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> **UNITED STATES ENVIRONMENTAL PROTECTION AGENCY**

**WASHINGTON D.C. 20460**

> **OFFICE OF THE ADMINISTRATOR**
>
> **SCIENCE ADVISORY BOARD**

December 23, 2008

EPA-CASAC-09-004

The Honorable Stephen L. Johnson

Administrator

U.S. Environmental Protection Agency

1200 Pennsylvania Avenue, N.W.

Washington, DC 20460

> Subject: Peer Review of EPA's *Risk and Exposure Assessment to Support
> the Review of the Secondary National Ambient Air Quality Standard for
> Oxides of Nitrogen and Sulfur: First Draft*

Dear Administrator Johnson:

The Clean Air Scientific Advisory Committee (CASAC) NO~x~ & SO~x~
Secondary National Ambient Air Quality Standards (NAAQS) Review Panel
held a public meeting on October 1-2, 2008 to review EPA's *Risk and
Exposure Assessment to Support the Review of the Secondary National
Ambient Air Quality Standard for Oxides of Nitrogen and Sulfur: First
Draft* (see Enclosure A for the Panel roster). The Panel discussed its
draft report on November 19, 2008 at a public teleconference. The
Panel's draft report was reviewed and approved by the chartered CASAC at
the public teleconference on December 19, 2008 (see Enclosure B for the
CASAC roster).

Overall, the Panel found the first draft of the Risk and Exposure
Assessment (REA) document to be a credible beginning in the development
of the assessments needed to support future rule-making. The Panel
recognizes the time constraints under which the present first draft REA
was prepared and that much of the analyses and the subsequent
interpretation have yet to be completed (e.g., Chapter 7 is focused
primarily on acidifying deposition and Chapter 8 only begins to explore
how a secondary NAAQS might be structured). The Panel has many
suggestions for strengthening the document in response to the Agency's
charge questions. Individual comments from the Panel members are
provided in Enclosure C.

The Panel strongly supports the up-front inclusion of a policy-focused
interpretation of each of the key scientific findings in the Integrated
Science Assessment (ISA). These policy interpretations should be
included in an Executive Summary, as well as in the applicable sections
of the REA. As discussed in prior reviews of the ISA and Scope and
Methods documents, it is critical that the REA give attention to all
forms of reactive nitrogen (Nr, which includes oxidized,
chemically-reduced and organic nitrogen forms) deposition because all
forms can contribute to both acidification and nutrient enrichment of
ecosystems. Moreover, the science indicates that ecological effects
could be ameliorated by decreasing deposition of any of those forms.
From a scientific standpoint, this intricate relationship indicates that
the applicable NAAQS standard(s) should address total reactive nitrogen
deposition. Thus, the Panel affirms that science-based secondary NAAQS
standards for nitrogen and sulfur should consider the ecological
consequences of total Nr deposition. However, it is noted that the
present interpretation of the regulatory authority of EPA recognizes
only oxidized forms of nitrogen and sulfur as Criteria Pollutants. The
Panel recommends that the EPA move forward with establishing
scientifically-based standards that effectively protect the environment,
while recognizing the current regulatory constraints.

***[Scope of the Review]{.underline}***

1.  *Chapters 1 and 2 provide the background, history, and framework for
    this review, including a discussion of our focus on the four key
    ecological effect areas (aquatic acidification, terrestrial
    acidification, aquatic nutrient enrichment, terrestrial nutrient
    enrichment). Is this review appropriately focused in terms of
    characterizing the important atmospheric and ecologic variables that
    influence the deposition and, ultimately, the ecologic impacts of
    nitrogen and sulfur? Does the Panel have any further suggested
    refinements at this time?*

Chapters 1 and 2 of the REA begin to satisfy the goals of providing a
clear and correct framing of the issues, providing a coherent method for
reaching conclusions required in the NAAQS review process, summarizing
the relevant policy questions and building on the ISA. The appropriate
effects are considered in the REA and the potential relationships
between atmospheric deposition and ecological effects are outlined.

The Panel commends EPA on its use of figures and diagrams throughout
Chapters 1 and 2: such illustrations help orient the reader and provide
a framework for discussion. It would be helpful if Figure 1.4-1 was
accompanied by descriptions in the text that explain how well each of
the steps can be executed, what the major uncertainties are, and where
each component is addressed in the later parts of the REA. Such
modifications would assist in guiding the reader through the material in
the document. It would also be beneficial for the Agency to include a
paragraph on the central concept of N and S "loading\" because this
concept is pivotal to the document. Similarly, the concept of "N
saturation" needs to be introduced earlier in the document with a clear
delineation of how this concept is, or should be, used in evaluating the
effects of N loadings. There should be greater coherence between the
text, figures and policy statements with respect to reduced and organic
forms of N: both forms of N are mentioned here and in the ISA, and are
important contributors to the effects being exhibited by ecosystems in
response to N deposition. In the present version of the REA, the
chemistry figures and the policy questions essentially address only the
oxidized form. The material should be modified to address
chemically-reduced and organic nitrogen.

Discussions of uncertainty in Section 2.4 are generic and qualitative:
it is unclear when uncertainty is being discussed and when variability
is the real issue. The document needs to be explicit that variability
and uncertainty are two important but different concepts, with different
impacts on establishing secondary NAAQS. The issue of uncertainty needs
to be paramount in the discussion of monitoring networks. The sparse
data from the existing network, the relationship between ambient
concentrations and dry deposition and our understanding of cloud water
deposition introduce significant uncertainty in estimates of total
deposition. The Panel recommends that Chapters 1 or 2 address
uncertainty with a discussion of the implications on EPA's ability to
perform the assessments outlined in Chapters 7 and 8. Additionally, the
uncertainty issue should extend to the discussion of climate change, for
which there are both beneficial and adverse effects of atmospheric Nr in
ambient air and deposition. The REA is unclear on how a change in the
secondary NAAQS will affect climate change and in what direction. If the
science is uncertain on the level and direction of effects on climate,
it should be clearly stated in the REA.

Exclusion of non-ecological public welfare effects of NO~x~ and SO~x~
(e.g., effects of N- and S-containing particulate matter on visibility
degradation and climate change, materials damage) continues to be an
area of concern for the Panel. To ensure that the current REA
meaningfully represents an assessment of environmental criteria, EPA
should state clearly in which Agency documents the omitted NO~x~/SO~x~
welfare effects will be treated and provide a short synopsis of the key
non-deposition effects in appropriate locations in the REA.

The Panel recognizes that including a discussion of the potential
primary NAAQS (i.e., based on public health) for NO~x~ and SO~x~, and
the current PM NAAQS, is premature at present. However, future drafts of
the REA should include an analysis of how the estimates of ecological
exposure and risk are impacted by the range of primary standards under
consideration and if the respective primary NAAQS would (or would not)
be adequately protective of the full range of environmental risks. Of
particular concern is that in the past, the secondary NAAQS for a number
of pollutants has been set identical to the primary NAAQS. As noted
later in this letter, the Panel finds the proposed approach for a
secondary NO~x~-SO~x~ NAAQS to be innovative, but has concerns about its
feasibility. Given the challenges the Agency may face with rulemaking
and implementation, a policy decision could be to once again set the
secondary NO~x~ and SO~x~ NAAQS to be identical to their respective
primary NAAQS. We recommend a full assessment of the implications of
making such a decision.

***[Air Quality Analyses]{.underline}***

1.  *To what extent are air quality characterizations and analyses
    presented in Chapter 3 technically sound, clearly communicated,
    appropriately characterized, and relevant to the review of the
    secondary NAAQS for NO~x~ and SO~x~?*

2.  *Section 3.2.1 describes an approach for evaluating the spatial and
    temporal patterns for nitrogen and sulfur deposition and associated
    ambient concentrations in the case study locations. This draft
    document includes the analysis for the Adirondacks case study. Does
    the Panel agree with this approach and should it be applied to the
    other Case Study Areas?*

3.  *Section 3.2.2 describes the relative contributions of ambient
    emissions of nitrogen and ammonia to nitrogen deposition for the
    case study areas. To what extent is the approach taken technically
    sound, clearly communicated, and appropriately characterized?*

The general nature of Question 1 leads the Panel to both address the
question and also to provide general comments on the current air quality
analyses. Assuming the many and important missing "placeholder" sections
are satisfactorily completed, the air quality characterizations and
analyses presented in Chapter 3 should provide a reasonably sound and
clearly communicated characterization of estimates of deposition of
total reactive nitrogen and acidifying species to the specific case
study areas. The Chapter, when completed, should also provide
information that is relevant to potential revisions to the current
secondary NAAQS for NO~x~ and SO~x~.

Given that most of Chapter 3 is devoted to the presentation of model
results from the Community Multiscale Air Quality (CMAQ) model and
Response-Surface Model (RSM), a major limitation of the current chapter
is the absence of any evaluation of model performance on simulated
levels and atmospheric deposition rates of the various forms and phases
of sulfur- and Nr-containing chemical species. It is critical that EPA
complete the placeholders that relate to model/measurement comparisons
and the characterizations of uncertainty in model results. For example,
plots of spatial and temporal variability with measurements would convey
how well the model captures the spatial and temporal patterns. Per the
panel's previous recommendations on the ISA, much of the needed
evaluation of the CMAQ model should be included in the ISA. There is
also a need -- either in the ISA or here in the REA -- for a more
detailed description of the RSM and an evaluation of its performance for
the S and N species. With the relatively extensive sets of air quality,
atmospheric deposition and environmental measurements available for the
Adirondacks, this may be a good case study area in which to evaluate
model performance prior to extending this approach to other case study
areas.

The complex terrain in sections of the Adirondacks also raises concerns.
It is not appropriate to compare the 12-km spatial resolution of the
modeled deposition with the spatial patterns in actual deposition
(including orographic precipitation increases and cloud water
deposition) or the spatial patterns in sensitive species and ecosystems.
A sensitivity analysis of variations within selected Adirondack model
grid cells could help evaluate the importance of spatial variability,
scale and resultant effects on deposition estimates.

The Panel was pleased to note the efforts of the Agency to link the
atmospheric models (relating emissions to deposition) with watershed or
landscape models (relating deposition to environmental effects). The
disparity in the time scales between atmospheric (i.e., CMAQ) and
watershed models is a major issue. Atmospheric models typically provide
predictions at relatively fine time scales (e.g., hourly) over a single
year, while the watershed models often provide results on scales ranging
from decades to centuries. To the extent possible, it would be helpful
if CMAQ could be run for a number of recent years (2002-2006), varying
both meteorology and emissions, to provide a better understanding of
inter-annual variability and longer-term spatial patterns. This would
provide a more robust basis for model-to-measurement and model-to-model
comparisons.

Assuming the model evaluations indicate reasonable performance for most
of the chemical species of concern, the Panel recommends that the model
results (for both sulfur and reactive nitrogen species) be used to
generate a number of maps that illustrate the spatial distributions of:

-   emissions (preferably interpolated to better illustrate
    high-emitting regions),

-   atmospheric concentrations (gaseous and aerosol and combined
    species),

-   deposition (wet, dry, total S, total N, oxidized N,
    chemically-reduced N, etc.), and

-   ratios of deposition to atmospheric concentrations and deposition to
    emissions.

The Panel recommends that the maps have a consistent spatial resolution
(e.g., 36 km) over the contiguous United States and a finer resolution
over the case study areas. Such maps would provide the reader a more
direct understanding of the spatial relationships that exist between
emission location, ambient concentrations and the resulting deposition.
The maps would also be useful in proposing a structure for a secondary
NAAQS.

In addition to these maps, the Panel recommends the EPA use scatter
plots of gridded model results to further illustrate the key
relationships between the deposition metrics most relevant to
environmental effects and alternative air quality metrics upon which the
secondary NAAQS might be based. The scatter plots could also be used to
provide information relevant to uncertainty analysis.

***[Case Study Analyses]{.underline}***

Before dealing with the specific charge questions with regard to the
Case Study Analyses, the Panel offers the following general comments.
The proposed use of ecological indicators that can be linked to varying
severity or magnitudes of effects (and related losses in ecosystem
services) goes beyond the concept of estimating critical loads at which
ecosystems experience no effects according to present knowledge. An
important consideration as these indicators are selected and further
developed is how to describe effect indicators of varying severity
rather than just providing a \"no-effects\" threshold. A continuum of
effect indicators will provide important information on the range of
adverse responses, and quantifying the response indicators to various
emissions and deposition levels will be important for the eventual
assessment of what ecological effects are considered to be adverse. A
separate section may be needed to discuss the ecological implications of
various levels of acid neutralizing capacity (ANC) and associated
effects, and its application to evaluating effects of acidifying
deposition. This discussion should include a consideration of the
implications for moving beyond single critical load "no-effects
threshold" approaches to more comprehensive approaches that offer
varying degrees of ecosystem protection within specified levels of
statistical probability.

The modeling approaches used to develop critical loads for these case
studies are very different. Evaluating these different approaches could
be very instructive. In particular, a discussion of the relative merits
of dynamic models vs. steady state models in these specific applications
is needed. For example, MAGIC does not effectively simulate watershed
nitrogen dynamics, so if watershed nitrogen dynamics is an important
component of the critical load there will undoubtedly be some errors.
Most forest ecosystems currently are losing exchangeable cations and
accumulating S and N, so by definition they are not steady-state
systems. Applying a steady-state model to such systems is problematic as
a critical loads assessment tool.

In the case study Attachments, the discussions of varying amounts of ANC
and their associated effects on ecosystem function differ from what is
presented in the main chapters of the REA document. A more consistent
approach is needed for setting the ANC limits of concern with respect to
ecosystem sensitivity to acidification and recovery from acidification.
The panel suggests that full protection of fish species (set at 100
μeq/L) should be considered in the case study scenarios.

It would be useful and instructive to include an N-limited site among
the case studies. Possible systems would be the rapidly-growing and
N-demanding Douglas-fir forest ecosystem in the Pacific Northwest or a
loblolly pine dominated forest stands in the Southeastern US. For better
understanding of the regional effects of N deposition in the southern
Sierra Nevada, EPA should consider a comparison of responses in mixed
conifer forests (e.g., the Kings River Project area) as compared to ANC
changes in the nearby lakes of the sub-alpine and alpine zone (e.g.,
such as leaching of nitrate to streams, lichen species composition, and
invasion of invasive grasses).

Additionally, it may be useful to include an up-front discussion of how
the acidity of the solid phase of the soil affects soil solution acidity
which can in turn affect surface water acidity. In an already acid soil
(whether acidic due to natural or anthropogenic processes), soil
solution acidity can increase or decrease instantaneously with the
introduction or removal of mineral acid anions (such as sulfate,
nitrate, or chloride) without any change in the soil solid phase. This
is sometimes referred to as the "intensity effect" and is described in
Reuss and Johnson (1986)[^1]. In contrast, acidification of the solid
phase of the soil can take a long time and is usually not reversible
without liming.

1.  *Attachment 2 presents a GIS analysis to define geographical areas
    that are sensitive to acidification and nutrient enrichment. Are the
    national geospatial datasets chosen adequate to identify sensitive
    areas? Are there other data sets that have not been identified by
    this analysis that we should consider? Does the panel agree with
    this approach or can they suggest alternatives?*

The selected datasets and the general GIS approach are appropriate for
this analysis, and the Panel has no recommendation for additional
datasets to consider. The period of coverage and spatial
representativeness (e.g., the lichen database) are possibly important
limitations that should be noted.

2.  *Attachment 3 presents our current progress on evaluating the effect
    of aquatic acidification in the Adirondacks. It describes the use of
    the MAGIC model to evaluate ANC levels in selected streams and lakes
    in Adirondacks and Shenandoahs. To what extent is the approach taken
    technically sound, clearly communicated, and appropriately
    characterized?*

The selection of the Adirondacks and the Shenandoah Park as case study
areas and the use of MAGIC as the modeling tool are appropriate;
however, this section needs to be edited for clarity. At present, it is
generally confusing, especially the modeling approach and descriptions
of MAGIC and ASTRAP models. Numerous errors make it difficult to fully
assess technical merits of the discussion in Attachment 3.

ANC has been selected as a metric to quantify the current acidic
conditions and biological impacts because, in many studies, it was found
to be the most appropriate single indicator of the biological response
of aquatic communities in the acid-sensitive ecosystems and it is
relatively easy to simulate using watershed biogeochemical models. Based
on the ANC values and fish populations responses, five classes of
biological responses (acute, severe, elevated, moderate and low
concerns) have been developed and can by used for evaluation of risk
assessment using the critical loads concept. As suggested above, for a
higher level of protection of fish species EPA should consider using a
more conservative value of 100 μeq/L instead of 50 μeq/L.

Some comparisons of these case study results with other efforts to
evaluate acid deposition/biogeochemical responses in each of these sites
(especially the Adirondacks) would be useful to indicate either
differences from or support for these modeling efforts.

3.  *Attachment 4 presents our current progress on evaluating the effect
    of terrestrial acidification. It outlines a plan to use the Simple
    Mass Balance Model to evaluate current deposition on forest soil ANC
    for sugar maple in Kane Experimental Forest and red spruce in
    Hubbard Brook Experimental Forest. To what extent is the approach
    taken technically sound, clearly communicated, and appropriately
    characterized?*

The selection of the study area is reasonable. Attachment 4 is highly
uneven. Substantial detail has been provided in some cases, while broad
generalizations are made in others. It is difficult for the reader to
ascertain the salient points in this chapter.

4.  *Attachment 5 presents our current progress on evaluating the effect
    of aquatic nutrient enrichment. It outlines a plan to evaluate how
    changes in nitrogen deposition affect the eutrophication index in
    two estuaries: Chesapeake Bay and Pamlico Sound. The analysis will
    model one steam reach (Potomac River and Neuse River) to determine
    the impact on the eutrophication index for the estuary. To what
    extent is the approach taken technically sound, clearly
    communicated, and appropriately characterized?*

The approach is appropriately characterized. The Chesapeake Bay has been
the focus of considerable efforts relating to the effects of nitrogen
loading on eutrophication. Extensive investigations have been made to
identify Nr sources within both the very large airshed and the much
smaller watershed areas of the Chesapeake region. However, a potential
drawback of the choice of both the Chesapeake Bay and Pamlico Sound
areas is that for both areas atmospheric nitrogen deposition is not
likely to be the dominant component of the total nitrogen loading, and
thus may not be as sensitive to atmospheric deposition changes as other
ecosystems where deposition is the major source of nitrogen loading.
Future assessments should consider including case studies of watersheds
where atmospheric deposition provides a greater proportion of the total
N loading.

5.  *Attachment 6 presents our current progress on evaluating the
    effects of terrestrial nutrient enrichment. It describes an approach
    to evaluate the effects of N deposition on the Coastal Sage Scrub
    community in California and mixed conifer forests in San Bernardino
    and Sierra Nevada Mountains. To what extent is the approach taken
    technically sound, clearly communicated, and appropriately
    characterized?*

The selection of coastal sage scrub (CSS) and mixed conifer forest
ecosystems is appropriate. Attachment 6 provides a comprehensive review
of existing scientific knowledge for these two ecosystems and the
findings have been clearly communicated. For development of critical
loads for CSS, accumulation of biomass of invasive grasses (critical
level for occurrence of catastrophic fires) could be considered. For the
mixed conifer forests, change in lichen communities is a good indicator
for ecosystem effects at the low end and nitrate leaching to surface
water is a good indicator at the high end of total Nr deposition loads.

***[Additional Effects]{.underline}***

> *1. In this chapter, we have presented results from some initial
> qualitative analyses for additional effects including the impact of
> sulfur deposition on mercury methylation, the impact of nitrous oxide
> on climate change, and the impact of nitrogen deposition on carbon
> sequestration. Are these effects sufficiently addressed in light of
> the focus of this review on the other targeted effects in terms of
> available date to analyze them?*

These descriptions and level of detail in Chapter 6 seem adequate, but
the relevant issues go beyond those associated with carbon
sequestration, mercury methylation and nitrous oxide emission changes.
The chapter would be much improved by providing a short summary that
describes additional welfare effects of SO~x~ and NO~x~ for which
deleterious impacts are expected (e.g., effects on visibility, climate
and materials; as well as the deposition-related terrestrial and aquatic
effects on which the REA currently focuses). Additional information is
needed as to the effect of changes in pH on mercury concentrations in
fish and other organisms. This summary should indicate both the
importance of these ecosystems to individual regions and, in the context
of the entire United States, the overall adverse ecological impacts. In
considering the impacts of nitrogen deposition on carbon sequestration,
the positive (e.g., increased forest growth and harvestable timber
production) and the negative relationships need to be considered and
presented in a balanced fashion.

***[Synthesis and Integration of the Case Study Results into the
Standard Setting Process]{.underline}***

1.  *The purpose of Chapter 7 is to summarize the Case Study results and
    characterize the relationship between levels of an ecological
    indicator and the associated degree of ecologically adverse effects.
    To what extent is this approach characterized at this point of the
    review? Does the Panel have any further suggested refinements at
    this time?*

Chapter 7 remains in a very early stage of development; thus it is
difficult to provide summary comments on the overall content and
direction of this chapter. The Chapter ends abruptly and seems
incomplete. Section 7.3 should be completed and a discussion of linkages
between ecological indicators and adverse effects in terrestrial
ecosystems is needed (similar to section 7.3.1 focusing on ANC in
freshwater systems).

In general terms, the outline and material included in the Chapter are
appropriate to the intended summary. Table 7.1 will be very important in
its final form in future drafts of the REA and thus EPA should carefully
consider its contents. The initial statement at the beginning of Section
7.2 strikes the right balance between important effects while
recognizing their variable and localized nature. As appropriate
throughout Chapter 7 (and the entire REA), the wording should be
scrutinized so that the reader is clear when NO~x~ and SO~x~ versus
total S or N deposition are the real drivers for the effects being
considered. In the summarized cases, the key metric is total deposition
irrespective of the original chemical forms of the airborne S and N
inputs.

***[Considerations in the Structure of the NOx/SOx Secondary
Standard]{.underline}***

1.  *Chapter 8 begins to explore how a secondary NAAQS might be
    structured to address the targeted ecological effects discussed in
    the risk assessment. The next draft of this document will include
    one or more examples of how this structure might be used to relate
    specific levels of air quality indicators with a corresponding
    ecological indicator for a given location and/or scenario. To what
    extent is the described approach technically sound, clearly
    communicated and appropriately characterized at this point of the
    review? Does the Panel have any further suggested refinements at
    this time?*

As noted previously, the Panel views that, scientifically, a NAAQS
standard developed to protect ecological systems should focus on total
acidifying deposition and excess nutrient enrichment, both of which
include chemically-reduced, organic and oxidized forms of total reactive
nitrogen. The current constraints have led EPA to focus on developing a
combined ambient standard that is limited to sulfur and nitrogen oxides,
but which may accommodate indirect consideration of contributions from
other forms of reactive nitrogen as well. The proposed approach is
scientifically well-founded: it is designed to lead to atmospheric
deposition rates that will protect at least some (and perhaps many) of
the target ecosystems as measured by specific ecosystem-based indicators
of adverse ecological effects (e.g., ANC). While the approach does not
directly include targeted decreases in atmospheric deposition of reduced
or organic forms of nitrogen, the approach does include consideration of
chemically reduced and organic nitrogen loadings as part of the already
existing conditions that contribute to acidification and nutrient
enrichment of sensitive ecosystems. As such, the approach could provide
for a substantial decrease in some of the adverse ecological effects of
acidification and nutrient enrichment in various part of the United
States.

The Panel concludes that the approach presented is novel and
environmentally relevant. The description should be clarified and more
detail should be provided, specifically with regard to how the approach
could be implemented in some of the proposed Case Study Areas. EPA
should clarify how the approach would promote controlling
chemically-reduced and oxidized nitrogen loadings as a means to
decreasing ecological acidification and nutrient enrichment.

Currently, the discussion in Chapter 8 on establishing an appropriate
linkage between ambient air concentrations and ecosystem effects, and
the importance of spatial and temporal scales, is limited. The Chapter
should show how the proposed approach directly addresses the Panel's
concerns that, from a scientific perspective, the resulting
environmentally-focused standard would include all reactive N
deposition. Further, the Panel has concerns about the feasibility of
implementing a standard based on this approach. There are a number of
complications that need to be addressed so as to fully inform
policy-makers, particularly in preparation for the development of an
appropriate Advanced Notice of Proposed Rule Making (ANPR). Critical
issues that need to be elaborated upon include:

1.  whether (or how) a standard will integrate the multiple indicators
    identified in the case studies,

2.  what are the appropriate spatial scales for each indicator and
    sensitive ecosystem,

3.  how varying levels of protection required by different ecosystems
    can be accommodated, and

4.  what level of protection is being provided to various ecosystems
    under alternative levels and forms of the standards.

