Earth Sciences Division (ESD) Department of Energy (DOE) Lawrence Berkeley National Laboratory (LBNL)

Meta-"Omics" Analysis of Microbial Carbon Cycling Responses to Altered Rainfall Inputs in Native Prairie Soils

This research is sponsored by the DOE-BER, Biological Systems Research on the Role of Microbial Communities in Carbon Cycling Program, under Contract No. DE-SC0004953


carbon cycleIn this project we are exploring the impact of climate change on the carbon cycle of native prairie soil in the US. Soils process and store large amounts of C; however, there is considerable uncertainty about the details that influence microbial partitioning of C into soil pools and what influential forces control the fraction of the C input that is stabilized.
We will employ a systems biology approach, considering the complex soil microbial community as a functioning system and use state-of-the-art pyrosequencing, metagenomics, meta-transcriptomic, and metaproteomic techniques.
These omics tools will be refined, applied to field experiments, and confirmed with controlled laboratory studies. Our experiments are designed to specifically identify microbial community mem bers and processes that are instrumental to C cycling in prairie soils and impacted by climate change events, such as altered precipitation.


1/ Further develop and optimize a combination of omics approaches to study how environmental factors affect microbially-mediated C cycling processes.
2/ Determine the impacts of long-term changes in precipitation timing on microbial C cycling using the RaMPs experiment.
Two field campaigns are planned for summer 2011. The first when plant growth is optimal and the second after plant senescence.
We will sample soils prior to a major rainfall event (when soils are relatively dry), shortly after wet-up, and at one more time as the soils begin to dry.
In addition to omics measurements, several soil enzymes involved in C cycling and soil respiration will be measured.
3/ Conduct laboratory experiments that vary moisture and C inputs to confirm field observations of the linkages between microbial communities and C cycling processes.



Research team

Oregon State University: David Myrold, Peter Bottomley, Lydia Zeglin *

=> Soil microbiology & microbial ecology, Project leader; RNA fractionation development; Illumina transcriptomics sequencing, 13C isotope analyses;group

Kansas State University: Ari Jumpponen, Charles Rice, Emmanuel Prestat*   

=> Mycology & soil science: Coordinate Kansas field sampling; 454 Titanium pyrotagged sequencing and bioinformatics

Lawrence Berkeley National Laboratory (ESD & JGI):  Janet Jansson, Susannah Tringe, Maude M. David*   

=> Molecular microbial ecology & omics: Protein and metabolite extractions from soil; metabolite profiling; data mining of Konza prairie metagenome; biostatistics and metadata correlations

Oak Ridge National Laboratory: Robert Hettich, Nathan Verberkmoes

=> Mass spectrometry, Shot gun metaproteomics and related bioinformatics; proteomic methods development

* Post-doctoral fellows

Picture (left to right): Maude David, Susannah Tringe, Stephanie Yarwood, Chuck Rice, David Myrold, Janet Jansson, Peter Bottomley, Nathan VerBerkmoes, and Lydia Zeglin. Missing from photo: Ari Jumpponen and Bob Hettich.

Research impact

ThOmicsis project addresses a key ecosystem in the United States that current climate models predict will be subjected to dramatic changes in rainfall patterns. The Mollisol soils of the Great Prairie, which are the focus of this work, are influenced both by tall grasses with extensive root systems and the microbes living in their proximity. Currently, the tallgrass prairie soils are thought to sequester more C than is released into the atmosphere, but it is not known what changes in rainfall and soil moisture will have on future C fluxes. In the worst case scenario, the balance will be tipped towards more C release from these soils than is taken up and sequestered in soil. If this were the case, due to the large land areas involved, the problem with increasing CO2 emissions to the atmosphere would be greatly aggravated. Because the consequences of changes in precipitation on microbial processing of C in soil are currently not known, we will take advantage of the RaMPs at the Konza Prairie field station that has experimentally altered rainfall inputs over the last decade.

For a complete description of the project: