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Aquatic Indicators

Ecological indicator: A characteristic of an ecosystem that is related to, or derived from, a measure of a biotic or abiotic attributes that can provide quantitative information on ecological condition, structure and function. An indicator can contribute to a measure of integrity and sustainability.

Currently, EMAP considers two principal types of indicators, condition and stressor (U.S. EPA, 1998). Condition indicators are biotic or abiotic characteristics of an ecosystem that can provide an estimate of the condition of an ecological resource with respect to some environmental value, such as biotic integrity. Stressor indicators are characteristics that are expected to change the condition of a resource if the intensity or magnitude is altered. EPA ORD's aquatic stressors research information.

 Lakes Physical Habitat, Fish, Fish Tissue, Zooplankton, Diatoms, Benthic Invertebrates,
 Rivers & Streams Water Quality, Physical Habitat, Macroinvertebrates, Fish, Fish Tissue, Periphyton, Data Collection
 Greatl Lakes Water Quality, Sediment, Biotic Assemblages, Habitat

Field Operations Manuals for sampling aquatic resources.


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Physical Habitat: The physical habitat shoreline and littoral surveys that the Surface Waters field teams conduct serve three purposes. First, this habitat information is absolutely essential to the interpretation of what lake biological assemblages "should" be like in the absence of many types of anthropogenic impacts. Second, the habitat evaluation is a reproducible, quantified estimate of habitat condition, serving as a benchmark against which to compare future habitat changes that might result from anthropogenic activities. Third, the specific selections of habitat information collected aid in the diagnosis of probable causes of ecological impairment in lakes.

In addition to information collected in the field by the shoreline and littoral surveys, the physical habitat description of each lake includes many map-derived variables such as lake surface area, shoreline length, and shoreline complexity. Furthermore, an array of information, including watershed topography and land use, supplements the physical habitat information. The shoreline and littoral surveys concentrate on information best derived "on the ground." As such, these survey results provide the all-important linkage between large watershed-scale influences and those forces that directly affect< aquatic organisms day to day. Together with water chemistry, the habitat measurements and observations describe the variety of physical and chemical conditions that are necessary to support biological diversity and foster long-term ecosystem stability. These characteristics of lakes and their shorelines are the very aspects that are often changed as a result of anthropogenic activities.

Development of a Technique for Lake Habitat Survey (LHS): Phase 2, 2006. SNIFFER project WFD42 www.sniffer.org.uk (Document pdf 9.2 MB, Field Guide pdf 3.8 MB, Executive Summary pdf)

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Fish Assemblages: Major objectives for the fish assemblage indicator work are to collect an index sample of the fish assemblage at each lake and to use the data derived from these samples to develop metrics of biological integrity. Biological integrity is a measure of the ability of the biotic components of an ecosystem to maintain a level of diversity and functional organization that is comparable to natural systems unimpacted by human disturbance (Karr and Dudley, 1981; Karr et al., 1986; Noss, 1990). Following the approach of Karr (1986) for use in streams, metrics are developed from numerical measures of various attributes of lake fish assemblage structure and composition.

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Fish Tissue Contaminants: The fish tissue contaminants indicator has characteristics of both response and diagnostic indicators (Paulsen et al. 1991). As a response indicator tissue contaminant levels can be used to infer effects on piscivorous populations in and around lakes. When response indicators identify lake degradation, the fish tissue contaminants indicator can also be used in conjunction with other diagnostic indicators (physical habitat, water chemistry, land use, population density, and other records of relevant anthropogenic stresses) to discover the probable causes. Analyses of fish tissue detect contaminants such as a number of organochlorinated pesticides, PCB congeners, and heavy metals, including mercury.

Zooplankton: Zooplankton are important components of the open water environment of lakes and ponds. Most species are microscopic and consist of crustaceans (copepods, cladocerans, and opossum shrimp), rotifers ("wheel-animals"), pelagic insect larvae (phantom midge), and aquatic mites. In lakes of the northeastern United States, more than 200 species have been recorded. Zooplankton are important elements of the food chain where they transfer energy from algae (primary producers) to larger invertebrate predators and fish. The zooplankton species assemblage responds to environmental stressors such as nutrient enrichment, acidification, and fish stocks. The effects of environmental stress can be detected through changes in species composition and abundance, body size distribution, and food web structure.

