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  • Diatom-based stream bioassessment: the effects of rare taxa and

    live/dead ratio

    Dissertation Proposal

    Ph. D. in Environmental Sciences and Resources

    Submitted by: Nadezhda D. Gillett

    January 2009

    Defense Date: 12:00 pm, February 3, 2009

    Dissertation Committee

    Portland State University

    Committee Members:

    Dr. Yangdong Pan, Chair

    Dr. Joseph Maser

    Dr. Ian Waite

    Dr. J. Alan Yeakley

    Graduate Office Representative: Dr. Jiunn-Der Duh

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    General Introduction

    The assessment of ecological integrity in streams and rivers is essential for the

    healthy, social and economic well-being of humans. However, human-induced stressors

    (e. g. agriculture, logging, urbanization, sewage contamination, etc.) alter the stream

    environment and the aquatic organisms by changing their habitat structure, flow regime,

    water quality, energy source and biotic interactions (Karr and Chu, 1999). Conceptually

    such alterations may cause the biota to respond in a predictable way by changing its

    energetics, nutrient cycling and community structure (Odum, 1985). Bioassessment

    focuses on changes in biotic community structure and function in response to human


    Diatom-based assessment has been an integral part of both national and regional

    bioassessment programs (Stevenson and Bahls, 1999; Peck et al., 2006). Accuracy and

    precision in diatom-based bioassessment need to be improved to meet the increasing

    demands of water resource management. Diatoms, a group of algae, are good

    bioindicators of water quality in streams and rivers (Stevenson and Pan, 1999). As

    primary producers, they are at the base of the food web in streams. Diatoms, with short

    life cycles, respond quickly to a variety of environmental conditions such as organic

    pollution (Lange-Bertalot, 1979), siltation (Bahls, 1993), pH (Pan et al., 1996) and

    eutrophication (Kelly and Whitton, 1995; Potapova and Charles, 2007). Diatom

    assemblages are species rich and each species may provide information about their

    environment (Lowe and Pan, 1996). Conventional diatom-based bioassessment

    programs, however, often draw assessment conclusions based on the responses of the

    common taxa to the environment, while the rare taxa in the diatom assemblages, regarded

    as noise, are often excluded from final assessment analyses or down-weighted (Pan et al.

    1996, 2000; Potapova and Charles, 2002, 2003). Based on the niche theory, several

    researchers assume that rare species may have narrow environmental requirements and

    therefore may be used as good indicators of pollution (Gaston, 1994; Potapova and

    Charles, 2004). This notion is not well supported by the current diatom literature.

    Bioassessment uses living organisms to evaluate environmental quality, with

    diatoms being an exception. A diatom sample comprises a mixture of live (chloroplast

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    containing siliceous cell walls) and dead (only siliceous cell walls) individuals which are

    not distinguished from each other in the conventional diatom analysis (Charles et al.,

    2002). This analysis involves the use of strong acid to remove the organic material in

    diatom cells to reveal the fine morphological features of their cell walls, which allows

    diatom identification to the lowest possible taxonomic level. It is unclear whether

    differentiating live and dead diatoms in an assemblage would significantly improve the

    accuracy and precision of diatom-based bioassessment. Several researchers have

    suggested that assemblages generated by the traditional method may better integrate

    spatial and temporal variability of environmental conditions in the sampled stream and its

    watershed, because the accumulation of live and dead diatoms over time may provide

    broad environmental information (Cox, 1998; Stevenson and Pan, 1999). However,

    Pryfogle and Lowe (1979) concluded that the traditional counting technique might mask

    the specific response of the live resident taxa to the local environmental conditions. In

    addition, dead diatoms from adjacent habitats might be a significant source of error in

    characterizing diatom communities and their signals about the local environment (Round,


    The US Environmental Protection Agency’s Western Environmental Monitoring

    and Assessment Program (WEMAP) provides a great opportunity to enhance the quality

    of diatom-based assessment. WEMAP sampled the western US streams and rivers with

    the major objective to assess the status of surface waters in the west. The project

    collected an extensive set of physical, chemical and biological data over the course of

    five years in 12 western states. Another important task of this project is to develop and

    evaluate the tools for assessing ecological conditions. Both of these objectives, as well as

    its large spatial coverage and probability-based sampling design, allow inferences to be

    made from a small number of samples about the extent of the whole study area. The

    extensive study area provides potential good natural and disturbance gradients which can

    be used to explore the roles of live/or dead diatoms and rare diatom taxa in


    My proposed research focuses on the potential roles of both rare taxa and

    live/dead diatoms in diatom-based stream bioassessment (Fig. 1). Specifically, I want to

    evaluate whether rare diatom taxa with either low abundance or small range size have

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    narrower ecological niches than common taxa and if so, I want to assess if the number of

    rare taxa can be used as an indicator of environmental conditions. I also want to assess

    the relationships between live/dead diatoms and human disturbance from a large scale

    study (12 western states) and a small scale study (Oregon coastal region).

    Fig. 1. Flow diagram of proposed research plan.

    Background Information


    The main goal of bioassessment is to evaluate whether a site or a system of

    interest (test site) is impaired based on biological indicators. This is usually done by a

    comparison to reference conditions with high physical, chemical and biological quality.

    The reference conditions can be defined for a region or for a site depending on the

    assessment objectives (US EPA, 2002). The regional reference condition represents

    natural state within a region for ecosystems with different geographical features (e.g.,

    climate, soil, topography and vegetation) and their biological communities (Hughes et al.,

    1986). The site-specific approach evaluates the conditions upstream from a point source

    pollution or in a matching watershed (Hughes et al., 1986). Due to the pervasive nature of

    human disturbance, a reference condition free of human disturbance may not exist and

    Importance of rare taxa in diatom-based stream bioassessment

    Do rare taxa with small range size inhabit narrow ecological niches?

    Live diatoms in bioassessment: a small regional study

    Do different metrics of diatom rarity respond to natural conditions or to human disturbance?

    Are the diatom assemblages generated by counting the traditional acid cleaned samples different from the live diatoms in the undigested samples?

    Do the assemblages from the two counts differ in their responses to the measured environmental variables?

    Live diatoms in bioassessment: a large scale study

    Can percent live diatoms be used as a metric of human disturbance?

    Dead diatoms in bioassessment

    Can percent dead diatoms be used as a metric of human disturbance?

    Do rare taxa with low abundance inhabit narrow ecological niches?

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    the phrase “reference condition for biological integrity” (biological condition without

    human disturbance in a watershed, e.g., national parks) has been proposed (Stoddard et

    al., 2006). Several definitions for reference conditions include: minimally disturbed

    condition (absence of significant human disturbance), least disturbed condition (least

    impacted current condition), historical condition (known lack of human influence in the

    past) or best attainable condition (desirable future condition with better management)

    (Stoddard et al., 2006). Reference site selection is often determined by proximity and

    influence by human population density and distribution, road density and land use in the

    watershed (logging, mining, agriculture, grazing and urbanization). Biological indicators,

    organisms with well-known response to disturbance, are used to detect deviations from

    reference conditions (Davies and Jackson, 2006).

    Bioassessment uses different groups of organisms (e.g., algae, macroinvertebrates

    and fish) to evaluate the environmental conditions of waters. Biological assemblages are

    often characterized using different biological attributes such as diversity, abundance, and

    functional groups. Diversity measures play an important role in bioassessment, because

    diversity is perceived as a correlate of environmental well bein

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