UNITED STATES ENVIRONMENTAL PROTECTION AGENCY

WASHINGTON D.C. 20460

OFFICE OF THE ADMINISTRATOR

SCIENCE ADVISORY BOARD

May 17, 2011

EPA-CASAC-11-005

The Honorable Lisa P. Jackson

Administrator 

U.S. Environmental Protection Agency

1200 Pennsylvania Avenue, NW 

Washington, DC 20460 

Subject: CASAC Comments on the Policy Assessment for the Review of the Secondary 

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

Sulfur (February 2011)

Dear Administrator Jackson: 

The Clean Air Scientific Advisory Committee (CASAC) Oxides of Nitrogen and Sulfur Oxides 

Secondary NAAQS Review Panel met on February 15-16, 2011 to consider the information in 

EPA’s Policy Assessment for the Review of the Secondary National Ambient Air Quality 

Standards for Oxides of Nitrogen and Oxides of Sulfur (February 2011) and to provide our 

recommendation on the review of the standard. The draft report was approved by the chartered 

CASAC at the public teleconference on May 12, 2011. Below, we offer our general comments 

and recommendations. The CASAC and Panel membership is listed in Enclosure A. More 

detailed consensus comments are presented in Enclosure B. Enclosure C is a compilation of 

individual panel member comments. 

Overall, we reiterate our previous comments from the review of EPA’s second draft of the Policy 

Assessment: “EPA staff has demonstrated through the Integrated Science Assessment (ISA), 

Risk and Exposure Characterization (REA) and the draft PA that ambient NOx and SOx can 

have, and are having, adverse environmental impacts. The Panel views that the current NOx and 

SOx secondary standards should be retained to protect against direct adverse impacts to 

vegetation from exposure to gas phase exposures of these two families of air pollutants. Further, 

the ISA, REA and draft PA demonstrate that adverse impacts to aquatic ecosystems are also 

occurring due to deposition of NOx and SOx. Those impacts include acidification and 

undesirable levels of nutrient enrichment in some aquatic ecosystems. The levels of the current 

NOx and SOx secondary NAAQSs are not sufficient, nor the forms of those standards 
2

appropriate, to protect against adverse depositional effects; thus a revised NAAQS is warranted.” 

(Russell and Samet, December 9, 2010, EPA-CASAC-11-003)

The final Policy Assessment is substantially improved from the last draft, and EPA staff has 

responded to most of our concerns raised in our previous comments. The Policy Assessment

develops a framework for a multi-pollutant, multimedia standard that is ecologically relevant and

reflects the combined impacts of these two pollutants as they deposit to sensitive aquatic ecosystems.

The final Policy Assessment clearly sets out the basis for the recommended ranges for each of the 

four elements (indicator, averaging time, level and form) of a potential NAAQS that uses 

ambient air indicators to address the combined effects of oxides of nitrogen and oxides of sulfur 

on aquatic ecosystems, primarily streams and lakes. As requested in our previous letters, the 

Policy Assessment also describes the implications of choosing specific combinations of elements 

and provides numerous maps and tabular estimates of the spatial extent and degree of severity of 

NAAQS exceedances expected to result from possible combinations of the elements of the 

standard.

We believe this final PA is appropriate for use in determining a secondary standard to help 

protect aquatic ecosystems from acidifying deposition of oxides of sulfur and nitrogen. EPA 

staff has done a commendable job in developing the innovative Aquatic Acidification Index 

(AAI), which provides a framework for a national standard based on ambient concentrations that 

also takes into account regional differences in sensitivities of ecosystems across the country to 

effects of acidifying deposition. 

CASAC supports the potential choices/ranges presented by EPA staff on the indicators, form, 

averaging time, and level that should be considered for a revised secondary NOx-SOx NAAQS. 

While each aspect of the standard is discussed separately in our attached comments, ultimately 

the final choice of the indicators, averaging time, form and level should be considered in an 

integrated fashion, accounting for the other considerations and uncertainties also discussed.

As EPA moves forward in this regulatory process, we recommend some attention be given to our 

residual concern that the available data may reflect the more sensitive water bodies and thus, the 

selection of percentiles of waterbodies to be protected could be conservatively biased. Further, 

we found some improvements could be made to the uncertainty analysis. Both of these concerns 

are discussed in our attached consensus comments. 

In summary, while we have identified areas for improvement in future work and topics that may 

need to be clarified in the current review, overall CASAC finds that the Policy Assessment

provides relevant scientific information needed for consideration in revising the secondary 

NAAQS for oxides of nitrogen and sulfur. We trust that our comments are useful to you and 

your agency in developing a proposal for a multipollutant NAAQS. 
3

Sincerely,

/signed/ /signed/

Dr. Armistead (Ted) Russell, Chair

CASAC Oxides of Nitrogen and Sulfur Oxides 

Secondary NAAQS Review Panel

Dr. Jonathan M. Samet, Chair

Clean Air Scientific Advisory Committee

Enclosures
4

NOTICE

This report has been written as part of the activities of the EPA's Clean Air Scientific Advisory 

Committee (CASAC), a federal advisory committee independently chartered to provide 

extramural scientific information and advice to the Administrator and other officials of the EPA. 

CASAC provides balanced, expert assessment of scientific matters related to issues and 

problems facing the Agency. This report has not been reviewed for approval by the Agency and, 

hence, the contents of this report do not necessarily represent the views and policies of the EPA, 

nor of other agencies within the Executive Branch of the federal government. In addition, any 

mention of trade names or commercial products does not constitute a recommendation for use. 

CASAC reports are posted on the EPA Web site at: http://www.epa.gov/casac.
5

Enclosure A: Rosters

U.S. Environmental Protection Agency

Clean Air Scientific Advisory Committee

Oxides of Nitrogen (NOx) and Sulfur Oxides (SOx) Secondary Review Panel

CHAIR

Dr. Armistead (Ted) Russell, Professor, Department of Civil and Environmental Engineering, 

Georgia Institute of Technology, Atlanta, GA

CASAC MEMBERS

Mr. George Allen, Senior Scientist, Northeast States for Coordinated Air Use Management 

(NESCAUM), Boston, MA

Dr. H. Christopher Frey, Professor, Department of Civil, Construction and Environmental 

Engineering, College of Engineering, North Carolina State University, Raleigh, NC

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

CONSULTANTS

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. 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. Charles T. Driscoll, Jr., Professor, Department of Civil and Environmental 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, Mechanical Engineering, Engineering and Applied Science, 

Washington University, St. Louis, MO

Dr Dale Johnson, Professor, Nat. Res. Env. Sci., College of Agriculture, Biotechnology, and 

Natural Resources, University of Nevada, Reno, Reno, NV
6

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

Institute, Palo Alto, CA

Dr. Myron Mitchell, Distinguished Professor and Director of Council on Hydrologic Systems 

Science, College of Environmental Science and Forestry, State University of New York, 

Syracuse, NY

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

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

Mr. David J. Shaw, Director, Division of Air Resources, Department of Environmental 

Conservation - New York State, New York State, Albany, NY, United States of America

SCIENCE ADVISORY BOARD STAFF

Dr. Holly Stallworth, Designated Federal Officer, Science Advisory Board Staff Office, 

Environmental Protection Agency, Washington, DC
7

U.S. Environmental Protection Agency 

Clean Air Scientific Advisory Committee (CASAC) 

CHAIR 

Dr. Jonathan M. Samet, Professor and Flora L. Thornton Chair, Department of Preventive 

Medicine, University of Southern California, Los Angeles, CA 

MEMBERS 

Mr. George A. Allen, Senior Scientist, Northeast States for Coordinated Air Use Management 

(NESCAUM), Boston, MA 

Dr. Joseph D. Brain, Cecil K. and Philip Drinker Professor of Environmental Physiology, 

Department of Environmental Health, Harvard School of Public Health, Harvard University, 

Boston, MA 

Dr. H. Christopher Frey, Professor, Department of Civil, Construction and Environmental 

Engineering, College of Engineering, North Carolina State University, Raleigh, NC 

Dr. Armistead (Ted) Russell, Professor, Department of Civil and Environmental Engineering, 

Georgia Institute of Technology, Atlanta, GA 

Dr. Helen Suh, Program Area Director, Environmental Health, National Opinion Research 

Corporation (NORC) at the University of Chicago, Boston, MA 

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

SCIENCE ADVISORY BOARD STAFF

Dr. Holly Stallworth, Designated Federal Officer, U.S. Environmental Protection Agency, 

Washington, DC 
8

Enclosure B: CASAC Consensus Comments

Below are CASAC’s detailed comments on each aspect of a potential NAAQS standard. 

Indicators

The use of total reactive oxidized nitrogen (NOy) and sulfur oxides (SOx) as atmospheric 

indicators of oxidized nitrogen (N) and sulfur (S) atmospheric concentrations is well justified. 

The use in the Aquatic Acidification Index (AAI) of NOy and SOx as atmospheric indicators of 

N and S concentrations is useful and corresponds with other efforts by EPA. As we have stated 

previously, CASAC also agrees that acid neutralizing capacity (ANC) is the most appropriate 

ecological indicator of aquatic ecosystem response and resiliency to acidification. It should be 

noted, however, that for some ecosystems, ANC does not fully characterize acidification 

attributes of systems and additional parameters such as an indicator of acidity or alkalinity (pH), 

dissolved organic carbon (DOC) and monomeric aluminum are important. While CASAC 

supports the use of the proposed SOx and NOy indicators, in combination with associated 

deposition transfer ratios from the Community Multiscale Air Quality (CMAQ) model, we 

encourage the Agency to exercise flexibility in considering alternative combinations of measured 

S and N chemical species and transference ratios that may be capable of producing comparable 

deposition estimates. The Air Monitoring and Methods Subcommittee report, (EPA-CASAC-11-

006), provides comments on the methods and measurements for implementing a new secondary 

NAAQS for oxides of N and S. Final decisions on the N and S indicators will need to take their 

recommendations into consideration.

Form

EPA has developed the AAI, an innovative “form” of the NAAQS itself that incorporates the 

multi-pollutant, multi-media, environmentally modified, geographically variable nature of 

SOx/NOy deposition-related aquatic acidification effects. With the caveats noted below, 

CASAC believes that this form of the NAAQS as described in the final Policy Assessment is 

consistent with and directly reflective of current scientific understanding of effects of acidifying

deposition on aquatic ecosystems. 

The form described consists of two general parts - a chemical component, and a spatial 

component. The chemical component, expressed in terms of the AAI equation, links an 

environmental indicator (a protective level of ANC in surface waters) to measurable 

concentrations of SOx and NOy in the ambient air. For any given spatial area and specified level 

of the standard, compliance can then be directly determined from new and continuing 

measurements of SOx and NOy. Given the importance of CMAQ and ecological model 

calculations in the equation, there is a continuing need to evaluate model performance in 

estimating the deposition terms and ecological components of the AAI to account for model 

uncertainties, and to make the model-dependent factors in the NAAQS increasingly transparent. 

Model performance issues are addressed further below.

The role of DOC and its effects on ANC, including differences in measured and calculated ANC 

values would benefit from further refinement and clarification. Some consideration should be 
9

given to how the supply of DOC affects overall sensitivity of aquatic ecosystems to total 

acidifying deposition, and the use of ANC as an indicator of surface water acidification. In 

future considerations of the standard, accounting for aluminum availability and sulfur retention 

and/or mobilization in soils also should be considered.

CASAC agrees that the spatial components of the form in the Policy Assessment are reasonable 

and that use of Omernick’s ecoregions (Level III) is appropriate for a secondary NAAQS 

intended to protect the aquatic environment from acidification – especially where there are 

geographical variations in the inherent sensitivity of ecosystems to pollutant effects. When 

considered in isolation, it is difficult to evaluate the logic or implications of selecting percentiles

(70th to 90th) of the distribution of estimated critical loads for lakes in sensitive ecoregions to 

determine an acceptable amount of deposition for a given ecoregion. However, when these 

percentile ranges are combined with alternative levels within the staff-recommended ANC range 

of 20 to 75 microequivalents per liter (μeq/L), the results using the AAI point to the ecoregions 

across the country that would be expected to require additional protection from acidifying 

deposition. Reasonable choices were made in developing the form. The number of acid 

sensitive regions not likely to meet the standard will be affected both by choice of ANC level 

and the percentile of the distribution of critical loads for lakes to meet alternative ANC levels in 

each region. These combined recommendations provide the Administrator with a broad but 

reasonable range of minimally to substantially protective options for the standard. 

The division of ecoregions into “sensitive” and “non-sensitive” subsets, with a more protective 

percentile applied to the sensitive areas, also seems reasonable. However, it is not entirely clear 

how the various sensitivity criteria will actually be defined and applied. The most relevant 

questions to answer are whether these areas currently suffer adverse effects to public welfare 

from anthropogenic-caused deposition and whether there is good scientific reason to expect 

improvement in the condition of these areas if anthropogenic deposition were decreased. There is 

likely to be some geographical variability in the capacity of soils to take up (and release) 

atmospheric sulfur and nitrogen that could be considered as part of the sensitivity criteria. Very 

low calculated critical loads that result from natural acidity are not an accurate reflection of the 

potential for adverse effects to public welfare from anthropogenic-caused deposition. Natural 

poorly buffered coastal plain areas are initially identified as sensitive areas based on low ANC, 

but are later identified as anomalous. These areas are found in CMAQ model runs that use a

single emission reduction scenario to be “non-responsive” to decreases in SOx and NOx 

deposition. While consideration of “responsiveness” is one of several screening criteria that 

might logically be applied, a more thorough assessment of responsiveness based on multiple 

emission/deposition-control scenarios and other factors would be helpful. The proposed rule 

should clearly specify how these or other screening criteria will be applied in assigning 

ecoregions to “sensitive” and “non-sensitive” categories.

