Biological monitoring, or biomonitoring, is the use of
biological responses to assess changes in the environment,
generally changes due to anthropogenic causes. Biomonitoring
programs may be qualitative, semi-quantitative, or
quantitative. Biomonitoring is a valuable assessment tool that
is receiving increased use in water quality monitoring
programs of all types.
There are two types of biomonitoring. One type of
biomonitoring is surveillance before and after a project is
complete or before and after a toxic substance enters the
water. The other type of biomonitoring is to ensure compliance
with regulations or guidelines or to ensure water quality is
Biomonitoring involves the use of indicators, indicator
species or indicator communities. Generally benthic
macroinvertebrates, fish, and/or algae are used. Certain
aquatic plants have also been used as indicator species for
pollutants including nutrient enrichment (Phillips and
Rainbow, 1993; Batiuk et al., 1992). There are advantages and
disadvantages to each. Macroinvertebrates are most frequently
used (Rosenberg and Resh, 1993). Biochemical, genetic,
morphological, and physiological changes in certain organisms
have been noted as being related to particular environmental
stressors and can be used as indicators.
The presence or absence of the indicator or of an indicator
species or indicator community reflects environmental
conditions. Absence of a species is not as meaningful as it
might seem as there may be reasons, other than pollution, that
result in its absence (e.g., predation, competition, or
geographic barriers which prevented it from ever being at the
site) (Johnson et al., 1993). Absence of multiple species of
different orders with similar tolerance levels that were
present previously at the same site is more indicative of
pollution than absence of a single species. It is clearly
necessary to know which species should be found at the site or
in the system.
Sentinel organisms, or indicator species that accumulate
pollutants in their tissues from the surrounding environment
or from food, are important biomonitoring devices (Phillips
and Rainbow 1993; Kennish 1992). The Mussel Watch is one such
use of a sentinel species (Phillips and Rainbow 1993; Kennish
1992). Filter feeders, such as bivalves (clams and mussels),
tend to concentrate metals in their gills or other tissues.
The widespread blue mussel (Mytilus edulis) accumulates metals
in certain tissues over time. As a result, M. edulis became a
species monitored in U.S. waters as well as internationally
for changes in levels of pollution (Phillips and Rainbow 1993;
Kennish 1992). Seaweeds, (e.g., Fucus spp.) accumulate metals.
Older algal tissue can be compared to newer tissue in the same
individual to determine the history of contaminants in an area
(Phillips and Rainbow, 1993). Metals and organochlorines
accumulate in finfish and territorial species or non-migratory
species such as pike, largemouth bass, can be used for an
accurate indication of mercury and organochlorine pollution in
a water body (Phillips and Rainbow, 1993).
||Copper (Cu), iron (Fe), manganese
|| Cu, Zn
||Cu, Fe, Pb, Zn
|| Most metals
|| Metals, metallothioneins
|| Cadmium (Cd), Pb
|| Cd, Pb
|| Cd, Pb
(Adapted from Phillips and Rainbow, 1993)
When the pollutant type is known or well understood, certain
indicators are more effectively used or are less expensive.
When stressors are not known and/or less is known about
species tolerance levels, multiple level assessment and more
intensive and expensive studies that may include toxicity
tests may be necessary (Johnson et al., 1993). Multiple level
assessment involves the monitoring of indicators and
behavioral changes of organisms. Indicators must display a
biochemical, genetic, morphological, or physiological change.
Behavioral indices are determined by particular species,
populations dynamics, or community changes.
Community level biomonitoring provides information on the
magnitude and ecological effects of the stressor on the
system. Cause and effect relationships are difficult to
establish and few definitely exist, because possible
confounding factors are often present (Johnson et al., 1993).
