Attachment F - EPA Responses to Services’ Input

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EPA Responses to Services’ Comments and Requests During Informal Consultation on the 

Approach and Outline for the Biological Evaluation of the 2013 VGP and sVGP 

EPA received the following noteworthy comments and requests from the Services on EPA’s 

proposed outline for this BE as part of informal consultation between the Agencies. The 

comments and questions were received in the Spring of 2012. The following document contains 

answers and explanations to these key comments and questions. 

EPA used the best scientific and commercial data available to prepare what we view as a useful 

and complete evaluation. EPA acknowledges and thanks the Services’ staff and management for 

providing feedback to EPA during the Agency’s development of this BE, which helped refine 

EPA’s approach. 

Comment 1: Add San Francisco as an RAA to capture smelt in the representative species 

analysis. 

Relevant Section in the BE: Section 4.1.6

EPA Response: EPA added San Francisco as an RAA and ensured the Delta Smelt was included 

in the RAA listed species. 

Comment 2: Add a Florida estuary as an RAA to capture the Johnson Seagrass and coral in the 

representative species analysis. 

Relevant Section in the BE: Section 4.1.7

EPA Response: EPA added Miami as an RAA and ensured the Johnson Seagrass, Staghorn 

Coral and Elkhorn Coral were included in the RAA listed species. 

Comment 3: Discuss the potential impacts of vessel discharges in intracoastal waterways.

Relevant Section in the BE: Section 5.2.6.1 

EPA Response: The impacts are discussed in Section 5.2.6.1. EPA believes the analysis in this 

section is generally representative of vessel discharges to intracoastal waterways for two primary 

reasons: 

• Several of the major water bodies (e.g., Elizabeth River, Charleston Harbor, Biscayne 

Bay) that are part of the Atlantic and Gulf intracoastal waterway were considered in 

developing the receiving characteristics for the estuary model; and 

• Even though a significant amount of vessel traffic may travel these waters on a daily 

basis, EPA believes that the daily vessel equivalent population is likely significantly 

lower in these waters than in a harbor environment. 

Comment 4: Provide a clear crosswalk between representative species and all species potentially 

impacted by vessel discharges covered under the VGP and sVGP.

Relevant Section in the BE: Section 5.2.5, Table 5-11, Appendix E, and Table E-1. 
Attachment F - EPA Responses to Services’ Input

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EPA Response: The listed sections provide a clear crosswalk between representative species and 

all species potentially impacted by the incidental discharges authorized under the permits, and 

the steps are as follows. EPA chose to evaluate the potential risk to listed aquatic and aquaticdependent species and their critical habitats in a subset of representative geographical areas 

(referred to as RAAs) selected to reflect the major ports of call and types of ecosystems 

potentially impacted by vessel discharges covered by the VGP and sVGP. EPA, with much 

appreciated assistance from the Services, selected seven RAAs for the BE analysis and evaluated 

risks from vessel discharges to the 82 aquatic and aquatic-dependant species and their critical 

habitats present in the RAAs. EPA grouped the 82 RAA listed species into 18 taxonomic groups; 

called listed species taxonomic groups. Next, EPA categorized each of the 612 listed species that 

may be affected by the VGP and sVGP into one of the 18 listed species taxonomic groups and 

used the in-depth analysis and risk conclusions for the RAA listed species taxonomic groups to 

inform the effects determinations for the broader list of all 612 aquatic and aquatic-dependent 

and their critical habitats that may be affected by the permit actions (see Section 7 of the BE for 

more discussion). 

Comment 5: Provide a transparent analysis for determining which federally listed species are 

potentially impacted by vessel discharges covered under the VGP and sVGP.

Relevant Section in the BE: Appendix E 

EPA Response: To logically and clearly determine the subset of federally listed species 

potentially impacted by VGP and sVGP discharges, EPA narrowed an initial list of over 1,900 

federally-listed species provided in the ECOs GIS dataset, by identifying the aquatic and aquaticdependent species that have more than limited exposure to “waters of the United States” using 

the following criteria: 

• Species is a fully-aquatic species (e.g., fish); 

• Species is an aquatic-dependent terrestrial species which has an important life-stage in 

aquatic ecosystems (e.g., amphibian); 

• Species is an aquatic-dependent terrestrial species which has a substantial portion of its 

diet directly from the aquatic environment (e.g., shorebird); 

• Species migration pattern includes an aquatic environment; or 

• Species critical habitat includes or is dependent upon an aquatic environment. 