Critical load calculations can be made either using the Model of Acidification of Groundwater in 

Catchments (MAGIC) or the F-factor approach. The critical loads calculated using the F-factor 

approach are consistently lower than those calculated using the MAGIC model. Either approach 

may result in an underestimate of the critical load component in the AAI equation in some 

regions. Calculations of critical loads for individual water bodies within each region can be 

accomplished using available data. The percentile of water bodies to select to meet the target 
10

ANC value is based on this distribution. The representativeness of the available data for an 

ecoregion is therefore important. The available data are more likely to reflect the more sensitive 

water bodies and are therefore not representative of the entire population of water bodies in a 

given ecoregion. Potential biases that would result from using the F-factor approach and the 

currently available water chemistry data should be identified and addressed. 

The potential biases in the critical load calculations and in the regional representativeness of 

available surface water chemistry data suggest that a given percentile of the distribution of 

estimated critical loads for surface waters may be protective of a higher percentage of surface 

waters in some regions. As indicated above, it is important that the performance of both 

atmospheric and ecological models on which the potential NAAQS is based be continually 

evaluated and refined. Periodically conducting direct measurements of ANC and other modeled 

chemical parameters in surface waters would also be a valuable way to assure that the 

combination of measured and modeled components of the NAAQS are performing as expected.

 

Averaging time 

Considering the cumulative nature of the long-term adverse ecological effects and the year-toyear variability of atmospheric conditions (mainly in the amount of precipitation), CASAC 

concurs with EPA that an averaging time of three to five years for the AAI parameters is 

appropriate. A longer averaging time would mask possible trends of AAI, while a shorter 

averaging time would make the AAI being more influenced by the conditions of the particular 

years selected. 

Level 

CASAC agrees with EPA staff’s recommendation that the “level” of the alternative AAI 

standards should be within the range of 20 and 75 μeq/L. We also recognize that both the 

“level” and the form of any AAI standard are so closely linked in their effectiveness that these 

two elements should be considered together.

Other Considerations

Adverse effects: Providing protection from adverse effects to public welfare is the motivation 

for this standard setting process. There is clear evidence that such adverse effects are occurring

in sensitive ecosystems in the United States as a result of anthropogenic acidic deposition. There 

are uncertainties about the magnitude of the economic value of the losses in ecosystem services, 

but CASAC believes that adverse effects to public welfare exist when fish species and other 

aquatic life that are native to an ecosystem are unable to survive.

Process for updating the AAI: EPA should provide values for the four elements of the AAI for 

each ecoregion as part of the proposed rule. These values may differ across the regions, but 

nationally consistent methods for their determination should be used. The suggestion was made 

that in some cases individual states might want to adjust some of these values with their own 

measurement data, but CASAC is concerned that this would be problematic unless the state’s 

measurement data are rigorously quality assured. However, it is extremely important to 
11

recognize that during each review cycle for the standard, new ecological and atmospheric data 

and modeling approaches should be considered to update and improve the values for the 

elements of the AAI, and that the national monitoring programs that supply data for these efforts 

are continued and, in some cases, expanded (e.g., National Acid Deposition Program, Clean Air 

Status and Trends Network, Temporally Integrated Monitoring of Ecosystems, Long Term 

Monitoring). This includes the estimates of ammonia and ammonium ion deposition, data and 

models used in the critical load calculations, data and models used to determine the deposition 

transference ratios, the retention rates for N and S, and weathering and runoff data. 

Chemically Reduced Nitrogen: Another issue raised in the context of the Aquatic Acidification 

Index (AAI) is the matter of chemically reduced forms of nitrogen (NHx = sum of NH3 and 

NH4

+

). CASAC fully understands that these chemically reduced forms of reactive nitrogen have 

not been identified as criteria pollutants. Nevertheless, aquatic ecosystems are well known to 

respond to these reduced forms of nitrogen as well as to oxidized nitrogen and to create acidity in 

the process, just as the deposition of nitric acid does. While policy and political considerations 

require different treatment of chemically reduced and chemically oxidized forms of nitrogen, the 

ecosystems upon which they fall do not so distinguish Thus, from a scientific perspective, it is 

very important to bear in mind that any controls on emissions of chemically oxidized forms, 

which originate primarily from fossil fuel combustion sources, will not address inputs of 

chemically reduced forms of reactive nitrogen, which originate primarily from animal operations 

and agricultural sources.

Uncertainties

It is difficult to judge the adequacy of the uncertainty analysis performed by EPA because of lack 

of details on data inputs and the methodology used, and lack of clarity in its presentation. 

Because of the limitations of the uncertainty analysis, it is difficult to see how this could be used 

to inform the choices for the standard.

In its analysis, EPA ignored some aspects of the variability in the parameters within an 

ecoregion. This omission could be critical in cases where this variability also affects the degree 

of confidence in a given value of a parameter. Instead of using the mean ecoregion values and 

the unexplained “bootstrapping” method to assign uncertainty, EPA could have used the 

variability of the distribution of the values in an ecoregion. If the distribution of values in an 

ecoregion is reasonably homogeneous, the effect of variability would be minimal. Under these 

conditions, the degree of confidence in the response surfaces for SOx and NOy is influenced 

solely by the uncertainty in the measurements or estimations of the AAI parameters. EPA’s 

uncertainty analysis does not include the impact of variability in judging the degree of 

confidence in the response surfaces by assuming average conditions and defining fixed levels of 

uncertainty for the average value of the parameters. In the future, EPA could perform uncertainty 

analysis at the water body level to account for variability of water bodies within an ecoregion to 

complement the analysis done for the ecoregion averages.

The parameters of the AAI equation are derived using air quality and aquatic models. Given that 

these models are being used in the standard setting process, a more rigorous model evaluation 

should have been conducted to provide more confidence in the use of the models. For example, 
12

CMAQ model evaluation statistics averaged over the continental U.S. are shown for modeled 

quantities which limit the understanding of how well it simulates deposition in acid-sensitive 

spatial areas of interest. The MAGIC model was evaluated by EPA for 104 water bodies, but 

results are shown only for four water bodies. It is important to know model results for the 

remaining 100 water bodies.

Recommendations for Future Research and Analysis

The innovative nature of this form of a combined NOx-SOx secondary NAAQS has prompted 

CASAC to identify a number of areas that should be the focus of further research. These areas 

are detailed here and have been documented in past transmittals, including the attached panelists’

comments. In many cases, EPA staff has been able to address the issues identified. Particular 

areas that would benefit from further study or consideration in potential revisions or 

modifications to the form of the NAAQS include sulfur retention and mobilization in the soils, 

aluminum availability, soil versus water acidification, and ecosystem recovery times. The 

important role that chemically reduced and organic forms of total reactive nitrogen have, not 

only in ecosystem acidification, but also in excess nutrient loading suggests that EPA identify 

ways to limit future emissions of reduced nitrogen (e.g., ammonia). Although the current focus 

on an ecological indicator of acidification effects on aquatic ecosystems is appropriate, some 

further linkage with associated effects on terrestrial ecosystems would be helpful in future work. 

The use of the chemiluminescence technique for measuring, NOy, has considerable merit. 

However, monitoring of individual ambient N chemical species that is more consistent with the 

current understanding of atmospheric deposition processes is also recommended for evaluation 

of dry deposition values generated by CMAQ. Nitric acid (HNO3), nitrogen dioxide (NO2) and 

ammonia gas (NH3) are routinely and reliably monitored with passive samplers. Since these 

species, in part, account for the majority of the dry deposited N, a commitment to their 

monitoring is encouraged. These measurements are especially important for reliable estimates of 

NHx deposition (factor F2 in the equation for calculation of AAI). Such empirical data would 

also help in calculation of the transference ratios from CMAQ model simulations. Ambient air 

monitoring with passive samplers in conjunction with the Clean Air Status and Trends Network 

(CASTNET) measurements, would greatly improve robustness of the available air chemistry 

data that would be essential for evaluation of the CMAQ outputs. The in situ measurements of 

total N & S deposition at a subset of monitoring sites are also recommended for evaluating 

CMAQ. An accompanying letter based on the work of the Air Monitoring and Methods 

Subcommittee will provide additional comments on these measurements. 
13

Individual Comments from the Panel

Policy Assessment for the Review of the Secondary National Ambient Air Quality 

Standards for Oxides of Nitrogen and Oxides of Sulfur (2011)

Contents

Dr. Praveen Amar....................................................................................................................... 14

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

Ms. Lauraine Chestnut............................................................................................................... 19

Dr. Ellis Cowling ......................................................................................................................... 21

Dr. Charles Driscoll .................................................................................................................... 26

Dr. H. Christopher Frey............................................................................................................. 29

Dr. Paul Hanson.......................................................................................................................... 32

Dr. Rudolph Husar ..................................................................................................................... 33

Dr. Dale W. Johnson................................................................................................................... 36

Dr. Naresh Kumar ...................................................................................................................... 40

Dr. Myron Mitchell..................................................................................................................... 45

Mr. Rich Poirot ........................................................................................................................... 49

Mr. Dave Shaw............................................................................................................................ 51

Dr. Kathleen Weathers............................................................................................................... 53
14

Dr. Praveen Amar

General Comments: 

First, EPA staff is to be commended for producing an outstanding document. This version of the 

Policy Assessment Document (PAD) is extremely well-written and articulates beautifully many 

complex scientific concepts of atmospheric processes, ecological processes, and ecological 

effects (both chemical and biogeochemical). The PAD is written in a highly policy-relevant 

language in that it makes an excellent and convincing case for the need for establishing new 

secondary National Ambient Air Quality Standards (NAAQS) for protection of sensitive aquatic 

ecosystems in the United States. It also makes the case for retaining the existing secondary 

NAAQS for SOx and NOx to protect against the known direct adverse effects. 

The proposed standard in this final PAD is expressed as a simple equation that explicitly takes 

into account the multi-pollutant nature of chemical species responsible for the adverse effects 

(NOy, NHx (only indirectly, see below), and SOx), as well as multi-media nature of ecological

effects (aquatic ecosystems (in this effort) and terrestrial ecosystems (in the future), both 

acidification (in this effort) and nitrogen nutrient enrichment effects (future effort). As a first 

order, the equation for AAI (Aquatic Acidification Index): 

AAI = F1-F2-F3 (NOy)-F4 (SOx) 

is the “form” of the “NAAQS” itself? The recommended indicator, ANC, is ecological in nature 

(and, not an “in-the-air” variable). Acid neutralizing capacity (ANC) is presented as the best 

measure of the capacity of an aquatic ecosystem to protect against acidifying deposition and has 

been strongly supported by our CASAC Panel in our previous deliberations and comments. The 

range of averaging time of three to five consecutive years for calculating average annual AAI 

values is consistent with the cumulative nature of the long-term adverse ecological effects, and 

this long-time average should be able to account for the generally large interannual variability of 

wet precipitation (rain, snow). It is also in agreement with our previous CASAC deliberations 

and comments.

In the future “real-world” implementation of the standard, the calculated values of AAI for a 

given spatial area (Omernick’s Ecoregion (Level III)) will be compared to the level of the AAI 

standard, yet to be chosen. The numerical value of “AAI standard” is directly related to the 

ecological indicator, ANC, and once the exact level of ANC (within the recommended range of 

20 to 75 micro equivalents per liter) is chosen, it determines the numerical values of the AAI 

standard. It is expected that EPA will provide/codify ecoregion-specific “look-up” tables to 

state/ local/regional/tribal agencies and other interested parties with values for all of the four 

factors (F1, F2, F3, F4), included as a part of the proposed Rule. 

To make a determination as to whether the ‘standard” is being met, one would simply need the 

measured air concentrations of NOy and SOx in a given ecoregion, together with the EPAprovided values of four ecoregion area-specific F1-F4 factors into the equation for AAI, and 

then compare resulting AAI value to the level of the standard. EPA should be asked for making 
15

this simplified approach available to implementing state/local/regional/tribal entities right in the 

Rule as it is promulgated. Otherwise, the rather complex nature (though entirely necessary and 

based on some beautiful, elegant, and well thought-out science) of this NAAQS, compared to the 

all the previous “simple” NAAQS (both primary and secondary) will result in technical, 

institutional, educational, pubic-outreach, and “cultural” barriers that may be difficult to 

overcome.

The complex nature of various components (and their variability over space and time as well as 

uncertainty in parameters as well as models, both atmospheric and ecological) requires that the 

approach finally selected is “more” than the sum of its parts. The suggested AAI approach, with 

its chemical components and spatial regions over which these components are averaged, is

indeed “more” than the sum of its individual parts and does a very good job of providing a 

rationale for secondary NAAQS.

It appears that the AAI framework has gone as far as it could go in addressing the reduced 

nitrogen (ambient NHx and its deposition). However, the framework only “takes into account” 

NHx to calculate what levels of NOx and SOx emission reductions might be required in the 

future to meet the secondary NAAQS based on AAI. Thus future control strategies and policy 

options most probably will not allow federal EPA (or, for that matter, states) to address and 

require reductions in U.S. ammonia emissions to meet the AAI standard. In this sense, it is a 

missed opportunity to directly and explicitly address ammonia emissions in the U.S., which 

unlike SOx and NOx emissions are currently increasing because of increased food production 

and increased activity in CAFO (confined animal feeding operations) sources. 