Using indicators at different organizational levels (for
example, individuals, species, community, ecosystem) may be
Biomonitoring measures may be used at the different, but
related, levels of analysis:
Levels of Organization and Associated Biomonitoring Measures
Individual - Organism - genetic mutations - reproductive
success - physiology - metabolism - oxygen consumption,
photosynthesis rate - enzyme/protein activation/inhibition -
hormones - growth and development - disease resistance -
tissue/organ damage - bioaccumulation Population -
survival/mortality - sex ratio - abundance/biomass - behavior
(migration) - predation rates - population decline/increase
Community - Abundance ("evenness") of an organism or
organisms - Biomass - Density of an organism or organisms -
Richness (variety) - number of species, size classes, or other
functional groups, per unit area or volume, or per number of
individuals. - Diversity - the richness given the relative
abundance of each species or group. Ecosystem - Mass
balance of nutrients (from Adamus and Brandt, 1990)
There are various indices used to assess the effects of
stressors on (aquatic) populations and communities:
Biotic Indices: generally specific to the type of
pollution or the geographical area; they are used to classify
the degree of pollution by determining the tolerance of an
indicator organism to a pollutant. Indicator species are
assigned scores for their tolerance level. Biotic indices
assume that polluted sites or systems will contain fewer
species than unimpacted sites or systems and the species that
are present will reflect their particular sensitivity to a
pollutant (Johnson et al., 1993). The measures are generally
weighted and may include indices such as richness, pollution
tolerance, trophic levels present, abundance, and deformities
(Adamus and Brandt, 1990). These indices were originally
devised for, and are most useful for, organic pollution
(Johnson et al., 1993).
Diversity Indices: the measure of the richness, or
number of distinct taxa (e.g., orders, families, species) at a
site, and the evenness, the relative abundance of different
taxonomic groups, determined by counts of all organisms
Comparison, or Similarity Indices - the comparison of
the community structure in richness and/or evenness over time
or over space.
Both the diversity index and the similarity index may use the
functional feeding group (e.g. herbivores, detrivores,
carnivores) as a measure of the community integrity rather
than taxa (i.e. species, genus, family).
On the level of the individual or species, biochemical and
physiological indicators may be examined (Johnson et al.,
1993). Some benthic macroinvertebrates such as stoneflies
(plecoptera), caddisflies (trichoptera), mayflies
(ephemeroptera), and shellfish, show increases or decreases of
certain enzymes, changes in DNA, RNA, amino acids, and protein
production, oxygen consumption and ion concentration, in
response to environmental stressors such as temperature
shifts, metals, and pesticides. Physiological indicators of
contamination include deformities, sores, or lesions (Phillips
and Rainbow, 1993; Kennish 1992).
The EPA Rapid Bioassessment Protocol for Use in Streams and
Rivers (Plafkin et al., 1989) uses community diversity in
assessing water quality. The absence of pollution sensitive
benthic macroinvertebrate groups (ephemeroptera, plecoptera,
and trichoptera) and dominance of pollution-tolerant groups
(oligochaetes or chironomids), is indicative of pollution.
Overall, low richness of benthic macroinvertebrates may
indicate impairment. However, naturally low nutrient levels in
pristine headwaters may be the cause of low productivity and
few benthic macroinvertebrate species exist in these
Pollutant stressors tend to cause slime and filamentous algae
productivity and/or fewer fish species and more tolerant
species than expected (Plafkin et al., 1989). The judgment of
impairment, based on these indicators should be made by an
Common Organisms used for Biomonitoring
Benthic macroinvertebrates Advantages:
Benthic macroinvertebrates are found in most aquatic
There are a large number of species, and different stresses
produce different macroinvertebrate communities.
Small order streams often do not support fish but do
support extensive macroinvertebrate communities.
Macroinvertebrates generally have limited mobility. Thus
they are indicators of localized environmental conditions.
Since benthic macroinvertebrates retain (bioaccumulate)
toxic substances, chemical analysis will allow detection in
them where levels are undetectable in the water resource.
A biologist experienced in macroinvertebrate identification
will, be able to determine relatively quickly whether the
environment has been degraded by identifying changes in the
benthic community structure of the water resource.
Benthic macroinvertebrates are small enough to be easily
collected and identified.
Sampling of macroinvertebrates under a rapid assessment
protocol is easy, requires few people and minimal
equipment, and does not adversely affect other organisms.
Macroinvertebrates are the primary food source for
recreationally and commercially important fish. An impact
on macroinvertebrates impacts the food web and designated
uses of the water resource.
State water quality agencies tend to collect
(Sources: Plafkin et al.,1989; Rosenberg and Resh, 1993; Klemm et
al., 1990) Example invertebrate indicators of specific
impairment types: Nutrient enrichment - increased
ratio of aquatic worms (oligochaetes) to aquatic insects -
increased ratio of midges (chironomids) to other aquatic insects
- increase of herbivorous mayflies (ephemeropterans) and midges
Low dissolved oxygen - increased ratio of aquatic worms to
aquatic insects - increased ratio of midges to other aquatic
insects Contamination by heavy metals - increased ratio of
aquatic worms to aquatic insects - increased ratio of midges to
other aquatic insects - increased abundance of water bugs and
water beetles - increased ratio of predators to herbivores and
detrivores Sedimentation - decrease in mayflies and midges
Low pH - loss of snails, clams, mussels, daphnids,
mayflies, midges Temperature - Releases of heated
effluents tend to reduce community richness (source: Adamus and
Benthic macroinvertebrates do not respond to all impacts.
