UNITED STATES ENVIRONMENTAL PROTECTION AGENCY 

 WASHINGTON D.C. 20460 

 

OFFICE OF THE ADMINISTRATOR 

SCIENCE ADVISORY BOARD 

November 18, 2008 

EPA-CASAC-09-002 

The Honorable Stephen L. Johnson 

Administrator 

U.S. Environmental Protection Agency 

1200 Pennsylvania Avenue, N.W.

Washington, D.C. 20460 

 

Subject: Peer Review of EPA’s Integrated Science Assessment (ISA) for Oxides of 

Nitrogen and Sulfur – Environmental Criteria (Second External Review 

Draft) 

Dear Administrator Johnson: 

The Clean Air Scientific Advisory Committee (CASAC or Committee) NOx & SOx

Secondary National Ambient Air Quality Standards (NAAQS) Review Panel (Panel) met on 

October 1-2, 2008 to review EPA’s Integrated Science Assessment for Oxides of Nitrogen and 

Sulfur – Environmental Criteria (Second External Review Draft) (EPA/600/R-08/083, August 

2008) (see Enclosure 1 for the Panel roster). This letter has been reviewed and approved by the 

chartered CASAC at the public conference call on October 30, 2008 (see Enclosure 2 for the 

CASAC Roster). Overall, the Panel found the second draft ISA to be much improved and very 

comprehensive. In this letter, the CASAC Panel offers general comments and recommendations 

to further strengthen the ISA followed by responses to the Agency’s charge questions. 

Comments from the individual Panel members are provided in Enclosure 3. 

1. EPA has done a good job in response to the Panel’s concern regarding imbalance in the 

discussion of NOx deposition vis-à-vis reactive nitrogen (Nr) deposition and how the 

various components of Nr contribute to acidification and nutrient enrichment. (Reactive 

nitrogen refers to the sum of NOx, reduced NHx, and organic nitrogen.) However, there 

remain instances in the second draft where appropriate adjustments have not been made. 

In finalizing the ISA, EPA should carefully consider if references to concentrations of

particular species and/or deposition effect are made correctly, and in particular whether 

and when the term “NOx deposition” should be replaced with “Nr deposition” for clarity 

and accuracy. 

2. The exclusion of the non-ecological welfare effects of NOx and SOx (e.g., effects of 

particulate matter on visibility degradation and climate, and materials damage) in this 
NAAQS review process continues to be an area of concern for the Panel. For a document 

entitled “Integrated Assessment for Oxides of Nitrogen and Sulfur – Environmental 

Criteria” a focus entirely on ecological effects makes its title a misnomer. The Agency 

maintains that these effects are discussed in the assessment documents of other criteria 

pollutants and consequently a full treatment in the current review is unnecessary. To 

ensure that the ISA represents a meaningful assessment of environmental criteria, EPA 

should either rename the document “Ecological Criteria” (which is probably not 

feasible) or keep “Environmental Criteria,” but state clearly in which Agency documents 

the omitted NOx/SOx welfare effects are treated and, at a minimum, provide a short 

synopsis of the key non-ecological effects in the appendix. 

3. Nitrogen is an essential and often limiting plant nutrient. In certain locations, the effects 

of increased Nr deposition may be viewed as ecologically and economically beneficial. 

The Agency should make certain that the treatment and discussion of the impacts of Nr 

deposition in the ISA are balanced. 

4. Given the importance of this document as a foundation for further analyses, there remains 

a general need to carefully review the draft for editorial integrity, with particular focus on 

clarity and accuracy. 

Responses to EPA’s Charge Questions: 

1. We have added an executive summary of the major findings and conclusions to the 

second draft ISA. We have also created a "key findings" section that is intended to 

provide highlights of these conclusions. We are seeking CASAC panel advice and 

comments on these additions to the ISA. To what extent do they provide an 

appropriate level of detail and convey the important scientific conclusions of the 

assessment? 

The Panel is pleased with the inclusion of an Executive Summary in the ISA report and 

found the general tone and scope to be appropriate. However, the Panel does recommend that the 

current draft of the key findings be merged into the executive summary to create a single 

summary document. 

The Executive Summary should incorporate additional conclusions from the ISA 

regarding the geographical distribution and magnitude of effects of current acidification and 

nitrogen deposition in various parts of the United States. An explanation of the implications of 

the extent of current acidification and nitrogen enrichment on ecosystems in terms of lost or 

degraded ecosystem services (e.g., changes in biodiversity, local species extinction, and lost 

habitat) should be considered. The authors should also include further explanatory text on 

emissions sources and atmospheric transport and transformation processes that lead to 

deposition. Brief statements summarizing recent and long-term trends in both ambient air 

concentrations and deposition loads should be clarified because they currently appear 

contradictory. 

The Panel cautions the Agency about the overly generalized statements in the current 

draft ISA that need to be qualified because they are not applicable to all ecosystems and 

2
locations. Acidification, nitrogen enrichment, and mercury methylation effects are indeed 

important for specific sensitive ecosystems within the United States, but generalizations need to 

be made more cautiously. 

The summary text (and both ISA and REA documents in general) should be carefully 

reviewed to determine where total reactive nitrogen is the appropriate term to use rather than 

oxides of nitrogen. EPA should also consult the specific wording suggestions provided within the 

individual Panel members’ written comments. 

2. Chapter 1 has been revised to clarify the scope or focus of this assessment on effects 

related to the deposition of nitrogen and sulfur compounds. In addition, we have

added a discussion of the framework for evaluation of causality for assessing 

ecological effects. Do these revisions adequately characterize the scope of the 

assessment? Does the CASAC panel have recommendations for revisions to the 

causality framework? Is it appropriately applied in the draft ISA? 

The CASAC Panel generally agreed that Chapter 1 provides a clear, concise introduction 

to the ISA. The chapter includes an outline of the intended scope of the current assessment, a 

brief history of past SOx and NOx NAAQS reviews, and a proposed framework for the 

determination of causality in relationships between the pollutants of concern and the resulting 

environmental responses. 

There have been substantial advances to the scientific evidence since the publication of

the most recent Air Quality Criteria Documents for NOx and SOx in 1993 and 1982, respectively. 

Several Panel members recommended expanding the historical summary of secondary SOx and 

NOx reviews and associated technical documents to include references to major EPA or 

inter-agency publications. A few examples include the 1985 EPA Acidic Deposition 

Phenomenon and Its Effects: Critical Assessment Document, the 1990 NAPAP State of Science 

and Technology and Integrated Assessment Reports, and the 1995 EPA Acid Deposition 

Feasibility Study report to Congress. 

The proposed framework for evaluation of causality is logical and clearly presented. 

This framework appears to be followed in subsequent chapters (3 and 4), which contain a 

number of concise, declarative statements that “the evidence is sufficient to infer a causal 

relationship between X causal agent and Y effect.” In most cases, the identified causal agents are 

usually “acidifying deposition” or “reactive nitrogen deposition,” and thus appear to be

non-specific to the traditional NOx and SOx criteria pollutant definitions. It would be helpful to 

include some similar statements of causality that relate emissions to air quality to deposition in 

Chapter 2. Additionally, expanding this causality framework to include a concept such as a 

“significantly contributing factor” as a subset of a “causal factor” (i.e. “the evidence is sufficient 

to infer a causal relationship between Nr deposition, for which oxidized N is a significantly 

contributing factor, and Y and Z effects”) is advised. This concept of a “significantly 

contributing factor” could be important in considering effects resulting from pollutant mixtures, 

as well as for considering effects which result from or are modified by the cumulative influences 

of both current and historical pollutant deposition. 

3
3. Chapters 2 and 3 from the first draft have been combined. Substantially more 

information has been included on NH3 emissions, NH3 measurement techniques, 

NH3 and NH4 concentrations. Additionally, information on NOx and SOx including 

ambient concentrations, deposition levels and their spatial and temporal 

relationships has been added. Have these revisions to Chapter 2 improved its 

assessment of the currently available scientific knowledge on atmospheric sciences 

and its relevance to the evaluation of environmental effects presented in later 

chapters? 

The revisions and additions to Chapter 2 have substantially improved the document. 

EPA has been very responsive to the Panel’s comments on the previous draft. As a result, this 

version is much improved and constitutes a solid scientific basis for the Risk and Exposure 

Assessment (REA). However, there are a few areas where additional information could provide 

useful context for evaluating the risk and exposure assessment work. In particular, because the 

REA relies so heavily on the Community Multiscale Air Quality (CMAQ) model predictions of

deposition, the section on chemical transport model (CTM) models should be augmented with 

specific CMAQ model performance statistics on wet- and dry-deposition. Also, comparisons 

should be made between measurements and model parameterizations for wet- and 

dry-deposition. Some discussion of sensitivity to critical parameters, such as dry deposition 

velocity, precipitation intensity, and depositional resistances, is needed as well. 

The additional maps were helpful for forming visual links between modeled emissions, 

concentration, and deposition. Nevertheless the varying spatial scales and color schemes make 

that comparison difficult. These linkages should be made more explicit either with maps in 

which the scales or colors are consistent, or with scatter plot comparisons in matched grid cells 

(e.g. concentration vs. deposition). 

The current title, ‘Source to Dose’ should be reworded as ‘Source to Deposition’ or 

something similar to reflect the environmental endpoint. Terms that might be unfamiliar to a 

more general audience (e.g., compensation point, ozone production efficiency, and nitrogen 

cascade) should be defined. Wherever possible, units should be consistent and clearly stated: it 

is not always clear if mass S really means mass of sulfur or whether it is really mass of sulfate, 

SO4

2-. We recommend the consistent use of mass of sulfur throughout the document, unless 

clearly stated otherwise. Also, it is important to note that all deposition flux units should be 

presented in kg/ha-yr rather than kg/ha. Similarly, the ISA should express all nitrate deposition 

data in units of kg/ha-yr of nitrogen. The summary section of Chapter 2 (Table 2-25) should be 

expanded to include information on the regional changes in wet- and dry-deposition in the 

western United States. 

Finally, the measurement section should include a discussion of passive samplers and 

additional discussion on historical emissions and deposition. The Panel recognizes that high 

quality historic data on emissions and atmospheric deposition of NOx, NHx, and total reactive 

nitrogen are limited, so more discussion as to how these values are currently estimated, both 

from field measurements as well as in atmospheric models (e.g., CMAQ), and their relevance to 

MAGIC and other water-quality models would be useful. In the interest of trimming some of the 

length of the chapter, some material could be put in the appendices: in particular, the 

4
tropospheric chemistry discussion and the high-time-resolution data (important but less relevant 

for ecological time-frames). 

4. We removed or eliminated redundancy, added summary sections, added additional 

references and reorganized Chapter 3. Revisions to the ecological effects sections are 

given below. Have the revisions improved the characterization of the ecological 

effects? 

a. Consistent with CASAC comments, we expanded our characterization of the 

quantification of chemical effects of acidification in aquatic ecosystems, added 

new conceptual diagrams, and further discussed interactions between 

acidification and plant disease. 

The revised Chapter 3 is logically organized and generally well written. It provides 

comprehensive information on the ecological effects of NOx, NHx, and SOx deposition in aquatic 

and terrestrial ecosystems – including acidification, nutrient enrichment, and sulfur-deposition 

induced methylation of mercury. The conceptual diagrams are useful and the discussion of 

interactions between acidification and plant disease is well written and up to date. 

Important items missing from Chapter 3 include: 

• Observation that despite recent decreases in acidifying deposition and some

improvement in surface water acid-base status there are widespread observations 

of ongoing soil acidification (i.e., decreases in soil exchangeable base cations); 

• Comparison of MAGIC with other watershed models (see Sullivan et al., 2006); 

• Recognition that mercury contamination occurs in terrestrial food webs (see 

Rimmer et al., 2005); and 

• Probable linkage between atmospheric N deposition and biogenic emissions of 

NO and VOCs. 

b. We expanded the discussion of quantitative relationships between nitrogen 

deposition and ecological effects, including published critical loads in the U.S. 

and Europe. In addition, the nitrogen enrichment section was expanded to 

include new discussions on carbon budgeting, biogenic nitrous oxide and 

methane. Information on the linkages between effects and both reduced and 

oxidized forms of nitrogen was emphasized, to the extent data were available. 

Information on the published critical loads data from Europe is mostly contained in Table 

3-24, as adapted from Acherman and Bobbink (2003). This table summarizes biological 

indicators and related critical loads for major ecosystem types in Europe and is probably 

sufficient for this document. However, the Panel recommends that the recent reports of the 

International Cooperative Program (ICP) Forests and ICP Modeling and Maps also be considered 

for updated information on critical load modeling efforts in European forests. The summary of 

the dose-response curves for N deposition and ecological indicators presented in Table 3-25 is 

valuable and should greatly help in developing a large-scale evaluation of critic loads in the US 

and their spatial adaptation. 

5
The section of Chapter 3 dealing with the carbon cycle of the Earth as related to N 

deposition is comprehensive and based on recently published studies. EPA staff should make 

sure that the presentation recognizes that nitrogen and sulfur are essential to plant growth, and 

thus can influence carbon sequestration, with nitrogen often being the limiting nutrient in 

terrestrial ecosystems. The evidence presented shows that ambient N deposition can result in 

increased atmospheric emission of N2O and CH4. 

c. The section on “other” welfare effects was updated to include information on the 

direct phytotoxic effects of nitric acid. 

Although a good discussion of direct effects of nitric acid is provided, it should be 

emphasized that most of the damaging effects of HNO3 have been observed in relatively 

short-term exposures at above-ambient concentrations of the pollutant. Long-term effects of 

lower air concentrations that more closely approximate ambient levels of HNO3 should be 

investigated. Similarly, visible injury to plant foliage due to exposure to NO, NO2 or NH3 have 

been demonstrated primarily at concentrations that rarely occur in ambient air. 

5. In revising the ISA, we have incorporated additional information on the 

indicators of exposure and ecological effects, including increased emphasis on 

quantified relationships in the presentation of information of results in tables 

and summary discussions in Chapter 4. What are the views of the CASAC panel 

on our revisions to focus on quantitative relationships between airborne nitrogen 

and sulfur compounds and ecological indicators? 

The effort made to perform an analysis of existing literature on ecological indicators 

relevant to deposition and acidification is commendable. The meta-analysis appears to be 

extensive and appropriate for the ISA. Much literature has been compiled, including a smattering 

of studies involving high application of N (up to typical fertilizer levels). A summary of

traditional forest and grassland fertilizer studies could strengthen this study, as well. Much of this 

literature is old, but still very relevant – especially the early fertilizer studies by C.O. Tamm et al. 

in Sweden. The tradeoffs associated with the use of nitrogen fertilizer in enhancing the 

productivity of forests, crops and grasslands versus the deleterious environmental impacts 

associated with excess nitrogen being released into the environment, especially surface waters, 

should be articulated more clearly. 

The analysis of indicators is particularly important since a secondary standard (if 

proposed and promulgated) needs to be expressed in terms of SOx, NOx, or NOx + NHx (Nr) and 

then properly linked to the effects through the relevant ecological indicators and causality 

frameworks. In the summary, it would be desirable to continue fortifying the linkages in the 

chain of causation between emission – atmospheric concentration – deposition – dosage – effect 

– ecosystem services. An example of such an end-to-end causality illustration would help. A 

synchronized array of trend charts for each parameter/indicator in the causality chain could be an 

effective way to illustrate the overall framework and key aspects of systems behavior. While it 

may not be necessary to have quantitative trend values for each of the parameters in the causality 

chain ensemble in the ISA, graphically indicating (e.g., dashed trend lines) the poorly understood 

parameters would be a more realistic representation of the current state of the causality 

6
framework. It is also appropriate to recognize how the causality framework may be used in both 

prospective and retrospective analyses. 

In summary, with incorporation of the Panel’s recommendations to strengthen the 

document, this second draft ISA will provide appropriate scientific support for the risk and 

exposure assessments. The CASAC was pleased to review this second draft of the ISA and looks 

forward to the Agency’s response. 

