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) NOx & SOx 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

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 

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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 NOx and SOx (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 NOx/SOx 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 NOx and SOx, 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 NOx-SOx 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 NOx and SOx

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

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 NOx and SOx? 

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? 

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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 NOx and SOx. 

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. 

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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

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. 

5
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? 

 

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.) 

6
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 

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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

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 SOx and NOx 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

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 

8
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 NOx and SOx 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

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 

9
10

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 NOx, SOx 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 NOx & SOx Secondary Clean Air Scientific Advisory Committee 

NAAQS Review Panel 

Enclosures 
Enclosure A 

U.S. Environmental Protection Agency 

Clean Air Scientific Advisory Committee 

NOx & SOx 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 

11
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) 

12
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)

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Enclosure C

Comments received:

Dr. Praveen Amar....................................................................................................................... 15 

Dr. Andrzej Bytnerowicz............................................................................................................ 17 

Ms. Lauraine Chestnut............................................................................................................... 20 

Dr. Ellis B. Cowling .................................................................................................................... 22 

Dr. Douglas Crawford-Brown ................................................................................................... 30 

Dr.Charles T. Driscoll................................................................................................................. 33 

Dr. Paul J. Hanson...................................................................................................................... 43 

Dr. Rudolf Husar ........................................................................................................................ 49 

Dr. Dale W. Johnson................................................................................................................... 52 

Dr. Donna Kenski........................................................................................................................ 55 

Dr. Naresh Kumar ...................................................................................................................... 62 

Dr. Myron J. Mitchell................................................................................................................. 65 

Mr. Richard Poirot ..................................................................................................................... 84 

Mr. David Shaw .......................................................................................................................... 89 

Dr. Kathleen C.Weathers........................................................................................................... 93 

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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?

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?

Question # 2 Response: 

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 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. 

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 

15
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 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:

 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? 

 

16
Dr. Andrzej Bytnerowicz 

Question 2 – 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 

SO4

2-, NO3-

 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:

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 – 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? 

17
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 

HNO3 and NH3 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. 

18
Specific comments: 

Page 13, 1st paragraph – also high levels of NH3 and NH4

+

 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, 1st 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:

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. 

19
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 

20
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 

21
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

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/c83c30afa465

6bea85256ea10047e1e1!OpenDocument&TableRow=2.1#2.

22
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 N2O in terrestrial ecosystems,” 

h) “alteration of biogeochemical flux of CH4 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 N2O flux in wetland ecosystems,” 

m) “alteration of CH4 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, NO2, and PAN and injury to vegetation” and 

s) “exposure to HNO3 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. 

23
Air Quality Analyses

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 NH3 of the deposition of total 

reactive nitrogen. Figure 3.2-42 shows that NH3 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 NH3, 10% occurs in the Potomac case study area in February. The 

24
largest impact of NH3, 73% occurs in the Neuse Case study in July. The Neuse case study has 

the largest overall impact of from NH3 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 HNO3, which limits ammonium nitrate (NH4NO3) 

formation (and for existing aerosol, a reduction in HNO3 shifts the equilibrium towards the gas 

phase), thereby increasing the lifetime of NH3. A net increase in NH3/NH4 results. Because the 

deposit velocity of NH3 is much higher than the deposition of NH4

+

 aerosol, dry deposition of 

NHx 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 HNO3, 

which limits ammonium nitrate (NH4NO3) formation (and for existing aerosol, a decrease in 

HNO3 emissions shifts the equilibrium towards the gas phase), thereby increasing the 

atmospheric lifetime of gaseous NH3. A net increase in the ratio of gaseous NH3 to NH4

+

 aerosol 

in the atmosphere results. Because the deposit velocity of gaseous NH3 is much larger than the 

deposition velocity of NH4

+

 aerosol, dry deposition of NHx increases. 

Case Study Analyses

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? 

25
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

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)

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 

26
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. 

27
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)

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. 

Integrating Across Species Contribution to 

Acidification:

A Proposed EPA Approach...

ANC Deposition

Load

Atmospheric

Concentrations

What is regulated

Total acidifying

deposition

Indicator

Physical

Regulatory

Acceptable depositional rate

Deposition from reduced N

DepNOx –

CNOx

DepNOx

–

CSOx

Allowed NOx+SOx deposition Current

Allowed

28
Applied to Nutrient Enrichment

? 

(your thoughts?)

Deposition

Load

Atmospheric

Concentrations

What is regulated

Total Nutrient Load

Indicator

Deposition from 

reduced N

Allowable Rn load

Non-atmospheric load

Allowed NOx 

deposition

29
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, 

30
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 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

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. 

31
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. 

32
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 (NOx) 

and sulfur dioxide (SO2). 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:

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 

33
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 

34
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:

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 2nd

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:

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. 

35
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 NO3/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 

36
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. 

37
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 NH4

+

. 

Page A3-1, line 15 Subscript 2. 

Page A3-1, line 20 hydrogen ion, and Aln+. 

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, 1st paragraph I suggest adding a sentence or two about 

immobilization/mobilization of SO4

2- and NO3-

 by plants/soil 

organic matter. 

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

Page A3-2, line 12 NO3

-

, Aln+

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+ + NH4

+

) – (SO4

2- + NO3-

 + ...) in (μeq/L) 

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

38
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 

SO4/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 Aln+

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 SO4

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/m2

-yr 

Page A3-22, line 24 This description needs to be expanded or clarified. There are 

more than 200 NADP sites. 

