Plant microbiomes
The phyllosphere, which is dominated by leaves, represents one of the largest terrestrial habitats for microorganisms, which influence their hosts with respect to growth and resistance to abiotic and biotic stresses. In addition, the microbiota that resides on the roughly one billion square kilometers of global leaf surfaces is sufficiently abundant to impact the global carbon and nitrogen cycles. Apart from its ecological and economic importance, the phyllosphere is also an excellent model habitat to study microbial physiology and adaptation. A long-term perspective of our laboratory is a systems-level understanding of the phyllosphere, with the aims of identifying organizing principles and ultimately developing predictive capabilities at the levels of the system and individual community members.
In our earlier work, we established cultivation-independent metaproteogenomic approaches to study natural phyllosphere (meta-) communities of microorganisms present on different plant host species. This strategy provided us with insights into the overall bacterial community composition and allowed us to identify abundant proteins as a proxy for characteristic proteins and functions of individual community members in the habitat. Our studies revealed a high consistency in bacterial communities at higher taxonomic ranks, and this consistency was also reflected in the metaproteomes of the microbiota on different plant species. Complementary analyses revealed that microbial communities of individual plant hosts are similar within a given environment.
We pioneered the use of synthetic microbial communities and gnotobiotic plant systems to study factors involved in microbe-microbe-plant interactions in the phyllosphere. We established a representative strain collection of leaf isolates from healthy Arabidopsis plants that can be used to establish causal relationships in reductionist approaches. We use isolates and synthetic communities to test for their ability to protect against the foliar plant pathogen Pseudomonas syringae pv. tomato DC3000 on Arabidopsis thaliana. Moreover, we analyze the colonization patterns of bacterial populations in the phyllosphere, with the ultimate goal of establishing assembly rules of bacterial communities in situ. Another current project concerns the identification of host factors that shape the composition of the bacterial community.
Keywords:
Synthetic communities experiments; Plant gnotobiotics; Functional genomics (including proteomics, metabolomics); Genetics; Microscopy
Funding:
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Project Members
- chevron_right Alan Pacheco, PhD
- chevron_right Andrea Ghigi
- chevron_right Andreas Keppler
- chevron_right Barbara Emmenegger, PhD
- chevron_right Basil Rast
- chevron_right Benjamin Daniel
- chevron_right Julien Massoni, PhD
- chevron_right Maria Berlanga Clavero, PhD
- chevron_right Michelle Roulier
- chevron_right Miriam Bortfeld-Miller, PhD
- chevron_right Noa Barak-Gavish, PhD
- chevron_right Paul Kramer y Rosado