On Page 7-38, the PAD suggests that because “NHx deposition exhibits greater spatial 

variability, as well as overall uncertainty than other terms,” an alternative approach might 

involve the use of more localized and/or contemporaneous modeling. Other approaches might 

involve the use of monitored NHx data. The other parts of the document suggest that states may 

choose alternative approaches for addressing NHx emissions and ambient levels. For the sake of 

consistency in any future implementation of the AAI standard, I recommend that a uniform 

national approach must be developed instead of the state-by-state approach. 

Consideration Associated with Alternative Standards:

It is not clear how the stated intent of the AAI standard to average AAI over three to five 

consecutive years would be actually met because there is “the lack of CMAQ modeling for 

multiple consecutive years.” (page 7-54). 

The PAD addresses the “responsiveness” of certain ecoregions (page 7-62, also see page 7-64, 

where “responsiveness to deposition change” is noted as one of the four parameters in 

delineating an ecoregion as relatively non-acid sensitive) to future reductions in SOx and NOx 

emissions. It makes a statement (page 7-62) that “expected emission changes over the next two 

decades should be far greater (my emphasis) than the 42% and 48% SOx and NOx reductions 

used in this analysis.” I do not think, based on the “rules on the book,” and general historic 

trends, and considering emissions from all sources (and, not just power plants), this statement is 
16

true. The expected reductions might even be smaller. Recognizing that 

“responsiveness”/emission sensitivity is used as one of the parameters (as noted above) to 

estimate certain ecoregions “likely not meeting alternative standards,” it may be important to 

evaluate the statement made next “with a consequent further reductions in ecoregions that would 

likely not meet alternative standards.” 

Finally, Section 7.6 on system uncertainties is an excellent summary of various new analyses 

done to undertake a rather rigorous and complete analyses of uncertainty, variability, and 

sensitivity in a common-sense manner. 
17

Dr. Andrzej Bytnerowicz

Comments

Generally this version of the Policy Assessment is a greatly improved document compared with 

its previous versions. I would like to complement the EPA staff for their efforts and persistence 

in developing the Policy Assessment that very well describes and justifies the rationale for 

developing a secondary standard for NOx and SOx. I support the proposed approach for 

implementing the ecologically-based new secondary standard for NOx and SOx that is based on 

the best available science and creative use of models. 

Chapter 7. Consideration of alternative standards for aquatic acidification

I have been specifically asked to comment on indicators described in this chapter. I have also 

made comment on other related issues discussed in this chapter. These comments mainly focus 

on the air chemistry part of the proposed methodology. I also make some suggestions for 

improving the existing national monitoring networks and methodologies. 

Chapter 7 is well organized and is written clearly and concisely. The introductory section 

provides a convincing reasoning why the new standard is needed and good overview of the 

proposed methodology. It also provides a justification why the present approach for multiple 

pollutants has been developed; why only the aquatic ecosystems have been selected for the 

secondary standard; considerations for using specific values of AAI for various ecological zones 

across the country; and considerations for the averaging time of the standard. 

I agree that at present using the total reactive oxidized nitrogen, NOy, measured with the 

chemiluminescence technique is justified. However, as the authors state on page 7-5, using 

individual ambient N species would be more consistent with the current understanding of 

atmospheric deposition science and has a better potential for more rigorous evaluation of dry 

deposition values. Although HNO3 is the strongest driver of N dry deposition, it is not a good 

indicator of dry deposition by itself (as the EPA has shown), but together with NO2 and NH3 it 

accounts for the majority of the dry deposited N. These chemical species can be routinely and 

reliably monitored with passive samplers. If these species are measured in conjunction with the 

CASTNET filter pack sampler, much more reliable data of HNO3, NH3 as well as particulate 

NO3 and NH4 concentrations from the network could be obtained. I will provide more detailed 

explanation of this proposed approach in the February 16th discussion on the monitoring 

methodologies that could support the new secondary standard for NOx and SOx. However, there 

are some pollutants, such as PAN as well as other organic N pollutants that are not easy to 

monitor on the regular basis. New approaches to monitoring of these pollutants should be 

comprehensively discussed. Considering all those technical problems and data gaps, the 

proposed use of CMAQ to provide the modeled values of N and S deposition is currently 

justified. However, the well-coordinated national efforts are needed to assure that the modeled 

values are verified against the experimental results. In this regard the passive samplers as well as

the remote sensing techniques seem to be the most promising methodologies in the near future. 

Potential utilization of these techniques is especially important for NHx – even if the agricultural 

sources are better characterized in the CMAQ predictions, emissions from multiple mobile 

sources (combustion engines) and their spatial trends are very difficult to model. Therefore,

reliable monitoring of the ambient NH3 and NH4 at a national scale is urgently needed. 
18

There is also a clear need for monitoring coarse particulate matter (PM) which is an important 

source of the atmospheric N and S into the aquatic and terrestrial ecosystems. Consequently, 

developing of monitoring techniques for coarse PM is recommended. 

In regard to choosing ecological indicators, a selection of the ANC is logical, well described and 

justified. The use of ANC has already been discussed at length between the EPA staff and the 

CASAC. This indicator is based on solid science and is well related to the combined deposition 

of NOy, SO2 & SO4 and NHx.

The transference ratios have to be verified since they are just products of the model. In this 

regard, the in situ measurements of total deposition are needed. The ion exchange resin

collectors, which have been used both in the East and the West, could be considered as a 

reference method for selected watersheds. These measurements should be matched with reliable 

measurements of the individual components of the NOy. 

In regard to the spatial aggregation, it is clearly stated that variation in the ecosystem sensitivity 

to N & S deposition has to be included in the development of a national standard. Selection of 

the Omernik’s classification with 84 defined regions seems logical. Remark – the text on pages 

7-32 and 7-33 as well as the caption for Figure 7.5 has to be checked since the numbers for the 

ecoregions and subdivisions are not consistent. Similarly – the last paragraph on page 7-34 is 

confusing and does not provide any explanation why the selected percentages of water bodies 

and ANC values were used to screen out regions with the overabundance of the high ANC 

values. 

The summary of system uncertainties (Section 7.6) and Table 7-6-1 with results of the 

uncertainty analysis are informative and useful. What I have found most interesting is that the 

highest uncertainties are caused by the transference ratios and the Neco. This fact clearly 

indicates that more information from the in situ atmospheric deposition measurement and the 

ecological effects evaluations are needed. It is especially important considering that the changing 

climate will provide additional uncertainties in regard to these parameters in future years. 

Therefore, sufficient efforts have to be undertaken to assure that the proposed methodologies are 

adequately tested and compared with the actual field measurements.

Table 7-6-1. “Summary of qualitative uncertainty analysis of key components of AAI”. 

(a) In regard to the “atmospheric concentrations to deposition” source of uncertainty, I have 

problems believing that the “knowledge –base uncertainty” is “low”. In the comments of the 

same table there is a statement that greater uncertainties reside in the information driving these 

calculations, such as the NH3 emissions. Therefore verification against the ground-level 

measurements (see my comments above) is needed. Without such comparisons I would be 

hesitant to agree that the uncertainty for this factor is “low”.

(b) In regard to “Dep NOy” & “Dep NHx” and the related comments in the table: again, testing 

of the models against ambient NOy and NHx experimental data is essential. I believe that the 

CASTNET results aided by the passive sampler data, the Ncore network and possibly in the 

remotely sensed data can be very useful in this regard. 

Appendix D containing Figures D-1 through D-9 and Tables D-3 & D-6. Information contained 

in those figures and tables is quite educational and can greatly help the Administrator in deciding 

what level of protection should be selected. Clearly, setting a standard at 75 ueq/L and 90th

percentile provides the best protection. Comparing the present scenarios with those with the 

reduced emissions shows benefits of the stricter NOx & SOx air pollution regulations. 
19

Ms. Lauraine Chestnut

This draft final of the Policy Assessment document is much improved over the last draft CASAC 

reviewed. It is responsive to comments on that draft. It presents the rationale and approach 

proposed for the NOx-SOx secondary NAAQS in a more coherent and comprehensive manner, 

making it easier to understand without getting bogged down in the many technical details.

I think there is sufficient scientific support for proceeding with the proposed secondary standards 

to protect aquatic resources from the effects of acidic deposition. This draft of the Policy 

Assessment addresses three important questions that were raised during the previous review:

1. Completion of the staff’s recommendations as to appropriate ranges for the indicator, 

form, averaging time, and level of the standard

2. A more thorough assessment of uncertainties and their implications for the application of 

the AAI

3. Examples of how the AAI would be calculated and applied for each ecoregion

I have some remaining concerns and questions on some specifics in the document.

Evidence regarding adversity of effects

This draft of the PA does a good job summarizing this evidence and how it applied in this case. I 

just have a couple minor issues. One is that uncertainty in the magnitude of the economic value 

of the effects on ecosystem services is not the same thing as uncertainty about whether the 

effects at current levels are adverse to public welfare. When effects are at the level where entire 

species of fish are unable to survive in their native waters as a result of human produced 

pollution, there is very little uncertainty that these effects are adverse to public welfare. This 

could be more strongly stated in the conclusions of Chapter 7. It is unnecessary to focus so much 

on the admittedly substantial uncertainty about the magnitude of the economic value of the 

effects on public welfare, for the purposes of setting this standard.

A minor note: I am still unclear about the differences between the estimates in Tables 4-3 and 4-

4 with regard to the different ANC thresholds.

Water quality data and selection of percentiles for calculation of alternative critical loads 

for an ecoregion

My understanding is that specific measures of water quality are needed for each water body in an 

ecoregion to calculate a critical load for that water body (for a given ANC target). Using all 

available data for water bodies in an ecoregion, a distribution of critical loads for the ecoregion is 

then obtained. From this distribution a critical load for a selected percentile of the population of 

water bodies in the ecoregion can be selected. This process presumes that the water quality data 

available are for a representative sample of water bodies in the region. I don’t know enough 

about the sources of these data to assess how reasonable this presumption is. If data are collected 

only for water bodies suspected of being sensitive to acidification, for example, then the data are 

not going to represent the whole population of water bodies in an ecoregion. In that case it is 

hard to know what a percentile of that distribution means. An even more troubling concern is 

that if data available for different ecoregions are based on different types of samples of water 

bodies, then there is no comparability in terms of what a given percentile means across the 

different ecoregions.
20

It may be appropriate to treat these water quality data as something that can be updated or 

substituted with improved data as they become available (or if states want to invest in better data 

collection); similar to what is proposed for handling reduced N.

Differentiation in the treatment of acid-sensitive and not acid-sensitive ecoregions

There are two issues here. One is that the rationale for using 50th percentile critical load for 

ecoregions that are not sensitive to acidification (i.e., with high buffering capacity) versus 70th to 

90th for sensitive ecoregions is not entirely convincing. If they are not sensitive, then wouldn’t 

the critical load at the 70th or 90th percentile still be quite high? I’m worried about stretching 

things when this is supposed to be a national standard. 

The second issue is the proposal that Atlantic coastal areas be treated as not sensitive because 

they appear to be unresponsive to large reductions in deposition levels. Is the scientific evidence 

convincing that these regions are naturally acidic and are therefore not adversely affected by 

human produced deposition? If so, then why were these regions not captured in the initial 

screening of naturally acidic areas? 

Time to recovery

The PA concludes that it is not possible to say anything about how long it would take for various 

ecoregions to recover with reduced deposition, other than to say the lower the deposition the 

more rapid the recovery. Maybe this is all that can be said, but it remains a policy-relevant 

question. Leaving it so open-ended leaves room for the argument that it is not worth investing 

much today for a recovery that won’t be seen until many decades in the future. Can nothing more 

specific be said based on evidence from the past 10-15 years with the Clean Air Act 

Amendments?
21

Dr. Ellis Cowling

Chairman Russell asked all members of this CASAC NOx/SOx Secondary NAAQS Review 

Panel to provide general comments “on any and all aspects” of the January 14 Policy Assessment 

and some of us to offer more specific comments on one or another topic within Chapter 7 titled 

“Consideration of Alternative Standards for Aquatic Acidification.” Both Dale Johnson and I 

have been asked to address the “Level” of the proposed alternative and integrated NOx and SOx 

NAAQS Secondary Standards. 

Accordingly, please find below both some general comments on the January 14, 2011 Policy 

Assessment document and some more specific comments on the recommended “Level” of the 

proposed integrated NAAQS Secondary Standard for NOx and SOx. 

General Comments:

EPA Staff have come a very long way toward their own self-declared objective of developing a 

scientifically sound “framework for a multi-pollutant, multimedia standard that is ecologically 

relevant and reflects the combined impacts of these two pollutants [total reactive nitrogen and 

sulfur] as they deposit to sensitive aquatic ecosystems!”

I applaud EPA staff’s significant achievements in the analysis and interpretation of current 

scientific understanding of atmospheric-deposition induced effects on aquatic and terrestrial 

ecosystems and in the development of science-based policy assessments and recommendations in 

the following areas of public welfare protection:

1) Recommending that the present separate NO2 and SO2 NAAQS Secondary Standards should 

be retained to continue to provide protection for vegetation from direct damage associated with 

exposures to gaseous SO2 and NO2.

2) Recognizing that these existing standards are neither appropriate nor adequate to provide 

protection of fresh water aquatic ecosystems from atmospheric deposition of total reactive 

nitrogen and sulfur compounds that are causing significant adverse public welfare impacts in 

acid sensitive in various regions across the United States.

3) Recognizing that both total reactive nitrogen and sulfur compounds are the principal causes of 

atmospheric-deposition-induced acidification effects on aquatic ecosystems and that a multiple 

pollutant approach to air quality management is essential to provide adequate protection of these 

ecosystems in various acid sensitive regions of the United States.

