UNITED STATES ENVIRONMENTAL PROTECTION AGENCY
                                   WASHINGTON D.C.  20460
                                                               OFFICE OF THE ADMINISTRATOR
                                                                 SCIENCE ADVISORY BOARD
                                     May 19, 2008

EPA-CASAC-08-012

The Honorable Stephen L. Johnson
Administrator
U.S. Environmental Protection Agency
1200 Pennsylvania Avenue, N.W.
Washington, DC 20460

       Subject:      Clean Air Scientific Advisory Committee's (CASAC) Peer Review of
                    EPA's Integrated Science Assessment (ISA) for Oxides of Nitrogen and
                    Sulfur - Environmental Criteria (First External Review Draft, December
                    2007)

Dear Administrator Johnson:

       The Clean Air Scientific Advisory Committee (CASAC) NOX & SOX Secondary National
Ambient Air Quality Standards (NAAQS) Review Panel met on April 2-3, 2008 to review EPA's
Integrated Science Assessment (ISA) for Oxides of Nitrogen and Sulfur - Environmental Criteria
(First External Review Draft, December 2007) (see Appendix A for the Panel roster). This letter
has been reviewed and approved by the chartered CASAC at the public conference call on May
5, 2008 (see Appendix B for the CASAC Roster).  While the Panel views that the first draft ISA
was informative, it also found that the first draft did not fully meet its objective.  The ISA should
be an informative, succinct, and useful summary of the evidence for consideration in the
NAAQS review process.  The Panel recognizes that this is a significant undertaking, particularly
noting that this is the first effort to consider developing standards that might integrate across
multiple criteria pollutants as has been recommended by a number of advisory bodies, including
National Academy committees.  In this letter, the CASAC Panel first offers general comments
and recommendations followed by responses to the Agency's charge questions.  Comments from
the individual Panel members are provided in Appendix C.

   1.  An Executive Summary would be valuable. It should bring forward the key points and
       findings from the individual chapters, with emphasis on the summary and conclusions.
       In addition to highlighting the findings and "take home" points from the ISA, an
       Executive Summary would also provide various linkages between the pollutants under
       consideration, their atmospheric dynamics, and their environmental effects. Further, the
       Panel recommends that the introductory chapter also include a table and associated
       discussion  of which effects are or are not being addressed in this NAAQS review and

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       why. This table and discussion should also identify where the associated information can
       be found in the ISA and in what other documents the effects that are not included are
       discussed (such as the PM ISA). Additionally, a summary of the data and studies that
       would reasonably be used to inform the setting of the secondary NAAQS should be
       presented in a second table (or tables). The Panel recommends that the critical data needs
       be included both  here and in the Conclusions chapter.

    2.  An issue pertinent to all of the chapters is an imbalance in how the various species  of
       total reactive nitrogen1 (Nr) (which includes oxidized, reduced and organic forms of
       nitrogen) are treated.  At present, there is significantly more emphasis and information
       for oxides of nitrogen than for reduced and organic nitrogen compounds. Greater
       consideration should be given to the emissions, dynamics, effects and linkages of reduced
       and organic nitrogen based on the current and growing recognition of the importance of
       these forms of Nr in the biogeochemical N cycle with respect to nitrogen enrichment and
       acidification.

    3.  The effects of Nr should also be considered in the context of multi-pollutant, multi-
       effects scenarios. Europe has been dealing with similar multi-pollutant, multi-effects
       challenges.  While their approach to policy development differs from the US, much can
       be learned specifically from how the science has supported  the development of European
       policies.  For example, European assessments of potential C sequestration in forests
       include probable  enhancement of growth as a result of Nr deposition in N-limited
       ecosystems, which are quite common. Special attention should be given to the scientific
       foundations that led to adoption of multiple-pollutant/multiple effects perspectives  and
       the concepts of Critical Loads and Target Loads in management of NOX, NHX, VOC,
       ozone, and PM within the European Union. The Panel has provided a number of
       references for your consideration in Attachment C.

    4.  A wide range of "indicators"  - including ambient air concentrations (gaseous and
       aerosol), deposition (wet and dry), and environmental (biogeochemical) - are discussed
       in the ISA and will later be utilized in the environmental risk and exposure assessments
       (REA).  It would be useful to provide some relevant information in the ISA to illustrate
       how some of these indicators are related to or  distinct from  others. Application of these
       indicators and their relationships should  be a focus throughout the document. For
       example, how do spatial  and temporal patterns of gaseous S and N compounds in the
       ambient air compare to emissions, aerosol concentrations, or deposition?

Responses to EPA's Charge Questions:

Atmospheric Sciences and Ecological Exposures

    1.  To what extent is the evidence on atmospheric chemistry and physics, air quality,
       and deposition and exposure sufficiently and correctly described, clearly
1 The term total reactive nitrogen includes all biologically, photochemically and radiatively
active compounds.

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       communicated, and relevant to the review of the secondary NAAQS for NO2 and
       SO2?

   2.  How well characterized are the relevant properties of the ambient air
       concentrations and deposition of NOX and SOX, including policy-relevant
       background concentrations, spatial and temporal patterns, and the relationships
       between ambient air concentrations and ecological exposures?

   3.  How sufficient is the information on atmospheric sciences and exposures for the
       purposes of evaluating and interpreting the ecological effects presented in Chapter 4
       of the draft ISA?

       In general, these questions align with Chapters 2 and 3. EPA staff has done a good job
identifying the key considerations included in these two chapters and necessary to respond to
these charge questions. However, more attention to identifying and quantifying linkages is
needed. EPA should also consider combining Chapters 2 and 3 into a single, more integrated
chapter.  This would effectively present the information in a "source to exposure"  format which
is more in line with the organization of the Draft IS As for the Primary NOX and SOX standards.

       The atmospheric chemistry and physics section was sufficient in coverage  and clearly
communicated, with the exception of the role of ammonia in gas and particle phase reactions of
the NOX-SOX-NHX system.  The air quality discussion was hindered by inadequate depictions of
the monitoring networks: mixing less relevant networks like ozone with SC>2 and NC>2 networks
obscured important information about SO2/NO2 monitor location and  density.  The document
concludes that the existing networks are sufficient, but various networks that could contribute
data  to assess concentrations and deposition each have significant shortcomings.  The SO2/NO2
monitors are sparse, primarily urban, and absent from large parts of the country. Similar
problems plague the particulate matter (PM) speciation network, which is also primarily urban
and thus poorly suited to characterize rural and remote areas. Monitoring networks like NADP
and CASTNET are critically important for the quantification of deposition and tracking spatial
and temporal patterns, but suffer from gaps in coverage as well, and cannot accurately
characterize exposure for the broad heterogeneity in sensitive ecosystems. Additional
monitoring data exist that ought to be incorporated in this document and used in the risk
exposure assessment (e.g., SEARCH). The dearth of ammonia, ammonium and organic Nr data
is a significant shortcoming that, while not immediately resolvable, could be addressed by
including a summary of data from research studies.

       Spatial and temporal trends in emissions and concentrations need to be better represented
in figures and/or tables. Emissions of SOX, NOX, N2O and NHX need to be better quantified, not
only  at the national level, but also at the regional level. Projections of future emissions  should be
included  in the ISA to put in to perspective the future importance of sulfur oxide and reduced,
organic and oxidized nitrogen emissions.  Explicit linkages between emissions, ambient
concentrations, and deposition should be made. EPA should consider showing maps of SC>2 (and
NOX) emissions adjacent to 862 concentrations and 864 deposition. The Panel recognizes that
this comparison may still be insufficient to provide the quantitative linkages that should
ultimately be made.

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       Air quality modeling appears to be essential to providing quantitative linkages between
source emissions and deposition fluxes. The current treatment of model capabilities and
accompanying uncertainties in their application should be bolstered. A particular need is to
expand discussions of model evaluation and the integration of model results and observations,
which are very limited spatially and in terms of species monitored.

Acidification

    4.  How well are the major effects of NOX and SOX on ecological acidification identified
       and characterized? To what extent do the discussions and integration of evidence
       across scales (e.g. species, communities, ecosystems, and regions) correctly represent
       and clearly communicate the state of the science?

    5.  How well has the ISA characterized the relationship between acidifying deposition
       levels of NOX and SOX and environmental effects?

    6.  How well characterized is the relative importance of the oxidized and the reduced
       forms of nitrogen on ecosystem acidification?

       The effects of SOX and NOX on ecological acidification were adequately identified,
characterized, and integrated across scales; however, the Panel has identified modifications or
additions for EPA's consideration.  A conceptual figure illustrating the highlighted processes
could be introduced at the beginning of the document to guide the reader through the entire
document. The Agency may consider identifying direct and indirect effects of deposition on
acidification.  For example, figures showing the direct links - e.g., deposition levels on the x-axis
and acidification response(s) on the y-axis - would be helpful. The importance of the SC>42" and
NOs" mobile anions needs to be highlighted. The Panel would also like the EPA to consider
further use of ecosystem functions (production, nutrient cycling, etc.) as response variables to
acidifying deposition.  The discussion of the natural and anthropogenic processes of soil
acidification should be moved to the beginning of the document.  Where possible, point out the
likely proportions that are due to natural versus anthropogenic causes.  Further consideration
might also be given to adding a discussion on the effects of capacity (change in soil acidity) and
intensity (changes in soil  solution, natural water). The former might take decades whereas the
latter changes more rapidly in response to the inputs, outputs and cycling of mineral acid anions
such as including N(V, SC>42" and Cl".

       Under indirect effects, the document should note that some important linkages have been
made between acidifying deposition and the interaction of other pollutants (e.g., ozone) and other
stressors (drought, pests, or pathogens), as well as other processes (fire). Relationships between
emission and deposition (or lack of such) should be reiterated here. Reduced and oxidized forms
of nitrogen were characterized well; though as previously noted, the influence of all forms of
reactive nitrogen on acidification (in addition to NOX)  should be balanced.

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Nitrogen Enrichment

    7.  How well are the major effects of NOX as it contributes to nitrogen enrichment of
       the ecosystems appropriately identified and characterized? To what extent do the
       discussions and integration of evidence across scales (e.g. various species,
       communities, ecosystems, and regions) correctly represent and clearly communicate
       the state of the science?

    8.  How well characterized are the relationships between ambient atmospheric nitrogen
       concentrations, nitrogen deposition and total nitrogen loads, and environmental
       effects?

    9.  To what extent has the draft ISA adequately characterized the contribution of
       oxidized and reduced forms of nitrogen to ecological effects related to nutrient
       enrichment?

       The impact of nutrient enrichment on terrestrial and aquatic ecosystems is a major focus
of this first draft ISA.  Although adequate attention is given to nutrient enrichment effects of
oxidized forms of reactive nitrogen (Nr), mainly NOX and N2O, the treatment of the
environmental effects of reduced and organic forms of reactive nitrogen (Nr) is inadequate.
Increased emphasis on the wet and dry atmospheric deposition of ammonium ion (NH4+),
gaseous ammonia (NH3) and inorganic Nr is needed in the Second Draft ISA.
       The Panel also recommends the further development of the quantitative relationships
between atmospheric concentrations of Nr, deposition rates and the resulting effects.  To the
extent practical, linkages between source(s) and effect(s) should be demonstrated. As noted
previously, additional potential environmental impacts from Nr-deposition and the resulting
nutrient enrichment should be further discussed, including such effects as increased plant growth
leading to carbon sequestration (including enhancement of production in combination with
increasing CO2), enhanced fire danger and increased potential of windthrow.  A further indirect
effect is that nutrient enrichment will modify the nitrogen cycling:  included in this modification
is the alteration of N inputs and outputs to/from the system as a result of biotic and abiotic
factors such as N fixation by plants and fires.
       Additional case studies should be also added to better represent the various U.S.
ecosystems and deposition scenarios. Examples for inclusion in the ISA are the mixed conifer
forests of the San Bernardino Mountains,  coastal sage and desert ecosystems of southern
California, which experience high gradients of N deposition.

Other Welfare Effects

    10. Several additional effects are discussed, including mercury methylation, direct gas-
       phase effects on foliage, and NiO as a greenhouse gas. How well does the draft ISA
       characterize the evidence on these topics?

       Section 4.4 of the report appropriately described available information and discussion of
additional NOX and SOX deposition-related welfare effects including the link between

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atmospheric ambient sulfate and mercury methylation; the direct phytotoxic effects of gaseous
nitrogen and sulfur oxides on vegetation (including HNOs); enhanced production of N2O from N
saturation; and the elevation of nitrate in surface water.  The EPA should expand this section to
include succinct discussions of the contribution of NOX and SOX to the production of particulate
matter and tropospheric ozone. Additionally, the Panel recommends that new sections be added
on the relationship between nitrogen deposition and carbon sequestration within natural
ecosystems and impacts on fires and other potential feedbacks. The discussion  should include
reasoning as to why certain effects are not more fully considered within the ISA in regards to
evaluating as secondary NAAQS for NOX and SOX.  This might simply be recognition that they
are fully considered elsewhere in documents related to other NAAQS.  The discussion of
methylation should be addressed in the context of the local, regional and global geochemical
cycling of both Hg and SOX and that the two share common sources. Further, to the extent
practical, the ISA should indicate the relative NOX and SOX contributions to each of the welfare
effects listed above (e.g., what fraction of global N2O emission are attributable to anthropogenic
N-enrichment).

Conclusions

   11. What are the views of the Panel on the appropriateness and comprehensiveness of
       the conclusions drawn in Chapter 5?

   12. How adequate is the draft ISA for providing information and guidance to future
       exposure, risk and policy assessments that may be prepared in support of this
       NAAQS review?

       Generally the Panel found that the conclusions, presented in Chapter 5 of the ISA, were
logically and appropriately drawn from the information presented in the preceding chapters and
annexes.  In some cases the concluding material could be more efficiently organized so that there
is better congruence between the conclusions and the information presented in the chapters.  The
Panel noted that the language employed is occasionally more subjective or speculative than
necessary. It would be more rigorous to employ a more consistent and liberal use of references
to document the concluding statements. The Panel also suggests that a condensed version of the
conclusions section be brought forward to the beginning of the ISA document as an executive
summary.

       While brevity is desirable throughout this ISA document, some of the concluding
sections were so pared down that they failed to convey much useful information. For example,
the summarization of case studies in Chapter 5 is inadequate to convey much detail about the
characteristics of the case study locations, the reasons for their selection, the implications and
significance of the environmental effects  of S and N deposition on ecosystem resources and
functions in these locations, or the intended future analyses in the environmental risk and
exposure assessments. Related effects of S  and N pollutants - such as on materials damage,
visibility and climate forcing - which are not the intended focus of this assessment, need to be
briefly summarized here, with pointers to locations where the relevant information can be
accessed in other documents.

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       A key basis for policy decisions is a clear demonstration that introduction of a control
strategy (e.g. decreasing Nr and S emissions) will produce the desired decreases in adverse
effects.  This calls for a demonstration that the existing evidence shows links between emissions,
atmospheric concentration, deposition, water and/or soil concentration, and harmful effects on
ecosystem resources, services and functions. This chapter should be the place at which this
crucial set of causal connections are summarized and judged as to their strength.

       The draft ISA provides  an appropriate review and summary of the science regarding the
effects of S and N deposition on ecosystem chemistry and biology and this will be very helpful
for the future risk and policy assessments. However, as noted above, the ISA document would
be more helpful if the implications of all effects on ecosystem functions were more clearly
articulated.  This will provide an essential link to the policy assessment regarding the adversity
of these effects.

       The degree to which this ISA is going to address economic valuation and ecosystem
services needs to be clarified. The ISA should specifically note that linkages between ecosystem
functions, changes in ecosystem services and ultimately to articulation of the welfare effects and
potential economic valuation will be developed in the subsequent risk and policy assessments.
Economic valuation is mentioned in the introduction to the ISA as a potential means to
determining what constitutes an adverse effect, but is not mentioned again in the main ISA
document, except for a lone table in the conclusions chapter that lists some economic valuation
study results and in the Appendix (as a review of the current literature). It is important to clarify
that economic valuation is not necessary for an assessment of the adversity of an effect, although
if available it would be useful.  Further, there was some discussion as to how far this ISA should
go in regards to ecosystem function-ecosystem service linkages, versus how much will be
covered in later documents (e.g., the REA documents).  To the degree the ISA does cover those
linkages, it should explore mapping relevant ecosystem functions (e.g., nutrient cycles,  system
acidification, productivity) that are  affected by Nr and SOx  onto specific ecosystem services
(ecosystem services as defined by the Millennium Ecosystem Assessment for example). The
resulting organizational sequence—from emission to deposition to effects on ecological function
to identifying where the affected ecosystem functions fit into ecosystem services—may provide
the scientific framework for the development, description and valuation of changes in ecosystem
services.

       In summary, the information provided in this first draft ISA needs to be further developed
to provide the range of information desired to review the  secondary NAAQS for NOX and SOX.
The need for the quantitative linkages between ambient air quality, depositional fluxes, and the
resulting effects to the extent practical cannot be overstated. This applies to not only nitrogen
and sulfur oxides, but reduced and organic forms of nitrogen as well.

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      The CASAC NOX & SOX Secondary NAAQS Review Panel was pleased to review the
first draft of the ISA for Oxides of Nitrogen and Sulfur - Environmental Criteria. We look
forward to review of the second draft and wish you well in this important endeavor.

                                Sincerely,
      /Signed/

Dr. Armistead (Ted) Russell, Chair
CASAC NOX & SOX Secondary
   NAAQS Review Panel

Enclosures
      /Signed/

Dr. Rogene Henderson, Chair
Clean Air Scientific Advisory Committee

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Appendix A: Roster of CASAC NOX & SOX Secondary NAAQS Review Panel

                     U.S. Environmental Protection Agency
                    Clean Air Scientific Advisory Committee
                  NOX & SOX Secondary NAAQS Review Panel

CASAC MEMBERS

Dr. Armistead (Ted) Russell  (Chair)., Professor, Department of Civil and Environmental
Engineering, Georgia Institute of Technology, Atlanta, GA

Dr. Ellis B. Cowling, University Distinguished Professor At-Large Emeritus, Colleges of
Natural Resources and Agriculture and Life Sciences, North Carolina State University, Raleigh,
NC

Dr. Douglas Crawford-Brown, Professor Emeritus and Director Emeritus, Department of
Environmental Sciences and Engineering and UNC Institute for the Environment, University of
North Carolina at Chapel Hill, Chapel Hill, NC

Dr. Donna Kenski, Data Analysis Director, Lake Michigan Air Directors Consortium,
Rosemont, IL

PANEL MEMBERS

Dr. Praveen Amar, Director,  Science and Policy, NESCAUM, Boston, MA

Dr. Andrzej Bytnerowicz, Senior Scientist, Pacific Southwest Research Station, USDA Forest
Service, Riverside, CA

Ms. Lauraine Chestnut, Managing Economist, Stratus Consulting Inc., Boulder, CO

Dr. Charles T. Driscoll, Jr., Professor, Environmental Systems Engineering, College of
Engineering and Computer Science, Syracuse University, Syracuse, NY

Dr. Paul J. Hanson, Distinguished R&D  Staff Member, Environmental Sciences Division, Oak
Ridge National Laboratory, Oak Ridge, TN

Dr. Rudolf Husar, Professor and Director, Mechanical Engineering, Engineering and Applied
Science, Center for Air Pollution Impact & Trend Analysis (CAPITA), Washington University,
St. Louis, MO

Dr. Dale Johnson, Professor, Department of Environmental and Resource  Sciences, College of
Agriculture, University of Nevada, Reno, NV

Dr. Naresh Kumar, Senior Program  Manager, Environment Division, Electric Power Research
Institute, Palo Alto, CA

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Dr. Myron Mitchell, Distinguished Professor and Director of Council on Hydrologic Systems
Science, College of Environmental and Forestry, State University of New York, Syracuse, NY

Mr. Richard L. Poirot, Environmental Analyst, Air Pollution Control Division, Department of
Environmental Conservation, Vermont Agency of Natural Resources, Waterbury, VT

Mr. David J. Shaw, Director, Division of Air Resources, New York State Department of
Environmental Conservation, Albany, NY

Dr. Kathleen Weathers, Senior Scientist, Institute of Ecosystem Studies, Millbrook, NY

SCIENCE ADVISORY BOARD STAFF
Ms. Kyndall Barry, Designated Federal Officer, 1200 Pennsylvania Avenue, NW
1400F, Washington,  DC, Phone: 202-343-9868, Fax: 202-233-0643, (barry.kyndall@epa.gov)
                                                                                    10

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Appendix B: Roster of the chartered CAS AC

                     U.S. Environmental Protection Agency
                   Science Advisory Board (SAB) Staff Office
              Clean Air Scientific Advisory Committee (CASAC)

CASAC MEMBERS

Dr. Rogene Henderson (Chair), Scientist Emeritus, Lovelace Respiratory Research Institute,
Albuquerque, NM

Dr. Ellis B. Cowling, University Distinguished Professor At-Large Emeritus, Colleges of
Natural Resources and Agriculture and Life Sciences, North Carolina State University, Raleigh,
NC

Dr. James D. Crapo, Professor, Department of Medicine, National Jewish Medical and
Research Center, Denver, CO

Dr. Douglas Crawford-Brown, Professor Emeritus and Director Emeritus, Department of
Environmental Sciences and Engineering and UNC Institute for the Environment, University of
North Carolina at Chapel Hill, Chapel Hill, NC

Dr. Donna Kenski, Data Analysis Director, Lake Michigan Air Directors Consortium,
Rosemont, IL

Dr. Armistead (Ted) Russell, Professor, Department of Civil and Environmental Engineering,
Georgia Institute of Technology, Atlanta, GA

Dr. Jonathan Samet, Professor and Chairman, Department of Epidemiology,
Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD
SCIENCE ADVISORY BOARD STAFF
Mr. Fred Butterfield, CASAC Designated Federal Officer, 1200 Pennsylvania Avenue, N.W.,
Washington, DC, 20460, Phone: 202-343-9994, Fax: 202-233-0643, (butterfield.fred@epa.gov)
                                                                                 11

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Appendix C:  Compilation of Individual Panel Member Comments on EP'A's Integrated Science
Assessment (ISA) for Oxides of Nitrogen and Sulfur - Environmental Criteria (December 2007)
Comments received:

Dr. Praveen Amar	13
Dr. Andrzej Bytnerowicz	18
Ms. Lauraine Chestnut	24
Dr. Ellis B. Cowling	26
Dr. Douglas Crawford-Brown	31
Dr. Charles T. Driscoll, Jr	35
Dr. Paul J. Hanson	57
Dr. Dale Johnson	65
Dr. Donna Kenski	71
Dr. Naresh Kumar	75
Dr. Myron Mitchell	78
Mr. Richard Poirot	87
Dr. Armistead Russell	95
Mr. David Shaw	101
Dr. Kathleen Weathers	107
                                                                               12

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                                 Dr. Praveen Amar
This write up addresses the first three charge questions from NCEA. The Charge Questions are
reproduced below:

1. To what extent is the evidence on atmospheric chemistry and physics, air quality, and
deposition and exposure sufficiently and correctly described, clearly communicated, and
relevant to the review of the secondary NAAQSfor NO 2 and SO 2?

2. How well characterized are the relevant properties of the ambient air concentrations and
deposition ofNOxandSOx, including policy-relevant background concentrations, spatial and
temporal patterns, and the relationships between ambient air concentrations and ecological
exposure?

3. How sufficient is the information on atmospheric sciences and exposures for the purposes of
evaluating and interpreting the ecological effects presented in Chapter Four of the draft ISA?

Response:

 Chapter 2 ( The Atmospheric Chemistry and Physics of Nitrogen and Sulfur Oxides, as well as
Annex AX1 with the same Title), and Chapter 3 ( Ecological Exposure to Oxides of Nitrogen
and Sulfur, and  to Ammonia and ammonium, as well as Annex AX2 with the same Title)
provide a  reasonably detailed description of the atmospheric science, air quality, deposition, and
exposure.  However, the Chapters can  and should be improved for more clear communication. It
is understandable that various sections have different authorships. These Chapters and other
chapters in the ISA would therefore benefit from the services of an expert technical/scientific
editor resulting  in a more readable ISA that more clearly communicates the important findings of
these Chapters (as well as other chapters).

Specific Comments to improve the ISA are provided below:

Page 2-2: Line 8: It is important to state the more important point first,  followed by a minor
point. Ammonia is included in this ISA, first because of its role in NOx and SO2 chemistry, and
its role in nitrification, and, second (and a distant second!), because its oxidation can be a minor
source of NOx.  There are other parts of this ISA that do suffer from the same issue. That is, first
order issues should be mentioned first.

A General comment about time scales of various chemicals/reactions: The ISA does a very good
job of providing time scales of various reactions and species. However, it would be very useful if
many of these important reactions' time scales are presented in a single Table, where readers can
compare them in one place and draw meaningful conclusions.

Page 2-4: Line 17: P (Os): Ozone Production Efficiency: It is an important concept. However, I
do not think it is clearly defined in the document (as number of molecules  of ozone produced per
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molecule of NOx over a certain time period and over a spatial extent, etc.).  I suggest it should be
explicitly defined first time it appears.

Page 2-7 (Lines 22-23): Awkward and an out-of-context reference to the fact that NO3 deposition
is a "complex function of wind speed." What does this mean? Needs an explanation.

General Comment about Section 2.2.2: Halogen Chemistry in the Marine Layer: This section is
written rather poorly and seems to be out of context with the main theme of SO2 and NOx
chemistry. I found it hard to follow. If it has important implications for the deposition of nitrogen
and sulfur compounds on coastal and non-coastal/regional scales, they should be stated.

Page 2-9, General Sulfur Chemistry: Besides SO2, SO3 though small in amount compared to SO2
(about 1 to 3 percent of total emitted SOx in stacks) has been known to cause visibility
degradation ("Blue plume" downwind of large power plants burning high sulfur coal, and
equipped with pollution controls of SCR and FGDs). It needs to be addressed here or in  the PM
document.

Page 2-10: Line 1: It is stated that aqueous-phase  oxidation of SO2 is responsible for about 80%
of the total oxidation (implying that the remaining 20 percent is by homogeneous gas phase
oxidation or by metal-catalyzed reactions). However, the ISA should note that the situation is lot
more complex than that.  For example, which of the various oxidation pathways dominates
depends on the details of the local accumulation of the co-pollutants such as ozone, hydrogen
peroxide, hydrocarbons, ammonia,  and catalytic metals ( Fe, Mn, and others).  This will have an
impact on final deposition levels of sulfur.

Page 2-14: A clear explanation of S (IV) and S (VI) would be helpful.

Page 2-21: Section on Satellites: A comment similar to the comment on Halogen Chemistry
above. This section appears to have been written out-of-context and needs to be integrated with
the larger context of estimating ecological exposures to S and N deposition and how satellite data
may be helpful in providing total loadings of S and N on larger scales that only satellites can
provide.  Same comment on Table 2.6-1. May be, the Table needs to be removed.

Page 3.2: SOx Emissions: Lines  14-18: The statement that sources other than electric utilities
"make only a very minor contribution" to overall  SO2 emissions is quite inaccurate and needs to
be corrected. In 2003, the non-EGU sources in the US contributed 31% of the total  SO2
emissions (at 5 mm tpy compared to about 11 mm tpy for EGUs). For example, industrial,
commercial, and institutional (ICI) boilers burning coal and oil produce about one mm tpy of
SO2 in the US.  Same text appears in the Annex and needs to be corrected. Also, the Summary
(page 3-59) needs to be corrected.

Page 3.9 NH? Emissions, Lines 23-28: Very awkward description of ammonia emissions. Three-
Way catalysts and ammonia emission from them are NOT the primary source of ammonia, and
therefore, a description of ammonia emissions must start with known large sources  of ammonia
(livestock and agricultural operations). Please rewrite for more effective communication and
drop the words "for these reasons..   ."
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A potentially important point about ammonia emissions is the geographic shift in ammonia
emissions that seems to have taken place in the US between 1980s and late 1990s and may still
be accelerating. The attached slide, courtesy of Dr. Bruce Hicks, NOAA, shows that the "center
of ammonia emissions" may be shifting from Midwest to the Southeast and the Carolinas. That
is, ammonia emissions (in N kg/ha) have increased by about 2 to 3 Kg/ha in the Southeast and
gone down by 1 to 2 kg/ha in the Midwest. This shift in density of ammonia emissions has
obvious implications on the regional atmospheric chemistry of SOx, NOx, and ammonia and the
resulting regional wet and dry deposition patterns for both sulfate and nitrates. ISA should
address the impact of this potential trend in geographic change in ammonia emissions.

Page 3-10:  Section 3.4: Evaluating Emission Inventories: The ISA should note that the first step
to evaluate emission inventories is not by looking at the ambient concentrations. The first  step in
evaluating reliability and accuracy of emission inventories needs to take into account the
methods and procedures that are used to produce emission inventories themselves (use of
emission factors, use of CEMs,  QA/QC methods, uncertainty in determining spatial and temporal
profiles, speciation factors for VOCs and primary PM emissions,  etc.).

