The term "periphyton" is sometimes used to refer to the benthic algae, while others use the term to refer to the entire attached community of microorganism, including algae, bacteria, fungi, and protozoa. To avoid confusion, this section will refer to the attached, bottom dwelling algae as benthic algae. Algae that are suspended or actively swimming in the water column, primarily in lakes, ponds, and backwater areas are the phytoplankton. Benthic algae are sensitive indicators of change in streams as well as being the primary producers within that ecosystem. The benthic algae are usually the dominant component of the periphyton. Because it is attached to the substrate, the algal community integrates physical and chemical disturbances to a stream. Other advantages of using the algal in water quality assessment are: the algal community contains a naturally high number of species, making data useful for statistical and numerical applications to assess water quality. Response time of the benthic algal community is rapid, as is recovery time, with recolonization after a disturbance often more rapid than for other organisms. Diatoms in particular are useful indicators of biological integrity because they are ubiquitous; at least a few can be found under almost any conditions. In addition, most can be identified to species by experienced biologists, and tolerance or sensitivity to specific changes in environmental conditions are known for many species. By using algal data in association with macroinvertebrate and fish data, the biological integrity of the entire ecosystem can be ascertained.

While in the field, qualitatively rank the algal community at each station. A score of 1 (lowest quality) to 5 (highest quality) is possible. Record scores and a description of the algal community in a logbook or on a field data sheet. While somewhat subjective, this information can be used later to support a detailed assessment of the algal community. The algae are carefully judged using the following ranking criteria:

Algae can be collected in the field and taken back to the laboratory for further analysis if a microscope is available. If so, the community can be studied in much greater detail. Qualitative collections should be made by scraping benthic algae from all available substrates. Collect a composite qualitative sample by sampling microhabitats in roughly the proportion that they occur at the site. Sample both riffles and pools, or select one major habitat type (usually riffle) if it occurs at all sites to be compared in the study. During drought periods, pools may be the only habitat available. Collect samples during stable low-flow conditions. After extremes of flooding or drought, allow at least a two week recolonization period before sampling. Collect samples using the following methods:

2. Use a suction device to collect algae from bedrock substrates. Press a section of PVC pipe equipped with a neoprene rubber gasket against the bedrock substrate so that the periphyton within the enclosed area can be dislodged with a stiff-bristled brush. Suction dislodged material into a filter flask using a hand-operated pump. This method can be used to obtain quantitative data from bedrock (modified from Douglas 1958).
1. Gently lift algal mats from depositional areas with a flat knife blade or by suctioning with a disposable pipette or a turkey baster.

After collection, samples can be taken back to the laboratory and examined under a microscope either in a live condition (preserve by placing samples in a cooler with ice) or "fixed" with a 4% formaldehyde solution (Caution is required when working with formaldehyde. Do not breathe it or let it get on your skin. If it does, wash the affected body part immediately.)

Several slides should be prepared and scanned under a compound microscope to identify the types and relative abundance (percentage) of each algal species present. A good book to start with for identification is "How to Know the Freshwater Algae" by G. Prescott (Third edition, 1978.)

Biologists use the following "Metrics" to analyze the algal community. They can be used if proper counting and identification techniques are used:

Taxa richness is an estimate of the total number of species present in the community, made by counting the number of species collected. It is only an estimated because in reality all the species present in a community are never collected. In general, taxa richness and the impairment that exists at a particular site within a waterbody are inversely related. Extremely low taxa richness indicates the possible occurrence of a toxicity problem (for example, acid mine drainage), while high taxa richness suggests clean water. However, extremely high taxa richness in small streams may indicate a minor degree of nutrient enrichment, while low taxa richness may be normal in small, naturally nutrient poor (oligotrophic) streams.

Certain taxa can be indicators of pollution. Autecological information on these indicator taxa is available in published references and is somewhat well known for diatom species in particular. Indicator categories are provided in the following table. Presence and relative abundance of indicator taxa is recorded and used in conjunction with other data to determine water quality impairment.

heading Bacillariophyceae) is estimated as follows:

Representatives from several divisions of algae are common from sites with good water quality. The number of divisions represented is reported as an indicator of diversity.

