The ultimate goal of this completed research was to improve our ability to predict ecosystem response to climate change. Our starting assumption was that plants and microorganisms mediate terrestrial ecosystem response to global climate change. While there are many groups of organisms that are critical to ecosystem function, we employed the simplifying construct that plants and microbes are the primary mediators.
This project was a collaborative project sponsored by the US Department of Energy, involving researchers from the Departments of Environmental Science, Policy and Management, Integrative Biology, University of California, Berkeley and the Earth Sciences Division, Lawrence Berkeley National Lab.
This project is currently inactive.
Can we enhance our ability to predict ecosystem response to future environmental changes by evaluating the genomic basis of the response of the primary mediators?
Ecosystem response to climate change potentially involves multiple levels of biological organization, ranging from genomes to whole ecosystem.
Our goal is to utilize current genomic, transcriptomic, and bioinformatic concepts and tools in order to identify and evaluate the essential components of the pathway of mediation.
Replicated annual grassland mesocosms contained within glasshouses are being exposed to three patterns of precipitation (i.e., 318, 678, and 1248 mm; applied with alternating wet and dry periods — these treatments were designed using 30-yr records of rainfall patterns for coastal California to reflect low, median, and high rainfall years) and two temperatures (i.e., ambient and ambient +3 degrees Celsius). The mesocosms contain three plant “communities”: Avena barbata, Erodium botrys, and mixed (7 species including Avena and Erodium). The mesocosms contain one of two soils (collected from Hopland and Sedgwick Field Stations, respectively). The mesocosms (154 total) are rooted in 50 x 75 cm schedule 40 PVC cylinders packed with three soil horizons to field bulk density with horizon depths from the field. The mesocosms were instrumented with TDR probes and psychrometers to follow soil moisture content and water potential throughout the seasons.
Biogeochemical (ecosystem) measurements include: nitrification potential, denitrifying activity, rate of gross nitrogen mineralization, rate of gross nitrification, rate of N2O production, soil O2 concentration, soil solution nitrate and ammonia concentrations, and ecosystem CO2 and methane exchange.
Plant indices being measured include: aboveground biomass, root biomass, canopy architecture, partitioning/allometry, fecundity, phenology, whole ecosystem gas exchange, leaf-level gas exchange, water-use efficiency and 13-carbon discrimination, elemental analysis, leaf pigments, enzymes activity, metabolites and expression of genes associated with carbon and nitrogen metabolism.
Soil microbial indices being measured include: microbial biomass (DNA), microbial activity (RNA), prokayotic community composition (phylochip), active prokaryote (rRNA phylochip), AM in roots (copy #), nitrifier numbers (qPCR and amoA DNA), nitrifier “activity” (qPCR and cDNA amoA), and species composition of ammonia-oxidizing bacteria (clone libraries of amoA).
- St.Clair SB, Sudderth EA, Castanha C, Torn MS and Ackerly DD (2009). Variation in soil moisture patterns and N availability alter plant productivity and species diversity in a model California grassland. Journal of Vegetation Science, 20, 860-870. (pdf)
- St.Clair SB, Sudderth EA, Fischer ML, Torn MS, Stuart SA, Salve R, Eggett D and Ackerly DD (2009). Variation in soil moisture and N availability modulates carbon and water exchange in a California grassland experiment. Global Change Biology, in press. (doi: 10.1111/j.1365-2486.2009.01862.x). (pdf)
- Leakey ADB, Ainsworth EA, Bernard SM, Markelz RJC, Ort DR, Placella SA, Rogers A, Smith MD, Sudderth EA, Weston DJ, Wullschleger SD and Yuan S (2009). Gene expression profiling – opening the black box of plant ecosystem responses to global change. Global Change Biology, 15, 1201–1213. (pdf)
- Wullschleger SD, Leakey ADB and St.Clair SB (2007). Functional genomics and ecology: a tale of two scales. New Phytologist, 176, 735-739. (pdf)
- Sudderth EA, St.Clair SB, Salve R, Fischer ML, Kleber M, Sudderth EB, Torn MS and Ackerly DD. Edaphic factors modify the impact of changing precipitation patterns on plant and ecosystem function in Avena barbata grasslands. New Phytologist.
- Salve R, Sudderth EA, Fisher ML, St. Clair SB and Torn MS. Precipitation and soil impacts on subsurface moisture dynamics in Avena barbata: Observations from a greenhouse experiment. Water Resources Research.
- Brodie EL, Dubinsky EA, Ackerly DD, Andersen GL and Firestone MK (2009). Are there predictable soil microbial community responses to climate change? Subsurface Biosphere Initiative seminar series, College of Oceanic and Atmospheric Sciences. Oregon State, University, Coravllis, OR.