Page 3-11,  Section 3.5.2 NO2: Say "NO2 interaction with vegetation is MORE DIFFICULT TO
UNDERSTAND than...."

Page 3-16 Line  10: Not clear about the distinction between "aerosol-phase" and "solid-phase".
Are they not the same in the context of atmospheric chemistry of aerosols?

Page 3-16, Line 7: "Title IV Reductions in NOX and SO2" and not N and S.

Page 3-17, Figure 3.6-3: The Title needs to be modified to indicate that the Figure also shows
trends, if any (2002 to  2006).

Page 3-19, Lines 8-10: Please rewrite for clarity.

Page 3-21:  Satellites: same comment as above. Please note the larger context of S and N
deposition.

Page 3-34:  Section 3-9: Harvard Forest: I have a comment similar to the comment on Halogen
Chemistry above. It reads as an independent piece without being integrated into the  ISA. It is
too long and not clear.  Please shorten it and rewrite.

Page 3.12 PRB Concentrations of NOx and SOx:  This is well-written section and does a very
good job of responding to the Charge Question 2 on the subject of PRB s of NO2, SO2, and nitrate
and sulfate deposition over various regions in the US and at different time scales.

Page 3-43 Regional-Scale CTMs, Also Annex AX-2 (AX2.10.1.1, Page AX2-62): The text notes
that the capabilities of a number of CTMs designed to study local and regional-scale air pollution
problems were summarized by Russell and Dennis (2000) and by others, including Arnold
(2003), etc. What is missing is the reference to recent peer reviews of the CMAQ system itself.
                                                                                     15

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The ISA needs to recognize that CMAQ modeling system has been extensively peer-reviewed.
The ISA document should refer in Chapter 3 and in Annex AX-2 to the three detailed written
reports of the external peer review panels. It would also be useful to include a short summary of
the major findings of the peer review reports that were published by the CMAS in years 2003,
2005, and 2007. They are available on CMAS website (ww^¥xmascente\o^  The three
references (they should be included both in Chapter 3 and Annex AX-2) are:
1. Amar, P., R. Bornstein, H. Feldman, H. Jeffries, D Steyn, R. Yamartino and Y. Zhang, 2004:
Final report: December 2003 Peer Review of the CMAQ Model. Report submitted to CMAS
Center, University of North Carolina at Chapel Hill, July, 24 pp.

2. Amar, P., D. Chock, A. Hansen, M. Moran, A. Russell, D. Steyn and W. Stockwell, 2005:
Final Report: Second Peer Review of the CMAQ Model. Report submitted to CMAS Center,
University of North Carolina at Chapel Hill, July,  33 pp.

3. Aiyyer, A., D. Cohan, A. Russell, W. Stockwell, S. Tanrikulu, W. Vizuete and J. Wilczak,
2007: Final report: Third Peer Review of the CMAQ Model. Report submitted to CMAS Center,
University of North Carolina at Chapel Hill, February, 25 pp.

A General Comment on Dry Deposition: The ISA needs to be more clear and explicit that we
only ESTIMATE dry deposition and therefore comments about total deposition (wet and dry)
and about the relative contribution of each pathway have a  level of uncertainty that is hard to
determine.

In summary, Chapters 2 and 3 and annexes address the first three charge questions on
atmospheric science and ecological exposure in a satisfactory manner. However, the whole
document needs a thorough technical and scientific editing job as well as a better integration of
some of the sections (Halogen Chemistry, Harvard Forest, satellites use) into the overall ISA.
Chapter 5: Findings and Conclusions

General Comment: This Chapter does a good job of summarizing the ISA with major
"take home" messages. As noted above for Chapter 2 and 3, this Chapter does need a thorough
scientific editing job for it to communicate complex concepts in a clear manner.

 Specific Comments follow:

 Page 5-2 Section 5.2.2: The conclusion drawn here that current routine monitoring is "adequate"
or 'fully adequate" after listing major problems with measurement of gaseous and paniculate
species does not seem to be justified. I think it is a matter of tone and the revised language
should indicate WHY the current network is adequate.
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Page 5-3 Line 30: Please see the comments for Chapter 2 about 862 emissions from sources
other than power plants. They are not "very little," since they are about 1/3 of the total SC>2
emissions.

Page 5-11: Lines 20-31: Not clear why there is no relationship between recent trend in N
deposition and trends in nitrate concentrations in surface waters. Have the recent reductions in
NOx emissions in the eastern US because of the "NOx SIP Call" taken into account?

Page 5-36:  Line 20: Please see my comment above on "adequate monitoring." Here, it says that
the monitoring networks are "inadequate." Need to be consistent.
                          Geographic Shift in Ammonia Emissions

                             (courtesy of Bruce Hicks, NOAA)
                                w Annual A%trugc AniiTiuma ll
                                ItWS in     - |JW tit
                                                                              as N

                                                                            <-2
                                                                            -2to-1
                                                                            -1 to -0,5
                                                                            •°-5to0'

                                                                            1 to 1.5

                                                                        -r — 9tft 1
                                                                        -T-^r., Us \\/ J
                                                                        faE- > 3
                                                                                      17

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                              Dr. Andrzej Bytnerowicz
General Comments:
Chapter 4 is well written and comprehensive and presents state of the scientific knowledge on
ecological effects of acidification, nitrogen nutrient additions and other welfare effects of N and
S. The chapter is very informative and is based on the relevant and current peer-reviewed
literature from North America and Europe.

Having said this, I would like to suggest that N effects are presented in a context of multi-
pollutant, multi-effects scenarios. Example of such an approach is the 1999 Gothenburg protocol
of the UN Convention of Long-range Transport of Air Pollutants recommending evaluation of
the combined effects of NOx, SOx, NH3, and VOCs on acidification, eutrophication and ground
levels ozone impacts (Working Group on Effects, 2004).
Specific comments:

Page 4-4, Figure 4.1 .-1. should be changed to Table 4.1 .-1.
Why eutrophication is not shown as a possible disturbance if forests?
In row 7 (atmospheric pollutant), the end products of deposition are shown, but not the pollutants
causing biological effects (e.g., NC>2, 862, HNOs, NH3, paniculate NOs, particulate NH4).

Page 4-5, point 7 - ammonia (NH3) should be listed as well.

Page 4-9, Figure 4.2-1 mixed up with Fig. 4.2-2.

Page 4-13, lines  12-27. Elevated levels of tropospheric ozone and land disturbances such as
catastrophic fires or withdthrows should be mentioned as factors affecting water resources of
ecosystems and their leaching potential.

Page 4-22, lines 25-27. This could be a good recommendation for future research needs.

Page 4-29, lines 27-28. Reduced cold tolerance is also caused by euthrophication.

Page 4-35, line 14. These effects on epiphytes, if I recall, were also caused by NC>2 and 862.

Page 4-35, section 4.2.2.2.3. The described effects are to a large extent not caused by acidity but
direct toxic effects of SO2 on plants.

Pages 4-38 through 4-44. Change SO4+ to SO42".

Page 4-66, lines 26-28. Reference is needed.
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Page 4-73, lines 28-32. It is a very important statement - clearly no single "definitive" critical
load for US ecosystems is possible. The eco-regional approach to the CL issue seems to make
most sense.

Page 4-98, lines 15-17. Is it contribution of gaseous HNOs or of total dissolved N(V?

Page 4-121, lines 18-20. In regard to changes in lichen species composition, there are differences
in responses to reduced vs. oxidized N. It has been proposed that elevated levels of HNO3 have
negative effects on sensitive lichens such as Ramalina menziesii in the San Bernardino
Mountains of southern California (Riddell et al., 2008). Such effects are attributed more to the
direct HNOs toxicity than NCV deposition. There is also a high probability that the reduced N
resulting from high NH3 and particulate NH4+ could affect lichens downwind of the Los Angeles
pollution sources area (Prof. Eva Barreno, personal communication). However, it has to be
remembered that the disappearance of lichens in southern California could also be caused by
high levels of ambient ozone in the area (Nash and Sigal,  1998; Sigal and Nash, 1983).

Page 4-122, lines 20-26. It should be added that increased mortality of the high elevation trees in
areas of elevated N deposition could be partially caused by their increased sensitivity to frost.

Page 4-129, section 4.3.3.1.4. This section should be incorporated into the forests section
(4.3.3.1.1) (see my remarks below).

Page 4-131, section 4.3.3.1.6. This section should be divided and moved into "forests" and "arid
& semi-arid" ecosystems (see my remarks below).

Page 4-147, lines 28-30. Transitional ecosystems (as mentioned in the previous sentences)
should also be added.

Page 4-152, lines 15-18.1 do not see a logical link here. If estuaries and coastal water are
inherently sensitive to increased N loading, this is not because of the high releases of N inputs
back to the atmosphere (high microbial activity). Increased release of N into the atmosphere can
be considered as an avoidance mechanism in the presence of excessive N loads.

Page 4-154, lines 21-24. Ranges of deposition that may be affecting sensitive species seem to be
mixed up - levels in alpine ecosystems should be lower than in other terrestrial ecosystems cited
in this ISA document (see Baron et al. 2000; Bowman et al., 2006).

Page 4-162, line 8. S deficiency level at <80 ug/g seems to be very low. In Scots pine foliage in
the pristine area of Europe the lowest recorded level of S was -400  ug/g (Molski et al.,  1981).

Page 4-176. Section on the direct effects of HNOs on plants should be considered and possibly
added.

Page 4-180, Table 4.2-2. Add "of after "Example".

Page 4-186, Table 4.2-9. Change "eith" to "with" in the second line.
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Page 4-189. Table 4.3-2. in the column "Factors that govern vulnerability", add a sentence
"Interactions with other contributing stressors such as elevated levels of ozone or drought".

Replies to the assigned questions:

7 A. How well are the major effects of NOx as it contributes to nitrogen enrichment of the
ecosystems appropriately identified and characterized?

Generally the effects of NOx contribution to the N enrichment of various ecosystems are well
described. These effects are divided into the terrestrial, transitional, aquatic (fresh water and
estuarine and coastal water) ecosystems. Two case studies (alpine and sub-alpine communities in
Colorado and in Chesapeake Bay) are described. Some other case studies could be possibly
added - such as the mixed conifer forest of the San Bernardino Mountains (Fenn and Poth, 1999;
2001; Fenn et al., 2003) and grassland ecosystems in the San Francisco Bay area (Weiss, 1999).

7B. To what extent do the discussions and integration of evidence across  scales (e.g.. various
species, communities, ecosystems, and regions) correctly represent and clearly communicate the
state of science?

Generally the effects (biogeochemical  processes and biological effects) have been described (as
in point 1) for the terrestrial, transitional and aquatic ecosystems from a perspective of the effects
indicators. Some confusion is caused by placing herbaceous and plants and shrubs (4.3.3.1.4) and
mycorrhizal and microbial activity (4.3.3.1.6) into separate sections. Information contained in
those sections should be incorporated into the forests (4.3.3.1.1)  and arid  and semi-arid
ecosystems (4.3.3.1.3). Lichens could stay alone since their evaluation surveys have been done
mostly for larger geographic areas encompassing various ecosystems (often including
agricultural or the urban-wildland interface). What is missing are the desert ecosystems - effects
of N deposition in these N-limited systems, especially in the vicinity of strong N sources areas,
should be mentioned. A good example is the Mojave Desert in California which is strongly
affected by N deposition from the Los Angeles area. There are only a few references referring to
those problems, however, research is ongoing at the University of California in Riverside (Allen
et al., 2008).

8. How well characterized are the relationships between ambient atmospheric nitrogen
concentrations, nitrogen deposition and total nitrogen loads, and environmental effects?

These relationships are not well described. This is mainly caused by a lack of sufficient
understanding of these relationships. Understanding responses of ecosystems to N addition are
often based on fertilization experiments, using mainly NH4NO3 or  (NH4)2SO4 additions and
assuming that these additions would simulate wide spectra of atmospheric N deposition
scenarios. More experiments on natural N deposition gradients,  with the  adequately identified N
components (gases, aerosols and soluble ions), should be conducted. Deposition of N to forest
ecosystems is calculated mostly from throughfall data with an assumption that wet and dry
deposition components are included. This approach has been used at large scales in Europe and
helped in calculating critical loads for N and S deposition and acidity (ICP Forests and ICP Maps
                                                                                       20

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and Modeling products). However, the N dry deposition component, especially when there is not
sufficient precipitation to remove N deposited on foliage and other surfaces to throughfall
solution, may be grossly miscalculated. The inferential method (using information on ambient
concentrations of major N deposition drivers, their deposition velocity as well as canopy
characteristics, such as leaf area index, LAI) may be helpful in such cases. This method could
also be applied in such ecosystems (grasslands, deserts, alpine and sub-alpine ecosystems) where
throughfall cannot be used at all or is very difficult to be applied.  The inferential method has
numerous limitations and uncertainties; however, it can be used for large geographic areas. This
method is the basis for the CASTNET estimates of N dry deposition at the national scale.  It has
to be remembered, however, that there is not enough data for ambient NH3, which is one of the
main drivers of N dry deposition.  In addition, understanding of N deposition in complex
(mountain) terrains is still poor.

9. To what  extent has the draft ISA adequately characterized the contribution of oxidized and
reduced forms of nitrogen to ecological effects related to nutrient  enrichment?

Contribution of reduced vs. oxidized forms of atmospheric nitrogen to nutrient enrichment
effects are not well understood and subsequently not well described in the ISA. The main reason
for that is an inadequate understanding of the chemical environment of ecosystems for which the
effects of N deposition are being described. As I mentioned  above, most of knowledge on the
ecosystem responses comes from  the fertilizer studies. Such experiments are well suited for
understanding biological effects of N in the wet deposition dominated ecosystems, such forests
in the eastern United States. However, in the arid and semi-arid ecosystems, where large portion
of N deposition may result from gaseous HNO3, NH3 or particulate NO3" or NH4+, fertilization
experiments may quite poorly mimic the real-world interactions between the atmosphere and
ecosystems (vegetation, soils and surface water components).

Recommendations:

    1.   While SC>2 and NOx concentrations should be monitored for health reason (primary
       standards), they have very limited application for evaluation of environmental
       (ecological) effects. Therefore there is a need for monitoring concentrations of major
       drivers of N & S  deposition. For S, this is mostly 864 in wet precipitation measured
       nationally (e.g. NADP network). However, for N, not only wet NO3 and NH4 deposition
       (also measured nationally), but also dry deposition of gaseous HNO3, NH3 and parti culate
       NO3 and NH4 as well  as the organic compounds should be included. Activities of the
       national monitoring networks, especially CASTNet should be continued  and expanded,
       especially in the underrepresented Western US.
    2.   For preliminary determination of HNO3 and NH3 "hot spots", use of passive samplers
       should be considered. Passive samplers have already been successfully used in
       monitoring networks in California: Sequoia National Park (Bytnerowicz  et al., 2003),
       Lake Tahoe (Gertler et al., 2006), or Joshua Tree National Park (Allen et al., 2008).
    3.   National efforts in ecological monitoring of N & S deposition effects are needed. Such
       efforts could be similar to those in Europe under the  auspices of the UN Economical
       Commission for Europe, namely the ICP Forests Level and ICP Modelling and Mapping
       efforts. Monitoring results from the ICP Forests Level II plots  have allowed for
                                                                                      21

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       determination of CL and their exceedances. The newly developed network for CL
       estimates on 17 US Forest Service Experimental Forests and additional 4 sites across the
       US will help to determine if the CL approach could be applied and be practical in the US.
       Research collaboration within the US and with the Canadian and European partners is
       planned. If successful, the monitoring efforts in the US FS could be expanded into a
       denser national network. It is envisioned that US FS Forest Inventory and Analysis (FIA)
       Phase 3 (Forest Health Monitoring) sites could be utilized. The Intensive Site Monitoring
       (ISM) site that would integrate the FIA Phase 3 and the  ICP Forests Level II-type plots
       will be established in the San Bernardino Mountains of  southern California in summer
       2008.
   4.  Effective collaboration between EPA, various national monitoring networks, and land
       management agencies such as US Forest Service or National Park Service, in developing
       a national program for monitoring and evaluation of N & S effects on ecosystems,
       including CL calculations, should be encouraged.

References:

Allen, E.B., L. E. Rao, RJ. Steers, A. Bytnerowicz, and M.E. Fenn. 2008. Impacts of
   atmospheric nitrogen deposition on vegetation and soils in Joshua Tree National Park. In R.H.
   Webb, L.F. Fenstermaker, J.S. Heaton, D.L. Hughson, E.V. McDonald, and D.M. Miller, eds.
   The Mojave Desert: Ecosystem Processes and Sustainability. University of Nevada Press, Las
   Vegas.  In press.
Baez, S., Fargione, J.,  Moore, D.L, Collins, S.L., and Gosz, J.R. 2007. Atmospheric nitrogen
   deposition in the northern Chihuahuan desert: Temporal trends and potential consequences. J.
   Arid Environ. 68, 640-651.
Bytnerowicz, A., Tausz, M., Alonso, R., Jones, D., Johnson, R., and Grulke, N. 2002. Summer-
   time distribution of air pollutants in Sequoia National Park, California.  Environmental
   Pollution, 118, 187-203
Fenn, M.E., Haeuber, R.,  Tonnesen, G.S., Baron, J.S.,  Grossman-Clarke, S., Hope, D., Jaffe,
   D.A., Copeland, S., Geiser, L., Rueth, H.M., and Sickman, J.O. 2003. Nitrogen emissions,
   deposition, and monitoring in the western United States. BioScience 53, 391-403.
Fenn, M.  E.,  and Poth, M. A.  1999.  Temporal  and spatial trends  in stream water nitrate
   concentrations in the  san Bernardino Mountains, southern  California. J. Environ. Qual., 28,
   822-836.
Fenn, M. E., and Poth, M. A. 2001. A case study of nitrogen  saturation  in westen U.S.  forests.
   Sci. World J., 1,433-439.
 Gertler, A., Bytnerowicz, A.,  Cahill,  T.  A., Arbaugh, M.,  Cliff, S., Kahyaoglu-Koracin, J.,
   Tarnay, L., Alonso, R.,  and Fraczek,  W. 2006. Local air quality threatens Lake Tahoe's
   clarity. California Agriculture, 60, 53-58.
 Molski, B., Bytnerowicz, A.,  and Dmuchowski, W.  1981.  Content  of sulphur  and fluorine
   compounds in Scots pine needles as an  indicator of air pollution in Poland. Silva Fennica, 15,
   4,419-421.
Nash, III,  T. H., and Sigal, L. L.  1998. Epiphytic lichens in the San Bernardiono Mountains in
   relation to oxidant gradients. In: Miller, P. R., McBride,  J. R.  (eds.)  Air Pollution in the
   Montane Forest of Southern California.  A Case Study of the San Bernardino Mountains. Ecol.
   Stud., vol. 134, Springer, New York, 223-234.
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Riddell, J., Nash III, T. H., and Padgett, P. 2008. The effect of HNO3 gas on the lichen Ramalina
   menziesii. Flora, 203, 47-54.
Sigal, L. L., and Nash, III, T. H. 1983. Lichen communities on conifers in southern California:
   an ecological survey relative to oxidant air pollution. Ecology, 64, 1343-1354.
Working Group on Effects.  2004.  Review and Assessment of Pollution Effects and Their
   Recorded Trends. UNECE Convention on Long Range Transboundary Air Pollution,
   Brussels, Belgium.
Weiss SB. 1999. Cars, cows, and checkerspot butterflies: Nitrogen deposition and management
   of nutrient-poor grasslands for a threatened species. Conservation Biology 13, 1476-1486.

Some literature citations supporting evidence of increased windthrow in forests
experiencing elevated N deposition:

Braun, S., Schindler, C., Vilz, R., Fluckiger, W. 2003. Forest damages by the storm "Lothar" in
       permanent observation plots in Switzerland:  the significance of soil acidification and
       nitrogen deposition. Water, Air and Soil Pollution,  142, 327-340.

Nilsson, C., Stjernsquist, I, Barring, L., Schlyter, P., Jonsson, A. M., Samuelsson, H. 2004.
       Recorded storm damage in Swedish forests 1901-2000. Forest Ecology and Management,
       1999, 165-173.

United Nations Economic Commisiion for Europe, The Condition of Forests in Europe, 2005
       Executive Summary, ENECE Geneva, 32 pp. ISSN 1020-587X.
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                               Ms. Lauraine Chestnut
Charge question 11 (appropriateness and comprehensiveness of conclusions?)

The review of relevant economic valuation studies is included only as an appendix and is not
incorporated into the conclusions. Table 5.5-2 lists some results of water quality valuation
studies in the Chesapeake Bay, but I don't see discussion of this table in the text. As a result of
both of these factors, the treatment of the economic valuation literature seems disconnected from
the review of the science. It is not clear how the review of the economics literature contributes
and fits into this ISA. There was mention in the introduction that economic valuation may be
helpful in assessing what effects are adverse, but I don't see any discussion of specifically how
the current literature may be useful in this regard in the appendix or in the  findings and
conclusions. If the ISA is not going to make the link between harmful effects on ecosystem
functions to the question of how these translate into welfare effects and associated economic
values, then this should be explained in the introduction. This link needs to be made  at some
point in this process, but it may be better addressed in the risk and policy assessments. If this is
EPA's intention, it needs to be stated in the introduction. The ongoing work of the SAB
Committee on Valuing the Protection of Ecological Systems and Services (C-VPESS) and
EPA's Ecological Benefits Assessment Strategic Plan should also be cited here as important
background materials for economic valuation methods.

It is also  important to stress that a determination of there being  an adverse  welfare effect does not
necessarily require that it be quantified in monetary value terms. Economic valuation studies
may be helpful in assessing when an affect is adverse, especially for direct use values. However,
for total value (including nonuse, bequest, and even some indirect use values) the public can only
assess these values when they are fully informed about what the changes to the ecosystem
resources and functions are, including an understanding of the implications of these changes on
the quality of the many ecosystem services that these resources provide. This information and
understanding has to have its foundations in the science. The conclusions in the ISA would be
more useful if they articulated the implications of the changes observed in  the various
ecosystems affected by N and S deposition in terms of changes or losses in ecosystem functions.

Charge question 12 (adequate information and guidance for the exposure, risk and policy
assessments?)

In reviewing the ISA I kept looking for two types of information that seem to be key to this
process of considering secondary standards:
1.  What information is there that tells us when a change in an ecosystem might be considered
   adverse?

2.  What levels of deposition/exposure can a system tolerate  without incurring adverse changes?

Perhaps these questions are to be addressed more explicitly in the risk assessment phase. I didn't
see them explicitly addressed in the ISA. A few observations related to the question of what
exposures can be tolerated include:
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1.  Exposures that can be tolerated vary for different resources and different locations according
   to several known characteristics.

2.  It will be very hard to say what levels of N deposition can be tolerated when there are
   significant other sources in aquatic systems (especially for estuaries).

3.  The answer may be different for recovery of currently injured resources than for prevention
   of future degradation.

4.  The question is complicated by episodic events (e.g. spring runoff) that cause temporary but
   damaging increases in exposures.

The ISA notes that the current secondary standards for 862 and NC>2 were not set to address the
effects of deposition, but has the case been made that these standards are not sufficiently
protective? Perhaps this is obvious, but if current standards are being met and adverse affects are
still occurring, then the standards are not adequate. Related to this issue is the question of
whether adverse effects of deposition will continue once the primary NAAQS for PM and ozone
are met. These standards are going to require further reductions in SC>2 and NOX emissions from
current levels. At what point in this process does it need to be assessed whether the reductions in
deposition that will result will be sufficient to protect ecosystem resources, or is this not
relevant?
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                                Dr. Ellis B. Cowling
    Individual Comments on the First External Review Draft of the Integrated Science
  Assessment for the Secondary National Air Quality Standards for Nitrogen Dioxide and
                                    Sulfur Dioxide
   These Individual Comments are developed in the form of responses to most of the 12
Charge Questions received from Kyndall Barry together with the final agenda for our
CASAC Peer Review on April 2, 2008.

   Chairman Ted Russell asked Andrzej Bytnerowicz and me to give special attention to Charge
Questions 7-9 in the attached list.  Thus I am very much looking forward to comparing notes
with Andrej during our Peer review on April 2, 2008.

   My responses to most of the Charge Question are presented below in ordinary type after
presentation of the Charge Questions in Bold Type.

1. To what extent is the evidence on atmospheric chemistry and physics, air quality, and
   deposition and exposure sufficiently and correctly described, clearly communicated,
   and relevant to the review of the secondary NAAQS for NO2 and SO2?

       Chapter 2 of this ISA gives a very thorough account of the major sources, and the
       chemical and physical transport, transformation, and atmospheric deposition processes
       for oxides of nitrogen and  sulfur. The schematic diagram  of the cycle of reactive
       nitrogen in Figure 2.2.1 gives a reasonably firm foundation for understanding those parts
       of the nitrogen cycle that involve oxidized forms of nitrogen.

       But this schematic diagram includes no mention or pictorial illustrations of the huge (mostly
       agricultural) sources of reduced and organic forms of reactive nitrogen that are critical to
       understanding both the nitrogen enrichment and acidification effects of atmospherically deposited
       nitrogen and sulfur on terrestrial and aquatic ecosystems.
       If EPA is serious about dealing with both nutrient enrichment and acidification of ecosystems
       induced by atmospheric deposition of total reactive nitrogen, the Agency needs to include in
       Chapter 2 of the Second Review Draft of this ISA for "NOx" and ""SOx," a similar schematic
       diagram for the major sources, transformation, transport and atmospheric deposition processes for
       reduced and organic forms of reactive nitrogen.
2. How well characterized are the relevant properties of the ambient air concentrations
   and deposition of NOx and SOx, including policy-relevant background concentrations,
   spatial and temporal patterns, and the relationships between ambient air
   concentrations and ecological exposures?
3. How sufficient is the information on atmospheric sciences and exposures for the
   purposes of evaluating and interpreting the ecological effects presented in Chapter 4 of
   the draft ISA?
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4. How well are the major effects of NOx and SOx on ecological acidification identified and
   characterized? To what extent do the discussions and integration of evidence across
   scales (e.g.  communities, ecosystems, and regions) correctly represent and clearly
   communicate the state of the science?
   The presentation of current scientific knowledge about the effects of NOx, SOx, and total
   reactive nitrogen in Chapter 4 of this First Draft ISA is very thorough and comprehensive.
   The discussion and integration of evidence across scales (communities, ecosystems, and
   regions is also reasonably complete.
5. How well has the ISA characterized the relationship between acidifying deposition levels
   of NOx and SOx and environmental effects?
6. How well characterized is the relative importance of the oxidized and the reduced forms
   of nitrogen on ecosystem acidification?
   Although Chapter 4of this First Draft ISA gives a very thorough and wide ranging account of
   the huge increase in scientific understanding of nitrogen enrichment and acidification effects
   of atmospherically deposited nitrogen and sulfur on the structure, specific components,
   functions, and ecosystem services provided by many different ecosystems in many different
   parts of this country, the attention given to comparison of the extent to which these many
   adverse effects are caused by atmospheric deposition of oxidized and organic forms of
   nitrogen vs oxidized forms of nitrogen is vanishingly small.
   The truth is that although there are short-term differences in the rapidity and specific species
   effects of nitrogen  enrichment effects induced by reduced vs oxidized forms of nitrogen, the
   long-term effects are essentially indistinguishable.
   Thus, the most important policy relevant decision that needs to be made with regard to the
   Second Draft ISA is to  set the stage more adequately for consideration of a "Total Reactive
   Nitrogen" approach in air quality management in this country and to refrain from trying to
   deal only with oxidized forms of nitrogen rather than the sum of oxidized, plus reduced, plus
   organic forms of reactive nitrogen.
7. How well are the major effects of NOx as it contributes to nitrogen enrichment of the
   ecosystems appropriately identified and characterized? To what extent do the
   discussions and integration of evidence across scales (e.g. various species, communities,
   ecosystems, and regions) correctly represent and clearly communicate the state of the
   science?
   The adverse effects of atmospherically deposited nitrogen and sulfur on terrestrial and
   aquatic ecosystems fall into two major categories that are reasonably well described in this
   First Draft Integrated Science Assessment for Oxides of Nitrogen and Sulfur - "Nutrient
   Enrichment" and "Acidification." Total reactive nitrogen deposition is the principal cause of
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   nutrient enrichment whereas both nitrogen and sulfur deposition are the principal causes of
   acidification in both terrestrial and aquatic ecosystems.
   Notably, however, in the context of this CAS AC Peer Review of the secondary standards for
   nitrogen and sulfur oxides, this First Draft ISA fails to demonstrate that it is not just oxidized
   forms of nitrogen and sulfur that induce major adverse ecosystem effects, but also chemically
   reduced and organic forms of nitrogen, and to a lesser extent, also reduced and organic forms
   of sulfur. In some very important parts of the US, atmospheric deposition of reduced and
   organic forms of nitrogen are larger in total load of reactive nitrogen than the total load of
   oxidized forms of nitrogen.
   The principal sources of oxidized airborne nitrogen and sulfur are combustion of fossil fuels
   used in production of electricity, industrial processes of many sorts, transportation vehicles,
   and both commercial and domestic home and water heating systems.  These matters are
   adequately covered in this First Draft ISA. But this is NOT true for the very important
   reduced and organic forms of nitrogen.
   The principal sources of air emissions of reduced and organic forms of nitrogen are
   agricultural operations that include fertilization of crops and forests, but even more
   importantly include animal rearing operations (principally chicken, turkey, and egg
   production units, swine farms, and both beef and dairy cattle farms) but also including other
   domestic animals such as horses, goats, sheep, and even companion animals. Municipal
   waste handling and processing facilities and septic tank systems are also important sources of
   air emissions of ammonia and ammonium ion.
   Please see the comment written in response to the first Charge Question listed above with
   regard to the need for a schematic diagram similar to Figure 2.1.1, but developed for reduced
   and oxidized forms of nitrogen rather than just for oxidized forms of nitrogen.
8. How well characterized are the relationships between ambient atmospheric nitrogen
   concentrations, nitrogen deposition and total nitrogen loads, and environmental effects?
   My impression is that the contributions of inorganic forms of nitrogen (principally nitrate
   ions and ammonium ion concentrations to total nitrogen loads in wet deposition are
   reasonably well characterized. On the other hand, the contribution of organic forms of
   nitrogen to total reactive nitrogen loads in wet deposition are not very well characterized.
   Also the contributions of gaseous ammonia, volatile organic acids and amines, and various
   nitrogen and sulfur aerosols to total nitrogen and sulfur loads are not very well characterized.
   At the same time, despite some of these uncertainties about specific air concentration, total
   loads,  and ecosystem responses, however, the general quantitative relationships between
   regional decreases and increases in total emissions of nitrogen and sulfur relationships and
   several different nutrient enrichment and acidification effects are reasonably well
   characterized.
9. To what extent has the draft ISA adequately characterized the contribution of oxidized
   and reduced forms of nitrogen to ecological effects related to nutrient enrichment?
                                                                                      28

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   The present Draft ISA does a pretty adequate job of characterizing the contribution of
   oxidized forms of nitrogen to nitrogen enrichment but has a long way to go with regard to the
   contribution of reduced forms of nitrogen to nutrient enrichment.
10. Several additional effects are discussed, including mercury methylation, direct gas-
   phase effects on foliage, and N2O as a greenhouse gas. How well does the draft ISA
   characterize the evidence on these topics?
   My impression is that the present draft ISA does a reasonably adequate job of describing the
   available evidence on these other topics.  I gather from some of the Charge Questions in the
   Draft Scope and Methods paper, however, that EPA is still trying to make up its mind about
   how much attention to give to these other effects that go beyond  the general issues of nutrient
   enrichment and acidification effects in both terrestrial and aquatic ecosystems.
11. What are the views of the Panel on the appropriateness and comprehensiveness of the
   conclusions drawn in Chapter 5?
   I could not be more delighted with the decision to provide this kind of bulletized presentation
   of major Findings and Conclusions from the various chapters of this draft ISA! It appears
   that a considerable and well-focused effort has been made to develop this series of very
   carefully crafted brief summary statements that:
   1)  Contain the distilled essence of the most important topics covered in each chapter, and
   2)  Are as directly relevant as possible to the overarching Key Policy Questions that should
       be the principal focus of all aspects of these NAAQS review processes:.

