Draft Scope and Methods Plan for 

Risk/Exposure Assessment: 

Secondary NAAQS Review for Oxides 

Of Nitrogen and Oxides of Sulfur
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 EPA-452/D-08-002 

March 2008 

Draft Scope and Methods Plan for Risk/Exposure Assessment: 

Secondary NAAQS Review for Oxides 

Of Nitrogen and Oxides of Sulfur 

Office of Air Quality Planning and Standards 

US Environmental Protection Agency 

Research Triangle Park, North Carolina 27711
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

Disclaimer 

This Draft Scope and Methods Plan for the review of the Secondary National Ambient 

Air Quality Standards for oxides of nitrogen and oxides of sulfur has been prepared by the Office 

of Air Quality Planning and Standards, U.S. Environmental Protection Agency (EPA). Any 

opinions, findings, conclusions, or recommendations are those of the authors and do not 

necessarily reflect the views of EPA. This document is being circulated to obtain review and 

comment from the Clean Air Scientific Advisory Committee (CASAC) and the general public. 

Comments on this document should be addressed to Dr. Anne W. Rea, U.S. Environmental 

Protection Agency, Office of Air Quality Planning and Standards, C539-02, Research Triangle 

Park, North Carolina 27711 (email: rea.anne@epa.gov). 

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Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

Table of Contents 

1. Context and Introduction ....................................................................................................... 1 

1.1 Context for this Scope and Methods Plan..................................................................... 1 

1.2 Introduction................................................................................................................... 2 

2. Background and Overview .................................................................................................... 5 

2.1 Legislative Requirements.............................................................................................. 5 

2.2 Background on Previous NO2 and SO2 Secondary NAAQS Reviews ......................... 6 

2.3 Overview of Ecological Risk Assessment and the Scope of the Secondary 

NAAQS Review for NOx and SOx ............................................................................... 7 

2.3.1 Overview of Risk Assessment Framework for Deposition-related 

Ecological Effects ............................................................................................. 9 

2.3.2 Overview of Nitrogen Deposition................................................................... 11 

2.3.3 Overview of Sulfur Oxides and Sulfur Deposition......................................... 13 

2.3.4 Targeted Effects for This Risk/Exposure Assessment.................................... 14 

2.4 Key Policy Relevant Questions .................................................................................. 16 

2.5 Proposed Schedule...................................................................................................... 19 

3. Analysis Plan ....................................................................................................................... 21 

3.1 Step 1 – Plan for assessment using documented effects; biological, chemical, 

and ecological indicators, and potential ecosystem services...................................... 26 

3.1.1 Documented Effects and Relevant Indicators of Effects for Each 

Ecosystem, Including Function and Service................................................... 26 

3.1.2 Potential Ecosystem Services ........................................................................ 30 

3.2 Step 2 – Define sensitive areas that exhibit effects using research findings and 

GIS mapping............................................................................................................... 31 

3.2.1 Defining Sensitive Ecosystems....................................................................... 31 

3.2.2 GIS Mapping................................................................................................... 32 

3.3 Step 3 – Select Risk/Exposure Case Study Assessment Area within a Sensitive 

Area ............................................................................................................................ 35 

3.4 Step 4 – Evaluate Current Loads and Effects to Case Study Assessment Area 

Including Ecosystem Services .................................................................................... 45 

3.4.1 Assess Data Availability and Adequacy......................................................... 45 

3.4.2 Compute Loading and Exposure for Each Ecosystem Effect:........................ 46 

3.5 Step 5 – Where Feasible, Scale Up Case Study Assessment Area Findings to 

Sensitive Areas ........................................................................................................... 51 

3.6 Step 6 – Assess the Current Ecological Conditions for Those Sensitive Areas ......... 52 

3.6.1 Calculate Response Curves for Each Indicator............................................... 52 

3.6.2 Calculate Desired Exposure Endpoint ............................................................ 52 

3.6.3 Develop GIS Maps and Overlay Loading and Indicators That Are 

Representative of Harmful Effects.................................................................. 52 

3.6.4 Using GIS Mapping, Compute the Extent That Loading Is Greater 

Than or Less Than the Harmful Effect Level (a.k.a. endpoint)...................... 52 

3.6.5 Assess Ecosystem Responses via Ecosystem Services and Valuation ........... 52 

3.7 Step 7 – Assess Alternative Levels of Protection Under Different Scenarios of 

Deposition From Ambient Sources ............................................................................ 55 

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4. References............................................................................................................................ 61 

Appendix A Identification of Sensitive Ecosystems ................................................................. A-1 

Appendix B Other Indicators – Nitrous Oxide .......................................................................... B-1 

Appendix C CMAQ Modeling................................................................................................... C-1 

Appendix D Multimedia Modeling............................................................................................ D-1 

Appendix E Valuation of Ecosystem Services ...........................................................................E-1 

List of Figures 

2-1. Risk assessment framework for deposition-related ecological risks. ............................... 10 

2-2. Schematic diagram of the cycle of reactive, oxidized nitrogen species in the 

atmosphere. ....................................................................................................................... 12 

2-3. Percent of Total U.S. Emissions of greenhouse gases in CO2 equivalents....................... 13 

2-4. Transformation of sulfur compounds in the atmosphere. ................................................. 14 

2-5. General flow of processes addressed in the risk/exposure assessment for NOx and 

SOx secondary standards. ................................................................................................. 16 

3-1. Seven step approach to planning and implementing risk/exposure assessment. .............. 25 

3-2. Ecosystem effects may range from near-field to far-field linkages.................................. 31 

3-3. Documented biological, biogeochemical, and physiographic linkages............................ 33 

3-4. Comparison of NAPAP-documented acid-sensitive ecoregions to CMAQ-moded 

nitrogen deposition............................................................................................................ 47 

3-5. Risk/policy assessment paradigm for deposition-related ecological risks........................ 56 

List of Tables 

2-1. Proposed Schedule for the Joint NO2 and SO2 Secondary NAAQS Review* .................. 19 

3-1. Summary of Indicators Categorized by Effect.................................................................. 27 

3-2. Key Indicators of Acidification Due to NOx and SOx ...................................................... 28 

3-3. Key Indicators of Nutrient Enrichment Due to NOx and SOx .......................................... 29 

3-4. Example Datasets Planned for GIS Analysis.................................................................... 34 

3-5. Summary of Indicators, Mapping Layers, and Models for Targeted Ecosystems............ 36 

3-6. SAB/EES Listing of Potential Assessment Areas for Evaluation of Benefits of 

Reductions in Atmospheric Deposition ............................................................................ 39 

3-7. Potential Assessment Areas Identified in the Draft ISA .................................................. 41 

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Key Terms 

Acidification: The process of increasing the acidity of a system (e.g., lake, stream, forest soil). 

Atmospheric deposition of acidic or acidifying compounds can acidify lakes, streams, 

and forest soils. 

Adverse Effect: The response or component of an ecosystem that is deemed harmful in its 

function. 

Air Quality Indicator: The substance or set of substances (e.g., PM2.5, NO2, SO2) occurring in 

the ambient air for which the National Ambient Air Quality Standards set a standard level 

and monitoring occurs. 

Alpine: The biogeographic zone made up of slopes above the tree line, characterized by the 

presence of rosette-forming herbaceous plants and low, shrubby, slow-growing woody 

plants. 

Acid Neutralizing Capacity: A key indicator of the ability of water to neutralize the acid or 

acidifying inputs it receives. This ability depends largely on associated biogeophysical 

characteristics. 

Arid Region: A land region of low rainfall, where “low” is widely accepted to be less than 

250 mm precipitation per year. 

Assessment Endpoint: An ecological entity and its attributes impacts to which are considered 

welfare effects, as defined in Clean Air Act Section 302(h), and that are analyzed in the 

assessment. 

Base Cation Saturation: The degree to which soil cation exchange sites are occupied with base 

cations (e.g., Ca2+, Mg2+, K+

) as opposed to Al3+ and H+. Base cation saturation is a 

measure of soil acidification, with lower values being more acidic. There is a threshold 

whereby soils with base saturations less than 20% (especially between 10–20%) are 

extremely sensitive to change. 

Biologically Relevant Indicator: A physical, chemical, or biological entity/feature that 

demonstrates a consistent degree of response to a given level of stressor exposure and 

that is easily measured/quantified to make it a useful predictor of biological, 

environmental, or ecological risk. 

Buffering Capacity: The ability of a body of water and its watershed to neutralize introduced 

acid. 

Critical Load: A quantitative estimate of the level of exposure to one or more pollutants, below 

which significant harmful effects on specific sensitive elements of the environment do 

not occur according to present knowledge. 

Denitrification: The anaerobic reduction of oxidized nitrogen (e.g., nitrate or nitrite) to gaseous 

nitrogen (e.g., N2O or N2) by denitrifying bacteria. 

Dry Deposition: The removal of gases and particles from the atmosphere to surfaces in the 

absence of precipitation (rain, snow) or occult deposition. 

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Ecological Dose: The concentration of a toxicant that inhibits a microbe-mediated ecological 

process by designated percentage; for example, ED50 inhibits 50%. 

Ecological Exposure: The exposure of a nonhuman organism to an environmental stressor. 

Ecological Risk: The likelihood that adverse ecological effects may occur or are occurring as a 

result of exposure to one or more stressors (U.S. EPA, 1992a). 

Ecological Risk Assessment: A process that evaluates the likelihood that adverse ecological 

effects may occur or are occurring as a result of exposure to one or more stressors (U.S. 

EPA, 1992a). 

Ecosystem: The dynamic, complex interaction of plants, animals, and microorganisms and the 

nonliving environment. 

Ecosystem Benefit: The value, expressed qualitatively, quantitatively, and/or in economic terms, 

where possible, associated with changes in ecosystem services that result either directly 

or indirectly in improved human health and/or welfare. Examples of ecosystem benefits 

that derive from improved air quality include improvements in habitats for sport fish 

species, the quality of drinking water and recreational areas, and the visual quality of 

scenic views. 

Ecosystem Function: The processes and interactions that operate within an ecosystem. 

Ecosystem Services: The ecological processes or functions having monetary or nonmonetary 

value to individuals or society at large. There are (i) supporting services, such as 

productivity or biodiversity maintenance; (ii) provisioning services, such as food, fiber, 

or fish; (iii) regulating services, such as climate regulation or carbon sequestration; and 

(iv) cultural services, such as tourism or spiritual and aesthetic appreciation. 

Elasticity: The percentage of change in the response variable for a 1% change in the input 

physical or meteorological characteristic. 

Eutrophication: The process by which nitrogen additions stimulate the growth of autotrophic 

biota, usually resulting in the depletion of dissolved oxygen. 

Greenhouse Gas: Those gaseous constituents of the atmosphere, both natural and 

anthropogenic, that absorb and emit radiation at specific wavelengths within the spectrum 

of infrared radiation emitted by the earth’s surface, the atmosphere, and clouds. This 

property causes the greenhouse effect. H2O vapor, CO2, N2O, CH4, and O3 are the 

primary greenhouse gases in the earth’s atmosphere. As well as CO2, N2O, and CH4, the 

Kyoto Protocol deals with SF6, hydrofluorocarbons, and perfluorocarbons. 

Nitrogen Enrichment: The process by which a terrestrial system becomes enriched by nutrient 

additions to a degree that stimulates the growth of plant or other terrestrial biota, usually 

resulting in an increase in productivity. 

Nitrogen Saturation: The condition when nitrogen inputs from atmospheric deposition and 

other sources exceed the biological requirements of the ecosystem. 

Occult Deposition: The removal of gases and particles from the atmosphere to surfaces by fog 

or mist. 

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Semiarid Regions: Those regions of moderately low rainfall, typically 25 to 50 centimeters 

(10 to 20 inches) of rainfall per year, where the natural vegetation is usually short grasses 

and shrubs and where the predominant land use may be as rangelands. 

Sensitivity: The degree to which a system is affected, either adversely or beneficially, by SOx or 

NOx pollution (e.g., from acidification or nitrogen nutrient enrichment). The impacts to 

natural environmental systems can be reflected in direct changes in growth or survival 

rates for individual species or changes at a community level reflected in shifts in 

measures such as species diversity. 

Target Load: A policy-based metric that takes into consideration such factors as economic costs 

and time frame for emissions reduction. This can be lower than the critical load if a very 

sensitive area is to be protected in the short term, especially if deposition rates exceed 

critical loads. 

Total Reactive Nitrogen: This includes all biologically, chemically, and radiatively active 

nitrogen compounds in the atmosphere and biosphere, such as NH3, NH4

+

, NO, NO2, 

HNO3, N2O, NO3

–

, and organic compounds (e.g., urea, amines, nucleic acids). 

Valuation: The economic or noneconomic process of determining either the value of 

maintaining a given ecosystem type, state, or condition or the value of a change in an 

ecosystem, its components, or the services it provides. 

Vulnerability: The degree to which a system is susceptible to, and unable to cope with, the 

adverse effects of NOx and/or SOx air pollution. Vulnerability is a function of the 

exposed and its sensitivity. 

Welfare Effects: The effects on soils; water; crops; vegetation; man-made materials; animals; 

wildlife; weather; visibility; and climate as well as damage to, and deterioration of, 

property; hazards to transportation; and the effects on economic values and on personal 

comfort and well-being, whether caused by transformation, conversion, or combination 

with other air pollutants (Clean Air Act Section 302[h]). 

Wet Deposition: The removal of gases and particles from the atmosphere to surfaces by rain or 

other precipitation. 

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Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

1. CONTEXT AND INTRODUCTION 

1.1 Context for This Scope and Methods Plan 

The U.S. Environmental Protection Agency (EPA) is currently conducting a joint review 

of the existing secondary (welfare-based) National Ambient Air Quality Standards (NAAQS) for 

nitrogen dioxide (NO2) and sulfur dioxide (SO2). We recognize that this is the first time that we 

have conducted a joint, multi-pollutant review of a secondary standard separate from the review 

of the primary standard. As discussed in the Integrated Review Plan (U.S. EPA, 2007a), this was 

done in recognition of the important linkages between ambient nitrogen and sulfur leading to 

deposition of ambient particles that can have significant impacts on the environment. We further 

recognize that a fully comprehensive assessment of such linkages and impacts is very complex 

and will extend beyond the time available in this review, as constrained by our court-ordered 

schedule. Thus, this Scope and Methods Plan is more narrowly focused on key aspects of the 

evolving scientific understanding to provide timely results to meet our court-ordered schedule. 

Our plan for the current review is to focus on the identification of sensitive ecosystems, the 

predominant linkages between ambient levels of nitrogen and sulfur, and the levels of deposition 

that create adverse effects in those ecosystems, building directly from the key findings of our 

Integrated Science Assessment (ISA). To the degree possible, our risk and exposure assessment 

will attempt to evaluate whether ecosystem damage is occurring in specific ecosystems under 

current ambient concentrations, and, if so, what alternative levels of ambient nitrogen and sulfur 

might be expected to allow various degrees of recovery of impacted systems and prevention of 

further damage. 

In particular, given the data and time constraints of our current review, we plan to base 

our overall assessment on a small number of local or regional case studies where adequate data 

are available to enable the quantification of some of the more important linkages, focusing on the 

impacts of acidification and enrichment for both terrestrial and aquatic systems. Along with these 

case studies, we plan to conduct statistical and spatial characterizations of existing national-scale 

databases on air quality, nitrogen and sulfur deposition, and ecosystem characteristics to help 

place the results of these local or regional case studies in a broader spatial context. The 

combination of these case studies and the national characterizations thus forms the body of our 

planned overall assessment. Additional case studies and more comprehensive investigations of a 

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Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

broader set of effects, linkages, and indicators may be identified during this process that might 

reasonably form the basis for further assessment in the next 5-year review cycle, when there will 

be a more robust database on which to develop a more comprehensive understanding of these 

relationships. 

1.2 Introduction 

The reviews of the primary NAAQS for NO2 and SO2 are addressed in separate plans 

released during the winter of 2006–2007. The revised, secondary NAAQS review process 

contains four major components: an integrated review plan, a science assessment, a risk/exposure 

assessment, and a policy assessment/rulemaking. This Scope and Methods Plan is the first phase 

of the risk/exposure assessment; it will describe the scope of the analyses to be performed and 

the tools and methods that will be used for the joint review of the secondary NAAQS for these 

pollutants. In this plan, the terms NO2 and oxides of nitrogen (NOx) and SO2 and oxides of sulfur 

(SOx) are not interchangeable. The terms NOx and SOx refer to the listed Criteria Air Pollutants 

for which EPA has regulatory authority under Sections 108 and 109 of the Clean Air Act (CAA), 

and for which criteria must be developed and reviewed every 5 years. It is necessary to 

distinguish between the definition of “nitrogen oxides” as it appears in the enabling legislation 

related to the NAAQS and the definition commonly used in the air pollution research and 

management community. In this document, the terms “oxides of nitrogen” and “nitrogen oxides” 

refer to all forms of oxidized nitrogen compounds, including nitric oxide (NO), nitrogen dioxide 

(NO2), and all other oxidized nitrogen-containing compounds transformed from NO and NO2. 

This follows usage in the Clean Air Act Section 108(c): “Such criteria [for oxides of nitrogen] 

shall include a discussion of nitric and nitrous acids, nitrites, nitrates, nitrosamines, and other 

carcinogenic and potentially carcinogenic derivatives of oxides of nitrogen.” By contrast, within 

the air pollution research and control community, the terms “oxides of nitrogen” and “nitrogen 

oxides” are restricted to refer only to the sum of NO and NO2, and this sum is commonly 

abbreviated as NOx. The category label used by this community for the sum of all forms of 

oxidized nitrogen compounds including those listed in Section 108(c) is NOy. 

The terms NO2 and SO2 refer to the specific air quality indicators (pollutant species) 

specified by the current standards whose concentrations are monitored to determine whether the 

NAAQS are being met in a given location. The ecological importance of both oxidized and 

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reduced forms of nitrogen has been widely recognized by the scientific community. Therefore, 

this risk/exposure assessment will also evaluate total reactive nitrogen (which includes both 

oxidized and reduced forms of nitrogen) and its impacts on public welfare. It is addressed in this 

NAAQS review because reduced forms of nitrogen may also cause many of the effects resulting 

from oxides of nitrogen (e.g., deposition-influenced nitrogen enrichment). 

Because NOx, SOx, and their associated transformation products are linked from an 

atmospheric chemistry perspective, as well as from an environmental effects perspective, and 

because of the National Research Council’s (NRC’s) 2004 recommendations to consider 

multiple pollutants in forming the scientific basis for the NAAQS, EPA has decided, for the first 

time since NAAQS were established in 1971, to jointly assess the science, risks, and policies 

relevant to protect the public welfare associated with oxides of nitrogen and oxides of sulfur. 

Though these interactions have been recognized historically by both the Clean Air Scientific 

Advisory Committee (CASAC) and EPA, and the science related to these interactions has 

continued to evolve and grow to the present day, providing ongoing support for considering them 

together. 

This Scope and Methods Plan is organized to provide information consistent with EPA’s 

1998 Guidelines for Ecological Risk Assessment (U.S. EPA, 1998) that is representative of the 

problem formulation phase of the risk assessment. The Scope and Methods Plan is organized to 

provide the following: 

 Background on NAAQS legislation, previous secondary reviews, an overview of 

ecological risk assessments, and the scope of this NAAQS review 

 A conceptual model of nitrogen and sulfur cycling 

 Key policy-relevant questions 

 EPA’s proposed schedule for the NOx/SOx secondary NAAQS review 

 An analysis plan that includes the identification of relevant indicators of effects, a 

proposed approach to select areas for the risk/exposure assessment, an evaluation of data 

and models to assess effects, plans for characterization of exposure, and plans for 

characterization of ecological effects 

 An assessment of alternative levels of protection under different scenarios of deposition 

from ambient sources. 

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EPA is consulting with CASAC, an independent scientific advisory committee 

established under the CAA, on this plan. In particular, given the context for this NAAQS review 

and the timing constraints for its completion, we are soliciting the advice from CASAC on how 

to best focus our current assessment activities to provide meaningful results to inform the 

regulatory portion of this review. To aid in this process, we have identified our initial priorities 

for each step in the process (i.e. case study areas, larger assessment areas, endpoints and 

indicators) for the overall risk/exposure assessment. As this review proceeds, the plan described 

here may be modified to reflect information received during the review process and to address 

advice and comments received from CASAC and the public. 
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

2. BACKGROUND AND OVERVIEW 

2.1 Legislative Requirements 

Two sections of the CAA govern the establishment and revision of the NAAQS Section 

108 (42 U.S.C. 7408) directs the Administrator to identify and list “air pollutants” that “in his 

judgment, may reasonably be anticipated to endanger public health and welfare” and whose 

“presence . . . in the ambient air results from numerous or diverse mobile or stationary sources” 

and to issue air quality criteria for those that are listed. Air quality criteria are intended to 

“accurately reflect the latest scientific knowledge useful in indicating the kind and extent of 

identifiable effects on public health or welfare which may be expected from the presence of [a] 

pollutant in ambient air. . . .” 

Section 109 (42 U.S.C. 7409) directs the Administrator to propose and promulgate 

“primary” and “secondary” NAAQS for pollutants listed under Section 108. A secondary 

standard, as defined in Section 109(b)(2), must “specify a level of air quality the attainment and 

maintenance of which, in the judgment of the Administrator, based on such criteria, is required to 

protect the public welfare from any known or anticipated adverse effects associated with the 

presence of [the] pollutant in the ambient air.” Welfare effects, as defined in Section 302(h) [42 

U.S.C. 7602(h)], include, but are not limited to, “effects on soils, water, crops, vegetation, manmade materials, animals, wildlife, weather, visibility and climate, damage to and deterioration of 

property, and hazards to transportation, as well as effects on economic values and on personal 

comfort and well-being.” The definition of public welfare in Section 302(h) was expanded in the 

1990 CAA amendments to state that the welfare effects identified should be protected from 

adverse effects associated with criteria air pollutants “whether caused by transformation, 

conversion, or combination with other air pollutant.” 

In setting standards that are “requisite” to protecting public health and welfare, as 

provided in Section 109(b), EPA’s task is to establish standards that are neither more nor less 

stringent than necessary for these purposes. In so doing, EPA may not consider the costs of 

implementing the standards (Whitman v. American Trucking Associations, 531 U.S. 457, 465–

472, 475–76 [2001]). 