- Bernard SM, Lindquist E, Wilks C, Ackerly DD and Andersen GL (2009). Developing molecular tools for studying the response of the wild grass Avena barbata to climatic changes. Evolutionary and Ecological Functional Genomics. Gordon Research Conference, Tilton, NH.
- Dubinsky EA, Brodie EL, Myint C, Ackerly DD, Van Nostrand J, Bird JA, Zhou J, Andersen GL and Firestone MK (2008). Predicting effects of climate change on the composition and function of soil microbiral communities. Annual Meeting American Geophysical Union. San Francisco, CA.
- Sudderth EA, Bernard SM, Placella SA, St. Clair SB, Brodie EL, Salve R, Herman DJ, Fisher ML, Torn MS, Firestone MK and Ackerly DD (2008). The effects of changing precipitation on ecosystem function in Avena barbata grasslands: linking microbial and plant responses in contrasting soil types. Ecological Society of American Annual Meeting. Milwaukee, WI.
- Brodie EL, Dubinsky EA, Myint C, Ackerly DD, Andersen GL and Firestone MK (2008). Are there predictable soil microbial community responses to climate change? American Society of Microbiology Annual Meeting. Boston, MA.
- Bernard SM, StClair SB, Sudderth EA, Torn MS, Ackerly DD and Andersen GL (2008). The long-term effects of drought and high temperature on N metabolism in a C3 grass. American Society of Plant Biologists. Annual Meeting Mérida, Mexico.
- Torn MS, Bernard SM, St.Clair SB, Fischer ML, Hopkins FM, Placella SA, Castanha C, Sudderth E, Herman DJ, Salve R, Ackerly DD and Firestone MK (2007). Linking the response of annual grasslands to warming and altered rainfall across scales of gene expression, species, and ecosystem. AGU, San Francisco, CA.
- Placella SA, Brodie EL, Bernard SM, Andersen GL, Herman DJ and Firestone MK (2007). Connecting Soil Microbial Nitrogen Transformations and Plant Nitrogen Processing. Oral presentation at the Ecological Society of America’s Annual Meeting, San Jose, CA.
- Bernard SM, StClair SB, Placella SA, Firestone M, Salve R, Ackerly DD and Andersen GL (2007). A molecular analysis of plant response to global climate change in an annual grassland. Ecological Society of America, General meeting, San Jose, CA.
- St. Clair SB, Castanha C, Sudderth EA, Torn MS, Firestone MK (2007). The influence of cumulative and temporal variation in soil moisture on California grassland plant processes. Talk presented to the Ecological Society of America, General Meeting, San Jose, CA.
- Torn MST, St.Clair SB, Ackerly DD, Andersen GL, Bernard SM, Brodie EL, Castanha C, Firestone MK, Fischer MK, Hopkins FH, Placella SA and Salve R (2007). Annual grassland response to altered precipitation and temperature: genes, species, and ecosystem. Ecological Society of America, General meeting, San Jose, CA.
- Brodie EL, Bernard SM, StClair SB, Placella SA, Herman DJ, Salve R, Torn MS, Ackerly DD, Firestone MK and Andersen GL 16S (2007). rRNA microarray analysis of shifts in microbial community composition in response to altered soil moisture and its implication for changes in nutrient cycling. Ecological Society of America, General meeting, San Jose, CA.
- Bernard SM, St. Clair S, Placella S, Firestone M, Torn MST, Ackerly DD and Andersen GL (2007). A molecular approach to understanding plant response to global climate change in a Californian grassland ecosystem. Plant biology and Botany- Joint congress, Chicago, IL.
- Placella SA, Brodie EL, Andersen GL, Herman DJ, and Firestone MK (2007). Linking Nitrification with Nitrifier Community Structure as Defined by High-Density Microarray. Poster presentation at the American Society for Microbiology General Meeting, Toronto, Canada.
- Placella SA, Bernard SM, St. Clair SB, Herman DJ, Andersen GL, Ackerly DD and Firestone MK (2007). Plant-Microbe Interactions and Global Change. Oral presentation at the Environmental Science, Policy, and Management Graduate Research Symposium, Berkeley, CA.
- St. Clair SB, Fischer ML, Torn MS and Ackerly DD (2006). The interactive effects of water, temperature, and community composition on California grassland CO2 fluxes. Ecological Society of America Annual Meeting, Memphis, TN.
- Bernard SM, Ball I, St.Clair S, Placella S, Firestone M, Torn MS, Ackerly DD and Andersen GL (2006). A molecular approach to understanding plant response to global climate change in a Californian grassland. Ecosystem. Gene in Ecology, Ecology in Genes. Kansas State University, Kansas City, Misouri.