       "What scientific evidence and/or scientific insights have been developed since the last
       review to indicate if the current public-health based and/or the current public-welfare
       based NAAQS need to be revised or  if alternative indicators, levels, statistical forms, or
       averaging times of these standards are needed to protect public health with an adequate
       margin of safety and to protect public welfare?

       "What scientific evidence and/or scientific insights have been developed since the last
       review to indicate whether,  and if so, what particular ecosystem components or other air-
       quality-related public welfare values, are more or less sensitive than the populations of
       humans for which primary standards are established and for this reason may require a
       different indicator, level,  statistical form, or averaging time of a secondary standard in
       order to protect public welfare. "

12. How adequate is the draft ISA for providing information and guidance to future
   exposure, risk and policy assessments that may be prepared in  support of this NAAQS
   review?
                                                                                     29

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I am a bit confused by this question. At first, I thought the question related to needs for information
and guidance for future NAAQS reviews, but then the question ends with "policy assessments
that may be prepared in support of this NAAQS review?
In any event, I do not recall that very much attention has been given in this First Draft ISA to
providing information and guidance with regard to either future or the present reviews for
secondary NAAQS standards for nitrogen  and/or sulfur.
                                                                                     30

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                           Dr. Douglas Crawford-Brown
This review focuses primarily on Chapter 5: Findings and Conclusions, although it draws on
information in the earlier chapters from which the Findings were drawn. My first very general
comment is that the Findings did, I believe, comport with the major conclusions one might draw
from the earlier chapters. At least, they summarized what I took to be most of the main points in
these earlier chapters, although I caution that I am not an ecologist and so there may have been
significant points made earlier that did not make their way into Chapter 5.

It was a bit hard (perhaps too hard) to get the subsections of Chapter 5 to match the way the
earlier chapters were organized. This is due largely to the fact that Chapter 5 itself does not have
any systematic approach to presenting the findings and conclusions  concerning effects (which is
really the focus of the NAAQS process). The effects are divided between Acidification; Nitrogen
Nutrient Enrichment; and Other Welfare Effects. Then these three major classes of effects are
subdivided in various ways (such as Aquatic; Terrestrial; etc). However, the subdivisions are not
consistent across the classes of effect. I suppose this might be because some of the subdivisions
are relevant for one class of effects and not others, but I can't see  any reason why this should be
the case. It would have been much more helpful to have the three  major classes subdivided into
the same set of subsections so the reader can quickly go through and find, for example, the
Biochemical Effects for all three classes. The needed information is all there, I just wanted a
more consistent structure to the presentation of it.

I also didn't understand the case studies. I could find no consistency in the way they were
approached, or any conclusions that could be drawn from them. There was no explanation of
what they  are doing within the document (i.e. what the reader is to take from them). They struck
me as an arbitrary set of rather poorly detailed cases - I'm sure the authors had some reasons for
selecting them, but this was not evident.

My final general quibble is with the highly qualitative nature of many  of the conclusions on
ecological effects, and the general presumption that an effect is the same as an adverse effect.
The chapter is littered with phrases such as "could cause", "are thought to", etc. There is an
implicit assumption throughout that ecosystems are in their optimal  states before NAAQS-
relevant sources are added to the world, and that all these sources can do is weaken ecosystem
health. Perhaps the authors don't intend this implicit assumption,  or the impression that the
phrases I mention count as strong evidence for any sort of belief, but I was left uneasy with many
of the conclusions for the reasons above.

I now have some specific comments on parts of Chapter 5:

1.  On Page 5-2 at the bottom, the authors conclude that measurements below the detection limit
cause "irresolvable uncertainty in these data". I  agree with the sentiment here, but there are
policy and regulatory decisions that can be made that don't have this "irresolvable uncertainty".
For example,  if the regulatory limit is well above the detection limit, and all the positive results
are below  the regulatory limit, then a large number of results below the detection limit does not
                                                                                      31

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prevent a decision as to whether a site is in compliance to be made with high levels of certainty.
Whether the "irresolvable uncertainty" has any implications for decisions depends entirely on the
kind of decision being taken.

2. On Page 5-4, first bullet, the authors state that "annual NOx has decreased < 35% over the
years". It was not clear whether this is to mean it has decreased by less than 35% of the baseline
year (1990) or has decreased TO LESS THAN 35% of the value in the baseline year.

3. On Page 5-6, the authors correctly state that it is possible that small amounts of SO2 may be
beneficial. It would be useful to indicate how this amount compares to the levels considered
under a NAAQS and the levels currently found in the environment. If the amounts that are
beneficial overlap the amounts found in the environment, this has significant implications for the
NAAQS. And it also would be useful to characterize the evidence for beneficial effects, since it
indicates that the exposure-response curve may be U-shaped. Focusing only on the "bad" effects
leaves the document open to charges of bias and presumes there is some sort of monotonic
increase of bad effects with exposure, or a threshold below which effects don't occur (but also
are not beneficial).

4. In that same paragraph, the authors state that lack of observation of a change doesn't mean
that no change is taking place (it may have been below the ability to detect such a change). I just
want to be sure it is also understood that this statement cannot be used to therefore justify
regulatory action; the evidence simply becomes neutral with respect to decisions being taken.

5. On Page 5-11, the  second bullet, the authors conclude that a lack of relationship may indicate
that the trends are on a time scale longer than is being  measured. Well, yes, this could be the
case. Or it could just  be that there IS no relationship. I find this pattern throughout the document:
a tendency  to explain away a lack of relationship as being due to some limitation in the data,
rather than  the simpler, and more truthful, claim that there has been no trend observed to date.

6. On Page 5-12, first bullet, line 16, the term "likelihood" is used. I couldn't figure out the sense
in which it  is being used here. I assume it is not in the  statistical sense.

7. On Page 5-15, last full paragraph, the final  sentence doesn't seem to me to follow from the
evidence presented, unless one assumes that ANC values are the sole determinant of acidic
episodes. I won't comment further on this, because it is not my area of expertise, but this implicit
assumption must be made and so I was left wondering where the evidence was given to support
it.

8. Throughout the discussion on NOx and SOx deposition, I could not find any recognition, or at
least explicit consideration, of deposition onto land that then enters a waterbody through run-off.
I am assuming it is being considered even if not called out directly in the text.(?)

9. On Page 5-17, last bullet, the issue of Hg increasing in fish is brought up. I realize that the
authors are suggesting here that this increase above "safe" levels is due in part to the effects of
acidic deposition, but this section is focused on effects and no specific effect is mentioned
(unless one takes the  increased Hg itself as an effect, which is what I presume the authors
                                                                                      32

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intend). But there should at least be some mention of the extent to which this increase in Hg is
due to the effects of acidic deposition and not just to loading of the original Hg into the waters.

10. On Page 5-18, first paragraph under 5.5, we find another instance in which a change is
automatically considered adverse. The argument is that excess N creates "unnatural rates in some
species and change in the competitive interactions...". This is then followed by the claim that
this will decrease ecosystem health and biodiversity. Again, I am not an ecologist, but my
reading of the literature suggests it is far from evident that all such changes weaken ecosystem
health (unless one assumes a priori that ecosystems are in their optimal state of health absent
increased N). Or the key may be in the term "excess". Perhaps the authors have some idea as to
what level of N constitutes an "excess" and are referring only to this condition, in which case we
have a tautology (the level of N that  is "excess" being by definition the level of N that causes
weakened ecosystem health). Without addressing this issue, the reader is likely to assume that
"excess" is the same as "increased",  which would not be true.

11. On Page 5-19  at the top, it seems to me that there is an assumption being made here that all N
in the system is bioavailable. I may be wrong in this, but it does seem to me that assumption is
inherent in the paragraph. At the bottom of that same page, the authors refer to the "availability
of NO3-. I wonder if they mean "bioavailability" or if the two terms are interchangeable.

12. On Page 5-21, line 13, it is noted that a change  in shoot-to-root ratio can be adverse. I would
guess it is adverse primarily if the ratio increases, not decreases.

13. On Page 5-26, line 12, it is mentioned that the function is not linear, but no indication is
given of the kind of non-linearity it represents. Some clarity here would be good (threshold,
positive second derivative, negative  second derivative, U-shaped, etc).

14. The Regional Trends sections struck me as unsatisfactory throughout the chapter. I was never
clear, in any of them, what important conclusions, related to a NAAQS decision, I was to take
away. It wasn't even made clear why a regional trend is of interest.

15. On Page 5-31, a list of biological measurements to assess eutrophic condition is provided.
But I don't see why this  list is here. I can find no way in which it informs the later discussion or
conclusions.

16. The discussion of Greenhouse Gases beginning on Page 5-35 is confusing, or at least given in
too much of a sketch. I haven't any idea what the reader is take away from this.

17. On Page 5-36, the first sentence states that in the chapter data were "integrated and
collectively considered in formulating conclusions". I don't think the chapter accomplished this,
or made it evident. I am  not saying the conclusions are wrong, or that the authors didn't have
good reasons for giving them. I am simply saying that the chapter doesn't lay out all clearly how
the data were "integrated and collectively considered". I would be more inclined to say that the
data were collected together, the authors considered them, and conclusions were formulated (in
ways that are not transparent to the reader).
                                                                                       33

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18. On Page 5-37, line 11, there is an instance of something that appears in other places in the
chapter. Some N and S deposition rates are mentioned, but there is no indication given as to
whether these are large or small compared to deposition rates one would expect under NAAQS
levels. The reader is left, therefore, wondering whether these deposition rates are significant with
respect to any decisions that must be taken under NAAQS.

19. The final sentence of the chapter is that "The Chesapeake Bay is an example of a large well-
studied estuary that receives 21 - 30% of its total N load from the atmosphere". This seems a
very odd way to end the  chapter, as this sentence is essentially a non sequitur and certainly
doesn't summarize any of the important conclusions.
                                                                                      34

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                             Dr. Charles T. Driscoll, Jr.
I have a few general comments that I will relay to you in this letter and the enclosed file has my
detailed comments.  I was disappointed in the ISA.  The scope is generally fine but the text is not
polished. It does not appear that the document was particularly well edited.  As a result, I have
considerable comments.

I have a few concerns with the document. Sections are highly redundant.  With a bit of editing, I
would guess that the length could be decreased 25%. The referencing of the document is
uneven. There are many instances where facts are stated that  are not common knowledge and no
citation is provided. I would think that this approach would not be acceptable. Other sections of
the document are referenced adequately.

There are several statements that are made which are incorrect.  I have either noted these or
corrected the text.

I do not like the approach as on 1-6, line 26 "Chapter 2 highlights".  This is grammatically
incorrect. A chapter is an inanimate object and cannot highlight anything. This is done
throughout  the document. It should be corrected.

The section on sampling and analysis for NOX and SOX (2.6) while interesting, is long and could
easily be put in an Appendix.

I understand that I really don't have much say in the matter, but interests would be best served if
the scope of the ISA was expanded to include base cation and Cl" deposition. Cl" is probably
largely derived from coal combustion or industrial processes at least away from the coast. Both
base cations are Cl" deposition can influence the acid-base chemistry of ecosystems.

•  In Chapter 3 (3-28), shouldn't some mention be made of cloud deposition?

•  In this section (3-28, 15), it is mentioned that NH3 is not included in deposition estimates.
   Another problem that isn't mentioned is DON deposition. This should be added to the text.

•  The document is made confusing by mixed units and symbols. Mass and molar, English and
   metric.  It seems that there is no unit or scale that is not used in this document.

•  Also different ways of expressing units are used (e.g., kg/ha-yr vs. kg ha"1 yr"1).  A consistent
   format should be used throughout the document.
                                                                                     35

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                  Specific Comments on Integrated Science Assessment
               for Oxides of Nitrogen and Sulfur in Environmental Criteria
Chapter 2

Page 2-2, line 5             Reference needed.

Page 2-3                   Figure title:  Define M, PAH, PAN

Page 2-4, line 6             Change to:  ... (e.g. nitrosamines, nitro-PAHs)

Page 2-5, line 23            Change to:  ... effectively no chemical or physical removal
                           mechanism in the ....

Page 2-10, line 24           Make italics:  in situ

Page 2-11, line 4            H+

Page 2-11, line 12           Change to:  ... compounds affect

Page 2-14, line 6            Change to:   ...  acidity, at adequate concentrations it affects...

Page 2-14, line 19           Change to:   For any [NHX] in the system...  condensed phase
                           (Reaction 2.4-4).

Page 2-16, line 17           Change to:  ... Earth's surface...

Page 2-19, line 27           Change to:   .... oversaturated with ....

Page 2-21, line 22           Make italics: in situ

Page 2-21, line 25           Change to:  An overview of the three satellite... backscatter is
                           contained in Table 2.6-1.

Page 2-21, line 27           Change to:  Total column [NCh]...  satellite is shown on Figure
                           2.6-1.

Page 2-23, line 9            Change to:  ...; see the more complete description ...

Page 2-28, line 12           Change to:  Excess NH3  alone or together with NOX can enhance
                           to terrestrial and aquatic ecosystems.

Page 2-29, line 7            Change to:  ... networks  is sparse over...
                                                                                     36

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Chapter 3

Page 3-1, line 11            Change to: In this section brief summaries... (NH4+) are provided.

Page 3-2                   Section 3.1.2.1 Soils.  This section needs some citations.

Page 3-2, line 20            Isn't N2 the dominant soil gas?

Page 3-2, line 30            Is there a typo here?  Do you mean "Although N2O is not
                           reactive...?

Page 3-3, line 4             Do you mean.. .oxidation of NH3 released ....?

Page 3-3, line 24            Is there a word or something missing? This sentence doesn't make
                           sense.

Page 3-3, line 28            What is meant by fuel N loadings?  Clarify.

Page 3-3, line 31            What section?

Page 3-4, Line 3 & 4        Need a reference

Page 3-4, line 23            Change to:   ... and this pattern remains...

Page 3-5, line 5             This sentence doesn't make sense, please clarify.

Page 3-5, line 9             What is meant by "stimulated through soil management"?

Page 3-5, line 12            You don't really want the brackets here do you?

Page 3-5, line 29            Cultivation of soil with high organics content is not an addition of
                           N as indicated in the sentence that follows.

Page 3-6, line 1             Change to:  ... of which a small portion

Page 3-6, line 30            Change to:  Data for 862 emissions... state level totals are
                           depicted in Figure 3.2-1.

Page 3-7, line 6             Change to:  The magnitude and spatial  distribution... in the ARP
                           is depicted in Figure 3.2-2 for the CONUS.

Page 3-7, line 7             Change to: .... continuing elevated density of SC>2 emission
                           sources in the ... compared to the West, particularly in the Central
                           Ohio River Valley.

Page 3-9, line 2             Change to:  ... increases with increasing fire intensity.
                                                                                      37

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Page 3-9, line 12            Change to:   ... emissions are lower. Reduced light levels...

Page 3-9, line 16            Change to:  However, note that...

Page 3-9, line 30            Need a citation

Page 3-12, line 23,24        Need citations

Page 3-14, line 7            Change to: The networks, sponsoring agencies... are listed in
                           Annex Table AX2.5-1.

Page 3-20, line 1            Does CASTNET really have cation data? I never knew that.

Page 3-20, line 19           Change to:  ... of ~ 90 sites. In addition the seven Atmospheric


                           Also doesn't AIRMon provide gas and particle chemistry and
                           estimates of dry deposition?

Page 3-22, line 31           Change to:  Contributions from several... than 30 years are
                           summarized in Annex Table AX2.5-5.

Page 3-23, line 9            Change to:  Ambient [NC^] ... through 2005 is shown in Figure
                           3.7-1.

Page 3-24, Para. 1           Need citations

Page 3-25, line 6            Change to:   ... evident along the Ohio ...

Page 3-25, line 7            Change to:  ... have been decreasing throughout...

Page 3-25, line 9,10         Define CMSAs and LOD

Page 3-26                  Figure title:  Lower case  c in concentration

Page 3-26, line 3            Change to:  The composite diel...  database is shown in Figure 3.7-
                           4.

Page 3-27                  Figure title:  Clarify what is meant by "in focus".

Page 3-27, line 1            Change to:   ... by sources some distance above the Earth's
                           surface.

Page 3-33, line 3            Change to:  Note, however, ...
                                                                                    38

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Page 3-33, line 26           Change to:  ... are problematic because ....

Page 3-34, line 4            Change to:  ... a similar relative decrease

Page 3-35                  Figure title:  Clarify what is meant by (V10

Page 3-36, line 26           Change to:  ... observed fluxes described here are compared in
                           Figure 3.9-5.

Page 3-44, line 28           Change to:  Results of a ..., respectively are shown in Figures
                           3.10-1 and 3.10-2.

Page 3-44                  In the comparison of measured and modeled deposition (e.g.
                           Figure 3.10-1) some discussion should be given on testing dry
                           deposition fluxes. Also in Figure 3.10-1 the fluxes are given on an
                           annual basis. What about patterns for other time intervals such as
                           monthly or weekly? The scatter should be much greater. Should
                           other predicted values for shorter time intervals be discussed?

Page 3-45, line 4            Why is this a critical load?  This definition seems inconsistent with
                           the remainder of the document. Please clarify.

Page 3-48                  The statement in the first paragraph that atmospheric load is equal
                           or exceeds riverine load (line 8) is inconsistent with the statement
                           in the 4th paragraph that atmospheric deposition is 10-40% of the
                           total load. This needs to be  clarified.  Also a reference for the 10-
                           40% contribution value needs to be referenced (Castro and Driscoll
                           2002?).

Page 3-50, line 4            Change to:  Several waterbodies ... to total N loads are listed in
                           Table 3.11-1.

Page 3-50, line 15           I do not believe the statement that 30-70% of the volume of animal
                           waste is emitted as NHa. This is not possible.  The statement needs
                           to be fixed.

Page 3-50, line 21           Change to:  Several important watersheds ... airsheds are listed in
                           Table 3.11-3 and 3.11-4.

Page 3-50, line 23           Reference is needed to justify the statement on larger airsheds for
                           oxidized N.

Page 3-51, line 1            Change title: 3.12 Background (PER) concentrations and
                           deposition of NOX and SOX
                                                                                      39

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Page 3-51, line 20           Change to:  The annual mean [NCh] ... [NCh] (bottom panel) are
                           shown in Figure 3.2-1.

Page 3-53                  Give complete figure title. Don't be lazy.

Page 3-54, line 8            Change to:  The highest values are ... Ohio River Valley (Figure
                           3.12-3 (upper panel)).

Page 3-54, line 23           Change to:  Results from ...  (Bey et al., 2001) is shown in Figure
                           3.12-5.

Page 3-55                  Again, give complete figure title

Page 3-56                  Again, give complete figure title

Page 3-59, line 7, 16        In addition to giving background concentrations, the summary
                           should provide deposition values.

Page 3-59, line 12           Give the reader the specific percentage that EGUs contribute to
                           SO2 emissions.

Page 3-59, line 29           Again, that statement about the NH3 contribution from animal
                           waste is incorrect and needs to be fixed.

Page 3-60, line 21,26        Again, the inconsistent statement about the atmospheric
                           contribution to the total estuarine input needs to be made
                           consistent. The 10-40% value is the correct statement (Castro and
                           Driscoll 2002).

Page 3-62                  Is this the original reference?  It is difficult to believe.


Chapter 4

** There needs to be a global search on this chapter on sulfate.  It should be SC>42".  The entire
chapter needs to be fixed. Also throughout the document, the authors refer to "inorganic Al".
There needs to be a global search on this.  This needs to be referred to as "dissolved inorganic
Al" or "monomeric inorganic Al". Much of particulate matter or soil is inorganic Al.  The
authors want to refer to dissolved inorganic Al. **

Page 4-1, line 8             Change to:  A discussion of acidification is presented in Section
                           4.2. Nitrogen (N) enrichment is discussed in Section 4.3.

Page 4-1, line 19            Change to:  ... , information is presented in this Integrated
                           Science Assessment (ISA) that was collected...
                                                                                      40

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Page 4-3, line 1             Change to:  Critical loads as a ... quantifying disturbance is
                           discussed in the following section.

Page 4-7                   Paragraph 1:   There is no discussion of target loads here.  Should
                           the text be expanded to address the concept of target loads?

Page 4-7, line 24            Change to:   ... is the accumulation of hydrogen ion (H+)  ...

Page 4-7                   Section 4.2.1.1: This section on soil acidification is woefully
                           inadequate.  Soil acidification is really the loss of base cations plus
                           the accumulation of acidic anions.  The authors should refer to van
                           Breemen et al. (1983) or Binkley and Richter (1987).

Page 4-9                   The incorrect figure is with this figure title.

Page 4-10, line  1            The statement of mobility of sulfate governing most aspects of soil
                           and water acidification is simply not true and demonstrates a
                           complete lack of understanding of the process. This needs to be
                           corrected.

Page 4-10, line  6            Change to:   ... deposited S is transported to the soil ...

Page 4-10, line  7            Change to:   ... acts as a mobile  anion at...

Page 4-10                  Paragraph 2:   References are needed to document statements made
                           in the paragraph.

Page 4-10, line  11           Change to:   ... leaching of cations, and ...

Page 4-10, line  13           Change to:   ... When S is transported from ....

Page 4-10                  Last paragraph: You need to clarify why accumulated sulfate is
                           slowly released from soil.

Page 4-11, line  2            Change to:   ... the accumulation of the historic legacy of
                           atmospheric S deposition in soil was ...

Page 4-11, line  9            Change to:   ... and the difficulty in discerning the effects of net
                           SC>42" description and net S mineralization make it difficult...

Page 4-12                  Paragraph 1:   Virtually all mass balance studies show N retention.
                           See Campbell et al. (2004) for example.

Page 4-12                  Paragraphs 1 and 2:  References are needed to document the
                           statements made.
                                                                                       41

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Page 4-12, line 9            Change to:  ... between atmospheric N deposition and the C:N...

Page 4-13, line 3            Add .. .leaching to surface waters in the eastern United States
                           (Aber et al. 2003)

Page 4-13, line 8            Change to:  ... Although concentrations of NOs" are typically less
                           than SC>42" in drainage waters...

Page 4-13, line 12           Change to:  ... leaching from forest ecosystems...

Page 4-13                  Paragraph 3 - References are needed...

Page 4-13, line 14           Clarify sentence

Page 4-13, line 20           Change to:  ... most noteworthy effect of ....

Page 4-14, line 1            Change to:  ... This pattern was likely due ...

Page 4-14                  Paragraph 2: References needed ....

Page 4-14, line 21           Change to:  ... S and N in acidic deposition enhance inputs of
                           strong acid anions that can accelerate ...

Page 4-14, line 25           Change to:  ... plant nutrients from  soil; and...

Page 4-15                  Paragraph 1: Reference needed....

Page 4-15, line 10           Change to:  ... documented decreases in base saturation of...

Page 4-15, line 16           This statement is not correct. Likens et al. (1996) and Kirchner
                           and Lydersen (1995) documented decreases in  stream
                           concentrations of base cations due to decreased leaching from the
                           soil exchange complex. They document decreases in soil
                           exchangeable pools  of base cations due to elevated acidic
                           deposition.

Page 4-15, line 27           Should cite Cronan and Schofield (1990)

Page 4-15, line 29           Change to:  ... deposition because inorganic monomeric ...
Page 4-16                  Paragraph 2:  References needed....

Page 4-16, line 30           Change to:  ... deposition tends to remain in solution ...

Page 4-17, line 1            Need to clarify this sentence. Changes in concentrations of base
                           cations do not necessarily result in increases in dissolved inorganic
                           aluminum.
                                                                                      42

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Page 4-17, line 8,9          Change to:   ... as chronic condition or episodic condition.
                           Chronic condition refers to annual ...

Page 4-17, line 11           Change to:   ... Episodic condition refers to ...

Page 4-17, line 12           Change to:   ... provide less neutralization of....

Page 4-17, line 18           Change to:   ... acidic deposition likely has substantially increased


Page 4-17, line 20           Change to:   ... Many streams that exhibit chemical conditions
                           during ...

Page 4-17, line 24           Need to define ANC

Page 4-17, line 25           Change to:  in the central Appalachian Mountain region ... (a
                           reference is also needed to document this statement)

Page 4-18                  Figure title. The figure is incorrect for the figure title and text
                           citation. Also in situ should be in italics.

Page 4-19, line 19           The statement here is not exactly correct.  The difference between
                           summer and spring ANC during baseflow conditions was on
                           average 30 jieq/L. This means that acidic episodes would occur on
                           average when summer ANC values reached 30 jieq/L.

Page 4-19, line 23           Define: episodic  ANC

Page 4-19, line 28           Change to:   ... contact with ANC supplying materials ...

Page 4-20, line 2            Change to:   ... this pattern can be ...

Page 4-20, line 6            Reference needed ...

Page 4-21, line 1            Make italics: in situ

Page 4-21, line 4            Change to:   ... during low flow, there is a shift to conditions of
                           moderate to severe episodic acidification during high flow that
                           showed higher ...

Page 4-22, line 28           Change to:  ... 2002), larger-term trends in ...

Page 4-22, line 28,29        Sentence not clear, please clarify

Page 4-23, line 12           Should the title be Terrestrial Ecosystems or Forest Ecosystems?
                                                                                       43

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Page 4-23                  4.2.2. Terrestrial Ecosystems. Should enhanced leaching of
                           nutrient cations from the canopy due to acidic deposition be
                           mentioned in this section?

Page 4-24                  Paragraph 1:  Reference needed

Page 4-24                  Paragraph 2 and elsewhere:  Throughout the document the authors
                           discuss soil horizons as though they are always and only
                           Spodosols. I don't believe that the only sensitive soils are
                           Spodosols. Aren't other soil types important?  When the authors
                           refer to O and B horizons, they need to clarify the geographic
                           context they are discussing, and if they are referring to all
                           Spodosols.