Seasonal variations may prevent comparisons of samples
taken in different seasons.
Drifting may bring benthic macroinvertebrates into waters
in which they would not normally occur. Knowledge of
drifting behavior of certain species can alleviate this
Certain groups are difficult to identify to the species
(Plafkin et al. 1989)
Fish are good indicators of long-term effects (several
years) and habitat conditions.
Fish communities represent a variety of trophic levels;
toxic substances tend to biomagnify, and thus fish
community structure reflects community health.
Fish are consumed by humans.
Fish are relatively easy to collect and identify.
Environmental requirements, life history information and
distribution are well known for most species.
Certain fish species such as salmon, trout, perch and
sculpins, are less tolerant of pollution than others. Bottom
dwellers are more tolerant of organic pollution since they are
adapted to lower oxygen levels. Predatory species that use
sight to hunt, such as pike, are sensitive to turbid
conditions (De Lange 1994).
Extensive fish kills are indicative of severe oxygen depletion
caused by organic pollution, oil slicks, or severe toxic
pollution, including toxic bacteria or plankton. Erratic
behavior, such as swimming close to the surface, slow
movements, swimming in circles, and gasping for oxygen, are
indicative of water contamination or severe oxygen depletion
(De Lange 1994).
Motility and migration cause difficulty in pinpointing a
pollutant as the cause of abnormalities in individuals or a
Monitoring only certain fish species will miss changes in
the benthic community or in other species in the community
that over time will affect the fish species.
Fish are not as sensitive as their food
(macroinvertebrates) to pollution and monitoring of fish
may not reflect severe changes in the invertebrate
An assessment of fish alone will not ensure "ecosystem
Example indicator fish species by impairment type:
Oxygen depletion Darter species
Salmonids Sculpin species Benthic insectivores
Sedimentation Darter species Salmonids Sculpin species Benthic insectivores
Degradation of pools and vegetative cover Sunfish species (Centrarchids) Minnow species (Cyprinids) Salmonids Physical and chemical
degradation of the water resource (long lived species) Suckers (Catostomids) Adult trout Minnows Catfish Tolerant species - distinguish
low from moderately degraded waters Green sunfish Common carp
White sucker Bullhead Creek chub Dace Trophic level Tolerance
(overall) used for the Index of Biotic Integrity Omnivores
Carp tolerant White sucker tolerant Bullhead minnow intermediate
Fathead minnow tolerant yearlings Insectivores Insectivorous cyprinids
intolerant to intermediate Juvenile trout intolerant Cutthroat
trout intolerant Rainbow trout intolerant Brook trout
intermediate White crappie intermediate Paiute Sculpin intolerant
Torrent Sculpin intolerant Prickly Sculpin intermediate
Reticulate Sculpin tolerant Madtom intolerant Carnivores Salmon
intermediate Bass intermediate Pike intermediate Walleye
intermediate Yellow perch intermediate Lake trout intermediate
(source: Plafkin et al., 1989)
Algal growth is dependent on sunlight and nutrient
concentrations. An abundance of algae is indicative of
nutrient pollution (De Lange 1994)
Algae are sensitive to some pollutants at levels which may not
visibly affect other organisms in the short term or may affect
other communities at higher concentrations.
(Plafkin et al., 1989)
Algae have very short life cycles and rapid reproduction.
This can also be a disadvantage.
Algae tend to be most directly affected by physical and
chemical environmental factors.
Sampling is easy and inexpensive, requires few people and
minimally impacts other organisms.
Standard methods exist.
Biomonitoring "Rapid Assessment" Measures for
Macroinvertebrates and Fish
Measure 1. Number of macroinvertebrate taxa (e.g. family,
genus) at site Reason for Use of Measure Taxa richness
tends to decline as water quality declines Issues
Difficulty in identification results in underestimatation.