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

7
Enclosure 1: Roster of CASAC NOx & SOx Secondary NAAQS Review Panel 

U.S. Environmental Protection Agency 

Clean Air Scientific Advisory Committee 

NOx & SOx Secondary NAAQS Review Panel 

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. Naresh Kumar, Senior Program Manager, Environment Division, Electric Power Research 

Institute, Palo Alto, CA 

Dr. Myron Mitchell, Distinguished Professor and Director, College of Environmental and 

Forestry, Council on Hydrologic Systems Science, State University of New York, Syracuse, NY 

Mr. Richard L. Poirot, Environmental Analyst, Air Pollution Control Division, Department of 

Environmental Conservation, Vermont Agency of Natural Resources, Waterbury, VT

8
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) 

9
Enclosure 2: Roster of the chartered CASAC 

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)

10
Enclosure 3: Compilation of Individual Panel Member Comments on EPA’s Integrated Science 

Assessment (ISA) for Oxides of Nitrogen and Sulfur – Environmental Criteria (Second External 

Review Draft)

Comments received: 

Dr. Praveen Amar ......................................................................................................................... 12 

Dr. Andrzej Bytnerowicz .............................................................................................................. 14 

Ms. Lauraine Chestnut.................................................................................................................. 17 

Dr. Ellis Cowling .......................................................................................................................... 19 

Dr. Douglas Crawford-Brown ...................................................................................................... 24 

Dr. Charles T. Driscoll.................................................................................................................. 28 

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

Dr. Rudolf Husar........................................................................................................................... 46 

Dr. Dale Johnson........................................................................................................................... 49 

Dr. Donna Kenski ......................................................................................................................... 53 

Dr. Myron J. Mitchell ................................................................................................................... 55 

Mr. Richard L. Poirot.................................................................................................................... 71 

Mr. David Shaw............................................................................................................................ 73 

11
Dr. Praveen Amar 

Question # 3: Chapters 2 and 3 from the first draft have been combined. Substantially more 

information has been included on NH3 emissions, NH3 measurement techniques, NH3 and NH4 

concentrations. Additionally, information on NOx and SOx including ambient concentrations, 

deposition levels, and their spatial and temporal relationships has been added. Have these 

revisions to Chapter 2 improved its assessment of the currently available scientific knowledge of 

atmospheric sciences and its relevance to the evaluation of environmental effects presented in 

the later chapters? 

Response: 

I would like to note that the previous Chapters 2 and 3, now combined in current Chapter 2, is a 

great improvement over the first ISA Draft. It is quite clear that very useful and relevant 

information has been included on reduced form of nitrogen (ammonia emissions, measurement 

techniques to estimate ambient levels of ammonia and inter comparison of these techniques, as 

well as concentrations of nitrate in particulate form). Equally useful is the more clear 

presentation on NOx and SOx (concentrations, deposition levels, trends in these levels, as well as 

spatial and temporal character of these two pollutants). EPA staff needs to be commended for 

this. 

I have several specific comments that are outlined below: 

1. I think the Title of the Chapter needs to change from “Source to Dose” to “Source and 

Exposure,” or something similar. This is because this Chapter is NOT about dose. In fact, a quick 

“search” shows that the word “dose” appears only once in this Chapter of more than 200 pages 

(page 2-116 to be exact). This is not surprising because this Chapter talks about emissions, 

concentrations, measurement techniques, trends, etc. but does not talk about dose. In fact, 

Chapter 3 is about “dose-response” and the word ‘dose” appears in that Chapter frequently and 

correctly. 

2. On page 2-2, please describe N cascade of Galloway in a little more detail since this is an 

important concept and not widely understood. 

3. Page 2-19: I do not understand “compensation point” of ammonia. Needs some clarification. 

What is being compensated? Ammonia?

4. Page 2-20: Line 10: I do not think “biogenic production” of ammonia from agriculture (chiefly 

from livestock) is the right word. It is as anthropogenic as it can get! 

5. P (O3): Ozone Production Efficiency: It is an important concept. However, I do not think it is 

clearly defined in the document (as number of molecules of ozone produced per molecule of 

NOx over a certain time period and over a spatial extent, etc.). I suggest it should be explicitly 

12
defined first time it appears. Just like N cascade, it is important concept and needs to be 

explained clearly. 

6. Page 2-20: Para under the Figure: I had made this comment on the first ISA Draft. Ammonia 

emission totals are dominated by livestock/fertilizer operations because they simply are. They 

are dominant source of ammonia in their own right and not because mobile sources are not. 

Please drop the words “for these reasons...” on line 9. 

7. I have not thoroughly read the section on Halogen Chemistry (page 2-41). Please make sure it 

is improvement on the version included in first draft and that it is integrated with the general 

theme of its relationship with, and effect on, SOx/NOx/NH3 chemistry. 

8. A general comment: please be consistent and clear that you mean to give quantitative values 

of nitrogen and sulfur deposition in the units of “N” and “S” for kg of N/ha/yr, and kg of 

S/ha/yr., etc. If they are given in terms of sulfate (SO4) or nitrate (NO3), they should be clearly 

labeled as such. I recommend “N” and “S”. To be inserted 

13
Dr. Andrzej Bytnerowicz

Question 4. Have the revisions improved the characterization of the ecological effects?

In general, Chapter 3 presents comprehensive information on ecological effects of SOx and 

NOx. The chapter is logically organized, contains current knowledge supported by large number 

of informative tables and figures. Good examples of very informative tables are Table 3-12 

presenting summary of knowledge on the effects of fire on nutrient concentrations in forests in 

California and Nevada and Table 3-15 summarizing N effects on forest carbon cycling. In 

summary – the revisions improved characterization of the ecological effects in the document. 

Summaries in the end of each sub-sections are very useful. Remark - summaries from Section 

3.2 are not listed in the Table of Contents. 

References in the text and list of citations are not always matching. Some of them are not cited 

properly. Examples of this deficiency are the references of Bytnerowicz et al., or Temple and 

Taylor (1983), incorrectly cited in the text as Temple (1983). 

Remark - careful technical editing of a final version of this document is recommended. 

 

Question 4a. Chemical effects of acidification in aquatic ecosystems

Information on acidifying effects of NOx and SOx aquatic ecosystems is comprehensive. 

Conceptual diagrams for this section have been correctly chosen. Examples of such diagrams are 

Figure 3.1 presenting fluxes of major ions associated with S depositions or Figure 3-5 showing 

the effects of acidic deposition on Ca supply in trees, their physiology, growth and resistance to 

environmental stresses. 

Discussion of interactions between acidification and plant disease is well written and up to date. 

Interaction of acidity with foliar, membrane-associated calcium, which influences responses of 

trees to changing environmental conditions, such as cold temperatures and winter injury, is very 

well described. Remark - a reference to Figure 3-5 should be made in the text. 

Question 4b. Quantitative relationships between nitrogen deposition and ecological effects 

Information on the published critical loads data from Europe is mostly contained in Table 3-24 

adapted from Acherman and Bobbink (2003). The table summarizes biological indicators and 

related critical loads for major ecosystem types in Europe and is probably sufficient for this 

document. However, I would like to recommend that the recent reports of the ICP Forests and 

ICP Modeling and Maps are also considered for updated information on CL modeling efforts in 

the European forests. Summary of the dose-response curves for N deposition and ecological 

indicators presented in Table 3-25 is valuable and should greatly help in developing a large-scale 

evaluation of critical loads in the U.S and its spatial extrapolation. 

14
The nitrogen enrichment section has been expanded and contains discussion on carbon 

budgeting, and fluxes of biogenic nitrous oxide and methane. Section on the carbon budget as 

related to N deposition is comprehensive and based on the recent scientific literature. Figure 3-35 

shows interactions between the N and C cycles while Table 3-15 summarizes N effects on forest 

carbon cycling in Europe and North America. The section is well organized and written and is 

supported by informative graphs and summary tables. Specific remark – page 3-136, citation of 

Sutton et al (2008) does not seem to be correct. Section on methane and nitrous oxide flux is 

based on the meta-analysis of the recently published studies. The presented evidence shows that 

N deposition results in higher concentrations of these greenhouse gases in the atmosphere. 

Question 4c. Other welfare effects 

Good discussion of direct effects of nitric acid is provided. However, it should be emphasized 

that the described damaging effects of HNO3 have been demonstrated in controlled experiments 

for relatively short-term exposures at highly elevated concentrations of the pollutant. Long-term

effects of lower, closer to ambient, levels of HNO3, should be investigated. Similarly, visible 

injury to plant foliage due to NO, NO2 or NH3 exposures have been demonstrated only at very 

high concentrations (controlled studies, industrial spills), at the levels that normally do not occur 

in ambient air. 

Table 3-28 on direct effects of SO2 should be moved closer to the text describing these effects. 

Remark - please see my above comments regarding a need for correct citation of references in 

this sub-section. 

Executive Summary

Although it generally adequately summarizes the ISA document, there are several deficiencies 

that should be resolved: 

1. In the Introduction, or in a footnote to it, it should be noted that 1 ppm = 1000 ppb. Readers 

less familiar with science may not know this fact, and both units are used throughout the text. 

2. In the section “Current concentrations and deposition in the US”, there are some statements 

that are not correct. For instance, on page 2, last paragraph of the first column, a statement is 

made that the highest mean N deposition of about 9 kg/ha/yr totals is in the Ohio River valley. 

This value seems to be too low – I suspect that this is only the wet portion of N deposition. On

the same page, the second paragraph of the second column, states that the model-predicted 

values in some regions of the Adirondacks are >20 kg N/ha/yr. In southern California the 

model-predicted total N deposition can be as high as 32 kg N/ha/yr. Actually, according to Fenn 

(2008), the highest values can be as high as >100 kg N/ha/yr on the western slopes of the San 

Bernardino Mountains. However, that high deposition mostly results from deposition of HNO3, 

NH3 and particulate NO3

-

 and NH4

+

, not NO and NO2 as the Executive Summary states. 

3. In the section “Ecological effects of N deposition” a clear statement is needed that ecological 

effects of NOx and SOx should be considered in a context of often unpredictable climate changes. 

15
Ecological effects of NOx and SOx will also depend on other stressors, such as elevated

background levels of ambient ozone, drought, insect and pathogens outbreaks, etc. 

 

4. On Page 6, 3rd paragraph of the first column – a statement “Exposures of NO2, nitric oxide 

(NO), peroxyacetyl nitrate (PAN) and nitric acid (HNO3) cause similar forms of plant injury and 

decreased growth” is not true. Characteristics of foliar injury caused by these various compounds 

are actually quite different (please see Bytnerowicz et al., 1998 for discussion of this issue). 

16
Ms. Lauraine Chestnut 

Charge Question 1: Executive summary and key findings 

The Executive Summary (ES) is a useful addition to the document, but it needs a little more 

detail to communicate more effectively the nature and magnitude of current harmful effects on 

ecosystems from N and S deposition in the US. As currently written, it describes the effects that 

can happen but says too little about the extent to which these are currently happening. The “key 

findings” document is largely redundant with the ES, but uses some nice formatting and boxes to 

highlight key points. I suggest merging these into one summary document and making use of text 

boxes to highlight some of the key conclusions. 

The “Scope” section needs a paragraph or two explaining the transport of emissions and their 

interaction in the atmosphere that result in N and S deposition. The first paragraph in Section 4-1 

on page 4-1 in the conclusions section provides a description of this at a level of detail that 

would be useful in the ES. 

A paragraph or two on the major sources of emissions that lead to N and S deposition would be 

helpful in this section. This information is well described in Chapter 2. 

The “Current concentrations” section needs to reconcile the information about declines in 

ambient concentrations from 1990 to 2005 versus the “10-fold increase” in deposition in the past 

100 years. It would be appropriate here and in the Introduction chapter to mention the Acid Rain 

Program (Title IV) as one of the main reasons for the decrease in emissions (especially SO2) 

from 1990 to 2005 and to note that the reductions from this program are now close to fully 

implemented and are leveling off. This program is not part of the NAAQS process, but it seems 

odd not to mention such a major program that was motivated by concern about the effects of acid 

deposition. 

In the section on “Ecological effects of acidification” there needs to be more descriptive 

information about the effects and their current extent and significance in the US. I’m not sure it 

comes through clearly that certain species of fish, particularly ones that people like to catch, have 

died off and cannot live in these acidified lakes and streams. I’m not sure the words “decline in 

fish species richness” quite gets the significance across. The discussions of the Adirondacks and 

Shenandoah and expectations of future acidification conditions at current deposition levels are 

good and are examples of the kinds of descriptive implications appropriate for the ES. 

In the section on “Ecological effects of N deposition” there needs to be more descriptive 

information about the extent and significance of eutrophication of estuarine ecosystems in the 

US. How many of the major estuaries in the US show significant eutrophication? What is the 

extent of losses to fisheries and habitat?

The “key findings” section will go away if merged into the ES, but material that is not 

duplicative should be brought into the ES. In that light here are some specific comments on the 

key findings: 

17
• The first box would be better labeled “main effects” than key findings. It describes the 

types of effects, but does not say how widespread or significant these effects are in the 

US at current deposition levels. 

• In the first paragraph after the first box, the parenthetical phrase after “secondary” is 

confusing. Ecological effects are public welfare effects, as I understand the language of 

the Clean Air Act. It would be more straightforward to just explain here that this ISA is 

focusing on ecological effects of deposition, and other welfare effects of PM, SO2 and 

NOx are dealt with elsewhere. 

• In the first set of bullets under effects of acidification, it would be helpful to distinguish 

between ecosystems that are sensitive and those that are experiencing significant effects 

on ecosystem functions at current deposition levels. 

• The second bullet on deposition levels is good, but seems out of place in this list. A little 

more location dimension to these numbers would be useful—perhaps a map. 

• It might be easier to for the reader if the sections on effects of acidification and N 

deposition were both subdivided into aquatic and terrestrial subsections. 

• The acidification section needs more description of where and how significant are current 

effects on ecosystems. The last paragraph in this section is good, but the heading needs to 

be qualified—some ecosystems that are currently experiencing harmful effects.... 

• Bullets under effects of nitrogen deposition: Separate the points about effects, deposition 

levels, and monitoring. The monitoring points need some explanation of why these 

monitoring limitations are problematic. Add some location information on the deposition 

rates. 

• In the section on effects of N deposition add information on where there are significant 

observed effects in the US now, and describe the extent of the effects. 

• The figure on interactions between carbon and nitrogen cycles needs some discussion. It 

in not clear what the implications are. 

Charge Question 2: Chapter 1 

Some discussion of how Title IV (Acid Rain Program) fits into this history would be appropriate. 

Also some mention of the 1995 “Acid deposition standard feasibility study” report to Congress 

would be appropriate as part of the background. 

Charge Question 4: Chapter 3 

Chapter 3 does a much better job now in describing the significance of the effects on ecosystems 

and of using the “case studies” as examples of these effects. Section 3.3.9 on ecosystem services 

affected by N deposition is good and helps set the stage for what comes in the REA. It would be 

useful if something similar were done for acidification in section 3.2. 

18
Dr. Ellis Cowling 

General Comments on the New NAAQS Review Processes

Before dealing with the details of my specific assignments during the October 1-2, 2008 meeting 

of CASAC I would like to offer a few general comments about the current efforts to streamline 

the NAAQS review processes and how these changes in process are playing out in the case 

of the CASAC Review of the Secondary (public-welfare based) NAAQS for NOx and SOx.

Many of us in CASAC have been very pleased that EPA has recently shown increased 

willingness to think more holistically – and in more fully integrated ways – about both the 

policy-relevant science and the practical arts of air quality management aimed at protection of 

both public welfare and public health. These shifts in both emphasis and approach have 

included: 

1) Increased emphasis on scientific questions that are as directly relevant as possible to 

well-defined policy questions of concern to EPA. This shift to greater policy relevancy 

in our scientific discussions within CASAC will increase efficiency in the preparation 

and CASAC review of NAAQS documents, and also help streamline the NAAQS review 

Process. For example, the following policy-defining statement was recommended as a 

guide during NAAQS review processes: 

“What scientific evidence and/or scientific insights have been developed since the last

review to indicate if the current public-health based and/or the current public-welfare 

based NAAQS need to be revised or if alternative levels, indicators, statistical forms, or 

averaging times of these standards are needed to protect public health with an 

adequate margin of safety and to protect public welfare?” 