Page 4-24, line 10           Why is the Bs horizon more sensitive than the Oa horizon in the
                           forest floor? I believe that the forest floor is more susceptible to
                           cation change from acidic deposition than the mineral soil. Most
                           of the roots are  in the forest floor.  Is a 20% loss of Ca2+ in the
                           forest floor less important than a 50% loss of Ca2+ in the mineral
                           soil?

Page 4-25, line 2            Do we actually  know that Al only becomes mobilized after Ca2+
                           becomes depleted? If this is true (I don't believe it) how about a
                           reference documenting it?

Page 4-26, line 10           Need a reference

Page 4-26, line 17           Change to:  ... nitrification rates are difficult to measure directly
Page 4-28, line 2            Do you mean terrestrial or forest?

Page 4-29, line 4            Has there been red spruce decline in the Southeast?  Please provide
                           a reference.

Page 4-29, line 14           Need a reference

Page 4-31, line 25,26        Change to:  ... A conceptual view.. .maple decline is provided in
                           Figure 4.2-2.

Page 4-33, line 6,7          Clarify sentence

Page 4-33                  I think Juice et al. (2006) shows some compelling data on sugar
                           maple response to Ca addition. The authors should consider
                           mentioning this work.
                                                                                      44

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Page 4-34, line 2,3          This section is on tree health.  Why mention soil cation depletion
                           here? Wouldn't it be more appropriate in the soil effects section?

Page 4-40                  Note that while temporal patterns in surface water N(V loss are
                           confusing and variable. Aber et al. (2003) shows that there are
                           spatial patterns across the region which are consistent with
                           atmospheric N deposition contributing to elevated NO3" leaching.

Page 4-41, line 18           Change to:   ... Efforts to explain the complex patterns in ...

Page 4-43, 14-16            Likens et al. (1998) showed increased losses of Ca2+ with flow
                           during the 1960s and a declining pattern in later years.

Page 4-44, line 18           How do Shenandoah streams show changes in soil sulfate
                           adsorption?  Please clarify.  One important observation that is
                           ignored in this report is that although surface water ANC appears
                           to be increasing, soil losses of exchangeable cations are continuing
                           despite reductions in acidic deposition. This observation should
                           me mentioned somewhere in the document.

Page 4-46, line 8-10         How large is large?

Page 4-46                  Do you really believe this statement is true? Virtually all studies
                           that measure major ion chemistry measure pH. I believe that ANC
                           is more commonly focused on because it is more straight forward.
                           pH is a non-linear measurement and its changes are difficult to
                           interpret as trends.

Page 4-47                  The statement that waters with ANC < 0  jieq/L have "no capacity
                           to neutralize acid inputs" is not true. An  ANC value below 0
                           |ieq/L simply means that H+ values are elevated (the solution pH is
                           below the equivalence point). This statement needs to be
                           corrected.

Page 4-48, line 7,8          Change to:   acidification (a decrease in ANC observed...)

Page 4-48, line 15           Where is Table 4.2-4?

Page 4-49, line 1            The units should be |ieq/L-yr.

Page 4-49, line 2            Change to:   ... represent significant trends towards...

Page 4-49, line 11           Change to:  ...  ANC below zero |ieq/L.

Page 4-49, line 20           Add Driscoll et al. (1988)
                                                                                      45

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Page 4-51, line 9,10         These conditions can also result in direct mortality as results from
                           in situ bioassays show (Van Sickle et al. 1996).

Page 4-51, line 12           Add reference

Page 4-51, line 15           Change to:   ... vigor, and reproductive success; and

Page 4-57, line 8            Table 4.2-6 - is missing

Page 4-57, line 15           Change to:   ... relationships are complex, however, ...

Page 4-57, line 22           Change to:   ... However, note that effects...

Page 4-60, line 16           Change to:   Note that the absence ...

Page 4-61                  Figure:  It would be helpful if a comment was made on the
                           consistency of Figure 4.2-11 with 4.2-10.  Although the line 4.2-10
                           is different. The values on the two figures  actually seem quite
                           similar. Is fish diversity response to acidification similar in the
                           Adirondacks and Virginia?

Page 4-66, line 6            What does this mean evaporative concentration? Please clarify.

Page 4-69, line 1            Change to:   ... conditions in the Park for ...

Page 4-69, line 14           Elsewhere in the document Al  concentrations are expressed in
                           |imol/L.

4-70, line 22                Aren't the USDA Forest Inventory Data (FIA) available? Please
                           clarify.

Page 4-71, line 9            Change to:  Note that the McNulty...

Page 4-72, line 1            Red spruce are generally  found at higher elevations.

Page 4-72, line 5            Change to:   ... sugar maple which are ....

Page 4-72, line 7            Change to:   ... areas where sugar maples appear to be ...

Page 4-73, line 28           Change to:  Note that critical loads...

Page 4-74                  4.2.4.3.2:   The text in this section is redundant with the previous
                           material presented.

Page 4-74, line 20           Give the specific %.
                                                                                       46

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Page 4-76, line 11           Change to:  ... 1991 levels of stream area that was suitable for
                           brook trout survival

Page 4-76, line 18           Change to:   ... required to restore watershed soils...
                           (Note throughout the document, the authors use the term buffering
                           capacity incorrectly. Please correct this.)

Page 4-76, line 25           Change to:   ... was partly because SC>42" adsorption
                           Also throughout the document, the authors refer to sulfur
                           adsorption.  I believe it is more appropriate to refer to sulfate
                           adsorption.

Page 4-77, line 30           Change to:   ... For aquatic ecosystems, ....

Page 4-79, line 30,31        Change to:   ... ANC have been increased through liming...

Page 4-80, line 14           Change to:   ... (e.g., pH,  Al, Ca, ANC, DOC, dissolved OC)...
                           Why  do the authors use the term dissolved OC? Why not use
                           DOC? Most readers will be familiar with this term.

Page 4-81, line 4            Change to:   ... increased  with lake pH and ....

Page 4-81, line 20           Change to:   .. .low weathering rates (Driscoll et al. 1991, Sullivan
                           et al.  2006a)

Page 4-82, line 2,3          Need a reference

Page 4-82, line 25,26        Need a reference

Page 4-84                  Figure 4.2-14:  Why not update this figure and show the most
                           complete time series of precipitation chemistry?

Page 4-84, line 23           Change to:   ... The hydrogen ion deposited  ....

Page 4-87, line 6            Change to:   ... model simulations coupled with population-level
                           extrapolations suggest that...

Page 4-87, line 23           Change to:   ... cations, hydrogen ion and ....

Page 4-89, line 15           This statement is not exactly true and needs to be qualified. These
                           authors provided an upper limit of organic acid content and as a
                           result greatly understated the number of fishless lakes due to acidic
                           deposition.  This is a very  important mistake  and needs to be
                           clarified.
                                                                                       47

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Page 4-89, line 22           Change to:   ... pH and ANC decreased substantially...

Page 4-89, line 26           Note that Van Sickle et al. (1996) was part of the ERP and not
                           subsequent to it.

Page 4-90, line 14           Change to:   ... from 1982-2000 in the original 16 ALTM ...

Page 4-90, line 15,16        Change to:   ... from 1992 to 2000 in the complete set of 48
                           ALTM lakes. (Note that 32 additional lakes were added to the
                           program in 1992). They found  ...

Page 4-92                  Figure 4.2-18.  You have the incorrect citation for this figure. It
                           should be Driscoll et al. (2003a).

Page 4-92, line 4            The population-base estimates need to be mentioned earlier in the
                           text where this study is first mentioned.

Page 4-93                  Figure title:  Change to:  ... ANC at three dates for the
                           population.

Page 4-94, line?             Note this citation is not correct. Chen and Driscoll (2004) applied
                           the model to the DDRP lakes.

Page 4-94                  Paragraph 2:   Why  not add a sentence or two on the modeled
                           changes in zooplankton and fish species diversity that are
                           discussed in  Sullivan et al. (2006b)?

Page 4-94, line 30-32        No! Watersheds that are sensitive to mercury deposition are
                           forested, have an abundance of wetlands, shallow hydrologic flow
                           paths, are unproductive and impacted by acidic deposition
                           (Driscoll  et al. 2007).

Page 4-95, line 27           Change to:   ... streams in the Park is linked ...

Page 4-95, line 28           Change to:   ... soils to adsorb  SC>42" is decreasing due to the long-
                           term accumulation of SC>42" on soil adsorption sites associated with
                           a legacy of elevated  acidic deposition.

Page 4-97, line 14           Change to:   ... At the low-ANC (~0 |ieq/L) ...

Page 4-97, line 16           Change to:   ... Increases in base cations tended to compensate...

Page 4-97, line 26           Change to:   ... NCV concentrations usually increased...

Page 4-97, line 29           Change to:   ... to the changes in ANC of Paine Run.. .River, and
                           contributed to decreases in ANC in Piney River.
                                                                                     48

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Page 4-98, line 3,4          Note that base flow ANC is controlled by bedrock geology.

Page 4-98, line 6            Note during high flow, the shallow flow paths diminishes contact
                           between ...

Page 4-98, line 5            Change to:   ..., probably because SC>42" adsorption ...

Page 4-99, line 1            Change to:   ... more vulnerable to adverse effects of episodic
                           acidification ...

Page 4-101                 Paragraph 1:  Isn't this material redundant with p. 76?

Page 4-101, line 8,9         These categories should have been defined previously in the text
                           when they are first mentioned.

Page 4-101, line 31          What are sensitive Si-based watersheds? Please clarify.
                           Somewhere the definition of sensitive southeastern watersheds
                           needs to be defined:  siliciclastic, granitic, and basaltic

Page 4-101, line 32          Is the loading kg S/ha-yr or as SO42"? Clarify.

Page 4-102, line 1           Change to:   ... Prior to the Industrial Revolution, most....

Page 4-102, line 3           Again, define Southeast watershed sensitivity and be consistent
                           using it throughout the text.

Page 4-102, line 10          Clarify what is meant by small areas

Page 4-104, line 7,8         Here you finally define the watershed sensitivity classes. Use
                           these terms throughout the text.

Page 4-104, line 25          Change to:   ... N is transported between air ...

Page 4-104, line 27          Change to:   ... because it is transported from the ....

Page 4-104, line 31          Change to:   ... Leaching from soil, ....

Page 4-104, line 32          I don't believe that nitrate leaching from atmospheric deposition
                           results in a violation of drinking water standards (>10 mg N/L).
                           Where?  I defy you to provide a reference(s).

Page 4-105                 Also mention causes of declines in submerged aquatic vegetation
                           (SAV) and causes of increases in nuisance algae species.

Page 4-105, line 3,4         see P. 112
                                                                                       49

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Page 4-105                 Note that nitrogen is also part of proteins, not only enzymes.

Page 4-106, line 29         Change to:   ... N leaches from soils to ....

Page 4-109, line 21,24       Delete parenthesis from NO3" plus NH4+ on both lines

Page 4-111, line 5-7         Redundant.  Denitrification has been defined previously.

Page 4-112, line 11,12       See below inconsistent with plot on p.  105

Page 4-112, line 19         Change to:   ... are generally thought to reduce ...

Page 4-112, line 22,23       The  methane response to nitrogen addition is confusing and
                           inconsistent. This section should be rewritten.

Page 4-113, line 5           Change to:  Note that the N enrichment...

Page 4-114, line 2           Change to:   ... in the eastern United States (Driscoll et al. 2003a).

Page 4-114, line 21         Change to:   ... fresh surface waters are: (1) elevated...

Page 4-114, line 22         Change to:   ... water; and (2) ....

Page 4-114, line 24,25       Need reference

Page 4-114, line 26         Change to:   ... in the Adirondacks (Aber et al. 2003)

Page 4-116, line 22         Change to:  ...  This pattern suggests that N ...

Page 4-116, line            Should you  mention increases in populations of nuisance algae?

Page 4-119, line 15         Change to:   ... not generally account for all wastewater inputs

Page 4-119, line 16-23       Should also cite Castro and Driscoll (2002).

Page 4-120                 Change to:  ...  Source: (Driscoll et al. 2003b).

Page 4-126, line 15         These units  do not make sense.  What is the areal basis of the
                           application?

Page 4-129, line 16         4.3.3.1.4 Herbaceous Plants and Shrubs - Move to forest section

Page 4-132, line 3           Change to:  ... This pattern suggests selective ...

Page 4-132, line 14         Change to:   ... In the reference plots,  five species...
                                                                                       50

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Page 4-132, line 14-16       I do not understand this sentence.  Please clarify.

Page 4-135, line 1           This would be much more useful if expressed as a loading rate.
                           The units shown here do not make sense mg/L-yr?

Page 4-135, line 32          Make italics: in situ

Page 4-138, line 17, 18      Make italics: in situ

Page 4-145, line 12          Make italics: in situ

Page 4-145, line 18          Change to:  ... (e.g., cyanobacteria, dinoflagellates)

Page 4-146, line 1           Note Driscoll et al. (2003) is not the original citation. It should be
                           (Valiela et al. 1990).

Page 4-147, line 27,28       Change to:  An overview of the sensitive ecosystems is given in
                           Table 4.3-2.

Page 4-152, line 9           Make italics: in situ

Page 4-152, line 28          Change to:  ... future outlook of the U.S. estuaries based ...

Page 4-154, line 2           Change to:  ... limited, though note that many ....

Page 4-160, line 26          Define very low.  Isn't it generally defined as <2 mg/L?

Page 4-163, line 27          Change to:  ... oxygen content, supply of labile organic carbon,
                           temperature, pH ...

Page 4-165, line 2           Please clarify the mass basis of the loading Kg S/ha or Kg SOVha?

Page 4-166, line 3,4         This statement is incorrect and misleading. High production of
                           sulfide will limit methyl mercury production (Benoit et al. 2003).
                           This sentence needs to be rewritten.

Page 4-166, line 30          Change to:  ... watershed soils and the transport of naturally...

Page 4-168                 Section 4.4.1.2.2:  There is no reference to effects of mercury on
                           song birds and terrestrial food chains (see (Rimmer et al. 2005).

Page 4-169                 No reference is made of Drevnick  et al. (2007) which suggests a
                           link between declines in atmospheric S deposition and fish Hg.
                                                                                      51

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Page 4-170, line 28         What is SC>42" deficit? I never heard of such a thing. Please
                           clarify.

Page 4-171, line 26         Change to:   ... Pollutants must be transported from the ....

Page 4-171, line 27         Change to:   ... Although the transport of pollutants...

Page 4-172, line 23-25       Change to:   ... concentrations of SO2. The effect of SO2 on
                           vegetation are summarized including some discussion of the
                           limited recent literature.

Page 4-176, line 27,28       Change to:   ... In Annex 7, a short list of GHGs and the
                           environmental factors.... of climate change are provided in Table
                           7-1.  A comprehensive...

Page 4-177, line 22         Change to:   ... The additional laboratory study  ...

Page 4-177, line 25         Change to:   ... 145 yr old beech tree ...

Page 4-179, line 4           Change to:   ... temperature, precipitation, and forest soil ...

Page 4-179, line 10         Change to:   ... show increasing temperature increases ...

Page 4-179, line 21         Change to:   ... ground water NO3" concentration is elevated ...

Page 4-179                 Again, I can't believe that atmospheric N deposition results in
                           surface water concentrations that approach drinking water
                           standards. Please provide a reference.


Chapter 5

Page 5-3, line 11            Change to:   ... networks is greatly limited over large ...

Page 5-5, line 23,24         As indicated before, this statement is not correct and inconsistent
                           with lines 25 and 30 immediately below. Please fix.

Page 5-6, line 1             What ecological effects does S deposition have on Chesapeake
                           Bay?

Page 5-6, line 14            Change to:   ... including topography vegetation, soil chemistry ..

Page 5-8, line 9             Change to:  ... There are several indicators of stress...

Page 5-9                   Paragraph 1: Need reference.
                                                                                       52

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Page 5-9                   Bullet:  A number of studies show ongoing soil acidification (i.e.,
                           net Ca2+ loss) despite decreases in acidic deposition (Bailey et al.
                           1996, Likens et al. 1998, Huntington et al. 2000).

Page 5-9, line 24            Change to:  ... as the pH decreases below 6.0

Page 5-10, line 14           Change to:  ... which tend to provide less neutralizing of ...

Page 5-12, line 12           The sentence as written does not make sense. Please change.
                           Change to:  ... Decreases in pH below values of 6.0 typically

Page 5-14, line 19           Change to:  ... in the pH range 5.0 to 6.0

Page 5-14                  Fourth bullet - Change to:   ... decrease in ANC below	|ieq/L.
                           Again, this sentence needs to be clarified. There is some threshold
                           ANC below which effects are evident. My guess is that it is about
                           100 |ieq/L.

Page 5-15, line 20           Change to:  ... that where chronically acidic during summer in the


Page 5-16                  Last bullet:  The authors should clarify that stream  surveys were
                           not conducted in the Adirondacks  or New England.

Page 5-16, line 28           Delete space before Maximum past...

Page 5-17                  Fourth bullet:  Again, this is a best case scenario because the study
                           overstated the  level of acidity associated with organic acids.  This
                           needs to be clarified.
Page 5-17, line 30           Change to:  ... with siliciclastic geology and ...

Page 5-19, line 19           Change to:  ... elevation, climate, species, composition ...

Page 5-19, line 26,27, 28    Change to:  :  communities. The ecological effects... studied in
                           recent years are summarized in Table 4.3-1.

Page 5-19, line 32           Change to:  ... ecosystems. Note that N saturation...

Page 5-20, line 16           Delete first sentence. Start paragraph with ... In general forest...

Page 5-23, line 1            Change to:  ... More than 30 kg N/ha-yr of ...

Page 5-28                  Last bullet.  N fluxes ... to the total N budgets are compared in
                           Table 5.5-1.
                                                                                       53

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Page 5-28, line 10           Change to:  ... N to total phosphorus was ...
                           (Note, also clarify if this ratio is on a molar or mass basis.)

Page 5-31, line 1            Change to:  ... Si:N ratio decreases below....

Page 5-31, line 6,7          Change to:  ... in community composition, reduces hypolimnetic
                           DO, decreases biodiversity, and causes declines in submerged ...

Page 5-32, line 26           Need a reference. Should the units here be metric?

Page 5-33, line 30           Change to:  ... influenced by oxygen content, supply of labil
                           organic carbon, temperature ...

Page 5-36, line 11           Change to:  ... average of 0.053 ppm. (space after 0.053)

Page 5-36, line 19           Change to:  ... Note that the regulatory....

Page 5-37, line 13           Change to:  ... forms of reactive nitrogen loading...

Page 5-38, line 2            Change to:  ... hypoxic zones,  loss of habitat and harmful ...

Page 5-39                  Third section. Base Cations.  Add references (Bailey et al. 1996,
                           Huntington et al. 2000).
                                                                                      54

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References:

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       Hallett, and J. L. Stoddard. 2003. Is nitrogen deposition altering the nitrogen status of
       northeastern forests? BioScience 53:375-389.
Bailey, S. W., J. W. Hornbeck, C. T. Driscoll, and H. E. Gaudette. 1996. Calcium inputs and
       transport in a base-poor forest ecosystem as interpreted by Sr isotopes (Paper
       95WR03642). Water Resources Research 32:14.
Benoit, J. M., C. Gilmour, A. Heyes, R. P. Mason, and C. Miller. 2003. Geochemical and
       biological controls over methylmercury production and degradation in aquatic
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Binkley, D., and D. Richter. 1987. Nutrient Cycles and H+ Budgets of Forest Ecosystems.
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Campbell, J. L., J. W. Hornbeck, M. J. Mitchell, M. B. Adams, M. S. Castro, C. T. Driscoll, J. S.
       Kahl, J. N. Kochenderfer, G. E. Likens, J. A. Lynch, P. S. Murdoch, S. J. Nelson, and J.
       B. Shanley. 2004. Input-output budgets of inorganic nitrogen for 24 forest watersheds in
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Castro, M. S., and C. T. Driscoll. 2002. Atmospheric nitrogen deposition to estuaries in the mid-
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Cronan, C. S., and C. L. Schofield. 1990. Relationships between aqueous aluminum and acidic
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       passerines in montane forest of northeastern North America. Ecotoxicology 14:223-240.
Sullivan, T. J., C. T. Driscoll, B. J. Cosby, I. J. Fernandez, A. T. Herlihy, J. Zhai, R. S.
       Stemberger, K. U. Snyder, J. W. Sutherland, S. A. Nierzwicki-Bauer, C. W. Boylen, T.
       C. McDonnell, and N. A. Nowicki. 2006a. Assessment of the Extent  to Which
       Intensively-Studied Lakes are Representative of the Adirondack Mountain Region. Final
       Report 06-17. New York State Energy Research and Development Authority, Albany,
       NY.
Sullivan, T. J., I. J. Fernandez, A. T. Herlihy, C. T. Driscoll, T. C. McDonnell, K. U. Snyder, and
       J. W. Sutherland. 2006b. Acid-base characteristics of soils in the Adirondack Mountains,
       New York. Soil Science Society of America Journal 70:141-152.
Valiela, I, J. Costa, K. Foreman, J. M. Teal, B. Howes, and D. Aubrey. 1990. Transport of
       groundwater-borne nutrients from watersheds and their effects on coastal waters.
       Biogeochemistry 10:177-197.
van Breemen, N., J. Mulder, and C. T. Driscoll. 1983. Acidification and alkalinization of soils.
       Plant and Soil 75:283-308.
Van Sickle, J., J. P. Baker, H. A. Simonin, B. P. Baldigo, W. A. Kretser, and W. F. Sharpe. 1996.
       Episodic acidification of small streams in the northeastern United States: Fish mortality
       in field bioassays. Ecological Applications 6:408-421.
                                                                                     56

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                                 Dr. Paul J. Hanson
My comments include general thoughts on the organization and content of the ISA, comments on
specific chapters and items within the text, and summary thoughts on the charge question to
which I was assigned.

General Comments:
       The Integrated Science Assessment (ISA) provides a concise, but occasionally cursory
overview of the key scientific issues for nitrogen and sulfur oxides related to atmospheric
chemistry and physics (Section 2), ecological exposures (Section 3), and effects (Section 4). The
section on effects is missing a brief discussion of the importance of NOxas an ozone precursor.
NOx-induced tropospheric ozone effects need not be covered in detail since they have recently
been reviewed as a part of the recent CAS AC evaluation of photochemical oxidants.
Nevertheless, the key role that NOx plays as a precursor to ozone in the troposphere must be
highlighted in the ISA.
       The ISA would benefit from the addition of a section on the complexity of N and S
biogeochemical cycles and the need to understand all natural and anthropogenic inputs and
outputs to these cycles.
       The most readable and best prepared section of the ISA was Section 5 on Findings and
Conclusions. In fact, I recommend that Section 5 be brought forward (at least in part) to  be
presented as a summary of the documents key conclusions.  Section 5 strikes the right balance
between the beneficial and adverse effects of N deposition that was largely missing within
Section 4. In a lead-off position within the ISA, the Findings and Summary material would
provide the key conclusions from which an interested reader might then search for additional
details and support within the document and its Annexes. All key conclusions within the
Findings and  Summary section must include parenthetical references to the pages within the ISA
or appropriate Annex that the reader could look to find justifications for the conclusions.
       For continuity with the previous Air Quality Criteria Documents (AQCD) for nitrogen
and sulfur oxides, summary materials from those documents that have not been changed by new
research might be brought forward and used within the ISA. For example, little new information
has become available on the direct effects of NOx and SOx on plant response, but the
quantitative understanding of the generally high ambient concentrations needed to illicit adverse
responses to direct NOx or SOx exposures should be reiterated within the ISA. Section 5
provides the general statements of limited direct effects at current ambient concentrations, but
Section 4 should include an overview of the key data from previous AQCDs in support of those
statements.
       When adverse effects are discussed within Section 4 of the ISA they should (where
possible) be referenced to the state of current exposures presented within Section  3. For  example,
the authors need to show the reader how to interpret a multi-year experimental exposure to 20 to
>100 kg N ha'V1 m the context of ambient levels that typically are maxed out near 10 kg N ha"

       The authors have not taken full advantage of the Annexes. By my count Annexes 1 and 2
were cited 7 and 11 times, respectively, but Annexes 3 through 10 were cited only 2,1,1,0, 1,0,0,
and 1 times, respectively.  The Annex material should serve as a source of expanded information
                                                                                      57

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for the reader to highlight key points made within the ISA. In their current form and level-of-use
the Annexes are not helpful to the reader.
       References to primary research articles and cross-references to key discussions within the
ISA and Annexes are often left out or ignored. This deficiency must be corrected. I offer some
suggestions in the specific comments listed below.
       A limited literature search for nitrogen deposition and impacts research conducted from
1991 through 2008 produced a number of research articles that are not mentioned or evaluated
within the ISA.
       As much as possible  the authors need to limit the use of subjective statements like
'maybe', 'if, 'probably', 'possibly... .etc'. Rewriting such statements to indicate the true
quantitative nature of the primary research conclusions would be a better approach.

Specific Comments:
Chapter 1
       Page 1-2 lines 5 to 22: Add a bullet asking if the form of the current secondary standard
       is appropriate for the evaluation of and protection against adverse effects.

       Page 1-5 lines 12 to 15: Even though no substantive research has been generated on the
       topic of gas phase responses to NOx and SOx since the publication of their most recent
       AQCDs, respectively, the ISA should include a brief overview and quantification of the
       air concentrations of gaseous forms of N and S necessary to generate adverse responses.

Chapter 2
       Page 2-16 line 10: The term sensitive ecosystem is used here prior to it being defined in
       the context of the ISA.

Chapter 3
       Page 3-11: Section 3.5.1 is inadequately referenced. The authors should either add
       references or point to a more detailed discussion within an Annex or to pages within a
       previous AQCD where such a discussion can be found. The following references might
       be quoted as a demonstration of how HNOs is incorporated into foliage:
              Hanson PJ, Garten CT (1992) Deposition of H NOs vapor to white oak, red maple and loblolly-pine
                  foliage -experimental-observations and a generalized-model. New Phytologist 122:329-337.
              Garten CT, Schwab AB, Shirshac TL (1998) Foliar retention of N-15 tracers: implications for net
                  canopy exchange in low-and high-elevation forest ecosystems. FOREST ECOLOGY AND
                  MANAGEMENT 103: 211-216.
              Vose JM, Swank WT (1990) Preliminary estimates of foliar absorption of N-15 labeled nitric-acid
                  vapor (HNOs) by mature eastern white-pine (Pinus-strobus) CANADIAN JOURNAL OF
                  FOREST RESEARCH 20:857-860.

       Page 3-11: A number of useful references could have been added/cited within this
       section. For example:
              Ammann M, Siegwolf R, Pichlmayer F, et al. (1999) Estimating the uptake of traffic-derived NO2 from
                  N-15 abundance in Norway spruce needles. Oecologia 118: 124-131.
              Boyce RL, Friedland AJ, Chamberlain CP, et al. (1996) Direct canopy nitrogen uptake from N-15-
                  labeled wet deposition by mature red spruce. CANADIAN JOURNAL OF FOREST RESEARCH
                  26: 1539-1547
              Nussbaum S, Vonballmoos P, Gfeller H, et al. (1993) Incorporation of atmospheric (NO2)-N-15-
                  nitrogen into free amino-acids by Norway spruce picea-abies (1) karst. Oecologia 94:408-414.
                                                                                           58

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       Qiao Z, Murray F (1998) Improvement of the N-15 dilution method for estimation of absorption of
           NOx by plants supplied with N-15-labelled fertilizer. New Phytologist 138:13-18.
       Segschneider HJ, Hutzen H, Forstel H, et al. (1993) Uptake of (NO2)-N-15 and metabolic transfer of
           the (NO2)-N-15 nitrogen to various nitrogen fractions of sunflowers. ISOTOPENPRAXIS 29:51-
           57.
       Vallano DM, Sparks JP (2008) Quantifying foliar uptake of gaseous nitrogen dioxide using enriched
           foliar delta N-15 values. New Phytologist 177: 946-???
       Vonballmoos P, Nussbaum S, Brunold C (1993) The relationship of nitrate reductase-activity to uptake
           and assimilation of atmospheric (NO2)-N-15-nitrogen in needles of norway spruce (Picea-abies
           [1] Karst). Isotopenpraxis 29: 59-70.

Page 3-11 lines 24 to 25: A reference is needed for this statement. Perhaps the following:
       Hanson PJ, Rott K, Taylor GE, et al. (1989) NO2 deposition to elements representative of a forest
           landscape. Atmospheric Environment 23:1783-1794.

Page 3-12 line 21: A reference is needed for the 1 ppb compensation point quoted here.

Figure 3.6-1: Why is this figure used? Shouldn't it be a summary of NOx and SOx
issues?

Figure 3.6-2. The caption should read 'Aggregate map of the majority of routine
U.S. monitoring stations.'

The Figure and brief paragraphs on page 3-17 seem unnecessary.

Section 3.7.1 would be improved with the inclusion of the graph demonstrating the nature
of NOx concentrations through time (i.e., over decades). Is this data not available? The
graphics provided for SOX and nitrogen and sulfur deposition in subsequent sections
nicely demonstrate the declining nature of N and S inputs to most regions from the late
1980s early 1990s in when compared to 2004 to 2006 data.