4) Developing a scientifically sound framework for relating air emissions of well characterized 

sulfur and nitrogen pollutants, to measurable ambient air concentrations of total reactive nitrogen 

and sulfur compounds, to atmospheric deposition of total acidifying deposition, doing this in 

reasonably well-defined acid-sensitive and non-acid sensitive regions of the US, where specific 

types of damage to fish and other aquatic biota and various other kinds of adverse impairments 

of ecosystem functions are occurring, and where acid neutralizing capacity (ANC) is universally 
22

recognized as the most reliable measure of aquatic ecosystem sensitivity to both chronic and 

episodic acidification processes, and where many of the factors that determine the time-frame 

and spatial distribution of biological response to decreases in allowable nitrogen and sulfur 

emissions and atmospheric deposition are reasonably well understood.

4) Development of the concept of an Aquatic Acidification Index (AAI) and a relatively simple 

mathematical equation by which to calculate and quantify the changes in nitrogen and sulfur 

pollutant emissions that will be needed to provide adequate protection for acid-sensitive aquatic 

ecosystems in various regions of the US.

5) Recognizing that the base of scientific understanding with regard to nitrogen- and sulfurinduced acidification effects on aquatic ecosystems is very much more substantial than the 

science base for understanding N and S induced nutrient enrichment effects on aquatic 

ecosystems and also for understanding both acidification and nutrient enrichment effects on 

terrestrial ecosystems.

Thus concluding that it is best (more wise in terms of public policy formulation) to begin an 

integrated multi-pollutant and multiple-ecological effects program by concentrating (at least for 

now) on development and implementation of a secondary NAAQS standard to protect aquatic 

ecosystems from acidification and to pursue further scientific research and assessment efforts 

before including nitrogen enrichment effects on aquatic ecosystems and either acidification and 

nitrogen enrichment effects on terrestrial ecosystems.

But also believing that the conceptual framework outlined in Item 3 (above) may provide a 

useful foundational framework that could later be adapted for use in dealing with both nitrogen 

enrichment effects on aquatic ecosystems and both acidification and nitrogen enrichment effects 

on terrestrial ecosystems.

6) Developing a policy assessment document that presents these many interrelated concepts and 

both atmospheric and ecological processes in a clear and logical fashion with very specific and 

clear presentation of the chemical indicators of choice, the statistical form and averaging time 

that would be appropriate, and the range of ANC levels that would be appropriate for 

consideration, promulgation and implementation to significantly decrease the presently occurring 

substantial adverse effects on public welfare in various regions of the United States. 

Specific Comments:

With regard to the Level of an Integrated NAAQS Secondary Standard I am persuaded by the 

ideas developed by EPA staff on pages 7-44 through 7-53 (including earlier advice that CASAC 

offered in its response to review of the Second External Review Draft of the Policy Assessment) 

that “target ANC levels in the range of 20 to 75μeq/L” are appropriate for consideration by EPA 

Administrator Jackson. As pointed out on pages 7-50 and 7-51, this range of target ANC values 

is consistent with those that have been implemented by other organizations including the 

UNECE in Europe, and the states of New York, Vermont, New Hampshire, and Tennessee in 

this country.
23

Additional Concerns:

With regard to public understanding of the concepts of total acidifying deposition and total 

reactive nitrogen in the context of further consideration of the alternative NAAQS standards 

developed in this nearly final Policy Assessment document, however, I am greatly concerned 

that the general tenor, focus, and content of this document will continue to lead the US public as 

a whole to continue to believe in the myth that it is only oxides of nitrogen and sulfur that are 

really injurious to public health and public welfare in this country. 

I am well aware that chemically reduced forms of reactive nitrogen are acknowledged and dealt 

with specifically as part of the description of total acidifying deposition that is the root cause of 

the acidification of aquatic ecosystems to which this whole Policy Assessment document is 

addressed. But the more or less constant and repeated use of use of the terms “oxides of nitrogen 

in the ambient air,” “nitrogen and sulfur oxides,” etc., and the comparatively infrequent use of 

the term “total reactive nitrogen” and “total acidifying deposition” leads to perpetuation of the 

myth that it is oxidized forms of nitrogen and sulfur that are the real causes of injury to public 

health and environment.

Consider the following statement on the first page of the Executive Summary:

“We have a high degree of confidence in the linkages between atmospheric oxides of 

nitrogen and sulfur, associated deposition of nitrogen and sulfur, and deposition-related 

aquatic acidification effects. Our objective in this Policy Assessment is to develop a 

framework for a multi-pollutant, multimedia standard that is ecologically relevant and 

reflects the combined impacts of these two pollutants as they deposit to sensitive 

aquatic ecosystems.”

Or also consider the repeated use of the diagram first shown on page ES-6 in the Executive 

Summary and repeated again on pages 7-9 and 7-26:

Conceptual design of the form of an aquatic acidification standard for oxides of nitrogen and sulfur.

Would it not be more appropriate (and more truthful!) for this very significant conceptual 

diagram to be reworded by: 1) leaving out the misleading words in the middle box of his diagram 

that refer only to “oxides of S and N,” 2) potentially changing the last line of the right-hand box 

to read “concentrations of NOy, SOx, and NHx,” and 3) changing the caption to read:

Conceptual design of the form of an aquatic acidification standard that includes all ecosystem-acidifying 

forms of nitrogen and sulfur.

I raise this general question about the potential of this otherwise very well-conceived and wellwritten Policy Assessment document to serve an important public educational purpose as well 

as a Policy Assessment purpose in very large part because of the following statements that are 

made in various chapters of this Policy Assessment document:
24

Page 7-78 --“In considering an indicator for oxides of nitrogen, we recognize that aquatic 

acidification results from and is best understood in terms of the deposition of total 

nitrogen, in both oxidized and reduced forms. Since the pollutant that is the focus of this 

review is oxides of nitrogen, not reduced forms of nitrogen, we conclude that it is 

appropriate to consider reduced forms of nitrogen separately, as a factor in the form of 

the standard, rather than as part of the indicator of the standard.”

Page 6-5 -- “ ... it is important that the structure of the [proposed] standards address the 

role of reduced nitrogen in determining the ecological effects resulting from deposition of 

atmospheric oxides of nitrogen and sulfur.”

Page 2-15 – “The key pollutants for this assessment are total oxidized nitrogen (NOY), 

total reduced nitrogen (NHX), and total oxidized sulfur compounds (SOx) in ambient air.”

Page 2-15 – “Total reduced nitrogen (NHX) includes ammonia, NH3, plus ammonium, 

NH4 (EPA, 2008) is introduced because NHx contributes to ... acidifying deposition, 

effectively behaving similarly to NOy.”

Page 2-15 – “Reduced nitrogen plus oxidized nitrogen is referred to as total reactive 

nitrogen.” –.

Page 2-38 – “The contribution of reduced nitrogen to total nitrogen deposition (Figure 2-

24) illustrates the strong influence of agricultural based ammonia emissions, particularly 

in upper Midwest and eastern North Carolina.”

Page 3-2 – “The chemical forms of nitrogen that may contribute to acidifying deposition 

include both oxidized and reduced chemical species.”

Page 3-19 – “Both oxides of nitrogen and reduced forms of nitrogen (NHx) contribute to 

nitrogen deposition. For the most part, nitrogen effects on ecosystems do not depend on 

whether the nitrogen is in oxidized or reduced form.”

Page 6-5 – “There are also important interactions between oxides of nitrogen and sulfur 

and reduced forms of nitrogen, which also contribute to acidification and nutrient 

enrichment.” 

Page 6-10 – “The evidence is sufficient to infer a causal relationship between N 

deposition, to which oxidized and reduced nitrogen contribute. .

Page 7-9 – “The [AAI] index also accounts for the contribution of reduced nitrogen to 

acidification.”

Pages 7-20 - 7-21 – “... we use the terms S and N in the CLANClim (N + S) term to broadly 

represent all species of sulfur or nitrogen that can contribute acidifying deposition. This 

follows conventions used in the scientific literature that addresses critical loads, and it 

reflects all possible acidifying contributions from any sulfur or nitrogen species. For all 

practical purposes, S reflects SOx as described in section 7.1, the sum of sulfur dioxide 

gas and particulate sulfate. However, N includes both oxidized forms, consistent with the 

ambient indicator, NOy, in addition to reduced nitrogen species, ammonia and 

ammonium ion, referred to as NHx. NHx is included in the critical load formulation 
25

because it contributes to potentially acidifying nitrogen deposition. Consequently, from a 

mass balance or modeling perspective, the form of the standard must account for NHx. 

However, N includes both oxidized forms, consistent with the ambient indicator, NOy, in 

addition to reduced nitrogen species, ammonia and ammonium ion, referred to as NHx. 

NHx is included in the critical load formulation because it contributes to [total] acidifying 

nitrogen deposition. Consequently, from a mass balance or modeling perspective, the 

form of the standard must account for NHx.”

Page 7-28 – “Equation 7-11 is the basic expression of the standard which translates the 

simple conceptual diagram into an explicit expression that relates ANC as a function of 

the ambient air indicators, NOy and SOx. Based on equation 7-11, we define an aquatic 

acidification index (AAI) that is more simply stated in terms that emphasize the ambient 

air indicators:

AAI = F1 – F2 – F3[NOy] – F4[SOx] (7-12)

where the AAI represents the long term (or steady state) ANC level associated with 

ambient air concentrations of NOy and SOx. The AAI is the potential the atmosphere 

affords in influencing ecosystem ANC. The factors F1 through F4 convey three 

attributes: a relative measure of the ecosystem’s ability to neutralize acids (F1), the 

acidifying potential of reduced nitrogen deposition (F2), and the deposition-toconcentration translators for NOy (F3) and SOx (F4).

Specifically:

F1 = ANClim + CLr/Qr ;

F2 = NHx/ Qr = NHx deposition divided by Qr;

F3 = TNOy/ Qr ; TNOy is the transference ratio that converts deposition of NOy to ambient 

air concentrations of NOy; and

F4 = TSOx/ Qr ; TSOx is the transference ratio that converts deposition of SOx to ambient 

air concentrations of SOx. .

F2 reflects the deposition of reduced nitrogen. Consideration should be given to 

specifying the value of F2 for each region based on the averaged modeled value across 

the region, using national CMAQ modeling that has been conducted by EPA. 

Consideration could also be given to alternative approaches to specifying this value, such 

as allowance for the use of air quality modeling conducted by States using more refined 

model inputs.

PS. After making this fairly long list of places in this Policy Assessment document that 

did refer to the importance of chemically reduced forms of nitrogen, I couldn’t help but 

wonder if this fairly long list didn’t of itself argue against the very point I am trying to 

make -- that the general tenor, focus, and content of this document gives undue and 

inappropriate emphasis to oxides of nitrogen and sulfur rather than to both chemically 

oxidized and chemically reduced forms of nitrogen and sulfur. 

Thus, I stand by my original assertion of a lack of balance in the document as a whole!
26

Dr. Charles Driscoll

I want to commend the staff of the U.S. Environmental Protection Agency (EPA) for their work 

on “Policy Assessment for the Review of the Secondary National Ambient Air Quality Standards 

for Oxides of Nitrogen and Oxides of Sulfur” (PA). The EPA staff has been very responsive to 

the comments and concerns of CASAC in the previous review of the PA. This draft of the PA is 

much clearer and transparent than the previous draft. EPA staff has clearly the indicator, form, 

averaging time and level that might be used for the proposed secondary NAAQS for oxides of 

nitrogen and sulfur. 

As indicated in our previous review, EPA staff has proposed an innovative approach that utilizes 

the aquatic acidification index (AAI). The AAI considers atmospheric concentrations of NOx

and SOx, the effects of reduced nitrogen deposition and the ability of watersheds to neutralize 

inputs of acidic deposition through the supply of basic cations and the retention of nitrogen.

The EPA staff conducted analysis to constrain values of the terms and conditions to apply the 

AAI. They showed for 19 acid-sensitive ecoregions, the ecoregions that would not meet the 

proposed secondary standard given alternative values of target ANC and percentile of waters to 

be protected. This is the type of analysis that CASAC requested in its previous review of the PA. 

This analysis gives CASAC and other reviewers of the PA an idea of the implications of a 

potential secondary standard and the extent of resources in ecoregions that are at risk with 

respect to acidification of freshwaters from acidic deposition.

These results of the EPA analyses make good sense given levels of atmospheric sulfur and 

nitrogen deposition and our understanding of acid-sensitive regions. In particular, considerable 

research has shown acidification effects on the Appalachian mountain areas. Less attention has 

been given to the coastal plains. However, these are very sensitive systems. They generally 

have high concentrations of naturally occurring organic acids. I believe that algorithms are 

available that could be applied in the AAI framework that could allow consideration of the 

effects of organic acids on the acid-base status of waters.

The EPA also provides some discussion of uncertainty associated with the AAI calculations. 

They are to be commended for doing this given the limited time available to revise the PA. This 

analysis provides a solid basis to conduct further uncertainty and sensitivity analysis.

In summary, although I have a few suggestions and comments, I have no difficulty supporting 

the PA.

Specific comments:

ES-3, paragraph 2 Brook trout is not a very sensitive fish species.

Figures throughout ES Figure titles should be provided for figures.

ES-4, line 1 ...growing in the eastern United States.
27

ES-4, second paragraph It might also be useful to refer to the results of 

Thomas et al. (2010) who show that there is a 

differential response of tree growth (some having a 

positive growth response; others a negative 

response) to increasing nitrogen deposition.

ES-6, paragraph 2, last line in paragraph ...effects in the future, including effects of nutrient

enrichment.

