CH 06 PDF
CH 06 PDF
CH 06 PDF
PERIPHYTON PROTOCOLS
Benthic algae (periphyton or phytobenthos) are primary producers and an important foundation of
many stream food webs. These organisms also stabilize substrata and serve as habitat for many other
organisms. Because benthic algal assemblages are attached to substrate, their characteristics are
affected by physical, chemical, and biological disturbances that occur in the stream reach during the
time in which the assemblage developed.
Diatoms in particular are useful ecological indicators because they are found in abundance in most
lotic ecosystems. Diatoms and many other algae can be identified to species by experienced
algologists. The great numbers of species provide multiple, sensitive indicators of environmental
change and the specific conditions of their habitat. Diatom species are differentially adapted to a wide
range of ecological conditions.
Periphyton indices of biotic integrity have been developed and tested in several regions (Kentucky
Department of Environmental Protection 1993, Hill 1997). Since the ecological tolerances for many
species are known (see section 6.1.4), changes in community composition can be used to diagnose the
environmental stressors affecting ecological health, as well as to assess biotic integrity (Stevenson
1998, Stevenson and Pan 1999).
Periphyton protocols may be used by themselves, but they are most effective when used with one or
more of the other assemblages and protocols. They should be used with habitat and benthic
macroinvertebrate assessments particularly because of the close relation between periphyton and these
elements of stream ecosystems.
Presently, few states have developed protocols for periphyton assessment. Montana, Kentucky, and
Oklahoma have developed periphyton bioassessment programs. Others states are exploring the
possibility of developing periphyton programs. Algae have been widely used to monitor water quality
in rivers of Europe, where many different approaches have been used for sampling and data analysis
(see reviews in Whitton and Rott 1996, Whitton et al. 1991). The protocols presented here are a
composite of the techniques used in Kentucky, Montana, and Oklahoma (Bahls 1993, Kentucky
Department of Environmental Protection 1993, Oklahoma Conservation Commission 1993).
Two Rapid Bioassessment Protocols for periphyton are presented. These protocols are meant to
provide examples of methods that can be used. Other methods are available and should be considered
based on the objectives of the assessment program, resources available for study, numbers of streams
sampled, hypothesized stressors, and the physical habitat of the streams studied. Examples of other
methods are presented in textboxes throughout the chapter.
The first protocol (6.1) is a standard approach in which species composition and/or biomass of a
sampled assemblage is assessed in the laboratory. The second protocol (6.2) is a field-based rapid
survey of periphyton biomass and coarse-level taxonomic composition (e.g., diatoms, filamentous
greens, blue-green algae) and requires little taxonomic expertise. The two protocols can be used
together. The first protocol has the advantage of providing much more accuracy in assessing biotic
Rapid Bioassessment Protocols for Use in Streams and Wadeable Rivers: Periphyton, Benthic
Macroinvertebrates, and Fish, Second Edition 6-1
DRAFT REVISION—September 25, 1998
integrity and in diagnosing causes of impairment than the second protocol, but it requires more effort
than the second protocol. Additionally, the first protocol provides the option of sampling the natural
substrate of the stream or placing artificial substrates for colonization.
Periphyton samples should be collected during periods of stable stream flow. High flows can scour the
stream bed, flushing the periphyton downstream. Recolonization of substrates will be faster after less
severe floods and in streams with nutrient enrichment. Peterson and Stevenson (1990) recommend a
three-week delay following high, bottom-scouring stream flows to allow for recolonization and
succession to a mature periphyton community. However, recovery after high discharge can be as rapid
as 7 days if severe scouring of substrata did not occur (Stevenson 1990).
Two sampling approaches are described for natural substrate sampling. Multihabitat sampling best
characterizes the benthic algae in the reach, but results may not be sensitive to subtle water quality
changes because of habitat variability between reaches. Species composition of assemblages from a
single habitat should reflect water quality differences among streams more precisely than multi-habitat
sampling, but impacts in other habitats in the reach may be missed.
The length of stream sampled depends upon the objectives of the project, budget, and expected results.
Multihabitat sampling should be conducted at the reach scale (30-40 stream widths) to ensure sampling
the diversity of habitats that occur in the stream. Ideally, single habitat sampling should also be
conducted at the reach scale. A shorter length of stream can probably be sampled for single habitat
samples than multihabitat samples because the chosen single habitat (e.g., riffles) is usually common
within the study streams.
macroinvertebrate or fish sampling (30-40 stream widths) so that as many algal habitats can be
sampled as is practical.
2. Before sampling, complete the physical/chemical field sheet (see Chapter 5; Appendix A-1, Form
1) and the periphyton field data sheet (Appendix A-2, Form 1). Visual estimates or quantitative
transect-based assessments can be used to determine the percent coverage of each substrate type
and the estimated relative abundance of macrophytes, macroscopic filamentous algae, diatoms and
other microscopic algal accumulations (periphyton), and other biota (see section 6.2).
3. Collect algae from all available substrates and habitats. The objective is to collect a single
composite sample that is representative of the periphyton assemblage present in the reach. Sample
all substrates (Table 6-1) and habitats (riffles, runs, shallow pools, nearshore areas) roughly in
proportion to their areal coverage in the reach. Within a stream reach, light, depth, substrate, and
current velocity can affect species composition of periphyton assemblages. Changes in species
composition of algae among habitats are often evident as changes in color and texture of the
periphyton. Small amounts (about 5 mL or less) of subsample from each habitat are usually
sufficient. Pick specimens of macroalgae by hand in proportion to their relative abundance in the
reach. Combine all samples into a common container.