For places where a complete continuous record exists it would be appropriate to include a
graphic showing the full trajectory of N and S deposition through measured time.

Captions for the Figure 3.8-x series need to include a description of the source of the data
within the figures.

Statements made at the top of page 3-41 need to be referenced to their source literature.
In general, Section 3 suffers from inadequate attribution of the primary source data.

The total and background axes with the figures on pages 3-52, 3-53, 3-55, and 356 should
be made the same. As drawn, the figures make it difficult to judge the level of
background N or S levels against current totals. I would also recommend that the bottom
graph in each of these figures be changed from a percentage of background to a
quantitative amount of the indicated  exposure measure above background. Low
background levels near zero make the calculation of percent changes of little value. That
is, a large percentage of a really small value is often still a really small value.
                                                                                    59

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       Page 3-58 lines 28: This is a key point. Where are the data or references to back it up? A
       citation to a publication, or another EPA report needs to be included here. Additional
       references are also needed on page 3-59.

       Please consider bringing the following Annex figures forward to this section of the ISA:
       AX4.1-1, AX4.1-2, AX4.1-3.

Chapter 4
       I would prefer to see this section organized along the lines of direct versus indirect effects
       of NOx and SOx. That approach has served the community well in the preceding
       AQCDs, and it better reflects that nature of the current N and S standards (gaseous
       exposures). Specifically Section 4.4.2 should be moved ahead of the discussion of
       acidification and nitrogen nutrient additions. This recommendation is not offered to
       perpetuate the use of a gaseous form of the welfare standard, but rather to recognize the
       history of NOx and SOx regulations. Delegating the primary effects of NOx and SOx
       exposures to a hidden corner at the back of the report seems inappropriate.

       Page 4-2 line 1: The term biosynthesis may need further definition.

       Section 4.1.3: The discussion of critical loads might be better located following the
       discussion of all direct and indirect effects. Redundant sections could all be combined
       together into a single section on the critical loads relevant to the combined and interacting
       effects  of the full range of adverse effects of N and S inputs. Such a section should
       describe the need for a comprehensive biogeochemical cycling-based assessment of the N
       and S cycles in support of the concept of critical  loads.

       Page 4-6 lines 10 and 11:  Where are the dose-response relationships?

       Page 4-7 line 28: A reference is needed for this statement.

       Page 4-8 line 1: A reference is needed for this statement.

       Figure 4.2-1  contains the wrong image. It has been inadvertently swapped with the figure
       for the image in Figure 4.2-2.

       Top of page 4-12: References to these statements are needed.

       Page 4-12 lines 20 and 21: A reference is needed for the C:N statement.

       Page 4-12 line 28: N may also be retained for long periods within plant biomass.

       Page 4-12 line 29: A reference is needed for this statement.

       At some point within Section 4 it would be useful to summarize the percent of US land
       area (perhaps within regions) anticipated to be impacted by direct effects of N and S
       forms, acidification, N deposition, etc. A table would suit this purpose  nicely.
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References are needed in Section 4.2.1.4 on base cation leaching.

Page 4-26 line 22: OC needs to be defined.

Section 4.2.2.2 is a good discussion (needing references) that might serve the reader
better if it occurred earlier in the document.

Page 4-28 line 25: Would it be appropriate to change the word "gradual" to
'accelerated'?

Page 4-29 lines 14 to 22: References for these statements are needed.

Page 4-31 line 10 and 11: The authors should be careful when using as phrase like
"contributed to". In many cases  the data probably showed only a correlation with an
observed effect rather than proof of a specific mechanism responsible for the effect.
Similarly, on Page 4-31  line 26, should  or could the word "indicated" be replaced with
'hypothesized'?

Page 4-33 lines 19 and 20: Can this statement be made more quantitative?

Section 4.2.4.1 is an excellent section that is well referenced. Use it as an example when
modifying other portions of Section 4.

Page 4-64 line 23: An "in review" paper is not an acceptable inclusion in the ISA.

Page 4-65 line 8: Were discussed regions acid naturally or have they developed acidity as
a result of anthropogenic N and  S additions? Can such a distinction be made?

Page 4-66 lines 26 to 28: Add the literature citation for this statement.

Page 4-70 line 21:1 think this heading should be numbered. Perhaps 4.2.4.2.2.

Bottom of page 4-70 and top of page 4-71. The text should be expanded to show the
components of the analysis of McNulty et al. (2007). The reader doesn't have sufficient
information. Is such information present in an Annex? If so, please direct the reader to
the text. How are variable rates of plant productivity used in this analysis?

Page 4-71 line 30: A reference for this statement is needed.

Page 4-104 lines 14 to 24: This material is unnecessarily redundant with material in
Sections 2 and 3.

Page 4-121 Iinel3: Is a change in productivity or biodiversity necessarily an adverse
effect? This question should be discussed in the context of N and S deposition or loading.
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Within section 4.4, the discussion on direct phytotoxic effects should be moved to the
front of Section 4. The discussion of direct phytotoxic effects should include a
description of the key exposure response relationships know to drive adverse direct
effects. Such information could easily be lifted and reused from prior AQCDs since little
new information is available on this topic. The following references published since the
last N and S AQCDs and should be considered for inclusion in the ISA discussion:
        Ammann M, vonBallmoos P, Stalder M, et al. (1995) Uptake and assimilation of atmospheric NO2-N
            by spruce needles (Picea abies): A field study. WATER AIR AND SOIL POLLUTION 85:1497-
            1502.
        Desantis F, Allegrini I (1992) Heterogeneous reactions of SO2 and NO2 on carbonaceous surfaces.
            ATMOSPHERIC ENVIRONMENT PART A-GENERAL 26:3061-3064.
        GunthardtGoerg MS, Schmutz P, Matyssek R, et al. (1996) Leaf and stem structure of poplar (Populus
            x euramericana) as influenced by O-3, NO2, their combination, and different soil N supplies.
            CANADIAN JOURNAL OF FOREST RESEARCH 26:649-657.
        Kainulainen P, Holopainen JK, Oksanen J (1995) Effects of so2 on the concentrations of carbohydrates
            and secondary compounds in scots pine (pinus-sylvestris 1) and norway spruce (picea-abies (1)
            karst) seedlings. New Phytologist 130: 231-238.
        Manninen S, Huttunen S (2000)  Response of needle sulphur and nitrogen concentrations of Scots pine
            versus Norway spruce to SO2 andNO2. ENVIRONMENTAL POLLUTION 107:421-436.
        MENG FR, COX RM, ARP PA (1994) Fumigating mature spruce branches with so2 effects on net
            photosynthesis and stomatal conductance. CANADIAN JOURNAL OF FOREST RESEARCH
            24:1464-1471.
        Qiao Z, Murray F (1997) The effects of root nitrogen supplies on the absorption of atmospheric NO2 by
            soybean leaves. NEW PHYTOLOGIST 136: 239-243.
        Qiao Z, Murray F (1998) The effects of NO2 on the uptake and assimilation of nitrate by soybean
            plants. ENVIRONMENTAL AND EXPERIMENTAL BOTANY 39:33-40.
        Thoene B, Schroder P, Papen H, et al. (1991) Absorption of atmospheric no2 by spruce (picea-abies 1
            karst) trees . 1. no2 influx and its correlation with nitrate reduction. New Phytologist 117:575-585.
        Vassilakos C, Katsanos NA, Niotis A (1992) Physicochemical damage parameters for the action of so2
            and no2 on single pieces of marble.  Atmospheric Environment 26: 219-223.
        Wolfenden J, Pearson M, Francis BJ (1991) effects of over-winter fumigation with sulfur and nitrogen
            dioxides on biochemical parameters and spring growth in red spruce (Picea-rubens Sarg) Plant
            Cell and Environment 14:35-45.
        Wulff A, Karenlampi L (1996) Effects of long-term open-air exposure to fluoride, nitrogen compounds
            and SO2 on visible symptoms, pollutant accumulation and ultrastructure of Scots pine and
            Norway spruce seedlings. Trees 10:157-171.


A brief section on the role of NOx as an ozone precursor should be added to Section 4.4.
This need not be very long, but it should provide  sufficient information to inform the
reader that NOx pollution is often indirectly responsible for known adverse effects of
photochemical oxidants on vegetation (and materials too  for that matter). The reader
could simply be pointed to the recent AQCD  for ozone and other photochemical oxidants.


Some mention should be made of the potential for anthropogenic N additions to fertilize
natural ecosystems leading to the sequestration of CCh from the atmosphere. This could be
added as  a counter point to the discussion of N2O emissions to be expected from N
saturated systems. If the authors don't provide this  discussion and show that the issue was
considered others will demand that it be  added later.


The Tables attached at the back of Section 4 should be embedded with the text to which
they apply or moved to their corresponding Annex.
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Chapter 5
       I really enjoyed reading Section 5.1 found it to be concise, informative and easy to
       follow. As I've already stated I believe it (or a portion of it) could be presented at the
       front of the document. I does, however, need to be populated with references to
       appropriate portions of the ISA, IS A-Annexes or other published work that support each
       statement.

       Page 5-2 line 13: Should "nitrification" be 'eutrophication'?

       Page 5-4 lines 16 to 18: Although this statement may be true, I don't believe it is
       supported within the current draft of the ISA.

       Section 5 might be rearranged to include:
              5.4 Direct Phototoxic Effects of NOx and SOx
              5.5 Indirect effects of acidification and nitrogen nutrient enrichment
              5.6 Other effects

       Page 5-7 line 29: Should this read 'Inorganic aluminum....'?

       Page 5-18 lines 19 and 20: Reword as ".. .ecosystems causes fertilization of trees
       and grasslands accelerating growth in  some species....
       The words "inadvertent" and "unnatural" seemed inappropriate to me.

       Page 5-19 line 9: Change to "When N increases to...."

       Page 5-20 lines 24 and 25: N is also retained in biomass.

       Page 5-37 lines 27 and 28: I would change "many forest ecosystems" to 'sensitive
       forest ecosystems'. There are many forest ecosystems that not show any adverse
       effects from this level of N deposition for a  long time (if ever).

       Most of the Tables should be used in their respective Sections and associated with
       some descriptive text. Table 5.7-1 is appropriate to the Summary and Findings
       section, and I would retain it. It would be helpful, however, to add a column to
       Table 5.7-1 to show how the experimental levels of N&S exposure actually relate
       to current N or S deposition rates. In many cases the experiments use N
       deposition rates that are an order of magnitude  above current levels.
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                  Draft Text for an Answer to ISA Charge Question #10:

Several additional effects are discussed, including mercury methylation, direct gas-phase
effects on foliage, and NiO as a greenhouse gas. How well does the draft ISA characterize
the evidence on these topics?

Designating the direct effects  of gas phase NOx and SOx as an additional effect is inconsistent
with prior AQCDs that appropriately delineated direct versus indirect effects of the defined
criteria pollutants. I would argue that the ISA should return to this format and characterize gas
phase effects of nitrogen and sulfur oxides as direct effects that are seldom expressed under
current atmospheric conditions. That discussion could be logically followed by a discussion of
the indirect effects of acidification, nitrogen nutrient additions, sulfur-induced mercury
methylation, the production of the greenhouse gas N2O, the production of tropospheric ozone,
the contributions of NOx and  SOx to visibility issues, and the interactive influence of global
anthropogenic N additions on carbon sequestration within natural ecosystems.  The last item on
the stimulation of ecosystem carbon sequestration is not currently discussed within the ISA, but
should be considered as an addition.

Some references related to N deposition and  carbon sequestration:
       Grace J (2004) Understanding and managing the global carbon cycle. Journal of Ecology 92:189-202.
       Hyvonen R, Agren GI, Linder S, et al. (2007) The likely impact of elevated [C02], nitrogen
           deposition, increased temperature and management on carbon sequestration in temperate and
           boreal forest ecosystems: a literature review. New Phytologist 173:463-480.
       Korner C (2000) Biosphere responses to C02 enrichment. Ecological Applications 10:1590-1619.
       Makipaa R, Karjalainen T, Pussinen A, et al. (1999) Effects of climate change and nitrogen deposition
           on the carbon sequestration of a forest ecosystem in the boreal zone. CANADIAN JOURNAL
           OF FOREST RESEARCH 29:1490-1501.
       Nadelhoffer KJ, Emmett BA, Gundersen P, et al. (1999) Nitrogen deposition makes a minor
           contribution to carbon sequestration in temperate forests. Nature 398:145-148.
       Norby RJ (1988) Nitrogen deposition: a component of global change analyses. New Phytologist
           139:189-200. Oren R, Ellsworth DS, Johnsen KH, et al. (2001) Soil fertility limits carbon
           sequestration by forest ecosystems in a C02-enriched atmosphere. Nature 411:469-472.
       Schindler DW, Bayley SE (1993) The biosphere as an increasing sink for atmospheric carbon -
           estimates from increased nitrogen deposition. Global Biogeochemical Cycles 7:717-733.
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                                   Dr. Dale Johnson
The quality of the review is very mixed, especially in Section 4. The first part is fraught with
inaccuracies, misconceptions, and bias, the last part is even handed and complete. Indeed, there
seems to be a real dichotomy between two different authors who seem to have written this
section, and the second one has a much more complete and balanced view of the situation.
Again, I stress the need for looking at all points of view - which in total this document does, but
only in certain parts and these parts do not adequately make their way into the summary sections.
The focus is on the negative effects, which leaves this document open for severe criticism once it
is released. There are several peer-reviewed publications that discuss and even demonstrate the
possibility that increased N deposition has or will increase terrestrial ecosystem C sequestration.
Below I cite some examples:

LeBauer, D.S., and K.K. Treseder. 2008. Nitrogen limitation of net primary productivity in
       terrestrial ecosystems is globally distributed. Ecology 89: 317-379.

This is a meta analysis of fertilizer studies that investigated latitudinal trends in response to N.
They note that most fertilizer applications differ from atmospheric deposition in that they are
greater in  quantity (at least over the short term) and pulse-like in time.  They also fully recognize
the potentially negative effects of too much N. The last sentence of their Conclusions reads:
"Increasing N deposition, particularly in the most rapidly developing regions, is likely to further
stimulate global NPP and slow the accumulation of atmospheric CO2."

Magnini, F., Mencuccini, M., Borghetti, M., Berbigier, P, Beringer, P., Delzon, S., Grelle, A.,
       Hari, P., Jarvis, P.G., Kolari, P., Kowalski, A.S., Lankreijer, H. Law. B.E., Lindroth, A.,
       Loustau, D., Giovanni, M., Moncreiff, J.B., Rayment, M., Tedeschi, V., Valentini, R. and
       Grace, J. 2007. The human footprint in the carbon cycle of temperate and boreal forests.
       Nature 447: 848-850.

A quote from their abstract: "After the confounding effects of disturbance have been factored
out, however, forest net carbon sequestration is found to be overwhelmingly driven by nitrogen
deposition, largely the result of human activities."

Pregitzer,  K.S., AJ. Burton, D.R. Zak, and A.F. Talhelm. 2008. Simulated  chronic nitrogen
       deposition increases carbon storage in Northern Temperate forests. Global Change
       Biology 14: 142-153.

This is a field study where applications of N at 30 kg ha-lyr-1 over two decades produced
greater C sequestration in surface soils and live woody tissues in northern hardwood forests in
Michigan.
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For the combined effects of CO2 and N:

Hungate, B.A., J.S. Dukes, M.R. Shaw, Y. Luo, and C.B. Field. 2003. Nitrogen and climate
       change. Science 302: 1512-1513.

The authors point out that model estimates of C sequestration due to elevated CO2 are probably
greatly inflated because they do not account for N limitation. They calculate some projected
increases in N deposition and estimate how much this could facilitate the modeled estimates of
CO2-enhanced C sequestration and it falls far short. So the point is that models that do not
incorporate N overestimate C sequestration and also implies that more N will lead to more C
sequestration.

Again, I must emphasize that this is meant to provide the other side of the N deposition issue and
in no way negates the well-documented negative effects of excessive N deposition on terrestrial
ecosystems. The problem with nitrogen in terrestrial ecosystems is that there is a very  short
plateau between  deficiency, where  increased growth with increased N inputs will occur, and
excess, where many negative effects such as soil and water acidification and water pollution
commence.

Specific comments:

p. 1-2, lines 5-22: Here I ask my recurring question: why the complete focus on adverse effects?
Nitrogen is the limiting nutrient for most terrestrial  ecosystems and therefore there is the distinct
possibility of beneficial effects as well. Again, I do  not advocate excusing air polluters on this
basis, but I think a fair and complete assessment requires that this side be discussed. To fail to do
so risks losing credibility for the entire effort.

p. 4-2, Title: The very title of this section clearly shows an bias toward adverse effects and such a
bias is completely unacceptable in a document that  purports to be scientifically objective.

p. 4-3, lines 7-8:  It is very hard to imagine that increasing N deposition will fail to cause
"change" in any  ecosystem, whether it be beneficial or harmful change. I think there is a need to
be more specific here.

p. 4-7, line 24: Acid cations that build up  during soil acidification include, importantly, A13+ as
well as H+.

p. 4-7 line 25: Soil acidification IS  a natural process. There is no doubt of this. Extremely acidic
soils can be found in pristine parts of the world. You should elaborate on such processes here -
carbonic acid, organic acids, plant cation uptake.

p. 4-7, line 28: Where have decreases in pH attributable to acidic deposition been found in the
US? You should cite references here.
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p. 4-8, line 6: The B horizon lies below the Oa horizon? Since when? This can happen in some
cases, but is the exception rather than the rule. What happened to the A and E horizons? Does
this author know anything about soils and soil genesis?

p. 4-8, lines 15-17: Actually, the situation with hardwoods is much more complicated than that
and this statement is misleading. Hardwoods, by taking up larger amounts of Ca, actually acidify
sub surface soil horizons more than conifers to even though they may enrich surface horizons
with Ca by litterfall recycling. There is a classic paper by Alban (1982) that clearly show this and
should be cited here. Also, an excellent source of information is the review paper by Stone
(1975).

p. 4-8, line 28 and throughout: "SO4+"?? Since when is sulfate a cation? This is an embarrassing
mistake.  Sulfate is an anion: SC>42"

p. 4-10, lines 5-6: Some oil crops have S demands that are in line with S deposition.

p. 4-10, lines 25-31: There are MANY other references besides Sullivan et al 2004 that show
this.

p. 4-11, line 30: Add this to the list: "3) greater growth causing more cation uptake and therefore
more soil acidification"

p. 4-12, lines 2-9: Ammonium is also acidifying: it is either taken up by plants or microbes,
thereby releasing H+, or is nitrified, creating nitric acid.

p. 4-14, lines 17-31: This is a good description of the leaching and acidification processes.

p. 4-15, lines 1-13: There are some significant problems with this section. First of all, it is
stoichiometrically impossible for the soil changes described by  Bailey et al to have been  caused
by any known level of acidic deposition -1 wrote a letter to the editor about this  and felt that
their reply was inadequate (Johnson, 2006). I insist that this be included in the discussion.
Secondly, there are several examples in the literature - even an entire book - written about
studies where plant cation uptake as well as atmospheric deposition has caused substantial soil
acidification (Johnson and Todd, 1990; Richter and Markewitz, 2001;  Trettin  et al., 1999). This
review of the soil acidification literature for the US is totally inadequate and misleading.

p. 4-16, lines 17-26: In nature, the rate of soil weathering seldom exceeds the  rate of acidification
- that is why soil naturally acidify. So it is not realistic to assume that  soil weathering will aid in
the recovery of acidified soils.

p. 4-18, Figure 4.2-2: It appears that you have the wrong figure here. I see a soil profile, not an in
situ bioassay.

p. 4-23, line 16: "lowered or INCREASED plant productivity"

p. 4-24, lines 2-3: why spell out potassium and sodium but not Ca and Mg?
                                                                                       67

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p. 4-24, line 30: Al is not toxic to all tree roots. Some plants tolerate it and like acidic soils.

p. 4-26, line 12: Do you mean Nitrogen to Carbon ratio? If so, the usual expression is carbon to
nitrogen ratio.

p. 4-31, lines 10-13:1 thought that the red spruce decline was largely attributed to climatic
factors. What about Art Johnson's work?

p. 4-37, lines 5-10: How about some of the N-loving invasive grasses in the southwestern US
like Bromus species? Edie Allen has shown thatN deposition clearly facilitates this in southern
California.

p. 4-43, line 22: Do you mean cation here?

p. 4-43, lines 25-26: In the study of Lawrence et al, did H+ and A13+ decrease to make up the
difference between base cation decreases and mineral acid anion decreases? Something surely
had to, otherwise charge balance was not maintained.

p. 4-44, lines 4-5: How were strongly acidic organic anions estimated?

p. 4-63: A discussion of capacity/intensity and anion mobility concepts for water acidification is
needed here. Namely, that a strong acid anion such as sulfate or nitrate passing through an acid
soil can mobilized H+ and A13+ with no delay because these acid cations are most available on
exchange sites to balance the  anions. This reaction does not require soil change and is instantly
reversible if strong acid anion inputs cease. This is quite a different matter from the case where
soils acidify. An already acidic soil, whether by natural acid production or by acid rain, is a
necessary but not sufficient condition for the acidification of soil water - strong acid anions are
also needed.

p. 4-84, lines 13-23: This is very interesting - we did not expect that soils of the northeast would
have such buffering with respect to sulfate. Very important point.

p. 4-91, Figure 4.2-17: The y-axis legends on this figure are messed up.

p. 4-104, line 30: "unnatural growth rates?" Again, this reflects the negative bias that seriously
detracts from this entire document. Just say increased growth rates and let the reader decide if it
is good or bad.

p. 4-105, lines 16-17: Once again, this statement reflects the negative bias that seriously detracts
from this entire document. I suspect that you would also be looking for negative effects if N
limitations were increased rather than decreased in the endless search for negative consequences.
Please let us simply state what we think will happen and leave out these value judgements.

p. 4-106, lines 9-10: At LAST! We see the mention of potential beneficial effects.
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p. 4-111, lines 3-17: Once again, there is too much negative bias here. I raise once again the
issue of global C and the potential for N pollution to make the terrestrial C balance better
(Kauppi et al., 1992; Magnini et al., 2007).

p. 4-121, lines 12-32: This is as close to a balanced presentation as I have yet seen in this
document. It needs to be up front along with all the potential negative effects.

p. 4-122, lines 15-16: Of course adding the limiting nutrient causes the next most limiting
nutrient to become limiting - everyone who has ever worked with fertilization knows this. Why
is this a bad thing? Is it healthier for a forest to be N limited than Ca, K, or Mg limited? Once
again, an unnecessary value judgement here.

p. 4-123-124: At last we see the new article by Magnini and a balanced discussion about it. I
think this kind of alternative view needs to be more up front as well.

p. 4-126: Good discussion of potential effects on grasslands and invasive species problems in
relation to N.

p. 4-127-128: Again, a very good discussion of potential N effects on arid and semi-arid lands. N
inputs in these areas could be a real problem and there is not much to be seen in the way of
benefits.

p. 4-161-162: Good discussion of the non-acidifying effects and biological role of sulfur.

p. 5-6, lines 19-31: Some of that good discussion and balanced treatment seen on the last pages
of section 4 need to make their way into this summary.

p. 5-7, line 29: Aluminum is toxic to SOME tree roots.

p. 5-8: Again, Some of that good discussion and balanced treatment seen on the last pages of
section 4 need to make their way into this  summary.

p. 5-12, lines 2-4: This is a very important yet seldom recognized point about surface water vs
soil acidification.

p. 5-18, lines 19-20: Once again, why must we say unnatural? Why not just INCREASED
growth rates? And then go on to elaborate about how you do not want this to happen in certain
places (if indeed you do want to maintain N deficiencies).

p. 5-21: Good summary about N effects on growth, both positive and negative.

References:

Bailey, S. W., S. B. Horsley, and R. P. Long.  2005. Thirty years of change in forest soils of the
       Allegheny Plateau, Pennsylvania.  Soil Sci. Soc. Am. J. 69:681-690.
                                                                                      69

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Johnson, D.W. 2006. Comments on "Thirty years of change in forest soils of the Allegheny
   Plateau, Pennsylvania." Soil Sci. Soc. Amer. J. 69: 2077.
Johnson, D.W., and D.E. Todd. 1990. Nutrient cycling in forests of Walker Branch Watershed:
   Roles of uptake and leaching in causing soil change.  J. Environ. Qual. 19: 97-104.


Kauppi, P.E., Mielikainen, K. and Kuusela, K., 1992. Biomass and carbon budget of European
   Forests, 1971 to 1990. Science, 256: 70-74.
Magnini, F., Mencuccini, M., Borghetti, M., Berbigier, P, Beringer, P., Delzon, S., Grelle, A.,
   Hari, P., Jarvis, P.O., Kolari, P., Kowalski, A.S., Lankreijer, H. Law. B.E., Lindroth, A.,
   Loustau, D., Giovanni, M., Moncreiff, J.B., Rayment, M., Tedeschi, V., Valentini, R. and
   Grace, J. 2007. The human footprint in the carbon cycle of temperate and boreal forests.
   Nature 447: 848-850.

Richter, D.D., and D. Markewitz. 2001. Understanding soil change. Soil sustainability over
   millennia, centuries, and decades. Cambridge University Press.

Stone, E.L. 1975.  Effects of species on nutrient cycles and soil change. Philos. Trans. R. Soc.
   Lond. Ser. B Biol. Sci., 721: 149-162.

Trettin, C.A., D.W. Johnson, and D.E. Todd, Jr. 1999. Forest nutrient and carbon pools: a 21-
   year assessment. Soil Sci. Soc. Amer. J. 63: 1436-1448.
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                                  Dr. Donna Kenski
Overall, this was a fine job summarizing a lot of data. The quality varied from section to section,
but most of the relevant information was here. Nevertheless there were some significant
shortcomings that should be addressed in future drafts. Most of my comments address the
presentation of air quality and emissions data, per Charge Questions 1-3.

The chemistry discussion is adequate. Most of the air quality issues were covered in Chapter 3,
and I found them lacking in several ways, especially with respect to the nitrogen species.
Section 3.1 needs a map of NOX emissions density (all sources) and a comparison, at least
nationally but preferably regionally, of the relative importance of each of the anthropogenic and
biogenic sources to total NOX emissions. We're told that soil contributes 10% of NOX emissions
globally, and 26% of NO in Illinois, but no estimates are given for soil NOX contribution to US
emissions either nationally or regionally.  Similarly for biomass burning. The statement that
increased wildfires will make emissions from this sector increasingly important should be
substantiated with quantitative data.  This information is too important to relegate to the Annex,
and Table 3.11-2 puts sources in priority order but is not quantitative. Table AX2-1 contains the
relevant information, and a shortened version of it, edited to eliminate the many small sources
and include only major categories would add significantly to this section. The section also needs
a description of NOX emission trends, parallel to the discussion of SOX emission trends in Sec.
3.2. While changes in NOX have not been as dramatic as those for SOX, they are documented and
the data are readily available. In addition, some information about future-year emissions
projections would be nice, along with a brief summary of recent and expected controls on NOX
and SOX sources. These analyses have been done by EPA already.  Another significant hole in
the emissions discussion was NH3. Although we're told that the NEI underestimated NH3
emissions by a factor of 2 or 3, we're never given an estimate of what those emissions are
(underestimate or not).

Section 3.6.1, and especially p.  3-15, lines 9-15 is somewhat misleading in  its description of the
monitoring networks.  Sure we have lots of ozone monitors,  but ozone monitors don't tell us
much about NOX or SOX or NH3. I don't understand why the authors of this section decided to
show us plots of ozone and PM2.5 air quality but not plots of SO2, NOX or NH3 concentrations .
While it is true as stated in lines 11-13 that NOX and SOX are often monitored at the same sites,
the number of NOX and SOX monitors is far less than for ozone or PM25. More relevant would
be a plot of just NO2 and SO2 monitors, which would make immediately apparent the significant
gaps in spatial coverage of measurements for these gases.  Figures 3.6-1 and 3.6-2 leave the
reader with the impression that the network of NOX/SOX monitors is much more dense than it
really is.  Including NATTS, HAPS,  CO, and lead sites in Fig. 3.6-2 only obscures the matter
further.  It may also be worth noting that monitors for both NOX and SOX have been cut from the
networks in recent years because their main purpose is perceived to be for comparing to the
primary NAAQS. As ambient concentrations for both NOX and  SOX have fallen well below the
standard throughout the US, the monitors are seen as a lower priority and unnecessary expense.
At the same time, monitoring budgets have been cut, leading to monitor shut downs.
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Another shortcoming of this section is that it does not address urban-rural differences.  Figure
3.6-3, for example, is of limited usefulness in assessing the composition of aerosol that impacts
the sensitive, mostly rural regions identified later; differences in urban and rural aerosols have
been noted by many. A similar plot, but based on IMPROVE data, would be an improvement, or
a plot that shows both urban and rural composition. The majority of monitors, both gas and
particle, are in urban areas; rural NOX and SOX monitors are rare. How does the lack of rural NOX
and SOX monitors affect estimates of N deposition?

