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Final Report: Microbial Community Assays
EPA Grant Number: R825433C045Subproject: this is subproject number 045 , established and managed by the Center Director under grant R825433
(EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).
Center: EERC - Center for Ecological Health Research (Cal Davis)
Center Director: Rolston, Dennis E.
Title: Microbial Community Assays
Investigators: Scow, Kate
Institution: University of California - Davis
EPA Project Officer: Levinson, Barbara
Project Period: October 1, 1996 through September 30, 2000
RFA: Exploratory Environmental Research Centers (1992)
Research Category: Center for Ecological Health Research , Targeted Research
Description:
Objective:The objective of this research project was to develop or adapt methods for measuring microbial community structure (targeting nucleic acids and fatty acids) and function in the environment. We conducted investigations in surface soils, contaminated groundwater, Clear Lake, and river sediments.
Summary/Accomplishments (Outputs/Outcomes):We analyzed sediment microbial community composition by phospholipid fatty acid (PLFA) analysis at different locations in mercury-contaminated portions of Clear Lake, and we related community composition to various environmental factors. We found that location within the lake most strongly correlated with microbial community composition; seasonal changes and depth-interval effects influenced composition, but were less important than lake location. Mercury methylation potential and sediment organic carbon content were significantly related to sediment PLFA composition, whereas porewater sulfate, total mercury concentrations, and organic matter carbon/nitrogen ratios were not. Mercury methylation potential per unit of microbial biomass was highest at lake locations with the highest abundance of biomarkers characteristic of sulfate-reducing bacteria in the genus Desulfobacter. In a second study, examining sediments at three other mercury-polluted sites, we found watershed and/or hydrology to be strongly related to microbial community composition. Microbial communities in the Cache Creek Watershed (Abbott, Reed, and Sulphur Bank) were more similar to each other than to the Mt. Diablo (Marsh Creek Watershed). Additionally, the two mine sites with stream hydrology (Abbott and Reed) grouped together separately from Sulphur Bank (lake) or Mt. Diablo (natural springs). We measured two PLFA biomarkers, Desulfobacter and Desulfovibrio, at each of these sites, and we suggest that these groups of bacteria may play a role in methylmercury production at the Abbott, Reed, and Sulphur Bank sites.
We also examined how organic carbon amendment (compost, vetch, or no amendment) and water additions (from air dry to flooded) affect microbial community composition. Using canonical correspondence analysis of PLFA data, we determined that flooded, carbon-amended (+C) microcosm samples were distinctly different from other +C samples and unamended (-C) samples. Overall, manipulating water and carbon content selects for microbial communities similar to those observed when the same factors are manipulated at the field scale.
We compared PLFA and total soil fatty acid methyl esters (TSFAME) with respect to their reliable detection limits, extraction precision, and ability to differentiate agricultural soils. Although less soil initially was extracted with TSFAME, total fatty acid content g-1 soil (DW) was more than sevenfold higher in TSFAME than PLFA-extracted samples. Sample extraction precision was much lower with TSFAME analysis than with PLFA analysis, with the coefficient of variation between replicates as much as fourfold higher with TSFAME extraction.
To measure the microbial community's response to radioactively labeled glucose or toluene, we coupled PLFA analysis of a soil microbial community with 13C isotope tracer analysis. Many microorganisms utilize glucose, and a relatively small subset of microorganisms utilizes toluene. We found the method to be effective in distinguishing the specific microbial population involved in the metabolism of toluene from other members of the soil community.
Finally, we developed two real-time quantitative polymerase chain reaction (PCR) methods to quantify two groups of environmentally important bacteria. One method targeted the 16S rRNA sequences specific to a methyl tert-butyl ether (MTBE)-degrading bacterium and led to the discovery of naturally occurring, MTBE-degrading populations. The other method targeted sequences for the gene responsible for ammonium oxidation, ammonia monooxygenase (amoA); we used amoA to describe population dynamics of ammonium oxidizers during nitrification in soil.
The following activities were accomplished:
• We analyzed sediment microbial community composition by PLFA analysis at four sites in California contaminated with mercury. The significance of this method is that it permits quantitative comparisons of microbial communities exposed to similar stressors across a landscape, measurement of the responses of populations to contamination or remediation activities, and the relation of environmental gradients to community composition.