Table 6-1. Summary of collection techniques for periphyton from wadeable streams (adapted from
Kentucky DEP 1993, Bahls 1993).
Substrate Type Collection Technique
Removable substrates (hard): gravel, pebbles, Remove representative substrates from water; brush
cobble, and woody debris or scrape representative area of algae from surface
and rinse into sample jar.
Removable substrates (soft): mosses, macroalgae, Place a portion of the plant in a sample container
vascular plants, root masses with some water. Shake it vigorously and rub it
gently to remove algae. Remove plant from sample
container.
Large substrates (not removable): boulders, bedrock, Place PVC pipe with a neoprene collar at one end
logs, trees, roots on the substrate so that the collar is sealed against
the substrate. Dislodge algae in the pipe with a
toothbrush, nail brush, or scraper. Remove algae
from pipe with pipette.
Loose sediments: sand, silt, fine particulate organic Invert petri dish over sediments. Trap sediments in
matter, clay petri dish by inserting spatula under dish. Remove
sediments from stream and rinse into sampling
container. Algal samples from depositional habitats
can also be collected with spoons, forceps, or
pipette.
4. Place all samples into a single water-tight, unbreakable, wide-mouth container. A composite
sample measuring four ounces (ca. 125 ml) is sufficient (Bahls 1993). Add recommended amount
of Lugol's (IKI) solution, "M3" fixative, buffered 4% formalin, 2% glutaraldehyde, or other
preservative (APHA 1995).
Rapid Bioassessment Protocols for Use in Streams and Wadeable Rivers: Periphyton, Benthic
Macroinvertebrates, and Fish, Second Edition 6-3
DRAFT REVISION—September 25, 1998
5. Place a permanent label on the outside of the sample container with the following information:
waterbody name, location, station number, date, name of collector, and type of preservative.
Record this information and relevant ecological information in a field notebook or on the
periphyton field data sheet (Appendix A-2, Form 1). Place another label with the same information
inside the sample container. (Caution! Lugol's solution and other iodine-based preservatives will
turn paper labels black.)
6. After sampling, review the recorded information on all labels and forms for accuracy and
completeness.
7. Examine all brushing and scraping tools for residues. Rub them clean and rinse them in distilled
water before sampling the next site and before putting them away.
8. Transport samples back to the laboratory in a cooler with ice (keep them cold and dark) and store
preserved samples in the dark until they are processed. Be sure to stow samples in a way so that
transport and shifting does not allow samples to leak. When preserved, check preservative every
few weeks and replenish as necessary until taxonomic evaluation is completed.
9. Log in all incoming samples (Appendix A-2, Form 2). At a minimum, record sample identification
code, date, stream name, sampling location, collector's name, sampling method, and area sampled
(if it was determined).
2. Before sampling, complete the 7. Store the filter in a cold cooler (not in water) and
physical/chemical field sheet (see eventually in a freezer.
Chapter 5; Appendix A-1, Form 1)
and the periphyton field data sheet
(Appendix A-2, Form 1). Complete habitat assessments as in multihabitat sampling so that the
relative importance of the habitats sampled can be characterized.
3. The recommended substrate/habitat combination is cobble obtained from riffles and runs with
current velocities of 10-50 cm/sec. Samples from this habitat are often easier to analyze than from
slow current habitats because they contain less silt. These habitats are common in many streams.
In low gradient streams where riffles are rare, algae on snags or in depositional habitats can be
collected. Shifting sand is not recommended as a targeted substrate because the species
composition on sand is limited due to the small size and unstable nature of the substratum.
Phytoplankton should be considered as an alternative to periphyton in large, low gradient streams.
4. Collect several subsamples from the same substrate/habitat combination and composite them into a
single container. Three or more subsamples should be collected from each reach or study stream.
5. The area sampled should always be determined if biomass (e.g., chlorophyll) per unit area is to be
measured.
Rapid Bioassessment Protocols for Use in Streams and Wadeable Rivers: Periphyton, Benthic
Macroinvertebrates, and Fish, Second Edition 6-5
DRAFT REVISION—September 25, 1998
1. Microslides should be thoroughly cleaned before placing in periphytometers (e.g., Patrick et al.
1954). Rinse slides in acetone and clean with Kimwipes®.
2. Place surface (floating) or benthic (bottom) periphytometers fitted with glass slides, glass rods,
clay tiles, plexiglass plates or similar substrates in the study area. Allow 2 to 4 weeks for
periphyton recruitment and colonization.
3. Replicate a minimum of 3 periphytometers at each site to account for spatial variability. The total
number should depend upon the study design and hypotheses tested. Samples can either be
composited or analyzed individually.
4. Attach periphytometers to rebars pounded into the stream bottom or to other stable structures.
Periphytometers should be hidden from view to minimize disturbance or vandalism. Avoid the
main channel of floatable, recreational streams. Each periphytometer should be oriented with the
shield directed upstream.