The REA as a whole needs to show how the results of the case studies
(specifically, the relationships between the observed chemical and
biological changes and N and S atmospheric deposition) can be linked to
the traditional NO~x~, SO~x~ and PM standards that are based on ambient
concentrations. It is imperative that this additional linkage
information is incorporated in the next draft of Chapter 8.

In summary, the CASAC Panel was pleased to review this first draft of
the *Risk and Exposure Assessment to Support the Review of the Secondary
National Ambient Air Quality Standard for Oxides of Nitrogen and
Sulfur*. The Agency's venture into new territory in the consideration of
multi-pollutant standards is laudable. Shifting to standards that focus
on ecological effects and employ metrics that are specifically relevant
to ecosystems will have some inherent complexities and difficulties, and
the Panel looks forward to following and contributing to the evolution
of suggested approaches.

> Sincerely,

***/Signed/ /Signed/***

Dr. Armistead (Ted) Russell, Chair Dr. Jonathan M. Samet, Chair

CASAC NO~x~ & SO~x~ Secondary Clean Air Scientific Advisory Committee

NAAQS Review Panel

Enclosures

Enclosure A

**U.S. Environmental Protection Agency**

**Clean Air Scientific Advisory Committee**

**NO~x~ & SO~x~ Secondary NAAQS Review Panel**

**CHAIR**

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

**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. Douglas Crawford-Brown**, Professor Emeritus, Department of
Environmental Sciences and Engineering, University of North Carolina at
Chapel Hill, Chapel Hill, NC

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

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

**Dr. Myron Mitchell**, Distinguished Professor and Director, College of
Environmental and Forestry, Council on Hydrologic Systems Science, 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)

Enclosure B

**U.S. Environmental Protection Agency**

**Clean Air Scientific Advisory Committee**

**CHAIR**

**Dr. Jonathan M. Samet**, Professor and Chair, Department of Preventive
Medicine, University of Southern California, Los Angeles, CA

**MEMBERS**

**Dr. Joseph Brain**, Philip Drinker Professor of Environmental
Physiology, Department of Environmental Health, Harvard School of Public
Health, Harvard University, Boston, MA

**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 Crapo**, Professor of Medicine, Department of Medicine,
National Jewish Medical and Research Center, Denver, CO

**Dr. H. Christopher Frey**, Professor, Department of Civil,
Construction and Environmental Engineering, College of Engineering,
North Carolina State University, Raleigh, NC, USA

**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

**SCIENCE ADVISORY BOARD STAFF**

**Dr. Holly Stallworth**, Designated Federal Officer, 1200 Pennsylvania
Avenue, NW, Washington, DC, Phone: 202-343-9867, Fax: 202-233-0643,
(stallworth.holly@epa.gov)

Enclosure C

**[Comments received:]{.underline}**

[**Dr. Praveen Amar 15**](#dr.-praveen-amar)

[**Dr. Andrzej Bytnerowicz 17**](#dr.-andrzej-bytnerowicz)

[**Ms. Lauraine Chestnut 20**](#ms.-lauraine-chestnut)

[**Dr. Ellis B. Cowling 22**](#dr.-ellis-b.-cowling)

[**Dr. Douglas Crawford-Brown 30**](#dr.-douglas-crawford-brown)

[**Dr.Charles T. Driscoll 33**](#dr.-charles-t.-driscoll)

[**Dr. Paul J. Hanson 43**](#dr.-paul-j.-hanson)

[**Dr. Rudolf Husar 49**](#dr.-rudolf-husar)

[**Dr. Dale W. Johnson 52**](#dr.-dale-w.-johnson)

[**Dr. Donna Kenski 55**](#dr.-donna-kenski)

[**Dr. Naresh Kumar 62**](#dr.-naresh-kumar)

[**Dr. Myron J. Mitchell 65**](#dr.-myron-j.-mitchell)

[**Mr. Richard Poirot 84**](#mr.-richard-poirot)

[**Mr. David Shaw 89**](#mr.-david-shaw)

[**Dr. Kathleen C.Weathers 93**](#dr.-kathleen-c.weathers)

# Dr. Praveen Amar

The charge is to respond to Questions #2 and 3 related to air quality
analyses. Specifically, the two questions are reproduced here:

Question \# 2 : Section 3.2.1 describes an approach for evaluating the
spatial and temporal patterns for nitrogen and sulfur deposition and
associated ambient concentrations in the case study locations. This
draft document includes the analysis for the Adirondacks Case Study.
*[Does the Panel agree with this approach and should it be applied to
the other Case- Study Areas?]{.underline}*

Question \# 3 : Section 3.2.2 describes the relative contributions of
ambient emissions of nitrogen and ammonia to nitrogen deposition for the
case-study areas. *[To what extent is the approach taken technically
sound, clearly communicated, and appropriately
characterized?]{.underline}*

**[Question \# 2 Response:]{.underline}**

The approach outlined in Section 3.2.1 should prove to be useful in that
it does propose to do a complete analysis of spatial and temporal
patterns of concentrations and deposition of sulfur and nitrogen
compounds (dry oxidized nitrogen, dry reduced nitrogen, wet oxidized
nitrogen, wet reduced nitrogen, dry sulfur deposition and wet sulfur
deposition). However, the analyses at the present time are based only on
CMAQ predictions (text says "CMAQ data"; "CMAQ predictions" is more
appropriate) are only for one year (2002), and for just one case-study
location (Adirondacks).

1.  At a minimum, before one can answer the question "Does the Panel
    agree with this approach and should it be applied to other
    case-study areas?" with a reasonable level of confidence, the
    proposed approach needs to include an independent as well as
    corroborative (by comparing it to model-predicted results) analysis
    that is based on *[measured]{.underline}* data for this case-study
    region (as well as the remaining case-study regions). It appears
    that modeled CMAQ results are reasonable, but it will increase the
    confidence in this approach if the measured data from NADP and
    CASTNet (and other networks in the Adirondacks region and other
    regions) corroborate the modeled predictions.

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2.  It is also important that before this approach is applied to other
    case-study areas, that the placeholders on Page 3-53 and 3-54 be
    completed. I would recommend that the analysis of inter-annual
    variation in N and S (for the years 2002-2006) deposition as well as
    uncertainty analysis (Section 3.2.1.5) be first completed for
    Adirondacks region before similar analyses are done for the other
    four case-study regions.

3.  Once the measured deposition data analyses are completed, Section
    3.2.1 should include a brief evaluation/comparison of CMAQ
    predictions for the four nitrogen and two sulfur components. As a
    part of this evaluation, the measured precipitation data and modeled
    (from MM5?) precipitation data (amounts and spatial patterns) should
    be compared. This is important since the modeled results in Section
    3.2.1 indicate strong correlations between amount of precipitation
    and wet deposition.

4.  A general comment on presentation of results on dry deposition of N
    and S: This section needs to be more clear and explicit that we only
    *[estimate]{.underline}* dry deposition (whereas we measure wet
    deposition) and therefore conclusions on total deposition (wet and
    dry) and on the relative contribution of each pathway have a level
    of uncertainty that is hard to determine, but needs to be
    acknowledged (for example, in Section 3.2.1.5 on Uncertainty).

**[Question \# 3 Response:]{.underline}**

This question involves the description of relative contributions of
ambient emissions of NOx and ammonia to deposition of nitrogen (total
nitrogen deposition (TND), oxidized nitrogen deposition (OND), and
reduced nitrogen deposition (RND)) for the eight case-study regions. It
asks if the approach used is technically sound, clearly communicated,
and appropriately characterized. Here are some comments:

1.  The "model of the model" or the RSM (Response-Surface Model) applied
    to CMAQ needs a more friendly description on how it works. On Page
    3-55, the text makes an effort but does not succeed in explaining
    what (and how) exactly RSM does. It appears that RSM is like an
    "instrumented CMAQ" model in that it "represents the outputs of the
    CMAQ model using statistical predictions." It is not clear to me
    what exactly these statistical predictions are. It might be useful
    to compare the "workings" of RSM with, say, Direct Decoupled Method
    (DDM) or other "process" models (that evaluate the relative
    contribution of various processes embedded in the model on model
    predictions). Has the RSM approach been applied by the general
    scientific and policy/regulatory communities outside the US EPA?

2.  To the extent RSM is essentially based on the "brute-force" approach
    of "zeroing out" NOx or ammonia emissions (recognizing there are
    some residual emissions for NOx that include international sources
    and lightning, and, for NH3, they include international,
    non-anthropogenic and point source emissions), I am not sure this is
    the right approach to accurately answer Question \# 3. Are there
    more appropriate approaches that do not "unduly stress" the CMAQ
    model that can better address this question of relative
    contributions?

3.  It is not clear to me how the twelve "emission control factors" on
    Page 3-56 were actually applied in the model. Were the emissions
    zeroed out only for the case-study region or for the whole modeling
    domain?

# Dr. Andrzej Bytnerowicz

[Question 2]{.underline} -- Current progress on evaluation the effects
of aquatic acidification in the Adirondacks and Shenandoah. To what
extent is the approach taken technically sound, clearly communicated,
and appropriately characterized?

Selection of the Adirondack Mountains and Shenandoah National Park for
estimation of ecological effects and risks caused by acidifying
deposition of N and S is well justified. The two areas experience high
levels of deposition, are characterized by a high density of
anthropogenically acidified lakes and streams, and there is a well
documented record of chemical and biological changes from many studies
with their results published in peer-reviewed literature.

The proposed approach is logical and technically sound. The wet
deposition data comes from the NADP/NTN networks operational in the
Adirondacks since 1978 and in the Shenandoah since 1980. Current
conditions were evaluated by a 3 step process that assessed trends in
surface water SO~4~^2-^, NO~3~^-^ and ANC concentrations; the percent of
watershed bodies that have different degree of acidity; and the percent
of water bodies receiving N & S deposition above the harmful levels
(exceedance of critical loads). Biological effects of acidity caused by
atmospheric N & S deposition are measured at the individual level as
fitness and at the community level as species richness and community
structure. ANC has been selected as a metric to quantify the current
acidic conditions and biological impacts because in many studies it was
found to be the best single indicator of the biological response of
aquatic communities in the acid-sensitive ecosystems. Relationship
between ANC and number of fish species showed that at the ANC values of
50-100 μeq/L, species richness begins to decline. Based on the ANC
values and fish populations responses, five classes of biological
responses (acute, severe, elevated, moderate and low concerns) have been
developed and can by used for evaluation of risk assessment using the
critical loads concept.

It will be interesting to see complete results of the planned
evaluations.

[Specific comments:]{.underline}

Page 32, Figure 5.1-2 - why there is such a high difference in the
"severe" category between the observed and MAGIC modeled outputs?

Page 33, Figure 5.1-3 -- change ANC units to μeq/L. In the same figure
-- why not to use more conservative value of 100 μeq/L instead of 50
μeq/L as the threshold of protection?

[Question 5]{.underline} -- Current progress on evaluating the effects
of terrestrial nutrient enrichment for coastal sage scrub and mixed
conifer forests of California. To what extent is the approach taken
technically sound, clearly communicated, and appropriately
characterized?

Selection of coastal sage scrub (CSS) and mixed conifer forest
ecosystems is appropriate because: (a) these ecosystems have high
geographic coverage and are located in the important wildland--urban
interface I highly populated areas, (b) they encompass a strong gradient
of N deposition from the low, background levels up to the highest levels
recorded in the US, (c) these ecosystems have been investigated for a
long time from a perspective of interactive effects of atmospheric
deposition, climate change fire and other stressors, (d) results of
these investigations are well documented in the peer-reviewed
literature.

If the goal of this chapter was to review the current state of science
for these two case studies, than the approach taken was technically
sound and findings have been clearly communicated. However, if results
of these two case studies were supposed to show how the relationships
between the observed chemical and biological changes and N atmospheric
deposition (possibly expressed as critical loads) could be linked to the
concentration-based NOx/SOx standards, then the used approach was not
inadequate and should be revised.

The chapter provides a comprehensive review of the existing scientific
knowledge for these two case studies. GIS maps show modeled N deposition
in portion of California encompassing the two selected ecosystems, CSS
threat from fire, and the presence of acidophyte lichens.
Three-dimensional maps illustrating loss of CSS in relation to different
levels of fire threats or N deposition could greatly help in developing
a probabilistic approach to the evaluation of N deposition risks to
important California ecosystems.

For development of CL for CSS, in addition to biodiversity changes or
changes in lichen communities, accumulation of biomass of invasive
grasses (critical level for occurrence of catastrophic fires) could be
considered (Anderson, 1982; Scifres and Hamilton, 1993; Gimeno et al.,
2009; Minnich and Franco-Vizcaino, 2009). For more information on this
subject please contact Drs. Richard Minnich and Edith Allen, UC
Riverside. For the mixed conifer forests, on the low end of N deposition
changes in lichen communities, and on its high end, nitrate leaching to
surface water, are good end points for CL estimates. Other, such as
possible changes in understory biodiversity changes could also be
considered and explored.

Data on N deposition levels was obtained from the NADP and CASTNET
networks and modeled N deposition distribution from the CMAQ model runs
for 2002, which were based on the 12 km grids. As the authors of this
analysis suggest, results from the 4 km grid would greatly improve
accuracy of predicted relationships between N deposition and the
biological effects.

Some data for the main drivers of N dry deposition in the San Bernardino
Mountains, gaseous HNO~3~ and NH~3~ from passive samplers have already
been published (Bytnerowicz et al, 2007). More results on distribution
of N nitrogenous gases monitored with passive samplers in southern
California and southern Sierra Nevada are currently being prepared for
publication (Andrzej Bytnerowicz, unpublished).

Suggestion: For better understanding of regional (southern Sierra
Nevada) effects of N deposition, comparison of responses in mixed
conifer forests (Kings River Project) such as leaching of nitrate to
streams, lichen species composition, and invasion of invasive grasses,
could be compared to ANC changes in the nearby lakes of the sub-alpine
and alpine zone.

[Specific comments:]{.underline}

Page 13, 1^st^ paragraph -- also high levels of NH~3~ and NH~4~^+^ are
deposited to CSS of southern California.

Page 29, Figure 3.1-1. Scale for N deposition is too coarse -- a bracket
6.83-70.04 kg N/ha/yr is not acceptable.

Page 33, 1^st^ paragraph -- bark beetle should be added as important
stressor in the mixed conifer forest ecosystem.

Page 44 and 45, section 5.2 -- for the mixed conifer forest also changes
of species composition of the under story vascular plants should be
considered.

Page 45, list of questions -- in regard to responses of lichens to N
deposition, effects of oxidized vs. reduced N should be considered. This
may be of interest because there is a potential shift towards less
reduced N due to the movement of dairy farms from the Los Angeles Basin
to California Central Valley.

[References:]{.underline}

Anderson, H. E. 1982. Aids to determining fuel models for estimating
fire behavior. USDA Forest Service Intermountain Forest and Range
Experiment Station, General Technical Report INT-122, Ogden, Utah.
http://www.fs.fed.us/rm/pubs_int/int_gtr122.pdf

Bytnerowicz, A., M. Arbaugh, S. Schilling, W. Fraczek, D. Alexander, P.
Dawson (2007) Air

pollution distribution patterns in the San Bernardino Mountains of
southern California: a 40-year perspective. *TheScientificWorldJOURNAL*
**7(S1)**, 98--109. DOI 10.1100/tsw.2007.57.

Gimeno, B. S., Yuan, F., Fenn, M. E., Meixner, T. 2009. Management
options for mitigating nitrogen (N) losses from N-saturated
mixed-conifer forests in California. In: A. Bytnerowicz, M. Arbaugh, A.
Riebau and C. Andersen (eds). Wildland Fires and Air Pollution,
Developments in Environmental Sciences, Vol 8, Elsevier, Amsterdam, pp.
425-455.

Minnich, R. A., Franco-Viscaino, E. 2009. A probabilistic view of
chaparral and

forest fire regimes in southern California and northern Baja California.
In: A. Bytnerowicz, M. Arbaugh, A. Riebau and C. Andersen (eds).
Wildland Fires and Air Pollution, Developments in Environmental
Sciences, Vol 8, Elsevier, Amsterdam, pp. 339-364.

Scifres, C.F., Hamilton, WT. 1993. Prescribed Burning for Brushland
Management: The South Texas Example. Texas A & M University Press,
College Station.

# Ms. Lauraine Chestnut

Charge question 1: Scope of the review

There seems to be some ambiguity regarding use of the term "sensitive."
It sometimes seems to mean an ecosystem that is vulnerable but not
necessarily harmed at current or historic deposition rates, and other
times it seems to mean that harm is occurring at current exposures. To
me, the word sensitive fits better for the former than for the latter.
For there to be harmful effects it would seem to require both
sensitivity and exposure. Thus, the selected case studies are
appropriately selected as not just sensitive, but currently being
affected by N and/or S deposition.

Pages 2-7 to 2.8

Descriptions of ecosystem services reduced or degraded as a result of
harmful effects on ecosystem functions are not only important inputs
into economic valuation and cost-benefit analysis, they are important in
helping policy makers and the public understand the significance of the
effects on the ecosystems.

It is important to recognize that economic valuation is best considered
relative to an alternative. In figure 2.3-2 it is unclear what an
economic value to "maintain" an ecosystem would be without specifying
what would happen if some action were not taken. There may be a value to
prevent a specified amount of degradation or a value to obtain a
specified improvement, but the value to simply "maintain" is probably
ambiguous.

Page 2-13

This discussion of uncertainty is pretty weak. One important note is
that variability is not the same thing as uncertainty. There may be a
lot of variability in how different ecosystems respond to the same
amount of N/S deposition but it may be able to specify this variability
with a great deal of certainty.

It is important to acknowledge uncertainty, but a critical thing here is
how to determine when there is enough known to be able to set reasonable
standards. The uncertainty issue will need to be taken up again when the
analysis is further along. A key question is whether there is enough
confidence in the results that they are useful to assist policy
decision-making. This requires more than just listing sources of
uncertainty, but necessitates an assessment of the significance of the
uncertainty and how it affects the results.

Case studies

The proposed use of ecological indicators that can be linked to varying
levels of effects (and related losses in ecosystem services) goes beyond
the idea of estimating critical loads at which ecosystems experience no
effects. This does not come through in the current draft until Chapter
7, and is a missing perspective in the various case study appendices. An
important consideration that has to be made as these indicators are
selected is their ability to be linked to effects of varying severity
rather than defining simply a \"no effects\" threshold, because this
will be important information for the eventual assessment what effects
are adverse.

The REA ultimately needs to describe the significance of the effects on
ecosystem function and services at current levels of exposure and at
alternative levels of exposure that might be achieved with alternative
standards in the case study areas. Selecting any secondary standard
probably requires more than a determination of a "safe" level because
the standard needs to protect against adverse effects, not just any
effects. The case study analyses seem to be headed in this direction and
I look forward to seeing this further fleshed out in the second draft.

Chapter 8

An important issue is that is not yet addressed is how the analysis will
deal with spatial scale in defining a potential standard. This is
complicated by expected variability in ecological response to deposition
in different locations even within a case study ecosystem. It is
unlikely to be reasonable or even feasible to set a standard to protect
the most sensitive ecosystems (or components of an ecosystem). The scale
decisions can be somewhat analysis driven in that the results may show
reasonable categories or groupings, such as X% of lakes in the
Adirondacks that would have an ANC of 50 or 100 at various ambient co

# Dr. Ellis B. Cowling

My individual comments on the August 2008 First External Review Draft of
the Risk and Exposure Assessment (REA) for the Secondary National
Ambient Air Quality Standards for Oxides of Nitrogen and Oxides of
Sulfur are organized below in response to each of the several Charge
Questions posed the Panel in preparation for the October 1-2, 2008 CASAC
meeting. As you will see, somewhat more detailed attention has been
given to the five Charge Questions on Case Study Analyses and the
recently received Chapters 7 and 8 than to other parts of this Risk and
Exposure Assessment as requested by the Chair.

**[Scope of the Review]{.underline}**

2.  **Chapters 1 and 2 provide the background, history, and framework
    for this review, including a discussion of our focus on the four key
    ecological effect areas (aquatic acidification, terrestrial
    acidification, aquatic nutrient enrichment, terrestrial nutrient
    enrichment). Is this review appropriately focused in terms of
    characterizing the important atmospheric and ecologic variables that
    influence the deposition and, ultimately, the ecologic impacts of
    nitrogen and sulfur? Does the Panel have any further suggested
    refinements at this time?**

My most serious reservation about the analysis framework for Chapters 1
and 2 is that chemically reduced forms of nitrogen (NHx), organic forms
of nitrogen (NCx), and total reactive nitrogen (Nr) all are not included
in the specific wording of any of the 20 policy-relevant questions that
are said to constitute the framework for this review on the effects of
nitrogen and sulfur pollution on acidification and nutrient enrichment
of aquatic and terrestrial ecosystems in the US.

This reservation is surprising in view of the very comprehensive
analysis regarding the importance of chemically reduced forms of
reactive nitrogen contained in the Integrated Science Assessment (ISA)
document and also in view of the October 31, 2007 *Resolution* from the
Science Advisory Board's Integrated Nitrogen Committee (INC) which makes
the following strong assertion from the INCs Committee's examination of
much of the same body of evidence reviewed in the ISA:

> "The current air pollution indicator for oxides of nitrogen, NOx, is
> an inadequate measure of reactive nitrogen in the atmospheric
> environment. The SAB's Integrated Nitrogen Committee recommends that
> inorganic reduced nitrogen (ammonia plus ammonium) and total oxidized
> nitrogen, NOy, be monitored as indicators of total chemically reactive
> nitrogen."

Please note the roster of current members of the SAB's Integrated
Nitrogen Committee whose collective competence with regard the public
welfare and public health effects of reactive nitrogen is very similar
to the collective competence of the CASAC Panel selected to review
Secondary NAAQSfor Oxides of Nitrogen and Oxides of Sulfur as can be
seen in the Determination Memo at
<http://yosemite.epa.gov/sab/sabproduct.nsf/02ad90b136fc21ef85256eba00436459/c83c30afa4656bea85256ea10047e1e1!OpenDocument&TableRow=2.1#2>.

The conclusionary statements written in **bold-type** in Chapter 4 of
the ISA indicate that:

> "The evidence is sufficient to infer a causal relationship between
> "acidifying deposition" (which includes NHx, and NCx, as well as NOx )
> and the following adverse acidification effects:

a)  "changes in biogeochemistry related to terrestrial ecosystems,"

b)  "changes in terrestrial biota,"

c)  "changes in biogeochemistry related to aquatic ecosysytems,"

d)  "changes in aquatic biota."

Also, "The evidence is sufficient to infer a causal relationship between
Nr (reactive nitrogen) deposition (which also includes NHx, NCx, and
NOx) and the following additional ecologically adverse nutrient-
enrichment effects:

e)  "alteration of biogeochemical cycling of N in terrestrial
    ecosystems,"

f)  "alteration of biogeochemical cycling of C in terrestrial
    ecosystems,"

g)  "alteration of biogeochemical flux of N~2~O in terrestrial
    ecosystems,"

h)  "alteration of biogeochemical flux of CH~4~ in terrestrial
    ecosystems,"

i)  "alteration of species richness, species composition and
    biodiversity in terrestrial ecosystems,"

j)  "alteration of the biogeochemical cycling of N,"

k)  "alteration of the biogeochemical cycling of C,"

l)  "alteration of N~2~O flux in wetland ecosystems,"

m)  "alteration of CH~4~ flux in wetland ecosystems,"

n)  "alteration of species richness, species composition and
    biodiversity in wetland ecosystems,"

o)  "alteration of biogeochemical cycling of C in freshwater aquatic
    ecosystems,"

p)  "alteration of species richness, species composition and
    biodiversity in freshwater aquatic ecosystems,"

q)  "alteration of the biogeochemical cycling of N in estuarine aquatic
    ecosystems,"

r)  "alteration of the biogeochemical cycling of C in estuarine aquatic
    ecosystems,"

s)  "alteration of species richness, species composition and
    biodiversity in estuarine aquatic ecosystems,"

> "The evidence is sufficient to infer a causal relationship between:

t)  "exposure to NO, NO~2~, and PAN and injury to vegetation" and

> s\) "exposure to HNO~3~ and changes to vegetation."