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Section 109(d)(1) requires that “not later than December 31, 1980, and at 5-year intervals 

thereafter, the Administrator shall complete a thorough review of the criteria published under 

Section 108 and the national ambient air quality standards . . . and shall make such revisions in 

such criteria and standards and promulgate such new standards as may be appropriate. . . .” 

Section 109(d)(2) requires that an independent scientific review committee “shall complete a 

review of the criteria . . . and the national primary and secondary ambient air quality 

standards . . . and shall recommend to the Administrator any new . . . standards and revisions of 

existing criteria and standards as may be appropriate. . . .” Since the early 1980s, this 

independent review function has been performed by CASAC of EPA’s Science Advisory Board 

(SAB). 

2.2 Background on Previous NO2 and SO2 Secondary NAAQS Reviews 

The current secondary NAAQS review for NOx/SOx will examine a number of issues that 

were of central importance in previous NAAQS nitrogen or sulfur reviews. For instance, in the 

previous review of the NO2 NAAQS, completed in 1995, welfare effects were assessed primarily 

with respect to effects of ambient concentrations of NO2 on vegetation by way of a literature 

review. A full risk assessment was not conducted for other welfare effects associated with NO2. 

The decision was made to retain the current standard for NO2 as the uncertainty and variability 

associated with the science at that time limited any other action. The 1995 NO2 review did state, 

however, that “growing evidence does indicate that the impact of nitrogen deposition on 

sensitive aquatic ecosystems may be significant,” that certain areas of the country, including “the 

Catskills, Northern Appalachians, Valley and Ridge Province, and Southern Appalachians all 

show some potential for chronic acidification due to NO3

-

” (U.S. EPA, 1995). Additional topics 

highlighted within the 1995 NO2 review also included the importance of acid neutralizing 

capacity (ANC) in surface water acidification, the influence of atmospheric nitrogen to 

eutrophication of the Chesapeake Bay, and the growing body of research on developing “critical 

loads” and “target loads” for nitrogen in various ecosystems. 

In the previous review of the SO2 NAAQS, completed in 1996, vegetation damage 

(growth, yield, and foliar injury) due to short-term and long-term exposures to SO2 were avoided 

by maintaining the current secondary 3-hour standard (0.053 ppm) (U.S. EPA, 1982). Data on 

the effects of long-term exposures affecting species richness and species diversity, reduced 

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growth, and premature needle drop were considered “weak and not developed well enough to 

provide the principal basis for selecting the level of a long-term SO2 standard” (U.S. EPA, 1982). 

The 1982 staff paper did note, however, that long-term SO2 concentrations may be affecting 

lichen and mosses, and that these should be considered in the larger context of regional acid 

deposition. (Note: the 1986 Addendum (U.S. EPA, 1986) and 1994 Supplement (U.S. EPA, 

1994) solely addressed human health effects.) 

The planned risk/exposure assessment described in this Scope and Methods Plan builds 

upon the methodology and lessons learned from the previous NAAQS reviews. This plan is 

based on our current understanding of the NOx and SOx scientific literature and is subject to 

change as the NOx/SOx ISA undergoes revision. Currently, the EPA’s Office of Research and 

Development’s (ORD) National Center for Environmental Assessment (NCEA) has compiled 

and synthesized the most policy-relevant science available to produce a draft of the ISA, which 

has been used in the development of the approach described here. The approach described in this 

plan may also be modified according to CASAC and public comments following their review of 

this document as well as any additional information contained in the final version of the ISA. 

2.3 Overview of Ecological Risk Assessment and the Scope of the Secondary 

NAAQS Review for NOx and SOx

The conventional framework for ecological risk assessment consists of three phases: 

 Problem Formulation, 

 Analysis, and 

 Risk Characterization. 

These phases have been described in more detail in the Guidelines for Ecological Risk 

Assessment (U.S. EPA, 1998) and other documents prepared by the Risk Assessment Forum 

(U.S. EPA, 1991, 1992a, 1992b). Generally, the Problem Formulation Phase describes the goals, 

breadth, and focus of the assessment including assessment endpoints, data needs, and anticipated 

analyses. It results in three products: (1) assessment endpoints that adequately reflect 

management goals of the ecosystem they represent, (2) conceptual models that describe key 

relationships between stressor and assessment endpoint or between several stressors and 

assessment endpoints, and (3) an analysis plan. The Scope and Methods Plan for the secondary 

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NO2/SO2 NAAQS Review represents the Problem Formulation Phase of the ecological risk 

assessment framework. The Analysis Phase of an ecological risk assessment might include 

environmental exposure profiles, the magnitude of spatial and temporal patterns of exposure, and 

summaries of the data analyses on effects and their association with assessment endpoints. The 

Risk Characterization Phase of an ecological risk assessment may be a quantitative or qualitative 

assessment that integrates exposure and effects profiles and estimates risks by categories, such as 

individuals or populations via modeling techniques. In the risk/exposure assessment, EPA plans 

to draw upon the ISA to develop quantitative and qualitative estimates of the risks of adverse 

welfare effects occurring as a result of current ambient levels of nitrogen oxides and sulfur 

oxides, levels that meet the current standards for NO2 and SO2, or levels that meet possible 

alternative standards. The issues that are addressed by the Analysis Phase and Risk 

Characterization Phase are part of the Risk/Exposure Assessment for the Secondary NAAQS 

Review for NOx and SOx. 

Welfare impacts from air pollution to ecosystems are a serious concern. There are many 

harmful environmental effects of air pollution, including acid rain, ozone formation, decreased 

visibility, and effects on climate. In addition to direct adverse impacts to the biological and 

biogeochemical components of natural ecosystems, these direct ecological impacts can affect the 

welfare amenities of ecosystems in terms of their aesthetic and recreational amenities. Impacts 

on climate are also considered welfare effects, such as those due to nitrous oxide, N2O. Welfare 

effects from the production of greenhouse gases such as N2O can also cause significant 

impairment of ecosystems through climate change processes. 

Against this broad background to welfare impact issues, this risk/exposure assessment 

will focus on ecological quality and its effects from acidification and enrichment related to 

nitrogen and sulfur air pollutants. In previous secondary reviews, acidification was evaluated for 

its damage to materials, including decay of buildings, statues, and sculptures that are part of our 

national heritage. The current assessment will focus on the influence of acid deposition on soil, 

forests, and waterbodies. Nitrogen deposition may also contribute to eutrophication (oxygen 

depletion) of water bodies, the symptoms of which include algal blooms (some of which may be 

toxic), fish kills, and loss of plant and animal diversity. These ecological changes impact human 

populations by changing the availability of seafood and creating a risk of consuming fish or 

shellfish contaminated from toxins produced by algal species that may be at an advantage in 

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Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

eutrophic systems as mentioned in the ISA. This reduces our ability to use and enjoy our coastal 

ecosystems, and causes an economic impact on people who rely on healthy coastal ecosystems, 

such as fishermen and those who cater to tourists. 

Visibility impairment and ozone formation are additional welfare effects that are being 

addressed in the particulate matter (PM) and ozone NAAQS reviews. Visibility is being 

addressed in a separate secondary review effort as part of the PM NAAQS standard review. 

Ozone pollution’s secondary impacts include damage to plant vegetation. Ozone is a secondary 

product of precursors NO2 and volatile organic carbon. A separate rule review effort is in place 

for ambient ozone concentration, and its secondary impacts will also not be addressed in this 

NOx and SOx risk/exposure assessment. 

In this current review, the appropriateness of NO2 as an indicator for NOx species and 

SO2 as an indicator for SOx species will be evaluated. This review will evaluate new information 

published in the peer-reviewed literature since the completion of the last NO2 (1995) and SO2

(1996) reviews, including assessments of the adequacy of the current secondary NAAQS, 

consideration of whether there is a possible need for a new single indicator or suite of indicators, 

as well as changed or retained level(s) and/or averaging times for the standards, which may 

include nitrogen and sulfur compounds other than NO2 and SO2. 

This Scope and Methods Plan is intended to facilitate consultation with the CASAC, as 

well as the public, and to obtain advice on the overall scope, approaches, and key issues in 

advance of the completion of such analyses and presentation of results in the first draft of the 

risk/exposure assessment. The risk/exposure assessment is intended to be a tool that, together 

with other information contained in the NOx/SOx ISA, can aid the Administrator in judging 

whether the current secondary standards are requisite to protect public welfare from any known 

or anticipated adverse effects, or whether these standards should be retained, revised, revoked 

and/or replaced with alternative standard(s) having different indicators to provide the required 

protection. 

2.3.1 Overview of Risk Assessment Framework for Deposition-related Ecological 

Effects 

The risk/exposure assessment framework is intended to serve as a conceptual map of the 

analytical and decision steps necessary to estimate the ecological risks associated with alternative 

9 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

forms and levels of standards for NOx and SOx. As noted in the Integrated Review Plan for this 

review (U.S. EPA, 2007a), the purpose of the risk/exposure assessment is to assess the potential 

adversity of impacts including the effects of the pollutants on ecosystem goods and services, the 

degree to which ecosystem functions are impaired, long-term trends in specific ecosystems 

(where available), and both monetized and non-monetized valuation of ecosystem services. The 

ability of the risk/exposure assessment to characterize these impacts will depend on a number of 

factors, including the state of the supporting science, the availability of data on ecosystem 

baseline conditions and/or responsiveness to changes in nitrogen and sulfur deposition, and the 

time available under the regulatory development process. 

The design of a risk assessment framework is discussed in the 1998 Guidelines for 

Ecological Risk Assessment (U.S. EPA, 1998). For this NOx/SOx risk/exposure assessment, EPA 

designed a flow diagram that represents how nitrogen and sulfur compounds move from “source 

to dose” in the environment. (See Figure 2-1.) This diagram represents the risk assessment 

framework for deposition-related ecological risks. It consists of two general activities: 

1) characterization of exposure and 2) characterization of effect. More specifically, this 

framework depicts the processes and transformations among atmospheric concentrations, 

deposition, ecosystem impacts, exposure to biologically relevant species, and ecosystem 

responses via ecosystem services and valuation. 

Figure 2-1. Risk assessment framework for deposition-related ecological risks. 

10 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

The ecosystem response may be expressed as an “endpoint” in the ecological risk 

assessment. For this review, the level of acidification and nitrogen and/or sulfur enrichment that 

results in a harmful effect may be deemed an endpoint. This risk assessment framework entails 

modeling to calculate ecosystem loading and exposure required to reach the endpoint. This load 

is also known as the critical load. A critical load analysis is a form of site-specific risk 

assessment. It considers exposure to and response by various ecosystem receptors to identify the 

amount of atmospheric deposition (or loading) above which adverse ecological effects occur, 

serving as the endpoint of the risk assessment. Critical load analysis, within a risk assessment 

framework, can be a potential indicator for policy analysis. 

Each component of the framework has a number of decisions required in implementing a 

framework to analyze alternative air quality standards. In an analytical world unconstrained by 

data and resource limitations, one could envision a nationwide comprehensive risk assessment 

covering all potentially affected sensitive ecosystems and all scientifically supported effects. 

However, as noted by the Science Advisory Board in their recent review of the analytical plan 

for the 2nd Prospective Analysis of the Costs and Benefits of the Clean Air Act, “a 

comprehensive quantitative national assessment of the ecological benefits of the CAA 

Amendments is not a realistic expectation.” We recognize this limitation in developing the 

framework for the NOx/SOx risk/exposure assessment, and in the following sections, we describe 

a detailed framework for assessing ecological risks that follows the principle of obtaining the 

maximum amount of policy-relevant risk information possible given the data, resources, and 

time limitations. 

2.3.2 Overview of Nitrogen Deposition 

The sum of mono-nitrogen oxides, NO2 and NO, typically are referred to as nitrogen 

oxides (NOx) in the atmospheric science community. More formally, the family of nitrogen 

oxides includes any gaseous combination of nitrogen and oxygen, e.g., NO2, NO, N2O, N2O3, 

N2O4, and N2O5. Total reduced nitrogen (NOy) includes all nitrogen oxides as well as gaseous 

and particulate nitrate species such as HNO3, PAN, and aerosol phase ammonium nitrates. 

Reduced atmospheric nitrogen species include ammonia gas (NH3) and ammonium ion (NH4

+

), 

the sum of which is referred to as NHx. Atmospheric nitrogen deposition often is delineated 

11 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

farther as dry (gas and particulate phases) or as wet (precipitation derived ion phase). (See 

Figure 2-2.) 

(Source: U.S. EPA, 2007e. ISA for Oxides of Nitrogen and Sulfur Environmental Criteria. December 2007, EPA/600/R-07/145A). 

Figure 2-2. Schematic diagram of the cycle of reactive, oxidized nitrogen species in the 

atmosphere. (IN refers to inorganic particulate species (e.g., Na+,Ca++), MPP to multiphase 

processes, hv to a solar photon, and R to an organic radical. Particulate phase organic nitrates 

are also formed from the species on the right side of the figure.) 

N2O has not been considered in setting previous NO2 NAAQS standards. In the first NOx

review, N2O was not considered an air contaminant because there was “no evidence to suggest 

N2O is involved in photochemical reactions in the lower atmosphere” (U.S. EPA, 1971). N2O 

was addressed in both the 1982 and 1993 criteria documents. In 1982, it was described as one of 

the eight nitrogen oxides that may be present in the ambient air, but “not generally considered a 

pollutant.” The effect of N2O on stratospheric ozone was described, and the criteria document 

noted that N2O may cause a small decrease in stratospheric ozone (U.S. EPA, 1982). Finally, the 

criteria document also concluded that N2O significantly contributes to the atmospheric 

greenhouse effect by trapping outgoing terrestrial radiation, and that the issue was being 

investigated, but that many years of research were still needed to reliably assess the issue. In 

1993, the criteria document again identifies N2O as an oxidized nitrogen compound that is not 

generally considered to be an air pollutant, but does have an impact on stratospheric ozone and is 

12 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

considered among the more significant greenhouse gases. These documents clearly consider N2O 

as within the scope of the listed nitrogen oxides criteria pollutant. 

The 2007 draft of the ISA (see Sections 2.2, 3.1 and 4.4 in U.S. EPA, 2007b) 

acknowledges N2O as a potent greenhouse gas and discusses N2O sources and emissions in the 

United States, as well as the biogeochemistry of the microbial mediated production via 

denitrification in natural ecosystems. Based on the current U.S. Greenhouse Gas (GHG) 

Inventory (U.S. EPA, 2007d), nitrous oxide contributes approximately 6.5 % to total greenhouse 

gas emissions (in CO2 equivalents) (Figure 2-3). 

Source: U.S. EPA, 2007d 

Figure 2-3. Percent of Total U.S. Emissions of greenhouse gases 

in CO2 equivalents. 

Since the definition of “welfare effects” includes effects on climate [CAA Section 

302(h)], we will include N2O within the scope of this review. However, it is most appropriate to 

analyze the role of N2O in anthropogenic climate change in the context of all of the greenhouse 

gases. Since that is outside the scope of this review, it will not be a quantitative part of this 

assessment. 

2.3.3 Overview of Sulfur Oxides and Sulfur Deposition 

SO2 is one of a group of substances known as SOx, which include multiple gaseous (e.g., 

SO2, SO, SO3, S2O3, S2O7) and particulate (e.g., ammonium sulfate) species (Figure 2-4). 

Acidification can result from the atmospheric deposition of SOx and NOx; in acid deposition, 

these species combine with water in the atmosphere to form sulfuric acid (H2SO4) and HNO3. 

Acidification is an environmental effect in which acid precipitation lowers the natural pH of 

waterbodies and/or damages terrestrial ecosystems. Over the past few decades, acidification of 

13 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

waterbodies has been recognized as an environmental issue throughout Europe and North 

America, and steps have been taken to control SOx and NOx emissions and to identify the 

recovery of the impacted ecosystems. Due to known acute effects on plants, in previous NAAQS 

reviews, SO2 served as the chemical indicator for SOx species. 

(Source: U.S. EPA, 2007e. ISA for Oxides of Nitrogen and Sulfur Environmental Criteria. December 2007, 

EPA/600/R-07/145A [adapted from Berresheim et al., 1995]). 

Figure 2-4. Transformation of sulfur compounds in the atmosphere. 

2.3.4 Targeted Effects for This Risk/Exposure Assessment 

The two classifications of effects that are targeted for this risk/exposure assessment are 

acidification and nitrogen and sulfur enrichment. Both effects occur in response to deposition of 

NOx and SOx. Acidification effects can occur from either nitrogen or sulfur deposition, and the 

relative contribution of each type of deposition depends on the characteristics of the affected 

ecosystem (see Section 4.2 of the ISA, U.S. EPA, 2007b). Nitrogen and sulfur enrichment 

represents a continuum of effects, and it can be characterized as a positive or negative effect, 

depending on the selected endpoint, location and baseline conditions of an ecosystem. 

Enrichment effects are caused by nitrogen or sulfur deposition, but are dominated by nitrogen 

deposition, which will be the focus of the risk/exposure assessment. Nitrogen enrichment in 

ecosystems may alter the native terrestrial species composition (i.e., from wildflower meadows 

to shrubs), and can result in eutrophication in aquatic systems (see Section 4.3 of the ISA, U.S. 

14 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

EPA, 2007b). Thus, the framework for this review highlights four main areas that will be 

evaluated for a risk/exposure assessment in this plan: 

1. Risks to terrestrial ecosystems from nitrogen enrichment effects 

2. Risks to aquatic ecosystems from nitrogen enrichment effects (eutrophication) 

3. Risks to terrestrial ecosystems from acidification effects (nitrogen and sulfur) 

4. Risks to aquatic ecosystems from acidification effects (nitrogen and sulfur) 

In addition to the four targeted effects listed above, we will address, as appropriate, 

impacts associated with nitrous oxide and the influence of sulfur enrichment on methylmercury 

production. Figure 2-5 provides a conceptual diagram of the processes we will need to model in 

our risk and exposure assessment. Atmospheric fate and transport is the initial point of departure 

for the analysis, and is fully integrated in the treatment of NOx, other reactive nitrogen species, 

and SOx. The results of the atmospheric fate and transport process are atmospheric loading of 

sulfur and total reactive nitrogen, as well as concentrations of N2O. As mentioned earlier, a 

quantitative assessment of N2O is not currently within the scope of this review. 

Atmospheric loadings of total reactive nitrogen and SOx lead to deposition of nitrogen 

and sulfur to terrestrial and aquatic ecosystems. In addition to the major ecological effects of 

acidification and nutrient enrichment, sulfur deposition also leads to enhanced methylmercury 

(MeHg) production in aquatic systems and, in turn, increases the risks for bioaccumulation and 

biomagnifications of mercury in food chains (see Section 4.4 in U.S. EPA, 2007b). This 

interaction between sulfur deposition and methylmercury production can exacerbate an already 

important mercury problem, especially in coastal and eutrophic waters subject to hypoxic algal 

blooms. The focus of the quantitative risk/exposure assessment will be the set of effects 

associated directly with acidification and nitrogen and sulfur enrichment, but we will also 

provide a qualitative assessment of potential impacts of sulfur deposition on waterbodies that are 

vulnerable to increased mercury methylation. 

15 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

Atmospheric

Fate and 

Transport

Total Reactive 

N and SOx

Deposition 

Processes

Acidification

N2O

Acidification

Terrestrial Aquatic Terrestrial Aquatic Terrestrial Aquatic

Enrichment MeHg 

Production

Nitrogen Sulfur

 

Figure 2-5. General flow of processes addressed in the risk/exposure assessment 

for NOx and SOx secondary standards. 

2.4 Key Policy Relevant Questions 

The 2007 Integrated Review Plan of the Secondary NAAQS for NO2 and SO2 introduced 

a series of policy-relevant questions to frame the approach EPA will take in this review (U.S. 

EPA, 2007a). The Review Plan indicated that issues of ecosystem susceptibility should be 

addressed, as well as the issue of whether individual effects or combined effects are more 

important to a given ecosystem (i.e., is it NOx or SOx acting individually that is important, or is it 

the combination of NOx and SOx that needs to be addressed). For example, both NOx and SOx

are associated with acidification effects, while nitrogen is associated with nutrient enrichment 

and eutrophication effects, and sulfur is associated with increased mercury (Hg) methylation. 

Both EPA and CASAC have acknowledged the importance of NOx, SOx, and their 

associated transformation products with respect to acidification effects on ecosystems. This 

review will focus on the ecosystem-related welfare effects that result from the deposition of these 

pollutants and their transformation products, rather than on the effects of aerosol NOx and SOx

that remain in the atmosphere. 

For this secondary NAAQS review of NOx/SOx, the primary policy-relevant questions 

include: 

16 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

 What are the known or anticipated welfare effects influenced by ambient NOx and SOx, 

and for which effects is there sufficient information available to be useful as a basis for 

considering distinct secondary standard(s)? 

 What is the nature and magnitude of ecosystem responses to NOx and SOx that are 

understood to have known or anticipated adverse effects, and what is the variability 

associated with those responses (including ecosystem type, climatic conditions, 

environmental effects, and interactions with other environmental factors and pollutants)? 

 What are the biologically relevant indices that adequately capture the relationship 

between ecosystem exposure and response for the known or anticipated welfare effects 

we are trying to protect? 

 To what extent do receptor surfaces influence the deposition of gases and particles (dry 

deposition), since dry deposition can contribute significantly to total deposition? 

 What are the appropriate air quality indicator(s), averaging time(s), form(s), and level(s) 

of standards that are requisite to avoid those ecosystem responses? 

 To what extent do the current standards provide the requisite protection for the public 

welfare effects associated with NOx and SOx? 

– Should the current secondary standards for NO2 (as an indicator of NOx) and SO2 (as 

an indicator for SOx) be retained, revised, or revoked and/or replaced with alternative 

standard(s) having different indicators to provide the required protection from known 

or anticipated adverse public welfare effects? 

– Can effects from NOx be distinguished from effects due to total reactive nitrogen? 