7-13, eqn 7-1, Note Ca2+ This equation should also include naturally 

occurring organic anions.

7-18, 1st paragraph, line 2 ...dominated by precipitation and 

evapotranspiration ...

7-18, 3rd paragraph, line 11 Do you mean less parameterization?

7-26, 1st paragraph, 2nd to last line 1980s

7-27 In a previous meeting, CASAC expressed concern 

over the assumption that no provision was given for 

watershed sulfur retention. I believe that a sulfur 

retention term, similar to Neco could be developed 

and applied in this framework.

7-30, 1st paragraph This is an important concept. It is too bad it is 

buried in the text. I urge EPA to pull this out and 

include it in the ES as well as the conclusions so the 

reader understands this point.

7-46, 1st paragraph Wow what a mess. This paragraph is horrible. 

Either re-write or indicate that surface waters that 

have been extremely impacted by acidic deposition 

would only have minimum ANC value of maybe 

-10 μeq/L. Within the ANC range of -10 to 100 

μeq/L, there is a correspondence of increases in pH 

with increases in ANC.

Reading this paragraph does not provide great 

confidence in the writer’s understanding of acidbase chemistry.

7-46, 2nd paragraph Again, brook trout is not a sensitive species.

7-47, 2nd paragraph ...below 50 μeq/L the sensitivity of surface waters

to acid inputs increases and negative...
28

7-47, 2nd paragraph, line 12 50 μeq/L

7-52, 2nd and 3rd paragraphs provide references for cost estimates.

7-56 It would be helpful to provide a map or a table with 

a better description of the sensitive ecoregions.

7-61, line 1 Do you mean Appalachian mountain areas instead 

of southern Appalachian mountain?

References:

(Thomas et al., 2010)

Thomas, R.Q., Canham, C.D., Weathers, K.C., Goodale, C.L., 2010. Increased tree carbon storage 

in response to nitrogen deposition in the US. Nature Geosciences 3, 13-17.
29

Dr. H. Christopher Frey

Chapter 7: The chapter is generally well organized and well written and more clearly and 

completely conveys the indicator, form, level, and averaging time than the previous draft. The 

chapter also does a good job of identifying the spatial extent of the ecosystem regions that will 

be used.

The term “non-acid sensitive” is unclear. It implies sensitivity to a non-acid. The intended 

meaning appears to be ‘insensitive to acid deposition’ and thus would more accurately be ‘acid 

deposition insensitive’ or ‘acid insensitive.’

p. 7-37. 90th percentile usually implies that 90 percent of the population has a value less than or 

equal to the specified value. However, here it appears that the complementary cumulative 

frequency is being used. This could be made clear.

p. 7-38. The monitor coverage in each eco region is not discussed. Are there regions that have 

more than one monitor? If so, should they be averaged?

p. 7-48: the text here claims that CASAC’s responses on the 2nd PA “provide support for 

focusing on target ANC levels in the range of 20 to 75 μeq/L.” However, this statement ignores 

that in the letter to the Administrator, CASAC clearly stated “Acid neutralizing capacity targets in 

the range of 20 to 100 μeq/L appear appropriate to consider at this time.” Thus, it is unclear as to 

how EPA reached a conclusion based on CASAC input that the upper limit should be only 75 μeq/L 

rather than 100 μeq/L. In fact, even the paragraph from CASAC’s response to the 2nd PA 

Charge Question 11, which EPA only partially quoted in the 3rd draft PA, goes on to state: “As a 

result, target ANC values of 20 to 100 μeq/L are in the range of appropriate values, while 

recognizing that there is additional protection at 50 to 100 μeq/L”

p 7-49. The quoted text from the CASAC response to Charge Question 22.C.ii importantly 

refers to “long-term” ANC levels. A long-term ANC level of 75 μeq/L does not necessarily lend 

support to a level of 75 μeq/L for a 3-5 year average, since it can decades or longer to reach the 

long term level.

p. 7-52. The ‘framing’ of this text is from the perspective of decreasing marginal protection as 

the level increases. However, conversely, this could be framed in terms of increasing certainty 

of protection as the level increases. Or, as the level is lowered, increasing certainty of loss of 

protection. The framing is quite important because it can bias the interpretation of the technical 

information. To avoid framing bias, all of these interpretations should be mentioned.

p. 7-53. It would be helpful to explain how CMAQ will be used operationally. For example, in 

order to have a 3-5 year average, consecutive annual CMAQ runs will be needed. The most 

recent averaging period can only be evaluated based on the most recently available CMAQ run, 

which may be one to three calendar years earlier than the current calendar year. Thus, nonattainment decisions would have a lag period of one to three years. Some discussion of this 

would be helpful.

p. 7-54. It would be helpful to have a table of all of the values that are input to F1, F2, F3, and 

F4, and of the values of F1, F2 (for those Fi derived from more than one input) associated with 

the ecoregions listed in Tables 7-5.1

Uncertainty/Sensitivity/Variability: 

Appendix F

p. F-3: ‘bootstrapping Monte Carlo type analysis’ – this term is very unclear. There are specific 

types of bootstrap and specific types of Monte Carlo analysis. A broader point, however, is that 

the statement on lines 13-17 seems to be contradicted by the analysis given in Appendix G. The 
30

latter is an uncertainty analysis of AAI except that it is inverted such that combinations of the 

SOx and NOy concentrations are inferred. This paragraph should be rewritten for clarity.

p. F-13, table F-4.2. The header should be more clear that it refers to Annual Mean Bias 

Statistics and that it is based on CASTNET sites in the Eastern Domain.

p. F-20. Why is there not a similar graph for SO2?

p. F-21: the data in these graphs are not interpreted in the text.

p. F-22. There is essentially no citation or interpretation of data in the associated figures. 

p. F-23. Define the box plots – mean? 95 percent frequency range? Since these are hourly data, 

why/how is this relevant to looking at annual averages or 3-5 year averages?

p. F-26. Are the data in the figure for 2002?

p. F-34, Figure F-15: define the meaning of the box and whiskers. Also for next page.

p. F-37. This comparison is not very informative, given that it is not on a consistent basis. The 

text could be more clear as to whether this comparison is really useful, other than just getting an 

idea of the typical magnitude of these transference ratios. It is not clear to the reader that these 

data can provide “extremely valuable diagnostic information.” What is “extremely” valuable 

about it? How can it be used to improve “CMAQ deposition processes”?

p. F-45: when translating “error in individual measurements” to regional values, one must pay 

careful attention to the spatial scale and averaging time. 

What is a “bootstrapping analysis of the parameters”? This is never explained adequately. There 

are many kinds of bootstrap. The basic input data are not clearly presented or described. The 

use of the term “parameter” here is sloppy.

Appendix G

The material in Appendix G is only useful if the reader can figure out what were there key inputs 

and the methodology used, neither of which are adequately addressed. For example, to merely 

describe the methodology as “bootstrapping” is not useful – there are many kinds of 

bootstrapping. What exactly was bootstrapped and how? The key input data should be clearly 

introduced and either presented or at least described or visualized if possible. The methods by 

which the data were bootstrapped should be clearly explained. The approach for Monte Carlo 

analysis and by which the probabilistic trade-off curves for SOx and NOx were derived must be 

adequately explained, including documentation of the key equation(s), key input distributions, 

analysis/simulation methods, and results. A rationale for using the mean values as the basis for 

the standard should be given. Some explanation should be given as to the implications of using 

upper or lower percentiles of the trade-off curve.

p. G-1: is there any statistical dependence among Neco, NHx, Tnoy, and Tsox? In what way is 

Neco from CMAQ?

There needs to be a table that clearly documents or explains the inputs to the ‘bootstrapping’ 

analysis, and associated figures that show the data.

How exactly were ‘these averaged values’ ‘bootstrapped using uncertainty in CMAQ modeling 

to obtain estimated uncertainty in the average values?’ What ‘uncertainty’ was used in CMAQ 

and how? What data were bootstrapped, and what kind of bootstrapping was done? For what 

averaging time? Geographic extent?

p. G-2: Results are shown but the input and method are not documented or adequately 

explained. For what averaging time? Annual averages? 3-5 year averages? Does “uncertainty” 

refer to a 95 percent probability range?
31

“Nleach was allowed to have 30% uncertainty.” (underline added). What is meant by 

“allowed”? Is this a judgment? Based on what? What type of distribution was assumed and 

why?

p. G-3: Figure G-2 – for what averaging time?

“Uncertainty in CMAQ values was included randomly...” what does this mean? How was this 

done? On what basis?

The text on the last few lines should be discussed more fully. What is the implication if the 

correlation is not zero? Is it possible to a sensitivity analysis to assess the results with 100% 

correlation?

p. G-4: is the ‘uncertainty’ range for a 95% probability range? What is the vertical line in each 

figure panel? What averaging time is used here?

p. G-5 “with the same uncertainty of 100%” – this is unclear. 

p. G-6: unclear as to how uncertainty is “bootstrapped” if it includes arbitrary ranges of 

uncertainty. Bootstrap typically implies reference to empirical data, either by resampling or by 

use of a parametric model fit to data. Bootstrap does not usually describe sampling from 

arbitrary distributions. What was resampled here? What is meant by and what is the basis for 

‘including’ 70 % uncertainty in BC and 5% uncertainty in Qo?

p. G-7: what is meant by “raw data” for these ecoregions? “The curve was then derived again 

using values from the derived distributions of...” this is not clear. There should be a basic 

equation or flow diagram to describe what was done. 

In what way was Neco treated separately from the CL selection? This is not clear.

p. G-8. The two figures given here are not interpretable given the lack of clarity regarding input 

data and methods used. For example, if these results are based on averaging times of less than 3-

5 years, then they would overestimate the uncertainty in the trade-off curves.
32

Dr. Paul Hanson

The summary of the available science is generally acceptable. I agree with the retention of the 

existing standard for protection human welfare from gaseous forms of nitrogen and sulfur oxides, 

and with the pursuit of a secondary standard based on ecosystems effects driven by total N and S 

deposition through the processes of acidification and nutrient enrichment. The focus on the 

development of a standard based on aquatic ecosystems seems appropriate and mandatory given 

the limited nature of data and defined response relationships for terrestrial ecosystems. 

I am not providing a list of specific comments on this Policy Assessment document, because it is 

in final form and will presumably not be changed. I do, however, want to comment on word 

choices in the Executive Summary to highlight a remaining concern. That concern is that the 

document (in places) continues to suggest that N and S deposition is an ever present and current 

danger to all ecosystems. The Policy Assessment (PA) document, the REA and the ISA before it 

support a conclusion that current levels of N and S deposition represent a potential adverse 

impact on sensitive ecosystems through a range of mechanisms. This version of the PA includes 

improved language from the previous draft, but occasionally falls into the trap of suggesting that 

N and S deposition are bad for all ecosystems.
33

Dr. Rudolph Husar

Comments are in italics.

General

Overall, this version of the PA document constitutes another significant improvement of this 

ground breaking regulatory document. The presentation of the proposed regulatory approach is 

much clearer and the document is much better structured and sections homogenized. This PA 

version shows strong responsiveness to past CASAC inputs. The content and structural 

improvements along with the cosmetic changes make this PA document nearly complete. 

I recognize that this the 11th hour for the PA. Nevertheless below are comments and some 

remaining questions, including some persistent ones, for consideration by EPA. 

Indicators for the Standard: 

NOy - Total reactive oxidized nitrogen, NOy, as the ambient air indicator for oxides of nitrogen.

The justification for the selection of atmospheric NOy as the oxidized N deposition indicator is 

not very compelling. HNO3 gas dry deposition and NO3 wet deposition contribute the 

overwhelming majority of oxidized N deposition. Both are measurable and measured 

parameters, why not use these as indicators for ox. N dep? The fact that NOy can be measured 

does not mean that it is a more robust indicator than HNO3 gas and NO3 wet dep. For receptors 

near the source, the effective multi-component ‘transmittance function’ is much different from 

the far source and applying CMAQ to properly account for these differences may be of tenuous 

robustness. 

If there are other reasons for NOy as the indicator, those should be explained more clearly. 

SOx - Sum of gaseous sulfur dioxide (SO2) and particulate sulfate (SO4) as the ambient air 

indicator for oxides of sulfur.

OK

Form of the Standard, AAI: 

The form of such a multi-pollutant, deposition-related standard, should be ecologically relevant 

and include link ambient air indicators for oxides of nitrogen and sulfur, the related deposition of 

nitrogen and sulfur, and the associated aquatic acidification effects in terms of the ecological 

indicator ANC. 

Aquatic acidification index (AAI), using a simple (??) equation to calculate an AAI value in 

terms of the ambient air indicators NOy and SOx and the relevant ecological and atmospheric 

factors that modify the relationships between the ambient air indicators and ANC. 

AAI = F1 [units deposition?]} – (F2[g/m2

,s] + F3[m/s]*(NOy) [g/m3] + F4[m/s]*(SOx)[g/m3])
34

The equation may be simple but the complications are embedded in the factors F1 to F4. Also, 

these factors rely heavily on model estimates, so these ‘simple’ terms in AAI arise from very 

complicated calculations and they are also the carriers of much of the uncertainly in AAI 

determination. So, I would remove the word ‘simple’. 

F1 – Ecosystem Neutralyzing Capacity 

F1 - Ecosytem’s natural ability to provide acid neutralizing capacity and to neutralize 

nitrogen deposition through plant uptake and other processes; F1 (as the other F factors) 

would be defined for each ecoregion by specifying ecoregion-specific values for each factor 

based on monitored or modeled data that are representative of each ecoregion. The AAI is to be 

evaluated over ecologically relevant regions, defined by Omernik Ecoregions, level III, 84. 