On the basis of this substantial body of accumulated evidence, I
recommend that a schematic diagram similar to Figure 1.3-1 be included
in Chapter 1 of the Second Draft REA document to illustrate the "cycle
of reactive, chemically **reduced** nitrogen species." I also recommend
that:

a)  Chemically reduced (NHx) and also organic forms (NCx) of total
    reactive nitrogen also be included among the nitrogen pollutants of
    concern in many of the 20 policy-relevant questions listed in
    Section 1.4 on pages 1-17 through I-20 in Chapter 1 of this First
    Draft REA, and

b)  Appropriate answers about both chemically reduced (NHx) forms of
    total reactive nitrogen, and, if possible also organic forms (NCx)
    of total reactive Nitrogen (Nr), be presented in Chapters 2, 3, and
    4 of the Second Draft REA when it is completed.

**[Air Quality Analyses]{.underline}**

4.  **To what extent are air quality characterizations and analyses
    presented in Chapter 3 technically sound, clearly communicated,
    appropriately characterized, and relevant to the review of the
    secondary NAAQS for NOx and SOx?**

> With the exception of the major reservations stated in answer to the
> Charge Questions about the Scope of the Review, I believe that the
> analyses presented in Chapter 3 are technically sound, clearly
> communicated, and appropriately characterized.

5.  **Section 3.2.1 describes an approach for evaluating the spatial and
    temporal patterns for nitrogen and sulfur deposition and associated
    ambient concentrations in the case study locations. This draft
    document includes the analysis for the Adirondacks case study. Does
    the Panel agree with this approach and should it be applied to the
    other Case Study Areas?**

> The approach used for evaluating the spatial and temporal patters for
> of N and S deposition and associated ambient concentration seems very
> reasonable to me. This approach proved to be useful in the Adirondacks
> Case study and I expect it to be reasonable for other case studies as
> well.

6.  **Section 3.2.2 describes the relative contributions of ambient
    emissions of nitrogen and ammonia to nitrogen deposition for the
    case study areas. To what extent is the approach taken technically
    sound, clearly communicated, and appropriately characterized?**

> I presume from examining the figures and associated text for the data
> presented on pages 3-63 through 3-112 that this question should have
> read:
>
> **" Section 3.2.2 described the relative contributions of chemically
> oxidized and chemically reduced forms to total reactive nitrogen for
> the Case Study areas. To what extent is the approach taken technically
> sound, ...etc."**
>
> On the assumption that my presumption is correct, I consider this
> combination of modeling and measurement approaches to be reasonable.
> But I must confess that it took me a very long time to finally
> understand the rationale behind the statement on lines 10-12 on page
> 3-13 that "In order to calculate total nitrogen (by which I suppose
> the author meant deposition of total reactive nitrogen) the two
> chemical species from the National Atmospheric Deposition Program
> (NADP) (i.e., NO3- and NH4+) were added together and then added to the
> total dry deposition values estimated from the Community Multiscale
> Air Quality model (CMAQ).
>
> It also took me a very long time to understand what was meant by the
> term "zero-out of NOx emissions" as used in most of the figure
> captions on pages 3-63 through 3-112) and periodically in the
> associated text.
>
> With regard to the questions of "clearly communicated and
> appropriately characterized" I offer the following comments:

1)  What a delight it was to find the following firm statement on lines
    15-20 on page 3-70:

> "Figures 3.2-42 examines the relative impact of emissions on NH~3~ of
> the deposition of total reactive nitrogen. Figure 3.2-42 shows that
> NH~3~ emissions represent a significant contribution to total reactive
> nitrogen in most case study areas, although the impact varies by
> season and by area. The smallest impact of NH~3~, 10% occurs in the
> Potomac case study area in February. The largest impact of NH~3~, 73%
> occurs in the Neuse Case study in July. The Neuse case study has the
> largest overall impact of from NH~3~ of any of the case study areas,
> across all four seasons."

2)  On lines 6 and 7 also on page 3-63 (and another case on lines 9 and
    10 on page 3-71) we find three very confusing sentences that reveal
    clearly why EPA's constant use of the terms "reduce," "reducing" and
    "reduction" is so often confusing and ambiguous:

> "One possibility is that reducing NOx reduces HNO~3~, which limits
> ammonium nitrate (NH~4~NO~3~) formation (and for existing aerosol, a
> reduction in HNO~3~ shifts the equilibrium towards the gas phase),
> thereby increasing the lifetime of NH~3~. A net increase in
> NH~3~/NH~4~ results. Because the deposit velocity of NH~3~ is much
> higher than the deposition of NH~4~^+^ aerosol, dry deposition of
> NH~x~ increases.
>
> The terms "reduce," "reducing" and "reduction" have both chemical and
> numerical meanings. Fortunately we have the unambiguous terms
> "decrease" and "decreasing" which have only a single (always
> numerical) meaning. So why not use the unambiguous term "decrease"
> instead of the word "reduce" when our intended meaning is numerical
> and thus reserve the term "reduce" for its chemical meaning?
>
> **Is this what was meant by the sentence quoted above?**
>
> "One possibility is that **decreasing** emissions of NOx **decreases**
> air concentrations of HNO~3~, which limits ammonium nitrate
> (NH~4~NO~3~) formation (and for existing aerosol, a **decrease** in
> HNO~3~ emissions shifts the equilibrium towards the gas phase),
> thereby increasing the atmospheric lifetime of gaseous NH~3~. A net
> increase in the ratio of gaseous NH~3~ to NH~4~^+^ aerosol in the
> atmosphere results. Because the deposit velocity of gaseous NH~3~ is
> much larger than the deposition velocity of NH~4~^+^ aerosol, dry
> deposition of NH~x~ increases.

**[Case Study Analyses]{.underline}**

1.  **Attachment 2 presents a GIS analysis to define geographical areas
    that are sensitive to acidification and nutrient enrichment. Are the
    national geospatial data sets chosen adequate to identify sensitive
    areas? Are there other data sets that have not identified by this
    analysis that we should consider? Does the Panel agree with approach
    or can they suggest alternatives?**

> I have only limited experience with the several data bases that were
> used in the GIS analysis used in an attempt to define geographic areas
> that are sensitive to acidification. Thus I have only limited
> professional experience on which to base a detailed judgment in
> response to this question.
>
> Nevertheless, my general impression derived from study of the summary
> map on page 18 of Attachment 2, and my general awareness of soil,
> vegetation, surface and ground waters, and the topographical,
> meteorological, and climatic factors that are relevant to
> acidification and nutrient enrichment, lead me to conclude that the
> GIS approach used is generally sound. I know of no additional data
> sets that should be included in this analysis.

2.  **Attachment 3 presents our current progress on evaluating the
    effect of aquatic acidification in the Adirondacks. It describes the
    use of the MAGIC model to evaluate ANC levels in selected lakes and
    streams in the Adirondacks and Shenandoah. To what extent is the
    approach taken technically sound, clearly communicated, and
    appropriately characterized?**

> I have no direct experience on which to base an informed judgment in
> response to this question. However, several of my colleagues tell me
> that the MAGIC model is very appropriate for these kinds of analyses.

3.  **Attachment 4 presents our current progress on evaluating the
    effect of terrestrial acidification. It outlines a plan to use the
    Simple Mass Balance Model to evaluate current deposition levels on
    forest soil ANC for sugar maple in the Kane Experimental Forest and
    red spruce in the Hubbard Brook Experimental Forest. To what extent
    is the approach taken technically sound, clearly communicated, and
    appropriately characterized?**

> I have studied Attachment 4 with considerable care and consider that
> the approach taken so far (since this is still a work in progress) is
> technically sound, clearly communicated, and appropriately
> characterized.

4.  **Attachment 5 presents our current progress on evaluating the
    effect of aquatic nutrient enrichment. It outlines a plan to
    evaluate how changes in nitrogen deposition affect the
    eutrophication index in two estuaries: the Chesapeake Bay and
    Pamlico Sound. The analysis will model one stream reach (Potomac
    River and Neuse River) to determine the impact on the eutrophication
    index for the estuary. To what extent is the approach taken
    technically sound, clearly communicated, and appropriately
    characterized?**

> I have studied attachment 5 with reasonable care and conclude that the
> approach taken in this case also is technically sound, clearly
> communicated, and appropriately characterized.

5.  **Attachment 6 presents our current progress on evaluating the
    effects of terrestrial nutrient enrichment. It describes an approach
    to evaluate the effects of nitrogen deposition on the Coast Sage
    Scrub community in California and in mixed conifer forests in the
    San Bernardino and Sierra Nevada Mountains. To what extent is the
    approach taken technically sound, clearly communicated, and
    appropriately characterized?**

> I have no experience with any of the western state ecosystems that are
> discussed in Attachment 6. Thus I have no professional experience on
> which to base an informed response to this question.

**[Additional Effects]{.underline}**

1.  **In this chapter, we have presented results from some initial
    qualitative analyses for additional effects including the impact of
    sulfur deposition on mercury methylation, the impact of nitrous
    oxide on climate change, and the impact of nitrogen deposition on
    carbon sequestration. Are these effects sufficiently addressed in
    light of the focus of this review on the other targeted effects in
    terms of available date to analyze them?**

> Chapter 6 provides a useful overview of the impact of sulfur
> deposition on methylation of mercury which seems to me to be very
> worthy of consideration with regard to setting appropriate limits on
> the amount of air emission of sulfur oxides that should be permitted
> in various regions of the US. I see little reason for worry about
> nutrient enrichment or acidification effects of carbon sequestration.
> I do believe, however, that nitrous oxide emissions should be
> incorporated in EPA's review of the NAAQS for nitrogen pollution and
> its effects on terrestrial and aquatic ecosystems.

**[Synthesis and Integration of Case Study Results into the Standard
Setting Process (Chapter 7)]{.underline}**

1.  **The purpose of Chapter 7 is to summarize the Case Study results
    and characterize the relationship between levels of an ecological
    indicator and the associated degree of ecologically adverse effects.
    To what extent is this approach technically sound, clearly
    communicated and appropriately characterized at this point of the
    review? Does the Panel have any further suggested refinements at
    this time?**

> I believe that the attempt being made in Chapter 7 to building a
> scientifically sound linkage between carefully selected ecological
> indicators and the extent and magnitude of ecologically adverse
> effects is a very complicated but very desirable goal.
>
> During my initial readings of Chapter 7, and even more Chapter 8
> during the few days between their availability to CASAC on September
> 23 and the CASAC meeting on October 1 and 2, it appeared to me that
> EPA was deliberately trying to build a case for making a modest
> decrease in emissions of nitrogen oxides (NOx \-- which is already
> recognized as a Criteria Pollutant ) --and of course would help
> decrease the adverse acidification and nutrient enrichment effects of
> total acidifying deposition and of total reactive nitrogen \-- without
> also having to develop the very challenging regulatory case for
> "listing" ammonia and ammonium ions" as Criteria Pollutants.
>
> At that time, my "seat-of-the-pants" inclination was to believe that
> the extent of decrease in reactive nitrogen pollution loads that are
> needed to protect sensitive terrestrial and aquatic ecosystems of this
> country probably cannot be achieved without taking steps to also
> include significant decreases in the amounts of chemically reduced and
> perhaps also organic forms of total reactive nitrogen.
>
> During the CASAC meeting in the Research Triangle Park on October 1
> and 2, 2000, however, and also during the EPA Science Advisory Board's
> Integrated Nitrogen Committee (INC) Workshop held in Washington DC on
> October 29 and 30, 2008, I began to see several things much more
> clearly:

1)  EPA already has full regulatory authority to limit air
    concentrations of oxides of nitrogen in order to protect sensitive
    ecological systems from adverse effects,

2)  The regulatory and political obstacles that would have to be
    overcome in order to "list" ammonia and ammonium ion as Criteria
    Pollutants are extraordinarily large,

3)  It would not be possible to meet the court-ordered regulatory
    deadlines for completion of the current NOx and SOx Secondary NAAQS
    Standard reviews if an attempt were made to overcome these very
    imposing regulatory and political obstacles,

4)  It would be possible to consider the amounts of NHx and NCx as part
    of the "already existing conditions that lead to acidification and
    nutrient enrichment of sensitive aquatic and terrestrial
    ecosystems,"

5)  It should be possible to determine what technically achievable
    extent of decrease in emissions of NOx might be sufficient to
    protect some if not all sensitive ecosystems in various parts of the
    US from the adverse ecological effects caused by
    reactive-nitrogen-induced acidification and nutrient enrichment of
    aquatic and terrestrial ecosystems, and

The present drafts of Chapters 7 and 8 indicate that OAQPS is seeking
first to determine, within EPA's **present** regulatory structure, if
decreases in emissions of nitrogen oxides (NOx) \-- which are already
recognized as a Criteria Pollutant \-- could achieve an adequate
decrease in the adverse acidification and nutrient enrichment effects of
N pollution that are now occurring in various parts of the United
States.

During our CASAC discussions with OAQPS on October 2, 2008, we were
assured that Chapters 7 and 8 of the Second Draft REA will deal much
more completely with the combined causal effects of both chemically
reduced (NHx) and chemically oxidized forms of reactive nitrogen (NOx).

**[Considerations in the Structure of the NOx/SOx Secondary Standard
(Chapter 8)]{.underline}**

1.  **Chapter 8 begins to explore how a secondary NAAQS might be
    structured to address the targeted ecological effects discussed in
    the assessment. The next draft of this document will include one or
    more examples of how this structure might be used to relate specific
    levels of air quality indicators with a corresponding ecological
    indicator for a given location and/or scenario. To What extent is
    the described approach technically sound, clearly communicated and
    appropriately characterized at this point of the review? Does the
    Panel have any further suggested refinements at this time?**

In Section 8.1 -- *Possible Structure of a Secondary Standard* -- the
diagram in Figure 8.1-1 was especially informative of the approach that
is currently being considered by OAQPS. The example given was based on
the ecological indicator ANC (acid neutralizing capacity) and assumed
that the pollutants of concern were not only the chemically oxides form
of reactive nitrogen (NOx) and sulfur (SOx) , but also the chemically
reduced forms of reactive nitrogen (NHx).

The attached diagrams were developed by Ted Russell in his role as Chair
of the CASAC NOx/SOx Secondary Standards Review Panel for presentation
to the SAB's INC Committee during the INC Workshop in Washington DC on
October 30, 2008. These two diagrams were designed to show how OAQPS
might include an estimate of chemically reduced nitrogen as one of the
"already existing conditions" that lead to acidification and/or nutrient
enrichment of aquatic and terrestrial ecosystems, and thus to provide a
basis for calculating the amount by which nitrogen oxide deposition
would need to be decreased in order to achieve an appropriate critical
load for acidification effects and a similarly appropriate critical load
for nutrient enrichment.

![](media/image2.wmf)

![](media/image3.wmf)

# Dr. Douglas Crawford-Brown

I am charged primarily with Scope of the Review, and so my comments are
primarily on that issue. The specific Charge Question addressed is:

"Scope of the Review: Chapters 1 and 2 provide the background, history
and framework for this review, including a discussion of our focus on
the four ecological effect areas (aquatic acidification, terrestrial
acidification, aquatic nutrient enrichment, terrestrial nutrient
enrichment). Is this review appropriately focused in terms of
characterizing the important atmospheric and ecologic variables that
influence the deposition and ultimately the ecologic impacts of nitrogen
and sulphur? Does the panel have any further suggested refinements at
this time?"

This review also considers Chapters 7 and 8, as these are the core of
the document in regards to an eventual regulatory decision.

As with my review of the ISA, my conclusion here is that the REA does in
fact satisfy the goal in the Charge Question, subject to the comments
below. The correct effects are considered (there may be more effects one
could note, but the ones considered here are the most significant and
are likely to bound the areas of concern adequately), and the correct
relationships to atmospheric and ecologic variables are considered
(again to the extent these are needed to draw the primary conclusions).
The document is well written, being easy to follow and nicely organized,
although the wheels fall off a bit -- or are not even present - in
Chapters 7 and 8). The authors have culled the most important
conclusions from an immense literature, focusing the reader properly
onto the key findings. A theme that will emerge below, however, is my
feeling that the available data and analyses may support the need for
considering a reduced NAAQS for NOx and SOx, but is insufficient to
suggest the actual ambient levels needed to avoid demonstrably adverse
effects (which I contrast with effects alone, which may or may not be
sufficient to deem adverse).

This document would benefit greatly from an Executive Summary similar to
the one in the ISA. There is a large amount of information here, but it
can be boiled down to a few key conclusions. My fear is that failing to
do that, the authors may find specific parts of the document picked in
the policy process because they support a desired conclusion and policy
solution. There needs to be a concise and unambiguous statement of the
key scientific conclusions, and an Executive Summary is exactly the
place to put these.

I found Chapter 1 very well written. The document lays out the relevant
policy questions and even relates these (in contrast to past documents)
clearly to the task of deciding whether the NAAQS needs to be revised
and, if so, how the information would be used to do that.

Figure 1.4-1 is quite interesting, but it also lays clear the one
glaring problem with a secondary NAAQS, since the key element is the
Ecological Effect Function. I don't see where such a function is
sufficiently well established to allow use in setting a secondary
standard, other than perhaps as an analogue to an effects threshold in
non-cancer human health risk assessment, probably with some margin of
safety inherent in it due to the inability to draw a proper line between
effect and adverse effect.

Chapter 2 begins by listing the appropriate effects, and I agree with
the selection of these based on the information in the ISA. Table 2.1-1
is particularly useful in providing a road map to the material in the
entire document. In the previous draft, I was unclear as to the purpose
of the case studies. In the present draft, this point is clearer, and I
agree with the idea that given the very large inhomogeneity in both
exposure conditions and species across different geographic areas, the
best that can be done is to select a few representative but sensitive
regions and determine where the ambient levels would need to be to
protect these. The one thing missing is a clear statement as to how
unique these case study areas are. One can't set national standards
based on a few outliers in the national distribution, and I believe a
better case can be made in the document as to why these particular areas
studied are not in the extremes of the tail of inter-site distributions
of sensitivity.

I particularly like the structure of the assessment outlined in the
seven steps. While the committee may have disagreements over specific
methodological issues, these seem to me the appropriate steps and an
innovative way to get at the issue of a secondary NAAQS that relies
maximally on available data. I fully support the EPA staff in this
choice of framework, even if in the end they must execute it somewhat
more qualitatively than might be desired. The point is that it is the
right way to be [thinking]{.underline} about the NAAQS.

The ecosystem services discussion in Chapter 2 was interesting to read.
It presented the subject well, and it is evident to me that ecosystem
services is one lens through which to view a secondary NAAQS (although
it doesn't capture issues such as inherent rights of other species). My
problem lies in a disconnect between the detailed discussion of
ecosystem services and the specific Ecological Effect Functions in
Figure 1.4-1. I don't believe the document, or even the current state of
the science, allows for development of such a Function needed to
determine how much a specific ecosystem service is impacted by a given N
or S loading, or how adverse is a given decline in ecosystem service. I
wouldn't be inclined to support a position that says [any]{.underline}
decline is automatically adverse; the same applies to my position on
human health imapcts. Due to this methodological and computational gap,
the Ecosystem Services discussion in Chapter 2 comes off as more
interesting than truly informative -- a good idea that can't quite be
pulled off when the data are analyzed.

The uncertainty discussion, as in almost all of the REAs we have
reviewed, is quite generic and qualitative. But given the nature of this
exercise, I am not sure a more quantitative approach to uncertainty
would inform the final decision. This is because, while there are
quantitative uncertainties having to do with the data and modelling, an
equally important uncertainty is the conceptual relationship between the
case studies and any sort of statement about the impact of a national
standard.

As Chapters 3, 4 and 5 are outside my area of expertise, especially with
respect to specifying where the staff should look for representative but
sensitive case study areas, I don't provide comments here, other than to
note that Chapters 4 and 5 are of little use given their sketchy nature.

The heart of the REA is found in Chapters 7 and 8. Table 7.1-1 agrees
with the information provided in Chapter 1, so at least the methodology
is consistent on this point. The framework of thinking laid out in this
Chapter is appropriate, although provided here in much too sketchy a
form for me to agree or disagree with how it is being executed. There
remain two areas in which substantial disagreement can arise between
individuals reviewing the document: (1) the methodological steps in
calculating impacts on a given case study site and (2) drawing summary
conclusions across sites. At the moment, the document does not fully
clarify the first, and the second issue is dealt with more through
aspirations than any clear approach. But I must withhold judgment until
the final report is prepared. The staff is at least headed in the right
direction, have a proper roadmap in front of them and have the expertise
on hand to carry out these tasks.

In Chapter 8, the phrase "uniform level of ecosystem protection" occurs,
and seems to become a key idea in how a NAAQS might be considered. This
idea really needs more of an explanation. Given the high levels of
inhomogeneity, and the fact that the conclusions rest ultimately on case
studies of sensitive areas, and the quite diverse kinds of effects being
considered, I don't understand what is meant by a "uniform level of
ecosystem protection". It surely doesn't mean that the level of effect
will be the same across all ecosystems in the country, or even that the
same ambient level will produce the same level of effect everywhere, or
that the effects will be equally adverse in some deeper sense. And there
is no common metric to which all these diverse effects can be reduced.
So, just what does it mean?

Again, Figure 8.1-1 is the right kind of structure, but I don't see how
the Ecological Effect Function will be developed as anything other than
a threshold model. And I don't see where a margin of safety is
recognized or introduced. But it is still the right conceptual approach
if it can be pulled off methodologically.

Much of the discussion in Section 8.2 seems to me of a policy nature,
belonging in a much earlier chapter. It almost comes across as being
filler here while the staff tries to figure out exactly how they will
execute the ambitious steps in Figure 8.1-1. I recommend moving it to
the front of the REA in either Chapter 1 or 2.

The rest of the Chapter 8 strikes me as a lot of scientific detail with
little to connect it all to the final calculations. I can't comment on
many of the equations proposed, because they relate more to
environmental transport and fate than to effects. But it is evident to
me that there is still a large gap between methodologies to estimate
deposition and methodologies to relate these loadings to any specific
effect that will drive a NAAQS.

# Dr. Charles T. Driscoll

The document "Risk and Exposure Assessment for Review of Secondary
National Ambient Air Quality Standards for Oxides of Nitrogen and Oxides
of Sulfur" is an effort by U.S. EPA staff to provide and discuss a
framework for establishing secondary standards of nitrogen oxides
(NO~x~) and sulfur dioxide (SO~2~). Overall, I found the framework
thought provoking and an interesting path forward in the establishment
of secondary standards. While I enjoyed reviewing the document, there
were several general technical issues that I am concerned about. There
are several wording and grammatical problems in the text that should be
addressed before the document is more widely circulated. Finally, there
are numerous small technical and wording problems in the document. I
have organized my comments around these three issues.

Unfortunately, the document is not complete. Major sections are missing
or partially complete. It is really a waste of time to conduct a review
of such a large and complex document when the document is incomplete.

**[Technical Issues:]{.underline}**

1\. *Case studies and modeling approach.* I think the approach of using
case studies to address the framework for secondary standards is a good
and appropriate one. I also generally think the specific case studies
that are advanced in the REA are appropriate and helpful. I generally
endorse the approach used. There are a few general comments/issues I
would like to address.\
\
The case studies for aquatic effects in the Adirondacks and the
Shenandoah Park regions, terrestrial effects on red spruce and sugar
maple in the East and terrestrial effects on coastal sage scrub and
conifer forests in California seem appropriate. I also like the two
estuarine sites to evaluate coastal effects. I do have some concerns
with the estuarine studies. First, it appears that the entire estuary
watershed will not be evaluated (i.e., Chesapeake-Potomac; Pamlico;
Neuse). Will this be a problem or is the scope of doing the entire
watershed just too great for this assessment? More problematic is
conducting analysis for two watersheds that are in fairly close
proximity? Although there is considerable information for Chesapeake Bay
and Pamlico Sound, wouldn't it make more sense to conduct one of these
case studies at a site with more contrasting features, with different
land cover, climatic or N sources? I would think interest's would be
best served by either selecting a northern estuary (e.g., Gulf of Maine,
Long Island Sound) or a Gulf estuary as a second site.

