U.S. Department of Energy, Office of Science

Program for Ecosystem Research

Research Project   An annual grassland exploration of scaling from genomes to ecosystem functioning

Principal investigator:   Mary K. Firestone

Project goal

To (1) evaluate the genomic basis of plant and soil microbial controls of terrestrial ecosystem response to climatic change and (2) create and validate models capable of scaling from measurements of genetic makeup of key components (organisms) to prediction of biogeochemical processes.

Conceptual model

Ecosystem being studied

California annual-grassland mesocosms located in glasshouses are being studies as model representations of grassland ecosystems comprising millions of hectares across the United States. Because these ecosystems are dominated by annual plants, the response of these ecosystems to changing patterns of precipitation and temperature may be evident over a relatively short time horizon, allowing relatively rapid assessment of the genomic basis of integrated plant/soil response to changing climate.

Soils and plants were collected from the Hopland Experimental Station (northwest California) and the University of California Natural Reserve System, Sedgwick Reserve (southwestern California).


The mesocosms have been constructed and the first growing season has been completed. Data to date indicate that the rainfall manipulation strongly affects microbial community structure, with no significant effect on bacterial or archaeal richness. System nitrification potential is associated with nitrifier community structure.

Why this is important

The response of ecosystems to climatic change depends on the integrated responses of many types of organisms. Yet the control of ecosystem response must ultimately be related to the genes of plants and microbes. Evaluating key genes of the major players will increase our mechanistic understanding and ability to predict how terrestrial ecosystems can be impacted by global environmental change.

LBNL mesocosms

California annual grassland mescosms being used in the project. Note the different plant communities. Probes for soil water content (TDR) at two depths, water potential (psychrometers) at three depths, and temperature at three depths are installed in each mesocosm. Nine-minute summaries of ambient air temperature, relative humidity, photosynthetic photon flux density, and evaporation rates are logged.


Replicated annual grassland mesocosms contained with 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 temperature (i.e., ambient and ambient +5 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.

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, phenolog transitions, root architecture, mycorrhization, leaf-level gas exchange, elemental analysis, leaf pigments, enzymes associated with carbon and nitrogen metabolism, metabolites associated with carbon and nitrogen metabolic pathways, gene expression associated with carbon and nitrogen metabolism, and water-use efficiency and 13-carbon discrimination.

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).

The measurements will be used to determine whether: (1) climatic change will alter the composition of the soil microbial community which can be related to changes in rates of N-cycling-processes that provide essential nutrients to plants and trace gas reactants; (2) the expression of plant genes related to nutrient uptake and metabolism will change in response to climatic change, particularly in roots; and (3) information on the soil environment, microbial dynamics, and molecular measurements of gene expression can be scaled to predict ecosystem function.


Mary K. Firestone, Lawrence Berkeley National Laboratory

Adam Arkin, Lawrence Berkeley National Laboratory

Margaret Torn, Lawrence Berkeley National Laboratory

David Ackerly, University of California, Berkeley (subaward)

Gary Andersen, University of California, Berkeley (subaward)

Funding period:   April 2005 to present