Factors F1 through F4 would be defined for each ecoregion by specifying ecoregion-specific 

values for each factor based on monitored or modeled data that are representative of each 

ecoregion.

Is this another novel aspect of this new standard (?): Defining the areas of compliance for 

regions (not points) and determining non-compliance by regionally ‘representative’ values of all 

AAI terms...or just the F factors? While the NOy and SOx observations would be the anchors to 

reality but it would be the CMAQ that (1) estimates the F3 and F4 factors...and (2) spatially 

extrapolates these observations for each ecoregion. 

This is a rather heavy burden for a model to carry. Could it happen that at the ‘representative’ 

observation site the location is compliant but the region is not compliant due to spatial gradients 

of any of the AAI terms? Can CMAQ withstand the scrutiny of the standard implementation 

process?

F2 - Acidifying deposition associated with reduced forms of nitrogen, NHx; 

So ammonia deposition estimate should be (1) entirely based on CMAQ, (or local model)? Why 

not use measured ammonia wet deposition data and model only the ‘transference ratios’. Why 

would model NHx wet deposition be more robust then the observations? See below re data 

assimilation. 

F3 and F4 : Transference ratios convert NOy and SOx conc. to deposition

Specifying the values for the transference ratios based on CMAQ modeling results alone is 

preferred to an alternative approach that combines CMAQ model estimates with observational 

data

The value judgment by EPA that CMAQ model estimates of the transference ratios in AAI is 

preferred to combined model-obs values is not shared by this reviewer. Yes, assimilating 

observations into atmospheric models is an inconvenience for the current models. However, 

regulatory arm of EPA could and should press its research arm to pursue such CAMQ data 

assimilation upgrade, particularly for wet deposition. Such a assimilation-enhanced CMAQ 
35

could benefit many applications of the official EPA regional model beyond this secondary 

standard. 

Since the units of F3 and F4 transference ratios are m/s, I still do not follow why these 

mysterious F factors could not be called effective [or total wet+dry] deposition velocities. By 

definition, the deposition velocity is the ratio of ambient concentration and deposition. 

Averaging Time for the Standard 

All calculated as annual average values, whether based on water quality and hydrology data or 

on CMAQ model simulations. The same annual averaging time for the ambient air indicators as 

is used for the factors in the AAI equation.

Annual average AAI values over 3 to 5 years to provide reasonable stability in the resulting 

index value, in light of the relatively high interannual variability expected. 

Agree, annual arithmetic average of atmospheric, deposition and ecological variables. No 

further comments now.

Level of the Standard 

The level of a standard based on the above indicators, alternative forms, and averaging times 

should be within the range of 20 to 75 μeq/L.

If Aquatic Acidification Index (AAI) is the standard and its units are μeq/L, then how does one 

combine the F1 [μeq/L] terms with the deposition terms F2, F3, F4 [g/m2

,s or meq/m2-yr]?
36

Dr. Dale W. Johnson

The primary topic assigned to me for review is “Levels” within Chapter 7, so I will first address 

that segment, then a few additional comments on other sections below.

Chapter 7 LEVEL

As I indicated in my last review, I see no problem with the ANC target levels chosen. Also as 

indicated in my last review, I do think that more attention should be given to capacity vs 

intensity effects of acidification. I have raised this several times, but still see some confusion, so 

I will take the liberty of providing an old paper and some visuals I use in class to illustrate this 

point. Figure 1 depicts the situation that most people think of when considering acidification, 

namely, that the soil acidifies and the waters passing through it (soil solution) also acidify as a 

result. This mechanism, which John Reuss (Reuss and Johnson, called the capacity effect, 

usually takes a long time, perhaps decades or centuries, and presumes that the soil begins in a 

non-acidic, or at least not extremely acidic, condition. Figure 2 illustrates a second mechanism 

by which soil solution can acidify: the soil is naturally acidic, but under pristine conditions, the 

soil solution is not necessarily acidic because the concentrations of strong acid anions (Cl-

, SO4

2-

, 

NO3

-

) are not high enough to balance a very high concentration of H+ or Al3+, which are the two 

major exchangeable cations on the soil in this case. When strong acid anions are introduced to 

this soil, however, acidification of the soil solution is instantaneous, as the incoming cations 

associated with these anions (whether acidic or basic) are exchanged with the soil and the soil 

releases H+ and Al3+ from the exchange sites into soil solution. The second mechanism is wellknown in soil science in that soil paste pH measured in 0.01 M CaCl2 is nearly always higher 

than when it is measured in water for exactly the same reasons (both methods of measuring soil 

pH are commonly employed). It is important to note that no change in the soil is required for 

the second mechanism. It is also important to note that acidic soils are a necessary but not 

sufficient condition for the acidification of soil solution. You may wonder if the second 

statement is really true; I attach a very old paper of mine which shows that acidic soils in Costa 

Rica (pH 4.0 to 4.9 in H2O; see Table 2) produce soil solution pH values around 6 (Figure 4). In 

the Alaskan site, soil pH ranges from 3.95 to 4.74, but in this case, soil solutions are acidic in 

forest floor and somewhat less so in the A2 horizon because of the presence of organic acids, but 

soil solution pH increases as the organic acids are precipitated out in the B2ir horizon (these are 

Spodosols). 

The differences in these two mechanisms are very important. In mechanism 1, acidification takes 

a long time to occur. In mechanism 2, however, acidification is instantaneous as soon as strong 

acid anions added to the system. Since there is no reason to believe that soils in humid regions 

spontaneously alkalize (desert soils do, but humid region soils spontaneously acidify, not 

alkalize), recovery from mechanism 1 is either slow or non-existent. Recovery in mechanism 2, 

however, closely tracks strong acid anion deposition (as we seem to be seeing currently in the 

Adirondack lakes, for example). John Reuss provided a succinct discussion of capacity and 

intensity effects on pp 71-72 in Reuss and Johnson (1986).

I hope this brief primer from my class notes does not come across as condescending, it certainly 

is not meant to be so; my intent is to illustrate what I have been talking about. This of course 
37

only applies to the scenario where waters flow through soil before entering lakes or streams, not 

surface flow or other mechanisms by which atmospheric deposition might enter aquatic systems 

more directly.

Given the above, I have problems with the statement on p. 7-49, for example, which states 

categorically that “Ecosystems become adversely impacted by acidifying deposition over long 

periods of time...”. The next paragraph on p. 7-49 is all about timing of acidification, and I really 

think that the above discussion is highly relevant to it. 

Other Comments:

p. 3-22, first whole paragraph: Finally we agree on how to state this issue of potential benefits of 

N deposition!

p. 3-25: I would add a segment on unintended consequences for C balance issues. Sensing great 

reluctance to do this on the part of the authors, however, I do not require it; I simply say that if I 

were an author, I would add it. 

p. 7-19: As I have indicated in previous reviews, this model seems to assume that there will be 

no response in base cation concentrations to inputs of strong acid anions. Am I wrong? If not, 

this flies in the face of experiences in nearly all artificial acidification experiments, not to 

mention what happens to soils when they acidify (capacity effect). For mechanism 2 above, this 

approximation is more realistic, but not in the cases where soils are assumed to be acidifying 

(mechanism 1). 

p. 7-43: The discussion of capacity and intensity effects above is relevant here. 

Reference:

Reuss, J.O., and D.W. Johnson. 1986. Acid Deposition and the Acidification of Soil and Water. 

Ecological Studies No. 59. Springer-Verlag, New York. 118 p.
38

Figure 1. Schematic diagram of the capacity effect. In this case, the soil is subjected to high rates 

of acid deposition. At first, most of the incoming acid is exchanged for base cations (BC), and 

the soil solution is not acidic. As the soil acidifies over time, a greater proportion of cations on 

the soil exchange sites are acidic cations and they therefore dominate soil solution as well. 
39

Figure 2. Schematic diagram of the intensity effect. In this case, the soil already naturally acidic. 

Under low strong acid anion deposition conditions, only low concentrations of acidic cations 

appear in soil solution because soil solution strong acid anion concentrations are low. With 

increased strong acid anion deposition and leaching through the soil, charge balance requires that 

soil solution total cation concentrations increase, and since the soil is acidic, exchange equations 

predict that the acidic cations will constitute a major proportion of this soil solution cation 

concentration increase. Soil solution acidity can increase or decrease very rapidly depending on 

strong acid anion inputs. No change in the soil exchanger itself is required. 
40

Dr. Naresh Kumar

This version of the Policy Assessment Document (PAD) for secondary standards of SOx and 

NOx is greatly improved in its presentation of key concepts, although many key issues still 

remain unaddressed. The specific comments on different elements of the standard are:

Indicators

The use of ANC as an ecological indicator for aquatic acidification is not fully supported. EPA 

recognizes that ANC is not itself the causative or toxic agent for adverse aquatic acidification 

effects, it proposes to use ANC as the indicator because it is associated with the causative agent, 

pH. However, the empirical data suggests that this relationship is not universal because of the 

broad distribution of dissolved organic carbon (DOC) and carbonates in real water bodies. Just 

because ANC is a more reliable indicator from a modeling perspective is not a good enough 

reason because convenience shouldn’t trump science when it comes to establishing national level 

standards. The empirical evidence shown by EPA to show relationship between adverse effects 

and ANC is derived from two regions of the country – Adirondacks and Shenandoah – and is not 

universal. EPA claims that ANC-deposition link is superior to the pH-deposition link because the 

relationship between pH and deposition is extremely nonlinear and complex. However, given 

that pH is a direct causative agent for adverse aquatic effects, EPA should have explored using 

pH as the aquatic indicator rather than completely dismissing it in favor of ANC

Form

The form of the proposed standard uses the aquatic acidification index (AAI) that links ambient 

indicators to deposition metrics. The major concern with using this form of the standard is that 

most of the parameters in the AAI equation are determined using models that have not been 

adequately evaluated. The specific comments are:

1. Lack of adequate model performance evaluation – Given that this is the first such use 

of models in establishing standards (rather than the use of monitored values); the burden 

on validating the used models has to be much higher than when they are used in a relative 

sense (e.g., during implementation of the standards). However, EPA has continued to 

ignore previous requests from the CASAC panel to conduct a comprehensive model 

performance for CMAQ. The performance statistics for the major species shown in Table 

F-2 are inappropriate and misleading because they show average biases over the whole 

country for one whole year. What one needs to know is how much the model may be 

biased at the ecoregion level, and the PAD has failed to do that. Even when showing 

monthly time-series plots, EPA uses domain-wide averages rather than show the timeseries at individual characteristic sites, as is the norm. EPA’s approach can be misleading 

because it can mask the true error by combining regions of over-predictions with regions 

of under-predictions (often termed as compensation of errors), and is unacceptable when 

EPA is proposing to use these models in establishing national standards. Independent 

model performance evaluations of CMAQ conducted by EPRI (and communicated to the 

CASAC panel) has shown that regional biases in predictions of species of concern (SO2, 

SO4, NO3, NH4, wet deposition) can range from -100% to +200%; something that is 
41

completely masked by EPA’s approach. The request to EPA from the CASAC members 

to conduct comprehensive evaluation has been made for each version of the PAD, REA 

and ISA, thus EPA has had enough time to conduct such evaluation, but it has failed to 

do so. Given the lack of a complete evaluation of CMAQ derived values with 

measurements and the lack of usefulness of the limited model performance that is shown, 

no degree of confidence can be placed in the use of the models to generate the desired 

parameters in the AAI equation. 

EPA has used the PRISM model to apply adjustments to wet deposition based on 

precipitation data. However, EPA has not shown how this selective application of bias 

adjustment affects the overall mass conservation. This also contradicts EPA’s assertion of 

not combining measured and modeled data in development of the transference ratios. 

The lack of robust model performance is also evident for the watershed models. In the 

appendix, EPA provides comparison of the MAGIC model results to calibration data; by 

definition, these align well because the model was calibrated to fit these data. EPA notes 

that the performance outside of the calibration period is not as good and refers to the 

REA document. However, the REA document shows model performance for two 

Adirondack lakes and two Shenandoah streams from a population of 104 waterbodies in 

the combined dataset. Unless EPA also shows the model performance for the remaining 

100 waterbodies, it is difficult to draw any conclusions on the adequacy of the model 

performance. EPA has failed to provide any reasons for not showing the model 

performance for all the waterbodies for which it conducted the analysis. A bigger concern 

may be the bias introduced by the use of the MAGIC model or the F-factor approach in 

calculating the critical loads. Evaluation of the MAGIC model at the 44 lakes in 

Adirondacks, as shown by EPRI in its comments to CASAC on the second draft of the 

PAD, indicated that the MAGIC model resulted in a “sum-of-strong-bases to sum-ofstrong-anions ratio” (tantamount to the F-factor) of 0.42 whereas the real data show a 

value of 0.87 (this would imply the critical load calculations using the MAGIC model 

would be biased low). EPA has shown that the F-factor approach gives critical loads that 

are even lower than the MAGIC model. Thus, no matter which approach is used by EPA 

(because of data limitations, EPA will most likely rely on the F-factor approach), the 

critical loads calculated will be biased low. This can have major implications on the level 

of the standards chosen.

2. Stability of transference ratios – A major concern with the transference ratios is that 

although they are the critical links between NOy and SOx ambient concentrations and 

their deposition, they are derived using a model that has not been adequately evaluated. 