The Methods summarized here are a modified version of those used by Kentucky (Kentucky DEP
1993), Florida (Florida DEP 1996), and Montana (Bahls 1993). For more detail or for alternative
methods, see Standard Methods for the Examination of Water and Wastewater (APHA 1995).
Many algae are readily identifiable to species level by trained personnel who have a good library of
literature on algal taxonomy (see section 6.3). All algae can not be identified to species because: the
growth forms of some algal species are morphologically indistinguishable with the light microscope
(e.g., zoospores of many green algae); the species has not been described previously; or the species is
not in the laboratory’s literature. Consistency in identifications within a laboratory and program is
very important, because most bioassessment are based on contrasts between reference and test sites.
Accuracy of identifications becomes most important when using autecological information from other
studies. Quality assurance techniques are designed to ensure "internal consistency" and also improve
comparisons with information in other algal assessment and monitoring programs.
2. Thoroughly mix the homogenized sample and pipette into a Palmer counting cell (see textbox for
alternative methods). Algal suspensions that produce between 10 and 20 cells in a field provide
good densities for counting and identifying cells. Lower densities slow counting. Dilute samples if
cells overlap too much for counting.
3. Fill in the top portion of the benchsheet for "soft" algae (Appendix A-2, Form 3) with enough
information from the sample label and other sources to uniquely identify the sample.
4. Identify and count 300 algal "cell units" to the lowest possible taxonomic level at 400X
magnification with the use of the references in Section 6.3.
! Distinguishing cells of coenocytic algae (e.g., Vaucheria) and small filaments of blue-green
algae is a problem in cell counts. "Cell units" can be defined for these algae as 10mm sections
of the thallus or filament.
! For diatoms, only count live diatoms and do not identify to lower taxonomic levels if a
subsequent count of cleaned diatoms is to be undertaken (See section 6.1.3.2).
! Record numbers of cells or cell units observed for each taxon on a benchsheet.
! Make taxonomic notes and drawings on benchsheets of important specimens.
5. Optional - To better determine non-diatom taxa richness, continue counting until you have not
observed any new taxa for 100 cell units or about three minutes of observation.
1. Subsample at least 5-10 mL of concentrated preserved sample while vigorously shaking the sample
(or using magnetic stirrer). Oxidize (clean) samples for diatom analysis (APHA 1995, see textbox
entitled “Oxidation Methods for Cleaning Diatoms”).
2. Mount diatoms in Naphrax® or another high refractive index medium to make permanent slides.
Label slides with same information as on the sample container label.
3. Fill in the top portion of the bench sheet for diatom counts (Appendix A-2, Form 4) with enough
information from the sample label to uniquely identify the sample.
4. Identify and count diatom valves to the lowest possible taxonomic level, which should be species
and perhaps variety level, under oil immersion at 1000X magnification with the use of the
Rapid Bioassessment Protocols for Use in Streams and Wadeable Rivers: Periphyton, Benthic
Macroinvertebrates, and Fish, Second Edition 6-7
DRAFT REVISION—September 25, 1998
references in Section 6.3. At minimum, count 600 valves (300 cells) and at least until 10 valves of
10 species have been observed. Be careful to distinguish and count both valves of intact frustules.
The 10 valves of 10 species rule ensures relatively precise estimates of relative abundances of the
dominant taxa when one or two taxa are highly dominant. Six hundred valve counts were chosen
to conform with methods used in other national bioassessment programs (Porter et al. 1993).
Record numbers of valves observed for each taxon on the bench sheet. Make taxonomic notes and
drawings on benchsheets and record stage coordinates of important specimens.
5. Optional - To estimate total diatom taxa richness, continue counting until you have not observed
any new species for 100 specimens or about three minutes of observation.
1. Relative abundances of "soft" algae are determined by dividing the number of cells (cell units)
counted for each taxon by the total number of cells counted (e.g., 300). Enter this information on
Appendix A-2, Form 3.
2. Relative abundances of diatoms have to be corrected for the number of live diatoms observed in the
count of all algae. Therefore, determine the relative abundances of diatom species in the algal
assemblage by dividing the number of valves counted for each species by the total number of
valves counted (e.g., 600); then multiply the relative abundance of each diatom taxon in the diatom
count by the relative abundance of live diatoms in the count of all algae. Enter this information on
Appendix A-2, Form 4. Some analysts prefer to treat diatom and soft algal species composition
separately. In this case, determine the relative abundances of diatom species in the algal
assemblage by dividing the number of valves counted for each species by the total number of
valves counted (e.g., 600).
3. Total taxa richness can be estimated by adding the number of "soft" algal taxa and diatom taxa.
Palmer counting cells are excellent for identifying and counting soft-algae in most species assemblages.
When samples have many very small blue-green algae or a few, relatively important large cells, other
slide preparation techniques may be useful to increase magnification and sample size, respectively.
Because accurate diatom identification is not possible in Palmer cells, we have recommended counting
cleaned diatoms in special mounts. However, if the taxonomy of algae in samples is well known,
preparation and counting time can be reduced by mounting algae in syrup. In syrup, both soft algae
and diatoms can be identified, but resolution of morphological details of diatoms is not as great as in
mounts of diatoms in resins (e.g., Naphrax®).
Assemblages with many small cells: We recommend a simple wet mount procedure when samples
contain many small algae so samples can be observed at 1000X. A small volume of water under the
coverglass prevents movement of cells when adjusting focus and using oil immersion. These
preparations usually last several days if properly sealed (see below).