2) More frequent discussion about both public-welfare and public-health impacts of 

mixtures of air pollutants; 

3) Separation of the preparation and review of documentation for a Secondary 

(public-welfare-based) NAAQS from the (previously always dominating) Primary 

(public-health-based) NAAQS review processes, 

4) The decision by the Science Advisory Board (SAB) of EPA in January 2007 to establish 

a special Integrated Nitrogen Committee (INC) with the following set of objectives: 

a) Identify and analyze, from a scientific perspective, the problems nitrogen presents 

in the environment and the links among them, 

b) Evaluate the contribution an integrated nitrogen management strategy could make 

to environmental protection, 

c) Identify additional risk management options for EPA’s consideration, and 

d) Make recommendations to EPA concerning improvements in nitrogen research to 

support risk reduction, 

19
5) The unprecedented decisions by EPA to undertake an integrated [simultaneous] 

review of the Secondary NAAQS for two Criteria Pollutants at the same time 

[Oxides of Nitrogen (NOx) and Oxides of Sulfur (SOx)], and to facilitate the 

required CASAC and public reviews of: 

i) an Integrated Science Assessment (ISA) for NOx and SOx -- to be issued in 

December 2008, 

ii) a Risk/Exposure Assessment (R/EA) -- to be completed by July 2009, 

iii) a Policy Assessment/Rulemaking document prepared in the form of an Advanced 

Notice of Proposed Rule Making (ANPR) -- by August 2009, and thus to 

achieve 

iv) Final Rule Making -- prior to a court-ordered deadline of October 19, 2010. 

In view of this demanding series of deadlines following our October 1-2 CASAC meeting, it is 

obvious that EPA and CASAC now have only about: 

i) 3 months to complete the Final ISA for NOx and SOx, and 

ii) 11 months in which to complete reviews of both the First and Second External 

Review Drafts and then to prepare a Final Draft R/EA for NOx and SOx. 

But we now have the considerable advantage that the new NAAQS review process envisions 

preparation of much more concise and much more policy-focused ISA and R/EA documents

for the present Integrated Secondary NAAQS for NOx and SOx than has historically been 

achieved in the encyclopedic Criteria Documents that have been prepared during the years 

since 1970. 

Specific Comments on the ISA for the Secondary Nitrogen and Sulfur Pollution NAAQS 

Standards

The present Second Draft ISA is a very huge volume which consists of: 

Chapter 1 – an appropriately short (10 page) “Introduction,” 

Chapter 2 – an exhaustive (202 page) analysis of “Source to Dose” relationships for both 

NOx and SOx,, 

Chapter 3 – a similarly exhaustive (237 page) analysis of Ecological and Other Welfare 

Effects. This chapter is appropriately focused on five critically important impacts of 

atmospherically deposited reactive nitrogen and sulfur compounds – acidification and 

nutrient enrichment of aquatic and terrestrial ecosystems and sulfur induced increase in 

methylation of mercury, 

Chapter 4 – a reasonably short (33 page) Summary and Conclusions chapter that includes 

many statements of conclusion from the science that is reviewed Chapters 2 and 3, 

Glossary – a very neat set of definitions for many of the specialized terms used in Chapters 

1-4, 

References – an exhaustive (124 page) list of (nearly 3000 scientific literature citations!) 

most of which are relevant to the possible revision of the current NAAQS standards for 

nitrogen and sulfur pollution. It would be very valuable to identify a limited number of 

20
these documents that are especially significant in terms of the policy purpose for which 

this ISA was written. 

Having carefully reviewed all of these several parts of this Second Draft ISA, I was: 

1) Generally satisfied with the parts of Chapters 1-3 that deal with oxides of nitrogen 

and sulfur, but was disappointed that much less attention continues to be given in 

Chapters 2 and 3 to the quantitative importance and significant biological impacts 

of chemically reduced forms of total reactive nitrogen. This is true with regard to 

both acidification and nutrient enrichment of aquatic and terrestrial ecosystems.

2) In spite of the ‘relatively less attention’ comment mentioned in comment 1 (above), I 

was very pleased to read in Chapter 4 the 23 bold-face-type statements regarding 

the “sufficiency of evidence to infer a causal relationship between ‘acidifying 

deposition’ and/or ‘Nr deposition’” and each of the many adverse acidification and 

nutrient enrichment effects of atmospheric deposition reactive nitrogen and sulfur 

pollution on aquatic and terrestrial ecosystems that are discussed in Chapters 2 and 

3.

3) At the same time, however, I was disappointed that almost all of the 

non-bold-faced-type conclusions among the Summary and Conclusions statements 

in Chapter 4 were notably lacking in specific articulation of the quantitative 

importance and significant biological impacts of chemically reduced and organic 

forms of reactive nitrogen in both terrestrial and aquatic ecosystems.

4) This lack of specific articulation of the quantitative importance and significant 

biological impacts of chemically reduced and organic forms of reactive nitrogen was 

especially worrisome in the final “Conclusion” statement in the Executive Summary 

of this ISA. 

Specific Comments on the Executive Summary of the ISA

This final Conclusion in the Executive Summary includes the following two statements 

both of which are incorrect and misleading in terms of their relevance to the policy 

purpose for which this ISA is being written:

“Acidification is driven by the deposition resulting from NOx and SOx pollution.” 

“In addition to acidification, deposition resulting from NOx, along with other 

sources of reactive nitrogen (e.g., fertilizers, waste water, and atmospheric 

ammonia deposition), causes a suite of ecological problems including biodiversity 

losses, disease, eutrophication, and harmful algal blooms.” 

Permit me to offer the following improved and more accurate wording of the final 

Conclusion of the Executive Summary (please note especially the explicit recognition of

both reduced and oxidized forms of reactive nitrogen -- both of these chemical forms of 

nitrogen are significant “Pollutants of Concern” as well as causal factors in both 

acidification and nutrient enrichment: 

21
Conclusion 

The three main effects of nitrogen and sulfur pollution presented in this ISA are 

acidification, nitrogen enrichment, and methylation of mercury. Acidification of 

ecosystems is driven primarily by atmospheric deposition of NOx, NHx, and SOx. 

These three pollutants cause a cascade of effects that harm both aquatic and terrestrial 

ecosystems including localized extinction of fish populations and other aquatic species, 

and slower growth and injury to forests. In addition to acidification, atmospheric 

deposition resulting from NOx and NHx emissions, along with other sources of reactive 

nitrogen (e.g., fertilizers and waste waters) cause a suite of ecological problems including 

biodiversity losses, disease in aquatic and terrestrial organisms, as well as eutrophication 

and harmful algal blooms in both fresh water, estuarine, and ocean ecosystems. Both

gaseous sulfur compounds and particulate sulfate can interact with methanogenic bacteria 

to produce methyl mercury, a powerful toxin that can bioaccumulate to toxic amounts in 

food webs at higher trophic levels (e.g., otters, king fishers.) 

Specific Comments on the Value of the Recently-Posted Document Titled

“Selected Recommendations and Findings from the Integrated Nitrogen 

Committee” and

an earlier Resolution by the Integrated Nitrogen Committee of EPA’s Science 

Advisory Board

As many of us on the CASAC NOx/SOx Secondary NAAQS Panel will recall, during our 

October 30, 2007 CASAC meeting, the following Resolution was received from the SAB’s 

Integrated Nitrogen Committee. 

Resolution from the Integrated Nitrogen Committee of the Science Advisory Board -- 

for Consideration by the CASAC Secondary NAAQS NOx and SOx Review Panel 

During the ongoing meeting of the EPA Science Advisory Board’s Integrated Nitrogen 

Committee (INC) -- meeting at SAB Headquarters in Washington DC on October 29-31, 2007 -- 

the several members and Chair of the INC, Dr. James Galloway of the University of Virginia, 

asked me (as the CASAC-designated liaison person to the Science Advisory Board’s Integrated 

Nitrogen Committee) to present the following Resolution (which was developed and approved 

by the INC) for consideration during the CASAC review of the NAAQS for NOx and SOx 

during our CASAC Conference Call Consultation on October 30, 2007. 

Resolution 

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. 

This Resolution is an important part of the scientific foundation and rationale behind my concern 

that the “Second External Review Draft of the ISA for Oxides of Nitrogen and Sulfur – 

Environmental Criteria” and the First Draft of the “Risk and Exposure Assessment for Review of 

the Secondary National Ambient Air Quality Standards for Oxides of Nitrogen and Oxides of 

22
Sulfur” are not consistent with the central idea of this Resolution – that both chemically reduced 

and chemically oxidized forms of reactive nitrogen must be considered in the current round of 

reviews of the NOx/SOx Secondary NAAQS Standards. 

Further justification for these ideas -- and policy recommendations that derive from the extended 

deliberations of the SAB’s Integrated Nitrogen Committee -- are contained in a recently 

completed Summary Document titled: “Selected Recommendations and Findings from the 

Integrated Nitrogen Committee.” This document was recently posted on the SAB website and 

thus is available for public review at the following URL: 

http://yosemite.epa.gov/sab/sabproduct.nsf/MeetingCal/EFB3E4663E2143F88525746

5006C5B32?OpenDocument

23
Dr. Douglas Crawford-Brown

I am charged primarily with Question 1, and so my comments are primarily on that question. 

However, since this Charge Question covers the Executive Summary and a “key findings” 

section, the review makes reference to other chapters where these materials are found. The 

specific Charge Question addressed is: 

1. We have added an executive summary of the major findings and conclusions to the 

second draft ISA. We have also created a "key findings" section that is intended to provide 

highlights of these conclusions. We are seeking CASAC panel advice and comments on these 

additions to the ISA. To what extent do they provide an appropriate level of detail and convey 

the important scientific conclusions of the assessment? 

The short answer is yes and yes. They provide the appropriate level of detail (with a few caveats 

noted below) and convey the most important conclusions from other chapters. As I will note 

below, however, it is less clear where this “key findings” section is located. Given the Charge 

Question, I had expected to find it in the Executive Summary or listed in the Table of Contents. 

It is in neither. 

In the Executive Summary on Page 1, there is a segue-way needed between gas and deposition 

effects. The first section ends by saying that the existing NAAQS were set on the basis of direct 

exposure to gases. Then the next paragraph begins by stating that this document focuses on 

deposition of NOx and SOx, which will be dominated by the particulate phase. A reader will 

wonder whether the current document is therefore a supplement to the previous NAAQS, or has 

changed the focus of concern – and if so, why. 

Then in the same area of the document, the authors state that understanding the ecological effects 

requires considering many reduced forms of N. While I agree with this, the statement does not 

say “in addition to the oxidized forms”, and so the reader will again be confused, wondering if 

the NAAQS has changed completely to deposition rather than gas phase, and to reduced rather 

than oxidized forms. It is simply a problem with the way this sentence is structured, not with the 

list of forms shown or the intent of the sentence. 

In the next paragraph, there is a discussion of the extent of decrease in NOx and SOx. The 

numbers are correct given data in later chapters, but there needs to be clarity as to what the 35% 

and 50% figures refer to. Are these mean annual levels measured at monitors; mean levels of 

exposure (perhaps population-weighted)? Something else? A few words of explanation would 

resolve this problem. 

And then later, the comment is made (correctly) that N deposition has been increased 10 fold 

over the past century. The problem with this statement is that it seems to contradict the finding 

that ambient levels have been in fact going down over the past decade. The problem lies, of 

course, in specifying the different periods of time over which the trends are being discussed. 

Surely N deposition has been going down as ambient levels have gone down, even if they went 

up quite a bit more prior to the recent decline. Or, is the difference between the two sections that 

24
the first refers specifically to NOx and the latter to all forms of N deposition, with perhaps the 

reduced forms continuing to go up (I doubt this is the case, but just want to be sure)? If I am

confused, the average reader probably will be as well. 

I fully support the conclusion on the inadequacy of the current monitoring network for 

deposition. Some more comment is needed on how that system might be better structured to 

resolve the specific areas of uncertainty found in the ISA. 

I believe the later chapters support the conclusion that “available evidence is sufficient to infer a 

causal relationship between acidifying deposition at current levels and effects on the following 

aspects of ecosystem structure and function: 

(1) biogeochemistry related to terrestrial and aquatic ecosystems; 

(2) biota in terrestrial and aquatic ecosystems.” 

As with the previous ISA, however, I remain less convinced that we can quantify this causal 

relationship sufficiently to determine an ambient concentration that would be judged to produce 

an acceptable level of impact, and nothing in the subsequent chapters makes me more 

comfortable with this task. Surely the ecosystem effects must be treated somewhat like the 

human health effects, where a change in some measure of health is not in itself evidence of 

unacceptably high adversity of effect. At some point, the changes noted in ecosystem measures 

of health do become high enough to consider not just present but adverse, but the ISA is not yet 

able to establish where that might be in most cases. I suspect this will drive the regulatory 

process to rely on the primary standards, with the secondary effects providing supporting 

evidence for the need to further lower ambient levels – even if it cannot specify how far they 

should be lowered. 

With respect to climate change, I disagree with the way the following statement is introduced 

and phrased: “N deposition often increases primary productivity. This does not necessarily 

increase C sequestration. C budgets are complicated by numerous factors that influence carbon 

exchange (e.g. climate).” The problem with the phrase is that in later chapters, the argument is 

made that nitrogen oxides can contribute to climate change both by being greenhouse gases and 

by reducing carbon storage in flora. The phrase “This does not necessarily increase C 

sequestration” is correct, but I would suggest that on average the increase in primary productivity 

will offset the adverse effects on plant growth. Perhaps I am wrong in this, but the later chapters 

don’t provide any data to suggest the correct answer one way or the other, and so the statement 

in the Executive Summary strikes me as an off-hand way to disarm a possibility that runs counter 

to the story being told (that NOx is bad for climate change). A much better scientific analysis is 

needed in the document to provide any firm conclusions one way or the other, or the impression 

will be left that the EPA staff have deliberately chosen only some aspects of the N-climate 

change connection to bolster their case. 

I agree completely with the focus on acidification and nitrogen enrichment as the two primary set 

of effects. There is sufficient evidence in later chapters to infer a causal relationship between 

current ambient levels in some geographic areas and adverse ecological effects. But I am less 

convinced by the methyl mercury argument. I don’t mean I don’t believe the case is made for 

sulfate leading to methyl mercury, but rather that I don’t see sufficient evidence to suggest that 

25
current levels of sulfate are causing methyl mercury concentrations that are of concern. I suppose 

the argument could be made that any methyl mercury increase is too much given current levels 

of methyl mercury in the food chain, but this argument isn’t made or supported in later chapters. 

On the issue of causal relationships, found in Chapter 1, the authors have done a good job of both 

classifying the causal categories and explaining the criteria for judging causality. As with 

previous ISAs, however, it is much less clear that any formal framework has been used to 

determine whether a given body of evidence does or does not satisfy these criteria, or how the 

criteria are to be balanced when one is satisfied but not another. The result is a purely subjective 

judgment of the strength of causality. I would agree that all judgments are in the end subjective, 

but there are judgments where the basis for that subjectivity is reached in a systematic fashion 

clearly elucidated, and judgments that result from reflection in a way that can’t be – or isn’t - 

described. I believe the current ISA falls into the latter group. I suspect, therefore, that different 

stakeholders would come to different judgments even when faced with the same information. 

Having said that, I still support the particular judgments of causality made in the ISA even if the 

document doesn’t let me see clearly the thinking that led to them. 

A significant problem I continue to have is that the causal judgments are too generic. The 

question that seems to be asked is whether there is a causal connection between deposition and 

effect at some level of deposition, rather than at the levels of deposition that currently exist or

might exist under alternative NAAQS. I always take it for granted that any substance will 

produce adverse effects at some level of exposure, and so I was looking for a bit more 

policy-relevant judgments of causal connections in the current document. The levels of 

deposition at which the causal connection has been established needs to be specified for each 

effect. 

With respect to the Key Findings section, I am generally comfortable that this reflects the major 

findings as described in other parts of the document. However, this section shares a problem I 

already noted above: that the claims of effects make little or no reference to the loadings and 

ambient concentrations at which the effects may be considered both causal and adverse. As a 

result, the reader is left with the impression that all of these effects may be taking place under the 

current NAAQS and would be alleviated with a lower NAAQS, neither of which is actually 

established elsewhere in the ISA. I think this problem is especially acute in the discussion of 

methyl mercury production, where I would disagree that evidence presented elsewhere in the 

ISA does not support a claim that sulfates currently are causing any of the fish advisories 

mentioned. 