EPA identified a total of 612 aquatic and aquatic-dependent species that may be potentially 

impacted by the VGP and sVGP. 

Comment 6: Provide a clear discussion of how EPA transferred risk conclusions from listed 

species in the RAAs to all listed species evaluated for the BE. 

Relevant Section in the BE: Section 7

EPA Response: EPA used the listed species taxonomic groups as the link to transfer risk 

conclusions from listed species in the RAAs to all listed species evaluated in the BE (see 

discussion for comment 4). EPA used risk conclusions for the subset of 82 listed aquatic and 

aquatic-dependent species and their critical habitats identified in the seven RAAs and species-
Attachment F - EPA Responses to Services’ Input

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specific assessments to inform EPA’s effects analyses for the full range of 612 listed species that 

may potentially be impacted by the VGP and sVGP. Additionally, EPA conducted species 

specific analysis on all species that may potentially be impacted the VGP and sVGP. For 

example, EPA assessed the concurrence of individual species distributions for the full range of 

species evaluated in this BE (612 listed species) with waters navigable by vessels covered under 

the permit actions (see Appendix E) to assess the applicability of risk conclusions from the 82 

RAA listed species for pollutants other than ANS. As a result of this analysis, EPA determined 

that 454 listed species are potentially exposed to both ANS and all pollutants in vessel discharges 

covered by the VGP and sVGP. In addition, EPA reviewed and considered relevant life history, 

habitat status, constituent element requirements, principle food sources, and major threat 

information for all 612 species evaluated in this BE to further refine the effects determinations. 

Comment 7: Discuss the potential synergistic effects of exposure to pollutant mixtures from 

vessel discharges covered under the VGP and sVGP on listed species. 

Relevant Section in the BE: Section 5.4.2

EPA Response: Evaluating and quantifying the effects of mixtures is challenging as the toxic 

effects of pollutants in mixture can be less than, greater than, or not appreciably different than 

those predicted for the same pollutants singly. Concentration addition is a common method used 

to assess mixture toxicity; however, this method is accurate only when the mixture consists 

solely of pollutants with the same toxicological mechanism of action such as metals or PAHs. 

While EPA notes that the low quantities of many of these incidental discharges likely means 

little potential impact, as an additional assessment of the risk posed to listed aquatic species from 

incidental discharges from vessels covered under the VGP and sVGP, EPA calculated the 

additive toxicity of metals and PAHs in mixture to assess impacts from vessel discharges. 

Comment 8: Discuss how EPA accounted for possible difference in sensitivity between a listed 

species and surrogate species used in the analysis. 

Relevant Section in the BE: Section 5.2.6.3, Section 5.4.1 

EPA Response: Although it is not expected that there would be such differences, to account for 

possible differences in sensitivity between a listed species and its surrogate species, EPA applied 

a safety adjustment factor of 2.0 to the Agency’s criterion continuous concentration when 

evaluating risk in the quantitative effects analysis to ensure that any sensitivity would be 

adequately captured. 

Comment 9: Discuss how EPA considered the issue of changes in ocean buffering related to 

climate change. 

Relevant Section in the BE: Section 5.2.6.1 

EPA Response: Exhaust gas scrubber discharges have the greatest potential to depress pH 

values in receiving waters as the discharge can have pH values as low as 3. As discussed in 

EPA’s economic and benefit analysis for the 2013 VGP, EPA believes that a maximum of only 5 

to 10 percent of effected vessels will install this scrubber technology by the end of the permit 

period. We further note that this is likely a high estimate of systems which would be used. EPA 

believes that the concurrence of site-specific changes in buffering capacity with a significant 
Attachment F - EPA Responses to Services’ Input

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population of vessels discharging exhaust gas scrubber water is highly unlikely to occur. EPA 

believes that any localized effects caused by direct exposure to an exhaust gas scrubber discharge 

plume will be brief such that risk effects to listed species considered in the BE are not of 

concern. 

Comment 10: Discuss how EPA evaluated the potential for pollutant loads from vessel 

discharges covered under the VGP and sVGP to contribute to water quality issues that are known 

stressors for listed species. 

