A Functional Genomics Database for Plant Microbiome Studies

Catalog of candidate genes involved in plant-microbe relationships.

Image courtesy of Asaf Levy, Joint Genome Institute, and Isai Salas Gonzalez, University of North Carolina

Phylogenetic tree of over 3,800 high quality and non-redundant bacterial genomes. The outer ring denotes the taxonomic group, central ring denotes the isolation source, and inner ring denotes the root-associated genomes within plant-associated genomes. Taxon names are color-coded based on phylum: green = Proteobacteria, red = Firmicutes, blue = Bacteroidetes, and purple = Actinobacteria.

The Science

Could marginal lands be bountiful fields for biofuel crops? To answer that question, scientists are investigating soil microbes, which can aid plant growth. Here, researchers isolated bacteria from around the roots of poplar trees, maize, and a type of mustard plant. They developed a catalog of the genetic material (genome) of the soil bacteria they found. In mining the data, they found genes involved in bacterial root colonization.

The Impact

Knowing how beneficial microbes and microbial communities colonize plants, along with subsequent plant-microbe interactions, could assist in growing food and energy crops with fewer chemical inputs. These inputs include fertilizer, pesticides, and fungicides.

Summary

To facilitate crop-breeding strategies for making plants more productive on marginal lands and more tolerant of stresses such as drought and low nutrient availability, researchers are focusing on understanding and promoting beneficial plant-microbe relationships. To date, most plant microbiome studies in the field have focused on community structure rather than function, but there is a need to understand microbial community functions to engineer the microbiome to support plant growth. In this study, researchers isolated bacteria from the root environments of Brassicaceae, poplar trees, and maize, and sequenced, assembled, and compared the genomes with thousands of publicly available genomes including bacteria from both plant and non-plant environments. This broad analysis allowed the researchers to identify genes enriched in the genomes of plant-associated and root-associated organisms. They found that plant- and soil-associated genomes were enriched in genes involved in sugar metabolism and transport, likely an adaptation to the production of photosynthesis-derived plant carbon compounds. Further, they found that numerous genes seem to mimic plant functions in a strategy similar to that employed by plant pathogens. The identification of two new, rapidly evolving protein families containing genes often used in offense or defense against another organism provides evidence for a “molecular arms race” between competing bacteria within the same environment. This research provides a valuable resource for researchers studying plant-microbe interactions to identify novel and potentially interesting genes and gain a better functional understanding of the plant microbiome that can be exploited for enhancing crop production.

Contact

BER Program Managers
Cathy Ronning
Biological Systems Science Division
Office of Biological and Environmental Research
Office of Science
Department of Energy
[email protected]

Dan Drell
Biological Systems Science Division
Office of Biological and Environmental Research
Office of Science
Department of Energy
[email protected]

Principal Investigator
Jeff Dangl
University of North Carolina at Chapel Hill and Howard Hughes Medical Institute
[email protected]  

Funding

The Department of Energy (DOE) Joint Genome Institute, Integrated National Science Foundation Support Promoting Interdisciplinary Research and Education, National Institutes of Health, Howard Hughes Medical Institute (HHMI), Gordon and Betty Moore Foundation, SystemsX.ch, European Research Council, DOE Office of Science Biological and Environmental Research (BER and U.S. Department of Agriculture National Institute of Food and Agriculture Plant Feedstocks Genomics for Bioenergy, and the DOE BER Genomic Science Program and Science Focus Area: Plant Microbe Interfaces (Oak Ridge National Laboratory) funded the research.

Publications

A. Levy, I.S. Gonzalez, M. Millelviefhaus, et al., “Genomic features of bacterial adaptation to plants.” Nature Genetics 50, 138 (2018). [DOI: 10.1038/s41588-017-0012-9]

Related Links

Joint Genome Institute press release: A Functional Genomic Database for Plant Microbiome Studies

Highlight Categories

Program: BER , BSSD

Performer: University , DOE Laboratory , SC User Facilities , BER User Facilities , JGI

Additional: Collaborations , Non-DOE Interagency Collaboration , International Collaboration