To the extent that the evidence suggests revision of the current secondary NOx/SOx

NAAQS is appropriate, ranges of standards will be identified (including different or alternate 

indicators, terms of exposure indices, averaging times, levels, and forms) that reflect a range of 

alternative policy judgments as to the degree of protection that is requisite to protect public 

welfare from known or anticipated adverse effects. To account for variability in ecosystem 

responses and land uses across the nation, ecosystem characteristics may be an important 

consideration in evaluating the form(s) of the standards. The form(s) of the standard(s) may be 

based on a complex formula that incorporates ecosystem characteristics, land uses, atmospheric 

17 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

transformations, climatic conditions, environmental effects and other interactions. In so doing, 

the following questions should be addressed: 

 Does the available information provide support for considering different NOx/SOx

chemical indicators or exposure indices? 

 Does the available information provide support for considering some joint standard(s) or 

are separate standards appropriate? 

 What range of levels and forms of alternative standards are supported by the information, 

and what are the uncertainties and limitations in that information? 

 To what extent do specific levels and forms of alternative standards reduce adverse 

impacts attributable to NOx/SOx, and what are the uncertainties in the estimated 

reductions? 

In order to be able to answer these questions, we believe that the relevant scientific and 

policy issues that need to be addressed in the science, risk/exposure, and policy assessment 

portions of this review include: 

 Identifying important chemical species in the atmosphere 

 Identifying the atmospheric pathways that govern chemical transformation, transport, and 

deposition of NOx and SOx to the environment 

 Identifying the attributes of ecosystem receptors that govern their susceptibility to effects 

from deposition of nitrogen and sulfur compounds 

 Identifying the relationships between ambient indicators and biologically relevant indices 

of effects, including ecosystem services associated with the indicator (but not excluding 

other non-economic evaluations) 

 Evaluating alternative measures to assess the adversity of effects on ecosystem services, 

including, for example, economic valuation 

 Evaluating if current levels may have a long-term impact due to cumulative loadings, and 

if this is relevant to a NAAQS review 

 Evaluating environmental impacts and sensitivities to varying meteorological scenarios 

and climate conditions 

18 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

19 DRAFT – March 2008

2.5 Proposed Schedule 

The proposed schedule for the joint NO2/SO2 secondary NAAQS review is shown in 

Table 2-1; underlined dates indicate the court-ordered schedule. Consultation with CASAC and 

the public on the first draft of the ISA and this Scope and Methods Plan is planned for April 

2008. Based on this consultation, the plan for the risk/exposure assessment may be revised as 

needed. The first draft of the risk/exposure assessment and the second draft of the ISA will be 

released to CASAC and the public in August 2008. EPA will receive comments on these draft 

documents from CASAC and the public at a meeting in October 2008. A revised risk/exposure 

assessment will be released in March 2009 followed by a CASAC and public review in May 

2009. The final risk/exposure assessment for the secondary NO2/SO2 NAAQS review will be 

released in July 2009. 

Table 2-1. Proposed Schedule for the Joint NO2 and SO2 Secondary NAAQS Review*

Stage of 

Review Major Milestone Draft Target Dates 

Literature search Ongoing 

Federal Register call for information December 2005 

Prepare the draft NO2/SO2 NAAQS Work Plan December 2005–August 2007 

Workshop on science/policy issues July 2007 

CASAC consultation October 2007 

Planning 

Prepare the final integrated NO2/SO2 NAAQS 

Work Plan 

December 2007 

Prepare first draft of the ISA December 2007 

CASAC/public review of the first draft of the ISA April 2008 

Prepare the second draft of the ISA July/August 2008 

CASAC/public review of the second draft of the 

ISA 

October 2008 

Integrated 

Science 

Assessment 

(ISA) 

Prepare the final ISA December 12, 2008

REA methodology released to the CASAC and 

the public 

February 2008 

CASAC/public consultation on the REA 

methodology 

April 2008 

First draft of the REA released to the CASAC and 

the public 

August 2008 

CASAC/public review of the first draft of the REA October 2008 

Second draft of the REA released to the CASAC 

and the public 

March 2009 

CASAC/public review of the second draft of the 

REA 

May 2009 

Risk/Exposure 

Assessment 

(REA) 

Final REA released July 2009 
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

20 DRAFT – March 2008

Stage of 

Review Major Milestone Draft Target Dates 

Publish ANPR August 2009 

CASAC review/public comment on ANPR October 2009 

Proposed rulemaking February 12, 2010

Policy 

Assessment/ 

Rulemaking 

Final rulemaking October 19, 2010

* Schedule may be modified, as necessary, to reflect actual project requirements and progress. 

Underlined dates indicate the court-ordered schedule. 
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

3. ANALYSIS PLAN 

Because ecosystems are diverse in biota, climate, geochemistry, and hydrology, response 

to pollutant exposures can vary significantly. Also, these diverse ecosystems are often neither 

abundant nor distributed evenly across the United States. To target acidification and nitrogen and 

sulfur enrichment, this Scope and Methods Plan focuses on four main ecosystem effects on 

terrestrial and aquatic systems identified in the ISA: 

 Terrestrial nitrogen enrichment 

 Aquatic nitrogen enrichment, including eutrophication 

 Terrestrial acidification due to nitrogen and sulfur 

 Aquatic acidification due to nitrogen and sulfur 

In addition to these four effects, we plan to address, as appropriate and within our time 

constraints, impacts associated with nitrous oxide (N2O)and the influence of sulfur enrichment 

on methylmercury production. Since these ecosystem effects are not found evenly distributed 

across the United States, we plan to perform risk/exposure assessment case studies for specific 

areas of the U.S. We plan to select these case studies from those areas of the United States where 

ecosystems are identified as sensitive to nitrogen and/or sulfur deposition effects. 

Once those sensitive areas are determined, we will decide how best to design and conduct 

case study analyses that contain the sensitive ecosystems of interest. These locations may vary in 

size from a single site to a region containing numerous lakes. Methods of assessments can 

include cluster analyses of regions with common ecosystem sensitivities (e.g., lakes and streams 

of the Adirondack Mountains), site-specific quantitative modeling analyses, qualitative analyses, 

and review and summary of previous risk/exposure assessments. From these qualitativequantitative analyses of sensitive areas and case studies in different regions of the U.S., we will 

discern if the results can be used for a broader characterization of national conditions to represent 

key components of our nation’s ecology. To be clear, this exercise is not a national-scale 

ecological risk assessment but, rather, is intended to be a qualitative analysis of multiple 

ecosystems’ quantitative-qualitative risk/exposure assessments. 

The risk/exposure assessment for the Secondary NAAQS for NOx and SOx will build 

upon the scientific information presented in the 2007 draft ISA (U.S. EPA, 2007b). The ISA 

21 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

documents ecological effects of nitrogen and sulfur deposition, biogeochemical indicators of 

effects, and areas of the U.S. where ecosystem effects have been studied. The ISA also 

recommends selected indicators and case studies as candidates for risk/exposure assessment and 

ecosystem services valuation. In this section, we will identify and describe how those 

recommendations can be considered in the assessment in order to provide information for policy 

decision making. 

The risk/exposure assessment will focus on ecosystem welfare effects that result from the 

deposition of total reactive nitrogen and sulfur. The anticipated spatial extent and diversity of 

ecological effects due to deposition of nitrogen and sulfur do not facilitate a nationwide analysis. 

Further, some areas of the United States are more vulnerable to the effects of deposition than 

others. Because of this diversity, we consider it valuable to formulate a strategy that is designed 

to protect sensitive systems, while allowing for flexibility in areas that are more resilient. As a 

result, this assessment intends to evaluate potential alternatives to current indices in an attempt to 

quantify the relationship between ambient concentrations of NOx and SOx and potential welfare 

effects. To create these indices, we plan to evaluate exposures and impacts in various ecosystem 

case studies with differing responses related to nitrogen and sulfur inputs and explore 

relationships between ambient concentrations and deposition of nitrogen and sulfur. 

As previously described, deposition of SOx and NOx compounds affects ecosystems in 

various adverse ways and at different spatial and temporal scales in diverse regions of the 

country. In its review of the analytical plan for the 2nd Prospective Analysis of the Costs and 

Benefits of the Clean Air Act, the Science Advisory Board recommended that EPA consider 

including studies of upland as well as coastal sites, because air deposition is often not the 

primary contributor of nitrogen in coastal sites, while it may be the dominant source in upland 

locations. The Analysis Plan Phase of a risk assessment includes selecting data that will be used, 

analyzing exposure (including spatio-temporal conditions), analyzing effects, and summarizing 

conclusions about exposure. 

In order to address the policy-relevant questions that are guiding the scope of this review, 

this risk/exposure assessment intends to evaluate the relationships between atmospheric 

concentrations, deposition, biologically relevant exposures, ecosystem effects, and ecosystem 

services. 

22 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

To evaluate the nature and magnitude of ecosystem responses associated with adverse 

effects, the risk/exposure assessment plans to examine various ways to quantify the relationship 

between air quality indicators, deposition of biologically accessible forms of nitrogen and sulfur, 

biologically-relevant indices relating to deposition, exposure and effects on sensitive receptors, 

and related impacts to ecosystem change and services. To the extent feasible, the risk/exposure 

assessment should also evaluate the overall load to the system for nitrogen and sulfur as well as 

the variability in ecosystem responses to these pollutants. The assessment intends to determine 

the exposure metrics that incorporate the temporal considerations (i.e., biologically relevant 

timeframes), pathways, and biologically relevant indices necessary to maintain the functioning of 

these ecosystems. In addition, the risk/exposure assessment plans to evaluate the contributions of 

atmospherically deposited nitrogen and sulfur relative to total loadings in the environment. For 

the atmospheric contribution to total nitrogen, we also plan to evaluate the contribution of NOx to 

total reactive nitrogen in the atmosphere relative to the contributions of reduced forms of 

nitrogen (e.g., ammonia, ammonium). 

The scope of the risk/exposure assessment will depend, in part, on the answers to the 

following questions: 

 What are the appropriate geographic scales and/or time frames for the risk assessment? 

Information that will be considered in addressing this question includes mapping datasets, 

research studies of sensitive ecosystems ranging in size from single lakes to stream and 

lake systems within a large geographic region (e.g., the Southern Appalachian 

Mountains), identification of representative ecosystem types, air pollution gradient 

studies, a weight-of-evidence approach incorporating both qualitative and quantitative 

information on risk, or some combination of the above. 

 How can regional variation of effects be taken into account? How should the 

risk/exposure assessment address acidification and nutrient-enrichment effects in 

different areas and ecosystem types (e.g., mesic, arid, mountain forests, alpine, 

subalpine)? 

 To what degree are assumptions supported by the available science regarding linkages 

between pollutants in ambient air, deposition, and measurable ecosystem effects, 

23 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

including effects on ecosystem services? What are the most useful metrics of both 

ambient pollution and the resulting effects? 

 To what degree should the risk/exposure assessment take the potential for recovery into 

account in selecting data for qualitative and quantitative assessments? 

 How can uncertainties be minimized and appropriately characterized? 

Because this risk/exposure assessment intends to focus on two basic secondary effects 

related to sulfur or nitrogen pollutants—acidification and enrichment—and because ecosystems 

may respond differently to these effects, it will be necessary to first perform risk/exposure 

assessment case studies unique to the effect and ecosystem type. We will assess the feasibility to 

consolidate effects and/or ecosystems in the risk/exposure assessment and, where feasible, 

perform a broader characterization. However, some ecosystems and their effects may be too 

unique to consolidate into a broad characterization. 

Upon completion of all risk/exposure assessment case studies, the results of the 

assessments performed for unique combinations of effects and ecosystem types will be presented 

together to facilitate decision making on the total effects of nitrogen and sulfur deposition. 

Ecosystem services that relate to the effects will be identified and valued if possible. Ecosystem 

services provide an additional way to compare effects across various ecosystems. The following 

is an overview of the risk/exposure assessment process, as well as more in-depth discussions on 

topics addressed in the seven steps (see Figure 3-1). 

Steps for Characterizing Ecological Effects 

The seven basic steps guiding the plan for the overall the risk/exposure assessment and 

the assessments for each case study area of interest are shown in Figure 3-1. These seven steps 

capture the components of the risk assessment framework by addressing the selection of effects, 

indicators and ecosystem services measured for exposure via atmospheric deposition of total 

reactive nitrogen and sulfur from ambient air. The initial steps of identifying effects, sensitive 

ecosystems, and potential indicators have been performed and documented in the ISA. In 

addition, the ISA identifies and reviews candidate multimedia models available for fate and 

transport analyses of a variety of ecosystems. The science documented in the ISA will play a key 

role in planning and conducting the risk assessment. It is possible that, for some of the desired 

case study areas, data may not be abundant enough to perform a quantitative assessment for each 

24 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

of the steps; in those cases, we may choose to execute some of these steps in a qualitative or 

semi-quantitative fashion. 

Step 1 Plan for assessment using 

documented effects; biological, 

chemical, and ecological indicators, 

and potential ecosystem services

Step 2 Define sensitive areas that 

exhibit effects using research 

findings and GIS mapping

Step 3 Select risk/exposure case 

study assessment area within a 

sensitive area

Step 4 Evaluate current loads and 

effects to case study assessment 

area including ecosystem services

Step 5 Where feasible, scale up 

case study assessment area findings 

to sensitive areas

Step 6 Assess the current 

ecological conditions for those 

sensitive areas

Step 7 Assess alternative levels of 

protection under different scenarios 

of deposition from ambient sources

Policy Decision

Integrated Science Assessment

Use 2002 CMAQ output to run 

selected multimedia models from 

the integrated Science Assessment

Figure 3-1. Seven step approach to planning and implementing risk/exposure assessment. 

25 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

3.1 Step 1 – Plan for Assessment Using Documented Effects; Biological, 

Chemical, and Ecological Indicators, and Potential Ecosystem Services 

3.1.1 Documented Effects and Relevant Indicators of Effects for Each Ecosystem, 

Including Function and Service 

To assess the impacts of total reactive nitrogen and sulfur loading, we plan to identify 

adverse terrestrial and aquatic effects due nitrogen and sulfur deposition. The impacts of 

acidification, nitrogen-induced eutrophication, and changes in species diversity due to nitrogen 

and/or sulfur saturation are documented in EPA’s 2007 ISA (U.S. EPA, 2007b). We plan to use 

this information to identify those ecosystems and ecosystem services that are considered most 

sensitive to acidification and nitrogen and sulfur enrichment and most informative for potential 

case study analyses in our overall risk/exposure assessment. 

Environmental indicators are measures that track environmental conditions over time. 

EPA’s Report on the Environment (ROE) (U.S. EPA, 2007c) defines an indicator as follows: 

A numerical value derived from actual measurements of a pressure, state or 

ambient condition, exposure, or human health or ecological condition over a 

specified geographic domain, whose trends over time represent or draw attention 

to underlying trends in the condition of the environment. 

Indicators of ecosystem response include chemical, biological, and habitat measurements, such 

as forest extent and type, land cover, lake and stream acidity, nitrogen and phosphorus in 

streams, and contaminates in fish tissue. 

Step 1 entails defining the biological and biogeochemical relevance of indicators for 

acidification and nitrogen and sulfur enrichment in order to select the most appropriate indicators 

for the risk/exposure assessment. The issue of which soil chemical and physical characteristics 

are most appropriate and the spatial variability in these characteristics will be addressed. For 

sulfur, the adsorption/desorption responses in soils may be important. In addition, we plan to 

consider the contribution of any internal sulfur sources (both organic sulfur mineralization and 

inorganic sulfur mineral weathering) to sulfate fluxes in soil, and the resultant differences in 

responses to decreases in sulfur deposition in surface and ground waters. For nitrogen, more 

attention will be focused on what soil features should be tracked; including how organic matter 

affects microbial processes. This characterization will also be linked to the role of vegetation, not 

only with respect to nitrogen cycling, but also in affecting organic matter quality via organic 

26 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

matter inputs to the soil. More detail on this approach to identifying indicators and a preliminary 

list of recommended indicators is provided below. 

Preliminary NOx and SOx Indicators: In the ISA, relevant indicators were divided into 

one or both of the response categories: acidification or nutrient enrichment. Table 3-1 presents 

acidification or nutrient enrichment indicators. 

Table 3-1. Summary of Indicators Categorized by Effect 

Acidification 

Ecosystem 

Type Nutrient Enrichment 

Ecosystem 

Type 

Acid stress index A Carbon budget (growth, carbon 

fixation, and respiration) 

T 

Acid neutralizing capacity A, T Concentration of chlorophyll A, T 

Alkalinity A Concentration of carotenoids T 

Aluminum, mobilization A Nitrogen, concentrations A 

Carbon to Nitrogen ratio T Photosynthetic rate A, T 

Calcium and magnesium 

concentrations 

T Phosphorus concentrations T 

Community structure A, T Species richness A, T 

Condition factor A Taxonomic density A, T 

Dissolved organic carbon A Thallus density T 

Dissolved organic nitrogen A Transpiration rate T 

Exchangeable cations T 

Forest health T 

Index of biotic integrity A, T 

Metal mobilization T 

pH A, T 

Soil-base saturation T 

Species composition A, T 

Taxonomic richness A, T 

A = Aquatic 

T = Terrestrial 

Key Acidification Indicators: Table 3-2 presents key indicators that play a significant 

role in surface water acidification and recovery (summarized from Skjelkvale et al., 2005). 

Specific indicators of acidification are discussed in more detail below. 

27 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

Table 3-2. Key Indicators of Acidification Due to NOx and SOx

Key Indicator 

Group Examples of Indicators Description 

Acid anions SO4

2-, NO3- Trends in these concentrations reflect recent 

trends in atmospheric deposition (especially SO4

2-) 

and in ecosystem responses to long-term 

deposition (notably NO3

-

 and desorbed SO4

2-). 

Base cations Ca2+, Mg2+, Σ(Ca2++Mg2+) These cations are mobilized by weathering 

reactions and cation exchange. These respond 

indirectly to decreases in SO4

2- and NO3- because 

a reduced input of acids will lead to a reduction of 

neutralizing processes in the soil, thereby reducing 

the release of base cations to soil- and runoff 

waters. 

Acidity pH, (Gran) alkalinity, 

ANC 

These indicators reflect the outcomes of 

interactions between changing concentration of 

acid anions and base cations. 

Organic acidity Dissolved organic carbon 

(DOC), total organic 

carbon (TOC) 

Organic acids are common natural sources of 

acidity in surface waters. 

Metals Al, iron (Fe) These metals are mobilized as a response to the 

deposition of SO4

2- and NO3-

. 

Biological Forest health, community 

structure, species 

composition, taxonomic 

richness, Index of Biotic 

integrity 

Ecological effects occur at four levels: individual, 

population, community, and ecosystem. Metrics 

have been developed for each level to assess the 

adverse effects of acids. 

ANC is an acidification indicator with relevance to soils, terrestrial ecosystems, and 

aquatic ecosystems and is a key indicator recommended in the ISA. ANC data are widely 

available for use in a risk/exposure assessment. Other indicators may be used in relation to 

particular ecosystems or specific sensitive areas. Chemical indicators such as pH or cation 

exchange capacity (CEC) are more widely available at the present time than the biological 

indicators.

Key Indicators of Nutrient Enrichment: Major indicators for nutrient enrichment to 

aquatic and terrestrial systems from air deposition of reactive nitrogen involve measurements 

based on available monitoring stations for wet deposition (NADP/national trend network [NTN]) 

and limited networks for dry deposition (CASTNET). Wet-deposition monitoring stations can 

provide more information on an extensive range of nitrogen species than is possible for drydeposition monitoring stations. This creates complications in developing estimates for total 

nitrogen deposition levels because dry-deposition data sources will likely be underestimated. 

Individual studies measuring nitrogen deposition to terrestrial ecosystems that involve 

28 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

throughfall estimates for forested ecosystems can provide better approximations for total 

nitrogen deposition levels, but such estimates and related bioassessment data, are not available 

for the entire country. For terrestrial ecosystems, low calcium to nitrogen ratios in soils are 

commonly related to increased nitrification and potential increases in soil acidity and releases in 

NO3 to receiving waters; however, these measurements are not always widely available. 

For aquatic ecosystems, the indicators for “nutrient enrichment” effects reflect a 

combination of inputs from all media (e.g., air, discharges to water, diffuse runoff, groundwater 

inputs). Major aquatic system indicators involve nutrient loadings (Heinz Center, 2006), 

indicators of excess algal standing crops (U.S. EPA, 2006), or, in larger waterbodies, 

anoxia/hypoxia in bottom waters. (See Table 3-3). For nitrogen, loadings or concentration values 

related to total nitrogen (a combination of nitrates, nitrites, organic nitrogen, and total ammonia) 

are encouraged for inclusion in numeric criteria as part of EPA-approved state water quality 

standards (U.S. EPA, 2000). Given the nature of the major indicators for atmospheric deposition 

and indicators for aquatic and terrestrial ecological systems, a data-fusion approach that 

combines monitoring indicators with modeling inputs and outputs is often used (Howarth, 2007). 

Table 3-3. Key Indicators of Nutrient Enrichment Due to NOx and SOx

Key Indicator Group Examples of Indicators Description 

Nitrogen deposition Nitrate or ammonia From wet or dry deposition monitoring 

stations and networks. 

Nitrogen throughfall 

deposition 

Nitrate, ammonia, organic 

nitrogen 

Special measurements in terrestrial 

ecosystem with corrections for nitrogen 

intercepted by plant canopies. 

Nitrogen loadings and fluxes 

to receiving waters 

Total nitrogen or constituent 

species combined with flow 

data from gauged stations 

Reflects a combination of inputs from all 

media (air, discharges to water, diffuse 

runoff, and groundwater inputs). Relative 

role of air deposition should ideally be 

compared with air deposition data and 

also with available (preferably multimedia) models. 

Other indicators of aquatic 

system nutrient enrichment 

(eutrophication) 

Algal standing crop (plankton 

and periphyton); 

anoxia/hypoxia for estuaries 

and large rivers 

Reflects a combination of inputs from all 

media (air, discharges to water, diffuse 

runoff, and groundwater inputs). Relative 

role of air deposition should ideally be 

compared with air deposition data and 

also with available (preferably multimedia) models. 