As to the quantified relationships on page 4, I am not sure I would call these relationships. They 

are instead levels at which effects have been noted. But it also is the case that the effects are not 

shown to be of levels considered adverse in any sense of that word defined in the ISA. 

 

26
Finally, there is a policy issue I would like to raise. I believe the ISA lays the appropriate 

groundwork for assessing whether current levels of N and S deposition are protective, and draws 

the right scientific conclusions on this issue. However, it is necessary to ask whether any 

continuing effects are due to the need for a lower NAAQS, or from a failure to fully enforce the 

current NAAQS. I see no discussion of that point, and would expect at least a sentence or two on 

this important issue. The policy solution is quite different depending on the answer. 

27
Dr. Charles T. Driscoll 

The second draft of the ISA is an improvement over the first draft. There are still many 

mistakes and errors that need to be fixed. Although the authors indicate they have eliminated 

redundancy, I find the document continues to be highly repetitive. 

I would like to see the units of deposition expressed as kg/ha-yr. 

I do not like the term acidifying deposition. Why introduce a new term? I understand where 

the authors are coming from, but we have three decades of acid or acidic deposition; why create 

unnecessary confusion?

Many references cited do not include the et al. 

I had difficulty with units and many of the figures. It would be very helpful to clarify the mass 

basis of concentrations, emissions, deposition (e.g., mass as S vs. mass as SO4). I had difficulty 

in the atmosphere section with English units. It is difficult to relate these to the metric units in 

the effects section. If it is necessary to present English units please also present their metric 

equivalent. 

I found several of the figure and tables very difficult to read due to small fonts. I understand 

that space is an issue but anything hat could be done to help this situation would be helpful. 

Sometimes there is a difference in the balance of the summary comments. Some comments are 

emphasized in the summary sections but are barely mentioned in the body of the text. I have 

tried to point these out in my specific comments. 

Specific comments:

Executive Summary

I liked the Executive Summary. I think it could be improved by adding some context to the 

beginning of the executive summary. 

Page 1, para 1, line 2 Concise? Please give me a break. 

Page 1, para 2, line 6 nitrogen 

Page 1, para 2, line 10 Define Nr 

Page 2, para 4, line 3 and 8 Change to... limited data exist 

28
Page 3, para 4, line 18 Change to... S deposition is generally the primary cause of chronic 

acidification with secondary contributions from nitrate due to N 

deposition. 

Page 3, para 4, line 18 Change to... 1980s and 1990s 

Page 3, para 4, line 20 Change to... were no longer acidic during baseflow in the... 

Page 3, para 5, line 3 Change to... Northeast, Southeast and Mountain West 

Page 4, para 4, line 6 between 5.5 and 10 kg N/ha-yr 

Page 5, para 2, line 1 Lichens are among the ... 

Page 6, para 1, line 8 This statement is misleading. Watersheds with high production 

of methyl mercury have been widely observed, not only the 

Northeast. 

Page 6, para 4, line 16 Rewrite sentence. Particulate sulfate interact with methanogenic 

bacteria. This sentence is not correct and doesn’t make sense. 

How about the activity of sulfate reducing bacteria generates 

methyl mercury?

Chapter 1. Introduction:

Page 1-1, line 1 Eliminate concise 

Page 1-4, line 19 Define PM 

Chapter 2:

Unfortunately I did not have an opportunity to review this section in detail and so therefore I do 

not have any detailed comments. 

I would like to see some discussion on values of deposition prior to the Industrial Revolution 

(background deposition). This would include sulfate, nitrate, ammonium, chloride, calcium, 

magnesium, sodium and potassium. This information is critical to ecosystem effects models. 

It would also be good to see some discussion of historical emissions from about 1850 forward. 

This is critical to ecosystem effects models. 

Finally, in the spirit of making suggestions to simplify the document I would ask the EPA to 

consider that this atmospheric chapter is to support the effects section. Ecological effects 

largely occur via deposition and over the time scale of decades. As a result the focus of chapter 

3 could be largely on long-term deposition patterns. Seasonal deposition is really not important 

in ecosystem effects. If it was desired a considerable portion of this material could be shifted to 

the annex. 

29
Chapter 3:

This section covers most of the major issues concerning ecological effects of air pollutants. It 

is comprehensive and generally well done. There are a few sections that are emphasized in the 

summary section but really were not discussed in the body of the chapter. For example there is 

now some literature suggesting that there is a compensatory response of dissolved organic 

carbon to changes in acidic deposition. I think the science is still developing here but this is an 

important point and it should be mentioned in the body of the chapter, possibly as a short section 

in 3.2.3.1. 

There is an analysis of the extent of N limitation in remote lakes that is presented in Chapter 4. 

This is an analysis of the stoichiometry of water chemistry from the National Surface Water 

Survey. This analysis helps quantify the extent of N limitation. I would urge that this analysis 

be presented in 3.3.3.3 or another section of chapter 3. 

MAGIC is an important tool used in the REA. I would like to see some text discussing how the 

structure of MAGIC affects prediction. This could include a comparison of MAGIC with other 

watershed models. For example see Sullivan et al. (2006). 

The science is emerging on mercury contamination in terrestrial food chains (e.g., Rimmer et al. 

2005). There should probably be some mention of mercury contamination in the terrestrial 

food chain. 

Finally a question. Is it worthwhile to mention the linkage of atmospheric N deposition and 

biogenic emissions of NO and VOCs? I don’t think the literature is compelling here but there 

may be some linkages between N deposition and soil emissions of NO and between foliar N and 

VOC emissions. Is this a welfare effect? It is a linkage with atmospheric chemistry. 

 

Page 3-4, line 25 I don’t understand the line at the end about wetlands. Aren’t 

wetlands included in other ecosystem services described above? 

Page 3-6, line 2 hydrogen ion 

Page 3-6, line 7 eastern U.S. 

Page 3-8, line 20 H+

Page 3-8, line 30 southeastern 

Page 3-10, line 1 northeastern 

Page 3-10, line 8 You should mean oxidizing NH4

+

Page 3-11, line 9 section ? 

30
Page 3-12, line 14 This statement is not correct. Under conditions of low soil base 

saturation (<20%) and elevated concentrations of strong acid 

anions, Al is mobilized from soil to drainage water (Cronan and 

Schofield 1990). 

Page 3-14 You discuss episodic acidification but fail to discuss chronic 

acidification. This seems a bit out of place without a discussion 

of chronic acidification. 

Page 3-16, figure title Italics in-situ

Page 3-17, line 12 above 0 μeq/L 

Page 3-17, line 13 Italics in-situ

Page 3-24, line 8 Do you mean N deposition?

Page 3-24, line 17 than forests 

Page 3-24, line 25 by oxidizing NH4

+

Page 3-25, line 16 pool of exchangeable base cations 

Page 3-26, line 13 northeastern U.S. 

Page 3-26, line 18 cite DeHayes et al. 1999 

Page 3-29, line 1 northeastern U.S. 

Page 3-30, 1st paragraph You should probably reference the study of St. Clair et al. (2005) 

who document a relationship between enzyme antioxidant levels in 

sugar maple foliage and soil and foliar calcium. 

Page 3-31, line 4 eastern U.S. 

Page 3-33, line 13 eastern North America 

Page 3-36, line 26 Acid neutralizing capacity is the most readily... 

Page 3-40, line 2 northeastern U.S. 

Page 3-42, line 3 and 32 eastern U.S. 

Page 3-45, line 17 is typically decreased by acidic deposition 

Page 3-46, line 16 I could not find Sullivan et al. in press in the references 

31
Page 3-48, line 34 northeastern U.S. 

Page 3-49, line 6 I question the statement that recent soil acidification appears to be 

modest. I refer the authors to (Likens et al. 1996, Bailey et al. 

1996, Bailey et al. 2005). I am also attaching a recently accepted 

paper Warby et al. (in press). The rates of soil nutrient cation lost 

are high. 

Page 3-49, line 12 northeastern U.S. 

Page 3-51, line 1 What is meant by “pre-disturbance”? 

Page 3-51, line 2 This sentence seems to be inconsistent with the text in 3-90. 

Page 3-51, line 6 The authors should look at Gbondo-Tugbawa and Driscoll (2003) 

who evaluate historical forest cutting and soil and water 

acidification.

Page 3-52, lines 26-28 The first two bullet points are at odds with the text in 3-90 and 

Zhai et al. (2008). 

Page 3-54, table 3.7 This table does not include Zhai et al. 2008, Chen et al. 2005b, c, 

Driscoll et al. 2001 among others. 

Page 3-55, line 19 eastern U.S. 

Page 3-55, line 22 an indication of acid base status 

Page 3-56, line 17 eastern U.S. 

Page 3-57, line 8 eastern U.S. 

Page 3-57, line 15 northeastern U.S. 

Page 3-57, line 28 Italics in-situ

Page 3-66, line 25, Page 3-67, line 3-4 

Up to this point in the text, I have not seen any literature on effects 

on birds and now it is mentioned in the summary. This does not 

seem appropriate. If it is not important enough to be discussed in 

the body of the text, it probably should not be in the summary. 

There was a paper by Hames et al. 2002 on acid rain effects on 

songbirds in the Northeast. 

32
Page 3-74, line 5 What is mildly acidic? Give an ANC value?

Page 3-83, line 2 that further reductions in acidic deposition 

Page 3-83, line 25 Do you mean suitable?

Page 3-87, line 11 As shown in Figure 3-22, N retention actually has been increasing 

in the Adirondacks. Correct statement. 

Page 3-103, line 24 Define GHG 

Page 3-117, line 27 Space after wetlands 

Page 3-118, line 7 Missing reference 

Page 3-127, line 26 Section?

Page 3-138, line 7 Should this be o

C?

Page 3-139, line 8 northern U.S. 

Page 3-139, line 10 table 

Page 3-143, line 1 Missing space 

Page 3-144, line 20 italics in-situ

Page 3-144, line 22 Usually this is referred to as the Experimental Lakes Area (ELA). 

Page 3-145, line 2 period 

Page 3-149, line 4 Change to... algal detritus 

Somewhere in 3.3.4 I believe studies have shown increased biogenic NOx emissions in 

response to N additions. Isn’t this a relevant consideration and 

shouldn’t it be included in the review? Also, I believe that foliar 

VOCs emissions are a function of foliar N which is influenced by 

atmospheric N deposition. Should this effect be addressed in this 

section?

Page 3-153, line 19 methanotrophic 

Page 3-158, line 7 denitrifying 

Page 3-161, line 19 Is positive relationship correct? This seems inconsistent with the 

remainder of the section. 

33
Page 3-169, line 2 Who is they?

Page 3-176, line 1 eastern U.S. 

Page 3-176, line 11 northern U.S. 

Page 3-176, line 13 table 

Page 3-176, lines 2 and 26 These sentences are identical. Do you really want the same

sentences on the same page?

Page 3-177, line 16 bioindicator 

Page 3-180, lines 4, 5 italics in-situ

Page 3-182, line 17 italics in-situ

Page 3-184, line 4 Change to... Among the most sensitive... 

Page 3-185, line 12 eastern U.S. 

Page 3-185, line 25 In the West, 

Page 3-186, line 12 NH4

+

 twice 

Page 3-192, lines 14, 15 Northeastern 

Page 3-196, line 6 italics in-situ

Page 3-200, line 4 and elsewhere 

Control should be changed to reference 

Page 3-206, line 26 Aren’t changes in biodiversity changes in structure?

Page 3-209, line 7 period 

Page 3-216, line 15 table 

Page 3-218, line 19 Change to... all fish consumption advisories 

Page 3-225, line 5 Methylation is prevalent in ecosystem in other regions besides the 

Northeast. This sentence should be changed. 

34
Page 3-227, somewhere in here 

Studies have also shown elevated concentrations of Hg in 

songbirds and bats via the terrestrial food chain. This should be 

mentioned (e.g., Rimmer et al. 2005). 

Page 3-228, 2nd paragraph You change the symbol for methyl mercury here. The text should 

be changed to be consistent. 

Page 3-232, lines 10, 11 The first letter of several of the names are in lower case. 

Page 3-236, line 1 H+

Chapter 4

Page 4-1, line 12 role in transporting N 

Page 4-4, line 19 Define p NO3

-

Page 4-4, line 23 Define FRM

Page 4-5, line 4 is very sparse over 

Page 4-6, line 7 and throughout the document 

I do not like the term acidifying deposition. Change to acidic or 

acid deposition. 

Page 4-6, line 13 energy by oxidizing NH4

+

 to NO3

-

Page 4-6, line 17 (see Table 4-1), including soil base saturation, aluminum

concentration and C:N ratio. 

Page 4-6, line 21 are increasingly neutralized by 

Page 4-7, line 8 toxicity, decreased ability of plant roots to take up nutrient cations, 

and elevated leaching of Ca2+ from needles 

Page 4-9, line 15 eastern U.S. 

Page 4-9, line 17 western U.S. 

Page 4-10, line 6 eastern U.S. 

Page 4-10, line 9 indicator of acid-base status 

Page 4-10, line 11 pH, Ca, SO4

2- and 

35
Page 4-10, line 20 Southern Appalachian Mountains 

Page 4-11, line 1, 17 eastern U.S. 

Page 4-11, line 19 the Central and Southern Appalachian Mountains 

Page 4-11, line 24 northeastern U.S. 

Page 4-13, bullet 1 Were effects on birds really discussed in Section 3? If not it 

probably should not be emphasized here. 

Page 4-14, line 30 Change to... were on average 30 μeq/L. 

Page 4-15, line 1 Change to: would need on average to recover 

Page 4-15, line 16 northeastern U.S. 

Page 4-15, line 23 Was DOC change discussed in Section 3? This is an important 

issue and probably deserves a paragraph in Section 3. 

Page 4-16, line 26 Change to... to a state more removed from a condition of N 

saturation. 

Page 4-18, line 8 West 

Page 4-18, line 27 western U.S. 

Page 4-20, line 27 western U.S. 

Page 4-23, line 3 southwestern U.S. 

Page 4-23, line 4 Sonoran Desert 

Page 4-23, line 20 Isn’t reducing biodiversity altering ecosystem structure?

Page 4-26, lines 10, 15 eastern U.S. 

Page 4-27, line 3 dissolved inorganic N?

Page 4-27, line 4 phosphorus 

Page 4-27, 1st paragraph Was this analysis of lake stoichiometry in the ELS discussed in 

Section 3? If not it should be as it is an important conclusion. 

Page 4-27, line 13 eastern and western U.S. 

36
Page 4-29, line 6 western U.S. 

Page 4-31, line 12 eastern U.S. 

Page 4-32, paragraph 2 Should these units be metric?

Page 4-34, line 10 This statement is incorrect. Methylation is a widespread 

phenomenon. It occurs in many areas besides the Northeast and 

southeastern Canada. 

References:

Bailey, S. W., J. W. Hornbeck, C. T. Driscoll, and H. E. Gaudette. 1996. Calcium inputs and 

transport in a base-poor forest ecosystem as interpreted by Sr isotopes (Paper 

95WR03642). Water Resources Research 32:14. 

Bailey, S. W., S. B. Horsley, and R. P. Long. 2005. Thirty years of change in forest soils of the 

Allegheny Plateau, Pennsylvania. Soil Science Society of America Journal 69:681-690. 

Cronan, C. S., and C. L. Schofield. 1990. Relationships between aqueous aluminum and acidic 

deposition in forested watersheds of North America and Northern Europe. Environmental 

Science and Technology 24:1100-1105. 

DeHayes, D. H., P. G. Schaberg, G. J. Hawley, and G. R. Strimbeck. 1999. Acid rain impacts on 

calcium nutrition and forest health. BioScience 49:789-800. 

Gbondo-Tugbawa, S. S., and C. T. Driscoll. 2003. Factors controlling long-term changes in soil 

pools of exchangeable basic cations and stream acid neutralizing capacity in a northern 

hardwood forest ecosystem. Biogeochemistry 63:161-185. 

Hames, R. S., K. V. Rosenberg, J. D. Lowe, S. E. Barker, and A. A. Dhondt. 2002. Adverse 

effects of acid rain on the distribution of the Wood Thrush Hylocichla mustelina in North 

America. Proceedings of the National Academy of Sciences of the United States of 

America 99:11235-11240. 