Wet mounts:
1. Clean coverglasses and place on flat surface.
Rapid Bioassessment Protocols for Use in Streams and Wadeable Rivers: Periphyton, Benthic
Macroinvertebrates, and Fish, Second Edition 6-9
DRAFT REVISION—September 25, 1998
4. Let dry for 24 hours. Alternatively, dry on slide warmer on low setting. Do not overdry or cells
will plasmolyze.
5. Place another . 1.0 mL of 10% TSM on cover glass and dry (overnight or 4 hours on a slide
warmer). Apply 10% TSM quickly to avoid patchy resuspension of the original layer of TSM and
algae.
6. Invert coverglass onto microscope slide; place slide on hot plate to warm the slide and syrup. Do
not boil, just warm. Press coverglass gently in place with forceps, being careful to keep all syrup
under the coverglass. The syrup should spread under coverglass.
7. Remove the slide from the hotplate. Cooling should partially seal the coverglass to the slide.
8. More permanently seal the syrup under slides by painting fingernail polish around the edge of the
cover glass and onto the microscope slide.
Special Note: If slides get too warm in storage, syrup will loose viscosity and become runny. Algae
and medium may then escape containment under coverglass. Store slides in a horizontal position.
The periphyton metrics presented here are used by several states and environmental assessment
programs throughout the US and Europe (e.g., Kentucky DEP 1993, Bahls 1993, Florida DEP 1996,
Whitton et al. 1991, Whitton and Kelly 1995). Each of these metrics should be tested for response to
human alterations of streams in the region in which they are used (see Chapter 9, Biological Data
Analysis). In many cases, diatom and soft algal metrics have been determined separately because
changes in small abundant cyanobacteria (blue-green algae) can numerically overwhelm metrics based
on relative abundance and because green algae with large cells (e.g., Cladophora) may not have
appropriate weight. However, attempts should be made to integrate diatoms and soft algae in as many
metrics as possible, especially in cases such as species and generic richness when great variability in
relative abundance is not an issue.
The metrics have been divided into two groups • If implementing a new program and only an
which may be helpful in developing an Index inexperienced analyst is available for the job,
of Biotic Integrity (IBI). Metrics in the first identifying diatom genera in assemblages can
group are less diagnostic than the second provide valuable characterizations of biotic
group of metrics. Metrics in the first group integrity and environmental conditions.
(species and generic richness, Shannon
diversity, etc.) generally characterize biotic • As analysts get more experience counting, the
taxonomic level of their analyses should
integrity ("natural balance in flora and
improve. The cost of an experienced analyst
fauna…." as in Karr and Dudley 1981) counting and identifying algae to species is not
without specifically diagnosing ecological much greater than analysis to genus.
conditions and causes of impairment. The
second group of metrics more specifically
diagnoses causes of impaired biotic integrity.
Metrics from both groups could be included in an IBI to make a hierarchically diagnostic IBI.
Alternatively, an IBI could be constructed from only metrics of biotic integrity so that inference of
biotic integrity and diagnosis of impairment are independent (Stevenson and Pan 1999).
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Macroinvertebrates, and Fish, Second Edition 6-11
DRAFT REVISION—September 25, 1998
Autecological information about many algal species and genera has been reported in the literature.
This information comes in several forms. In some cases, qualitative descriptions of the ecological
conditions in which species were observed were reported in early studies of diatoms. Following the
development of the saprobic index by Kolkwitz and Marsson (1908), several categorical classification
systems (e.g., halobian spectrum, pH spectrum) were developed to describe the ecological preferences
and tolerances of species (see Lowe 1974 for a review). Most recently, the ecological optima and
tolerances of species for specific environmental conditions have been quantified by using weighted
average regression approaches (see ter Braak and van Dam 1989 for a review). We have compiled a
list of references for this information in Section 6.4. These references will be valuable for developing
many of the metrics below.
1. Species richness is an estimate of the number of algal species (diatoms, soft algae, or both) in
a sample. High species richness is assumed to indicate high biotic integrity because many
species are adapted to the conditions present in the habitat. Species richness is predicted to
decrease with increasing pollution because many species are stressed. However, many habitats
may be naturally stressed by low nutrients, low light, or other factors. Slight increases in
nutrient enrichment can increase species richness in headwater and naturally unproductive,
nutrient-poor streams (Bahls et al. 1992).
2. Total Number of Genera (Generic richness) should be highest in reference sites and lowest in
impacted sites where sensitive genera become stressed. Total number of genera (diatoms, soft
algae, or both) may provide a more robust measure of diversity than species richness, because
numerous closely related species are within some genera and may artificially inflate richness
estimates.
3. Total Number of Divisions represented by all taxa should be highest in sites with good water
quality and high biotic integrity.
4. Shannon Diversity (for diatoms). The Shannon Index is a function of both the number of
species in a sample and the distribution of individuals among those species (Klemm et al.