29 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

3.1.2 Potential Ecosystem Services 

We plan to identify the primary ecosystem service(s) for each of the effect classes (e.g., 

acidification or enrichment) and for major ecosystem types and components (e.g., terrestrial 

ecosystems, soils, aquatic ecosystems). These services may be characterized as: supporting 

services that are necessary for all other services (for example primary production), provisioning 

services (food, fuelwood), regulating services such as climate regulation or flood control, and 

cultural services including spiritual or religious values, aesthetic values, recreation values among 

others. 

Define Change for Each Ecosystem Service: We intend to characterize the type of 

change, positive or negative, for each ecosystem service. This will be expressed in different 

ways, relative to the type of environmental system. 

Identify the Indicator of Change: We plan to identify indicators for the major types of 

change. These indicators may use chemical/physical properties (e.g., ANC), or they may involve 

biological endpoints (e.g., bioassessment metrics, such as a fish or benthic invertebrate Index of 

Biotic Integrity [IBI]). 

Identify Databases of Indicator Conditions: The indicators selected will relate to 

available compendiums of literature abstracts or actual database systems (as stand alone files or 

accessed through Web portals) to provide readily available and transparent ways to document the 

nature of the indicators and the indicator conditions used to define the environmental 

impairments. 

Identify and Address Temporal Issues: Different ecoregions or biological provinces 

may understandably display differing degrees of susceptibility to impairments or differing 

recovery potential, depending on past land use or pollution histories. Some ecological systems 

may be capable of fairly rapid recovery responses once pollutant loadings are significantly 

abated; other systems, such as larger estuarine aquatic systems, may require much longer 

recovery times. These temporal issues will be documented in the analyses as possible. 

30 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

3.2 Step 2 – Define Sensitive Areas That Exhibit Effects Using Research 

Findings and GIS Mapping 

3.2.1 Defining Sensitive Ecosystems 

Some ecosystems and areas of the United States are more sensitive than others to the 

effects of nitrogen and sulfur deposition (i.e., acidification and nitrogen and sulfur enrichment). 

In the risk/exposure assessment, we plan to begin with those ecosystems and case study areas 

identified in the ISA and consider potential near-field and far-field linkages. 

Identify Biological, Biogeochemical, and Physiographic Linkages in These 

Ecosystems: Linked systems will be identified (e.g., upland terrestrial/aquatic areas linked to 

downstream estuarine system) where possible. Especially for larger watershed or basin-scale 

systems, some components of these study areas (e.g., estuaries linked to inland fluvial drainage 

areas) should show both direct near-field effects from nitrogen or sulfur enrichment as well as 

linked, far-field effects related to loadings from the inland drainage areas (Figure 3-2). 

Figure 3-2. Ecosystem effects may range from near-field to far-field linkages. 

Assess Significance of Linkages: The spatial extent of linkages supports different scales 

of risk assessment. For example, nutrient criteria could serve as the anchor of a broader-scale 

characterization of U.S. aquatic systems. Inland acid-sensitive waters in the eastern United States 

and nitrogen-sensitive ecosystems in the Rocky Mountains and other parts of the western United 

States may support a large-scale, special-area assessment. Ecosystem effects in special areas, 

such as the Adirondack Mountains or Class I areas of the United States may support area-level 

assessments. If the linkages are geographically significant, we plan to evaluate and determine the 

maximum scale of the case study area based on the linkages. The resultant case study area may 

be a common ecosystem, a subbasin, a riverbasin, or an airshed, and may be local, subregional, 

31 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

32 DRAFT – March 2008

or regional in scale. If an area is identified as not having important linkages, then that area may 

be a good candidate for a case study area (e.g., local research of MeHg formation in Devil’s 

Lake, WI). 

Of special interest will be the characterization of linkages that reflect conditions for all 

parts of the country. For instance, national nutrient criteria for rivers and lakes can provide the 

foundation for national-scale characterizations involving nitrogen-enrichment effects for aquatic 

systems related to loadings from air deposition and other nitrogen sources. Available information 

on the nitrogen sensitivity of estuarine systems can further extend the scope of these analyses to 

include estuarine and other near-coastal waters. Information that deals with special case study 

areas (e.g., the Adirondack Mountains or special alpine and subalpine ecosystems in the West) 

that reflect impacts affecting sizeable regions may also be of interest. Figure 3-3 provides 

examples of significant linkages. 

3.2.2 GIS Mapping 

To describe the national picture, we plan to map the locations of those sensitive 

ecosystems identified in Section 3.2.1 and identify the characteristics of the biological and 

biogeochemical properties that create the sensitivity. Identifying the key properties of sensitive 

systems may aid in estimating the sensitivity of currently unmapped areas. Sensitive areas can be 

identified at different spatial scales by using different approaches for defining the boundaries of 

the mapped units. Flexibility in the way sensitive areas are identified will enhance the utility of 

the highest-quality data. Such flexibility also facilitates identifying important ecological services 

or related welfare values of these sensitive natural systems. For instance, primary data 

collections are often made at the spatial level of small plots or stands. Geographic Information 

System (GIS)–based spatial analysis tools may be used to gain more insights from the collection 

of data. Models are often used to supplement direct measurements for larger spatial units, which 

may be reasonably localized catchments or land-cover patches. Integrated systems using 

monitoring, modeling, and interpolation approaches are often applied for larger watershed units 

or physiographical areas related to characteristics of soils, topography, or surficial geology. 

Sensitive areas may be defined by focusing primarily on terrestrial or aquatic system features. 

Examples of datasets and GIS maps that can be used to locate ecosystem types are given in 
Secondary NAAQS Review for Oxides of Nitrog

Figure 3-3. Documented biological, biogeochemical, and physiographic linkages. 

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Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

34 DRAFT – March 2008

Table 3-4. These materials may also be of value in identifying a list of nitrogen- and 

sulfur-sensitive ecosystem services and patterns and trends due to changes in reactive nitrogen 

and sulfur inputs (Section 3.7 describes this step). 

Table 3-4. Example Datasets Planned for GIS Analysis 

Ecosystem 

Type Description 

Effect of 

Interest 

Indicator 

Parameter 

Internet Link or Other 

Resource 

Lakes, rivers, 

estuaries 

Nutrient criteria 

for lakes, rivers, 

and estuaries 

 NE TN for lakes 

and rivers 

www.epa.gov/waterscience/

criteria/nutrient/ecoregions

Lakes, rivers, 

estuaries 

Acid sensitive 

waters of the 

United States 

ACID pH, ANC epamap4.epa.gov/cmap/vie

wer.htm

All National atlas of 

Class I areas 

NE and ACID All www.nationalatlas.gov/mld/f

edlanp.html

All Ecoregions of 

the United 

States 

NE and ACID All nationalatlas.gov/atlasftp.ht

ml#ecoomrp

All Soil 

characterization 

data 

NE and ACID pH, ANC, 

exchangeable 

Ca2+, dissolved 

organic content 

www.ncgc.nrcs.usda.gov/pro

ducts/datasets/statsgo/descr

iption.html 

Lakes, rivers, 

estuaries 

Total nitrogen 

deposition and 

other analytes 

NE NH4

+ epamap4.epa.gov/cmap/vie

wer.htm

Forests and 

grasslands 

U.S. vegetation NE and ACID N and S ivm.cr.usgs.gov/products.ph

p Also available from 

NationalAtlas.gov

Rivers, lakes, 

estuaries 

Surface water 

quality 

Many www.epa.gov/storet

Highelevation–

based lakes 

and rivers 

U.S. elevation 

map 

ACID S ESRI 8.3 data disks 

All Land cover NE and ACID N and S www.mrlc.gov/mrlc2k_nlcd.a

sp

All NADP grid files NE and ACID N and S nadp.sws.uiuc.edu/isopleths/

grids.asp 

Note: NE = nutrient enrichment, ACID = acidification, TN = total nitrogen, S = sulfur, N = nitrogen 

Recommended Mapping Layers and Models: Table 3-5 summarizes the current plan 

for GIS mapping layers and models to be applied in the risk/exposure assessment of targeted 

sensitive ecosystems. This plan is preliminary and will be reassessed as EPA proceeds in 

performing the seven steps for characterizing ecological effects. 
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

35 DRAFT – March 2008

3.3 Step 3 – Select Risk/Exposure Case Study Assessment Area Within a 

Sensitive Area 

We intend to use the sensitive areas identified via Step 2 to select/delineate case study 

assessment areas for the risk/exposure assessment. Where case study or ecosystem-specific data 

are available, a subset of maps for the case study assessment area may be created. 

Complementary to these efforts, we may use a statistical cluster analysis to group ecosystem 

units into similar sets. Clustering ecosystems might reduce the number of locations that need to 

be modeled to adequately characterize the variability in ecosystem response to changes in 

nitrogen and sulfur deposition. 

In selecting areas to assess ecological effects from air deposition, the SAB Ecological 

Effects Subcommittee (EES) suggests consideration of (1) clear quantifiable ecological effects 

due to air pollution, (2) the degree to which a significant component of ecological effects are 

attributable to air pollution, (3) the responsiveness of ecosystem services to changes in air 

pollution,(4) the cumulative impacts of multiple air pollutants, (5) the abundance of ecological 

effects and economic benefit cost analysis, and (6) the visibility to the public and value of 

resources at risk (U.S. EPA, 2005). While these recommendations were made in the context of a 

prospective cost-benefit analysis, many of these recommendations are sound in the context of our 

NAAQS risk analysis. The EES also provided some specific critiques and recommendations of 

specific potential case study assessment areas. We plan to evaluate their comments as part of our 

case study assessment area selection process. Among other points the EES emphasized are as 

follows: 

 “Be cautious in any chosen assessment area when using surrogate sources to quantify 

ecological effects of air pollutants. For example, ‘New’ nitrogen (or mercury) derived 

from air pollutants is generally more bioavailable than ‘old’ nitrogen (or mercury). 

Moreover, ecosystems and associated organisms respond differently to different species 

and sources of nitrogen (and mercury).” (p. 6).
Secondary NAAQS Review for Oxides of Nitrog

Table 3-5. Summary of Indicators, Mapping Layers, and Models for Targeted Ecosystems 

Targeted 

Ecosystem 

Effect Indicator(s) Mapping Layers Model(s) 

Terrestrial Nitrogen Enrichment 

CEC C:N ratios Ca:Al ratios Air wet/dry deposition (corrected for throughfall using available data) 

Forest soils from USFS Forest type from USFS Statsgo soils NLCD CMAQ (N) by HUC 

MAGIC; PnET-BCG 

Aquatic Nitrogen Enrichment and Eutrophication 

Nitrate and ammonia, total nitrogen (major reactive N species) Al toxicity data Chl-a (algal standing crop) anoxia/ hypoxia (primarily estuaries and tidal rivers) N loadings for sub-watersheds or larger basins and Estuarine Drainage Areas (EDAs) EPA NCCR WQ index and NOAA Estuarine-Coastal Eutrophication Index Diatom data for N-limited systems 

STORET retrievals USGS NAWQA information USGS SPARROW information WQS Nutrient Criteria for rivers and lakes EPA NCCR and NOAA estuarine eutrophication indicators NOAA EDAs EPA/NOAA airsheds for major Atlantic and Gulf estuaries CMAQ (N) by HUC 

USGS SPARROW PnET-BCG 

Aquatic Sulfur Enrichment (MeHg Focus) 

MeHg (ambient) MeHg (tissue residues) Sulfur (ambient and sediments) 

Devils Lake, WI, area Limit to review of 

previous research 

ExaLakothMeCofor nor

Terrestrial Acidification Due to Nitrogen and Sulfur 

Soil ANC Soil pH CEC Inorganic Al Ca:Al ratio 

Special areas (e.g., Class I areas, the Adirondack Mountains) CMAQ (N & S) by HUC Forest soils from USFS Statsgo soils USFS lichen USFS forest types 

MAGIC; ILWAS; PnET-BGC 

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Secondary NAAQS Review for Oxides of Nitrog

37 D

Targeted 

Ecosystem 

Effect Indicator(s) Mapping Layers Model(s) 

Aquatic Acidification Due to Nitrogen and Sulfur 

ANC pH Al NO3 and SO4 fluxes or loadings 

Acid-sensitive waters Select Class 1 areas EPA STORET USGS NWIS CMAQ (N & S) by HUC 

MAGIC; PnET-BGC; SPARROW 

Note: CEC = cation exchange capacity, C:N = carbon:nitrogen, Ca:Al = calcium:aluminum, Chl-a = chlorophyll a, NCCR = National Coas

= water quality, NOAA = National Oceanic and Atmospheric Association, S = sulfur, USFS = U.S. Forest Service, NLCD = National Land hydrological unit, STORET = STOrage and RETrieval, USGS = U.S. Geological Survey, NAWQA = National Water Quality Assessment quality standards, NWIS = National Water Information System, ILWAS = Integrated Lake-Watershed Acidification Study. 
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

 “It is important to choose [assessment areas] where atmospheric deposition itself can be 

distinguished from other sources contributing to ecological effects of interest. Thus, 

selection of an [appropriate assessment] area should be based not only on the type of 

ecosystem and its geographical location, but on the sources and types of air pollutants 

that impact it.” (p. 7) 

 “The EES encourages the EPA to consider sites in different regions with different 

resources at risk to help bring attention to the importance of ecosystem valuation.” EPA 

could take advantage of the “opportunity to examine the effects of control of multiple 

pollutants individually and in combination.” (p. 7) 

The EES also provided a summary table listing potential case study areas for examining 

ecological benefits of reducing atmospheric deposition. This table is reproduced in Table 3-6. 

The ISA also recommended case study areas as candidates for risk/exposure assessments 

(Table 3-7). Special emphasis was given to the following: 

 Adirondacks 

 Shenandoah National Park 

 Chesapeake Bay 

 Alpine and subalpine areas of the Rocky Mountains. 

We plan to consider these case study areas and any additional sites identified by the Step 2 

mapping exercise in our selection of risk/exposure assessment areas. Options for selecting case 

study assessment areas include site-specific quantitative modeling analysis, qualitative analysis, 

cluster analysis, and review and summary of previous risk/exposure assessments. It is likely that 

since multiple risk/exposure assessments may be needed depending on the number of effects 

characterized, a combination of assessment methods will be used. 

38 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

Table 3-6. SAB/EES Listing of Potential Assessment Areas for Evaluation 

of Benefits of Reductions in Atmospheric Deposition 

Ecosystem/ 

Region 

Main CAA 

Pollutant(s) 

Percentage(s) 

Attributable to 

Atmospheric 

Deposition 

Quantitative 

Ecological and 

Economic 

Information EES Comments 

Coastal 

Waquoit Bay Nitrogen 30% Yes High priority. Higher loading 

from non-depositional 

sources may confound 

analysis. 

Chesapeake 

Bay 

Nitrogen 20–30% Yes High priority. Loading from 

diverse sources, particularly 

agricultural, may confound 

analysis. 

Long Island 

Sound 

Nitrogen; 

Mercury 

Nitrogen = 23–

35%; Mercury = ? 

Yes High priority. High nitrogen 

loading from wastewater 

treatment plants may 

confound analysis. 

Everglades Mercury 20–85% Ecological = yes; 

Economic = 

uncertain 

Medium priority. Reduction in 

atmospheric deposition has 

already resulted in decreased 

mercury burdens in fish and 

other biota. 

Lake 

Michigan 

Mercury 87% Ecological = yes; 

Economic = lacking 

Medium priority. Lack of 

quantitative economic data 

may restrict analysis. 

Barnegat Bay Nitrogen 50% total 

Direct deposition 

30–39% 

Yes High priority. Direct linkage of 

ecological effects with 

atmospheric deposition; 

quantitative economic data 

exist. 

Tampa Bay Nitrogen; 

Mercury 

Nitrogen = 25–30% Yes Medium priority. Examined in 

previous EPA efforts. 

Variability in loading data may 

confound analysis. 

Gulf of Maine Nitrogen Low ? Low priority. Linkage of 

nitrogen loadings and 

ecological impacts is not well 

established. Major source of 

nitrogen is open-ocean influx. 

Casco Bay Nitrogen; 

Mercury 

Nitrogen = 30–40%

Mercury = 84–92% 

Yes Medium priority. Good data 

on ecological and economic 

impacts are available. 

39 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

40 DRAFT – March 2008

Ecosystem/ 

Region 

Main CAA 

Pollutant(s) 

Percentage(s) 

Attributable to 

Atmospheric 

Deposition 

Quantitative 

Ecological and 

Economic 

Information EES Comments 

Forested 

Adirondacks Nitrogen; 

Sulfur; 

Mercury 

Nearly 100% Yes High priority. Good 

quantitative ecological and 

economic data exist. Previous 

studies can be augmented 

readily. 

Catskills Nitrogen; 

Sulfur 

Nearly 100% Yes Medium priority. Economic 

data may be lacking. Issues 

similar to the Adirondacks. 

Southern 

Appalachian 

Mountains 

Nitrogen; 

Sulfur 

Nearly 100% Yes Medium priority. Economic 

data on fisheries are 

available. Issues similar to the 

Adirondacks. 

Rocky 

Mountains 

Nitrogen Nearly 100% Yes Medium priority. Levels of 

nitrogen loading much lower 

than for northeastern 

locations. Economic data may 

be lacking. 
Secondary NAAQS Review for Oxides of Nitrog

Table 3-7. Potential Assessment Areas Identified in the Draft ISA (U.S. EPA, 2007b) 

Area Indicator 

Detailed 

Indicator Area Studies Models References in EPA, 2

Aquatic Nutrient Enrichment; Terrestrial Nutrient Enrichment; Mercury Methylation 

PIRLA I and II; Adirondack Lakes Survey; Episodic Response Project; EMAP 

MAGIC; PnET-BGC 

Baker and Laflen, 1983; Baker eBaker et al., 1990c; Baker et al., et al., 2003; Chen and Driscoll, 2et al., 1983; Cumming et al., 199al., 1987a; Driscoll et al., 1991; 1998; Driscoll et al., 2001a; Dris2001b; Driscoll et al., 2003b; Dr2003c; Driscoll et al., 2007a; Dri2007b; Evers et al., 2007; GAO, Havens et al., 1993; Ito et al., 20et al., 1994b; Landers et al., 198et al., 2007; NAPAP, 1998; Sieg1989; U.S. EPA, 2003; Sullivan Sullivan et al., 2006a; Sullivan eU.S. Environmental Protection A1995b; Van Sickle et al., 1996; W2002; Wigington et al., 1996; Zh

Adirondacks 

Aquatic Acidification 

ILWAS Gherini et al., 1985 

Shenandoah National Park 

Aquatic Acidification; Terrestrial Nutrient Enrichment 

Shenandoah Watershed Study; Fish in Sensitive Habitats (FISH) study 

MAGIC Baker and Christensen, 1991; B

1990b; Bulger et al., 1999; BulgeCosby et al., 2006; Dennis and BDennis et al., 1995; Deviney et aEshleman and Hyer, 2000; Eshl1995; Eshleman et al., 1998; Ga1983; Hyer et al., 1995; MacAvo1995; Molot et al., 1989; SchofieDriscoll, 1987; Sullivan et al., 20et al., 2007a; Webb et al., 1995 

41 D
Secondary NAAQS Review for Oxides of Nitrog

42 D

Area Indicator 

Detailed 

Indicator Area Studies Models References in EPA, 2

Chesapeake Bay 

Aquatic Nutrient Enrichment; Aquatic Nitrogen Limited Eutrophication 

Bricker et al., 1999; Bricker et al

Boesch et al., 2001; Boyer et al.and Howarth, 2002; Cooper and Fisher and Oppenheimer, 1991; Perry, 1997; Howarth, 2007; Ke1983; Malone, 1991, 1992; Offic1984; Orth and Moore, 1984; Tw1985 

Alpine and Subalpine Communities of the Eastern Slope of the Rocky Mountains in Colorado 

Aquatic Nutrient Enrichment; Terrestrial Nutrient Enrichment 

biomass production; NO3

leaching; species richness 

Baron et al., 1994; Baron et al., 2006; Bowman, 2000; Bowman 1998; Bowman et al., 1993; Bow1995; Bowman et al., 2006; BurFenn et al., 2003a; Fisk et al., 19Ranker, 2001; Rueth et al., 2003and Vaccaro, 2001; Sherrod and 2001; Steltzer and Bowman, 199al., 2006; Williams and TonnessWilliams et al.,1996a; Wolfe et a

Beartooth Mountain, Wyoming 

Aquatic Nutrient Enrichment 

algae composition switch 

Saros et al., 2003 

Fernow Experimental Forest near Parsons, West Virginia 

Terrestrial Nutrient Enrichment 

forest growth Adams et al., 1997, 2000; DeWa

2006; Edwards and Helvey, 199al., 2006; Peterjohn, 1996 

Uinta Mountains of Utah and the Bighorn Mountains of central Wyoming 

Aquatic Acidification 

lake NO3

concentrations 

Western Lakes Survey 

U.S. EPA, 1987 

Pamlico estuary in North Carolina 

Aquatic Nitrogen Limited Eutrophication 

hypoxia; phytoplankton bloom 

Paerl et al., 1998 
Secondary NAAQS Review for Oxides of Nitrog

43 D

Area Indicator 

Detailed 

Indicator Area Studies Models References in EPA, 2

Bear Brook, Maine 

Aquatic Acidification; Terrestrial Nutrient Enrichment 

sugar maple; red spruce 

Elvir et al., 2003 

Harvard Forest 

Terrestrial Nutrient Enrichment 

forest growth— species 

Magill et al., 2004; Magill, 2004 

Southern California 

Terrestrial Nutrient Enrichment 

forest growth—species; coastal sage scrub 

Fenn et al., 1996, 2003a; Takem2001 

Jasper Ridge Biological Preserve in California 

Terrestrial Nutrient Enrichment 

grasslands Zavaleta et al., 2003 

Allegheny Mountains of West Virginia 

Aquatic Acidification 

high streamwater or lake NO3

concentrations 

Gilliam et al., 1996 

Catskill Mountains of New York 

Aquatic Acidification 

high streamwater or lake NO3

concentrations 

Murdoch and Stoddard, 1992; S

Great Smoky Mountains in Tennessee 

Aquatic Acidification 

high streamwater or lake NO3

concentrations 

Cook et al., 1994 

Loch Vale, Colorado 

Terrestrial Nutrient Enrichment 

old-spruce growth 

Rueth et al., 2003 

Terrestrial Nutrient Enrichment 

tundra composition switch 

Rocky Mountain National Park, Colorado Aquatic Nutrient 

Enrichment 

diatom shifts Interlandi and Kilham, 1998 
Secondary NAAQS Review for Oxides of Nitrog

44 D

Area Indicator 

Detailed 

Indicator Area Studies Models References in EPA, 2

Rocky Mountain National Park, Colorado 

Aquatic Acidification 

subalpine lakes MAGIC Sullivan et al., 2005 

Lake Tahoe, California 

Aquatic Nutrient Enrichment 

primary productivity; chlorophyll a 

Goldman, 1988; Jassby et al., 1

Little Rock Lake, Wisconsin 

Aquatic SulfurEnhanced Mercury Methylation 

bioaccumulation of Hg in freshwater fish 

Hrabik and Watras, 2002; Watra1989; Watras et al., 2006 

Southern Appalachians 

Aquatic Acidification 

Streams MAGIC Sullivan et al., 2004 

Hubbard Brook, New Hampshire 

Terrestrial Acidification; Aquatic Acidification 

forest ecosystem; soils; streams 

many studies for decades 

PnET-BGC Gbondo-Tugbawa and Driscoll, 

Gbondo-Tugbawa et al., 2002 
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

3.4 Step 4 – Evaluate Current Loads and Effects to Case Study Assessment 

Area Including Ecosystem Services 

This step involves evaluating the deposition and terrestrial and aquatic fate and transport 

of nitrogen and sulfur, as well as the ecological effects, and their subsequent effect on ecosystem 

services, resulting from exposure to certain levels of nitrogen and sulfur. Depending on the 

adequacy and abundance of data for areas, the evaluation may entail computer modeling, 

statistical analysis, or qualitative analysis. 