Likens, G. E., C. T. Driscoll, and D. C. Buso. 1996. Long-term effects of acid rain: Response and 

recovery of a forest ecosystem. Science 272:244-246. 

Rimmer, C. C., K. P. McFarland, D. C. Evers, E. K. Miller, Y. Aubry, D. Busby, and R. J. 

Taylor. 2005. Mercury concentrations in Bicknell's Thrush and other insectivorous 

passerines in montane forest of northeastern North America. Ecotoxicology 14:223-240. 

37
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. 

Zhai, J., C. T. Driscoll, T. J. Sullivan, and B. J. Cosby. 2008. Regional application of the 

PnET-BGC model to assess historical acidification of Adirondack lakes. Water 

Resources Research 44, W01421:doi:10.1029/2006WR005532. 

38
39
40
41
42
Dr. Paul J. Hanson 

 

I found the second draft of the Integrated Science Assessment (ISA) to be greatly 

improved. Panel suggestions on the first draft appear to have been incorporated for the most part. 

The requested Executive Summary is well crafted and a nice introduction to the ISA, but some

wording changes may still be in order. My specific comments and editorial suggestions are 

listed below. 

Specific comments and suggested edits: 

Executive Summary 

Page two, second column: Change to “Numerical modeling experiments can help fill in 

these data gaps and suggest that local and even regional areas of high concentration and 

deposition may exist where measured data are unavailable. Subscript the 2 in NO2. 

Page 4 last paragraph: The last statement is not correct. The onset of leaching is not a fixed 

constant that applies to all eastern forests. This text should be changed to indicate that such a 

threshold applies to a defined set of sensitive eastern forests. 

Page 5: Change the first two sentences to: “N deposition often increases primary 

productivity, but may not lead to enhanced carbon sequestration.” In the first paragraph 

change “However, alteration...” to ‘Alteration...’ I would add the word possible to the 

following: “The increase in growth is greater for some species than others, leading to possible

shifts in population dynamics, species composition, community structure and, in extreme 

instances, ecosystem type.” Growth changes are not a guarantee of cascading effects. The 

paragraph on lichens seemed too general. Are the limits for lichen response true for all 

ecosystems, or only sensitive ones? 

Page 5 last paragraph: Should organisms be animals? Elemental mercury is taken up by plants. 

Page 6 third paragraph: Change to “Acute exposures to NO2,....” Delete the word “Overall”. 

Page 6 last paragraph: Consider the following changes: 

“...deposition resulting from NOX and SOX pollution. It causes a cascade of effects that 

harm susceptible terrestrial and aquatic ecosystems, including slower growth and injury 

to forests, and localized extinction of fishes and other aquatic species. In addition to 

acidification, deposition resulting from NOx, along with other sources of reactive 

nitrogen (e.g., fertilizers, wastewater, and atmospheric ammonia deposition), causes a 

suite of ecological changes within sensitive ecosystems including biodiversity losses, 

disease, eutrophication, and harmful algal blooms. Particulate sulfate can interact with 

methanogenic bacteria to produce methylmercury, a powerful toxin that can 

bioaccumulate to toxic amounts in higher trophic levels (e.g. otters and kingfishers). 

Chapter 1: No comments. 

43
Chapter 2 

The font size for the text within figures on pages 2-96 through 2-100 is too small. These 

figures need to be adjusted. 

Figures 2-41 , 2,42, 2-43, and 2-44: Using the same color scheme for an alternate range of 

concentrations in the comparison of Total vs. background concentrations masks what should be 

the main message of these figures. Background levels are very, very low. The need to 

visualize where background levels are highest over a range from very-low to low seems 

unnecessary. If the authors really want this specificity they should choose an alternate color 

scheme for the background map. 

Chapter 3 

Tables 3-11 to 3-26 within Section 3.3 provide an appropriate and site-specific level of

detail to allow the readers to understand the indicators and levels of deposition of importance for 

specific ecosystems and the responses being highlighted. 

Chapter 4 

For the bolded conclusion statements on pages 4-17 through 4-31 determine if you can 

change “alteration” to a statement of directional change if the data warrant (e.g., change 

alteration to increase in the statement of N deposition effects on N2O emissions). 

Comments on the Key Findings draft (1 October 2008): 

Page 1 first yellow box: 

In the third paragraph I recommend changing the word “problems” to ‘changes’ to avoid the 

judgmental nature of the first term. As with many other locations in the document it is 

important that this statement not be interpreted as applying equally to all ecosystems throughout 

the United States. 

Second yellow box: 

While the statement may be factually correct it tends to imply that acidification leading to 

adverse effects is taking place in all ecosystems. I don’t believe this is true. One size doesn’t 

fit all and levels of deposition, acidification, and adverse effects are not consistent across the US. 

The bullets at the top right portion of page 1 are just right in my opinion. They contain the 

detail needed for the reader to draw the appropriate conclusion. 

Right hand column of Page 2 – yellow box: 

I would change the first lines to “Nitrogen deposition causes ecosystem element 

enrichment and eutrophication....” 

Page 2, second column, first bullet: 

Modify the text to read “....nitrogen enrichment. However, most ecological experiments and 

observations have .....” 

44
Page 2, second column, third bullet: 

Is Ammonia always 80% of total reduced N or only in locations with high N deposition totals?

Page 2, second column, last bullet: 

Add the words ‘insensitive ecosystems’ to the end of the bullet. 

Page 3, column 1, first bullet: 

I don’t believe that this statement is true in natural ecosystems dominated by nitrogen 

fixing species (alder thickets/forests; and perhaps early successional oldfields). The last 

statement of this bullet needs further expansion. I’m not clear on the intent. 

Page 4, first column, first bullet under the Biological Effects heading: 

Near the end of the statement the terms ‘terrestrial ecosystems’ is too general. This is 

not true for all terrestrial ecosystems. 

Page 4: 

Bullets ending column 1 and beginning column 2 are well worded. 

Page 4, second column, yellow box: 

The statement suggesting that 5.6 to 10 kgN/ha/y drives the onset of nitrate leaching in

eastern forests is wrong. It only applies to specific systems and locations within eastern US 

forests. 

I agree with the suggestion of one panel member (can’t remember who) that spatially explicit 

information on the areal extent of acidification, nitrogen enrichment, and sulfate effects on 

mercury methylation might all be made clear in the executive summary. 

45
Dr. Rudolf Husar 

These comments pertain primarily to Charge Question 5 with brief comments on other sections. 

ISA Charge Question 5. In revising the ISA, we have incorporated additional information on the 

indicators of exposure and ecological effects, including increased emphasis on quantified relationships in

the presentation of information of results in tables and summary discussions in Chapter 4. What are the 

views of the CASAC panel on our revisions to focus on quantitative relationships between airborne 

nitrogen and sulfur compounds and ecological indicators? 

• It is commendable that effort was made to perform an analysis of existing literature on

indicators relevant to deposition and acidification. The meta-analysis appears to be

extensive and appropriate for the ISA 

• The analysis of indicators is particularly important since the a secondary standard (if 

proposed and promulgated) needs to be expressed in terms of Sox / Nox and then 

properly linked to the effects through the indicators and a causality framework. 

• It would be desirable to continue fortifying the linkages in the causality chain between 

emission - atmospheric concentration – deposition – dosage – effect – ecosystem

services. 

• An example of such an end-to-end causality illustration would help. A synchronized 

array of trend charts for each parameter/indicator in the causality chain could be an 

effective way to illustrate the overall framework and key aspects of systems behavior. 

• In the ISA it may not be necessary the have quantitative trend values for each of the 

parameters in the causality chain ensemble. In fact, graphically indicating (say dashed 

trend lines) the poorly understood parameters would be a more realistic representation of 

the current state of the causality framework. 

A recurring general concern regarding the ISA, voiced by several panel members over multiple 

meetings, is the near-complete avoidance of the non-ecological welfare effects of NOX and 

SOX, such as particle effects on visibility and climate, materials damage etc. It is understood 

that some of these effects are discussed in other assessment documents and full treatment of

these in this ISA is not necessary. 

This document is titled “Integrated Assessment for Oxides of Nitrogen and Sulfur –

Environmental Criteria” but by design, it focuses on the ecological effects. Fine, no problem

here. However, since Environment includes air, land, water, biota I see two possibilities: 

• Either rename the document to ‘Ecological Criteria’ – probably not feasible 

• Or keep “Environmental Criteria” but state it clearly 

o in which docs other NOx/Sox welfare effects of are being treated 

o provide a short synopsis of the key non-ecological effects in the 

appendix, so this ISA document can meaningfully represent an 

assessment of Environmental Criteria. 

46
Detailed Comments on Specific Sections of ISA Document 

Page 1-3: The schematic Figure on the biogeochemical cycles of NOx and SOx is good. 

However, during the June 2008 CASAC it was suggested that 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. 

Page 2-47: Figure 2-20 is again a qualitative schematic of the sulfur flows in the and out of 

the atmosphere. At the minimum, estimating the magnitude of dry and wet deposition 

would be most helpful. 

Page 2-47: Multi-phase SOx chemistry is reviewed in considerable detail including the 

relative humidity effects on deliquescence. It is puzzling why this detailed behavior of 

particles is relevant for ISI which is to support ecological effects and not the atmospheric 

effects of particles. 

Page 2-54: Same comment as above. Why discuss deliquescence of nitrate particles when 

atmospheric effects of particles are not considered. 

Page 2-56: Section 2.6.5 “Transport-Related Effects” is a rather haphazard collection of 

references that neither explain the general features of S and N transfer in the atmosphere nor 

is a comprehensive list of literature. Calling it Transport Effects is misleading, since the 

section covers transport processes and phenomena, not effects. 

In addition to Transport Phenomena a statement on the general role of meteorological 

processes shaping pollutant transport, governing thermodynamics (e.g. gas-particle 

equilibrium and reaction kinetics) and removal processes. Shoving the precipitation pattern 

would provide considerable explanatory support to the pattern of S and N deposition and the 

resulting effects. An explicit discussion of the atmospheric life time of various sulfur and 

nitrogen species would be most helpful. 

Page 4-1: Chapter 4, “Summary and Conclusions” supposed to summarize the content of 

Chapter 2 (Emissions, Atmospherics) and Chapter 3 (Ecological Effects) of NOx and SOx. 

The way in which Chapter 4 has been written, only about 10% of the 40 page summary deals 

with the emissions, ambient concentrations, transport and deposition. 90% is about the 

effects and associated summary tables. Table 4-4 for N is useful and similar compilation for 

S would be useful as well. Given the sizable effort invested in the compilations this 

Chapter appears to be an integration Chapter rather than just a Summary Chapter. 

Page 4-1 Line 11: Section 4.1.1 “ Relevant Chemical Families and Constituent Species” 

is a single paragraph, loaded with inaccuracies and dubious rationale. Examples: 

“particulate nitrate is .... not a member of the oxidized N family of species” . So, 

particulate nitrate is not an oxidized N? Line 17: “Only SO2 is present in concentrations 

47
relevant for atmospheric chemistry and environmental exposures. “ So, the 10,000 

excess death per year, mostly from sulfate are not relevant?

Page 4-2 Line 1: Stating that the 2001 US NOx emissions were approximately “~23.19 Tg” 

is misleading since it implies that the accuracy of US NOx emissions is known with better 

than 1% accuracy. For most of us the NOx emission accuracy is not better than 20% , i.e. 

23+/ - 2 Tg. 

Page 4-2 Line 5: “Biogenic NOx sources .....include biomass burning, lightning, and 

soils”. I wonder which biota in the sky are responsible for lightning??

Page 4-2 Line 5: “Biogenic NOx sources are substantially smaller than anthropogenic .....”. 

On global scale anthropogenic and natural nitrogen emissions to the atmosphere are 

comparable (http://www.visionlearning.com/library/module_viewer.php?mid=98). 

Page 4-5 Line 1: It is true that the measurements of particulate NO3 and NH4 are subject to 

positive and negative errors. However, the measurement of particulate sulfate is among the 

most accurate and reliable among the sampling methods. 

Page 4-5 Line 5: “This assessment concludes that...”. This complicated sentence is

incomprehensive. 

Page 4-10 Line 26: “However, there is no apparent relationship between recent trends in N 

deposition and trends in NO3 concentrations in these surface waters.” This statement has 

significant consequences regarding the conclusions as stated below. 

Page 4-27 Line 8: “The evidence is sufficient to infer a causal relationship between N 

deposition and the alteration of biogeochemical cycling of N in fresh water aquatic 

ecosystems”. Is this consistent with the statement that N deposition trends are not matched 

by corresponding N concentration trends? 

48
Dr. Dale Johnson 

This draft is an improvement in some ways but I believe that it needs to include assessments of 

the possibility of beneficial effects of N deposition. It now contains detailed descriptions of N 

and S cycles and recognized the fact that nitrogen (but not sulfur) is often a limiting nutrient. It 

now considers the potential for N deposition to enhance production and C sequestration 

specifically within the body of the text – and then summarily dismisses such a possibility and 

mentions nothing of it in summary statements. It appears that the treatment of the potential 

benefits of sulfur are discussed much more extensively than those for nitrogen (although I fully 

recognize that N deposition is probably not important for crop systems, given how much they are 

fertilized). 

 

Specific comments: 

p. 3-7, lines 1-3: In addition to these studies, are the very detailed studies of Richter and 

Markewitz (2001) which show long-term soil acidification due to both tree uptake and 

atmospheric deposition. The fourth resampling of Walker Branch Watershed will also soon be 

published (Johnson et al., 2008) and I will send a copy. It documents continued declines in 

exchangeable Ca2+ and Mg2+ with the exception of cases where decomposing logs enrich Ca2+. 

The Ca declines are attributed mostly to uptake where the Mg2+ declines attributed mostly to 

leaching, augmented by acid deposition. 

p. 3-12: I do not think the study by Bailey et al is by any means the most thorough resampling 

study in the US. The Richer and Markewitz study is much more comprehensive and detailed, and 

fully deals with the causes of soil change in a quantitative manner, which the Bailey study does 

not. As noted in my last review, while Bailey did evaluate the role of uptake in causing the soil 

changes they observed, they have grossly overestimated the potential role of acidic deposition in 

the soil changes they observed – it would have taken a prolonged S deposition rate of something 

like 200 kg ha-1 yr-1 for many decades, for example, to produce such changes as they saw in 

some cases. It is simply not logical to blame acidic deposition for that magnitude of change. I 

wrote a letter to the editor on this (Johnson, D.W. 2006. Comments on “Thirty years of change in 

forest soils of the Allegheny Plateau, Pennsylvania.” Soil Sci. Soc. Amer. J. 69: 2077.), to which 

they responded, which the authors of this document should look at if they intend to highlight the 

Bailey studies as hallmark studies showing soil acidification by acid deposition. I noted this in 

my last review of this document, but this comment was apparently overlooked. The authors may 

choose to dismiss my letter and accept Bailey’s conclusions, but they should at least 

acknowledge the controversy. 

p. 3-13, line 33 to p. 3-14, line 1: Once acidified, it is unlikely that Al levels in soils will decline 

again unless the soils are limed. 

p. 3-26, lines 6-12: What about the effects of N on N-deficient sytems?

p. 3-43, line 5: The base cation decline could be explained as a simple consequence of charge 

balance. 

49
p. 3-75, lines 1-17: This is amazing. So we do not even know if our forests are growing at a 

faster or a slower rate. A fundamental piece of knowledge that is missing while we speculate 

about effects. 

p. 3-104, lines 17-23: The beginning of this paragraph acknowledges that N can be both 

beneficial and detrimental – so I would add to the end of it something like the following: “ or 

on the other hand, improved forest health by alleviation of N deficiency, increased productivity 

and C sequestration”. 

p. 3-115: Good segment on disturbance – there are also many other references on the effects of 

fire, including effects on water quality – see references below. 

p. 3-131, lines 1-11: It is very common in commercial fertilizer studies as well as pollution N 

addition studies for trees to take up only a fraction of applied N unless it is applied to foliage. 