> The other general technical comment is that the approaches used to
> develop critical loads for these case studies are very different.
> Evaluating these different approaches could be very instructive but
> also problematic. I like the approach proposed of using a dynamic
> acidification model for the Adirondack and Shenandoah case studies.
> Note, however, that MAGIC does not effectively simulate watershed
> nitrogen dynamics. So if this is an important component of the
> critical load, there will undoubtedly be some errors. I find it
> disconcerting that for the terrestrial acidification assessment a
> steady-state model is being used. First, is it a good idea to use a
> dynamic model for the aquatic assessment and a steady-state model for
> the terrestrial assessment? While I agree with the authors that
> critical loads are a steady-state phenomenon, ecosystems are not.
> Forest ecosystems are losing exchangeable cations and presumably
> accumulating sulfur and nitrogen. This makes these systems by
> definition not a steady-state and increasingly sensitive to inputs of
> acidic deposition. While the application of a steady-state model is
> easy, it would seem to be problematic as an assessment tool. There are
> clear limitations in using a steady-state model for critical loads
> assessments. Finally, I don't understand how the critical loads will
> be determined for the coastal and terrestrial nutrient case studies.
> SPARROW is a statistical model and it is not clear how this can be
> used to evaluate greater and lower N loads.

2\. *Nitrogen saturation.* Throughout the text, N saturation is referred
to. However, I could not find any discussion of this phenomenon in the
introductory sections. It is discussed in the ISA but not (that I could
find) in the REA. A brief summary of N saturation might be helpful.

3\. *Time scale disconnect.* There appears to be a disconnect between
the time scales used for the atmospheric modeling and the effects
assessments. Ecosystem effects of air pollutants are largely manifested
over decades to multiple decades. Certainly the simulations conducted by
MAGIC are conducted with what I believe to be the appropriate temporal
perspective. I believe the time-scale for nutrient effects on ecosystems
similarly have a long-term perspective. In contrast, the deposition/CMAQ
analysis seems to be largely focused on a short-term or seasonal
perspective. Why? There seems to be a complete disconnect in the
atmospheric and effects modeling concerning time-scale of analysis.
Isn't the primary concern here ecological effects? Do seasonal or
monthly patterns in air concentration or deposition have any relevance
for this long-term analysis of ecosystem effects?

4\. *Climate.* I am a bit surprised that no discussion is given to
changing climate. The framework to be developed is examining effects
that will play out over the next decades. It is projected that climate
will also change substantially over the same period. Climate change will
affect hydrology and ecosystem response to air pollution. Climate change
should be mentioned and needs to be addressed in future assessments.

5\. *Establishing standards around ambient air concentrations.* In
Chapter 8, limited discussion was advanced in establishing ecosystem
effects around ambient air concentrations. While I can see that this
might be a desirable objective, as we currently have primary standards
and some quasi secondary standards based on ambient air concentrations.
However, for ecosystem effects, I do not see this approach as workable.
I think the standard needs to be based ultimately on total sulfur and
total nitrogen deposition. There are many species of sulfur and nitrogen
all which contribute to ecological effects but having different
residence times in the atmosphere. These residence times vary in time
and space. The key driver of ecological effects is long-term total
deposition. Establishing standards around ambient air concentrations
would seem to be intractable.

6\. *Spatial variability in sensitivity.* I'm not sure if this
consideration is relevant for the nutrient case studies, however, the
acidification case studies will exhibit considerable spatial variability
in sensitivity to acidic deposition. There is a range of ecosystem
sensitivity to acidification from highly sensitive to highly
insensitive. How will this range of ecosystem response to acidic
deposition be addressed when establishing the critical load? Will all
ecosystems be protected? 90%, 50%. Some discussion of this consideration
would be helpful.

**[Written Document Considerations:]{.underline}**

1\. *Written perspective.* The document is written from the "we"
perspective (i.e., we did this..., we analyzed that...). I find this
approach somewhat disconcerting. The reason being it is not clear who
owns the document. Is this EPA's document or the contractor's document?
Who are we? I would like to see the document altered.

2\. *Typos, errors, writing mistakes.* As with the last draft of the
ISA, the REA (and the 2^nd^ draft of the ISA) is filled with mistakes
and typos. I point out many of these in my specific comments (see
below). However, these are by no means all the mistakes. This document
needs to be carefully read, proofread and edited for consistency and to
eliminate the mistakes.

3\. *Redundancy.* There are many redundant sections in the document.
This makes a very long document, longer than it needs to be. The
document should be edited to eliminate the redundant text.

4\. *Tense.* The REA switches back and forth from the past to present
tenses. I can see writing in either tense. However, the document should
be edited so it is written in a consistent tense.

**[Specific comments:]{.underline}**

Page 1-2, line 16 Units of ANC µeq/L?

Page 1-11, line 24 I don't agree with the statement. Most published
studies document inputs of oxidized and reduced N. A few don't, but most
do.

Page 1-12, line 10 Space missing.

Page 1-12, line 13 I would change the wording. Acidification is an
environmental effect due primarily to sulfur and secondarily nitrogen in
most environments.

Page 1-13, line 12 As above, need to define N saturation.

Page 1-13, line 19 Change air to atmosphere.

Page 1-15, line 22 alpine

Page 1-16, line 12 It is incorrect to state that watersheds conducive to
methylation are found in the northeastern U.S. and southeastern Canada.
They are found all over. See Figure 6.1-3.

Page 2-2, table 2.1-2 Under aquatic acidification also include
hydrologic flow paths under sensitivity variable.

Page 2-4, line 15 Eliminate comma

Page 3-7 I would like to see this section expanded to include a section
of background (pre Industrial Revolution) deposition, including sulfate,
nitrate, ammonium and basic cation deposition.

Page 3-8 I would like to see a brief description of organic N
deposition, including sources.

Page 3-9, thru 12 There is a summary of spatial deposition patterns. The
discussion of how these maps are produced is in the section that follows
(3-12). The methods section should be moved in front of the maps. Also,
the maps are generated for 2002. Some discussion should be given as how
representative this year is, given year-to-year variability in
deposition. Moreover, it is critical to clarify on the deposition maps
the units of mass (e.g., Kg N/ha-yr or kg NO~3~/ha-yr).

Page 3-12, line 10 data are ...

Page 3-13, line 1 data were...

Page 3-13, line 6 Change to... kg/ha-yr.

Page 3-13, line 7 data were...

Page 3-16, line 5 Need to clarify the time interval kg/ha-yr?

Page 3-16, table 3.2-2 It is not clear what this table is. Some
additional text is necessary.

Page 3-19 It would be helpful to put the Adirondack Park and the
Shenandoah National Park boundaries and the Chesapeake and Pamlico
watershed areas on the map so the reader can understand the scope of the
analysis relative to the total resource.

Page 3-25, line 7,8 Change to... kg N-ha/yr.

Page 3-35, line 12 Change to... fairly uniform.

Page 3-36, figure 3.2-14 Why show figures of both monthly and seasonal
deposition? Isn't this redundant?

Page 3-38, figure 3.2-16, 17, 18, 19

These figures are difficult to read and are they really helpful?

Page 3-40, line 4 Change to... generally uniform...

Page 3-50, lines 3, 17 and Page 3-51, line 6

Change...drop to decrease

Page 3-50, figure 3.2-28 and elsewhere

Aren't the monthly patterns in wet deposition strongly driven by the
quantity of precipitation? Wouldn't patterns for a different year with
different precipitation patterns be different? As a result, this
temporal section is misleading because it is strongly affected by the
meteorology for that year. If true, why include all this analysis? As a
minimum, this fact should be clarified and some data provided on 2002 as
a reference year.

Page 6-1, line 3-4 Rephrase. Every wetland has sulfate. The production
of methyl mercury is largely mediated by sulfate reducing bacteria.

Page 6-1, line 22 Also phosphorus (or N) can be important as it
regulates aquatic productivity and therefore mercury concentrations in
aquatic organisms (Driscoll et al. 2007).

Page 6-2, line 4 Change to...Industrial Revolution.

Page 6-2, line 28 This sentence needs to be clarified. Ionic mercury can
be reduced and evaded and separately methylated. Methyl mercury is not
reduced. Where does this 1-2% come from? The extent of methylation is
highly variable from ecosystem to ecosystem.

Page 6-4, line 14-16 Why is methane needed? Why do you need HgS in the
equation? Define MeHg^+^.

Page 6-4, line 20 Also anoxic conditions.

Page 6-4, last paragraph There are other studies that probably should be
cited (Branfireun et al. 1999), (Jeremiason et al. 2006).

Page 6-5, line 12 Change to...methylation can occur within.

Page 6-5, figure 6.1-2 Hg can also be supplied from sediments.

Page 6-6, line 3 Change to... anoxia, sulfate).

Page 6-6, line 5 Change to... response, hydrology, nutrient loading,
limnology).

Page 6-10, line 4 Is this really true? I do not believe it. % methyl
mercury is highly variable. Need to correct.

Page 6-12, line 5 Change to... oxidizing NH~4~^+^.

Page A3-1, line 15 Subscript 2.

Page A3-1, line 20 hydrogen ion, and Al^n+^.

Page A3-1, line 20 and throughout the document

I don't think the writers of this document understand the concept of
buffering capacity. Buffering capacity is the resistance of a system to
changes in pH. I would recommend eliminate using the term here and
elsewhere or change the phrasing to use it correctly. An alternative
could be acid neutralizing capacity or acid-base status.

Page A3-2, 1^st^ paragraph I suggest adding a sentence or two about
immobilization/mobilization of SO~4~^2-^ and NO~3~^-^ by plants/soil
organic matter.

Page A3-2, line 10 There are numerous chemical indicators.

Page A3-2, line 12 NO~3~^-^, Al^n+^

Page A3-2, line12 Change to... of base cations; and ANC.

Page A3-2, line 27 Change to... precipitation enters the soil and soil
water to emerge...

Page A3-2, line30 K^+^ + Na^+^ + NH~4~^+^) -- (SO~4~^2-^ + NO~3~^-^ +
...) in (µeq/L)

Page A3-3, line 5 Change to... low pH.

Page A3-3, line 6 Change to... This is the acid neutralizing capacity
(ANC), or the ...

Page A3-5, line 4 acidic surface waters (14%; ANC\<0 µeq/L).

Page A3-5, line 26 United States

Page A3-6, line 24 Need to define the time and mass basis of deposition
(e.g., kg SO~4~/ha-yr or kg S/ha-yr).

Page A3-7, line 12 Change to... weathering rates and limited
neutralizing of acid inputs.

Page A3-8, line 5 Again need to define the time and mass basis of
deposition.

Page A3-9, line 19 Al^n+^

Page A3-9, line 21 with limited leaching

Page A3-9, line 23 EPA-administered Long-Term Monitoring (LTM) program.

Page A3-15, line 12 SO~4~^2-^

Page A3-16, line 9 comma

Page A3-16, line 19 it's the acid neutralizing capacity of a ...

Page A3-16, line 21 The acid neutralizing capacity of a ...

Page A3-17, line 3 20 µeq/L (limited protection)

Page A3-16, line 12 This sentence makes no sense. At ANC = 0 µeq/L a
water is chronically acidic.

Page A3-17, line 8 Sub and super script

Page A3-20, line 5 Units should be eq/ha-yr.

Page A3-20, line 7,8 I would eliminate the term occult deposition simply
call it cloud and fog deposition.

Page A3-20, line 10 Units meq/m^2^-yr

Page A3-22, line 24 This description needs to be expanded or clarified.
There are more than 200 NADP sites.

Page A3-28. line 25 in the catchment

Page A3-29, line 19 400 meq/m^3^

Page A3-29, line 24 The titles used for these classes should be
consistent with the titles established in table 4.1-1 on A-14.

Page A3-33 There needs to be some discussion on the time and nitrogen
retention assumptions used to obtain critical loads.

Page A4-1 I would change the title to Forest Acidification Case Study.

Page A4-1, line 17 hydrogen ions

Page A4-1, line 19 where strong acids

Page A4-4 Should also consider citing the recent paper by (Warby et al.
(in press)) attached), which shows widespread soil acidification in the
Northeast.

Page A4-5, line 14 This statement needs to be reworded. Al mobilization
occurs under low % base saturation and high concentrations of acid
anions. The statement as it stands is incorrect.

Page A4-9, line 18 Should be (Driscoll et al. 2001).

Page A4-10 It would be helpful to cite the study by (St. Clair et al.
2005) which shows decreases in foliar antioxidant enzymes in sugar maple
in response to lower foliar and soil Ca^2+^ in Pennsylvania.

Page A4-19, line 1 Again need to specify the mass and time basis of
deposition.

Page A4-28, line 10 acidity input neutralized by

Page A4-28, line 18 parties

Page A4-49 Need to indicate the units of the figure.

Page A4 References Should be BioScience.

Page A5-18, 1^st^ paragraph Need to use metric units.

Page A5-26, line 6 Need to define Nr.

Page A5-30 SPARROW is a steady-state model. Will need to demonstrate how
you can use it.

Page A5-55, line 7 were from

Page A5-58, line 6, 8 Does the SAV coverage really have this level of
significant figures?

Page A6-10, line 1 Change to... Mediterranean climate. This climate
is...\\

Page A6-25, line 16 result of long-term elevated N deposition rather
than pulses

Page A6-42, line 7 data are

Page 7-3, line 12 Change to... where strong acids are

Page 7-11, line 2 catchment to neutralized acid anion deposition is
known as acid neutralizing capacity.

Page 8-1, line 14 There cannot possibly be a uniform level of ecosystem
protection due to the inherent variability in ecosystem sensitivity.

Page 8-4, figure 8.1-1 Add climate as a variable/fixed factor.

Page 8-5, line 2 What is meant by the point of deposition?

Page 8-8, line 14 What about forest acidification?

Page 8-8, line 14 How can you say whether precipitation occurs or not.
Is there a location where precipitation does not occur? Rewrite
sentence.

Page 8-10, line 24. Do you mean deposition is expressed or an
equivalence basis? Please clarify.

Page 8-11, line 4 This sentence makes no sense and should be rewritten.

Page 8-14, line 1 data are

Page 8-14, line 20 Do you mean equivalence ratio?

**[References:]{.underline}**

Branfireun, B. A., N. T. Roulet, C. A. Kelly, and J. W. M. Rudd. 1999.
In situ sulphate stimulation of mercury methylation in a boreal
peatland: Toward a link between acid rain and methylmercury
contamination in remote environments. Global Biogeochemical Cycles
**13**:743-750.

Driscoll, C. T., Y.-J. Han, C. Y. Chen, D. C. Evers, K. F. Lambert, T.
M. Holsen, N. C. Kamman, and R. K. Munson. 2007. Mercury contamination
in forest and freshwater ecosystems in the Northeastern United States.
BioScience **57**:17-28.

Driscoll, C. T., G. B. Lawrence, A. J. Bulger, T. J. Butler, C. S.
Cronan, C. Eagar, K. F. Lambert, G. E. Likens, J. L. Stoddard, and K. C.
Weathers. 2001. Acidic deposition in the northeastern United States:
Sources and inputs, ecosystem effects, and management strategies.
BioScience **51**:180-198.

Jeremiason, J. D., D. R. Engstrom, E. B. Swain, E. A. Nater, B. M.
Johnson, J. E. Almendinger, B. A. Monson, and R. K. Kolka. 2006. Sulfate
addition increases methylmercury production in an experimental wetland.
Environmental Science and Technology **40**:3800-3806.

St. Clair, S. B., J. E. Carlson, and J. P. Lynch. 2005. Evidence for
oxidative stress in sugar maple stands growing on acidic, nutrient
imbalanced forest soils. Oecologia **145**:258-269.

Warby, R. A. F., C. E. Johnson, and C. T. Driscoll. (in press).
Continuing acidification of organic soils across the northeastern USA:
1984 - 2001. Soil Science Society of America Journal.

# Dr. Paul J. Hanson

The Risk and Exposure Assessment (REA) ... represents a good beginning,
but many sections are not yet complete or only partially complete making
it difficult to judge the full intent or appropriateness of the
document.

[Specific comments and suggested edits:]{.underline}

**Front matter**:

Page xii: Should the definition of ecological dose be limited to
toxicants that inhibit *[microbe-mediated ecological
processes]{.underline}*? I would think that the term should apply to all
biological organisms. It may be that it is a term that dominates
microbial studies.

Top of Page xiii: The most common example of an ecosystem benefit would
probably be an increase in productivity. Why isn't this an example?

Page xiii: The difference between elasticity and sensitivity (page xv)
isn't clear. Is there a reference for the use of the term elasticity
that might be placed here?

Page xv: The precipitation range for semi-arid regions should probably
be 250 to 500 mm. It certainly shouldn't be the same as the definition
for arid systems.

**[Chapter 1]{.underline}**

Page 1-3 line 8: I recommend the following wording change "...both
ambient [air]{.underline} and [surface]{.underline} deposited species of
NOx and SOx...

Page 1-10 line 23: N~2~O is nitrous oxide not nitrogen dioxide.

Page 1-12 line 9: For parallel structure I would add the spelled out
version of sulfur dioxide.

Page 1-13 line 5: Remove the semicolon.

Page 1-13 line 13: I would change "direct effects" to 'direct adverse
effects'. There is some evidence for localized N uptake.

Page 1-14 line 11: The text must be changed to "..detail on how
acidification affects sensitive ecosystems....." Don't leave the reader
with the impression that acidification is having effects on all
ecosystems.

Page 1-14 line 17: I don't understand "re-acidification". This concept
needs to be further developed.

Page 1-14 line 31: Add 'productivity' to the list of changes driven by N
deposition.

Page 1-15 line 14: This threshold for N saturation is only relevant for
some, but [not all]{.underline} eastern forests. Those levels of N
deposition would be easily assimilated by much of the upland oak forests
throughout the eastern United States growing on deeps soils with ample
base saturation. Page 3-186 of the ISA states "there is currently no
published national assessment of empirical critical loads for N in the
U.S......" Table 3-25 is a nice summary of what is known. The REA needs
to reflect the limited amount of data available for developing
quantifiable thresholds, and appropriately characterize those ecosystems
for which it might appropriately be applied. Avoid inappropriate
extrapolations. Lines 14 to 19 on page 4-16 of the ISA include good
statements that should be used within the REA to qualify the nature of
ecosystem sensitivity.

Page 1-15 lines 21 and 22: Similarly, the wording may need to be changed
here to suggest if these levels represent an appropriate threshold for
all or just some sensitive grasslands.

Page 1-15 line 30: Add a reference for the sentence ending on this line.

Figure 1.3-3 still doesn't show the productivity enhancement effect of
N, which is clearly a dominant process in the N cycle.

Bottom of page 1-17: Should some mention be made at this point to N
standards for water pollution? It isn't necessary, but might be a useful
connection. Section 3.3.6 of the ISA and the associated annex might be
cited.

Figure 1.4-1 doesn't adequately capture the integrated nature of NOx and
SOx pollution that is being attempted in this document. Are they truly
intertwined all along this process or do they only come together after
deposition takes place?

**[Chapter 2]{.underline}**

In Table 2.1-1 ANC should be defined, productivity should be added as an
ecosystem service where appropriate, and N leaching might be added as an
indicator of terrestrial nutrient enrichment. The characteristics of
sensitivity for terrestrial nutrient enrichment might be updated.

Sections of Table 2.3-1 still need to be filled in.

**[Chapter 3]{.underline}**

Page 3-4 lines 6 and 7: Check the wording. 30 to 70% of the animal
wastes can't be emitted as NH~3~. Should it read 30 to 70% of the N
losses from animal wastes?

Page 3-5 lines 10 to 15: Are there not any natural sulfur emissions in
and around Yellowstone or in other hot springs areas of the country? I
realize they may be inconsequential....

Pages 3-10 to 3-11: Question: Have all of the emissions reductions
resulting from past clean air legislation been realized? Will new
standards for ozone impact the likely deposition rates for N in the
future? Should such a discussion be included someplace in this document?

Chapter 3 doesn't include much on temporal changes in deference to the
maps of recent conditions. Those are fine, but I think some discussion
of where we have been and where we are going should be included in the
REA. Figures 2-59 or 2-103 from the ISA might be considered.

Page 3-12: Super and subscripts for charge are missing for SO~4~^-2^,
NO~3~^-^, and NH~4~^+^.

Question: Do the QMAC estimates of deposition to terrestrial systems
include foliar uptake of NO or NO~2~ near urban areas or along major
roadways where air concentrations are high enough to drive this pathway?

Table 3.2-2 is not well defined. It needs references.

I was disappointed by how much information was still not added to the
document (especially in this Chapter). We are being asked to provide
comment on a document that has a lot missing from it.

Captions to Figure 3.2-12, -13, and -14 need to be reworded to
"...nitrogen deposition by [source and]{.underline} quarter.... The most
interesting data in many cases has to do with the source of N forms
rather than the season of the year.

Figures 3.2-22, -23, -24, and -25 lack units (presumably kg/ha as for
N).

Captions to Figure 3.2-27 and -28 need to be reworded to "...sulfur
deposition by [source and]{.underline} quarter....

Page 3-54: Again...we don't have much to review yet.

Page 3-54 line 14: Reword as...."Public welfare effects associated with
direct exposure to NOx and SOx do not occur for current ambient
concentrations."

Page 3-54 line 23: The discussion on pages 1-10 and 1-11 seems to
disagree with this statement. The REA has already been defined to deal
with total reactive N.

The discussion of Data and Tools (Section 3.2.2.2) should probably be
presented earlier within Chapter 3 (perhaps around page 3-17).

Figures 3.2-35 and -36: Adding pixels for actual forest cover within
these maps would be useful to better reflect the actual extent of the
forest types. The coastal sage map (Figure 3.2-37) appears to be drawn
this way.

The text for Figures 3.2-39, -40, -41, -42, -43, and -44 is way too
small and the figure captions are inadequate. Please revise.

Page 3-70: At this point of the discussion it occurred to me that a case
study for an area dominated by NH3 deposition (i.e., Iowa, Minnesota,
Illinois) should probably be added to the REA. It wouldn't necessarily
show adverse effects, but it would complete the picture of total
reactive N deposition across the US. Page 3-103 of the ISA provides some
rationale for not including such a case study since agricultural areas
are overwhelmed by fertilizer additions. However, limited natural areas
(forests, prairies) are embedded within areas dominated by agriculture.

**[Chapter 4]{.underline}**: Incomplete and not reviewed.

**[Chapter 5]{.underline}**: Incomplete and not reviewed.

**[Chapter 6]{.underline}**

Figure 6.1-4: SRB should be defined in the figure caption.

Page 6-16 line 13: Remove the word "often". Fungi should probably also
be recognized as an important contributor to decomposition.

Increased nitrogen does affect the N content of green leaves. Is this
pattern well established for litterfall as well? Does the pattern differ
by vegetation type (i.e., trees, grasses, crops...)?

Page 6-17: Some of this material might be better left to the ISA
document. Lines 24 to 28 are not needed here.

Page 6-19: How the contribution of atmospheric deposition to upland
watersheds actually finds its way into waterways isn't clear. The
'filtering' effect of upland vegetation will vary tremendously from
location-to-location. This concept needs to be made clear in the
document.

Chapter 6 seems to lack summary conclusions:

What terrestrial systems are at risk? What percent of US land area?

What aquatic systems are at risk? What percent of US freshwater area?

**[Chapter 7]{.underline}**

Page 7-5 line 4: Replace "ecosystem health" with another term. It isn't
and perhaps can't be defined.

Page 7-5. Line 7: Change to "this is hypothesized to change...." Or
provide the references that show proof.

Page 7-5 line 21: Spell out CSS.

Page 7-7 Table 7.1-1: Replace "tree health" with a more meaningful term
or terms such as rate of growth, survival....

Page 7-8: The deposition levels proposed are appropriate for 'sensitive'
ecosystem, but not all ecosystems. A concept of one size does not fit
all will need to be worked into the conclusions of the REA. While
protection of sensitive systems may be a justification for a new
standard and level, it shouldn't be interpreted as having the same
effect on all areas of the US. That is, lowering inputs to areas
currently unaffected will not help them. Pages 3-78 and 3-79 of the ISA
include text that might be useful in clarifying this point.

Chapter 7 ends abruptly and seems incomplete.

**[Chapter 8]{.underline}**

Page 8-1 lines 14 and 15: The concept of achieving a standard based on a
"uniform level of ecosystem protection" seems at odds with the REA
document. The REA clearly states that the impacts of N and S deposition
are localized throughout the US and subject to the correct combinations
of deposition and susceptibility of the target terrestrial and aquatic
ecosystems.