Figures 3.7-2 and 3.7-3, which compares ambient 862 and 864 concentrations in the early 1990s
with more recent data, are very effective, but the text or caption should note whether Fig. 3.7-3 is
showing SC>4 concentrations in particulates or in rainfall - its not clear which. A similar set of
plots should be  shown for NOX and NH3.

I didn't like Fig. 3.7-4 when it showed up in the SOX primary ISA (as I recall from discussions,
none of the panel did) and  I still don't like it. It is not effectively communicating information
about SO2 concentrations;  replotting on a log scale would make it much more informative.
Especially in this context, the extreme values are less informative than the rest of the
distribution.

Figures 3.8-1 thru 3.8-4 are also ineffective. It is difficult to distinguish meaningful differences
by comparing the size of the pies in the upper and lower plots, and also to tell if there have been
changes in the geographic  distribution of the various forms of S and N deposition. NADP
produces a much more effective set of plots, at least for wet deposition, similar to Fig.  3.7-2;
perhaps those could be substituted here (see http://nadp.sws.oiuc.edu/isopleths/annualmaps.asp)
or these could be reworked to show the data in a similar fashion.  At least change the pies to bar
charts as in Fig. 3.2-1.

Section 3.6.4 on satellite observations was too brief to be useful. It seems clear that the
technology holds great promise; it would be helpful to see some support of that notion, rather
than just have a laundry list of satellites without any indication of their strengths and weaknesses.
Is there useful data for our purposes (N and S deposition) being produced by the satellites now?
If so report it here.

Section 3.6.5 could be removed to Annex 2.

This chapter should have left us with an understanding of the relative importance of NOX, NFL?,
and organic nitrate deposition nationally and regionally, but at the end I still felt unable to assess
those except in a qualitative way.

Ultimately, the question we want to answer is, what kind of secondary standard would  be
adequately protective of our sensitive ecosystems.  Here I think the ISA was not very helpful. I
was searching for information that explicitly linked ambient concentrations or emissions with
deposition and more importantly with acidification effects. How are ambient concentrations
related to deposition?  Are these essentially equivalent?  Can we compare (using GIS tools or
other quantitative techniques) the distribution of concentrations (or deposition) to the distribution
of sensitive ecosystems?
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Some other general comments:

The various chapters and subsections make occasional mention of shortcomings in the data and
areas that are poorly understood, but these shortcomings aren't collectively addressed anywhere.
These data gaps and research needs should be explicitly discussed and summarized in the
conclusions.  Doing so would help us better understand some of the limits to our knowledge and
also hopefully help EPA target research efforts and support future reviews.

Another concern I have is that NHX isn't addressed comprehensively here because the focus is
NOX and SOX, and it may not be comprehensively discussed in the PM ISA, because the focus
there is PM. When or where does NHX get its due? If we always consider it as a smaller part of
something else, it may never get dealt with adequately.  I appreciate that NHx's contributions to
deposition and acidification were discussed here at some length, but we seem in danger of
marginalizing its very important role in nitrogen and sulfur deposition because it is a lesser
player, without doing the research to adequately characterize its role.

More specific comments:

p. 2-29 line 6-7 The concluding sentence, that coverage of monitoring networks is thin over large
expanses of the US, is true, but not a conclusion that follows from the previous discussion, which
is only about the adequacy of the monitoring techniques. It is a statement more appropriate for
Sec.  3.6.1.

p.3-7 line 7-9 overrepresentation is a poor word choice. Perhaps higher density would be better.

p. 3-13, eqn 3.5-4 Isn't the second = sign supposed to be a + ?

p. 3-16, caption to Fig. 3.6-2 should be ..majority of routine...

p. 3-35, caption to Fig. 3.9-1 should read .. .25th and 75th quartiles...

p. 4-7  Throughout this Section (4.2) the concept of base saturation is discussed and a few
benchmark figures (base saturation less than 20%, for example) are mentioned, but it does not
explain how base saturation is quantified until p. 4-24. A brief definition at the beginning of this
section would be a useful addition since it may not be familiar to the many in the atmospheric
community.

pp. 4-7 - 4-191  Somehow in this entire chapter, SO42" morphed into SO4+.  Search and replace
gone awry?  Very disconcerting.

pp. 4-9, 4-18  Figures 4.2-1  and 4.2-2 have been switched.  The captions are correct but the
figures themselves are reversed.

p. 4-24 Later in the document there are maps of sensitive areas (although not enough—much
more of the data could/should have been summarized graphically). Any available to show soil
base saturation, or Ca: Al ratios, which might be helpful here?
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p. 4-24  Change in terms soil water -> soil solution is confusing. Are these the synonyms or is
there some subtle difference?

p. 4-26 line 12  Calcium should be Carbon

p. 4-64, section 4.2.4.2 This section suffers from a lack of integration.  It's difficult to assess the
extent and distribution of these sensitive areas without some graphical help. Figure 4.2-12 is a
start, but only tells part of the story; Figure AX4.3-2 does a much better job showing the location
and extent of acidification.  Also, acidified streams and lakes are sometimes mentioned
separately and sometimes together; it is not clear whether regions with acidified streams
necessarily also have acidified lakes,  and vice versa.

p. 5-16, lines 5-14 Although this section is supposed to be about recent trends in acidification
recovery, this last bullet doesn't say anything about recovery and seems out of place.  The parent
section 4.2.4.2.1 emphasizes that this WSA survey is summer data and therefore biased low, but
that caveat is not repeated here, as it should be.  These results also don't jive with later data (i.e.,
on p. 5-17, 66% of Adirondack streams currently have high Al). It would be useful to have a
graphical assessment of the geographic extent of acidification either here or as suggested earlier,
in section 4.2.4.2.  Figure AX4.3-2 is very helpful in this regard.

p. 5-36 lines 19-23 Absolutely true that regulatory networks cannot adequately characterize
regional heterogeneity (on a scale that matches that of the sensitive ecosystems) and hotspots.
But the statement about hotspots identified at research sites was not discussed in the text, except
in reference to Hg. If this is documented it should be discussed in the body of the ISA,  not
mentioned first in the  summary.

p. 5-36, line 25 lead should be led

p. 5-38 This section comes to an abrupt end; is something missing?
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                                 Dr. Naresh Kumar


Information provided in the Integrated Science Assessment document on atmospheric chemistry
and physics, air quality, and deposition and exposure is concise, but sufficiently comprehensive.
Specific comments are:

Page 2-2, Lines 6 & 7: Nitric acid doesn't contribute to the acidity of particles, so there is a need
to reword the sentence.

Page 2-2, Lines 23  & 24: It would be meaningful to mention the contribution to NOx emissions
from mobile sources and electric utilities (e.g., According to NEI 2003, 55% of NOx emissions
were from mobile sources and 22% were from electric utilities).

Page 2-5, Line 7: The following reactions should be added before Equation 2.2-2

                    O3 + NO2 -» NO3 + O2
                    NO3 + NO2 -» N2O5

Page 2-5, Line 15: The nitrate radical, NO3 should be included as part of the photolysis.

Page 2-6, Lines 7 thru' 16: The paragraph should also mention the negative radiative forcing
caused by nitrate particles.

Page 2-6, Line 28: Add "from the free troposphere" at the end of the sentence.

Page 2-7, Line 9: Add "except at lower temperatures" at the end of the sentence.

Page 2-8, Line 13: There is no SC>42" in Equation 2.2-15.

Page 2-8, Line 22: "diatonic" should be "diatomic".

Page 2-9, Line 31: Change "high" to "moderate"

Page 2-9, Line 32: After "in the aqueous phase in cloud droplets", add "by reaction with H2O2,
O3 or O2 through catalysis by Fe and Mn.

Page 2-10, Line 7: After "highly soluble", add "as well as hygroscopic".

Page 2-11, Line 3: "Methane sulfuric acid" should be "methanesulfonic acid".

Page 2-12, Figure 2.3-1: Include Fe, Mn and O2 where reaction from S(IV) to S(VI) is shown.

Page 2-13, Line 18: Add manganese (Mn) to the list of metals that can catalyze oxidation by O2.
                                                                                     75

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Page 2-17, Line 17: Include Edgerton et al., 2006 and Edgerton et al., 2007 in the list of
references on newer methods for measuring nitrate, ammonia and ammonium. SEARCH
network has been in place since 1999 and has been widely used by the community, but there is
no mention of this network anywhere in the ISA document.

Page 2-21, Line 12: H2SO4 should be changed to SO2.

Page 2-24, Line 22: Add "for IMPROVE and thermal-optical transmittance (TOT) for STN" at
the end of the sentence.

Page 2-25, Line 2: Change "well correlated" to "moderately well correlated".

Page 2-26, Line 1: Remove NH4NO3 from the list.

Page 2-26, Line 6: After "PMio", add ", partly because NOs" contributes smaller fraction to PMio
and partly because NO3- is present in a non-volatile form, such as NaNO3, in the coarse mode.".

Page 3-1, Lines 23 & 24: Electrical utilities and various industries account for about one-third of
anthropogenic NOx emissions (not roughly half).

Page 3-20, Line 13: Add description  of the SEARCH network. Here is the suggested description
to choose from:

Southern Company and EPRIfunded SEARCH program has provided a highly instrumented eight-
station network since 1998 (and continuing till at least 2010) in the states ofAL, FL, GA and MS
(Hansen et al, 2003). At present, the suite of measurements made at all sites includes:

   1.  24-hr'PM2.5filter samples, analyzed for mass, ions (sulfate, nitrate, ammonium), organic
       carbon(OC), elemental (black) carbon (EC orBC), and elements as measured by X-ray
      fluorescence (XRF);

   2.  24-hr PMcoarse mass, ions, and XRF elements;

   3.  24-hr gaseous ammonia as collected with an annular denuder;

   4.  continuous (minute to hourly) PM2.smass, OC, EC, ammonium, nitrate, and sulfate; light
       scattering and light absorption;

   5.  continuous gaseous ozone, nitric oxide, nitrogen dioxide, total oxidized nitrogen (NOy), nitric
       acid, carbon monoxide, and sulfur dioxide; and

   6.  continuous 10-m meteorological parameters: wind speed, wind direction, temperature,
       relative humidity,  solar radiation, barometric pressure and precipitation.

Page 3-23, Line 22: SEARCH sites have also measured nitric acid (Zhang et al., 2006; Blanchard
and Hidy, 2003) since 1998  and the measured hourly concentrations range from less than 1 ppb
to more than 10 ppb.
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Page 3-42, Line 14: Add "international transport" as one of the issues addressed by global
CTMs.

Page 3-43, Line 17:1 suggest adding Arnold and Dennis (2006) reference, as they went beyond
just testing the operational model performance.

Page 3-47, Line 27:1 suggest adding appropriate references to the SEARCH sites here.
References:

    •   Arnold, J.R. and Dennis, Robin L. (2006). Testing CMAQ chemistry sensitivities in base case and
        emissions control runs at SEARCH and SOS99 surface sites in the southeastern US. Atmos. Environ. 40
        (26) 5027-5040.

    •   Blanchard, C.L. and Hidy, GM. (2003). Effects of changes in sulfate, ammonia, and nitric acid on
        particulate nitrate concentrations in the southeastern United States. J. Air Waste Mange. Assoc. 53 283-
        290.

    •   Edgerton, E.S., Hartsell, B.E., Saylor, R.D., Jansen, J.J., Hansen, D.A., and Hidy, G.M. (2006). The
        Southeastern Aerosol Research and Characterization Study: Part III. Continuous Measurements of PM25
        Mass and Composition.  J. Air Waste Mange. Assoc. 56, 1325-1341.

    •   Edgerton, Saylor, Hartsell, Jansen, Hansen (2007) Ammonia and Ammonium Measurements from the
        SoutheasternU. S., Atmos. Environ., 41, 3339-3351.

    •   Hansen, D.A., Edgerton, E.S., Hartsell, B.E., Jansen, J.J., Kandasamy, N., Hidy, G.M., and Blanchard, C.L.
        (2003). The Southeastern Aerosol Research and Characterization Study: Part 1 - Overview. J. Air Waste
        Mange. Assoc. 53  1460-1471.

    •   Zhang, Y., Liu, P., Queen, A., Misenis, C., Pun, B., Seigneur,  C., and Wu, S.-Y. (2006). A comprehensive
        performance evaluation of MM5-CMAQ for the Summer 1999 Southern Oxidants Study episode—Part II:
        Gas and aerosol predictions. Atmos. Environ. 40 (26) 4839-4855.
                                                                                                77

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                                Dr. Myron Mitchell
General Comments
The December 2007 version of the "Integrated Science Assessment for Oxides of Nitrogen and
Sulfur - Environmental Criteria" has done a very good job in summarizing a substantial amount
of information. Included within this analysis is discussion on the relevance of this information to
policy decisions.  There is some reference and discussion to results from European analyses.  It
would be interesting to make some further explicit comparisons of the success or lack of success
of the European analyses including the relevance of these analyses to both interpretations and
policy implications in the United States.

In the various sections, however, there is sometimes substantial repetition and overlap.  Some of
this is likely inevitable, but having additional cross referencing among chapters would also be
helpful.  Removing some of this overlap will make the document more readable and reduce the
overall length. In Chapter 3 (ECOLOGICAL EXPOSURES TO OXIDES OF NITROGEN
AND SULFUR, AND TO AMMONIA AND AMMONIUM) some further discussion of the
issues related to model parameterization, assumptions and differences in the predictions of
concentrations and deposition would be helpful in placing results in the context of the overall
confidence levels of predicted values both across temporal and spatial scales.

In Chapter 4 (EFFECTS OF ACIDIFICATION AND NITROGEN ENRICHMENT ON
ECOSYSTEMS AND OTHER WELFARE EFFECTS) more attention should be given to the
potential importance in at least some watersheds of other sources of sulfate that will affect the
recovery from acidification. These sources can include organic sulfur mineralization and the
weathering of sulfur bearing minerals.

In Chapter 5 (FINDINGS AND CONCLUSIONS), this information should be converted to an
Executive Summary in which the salient features of the document are articulated.

Inclusion in the assessment of the impact of total reactive nitrogen would help strengthen the
importance of all  reactive nitrogen chemical species including ammonium to the total nitrogen
loading of ecosystem.

More Detailed Comments

Page        Comment

xx           Change to: Dr. Myron Mitchell, Distinguished Professor and Director of Council
             on Hydrologic  Systems Science, College of Environmental and Forestry, State
             University of New York,  Syracuse, NY

xxxv        Change to: The removal of gases and particles from the atmosphere to surfaces by
             rain or other forms of precipitation
                                                                                   78

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2-2           Change to: contributing to the acidity of cloud, fog, and rain water and ambient
              particles in the atmosphere.

2-3           Change to: few hours during summer days of high photon flux to roughly 24 h
              during winter with less

2-4           Change to:
2002).        The mechanisms for transporting the NOx precursors, the factors controlling the

2-6           Change to: on the conventional 100-year time horizon of-296 - i.e., N2O is
              nearly 300 times more effective on a per molecule basis for trapping heat in the
              atmosphere than carbon dioxide (CO2)(IPCC,

2-13          Indicate location of "Mace Head" in line 3.

2-18          Be more explicit in what is the interference by NOz compounds in line 1.

2-20          Reword to clarify the issue related to: also lead to artifact volatilization and
              associated positive bias in [HNO3] measured downstream

2-20          Would this be an appropriate place to discuss issues related to differences
              between CASTNET and the Canadian (CAPMoN) dry deposition comparisons. I
              believe most of the differences are associated with the dry deposition modeling
              versus the actual measurements of gaseous chemical species.

2-22          Figure 2.6-1 needs to provided with better resolution  of the contour lines.

2-24          Should Teflon be indicated to be  a registered name?  ®

3-1           Delete: (The category label for NH3 and NH4+ is NHX.)

3-1           Substitute "approximately" for "roughly" here and elsewhere in the document.

3-2           Change to: Where N is in excess  of biotic demand, gaseous N emissions increase
              by microbial transformation.

3-2           The issue related to "Although N2 is not reactive in the troposphere, N2O is a
              greenhouse gas (GHG) with a significant global warming potential (GWP) from
              its direct radiative forcing and from its..." maybe should be linked to the
              discussion in Chapter 2.

3-3           Change to: Emission rates of NO from cultivated soils depend chiefly on N
              fertilization levels

3-3           Change to: can have wide variation around this value
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3-3          Change to: N in plants is present mostly as amine (NH2) groups in amino acids.

3-3          Change to: will make emissions from this source increasingly important

3-8          This statement needs clarification: Emissions of SC>2 from burning vegetation are
             generally in the range of 1 to 2% of the biomass burned (e.g., Levine et al., 1999).

             This would suggest that 1 to 2% of biomass gets converted to 862. This seems to
             high with respect to the average S concentration in vegetation.  Does this study
             suggest that 1 to  2% of the S in biomass is converted to SC>2?

3-9          Be more explicit about which pattern in the statement: Anthropogenic emissions
             of NH3 show a strikingly different pattern from those of NOx or SC>2.

3-10         Does the statement "Results from some more recent emissions evaluation studies
             have been mixed, with some studies showing agreement to within ±50%" imply
             that some of these studies show that agreement is greater than 50%?

3-21         Figure 3.6-7. Routinely operating North American precipitation and surface water
             networks: Upper left, Canadian Air and Precipitation Monitoring Network
             (CAPMoN); upper right, Integrated Atmospheric Monitoring Deposition Network
             (IADN); bottom, National Atmospheric Deposition Monitoring Program (NADP)
             with TIME/LTM surface chemistry sites.

             This figure shows a symbol of N-saturated forests.  What is the source of this
             designation?  What is the coverage associated with the symbol? Other Ecological
             Resources are also noted, but the source of these designations is not included in
             the figure legend.

3-22
3-23         Some further discussion of differences of these European monitoring efforts
             compared to those in the U.S. may be helpful. Also, some discussion on
             differences with the Canadian monitoring efforts should be included.

3-47         Change to: parameterizations of atmospheric chemical and physical processes in
             models.

3-48         Change to: In a watershed, everything that is deposited in its area

4-1          Change: Structure refers to the  species richness, abundance, and community
             composition that ultimately relate to ecosystem biodiversity.

             To something like: Structure may refer to a variety of measurements including the
             species richness, abundance, community composition as well as landscape
             attributes.  The biotic components comose the biodiversity of an ecosystem.
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4-1           Change to: Competition among and within species and tolerance to environmental
              stresses are key elements of survivorship

4-1           Change to: Function refers to the suite of processes and interactions among the
              ecosystem components and their environment that such as nutrient and energy
              flow as well as other attributes including water dynamics and the flux of trace
              gases.

4-2           Change to: related to functions of energy flow and nutrient cycling

4-2           Change to: Energy moves from one organism to another through food webs, until
              it is ultimately released as heat. Nutrients and water can be recycled. Air pollution
              alters the function of ecosystems when elemental cycles or the energy flow is
              altered.  This alteration can also be manifested in changes in the biotic
              composition of the ecosystem.

4-6           The use of "we" seems awkward in this type of discussion.  I would suggest
              rewording.

4-8           It may also be useful to include the term "forest floor" when discussing the O
              horizon of forest soils.

4-8           For the documentation of soil acidification the following reference should be
              included: Sullivan, T.J., IJ. Fernandez, A.T. Herlihy, C.T. Driscoll, T.C.
              McDonnell, N.A. Nowicki, K.U. Snyder, and J.W. Sutherland. 2006. Acid-base
              characteristics of soils in the Adirondack Mountains, New York. Soil Science
              Society of America Journal 70: 141-152.

4-11          Not only is the fate  of carbon-bonded sulfur an issue, but also the fate of ester
              sulfate needs to be considered.

4-11          This might the be place to at least mention that sulfate isotopic  have indicated the
              potential for the net mineralization of organic S contributing to sulfur imbalances
              for watersheds. This has been  found in  studies both the United States and Europe.
              Some relevant references would include:

              Novak, M. M. J.  Mitchell, I. Jackova, F. Buzek, J. Schweigstillova, L. Erbanova,
              R. Prikryl and D.  Fottova. 2007. Processes affecting oxygen isotope ratios of
              atmospheric and ecosystem sulfate in two contrasting forest catchments in Central
              Europe. ES&T 41(3): 703-709. DOT: 10.1021/es0610028

              Likens, G.E., C.T. Driscoll, D.C. Buso, M.J. Mitchell, G.M. Lovett, S.W. Bailey,
              T.G. Siccama, W.A. Reiners, C. Alewell. 2002. The biogeochemistry of sulfur at
              Hubbard Brook. Biogeochemistry 60:235-316.
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             Gbondo-Tugbawa, S.S., C.T. Driscoll, MJ. Mitchell, J.D. Aber and G.E. Likens.
             2002. A model to simulate the response of a northern hardwood forest ecosystem
             to changes in S deposition. Ecological Applications 12:8-23.

             In addition, some mentioned should be included about the potential role of
             weathering reactions for contributing to sulfate in some watersheds. A good
             example is:

             Shanley, J.B., B.  Mayer, MJ. Mitchell, R.L. Michel, S. Bailey and C. Kendall.
             2005. Tracing sources of streamwater sulfate during snowmelt using S  and O
             isotope ratios of sulfate and 35S activity. Biogeochemistry 76:161-185

4-14         The is also strong evidence of the importance of winter time processes  and the
             possible linkage to climate in affecting nitrate losses. See for example:

             Eimers, M.C., Buttle, J.M., Watmough,  S.A., 2007. The contribution of rain-on-
             snow events to annual NOs-N export at a forested catchment  in central  Ontario,
             Canada. Applied Geochemistry, 22:  1105-1110.

             Campbell, J.L., M. J. Mitchell, P. M. Groffman, L.  M. Christenson. 2005. Winter
             in northeastern North America:  An often overlooked but critical period for
             ecological processes. Frontiers in Ecology 3(6):314-322.

             Park, J, MJ. Mitchell, PJ. McHale, S.F. Christopher and T.P. Myers.  2003.
             Interactive effects of changing climate and atmospheric deposition on N and S
             biogeochemistry in a forested watershed of the Adirondack Mountains, New York
             State.  Global Change Biology 9:1602-1619.

4-20 to
4-22         There is evidence that episodic acidification associated with droughts and the
             mobilization of sulfate is also important. This has been shown for studies in
             Canada and the northeast U.S.  See for example:

             Eimers, M.C., Watmough, S.A., Buttle,  J.M., Dillon, PJ., 2007. Drought-induced
             sulphate release from a wetland in south-central Ontario. Environmental
             Monitoring and Assessment, 127: 399-407.

             Eimers M.C.  and Dillon P J. 2002. Climate effects on sulphate flux from forested
             catchments in south-central Ontario. Biogeochem. 61: 337-355.

             Mitchell, MJ. K.B. Piatek,  S. Christopher, B. Mayer, C. Kendall and P. McHale.
             2006. Solute sources in stream water during consecutive fall  storms in a northern
             hardwood forest watershed: a combined hydrological, chemical and isotopic
             approach.  Biogeochemistry 78: 217-246.
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4-26          Should this heading be Changed to: 4.2.2.1.3 Soil Nitrogen: Carbon to Nitrogen
              Ratio

              Not sure if the emphasis is on Ca and if the ratio indication is appropriate.
4-33
& Elsewhere  Change SO4+ to: SO42"

4-39          Change to: The increasing trend in Virginia streams is presumably the result of
              decreased soil solution sulfate concentration and net desorption in the soil in
              response to decreased  S deposition.

4-41          As indicated above (see comments for 4-14) that there is other evidence that
              changes in winter time conditions can affect nitrate export.

4-42          Other studies in the Adirondacks have also identified the importance of within
              lake processes in affecting nitrate losses from lake/watersheds.  See for example:

              Ito, M., M. J. Mitchell, C.T. Driscoll, R. M. Newton,  C.E. Johnson, and K.M.
              Roy. 2007.Controls on surface water chemistry in two lake-watersheds in the
              Adirondack region of New York:  differences in nitrogen solute sources and sinks.
              Hydrological Processes 21:1249-1264.

              Ito, M., MJ. Mitchell, C.T. Driscoll and K.M. Roy.  2005. Nitrogen input-output
              budgets for lake-watersheds in the Adirondack region of New York.
              Biogeochemistry. 72:283-314.

4-44          Change to: with the exception of streams in Shenandoah National Park, Virginia,
              which appear to exhibit decreases in adsorbed sulfate in soils.

4-62 to
4-63          The discussion in this section needs to differentiate between bedrock geology and
              surficial geology. Surficial geology is a much more important predictor of the
              sensitivity to acidification than bedrock geology. Differences in surficial geology
              can be  especially important for predicting sensitivity to acidification within a
              region.

4-73          Some of this discussion on critical loads is repetitious from previous sections
              although this previous section is referenced.

4-82          I don't believe the following statement is true for the Adirondacks: However,
              recent research suggests that N has accumulated in soils over time in the
              Adirondacks and that some forests have exhibited declining retention of N inputs.
              The result has been increased leaching of NO3 to surface waters.
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              See for example:

              Mitchell, M.J., C.T. Driscoll, S. Inamdar, G. McGee, M. Mbila, and D. Raynal.
              2003. Nitrogen biogeochemistry in the Adirondack mountains of New York:
              hardwood ecosystems and associated surface waters. Environmental Pollution
              123:355-364.

              Mitchell, M.J.,  C.T. Driscoll, J. Owen, D. Schaefer, R. Michener, and D.J.
              Raynal. 2001 Nitrogen biogeochemistry of three hardwood forest ecosystems in
              the Adirondack Mountains. Biogeochemistry 56: 93-133.

4-112         Wetlands after droughts can also serve as nitrate sources when rewetted. See for
              example:

              Watmough S.A., Eimers M.C., Aherne J. and Dillon PJ. 2004. Climate effects on
              nitrate export from forested catchments in south-central Ontario. Environ. Sci.
              Technol. 38(33): 2383-2388.

              Also, some mention of the role of N-fixation should be included for wetlands; see:
              Kurd, T. M., D. J. Raynal, and C. Schwintzer. 2001. Symbiotic N-fixation of
              Alnus incana spp. rugosa in shrub wetlands of the Adirondack Mountains, New
              York. Oecologia 126:  94-103.

4-129         The following paper could be referenced showing the effect on N additions on
              understory communities in the Adirondacks:

              Kurd, T.M., A.R. Brach, and D.J. Raynal.  1998. Responses of understory
              vegetation of Adirondack forests to nitrogen additions. Can J. For. Res. 28: 799-
              807.

4-162         There is fairly good evidence that for forest ecosystems with closed canopies that
              throughfall sulfate is a good estimate of total sulfur deposition.  See: Lovett
              G.M., Thompson A.W., Anderson J.B. and Bowser JJ. 1999. Elevational patterns
              of sulfur deposition at a site in the Catskill Mountains, New York. Atmospheric
              Environment 33:617-624.

4-162
to
4-170         The discussion on the  formation of MeHg needs to emphasize the
              interrelationship with  sulfate concentrations and the role of sulfate reducing
              bacterial.  Such focus will help emphasis that theme of this report relates nitrogen
              and sulfur.  The extensive discussion on Hg biogeochemistry and environmental
              effects can be condensed.

4-179         An evaluation of nitrate sources to waters with respect to atmospheric deposition
              needs to separate how nitrogen deposition loading leading to more nitrate loss
                                                                                     84

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             versus atmospherically deposited N being found directly in drinking water. Forest
             watershed level work using stable isotopes shows predominantly that almost all of
             the nitrate in surface and ground waters has been biotically derived. See for
             example:

             Burns, D. A. and Kendall, C.: 2002, Analysis of 615N and 618O to differentiate
                s sources in runoff at two watersheds in the Catskill Mountains of New York',
             Water Res. Res. 38(9), 1-11.

             Piatek, K.B., M.J. Mitchell,  S.R. Silva and C. Kendall. 2005. Sources of nitrate in
             Adirondack surface water during dissimilar snowmelt events. Water, Air and Soil
             Pollution 165:13-35.

             Kendall, C.: 1998, 'Tracing  nitrogen sources and cycling in catchments', in C.
             Kendall and J. J. McDonnell (eds), Isotope Tracers in catchment hydrology,
             Elsevier Science, BV, pp.  519-576.

5-36
to
5-37         The conclusion section should then be shorted and include information on the
             overall approach of the study including important resources to be used and
             potential limitations.

5-3          Not sure we have  good estimates for some pollutants such as ammonia. This
             statement seems contradictory:

             Despite the aforementioned  limitations, for the purposes of identifying and
             quantifying the atmospheric concentrations and deposition totals causing
             ecological effects, these measurement techniques and sampling frequencies are
             fully adequate. Nevertheless, the coverage of the networks is very thin over large
             expanses of the interior United States.

5-6          As stated previously the importance of superficial geology needs to be
             emphasized.

5-36
to
5-42
to
5-44         TABLE 5.7-1. SUMMARY OF NITROGEN DEPOSITION LEVELS AND  THE
             CORRESPONDING EFFECTS OF ACIDIFICATION AND NUTRIENT
             ENRICHMENT ON ECOSYSTEMS.

