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Mapping soil carbon from cradle to grave: using comparative transcriptomics, proteomics and metabolite analysis to identify the microbial blueprint for root-enhanced decomposition of organic matter.

EMSL Project ID


In this JGI-EMSL project, we will investigate how living roots impact the functional capacity of the detritosphere (litter and surrounding soil) microbiome that is actively mediating decomposition processes. We hypothesize that the input of root-exudates alters soil microbial expression of biomolecules (transcripts, enzymes, metabolites) involved in execution and control of the decomposition of organic C compounds. We propose to analyze soil taken from a California grassland, incubated under controlled greenhouse conditions, and grown with a common annual grass (Avena fatua). Our experimental system combines the reality of soil containing plant litter and live roots with the defined environment of mesocosms replicated in a greenhouse. The time frame of our sampling scheme is chosen as a result of extensive background work which provides a powerful context allowing a refined experimental system and well-honed research questions.
The work we propose on microbial community systems biology brings to bear a multi-omics approach to address important questions using dynamic soil systems sampled over time, with replication. Our analytical approach uses PCR-independent sampling and employs stable isotopes, introduced at realistic levels (as natural exudates and litter) to target functional groups mediating litter decomposition in the presence and absence of live roots.
Our primary objective is to determine how organic C transformation and decomposition in soil is altered by the interactions between plant roots and the soil microbial community (bacteria, archaea, fungi, microfauna). We propose to use the JGI’s significant sequencing capacity and expertise to sequence 24 metatranscriptomes from soil, analyzing the evolution of the detritosphere microbiome at four timepoints over 30 days for transcripts related to organic C decomposition. The availability of two metagenomes and 50 sequenced genomes from our experimental soil (CSP #653) will significantly aid our transcriptome analysis and assignment.
We will collaborate with EMSL scientists to determine the temporal patterns of protein expression (metaproteomics), the assimilation of 13C-enriched exudate compounds by identified microorganisms (Protein-SIP), and the identity and quantity of three classes of metabolic products of root litter degradation using GC/MS and LC/MS analysis (metabolomics). The proposed analyses will result in coordinated transciptomes, proteomes, and metabolomes of a detritosphere microbiome in the presence and absence of plant roots. These analyses will be done on samples defining a temporal period of maximum root activity (9, 12, 18, 27 days). As a result of an on-going DOE genomics project, these samples are in hand, thus making the 18 month timeframe ideal.
Our work targets the rhizosphere, the nexus of plant-soil-microbial interactions critically important in C-cycling and biofuel crop soil fertility. Gaining quantitative understanding of carbon cycling in the rhizosphere is directly relevant to the DOE-BER Global Carbon Cycling and Sequestration mission to develop a mechanistic understanding of fundamental parts of the carbon cycle that ultimately relate to C sequestration.

Project Details

Project type
FICUS Research
Start Date
End Date


Principal Investigator

Mary Firestone
University of California, Berkeley

Team Members

Erin Nuccio
Lawrence Livermore National Laboratory

Eoin Brodie
Lawrence Berkeley National Laboratory

Jennifer Pett-Ridge
Lawrence Livermore National Laboratory

Thomas Metz
Pacific Northwest National Laboratory

Mary Lipton
Environmental Molecular Sciences Laboratory