Page 8-4 Figure 8.1-1: An air quality based estimate of total N and S
form deposition may not be sufficient information to judge impacts on
acid neutralizing capacity. A data layer on extant edaphic conditions is
needed. The deposition metric should probably also be enhanced to allow
for the estimation of biological immobilization (i.e., plant and
microbial uptake of some fraction of the total deposition).

Page 8-5 lines 1 to 3: Plant uptake needs to be included in this list.

Page 8-28 lines 2 to 9: I don\'t agree with the assumption that annual
accumulation of N inputs into wood increment can be ignored in this
analysis. Except for low or no productivity ecosystems this is a
significant sink for atmospheric N deposition that must be included in
the calculation of N available for other soil interactions.

Section 8. 4 is incomplete. More material is needed.

**Attachment 3**

Page 1 line 16: The phrase "a host of biogeochemical processes" is too
vague. Please expand this concept.

**Attachment 4**

Pages 2 and 3: Table 1.1-1 is not filled in. The term forest health
should be replaced.

Pages 12 and 13: Table 1.2-2 is not complete.

Page 31: The authors conclude that the simple mass balance method would
be used in the REA. What caused the authors to exclude the dynamic model
method? Lack of input data? Lack of validation?

Page 32: All evapotranspiration [does not]{.underline} occur at the
surface of the soil profile. Did the authors mean to imply evaporation
alone?

Page 42 line 17: Is the nitrogen immobilization mentioned here microbe
and plant or just microbe?

Figure 3.1-2 is missing units.

Page 53: The conclusions need work. The imbalances for Ca, Mg, and Al
suggested for forest soils are for localized sensitive systems. As
worded, the conclusions would be taken as a broad generalization for all
US ecosystems.

**Attachment 5:** No comment

[Attachment 6]{.underline}

Page 6: Table 1.2-2 is missing too much information to be fully
evaluated.

The studies cited and discussed for the CSS system should be closely
evaluated to determine which were based on manipulative studies capable
of determining cause-and-effect relationships versus those that
represent correlation studies for which relationships between known
variables and measured responses were assumed to be viable explanations
for adverse responses.

Studies highlighted in the ISA within Tables 3-15, 3-17, 3-18, and 3-19
might have a larger presence within the REA.

Figure 5.1-1 and -2: In my opinion the change in CSS seen in Figure -1
doesn't correlate very well with the dominant deposition patterns in -2.
How well does N deposition really correlate with change? How much does
land use change through time get in the way of the interpretation of N
deposition cause and effects in this case study?

Page 46 lines 4 versus line 15: The conclusion of "compelling evidence"
on line 4 does not seem to agree with the authors conclusion about the
research still underway on line 15. A word change seems in order.

Page 47 line 5: Is a modification of a valued ecosystem an ad

# Dr. Rudolf Husar

These comments are addressing primarily the 1st draft REA section:
Additional Effects. It also includes both general comments on the
approach to the REA as well as comments on sections of the the first REA
draft document.

## Comments on REA Chapter 6: Additional Effect

## 

1.  *Charge: In this chapter, we have presented results from some
    initial qualitative analyses for additional effects including the
    impact of sulfur deposition on mercury methylation, the impact of
    nitrous oxide on climate change, and the impact of nitrogen
    deposition on carbon sequestration. Are these effects sufficiently
    addressed in light of the focus of this review on the other targeted
    effects in terms of available data to analyze them?\
    *

Overall, this chapter is a good effort to illustrate additional,
non-ecological risks associated with anthropogenic N and S. Indirect
sulfur impacts are well captured by the problem of sulfur-induced
methylation of mercury, which then causes the effects in biota. The
interaction of nitrogen and carbon cycles is also properly illustrated
in the section on nitrogen-induced changes in the carbon sequestration.

The utility of the section on N~2~O impact on climate is less obvious.

This chapter is clearly a first draft. In the introduction it would be
helpful to provide more extensive rationale and criteria on the general
approach for selecting these Additional Effects. The rationale should
also include why some obvious additional effects on materials,
visibility and soil are not being considered. See further discussion
regarding these effects in the general comments on REA below.

### 6.1 Sulfur and Mercury Methylation 

Page 6-2 Line 10: Currently, i.e. since 1995, coal combustion was,
indeed, the main cause of anthropogenic mercury deposition. However,
prior to the regulatory action, around 1990, the anthropogenic mercury
emissions were dominated by other sources. Since deposited mercury has a
long residence time in soil and biota, much of the mercury methylation
occurs on the accumulated mercury from solid waste and other
agricultural, medical, residential usages.

Page 6-2 Line 13: Atmospheric mercury particles cannot possibly remain
in the atmosphere for more than two years. Even stratospheric particles,
have atmospheric residence time of less than two years. As with the rest
of ambient aerosols their atmospheric residence time is less than a week
in the planetary boundary layer and less than 3-4 weeks in the
mid-troposphere.

Page 6-3: Figure 6.1-1 represents the mercury cycle in the ecosystem. It
has many compartments and arrows representing the mercury flow and
transport/transformation processes. It is recognized that full
quantification of the mercury cycle through air, water, land and biota
is not possible at this time. However, it would be helpful, at least in
the text, to highlight the main flows and processes that dominate the
mercury cycle.

### 6.2 Nitrous Oxide 

Page 6-10: I find little justification for this section on the climate
impact due to anthropogenic N~2~O. As stated in the REA, N~2~O
contributes only about 6% of GHGs and the man-induced sources of
atmospheric N~2~O are only 10% of that, i.e. .6% of the GHGs.

Page 6-12 Line 31: The statement "that nitrogen addition increased N~2~O
emission by 215%" could benefit from a reference, compared to what?

### 6.3 Carbon Sequestration

Page 6-13: This section is an appropriate illustration of the
interdependence of nitrogen (sulfur?) and carbon cycles through air,
land, water and biota. The meta-analysis of existing literature is an
appropriate method for illustrating the interdependencies of the earth
system components and how changes in one set of environmental chemicals
may have intended and unintended consequences throughout the earth
system.

## General comments on the first draft REA 

This REA focuses on ecosystem welfare effects that result from the
deposition of total reactive nitrogen and sulfur." I concur with D.
Johnson that exclusive focus on "negative" effects of N and S deposition
is a flawed approach. It ignores the broader context and the full
dynamics of eco system responses to anthropogenic N and S deposition.
The beneficial effects of atmospheric S and N fertilization should also
be considered. This would also require definitions and/or conventions on
what's harmful and what's beneficial.

The man-induced nitrogen and sulfur deposition should be compared
quantitatively to the naturally occurring N, S flows. This will allow
estimating the significance of the man-induced stress, compared to the
naturally occurring values. By avoiding such broader context, the risk
assessment will be susceptible to criticisms of incompleteness and
possibly irrelevance to actual ecological risk estimation.

Page 1-2 Line 9: "In the Act (Section 109 B 2) the purpose of the
secondary NAAQS is to protect the public welfare from ***any*** known or
anticipated adverse effects..." Clearly, a secondary NAAQS includes all
welfare effects, not only the effects on the ecosystem. This fact is not
followed through in the REA and ISA.

Page 1-2 Line 19: "Adverse public welfare effects are based on an
assessment of how ecologically adverse impacts translate into adverse
impacts on public welfare" In this sentence as well as throughout the
REA welfare effects only include effects on ecosystem . As stated above
welfare effects include damage to materials, visibility, soils, climate.

## Specific comments on sections of the first draft REA

Page 1-13: Figure 1.3-2 representing the sulfur cycle should be made
more quantitative. The schematic Figure on the biogeochemical cycles of
sulfur is good. However, such a general Figure should be fortified by
adding magnitudes to the flows represented by the arrows. The transfer
rates, say over the US, can be estimated from the model runs, or based
on the empirical evidence. There is ample literature on biogeochemical
cycles that estimates the magnitude and importance of the various flow
rates.

Page3-5 Line 4: " ....combustion of fossil fuels by electric utilities
(\~66%) " This percentage is inconsistent with 71% EGU contribution
shown in the pie diagram, Figure 3.1-5.

Page 3-8: The section layout for 3.1.4 on Deposition starts with the
total deposition maps that are obtained by combining the model and
measured values. The description of the data and tools is given after
that. The customary approach is first to present the input data, tools
and methods and then the resulting computed values. Also, as discussed
at the October CASAC meeting, a separate section on CMAQ model
comparison with the observations for the key N, S species would be most
desirable.

Page 3-8: Section 3.1.4.1 on Nitrogen Deposition has many useful
quantitative numbers. However, the source and estimation methods for
these estimates are not well documented.

Page 3-10: The useful Figure 3.1-7 on oxidized N deposition should be
augmented with separate Figures for dry and wet deposition of N. The wet
deposition Figure should also compare the model and measured oxidized N
deposition.

Page 3-11: Ditto for reduced N deposition.

Page 3-12: Ditto for reduced S deposition.

Page 3-12: Section 3.2. could be subdivided such that the procedures for
model-observation data fusion has a more extended separate sub-section.

# Dr. Dale W. Johnson

As has been noted in previous reviews, I feel that this document is
unbalanced with respect to the effects of nitrogen deposition. Some very
simple facts need to be acknowledged and considered: 1) most terrestrial
ecosystems in the USA are nitrogen-deficient; therefore 2) increased
inputs of N are likely to cause growth increases; 3) growth increases
will almost certainly result in increases in carbon (C ) sequestration,
which in turn may have inadvertent benefits for the CO~2~ / climate
problem. This is not to diminish any statements about the negative
effects of N deposition, it is simply to add balance to this document.
As scientific reviewers, we have the responsibility to treat this and
all other subjects in a completely objective manner.

Below are some specific comments, some editorial in nature, some
technical in nature, and some where I see this lack of objectivity and
balance. Following that I will address the specific questions assigned
to me.

Specific comments:

p\. 1-13, lines 4-7: This is a balanced statement -- the review of
effects should really flow from this approach, considering both
increased productivity (which may be beneficial in some cases,
detrimental in others) and increased soil acidity and eutrophication.

p\. 1-15, line 14: 5.6 to 10 kg ha^-1^ yr^-1^? Can you really narrow
this down to one decimal point?

p\. 1-15, line 17: should include "and carbon sequestion" after "carbon
cycling".

0\. 1-17, line 13: From a soils point of view, the effects of NOx really
cannot be readily distinguished from the effects due to total reactive
nitrogen -- both are transformed in the soil rather extensively.

p\. 2-5, line 25: should add "timber production and carbon
sequestration" after "water". I note that timber production is mentioned
page 2-7, lines 19-20, but only in the context of how soil acidification
might negatively affect it. Soil acidification may well negatively
affect timber production, and the latter statement should stay as it is,
but increased N deposition will probably also increase timber production
and this needs to be acknowledged.

p\. 2-9, line 27: should add "timber production and carbon
sequestration" after "water quality"

Attachment 1, p. 3: I see Carbon Sequestration is listed as a potential
section 6.3 -- this is a good thing. Looking forward to seeing it.

Attachment 3, p. 1, lines 17-26: There needs to be a discussion of the
effects of mineral acid anions on soil solution (what Reuss calls
intensity effects, which can happen very quickly) in addition to the
discussion of how they affect soils (capacity effects, which take a long
time to occur). Reuss points out in his 1983 paper (Reuss, 1983) and in
our small book (Reuss and Johnson, 1985), both of which are cited later
in the Terrestrial Case Study, that Al^3+^ increases to the 3/2 power of
Ca^2+^, for example, as total mineral acid anion (e.g., nitrate and
sulfate) concentrations increase, and this happens even if there is NO
CHANGE IN THE SOIL AT ALL. Thus, if the soil is already acid, the
introduction of mineral acid anions will cause the immediate
mobilization of Al and acidification of soil solutions and probably
surface waters long before any change in the soil takes place.
Conversely, if the mineral acid anion concentrations are reduced, one
should see a very rapid recovery. In short, the soil solution can change
very quickly and almost independently of the soil, and this has major
implications for the effects of N and S deposition on aquatic
ecosystems.

Attachment 4, p. 1. lines 16-29: Same exact comment above applies here
and in this case, our small book is cited as a source but only part of
the story (the soil part, not the soil solution part) is reviewed. This
is an important point -- please include it in the next draft.

Attachment 4, p. 5, lines 10-17: Same comment as above here. It is not
necessarily true that "inorganic Al does not become mobilized until
after soil Ca is depleted" if the soil is already acidic, as many
unpolluted soils indeed are.

Question 4 Response: The revisions have improved the characterization of
adverse ecological effects, but I see no real consideration of the
potential positive effects of N deposition as yet. Timber production is
mentioned, but only in a negative context and I see little or nothing on
C sequestration. The one pager for section 5 refers to case studies and
gives no indication that this approach will be changed.

Question 4b: I see no discussion on effects on carbon budgeting as yet
-- have I missed something? I do see Carbon Sequestration is listed as a
potential section 6.3 -- this is a good thing. Looking forward to seeing
it.

Chapters 7 and 8 (Sent 19 Sept 2008)

Chapter 7: We are asked if the approach is technically sound to consider
"ecologically adverse effects". For the most part, yes, it is. However,
once again, I note that this section focuses entirely on negative
effects of N. This document should also consider cases where increased
production could be a positive effect -- such as on timber production
and C sequestration.

p\. 7-1, lines 21-27: This is a real mouthful. Can it be simplified and
broken into at least two sentences?

p\. 7-3, line 12: Why "inorganic and mineral acids"? They are basically
the same thing.

Section 7.1.4:

Chapter 8: Many questions are posed to the panel here and I will not
repeat them. I had problems with the conceptual framework for the
calculations, as noted below.

Section 8.3.3: I had a very difficult time following this section and do
feel like I ought to be able to. It would help a great deal if units
could be specified in the various equations and the assumptions were
clearly spelled out in the beginning. For example, is it assumed that
base cation concentrations will remain at pre-industrial levels? The
equations would suggest so, as would the statement on p. 8-29, lines
13-15. I cannot really agree with the assumption state here that
"pre-industrial base cation concentrations effectively set the long-term
capacity of the catchment to neutralize acidic deposition because it
represents the only source of base cation input that is sustainable over
the long-term". For one thing, soils in humid regions always naturally
acidify and therefore there is no long-term steady state base cation
flux until soils become extremely acidic-- it is always slowly
decreasing. I also think that the implicit assumption here that base
cation concentrations in streams will not increases over the long-term
in response to acidic inputs is flawed -- some soils have a very large
exchangeable base cation pool and could buffer such inputs for a much
longer term than the typical attention span of scientists and policy
makers, let alone the public.

p\. 8-29, lines 18-19: This statement makes no sense. At steady state,
the leaching rate of base cations is, by definition, equal to weathering
inputs, not "at lesser or greater rates".

# Dr. Donna Kenski

Overarching concerns: EPA staff have clearly made a great effort in
pulling this document (and its companion ISA) together, and should be
commended for the high-quality (and quantity) produced thus far.
Nevertheless its current incomplete status and the pressing schedule
make it hard to see how all the remaining tasks can be completed, and
reviewed, in sufficient time to meet the predetermined deadlines. Staff
and contractors to EPA need to be realistic in judging how much can
really be done in the remaining months. If it is time to set priorities,
perhaps that is something that can be discussed at this meeting.

The CAA requirement that the secondary standard be in the form of a
concentration standard is going to require us to tolerate a much higher
level of uncertainty than usual in the standard setting process, because
of the need to employ multiple models to characterize the
concentration-deposition-ecological effect-ecological indicator linkage.
Consequently, the REA in general needs to be much more comprehensive and
transparent in describing the levels of uncertainty encountered at each
of these steps and their impacts on overall uncertainty. For example, so
much hinges on the CMAQ estimates of deposition, and yet there is little
information given in the REA or the ISA on CMAQ performance. It seems
from the ISA that CMAQ has really only been evaluated in terms of its
annual estimates of aerosol deposition, and those are accurate to within
a factor of 2. No CMAQ performance evaluation is given for deposition to
specific locations, particularly locations that share characteristics of
the sensitive areas focused on in this analysis. Likewise, none is given
for measurements with a shorter time frame than annually. A clear-eyed
discussion of these uncertainties for CMAQ and for the other models used
to support the REA (MAGIC, ASTRAP, Sparrow) is a critical component that
needs to be incorporated.

Charge Questions: Scope of the Review

1.  *Is the review appropriately focused in terms of the targeted effect
    variables and in terms of characterizing the important atmospheric
    and ecologic variables that influence deposition and ultimately the
    ecologic impacts of nitrogen and sulfur? Does the Panel have any
    further suggested refinements at this time?*

Generally, the review seemed to focus on appropriate variables, although
as noted above, the complete scope may be too broad to accomplish before
the court's deadline. The policy-relevant questions posed in Sec. 1.4
weren't actually addressed directly (perhaps it's still too soon, given
the incomplete case studies) but I did note that questions 3 and 4 of
that list (i.e., to what extent do receptor surfaces influence dry
deposition, and can effects of NOx be distinguished from effects due to
total reactive nitrogen) did not seem to be discussed or addressed by
any of the case studies in Attachments 3-6, although Chap. 3 did present
a nice graphical characterization of the areas and their relative
proportions of NOx vs total and other forms of N nitrogen. However, most
of that was modeled data and little comparison to measured values was
presented for comparison. Perhaps more of that is coming in the second
draft, since there were lots of missing sections to Chap. 3.

Similarly, the list of issues on p. 1-20 should include evaluating the
impacts of atmospheric deposition relative to other paths (nitrogen
runoff from agricultural lands, for example). This might be what is
meant by the last bullet, but it wasn't clear; perhaps it could be made
more explicit.

Air Quality Analyses (Chapter 3)

1.  *To what extent are the air quality characterizations and analyses
    presented in Chapter 3 technically sound, clearly communicated,
    appropriately characterized and relevant to the review of the
    NAAQS?*

The analyses in Chap. 3 could more accurately be described as modeled
estimates of air quality, rather than air quality characterizations,
which I think of as based on measured data. While the graphs were useful
and logically presented, there was very little measured data given for
comparison, so it is not possible to judge their 'soundness'. Combined
with the lack of CMAQ validation discussion (mentioned above), it
becomes more important to see these in the context of measured data as
well. But this may be premature if the next draft is meant to include
such comparisons.

I would have liked more discussion of the monthly patterns of deposition
shown, for example, in Figs 3.2-14 through 3.2-19. Clearly wet
deposition is driven largely by precipitation, but what drives the other
components of deposition? Are these emission patterns or meteorological
patterns or biological activity patterns? Some discussion of the
importance of these various temporal scales for the ecological effects
modeled is probably appropriate as well. A minor complaint on the
communication of the results: the color scheme for Figures like 3.2-6
etc. is not intuitive. The scheme used was almost a rainbow-like scale,
which is easy to interpret and would have been fine, but instead green
was sandwiched between yellow and orange, breaking the natural
progression of colors (red -\> orange -\> yellow) that most of us have
internalized and making it harder to visually establish a continuous
gradient of concentration changes.

2.  *Section 3.2.1 describes an approach for evaluating the spatial and
    temporal patterns for N and S deposition and associated ambient
    concentrations in the case study locations. This document includes
    the analysis for the Adirondacks case study. Does the Panel agree
    with this approach and should it be applied to the other case study
    areas?*

It was a sound approach and a useful exercise that may give as clear a
picture of deposition as we're likely to get. With the additions/changes
noted above, I would welcome this analysis for the other areas.

3.  *Section 3.2.2 describes the relative contributions of ambient
    emissions of nitrogen and ammonia to nitrogen deposition for the
    case study areas. To what extent is the approach taken technically
    sound, clearly communicated, and appropriately characterized?*

This was an interesting exercise that was very useful in establishing
the relative importance of NOx and NH3 emissions to overall N deposition
and the relative responsiveness of deposition to changes in emissions.
It was very helpful to establish this kind of personal internal
calibration in a strong visual way. It is also a critical comparison to
establish in making a strong case for the ability of a NOx-concentration
based standard to be sufficiently protective, despite our understanding
that impacts are really driven by total nitrogen. Given the lack of
spatial and temporal variability in the contributions of NOx to oxidized
N and NH3 to reduced N, those maps probably don't need to be shown, just
described instead. The results look perfectly logical and convincing,
although I resist accepting these results completely until seeing
further documentation of CMAQ's performance. The REA notes that the RSM
has been validated for PM and O3, but it's not clear whether that
validation translates to deposition parameters as well. Presumably the
missing section 3.2.2.5 on uncertainty will address some of these
issues. Again, as above, the color scale on all these plots is
counterintuitive. Using the color red to depict no impact and green for
100% impact is contrary to general mapping conventions and at least in
my case, caused me to continually misinterpret the plots.

Case Study Analyses (Attachments 2-6)

6.  *Att. 2: Are the national geospatial datasets chosen adequate to
    identify sensitive areas? Are there other data sets that have not
    been identified by this analysis that we should consider? Does the
    panel agree with this approach or can they suggest alternatives?*

I have no knowledge of other datasets that could be useful to this
effort. Some of the data were quite old (1971 for the range of red
spruce) and caused me to wonder whether the range could have changed
significantly in the intervening 37 years. Perhaps the authors could
comment on the issues that might be affected by such old observations.
Similarly, the dataset on acidophytic lichens was clearly not complete,
or at least spatially representative, and impacts the results. One can't
protect lichens that haven't been identified as sensitive, and the
current map, which shows clusters of lichens within some states but none
in neighboring states, strongly implies that some species have not been
identified in those neighboring states.

7.  Att. 3: re MAGIC model to evaluate ANC levels in selected streams
    and lakes in Adirondacks and Shenandoahs. To what extent is the
    approach taken technically sound, clearly communicated, and
    appropriately characterized?

The selection of MAGIC is appropriate, but this section was poorly
written and extremely confusing, especially the modeling approach and
description of MAGIC and ASTRAP. I think the dates given for scaling the
historic data to deposition are wrong in several places, but the text
was too convoluted to tell for sure. Also it would have been nice to see
a map or at least a better description of how the ASTRAP sites are
connected to the MAGIC sites. The classes and descriptions of ANC limits
kept changing within the text and figures and should be made consistent.
The discussions of critical load frequently mixed up the concepts of
greater than-less than and above-below, adding to the confusion. It was
very difficult to wade through the errors and try to make sense of what
was really being accomplished here. The approach may be sound, but can't
be assessed on the basis of what was presented. It was certainly not
communicated or characterized in a satisfactory way.

8.  *Att. 4: use of SMB model to evaluate current deposition on forest
    soil ANC for sugar maple in Kane Experimental Forest and red spruce
    in Hubbard Brook Experimental Forest. To what extent is the approach
    taken technically sound, clearly communicated, and appropriately
    characterized?*

The selection of the study area was reasonable and the description of
the method was clear. Without results it's not possible to say too much
more. The Table 3.1-2 had some numbers that need to be explained
further, however. The range of critical N loads vary by a factor of 10
over the 3 study periods shown, and each of the methods gives very
different results. Why the big difference? The text mentions biomass
changes; is this the sole reason? Is this magnitude of change in biomass
typical? How comparable are the methods? The text in Section 1.1.1 was
unnecessarily repetitive and could be tightened up; no need to quote the
ISA at such length.

9.  *Att. 5: Aquatic nutrient enrichment---evaluate how changes in N
    deposition affect the eutrophication index in two estuaries:
    Chesapeake Bay and Pamlico Sound. To what extent is the approach
    taken technically sound, clearly communicated, and appropriately
    characterized?*

10. *Att. 6: Terrestrial nutrient enrichment---evaluate effects of N
    deposition on CSS community in California and mixed conifer forests
    in San Bernardino and Sierra Nevada Mountains. To what extent is the
    approach taken technically sound, clearly communicated, and
    appropriately characterized?*

Additional Effects (Chap. 6)

1.  *Impacts of S deposition on Hg methylation, impacts of NO on climate
    change, and impact of N deposition on C sequestration. Are these
    effects sufficiently addressed in light of the focus of this review
    on the other targeted effects and in terms of the data available to
    analyze them?*

This was an adequate review of these effects. The focus appropriately
belongs on acidification and enrichment effects.

Synthesis and Integration of Case Study Results into the Standard
Setting Process (Chap 7)

1.  *Purpose is to summarize the case study results and characterize the
    relationship between levels of an ecological indicator and the
    associated degree of ecologically adverse effects. To what extent is
    the approach taken technically sound, clearly communicated, and
    appropriately characterized? Does the Panel have suggested
    refinements?*

I'm still uncertain about exactly how the case studies ultimately are
used. Are they merely for scientific support and justification, or do
the model results from them get incorporated eventually into a
quantitative relationship that can be plugged into the framework
presented in Chapter 8? I think the confusion stems from the incomplete
nature of this chapter. When it is fleshed out in the next version with
real data, the application of the case study results should be obvious.