3.4.1 Assess Data Availability and Adequacy 

Determine Which Indicators Have Monitoring Data and/or Modeling data Available 

for Analysis: The ISA contains a review of recent (2000 to present) monitoring programs for 

targeted ecosystem effects and associated indicators. We propose to use ANC as the first choice 

of acidification indicators. However, we may consider other indicators if we determine that data 

are insufficient or other factors demonstrate a need to change indicators. Nitrogen and sulfur 

enrichment have both terrestrial and aquatic impacts, making the selection of indicators more 

challenging. Currently, we have narrowed the list of indicators for additional evaluation to the 

following: 

 Wet and dry nitrate and ammonia deposition 

 Nitrate, ammonia, organic nitrogen throughfall deposition for terrestrial ecosystems 

 Total nitrogen or constituent species’ loadings and fluxes to receiving waters from runoff, 

air, discharges, and groundwater inputs 

 Algal standing crops and anoxia/hypoxia for aquatic systems. 

Environmental monitoring data and programs will be used to detect long- and short-term 

effects of nitrogen and sulfur deposition. Therefore, we will consider the conditions of the 

monitoring programs supplying data for this assessment; for example, nationally sponsored, 

long-term studies versus short-term academic research. 

The ISA also reports literature available to assess impacts on ecosystem services that can 

be used to more fully describe the importance of effects on services that are important to the 

public. 

45 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

Evaluate the Adequacy of Spatio-temporal Data and the Statistical Adequacy of 

Available Data: We plan to evaluate the spatial adequacy of available monitoring data 

including GIS mapping of documented data to identify any meaningful spatial gaps. For each 

ecosystem effect, we plan to determine if there is a temporal dimension to exposure. That is, if 

effects “lag” behind exposure at different scales of time, we plan to develop an approach to 

address those time-steps (e.g., measure effects on a daily or annual scale), and we plan to seek 

and assess data available for candidate indicators from both monitoring and modeling data that 

address the temporal dimensions required. 

We intend to review and determine the best indicators for acidification and nitrogen and 

sulfur enrichment for each targeted ecosystem effect. To accomplish this, we plan to identify 

spatial and temporal gaps, document uncertainties and limitations raised in the research 

literature, and raise any additional points about uncertainty identifiable through either statistical 

analysis or qualitative evaluation (depending on the form of information available). 

Resolve Gaps and Disadvantages (e.g., integrate datasets and/or models; 

interpolate): The location and type of ecosystem effects resulting from nitrogen and sulfur 

deposition do not lend themselves to a traditional large-scale risk/exposure assessment. This is 

due to both the isolated or regional effects observed and the potential lag in time for observed 

effects. Therefore, it will likely be necessary to resolve spatial and temporal gaps in data needed 

to perform a risk/exposure assessment. We propose to resolve gaps through a combination of 

integrating datasets, modeling, and interpolation/extrapolation. We plan to use CMAQ output 

data at 12 km grids for regions of interest, and an appropriate multimedia model to address 

spatial data needs for terrestrial and aquatic exposure assessments for the targeted ecosystem 

effect. Additional information on CMAQ and multimedia models is presented in Appendices C 

and D, respectively. 

3.4.2 Compute Loading and Exposure for Each Ecosystem Effect: 

We plan to use current data and models to analyze reactive nitrogen and sulfur loads and 

exposures. Major categories of loading data include the following: 

 Atmospheric deposition across the landscape (available from CMAQ modeling for 2002 

for 8-digit hydrological units [HUCs] and a 12-km grid) (Figure 3-4 presents past 

46 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

applications of CMAQ modeling to support the evaluation of National Acid Precipitation 

Assessment Program [NAPAP]–monitored acidification effects in the United States.) 

 Atmospheric deposition monitoring data (National Atmospheric Deposition Program 

[NADP] and Clean Air Status and Trends Network [CASTNET]) 

 National Pollutant Discharge Elimination System (NPDES) point source discharge data 

 Agricultural runoff modeling 

 Urban non-point source runoff modeling 

 Other urban or rural loading sources (e.g., onsite septic system modeling). 

Figure 3-4. Comparison of NAPAP-documented acid-sensitive ecoregions 

to CMAQ-modeled nitrogen deposition. 

CMAQ Deposition Modeling: It is necessary to understand the role of receptor surfaces 

(i.e., land use/land cover) influencing atmospheric deposition. Receptor surfaces affect the dry 

deposition of gases and particles. Dry deposition can contribute significantly to total deposition 

(in many locations and for many chemical species >50% of total deposition). CMAQ modeling 

should account for the role of deposition due to both atmospheric conditions and land cover. We 

plan to use land cover datasets, such as the National Atlas, to support our analysis of the role of 

land cover in targeted ecosystem effects. Appendix C provides a more extensive description of 

CMAQ modeling plans for this risk/exposure assessment. 

Multimedia Modeling: The ISA (U.S. EPA, 2007e) provides a survey of multimedia 

models, and a summary of the ISA review is in Appendix D. The recommended models for the 

risk/exposure assessment are presented here. The two distinct environmental effects of nitrogen 

and sulfur deposition for which indicators can be defined and models identified based on past 

47 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

48 DRAFT – March 2008

applications, geographic applicability, and use of atmospheric inputs are acidification and 

nitrogen and sulfur enrichment. 

To provide more detail for the models, those that readily accept atmospheric deposition 

inputs of the same nature as CMAQ output (flux in mass per area per time) are presented in bold. 

Those that accept atmospheric concentration data (mass per volume) are presented in italics. 

Although these classifications note whether a model accepts atmospheric deposition input, they 

do not specify whether temporal and spatial resolutions will match between the atmospheric and 

ecosystem models. 

Acidification 

As explained in Appendix A, acidification is an environmental effect in which acid 

precipitation lowers the natural pH of waterbodies and/or damages terrestrial ecosystems. The 

key indicators of acidification likely to be considered in any modeling efforts to determine the 

effects of acidification on an ecosystem include both chemical measurements and 

ecological/biological indices and factors. The biological indicators of acidification can be found 

in both terrestrial and aquatic systems; however, models are much less developed for simulating 

or estimating measures of the biological indicators on land. The chemical indicators of acidity 

are much more likely to be included in a model. 

Both MAGIC and WARMF1

 account for several of the chemical indicators of 

acidification for both terrestrial and aquatic systems. Either of these models could be used for an 

acidification analysis, although WARMF contains a more robust analysis with higher-level 

processes, including biological processes, and a GUI. 

The ILWAS and WARMS models both provide for acidification indicators but have 

limited applications outside of their development areas of Illinois and Ontario, respectively. 

ILWAS is a highly parameterized model. 

The TMDB/IBIS model does not include the minerals as its state variables but does 

simulate nitrogen and carbon, as well as vegetation, which could be considered a measure of 

forest health. This model can be used on a global scale. 

 

1

 WARMF currently accepts atmospheric deposition in concentration form; however, EPRI and Systech 

Engineering, Inc., the developers of WARMF, have recently undertaken a project to modify WARMF to accept 

depositional fluxes such as those output by CMAQ. 
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

49 DRAFT – March 2008

Several of the terrestrial/watershed models could be used to provide input loads to a 

receiving-water model for acidification studies. The choice of model would depend on the timestep needed and the geographic location of analysis. Applicable terrestrial/watershed models 

include PnET-BGC, DayCent, Century 4/5, NuCM, and SAFE. 

Our current intention is to run MAGIC for a case study area to look at changes in ANC. 

The other models may be considered if further analysis would prove useful. 

Nitrogen Enrichment 

Indicators of nitrogen enrichment are addressed in detail in Section 3.1.1. Atmospheric 

deposition has been shown to increase nitrogen enrichment in Atlantic Coast estuaries and is now 

of concern in high-altitude, alpine lakes. Because the key indicators for nitrogen enrichment 

depend on measurements of nitrogen, there are many models available to estimate the ecosystem 

effects, but special attention should be paid to how these models simulate the nitrogen cycle and 

whether biological processes, which are vital to the cycle, are included. Nitrogen, either total or 

speciated, is probably the most highly modeled chemical parameter in ecosystems. Both 

receiving-water and terrestrial/watershed models may be used in these analyses. Additionally, it 

is possible to use a combination of models so that a watershed model provides input loadings to 

the receiving water model. 

The following receiving-water models all estimate speciated nitrogen (e.g., ammonia, 

nitrate, organic, or total) and can be used in most geographic locations: AQUATOX, QUAL2K, 

WASP, and the CE-QUAL family of models. 

The THMB/IBIS model simulates the nitrogen cycle, but has limited geographic 

applicability for small sites. It is more applicable for large-scale simulations. 

HSPF, SWAT2

, and WARMF simulate the nitrogen cycle across land and water; 

however, SWAT contains a more simplified approach to the nitrogen cycle in reservoirs and 

lakes. HSPF accepts the atmospheric flux of nitrogen that is output by CMAQ. While SWAT 

currently only considers a state nitrate concentration in wet deposition, WARMF currently 

 

2

 SWAT currently accepts only a static input nitrate concentration in precipitation. An untested concept to utilize 

SWAT’s fertilizer management function to simulate atmospheric deposition may provide a work-around function. 
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

accepts atmospheric concentrations of NOx, ammonia, and nitrate in both wet and dry 

atmospheric conditions. 

Nitrogen enrichment, more than acidification, may be measured across the terrestrial 

landscape, in addition to waterbodies. Many of the terrestrial/watershed models may be used for 

nitrogen enrichment analyses, with the choice depending on time-step, geographic location, 

nitrogen species desired, and simulation of the nitrogen cycle within the model. For daily 

simulations, possible models include: DayCent, DNDC, DRAINMOD-N II, EPIC/APEX, 

GLEAMS, INCA, RHESSys, and GT/MEL. For longer-term simulations (monthly, annual), the 

following models may be used: Century, MAGIC, MERLIN, PnET-BGC, ReNuMa, and 

SPARROW. 

Approach for Selecting Geographic Regions to Model: Selection of geographic 

regions of the United States to model will depend on a number of factors: 

 Observed data that are indicative of the ecosystem and response of interest or observed 

characteristics of an ecosystem that implies it has the potential to respond 

 Availability of a model capable of analyzing the region of interest 

 Availability of model input data for the region. 

It may be possible to explore adapting an existing model to an untested geographic area 

or using synthetic or surrogate data if there is a geographic region of particular interest with 

insufficient model input data. In contrast, if there are multiple geographic regions suitable for 

modeling, we intend to examine the feasibility of clustering the regions, increasing the scale of 

the modeling to capture the regions, or selecting the one region with the best potential to provide 

valid and representative data on ecosystem response. 

Assess Uncertainty in Loading and Exposure Computations: The risk/exposure 

assessment will need to account for the fact that current runoff models vary in resolution. Runoff 

and other fate and transport models should be selected to adequately address the differing 

complexities of the identified sensitive ecosystems. To the extent possible, the analyses should 

try to include all reactive nitrogen species, recognizing that inventories may need improving. 

Most likely, the assessments will initially be a snapshot of the loadings and exposures with more 

dynamic assessments to follow in future reviews. Where possible, the focus will be to develop 

50 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

the best available numeric measures of the loading contribution from all major sources, so that 

the contributions from air deposition sources can be analyzed relative to all other major 

anthropogenic or natural sources for sensitive ecosystems across the country. 

3.5 Step 5 – Where Feasible, Scale-Up Case Study Assessment Area Findings 

to Sensitive Areas 

Several approaches can be applied to take the results of analyses for specific case study 

assessment areas and relate these findings to more spatially extensive sensitive areas. For 

instance, analyses using MAGIC taking advantage of good quality Temporally Integrated 

Monitoring of Ecosystems (TIME) and Long-Term Monitoring (LTM) data sets may be scaled 

up to several extensive ecological and physiological provinces such as the Adirondacks, the 

Appalachian Plateau (primarily in Pennsylvania), and the Ridge & Blue Ridge Provinces (largely 

in the Shenandoah National Park and along the Shenandoah Parkway). Where the TIME/LTM 

datasets have previously been applied to define the extent of sensitive areas, scaling up the new 

analyses to the same previously used larger sensitive areas may be readily justified. Where the 

case study assessment areas are defined using clusters of sampling sites, more sophisticated GISbased spatial interpolation techniques may be applied where the case study assessment area sites 

are related to bounding polygons reflecting standard ecoregion delineation systems (e.g., the 

EPA Omernik Level II ecoregions or the aggregated Omernik ecoregions developed for EPA 

criteria for numeric nutrient criteria for lakes and streams). Statistical cluster analysis techniques 

may be applied to provide a means for objectively grouping localized case study assessment 

areas into larger sensitive areas. For larger case study assessment areas such as the Chesapeake 

Bay system, available national indicator products such as the USGS SPARROW models for 

HUC8 (sub-basin) watersheds, or EPA and NOAA estuary eutrophication indicators may be 

considered as tools to document similarities and differences for major estuarine and near coastal 

aquatic systems, taking into account the relative importance of atmospheric deposition of 

pollutants such as nitrogen to sources within estuarine drainage areas related to point source, 

urban, or rural nutrient loadings. 

A qualitative or semi-quantitative characterization of these larger sensitive areas may be 

developed, depending on data availability and time constraints. Where feasible, we plan to also 

discuss the effect on related ecosystem services of these sensitive areas. 

51 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

3.6 Step 6 – Assess the Current Ecological Conditions for Those Sensitive 

Areas 

3.6.1 Calculate Response Curves for Each Indicator 

If feasible, we intend to generate indicator response curves from the multimedia model 

runs. The response curves can supply useful information about the degree of impairment and 

sensitivity of the system. 

3.6.2 Calculate Desired Exposure Endpoint 

Once the sensitive ecosystems response curves are generated, it may be possible to 

calculate a desired exposure endpoint. This requires similar information and steps required for a 

critical load analysis. Critical load analyses may be considered, where appropriate, in identifying 

ways to select endpoints in terms of ecosystem responses relative to atmospheric levels 

(concentrations or loadings) of nitrogen and sulfur. A detailed description of critical loads and its 

use as an analysis tool are presented in the ISA (U.S. EPA, 2007b). 

3.6.3 Develop GIS Maps and Overlay Loading and Indicators That Are Representative of 

Harmful Effects 

For each targeted ecosystem effect, we plan to create GIS maps from the modeling and 

monitoring data generated/compiled for selected indicators. Then, a second data layer can be 

created to represent the level of exposure at which harmful effects based on the indicator, and 

these data layers can be combined to facilitate mapping. 

3.6.4 Using GIS Mapping, Compute the Extent That Loading Is Greater Than or Less 

Than the Harmful Effect Level (a.k.a. endpoint) 

We plan to use GIS to compute the difference in exposure relative to the response-based 

harmful effect level. We recognize that the loading and exposure may be less than or greater than 

the findings of the exposure response research. Based on our findings, we plan to determine if a 

particular geographic region requires additional analysis or if we are able to proceed to Step 7. 

3.6.5 Assess Ecosystem Responses via Ecosystem Services and Valuation 

One component of an integrated assessment of risks to the public welfare involves 

determining what level of ecosystem response translates into an effect that could reasonably be 

considered adverse to the public welfare. There are a number of ways to do this, including the 

following: 

52 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

 Direct measures of quantities that are of known value to the public (e.g., numbers of 

endangered species) 

 Translation of ecosystem attributes into measures of ecosystem services, which can then 

be quantified 

 Direct economic valuation of ecosystem functions and services, including use and nonuse 

values (values that do not require an individual’s direct use of an ecosystem—for 

example, the value of preserving an endangered species habitat, even though that 

individual will ever see that species in the wild) 

 Direct nonmonetary valuation of ecosystem functions based on enumeration of 

preferences using nonmonetized indices of preferences. 

The specific methods used to evaluate adversity will depend on the availability of data 

and methods for the indicators of interest related to acidification and nutrient enrichment and on 

an assessment of the appropriateness of each type of quantification in comparing different levels 

and forms of the standards. In our initial assessment of the available data, given the timeframe 

for this NAAQS review, we have determined that the most useful approaches will be those 

focusing on quantifying the link between changes in ecosystem indicators and ecosystem 

services. Linking these changes in ecosystem services to changes in economic values will likely 

be beyond the scope of the current assessment. A brief discussion is provided in Appendix E on 

how valuation approaches might be used to combine and/or compare changes across ecosystem 

services. 

The EPA SAB Committee on Valuing the Protection of Ecological Systems and Services 

(SAB CVPESS) has recently drafted major recommendations for improving ecological benefits 

assessment to facilitate consideration of ecosystem benefits in the decision-making process. This 

SAB panel recommends taking “a more comprehensive approach to assessing, valuing, and 

reporting on the ecological benefits of its actions” (SAB CVPESS, 2007). The conceptual model 

described in Figure 2-5 that links atmospheric concentrations and deposition to ecosystem 

effects and biologically relevant indicators, and tying these to ecosystem services and valuation 

is supported by the SAB panel. One of the critical gaps identified by the SAB panel is 

“identifying how the biophysical effects of an action on an ecosystem will in turn impact the 

ecosystem services of importance to the public” (SAB CVPESS, 2007). 

53 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

In broad terms, the most important information gap in this review is an incomplete 

understanding of how hydrological and biogeochemical processes (e.g., cycling of H2O, N, C, P) 

interact to control the response of ecosystem services to NOx and SOx and other forcing variables 

(e.g., climate). A major consequence of these interactions is that ecosystem services tend to be 

linked or “bundled,” so that actions taken to improve one may result in an improvement or 

deterioration of other services. Thus, when ecosystem services are quantified and their ecological 

response functions to NOx and SOx are modeled, it is imperative that the entire bundle of 

services be evaluated, and that the linkages and tradeoffs among ecosystem services be included 

in the quantification (i.e., ecological tradeoff functions [ETFs]). The key feature distinguishing 

the services from the underlying ecosystem function or processes is the explicit involvement of 

beneficiaries, so consideration of which ecosystem services to target in assessment activities 

involves consideration of the relative demand for the service, its spatial distribution, and its 

magnitude. 

Ecological Response Functions (ERFs) and Ecological Tradeoff Functions (ETFs) can be 

developed to quantify the response of a service to changes in NOx/SOx concentrations and the 

tradeoffs between different services given these ambient air quality drivers. Many of the services 

of importance in assessing risk of NOx and SOx have not been quantified (i.e., developed ERFs 

and ETFs) or adequately scaled for a comprehensive evaluation of the benefits of these services. 

Such research is being planned, and will, no doubt, contribute to future NOx/SOx assessments. 

Therefore, at this time, data mining will be central to developing at least a preliminary 

assessment of potential impacts of NOx/SOx deposition and acidity on ecosystem services. In the 

current plan, process-based models are being considered to be used to (1) synthesize/link the 

suite of ERFs and ETFs and (2) generate maps and summaries of ecosystem services and 

tradeoffs in response to current and future ambient air indicators for NOx and SOx. The collection 

of response and tradeoff functions will aid in the valuation of the services at risk to these criteria 

pollutants where possible. 

A risk/exposure assessment approach using the most relevant and best available data on 

deposition, acidity, and measured effects will benefit from spatial and temporal mapping. In 

preparation for the NOx/SOx risk/exposure assessment, a suggested series of mapping exercises 

would proceed in the following order: 

54 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

1. Identify areas/regions of the country receiving high levels of NOx/SOx deposition and 

acidity impacts. 

2. In those regions, identify ecosystems sensitive to elevated levels of nitrogen and 

sulfur, using some common selection criteria. 

3. In those sensitive ecosystems, ask what ecosystem services are expected to be 

prevalent and “valued” (i.e., some subset of all potential services). 

4. In those areas, identify what data are available to develop ERFs and ETFs, at least to 

a qualitative degree that would enable production of spatial and temporal maps to 

identify different degrees of protection that would exist under alternative secondary 

NAAQS. Chan et al., (2006) produced such maps for several ecosystem services in 

the Central Coast ecoregion of California. The linkage and comparison of multiple 

ecosystem services in the region would provide information for consideration of 

tradeoff value of one service versus another. 

Both economic and biophysical valuation can be considered in determining adverse 

effects and can be used in determining benefits of protection. As noted above, valuation is a 

useful way to compare disparate ecosystem impacts, and it is a potentially important component 

in the risk characterization phase of the risk assessment. As a result, an additional step in the 

above process is to identify potentially relevant economic valuation studies for ecosystem 

services and map the location of these studies relative to the available data on ecosystem 

services. Note that while we are considering all potential methods for obtaining ecosystem 

valuation estimates, the current focus of this plan is to use literature-based estimates of 

ecosystem service values previously identified in the ISA that can be applied in a valuation 

transfer approach. Realization of concepts like the conjoint analysis approach would require time 

and resources, which are not available for the current analysis, but which should be considered 

for future reviews. 