• We coupled PLFA analysis of a soil microbial community with 13C isotope tracer analysis to measure the microbial community's response to the addition of a contaminant, toluene, used by a relatively small subset of microorganisms. Our study showed that coupling 13C-tracer analysis with PLFA analysis is an effective tool for distinguishing a specific microbial population involved in the metabolism of a labeled substrate in complex environments such as soil.
• We developed a real-time quantitative PCR method for detecting the MTBE-degrading bacterial strain PM1. This is significant because it is now possible to quantify the density of a naturally occurring bacterium involved in MTBE biodegradation in groundwater, and to relate densities to biodegradation rates. The quantitative PCR method for PM1 will be commercially available (through Regenesis, Inc.) and currently is being used by industry (responsible parties, engineering firms) to estimate the potential for MTBE bioremediation by biostimulation.
• We developed a quantitative real-time PCR assay targeting the amoA gene to estimate population sizes of ammonium-oxidizing bacteria in soil. This is the first reported method that quantifies this important group of bacteria in soil. This also is the first study to demonstrate the relationship between ammonium oxidation kinetics and densities of amoA genes. These findings will be useful to other investigators studying microbial community structure.
Supplemental Keywords:ecosystem, ecosystem protection, environmental exposure and risk, geographic area, international cooperation, water, terrestrial ecosystems, aquatic ecosystem, aquatic ecosystem restoration, aquatic ecosystems and estuarine research, biochemistry, ecological effects, ecological indicators, ecological monitoring, ecology and ecosystems, environmental chemistry, restoration, state, water and watershed, watershed, watershed development, watershed land use, watershed management, watershed modeling, watershed restoration, watershed sustainability, agricultural watershed, exploratory research environmental biology, California, CA, Clear Lake, Lake Tahoe, anthropogenic effects, aquatic habitat, biogeochemical cycling, ecological assessment, ecology assessment models, ecosystem monitoring, ecosystem response, ecosystem stress, environmental stress, environmental stress indicators, fish habitat, hydrologic modeling, hydrology, integrated watershed model, lake ecosystems, lakes, land use, nutrient dynamics, nutrient flux, water management options, water quality, wetlands. , Ecosystem Protection/Environmental Exposure & Risk, Water, INTERNATIONAL COOPERATION, Geographic Area, Scientific Discipline, RFA, ECOSYSTEMS, Ecosystem/Assessment/Indicators, Water & Watershed, exploratory research environmental biology, Aquatic Ecosystems & Estuarine Research, Ecological Monitoring, Aquatic Ecosystem, Ecological Indicators, Biochemistry, Watersheds, Environmental Chemistry, Ecological Effects - Environmental Exposure & Risk, Monitoring/Modeling, Ecology and Ecosystems, Environmental Monitoring, State, biomarkers, runoff, water quality, California (CA), wildlife habitat, watershed modeling, watershed land use, marine food web, watershed management, watershed restoration, immunoassay, Clear Lake, microbial ecology, ecological risk, ecology assessment models, ecosystem health, Clear Lake , environmental stress indicators, anthropogenic effects, microbial assays, fish habitat, land use, wetlands, watershed development, aquatic habitat, agricultural watershed, aquatic ecosystems, environmental stress, lake ecosysyems, watershed sustainablility, bioassay, ecological assessment, hydrology, water management options, biomarker, ecosystem stress, ecosystem response, ecosystem monitoring, nutrient dynamics
Relevant Websites:
Progress and Final Reports:
1999 Progress Report
Original Abstract
Main Center Abstract and Reports:
R825433 EERC - Center for Ecological Health Research (Cal Davis)
Subprojects under this Center:
(EPA does not fund or establish subprojects; EPA awards and manages the overall grant for this center).