Richness measures counts at the level of the order or family may
ignore the range of pollution tolerance across the family, genus,
or even species level. Measure 2. Number of EPT benthic
macroinvertebrate taxa (ephemoptera, plecoptera, and trichoptera)
to species level if possible Reason for Use of Measure
These orders tend to be sensitive to pollutants Issues
Species level keys only available for 1/2 of taxa.
Presence/absence of taxa is a measure as well. Part of Plafkin et
al., 1989. Measure 3. Number of aquatic worms, midges,
and/or snails Reason for Use of Measure: Abundance of such
groups indicates nutrient enrichment, low dissolved oxygen, and
heavy metal contamination. Issues Measure is most useful
if you can see a change over time. Measure 4. Niche
Occupant Forms Counts are of number of forms, not individuals
Reason for Use of Measure Number of niche occupant forms
declines as water quality declines Issues: Based on taxa
that a novice biologist can discern. Faster. May count different
life stage of same taxon as different taxa and therefore
overcount. Measure 5. Number of native fish species;
benthic species (sucker species); darter species; pool species
(sunfish species); long-lived species; tolerant species;
intolerant species Reason for Use of Measure: Determines
level of degradation Issues: Knowledge of water body
composition prior to pollutant makes measure most accurate.
Introduction or stocking of species may cause a misrepresentation
of actual stream integrity.
Evenness (Abundance) Measures
Measure 1. Number of individuals Reason for Use of
Measure Pollutants may cause numbers or biomass to increase
(for example, nutrients) or decrease (for example, pesticide).
Issues: Competition and predation cause population changes
as well. Simple counts of individuals will miss more subtle
indications of stress such as physical condition or physiological
changes. Used by Plafkin et al., 1989. Measure 2. Ratio of
ephemoptera, plecoptera, and trichoptera (EPT) (benthic
macroinvertebrate) species to chironomids (midges) Reason for
Use of Measure: Chironomids (midges) are considered more
pollution-tolerant. In particular, chironomids respond to
nutrient enrichment and eutrophic conditions (Adamus and Brandt,
1990). EPT taxa are more sensitive to heavy metals. Issues
At the species level of chironimids, a range of pollution
tolerances exists. Habitat can influence abundance. Mean size of
kick screen must be small enough to ensure chironimids are
captured. Measure 3. Ratio of individuals in numerically
dominant taxa to total number of individuals Reason for Use of
Measure: Domination by few species or families indicates
stress or conditions which preferentially support particular taxa
such as nutrient enrichment, low dissolved oxygen, and toxic
contaminants. Issues Unstressed habitats may have few
taxa. Measure 4. Proportion of tolerant fish species of
total number collected Reason for Use of Measure:
Domination by few species or families indicates stress or
conditions which preferentially support particular taxa such as
nutrient enrichment, low dissolved oxygen, and toxic
contaminants. Measure 5. Proportion of fish with
disease/deformities, etc. Reason for Use of Measure: High
levels of toxic compounds may generate physical abnormalities.
Functional Feeding Group Measures
Measure 1. Ratio of shredders to total. Collect samples
from leaves or other coarse particulate organic matter (CPOM).
Reason for Use of Measure: Shredders and their microbial
food are sensitive to toxic substances and habitat modification.
Issues Identifications must be accurate. Counting the same
taxon of a different age group is a problem. Seasonality
influences data; easily processed litter such as maples and birch
generally have high shredder content in the winter; whereas oak,
beech, pine litter have high shredder content in the summer
(Plafkin et al., 1989). Measure 2. Ratio of scrapers to
collector feeders Reason for Use of Measure These groups
indicate availability of food resources. Collector-feeder
dominance indicates organic enrichment. Decline of filtering
collectors is indicative of toxic contaminants, as toxicants bind
to their food particles. Issues Some scrapers are
pollution-tolerant. If toxic compounds are present in the organic
matter, this measure may not be clearcut. Identifications must be
accurate. Measure 3. Ratio of specialists to generalists.
Reasons for Use of Measure Specialists are restricted to
specific food sources; generalists use a broader range of food
sources. Issues Assumes that generalists are more
pollution-tolerant and become numerically dominant. Difficult to
identify whether and organism is definitely one or the other.
Measure 4. Proportion omnivorous, insectivores,
carnivorous fish Reason for Use of Measure Assumes there
would be more omnivorous fish as environment deteriorates; as the
invertebrate community is reduced, insectivores decrease; top
carnivores will bioaccumulate pollutants so their presence is
indicative of high integrity. Issues Score habitat using
Plafkin et al. (1989) system. (Adapted from Resh and Jackson,
1993; Plafkin et al., 1989; Adamus and Brandt, 1990)
Collection of a representative sample and accounting for
inherent high variability is a much larger issue for
biomonitoring than it is for physical or chemical monitoring.