             To this table could be added the results from the Adirondack Manipulation and
             Modeling Program (AMMP): Mitchell, M.J., C.T. Driscoll, J. Owen, D. Schaefer,
             R. Michener,  and  DJ. Raynal. 2001. Nitrogen biogeochemistry of three hardwood
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forest ecosystems in the Adirondack Mountains. Biogeochemistry 56: 93-133.)

This study included experimental additions of ammonium sulfate and nitric acid
(14 and 28 kg N ha"1 yr"1).  The biogeochemistry of nitrogen (N) was evaluated
for three forest ecosystems [Woods Lake (WL), Pancake-Hall Creek (PHC) and
Huntington Forest (HF)] in the Adirondack region. Bulk N deposition was higher
at sites in the west than those in the central and eastern Adirondacks. These higher
atmospheric N inputs were reflected in higher bulk throughfall fluxes of N (WL
and PHC, 10.1 and 12.0 kg N ha"1 yr"1, respectively) in the western Adirondacks
than at HF (4.6 kg N ha"1 yr"1) in the central Adirondacks. The greatest increase
in nitrate loss in response to the experimental treatments occurred at HF where the
HNO3 additions resulted in the highest nitrate concentrations and lowest N
retentions.
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                                 Mr. Richard Poirot
Generally, I think the document provides a thorough and useful summary of the state of
knowledge relating to the ecological effects of S & N deposition - primarily through
acidification and nitrogen enrichment. Several other welfare effects of these pollutants are briefly
discussed, although there is no mention of materials damage. As indicated in previous comments,
I think it might have also been useful to consider the important welfare effects of sulfate and
nitrate aerosols under both this secondary SOx/NOx review, as well as in the PM review
(copy/paste).  Excluding aerosol effects here seems to point to an advance decision that some
sort of deposition, critical loads, or critical loads exceedance-type indicators are being considered
as a possibility for secondary S and N (hopefully including reduced N) NAAQS.

This flexibility in considering alternative indicators would be a welcome change in the Agency's
approach to secondary (or primary) NAAQS, as I think previous reviews have been constrained
to consideration of indicators based on the named gaseous criteria pollutants - SO2 or NO2 -
even though I think the Clean Air Act provides ample encouragement to consider the effects of
secondary transformation products and combinations with other pollutants. Since this ISA
represents a beginning of the new, streamlined NAAQS review process, its difficult to get a
sense of just how far the information and analysis should be taken or "set up" in this document,
what belongs in the risk/exposure assessment, and what should be left to the ANPR. If there is
really going to be consideration of several deposition-related indicators in this review cycle, I
think there should be additional discussion of the options - like critical loads - up front in this
ISA, since these are the kind of alternative limits to be evaluated in the risk/exposure assessment,
and should definitely not be introduced for the first time in the ANPR.

Another general comment is that I think the document is unnecessarily silent on projected future
reductions in S and N emissions that will result from the CAIR rule.  We would like to have a
better sense of what kinds of effects have occurred, are  currently occurring, and are expected to
occur as future "on the books" emission reductions occur. At some point before this review is
completed, there will likely be some consideration of how NAAQS which relate to location-
specific effects and measurements may interact with the receptor location-insensitive emissions
cap & trade approach that has become the preferred regulatory approach for further reductions in
S and N emissions.

Chapter 2
The 1st half of the chapter's discussion of atmospheric chemistry seems reasonably thorough,
although it might more logically follow the discussion of emissions at the beginning of Chapter
3.  Its not clear whether this level of detail on atmospheric chemistry is needed in this new-style
"Integrated Science Assessment" (as compared to a criteria  document or an annex to this ISA).
Any excess information here is harmless, but every attempt should be made to make the
discussion relevant to those aspects of atmospheric chemistry that may be especially critical to
understanding  the sources exposures and environmental effects of these S & N pollutants (or
other pollutants like Hg the effects of which emissions of these pollutants may affect).
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By contrast, the very brief 2-paragraph section 2.5 on Atmospheric Transport conveys almost no
useful information (and there's not all that much more detail on transport provided in the
Annex). I think this section needs work and might more logically be either tightly focused on
those aspects of atmospheric chemistry which in turn affect the transport and ultimate deposition,
or expanded and combined with the section on chemical transport models (CTM) at the end of
chapter 3.

The 2nd half of chapter 2 seems unnecessarily limited to measurements of the "named" NOx and
SOx criteria pollutants, with additional tangential discussion of artifactual gains and losses of S
& N species in PM mass measurements (which is somewhat beside the point).  At the same time,
this discussion of measurements, networks, & limitations seems unnecessarily disconnected from
discussion of the same topics for measurements, networks & limitations  of gaseous & aerosol
concentrations, and wet and dry deposition which are included in the first half of Chapter 3
(which actually has relatively little direct discussion of "Ecological Exposures" until the section
on Harvard Forest Flux measurements on p. 3-34).  I think it would be better to combine all these
discussion of measurements of the relevant gaseous, aerosol, wet and dry deposition networks in
a single section.  Emissions to chemistry & transport to concentrations to deposition and
exposures seems like a more logical way to present this information.

Specific Comments
p. 2-1, lines 13-27 (& footnote 1): Possibly you could also include a mention here of the CAA
definition of "welfare effects" modified in Section 302 (h) of the 1990 CAA to include the
phrase: ".. .whether caused by transformation, conversion, or combination with other air
pollutants". All gaseous, aerosol and deposition oxidation products of (traditionally defined)
SOx & NOx emissions should be clearly on the table for consideration, and "combination with
other pollutants" may help open the door to considering effects resulting from both oxidized &
reduced N emissions.

p. 2-2, line 7: If you changed "particles" to "aerosols" (which includes the suspending gaseous
medium), you could leave (gaseous) FENOs on the list.

p. 2-3, Figure 2.2-1: Some inorganic nitrates - like NH4NO3- can also be transported to remote
regions under low temperatures. Generally this section seems overly brief.

p. pages 2-7 to 2-98:  This is an interesting and thorough discussion, but there needs to be a
clearer connection made between this halogen chemistry and either the emissions, transport or
deposition of S & N compounds. You might also add somewhere here that free Cl & Br released
by these reactions can also contribute to the conversion of Hg° to Hg2+, enhancing the potential
for wet & dry Hg deposition to the environment.

p. 2-9 line 29:  Add "gaseous" before "species".

p. 2-16, line 29:  Formation of aerosol NFLjNOs can also substantially enhance the atmospheric
lifetime(s) and transport distance (for both oxidized & reduced N). At some point (not sure
where) you should also add some discussion of both current and projected future aerosol

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sulfate/nitrate/ammonium/acidity relationships, as lower levels of acidic sulfate may lead to
increased levels (& longer transport distances) of aerosol nitrate.

p. 2-16, lines 26-29: This discussion seems overly simplified. Yes, NO and NC>2 are less soluble
than SO2, but they are also much more reactive and, with their "longer-lived reservoir species
HNNOs" do not necessarily transport over longer distances than SC>2 and its transformation
products.

p. 2-17, lines 7, 9, 13,  14: Here it looks like you use "NOx" with several different meanings, and
while you claim (line 14) to limit the chapter to FRM/FEM, the chapter quickly moves beyond
FRMs for NO/NO2 to more exotic species & methods.

p. 2-21, lines 15-19: I think this is stated backward. There is more likely to be volatilization loss
of NCV from (relatively acidic) PM2.5 filters (if Teflon - not nylon)  and more likely to be
positive nitrate artifacts on alkaline PMio (or PMio-2.5 filters), unless preceded by HNOs
denuders.

p. 2-21, line 22 - p. 2-22, line 8: This is a limited discussion and wimpy illustration of current
satellite sensing potential for NC>2. See for example :
http://datafedwiki.wustl.edu/index.php/2007-07-l 8_ESIP_Demo_OMI_NO2
for a better illustration of & links to OMI NC>2 data and images.

p. 2-24, line 22: Traditionally the STN network has employed thermal-optical transmittance
(TOT), while the IMPROVE network has used TOR. Currently, STN sites are transitioning to
TOR in a phased process - over several  years.

p. 2-24, line 23: IMPROVE sample frequency changed from twice a week (Wed & Sat) to 1 in 3
day (same as STN) in Sept.  2000.

p. 2-24, lines 27-31: IMPROVE denuders are coated with a combination of carbonate and
glycerin.

p. 2-25, lines 13-22: Its not clear what kind of sampling you're referring to here.  Glass fiber
filters with basic coarse particles on the  filters would be indicative of TSP samplers currently
used primarily for sampling for Pb NAAQS. These are very rarely analyzed for SO4, NOs, Cl, or
PM mass (which is irrelevant for TSP).  Quartz filters can also have (smaller than glass but
significant) positive artifacts from SO2 or HNOs. Denuders are not really much of an option for
hi-vol PMio samplers - on which quartz filters are typically run, but yes, denuders on lo-vol
Teflon filter PMio or PMio-2.5 (by dichot) sampling would help eliminate artifacts.

p. 2-26, lines 6-7:  Actually, the loss of pNOs from FRM PM2.s samples is likely to be greater
than for the "other simple collection systems described above". Also, the discussion in the
following several paragraphs is interesting &  informative, but relates primarily to how nitrate
sampling losses affect PM2.s mass measurements (not nitrate measurements, which are usually
not conducted on these Teflon filters). This reminds me to lament again that its too bad aerosol
                                                                                      89

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nitrate is "off the table" in this NAAQS review - since it is not fully included in our
measurement-based definition of PM.

p. 2-27, lines 4,5:  I would add "nitrate" after "ammonium" (ammonium sulfate is very stable).
Also, changes in the equilibrium between aerosol and gaseous precursors can be due to factors
other than T, RH and acidity - such as changes in the precursor gas concentrations - for example
rapid loss of (sticky) HNOs & NHa concentrations in the indoor environment.

p. 2-27, lines 3-21: Why not move the discussion of negative pNH4 artifacts adjacent to the
discussion of positive pNH4 artifacts beginning line 21, p. 2-25. Also I question your implication
that negative artifacts generally exceed positive artifacts for NH/t. Can you provide a reference
for this? NH4 is not measured in IMPROVE and NH3 denuders are not used in STN - which does
attempt to quantify NH/t. What is the intended meaning of the occasional [ ] in this paragraph?

Chapter 5
This chapter provides a concise summary of the information presented in the preceding chapters.
It was generally well-written, but as with the other chapters, there were sections that were
choppy  (multiple authors?)  or where the language would benefit from some more careful editing
for clarity.  In some cases, the brevity (highly desirable) seems too brief to convey useful
information and would benefit from a bit more detail. The use of references is not consistent
from section to section and  I suggest using more rather than fewer (they don't take much room
and inspire confidence). In some sections the language is unnecessarily vague ("very large",
"higher than might be expected", etc.) or speculative ("may occur", "is probably ongoing", etc.).
In many cases, a good point is being introduced that could easily be restated more objectively.

It should be clear that this is a "summary" (which is fine), but not intended as an integrative
synthesis or winnowing down of crucial information. There are no  new insights provided here,
and the  chapter doesn't lead in any obvious directions toward selection of alternative or specific
indicators.  For the most part,  the more detailed and useful information is presented in the
preceding chapters. A strong point of Chapter 5 is a series of excellent summary tables at the end
(especially Table 5.7.1 on N deposition & effects).   These tables start to provide a sense of what
kinds of effects are occurring in what regions at what loading rates. I would have liked to see
this information taken a bit  further to more directly address the concept of critical loads (and
exceedances of critical loads), in ways that might provide more advance insights into possible
elements (indicators, averaging times, levels & forms) of new secondary NAAQS.

Specific Comments
p. 5-1, line 32: You could add pSO4 as parallel to pNO3 in line 29.

p. 5-2, line 7"  "controlling  862 oxidation" isn't really the right term here.  Could reword as
something like ".. .altering the chemistry of 862 oxidation products by neutralizing..."

p. 5-2, line 23: "adequate" (a questionable judgment here), could be improved by adding "for
determining compliance with current NAAQS".
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p. 5-3, line 3: "regulatory" doesn't seem quite right here (& in several other instances).  We have
no "regulations" for required monitoring of NH3.

p. 5-3, line 7: You could add a bullet or 2 here describing routine methods/networks and
limitations for monitoring of wet (&/or dry) deposition of S & N compounds.

p. 5-3, line 31: Can you be more quantitative than "very little..."

p. 5-4, line 5: Same as previous comment. What % does "substantially smaller" mean?

p. 5-4, line 19: You could add "atmospheric" before "N".

p. 5-4, line 23: Do you mean ".. .emitted to the atmosphere..."?

p. 5-4, line 26:  There are not "regulatory" monitoring networks for deposition (although maybe
there should be).

p. 5-5, lines 23-26: Its not clear what you mean by "riverine flow in the absence of deposition"
(some of the riverine flow N is from deposition to upland surface waters or catchments, some is
from non-atmospheric sources, and then there's some directly deposited to the surface waters of
the coastal estuary). Also, its not clear what the 11, 5.6 & 5.6 kg N ha-1 refer to here.

p. 5-6, line 21:  You could replace "understood" (speculative) with "described in detail".

p. 5-7, line 23: Can you use a more objective phrase than "thought to be"?

p. 5-8, line 30:  Can you use a more objective phrase than "may occur"? For example, have such
effects been observed anywhere? If not, you might express these as logical expected outcomes
which have not been observed to date...

p. 5-9, line 27: "Consequently" doesn't seem quite right. Organic matter build-up isn't
necessarily a consequence  of "fungi that feed on organic debris..."  unless they are less efficient
than the bacterial consumers they replace, in which case say so..

p. 5-10, line  1:  You could replace "expanded" with something like  "reflected a substantial
increase in..."  The CD didn't expand knowledge; it just documented it.

p. 5-11, line  16 (& also 5-12, lines 2 and 29 & elsewhere):  There are several different indications
of a uniquely different situation in the Mid-Appalachian region.  It would be useful to provide
some explanation of reasons for this difference. Maybe you could do this in the case studies
(make it clear there why Shenandoah is different from the Adirondacks) and have pointers to that
discussion whenever you indicate a 'Shenandoah exception' elsewhere in the document.

p. 5-12, line 28: Add "in"  after "decreased".

p. 5-13, line 2 "Al generally becomes the greater health risk" Greater than what?
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p. 5-13, line 19: I assume that by "the most serious effects" you mean something like "more
serious than long term", which I find very counter-intuitive - and would need more convincing
to accept as absolute truth. I don't see any need to play off the severity of chronic vs. acute
acidification against each other, nor do I like the policy implication that its only the episodes that
matter.

p. 5-15, line 9: This is a good example of overly speculative phrasing ("acidification that has
occurred to date has likely been very limited").  You could say roughly the same thing more
objectively by indicating that "acidification that has been observed to date has been very
limited").

p. 5-15, line 9,10: Not clear what "Episodic acidification does occur" means here. In the West?

p. 5-15, lines 29-30: I'm surprised that the absolute concentrations of SO42" (as well as its % of
total ion concentration) did not also decrease. If they did, why not say this as well, as a decrease
in the % could be due to an increase in something else.

p. 5-16, line 18 (& next few pages): These case studies seem like they need some additional
detail. I'm not quite sure what's the intended point. Maybe you could put some emphasis on the
similarities & differences between the focus regions.  For example what were the past & current
deposition levels in the Adirondacks - to compare with those reported subsequently for
Shenandoah? Possibly an additional 'case study' for an acid-sensitive alpine Western ecosystem
would round out the regional coverage, and would also help emphasize the extreme sensitivity in
these fragile ecosystems which will not benefit from CAIR emissions reductions.

p. 5-16, lines 30-32: This is  awkwardly worded. I assume you mean that the number of lakes
with ANC < 50 has more than doubled from pre-industrial times (it's not the estimate of the # of
pre-industrial low ANC lakes pre-industrial lakes that's changed).

p. 5-17, lines 8-10: It seems like these future projections are out of place here.  I would move
them to after line 23.

p. 5-18, line 32: Add "assessments of before "the impacts".

p. 5-21, lines 10, 12-17, 23 & elsewhere: At some point, it would be useful to add some direct
discussion of N-fertilized "growth" enhancements vs. other consequences of this fertilization &
growth. In some places an impression is given that "growth" is always good, or good up to a
point beyond which other adverse consequences can result. Possibly also add some discussion of
combined effects of N fertilization + climate change.

p. 5-23, line 4: Can you give a quantitative example of what you mean by "very high"?

p. 5-24, lines 3-4: Can you use a more objective term than "are thought to include"? Could you
say something like "Observed effects...  have included.
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p 5-24, line 5:  Same comment as above,  "would be considered relatively low" by whom?
Compared to what?

p. 5-27, line 1: This is an interesting observation. I wonder why? Also, "disproportionately
high" compared to what?

P 5-27, lines 7-10: It might be helpful to provide some comparative info on N dep rates in
Netherlands vs. US.

p. 5-30, line 25 and following paragraph. I think this section should extend beyond the current
discussion  - focused largely on primary productivity - and describe some of the biogeochemical
effects of excess growth and decomposition on dissolved oxygen, etc.

p. 5-30, line 31: Could you say "N-limited", rather than "N-deficient"?

p. 5-31, lines 18-30: You might add "turbidity" to this list. Its not a "biological" measurement,
but neither is DO.

p. 5-33, line 10: Can you state this more objectively than "probably ongoing"?

p. 5-33, line 14: Aren't current inputs in this region much lower than 10 kg N ha"1 yr"1?

p. 5-34, line 3: You could add "SO4 deposition and" before "Hg methylation".

p. 5-34, line 10:  Why are DIC & DOC in ( )?

p. 5-36, line 19: There are no "regulatory networks" for S or N deposition.

p. 5-36, line 20:  You could add ", elevational gradients and" before "hotspots" to emphasize a
particularly important inadequacy of existing deposition networks.

p. 5-36, line 22:  Add a (cite) where indicated.

p. 5-37, lines 2-4:  Is it possible you meant "high elevation areas of the West"  in line 4?
Otherwise including both the Appalachians and high elevation seems redundant.  And if you did
mean the "West" (which would be true) you might describe the first region as  "New York / New
England" to include the Adirondacks & Catskills. Possibly also  add a mention of sensitive areas
in Canada which might benefit from future reductions in US S and or N emissions.

p. 5-37, line 11:1 hesitate to criticize this presentation of quantitative "limits" here, since I think
more such numbers would be useful in this section, but in this case, I think N deposition rates are
already below  this 9-15 kg N ha"1 yr"1 limit, while the low bound limit of 0 kg  S ha"1 yr"1 suggests
that no amount of S reduction would prevent re-acidification (which doesn't make sense). It
might also be useful here to provide some indications of how these ranges compare to both
current deposition levels and future projections under of CAIR and contrast these with the
estimated damage thresholds in both Adirondacks and Shenandoah.
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p. 5-37, line 14: As in a previous comment, you are implying here that "growth" in some
ecosystems is a beneficial outcome - to be contrasted with "adverse effects" in others.  I think
this could be fixed by changing "ecosystems" to something like "ecosystem components".

p. 5-37, line 19: Insert "Adding" before "excess" or change "to" to "in".

p. 5-37, line 26: Should be "West" coast.

p. 5-39, end of 1st line under Nitrate: Add s to 1980. And 2nd to last line: Could you add example
parenthetical "X ueq/L)" to indicate what is meant by "Very High".

p. 5-42:  Table 5.7.1 provides a very useful quantitative summary of effects of N deposition on
acidification and nutrient enrichment that have been identified in recent studies. Would it be
possible to provide a similar summary table providing quantitative of S deposition (or S+N
deposition where applicable) on acidification? It is curious that these concluding summary
tables include some international observations but seem to have no Canadian references.
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                               Dr. Armistead Russell
While I think the current ISA for Oxides of Nitrogen and Sulfur-Environmental Criteria provides
much of the needed information for the process of reviewing the secondary NAAQS for NOx
and SOx, at present the document is in need of significant modification to provide such
information efficiently and effectively. The document should be read and edited for relevancy of
the information being provided, and how it is provided, to the ultimate goal of the review of, and
providing the scientific basis for possibly changing, the associated secondary NAAQS.

One step  in this process would be to look at Chapter 5 and edit what is presented there to
specifically provide a summary of what information is needed to provide a scientific foundation
for a review of the standard. Having edited the summary chapter, then go back and write the
chapters to bring forth the specific points needed to provide the basis for what is in Chapter 5.

Unlike the ISA's for the two associated primary NAAQS, this document begins in Chapter 2
with the more traditional Criteria Document approach of reviewing the atmospheric physics and
chemistry of NOx and SOx, as opposed to a "Source to Dose" presentation, which here would be
source  to exposure or load.  The latter approach led to a much more efficient presentation of the
key concepts, data and science. As  it currently reads, aspects of Chapter 3 seemed to be
somewhat repetitive of information  in Chapter 2, and the flow is awkward. Taking a source to
exposure/load also leads back to the key idea that the increased environmental exposures can be
linked to  a source, which is what is  controlled. Maybe it is due, in part, to lack of scientific
investigation, but it is this type of information that is required for this review. In revising the
current Draft ISA, it might be good  to have someone read Chapter 5, the Conclusions, first, and
then identify what are the major points, and what is needed to support the  key findings as to the
environmental implications of anthropogenically-influenced increased exposures  and loads.
Then, the degree to which those key findings are supported in Chapters 1-4 can be assessed, and
the discussion of tangential information can be streamlined.

Chapter 2:

As noted above, I think the ISA would benefit from a Chapter 2 that goes  from Sources to
Environmental Exposure/Load.  Chapter 3 should be integrated in.  In addition to having
atmospheric chemistry and physics, aquatic and  soil chemistry and physics should be added.
This would save much repetition later on in the report (e.g., about what leads to acidification, its
affect, mobilization of aluminum, etc.). Fig. 2.2-1 could have a twin(s) showing what is
happening in surface water and the soil-water matrix.

On page 2-3,  line 16, one should note they are referring to US emissions.  Lines 19-23 are a bit
confusing at present.  What is important, here, is that virtually all of the fuel-bound sulfur gets
oxidized to a volatile component (SO2 or SO3),  and that there is very little natural, oxidized
sulfur in air over the US, so the sulfur emitted from burning a fuel is quantitatively related to that
in the fuel.
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The section on Measurement Methods needs to be refocused. The major question to be
addressed here is if the current methods employed in the field provide reliable measurements of
NOx, NH3, NH4+, NO3", SO2 and SO/f for levels of interest, and this should be answered
quantitatively. At present, there is discussion of the various measurement approaches (some is
needed) and lots of discussion on possible interferences, but never does one get the answer to
what is the typical uncertainty in the measurements at a typical monitor in the US and how that
impacts our ability to accurately quantify environmental exposures.  I suspect that the methods
employed for most of the species, while subject to some interferences, provides fine data, and
that the level of uncertainty is such that we need not concern ourselves with possible
interferences and biases.  The major exception, of course, is ammonia, which is not even
discussed. What really limits our ability to quantify deposition accurately (e.g., do we need more
accurate measurements, different kinds?). Quantify the problems, let the reader assess if they are
of concern.

More specific comments:

2-1:24-27: What about pSO4?
Rxn 2.2-2: Balance the reaction.
2-5:13: Reactions 2.2-1  and 2.2-2.
Section  2.2.2 It is not apparent the need for so much on Cl chemistry.  Also, this section should
be preceded  by a more comprehensive discussion of N2O5. I would be very tempted to
minimize this discussion.

2-9:25:  Not sure why you use monomeric.  What polymers do you have in mind?
2-10: 28: In both cases, NO3 and H are radicals, not ions.
2-11:2 Ravishankara.
2-13:28:  A second reaction for comparison should be added (i.e., the ozone reaction).
2-14:10:  What chemistry of NO3- formation is being discussed?
2-15:1:  Ammonium nitrate formation as well.
2-17:30 Remove "all".
2-21:  Section 2.6.2.2 needs to address  accuracy more directly.
2-22...:  Section 2.6.3 should be more quantitative.

A section on NH3 measurement is needed.

2-27:  Section 2.7.1:  It is weird that pNO3 is included here, pSO4 is not.
2-28:28:  There is a  summary paragraph for NH3 that is about as long as those for the other
species, but where is this drawn from?

At present, the summary is a  bit sparse.
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Chapter 3

The Chapter beings with a discussion of sources, which as noted above, should go in a more
integrated Chapter 2. It seems a bit unnatural to not start "the story" with sources.  Also, while
this chapter starts with sources, one does not get a quantification of such. One should not have to
go to the Annexes to get a reasonably quantitative overview.  A single table showing the
contributions of, say, mobile, non-mobile, utility, biogenic and agricultural sources to oxidized
NOx, N2O, reduced N and SOx is required.  This might be done on a tons of S and N basis for
ready comparison between the oxidized and reduced forms.  Some estimate of the transport to
North America might also be provided.  (A sister Table showing the fate of the above is also
suggested.)

A Table of fate of reduced N,  oxidized N and SOx is suggested, showing the masses dry and wet
deposited by species, as well as the amount transported away from the continent and associated
estuaries. Having this table integrated with the table of sources might be of interest from a mass
balance perspective.

Figure 3.7-4 As discussed during the SOx-Primary ISA review, this figure is not very effective.
First it refers to "... in  focus" in focus of what? Further, most of the data is very much at the
bottom end, so it is difficult to see what is really happening, and it needs to include more
information (what years...). I would have it provide the mean, median, 5 & 95%iles, and the
extreme value. Further, it might be given on a log scale as most of the lower level information is
now lost.

There is a bit of a contradiction in Chapter 3.  On page 3-8, line 11, it says the ratio of N-to-S is
14, close to that in the tissue.  The prior line says that approximately half of the S is in the ash.
Please  explain further.

In considering emissions, it would be good to also provide some information as to future
emissions for perspective. CAIR is going to significantly lower emissions in areas where they
are currently high. This is important for our further consideration as to how a standard might
impact air quality.

Section 3.13 Summary.

This section starts out very roughly. 3.13.1 reads more like a set of bullet points in sentence
form. The last paragraph (3-161,14-6):  Is this what you really mean to say, and from what part
of the report is it distilled? Table 3.11.1 is rather more concrete at 21%, but does not indicate the
reduced N fraction. Also, the  first sentence of 3.12.2 is not really taken from something in the
text (I might add this to the prior text).

3-60:26 change to "... surface  of some coastal..."

What this chapter (or what should become a section of Chapter 2) needs is to focus on what one
wants to  know, as this section currently has some stuff I like to know, and some of what is not
needed to assess a NAAQS. What is really needed? I would say a best estimate (map) of total N
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and S deposition, a list of estuaries suffering eutrophication with estimates (and uncertainties) of
what is contributing.  There was too little on ammonia(um) deposition.

Specific comments:

3-2:30:  This sentence contains a non-sequiter.
3-3:2: Reactions, not reactivities.
3-4:16:  I would remove "small"
3-4:24:  "... for example, is estimated to have decreased.
3-9:16:  Remove "However"
3-13:13 "is a smaller loss process than its net thermal decomposition"
3-13:28 Remove "which"
3-14:  Section 3.5.5. the source strength given is not a source strength unless one knows the
volume. Further, more information on how robust this value might be nationally is needed.
3-23:  Section 3.7 is somewhat repetitive of prior sections.
3-23:23-29: What is this paragraph trying to say?
3-23:28:  Higher than what?
3-24:1-8: Much more quantitative information is available, e.g., annual average concentrations
of the various individual oxidized nitrogen species.
Figure 3.7-2: Put Figure 3.7-3 right below this figure for comparison. Also, can you provide the
same figures for oxidized nitrogen species of interest?
3-26:2 "for more complete descriptions"
3-26:7:  This is  not seen in Fig. 3.7-4.
3-28:6:  "correlative"?
3-28:29 "...mean oxidizedN..."
3-36:6:  Units on deposition velocity?
3-36:7-7: Is this a major extrapolation. Please clarify.
Fig. 3.9-3:  How significant is "a", and the units for concentration are non-standard.
3-41:3-5: Further explanation as to "why" is needed.
3-43:26-27: Same  should be added for regional scale.
3-47:19-17: I would note all of the evaluation work and measurements done by/for the state,
RPO's and  EPA. It may not get published in the open literature, but these groups probably do
most of the model evaluations done.
3-48:12 "This"?
3-50:  What is needed here are the best estimates of N deposition using CMAQ.
Figure 3.12-3:  How about adding NH3?

Chapter 4:

Chapter 4 reads more like the old Criteria Documents, being rather exhaustive and sometimes
appearing to lose the point.

Also,  maybe I missed this,  but this chapter seems to have ad hoc decided to use SC>4+ instead of
using  SO4= (or SO42").  Why?