Even so, as noted on lines 9-11, growth increases to this small proportion of plant uptake are 

common. 

p. 3-133, lines 1-8: Of course it is true that when you add a limiting nutrient you will run up 

against the next limiting nutrient – this is very well known. Is this then a wholly bad thing or was 

the addition of the limiting nutrient “good” to start with?

p. 3-133, lines 9-12 through p. 3-133, lines 1-10: By my reading, there were 6 positive responses 

to N listed in Table 3-15, and some were at the “moderate to high” levels of N addition. I count 

three negative responses, including the one by McNulty which is so prominently highlighted, and 

three which showed both positive and negative responses, depending on time and which species 

was being looked at. AND, I will wager that if you included fertilization studies in commercial, 

fast-growing forests, you would find a very high proportion of positive growth responses indeed. 

p. 3-135, Regional Trends.... It is a shame that we do not have the data to know whether forest 

growth has increased, decreased, or stayed the same from the forest inventory system. The 

Europeans have this, yet we seem not to. That being the case, apparently, I do not find this 

segment particularly illuminating, although it may the best we can do. 

p. 3-136, lines 3-17: I am glad that the authors included a discussion of the Magnini paper – even 

though they do dismiss it rather easily. I am not sure I agree with that – nitrogen is, as is 

acknowledged in this document – a limiting nutrient and it seems highly probable that adding it 

will cause increased growth. The authors opinions obviously differ from mine. At least it was 

discussed. 

p. 3-162, Trees: The view here seems to be that there is nothing good about “altered growth 

rates”. Can’t altered growth rates be a “good” thing if they are in the positive direction and in, for 

example, commercial forests? Does this not bear even the slightest mention?

3-163 to 3-175: A very good review of N effects from the pollutant point of view. Do traditional 

forest fertilization studies tell us anything more?

50
3-164 Grasslands: It would be good to mention the cheatgrass issue in the Great Basin here. 

Cheatgrass is a nitrophile and increased N deposition will undoubtedly facilitate the spread of 

this noxious species also. 

p. 3-191, line 13: I would add “increased growth” after “sensitive” 

p. 3-206, lines 4 and 8-18: “forest yields” is mention in the headlines, but no mention of 

increased timber yield is mentioned in the following paragraph – all is negative. 

p. 3-212 to 3-218: A very good, thorough and objective treatment of sulfur. 

General References 

Johnson, D.W., D.E. Todd, C.F. Trettin, and P.J. Mulholland. 2008. Changes in Soil 

Exchangeable K+

, Ca2+, and Mg2+in Forests of Walker Branch Watershed, 1972-2004. Soil 

Sci. Soc. Amer. J. (in press) 

Richter, D.D., and D. Markewitz. 2001. Understanding Soil Change: Soil Sustainability over 

Millennia, Centuries, and Decades. Cambridge University Press. 255p 

Richter, D.D., D. Markewitz, H.L. Allen, R. April, P.R. Heine, and R. Urrego. 1994. Soil 

chemical change during three decades in an old-field loblolly pine (Pinus taeda L.) 

ecosystem. Ecology 75:1463-1473. 

Trettin, C.A., D.W. Johnson, and D.E. Todd, Jr. 1999. Forest nutrient and carbon pools: a 

21-year assessment. Soil Sci. Soc. Amer. J. 63: 1436-1448. 

References on the effects of fire:

Adams, M.A., Iser, J., Keleher, A.D., and D.C. Cheal. 1994. Nitrogen and phosphorus 

availability and the role of fire in heathlands at Wilsons Promontory. Aust. J. Bot. 

42:269-281. 

Baird, M., Zabowski, D., and R.L. Everett. 1999. Wildfire effects on carbon and nitrogen 

in inland coniferous forests. Plant Soil 209:233-243. 

Bayley, S.E., Schindler, D.W., Parker, B.R., Stainton, M.P., and K.G. Beaty. 1992. 

Effects of forest fire and drought on acidity of a base-poor boreal forest stream: 

similarities between climatic warming and acidic precipitation. Biogeochem. 17:191-204. 

Certini, G. 2005. Effects of fire on properties of forest soils: a review. Oecologia 143: 1-10. 

Chorover, J., Vitousek, P.M., Everson, D.A., Esperanza, A.M., and D. Turner. 1994. 

Solution chemistry profiles of mixed-conifer forests before and after fire. Biogeochem. 

26:115-144. 

DeBano, L.F. and C.E. Conrad. 1978. The effect of fire on nutrients in a chaparral 

51
ecosystem. Ecology. 59(3):489-497. 

Dyrness, C.T., Van Cleve, K., and J.D. Levison. 1989. The effect of wildfire on soil 

chemistry in four forest types in interior Alaska. Can. J. For. Res. 19:1389-1396. 

Grier, C.C. 1975. Wildfire effects on nutrient distribution and leaching in a coniferous 

ecosystem. Can. J. For. Res. 5:599-607. 

Hauer, F.R., and C.N. Spencer. 1998. Phosphorus and nitrogen dynamics in streams 

associated with wildfire: a study of immediate and longterm effects. Int. J. Wildland 

Fire 8(4):183-198. 

Khanna, P.K. and R.J. Raison. 1986. Effect of fire intensity on solution chemistry of 

surface soil under a Eucalyptus pauciflora forest. Aust. J. Soil Res. 24:423-434. 

Khanna, P.K., Raison, R.J., and Falkiner, R.A. 1994. Chemical properties of ash derived 

from Eucalyptus litter and its effects on forest soils. For. Ecol. Manage. 66:107-125. 

Knight, H. 1966. Loss of nitrogen from the forest floor by burning. For. Chron. 

42(2):149-152. 

Neary, D.G., C.C. Klopatek, L.F DeBano, PF. Ffolliot. 1999. Fire effects on belowground 

sustainability: a review and synthesis. For. Ecol. Managem. 122: 51-71. 

Raison, R.J. and J.W. McGarity. 1980. Some effects of plant ash on the chemical 

properties of soils and aqueous suspensions. Plant Soil 55:339-352. 

Rashid, G.H. 1987. Effects of fire on soil carbon and nitrogen in a Mediterranean oak 

forest of Algeria. Plant Soil 103:89-93. 

Trabaud, L. 1994. The effect of fire on nutrient losses and cycling in a Quercus coccifera

garrigue (southern France). Oecologia, 99: 379-386. 

Williams, M.R. and J.M. Melack. 1997. Effects of prescribed burning and drought on the 

solute chemistry of mixed-conifer forest streams of the Sierra Nevada, California. 

Biogeochem. 225-253. 

52
Dr. Donna Kenski

Overarching comments: 

There is an impressive amount of new material in this new draft. EPA has been very responsive 

to the panel’s comments on the previous draft. As a result this version is much improved and 

constitutes a solid scientific basis for the REA. I find only one major shortcoming, and that is 

in its discussion of CMAQ’s performance characteristics. After reviewing the REA and noting 

its reliance on CMAQ, it seems more important than ever to thoroughly describe CMAQ’s 

performance especially with respect to modeling wet and dry deposition. The ISA includes 

plenty of useful new information on CMAQ, all of which is a welcome addition, including the 

Tampa Bay modeling exercise (although the accompanying Figs. 2-29 through 2-37 are so small 

as to be practically unreadable). The existing text on CTM deposition performance (Sec. 

2.8.3.2) compares results for 23 different models (including CMAQ?), but no CMAQ specific 

data are given. Is the factor-of-2 performance of these models for wet deposition adequate for 

supporting the REA analyses and the standard-setting process? Dry deposition performance is 

probably even more variable. Section 2.8.4 has some limited statistics on RADM performance 

– but the REA doesn’t propose any applications of RADM, so do we really need this? A more 

thorough discussion of these deposition uncertainties, specific to CMAQ as much as possible, is 

still needed. 

Charge Questions: 

Exec. Summary: This was a great addition that was just the right length and tone. I liked the 

simple summaries of causal evidence and the emphasis on current concentrations. 

Chap 1: Addition of the causality framework was helpful. The way the causal judgments 

were carried through the document was great – i.e., in the summary, throughout Chapt. 3, and in 

the conclusions in Chap. 4. 

Chap 2: Nice review of NH3 measurement methods. Expanded information on CTM models, 

especially CMAQ, is well written and very helpful, although still more is needed on CMAQ 

performance with respect to wet and dry deposition. The additional tables on various 

monitoring programs are nice (although hard to read – the font size in all tables has shrunk a 

little too much). I also like the new maps and the source attribution summary. All in all, this 

is a much stronger section than it was. 

Chap 4: Like the executive summary, I thought this summary chapter was just about the right 

length and struck the right tone. 

Specific comments, typos, etc: 

p. 2-2, Table 2-1: Improved formatting and detail in this table makes it much easier to read. 

p. 2-4, line 4; remove ‘the’ 

53
p. 2-4, lines 5-8: It seems more appropriate to consider all electricity generation together for 

this analysis, rather than split it into utility and industrial categories. Then it’s clear that 

electricity generation is almost equal to mobile sources in NOX emissions. 

p. 2-4 thru 2-6: the added maps, figures 2-1 through 2-4, are very nice. 

p. 2-7, lines 29-30: marine transport is 60% of land-based NOx in Europe? Can that be true?

p. 2-20, lines 3-5: although vehicle NH3 is only 8% of total NH3, it can be locally significant 

(i.e., in cities). This is evident in Fig. 2.12 but bears noting in the text as well. 

p. 2-27, Figure caption. Good clarification and explanation of this figure! 

p. 2-30, top of page: 2NO2O5 should be N2O5 

p. 2-30, line 13: what is ‘organic coating’ referring to? Organic compounds on the particle 

surface? Not clear. 

p. 2-34, line 30: instantiations?

p. 2-37, line 4: incomplete sentence. 

p. 2-38, line 35: should snow be soot?

p. 2-95, Fig. caption 2-27 is garbled. 

p. 2-96, line 2: predations ->predictions 

p. 2-101, line 9: incomplete sentence 

p. 2-122, line 14: change first ‘and’ to ‘by’ 

p. 2-122, lines 17-21: Note that SEARCH makes continuous NH3 measurements at several 

sites (not all of the network though). Discussion of their denuder difference method might be 

added to the text. 

p. 2-155, Fig. 2-75: Isn’t this a map of particle NO3 concentration (not gas phase)? 

p. 2-161: Figure 2-80 is the same as Figure 2-74 

p. 2-199, line 15: Section 0?

p. 4-1, line 14: typically

54
Dr. Myron J. Mitchell 

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

Be consistent in the order of multiple citations throughout the document. Either cite by date or 

alphabetically. Within the document the citations are not complete or consistent including the 

need to use letters for multiple citations by the same author and same year. It would be helpful to 

have unified and consistent units throughout the document. There is a mixture of English and 

metric units (i.e., SI) in the current document. The correct SI abbreviations and units should be 

used throughout the document. If English units are used, the equivalent values using SI units 

provided in parenthesis would be helpful. 

Responses to Charge to the CASAC NO /SO Secondary Review Panel 

1. We have added an executive summary of the major findings and conclusions to the second 

draft ISA. We have also created a "key findings" section that is intended to provide highlights of 

these conclusions. We are seeking CASAC panel advice and comments on these additions to the 

ISA. To what extent do they provide an appropriate level of detail and convey the important 

scientific conclusions of the assessment?

In general the information level in the executive summary is suitable. However, the executive 

summary and key findings need to be placed in the broader context of other environmental issues 

including climate change, invasion of exotics, extreme events, changes in CO2 concentration etc. 

These other environmental affects can dampen and/or amplify the environmental effects

associated with SOx and NOx. Some changes related to other effects are suggested within my 

detailed comments. Within the key findings there are a number of issues that need to be 

addressed and these are provided within my detailed comments. 

2. Chapter 1 has been revised to clarify the scope or focus of this assessment on effects related to 

the deposition of nitrogen and sulfur compounds. In addition, we have added a discussion of the 

framework for evaluation of causality for assessing ecological effects. Do these revisions 

adequately characterize the scope of the assessment? Does the CASAC panel have 

recommendations for revisions to the causality framework? Is it appropriately applied in the draft 

ISA? 

The information provided in Chapter 1 seems appropriate with respect to the overall approach. 

3. Chapters 2 and 3 from the first draft have been combined. Substantially more information has 

been included on NH3 emissions, NH3 measurement techniques, NH3 and NH4

+

 concentrations. 

Additionally, information on NOx and SOx including ambient concentrations, deposition levels 

and their spatial and temporal relationships has been added. Have these revisions to Chapter 2 

improved its assessment of the currently available scientific knowledge on atmospheric sciences 

and its relevance to the evaluation of environmental effects presented in later chapters? 

55
There is certainly more detail on atmospheric chemistry in Chapter 2. I am not certain whether 

all of this detail including issues related to analytical technique, artifacts, differences in 

instrumentation, etc. are necessary with respect to having sufficient information to set standards. 

I would suggest placing some of these details in an appendix. More explicit linkages need to be 

made on what we know as well as what we do not know and how this information is needed for 

setting standards for NOx and SOx. The details provided in this section are somewhat 

overwhelming including extensive graphics and results from specific sites. A clear summary of

what is known related to setting NO and SO standards would help bring all of this information 

into focus. In particular the issues relating to the estimates of deposition velocities need to have 

a central place in this document. One example that I am aware of is for the Egbert, Ontario site 

in Canada where both concentration measurements and deposition values were compared using 

CASTNET and CAPMoN approaches. The concentration data are almost identical, but the 

deposition estimates are quite different. The issue related to confidence in modeled deposition 

velocities needs to be placed in the context of the CMAQ predictions. The flow of information 

could be improved with better use of headings to direct the reader to the content of major 

sections. Also, some further discussion is warranted about how other factors such as climate 

change, extreme events (e.g. fire, hurricanes, ice storms), invasion of exotics, etc. can also have 

a major impact on ecosystem response and can have a major influence on the expression of 

acidic deposition impacts on ecosystems. These results need to be placed in an historical 

framework since for the effects analyses the longer time scales (i.e., decades) are most relevant. 

4. We removed or eliminated redundancy, added summary sections, added additional references 

and reorganized Chapter 3. Revisions to the ecological effects sections are given below. Have the 

revisions improved the characterization of the ecological effects?

This section has many problems in the citations and references. Some of the sections in this 

chapter are redundant. For example in section 3.2.1.3 there is a review of N accumulation and 

nitrate leaching and in section 3.3.2 there is a section on N enrichment effects on N cycling. A 

major challenge is placing the nitrogen atmospheric deposition concerns in the context of other 

environmental issues including wastewater treatment and fertilizer contributions to the nitrogen 

loading to surface waters. It is clear that there are often quite different current conditions and 

responses among regions such as the Rocky Mountain West versus the Northeast especially with 

respect to nitrogen. The need for different standards or approaches needs to be considered that 

focus on specific types of ecosystems (e.g., alpine, northern hardwoods, etc.). It would be helpful 

to have some better comparisons among model predictions (e.g., MAGIC versus PnET-BGC as 

well as other models). Also, some better use of the PIRLA I and PIRLA II results in showing the 

historical patterns of acidic deposition. 

a. Consistent with CASAC comments, we expanded our characterization of the 

quantification of chemical effects of acidification in aquatic ecosystems, added new 

conceptual diagrams, and further discussed interactions between acidification and plant 

disease. 

Certainly more details are provided. However, there is considerable redundancy in the 

document. A clearer delineation of particular areas of focus is needed. 

56
b. We expanded the discussion of quantitative relationships between nitrogen deposition 

and ecological effects, including published critical loads in the U.S. and Europe. In 

addition, the nitrogen enrichment section was expanded to include new discussions on 

carbon budgeting, biogenic nitrous oxide and methane. Information on the linkages 

between effects and both reduced and oxidized forms of nitrogen was emphasized, to the 

extent data were available. 

The more you can do to pull together information from these divergent informational sources 

and provide those points that indicate divergence or divergence related to deposition and 

ecological effects will improve this document. 

c. The section on “other” welfare effects was updated to include information on the direct 

phytotoxic effects of nitric acid. 

The inclusion of additional information on the direct phytotoxic effects of nitric acid was helpful. 

5. In revising the ISA, we have incorporated additional information on the indicators of exposure 

and ecological effects, including increased emphasis on quantified relationships in the

presentation of information of results in tables and summary discussions in Chapter. 

This revised version certainly is more complete than the previous version. A major challenge is

placing the issues related to NOx and SOx effects in the context of other ecosystem changes 

including effects due to climate change, invasion of exotics, extreme events. There is also 

substantial reliance on a variety of models that are used to predict a variety of parameters. 

