Microbial networks & Communities

Plants harbor diverse arrays of microbes that can impact host phenotypes and fitness. Greater insights into the ecological forces that structure these microbial communities are needed to develop effective strategies to promote host health and resist pathogen invasion. We use GWAS mapping to determine the host factors that shape microbial communities growing within Arabidopsis thaliana, and use controlled experiments to test the importance of candidate host factors in shaping these microbial communities. We also explore species interactions with the aim of understanding community assembly across host genotypes. Ultimately, our goal is to enhance plant resistance by identifying conditions that favor protective microbes.

Ongoing Projects

Spatial and temporal dynamics of Arabidopsis thaliana associated microbial communities in nature

Plant fitness and ecosystem functions are influenced by the microorganisms living in and on leaves (the phyllosphere) and roots (the rhizosphere). In order to understand the ecological roles and evolutionary histories of these plants we must understand what these microbes are and how they colonize and interact with plant tissues and with each other. We are using sequence based methods to characterize the structure and dynamics of microbial communities in order to infer the ecological drivers of host associated microbial communities.

Collecting Microbial Network Members & Hub Species

Although patterns of association can provide insights into microbial ecology, mechanistic understanding requires experimentation. We are cultivating the microbes that are associated with A. thaliana in Sweden, France and North America. We have already cultivated and identified thousands of bacterial and fungal OTUs within plant tissues, and are now focused on finding species that have been identified as ecological hubs in nature. Our aim is to capture and culture these hub taxa to study their role in microbial community assembly through synthetic microbial communities derived from natural A. thaliana isolates.

Genomics of Pathogen-Pathogen Interactions During Co-Infection

Most plants in nature are co-infected by multiple pathogens at the same time. We study how competitive and synergistic interactions between pathogen strains alter infection outcomes and pathogen fitness, using novel high-throughput phenotyping and GWAS methods to map the repertoire of genes mediating pathogen-pathogen interactions.

Selected publications:

Brachi, B., Filiault, D., Darme, P., Le Mentec, M., Kerdaffrec, E., Rabanal, F., Anastasio, A., Box, M., Duncan, S., Morton, T., Novikova, P., Perisin, M., Tsuchimatsu, T., Woolley, R., Yu, M., Dean, C., Nordborg, M., Holme, S. and J. Bergelson (2017) Plant genes influence microbial hubs that shape beneficial leaf communities. Biorxiv, http://dx.doi.org/10.1101/181198
We characterized the leaf microbiota within 200 Swedish accessions planted across four field sites and two years in the North and South of Sweden. We found strong effects of host genotype on the microbial community. This ‘host control’ of the microbial community appears focused on ecological hubs species which then influence the relative abundance of co-occurring microbial species.
Horton, M. W., Bodenhausen, N., Beilsmith, K., Meng, D., Muegge, B.D., Subramanian, S., Vetter, M.M., Vilhkálmsson, B.J., Nordborg, M., Gordon, J. and J. Bergelson (2014) Genome-wide association study of Arabidopsis thaliana leaf microbial community. Nature Communications, 5 (November). https://doi.org/10.1038/ncomms6320
This study is the first demonstration that genetic variation among hosts within a species is associated with the structure of the microbial community within leaves for A. thaliana plants grown under field conditions. GWAS identified genes for plant defense and cell wall integrity impact variation in the microbial community.

Bodenhausen, N., Horton, M.W. and J. Bergelson (2013) Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana. PLoS ONE, 8(2). https://doi.org/10.1371/journal.pone.0056329
Sampling wild A thaliana across four sites in Michigan and Indiana for epiphytic and endophytic bacteria associated with roots and leaves revealed differentiation of the microbial communities resident in different plant tissues and at different sites.

University of Chicago, Dept. of Ecology & Evolution