Considerations in the Structure of the NOx/Sox Secondary Standard (Chap
8)

1.  *Is the suggested overall structural framework for a secondary
    standard technically sound and logically presented?*

The recently added Chapter 8 was very lucid and well written, presenting
a helpful blueprint for how to move from ambient concentrations to
possible secondary standard. I found no technical or logical fault in
it.

2.  *Is the description and development of the deposition transformation
    function (Fig 8.1.1) between air quality indicators and the
    deposition metric clear and technically sound?*

3.  *Is the description and development of the ecological effect
    function (Fig. 8.1.1) between the deposition metric and the
    ecological indicator clear and technically sound?*

4.  *Does the discussion adequately capture the potential use of
    categorical variables versus continuous variables when accounting
    for the variability of atmospheric, landscape, and ecological
    factors?*

These were all fine.

5.  *Are there any key elements missing from the framework?*

There needs to be a more complete discussion of how a standard can
accommodate geographic variation; i.e., how to equitably control NOx and
Sox to adequately protect sensitive areas without overcontrolling in
areas that are far less sensitive to acid deposition. Section 8.3.1 made
reference to varying factors within the transformation function by
location, and the fact that deposition loads will vary by location, but
it was not clear from the text how this translates to variation in the
standard. It seems that the standard must account for different
concentrations in different regions, but how that is specified is still
pretty fuzzy.

Another big piece that is missing is the discussion of CMAQ (or other
model) uncertainties. It was interesting that this is the first place in
the REA (Sec. 8.3.2.1.2) where CMAQ performance evaluation (or the lack
thereof) is mentioned. Given the very heavy reliance of the REA analyses
on CMAQ (a necessary reliance, admittedly), it is critical to have its
performance characterized as thoroughly as possible so that the
Administrator and others can assess a proposed standard's potential for
success.

Section 8.3.2.2.2 leaves aggregation methodology as an open research
issue. Does this mean it will be resolved in the next draft by work the
staff is doing? If not what are the implications of leaving this issue
unresolved?

6.  *Does the framework need to be expanded or revised to accommodate
    the appropriate consideration of ecological indicators besides ANC
    when developing a secondary NAAQS for NOx and Sox*

Isn't that the point of the case studies? It seems premature to answer
this question until those results are complete. ANC seems adequate for
acidification effects, but the other case studies weren't really far
enough along to evaluate. The chapter should include some discussion of
how the standard might account for multiple indicators.

7.  *Does the panel have any further suggested refinements at this
    time?*

Section 8.3.2.4 needs additional attention. It mentions possible work on
MCIP and CMAQ to incorporate measurements, which would be great and I
highly encourage. But is it really possible to produce results and
incorporate them into the next draft?

Section 8.3.3 on the deposition-indicator links could benefit from a
discussion of how influential the various parameters are on the outcome,
at least in a qualitative sense. It would help the reader (and
presumably the Administrator) evaluate which are the critical parameters
controlling the relationship. There also needs to be some discussion or
graphical analysis of the geographic sphere of influence of NOx/SOx
concentrations on each sensitive area. For example, if the indicator
were set at an ANC of 50 ueq/L in the Adirondacks, how much would NOx
and Sox need to be reduced to reach that ANC, and over what geographic
area? Somewhere the document needs to lay out that visual frame of
reference for the geography of influence on the sensitive areas. We know
that deposition is some function of distance, and that high
concentrations close to a sensitive receptor will be more influential
than the same concentrations far way; how far away is far enough to have
negligible impact?

Specific comments, typos, etc.:

> p\. 3-3, Fig 3.1.2 (also Fig 3.1-5) Avoid use of pie charts, as they
> make it difficult to make quantitative comparisons. Bar charts are
> almost always preferable. The use of 3-D unnecessarily complicates
> these figures and also makes it more difficult to visually compare the
> slices of the pies.
>
> p\. 3-4, lines 12-13: Fig. 3.1-4 actually shows facilities, not annual
> emissions by state.
>
> p\. 3-6, lines 14-16: Is the NEI fire inventory error corrected here?
> If not, a statement about the correct magnitude of fire emissions
> should be added.
>
> p\. 3-8, line 9: Figure 3.1-6 shows total N deposition in Ohio and
> Pennsylvania of \>20 kg/ha/yr, definitely much more than the 9.2-9.6
> kg/ha/yr cited here. Which is correct? This and the following figs
> 3.1-7,8,and 9 are nice but the colors are difficult to distinguish in
> the printed version.
>
> p\. 3-50, line 1: ARD -\> ADR
>
> p\. 3-57, line 10: remove question mark
>
> p\. 6-7 caption to Fig. 6.1-3: watershed should be plural
>
> p\. 6-18, line 6: Not clear what 'further stabilizing soil carbon
> compounds' actually means. Do they then have longer lifetimes?
>
> p\. 6-23, line 12: Onondagal -\>Onondaga
>
> p\. 7-1, line 28: area should be plural
>
> p\. 8-14: Equation numbers don't follow the text
>
> Attachment 2, p. 2, line 14: remove 'is'
>
> Attachment 2, p. 3, line 19: is this really 51 inches, or should it be
> cm, as 4.1.11 says about this same dataset?
>
> Attachment 2, p. 7, line 17: remove 'Sulfur Containing'
>
> Attachment 2, p. 7, line 26: remove 'Nitrogen Containing Chemical
> Species'
>
> Attachment 2, p. 8, line 9: remove 'deposited'
>
> Attachment 2, p. 11, line 8: remove 'Nitrogen Containing Chemical
> Species'
>
> Attachment 2, p. 11, line 18: Containing -\> Including
>
> Attachment 2, p. 16, line 4: remove meter
>
> Attachment 3: fix the subscripts and superscripts throughout. Too many
> grammar errors and typos to enumerate here -- this whole section needs
> careful editing.
>
> Attachment 3, p. 6, line 24: deposition is more like 17 and 13 kg/ha
> according to the Figure 3.1-1, not 15 and 10.
>
> Attachment 3, p. 8, line 4: deposition is more like 18 and 11 kg/ha
> according to Fig. 3.2-1. This makes me distrust the % declines in
> these species, here and on p. 6, but I didn't recalculate them.
>
> Attachment 3, p. 12, Fig. caption: 12 streams are shown, not 13. Lots
> of other typos in this caption.
>
> Attachment 3, p. 16, line 26: \>50 should be \<50
>
> Attachment 3, p. 17, lines 6-8: Fig. 4.1-2 doesn't imply that biota
> are not often harmed below and ANC of 100, only that the harm is less
> severe than for lower ANC
>
> Attachment 3, p. 17, line 12: It doesn't make sense to say that an ANC
> of 0 protects surface waters from becoming acidic. waterbody
>
> Attachment 3, p. 17, line 17: change 'deposition -- critical load' to
> 'deposition less than critical load'
>
> Attachment 4, p. 1, line 6: should be 'sulfur loads *to* and effects
> *on* a chosen...'
>
> Attachment 4, p. 10, line 4: on -\> at
>
> Attachment 4, p. 11, line 16: not clear, reword
>
> Attachment 4, p. 11, lines 21-22: not clear, reword
>
> Attachment 4, p. 23, line 22: HBEF
>
> Attachment 4, p. 25, line 8: litterfall
>
> Attachment 4, p. 33, line 17: put weathering on its own line
>
> Attachment 4, p. 38, line 13: Arrhenius
>
> Attachment 4, p. 48 and 49: It would be helpful for these figures to
> include the HBEF as well; its very hard to place it accurately given
> the map on p. 21

# Dr. Naresh Kumar

COMMENTS ON SECTION 6.1. SULFUR AND MERCURY METHYLATION

GENERAL COMMENTS

The section begins with a segment on the chemistry and physics of
mercury atmospheric transport, fate, and deposition, followed by a more
detailed segment discussing the chemical determinants of mercury
methylation.

The two segments of the section differ greatly in their accuracy,
completeness, and understanding of mercury chemistry and environmental
behavior. While the second part, on mercury methylation specifically, is
generally complete and accurate, the first, background, segment has a
number of factual errors, misinterpretations, and erroneous conclusions
in it.

As two examples, the first segment presents an erroneous picture of the
behavior of elemental mercury (or Hg^0^) in the environment, and of
"methylmercury" (dimethylmercuric salts) in organisms. In the first
case, Hg^0^ is presented as being "reduced" in surface ecosystems to
become methylmercury; in reality, Hg^0^ is the reduced form, and plays
no part in methylation, which occurs through bacterial action on the
oxidized form, divalent mercury (or Hg^+2^ in the text). In the second
case, methylmercury is openly stated to be "lipophilic," or
preferentially attached to fatty tissues in fauna, when in fact
methylmercury is lipophobic and associated with protein sulfhydryl
groups, in muscle tissue.

The entire section need to be thoroughly reviewed and rewritten from the
beginning to more accurately reflect our basic understanding of mercury
chemistry, transport, and fate in the environment. Specific comments on
the text follow.

SPECIFIC COMMENTS

-   To date, there has been *no* unequivocal demonstration of sulfate
    limitation in US or global waterways such that natural sulfate
    addition or subtraction alone has produced a change in methylation
    rates or mercury in fish. Such demonstrations have occurred only in
    experimental manipulations of microcosm ecosystems. Since fish take
    up only a fraction of the methylmercury in the water column and
    biota of lower trophic levels, there is always an excess of MeHg in
    studied water bodies. And downtrends in sulfate addition have always
    been matched by downtrends in divalent mercury deposition, so that
    it is not possible to separate sulfate availability from divalent
    mercury burden.

-   It is mentioned that *"Mercury concentrations have increased
    approximately 2 to 5 times since the onset of the industrial
    revolution and appear in even the most remote locations on the Earth
    (Munthe et al., 2007; U.S. EPA, 2006)."* The accepted global average
    ratio of atmospheric mercury mass now compared to the period prior
    to the Industrial Revolution is in the range of 2 to 3, not 2 to 5.
    Ratios higher than 3 can be found in local, single-instance
    measurements of concentrations in, e.g., an ice core, but these are
    characteristic of individual locations and not the global balance of
    mercury.

-   It is stated in the text that *"In the United States, the primary
    source of mercury to ecosystems is atmospheric deposition due to
    coal combustion (e.g., coal-fired electric utilities). Other sources
    include municipal waste combustion, medical waste incineration,
    chlor-alkali plants, and industrial boilers."* This sentence appears
    to propagate the common misconception that mercury emissions
    (anywhere) are proportioned exactly the same as mercury deposition
    (anywhere else). This is obviously incorrect, since both total and
    wet deposition of mercury at any location on earth (or in the United
    States) is made up of contributions from hundreds of sources at
    widely varying distances upwind, and is not linearly proportional to
    the fraction of total emissions each source, or source type, makes
    up. Therefore, it should be noted that a significant amount of
    mercury depositing within the United States originates in other
    countries, primarily mainland Asia. The sources of mercury
    depositing to U.S. ecosystems varies widely, both geographically and
    by source, depending on the proximity of U.S. sources and the
    precipitation climatology of the setting.

-   It is mentioned that, *"Depending on the particulate association and
    oxidation state, atmospheric mercury particles can remain suspended
    in the atmosphere for more than 2 years (Evers et al., 2007; U.S.
    EPA, 2006)*." This sentence should be rewritten or *deleted.* There
    is no relation between "particulate association" (an unexplained
    term) and oxidation state for mercury; most of the mercury bound to
    particles is divalent mercury (or "Hg^+2^" as used in the report).
    But the statement that such particle-bound mercury has an
    atmospheric lifetime of more than 2 years is not true; due to
    gravitational settling, coagulation, etc., Hg~p~ has an average
    lifetime in the atmosphere of several days to about two weeks, no
    more. And no source of mercury emissions to the atmosphere issues
    more than about 3% of mercury mass in the form of particle-bound
    mercury, in any case. It is suggested inserting something like this:
    *"There are three primary forms of mercury in atmospheric sources of
    the substance: elemental mercury, reactive gaseous mercury, and
    particle-bound mercury. Once emitted, the three forms behave very
    differently in the atmosphere and deposit over very different
    geographic patterns. It generally takes hundreds or thousands of
    miles for half of the emitted gaseous elemental mercury to deposit
    to ground level, while half of the reactive gaseous mercury will
    deposit within about 150 miles of the source. Particulate-bound
    mercury, generally 3 percent or less of the emitted mercury mass,
    deposits in intermediate patterns (M. Cohen, 2004)."*

-   *The text states that, "When deposited into terrestrial and aquatic
    ecosystems, elemental mercury is oxidized to reactive mercury (Hg+2)
    (Ambrose et al., 2005; U.S. EPA, 2006)."* A number of statements
    need to be corrected or nuanced in this passage. Any "deposition" of
    elemental mercury occurs by gas-phase transfer at ground level from
    regions of higher concentration (that is, the atmosphere) to regions
    of lower concentration (to plant stomata, soil pores, interstitial
    spaces, etc.), basically a down-gradient mass transfer. There is
    nearly no oxidation of elemental mercury to the divalent form
    occurring at the ground surface; more likely is removal of elemental
    mercury back to the atmosphere by revolatilization, or evasion.
    There may also be a net output of elemental mercury from the surface
    by insolation (solar radiation) producing photoreduction of divalent
    mercury, or demethylation and photoreduction of monomethylmercuric
    halides.

-   The entire sentence where methylmercury is stated to be "lipophilic"
    needs to be corrected. First, mercury cannot be "reduced and
    methylated to methylmercury"; the reduced form of mercury is the
    insoluble elemental mercury, Hg^0^; because of its insolubility in
    water, it is unavailable to sulfate-reducing bacteria for the
    methylation process. Of the "deposited mercury pool," typically half
    or more is (wet-deposited) divalent mercury, most of the remainder
    dry-deposited elemental mercury; of the amount of divalent mercury
    dissolving in water bodies, between 1% and 10% may be methylated and
    dissolved in the water column. Of this 1% to 10% (depending on the
    particular water chemistry; higher fractions for more anoxic
    waterways), perhaps 10% of that (or 0.1% to 1% of the dissolved
    divalent mercury) may be taken up into the food web. Second, mercury
    is most certainly *NOT* lipophilic, but rather ***lipophobic***: it
    attaches to protein-based sulfhydryl groups and resides primarily in
    muscle and nerve tissue ("fish flesh"). This distinction is
    important because it is the root of the finding that cooking fish
    which may be mercury-laden will in fact not decrease, but increase,
    the concentration of the mercury in the cooked product. Any fat that
    is cooked off is mercury-free, and the lower weight cooked fish
    remaining has the same mass of mercury as prior to cooking, but in a
    lower-weight portion of fish (with some fat and water mass cooked
    off), hence higher net mercury concentration.

-   There seems to be a faulty reference in the sentence ***"**The
    majority of U.S. waters are sulfate-limited (Harmon et al., 2007);
    therefore, decreases in sulfate are likely to promote decreases in
    methylmercury."* Harmon et al., 2007, "Using Sulfate-Amended
    Sediment Slurry Batch Reactors to Evaluate Mercury Methylation,"
    *Arch. Environ. Contam. Toxicol. 52*, 326--331 (2007); \[DOI:
    10.1007/s00244-006-0071-x\] does not have a single word to say about
    sulfate-limited waterways. The term "-limited," in fact, occurs only
    once in the document, in the introduction, with no reference to the
    state of U.S. waters.

# Dr. Myron J. Mitchell

**General Comments** (For these general comments my responses are in
*italics*.)

*The document and associated attachments are extensive and it is a major
challenge to provide a*

*cohesive approach to presenting this information. I recognize the
difficulty and complexity of*

*pulling all of this together. The potential for providing clearer
linkages in this document to the*

*"Integrated Science Assessment for Oxides of Nitrogen and Sulfur --
Environmental Criteria"*

*may help maintain focus and reduce the size of the document. More
consistency is needed in the*

*use of terms such as oxides of sulfur, oxides of nitrogen, sulfur
oxides, nitrogen oxides, SO~x~, NO~x~, etc. Also, in the document there
are differences in criteria for sensitivity of various parameters such
as ANC. Careful editing would help focus the document and reduce
redundant information. The draft document has many noun trains such as
"draft revised criteria document".*

**Responses to Charge to the CASAC NO~x~/SO~x~ Secondary Review Panel**

Scope of the review (Chapters 1 and 2):

1\. Chapters 1 and 2 provide the background, history, and the framework
for this review,

including a discussion of our focus on the four key ecological effect
areas (aquatic acidification,

terrestrial acidification, aquatic nutrient enrichment, terrestrial
nutrient enrichment). Is this

review appropriately focused in terms of the targeted effect areas and
in terms of characterizing

the important atmospheric and ecological variables the influence the
deposition and, ultimately,

the ecological impacts of nitrogen and sulfur? Does the Panel have any
further suggested

refinements at this time?

*Chapter 1 needs a more balanced introduction with respect to the
impacts of S and N gaseous*

*constituents and deposition with greater attention earlier in each
chapter on the effects of N on*

*ecosystem structure and function including the alteration of species
composition. In Chapter 2*

*(Section 2.4) the description of errors in the analyses needs a more
rigorous approach that more*

*clearly identifies specific issues related to sources and amount of
errors. In its current form*

*Chapter 2 provides very broad descriptions that do not clearly identify
the major sources of*

*error that are important to the current assessment. Possibly reference
to subsequent chapters*

*that more clearly delineate these errors would be helpful.*

Air quality analyses (Chapter 3):

1\. To what extent are the air quality characterizations and analyses
presented in Chapter 3

technically sound, clearly communicated, appropriately characterized,
and relevant to the review

of the secondary NAAQS for NO~x~ and SO~x~ ?

*The terminology and analyses associated with "policy-relevant
background concentrations" is*

*confusing. Some consideration is needed of the adequacy of the current
monitoring network in*

*evaluating air quality especially in relationship to measurements in
urban settings.*

2\. Section 3.2.1 describes an approach for evaluating the spatial and
temporal patterns for

nitrogen and sulfur deposition and associated ambient concentrations in
the case study locations.

This draft document includes the analysis for the Adirondacks case
study. Does the Panel agree

with this approach and should it be applied to the other Case Study
Areas?

*This can be a helpful approach. However, within each of these regions
there have been other*

*measurements made of associated parameters including precipitation
amount, atmospheric*

*deposition, etc. It does not appear that any substantial attempts are
being made in this document*

*to compare these current results with previously published results?
There is a major emphasis*

*on providing both spatial and temporal patterns using the CMAQ modeling
results. Shouldn't*

*these modeling results be compared with other results of deposition
measurements for this*

*region? Having some comparisons with these other measurements would be
helpful in evaluating*

*the CMAQ deposition estimates. The issues and problems associated with
making measurements*

*of air pollution concentrations and converting them to deposition by
various inferential*

*procedures needs to be clearly articulated.*

3\. Section 3.2.2 describes the relative contributions of ambient
emissions of nitrogen and

ammonia to nitrogen deposition for the case study areas. To what extent
is the approach taken

technically sound, clearly communicated, and appropriately
characterized?

*Clarification is needed on the relative importance of the emission
sources including the accuracy*

*of these emission estimates, atmospheric chemical conversions and the
estimates of deposition*

*velocities in evaluating the results of these model outputs. Too much
of this section describes*

*model output with little supporting evidence of the relationships
noted.*

Case Study Analyses (Attachments 2-6):

*These attachments are extensive and it would be most helpful if they
were more targeted to the*

*issues and needs of the "Risk and Exposure Assessment to Support the
joint Review of the NO~2~*

*and SO~2~ Secondary National Ambient Air Quality Standards".*

1\. Attachment 2 presents a GIS analysis to define geographical areas
that are sensitive to

acidification and nutrient enrichment. Are the national geospatial
datasets chosen adequate to

identify sensitive areas? Are there other data sets that have not been
identified by this analysis

that we should consider? Does the Panel agree with this approach or can
they suggest

alternatives?

*In general, the selected regions and associated data sets appear to be
appropriate for this*

*analysis.*

2\. Attachment 3 presents our current progress on evaluating the effect
of aquatic

acidification in the Adirondacks. It describes the use of the MAGIC
model to evaluation ANC

levels in selected lakes and streams in the Adirondacks and Shenandoahs.
To what extent is the

approach taken technically sound, clearly communicated, and
appropriately characterized?

*There is some differences in the deposition estimates being used for
estimates using the MAGIC*

*versus other approaches in the document (e.g., ASTRAP versus CMAQ).
Will this result in some*

*issues relating to congruity of analyses in the document? These
analyses have a specific focus*

*on the Grimm and MAGIC models. There have been other efforts to
evaluate acid*

*rain/biogeochemical responses in each of these sites (especially the
Adirondacks) and hence it*

*would be useful to include some of these other results to indicate
either differences or support of*

*these current modeling efforts. In these discussions different levels
of ANC are suggested that*

*differ than for other sections in the document. A more consistent
approach is needed on setting*

*the ANC limits of concern with respect to sensitivity to acidification
and recovery from*

*acidification. Possibly a separate section is needed with respect to
ANC and its application to*

*evaluating acidity and the various levels that are used. This would
need to be included before*

*the case studies section.*

3\. Attachment 4 presents our current progress on evaluating the effect
of terrestrial

acidification. It outlines a plan to use the Simple Mass Balance Model
to evaluate current

deposition levels on forest soil ANC for sugar maple in the Kane
Experimental Forest and red

spruce in the Hubbard Brook Experimental Forest. To what extent is the
approach taken

technically sound, clearly communicated, and appropriately
characterized?

*This portion of the document is highly uneven with in some cases
substantial detail provided and*

*in other places there are broad generalizations. This makes it
difficult for the reader to*

*ascertain the salient points.*

4\. Attachment 5 presents our current progress on evaluating the effect
of aquatic nutrient

enrichment. It outlines a plan to evaluate how changes in nitrogen
deposition affect the

eutrophication index in two estuaries: the Chesapeake Bay and Pamlico
Sound. The analysis will

model one stream reach (Potomac River and Neuse River) to determine the
impact on the

eutrophication index for the estuary. To what extend is the approach
taken technically sound,

clearly communicated, and appropriately characterized?

*The Chesapeake Bay has been the focus of considerable efforts relating
to the effects of nitrogen*

*loading on eutrophication. There have been extensive investigations on
this site and there are*

*extensive data sets that can be used in the analyses. A major drawback
of this site, however, is*

*that it is not likely that atmospheric nitrogen loading is a major
component of the total nitrogen*

*loading. Hence, the Chesapeake Bay will not be very sensitive to
changes in atmospheric*

*nitrogen inputs. Although the information on the Neuse River is less
extensive, there are similar*

*problems with the overall importance of atmospheric N loading. In
attachment 5, page 20 it is*

*indicated that "Previous studies have estimated that wet atmospheric
deposition of nitrogen (WAD-N), as deposition of dissolved inorganic
nitrogen (DIN: NO^-^~3~ , NH~3~ /NH^+^ ) and dissolved*

*organic nitrogen, may contribute at least 15% of the total externally
supplied or "new" nitrogen*

*flux to the coastal waters of North Carolina".*

5\. Attachment 6 presents our current progress on evaluating the effect
of terrestrial nutrient

enrichment. It describes an approach to evaluate the effects of nitrogen
deposition on the Coastal

Sage Scrub community in California and in mixed conifer forests in the
San Bernardino and

Sierra Nevada Mountains. To what extent is the approach taken
technically sound, clearly

communicated, and appropriately characterized?

*The selection of the Coastal Sage Scrub community in California and in
mixed conifer forests in*

*the San Bernardino and Sierra Nevada Mountains needs some further
justification versus other*

*regions including the alpine and subalpine communities of the eastern
slope of the Rocky*

*Mountains in Colorado. These sites in California are certainly
important and interesting sites,*

*but it may be difficult to separate the effects of nitrogen deposition
versus other air pollution*

*components, especially ozone.*

Additional Effects (Chapter 6):

1\. In this chapter, we have presented results from some initial
qualitative analyses for

additional effects including the impact of sulfur deposition on mercury
methylation, the impact of nitrous oxide on climate change, and the
impact of nitrogen deposition on carbon sequestration. Are these effects
sufficiently addressed in light of the focus of this review on the other
targeted effects and in terms of the available data to analyze them?