These models have different spatial and temporal resolutions. Also, some clearer delineation is 

needed on the overall model performance and the confidence of predictions. How does this 

confidence effect the ability to make accurate assessments of the effects of NOx and SOx? 

Specific Comments 

For Key Findings the following issues need to be addressed: 

This statement is not true:

Particulate sulfate can interact with methanogenic bacteria to produce methylmercury. 

This relationship is for sulfate in soil and wetlands not “particulate sulfate”. 

For the statement:

The sensitivity of terrestrial and aquatic ecosystems to acidification from sulfur and nitrogen 

deposition is predominantly governed by surficial geology. 

Change to include regional differences. 

For the statement:

In aquatic ecosystems, ecological effects are linked to changes in surface water chemistry, 

including sulfate concentration, nitrate concentration, sum of base cations, acid neutralizing 

capacity, surface water inorganic aluminum concentration, and surface water pH. 

Also indicate these effects are influenced by historical inputs to these systems. 

57
For the statement:

At least one important component of N, ammonia, is not measured routinely in any national 

network, but may account for greater than 80% of total reduced nitrogen deposition. 

This statement gives impression that N deposition is greatly underestimated without the inclusion 

of NH3. Provide clarification on the degree of the relative importance of NH3 deposition across 

the U.S. 

For the statement:

Existing monitoring networks are inadequate to characterize the full extent of regional 

heterogeneity in nitrogen and sulfur deposition, and very likely underestimate the total nitrogen 

deposition across wide areas of the U.S. 

Indicate where the actual geographical problems occur. 

The following statement is not true:

Atmospheric nitrogen deposition is the main source of new nitrogen to terrestrial ecosystems. 

Across terrestrial ecosystems for the total U.S. N fertilizers are the dominant form of input. 

Clarify that N atmospheric deposition’s relative importance varies among regions. 

For the following statement:

Nitrogen deposition causes changes in ecosystem carbon budgets. However, whether nitrogen 

deposition increases or decreases ecosystem carbon-sequestration remains unclear. For example, 

a limited number of studies suggest that nitrogen deposition may increase carbon-sequestration 

in forests, but has no apparent effect on carbon-sequestration in non-forest ecosystems.

Clarify that these effects are highly spatially variable including whether there are decreases or 

increases in C sequestration. 

For the following statement:

Productivity of many freshwater ecosystems and most estuaries and coastal water ecosystems is 

nitrogen limited. 

This suggests that N is the major limiting nutrient for freshwater systems. This is not generally 

true. This statement needs to be placed in context of P which often as important than N as a 

limiting nutrient for freshwater systems. 

For the following statement and related section:

Biological effects, Multiple biological indicators have shown that nitrogen deposition alters 

ecosystem structure. 

This section needs to be placed in the context of other agents of change including climate, exotic 

introductions, extreme events, etc.

58
Page Line Comment

xvii Change to “chloride ion.” 

xviii Change to “fluoride ion” 

1 Within the body of the text “Nitrogen” should be changed to “nitrogen”. 

1 Throughout the text corrections need to be made for subscripts that are lacking in 

some cases (e.g., NO3 should be NO3, NO2 should be NO2, SOX should be SOx, 

etc.). 

1 Change to “In the years 2004-2006, S deposition in the United States.” 

2 Change “inferred” to “modeled.” 

2 Change to “Although deposition in most areas of the United States was dominated 

by wet deposition, there were some exceptions, including parts of California here 

N deposition was primarily dry.” 

2 Change to “The sparse coverage of monitoring sites in many areas, especially in 

the rural West, results in little or no data on deposition totals in a substantial 

number of potentially sensitive places.” 

2 Change to “Numerical modeling efforts can help fill-in these data gaps and may 

suggest that local and even regional areas of high concentration and deposition 

exist where currently no data exist. 

4 Some of most severe acidification may also occur during the summer after periods 

of drought especially in those watersheds with substantial portions of wetlands. 

These rewetting episodes are associated with acidification due to the oxidation of 

previously reduced sulfides. 

2-1 8-18 Isn’t there some merit in changing the definition of nitrogen oxides to be the same

as that used by atmospheric scientists and air quality control experts?

2-4 2 Change “Roughly” to “Approximately.” 

2-6 6 Change to “The N content in fossil fuels and chemical forms vary strongly.” 

2-6 7 Change “running” to “operating conditions”. 

2-7 35 I thought that the effect of “stack height” effect was relatively minor with respect 

to the overall dispersion distance of pollutants from combustion. 

2-8 16 Change to “of the various products of N transformations.” 

59
2-8 22 Change to “synthetic and organic N fertilizers.” 

2-8 29 Change to “N metabolism in soils is strongly dependent on soil substrate 

concentrations of both N and labile carbon constituents as well as physical.” 

2-8 30 Change to “Where available N.” 

2-9 11-12 Change to “such as the differences between shortgrass and tallgrass prairie for 

example.” 

2-9 18-19 Change to “Local contributions to soil NOx can be greater per unit area than the 

global average.” 

2-10 28 Delete extra “,” in “(e.g.,,.” Note this occurs twice in this line. 

2-11 14-16 This statement is a little confusing. It suggests there a combination of both 

atmospheric residency time as well as heat trapping efficiency that produces this 

value of 300? These two parameters need to be clearly separated. Isn’t the heat 

trapping capacity on a per molecule 310 times that of carbon dioxide?

2-11-12 Reword as follows: However, N2O is an intermediate product along with NO 

from the complex soil metabolism described in Section 2.2.2.1. A brief 

description of N2O emissions and its contribution to the U.S. GHGs is described 

below. 

2-12 16-17 Delete: These emissions resulted from the fuel combustion, industrial practices, 

and stimulation of biogenic sources through agricultural practices enumerated 

above. 

2-12 18-19 Change to “From 1990 and 1998.” 

2-12 23 Change to “Biogenic production of N2O from soil accounted for > 75%.” 

2-12 27 Change to “may be affected by environmental conditions.” 

2-12 28-29 Change to “enhancing denitrification, and potentially increasing N2O emissions.” 

2-13 8 Change to “emissions originated from.” 

2-13 10 Change to “either as SO2 or SO3.” 

2-13 14 Change to “can not accurately be used to calculate the contribution of local 

sources to selected environmental.” 

2-13 18-19 Delete “with most counties east of the Mississippi River in warmer colors (greater 

emissions densities) than most counties in the West.” 

60
2-15 6 Change to “98 and 160 tons total SO2 per square mile, respectively.” 

2-18 4 In addition to carbon-bonded S (amino acid) there is also inorganic sulfate. 

2-22 1-3 This is a confusing sentence that needs to be reworded. 

2-22 10 Change to “have been performed for a number.”

2-22 12 Change to “it can be treated conservatively on these scales.” 

2-23 30 Change to “may have been underestimated or were increasing.” 

2-24 6 Change to “proved useful for estimating.” 

2-25 11 Change to “volatility. This pattern, however, has not appeared in previous 

emissions factors and inventories.” 

2-26 10 Change to “available in numerous references (Seinfeld.” 

2-26 11 Change to “recounted here with special attention to.” 

2-26 12-13 Change to “are schematized in Figure 2-15. NO2, itself an oxidant, can react to 

form.” 

2-26 16-17 Change to “to HNO3 and can contributing to the acidity of cloud, fog, and rain 

water.” 

2-27 Figure Caption 2-15 As stated previously it would be helpful to have the 

definitions of “NOx” and “NOy” be consistent with the atmospheric science 

literature. 

2-29 2 Delete “highways.” 

2-29 7 Change to “Reaction 7:.” 

2-29 14 Delete “schematic.” 

2-29 17 Change to “this chapter are:.” 

2-30 2 Change to “NO3:.” Note I would suggest that if reactions are provided after a 

statement this statement should end with a “:” throughout the document. 

2-32 15-16 Be consistent in the order of multiple citations throughout the document. Either 

cite by date or alphabetically. 

2-34 4 Change to “decomposition ranges.” 

61
2-34 6 Change to “uptake by vegetation.” 

2-34 7 Change to “Reaction 21 is thermally.” 

2-34 11 Change to “concentrations of their precursors.” 

2-34 12 Change to “found in most environments, ranging from remote.” 

2-34 14 Change to “downtown metropolitan areas, especially.” 

2-35 5 Change to “because many factors important for P(O3) are omitted.” 

2-35 6 Change to “VOCs that are mostly absent during early morning hours.” 

2-35 11-12 Delete “at a monitoring site in Shenandoah National Park, VA.” 

2-35 18 Change “from commercial aircraft are very similar.” 

2-35 20 Delete “included in model calculations.” 

2-35 27 Change to “(1998, 2001).” 

2-35 32 What is implied by the use of the term “correlation patterns”? See also page 2-36, 

line 1. 

2-36 7 Change to “2001 , 2003).” 

2-37 10 Change to “Brown et al. (2006) found.” 

2-38 1-2 Change to “available for reaction thus increasing P(O3).” 

2-38 5 Change to “amounts. However, only.” 

2-38 8-11 Change to: “It is important to recognize that the studies of both Schultz et al. 

(2000) and Singh et al. (1996) involved aircraft sampling at high altitude that can 

significantly under-represent sea salt aerosols. These aerosols are important 

contributors to total NO3 (defined to be HNO3 + pNO3 ) and large fractions of 

NOY(Huebert, 1996).” 

2-38 12 Change to “budgets based upon their studies.” 

2-38 14 Change to “domine, 2002) that.” 

2-38 19 Change to “Hence, HNO3 recycling.” 

2-38 33 Delete “observed.” 

62
2-38 34 Change “(Reaction 18) constitutes a.” 

2-39 6 Change to “and kerosene soot, and found that.” 

2-39 16 Delete “observed.”. 

2-39 18 Change to “Longfellow et al. (1999).” 

2-39 20 Change to “NO3/N2O5 and HO2/HO2NO2.” 

2-40 11-12 Change to “Daytime observations of HNO2, when rapid photolysis depletes 

ambient concentrations to very low levels, implies large sources of 

photoinduced.” 

2-48 4 Change to “Jacobson (2002).” 

2-48 12 Change to “~5 x 10-3 with.”

2-50 6-7 Is there still a quantifiable plum “further downwind”. Why are conditions even 

“more oxidizing than in background air”?

2-55 18 The correct abbreviation for moles is “mol” not “M”. 

2-56 2 Change to “throughout the Earth’s boundary layer.” 

2-56 8-9 Does the term “reservoir species” imply chemical species with larger “τ”? 

2-56 19-20 Change to “Photochemical activity is enhanced by higher temperatures and 

sunlight.” 

2-57 1 Change to “distances from their sources.” 

2-59 26-27 The format here is mixed up and needs a “)” at the end. 

2-60 1 Change to “(2007)”. There are two 2007 references that need to be designated 

with letters.

2-60 1 Delete “parts per billion” and “[]”. 

2-60 7 See other comment about Dunlea et al. references. 

2-60 2-34 Change to “The daily average interference for an episode during the summer of 

2002 was modeled. Concentration fields for NOz species and conversion 

efficiencies for NOz species ranged from ~20% in Baltimore to ~80% in Madison, 

VA. 

63
2-61 1 Change to “activity was highest.” 

2-61 2 Change to “compounds were greatest” 

2-61 7 Delete “On the whole.” 

2-61 10 What is meant by "can be changing rapidly"? Do you mean changing rapidly in 

the literature

2-65 7 Change to “normal” to “typical.” 

2-65 12-17 These statements are important in relating the results to actual needs and 

determination of standards. Similar types of statements are needed throughout the 

document to focus the results on those issues which are policy relevant. 

2-66 4-5 This sentence needs to be reworded since “and of the particles against deposition”

does not make sense. See also line 9. 

2-66 11-13 Delete the term “standard” in these statements. There is no actual standard 

configuration for these devices. 

2-69 1 Clarify what is meant by “In addition to the elevation by EPA.” 

2-69 2 Delete “and reported by.” 

2-69 3-6 Change to “The methods included the use of a tunable diode laser (TDL) 

absorption spectrometer, a wet scrubbing long-path absorption photometer 

(LOPAP), a wet effusive diffusion denuder (WEDD), an ion mobility 

spectrometer (IMS), a Nitrolux laser acousto-optical absorption analyzer, and a 

modified CL analyzer.”

2-69 11-13 Change to: “Hence comparisons of ambient NH3 instruments have confirmed that 

no single technique has yet been identified that provides automated, high quality 

results for continuously determining NH at low concentrations.” 

2-71 5 Be more explicit in using the term “positive artifact” here and elsewhere. Does 

this mean to suggest that there are overestimates of concentration measurements?

Would a better term be something like artifacts resulting in overestimates. 

2-71 11 See the comment above and modify to avoid confusion I the term “negative 

interference.” 

2-78-81 This section could benefit with more focus on the issues related to evaluating SOx

and NOx at the scales important for this assessment with respect to chemical 

transport models CTMs.

64
2-81-83 Is this review of global scale issue important for the issues associated with 

regional/local situations. At a minimum this section could be reduced playing 

particular attention to those global aspects that can have regional implications. 

2-87 3 In the Picketering et al. citations remove “;”. These format errors need to be 

corrected throughout the document. 

2-88 The previous pages (2-78 to 2-87) need to have a clearer linkage to this deposition 

section. 

2-89 9-13 Certainly a major issue that needs focus are the errors and problems with 

estimating dry deposition and a considerable amount of these concerns related to 

the calculations of deposition velocities. 

2-90 13-15 The statement that “Deposition rates are independent of leaf area or stomatal 

conductance, implying that deposition occurs to branches, soil, and the leaf cuticle 

as well as leaf surfaces” is misleading since leaf area and stomatal conductance 

are important, but that other factors also need to be included. 

2-93-95 The section on “Air Quality Model Evaluation” is a critical part of this document. 

2-94 3-5 These errors can lead to erroneous predictions especially with respect to those 

associated with future air quality estimates. 

2-101-202 Figures 2-38 and 2-39 suggest that the model results are quite different than those 

for the NADP network sites. Doesn’t this bring into question the model validity 

for predicting these wet deposition amounts?

2-104 12-13 Suggesting that Ext-RADM provides “good” agreement when R2

 values are

between 0.4 to 0.7 for most species is misleading since at lower values less than 

50% of the variation is being explained. 

2-105 1-4 These statements suggest a better Ext-RADM result. Is this due to the value 

representing a larger spatial unit and also an estimate for a longer period? 

2-108 1-4 I am not sure of the rationale for including in PRB the anthropogenic sources 

outside of U.S., Canada and New Mexico. 

2-120 Are the measurement protocols in State and Local Air Monitoring Systems 

(SLAMS) networks sufficiently similar for these measurements to be comparable 

to CASTNET. 

2-131 10 Incomplete sentence. 

2-198-202 Having this summary is helpful in placing the large amount of information 

provided in the document in context. Some further inclusion of statements relating 

65
to problems with respect to dry deposition estimates including the issues 

associated with estimating deposition velocities needs to be included. 

2-199 18-21 This sentence needs to reworded and likely separated into a series of sentences. 

3-4 25-26 Why are wetlands given special attention here?

3-7 Figure 3-2 caption. Change to “Diagram illustrates soil horizons commonly 

found”. 

3-9 8 Change to “(Shanley et al., 2005).” 

3-9 14-15 References are not cited correctly (these are multiple authors) including a need for 

a letter designation for Driscoll et al. (2001) 

3-9 20 See comment above regarding citation. It appears that this section has many cases 

where the references are not cited correctly including the absence of showing that 

the references are multiple authors.

3-11 9 Section “0"? 

3-12 17 Another line with incorrect referencing being used. 

3-12 30 Another line with incorrect referencing being used. 

3-16 Figure 3-3 needs a reference. 

3-17 Figure 3-4 needs a reference. 

3-19 3-9 Even in the West the nitrate in surface waters during snowmelt is mostly 

microbially derived and is not from direct atmospheric input. These statements 

confuse this issue. 

3-22 4 There are also large differences in tree species to tolerance of different levels of 

Al. Note this is indicated later in line 14. A clear statement is needed of the 

major factors associated with Al toxicity. 

3-22 14 Figure 3-5 does not clear depict that Al stress varies with species as suggested 

with this reference. 