Algal divisions common in Kentucky streams include:

Chlorophyta: Green algae. Found in almost all lakes and streams, in a variety of environmental conditions. Cladophora is a common green algae that forms long filaments attached to rocks and other solid substrates in streams. Its filaments can grow up to 2 meters long, especially in nutrient enriched streams.

Other examples are: Hydrodictyon (water net), Spirogyra, Chlamydomonas.

Cyanophyta: Bluegreen algae. Because of their bacteria-like morphology, they are sometimes classified as bacteria, but they are an important part of the periphyton community. Because they are photosynthetic organisms, they are discussed here with the algae. The "bluegreens" are important environmentally because they can fix nitrogen and store phosphorus, so they can thrive when nutrient and other environmental conditions do not favor the other algae. They can form noxious blooms in ponds, lakes, and reservoirs. These blooms can cause oxygen depletion (resulting in fish kills), and taste and odor problems in drinking water, and can sometimes be toxic to livestock. In streams, the bluegreen algae are usually less troublesome, and are found in waters ranging from pristine to severely polluted.

Examples of bluegreen algae: Anabaena, Aphanizomenon, Microcystis, Oscillatoria, Phormidium.

Chrysophyta: Yellow-green algae or Golden-brown algae (diatoms). The most common group are the diatoms, called golden-brown algae because of the golden to rich brown color that mats of these microorganisms can form on almost any substrate in the stream. Diatoms are found in every aquatic habitat and are the group of algae most commonly used in water quality analysis. They are found in a wide range of environmental conditions, some species are tolerant of pollution while others are extremely sensitive.

Common diatoms include: Navicula, Nitzschia, Cymbella, Gomphonema.

Other non-diatom Chrysophyta include the filamentous Vaucheria and the planktonic Synura.

Rhodophyta: Red algae. There are several genera of freshwater red algae in Kentucky. They may be olive-green, maroon, brown, or green in color. There texture is sometimes rough, as in Lemanea or can be extremely slimy, as in Batrachospermum. They are most often found in cool shady streams with fairly good water quality, and further study of this group may result in their use as good water quality indicators.

Euglenophyta: Euglenoids. Common in ponds and nutrient rich lakes and reservoirs, these organisms are planktonic and equipped with flagella for movement in the water column.

Common genera include: Euglena, Trachylomonas, Phycus

Pyrrophyta: Dinoflagellates. Also planktonic and more common in ponds, lakes and reservoirs than in streams or rivers. Related to organisms that cause red tide shellfish poisoning in the marine environment, but not known to cause any similar problems in freshwater. They can, however, cause blooms that result in taste and odor problems in drinking water reservoirs.

1. Chlorophyll a

Chlorophyll a analyses are performed using U.S. EPA Method 445.0 (1992) (preferred method) or Standard Methods for the Examination of Water and Wastewater (American Public Health Association (1992).

Benthic chlorophyll a values are used as an estimate of algal biomass. Chlorophyll a values can be extremely variable because of the patchiness of benthic algal distribution; therefore, assessments are based on a mean of three or more replicate samples. These values are used to compare biomass accrual at the same station over time or between stations during the same sampling period. High chlorophyll a values may indicate nutrient enrichment, while extremely low values may either indicate low nutrient availability, toxicity, or low-light availability because of shading, sedimentation, or high turbidity. Chlorophyll a values are used to support community structure analyses.

Ash-Free Dry-Weight (AFDW) samples are analyzed in accordance with Standard Methods (APHA 1992). Benthic AFDW values are used as an estimate of total organic material accumulated on the artificial substrate. This organic material includes all living organisms (algae, bacteria, fungi, protozoa, and macroinvertebrates) as well as non-living detritus. Ash-free dry-weight values have been used in conjunction with chlorophyll a as a means of determining the trophic status (autotrophic vs. heterotrophic) of streams. The Autotrophic Index (AI) is calculated as:

AI=AFDW(mg/m²) / chlorophyll a (mg/m²)

High AI values (>200) indicate the community is dominated by heterotrophic organisms, and extremely high values may indicate poor water quality. This may be a result of organic (sewage) or other pollution; however, this index should be used with discretion, as non-living organic detritus can artificially inflate the AFDW value.