1990). Because species richness and evenness may vary independently and complexly with
water pollution. Stevenson (1984) suggests that changes in species diversity, rather than the
diversity value, may be useful indicators of changes in water quality. Species diversity,
despite the controversy surrounding it, has historically been used with success as an indicator
of organic (sewage) pollution (Wilhm and Dorris 1968, Weber 1973, Cooper and Wilhm
1975). Bahls et al. (1992) uses Shannon diversity because of its sensitivity to water quality
changes. Under certain conditions Shannon diversity values may underestimate water quality
e.g., when total number of taxa is less than 10. Assessments for low richness samples can be
improved by comparing the assemblage Shannon Diversity to the Maximum Shannon Diversity
value (David Beeson1, personal communication).
5. Percent Community Similarity (PSc) of Diatoms. The percent community similarity (PSc)
index, discussed by Whittaker (1952), was used by Whittaker and Fairbanks (1958) to
compare planktonic copepod communities. It was chosen for use in algal bioassessment
because it shows community similarities based on relative abundances, and in doing so, gives
1
David Beeson is a phycologist with Schafer & Associates, Inc.
more weight to dominant taxa than rare ones. Percent similarity can be used to compare
control and test sites, or average community of a group of control or reference sites with a test
site. Percent community similarity values range from 0 (no similarity) to 100%.
s s
PSc ' 100&.5Ei'1*ai&bi* ' Ei'1min(ai,bi)
where:
6. Pollution Tolerance Index for Diatoms. The pollution tolerance index (PTI) for algae
resembles the Hilsenhoff biotic index for macroinvertebrates (Hilsenhoff 1987). Lange-
Bertalot (1979) distinguishes three categories of diatoms according to their tolerance to
increased pollution, with species assigned a value of 1 for most tolerant taxa (e.g., Nitzschia
palea or Gomphonema parvulum) to 3 for relatively sensitive species. Relative tolerance for
taxa can be found in Lange-Bertalot (1979) and in many of the references listed in section 6.4.
Thus, Lange-Bertalot’s PTI varies from 1 for most polluted to 3 for least polluted waters when
using the following equation:
Enit i
PTI '
N
where:
ni = number of cells counted for species i
ti = tolerance value of species i
N = total number of cells counted
In some cases, the range of values for tolerances has been increased, thereby producing a
corresponding increase in the range of PTI values.
7. Percent Sensitive Diatoms. The percent sensitive diatoms metric is the sum of the relative
abundances of all intolerant species. This metric is especially important in smaller-order
streams where primary productivity may be naturally low, causing many other metrics to
underestimate water quality.
8. Percent Achnanthes minutissima. This species is a cosmopolitan diatom that has a very
broad ecological amplitude. It is an attached diatom and often the first species to pioneer a
recently scoured site, sometimes to the exclusion of all other algae. A. minutissima is also
frequently dominant in streams subjected to acid mine drainage (e.g., Silver Bow Creek,
Montana) and to other chemical insults. The percent abundance of A. minutissima has been
found to be directly proportional to the time that has elapsed since the last scouring flow or
episode of toxic pollution. For use in bioassessment, the quartiles of this metric from a
Rapid Bioassessment Protocols for Use in Streams and Wadeable Rivers: Periphyton, Benthic
Macroinvertebrates, and Fish, Second Edition 6-13
DRAFT REVISION—September 25, 1998
population of sites has been used to establish judgment criteria, e.g., 0-25% = no disturbance,
25-50% = minor disturbance, 50-75% = moderate disturbance, and 75-100% = severe
disturbance. Least-impaired streams in Montana may contain up to 50% A. minutissima
(Bahls, unpublished data).
9. Percent live diatoms was proposed by Hill (1997) as a metric to indicate the health of the
diatom assemblage. Low percent live diatoms could be due to heavy sedimentation and/or
relatively old algal assemblages with high algal biomass on substrates.
The ecological preferences of many diatoms and other algae have been recorded in the literature. Using
relative abundances of algal species in the sample and their preferences for specific habitat conditions,
metrics can be calculated to indicate the environment stressors in a habitat. These metrics can more
specifically infer environmental stressors than the general pollution tolerance index.
10. Percent Aberrant Diatoms is the percent of diatoms in a sample that have anomalies in striae
patterns or frustule shape (e.g, long cells that are bent or cells with indentations). This metric
has been positively correlated to heavy metal contamination in streams (McFarland et al.
1997).
11. Percent Motile Diatoms. The percent motile diatoms is a siltation index, expressed as the
relative abundance of Navicula + Nitzschia + Surirella. It has shown promise in Montana
(Bahls et al. 1992). The three genera are able to crawl towards the surface if they are covered
by silt; their abundance is thought to reflect the amount and frequency of siltation. Relative
abundances of Gyrosigma, Cylindrotheca, and other motile diatoms may also be added to this
metric.
12. Simple Diagnostic Metrics can infer the environmental stressor based on the autecology of
individual species in the habitats. For example, if acid mine drainage was impairing stream
conditions, then we would expect to find more acidobiontic taxa in samples. Calculate a
simple diagnostic metric as the sum of the percent relative abundances (range 0-100%) of
species that have environmental optima in extreme environmental conditions. For example (see
Table 6-2):
% acidobiontic + % acidophilic
% alkalibiontic + % alkaliphilic
% halophilic
% mesosaprobic + % oligosaprobic + % saprophilic
% eutrophic
13. Inferred Ecological Conditions with Simple Autecological Indices (SAI) - The ecological
preferences for diatoms are commonly recorded in the literature. Using the standard ecological
categories compiled by Lowe (1974, Table 6-2), the ecological preferences for different diatom
species can be characterized along an environmental (stressor) gradient. For example, pH
preferences for many taxa are known. These preferences (1i) can be ranked from 1-5 (e.g.,
acidobiontic, acidophilic, indifferent, alkaliphilic, alkalibiontic, Table 6-2) and can be used in
the following equation to infer environmental conditions (EC) and effect on the periphyton
assemblage.