There is significant repetition in this chapter.  Much of what is in 4.2.1.4 is in pages 4.10-12.
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4-1:22: interacting
4-2:6: "...when the nutrient..."
Figure . 1-1:  For the forest critical chemical limit, what are the units of 1.0?  For the Lake, is "0"
sensible?
4-7:13 Might you add surface water acidification?
4-8:4: Define Oa
4-8-29:  What about NHX?
Fig. 4.2-1: Wrong figure.  (Switch with 4.2-2)
4-11:25:  Replace "This" with "The"
4-13:22:  "... forested areas2 it is  ..."
4-15:27 Define "%" of what.
4-16: "...acidic deposition moblizes..." no comma.
4-16:14-16: Repetitive.
4-19:11-12:  Same paragraph.
4-19:16:  "...general... generally..."
4-19:28 "or neutralizing"
Fig. 4.2-3 Probably should define ANC in the caption and also add the 0 lines.
4-22:30 All the "in summary" statements get a bit old.
4-24:3:  [K]
Section 4.2.22:  Repetitive of prior material.
Fig. 4.2-6: "Bad death"? As opposed to "Good death"?
4-39:25-26:  Sentence needs a bit more explanation.
4-43:: 19: "linearly"
4-44:31:  Context needed for 5.0, 5.5 and 6.0. Reference to what effects.
4-49:  Should not ANC measurement be up front in measurement methods?
4-49:9: Repetitive.
4-49:14:  Small is not defined, and why is this viewed as small?
4-49:23-24:  Unclear clause at the end.
4-50:  Lines 21-22 and 25-26 appear to be contradictory.
4-54:20:  Be specific as to at what level.
4-64:23:  Lawrence no longer in review, I think.
4-123:L24...: Again, seems repetitive.
4-129:17 Reviewing only the negative  effects appears one-sided.
4-130:2:  "Results of these studies..."
4-132:30: Confirmed?  Support?
4-135:1:  What would this equate to in terms of deposition?
4-148:29: define stges.
4-150:26: "probably"? Cite.
4-152.19-27: Largely repetitive.
4-154:5-9 The term significant here must be purely definitional. What is meant by, or
determines, significant?
4-156:4...: Repetitive.
4-157:14 "Niwot Ridge where..." remove comma.
Section 4.4.1.2  can be shortened.
4-168:19-21. This need not be stated.  It has to be.
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4-174:3-14.  Be quantitative... at what levels are the impacts found?
4-177:12-31 Use same units as before.
4-177:3-: Provide units on coefficients.
4-178:9-14:  Discuss exactly what was measured, provide uncertainties.
4-179:24-25: Is this likely an issue?
4-179: Provide a summary.

Chapter 5:

This chapter is still a bit choppy, but primarily should be revised by asking the question:  What
information specifically is needed to provide the scientific basis for reviewing the NAAQS
secondary NOx and SOx standards.

Specifics:

5-3:8-12: What about ammonia?
5-12:28:  "... decreased in some..."
5-12:31: be a bit more specific as to how.
5-13:29-30:  Could just be my memory, but I don't recall this.
5-16-28:  Remove extra "."
5-16:30 Try  not to use "many" as opposed to giving a specific fraction.
5-18:5: rearrange sentence" "contributions of CA...acidity) from some ..."
5-20:16: "...section discusses..."
5-20:31: "is it "of or "by"?
5-26:8-28: These are important points, but they did not seem to come out very distinctly in the
chapters. (same with 5-27:15-20).
5-28:22: "AQCD, further studies suggest productivity..."
5-31:6: awkward sentence.
5-37:16 remove "in"

Overall:  Probably the single biggest limitation in this document is acknowledged early on: It
does not try to establish critical loads, without which it becomes difficult to know what levels of
environmental exposures are acceptable or not.  Decision makers and advisors need such
information, even if it is fraught with "uncertainties." (I put uncertainties in quotation marks as
it seems as though we use that as a reason to not go forward, which is not the case.)  The second
real need of this ISA is to dig more in to the reduced nitrogen deposition issue.
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                                   Mr. David Shaw
Chapter 1 Comments
Message of the document
This chapter drives the whole document and as such it should say up front that a major part of
this assessment is examining. A primary unit of measure is shown throughout as deposition, so it
must state the strength of a deposition approach to both of these contaminants. I also feel that
the purpose and consequences of evaluating N and S in tandem should be addressed. While the
chapter opens with a statement of eliminating particulates in the scope of this scientific analysis,
I do not feel that this is not an appropriate message.
Framing Questions
Some of the framing questions (pg 1-2) are awkward (e.g. bullet 3 line 13) and don't focus the
work as well as the more succinct language below (proposed by E.Cowling). Individual
Comments on the September 2007 Draft Plan for Review of the Secondary National Air Quality
Standards for Nitrogen Dioxide and Sulfur Dioxide October 26, 2007. I suggest substituting the
framing questions for these:

       "What scientific evidence and/or scientific insights have been developed since the last
       review to indicate if the current public-health based and/or the current public-welfare
       based NAAQS need to be revised or if alternative levels, indicators,  statistical forms, or
       averaging times of these standards are needed to protect public health with an adequate
       margin of safety and to protect public welfare?"

       "What scientific evidence and/or scientific insights have been developed since the last
       review to indicate whether, and if so, what particular ecosystem components or other air-
       quality-related public welfare values, are more or less sensitive than the populations of
       humans for which primary standards  are established and for this reason may require a
       different level, indicator, statistical form, or averaging time of a secondary standard in
       order to protect public welfare?"

Format
The format calls for a summary of findings at the end of each major segment of each chapter
which the authors do, but they should also, as much as possible, discuss the  relevance of each of
those findings with the two questions above. This should be expressed in Section 1.3. The
format should also require that the conclusions in Chapter 5 restate these original questions and
summarize all findings within the two reworded framing questions.  The summaries would serve
the document best by ensuring that all the material is summarized in a clear and concise manner.

The deposition monitoring network maps are too  small to show adequacy of the network.
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Gaps in legislative background and history of the current review
CAIR should be mentioned in the regulation portion of this discussion.

Major scientific, multi-state and national surveys and summary reports of the period (i.e., since
SC>2 NAAQS 1982) need to be mentioned, included but not limited to the EPA Eastern and
Western Lake Surveys, the National Acid Precipitation Assessment Program (NAPAP), the
NAPAP Integrated Assessment in 1991, and the EPA Acid Deposition Standard Feasibility
Study Report to Congress in 1995. Significant state surveys like the Adirondack Lakes Survey in
1984-1987 and the ongoing Adirondack Long Term Monitoring of lakes and streams should also
be included.

The recent progression of the importance of N in acidification should be given more attention.
For example, the recent chemical recovery signal in Adirondack lakes appears closely linked
with N deposition. Recent data show stream acidification is also highly correlated.

Section 1.1.3 SOX. Include the primary standard for SOX.  Fill in the history gap between 1988
and 2006.

Section 1.1.4. Include what led to the development of a deposition approach to this secondary
standard as opposed to  an ambient air standard. Add what other states may have done with
respect to 1) more stringent primary standards or 2) proposals of secondary standards or other
regulations to protect the environment from NOX and SOX.

Current levels of ambient and deposition N and  S are improved because of all efforts to attain
clean air, which should include major state efforts such as New York State's NYS Sulfur
Dioxide Control Program in 1985 that evolved into its Acid Deposition Control Program.
Several northeast  states (NH,VT, CT and ME) have discussed or proposed S and N deposition
standards to protect forests.
Particulate of NOX and SOX omission

The first paragraph states "The scope of the joint NOX and SOX ISA is limited to welfare topics
that do not duplicate those addressed by the forthcoming particulate matter (PM) science
assessment.  The welfare effects of visibility impairment and climate interactions associated with
particulate NOX and SOX will be addressed within the secondary PM NAAQS."  The omission of
particulate phase NOX and SOX limits the potential for setting standards in the future using both
PM and oxides of Nitrogen and Sulfur standards. Furthermore, PM plays a significant role in
nitrogen and sulfur deposition. I feel that separating out the effects of gas- versus aerosol-phase
S/N will be difficult, since wet and dry deposition can include both phases, and atmospheric
chemistry and transport affect both phases.  The ISA clearly states that "particulate NOX and SOX
will be addressed with the secondary PM NAAQS review," and it therefore becomes crucial that
these two review process tracks are highly consistent with each other. One cannot proceed
independently of the other track.
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Implementation of a secondary standard(s)
It is important to state that this document covers the setting of a secondary standard(s) but not, at
this point, the implementation of a secondary NAAQS.  They would need to be developed or
	This would be very difficult because at present, there are no adequate source-receptor
models to provide the level of control that would be required to meet the secondary NAAQS, if
the deposition standards were exceeded in any particular area.
Charge Questions

Question #1
To what extent is the evidence on atmospheric chemistry and physics, air quality, and
deposition and exposure sufficiently and correctly described, clearly communicated, and
relevant to the review of the secondary NAAQS for NOi and SOi?	

       The information on gas-phase chemistry and physics is sufficient and well-presented in
       Chapters 2 and 3.
       Since both gas-phase and particulate S/N are involved in deposition, the ISA would
       benefit from inclusion of more chemistry and physics on the particulate side in these
       chapters as well.
       Clearly communicated - see "Format" section.  Summaries are graded as poor.
Question #2
How well characterized are the relevant properties of the ambient air concentrations and
deposition of NOX and SOX, including policy-relevant background concentrations, spatial
and temporal patterns, and the relationships between ambient air concentrations and
ecological exposures?	

       There is enough information on urban NC>2 and SC>2 to characterize ambient levels, but
       not enough information in rural areas and sensitive ecosystems.
       In general, emission inventories for SO2, whose sources are well-characterized, are more
       reliable than estimates for emissions of NOX; and certainly far more reliable than NH3
       emissions.
       There is more information, in terms of spatial coverage, on wet deposition
       and NH4 than ambient SO2, NO2, or NH3
Question #3
How sufficient is the information on atmospheric sciences and exposures for the purposes
of evaluating and interpreting the ecological effects presented in Chapter 4 of the draft
ISA?

There is an inherent danger here of assuming that all areas of ecological effects are equally
important or equally developed in the literature, which in my view, they are not.  The danger is
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the inevitable conclusion that the sufficiency of the information will not be adequate for all of
them.

A better use of time would be to go to the bigger questions framed above that have to do with the
interaction between the primary and the secondary standards, and the value and need for
establishing deposition standards.

General Comments

Deposition-based Standard
The draft ISA demonstrates a strong interrelationship between deposition data and effects to
ecosystems as shown in Table 5.7-1.  Concentration-based standards are not biologically relevant
to most resources at risk from air pollution (surface waters, groundwater, soils, etc).  It is
important that other EPA programs (i.e. CAMD) are reviewing or participating in this ISA. All
programs  should be aware  of the proposed move forward to a multi-pollutant approach and this
new pathway.

One or multiple secondary standard
One secondary standard for the US or several according to various sensitive receptor areas in the
country? Primary standards protect only one organism, people, and they are  distributed
throughout the country, so  generally one size does fit all.  Secondary standards protect sensitive
ecological receptor areas (ER) which are not evenly distributed and have multiple sensitive
components within them.  Are we setting one secondary standard for the country? Have we
identified all of the sensitive environments that we wish to track and to protect?

Within each sensitive environment, have the ecological assessments identified a single or
multiple deposition targets? Shouldn't each ecological area have one targeted? Have the major
eutrophication-stressed estuaries picked a limit for NOX and NHX?

Critical loads may be an area of interest. I feel there is a need for discussion  on the state of
knowledge of critical loads. While there may not be a high resolution understanding (small
blocks) areas can be defined by forest or east vs west.  The EU has critical loads in place.

Emphasis on Certainty
While there  is uncertainty surrounding some data or modeling, I feel that it is important to
emphasize that solid and certain data does exist which the scientific  community has accepted.

Climate change
There may be a need for analysis of the effects of the SOX and NOX deposition on climate
change. In addition, the effects of climate change on SOX and NOX pollution.

Adequacy of existing air monitoring network
          The density of SO2 and NO2 monitors is adequate to track the primary standard, but is
          not adequate for the secondary standard.
          The bulk of the  ambient SO2 and NO2 monitors, as well as the Speciation Trend
          Network for fine particulate SO4 and NOs, are  located in urban and suburban areas.
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          There is no national NH3 monitoring program, and what little information is available
          for ambient concentrations is research-oriented.
          There is information on fine particulate SC>4 and NOs at > 100 Class I areas through
          the IMPROVE program, but this is probably not adequate to characterize all sensitive
          ecosystems across the nation.
          The major deposition networks (CASTNet, NADP/NTN) were generally established
          to track the effects of emissions reductions from the energy generation sector.
          In terms of data coverage, there are more wet deposition monitors measuring SO4,
          NOs, and NH4 than there are ambient NC>2 monitors, however these networks are not
          generally capable of characterizing deposition in urban areas or many rural areas
          (especially in the western US).
          Dry deposition of S/N is inferred rather than measured directly by routine networks
          like CASTNet, but even so there are far fewer dry deposition sites compared to wet.

Transformation Products
Clarify which N pollutants are being discussed.  Research which oxidized N compounds are
relevant and feasible to monitor. While NOy may be more appropriate, there is a need to discuss
the difficulty of measuring individual compounds. Chapter 2 does describe some of the
heterogeneous chemistry between NOy and halogens, but does not really cover ammonium
nitrate/sulfate formation.  Halogen chemistry plays an important role in urban coastal settings,
but ammonium nitrate/sulfate chemistry is important over vast regions of the continent.

NOX as a precursor
NOx should be discussed as a precursor to the following:
   Ozone
   Ambient nitrates
   N deposition
   Fine particulates

Inclusion of NiO
   N2O is certainly a greenhouse gas, but is not a component of NOy, nor is it relevant to
   Os/PM/haze formation or N deposition (and  subsequent acidification or nutrient enrichment).
   More information on particulate N would be favored over N2O analysis.

Dry deposition
There are different monitoring networks for sulfur and nitrogen. Monitoring network not
adequate for dry deposition

Emissions inventories
Are emission inventories adequate for each, SOX, NOX and NHX? For the primary and secondary
standard?  In general, emission inventories for SO2, whose sources are pretty well-characterized,
are more reliable than estimates for emissions of NOX; and certainly far more reliable than
emissions.
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Multiple indicators and multiple sensitive areas.
States may contain several sensitive regions.  Sensitive regions like the Adirondack Mountains
will have multiple natural resources with different indicators and/or critical thresholds (see
Figure 4.1 .-1, page 4.4).  Have all the sensitive areas within the US been identified (Alaska and
Hawaii have none?)? Will each state be responsible for verifying these areas? Is there is enough
data to do that in each area?  Or whether there will be a blanket single indicator for each sensitive
region? What is the more quantifiable indicator of ecological health? Has the effects literature
(for the case study areas where the literature is more complete) identified the most representative
indicator to protect the whole area?
Other editorial comments:
1. Figure 4.2-2 wrong diagram for the caption.
2. pg 4-41, line 6 Figure 4.2-2 should be Figure 4.2-8.
3. pg 5-10 line 12. Spring chemistry is not baseflow condition for streams in the Eastern US.
4. Glossary. Add base cation surplus, chronic acidification, episodic acidification...
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                               Dr. Kathleen Weathers
This chapter was rather unbalanced in writing style as well as analysis and synthesis.  It was
often difficult to identify the salient points (bottom lines) in much of the first part of the
document (until 4.3). There were inaccuracies and often unqualified (under referenced), value-
laden language was used (see specific comments, below).  Consider reorganizing and rewriting
the chapter, using one voice, and organizing the chapter around a conceptual model. The
integrative tables that are at the end of the document could be used to guide a discussion on the
overarching effects of acidification and nitrogen enrichment on ecosystems.  Supporting
information could then be revised, condensed and used to underpin this synthesis.

4a How well are the major effects ofSOx andNOx on ecological acidification identified and
characterized?
4b To what extent do the discussion and the integration of evidence across scales (e.g., species,
communities and ecosystems and regions) correctly represent and clearly communicate the state
of the science?

The major acidification effects, which have been indirectly or directly liked to the (wet,
sometimes wet + dry) deposition of sulfur and nitrogen, have been identified and characterized in
this chapter. The relative importance and certainty of various effects was less well characterized.

Categorization of biological and chemical effects is a useful  way to partition.

Again, I suggest adding  a conceptual model to the beginning of this section.  The table
(identified as Fig. 4.1-1) and its associated description is a start. However, I do think that it is
more logical to consider deposition as a driving variable and various ecosystem (i.e., export
rates, nutrient or pollutant cycling, acidification process, productivity) or ecological properties as
response to variables rather than the other way around, despite the suggestion that working from
top to bottom is inherent in the critical load approach.

Much of the text details  studies that have explored the effects of acidification on the various foci
of ecological  studies  (as listed above). The coverage of the literature is not as broad as it might
be; it relies heavily on a limited set of research/researchers' work.  There is also much supporting
literature in this chapter from past decades. It is very useful  to cite these foundational studies,
but also important to note what the relevant (to this time period) bottom lines are, especially in
situations  where the environmental conditions have changed significantly in the interim. One
suggestion is to identify what is new (recent results, or synthesis efforts) and what has been
known for some time. I am concerned that studies whose results,  for example,  point to how
ecosystems responded to the deposit!onal regime in the 1980s and 1990s may be dismissed, or
questioned as relevant in 2008. However, there have been a number of integrated studies over
the past several years, both modeling efforts and synthesis whose  results are cited. Thus, it
would be useful to identify which class of results is timeless, i.e., where the findings still hold
despite significant  changes in emissions and/or deposition over time. Integration and synthesis is
a challenging task.
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5. How well has the ISI characterized the relationship between acidifying deposition levels of
NOx and SOx and ecological effects.

The characterization could be made more direct. As one example, studies that highlight
deposition, whether estimated across the landscape or to a site (e.g., Lovett and Reuth 1999), or
controlled through experimental additions (Harvard Forest, Catskills, Bear Brook additions, for
example), were not highlighted or cited well throughout the text.

The ecosystem approach was underscored in the first part of the chapter. Thus framing the
relationships of deposition and ecological responses using a mass balance approach would be an
other logical way to organize the discussion. In this way, it would be possible to move from the
influence of S and N on watersheds, to communities and species within watersheds. Consider
including a table or a section that summarizes the relationships between deposition and
ecological effects toward the beginning of the chapter.

I appreciated the introduction of critical loads as a way that the EU and others have considered
successfully the relationship between atmospheric deposition and environmental effects; it is an
important approach to explore in this  document.

The word/concept "thresholds" is used in numerous cases.  It should be (re) defined in this
section. A summary section or table identifying ecological thresholds that have been
documented (the response variable and the actual threshold) would be very useful.
Even if it turns out that few have been defined,  it would be useful exercise.

An introductory paragraph about the (legitimate/defensible) use of models and a brief character-
ization (i.e., table about the nature and utility of the various models, and their results, that are cite
d throughout this  chapter) would be a useful addition. Also, wherever there are multiple model
results for an ecosystem or region, a summary of the similarities (e.g., page 4-87 for the
Adiriondacks) as well as the differences in model results and whether there has been any in-
dependent validation or verification of the models should accompany the comparison. It is also
critical to point out which models consider biological interactions (the bio part of biogeo-
chemistry) and which do not. Since N is very biologically active, and tree species can have a
considerable effect on N loss from ecosystems (e.g, Lovett et al. 2000, 2002, 2004), use of any
models that do not consider the influence of biology on geochemical cycles should be very well
justified. And, the details, strengths and weaknesses of models that do include biological process
ing should likewise be revealed.

6. How well characterized are the oxidized and reduced forms of nitrogen on acidification

The N cascade section was good. Consider including the first part of the N cascade section and a
 parallel sulfur section at beginning of this chapter.

Make clear that in addition to HNO3 wet and dry deposition, some areas of the country are exper
iencing a rise in NH3 emissions and NH4 wet deposition (NADP data show this increase). Al-
though there are fundamental differences in ecological  processing when reduced vs oxidized
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nitrogen is added to an ecosystem, it would be useful to point out that there may be downstream
acidification/eutrophication effects if nitrogen demand is exceeded and nitrogen is leached as a
result of NH4-N deposition (in addition to the brief mention on page 4-145).

A few overarching comments:

Total deposition, wet+snow+dry+fog, in places where it matters, is still poorly characterized for
most places on the planet, especially in non-homogeneous terrain (e.g., see Weathers et. al. 2000,
2006). Getting reasonable estimates of total deposition, especially across space, and relating
emissions to deposition are still active areas of research.  These facts  can be problematic when
deposition is used as the independent variable or treatment for any of a suite of ecological
responses. I do not think that this challenge — obtaining and using reasonable estimates of
deposition — renders specific studies either inadequate or wrong.  However, it does underscore
the need for multiple lines of evidence to identify, with some confidence, the effects of N and S
on loading ecosystems, species, and communities. These multiple lines of evidence often come
through the use of experimentation (especially loading studies), modeling, theory, long-term
analyses, and use of deposition gradients (where there are surely large differences in deposition
even if the absolute numbers have large uncertainties associated with them). I think that pointing
out the importance and power of multiple lines of evidence in supporting current understanding
about the effects of NOx and SOx on ecological systems would be a useful thing to do at the
beginning of this section.

I like the case studies, but they could be used more effectively, perhaps to highlight parts of a co
nceptual model.  Make clear why particular case studies are being used.

Some details:

The  charge on sulfate is  incorrectly identified throughout the text: sulfate is an anion, not a
cation, and it's divalent,  not monovalent. I note, however, that there is correct inference for
sulfate's behavior throughout the text (i.e. it is listed/included in discussions about mobile
anions).

Decomposition should be added as an important process in section 4.1.1  and food webs vs food
chains are more realistic descriptions of energy movement within ecosystems.

There are many places in the text where references are missing, but necessary. The references
also  seem quite biased toward specific researchers or research groups.

Correct the text for reduction/oxidation reactions and products (the transformation from ammon-
ium to nitrate is oxidation, for example).

Figures 4.2-1 and 4.2-2 are transposed.

Y axis on Fig. 4.2-6: "Bad?" death?

Do the colors mean anything on Fig. 4.2-12?
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It seems to me that much of the fish data that include abundance, biodiversity, and total numbers
of species present as response variables are potentially confounded by freshwater stocking activit
ies. Perhaps stocking did not influence the results or was not practiced in many of the focal
surface waters. If that is true, it would help to say so, if it is not, it may still be worth mentioning
this confounding point.

I believe that the original reference to N saturation was Agren and Bosatta (1988) (page 4-106).

Equating throughfall N flux with atmospheric N deposition is not warranted in many locations in
 the US because of variable uptake and leaching in the canopy (page 4D110).  Throughfall
deposition or flux is often considered to be a good indicator of what is deposited to the forest
floor, but not necessarily what is deposited from the atmosphere to canopies when the nutrient,
ion or element of interest is biologically reactive/active.  Sulfur, however, has often been con-
sidered an exception. In regard to sulfur in throughfall, research that has  suggested its utility as
an indicator of total deposition should be included as well as the one on page 4-162 (Cape) that
questions it. For example, many papers, including Garten and Lindberg; Lindberg and Johnson;
Lovett; Weathers et al.; and more have pointed to its utility.

Words such as "harmful" or "negative effects" without qualification should be avoided; if used
they should be qualified with specific environmental terms (e.g., harmful physiological effects of
acidity on fish biota). Also "ecosystem or ecological health" is ill defined and often a lightning
rod-word. I suggest defining it, or  better yet, don't use it.

Consider doing a publication count by year on the topic of acidification/critical loads.

Listed below are some relevant articles whose results should be considered when revising the ISA:

Butler, T. J., G. E. Likens, F. M. Vermeylen, and B. J. B. Stunder.  2005.  The impact of changing
       nitrogen oxide emissions on wet and dry nitrogen deposition in the northeastern USA.  Atmos.
       Environ.   39:4851-4862.
Burgin, A.J. and S. K. Hamilton. 2007. Have we overemphasized the role of denitrification in aquatic
       ecosystems? A review of nitrate removal pathways. Front. Ecol. Environ. 5:89-96
       [indirect effects of S on N biogeochemistry]
Caraco, N.F. 1993. Disturbance of the phosphorous cycle: a case of indirect effects of human activity.
       Trends in Evolution and Ecology 8:51-55. [indirect effects of S on P biogeochemistry]
Caraco, N.F., J.J. Cole, G.E. Likens, G.M. Lovett, and K.C. Weathers. 2003. Variation in NO3 export
       from flowing waters of vastly different sizes: Does one model fit all? Ecosystems 6:344-
       352. [N deposition and what influences nitrate in aquatic systems draining various source  areas]
Groffinan, P.M., J.S. Baron, T. Blett,  A.J. Gold, I. Goodman, L.H. Gunderson, B.  Levinson, M. Palmer,
       H.W. Paerl, G.D. Peterson, N.L. Poff, D.W. Rejeski, J.F. Reynolds, M.G. Turner, K.C. Weathers
       and J. Wiens. 2006. Ecological thresholds: An important concept with no  practical application, or
       the key to successful environmental management? Ecosystems 9:1D13. [a very cursory examinati
       on of the concept and difficulties surrounding thresholds; acid deposition used as an example]
Kelly, V.R., G.M. Lovett, K.C. Weathers, and G.E. Likens. 2005. Trends in atmospheric ammonium
       concentrations in relation to atmospheric sulfate  and local agriculture. Environmental Pollution
       135:363-369.
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Kelly, V.R., G.M. Lovett, K.C. Weathers, and G.E. Likens. 2002. Trends in atmospheric concentration
       and deposition compared to regional and local pollutant emissions at a rural site in southeastern
       New York, USA. Atmospheric Environment 36:1569-1575.
Likens, G. E., D. C. Buso, and T. J. Butler.  2005. Long-term relationships between SO2 and NOx
       emissions and SO42- and NO3-concentration in bulk deposition at the Hubbard Brook
       Experimental Forest, New  Hampshire.  J. Environ. Monitor.  7(10):964-968.
Lovett, G.M., K.C. Weathers, and M.A. Arthur. 2002. Control of nitrogen loss from forested watersheds
       by soil C:N ratio and tree species composition. Ecosystems 5:712-718.
Lovett, G.M., K.C. Weathers, and M.A. Arthur. 2004. The influence of tree species on nitrogen cycling in
       the Catskill Mountains, New York. Biogeochemistry 67:289-308.
Lovett, G.M., K.C. Weathers, and M.A. Arthur. 2001. Is nitrate in stream water an indicator of forest
       ecosystem health in the Catskills. Pp. 23-30.  In: M.S. Adams (ed.). Catskill Ecosystem Health.
       Purple Mountain Press, Fleischmanns, New York.
Lovett, G.M. 1994. Atmospheric deposition of nutrients and pollutants to north America: an ecological
       perspective. Ecol. Apps. 4:629-650.
Lovett, G.M. and H. Reuth.  1999.  Soil nitrogen transformations in beech and maple stands along a
       nitrogen deposition gradient. Ecol. Apps. 9:1330-1334.
McNeil, B.E., J.M. Read and C.T. Driscoll.  2007. Foliar nitrogen responses to elevated atmospheric
       nitrogen deposition in nine temperate forest canopy species.  Environ. Sci. and Technol 41:5191-
       5197.
Simkin, S.M., D.N. Lewis, K.C. Weathers, G.M. Lovett, and K. Schwarz. 2004. Determination
       of sulfate, nitrate and chloride in throughfall using ion-exchange resins. Water, Air and
       SoilPollution 153: 343D354.
Templer, P.H., M.A. Arthur, G.M. Lovett and K.C. Weathers. 2007. Plant and Soil Natural Abundance
       15N: Indicators of relative rates of nitrogen cycling in temperate forest ecosystems. Oecologia. 1
       53: 399-406.
Templer, P.H., G.M. Lovett, K.C. Weathers, S.E.G. Findlay, and T.E. Dawson. 2005. Influence of tree
                 15
       species on N sinks and forest N retention in the Catskill Mountains, New York, USA.
       Ecosystems 8:1-16.
Weathers, K.C., G.E. Likens, and T.J. Butler. 2006. Acid rain. Pp. pp. 1507-1522. In: W. Rom (ed.).
       Environmental and Occupational Medicine, 4th edition. Lippincott-Raven and Wilkins
       Publishers, Philadelphia
Weathers, K.C., S.M. Simkin,  G.M. Lovett,  and S.E. Lindberg. 2006. Empirical modeling of atmospheric
       deposition in mountainous landscapes. Ecological Applications 16:1590-1607.  [Review of
       deposition in heterogeneous terrain, use of throughfall sulfate as an indicator of total deposition;
       quantification of hotspots of S and N deposition, in general and Acadia  and Great Smoky Moun
       tain National Parks, in particular]
Weathers, K.C., G.M. Lovett, G.E. Likens, and R. Lathrop. 2000. The effect of landscape features on
       deposition to Hunter Mountain, Catskill Mountains, New York. Ecological Applications  10:528-
       540. [quantification of hotspots of S and N deposition]
Weathers, K.C., G.E. Likens, F.H. Bormann, J.S. Eaton, W.B. Bowden, J.L.  Anderson, D.A.
       Cass, J.N. Galloway, W.C. Keene, K.D. Kimball, P. Huth, and D. Smiley.  1986. A
       regional acidic cloud/fog event in the  eastern United States. Nature  319:657-658.
       [importance of fog or  clouds in delivering acidifying substances to ecosystems].
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