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Sediment Diatoms: The diatom indicator is unique in that it can potentially tell us the "original" or pristine condition of the lake. None of the other indicators can provide this information. Thus, sampling the sediments in a precise and consistent manner is particularly critical. To assess the original condition, sediments dating from that time need to be collected. A general understanding of the diatom indicator and the sampling and analysis process will enhance sample collection.

Benthic Invertebrate Assemblages: Bottom dwelling invertebrates have long been used as indicators of water quality throughout this country and abroad. In the United States their use as living monitors of environmental conditions has principally been applied in environmental assessments of rivers and streams. However, European biologists have used benthic invertebrates for purposes of classifying lakes as to trophic status since the 1920s. Although their use for this purpose has not been as widespread in North America as it has been in Europe, these organisms show great potential as indicators of the biotic integrity and ecological condition of this Nation's lakes and reservoirs.

Currently there are a number of indices of biotic integrity for invertebrate assemblages in streams, but these indices have not been widely applied to lake assemblages. Benthos sampling is restricted to the sublittoral zones of EMAP sample lakes.

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Rivers & Streams

Water Quality  Physiochemical water quality characteristics affect the ability of species to persist in a given lotic habitat. Water quality data are collected to determine the acid-base status, trophic condition (nutrient enrichment), and chemical stressors. Physical parameters include light penetration (e.g., turbidity, suspended solids), temperature and ionic strength (e.g., conductivity). Chemical parameters include the concentrations of dissolved gases, major cations, anions, and nutrients (i.e., nitrogen, phosphorus).

EMAP:  Data are collected from each stream for a variety of physical and chemical constituents. Information from these analyses is used to evaluate stream condition with respect to stressors such as acidic deposition (of importance to the TIME project), nutrient enrichment, and other inorganic contaminants. In addition, streams can be classified with respect to water chemistry type, water clarity, mass balance budgets of constituents, temperature regime, and presence of anoxic conditions. Examples of relationships between stream chemistry and watershed-level land use data are described in Herlihy et al. (1998).

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Physical Habitat  Stream physical habitat includes all those structural attributes that influence or sustain organisms within the stream. Habitat assessments generally provide a critical understanding of a stream's ecology. Some common physical habitat attributes are stream size, channel gradient, channel substrate size and type, habitat complexity and cover, and riparian vegetation cover and structure. The understanding of the physical habitat of an area allows for better assessments of the stream ecosystem and human caused effects.

EMAP Western Pilot:  Naturally occurring differences among surface waters in physical habitat structure and associated hydraulic characteristics contributes to much of the observed variation in species composition and abundance within a zoogeographic province. The structural complexity of aquatic habitats provides the variety of physical and chemical conditions to support diverse biotic assemblages and maintain long-term stability. Anthropogenic alterations of riparian areas and stream channels, wetland drainage, grazing and agricultural practices, and stream bank modifications such as revetments or development, generally act to reduce the complexity of aquatic habitat and result in a loss of species and ecosystem degradation.

Stressor indicators derived from data collected about physical habitat quality will be used to help explain or diagnose stream condition relative to various condition indicators. Important attributes of physical habitat in streams are channel dimensions, gradient, substrate characteristics; habitat complexity and cover; riparian vegetation cover and structure; disturbance due to human activity, and channel-riparian interaction (Kaufmann, 1993). Overall objectives for this indicator are to develop quantitative and reproducible indices, using both multivariate and multimetric approaches, to classify streams and to monitor biologically relevant changes in habitat quality and intensity of disturbance. Kaufmann et al. (1998) discuss procedures for reducing EMAP field habitat measurements and observations to metrics that describe channel and riparian habitat at the reach scale.

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Aquatic Macroinvertebrate Assemblage:  Aquatic macroinvertebrates play important functional roles in lotic ecosystems and are good indicators of stream quality. Aquatic macroinvertebrates represent a fundamental link in the food web between organic matter resources (e.g., leaf litter, periphyton, detritus) and fishes. Within specific biogeographical regions, aquatic macroinvertebrate assemblages respond in predictable ways to changes in stream environmental variables. Because many aquatic macroinvertebrates have limited migration patterns or a sessile mode of life, they are particularly well suited for assessing site-specific effects.