EPA has shown the year-to-year change in transference ratios using the same model to 

evaluate its stability. However, the bigger concern is not the stability from year-to-year, 

but the variability in the ratios as determined from different models. EPA agrees that 

transference ratios constructed from different modeling platforms do exhibit significant 

differences; however those results are not shown. The fact that the choice of a model is so 

critical in determining the link between the ambient indicators (NOy and SOx ambient 

concentrations) and deposition, it further affirms why an adequate model performance 

needs to be part of the process. EPA contends, “the use of a modeled constructed 
42

transference ratio is based on the same premise by which we use models to estimate 

deposition in the first place”. However, two wrongs don’t make it right. It is wrong to use 

a model without adequate performance evaluation to estimate deposition when 

establishing a national standard, and it doubly wrong to use that as a reason to endorse 

the use of the same model for establishing a critical link in the form of the standard (the 

AAI). 

3. Spatial Aggregation – EPA is proposing to use ecoregion Level III as spatial areas over 

which values for the factors in the AAI equation are quantified. There are a total of 84 

such regions in the contiguous Unites States. One problem with using such large spatial 

regions to define the standard is that one has to use averaged quantities over regions that 

can be quite inhomogeneous and disparate. A more critical issue is whether use of these 

ecoregions may introduce biases in calculation of critical loads. Water bodies that are 

actively sampled in the U.S. are most often predominantly located in the more acid 

sensitive regions. Using these sampled data to calculate critical loads for the whole 

ecoregion will lead to critical loads that are biased low. The representativeness of 

available data to use for an ecoregion is a critical issue that has not been addressed by 

EPA. The biases resulting from use of currently available water chemistry data would 

imply that a given percentile of the distribution of estimated critical loads for surface 

waters would be protective of a higher percentage of surface waters in most regions

because of un-representativeness of the data. For example, critical load calculated based 

on 70th percentile of waterbodies for which data are available will be lower than the 

critical load calculated based on 70th percentile of all waterbodies in the whole ecoregion 

because of skewness of data towards more acid-sensitive waterbodies.

Level

EPA suggests a level of the standard in the range of 20-75 μeq L-1 for the ecological indicator, 

ANC. Rather than choosing a number arbitrarily in this recommended range, we should consider 

all the factors that are critical in linking adverse aquatic effects to causative agents and also 

examine the factors that may be causing biases in EPA’s approach before deciding on the ANC 

level for the standard. EPA has rightfully stated that pH is a better causative link with adverse 

aquatic effects, so one should use studies linking pH to adverse effects when determining an 

appropriate level. Table 3-1 on Page 3-8 shows different studies linking fish mortality response 

to pH. The range of pH values causing fish mortality is between 4.5 and 6 for various studies 

except one study where the pH was at 6.5. Assuming a conservative value of 6.5 for pH that 

causes adverse effects, one can determine that the corresponding ANC (from Figure 7-2) is about 

25 μeq L-1. This would be a better approach than relying on a single study linking ANC with 

adverse effects (Figure 7-4), which shows increasing effects from 0 to 100 μeq L-1, but also 

shows increasing uncertainty above 20 μeq L-1. In regions where ANC is low, but inorganic 

aluminum levels are also low, the fish populations have been shown to be thriving, so one 

shouldn’t rely only on a single study. Another study in western Virginia showed that at ANC 

above 50 μeq L-1, the brook trout populations were not affected.

Another factor that is important is that as shown previously, EPA’s approach would lead to 

critical load values that would be biased low because of the aggregation at the ecoregion level 
43

and because of the use of the MAGIC model and the F-factor approach. This would in turn cause 

the NOy and SOx allowable levels to be biased low. Thus, in the absence of any other criteria, 

selection of the ANC level should be conservative towards the low end of the recommended 

range of 20-75 μeq L-1 to balance against the biases introduced by the EPA approach. Moreover, 

in this case the evidence suggests (as explained previously) that the appropriate ANC value in 

absence of any bias should be about 25 μeq L-1. However, given the other biases, one can justify 

20 μeq L-1 as the appropriate ANC value for the standard.

The choice of the percentile of waterbodies to be protected in an ecoregion is also an important 

part of the standard. EPA has recommended a range of 70th percentile to 90th percentile of 

waterbodies to be protected in ecoregions classified as acid-sensitive. However, given the fact 

that most of the data for estimation of critical loads is predominantly available at waterbodies in 

acid-sensitive regions, these percentile levels could lead to an extremely strict standard. Consider 

a thought experiment where an ecoregion has 1000 waterbodies of similar sizes and assume that 

200 of those waterbodies are acid-sensitive. Now assume that a total of 100 waterbodies in this 

ecoregion have water chemistry data with 80 of those waterbodies to be acid-sensitive and the 

other 20 to be non acid-sensitive. These numbers are not out of ordinary and may be quite 

realistic. A critical load based on 70th percentile of these 100 waterbodies (for which data are 

available) would represent an extremely acid-sensitive waterbody and may be overly protective 

of all the acid-sensitive waterbodies in that region, notwithstanding the large number of non 

acid-sensitive waterbodies. A percentile level of 70 or larger is appropriate only if majority of the 

waterbodies in an ecoregion are acid-sensitive or if the data are available in equal proportion for 

both acid-sensitive and non acid-sensitive water bodies. Given that this is not the case, a 50th

percentile may be a more appropriate level, although still conservative because of the skewness 

in availability of data.

Uncertainty Analysis

It is difficult to judge the adequacy of the uncertainty analysis performed by EPA because of lack 

of details. The purpose of the uncertainty analysis as requested by CASAC was to estimate the 

degree of confidence in the response surfaces of NOy and SOx given the high degree of 

uncertainty in the individual terms of the AAI. The way the EPA has conducted the uncertainty 

analysis using bootstrapping, the uncertainties in individual terms may have been minimized. For 

example, EPA assumed an uncertainty analysis of 100% for Ndep at the grid level, but averaged 

over the ecoregions the bootstrapped distribution resulted in an uncertainty of only 10% and 15% 

for the two ecoregions. It seems the law of large numbers is at play here, i.e., when averaged 

over a large number (because of the large ecoregions) the average distribution will be closer to 

the expected value. Thus, EPA’s approach of using bootstrapping seems questionable. By 

focusing on the uncertainty of the average parameters, EPA has ignored the variability of the 

values in the ecoregion, which is a critical omission because variability also affects the degree of 

confidence in a given value of a parameter.

Instead of using the mean values and the questionable bootstrapping method to assign 

uncertainty, EPA should have used the distribution of the actual individual parameters in an

ecoregion. If the distribution in an ecoregion is homogeneous, the effect of variability would be 

minimal. Under those conditions, the degree of confidence in the response surfaces for SOx and 
44

NOy is influenced solely by the uncertainty in the measurements or estimations of the AAI 

parameters. EPA’s uncertainty analysis ignores the impact of variability in judging the degree of 

confidence in the response surfaces by assuming average conditions and defining fixed levels of 

uncertainty for the average value of the parameters, and thus doesn’t serve the purpose as 

intended by the CASAC. Thus, the uncertainty analysis performed by EPA doesn’t provide any 

insights into the confidence level of the standard because of the lack of clarity and the 

arbitrariness of the assumptions used. It is almost as good or as bad as the qualitative uncertainty 

analysis performed earlier and repeated in this version of the PAD. Both these analyses 

(qualitative and quantitative) purport to undermine the actual uncertainty in the system. 
45

Dr. Myron Mitchell

Comments on “Indicators” in Chapter 7 entitled “CONSIDERATION OF ALTERNATIVE 

STANDARDS FOR AQUATIC ACIDIFICATION”.

General Comments

The introduction to this chapter (p. 7-1 through 7-3) does a good job of giving an overview of the 

overall approach and its rationale. Throughout this Chapter and the entire document the term 

“species is used extensively”. I would suggest that in future documents for those places when 

the “species” refers to “chemical species” that this term be provided explicitly so as to avoid any 

confusion with “biological species”. In the Panel’s previous discussions it was strongly 

suggested that the importance of ammonium and ammonia atmospheric deposition be 

incorporated into the standard. The beginning of this chapter (Section 7.1.2) suggests that only 

the NOy chemical species be utilized in the standard, but later (pages 7-21 through 7-23) the 

importance for incorporating NHx deposition is included. More consistency in the Chapter 

would have been helpful. In some of the discussions of this section the consistency of the 

arguments for the use of individual nitrogen species versus NOy chemical species could have 

been improved. However, it is indicated (page 7-9) that “The index also accounts for the 

contribution of reduced nitrogen to acidification”. In general the Chapter provides important 

arguments that link the aquatic acidification index (AAI) to ANC (Acid Neutralizing Capacity) 

and the use of ANC as important parameter for evaluating the effects of S and N deposition. I 

am still concerned with respect to the discussion of how internal S sources are not treated in the 

model formulation:

CLANClim(N + S) = ([BC]0* - [ANClim])Q + Neco (7-2)

as well as the version to be used in the actual Aquatic Acidification Index (AAI):

AAI = F1 – F2 – F3[NOy] – F4[SOx] (7-12)

where 

F1 = ANClim + CLr/Qr ;

F2 = NHx/ Qr = NHx deposition divided by Qr;

F3 = TNOy/ Qr ; TNOy is the transference ratio that converts deposition of NOy to ambient air

concentrations of NOy; and

F4 = TSOx/ Qr ; TSOx is the transference ratio that converts deposition of SOx to ambient air

concentrations of SOx.

It is indicated in the text (page 7-20) that more details are provided in Appendix B, but I do not 

see any treatment associated with internal S sources. There is no consideration in the appendix 

of the potential importance of organic S mineralization, sulfate desorption or the weathering of 

sulfur minerals. The assumption of the sulfur content in these ecosystems to be in steady state is 

not correct. In future efforts the importance of this internal S source in affecting ecosystem 

response to atmospheric deposition needs to further consideration by EPA.
46

There is extensive discussion related to the rationale for using “transference ratios” versus 

“deposition velocities (pages 7-23 through 7-26). Some of this discussion does not match well 

with the introductory aspects of the chapter that suggest the importance of using deposition 

velocities of individual chemical species (e.g., pages 7-5 through 7-7). There is considerable 

argument provided on the use of CMAQ to develop transference ratios (pages 7-23 through 7-

26). The selection of the Omernik’s ecoregion classification for geographical separation is well 

justified and builds upon previous efforts by EPA. The selection of ecoregion level III resolution 

seems appropriate although it will certainly be challenging to provide parameters for the 84 

defined regions. The further delineation of two broad groupings of ecoregions (acid sensitive 

and relatively non-acid sensitive) is a useful approach in moving this effort forward. It was also 

helpful to identify those ecoregions with insufficient data needed and to use to use median values 

of CLr and Qr from all the relatively non-acid sensitive ecoregions.

Although I agree that for the current standards the appropriate focus is on chronic acidification 

(annual averages) as discussed in Section 7-3, there should be some statement that indicates that 

with climate change resulting in greater amplitudes in hydrological events that episodic 

acidification may become a more dominate and important factor in the future. The discussion on 

the need to focus on a range of ANC values is useful, but it is not completely clear why the final 

selection of the range was from 25 to 75 μeq L-1 versus 0 to 100 μeq L-1 (pages 7-46 through 7-

47) . However, some later arguments (e.g.., pages 7-50 through 7-51) including what standards 

have been set by others helps to justify the former range. 

Section 7.5 on “Considerations associated with alternative standards” provides some useful 

discussion on the applications of various standards and how their utilization effects attainment 

among the various ecoregions. The discussion is useful on how the implementation of the 

standard is affected within the target ANC range of 20 to 75 μeq/L and within representative 

percentile values within the range of the 70th to 90th percentile identified in Section 7.2.5.3 with 

higher percentiles corresponding to a lower critical loads. The overall findings as outlined in this 

section provide supportive information on the implementation of the AAI approach with results 

being consistent with known spatial and temporal factors associated with surface water 

acidification and potential for recovery. Will the implementation of this approach and resultant 

standard have any support for those geographic regions that are more concerned with N 

enrichment in affecting ecosystem structure and function versus acidification?

Table 7-6-1 that provides a “Summary of Qualitative Uncertainty Analysis of Key Components 

of the AAI” is very important”. I am not sure that all of the uncertainty associated with the 

model formulations is clearly articulated including current and future uncertainty about the 

estimates of Neco. There is no indication in the table of any implications associated with the 

assumption that the sulfur inputs and outputs are not in steady state.

The Summary Section (7.7) is a useful synthesis of the overall approach to this new standard. On 

page 7-77 it is stated that “consideration should be given to establishing a new ecologically 

relevant standard(s) to provide increased protection from deposition-related effects of oxides of 

nitrogen and sulfur on sensitive ecosystems”. Clearly this approach considers the combined 

effects of N and S deposition on acidification, but will the absence of nutrient effects 
47

compromise the goal in the establishment of an “ecologically relevant standard”?

Throughout the document the term “neutralize nitrogen deposition” is used and its meaning may 

be confused. When this term is first used it should be defined as gaseous loss and N storage 

(e.g., page ES-8 and 7-18).

Specific Comments (Changes are indicated in italics)

Page(s) Comment

7-3 In discussing the effects of atmospheric deposition of N 

and S compounds it should be mentioned that not only is the effect 

associated with “acidification”, but also to the generation of mobile anions 

(e.g., SO4

2- and NO3-

).

7-11 Change to “low pH”.

7-11 Change to “ANC is a more useful indicator”.

7-11 Change to “acidification through the input of strong acid, 

mobile anions (e.g., NO3

- and SO42-

) that may shift”.

7-11 Change to “transformation through soil S and N 

mineralization and nitrification processes and subsequent drainage from 

terrestrial ecosystems”.

7-11 Change to “surface water pH; trivalent aluminum, Al+3, 

concentrations;”.

7-12 Change to “Aluminum and some other metals may be 

causative toxic agents that directly impair biological functions”.

