1. Benthic Assessments One benthic ecologists concerns and suggestions Fred Nichols USGS, retired

2. Introduction Where I am coming from As a marine invertebrate ecologist, I want to know why species live where they do. That is, what determines their distribution and abundance in space and time? As a marine invertebrate ecologist, I want to know why species live where they do. That is, what determines their distribution and abundance in space and time? With respect to evaluating human influences on invertebrates, it is important to first define natural variability, in both species and their environment. With respect to evaluating human influences on invertebrates, it is important to first define natural variability, in both species and their environment. It is against the background of natural variability that the effects of human stressors should be measured. It is against the background of natural variability that the effects of human stressors should be measured.

3. Evolution of indices/assessments (Nichols version) Long history of evaluating the relative abundance of tolerant vs. sensitive species. Long history of evaluating the relative abundance of tolerant vs. sensitive species. The concept of trophic indices applied to continental shelves, e.g., organic enrichment off Los Angeles The concept of trophic indices applied to continental shelves, e.g., organic enrichment off Los Angeles Index of Biological Integrity applied to freshwater systems, contrasting impacted with pristine streams or watersheds (James Karr) Index of Biological Integrity applied to freshwater systems, contrasting impacted with pristine streams or watersheds (James Karr) EPA EMAP expanded a condition index concept to estuaries EPA EMAP expanded a condition index concept to estuaries

4. Introduction What we have learned about estuaries Distribution and abundance are determined by many factors such as dispersal of larvae, substrate type, food availability, predation, and physical stressors. Distribution and abundance are determined by many factors such as dispersal of larvae, substrate type, food availability, predation, and physical stressors. Abundances of individual species fluctuate widely over time. Abundances of individual species fluctuate widely over time. Most species, particularly estuarine species, are durable – they tolerate a varying environment. Most species, particularly estuarine species, are durable – they tolerate a varying environment. We continue to be surprised by the very large ecosystem changes that periodically occur (e.g., in the benthos, plankton and fish communities). We continue to be surprised by the very large ecosystem changes that periodically occur (e.g., in the benthos, plankton and fish communities).

7. Introduction What we have learned (2) Most estuarine and coastal environments are somewhat contaminated. Most estuarine and coastal environments are somewhat contaminated. At heavily contaminated sites, the effects are usually obvious - few species survive. At heavily contaminated sites, the effects are usually obvious - few species survive. We are steadily making progress in understanding how individual species respond to contamination. We are steadily making progress in understanding how individual species respond to contamination. Distinguishing clearly between the effects of natural factors and the effects of low to moderate contamination on community composition in estuaries has been exceedingly difficult, despite decades of good effort. Distinguishing clearly between the effects of natural factors and the effects of low to moderate contamination on community composition in estuaries has been exceedingly difficult, despite decades of good effort.

8. Role of Benthic Assessments EMAP, IBI, etc. It is indeed important to take geographically comprehensive approaches in evaluating the condition of estuarine/coastal benthic habitats, e.g., the Triad approach: It is indeed important to take geographically comprehensive approaches in evaluating the condition of estuarine/coastal benthic habitats, e.g., the Triad approach: Define community composition Define community composition Assess contaminant distributions Assess contaminant distributions Carry out bioassays Carry out bioassays Such studies provide objective means of describing contaminant distributions and distinguishing those sites that seem to be most affected by contaminants. Such studies provide objective means of describing contaminant distributions and distinguishing those sites that seem to be most affected by contaminants.

9. My Primary Concerns A. Interpreting contaminant effects on communities from limited sampling in physically dynamic environments. B. Tracking the status of environmental condition over time, i.e., trends.

10. A.Contaminant effects in dynamic environments I nfluence of salinity (1) Benthic community structure in river-dominated estuaries is in large part determined by physical processes, of which salinity is a key indicator. Benthic community structure in river-dominated estuaries is in large part determined by physical processes, of which salinity is a key indicator. Physically dynamic estuaries like San Francisco Bay exhibit large and often sudden changes in salinity. Physically dynamic estuaries like San Francisco Bay exhibit large and often sudden changes in salinity. Species distributions and abundances can change dramatically in response to the changing conditions. Species distributions and abundances can change dramatically in response to the changing conditions.