3.7 Step 7 – Assess Alternative Levels of Protection Under Different Scenarios 

of Deposition From Ambient Sources 

A secondary NAAQS standard, while national in scope, might have a form that allows for 

consideration of regional heterogeneity in ecosystem sensitivity and heterogeneity in 

55 DRAFT – March 2008
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56 DRAFT – March 2008

atmospheric composition of nitrogen and sulfur deposition either alone or combined. Such a 

form should be designed to provide for the adequate protection of sensitive ecosystems and to 

allow flexibility for those ecosystems with more ecological resilience. Assessing alternative 

levels of protection with different loadings scenarios under different forms of the standards will 

be an important step in this process. 

We intend the risk/exposure assessment to characterize exposure and ecological effects 

associated with current levels of nitrogen and sulfur deposition as described in this Scope and 

Methods Plan. However, the NAAQS are based on ambient concentrations of NOx and SOx in 

the atmosphere, and, therefore, additional analyses are required to move from deposition-based 

risk estimates to policy-relevant ambient indicators. The policy assessment will build upon the 

current conditions risk/exposure assessment to develop these policy-relevant ambient indicators 

(Figure 3-5). This requires synthesizing the ecosystem responses, biological indicators, and 

ecosystem effects related to deposition loadings and translating those loadings back to their 

corresponding ambient air conditions. 

Figure 3-5. Risk/policy assessment paradigm for deposition-related ecological risks. 

RISK/EXPOSURE ASSESSMENT

POLICY ASSESSMENT
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

After the current conditions risk/exposure assessment develops an understanding of 

baseline conditions, it will be necessary to define the amounts of risk under varying levels and 

forms of the standards. The risk/exposure assessment intends to establish whether current levels 

are causing effects, which ecosystems are most sensitive to those effects, and the magnitude of 

the risks existing at current levels. After this baseline is established, modeling techniques can be 

used to change the ambient level and examine how the corresponding exposures and risks 

change.In this way, dose-response curves can be generated that establish the range of impacts 

and effects associated with nitrogen and sulfur inputs. For example, suppose at a particular level 

of loading (X), a negative effect is observed (Y). This analysis can be used to establish what X is 

equivalent to in terms of ambient concentrations, so that Y can be reduced or avoided. Several 

iterations of this process may be needed to examine different forms and levels of the standard(s) 

and determine if the form(s) of the standard(s) has an impact on the risk associated with that 

form.

Some of the issues associated with this type of analysis include: 

 What adverse effects are we trying to protect against? 

 If total nitrogen is the relevant biological indicator, what is the relative contribution of 

oxidized versus reduced forms of nitrogen, and what is the ambient contribution 

compared to other sources? 

 Do these effects occur due to different ambient levels and/or forms of nitrogen and 

sulfur? 

 How should alternative levels be selected (i.e., via a dose response curve, based on 

threshold events, or is another method more appropriate)? 

 What are the correct temporal and spatial scales for the level of the ambient air indicator 

and how do they relate to the temporal and spatial scales of the deposition indicator? 

 What are the associated uncertainties? 

In determining the appropriate level and form of a standard, we plan to evaluate 

alternative levels and forms of the standard and evaluate the ecological risks associated with 

those levels and forms. Due to limits in data, modeling, and time, we are not able to conduct a 

national assessment. Instead, we plan to extend the assessment area analysis approach used in the 

57 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

current conditions analysis. Our initial thoughts on evaluating the appropriate level and form of 

the standard using the assessment area analyses approach include the following: 

1. Identify the relative contribution of loadings associated with atmospheric deposition 

of nitrogen and sulfur. 

2. Identify the most critical impacts from nitrogen and/or sulfur loadings (i.e., 

acidification, nutrient enrichment, or eutrophication). 

3. Identify the contribution to atmospheric loadings from total reactive nitrogen, NOx, 

and SOx.

4. Identify the biogeochemical indicators/resources of concern in the assessment area 

and the ecosystem services associated with those indicators. 

a. Determine the ecosystem service effects associated with the most-critical impacts. 

b. Bundle ecosystem services to find common metrics for comparison across 

locations. 

5. Define the exposure-response (loading-response) functions (ERFs) for the ecological 

indicators of concern. 

6. Estimate the loadings/exposures associated with current and alternative levels of the 

NOx and SOx standards (using CMAQ modeling). 

a. Analyze the relationships between NOx, SOx, and other reactive forms of 

nitrogen. 

b. Assess the impacts of meteorological variability on these relationships. 

7. Estimate the ecosystem impacts associated with estimated loadings. 

8. Convert estimates of individual ecosystem risks to common units using 

a. economic valuation based on benefits transfer from existing literature estimates 

b. biogeochemical equivalents using ecological tradeoff functions (ETFs). 

9. Combine individual risk estimates to produce overall impact estimates. 

Results from individual assessments can be evaluated relative to the national maps of ecosystem 

types and sensitivities. This analysis may characterize how well the assessment areas represent 

58 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

overall national ecosystem types and sensitivities, and how similar impacts of alternative 

standards might be across ecosystems throughout the country. The output of the quantitative 

assessment and the science assessment feed the policy assessment, so that it can examine a range 

of alternative standards applicable for the agency to consider. The following are questions to 

address in identifying specific elements of standards: 

 How do alternative levels and forms of the standards relate to a given exposure metric? 

 What are the appropriate averaging times for alternative levels and forms of the 

standards? 

 What alternative levels of the standards should be considered? 

 Should there be alternative levels of the standards (i.e., individual NOx and SOx standards 

or a combined NOx/SOx standard)? 

 Do the ambient air indicator forms allow for site-specific protection while maintaining 

national consistency? 

 Does the ambient air indicator adequately account for the effects of total reactive 

nitrogen? 

 Does the form of the standard have an impact on the risk? 

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Available at http://www.epa.gov/ttn/naaqs/standards/no2so2sec/index.html. 

U.S. EPA (Environmental Protection Agency). 2007b. Preliminary Draft Excerpts of the 

Integrated Science Assessment for the NOx and SOx Secondary Draft document. 

Presented at the PM Secondary NAAQS Kickoff Meeting and NOx/SOx Secondary 

NAAQS Workshop, Chapel Hill, NC, sponsored by the U.S. Environmental Protection 

Agency, July 16–19. 

U.S. EPA (Environmental Protection Agency). 2007c. EPA’s Report on the Environment, SAB 

Review Draft. Office of Research and Development, Washington, DC. EPA 841-B-06-

002. December. 

U.S. EPA (Environmental Protection Agency). 2007d. The U.S. Inventory of Greenhouse Gas 

Emissions and Sinks: Fast Facts. Office of Atmospheric Programs. EPA 430-F-07-004. 

April. 

U.S. EPA (Environmental Protection Agency). 2007e. Integrated Science Assessment for Oxides 

of Nitrogen and Sulfur Environmental Criteria. Office of Research and Development, 

Research Triangle Park, NC. EPA/600/R-07/145A, December. 

61 DRAFT – March 2008
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62 DRAFT – March 2008

U.S. EPA (Environmental Protection Agency). 2006. Wadeable Streams Assessment. Office of 

Research and Development, Washington, DC. EPA/600/R-07/045. May. 

U.S. EPA (Environmental Protection Agency). 2005. EPA-COUNCIL-ADV-05-001 Advisory on 

Plans for Ecological Effects Analysis in the Analytical Plan for EPA’s Second 

Prospective Analysis—Benefits and Costs of the Clean Air Act, 1990–2020. June 23. 

U.S. EPA (Environmental Protection Agency). 2003. Response of Surface Water Chemistry to 

the Clean Air Act Amendments of 1990. U.S. EPA Office of Research and Development, 

National Health and Environmental Effects Research Laboratory, Research Triangle 

Park, NC. EPA/620/R-03/001. 

U.S. EPA (Environmental Protection Agency). 2000. Nutrient Criteria Technical Guidance 

Manual: Rivers and Streams. Office of Water, Washington, DC. EPA-822-B-00-002. 

July. 

U.S. EPA (Environmental Protection Agency). 1998. Guidelines for Ecological Risk Assessment. 

Risk Assessment Forum. EPA/630/R-95/002F. April. 

U.S. EPA (Environmental Protection Agency). 1995. Review of the National Ambient Air Quality 

Standards for Nitrogen Dioxide: Assessment of Scientific and Technical Information. 

OAQPS Staff Paper. EPA-452/R-95-005. September. 

U.S. EPA (Environmental Protection Agency). 1994. Review of the National Ambient Air Quality 

Standards for Sulfur Oxides: Assessment of Scientific and Technical Information. 

Supplement to the 1986 OAQPS Staff Paper Addendum. EPA 452/R-94-013. September. 

U.S. EPA (Environmental Protection Agency). 1992a. Framework for Ecological Risk 

Assessment. Risk Assessment Forum. EPA/630/R-92/001. February. 

U.S. EPA (Environmental Protection Agency). 1992b. Report on the Ecological Risk Assessment 

Guidelines Strategic Planning Workshop. Risk Assessment Forum. EPA/630/R-92/002. 

February. 

U.S. EPA (Environmental Protection Agency). 1991. Summary Report on Issues in Ecological 

Risk Assessment. Risk Assessment Forum. EPA/625/3-91/018. February. 

U.S. EPA (Environmental Protection Agency). 1986. Review of the National Ambient Air 

Quality Standards for Sulfur Oxides: Updated Assessment of Scientific and Technical 

Information. Addendum to the 1982 OAQPS Staff Paper. EPA 450/05/86-013. 

December. 

U.S. EPA (Environmental Protection Agency). 1982. Review of the National Ambient Air Quality 

Standards for Sulfur Dioxide: Assessment of Scientific and Technical Information. 

OAQPS Staff Paper. EPA-450/5-82-007. November. 

U.S. EPA (Environmental Protection Agency). 1971. Air Quality Criteria for Nitrogen Oxides. 

Air Pollution Control Office. No. AP-84. January. 
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

APPENDIX A 

IDENTIFICATION OF SENSITIVE ECOSYSTEMS 

A.1 Targeted Ecosystem Effects 

One of the central issues in this secondary NAAQS review is determining which 

ecosystems are sensitive to nitrogen and sulfur deposition and their degree of sensitivity 

compared to one another. Characteristics to determine sensitivity may include, but are not 

limited to, (1) potential nitrogen and sulfur retention rates; (2) potential nitrogen and sulfur 

uptake rates, which might include vegetative uptake, potential denitrification, and potential 

mobilization of nitrogen and sulfur; (3) potential residence time based on local hydrology 

(precipitation rates, conductivity) and geology (bedrock type, pervious surfaces, soil properties); 

and (4) total supply of nitrogen and sulfur, including current and historical atmospheric 

deposition and other nonatmospheric sources (e.g., applied fertilizers, sewer leaks, point 

sources). Other ecosystem-specific characteristics that may help assess sensitivities include 

threatened and endangered species data where available, land cover, land-use type (including 

Class I, National Park, and Fish and Wildlife Refuges and National Wilderness areas), species of 

community shifts (or invasive species), and baseline nitrogen and sulfur loading estimates. 

Where ecosystem-specific data are available, a subset of maps for the study region may be 

created. Complementary to these efforts, we may use statistical cluster analysis to group 

ecosystem units into similar sets. By clustering ecosystems, we might reduce the number of 

locations that need to be modeled to adequately characterize the variability in ecosystem 

response to changes in nitrogen and sulfur deposition. 

These types of analyses may aid in determining whether area-based risk/exposure 

assessments are appropriate for looking at nitrogen and sulfur effects on various ecosystems and 

geographic regions as a means of extrapolating these impacts to characterize the entire country. 

For those areas where data are available, watershed models (e.g., MAGIC, PnET-BGC, 

DayCent-chem) may be useful for evaluating the emission-deposition-ecosystem response 

linkage. 

These are the main questions the risk/exposure assessment will address: 

 If we can identify appropriate biologically relevant indicators, can we establish a link 

between deposition of NOx (and/or reactive nitrogen), SOx, and ecosystem response? 

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 What ecosystem services are associated with changes in emissions? 

Ecosystem response to nitrogen and sulfur deposition varies across the landscape, 

depending on the local physical, chemical, and biological characteristics. Atmospheric 

deposition effects range from species alterations (due to nutrient enrichment) to anthropogenic 

eutrophication of estuaries to acidification of forests, lakes, and streams. This Scope and 

Methods Plan focuses on five ecosystem effects on terrestrial and aquatic systems. 

A.1.1 Terrestrial Nitrogen Enrichment 

Deposited nitrogen compounds can act as a fertilizer to increase the productivity of plants 

and algae. However, too much nitrogen can lead to a surplus of nutrients, resulting in overnutrient enrichment. Table A-1 presents examples of nitrogen enrichment effects, which can 

impact species diversity by favoring nitrogen-tolerant species over other species that are more 

sensitive to nitrogen limits. Certain ecosystems may be dominated by species that have a 

competitive advantage in low nitrogen environments. When nitrogen increases, species that are 

normally kept in check by low nitrogen levels flourish and out-compete the other species in the 

community; thereby, potentially altering species’ composition and diversity, nutrient cycling, 

and other ecosystem properties and functions. New plants may also move into ecosystems that 

are enriched in nitrogen, further challenging the native species. Animals that depend on specific 

plants for habitat and food may then be threatened by the changes to the plant communities that 

result from nitrogen inputs. 

Table A-1. Examples of Nitrogen Enrichment Effects 

Nitrogen Load 

(kg N ha-1• yr-1) Nitrogen Enrichment Effects 

>1.5 Altered algal communities in high-elevation freshwater lakes. (Colorado) 

Elevated N in tree leaf tissue high-elevation forests. (Colorado) 

3 to 8 Mortality of sensitive lichen species. (West Coast) 

5 to 35 A transect of 68 acid grasslands; species richness declines as a linear function of 

the rate of inorganic nitrogen deposition, with a reduction of one species per 4-m2

quadrat for every 2.5kg N-1 yr-1. (United Kingdom) 

7 Community-level shifts in ombrotrophic bogs. (North Central and Eastern United 

States) 

<8 to 10 N retained or denitrified (i.e., limited leaching). (many U.S. forests) 

10 to 15 Change in plant species’ competitive interactions lead to community-level shift in 

native grassland. (California) 

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Increased nitrogen deposition in western grass/shrub lands is also implicated in increased 

fire frequency in some areas because the nitrogen over-enrichment has favored the growth and 

production of fire-prone grass species. Emerging research has also linked increased nitrogen 

deposition to habitat alteration for threatened species. 

Nitrogen enrichment, in combination with ozone exposure, causes major changes in tree 

health by reducing fine-root biomass and carbon allocation below ground and by greatly 

decreasing the lifespan of pine foliage. Nitrogen enrichment results in greater leaf growth, while 

ozone causes premature leaf loss at the end of the growing season. The net result of these 

pollutants is significant litter accumulation on the forest floor. Nitrogen cycling rates in soil are 

also stimulated by high nitrogen inputs, resulting in large leachate losses of nitrate from these 

watersheds and elevated fluxes of nitric oxide gas from soil. In coastal sage ecosystems that 

occur in low-elevation sites in this region, greenhouse and field studies indicate that nitrogen 

deposition may be one factor that enhances the invasion of exotic annual grasses. 

A.1.2 Aquatic Nitrogen Enrichment and Eutrophication 

Atmospheric deposition of nitrogen is a significant source of total nitrogen to many 

estuaries in the United States. National Oceanic and Atmospheric Association (NOAA) has 

calculated the amount of nitrogen entering estuaries ultimately attributable to atmospheric 

deposition for many of the East Coast estuaries. The amount of nitrogen entering estuaries due to 

atmospheric deposition varies widely, depending on the size and location of the estuarine 

watershed and other sources of nitrogen in the watershed. A number of uncertainties may result 

in a greater relative contribution of atmospheric deposition in some places. In addition, episodic 

inputs, which may be ecologically significant, may be higher than the annual average. Studies 

have shown that atmospherically deposited nitrogen (AD-N) contributes from 20 to >40% of the 

new nitrogen flux to estuaries and waters along the East Coast (Whitall and Paerl, 2001). The 

areas with the highest deposition rates stretch from Massachusetts to the Chesapeake Bay, and 

along the Central Gulf Coast. 

The supply of nitrogen tends to limit the productivity of coastal ecosystems. However, 

nitrogen over-enrichment can alter a series of complex biogeochemical cycles that affect 

community processes (e.g., competition, community structure) and ecosystem processes (e.g., 

ecosystem efficiency, decomposition). Approximately 60% of estuaries in the United States 

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(65% of the estuarine surface area) suffer from over-enrichment of nitrogen, resulting in 

excessive algal growth, the outcome of which is eutrophication—the depletion of oxygen 

concentrations as the algae die and decompose. Symptoms of eutrophication include changes in 

the dominant species of phytoplankton (the primary food source for many kinds of marine life), 

low levels of oxygen in the water column, fish and shellfish kills, outbreaks of the toxic 

dinoflagellate, such as Pfiesteria piscicida, and cascading population changes up the food chain. 

In addition, encrustation and increased levels of turbidity in the water due to large amounts of 

algae can kill off submerged aquatic vegetation, which is an important habitat for many estuarine 

fish and shellfish species. 

Often the most severe result of eutrophication is the depletion of dissolved oxygen (DO) 

in the water column by the decomposition of organic matter, produced within the ecosystem as a 

result of the nitrogen saturation. Anoxia (lack of oxygen) or hypoxia ( DO concentrations lower 

than required by indigenous organisms) is a particular concern in coastal estuaries that exhibit 

density stratification (the division of water into layers with different temperatures and oxygen 

content), which occurs mostly during the summer months. Organic matter produced in lighted 

surface waters either sinks to the bottom waters where it decomposes, consuming oxygen 

inventories that are not replenished by photosynthesis, or it mixes with oxygen-rich surface 

waters. These low-oxygen zones may cause massive deaths of aquatic life and reduce the 

population densities of many important commercial fish and shellfish. Hypoxic bottom waters 

have expanded during the latter 20th century in many coastal ecosystems, including large areas 

of the continental shelf of the northern Gulf of Mexico near the mouth of the Mississippi River. 

Many of the highly eutrophic estuaries are along the gulf and mid-Atlantic coasts, overlapping 

many of the areas with the highest nitrogen deposition, but there are eutrophic estuaries in every 

region of the conterminous U.S. coastline. 

Emerging ecological studies in the western United States demonstrate that some aquatic 

and terrestrial communities are significantly altered by increased nitrogen deposition. The major 

concerns are for ecological systems that are naturally adapted to low-nitrogen inputs, because 

increases related to anthropogenic atmospheric deposition can lead to nitrogen saturation. Where 

the inputs of nitrogen exceed the ecological system’s need for them, excess nitrogen is leached 

into surrounding waterways. Although much of the western United States is exposed to relatively 

low deposition of nitrogen, hotspots of nitrogen deposition occur downwind of large 

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metropolitan areas or large agricultural operations. Some of the most sensitive systems affected 

by the elevated nitrogen deposition include high-elevation catchments in Colorado and chaparral 

catchments in the southwestern Sierra Nevada Mountains. The primary concerns in the West 

have been for the critical load of nitrogen deposition, which affects both terrestrial and aquatic 

resources through eutrophication and/or nitrogen enrichment, thereby altering community 

structure. 

The over-enrichment of nitrogen deposition in high-elevation lakes has led to increased 

biomass of phytoplankton, resulting in eutrophication and shifts in diatom community 

composition. In the western United States, episodic acidification is also an important issue for 

surface waters throughout high-elevation areas. Where soils are sparse, as in alpine regions, most 

snowpack nitrogen is flushed to surface waters early in the snowmelt period. In addition to highelevation lakes, snowpack nitrogen has also been reported to cause temporary acidification of 

alpine streams. Snowmelt-related temporary acidification of alpine lakes and streams and 

associated effects have been reported in numerous studies, largely for CAA Class 1 areas in the 

southern and central Rocky Mountains. 

Increased nitrogen deposition in western arid and semiarid grass/shrub lands is also 

implicated in increased fire frequency in some areas because the nitrogen over-enrichment has 

favored the growth and production of fire-prone grass species. Emerging research has also linked 

increased nitrogen deposition to habitat alteration for threatened species. Nitrogen fertilization 

experiments in arid and semiarid plant communities have shown that changes in plant biomass 

associated with increased nitrogen deposition tend to alter species’ composition, with negative 

impacts on biodiversity. Such plant community changes resulting from experimental fertilization 

have been reported in Joshua Tree National Park in California, coastal sage shrub communities 

of southern California, areas in the Chihuahuan Desert and Mojave Desert, and for arid grassland 

areas on the Colorado Plateau. 

A.1.3 Aquatic Sulfur Enrichment 

Atmospheric deposition of sulfur to primarily aquatic environments with high 

concentrations of organic matter leads to an increase in production of MeHg. The increased 

availability of sulfur as sulfate in lakes and streams due to the deposition of SOx accelerates the 

conversion of elemental mercury and mercuric salts to highly toxic, bioaccumulative, and 

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persistent MeHg compounds that build up in living tissue and increase in concentration up the 

food chain. Sulfate-dependant bacteria, along with methanogenic (methane-producing) 

microorganisms, are involved in the conversion of Hg2+ to MeHg under the anaerobic conditions 

found in wetlands, river sediments, and in certain soils. The presence of sulfates stimulates the 

growth of these methylating microbes. Acid rain is thought to increase biomethylation as more 

MeHg is formed under acidic conditions (less than a pH of 6). 

The “cause-and-effect relationship” between sulfur and mercury deposition from the 

atmosphere has been demonstrated in the lab and in small-scale field experiments. Using sulfate 

levels equivalent to historical levels of sulfate deposition from acid rain in the northeastern 

United States, researchers in Minnesota have been able to the confirm a surge in MeHg levels 

with increasing levels of sulfates in a large-scale, fresh water wetland ecosystem (Jeremiason et 

al., 2006). While an in-depth assessment of mercury methylation relative to NOx and SOx inputs 

is not feasible at this time, reducing NOx and SOx inputs may also reduce the mercury 

methylation potential of some systems. 