SAIEC =E 1ipi
14. Inferred Ecological Conditions with Weighted Average Indices are based on the specific
ecological optima ($i) for algae, which are being reported more and more commonly in recent
publications (see Pan and Stevenson 1996). Caution should be exercised, because we do not
know how transferable these optima are among regions and habitats. Using the following
equation, the ecological conditions (EC) in a habitat can be inferred more accurately by using
the optimum environmental conditions ($i) and relative abundances (Di) for taxa in the habitat
(ter Braak and van Dam 1989, Pan et al., 1996) than if only the ecological categorization were
used (as above for the SAI). Optimum environmental conditions are those in which the highest
relative abundances of a taxon are observed. These can be determined from the literature or
from past surveys of taxa and environmental conditions in the study area (see ter Braak and
van Dam 1989). In a pH example, the specific pH in a habitat can be inferred if we know the
pH optima (Hi) of taxa in the habitat, and use the following general equation:
WAIEC = G$ipi
WAIpH = G Hipi
15. Impairment of Ecological Conditions can be inferred with algal assemblages by calculating
the deviation ()EC) between inferred environmental conditions at a test site and at a reference
site.
Compare inferred ecological conditions at the test site to the expected ecological conditions (ECex) of
regional reference sites by using either simple autecological indices (SAIEC) or weighted average indices
(WAIEC):
Table 6-2. Environmental definitions of autecological classification systems for algae (as modified or
referenced by Lowe 1974). Definitions for classes are given if no subclass is indicated.
Classification System/ Conditions of Highest Relative
Ecological Parameter Class Subclass Abundances
pH Spectrum Acidobiontic Below 5.5 pH
Acidophilic Above 5.5 and below 7 pH
Indifferent Around 7 pH
Alakaliphilic Above 7 and below 8.5 pH
Alkalibiontic Above 8.5 pH
Nutrient Spectrum - based on Eutrophic High nutrient conditions
P and N concentrations
Rapid Bioassessment Protocols for Use in Streams and Wadeable Rivers: Periphyton, Benthic
Macroinvertebrates, and Fish, Second Edition 6-15
DRAFT REVISION—September 25, 1998
Measurement of periphyton biomass is common in many studies and may be especially important in
studies that address nutrient enrichment or toxicity. In many cases, however, sampling benthic algae
misses peak biomass, which may best indicate nutrient problems and potential for nuisance algal
growths (Biggs 1996, Stevenson 1996).
Biomass measurements can be made with samples collected from natural or artificial substrates. To
quantify algal biomass (chl a, ash-free dry mass, cell density, biovolume cm-2), the area of the substrate
sampled must be determined. Two national stream assessment programs sample and assess
area-specific cell density and biovolume (USGS-NAWQA, Porter et al. 1993; and EMAP, Klemm and
Lazorchak 1994). These programs estimate algal biomass in habitats and reaches by collecting
composite samples separately from riffle and pool habitats.
Ash-free dry mass is a measurement of the organic matter in samples, and includes biomass of
bacteria, fungi, small fauna, and detritus in samples. A detailed description of analysis is beyond the
scope of this chapter, but standard methods (APHA 1995, USEPA 1995) are readily available. The
analysis is relatively simple and measures the difference in mass of a sample after drying and after
incinerating organic matter in the sample. We recommend using AFDM versus dry mass to measure
periphyton biomass because silt can account for a substantial proportion of dry mass in some samples.
Ash mass in samples can be used to infer the amount of silt or other inorganic matter in samples.
Cell densities (cells cm-2) are determined by dividing the numbers of cells counted by the proportion of
sample counted and the area from which samples were collected. Cell biovolumes (mm3 biovolume
cm-2) are determined by summing the products of cell density and biovolume of each species counted
(see Lowe and Pan 1996) and dividing that sum by the proportion of sample counted and the area from
which samples were collected.
Rapid Bioassessment Protocols for Use in Streams and Wadeable Rivers: Periphyton, Benthic
Macroinvertebrates, and Fish, Second Edition 6-17
DRAFT REVISION—September 25, 1998
natural substrate and requires no laboratory proc essing, but hand picked samples can be returned to
the laboratory to quickly verify identification. It is a technique developed by Stevenson and Rier2.
2. Establish at least 3 transects across the • viewing bucket with 50-dot grid [Make the
habitat being sampled (preferably riffles viewing bucket by cutting a hole in bottom of
large ($0.5 m diameter) plastic bucket, but leave
or runs in the reach in which benthic
a small ridge around the edge. Attach a piece of
algal accumulation is readily observed
clear acrylic sheet to the bottom of the bucket
and characterized). with small screws and silicon caulk. The latter
makes water tight seal so that no water enters the
3. Select 3 locations along each transect bucket when it is partially submerged.
(e.g., stratified random locations on right, Periphyton can be clearly viewed by looking
middle, and left bank). down through the bucket when it is partially
submerged in the stream. Mark 50 dots in a 7 x
4. Characterize algae in each selected 7 grid on the top surface of the acrylic sheet with
location by immersing the bucket with a waterproof black marker. Add another dot
outside the 7 x 7 grid to make the 50 dot grid.]