*These descriptions seem adequate, but certainly the issues go beyond
those associated with*

*carbon sequestration. Some additional discussion of the importance of
mercury being found in*

*other components of the ecosystems including song birds should be
included.*

The purpose of Chapter 7 is to summarize the Case Study results and
characterize the

relationships between levels of an ecological indicator and the
associated degree of ecologically

adverse effects. To what extent is this approach technically sound,
clearly communicated and

appropriately characterized at this point of the review? Does the Panel
have any further

suggested refinements at this time.

*In its current form this Chapter is highly descriptive. Future
revisions will need to include more*

*specific quantitative results that show a clear relationships to the
assessment.*

Chapter 8 begins to explore how a secondary NAAQS might be structured to
address the targeted

ecological effects discussed in the risk assessment. The next draft of
this document will include

one or more examples of how this structure might be used to related
specific levels of air quality

indicators with a corresponding ecological indicator for a given
location and/or scenario. To

what extent is the described approach technically sound, clearly
communicated and appropriately

characterized at this point of the review? Specifically, we are asking:

-   Is the suggested overall structural framework for a secondary
    standard technically sound

and logically presented?

-   Is the description and development of the deposition transformation
    function (Figure 8.11) between air quality indicators and deposition
    metic clear and technically sound?

-   Is the description and development of the ecological effect function
    (Figure 8.1-1)

between the deposition metric and ecological indicator clear and
technically sound?

-   Does the discussion adequately capture the use of categorical
    variables versus continuous

variables when accounting for the variability of atmospheric, landscape
and ecological

factors?

-   Are any key elements missing from the framework?

-   Does the framework need to be expanded or revised to accommodate the
    appropriate

consideration of ecological indicators besides ANC when developing a
secondary

NAAQS for NOx and SOx?

-   Does the panel have any further suggested refinements at this time?

*Providing a clear scientific linkage that is policy relevant between
concentrations of SO~x~ and NO~x~ and resultant S and N deposition and
subsequent translation to ecosystem level effects is a*

*major challenge. There are good linkages between concentrations of
SO~x~ and NO~x~ and deposition, but the linkage to ecosystem level
effects is more complicated due to inherent variability across the
United States of the sensitivity of these systems. There are major
problems with respect to both having confidence in calculated deposition
velocities and how to ascertain "functional forms". A clear delineation
of which ecosystem types are most important with respect to specific
ecological effects (e.g., acidification in the northeast, N deposition
affecting biological community structure in the mountain west, etc.) is
required. Such categorization will be very important in setting
secondary standard(s) that will be relevant to those effects which are
of greatest importance to various regions that have different relative
representations of various*

*ecosystem types.*

**Specific Comments in which *italics* indicate specific changes.**

Page(s) Lines(s) Comment

xv 3-5 Why should this definition only include terrestrial ecosystems?

1-1 8 Change to "The NAAQS *have been* established for pollutants".

1-2 8 Change to "complex interactions among relevant *chemical* species

> of".

1-3 10 Clarify more specifically who is "we". Do you mean EPA?

1-3 19 "Chapter 2\" should be in bold font.

1-4 1-5 This does not agree with provided definition on nitrogen

> enrichment (page xv, lines3-5)

1-5 13 Change to "*This draft*".

1-5 15 Delete "held".

1-5 24 Change to "identified the critical *components* to be".

1-5 25 Specify the title of the "Administrator" here and elsewhere in
the

> document.

1-6 5 Change "NAAQS for NO2 *was set at* 0.053 ppm".

1-6 10 Change to "secondary NAAQS values for SO~2~ under".

1-6 13 Change to "of evidence from vegetation effects ".

1-6 19 Change to "EPA was aware that SO~x~ has other".

1-6 25 Here and elsewhere be consistent in the use of terms SO~x~ and

> sulfur dioxides.

1-7 17 Change "completed by EPA at *this time*".

1-7 20-23 Change to "Administrator's conclusions that (1) based upon the

> then-current scientific understanding of acid deposition, it would
>
> be premature and unwise to prescribe any regulatory control
>
> program, and (2) when the scientific uncertainties had been
> *substantially* reduced through ongoing research efforts, EPA would
>
> draft and support an appropriate set of control measures".

1-8 3 Change to "*Due to* the complexities and *substantial* remaining".

1-8 20-21 Change to "long-term".

1-9 28 Be more explicit with respect to this "Federal Register notice".

1-10 7 Why "beyond full implementation of Title IV...."?

1-10 7 Change "to presented in the *2005 NAPAP* Report".

1-10 10 Be more specific with respect to which "recent reports".

1-10-11 It would preferable to start with a clearer definition of the
different

> forms of nitrogen oxides and then discuss some of the confusing
>
> terminology.

1-11 6 Are another group of individuals using different terminology for

> nitrogen oxides?

1-11 12 Change to "deposition of *reactive* nitrogen"

1-11 19 Change to "In many *regions*".

1-11 22 Change to "assessing *the impacts of nitrogen deposition*".

1-11 24-26 This is not true most research does consider separately the
oxidized

> and reduced forms of nitrogen inputs especially for natural
>
> ecosystems. In many cases the total input of reduced nitrogen is
>
> less well known than that of oxidized nitrogen.

1-12 13-14 With reduction in S deposition the relative importance of N

> deposition in contributing to acidification has increased. This
>
> should be noted in this introductory information.

1-13 5 The statement "sometimes limiting" with respect to N is

> misleading. Nitrogen is often a limiting nutrient with respect to
>
> primary production in terrestrial ecosystems. Even though N may
>
> be a limiting nutrient does not necessarily imply, however, that
>
> there may not be substantial ecosystem damage. Changing N
>
> inputs can alter ecosystem structure including altering the system
>
> from a more desirable state. Such factors are especially important
>
> with respect to the evaluation of N deposition in the western U.S.
>
> Such secondary effects need to be considered in setting standards.

1-13 6 Change to "acidification, nutrient enrichment, eutrophication,
and

> changes in species composition".

1-14 7-9 Other effects including changes in species composition and

> community structure need to be included for both terrestrial and
>
> aquatic systems especially associated with N inputs.

1-14 10-24 Clearly there have been substantial studies of acidic
deposition

> effects in the eastern U.S., but some consideration is needed of
>
> effects in the western U.S. where the effects appear to be
>
> substantially different especially with respect to N deposition
>
> influences.

1-14 26 Does the reference to "high elevation lakes" refer to the
western

> U.S.?

1-14 31 In this section the issue of changes in "community composition"
is

> mentioned and this needs to be included earlier in the document.

1-15 1-4 This statement on alteration of aquatic communities needs to be

> made congruous with earlier statements on overall effects of S and
>
> N deposition.

1-15 22 Change to "*a*lpine".

1-16 5 Provide some information on what are these "other factors". Do

> you mean periods of relatively high microbial activity?

1-16 8 Be more explicit on the relationship (e.g., positive or negative)

> between "oxygen content, temperature, pH, and supply of labile
>
> organic carbon".

1-16 11 Be more explicit on what are these conditions. Do you mean for

> conditions the amount of wetlands and linkages to drainage
>
> waters?

1-16 Figure 1.3-3 should explicitly have a category for changes in
species composition that may differ from altered biodiversity.

2-1 9-12 This listing needs to explicitly include effects on community

> structure and species composition.

2-1 16-18 This statement begins to raise the issue associated with
different

> effects depending on region in the U.S.

2-1-2 The absence of case studies in the Rocky Mountain west is

> problematic.

2-4 This introduction can be improved with a more focused approach.

> There is considerable repetition in this part of the document.

2-5 4-5 Change to "data *were not sufficiently available* to perform".

2-5 18 Clarify in scaling-up clarify how this will be done with respect
to

> sensitive areas (e.g., will this be done for all sensitive areas or
> will
>
> the scaling be a function of other sensitive areas with similar
>
> characteristics?

2-6 27 Change to "*need* for them".

2-6 28 A citation is needed for the "MEA" here. Later it is indicated
that

> MEA (2005).

2-7 3 Care should be made in the use of the term "regulating" since this

> term has a different meaning in the context of environmental
>
> regulations such as those associated with laws formulated by the
>
> EPA. Maybe a clarifying phrase is needed to avoid any confusing
>
> recognizing that the term regulation has a different meaning in an
>
> ecological context.

2-6 14 Are there different references for the MEA? Here it is indicated:

> MEA, 2005b. Also see Line 17 (MEA, 2005b).

2-7 This section needs some further articulation with respect to the

> description of ecosystem services. Is this description based solely
>
> on what is provided in (U.S. EPA, 2006)? It would be helpful to
>
> provide some further references that link these statements to other
>
> informational sources.

2-7 16 Change to "interest in the risk assessment *described in the
current*

> *document*".

2-7 20-22 A better description is needed that clarifies the association
of NO~x~

> deposition and eutrophication.

2-7 23-25 This statement is poorly worded.

2-7 26-31 The wording of this section needs much better clarification.
It is

> confusing whether a linkage or several linkages are being
>
> evaluated.

2-8 Figure 2.2-2 Ecosystem Services: the ecological processes or
functions having

> monetary or non-monetary value to *individuals or society*.

2-9 1-2 Change to "We have begun identifying the primary ecosystem

> service(s) affected by *either* acidification *and/or* enrichment and
>
> for major ecosystem types and components (i.e., terrestrial
>
> ecosystems, soils".

2-9 4 Change to "The impacts *affecting* various".

2-9 6-7 Change to "*These impacts on ecosystem services* will be".

2-9 10 Change to "tourism. *Effects on fisheries* (decreased".

2-9 21 Change to "tourism. Effects on fisheries".

2-9 27-28 Change to "hazard mitigation. *Methods for evaluating linkages
to*

> *measurements and ecosystem* services may include".

2-10 5 Clarification is needed on what is meant by "community".

2-10 7 Change to "changes in stand density, shifts in". Densification is

> jargon. Change to "shifts in lichen community species composition".

2-10 14 Delete "intake".

2-10 15-16 Why distinguish between "Native Americans and Alaska native

> Villagers"?

2-13 2-4 Change to "*Our approach in evaluating risk assessment relies*

> *upon various analytical tools and techniques, data sources, and*
>
> *other forms of analyses each of which has inherent uncertainties* ".

2-13 6 Change to "affect the *level* of its response".

2-13 10-11 This is not a very succinct or complete description of the
errors

> associated with modeling approaches.

2-13 12 Change to "involved *with the transformation and fluxes of
nitrogen*

> *and sulfur constituents*".

2-13 14-15 It would be more helpful to be more explicit in describing
the

> sources of uncertainty. For example with respect to deposition,
>
> wet deposition of S and N can be relatively well characterized
>
> compared to dry deposition. The major issue associated with the
>
> errors related to dry deposition are associated mostly with the
>
> modeling of deposition velocities. Also, be more specific in what
>
> is being implied with the use of the term "ecological modeling".

2-13 14-21 This section needs to include more specific information. It
would

> be most helpful to explicitly state the major sources of error in risk
>
> estimates.

2-13 22-30 These statements are very general. At a minium specific
examples

> need to be supplied that show actual examples of these errors and
>
> importance to the assessment.

2-14 2-3 It is anticipated that these discussions will provide
sufficient detail

> on these sources of error in risk assessment.

2-14-15 References should also include citations to the actual
literature and

> not rely solely on EPA documents.

3-1 10 Change to "The deposition *results*".

3-1 26 Change to "The total amount of NO~x~ emitted in the USA in
2002\".

3-2 3-4 Change to "primary emitters of NO~x~, mainly as NO and NO~2~\".

3-2 5 Change to "utilities, with *additional* contributions".

3-2 9 Change to "remainder of anthropogenic emissions".

3-2 10 Delete "component".

3-2 15-16 Delete "in the pie charts in".

3-2 16-17 Change to "*Results are shown on both a national* basis
(contiguous

> states only) as well as for the eastern".

3-2 18 Delete "For this display".

3-3 1-2 Delete "Note that emissions from Alaska and Hawaii are not

> included in any of these charts".

3-3 5-6 (not shown) with the on-road sector *being* the largest
contributor,

> followed by emissions".

3-3 8 Change "overall" to "*national*".

3-3 12 The figure caption needs more information (e.g. that Hawaii and

> Alaska are excluded in these results).

3-3 15 Change to "*contiguous* states".

3-4 3 Change to "emissions *from* fertilized".

3-4 5 Clarify what is meant by "30%--70%". Does up to 70% of the

waste mass be converted to emitted NH~3~?

3-4 9 Change to "impact from *the input of* total reactive".

3-4 10 Explicitly state what is meant by "This".

3-4 12 Change to "Total *USA* emissions of".

3-5 9 Change to "utilities using *coal*".

3-5 12 Change to "up to 10 *ppm*".

3-5 13 This becomes a little confusing since the figure does not provide

> emission data from Hawaii and Alaska. Why not include values
>
> for these states in these figures.

3-5 13-14 Sulfur is found in other forms besides amino acids in
vegetation so

> change to "Sulfur is a macronutrient (typically being 1 to 2%) and
>
> is released as SO~2~ if vegetation is combusted (Levine and Pinto,
>
> 1998)". Also, there can be other forms of gaseous releases of
>
> sulfur components from vegetation (as well as soil) including H~2~S,

COS, methyl mercaptan, etc. I am not sure where in the document

> these biogenic sulfur sources should be included.

3-6 1-2 Delete since information has been included in my suggested

> modification.

3-6 3-6 Change to "The *proportion* of SO~2~ emissions from major
sources

> are shown in Figure 3.1-5 both on a national total basis well as for
>
> the eastern and western United States".

3-6 6 Why not include Alaska and Hawaii for completeness?

3-6 14-16 The relative importance of this error needs to be stated
explicitly.

3-7 2-5 Not sure the term \"policy-relevant\" is a useful term with
respect to

> defining background concentrations. What is the basis of the actual
>
> value being used? Is it based on a specific time period or some
>
> calculation that attempts to separate out natural versus
>
> anthropogenic emissions? How can the general effects of N
>
> fertilizers and N atmospheric deposition in affecting NO~2~ flux be
>
> evaluated? Is this 100 ppt based on some type of area weighted
>
> basis or some other form of calculation?

3-7 4 Delete "policy-relevant"?

3-7 25 Change to "This source distinction and quantification will".

3-8 13-14 Further information should be provided on the source and
methods

> for estimating these deposition values. This information is
>
> provided later on page 3-13. This information should be provided
>
> earlier in the document.

3-8 19 Not sure what "Great Waters" means.

3-8 19-23 References are needed here.

3-9 Figure 3.1-6. Reduce the significant digits in the figure legend to
nearest 1/10th.

3-10 Figure 3.1-7. Reduce the significant digits in the figure legend to
nearest 1/10th.

3-11 Figure 3.1-8. Reduce the significant digits in the figure legend to
nearest 1/10th.

3-11 9-10 Further details on how these deposition estimates were derived

> should be provided. This information is provided later on page 313.
> This information should be provided earlier in the document.

3-12 Figure 3.1-9. Reduce the significant digits in the figure legend to
nearest 1/10th.

3-12-13 See previous comments on the placement of this information

> within the document.

3-12-16 Isn't much of this information relevant to the overall
predictions of

> N and S deposition. It was not clear why this more extended
>
> discussion was focused on the case studies. Was there a different
>
> type of analyses done for deposition for the case study regions than
>
> for the overall U.S.?

3-16 Aren't all these abbreviations already provided and hence Table

> 3.2-1 can be deleted.

3-16 Are these formulas included to show the conversions from formula

> compound mass to nitrogen or sulfur mass? If this is there only
>
> use then Table 3.2-2 should be deleted.

3-17 11 Has the western case study been identified?

3-20 Within each of these regions there have been other measurements

> made of associated parameters including precipitation amount,
>
> atmospheric deposition. Is there any attempt being made in this
>
> document to compare these current results with previously
>
> published results?

3-23 There are well established geographic patterns in N and S

> deposition across the Adirondacks. Shouldn't these be
>
> acknowledged? There has also been substantial work on deposition
>
> estimates in the Adirondacks using other approaches. For wet only
>
> deposition for example see: Ito, M., M.J. Mitchell and C.T.
>
> Driscoll. 2002. Spatial patterns of precipitation quantity and
>
> chemistry and air temperature in the Adirondack Region of New
>
> York. Atmospheric Environment 36:1051-1062. Also other
>
> studies have evaluated the relative contribution of wet and dry
>
> deposition. See for example: 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. Would
>
> some comparisons with other investigations be warranted?

3-25 This repeats a previous comment with respect to the inclusion of

> previous analyses of these regions in these cases studies.

3-26-53 There is considerable detailed treatment of the results provided
by

> the CMAQ modeling including temporal and spatial results. With
>
> so much emphasis on these model results it would be useful to
>
> provide some other confirmation of these deposition values.

3-54 14-15 This is not entirely true. There can be instances were
ambient

> concentrations of NO~x~ and SO~x~ are directly deleterious. These
>
> conditions, however, have not been generally found in the USA
>
> during the period of concern associated with acidic deposition
>
> effects. For Europe conditions in the "black-triangle" and other
>
> centers of high pollutant concentration there were direct impacts
>
> especially associated with SO~x~.

3-55-70 The format and output of the CMAQ modeling runs are provided

> in some detail. Some further comparison of the CMAQ results,
>
> especially, in the areas of test cases, would be helpful in providing
>
> some objective measurements of the model results.

3-70-72 The model results need to be verified with actual data that show

> these relationships. Clearly the model functional relationships and
>
> parameterization will effect overall model output. It is important
>
> that it be clearly identified when model outputs are producing
>
> results that have been verified elsewhere or whether there are
>
> currently no empirical and experimental results that provide data to
>
> verify these results. Such arguments can also be made for the other
>
> N gaseous constituents.

3-70 16 It is suggested that there is "statistical imprecision in the

> modeling". There are other important sources of model error that
>
> need to be considered including uncertainty in model formulations.

3-82 7-9 Statements such as "Figure 3.2-55 shows that NO~x~ emissions

> account for almost all oxidized nitrogen deposition in the
>
> Adirondacks Case Study Area, while Figure 3.2-56 shows that NH~3~
> emissions account for almost all reduced nitrogen deposition" have
> important implications with respect to making recommendations
> associated with NO~x~ emission controls. Are these results verifiable
> and can the emissions also be linked to specific geographical areas?

3-87 How are these high emission locations ascertained? Is this a

> function of the location of specific monitoring locations (e.g.,
>
> CASTNET sites).

3-112 This section on uncertainty (3.2.2.5) that has yet to be completed

> needs to include not only statistical issues, but also uncertainties
> in
>
> the model formulations and associated parameters.

3-113-114 This is a relatively limited reference list with considerable
reliance

> on EPA documents. This section would be strengthened by
>
> inclusion of results from the peer reviewed scientific literature that
>
> support the suggested findings.

4-1

5-1 The sections on "ACIDIFICATION" and "NUTRIENT

> ENRICHMENT" include only outlines, but the suggestion of the
>
> importance of providing uniform terminology is encouraging.

6-1-10 This section gives a useful review of recent findings linking the

> cycling of S and Hg. This section also includes more references to
>
> the referred literature related to this topic

6-10-13 The section on NITROUS OXIDE provides additional information

> on this N gas and provides a clear indication of the importance of
>
> this gas including its linkage with N deposition and is important
>
> role as a "greenhouse" gas.

6-13-18 The synopsis on CARBON SEQUESTRATION provides a useful

> overview of important interactions between N deposition, warming
>
> and the carbon cycling in terrestrial ecosystems. This is a very
>
> large and important subject area. As suggested a detailed analyses
>
> is beyond the scope of this review. The term carbon sequestration
>
> does not really capture the total content of this section.

6-19-22 More emphasis in the description of aquatic effects should be

> placed on changes in the phytoplankton community structure that
>
> has been most noted in the western U.S.

7-1

7-15 In its current version this "Synthesis and Integration of Case
Study

> Results" is highly descriptive. This will need to be improved with
>
> specific quantitative results that show a clear relationships to the
>
> assessment.

8-1

8-30 Clearly providing a clear scientific linkage that is policy
relevant

between concentrations of SO~x~ and NO~x~ and resultant S and N

> deposition and subsequent translation to ecosystem level effects is
>
> a major challenge. Clearly there are good linkages between
>
> concentrations of SO~x~ and NO~x~ and deposition, but the linkage to
>
> ecosystem level effects is more complicated due to inherent
>
> variability across the United States of the sensitivity of these
>
> systems to acidification, eutrophication and changes in biotic
>
> composition. It will be important to formulate an approach that
>
> takes into account these geographical patterns of sensitivity.

8-4-5 Figure 8.1-1 needs to indicate in some format that these
ecological

> indicators may not be constant over the United States (e.g., N
>
> deposition levels with respect to changes biotic community
>
> structure being more sensitive in the Mountain west than the
>
> eastern U.S.). These issues are outline on lines 1-7, page 8-5.

8-5 22 The problem in not including reduced N chemical species in any

> formulations associated with N deposition effects is highly
>
> problematic. I am not sure it is feasible to focus solely on NO~x~.

8-9 There are major difficulties in setting national standards for SO~x~

> and NO~x~ concentrations without taking into account regional
>
> effects.

8-13 As suggested the development of these "functional forms" will be

> critical and may have both spatial as well as temporal components.

8-13 Clearly EPA is making heaving reliance on the CMAQ model

> suggesting the importance of validating results using other
>
> approaches and the linkages between gaseous concentrations and
>
> specific deposition levels.

8-14-17 The issues of deposition velocities are not trivial. For example

> look at the differences in deposition associated with the estimates
>
> at the same site for CAPMoN and CASTNET. Although
>
> CAPMoN and CASTNET provide similar concentrations of gases
>
> the deposition velocities are higher for CAPMoN verus
>
> CASTNET.

8-23 The discussion of uncertainties needs to include the various issues

> associated with the calculation of deposition velocities.

Attachments

2, pg 2 5 Change "to reflect *most recent* conditions".

2, pg 2 14-15 Not sure that there is a relationship between steepness
and base

> cation leaching rates versus the role of slope in affecting the
>
> contact of drainage waters to soils and the relative contributions of
>
> ground waters to drainage with groundwaters generally being more
>
> rich in base cations than waters derived from shallower soil
>
> sources.

2, pg 3 30 Isn't a threshold of 400 μeq/L or less considered acid
sensitive?

> Would a threshold of 100 μeq/L better? Also, note that the correct
>
> symbol for liter is "L" not "l". Change for entire document.

2, pg. 5 Figure 3.2-1. Give a citation for the Acid Sensitive Waters

> (USGS).

2, pg. 7 Why was there no selection of a threshold for sulfate
deposition?

> Is this awaiting the determination of critical load? At a minimum the
> European critical load could be used.

2, pg 8 Same comment for total N and S deposition and the assignment of

> a value as that provided by sulfate.

2, pg. 9 The inclusion of high elevation could also be justified by
other

> criteria such as the potential contribution of occult (fog)
>
> deposition. If occult deposition accounted for in the CMAQ
>
> estimates. This also relates to rationale provided with respect
>
> topographic position (Attachment 2, page 17).

2, pg 9 25-28 This is confusing with respect S and N deposition since it
was

> suggested above that no criteria for S and N deposition were
>
> defined. If these top quartiles are used the actual values need to be
>
> supplied that make up these quartiles. Also, the year or years from
>
> which these deposition data are derived needs to be given
>
> explicitly.

2,pg 10 14 Why "Total nitrogen (Kjeldahl)". Do you mean total dissolved

> nitrogen or total dissolved Kjeldahl nitrogen. Why exclude nitrate
>
> in surface waters?

2,pg 11 Although there are weak linkages between N deposition and N

> solute concentrations in surface waters, it would be preferable to
>
> provide the data layer of actual N solute concentrations in surface
>
> waters.

2, pg12 18-19 Provide these nutrient concentrations available from the
National

> Nutrient Database. Provide a citation for this and the other data
>
> bases.

2, pg 15 These N deposition data layers seem to be redundant from data

> layers previously described.

2, pg 16 More clearly delineate the difference between "content" and

> concentration". Content should be reserved for the total amount
>
> (mass, molar value) of a an element on a per unit area while
>
> concentration is the amount (mass, molar value) of an element per
>
> unit of mass (sometimes) expressed as %.

2,pg 18 The delineation of the location of acidophilic lichens appears
to

> have a strong boundary based upon state borders especially notable
>
> in Arizona and an absence in New Mexico.