A.1.4 Terrestrial Acidification Due to Nitrogen and Sulfur 

The current understanding of the effects of acidifying deposition on forest ecosystems has 

focused increasingly on the biogeochemical processes that affect plant uptake, retention, and 

cycling of nutrients within forested ecosystems. Research results from the 1990s indicate that 

decreases in base cations (e.g., calcium, magnesium, potassium) from soils are at least partially 

attributable to acid deposition in the northeastern and southeastern United States. Base cation 

depletion is a cause for concern because of the role these ions play in acid neutralization, as 

discussed above: In the case of calcium, magnesium, and potassium, these are essential nutrients 

for plant growth and physiology (e.g., nutrient uptake). As mobile aluminum increases due to 

soil acidification, the calcium/aluminum ratios change, which is partly related to the higher 

affinity of aluminum during passive uptake by roots. The change in these relative nutrient 

proportions has been correlated with declining forest health. Recent research indicates that the 

loss of cations also leads to aluminum leaching from the soil to stream waters, which can have 

harmful effects on fish. 

The loss of calcium from forest soils and forested watersheds has now been documented 

as a sensitive, early indicator of the soil response to acidifying deposition for a wide range of 

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forest soils in the northeastern United States (Likens, Driscoll, and Buso, 1996). There is a strong 

relationship between acid deposition and leaching of base cations from soils in hardwood forests 

(e.g., maple, oak), as indicated by long-term data on watershed mass balances, plot- and 

watershed-scale acidification experiments in the Adirondack Mountains and in Maine, and 

studies of soil solution chemistry along an acid-deposition gradient from Minnesota to Ohio. 

A.1.5 Aquatic Acidification Due to Nitrogen and Sulfur 

Acidifying deposition causes acidification of sensitive surface waters. The effect of 

acidifying deposition on aquatic systems depends largely upon the ability of the ecosystem to 

neutralize the additional acid. This is referred to as an ecosystem’s ANC. 

ANC levels depend largely on a watershed’s physical characteristics: geology, soils, and 

size. Water systems that are sensitive to acidification tend to be located in small watersheds that 

have few alkaline minerals and shallow soils. Large, forested watersheds have been shown to 

acidify during large rainfall and snowmelt episodes. As acidity increases, aluminum leached 

from soils and sediments flows into lakes and streams and can be toxic to aquatic species. The 

lower pH levels and higher aluminum levels that result from acidification make it difficult for 

some fish and other aquatic species to survive, grow, and reproduce. In some waters, the number 

of fish species able to survive has been directly correlated to water acidity. Acidification can also 

decrease fish population density and individual fish size. 

In western regions, some high-elevation lakes, particularly in the Rocky Mountains, have 

become acidic, especially during snowmelt. However, while many western lakes and streams are 

sensitive to acidification, they are not subject to continuously high levels of acid deposition, and, 

therefore, have not become chronically acidified. During the 1980s and 1990s, an integrated 

study of atmospheric deposition, terrestrial ecosystems, and aquatic ecosystems was conducted 

in several watersheds in the Sierra Nevada Mountains to determine if acidifying deposition was 

affecting these areas and to infer the implications of acidification on surface waters in the region. 

Chronic acidification of high-elevation surface waters in the Sierra Nevada Mountains was not 

found, but episodic changes in stream water chemistry did occur. In many of the watersheds 

studied, for example, the pH decreased as the waters became more acidic with increasing runoff, 

reaching a minimum during peak snowmelt. 

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Anthropogenic atmospheric nitrogen and sulfur deposition impacts the surface seawater 

chemistry by increasing acidification and reducing alkalinity. The impacts of these changes are 

more substantial in coastal waters where the ecosystems are more vulnerable due to other human 

impacts, such as nutrient enrichment and pollution. Ocean acidification is a significant threat to 

coral reefs and coastal benthic and planktonic foodwebs which, in turn, impacts fish populations. 

A.2 Additional Effects Related to Acidification and/or Nutrient Enrichment on 

Sensitive Ecosystems 

It important to note that several additional indicators are worthy of investigation: 

 Nitrogen saturation 

 Maple decline 

 Ammonia air deposition and toxicity to native mussels 

 Relationship between acidity/nutrient enrichment and mercury methylation 

 Sensitive areas for acidity/nutrient enrichment impacts. 

A concise summary of information on each topic is introduced in the following sections. 

A.2.1 Nitrogen Saturation 

Terrestrial and aquatic ecosystems in the eastern and northeastern United States receive 

nitrogen deposition loadings related to air pollution that are far in excess of natural background 

levels. When combined with other acid rain impacts to soil systems and receiving waters, the 

terrestrial ecosystem, in particular, can become nitrogen saturated. This leads to the increased 

“leakage” of nitrogen into groundwater and surface water. Studies are now documenting similar 

concerns for sensitive areas that often involve national parks in the Appalachians (e.g., Smoky 

Mountains National Park), the Rocky Mountains, the Cascades, and other areas in the West. 

Several forests throughout the United States are beginning to show signs of nitrogen saturation, a 

condition where the inputs of nitrogen exceed the forest’s need for them and excess nitrogen is 

leached into surrounding waterways. Significant studies include those identified by Driscoll and 

colleagues (2001); Fenn and colleagues (2003); and NAPAP (2005). 

A.2.2 Maple Decline 

Maple decline is a generalized term for a set of symptoms that may be applied to any 

species of tree suffering a wide range of different stressors, resulting in a loss of vigor or habitat. 

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These symptoms have been studied for the northeastern United States in recent decades, with a 

focus on native maples, such as the sugar maple. In rural areas, maple decline is often attributed 

to soil acidification caused by acid rain. Soils that have developed from nutrient-poor parent 

materials, such as sandstone, quartzite, and granite are most sensitive to acidification. Some of 

the best-documented work has been conducted at the Hubbard Brook Experimental Forest 

(HBEF), a 3,160-hectare reserve near North Woodstock, NH, where scientists have measured 

soil composition for the past 50 years. A recent study (Juice et al., 2006) documents how 

scientists added nutrients in a test plot to replicate soil conditions that existed prior to the loss of 

sugar maples over the past 25 years. This reproduced the favorable soil conditions that existed 

prior to 20th-century industrial pollution, with the result that sugar maples on the test plot 

rebounded dramatically. Nitric and sulphuric acid in acid rain leaches calcium from the soil. 

Calcium is the second most abundant plant nutrient after nitrogen. In addition, the loss of 

calcium leads directly to acidic soils. When soils become too acidic, trees such as sugar maples 

become stressed and have a harder time growing or producing seeds and seedlings. 

A.2.3 Ammonia Air Deposition and Toxicity to Native Mussels 

Across North America, populations of freshwater mussels have fallen drastically to the 

point where more than 70% of native unionid mussel species are considered endangered, 

threatened, or of special concern. Ammonia toxicity is of concern for the survival of juvenile 

mussels (the most sensitive life stage), and EPA’s Office of Water (OW) is pursuing studies to 

consider revisions to its total ammonia criterion guidance to provide protections against acute or 

chronic toxicity (U.S. EPA, 2005). 

A.2.4 Relationship between Acidity/Nutrient Enrichment and Mercury Methylation 

Research recently summarized for the northeastern United States suggests a relationship 

between sulfur deposition and processes promoting mercury methylation, which increases the 

risks for bioaccumulation and biomagnification in food chains. Ongoing research in the Gulf of 

Mexico is also addressing the following three research goals: 

 Research Goal 1 – Test the hypothesis that rates of MeHg production in coastal sediments 

are in part controlled by temporal and spatial hypoxia patterns that result from coastal 

eutrophication, and that maximum MeHg production occurs in regions adjacent to 

hypoxic zones. 

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 Research Goal 2 – Test the hypothesis that coastal eutrophication and hypoxia can result 

in elevated MeHg accumulation and biomagnification in red snapper and gray snapper, 

both commercially and recreationally important fish species in this region. 

 Research Goal 3 – Test the hypothesis that anglers who proportionately consume fish 

from areas of higher MeHg production related to hypoxia will have higher rates of 

mercury exposure (as measured by the concentration of mercury in hair) than anglers 

consuming similar amounts of fish from other coastal Louisiana locations where hypoxia 

does not occur. 

The EPA ORD has also done some preliminary work on developing large-basin 

multimedia modeling systems that would handle impacts from nutrients (especially nitrogen 

species) and the complicated processes related to mercury. Significant sources identified include 

Chesney and colleagues (2006), Driscoll and colleagues (2007), and Evers and colleagues 

(2007). 

A.3 Sensitive Areas for Acidity/Nutrient Enrichment Impacts 

Research accomplished through the NAPAP (2005) has identified spatial areas in terms 

of both terrestrial and aquatic ecosystems that show sensitivity to impacts from acid rain–related 

air pollution (Figure A-1). The NAPAP has been able to develop GIS layers of such sensitive 

areas as ecoregions or hydrologic basins. 

The degree to which other types of sensitive areas (related to such themes as nitrogen 

saturation, maple decline, or the locations of waterbodies showing nitrogen limitations) can be at 

least robustly defined in terms of their geographical extents could be examined. Where such 

geospatial data stratification materials can be identified, this would be helpful in both the 

analysis of indicators and in the development and interpretation of results from models. An 

examination of these materials would also be useful in identifying critical loads for acidification 

and nutrient enrichment stressors, which in most cases will vary for different ecoregions and 

waterbody types. 

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Figure A-1. Sensitive ecological receptors in the United States. 

References 

Chesney, E., R. Lincoln, M.S. Bank, D.B. Senn, D.J. Vorhees, P. Grandjean, and N.N. Rabalais. 

2006. Exploring Links Between Mercury, the Coastal Environment, and Human Health in 

Coastal Louisiana. Available at http://www.sdafs.org/laafs/MeetingProgram200616.pdf. 

Driscoll, C.T., Y.-J. Han, C.Y. Chen, D.C. Evers, K.F. Lambert, T.M. Holsen, N.C. Kamman, 

and R.K. Munson. 2007. Mercury contamination in forest and freshwater ecosystems in 

the northeastern United States. BioScience 57(1):17–28. 

Driscoll, C.T., G.B. Lawrence, A.J. Bulger, T.J. Butler, C.S. Cronan, C. Eager, K.F. Lambert, 

G.E. Likens, J.L. Stoddard, and K.C. Weathers. 2001. Acidic deposition in the 

northeastern United States: sources and inputs, ecosystem effects, and management 

strategies. BioScience 51:180–198. 

Evers, D.C., Y.-J. Han, C.T. Driscoll, N.C. Kamman, M.W. Goodale, K.F. Lambert, T.M. 

Holsen, C.Y. Chen, T.A. Clair, and T. Butler. 2007. Biological mercury hotspots in the 

northeastern United States and southeastern Canada. BioScience 57(1):29–43. 

Fenn, M.E., R. Haeuber, G.S. Tonnesen, J.S. Baron, S. Grossman-Clarke, D. Hope, D. Jaffe, S. 

Copeland, L. Geiser, H.M. Rueth, and J.O. Sickman. 2003. Nitrogen emissions, 

deposition, and monitoring in the western United States. Bioscience 53(4):391–403. 

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 A-12 DRAFT – March 2008

Jeremiason, J.D., D.R. Engstrom, E.B. Swain, E.A. Natur, B.M. Johnson, J.E. Almendinger, 

B.A. Monson, and R.K. Kolka. 2006. Sulfate addition increases methylmercury 

production in an experimental wetland. Environ. Sci. Technol. 40(12)3800–3806. (DOI: 

10.1021/es0524144). 

Juice, S.M., T.J. Fahey, T.G. Siccama, C.T. Driscoll, E.G. Denny, C. Eagar, N.L. Cleavitt, R. 

Minocha, and A.D. Richardson. 2006. Response of sugar maple to calcium addition to 

northern hardwood forest at Hubbard Brook, NH. Ecology 87(5):1267–1280. 

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

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

NAPAP (National Acid Precipitation Assessment Program) 2005. National Acid Precipitation 

Assessment Program Report to Congress: An Integrated Assessment. National Acid 

Precipitation Assessment Program. National Oceanic and Atmospheric Administration, 

Silver Spring, MD (NAPAP coordination now under the U.S. Geological Survey). 

General information on NAPA is available at: http://ny.cf.er.usgs.gov/napap/index.html. 

The 2005 report can be downloaded from the following url: 

http://ny.cf.er.usgs.gov/napap/index.html. 

U.S. EPA (Environmental Protection Agency). 2005. Mussel Toxicity Testing Workshop. 

Conducted by U.S. EPA HQ and EPA Region 5, Chicago, IL. August 23–24. 

Whitall, D.R. and H.W. Paerl. 2001. Spatiotemporal variability of wet atmospheric nitrogen 

deposition to the Neuse River Estuary, North Carolina. Journal of Environmental Quality

30:1508–1515.
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APPENDIX B 

OTHER INDICATORS – NITROUS OXIDE 

NAAQS’ purpose to protect welfare entails not only ecological welfare, but also other 

forms of welfare that are potentially impacted, such as materials, climate change, and visibility. 

N2O is a naturally occurring greenhouse gas; however, human activities have increased 

atmospheric concentrations by 18% since the preindustrial era (IPCC, 2001). The global 

warming potential of CO2 is 1, while the global warming potential of N2O is 310, indicating that 

a molecule of N2O is 310 times more effective in trapping heat in the atmosphere than CO2 over 

a 100-year period. Based on the current U.S. Greenhouse Gas (GHG) Inventory (U.S. EPA, 

2007), nitrous oxide contributes approximately 6.5% to total greenhouse gas emissions (in CO2

equivalents) 

Elevated nitrogen loading to ecosystems can significantly enhance the production of N2O. 

For example, the nitrogen nutrient loading in water bodies can enhance N2O emissions from the 

bacterial breakdown of nitrogen from these sources. In another example, numerous studies have 

shown that N2O emissions from soils increase upon artificial nitrogen additions (Brumme and 

Beese, 1992; Matson et al., 1992; Klemedtsson et al., 1997; Papen et al., 2001). Regions with 

elevated atmospheric nitrogen deposition due to anthropogenic activity also show increased N2O 

emissions (Butterbach-Bahl et al., 1998, 2002). Nitrous oxide emissions from soils are also 

influenced by precipitation and temperature. The Photosynthesis-Evapotranspiration-Model–

Nitrogen–Denitrification-Decomposition (PnET-N-DNDC) model is designed to simulate and 

predict soil carbon and nitrogen biogeochemistry in temperate forest ecosystems and to simulate 

the emissions of N2O and NO from forest soils. The model couples the PnET model, the DNDC 

model, and a nitrogen module that are further described in Li and colleagues (1992, 1996, 2000), 

Li (2000), and Stange and colleagues (2000). The capacity of this model to simulate nitrogen 

trace gas emissions from forest soils was tested by comparing model results with results from 

field measurements at 19 different field sites across Europe and 1 site in the United States (Kesik 

et al., 2005). Denitrification is described in the model as a series of sequential reductions driven 

by a microorganism using nitrogen oxides as electron acceptors under anaerobic conditions. As 

intermediates of the processes, NO and N2O are tightly controlled by the kinetics of each step in 

the sequential reactions. Interactions between temperature, precipitation, and forest soil NO and 

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N2O emissions in Europe were investigated using PnET-N-DNDC (Kesik et al., 2006) abiotic 

parameters that are included in the model and are summarized in Table B-1. 

Table B-1. Parameters Included in the PnET-N-DNDC Model as Modeled 

for European Forest (Kesik et al., 2006) 

Forest Properties Soil Properties 

Daily Climate Input 

Parameters Tree Species/Genera 

Forest type 

Age 

Above and below 

ground biomass 

Plant physiology 

parameters 

Texture 

Clay content 

pH 

Soil organic carbon 

content 

Stone content 

Humus type 

Precipitation 

Min and max air temps 

Inorganic [N] in Precip 

Pine 

Spruce 

Hemlock 

Fir 

Oak 

Birch 

Beech 

Slash Pine 

Larch 

Cypress 

Evergreen Oak 

References 

Brumme, R., and F. Beese. 1992. Effects of liming and nitrogen fertilization on emissions of 

CO2 and N2O from a temporate forest. Journal of Geophysical Research 97:12851–

12858. 

Butterbach-Bahl, K., L. Breuer, R. Gasche, G. Willibald, and H. Papen. 2002. Exchange of trace 

gases between soils and the atmosphere in Scots pine forest ecosystems of the 

northeastern German lowlands 1. Fluxes of N2O, NO/NO2 and CH4 at forest sites with 

different N-Deposition. Forest Ecology and Management 167:123–134. 

Butterbach-Bahl, K., R. Gasche, C. Huber, K. Kreutzer, and H. Papen. 1998. Impact of nitrogen 

input by wet deposition on N-trace gas fluxes and CH4-oxidation in spruce forest 

ecosystems of the temperate zone in Europe. Atmos. Environ. 32:559–564. 

IPCC, 2001: Climate Change 2001: Synthesis Report. A Contribution of Working Groups I, II, 

and III to the Third Assessment Report of the Intergovernmental Panel on Climate 

Change. 398 pp. Edited by R.T. Watson and the Core Writing Team., Cambridge, United 

Kingdom, and New York, NY: Cambridge University Press. 

Kesik, M., P. Ambus, R. Baritz, N. Brüggemann, K. Butterbach-Bahl, M. Damm, J. Duyzer, L. 

Horváth, R. Kiese, B. Kitzler, A. Leip, C. Li, M. Pihlatie, K. Pilegaard, S. Seufert, D. 

Simpson, U. Skiba, G. Smiatek, T. Vesala, and S. Zechmeister-Boltenstern. 2005. 

Inventories of N2O and NO emissions from European forest soils. Copernicus GmbH on 

behalf of the European Geosciences Union (EGU). Sweden. 

Kesik, M., S. Blagodatsky, H. Papen, and K. Butterbach-Bahl. 2006. Effect of pH, temperature 

and substrate on N2O, NO, and CO2 production by Alcaligenes faecalis p. Journal of 

Applied Microbiology 10 (3)655–667. 

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Klemedtsson, A., L. Klemedtsson, K. Burglund, P. Martikainen, J. Silvola, and O. Oenema. 

1997. Greenhouse gas emissions from farmed organic soils: a review. Soil Use of 

Management 13:245–250. 

Li, C. 2000. Modeling trace gas emissions from agricultural ecosystems. Nutr. Cycl. Agroecosys. 

58:259–276. 

Li, C., J. Aber, F. Stange, K. Butterbach-Bahl, and H. Papen. 2000. A process-oriented model of 

N2O and NO emissions from forest soils: 1. Model development. Journal of. Geophysical 

Research 105:4369–4384. 

Li, C., S. Frolking, and T.A. Frolking. 1992. A model of nitrous oxide evolution from soil driven 

by rainfall events: 1. Model structure and sensitivity. Journal of Geophysical Research

97:9759–9776. 

Li, C., V. Narayanan, and R. Harriss. 1996. Model estimates of nitrous oxide emissions from 

agricultural lands in the United States. Global Biogeochemical Cycles 10:297–306. 

Matson, P.A., S.T. Gower, C. Volkmann, C. Billow, and C.C. Grier. 1992. Soil nitrogen cycling 

and nitrous oxide fluxes in fertilized Rocky Mountain Douglas-fir forests. 

Biogeochemistry 18:101–117. 

Papen, H., M. Daum, R. Steinkamp, and K. Butterbach-Bahl. 2001. N2O and CH4-fluxes from 

soils of a N-limited and N-fertilized spruce forest ecosystem of the temperate zone. J. 

Appl. Bot. Angew. Bot. 75:159–163. 

Stange, F., K. Butterbach-Bahl, and H. Papen. 2000.A process-oriented model of N2O and NO 

emissions from forest soils, 2. Sensitivity analysis and validation. Journal of Geophysical 

Research 105(15)4385–4398. 

U.S. EPA (Environmental Protection Agency). 2007. The U.S. Inventory of Greenhouse Gas 

Emissions and Sinks: Fast Facts. Office of Atmospheric Programs, EPA 430-F-07-004. 

April. 

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APPENDIX C 

CMAQ MODELING 

The 1998 Guidelines for Ecological Risk Assessment (U.S. EPA, 1998) state that “At the 

beginning of the analysis phase, the [risk] assessor critically examines the data and models to 

ensure that they can be used to evaluate the conceptual model developed in problem 

formulation.” The assessor evaluates the strengths and limitations of different types of data and 

evaluated measurement or modeling studies to be used, including accounting for uncertainty. 

This section presents our current thoughts for using existing ambient air quality and deposition 

monitoring data, as well as the application of atmospheric and multimedia models to predict 

ecological risk and exposure. 

C.1 Atmospheric Modeling 

The atmospheric processes that transform and transport ambient NOx and SOx to 

deposition species are similar. (NOTE: In addition, NOx and SOx interact photochemically in the 

PM formation. Further, since NOx participates in both the ozone and PM photochemistry, those 

pollutants are linked and need to be simulated together in a single model.) Therefore, we intend 

to use the same process model for atmospheric fate, transport, and deposition. We plan to use the 

CMAQ model, a peer-reviewed, state-of-the-art model of the atmosphere. The 2002-based 

CMAQ modeling platform will likely be used as the tool for the air quality modeling. 

As shown in Figure C-1, the CMAQ modeling domain covers the continental United 

States and portions of Canada and Mexico. There are two 12 x 12 km horizontal-grid resolution 

modeling domains, an eastern United States domain (outlined in red), and a western United 

States domain (outlined in blue). The modeling domain contains 14 vertical layers, with the top 

of the modeling domain at about 16,200 meters. 

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Figure C-1. CMAQ 12-km eastern and western United States modeling domains. 

The key inputs to the CMAQ model include emissions from anthropogenic and biogenic 

sources, meteorological data, and initial and boundary conditions. The CMAQ meteorological 

input files were derived for the entire year of 2002 from a simulation of the Pennsylvania State 

University/National Center for Atmospheric Research Mesoscale Model (Grell et al., 1994). This 

model, commonly referred to as MM5, is a limited-area, nonhydrostatic, terrain-following 

system that solves for the full set of physical and thermodynamic equations, which govern 

atmospheric motions. Anthropogenic and biogenic emissions from the 2002 CMAQ modeling 

platform were obtained from the 2002 National Emissions Inventory (NEI). These data were then 

processed using the Sparse Matrix Operator Kernel Emissions (SMOKE) processing system. 