Relevant Section in the BE: Section 4, Section 5.5 

EPA Response: Using the best scientific and commercial data available, including USFWS and 

NMFS species factsheets, EPA reviewed the known threats for each of the 82 listed RAA species 

(see Table 4-19) and assessed the potential for permitted vessel discharges to contribute to the 

known stressors for each species. EPA determined that 23 of the 82 RAA species are sensitive to 

water pollution and other related water quality problems that could potentially originate from or 

be contributed by incidental vessel discharges covered under the VGP and sVGP; however, none 

of the species-specific threat information identified incidental vessel discharges as a specific 

pollution source of concern. As discussed throughout Section 4, the RAAs evaluated in the 

effects analysis are impacted by pollutant sources other than vessel discharges such as industrial 

discharges, urban storm water, superfund sites, and agricultural runoff (see RAA-specific 

discussions of water quality impairments). Given that pollutant loads from vessel discharges are 

comparatively lower than those from other sources in the RAAs, and given that the estimated 

RQs from vessel discharges alone are extremely low, EPA believes that vessel discharges 

covered under the VGP and sVGP are unlikely the major pollution sources for listed species with 

identified sensitivities to water pollution. 

Comment 11: Discuss potential ways EPA could use monitoring data collected as part of 

requirements in the VGP and sVGP to improve the BE analysis. 

Relevant Section in the BE: Section 5.2.6.1 

EPA Response: EPA used the most robust data sources available to develop the pollutant loads 

used in the modeling analysis; however, data gaps exist for certain combinations of vessel types, 

discharges, pollutants, and vessel populations. Although EPA used best professional judgment to 

extrapolate the pollutant concentrations and flow information among the different vessel types 

and vessel populations, the extrapolation of information represents a source of uncertainty in the 

analysis. Data collected as part of the monitoring requirements proposed in VGP and sVGP will 

improve the quality of information used for EPA’s future analyses. For example, EPA requires 

monitoring of ballast water treatment system metrics and certain discharge parameters. EPA can 

later use these results to evaluate the whether ballast water treatment systems continue to 

perform after installation, and whether we are continuing to meet our objectives of reducing risk 

from ballast water discharges. 

Comment 12: Describe the techniques available for ANS control and include a discussion of the 

feasibility or infeasibility of each option to document why the control option selected by EPA is 

the most effective control option that is feasible/reasonable. 
Attachment F - EPA Responses to Services’ Input

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Relevant Section in the BE: Sections 6.1.2 and 6.1.3. 

EPA Response: These issues are addressed in the VGP and sVGP Fact Sheets (see Part 4 of the 

VGP Fact Sheet). In the BE, options for control of ANS introduction via ballast water discharge 

are addressed in Section 6.1.2 (Reducing Propagule Pressure by Ballast Water Management), 

subsections 6.1.2.1 through 6.1.2.8. Options for control of ANS introduction via biofouling are 

addressed in Section 6.1.3 (Reducing Propagule Pressure by Biofouling Management), 

subsections 6.1.3.1 through 6.1.3.4. EPA revised the outline and content presented in these 

sections to address this comment. EPA notes that the Clean Water Act requires effluent limits 

based upon best available technology, which may be different than how the Services’ defines 

“feasible/reasonable.” 

Comment 13: Describe overall variability, seasonal and regional factors influencing propagule 

pressure. 

Relevant Section in the BE: For ballast water discharge, see Sections 5.1.1.3.1 (Volume and 

Discharge of Ballast Water), 5.1.1.3.2 (Abundance and Diversity of Organisms in Ballast Water), 

and especially 5.1.1.3.3 (Variability of Propagule Pressure from Ballast Water). For biofouling, 

see Sections 5.1.1.4.1 (Extent of Fouling on Commercial Vessels), 5.1.1.4.2 (The Relationship of 

Biofouling to Underwater Ship Husbandry), 5.1.1.4.3 (Abundance and Diversity of Organisms 

Entering U.S. Coastal Waters on Vessel Hulls), and especially 5.1.1.4.4 (Variability of Propagule 

Pressure from Fouling Organisms). 

EPA Response: EPA revised the outline and content presented in Sections 5.1.1.3.1, 5.1.1.3.2, 

5.1.1.3.3, 5.1.1.4.1, 5.1.1.4.2 , 5.1.1.4.3 and 5.1.1.4.4 to include discussion responsive to these 

issues. EPA also directs the Services to the recently completed National Academy of Sciences 

report referenced in this BE. 

Comment 14: Describe other mechanisms for introduction of ANS that would be subject to 

regulation under this action (e.g., anchor system, sea chest, internal seawater piping system, 

bilge, etc.). 

