Assessment of Multiple Stresses on Soil Microbial Communities

EPA Grant Number: R825433C066
Subproject: this is subproject number 066 , 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: Assessment of Multiple Stresses on Soil Microbial Communities
Investigators: Scow, Kate
Institution: University of California - Davis
EPA Project Officer: Packard, Benjamin H
Project Period:    
RFA: Exploratory Environmental Research Centers (1992) RFA Text |  Recipients Lists
Research Category: Targeted Research


Microbes are primary agents of decomposition and nutrient and energy flow in all ecosystems. Microbial food web interactions and population dynamics are potentially very complicated, with as many as 1000 species present in a gram of soil. Changes in microbial communities in response to stresses are poorly understood, primarily because they are difficult to measure. Previously existing methodology in microbial ecology has been dependent on culturing (most environmental species cannot be cultured), or lacked the sensitivity to detect changes in response to known biological stressors such as pesticides. New methods which allow detection of changes in microbial community structure and function will provide novel information about the potential of ecosystems to withstand stresses and decompose toxins. Once developed, such methods are applicable to any ecosystem, including aquatic and terrestrial.


Two major analytical challenges are being addressed. First, methods being developed are community (as opposed to pure culture or species-selective) measures of microbial structure and function. Second, methods are being adapted for use in complex environmental media such as soil and sediment. Promising methods are tested for sensitivity in detecting responses along known stress gradients. Methods which have already been adapted include BIOLOG (a measure of potential community metabolic ability), modeling analysis of substrate-induced respiration kinetics (SIR), and community phospholipid fatty acid (PLFA) analysis. An additional challenge is posed by data sets generated BIOLOG and PLFA methods. These methods generate over 50 test responses simultaneously and are most powerful when analysed with multivariate statistic which allow direct identification of relationships between the response pattern and environmental or stress gradients. We have found redundancy analyis (RDA) and canonoical correspondence analysis (CCA) to be extremely useful in analyzing large BIOLOG and PLFA data sets.

Sensitivity of BIOLOG and SIR methods have now been tested with a wide variety of stressors, including organic and inorganic agricultural chemicals (metam sodium, kocide, polyacrylamide), pesticide degradation products (p-nitrophenol), and water and carbon-supply gradients. Microcosm studies using dose gradients of metam sodium, one of the most-used agricultural chemicals in California, showed that both BIOLOG and SIR could easily detect differences in microbial communities along a concentration gradient in field-relevant dose ranges. In a similar study using field-relevant concentration both methods also detected changes due to "Kocide", a widely-used copper hydroxide pesticide. "Soil-fix IR", a polyacrylamide soil conditioner, also caused changes detected by BIOLOG in a microcosm study.

Ability of BIOLOG and SIR to distinguish changes due to multiple stress was tested in a microcosm study using dose gradients of metam sodium and p-nitrophenol, a parathion degradation product. BIOLOG and SIR were both able to differentiate dose levels along both gradients, indicating that they may be very sensitive tools to monitor changes in the functional abilities of soil microbial communities in soil and sediment systems subject to multiple stresses gradients. This conclusion is supported by analysis of soil samples from a field-replicated study of carbon and water dynamics in rice agriculture. Differences in BIOLOG patterns were significantly related to carbon input and flooding treatments in this study. Traditional measures of microbial biomass were not able to detect.

Expected Results:

Future work will focus on further development of Randomly Amplified Polymorphic DNA (RAPD) analysis for characterizing total soil DNA and community PLFA profiles. These approaches have already proven fruitful in fingerprinting soil from different locations, under different management practices, and exposed to different stressors. These methods will be available to characterize natural microbial communities in field samples collected from different Center project sites. Taxon-specific 16S rDNA probes to be used with community DNA extracted from soil and sediment are also under development and will provide a bridge between functional and structural changes. Both the DNA probes and PLFA profiles will help link impairments of specific microbial functions, such as decomposition, pollutant degradation, and nutrient cycling, to exposure to various stress gradients. The Transport and Fate Core can use the molecular and kinetic approaches developed here in the assessment of biodegradation kinetics.

Supplemental Keywords:

Aquatic ecosystem, California, environmental statistics, soil analysis, nutrients, microbial food web, pesticides, ecosystem modeling, DNA analysis, biodegradation, watersheds., RFA, Scientific Discipline, Ecosystem Protection/Environmental Exposure & Risk, Ecology, exploratory research environmental biology, Ecosystem/Assessment/Indicators, Ecosystem Protection, Ecological Effects - Environmental Exposure & Risk, Ecological Risk Assessment, Ecology and Ecosystems, Agronomy, Ecological Indicators, Agricultural Engineering, stressors, microbial communities, agricultural environments, multiple stressors, soil, agriculture, agrochemcial, metam-sodium, agriculture ecosystems

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