In addition to understanding the relationship between ambient concentrations and 

deposition, we also need to understand how the existing patterns of deposition modeled using 

CMAQ may vary with variability in meteorology (e.g., temperature, precipitation). By making 

use of the 5 years of CMAQ simulations conducted for the joint EPA/Centers for Disease 

Control and Prevention (CDC) project, we may be able to provide a quantitative assessment of 

the variability in deposition patterns induced by the meteorological variability between years. 

This assessment plans to include statistical analyses designed to compare the magnitude and 

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spatial patterns of deposition for sulfur and nitrogen containing species predicted by CMAQ 

across the 5 years modeled. The analysis intends to highlight the similarities and differences in 

the distribution of monthly, seasonal, and annual wet, dry, and total deposition for grid cells 

covering selected watersheds, forested ecosystems, and croplands. Specifically, for each 

geographic area we plan to calculate (1) the 5-year average in monthly, seasonal, and annual 

nitrogen and sulfur deposition and (2) the range in the deposition for each of these time periods 

within the 5 years modeled. This information may be presented in tabular and graphical forms to 

reveal (1) how deposition varies by year, season, and month for the 5 years, on average, and (2) 

how monthly and seasonal deposition in the individual years compares to the 5-year average. We 

may also examine the spatial variation in deposition within and between the selected geographic 

areas. For this we plan to prepare histograms showing the distribution of deposition by month 

and season across the multiple grid cells within each of the selected geographic areas. The results 

may be analyzed to compare the distribution and range of values for the different areas. The 

feasibility of using statistical techniques to quantify year-to-year variability in the spatial patterns 

of predicted deposition within a geographic area may be explored. 

C.2 Ambient Air Concentration Data and Deposition Data 

Because the risk/exposure assessment will ultimately be used to assess current and 

alternative ambient NOx and SOx standards, the risk assessment will need to characterize both 

the effects associated with the deposition of nitrogen and sulfur and the relationship between 

ambient concentrations at a specific geographic resolution and deposition at “downstream” 

receptors. Figure C-2 shows the flow of information and modeling we propose to use to 

characterize the ambient levels of NOx and SOx and estimates of nitrogen and sulfur deposition. 

As shown in Figure C-2, in addition to CMAQ modeling, we plan to evaluate the 

available observational data on deposition for use in characterizing ambient and deposition 

surfaces across the United States. There are a number of databases of ambient monitoring data, 

most of which are collected in EPA’s Air Quality System (AQS). There are also databases of 

deposition monitoring data, including the NADP, the CASTNet, and the Park Research and 

Intensive Monitoring of Ecosystems NETwork (PRIMENet). 

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Ambient and 

Deposition Surfaces Monitoring

Emissions Meteorology

CMAQ Modeling

Figure C-2. Development of ambient NOx and SOx and nitrogen 

and sulfur deposition characterizations. 

We plan to assess the feasibility of combining data from modeling and monitoring to 

produce ambient air quality and deposition surfaces that are grounded in observational data but 

make use of the models’ ability to capture the impacts of emissions and meteorology on the 

geographic gradients of air quality and deposition. To assess the feasibility of combining data, 

we intend to implement one or more methods on data associated with a region of interest to this 

project. The estimated air quality and deposition surfaces will be helpful in assessing baseline 

risks and serve as baselines for assessing the impacts of attaining alternative standards. 

References 

Grell, G., J. Dudhia, and D. Stauffer. 1994. A Description of the Fifth-Generation Penn 

State/NCAR Mesoscale Model (MM5), NCAR/TN-398+STR. 138 pp. National Center for 

Atmospheric Research, Boulder CO. 

U.S. EPA (Environmental Protection Agency). 1998. Guidelines for Ecological Risk Assessment. 

Risk Assessment Forum. EPA/630/R-95/002F. April. 

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APPENDIX D 

MULTIMEDIA MODELING 

Atmospheric modeling for this quantitative risk/exposure assessment intends to use, 

where possible, the CMAQ modeling system. The outputs from the CMAQ model must be 

linked to one or more multimedia models (e.g., models for terrestrial systems or aquatic systems) 

to determine the environmental effects of atmospheric deposition of NOx and SOx. For this 

analysis, there is a need to consider models that can potentially handle all types of total reactive 

nitrogen (e.g., consideration of such species as ammonia and nitrous oxide) and models that can 

combine analyses of sulfur with mercury methylation processes. 

The choice of multimedia models to determine and quantify these effects is not as clear 

as in the atmospheric modeling. With multimedia models, there are numerous technical 

formulations, parameterizations, and geographic considerations to consider in choosing the 

correct model for the task at hand. This decision depends on desired outcomes and simulated 

parameters. Outcomes may range from quantified, speciated sulfur or nitrogen concentrations in 

the soil and surface water to measures of species’ richness in a forest landscape. Not all effects 

can be estimated with multimedia models, so a decision on the models to use must balance the 

pros and cons of the models that are available. 

D.1 Model Characterization 

The 35 models listed in Table D-1 represent a wide diversity of types of ecosystems; 

history, location, and spatial/temporal scale of application; scientific acceptance and 

organizational and agency support; complexity and requirements; state variables and processes; 

and management uses. Each model was examined to elucidate the necessary information for 

choosing the appropriate multimedia model. Of the 35 models, 9 are classified as receiving-water 

models, and 26 are classified as terrestrial/watershed models, although these distinctions are 

somewhat arbitrary. In recognition of some models having enough common features or history of 

integration to warrant merging of the discussion, the table also presented several models 

together; however, although presented collectively, these models may not share the same history, 

theory, development, and application. 

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Table D-1. Information Detailed for Each Model of Interest 

Model Information 

Name Model type 

Description Indicators 

Supporting organization(s)/agency endorsements Resource requirements 

Scientific acceptance Data requirements 

Type of ecosystems modeled Model performance/evaluation 

Where has it been applied? Model technological integration 

Spatial scale Key environmental/ecological processes 

Transferability Management use 

Temporal features Citations/URLs 

Model inputs related to deposition Notes (miscellaneous) 

Table D-2 presents a more concise overview of the models identified; information is 

presented that summarizes both the type of ecosystem that the model has been designed to 

represent and the relative level of complexity with which the model considers system 

components and processes. Model complexity was measured by the underlying theory and the 

effort necessary to parameterize a model. For instance, an empirical model that requires only 

basic nutrient information and relies on many assumptions would constitute a low level of 

complexity, whereas a mechanistic model with a large number of variables to parameterize 

would constitute a highly complex model. Complexity does not necessarily suggest desirability, 

utility, or credibility, as these concepts are highly context-specific. All of the models presented 

have arguably demonstrated substantial technical acceptance based on their historical use, 

presence in peer-reviewed publications, and degree of agency support. Further discernment 

regarding “quality” or applicability of the different models to support elements of the secondary 

NO2 and SO2 NAAQS should carefully consider a variety of contextual drivers when using an 

integrated modeling approach. 

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Table D-2. Supported Model Components And Level Of Representation 

Model 

Urban Rural Agriculture Forest River Lake Reservoir Estuary Coastal Groundwater 

AQUATOX — — — — ■ ■ ■ — — — 

QUAL2K — — — — ◙ — — — — — 

WASP7 — — — — ■ ■ ■ ■ ■ — 

CE-MODELS — — — — ■ ■ ■ ■ ■ — 

ILWAS — □ — ◙ ◙ ◙ ◙ — — □

LWWM ■ — — — ■ ■ ■ ■ ■ ◙ 

RCA — — — — ■ ■ ■ ■ ■ — 

THMB/IBIS — ◙ ◙ ◙ ◙ — — — — ◙ 

WATER MODELS 

WARMS — — — — — ◙ ◙ — — — 

HSPF/LSPC ■ ■ ■ ■ □ □ □ — — □

PLOAD □ □ □ □ — — — — — — 

SWAT ◙ ■ ■ ■ ■ ◙ ◙ □ — ■

WARMF ■ ■ ◙ ■ ■ ■ ■ — — ◙ 

BIOME-BGC — ■ ◙ ■ — — — — — — 

PnET-BGC — ◙ — ◙ ◙ ◙ ◙ — — — 

CENTURY 4/ CENTURY 5 — ■ ■ ■ — — — — — □

DayCent — ■ ■ ■ — — — — — □

DNDC — □ ◙ □ — — — — — — 

DRAINMOD — □ ■ — □ — — — — ◙ 

EPIC/APEX — ◙ ■ □ — — — — — □

GLEAMS — ◙ ■ □ — — — — — ◙

Hole-in-the-pipe — ■ — ■ — — — — — — 

INCA — ◙ ◙ ◙ □ — — — — — 

MAGIC — ◙ — ◙ ◙ ◙ ◙ — — ◙

MERLIN — ■ □ ■ — — — — — □

NLOAD/NLM/ELM □ □ □ □ — — — □ — □

NuCM — ◙ — ■ — — — — — — 

ReNuMa ◙ ◙ ◙ ◙ — — — — — □ 

NWPCAM □ □ □ □ □ — — — — — 

RHESSys — ■ ■ ■ □ — — — — — 

SAFE — ■ — ■ — — — — — ◙

Simple Mass Balance □ □ □ □ □ □ □ □ □ — 

SPARROW □ □ □ □ □ — □ — — — 

TOPMODEL or GT/MEL — ◙ ◙ ◙ ◙ — — — — — 

WATERSHED/TERRESTRIAL MODELS 

WATERSN □ □ □ □ — — — — — — 

— Not supported 

□ Relatively simple representation of features and processes

◙ Moderate level of representation of features and processes

■ Most complex representation of features and processes 

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D.2 Multimedia Model Selection 

There are four basic steps necessary to undertake a modeling effort to examine the effects 

of nitrogen and sulfur deposition (RTI 2007): 

1. Choose the specific question/problem to address. 

2. Choose the best models based on model formulation (e.g., are biological processes 

considered?), desired output, study area, data availability, and necessary 

uncertainty/sensitivity analyses for the models. 

3. Determine and set up any processes/algorithms necessary to match atmospheric 

modeling output (assumed to be from CMAQ) to the chosen receiving water or 

terrestrial/watershed model. 

4. Obtain the data needed for model parameterization. 

The model details presented in the summary table and concluding discussion should 

assist the reader in making an informed decision on the best model for a task. The difficulty with 

this area of work lies with the desire to utilize atmospheric modeling in combination with the 

receiving-water and terrestrial/watershed models. The multi-media approach to modeling is still 

in development, so, at this time, not many models are set up to immediately accept the output 

from an atmospheric model such as CMAQ. Several of the models examined accept atmospheric 

concentration or flux data, but the time-step, spatial resolution, and exact species required might 

all differ from the atmospheric model output. For those models that accept atmospheric inputs in 

a form other than that output by CMAQ, efforts can be made to reconcile the outputs of the 

atmospheric model and the inputs of the ecosystem model. 

Most applications for the determination of acidification effects have taken place in the 

northeastern United States because of the interest in quantification of acid rain effects. A specific 

effort was made to determine which models of the 35 could apply to other regions of the United 

States. 

Review of past applications and technical documentation for each of the 9 receiving 

water models reveals that 4 of the 9 models are accepting of parameters for all regions of the 

country. These models are: AQUATOX, the CE-QUAL family of models, QUAL2K, and 

WASP. The WARMS model has been used in Canada; therefore, it may be applicable in more 

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alpine regions of the United States. The remaining 4 models have either been developed for a 

specific area of the country or show limitations in their extension beyond the regions in which 

they have already been applied. 

A listing of the terrestrial/watershed models that show promise in applications across the 

United States, specifically in western states, follows with a short explanation of support. 

 BIOME-BGC – validated with western locations, including arid, cold, western climates 

 CENTURY 4/5 – has been used in the Great Plains and Rocky Mountain areas of the 

United States 

 DayCent (DayCent-Chem) – validated in an alpine/subalpine watershed of Colorado and 

used at other sites across the United States 

 EPIC/APEX – used across the country, but only for agricultural lands 

 GT/MEL – a relatively new model that has been tested in the western Oregon Cascades 

 HSPF – used in applications across the country 

 MAGIC – used worldwide and on many types of systems but does not include biological 

processes directly and lacks features to simulate processes involving nitrogen 

 Mass balance – may be applied anywhere data are available 

 MERLIN – no applications uncovered for U.S. sites but has been used in locations in 

Europe 

 PLOAD – a screening-level model that may be applied anywhere data are available 

 PnET-BGC – many applications in the northeastern United States; developed for forest 

landscapes 

 RHESSys – used in applications in the mountains of Montana 

 SAFE – wide applications in forest systems 

 SWAT – used throughout the country, but does not readily accept the atmospheric 

deposition inputs required for this study, although a workaround may be possible 

 WARMF – used across the country (currently utilizes atmospheric concentration data; a 

newly undertaken project will modify WARMF to accept atmospheric deposition fluxes 

to make it more compatible with CMAQ). 

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References 

RTI International. 2007. Review of Candidate Fate and Transport and Ecological Models. Final 

Report. Report for the Office of Air Quality, Planning, and Standards, U.S. 

Environmental Protection Agency, Research Triangle Park, NC. 
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

APPENDIX E 

VALUATION OF ECOSYSTEM SERVICES 

E.1 Introduction to Ecosystem Services 

The definition of adverse is “unfavorable or antagonistic in purpose or effect.” One way 

to assess adverse effects on welfare is through quantification of ecosystem services. The adverse 

effect would be the loss or reduction of those services through the effects of NOx and SOx on the 

underlying ecological processes and functions that constitute the service. EPA defines ecosystem 

services as the outputs of healthy, intact ecosystems and the underlying ecosystem processes and 

functions that contribute to human well-being (U.S. EPA, 2006). As articulated by the 

Millennium Ecosystem Assessment (United Nations, 2005) from the United Nations, these 

include provisioning services (e.g., clean water, food, wood, fiber, fuel), regulating services (e.g., 

water purification, climate regulation), supporting services (e.g., nutrient cycling, soil 

formation), and cultural services (e.g., recreation, spiritual). Regulating services are of key 

importance to EPA because they directly impact air and water quality, and they have strong links 

to human heath and well-being. Therefore, assessing changes in ecosystem services may be one 

means of assessing whether an effect is adverse. Key issues are how to aggregate across different 

ecosystem services or how to select a representative ecosystem service that is most sensitive to 

deposition effects. Some potential indicators of ecosystem services include the quality of a 

critical habitat, biodiversity, species composition, controlling/limiting invasive species, and pest 

outbreaks. Determining the exposure-response relationships of NOx and SOx on the ecosystem 

service and the underlying ecological process and function will provide a broader focus in 

determination of adverse impacts. For more background information on ecosystem services, see 

The Integrated Review Plan for the Secondary National Ambient Air Quality Standards for 

Nitrogen Dioxide and Sulfur Dioxide (U.S. EPA, 2007). 

Economic Valuation. A succinct statement of the economic approach to valuation is in 

the Ecological Benefits Assessment Strategic Plan (EBASP) (U.S. EPA, 2006): “Economists 

generally attempt to estimate the value of ecological goods and services based on what people 

are willing to pay (WTP) to increase ecological services or by what people are willing to accept 

(WTA) in compensation for reductions in them. To enable a comparison of policy options, a 

common unit is needed to express the value of ecological goods and services. The dollar is the 

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preferred unit for valuation, because there is an extensive body of literature addressing its 

application and interpretation and it is easily compared with costs for considering the net effects 

of alternative policy choices. Three primary approaches for estimating these values exist: 

market-based methods, revealed preference methods, and stated preference methods (U.S. EPA, 

2006).” The EBASP document continues by further explaining these types of economic 

monetary valuation methods. 

For market-based valuation, for many regions of the country, there are diverse crop 

assemblages, including timber for building materials, timber for pulp and paper, biofuel crops, 

grain and soybean feed crops, grass seed, orchard crops, row crops, Christmas trees, and 

horticultural crops. There are numerous methods and data for valuation of these market 

commodities. 

A useful approach to pursue with economists would be mapping the monetary values of 

ecosystem services by land use across the ecosystem service district, using the approach 

described in Troy and Wilson (2006). This approach will first require mapping biophysical 

measurements of services as discussed in Section 3.2. Then, economics expertise will be needed 

to apply monetary values to these services as well as to other services, for which there are 

transferable methods and values from studies elsewhere, using the “Environmental Valuation 

Reference Inventory” ([http://www.evri.ca/english/default.htm] and other sources of 

information). 

Biophysical Valuation. Because monetization of many ecosystems services is either 

very difficult or problematic for a number of reasons, nonmonetary valuation using biophysical 

measurements and concepts will be pursued in addition to economic valuation. One approach 

that fits well with the empirical and modeling data is what has been called relative value 

indicators or relative benefit indicators (Wainger et al., 2001; Boyd and Wainger 2003). In this 

approach, a set of indicators is defined that reflect site and landscape features that affect (1) the 

quality and quantity of ecosystem functions or services, (2) the availability of complementary 

goods and services, (3) the scarcity of goods and services, and (4) the reliability of the flows of 

ecosystem services. These indicators are then aggregated into a combined site or place-based 

index using standardized scoring (Wainger et al., 2001). This is an explicit approach to a 

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“bundling” of services. The development of ERFs and ETFs in Section 3.7 may be adapted to 

such an approach. 

A related approach derives from an economic method that develops “productivity 

indexes” and now calls these “environmental performance indexes” (Färe et al., 2004). This 

approach attempts to combine positive and negative outcomes from a system (e.g., factory, 

region, county) into a single index of performance. To the degree that this approach is sciencebased, it can be developed with available data and offers potential in a qualitative risk 

assessment. 

A second approach to biophysical valuation assigns values to ecosystem goods and 

services through the use of the common currency of energy. This approach has been supported in 

part by the EBASP (U.S. EPA, 2006) and other reviews of valuation. A comprehensive, holistic 

method of energy-based valuation is the energy systems analysis of environmental accounting 

developed by H. T. Odum (1996). A similar approach has been developed by Bakshi and 

colleagues (Hau and Bakshi, 2004a, 2004b; Ukidwe and Bakshi, 2004, 2005). There is extensive 

literature supporting and elaborating on these approaches. 

By describing the differing bundles of ecosystem services under varying levels of NOx

and SOx, and offering choices between those bundles, tradeoff or indifference curves can also be 

generated reflecting individual- and population-level preferences for different ecosystem 

functions. These tradeoffs can be presented to survey respondents using methods such as 

conjoint analysis to provide measures of preferences for different levels of ecosystem functions 

as expressed through ecosystem service levels. Table E-1 shows an example of how ecosystem 

services information might be presented to a survey respondent in a conjoint analysis framework. 

The results of a conjoint analysis can be used to convert all ecosystem services to a 

common unit based on preference weightings for different types of services. This may allow 

ecosystem services to be combined for comparing impacts across alternative forms or levels of 

NOx and SOx standards. 

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Table E-1. Example Survey Design for Preference-Based Ecosystem Tradeoffs 

Water Quality Habitat

Food and Fiber 

Production

Carbon 

Sequestration

Scenario 1 Drinkable Low diversity High High

Scenario 2 Drinkable High diversity Low Low

Scenario 3 Swimmable Medium diversity Medium Medium

Scenario 4 Boatable Low diversity High Medium

Scenario 5 Swimmable Low diversity Low Low

Highly 

Desirable Quite Desirable Desirable

Slightly 

Desirable

Neither 

Desirable 

nor 

Undesirable

Slightly 

Undesirable Undesirable

Quite 

Undesirable

Highly 

Undesirable

Scenario 1 1 2 3 4 5 6 7 8 9

Scenario 2 1 2 3 4 5 6 7 8 9

Scenario 3 1 2 3 4 5 6 7 8 9

Scenario 4 1 2 3 4 5 6 7 8 9

Scenario 5 1 2 3 4 5 6 7 8 9

Ecosystem Services Scenario Descriptions

Scenario Rating

Please rate how desirable each scenario is overall by circling one of the numbers in each row of the following table:

Example Conjoint Scenario Rating Form

References 

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Analysis to Evaluate Environmental Trades and Compensation Resources for the Future. 

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Hau, J.L., and B.R. Bakshi. 2004a. Expanding exergy analysis to account for ecosystem products 

and services. Environmental Science and Technology 38:3768–3777. 

Hau, J.L. and B.R. Bakshi. 2004b. Promise and problems of emergy analysis. Ecological 

Modeling 178:215–225. 

Odum, H.T. 1996. Environmental Accounting: Energy and Environmental Decision Making. 

370 p.p. New York: John Wiley & Sons, Inc. 

Troy, A., and M.A. Wilson. 2006. Mapping ecosystem services: practical challenges and 

opportunities in linking GIS and value transfer. Ecological Economics 60:435–449. 

Ukidwe, N.U., and B.R. Bakshi. 2005. Flow of natural versus economic capital in industrial 

supply networks and its implications to sustainability. Environmental Science and 

Technology 39:9759–9769. 

Ukidwe, N.U., and B.R. Bakshi. 2004. Thermodynamic accounting of ecosystem contribution to 

economic sectors with application to 1992 U.S. economy. Environmental Science and 

Technology 38:4810–4827. 

United Nations. 2005. Millennium Ecosystem Assessment Reports. Available at 

http://www.millenniumassessment.org/en/index.aspx. 

 E-4 DRAFT – March 2008
Secondary NAAQS Review for Oxides of Nitrogen and Oxides of Sulfur 

 E-5 DRAFT – March 2008

U.S. EPA (Environmental Protection Agency). 2007. Plan for Review of the Secondary National 

Ambient Air Quality Standards for Nitrogen Dioxide and Sulfur Dioxide. Available at 

http://www.epa.gov/ttn/naaqs/standards/no2so2sec/index.html. 

U.S. EPA (Environmental Protection Agency). 2006. Ecological Benefits Assessment Strategic 

Plan. P. A-4. Washington, DC. EPA 240-R-06-001. October. 

Wainger, L.A., D. King, J. Salzman, and J. Boyd. 2001. Wetland value indicators for scoring 

mitigation trades. Stanford Environmental Law Journal 20:413–478. 
United States 

Environmental Protection Agency 

Office of Air Quality Planning and Standards 

Health and Environmental Impacts Division 

Research Triangle Park, NC 

Publication N