R825433C001 Potential for Long-Term Degradation of Wetland Water Quality Due to Natural Discharge of Polluted Groundwater
R825433C002 Sacramento River Watershed
R825433C003 Endocrine Disruption in Fish and Birds
R825433C004 Biomarkers of Exposure and Deleterious Effect: A Laboratory and Field Investigation
R825433C005 Fish Developmental Toxicity/Recruitment
R825433C006 Resolving Multiple Stressors by Biochemical Indicator Patterns and their Linkages to Adverse Effects on Benthic Invertebrate Patterns
R825433C007 Environmental Chemistry of Bioavailability in Sediments and Water Column
R825433C008 Reproduction of Birds and mammals in a terrestrial-aquatic interface
R825433C009 Modeling Ecosystems Under Combined Stress
R825433C010 Mercury Uptake by Fish
R825433C011 Clear Lake Watershed
R825433C012 The Role of Fishes as Transporters of Mercury
R825433C013 Wetlands Restoration
R825433C014 Wildlife Bioaccumulation and Effects
R825433C015 Microbiology of Mercury Methylation in Sediments
R825433C016 Hg and Fe Biogeochemistry
R825433C017 Water Motions and Material Transport
R825433C018 Economic Impacts of Multiple Stresses
R825433C019 The History of Anthropogenic Effects
R825433C020 Wetland Restoration
R825433C021 Sierra Nevada Watershed Project
R825433C022 Regional Transport of Air Pollutants and Exposure of Sierra Nevada Forests to Ozone
R825433C023 Biomarkers of Ozone Damage to Sierra Nevada Vegetation
R825433C024 Effects of Air Pollution on Water Quality: Emission of MTBE and Other Pollutants From Motorized Watercraft
R825433C025 Regional Movement of Toxics
R825433C026 Effect of Photochemical Reactions in Fog Drops and Aerosol Particles on the Fate of Atmospheric Chemicals in the Central Valley
R825433C027 Source Load Modeling for Sediment in Mountainous Watersheds
R825433C028 Stress of Increased Sediment Loading on Lake and Stream Function
R825433C029 Watershed Response to Natural and Anthropogenic Stress: Lake Tahoe Nutrient Budget
R825433C030 Mercury Distribution and Cycling in Sierra Nevada Waterbodies
R825433C031 Pre-contact Forest Structure
R825433C032 Identification and distribution of pest complexes in relation to late seral/old growth forest structure in the Lake Tahoe watershed
R825433C033 Subalpine Marsh Plant Communities as Early Indicators of Ecosystem Stress
R825433C034 Regional Hydrogeology and Contaminant Transport in a Sierra Nevada Ecosystem
R825433C035 Border Rivers Watershed
R825433C036 Toxicity Studies
R825433C037 Watershed Assessment
R825433C038 Microbiological Processes in Sediments
R825433C039 Analytical and Biomarkers Core
R825433C040 Organic Analysis
R825433C041 Inorganic Analysis
R825433C042 Immunoassay and Serum Markers
R825433C043 Sensitive Biomarkers to Detect Biochemical Changes Indicating Multiple Stresses Including Chemically Induced Stresses
R825433C044 Molecular, Cellular and Animal Biomarkers of Exposure and Effect
R825433C045 Microbial Community Assays
R825433C046 Cumulative and Integrative Biochemical Indicators
R825433C047 Mercury and Iron Biogeochemistry
R825433C048 Transport and Fate Core
R825433C049 Role of Hydrogeologic Processes in Alpine Ecosystem Health
R825433C050 Regional Hydrologic Modeling With Emphasis on Watershed-Scale Environmental Stresses
R825433C051 Development of Pollutant Fate and Transport Models for Use in Terrestrial Ecosystem Exposure Assessment
R825433C052 Pesticide Transport in Subsurface and Surface Water Systems
R825433C053 Currents in Clear Lake
R825433C054 Data Integration and Decision Support Core
R825433C055 Spatial Patterns and Biodiversity
R825433C056 Modeling Transport in Aquatic Systems
R825433C057 Spatial and Temporal Trends in Water Quality
R825433C058 Time Series Analysis and Modeling Ecological Risk
R825433C059 WWW/Outreach
R825433C060 Economic Effects of Multiple Stresses
R825433C061 Effects of Nutrients on Algal Growth
R825433C062 Nutrient Loading
R825433C063 Subalpine Wetlands as Early Indicators of Ecosystem Stress
R825433C064 Chlorinated Hydrocarbons
R825433C065 Sierra Ozone Studies
R825433C066 Assessment of Multiple Stresses on Soil Microbial Communities
R825433C067 Terrestrial - Agriculture
R825433C069 Molecular Epidemiology Core
R825433C070 Serum Markers of Environmental Stress
R825433C071 Development of Sensitive Biomarkers Based on Chemically Induced Changes in Expressions of Oncogenes
R825433C072 Molecular Monitoring of Microbial Populations
R825433C073 Aquatic - Rivers and Estuaries
R825433C074 Border Rivers - Toxicity Studies