3, pg 10 Here and elsewhere "μM" is not a correct abbreviation. The

> abbreviation for mole is "mol".

3, pg 12 Note that these ANC levels are lower than those suggested to be

> considered to be of concern in Attachment 2.

3, pg 15 There have been other models (e.g,. PnET-BGC) that have been

> applied particularly to the Adirondacks to evaluate especially
>
> temporal patterns of acidification. Wouldn't it be helpful to at
>
> least do some comparisons using other models besides MAGIC.

3, pg 18 8 Change to "SO~4~ ^2-^".

3, pg 21 Clarify how the ratios of wet to dry deposition were derived.

3, pg 22 15 Are the total deposition values used in the MAGIC
calculations

> different from deposition estimates used elsewhere in the entire
>
> document?

3, pg 22 27-29 Some elaboration on how ASTRAP derived deposition would
be

> helpful and how these estimates confirm or differ with the CMAQ
>
> estimates.

3, pg 23-26 There is considerable discussion of the calibration of MAGIC
in

> this section. Some of this could be reduced and inclusion of other
>
> ways of comparing model output with other published results
>
> including other models (e.g. PnET-BGC) would provide additional
>
> perspectives of these results.

3, pg 29 Similar to previous comments, although the discussion and

> definition of the F-factor provides background information this is
>
> not a novel approach, but rather one that could be cited. More
>
> emphasis of the validation and comparisons with actual
>
> measurements versus description of the model development would
>
> be more helpful.

3, pg 31 Figure 5.1-1. Trends in LTM monitored lakes in the Adirondacks

> of New York would be improved if specific lake classes were used.
>
> It is not clear from these figures how a general trend for the LTM
>
> monitored lakes were obtained.

3, pg 32 Figure 5.1-2. The modeled values appear to be substantially

> different that those of the measured values. Doesn't this bring into
>
> question to validity of the predictions for 2010? I don't believe the
>
> results of this figure are discussed within the document.

3, pg 35 Clearly the document is incomplete at this stage.

4, pg 1-2 This seems repetitious of information provided in the main

> document.

4, pg 5 "M" is not the correct SI abbreviation for mole. The correct

> abbreviation is "mol".

4, pg 4-9 Not sure that this much restating of what has previously been

> found about Al and Ca relationships is needed.

4, pg 11 Would it be more efficient to cross reference the description
of

> ecosystem services as provided in the main document?

4, pg 18-20 Are the details of the history of the Kane Forest needed in
this

> document?

4, pg 21-25 Similarly to the previous comment, are all these details
about

> Hubbard Brook needed for this document?

4, pg 26-47 This is difficult to follow due to the level of detail.
Perhaps a more

> generalized format in which could be imbedded specific references
>
> to the literature or the inclusion of appendices so that the major
>
> theme of the discussion is not lost.

4, pg 50 Not sure of the importance of the inclusion of the section on

> "Implications for other systems" in this document.

4, pg 51-52 The uncertainties issues need to be better integrated into
the overall

> document.

4, pg 53 The "Conclusions" summarize the important issues and these

> issues should be the focal points of this entire section with a need

6, p 43 The figure on this page (Figures 5.1-1 5.1-2) appears to have an

> inappropriate numbers. Shouldn't they be 6.1-1 and 6.1-2?

# Mr. Richard Poirot

These comments pertain primarily to REA Chapter 3 (Sources, Ambient
Concentrations, and Deposition), for which the following charge
questions were provided.

> **Question 1**: To What Extent are the air quality characterizations
> and analyses presented in chapter 3 technically sound, clearly
> communicated, appropriately characterized, and relevant to the
> secondary NAAQS for NOx and SOx?
>
> **Question 2**: Section 3.2.1 describes an approach for evaluating the
> spatial and temporal patterns for nitrogen and sulfur deposition and
> associated ambient concentrations in the case study locations. This
> draft document includes the analysis for the Adirondacks Case Study.
> *[Does the Panel agree with this approach and should it be applied to
> the other Case- Study Areas?]{.underline}*
>
> **Question 3**: Section 3.2.2 describes the relative contributions of
> ambient emissions of nitrogen and ammonia to nitrogen deposition for
> the case-study areas. *[To what extent is the approach taken
> technically sound, clearly communicated, and appropriately
> characterized?]{.underline}*

Assuming the many and important missing "placeholder" sections are
filled in, I think the air quality characterizations and analyses
presented in chapter 3 will provide a technically sound, clearly
communicated, appropriately characterized, and relevant to the secondary
NAAQS for NOx and SOx (although it still remains unclear to me what kind
of 2ndary standards are being contemplated). Many of these placeholders
refer to evaluations of model performance, and since the majority of the
chapter consists of presentation of intensively graphical model results,
filling the placeholders will be key to providing confidence in the
model results. The technical approach appears to be reasonable, but
without a better sense of model performance (including both CMAQ and the
RSM meta-model), the technical soundness and relevance to NAAQS can't
really be evaluated.

The presentation of the information is clear (even beautiful), but there
is minimal discussion or interpretation of the graphical results, which
makes it difficult to maintain interest in looking so many pictures.
Conversely, it might be informative to poll the model results in ways
that might provide a better understanding of relationships among the
various metrics of air quality, deposition and environmental effects.
For example: what would the maps look like that show the ratios of S
deposition to S emissions; N (oxidized) deposition to N (oxidized)
emissions; N (reduced) deposition to N (reduced) emissions. What would
maps look like that show ratios of S (or N) deposition to ambient SO~2~
(or NO~2~) concentrations? What if modeled S emissions were rolled back
to show alternate lower maximum levels of SO~2~ (and/or NO~2~) -- what
would be the subsequent changes in S (and/or N) deposition in sensitive
downwind areas? If sections of the Adirondacks were considered to be
experiencing adverse levels of acidifying deposition, how could the
models be used to determine the "significant contributing area" -- or
perhaps some combination of emission size, and frequency upwind -- such
that a non-attainment area might be defined to better include the
contributing emissions? A possible approach for an improved secondary
SOx or NOx NAAQS might consider (much) lower levels but averaged over
larger areas or longer averaging times.

With the caveat that the model performance needs to be more clearly
examined and documented, I think the more detailed approach applied here
for the Adirondack case study is reasonable, and could be applied to
other case study areas. One possible concern -- possibly more relevant
to the Adirondacks than to most of the other case study areas -- is
whether the 12 km gridding might be coarse relative to the spatial
variability in deposition, terrestrial & aquatic ecosystems and
associated effects. Potentially the larger grid cells may fail to
adequately capture orographic increases in precip volume & deposition
and the additional increases from occult deposition at highest
elevations (or in certain coastal areas) -- in comparison with
variations in sensitive terrestrial and aquatic biota within these grid
cells . See for example: Miller, E.K. et al. 1993. Atmospheric
deposition to forests along an elevational gradient at Whiteface
Mountain, NY USA. Atmos. Environ. 27A:2121-2136.

![](media/image4.wmf){width="5.996527777777778in"
height="4.503472222222222in"}

Possibly this influence of occasionally large terrain, deposition and
species variations within the relatively large grid cells could be
evaluated by conducting a higher resolution sensitivity analyses within
selected grid cells in the Adirondacks case study area. Alternatively,
it might at least be possible to disaggregate the coarser modeled dry
dep. estimates to combine with the higher resolution wet dep. estimates
from the Grimm & Lynch approach. Arguably the dry dep totals and
variability may be less important than wet dep at more remote receptor
locations. Possibly also a terrain-based cloud deposition model could be
added to provide added detail for higher elevations or in coastal areas.

Regarding the soundness of the technical modeling approach to estimate
the relative contributions of ambient emissions of oxidized and reduced
nitrogen to nitrogen deposition for the case-study areas -- the approach
seems sound but again there is a need to evaluate the performance of the
models (CMAQ + RSM). Trust but verify. This evaluation could/should
extend where possible to subcomponents of the models such as emissions
inputs and space/time patterns of modeled estimates of wet oxidized N
and wet reduced N deposition.

That being said, I do like the approach of directly linking the
estimates of changes in Nr deposition to changes in specific emission
sources. I would think a similar approach could also be taken to zero
out and otherwise reduce SOx emissions from different source categories.
Down the road, this may allow a bundling & comparing of projected
"optional" future emission controls (small, medium, large, etc.) to
desired reductions in deposition in sensitive areas, in comparison to
the associated concentrations in atmospheric NOx & SOx concentrations
(in the event the layers say we have to stick with the traditional
indicators). What new NAAQS limits of these indicators (perhaps averaged
over larger - or much larger - areas than single monitors) would be
necessary to achieve the desired reductions of Nr and/or S deposition in
sensitive areas?

In addition, if you were to add various levels of SOx (and NOx) emission
reductions to your modeled scenarios, it would be a snap to calculate
and display the resulting changes in sulfate and nitrate aerosols (and
in their visibility effects) that would result from any changes in S & N
emissions or deposition or SO~2~ & NO~2~ concentrations. This would
allow you to (a) consider a more complete set of welfare benefits that
would result from any revised NAAQS based on deposition effects and/or
(b) might lead to and help justify alternative ambient air indicators --
for example the sum of total atmospheric oxidized S and N compounds (sum
in ug/m3 of S from SO2 and pSO4 and N from NO, NO2, HNO3, and pNO3 or
somesuch) -- that might not be considered if only deposition-related
effects are considered, but which might, set at the right levels, result
in large deposition-related benefits.

**Other Minor Comments:**

p\. 3-1 lines 16-23: This is a good example of what seems like an
intentional sense of vagueness regarding which pollutants and secondary
transformation products are or are not the subject of this review,
and/or available as potential indicators for secondary NAAQS. Why are
nitric acid and PNO3 considered part of "NOx", while SOx includes only
gaseous SO~2~?

p\. 3-4, Figure 3.1-3: This figure just doesn't look right -- and seems
inconsistent with the reduced nitrogen deposition map in Figure 3.1-8 on
p. 3-11.

p\. 3-4, lines 3-5: Does confined feeding really increase animal wastes,
or does it just increase atmospheric emissions from them?

p\. 3-4, line 12: Figure 3.1-4 does not show annual 2002 SO~2~ emissions
"by state".

p\. 3-5, line 4: I would change "Industrial" to "Anthropogenic".

p\. 3-5, lines 10-15: Should marine DMS emissions be mentioned here?

p\. 3-6, lines 14-16: Can you provide any quantitative indication of how
large these fire SO~2~ emission underestimates are?

p\. 3-8, lines 5-7: Does this increased deposition of reduced nitrogen
also pertain over the 100-year period of the preceding sentence. Can you
say something more precise about trends over the past several decades?

p\. 3-12, lines 10-14: This description relates to how NADP interpolates
its wet deposition data. However, later you indicate using the
precip-volume-enhanced estimates from Grimm & Lynch (2004). So which was
it? One general concern is that the 12 km gridding may overly smooth
some of the more extreme orographic increases in precip -- and you seem
to exclude cloud water deposition. Possibly this could be handled by
conducting some sensitivity analyses for grid cells containing higher
elevation terrain -- especially for the Adirondack and Shenandoah case
studies.

p\. 3-16, line 11: Why not also describe CASTNet (& AIRMoN dry) data for
HNO~3~, NO~3~, NH~4~, SO~4~?

p\. 3-23, lines 4&5 and lines 11&12: say roughly the same thing twice.

p\. 3-23, line 7: "(25% wet vs. 6% dry)" and 69% what?

p\. 3-23, line 12: Change "does" to "do".

p\. 3-54, line 17: You could add "current and historical" before
"atmospheric deposition".

p\. 3-55, lines 20-21: Can you provide any indication of if and how well
the RSM technique (and for that matter the underlying CMAQ model) works
for all the SOx, NOx and reduced N species you will use it for?

p\. 3-57, line 5: Am I missing something or did you only use a couple
(zero-outs) of these 210 control runs? So what was the purpose of the
other runs?

p\. 3-71, line 8: Delete one "deposition" in "greater deposition of
oxidized nitrogen deposition".

p\. 3-71, lines 8-15: I would think formation of aerosol NH~4~NO~3~
would tend to increase the transport distance, but would not lead to any
net decrease or increase in Nr deposition. It all gets deposited
eventually. An exception might be if aerosols persist long enough to
transport out of the (US or North American) domain.

p\. 3-73: I must have blinked somewhere, because I didn't expect to see
this large, international "sugar maple case study" area discussed
previously. Its not listed as a "Case Study Location" in Table 2.1-1 on
page 2-2&3. It reminds me to ask for a clearer "up-front" description (&
map) of all the intended case study areas.

# Mr. David Shaw

**General Comments**

Thank you for addressing the outcome of this REA. I believe that this
makes the document more focused.

I still feel that a specific goal of this assessment should be to
identify and report sensitive areas which do not have adequate
monitoring. Adopting this longer view in this analysis will enable the
next review process to start from a stronger point. In identifying areas
without adequate monitoring data, we may be able to start the process of
getting a stronger data record of results for future analysis. It is my
hope that this will lead to better modeling due to better data.

While there are certainly areas that are deficient in monitoring data,
there definitely are areas of strong monitoring data with analysis. I
still feel that the areas of certainty do not receive equal treatment as
uncertainty. I feel we must be clear that we do understand causes,
effects and variability in our ecosystem response.

On this note, the analyses presented in Chapter 3 of the REA rely
heavily on modeling and don't always reinforce where the measurements
are the strongest. It is important to emphasize where we have the most
confidence (e.g. wet deposition, ANC measurements in case study areas)
and the least confidence (e.g. air concentrations and dry deposition of
NOx/SOx, where measurements are lacking). Much of the information on dry
deposition will come from CMAQ, and the measured data from CASTNet and
other special studies could be used to assess the model at selected
locations.

**Charge Questions**

***Scope of the Review***

***Question 1***

***Chapters 1 and 2 provide the background, history, and the framework
for this review, including a discussion of our focus on the four key
ecological effect areas (aquatic acidification, terrestrial
acidification, aquatic nutrient enrichment, terrestrial nutrient
enrichment). Is this review appropriately focused in terms of the
targeted areas and in terms of characterizing the important atmospheric
and ecologic variables that influence the deposition and, ultimately,
the ecologic impacts of nitrogen and sulfur? Does the Panel have any
further suggested refinements at this time?***

**Pages 1- 1 to 1-10:**

I feel that this gives good overall information on the Rational,
Background and History. It might also be a good place to address other
pollutants associated with NO~x~ and SO~x~ analyzing the whole set of
problems associated with these pollutants.

**Page 1-8 lines 3-5:**

Lines 3-5 state that 'in spite of the complexities and
uncertainties....' it became clear that a program to address acid rain
was needed. In actuality, it was the evidence of a preponderance of the
scientific data of the NAPAP effort which made it clear that an acid
rain program was needed. This builds on one of my general comments
regarding an emphasis on uncertainty rather than giving equal treatment
to those areas where certainty exists.

**Page 1-16:**

I would recommend adding a discussion on critical loads as the
organizing principle of this RAE assessment. Include the current
understanding of ecological indicators and how levels of the proposed
standard will be integrated.

**Page 1-20:**

It would be helpful to explain how the existing monitoring data will be
used to evaluate the success of the proposed standard? How and when will
the existing monitoring networks be evaluated for adequacy of measuring
ecosystem response?

**Page 2-10:**

I appreciate the effort in adding sulfur and mercury methylation. The
fact that it will be addressed will make this a stronger analysis.

**Page 2-11, Table 2.3-1:**

I feel that it would be beneficial to add to Cultural Services "chemical
and biological degradation of Constitutionally (federal and states)
protected Wilderness areas". This would apply to several if not all
Targeted Effect Areas. The point being that the ADK case study area, for
example, represents a 6 million acre region, 43% of which is protected
by the NYS Constitution as 'forever wild' Forest Preserve. Here, tree
cutting is not allowed, yet atmospheric deposition damages forests and
diminishes aquatic ecosystems within these forests. The remaining 57% is
devoted principally to forestry, agriculture, and open-space recreation,
a portion of which is sensitive to negative effects of atmospheric
deposition. This landscape holds an additional cultural value to New
Yorkers especially, and to others from the US and around the world.

**Pg 2-12:**

In the box where "provisioning services" and "cultural services" for
Sulfur and Mercury Methylation are provided, fish kills is listed as an
ecological impact. From the literature that I am familiar with, fish
kills or declines in fish populations are not a good indicator of MeHg,
however, declines in the success of species higher in the food web such
as loons and humans occur because of MeHg neuron toxic effects and bio
accumulation.

***Air Quality Analysis***

***Question 1***

***To what extent are the air quality characterizations and analyses
presented in Chapter 3 technically sound, clearly communicated,
appropriately characterized, and relevant to the review of the secondary
NAAQS for NO~x~ and SO~x~?***

**Sections 3.1.4 and 3.2:**

It seems as if the dataset discussion (Section 3.2) would be more
beneficial if it appeared before the composite deposition maps (Section
3.1.4). These composite maps consist of modeled dry and
measured/interpolated wet deposition. For these maps, are the units
actually kg ha^-1^ y^-1^, or are they kg N ha^-1^ y^-1^ and kg S ha^-1^
y^-1^? Some mention should be made that the dry deposition estimates are
generally consistent with whatever measurements (e.g. CASTNet) are
available, that one year of modeling is adequate to capture the
seasonal/spatial variability in the predictions (i.e. this is not an
atypical year), and that other photochemical models are capable of
estimating dry deposition and could be used to perform such an analysis.

**Section 3.2.1.2:**

I am interested to know why SO~2~ and NO~2~ from SLAMS/NAMS monitors are
not included in the measured database? While there may not be many NO~2~
monitors in rural areas, there should still be some measurements of
SO~2~ in the case study areas.

**Page 3-21 ADK case study area:**

There are several questions regarding the selection of this study that
would be of interest to note in the REA:

How were the 44 lakes and ponds selected?

How was the subset of 15 lake sites selected for geographic variation in
deposition assessment?

How representative are these sites of the whole region?

Is there an elevational stratification?

Are any of the intensive study sites part of the current Adirondack
monitoring programs (e.g., ALTM, TIME, AEAP)?

Have any or will any of the model results be compared with existing long
term monitoring data?

Some important facts to point out regarding this region is that 22% of
it is above 600 m were the sensitive spruce fir forest community becomes
dominant. Further up above 900 m are key signature mountain peak
ecosystems containing over 100,000 acres.

Monitors are not measuring any deposition data above 610 m in NYS, with
the exception of the top of Whiteface Mountain.

**Pages 3-35 through 3-37, and 3-50 through 3-53:**

It may not be necessary to include the additional information on a
monthly basis. The form of the annual NAAQS looks to be seasonal or
annual, so presenting deposition on a seasonal basis seems to be
adequate to capture the variation over the course of a year.

**Figures 3.2-29 through 3.2-44:**

I would recommend that the metrics for these figures are clearly stated.
Also, it would be helpful to confirm that the "whiskers" are the minimum
and maximum and that the boxes are 25^th^/75^th^ percentiles.

**Figures 3.2-45 onward:**

It might help the reader to reverse the color scheme, that is display
the smallest impacts in green and the largest impacts in red.

**Misc.**

In the introduction there are many references to "...noted ***below***
in Section 1.x...." I would recommend removing the word "below" in each
of these references.

Page 1-3 line 19, "Chapter 2" should be

# Dr. Kathleen C.Weathers

*Overarching comments on Chapters 7 and 8*:

First, I think that the case study approach is useful and appropriate
for this analysis. Next,

Chapter 8 provides some interesting ideas to ponder. Finally, the
incompleteness of this document makes it difficult to provide much in
the way of pithy comments. In addition, there's much editing that will
need to be done on these chapters.

*Case Studies:* As we discussed during the first meeting of the Panel,
the choice of case studies is critical. My biggest concern about the
case studies identified in this draft is whether they are representative
enough. That the there is sufficient data and information for a case
study is, of course, a major criterion. Further, their use should be
supported and justified in regard to the suite of impacts of air
pollution they illustrate with regard to direct and indirect effects of
atmospheric N and S. I question the use of the Chesapeake Bay/Pamlico
Sound in this regard, mainly because atmospheric N deposition to the
region is not a large proportion of N inputs to the ecosystem. Thus,
unless it is used as a contrasting example of a system in which the
atmospheric deposition of N is not a major component of N loading (I
note that this contrast could have utility), the Chesapeake Bay/Pamlico
Sound regions may not be the most illustrative case study to use. I do
think that, if feasible, evaluating deposition impacts on a coastal
ecosystem(s) would be instructive.

I mentioned in my last review that I thought Day-Cent-Chem should be
considered as a potential model to be used for these case study
analyses. It has some advantages over Magic, and some parallels with
other biogeochemical models (PNET-BGC, for example).

Would it be possible to consider in some creative way a "case study"
that summarizes and synthesizes experimental manipulations of N and S
inputs (e.g., Harvard Forest, Catskill Mountains, NY, Bear Brook, ME, Mt
Ascutney)?

*Conceptual pieces:* I agree with using a "weight-of-evidence" approach,
which I interpret to mean that assessing effects using a suite of
different tools (modeling, experiments, theory, long-term monitoring)
can be used to provide the most robust syntheses. The IPCC has used this
approach successfully.

As the authors of this document are no doubt well aware, ecosystems are
affected by the amount (and sometimes concentration) of a pollutant or
nutrient that is actually makes its way to the ecosystem --- i.e., that
is deposited. Working backwards from that fact suggests that what will
be necessary is a set of standards that consider actual loading ---
deposition --- to ecosystems, rather than atmospheric
concentration-based standards that identify the role of "modifying
factors." The devil's in the details of Figure 8.1-1! As research has
demonstrated, for some chemical species,

there may be little connection between emissions and total deposition
downwind, much less all of the biologic and geochemical transformations
that happen from deposition to terrestrial processing to surface water
effects (or not).

As noted in this REA, lining up the spatial and temporal scales of
analysis and output are critical

issues, for example, high temporal resolution (air concentrations and
deposition on an hourly

basis, for example) but low spatial resolution (across the country) may
be exactly the opposite of

what would be most useful for assessing ecosystem effects.

The likelihood that current rates of deposition will show immediate
effects on downstream

ecosystems for nutrients such as N is quite low. Rather, capturing the
longer-term average loads

and patterns of deposition is likely to be more relevant.

The derivation of deposition metrics and transformation functions were
at once described in

great detail and in not enough detail. Seeing the forest for the trees
will be very important. See

comments about a deposition standard, above.

*General comments on Chapters 7 and 8:*

Note that I have not offered detailed editorial comments for this
review.

I'm not sure that I agree (page 7-2, lines 15-16) with the statement
that it is the increase in sulfur

and nitrogen content of soils that is the sole reason for alteration of
major biogeochemical

processes. Also, just below, missing from the description of acidic
deposition's effects on aquatic

system are the properties of the adjacent terrestrial watershed,
including hydrologic pathways.

And, at the end of this paragraph, the reasons why the results from the
case studies for the

Adirondacks and Blue Ridge Mountains might be applicable to the rest of
the Appalachians and

the Northeast should be identified.

There appears to be some confusion about terrestrial acidification, or
at least the beginning of the

terrestrial acidification should be rewritten for completeness (i.e.,
natural and anthropogenic

acidification occur in soils), accuracy, and clarity.

I appreciate the importance of the statements on pages 8-12, lines 9-13
in regard to a national

transformation function with local modifying factors within it. This is
very important given the

importance of landscape (in its broadest sense) in influencing inputs.

I note the absence of cloud or fog deposition in Section 8.3.2.1. I
suggest mentioning in the text

that it will not be included directly here. This vector can be
critically important, but only in

coastal and mountainous ecosystems.

Surely the intention in the Catchment parameter section is to use GIS
databases (not actual

topographic maps)?

Be sure to label figures clearly as well as be clear when discussing
total (wet + dry? or Nr, or?)

deposition. Note annual or seasonal as well in the text.

Organic nitrogen, in regard to both its atmospheric input (less known)
and output (more known)

via surface waters should be at least mentioned as part of the N effects
picture. While it is not

directly part of NOx/SOx emissions, it is nonetheless important and it
is becoming especially

relevant in regard to climate change.

Such terms as ecosystem services, and ecosystem health, should be
explicitly, consistently, and

clearly defined among and within these NAAQS review documents.

[^1]: Reuss J.O., and D.W. Johnson.  1986.  Acid Deposition and the
    Acidification of Soil and Water.  Chapter 7.5: Capacity versus
    Intensity. Ecological Studies No. 59.  Springer-Verlag, New York,
    Pages 71-72.)