11. Contaminant effects in dynamic environments Influence of salinity (2) EMAP-type studies, typically based infrequent sampling, assume that the relationship between community composition and salinity is defined at the time of sampling. EMAP-type studies, typically based infrequent sampling, assume that the relationship between community composition and salinity is defined at the time of sampling. Salinity measured at the time of sampling does not necessarily define the conditions under which community composition was established. Salinity measured at the time of sampling does not necessarily define the conditions under which community composition was established. The benthic community in the upper reaches of the Bay can be markedly influenced by water transport/salinity conditions months before the time of sampling. The benthic community in the upper reaches of the Bay can be markedly influenced by water transport/salinity conditions months before the time of sampling. The physical regime at the time of recruitment is probably a much more meaningful influence on community structure than physical conditions at the time that one collects adults. The physical regime at the time of recruitment is probably a much more meaningful influence on community structure than physical conditions at the time that one collects adults.

12. Contaminant effects in dynamic environments Influence of salinity (3) Infrequent sampling means that important events (storm, drought, flood, arrival of new predator, etc.) that determine species distributions/abundances are missed. Infrequent sampling means that important events (storm, drought, flood, arrival of new predator, etc.) that determine species distributions/abundances are missed. One should have an understanding of antecedent physical conditions when interpreting community composition at any moment in time. One should have an understanding of antecedent physical conditions when interpreting community composition at any moment in time. The combination of a fluctuating environment and infrequent sampling makes the interpretation of non- lethal human effects on community composition very challenging. The combination of a fluctuating environment and infrequent sampling makes the interpretation of non- lethal human effects on community composition very challenging.

13. B. Tracking environmental condition Tracking environmental condition, including contaminant effects, over time is critical to evaluating water quality management and policy decisions (adaptive management). Tracking environmental condition, including contaminant effects, over time is critical to evaluating water quality management and policy decisions (adaptive management). Geographically comprehensive but temporally limited sampling, combined with natural variability and few reference site options, can preclude meaningful biological community trends analysis Geographically comprehensive but temporally limited sampling, combined with natural variability and few reference site options, can preclude meaningful biological community trends analysis The goal should be to develop strategies that provide resource managers and decision makers with defensible trends information The goal should be to develop strategies that provide resource managers and decision makers with defensible trends information The challenge is to identify trends in human impacts (e.g., with the Triad approach) in shallow, physically dynamic estuaries where the time scales of important natural change in the community are typically shorter or longer than most sampling frequencies. The challenge is to identify trends in human impacts (e.g., with the Triad approach) in shallow, physically dynamic estuaries where the time scales of important natural change in the community are typically shorter or longer than most sampling frequencies.

14. Conclusions and Recommendations (1) Distinguishing human-induced effects on estuarine benthic community structure, other than at highly impacted sites, is a major and, I think, largely unmet challenge. Distinguishing human-induced effects on estuarine benthic community structure, other than at highly impacted sites, is a major and, I think, largely unmet challenge. To measure the effectiveness of actions taken to improve conditions in estuarine systems, the next generation of studies should focus on investigations designed specifically to evaluate trends, i.e., to measure both the short- and long-term patterns of variability and change in these systems. To measure the effectiveness of actions taken to improve conditions in estuarine systems, the next generation of studies should focus on investigations designed specifically to evaluate trends, i.e., to measure both the short- and long-term patterns of variability and change in these systems. Such studies should incorporate measures of natural perturbations of the environment in the analysis of the effects of contaminants on community structure Such studies should incorporate measures of natural perturbations of the environment in the analysis of the effects of contaminants on community structure

15. Conclusions and Recommendations (2) Making substantial progress in evaluating the effects of contaminants on the Bays ecosystem will require Making substantial progress in evaluating the effects of contaminants on the Bays ecosystem will require deciding what tractable questions can be answered with future assessment studies, and deciding what tractable questions can be answered with future assessment studies, and establishing permanent, frequently sampled sites in the areas of most concern. establishing permanent, frequently sampled sites in the areas of most concern. Because of the scope of the challenge, the greatest focus should perhaps be on those areas of San Francisco Bay that are known to be heavily contaminated, with the goal of: Because of the scope of the challenge, the greatest focus should perhaps be on those areas of San Francisco Bay that are known to be heavily contaminated, with the goal of: Distinguishing between natural and human induced impacts Distinguishing between natural and human induced impacts Tracking impacts over time to establish long-term trends. Tracking impacts over time to establish long-term trends.

16. Conclusions and Recommendations (3) We should urge more coordination among studies of the benthos, plankton and fish communities because they are so closely interconnected in a single food web. Each of these communities is critical to an understanding of overall conditions and trends in the estuary. We should urge more coordination among studies of the benthos, plankton and fish communities because they are so closely interconnected in a single food web. Each of these communities is critical to an understanding of overall conditions and trends in the estuary. We need to pay attention to what the individual species themselves, by their distribution and abundance patterns over time, are telling us about what is going on in the environment. We need to pay attention to what the individual species themselves, by their distribution and abundance patterns over time, are telling us about what is going on in the environment.