3-25 2-5 The term buffering is not correctly used here. Reword to : Once base saturation 

decreases to a critical level (approximately 15–20%), inputs of H2SO4 and HNO3

result in exchange of inorganic Al. 

3-25 9-10 Change to “ If the C:N ratio of soils falls below about 20 to 25, nitrification is 

stimulated resulting in net nitrification and increased acidity.”

66
3-27 Figure 3-6 needs a reference. 

3-34 18-21 Also grasslands tend to be found on soils with relatively high pH and % base 

saturation. Aren’t grassland associated with acidic soils less common?

3-39 16 Change to “in most affected.” 

3-39 22 Delete “to a greater extent than SO4

2- .”

3-39 23-24 Delete “The importance of NO3 as an agent of acidification varies by region.” - 

3-39 29 Delete “Average.” 

3-40 1 Change to “Surface water NO concentrations have changed over time and these ! 

trends vary by regions”. 

3-40 19 Change “outbreak of gypsy moths, which consumed foliage” to “gypsy moth 

defoliation.”

3-40 20-21 Delete “ in affected watersheds.” 

3-40 32-33 Change to “annual air temperatures were strongly related to average annual NO3-

concentrations in stream water”. 

3-41 5-6 Was it really suggested that an increase in pH stimulated primary productivity? If 

this is the case this should be attributed to the authors of the article. 

3-41 9 Change to “between recent temporal trends.” 

3-42 1-2 Change to “(Aber, 2003). Moreover, spatial patterns of NO3 concentrations in 

surface water across the Northeastern U.S. are consistent with atmospheric N 

deposition values although there is considerable variation in these concentrations 

based upon watershed attributes. 

3-42 15-16 Change to “Within western Virginia and in Shenandoah National Park, 

concentrations of base cations in streams did not exhibit significant temporal 

trends from 1988 to 2001.” 

3-42 16-17 If sulfate concentrations did not change indicate this explicitly versus an indirect 

reference to the role of sulfate adsorption. 

3-43 1-2 See comment above regarding the results from Virginia. 

3-43 6-7 Delete “The pH of water quantifies the hydrogen ion concentration, which is toxic 

to many forms of aquatic life.” 

3-43 12 Explain the derivation of these three pH reference levels. 

67
3-43 22 Change to “southwestern Adirondacks acidified more compared to other lakes in 

the Adirondacks since preindustrial time.” 

3-44 6 Should this be “(0.18 μeq/L/yr)”?

3-45 1 Be explicit in referring to this study. I assume this is Stoddard et al. (2003). 

3-45 18 Do you mean by more stable that ANC is not affected by ambient CO2

concentrations? Make this more explicit. 

3-45 29 Explain these three cutoff values for ANC. 

3-45 33 Change to “the oxidation of chemically reduced S-containing minerals.” 

3-47 11-14 Delete “ANC can be measured in the laboratory by Gran titration or calculated on 

the basis of the difference between the base cation sum and the mineral acid anion 

sum. Acidic waters are defined as those having ANC less than or equal to zero 

μeq/L”. 

3-48 33 Not sure the term “limited” is appropriate. 

3-50-51 References are needed in this text to support the statements. 

3-52 The following study provides additional information on ANC patterns within the 

Adirondacks using a mass balance approach: Ito, M. M.J. Mitchell, C.T. Driscoll 

and K.M. Roy. 2005. Factors affecting acid neutralizing capacity in the 

Adirondack region of New York: a solute mass balance approach. Environmental 

Science and Technology 39:4076-4081. 

3-54 I believe some PnET-BGC simulations by Driscoll’s group have also been done 

that would provide other estimates of the recovery of ANC. 

3-56 8 Change to “rain events.” 

3-76 32-33 References needed to support this statement. 

3-79 1-2 A major problem in making wide scale regional projections is that it is well 

known that the response even within relatively small areas (e.g. almost adjacent 

watersheds) that the response to acidic deposition can be quite marked. 

3-79 3-6 It needs to be emphasized that the water pathways and soil depth can be very 

important in the capacity to neutralize the effects acidic inputs. 

3-79 13 It should also be stated that this is a threshold which is generally necessary, but 

does not always result in enhanced nitrate loss. 

68
3-80-81 Some inclusion of issues associated with how biotic response can also be altered 

by other factors such as climate change, invasion of exotics, extreme events (e.g., 

drought, ice storms, hurricanes, etc.) 

3-87 Figure 3-19. Why not cite NADP/NTN as the source versus Sullivan et al. 

(2006a). Also, the more recent data should be included. 

3-88 In reviewing the results from the Adirondacks focus on those findings specific to 

the Adirondacks versus generalities associated with acidification of ecosystems. 

3-89 The PIRLA I and PIRLA II projects provided some of the most definitive 

evidence of historical changes in acidification of the Adirondacks. Inclusion of 

some of the figures produced from this project would strengthen the document. 

3-89-90 The inclusion of figures showing side by side comparison of MAGIC and 

PnETBCG hind casting would be instructive especially if placed in the context of 

the PIRLA reconstructions. 

3-90 8 Provide figures or tables clearly showing similarities and differences between the 

MAGIC and PnET-BGC simulations. 

3-91 Table 3-10. Reference needed 

3-102-123 The structure of the document results in redundancy with some of the information 

in this section also being presented in previous sections of Chapter 3. 

3-127 9 Certainly atmospheric deposition is an important contributor, but it also needs to 

be stated that other forms of N input generally exceed that from the atmosphere. 

3-127 23 Even for those watersheds exhibiting substantial nitrate loss the vast majority of 

the N inputs are either being stored or being denitrified within these watersheds. 

3-128 1-2 Change to “higher rates of deposition with some of these watersheds showing 

little nitrate losses.” 

3-128 12-19 Wetlands can also be sources of nitrogen due to nitrogen fixation such as that 

associated with alders. 

3-128 23-24 The case for freshwater eutrophication is not strong. The strongest evidence is 

associated with changes in the biotic assemblages of lakes especially in the 

Mountain West. 

3-129 1-4 A more conservative statement is warranted with respect to the contribution of 

atmospheric deposition so that it is clear that in general this is not the dominant 

source of N input that is causing eutrophication. 

69
3-129 19-25 It should be emphasized that there is also an issue of transient effects where over 

the short term the additional N results in additional C fixation (e.g. enhanced 

primary productivity) but this will not continue as other factors limit production 

over extended periods. 

3-130 21 Change to “beech.” 

3-130 25-31 This affect on frost hardiness needs to be linked to issues of red spruce dieback at 

high elevations. 

3-133 6-7 Some further elaboration is needed related to results in Europe that have shown 

that experimental N additions have resulted in higher forest growth and this high 

growth resulted in other nutrient deficiencies especially in the form of Mg. 

3-133-136 This discussion on “N Deposition Effects on Productivity and C Budgets in 

Terrestrial Ecosystems” is generally well done and provides a good synopsis of 

existing information. 

3-142 1-13 The discussion on the historical aspects of N limitation in North American lakes 

is interesting, but it is important to ascertain which is the type of lake nutritional 

status are the goals of any regulatory programs. It is not likely that there would be 

a strong mandate to return to pre-Columbian conditions. This situation may be 

different with respect to desirable endpoints between the eastern and western U.S. 

3-146 14-15 This needs to reworded so as not to give the impression that the N is the major 

limiting nutrient for most lakes. Clear articulation of differences between more 

pristine versus more developed regions is likely required. 

3-147-151 The section on estuaries is generally thorough a provides a good review of the 

influence of N availability on productivity and other aspects of importance to 

biogeochemical and biotic responses. 

3-162 10 Change to “100 y.’ 

3-166 16 Change to “documented.” 

3-152 33-34 It needs to be explicitly stated that atmospheric N loadings is not the sole 

contributor to the increased N loading in estuaries. 

R-30 There are two Dunlea et al. (2007) references that need to be designated “a” and 

“b” respectively.

70
Mr. Richard L. Poirot 

These comments pertain primarily to Charge Question 2 and Chapter 1 of the 2nd draft ISA. 

Question 2. Chapter 1 has been revised to clarify the scope or focus of this 

assessment on effects related to the deposition of nitrogen and sulfur compounds. In 

addition, we have added a discussion of the framework for evaluation of causality 

for assessing ecological effects. Do these revisions adequately characterize the scope 

of the assessment? Does the CASAC panel have recommendations for revisions to 

the causality framework? Is it appropriately applied in the draft ISA?

Chapter 1 provides a clear, concise introduction to the ISA, including a brief history of past 

NAAQS reviews, an outline of the intended scope of the current assessment, and a proposed 

framework for the determination of causality in relationships between the pollutants of concern 

and the resulting ecological responses. Overall I think this chapter looks good, and my 

comments are mostly minor. 

While the scope of the assessment is relatively broadly defined – to include for example

consideration of ecological effects resulting from N-nutrient enrichment from deposition of both 

oxidized and reduced nitrogen – there still seems to be a rather intentional avoidance of 

questions of how such effects or environmental effects may be related to alternative kinds of

NAAQS air-quality-related indicators. This question does get taken up to some extent in 

Chapter 8 of the Risk and Exposure Assessment. However, it might also be useful to add some

discussion and display of the inter-relationships among various air quality, deposition and effects 

metrics as part of the ISA. It would be useful to know up front if deposition-based or critical 

load-type NAAQS are a possibility, or are we stuck with SO2 and NO2, again? 

As indicated in previous comments, I think its unfortunate that the scope of this assessment was 

narrowed to exclude consideration of visibility effects from aerosol phase sulfur and nitrogen 

compounds. I think it would have been possible to copy/paste the same discussion of these 

effects in both the SOx/NOx and PM secondary NAAQS ISAs (and then decide which NAAQS - 

if any - would be most effective for addressing all the welfare effects of S & N emissions). In 

the current case it might also have led to consideration of useful alternative NAAQS indicators – 

which consideration of aerosol concentrations & effects would help justify. It can also be noted 

that the working definitions of NOx and SOx are somewhat awkward here, as NOx is taken to 

include nitric acid and aerosol nitrate, while SOx includes only the gaseous oxidized sulfur 

compounds. 

The historical summary of the secondary SOx and NOx NAAQS reviews is exceedingly brief, 

and it seems incomplete for example to mention the 1984 EPA Acid Deposition Critical 

Assessment Document without also mentioning the 1990 NAPAP State of the Science and 

Technology and Integrated Assessment Reports, the 1990 CAA Amendments (Title IV), and 

1995 EPA Acid Deposition Standard Feasibility Study Report to Congress. Granted, these 

were not part of the NAAQS review per se, but the 1996 decisions not to revise the secondary 

SOx or NOx NAAQS were related to these other activities, and represented a clear decision that 

71
the environmental effects of these pollutants were better addressed by other regulatory 

mechanisms. 

The proposed framework for evaluation of causality is logical and clearly presented. So far as I 

can tell, it appears to be appropriately (and effectively) applied elsewhere in the document – 

where chapters 3 and 4 contain a number of clear, persuasive statements that “the evidence is 

sufficient to infer a causal relationship between ...X and Y”. With the exception of a few 

such statements on direct vegetation effects from exposures to specific gaseous S and N 

compounds, the identified “causal agents” are almost always either “acidifying deposition” or

“reactive nitrogen deposition”, and thus appear to be intentionally non-specific to the 

traditional criteria pollutant definitions. I think this is fine – even preferable – if secondary 

NAAQS are being considered that might be deposition-based, combine S&N or combine 

oxidized and reduced nitrogen. If such alternative metrics are not being considered, than maybe 

some of these bullets might be rephrased in more pollutant-specific terms. Also perhaps there 

could be some causality conclusions in chapter 2, in which causal relationships might be inferred 

between (current and historical) emissions, ambient air concentrations and deposition of various 

S and N compounds. 

Possibly also, the concept of a “significantly contributing factor” could be introduced here (and 

used later) as a sort of subset of a “causal factor” (i.e. “the evidence is sufficient to infer a causal 

relationship between Nr, for which oxidized N is a significantly contributing factor, and Z 

effects...”). This concept of significant contributing factor could be important in considering 

effects resulting from pollutant mixtures, as well as for considering effects which result from or 

are modified by the cumulative influences of both current and historical pollutant deposition. 

I think the description of the 2-step process in the causality framework could be more clearly 

presented. There’s a bit of a logic problem with saying first we will determine the causal 

relationship and then we will determine what effect has been caused. In reality, the process 

seems to be more one of starting with identifying rather broad, general causal relationships (for 

example between total Nr deposition and alteration of terrestrial species richness) and then in 

step 2 winnowing this down to identify more pollutant-specific and/or species-specific 

relationships at specific ranges of concentrations/exposures. Additional confusion is introduced 

by apparent inconsistencies between the 2 steps in the causality framework as described in lines 

4 and 5 page 1-7, and the subsequent discussion of 2 steps in sections 1.6.1 and 1.6.2. In the 

first case, step 2 refers narrowly to the determination of whether levels of exposure can be 

defined at which effects of concern can be observed (kind of a yes/no threshold answer). In the 

second case (section 1.6.2), step 2 is more broadly and comprehensively defined to consider 

effects over a range of exposure conditions with evaluation of the shapes of exposure-response or

concentration-response functions. Presumably this would also include consideration of 

estimated future ecological responses to changes (increases or decreases) in pollutant 

concentration and deposition. For the most part, this ISA seems much more focused on step 1 

type conclusions – although there are some very useful tabular presentations of quantitative 

relationships between N deposition levels and specific ecological effects such as in Table 4-4. 

I wonder if the intent is to intentionally focus on step 1-type conclusions in the ISA and then 

develop more detailed quantitative evaluations of ecological response (i.e. step 2) in the Risk and 

Exposure Assessment. If this is the intent, why not make it clear?

72
Mr. David Shaw

General Comments 

The executive summary is an excellent contribution to the ISA. This addresses some of my

previous concerns regarding a clear message of the document. 

Executive Summary, Page 2: 

The paragraph which begins with “Expanding urbanization...” has a last sentence explaining 

heterogeneous deposition. This last sentence might be benefited by the addition transport. 

It seems that it would serve the assessment better to have Section 1.7 (page 1-10) appear at the 

beginning of Chapter 1. 

Charge Questions 

Chapter 1 has been revised to clarify the scope or focus of this assessment on effects related to 

the deposition of nitrogen and sulfur compounds. In addition, we have added a discussion of 

the framework for evaluation of causality for assessing ecological effects. Do these revisions 

adequately characterize the scope of the assessment? Does the CASAC panel have 

recommendations for revisions to the causality framework? Is it appropriately applied in the 

draft ISA?

I feel that the scope has been properly modified to include both oxidized and reduced forms of 

nitrogen. Furthermore, I am pleased at the use of “acidifying deposition” throughout the 

document. This reflects the actual concern of this type of deposition. 

Section 1.1, Page 1-3: 

I still feel that particulate matter should not be omitted from this document. As my previous 

comments state: 

PM plays a significant role in nitrogen and sulfur deposition. I feel that separating out the 

effects of gas- versus aerosol-phase S/N will be difficult, since wet and dry deposition can 

include both phases, and atmospheric chemistry and transport affect both phases. The ISA 

clearly states that “particulate NOx and SOx will be addressed with the secondary PM NAAQS 

review,” and it therefore becomes crucial that these two review process tracks are highly 

consistent with each other. One cannot proceed independently of the other track. 

Section 1.6, Table 1-1: 

While the causality framework does seem appropriate, it is unclear as to how much weight is 

given to each aspect. I do appreciate that it clearly states that that scientific evidence will not 

have to meet all of the aspects of causality, but it might benefit the group to understand how each 

will be considered in the weighting process (i.e. if no consistency then not used). 

73
Section 1.6.1, Table 1-2: 

Again, while the descriptors for weight of evidence seem appropriate, I wonder if these could 

somehow be associated with the causality aspects. For example, given a “weight” in the form

of a number for each aspect, add all the aspect numbers for a total. When this total is 

calculated, apply to the weight of evidence table. Perhaps “sufficient to infer a causal 

relationship” is used for aspect numbers of 30 or higher (depending on how the number scheme

is set). 

Misc. 

Page 1-6, line 16: 

Should read “...analyses used appropriately and...” 

Executive Summary 

There is inconsistency in how NOx and SOx is typed. 

74