50-dot grid (7 x 7 + 1) in the water.
• meter stick
! First, characterize macroalgal
• pencil
biomass. • Rapid Periphyton Survey Field Sheet
C Observe the bottom of the stream
through the bottom of the
viewing bucket and count the
number of dots that occur over macroalgae (e.g., Cladophora or Spirogyra) under which
substrates cannot be seen. Record that number and the kind of macroalgae under the dots
on RPS field sheet.
C Measure and record the maximum length of the macroalgae.
C If two or more types of macroalgae are present, count the dots, measure, and record
information for each type of macroalgae separately.
! Second, characterize microalgal cover.
C While viewing the same area, record the number of dots under which substrata occur that
are suitable size for microalgal accumulation (gravel > 2 cm in size).
C Determine the kind (usually diatoms and blue-green algae) and estimate the thickness
(density) of microalgae under each dot using the following thickness scale:
0 - substrate rough with no visual evidence of microalgae
0.5 - substrate slimy, but no visual accumulation of microalgae is evident
1 - a thin layer of microalgae is visually evident
2 - accumulation of microalgal layer from 0.5-1 mm thick is evident
3 - accumulation of microalgae layer from 1 mm to 5 mm thick is evident
4 - accumulation of microalgal layer from 5 mm to 2 cm thick is evident
5 - accumulation of microalgal layer greater than 2 cm thick is evident
Mat thickness can be measured with a ruler.
C Record the number of dots that are over each of the specific thickness ranks separately for
diatoms, blue-green algae, or other microalgae.
2
S.T. Rier is a graduate student at the University of Louisville.
Rapid Bioassessment Protocols for Use in Streams and Wadeable Rivers: Periphyton, Benthic
Macroinvertebrates, and Fish, Second Edition 6-19
DRAFT REVISION—September 25, 1998
6. QA/QC between observers and calibration between algal biomass (chl a, AFDM, cell density and
biovolume cm-2 and taxonomic composition) can be developed by collecting samples that have
specific microalgal rankings and assaying the periphyton.
A great wealth of taxonomic literature is available for algae. Below is a subset of that literature. It is
a list of taxonomic references that are useful for most of the United States and are either in English, are
important because no English treatment of the group is adequate, or are valuable for the good
illustrations.
Camburn, K.E., R.L. Lowe, and D.L. Stoneburner. 1978. The haptobenthic diatom flora of Long
Branch Creek, South Carolina. Nova Hedwigia 30:149-279.
Collins, G.B. and R.G. Kalinsky. 1977. Studies on Ohio diatoms: I. Diatoms of the Scioto River
Basin. Bull. Ohio Biological Survey. 5(3):1-45.
Cox, E. J. 1996. Identification of freshwater diatoms from live material. Chapman & Hall, London.
Czarnecki, D.B. and D.W. Blinn. 1978. Diatoms of the Colorado River in Grand Canyon National
Park and vicinity. (Diatoms of Southwestern USA II). Bibliotheca Phycologia 38. J. Cramer. 181 pp.
Dawes, C. J. 1974. Marine Algae of the West Coast of Florida. University of Miami Press.
Dillard, G.E. 1989a. Freshwater algae of the Southeastern United States. Part 1. Chlorophyceae:
Volvocales, Testrasporales, and Chlorococcales. Bibliotheca, 81.
Dillard, G.E. 1989b. Freshwater algae of the Southeastern United States. Part 2. Chlorophyceae:
Ulotrichales, Microsporales, Cylindrocapsales, Sphaeropleales, Chaetophorales, Cladophorales,
Schizogoniales, Siphonales, and Oedogoniales. Bibliotheca Phycologica, 83.
Dillard, G.E. 1990. Freshwater algae of the Southeastern United States. Part 3. Chlorophyceae:
Zygnematales: Zygenmataceae, Mesotaeniaceae, and Desmidaceae (Section 1). Bibliotheca
Phycologica, 85.
Dillard, G.E. 1991. Freshwater algae of the Southeastern United States. Part 4. Chlorophyceae:
Zygnemateles: Desmidaceae (Section 2). Bibliotheca Phycologica, 89.
Drouet, F. 1968. Revision of the classification of the oscillatoriaceae. Monograph 15. Academy of
Natural Sciences, Philadelphia. Fulton Press, Lancaster, Pennsylvania.
Hohn, M.H. and J. Hellerman. 1963. The taxonomy and structure of diatom populations from three
North American rivers using three sampling methods. Transaction of the American Microscopal
Society 82:250-329.
Jarrett, G.L. and J.M. King. 1989. The diatom flora (Bacillariphyceae) of Lake Barkley. U.S. Army
Corps of Engineers, Nashville Dist. #DACW62-84-C-0085.
Lange-Bertalot, H. 1980. New species, combinations and synonyms in the genus Nitzschia.
Bacillaria 3:41-77.
Patrick, R. and C.W. Reimer. 1966. The diatoms of the United States, exclusive of Alaska and
Hawaii. Monograph No. 13. Academy of Natural Sciences, Philadelphia, Pennsylvania.