EMAP Western Pilot: Benthic macroinvertebrates inhabit the sediment or live on the bottom substrates of streams. The macroinvertebrate assemblages in streams reflect overall biological integrity of the benthic community , and monitoring these assemblages is useful in assessing the status of the water body and discerning trends. Benthic communities respond differently to a wide array of stressors. As a result of this, it is often possible to determine the type of stress that has affected a benthic macroinvertebrate community (Plafkin et al., 1989; Klemm et al., 1990; Barbour et al. 1999). Because many macroinvertebrates have relatively long life cycles of a year or more and are relatively immobile, macroinvertebrate community structure is a function of past conditions.

Two different approaches are currently being evaluated to developing ecological indicators based on benthic invertebrate assemblages. The first is a multimetric approach, where different structural and functional attributes of the assemblage are characterized as "metrics". Individual metrics that respond to different types of stressors are scored against expectations under conditions of minimal human disturbance. The individual metric scores are then summed into an overall index value that is used to judge the overall level of impairment of an individual stream reach. Examples of multimetric indices based on benthic invertebrate assemblages include Kerans and Karr (1993), Fore et al. (1996) Barbour et al. (1995; 1996), and Klemm et al. (In press).

The second approach being investigated is to develop indicators of condition based on multivariate analysis of benthic assemblages and associated abiotic variables. Examples of this type of approach as applied to benthic invertebrate assemblages include RIVPACS (Wright, 1995), and BEAST (Reynoldson et al., 1995). Rosenberg and Resh (1993) present various approaches to biological monitoring using benthic invertebrates, and Norris (1995) briefly summarizes and discusses approaches to analyzing benthic macroinvertebrate community data.

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Fish and Aquatic Vertebrate Assemblage:  The fish and other aquatic vertebrates can indicate stream and riparian quality. Extensive life history information is available for many species, and because many are high order consumers, they often reflect the responses of the entire trophic structure to environmental stress. Also, fish provide a more publicly understandable indicator of environmental degradation. Fish generally have long life histories and integrate pollution effects over longer time periods and large spatial scales.

EMAP Western Pilot: Aquatic vertebrate assemblages of interest to EMAP include fish and amphibians. The fish assemblage represents a critical component of biological integrity from both an ecosystem function and a public interest perspective. Historically, fish assemblages have been used for biological monitoring in streams more often than in lakes (e.g., Plafkin et al., 1989; Karr, 1991). Fish assemblages can serve as good indicators of ecological conditions because fish are long-lived and mobile, forage at different trophic levels, integrate effects of lower trophic levels, and are reasonably easy to identify in the field (Plafkin et al., 1989). Amphibians comprise a substantial portion of vertebrate biomass in streams of many areas of the U.S. (Hairston, 1987; Bury et al., 1991). Reports of dramatic declines in amphibian biodiversity (e.g., Blaustein and Wake, 1990; Phillips, 1990) has increased the level of interest in monitoring these assemblages. Amphibians may also provide more information about ecosystem condition in headwater or intermittent streams in certain areas of the country than other biological response indicators (Hughes, 1993). The objective of field sampling is to collect a representative sample of the aquatic vertebrate assemblage by methods designed to 1) collect all except very rare species in the assemblage and 2) provide a measure of the abundance of species in the assemblages (McCormick, 1993; Reynolds et al., 2003). Information collected for EMAP that is related to vertebrate assemblages in streams includes assemblage attributes (e.g., species composition and relative abundance) and the incidence of external pathological conditions.

Indicators based on vertebrate assemblages are being developed primarily using the multimetric approach described in Section 1.3.5 for benthic macroinvertebrates, and originally conceived by Karr and others (Karr et al., 1986). Simon and Lyons (1995) provide a recent review of multimetric indicators as applied to stream fish assemblages. (McCormick et al. (2001) provide an example of a multimetric indicator developed for the Mid-Atlantic region using EMAP data, based on an evaluation process described by Hughes et al. (1998).

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Fish Tissue Contaminants:

EMAP Western Pilot: Indicators of fish tissue contaminants attempt to provide measures of bioaccumulation of toxic chemicals in fish. The primary purpose of determining contaminant levels in fish tissue is to provide a measure of the potential exposure of stream systems to toxic compounds. It is also meant to be used in conjunction with the other stressor indicators (physical habitat, water chemistry, land use, population density, other records of relevant anthropogenic stresses) and condition indicators (fish, macroinvertebrates, periphyton) to help diagnose whether the probable cause of stream degradation, when it is shown by the condition indicators to occur, is water quality, physical habitat, or both.