39
Page A3-28. line 25 in the catchment 

Page A3-29, line 19 400 meq/m3

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 Ca2+ 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, 1st 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. 

40
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:

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. 

41
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. 

 

42
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: 

Front matter: 

Page xii: Should the definition of ecological dose be limited to toxicants that inhibit microbe-mediated 

ecological processes? 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

Page 1-3 line 8: I recommend the following wording change “...both ambient air and surface deposited 

species of NOx and SOx... 

Page 1-10 line 23: N2O 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 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 

43
“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

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

Page 3-4 lines 6 and 7: Check the wording. 30 to 70% of the animal wastes can’t be emitted as NH3. 

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 SO4

-2, NO3-

, and NH4

+

. 

Question: Do the QMAC estimates of deposition to terrestrial systems include foliar uptake of NO or NO2

near urban areas or along major roadways where air concentrations are high enough to drive this 

44
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

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 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: Incomplete and not reviewed. 

Chapter 5: Incomplete and not reviewed. 

Chapter 6 

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. 

45
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

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

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 

46
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 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

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 

47
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 

48
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 N2O 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. 

49
6.2 Nitrous Oxide 

Page 6-10: I find little justification for this section on the climate impact due to anthropogenic 

N2O. As stated in the REA, N2O contributes only about 6% of GHGs and the man-induced 

sources of atmospheric N2O are only 10% of that, i.e. .6% of the GHGs. 

Page 6-12 Line 31: The statement “that nitrogen addition increased N2O 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. 

50
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. 

51
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 CO2 / 

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 

52
Johnson, 1985), both of which are cited later in the Terrestrial Case Study, that Al3+ increases to 

the 3/2 power of Ca2+, 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. 

53
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”. 

54
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. 

55
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 

56
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? 

57
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? 

58
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. 

59
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’ 

60
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 

61
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 Hg0

) in the environment, and of “methylmercury” (dimethylmercuric salts) in 

organisms. In the first case, Hg0 is presented as being “reduced” in surface ecosystems to 

become methylmercury; in reality, Hg0

 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, 

62
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., Hgp 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 

63
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, Hg0; 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. 

64
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, SOx, NOx, 

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 NOx/SOx 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 NOx and SOx ? 

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 

65
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 NO2 

and SO2 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? 

66
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: NO3 , NH3 /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 

67
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? 

68
• 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 SOx and 

NOx and resultant S and N deposition and subsequent translation to ecosystem level effects is a 

major challenge. There are good linkages between concentrations of SOx and NOx 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. 

69
1-6 5 Change “NAAQS for NO2 was set at 0.053 ppm”. 

1-6 10 Change to “secondary NAAQS values for SO2 under”. 

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

1-6 19 Change to “EPA was aware that SOx has other”. 

1-6 25 Here and elsewhere be consistent in the use of terms SOx 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 

70
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 “alpine”. 

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

you mean periods of relatively high microbial activity? 

71
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 

72
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 NOx 

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”? 

73
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 NOx emitted in the USA in 2002". 

3-2 3-4 Change to “primary emitters of NOx, mainly as NO and NO2". 

3-2 5 Change to “utilities, with additional contributions”. 

3-2 9 Change to “remainder of anthropogenic emissions”. 

3-2 10 Delete “component”. 

74
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 NH3? 

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 SO2 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 H2S, 

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

these biogenic sulfur sources should be included. 

75
3-6 1-2 Delete since information has been included in my suggested 

modification. 

3-6 3-6 Change to “The proportion of SO2 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 NO2 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. 

76
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. 

77
3-54 14-15 This is not entirely true. There can be instances were ambient 

concentrations of NOx and SOx 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 SOx. 

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 NOx emissions 

account for almost all oxidized nitrogen deposition in the 

Adirondacks Case Study Area, while Figure 3.2-56 shows that 

NH3 emissions account for almost all reduced nitrogen deposition” 

have important implications with respect to making 

recommendations associated with NOx 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 

78
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 SOx and NOx 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 SOx and NOx 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 

79
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 NOx. 

8-9 There are major difficulties in setting national standards for SOx 

and NOx 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. 

80
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 

81
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 “SO4

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 

82
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? 

83
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?

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?

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 SO2 (or NO2) concentrations? What if modeled S emissions were 

rolled back to show alternate lower maximum levels of SO2 (and/or NO2) – 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 

84
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. 

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. 

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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 SO2 & NO2 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 SO2? 

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 SO2 emissions “by state”. 

p. 3-5, line 4: I would change “Industrial” to “Anthropogenic”. 

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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 SO2

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 HNO3, NO3, NH4, 

SO4? 

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 NH4NO3 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 

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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. 

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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 NOx and SOx analyzing 

the whole set of problems associated with these pollutants. 

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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 NOx and SOx? 

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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 SO2 and NO2 from SLAMS/NAMS monitors are not included in the 

measured database? While there may not be many NO2 monitors in rural areas, there should 

still be some measurements of SO2 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 

25th/75th 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. 

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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 

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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). 

93
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. 

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95

Such terms as ecosystem services, and ecosystem health, should be explicitly, consistently, and 

clearly defined among and within these NAAQS review documents.