Kick seine: Requires 2 or more people. One person
places a four by four feet nylon mesh screen seine is
placed along the bottom at an angle that will allow riffle
areas to be easily sampled for benthic macroinvertebrates.
Another individual kicks the stream bottom down to 2 inches
to loosen macroinvertebrates for collection, upstream of
the net. The net is then removed from the water and
organisms are classified.
Sweep nets: Used to sample invertebrates from the
water column as well as communities attached to wetland
plants. The nets are at the end of a pole which is placed
on the bottom of the water body and swept up vertically
through the water column or swept a standard length of
vegetation. (Adamus and Brandt, 1990)
Dredges or core samplers: A specified area is
enclosed and sediments and the associated organisms are
retrieved. Fast moving organisms can and do escape. Core
samplers are particularly useful in wetlands that are dry.
(Adamus and Brandt, 1990)
Artificial substrates: Plastic plants or other
sterile surfaces allow objective sampling and sample
collection in locations that are difficult to sample
(Plafkin et al., 1989). Such artificial substrates should
remain in place for at least a month (Adamus and Brandt,
1990) and the average is 8 weeks (Plafkin et al., 1989).
Emergence traps and funnel traps: Nets or funnels
placed at or just above the water surface trap adult
aquatic insects emerging from the water (Adamus and Brandt,
1990). These will not collect benthic organisms such as
aquatic worms and snails.
Sampling Techniques- Finfish
Sample as soon as water temperatures are favorable.
Sampling time considerations include migration, spawning, and
dispersal. Nighttime sampling is suggested, particularly for
catfish and perch.
Electrofishing: A technique which stuns fish,
allowing them to be caught, identified, measured, and
released quickly. Permits are required. Water body inlets
and outlets can be blocked with nets to prevent fish from
escaping the electrical field. Electrofishing can also
guide fish into nets. Electrofishing accuracy decreases
with turbididty and plant density. Collections may be
size-biased in favor of larger individuals and species.
Electrofishing is not effective in wetlands recieving acid
mine drainage (Adamus and Brandt, 1990).
Seines: Nets pulled through the water to capture
fish. Seines can allow an estimate of species richness. A
mesh size of 1/8 is recommended for fish.
Sweep nets or lift nets: Nets are placed on the
bottom and lifted to capture fish, particularly small
schools of fish.
Some sources of information and techniques for biomonitoring:
Batiuk, R.A., R.J. Orth, K.A. Moore, W.C. Dennison, J. C.
Stevenson, L.W. Staver, V. Carter, N.B. Rybicki, R.E. Hickman,
S. Kollar, S. Bieber, P. Heasly. 1992. Chesapeake Bay
Submerged Aquatic Vegetation Habitat Requirements and
Restoration Targets: A Technical Synthesis. EPA: Annapolis,
De Lange, E. 1994. Manual for Simple Water Quality Analysis.
International Water Tribunal (IWT) Foundation:Amsterdam.
Kennish, M.J. 1992. Ecology of Estuaries: anthropogenic
effects. CRC Press: Boca Raton.
Klemm, D.J.. et al., 1990. Macroinvertebrate field and
laboratory methods for evaluating the biological integrity of
surface waters. EPA:Cincinnati, OH.
McDonald, B., W. Borden and J. Lathrop. 1990. Citizen stream
monitoring, a manual for Illinois. Illinois Department of
Energy and Natural Resources:Illinois.
Mitchell, M.K., W. B. Stapp. 1992. Field Manual for Water
Quality Monitoring, an environmental education program for
schools. GREEN:Ann Arbor, MI.
Phillips, D.J.H., P.S. Rainbow. 1993. Biomonitoring of Trace
Aquatic Contaminants. Elsevier Applied Science: New York, NY.
Plafkin, J.L. M.T. Barbour, K.D. Porter, S.K. Gross, R.M.
Hughes. 1989. Rapid Assessment Protocols for Use in Streams
and Rivers: Benthic Macroinvertebrates and Fish. EPA:
Washington, D.C. Rosenberg, D.M., V. H. Resh (eds). 1993.
Freshwater Biomonitoring and Benthic Macroinvertebrates.
Chapman & Hall:New York, NY.