7-13 Change to “solution must satisfy the condition that the sum 

of negatively charged species must be balanced by the sum of positively 

charged species”.

7-15 Not sure what the meaning of the statement of 

“relationship can be extremely nonlinear” is trying to convey.

7-16 Change to “as temperature, partial pressure of CO2, 

mixing conditions of a water body, and the levels of other several 

chemical species in the system including HCO3

-

“.

7-17 Change to “since the onset of marked increases in 

anthropogenic nitrogen and sulfur deposition”.
48

7-18 It is stated that “based on an ecosystem’s inherent 

generation of ANC and ability to neutralize nitrogen deposition through 

biological and physical processes”. I do not know how “physical” 

processes neutralize nitrogen deposition.

7-18 Change to “whereas steady state models depend on far less 

parameterization and generalization of processes that is afforded”.

7-19 Change to “addressed as well as the ability to perform 

modeling that provides relevant information for different geographic areas 

across the country.

7-34 Change to “as to screen out regions with high proportions 

of high ANC values”.

7-38 Change to “Of these terms, NHx deposition perhaps 

exhibits greater spatial variability, as well as overall uncertainty, than the 

other deposition terms”

7-40 Change to “they may contain some water bodies that are 

acid sensitive”.
49

Mr. Rich Poirot

Form

Given the multi-pollutant, multi-media, environmentally modified, geographically variable 

nature of SOx/NOx-related aquatic acidification effects, the form of any national ambient air 

standard intended to address those effects is guaranteed to be complex. The form of the NAAQS 

proposed in this final PA is unavoidably complex, but is also entirely consistent with and directly 

reflective of the current scientific understanding of the problem. Each element or range of 

options for the form presented in section 7.2 of the PA is logically derived, well justified and 

clearly explained. The high clarity of presentation, added specificity of details, and staff 

recommendations of options or ranges of options for individual elements of the form are all 

notable improvements from the previous draft PA, and are directly responsive to previous 

CASAC review comments. 

The proposed form consists of two general parts - a chemical component, and a spatial 

component. The chemical component (AAI) links an environmental indicator (a protective level 

of ANC in surface waters) to measurable concentrations of SOx and NOy in the ambient air. 

This chemical component can be expressed in terms of the (7-12) equation: AAI = F1 – F2 –

F3[NOy} – F4[SOx]. For any given spatial area and target ANC value, each of the “F” factors in 

this equation can be developed from pre-existing measurement and model data. For any 

specified level of the standard, compliance can then be directly determined from new and 

continuing measurements of SOx and NOy.

The proposed form also includes a spatial component which would define the spatial areas 

(Omernick’s Ecoregions, Level III), over which separate, spatially aggregated, chemical AAI 

calculations would apply. It divides those ecoregions into subsets considered “sensitive” and 

“non-sensitive” to acidification, and also proposes separate ranges of percentiles of critical loads 

for surface waters to be protected from acidification within each sensitivity category. The 

current staff recommendations include a using a more protective range of the 70th to 90th

percentile critical load values in acid sensitive ecoregions and the 50th percentile critical load in 

non-sensitive areas (either averaged across individual areas or across all non-sensitive areas).

The proposed chemical component of the form appears to be technically sound and the AAI 

equation directly parallels the conceptual model of our scientific understanding of the problem. 

Since the F terms can be derived from existing data, the inherent complexities of the form could 

presumably be reduced to a nomograph or set of look-up tables, developed in advance for each 

ecoregion. It is notable that the important factors F2, F3 and F4 would be entirely derived from 

CMAQ model results. This partial reliance on CMAQ represents a significant departure from 

previous NAAQS proposals. This isn’t necessarily a problem, and there may be several benefits 

to combining models and measurements in setting this (or other future) NAAQS, as well as in 

the implementation phase. The accuracy of the factors supplied here by the model is also 

inherently difficult to evaluate (almost by definition, since if there were good measurements 

available to evaluate, the model results wouldn’t be needed). For a standard with a form like this 

to be effective, it will be important to continually scrutinize model performance, adding 

measurements where possible to help evaluate and improve model performance, and to publicly 
50

expose all the relevant details of the model calculations (i.e. show us all the gridded 

concentration and deposition fields – not just the ecoregion AQI look-up tables).

The proposed spatial components of the form also generally appear to be sound, and the use of 

Omernick’s ecoregions (Level III) seems like an appropriate and positive new development for 

secondary NAAQS intended to protect the environment – especially where there are 

geographical variations in the inherent sensitivity of ecosystems to pollutant effects. It is 

difficult to evaluate the logic or “wisdom” of the proposed percentiles (70% to 90%) for critical 

loads of lakes in sensitive ecoregions when taken in isolation. However, when these percentile 

ranges are combined with alternative levels within the staff recommended ANC range of 20 to 

75 μeq/L, the resulting range of combined levels and forms appears to generally focus on the 

right problem areas, and to indicate reasonable degrees of the problem severity (especially at the 

higher percentiles and levels). This “logical performance” of the combined proposals of level 

and form provides confidence in the overall design of the standard, in the individual elements of 

the level and form, and in the ranges recommended by staff. These combined recommendations 

provide the Administrator with a broad but reasonable range of adequate to minimally protective 

options for the standard.

The division of ecoregions into “sensitive” and “non-sensitive” subsets, with a more protective 

percentile applied to the sensitive areas, seems reasonable. It’s not entirely clear, however, how 

the various sensitivity criteria will actually be applied. The naturally poorly buffered coastal 

plain areas (regions 8.5.4, 8.5.1, 8.3.5, and 8.5.3) are initially identified as sensitive areas, are 

included as such in Tables 7-5 and in the various appendices, and exhibit some of the most 

extreme potential exceedances at the 70th through 90th percentiles at all potential levels of the 

standard. But these areas are later identified as anomalous, and found in CMAQ model runs with

future SOx & NOx emissions reductions to be “non-responsive” to SOx and NOx deposition 

changes. It is suggested (p. 7-63) that “responsiveness to deposition change” might be included 

as one of the acid sensitivity criteria, in which case these coastal plain areas would be designated 

non-sensitive. So are they in or out, and if they are out, is the lower 50th percentile sufficient to 

assure that they will not be identified as out of (or at least not way out of) compliance?

I think adding the “responsiveness” criteria to determine relative sensitivity is reasonable and 

appropriate, especially in a case like this where the scientific understanding of ecological 

response to changing atmospheric loading is reasonably well understood, can be further 

documented with observations from the recent past, and can be periodically evaluated by 

“ground truth” (surface water) data as the standard is implemented. In the event that subsections 

of ecoregions exhibit substantially greater (or lower) responsiveness than the region as a whole, 

consideration should be given to further dividing those regions. Establishing such subregions 

may also be desirable for regions which exhibit large spatial variability in TSOx, or TNOy ratios or 

SOx, NOy concentrations. I encourage the Agency to include “responsiveness to deposition 

change” in its initial screening criteria to determine relative “sensitivity”, and think it will also be 

a useful metric for determining and evaluating strategies in the implementation phase. Since 

determination of responsiveness, is like several other elements of this NAAQS, dependent on 

CMAQ model performance, it will be important to continually scrutinize model performance, 

adding measurements where possible to help evaluate and improve model performance, and to 

publicly expose all the relevant details of the model calculations.
51

Mr. Dave Shaw

General Comments

I appreciate the scope and challenge of your task in establishing a NAAQS which will 

appropriately protect our ecosystems and linking that with ambient air concentrations. The form 

of the standard needs to be ecologically relevant and I believe that the form proposed in this 

latest version of the Policy Assessment (PA) is a rather good one, albeit with some 

considerations and concerns.

First and foremost, I do not see where the PA has addressed a concern which I have documented 

with each set of my previous comments. The concern is the lack of real monitored data. A clear 

commitment to the development of a relevant, reliable and consistent monitoring network needs 

to be shown. This should include a timeframe as well as expectations. By including a plan, and 

taking advantage of this multi-pollutant approach, we can make the best use of limited resources, 

for example, by using one monitoring location for several pollutants.

In addition to air monitoring, the PA needs to address what appears to be a lack of commitment 

to adequately measuring water quality indicators. If this is not addressed, the success or failure 

of the overall program will be indeterminate. The PA discusses the TIME and LTM programs, 

but this does not reach into each ecoregion. I recommend establishing a federally funded effort 

to measure water quality at 5-10 lakes in each ecoregion monthly starting as soon as possible. It 

would be advantageous to focus most of the water sampling on the moderately impacted lakes 

which are likely to show the most significant progress from changes in air quality over the 

timeframe of subsequent NAAQS reviews.

While the need for real data is clear, it is understandable that model predictions must be used in 

such a complex effort, it is unfortunate that so much of the F3 and F4 factors are based on model 

predictions. CMAQ is certainly well-tested and constantly being improved, but it has a vast 

array of options. For example, chemical mechanisms, physical packages (boundary layer 

dynamics, clouds, etc.), and initial/boundary conditions are only a few that you can get a range of 

answers for. States, MJO’s, tribes, and other entities may want to use different, perhaps more 

recent, meteorological years, different emission inventories, which may give more reliable 

results, but different from other entities across the United States.

The use of the target ANC/critical load approach for surface waters has sound scientific footing 

and I feel is a proper method to move forward with for this multi-pollutant approach. The area 

that I have some concern with is the linkage which relates back to ambient air concentrations of 

NOy and SOx. Each of the four F factors, especially NHx deposition (F2) and transference ratios 

(F3 and F4) have uncertainties and cannot be tested/verified. High quality representative air and 

water quality monitoring data are necessary in order to develop these modeled relationships. 

Again, this is why the program must have a strong emphasis on environmental monitoring.

I am focusing on data because model predications are based on collected data, so the model 

outcome can only be as good as the data which is used. If EPA decides to rely on model data 

over real data, model outcomes will become less reliable and as a result may become less 
52

protective. On that note, it would be helpful to have some discussion comparing modeled 

estimates of transference ratios at co-located CASTNet/NADP sites where you have measured 

wet and estimated dry deposition.

Because this approach is so model dependent, some discussion on the response during a situation 

where the concentrations of NOy and SOx are within the allowable limits but the lakes still do not 

meet the critical ANC in X percent of the lakes/streams would be helpful. This scenario seems 

possible within ecoregions such as the Adirondacks where there is a lot of spatial variability 

between different lake classes.

I believe that the PA should be very clear about what the standard is and how progress will be 

assessed. Is the standard the AAI, the ambient air concentrations of NOy and SOx, or the ANC? 

Also, the PA needs to maintain a consistency in labeling tables and such with the word 

“standard.” 
53

Dr. Kathleen Weathers

This final version of the PA shows considerable improvement over the previous draft that the 

committee reviewed. It is a huge undertaking and the EPA staff has clearly worked hard. I 

continue to applaud the creation of a multi-pollutant, multi media standard that is linked to 

deposition and ecosystem responses.

General Comments:

This version contains much clearer descriptions and general justification for the various aspects 

of the standard. And, while I think that a standard that is applied to 80+ ecoregions will present 

challenges, it is far more realistic given that ecosystem responses to atmospheric deposition are 

modulated by chemical, physical and biological features of the landscape, and that these features 

also vary across the landscape. That the coastal plain regions showed up prominently (Chapter 7, 

Figures in Appendix D) in the preliminary assessment was surprising (vs the Appalachians). 

While I agree with the discussion in Chapter 7 about the likely ecological reasons for this 

(organic vs mineral acids), I was less clear what the practical implications are, and how, 

specifically, the coastal plains regions might be dealt with in regard to the standard.

The uncertainty discussion is much improved in chapter 7. As expected there are considerable 

uncertainties in all aspects of the AAI—it is the state of the science and the state of the models. 

The goal of reducing uncertainties and further testing and refining both the models and data 

collection in the future (esp. section F-50) is quite important. I found interesting, and not too 

surprising that, in general, base cation weathering, and Q, for most locations, had a greater 

influence on AAI than transference ratios (Appendix, page F-11 in final version of PAD). These 

results highlight research and monitoring needs.

The AAI is an innovative and ecologically relevant form. It considers the complex interactions of 

ecological systems from emissions to deposition to ecological effects via complicated 

biogeochemical reactions within ecosystems. There is much modeled and measured information 

and data packed within the AAI, as we have discussed at length in the past, including 

consideration of NHx inputs to ecosystems.

Atmospheric NOy and SOx are the indicators that this standard has to “work with.” As noted 

throughout this review, other forms of N (e.g., NHx) are important to ecological function, on the 

rise, and should be considered explicitly (not just as an “offset” in the AAI) in the future.

ANC is a scientifically defensible indicator of aquatic acidification, and its proposed (range) 

level is appropriately supported by the literature.

Multiyear averaging time to smooth out anomalous years makes sense. However, it does not 

make complete sense to me to run CMAQ on a daily time step when 3-5 year averaging would 

be used. Also, I don’t completely buy the argument that it’s the temporal, rather than the spatial 

heterogeneity that is most important to capture in modeling deposition, especially since CMAQ 

still cannot resolve finer (spatial) scale deposition to heterogeneous, ecologically sensitive 

mountainous regions. An important goal should be to generate annual deposition over finer 

spatial scales and complex terrain. (I note that there is vague reference to doing this in section 

F.5 of the Appendices—more detail would have been useful.)
54

I cannot stress enough the importance of gathering spatially explicit monitoring data and 

stimulating and supporting ecosystem based research to the fill the significant gaps we have 

identified during this process, from inputs (deposition) to biogeochemical processes within and 

among ecosystems. I should hope that the next review will be made much more straightforward, 

and uncertainties will be much reduced as a result.