Patrick, R. and C.W. Reimer. 1975. The Diatoms of the United States. Vol. 2, Part 1. Monograph
No. 13. Academy of Natural Sciences, Philadelphia, Pennsylvania.
Prescott, G.W. 1962. The algae of the Western Great Lakes area. Wm. C. Brown Co., Dubuque,
Iowa.
Prescott, G.W., H.T. Croasdale, and W.C. Vinyard. 1975. A Synopsis of North American desmids.
Part II. Desmidaceae: Placodermae. Section 1. Univ. Nebraska Press, Lincoln, Nebraska.
Prescott, G.W., H.T. Croasdale, and W.C. Vinyard. 1977. A synopsis of North American desmids.
Part II. Desmidaceae: Placodermae. Section 2. Univ. Nebraska Press, Lincoln, Nebraska.
Prescott, G.W., H.T. Croasdale, and W.C. Vinyard. 1981. A synopsis of North American desmids.
Part II. Desmidaceae: Placodermae. Section 3. Univ. Nebraska Press, Lincoln, Nebraska.
Prescott, G.W. 1978. How to know the freshwater algae. 3rd Edition. Wm. C. Brown Co.,
Dubuque, Iowa.
Simonsen, R. 1987. Atlas and catalogue of the diatom types of Friedrich Hustedt. Vol. 1-3. J.
Cramer. Berlin, Germany.
Rapid Bioassessment Protocols for Use in Streams and Wadeable Rivers: Periphyton, Benthic
Macroinvertebrates, and Fish, Second Edition 6-21
DRAFT REVISION—September 25, 1998
Smith, M. 1950. The Freshwater Algae of the United States. McGraw-Hill, New York, New York.
Taylor, W. R. 1960. Marine algae of the eastern tropical and subtropical coasts of the Americas.
University of Michigan Press, Ann Arbor, Michigan.
Whitford, L.A. and G.J. Schumacher. 1973. A manual of freshwater algae. Sparks Press, Raleigh,
North Carolina.
Wujek, D.E. and R.F. Rupp. 1980. Diatoms of the Tittabawassee River, Michigan. Bibliotheca
Phycologia 50:1-100.
Beaver, J. 1981. Apparent ecological characteristics of some common freshwater diatoms. Ontario
Ministry of the Environment. Rexdale, Ontario, Canada.
Fabri, R. and L. Leclercq. 1984. Etude écologique des riviéres du nord du massif Ardennais
(Belgique): flore et végétation de diatomeées et physico-chimie des eaux. 1. Station scientifique des
Hautes Fagnes, Robertville. 379 pp.
Fjerdingstad, E. 1950. The microflora of the River Molleaa with special reference to the relation of
benthic algae to pollution. Folia Limnologica Scandanavica 5, 1-123.
Hustedt, F. 1938-39. Systamatische und ökologische Untersuchungen über die Diatomeen-Flora von
Java, Bali und Sumatra nach dem Material deter Deutschen Limnologischen Sunda-Expedition.
Allgemeiner Teil. I. Ubersicht über das Untersuchungsmaterial und Charakterisktik der Diatomeenflora
der einzelnen Gebiete. II. Die Diatomeen flora der untersuchten Gesässertypen. III. Die ökologische
Faktoren und ihr Einfluss auf die Diatomeenflora. Archiv für Hydrobiologie, Supplement Band,
15:638-790 (1938); 16:1-155 (1938); 16:274-394 (1939).
Hustedt, F. 1957. Die Diatomeenflora des Flusssystems der Weser im Gebiet der Hansestadt Bremen.
Abhandlungen naturwissenschaftlichen. Verein zu Bremen, Bd. 34, Heft 3, S. 181-440, 1 Taf.
Lange-Bertalot, H. 1979. Pollution tolerance of diatoms as a criterion for water quality estimation.
Nova Hedwigia 64, 285-304.
LeCointe C., M. Coste, and J. Prygiel. 1993. "OMNIDIA" software for taxonomy, calculation of
diatom indices and inventories management. Hydrobiologia 269/270: 509-513.
Palmer, C. M. 1969. A composite rating of algae tolerating organic pollution. Journal of Phycology 5,
78-82.
Rott, E., G. Hofmann, K. Pall, P. Pfister, and E. Pipp. 1997. Indikationslisten für Aufwuchsalgen in
österreichischen Fliessgewässern. Teil 1: Saprobielle Indikation. Wasserwirtschaftskataster.
Bundesminsterium für Land- und Forstwirtschaft. Stubenring 1, 1010 Wein, Austria.
Slàdecek, V. 1973. System of water quality from the biological point of view. Archiv für
Hydrobiologie und Ergebnisse Limnologie 7, 1-218.
Van Dam, H., Mertenes, A., and Sinkeldam, J. 1994. A coded checklist and ecological indicator
values of freshwater diatoms from the Netherlands. Netherlands Journal of Aquatic Ecology 28,
117-33.
Watanabe, T., Asai, K., Houki, A. Tanaka, S., and Hizuka, T. 1986. Saprophilous and eurysaprobic
diatom taxa to organic water pollution and diatom assemblage index (DAIpo). Diatom 2:23-73.
Rapid Bioassessment Protocols for Use in Streams and Wadeable Rivers: Periphyton, Benthic
Macroinvertebrates, and Fish, Second Edition 6-23