The various studies that have been done on fish tissue contaminants have focused on different parts of the fish: whole fish, fillets, livers. For EMAP-SW, the focus is on whole fish because of the emphasis on the ecological health of the whole stream (as opposed to a focus on human health concerns). Whole fish are a better indicator of risk to piscivorous wildlife than fillets. It is hoped to also be able to say something about risks to human health by analyzing whole fish. Whole fish also present fewer logistical problems for field crews (no gutting required in the field) and the analytical lab (no filleting necessary). Yeardley et. al. (1998), Peterson et al. (2002), and Lazorchak et al. (2003) provide examples of the use of fish tissue contaminant data in EMAP studies.

Samples are prepared for two major categories of fish species. One sample is prepared using a species whose adults are small (e.g., small minnows, sculpins, or darters). The second sample is prepared using a species whose adults are of larger size (e.g., suckers, bass, trout, sunfish, carp). In addition to being more ubiquitous than the larger fish (and therefore more likely to be present in sufficient numbers to composite), small fish have other advantages over large fish. Most importantly, it may be possible to get a more representative sample of the contaminant load in that stream segment (although it could be at a lower level of bioaccumulation) by creating a composite sample from a larger number of small individuals than by compositing a few individuals of larger species. The major advantage that larger fish could potentially offer, whether predators (piscivores) or bottom feeders, is a higher level of bioaccumulation and thus greater sensitivity to detect contaminants. The relative bioaccumulation of contaminants by large and small stream fish is not known, thus the reason for preparing two samples in this study.

Periphyton:  Periphyton are algae, fungi, bacteria, protozoa, and associated organic matter associated with channel substrates. Periphyton are useful indicators of environmental condition because they respond rapidly and are sensitive to a number of anthropogenic disturbances, including habitat degradation, contamination by nutrients, metals, herbicides, hydrocarbons, and acidification.

EMAP Western Pilot: Periphyton are the algae, fungi, bacteria, and protozoa associated with substrates in aquatic habitats. These organisms exhibit high diversity and are a major component in energy flow and nutrient cycling in aquatic ecosystems. Many characteristics of periphyton community structure and function can be used to develop indicators of ecological conditions in streams (Hill et al., 1999). Periphyton are sensitive to many environmental conditions, which can be detected by changes in species composition, cell density, ash free dry mass (AFDM), chlorophyll, and enzyme activity (e.g., alkaline and acid phosphatase). Each of these characteristics may be used, singly or in concert, to assess condition with respect to societal values such as biological integrity and trophic condition.

A hierarchical framework is being used in the development of the periphyton indices of stream condition. The framework involves the calculation of composite indices for biotic integrity, ecological sustainability, and trophic condition. The composite indices will be calculated from measured or derived first-order and second-order indices. The first-order indices include species composition (richness, diversity), cell density, AFDM, chlorophyll, and enzyme activity (e.g., Saylor et al., 1979), which individually are indicators of ecological condition in streams. Second-order indices will be calculated from periphyton characteristics, such as the autotrophic index (Weber, 1973), community similarity compared to reference sites, and autecological indices (e.g., Lowe, 1974; Lange-Bertalot, 1979; Charles, 1985; Dixit et al, 1992). Hill et al. (2000, 2003) describe the development of a multimetric index based on periphyton assemblages in wadeable streams.

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Data Collection:  Methods of data collection have been developed for each of the core indicators. In-depth explanation of data collection methods used for the EMAP Western Pilot are available in "Surface Waters Western Pilot Study: Field Operations Manual for Wadeable Streams". Download the Surface Waters Manual (pdf 38MB)

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Great Rivers Metrics and Indicators

Water Quality
  • Dissolved oxygen
  • Dissolved N (NOx, ammonia)
  • Conductivity
  • pH
  • Metals (As, Pb, Se, CU, Fe, Ni)
  • Temperature
  • Anions & Cations
  • Turbidity, suspended matter
  • Alkalinity
  • Total & Dissolved P, N, & C
  • Elemental particle analysis
  • Particulate stable isotopes
  • Chlorophyll
  • Enzyme activity
  • Toxicity
  • Total and volatile matter
  • Chemistry (organics, inorganics)
Biotic Assemblages
  • Fish
  • Tissue contaminants
  • Invertebrates
  • Littoral benthos
  • Snags
  • Zooplankton
  • Phytoplankton
  • Periphyton
  • Submersed aquatic vegetation
  • Littoral
  • Vegetation cover
  • Substrate
  • Velocity
  • Woody debris
  • Riparian
  • Vegetation cover
  • Invasive/exotic species

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