Title: Collaborative Research: MSB: Defining Plant-Associated Metagenomics.
NSF-IOS-0958245
04/15/10-03/31/14
Together with co-PI Prof. Ruth Ley at Cornell and our sub-contractor, the DOE-JGI lab and Dr. Susannah Tringe Green, we describe the root rhizosphere and endophyte metagenomes of Arabidopsis and corn across the genetic diversity of these species and in various wild soils.
Project summary: Essentially all land plants grow in intimate association with complex microbial communities both above the ground (phyllosphere) and below the ground on roots and the immediately surrounding area (rhizosphere). The relationships between a microbiota (the community of microbes intimately associated with a plant) and its host can vary from pathogenic to mutualistic or commensal. The microbiome (the set of genes encoded by any particular microbiota) can perform ecosystem services such as providing the host plant with one or more critical nutrients, protecting a plant from pathogens, producing functional plant hormones, and providing tolerance to abiotic stress. The plant, in turn, provides the microbiome with an improved environment that may include a more favorable pH, reduced predation or microbial competition, and a cuisine of energy sources released by rhizodeposition. Decaying plant tissue and carbon-rich root exudates release large amounts of fixed atmospheric carbon to the soil, making the rhizosphere a large carbon sequestration zone.
The field of host-associated metagenomics is predicated on the conviction that an understanding of a complex genome, for example, the human genome, is incomplete without a corresponding understanding of the associated micobiome. This conviction is supported by reams of data for animal biology, and it is appropriate to apply this to plant genomics as well. Such research will ultimately lead to predictive interventions that will increase plant health and productivity, carbon sequestration, and disease resistance through the rational utilization of the probiotic capacity of soils and the local environment.
The rhizosphere microbiome is a paradigmatic example of Dawkins’ ‘extended phenotype’ in the same way that the human gut microbiome is a key component of our own extended phenotype. Plant genotype, both within and between species, has been correlated with differences in the associated microbiome, with consequent phenotypic associations to plant growth, development, and performance. The distinctive ‘terroir’ that flavors wine, the yield of maize and other crops, and the productivity of any plant community relies in part on the respective rhizosphere microbiome. The microbiota is most simply viewed as an extension of each plant’s genome; we do not know any plant genome’s full functional capacity until we also know the functional capacity and assemblage drivers on its associated microbiome.
We assembled a collaborative interdisciplinary team including the head of the Microbial Ecology program at DOE-JGI, who is a world leader in the analysis of environmental microbiomes, and a talented junior PI at Cornell who is an expert in host-associated metagenomic analyses. We propose to define the rhizosphere microbiota, and associated microbiome, across the genetic diversity of two important model plant species: Arabidopsis thaliana, the premier model for rapid discovery in plant biology, and Zea mays, the premier model for genetic dissection of complex traits in crops. Our consortium requests NSF funds for personnel to generate samples efficiently and to analyse the data. Our results will set the stage for exploitation of natural variability for association mapping of underlying traits in both plant species. Our proposal is in line with the goals of several NSF Programs, particularly Microbial Systems in the Biosphere (MSB) and is aligned with the inclusion of metagenomics as a priority in the NSF FY201 budget request to Congress.
PI: Jeff Dangl, Biology, CB#3280, Univ. of Chapel Hill, Chapel Hill, NC 27599
Co-PI: Ruth Ley, Dept. of Microbiology 260A Wing Hall Cornell University Ithaca, NY 14853
Contractor: Susannah Green Tringe, JGI Production Genomics Facility, 2800 Mitchell Drive, Walnut Creek, CA 94598