Relevant Section in the BE: Sections 5.1.1.5 (Other Vessel Discharges Potentially Harboring 

ANS), 6.1.3.3 (Management of Biofouling in Seawater Cooling Systems) and 6.1.4 (Control of 

ANS Discharges in Chain Locker Effluent). 

EPA Response: Other vessel discharge vectors for ANS introduction (chain locker effluent, sea 

chests, seawater cooling systems, and fish hold effluent) are briefly discussed. However, these 

sources have generally not been identified as primary sources of concern onboard vessels, and a 

profound lack of data regarding these vectors prevents a meaningful analysis. This opinion is 

based upon EPA’s review of the most recent and authoritative studies and literature. For 

example, the 2011 Biennial Report on the California Marine Invasive Species Program (Takata 

et al., 2011) states: 

“Commercial ships transport organisms through two primary mechanisms – ballast water 

and vessel fouling”. 

This report goes on address prevention of ANS introduction via vector management, specifically 

ballast water management and vessel fouling management; other mechanisms of vessel-mediated 

ANS introduction are not even mentioned. 
Attachment F - EPA Responses to Services’ Input

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Australia’s National System for the Prevention and Management of Marine Pest Incursions 

published a study of the Relative Contribution of Vectors to the Introduction and Translocation 

of Invasive Marine Species (Takata et al., 2006) which identified a number of ANS transport 

mechanisms in the marine environment that have largely been associated with commerce and 

exploration. A number of these mechanisms are only relevant historically (wooden vessels, dry 

ballast, etc.). As the authors state: 

“While it is believed that these (historical) transport mechanisms have ceased, others 

have become more apparent (e.g., ballast water)” 

Generally, we believe vessel discharge vectors other than ballast water and biofouling are 

discountable. EPA revised the outline and content presented in Sections 5.1.1.5, 6.1.3.3 and 6.1.4 

to include discussion, to the extent information is available, to address this request from the 

Services. 

Comment 15: Describe the mechanisms by which ANS can affect listed species (e.g., 

competition, infection, altered food web, predation, biogeochemistry). 

Relevant Section in the BE: Section 5.1.1.7.4 (Mechanisms by which ANS Impact Native 

Species) 

EPA Response: EPA revised the outline and BE to add Section 5.1.1.7.4 to be responsive to this 

request from the Services. 

Comment 16: Describe “how” and, as much as possible, to what extent ballast water 

treatment/effective hull management reduces risk from ANS. 

Relevant Section in the BE: Section 5.1.1.6.2 (Discharge (Release and Inoculation): Propagule 

Pressure), 6.1.1 (Mitigating Risk of ANS by Reducing Propagule Pressure), 6.1.2 (Reducing 

Propagule Pressure by Ballast Water Management) and 6.1.3 (Reducing Propagule Pressure by 

Biofouling Management). 

EPA Response: EPA revised the outline and content presented in Section 6.1.1 to be responsive 

to this request from the Services. As discussed in this section of the BE, the risk reductions 

achieved by ballast water treatment/effective hull management are fundamentally based on 

reducing propagule pressure. This is also addressed in Section 5.1.1.6.2. Sections, 6.1.2 and 6.1.3 

document the extent to which ballast water treatment/effective hull management mitigate the risk 

of ANS invasion. EPA has incorporated requirements in the permits for hull management to 

reflect these concerns/issues. 

Comment 17: Please include other vectors, or provide reasons why the threats from those 

vectors are discountable. 

Relevant Section in the BE: See response to Comment 14 
Attachment F - EPA Responses to Services’ Input

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EPA Response: See response to Comment 14. Additionally, EPA did not address other nonvessel vectors for ANS introduction (aquaculture, exotic animal trade, etc.) because these are not 

within the scope of the VGP or the sVGP. 

References

Takata, L. Falkner, M. and S. Gilmore. 2006. Commercial Vessel Fouling in California: 

Analysis, Evaluation, and Recommendations to Reduce Nonindigenous Species Release 

from the Non-Ballast Water Vector. Produced for the California State Legislature by the 

California State Lands Commission, Marine Facilities Division. April 2006. Retrieved 

from http://groups.ucanr.org/Ballast_Outreach/files/25918.pdf. 

Takata, L., Dobrowski, N., Scianni, C. and M. Faulkner. 2011. 2011 Biennial Report on the 

California Marine Invasive Species Program. Produced for the California State 

Legislature by the California State Lands Commission, Marine Facilities Division. 

January, 2011.