ViPS Invited Seminar October 2019

Eric Kemen, University of Tübingen, Germany

Date: 9th October 2019

Time: 13:15

Title: Inferring Microbiota Functions in the Plant Phyllosphere

Location: Seminar room 2012, Biocentre 2, Viikinkaari 5

Host: Kirk Overmyer

Abstract: Pathogenic host-microbe interactions within the phyllosphere have often been portrayed as binary or ternary interactions between a host and a small number of microbes.  Recent studies indicate, however, that commensal microbes are far more important during pathogenesis than previously expected. In fact, the leaf microbiome sensibly changes composition in presence of an ongoing infection, and the interplay between pathogens and the rest of the microbiome is intense. Cause and consequence of such microbiome-pathogenicity links still remain difficult to decode. Main reasons are significant gaps in the characterization of entire clades of leaf microbes, particularly within the eukaryotes.

To analyze interactive queues in the phyllosphere, we first dissect prokaryotic and to a unprecedented depth eukaryotic diversity of natural field samples on a broad geographic scale. Second, we develop a network analysis based approach able to identify commensal microbes as drivers of changes within natural microbial networks (driver nodes) and test those under laboratory conditions. We hypothesize that those driver nodes are responsible to shift microbial communities form a healthy to a detrimental, pathogen susceptible or even pathogen promotive stage.

As a primary data source with natural variation, we performed a sampling transact across Europe, focusing on the phyllosphere of Arabidopsis thaliana with and without white rust symptoms caused by the protist pathogen Albugo laibachii. Investigating Albugo laibachii promotive communities we could identify several microbes such as  a basidiomycete yeast of the genus Dioszegia being a driver of Albugo infection. To validate our computational approach, we provide experimental evidence of a direct driving effect of the basidiomycete yeast Dioszegia (driver node) and other selected bacteria (driver nodes) in promoting Albugo laibachii reproductive fitness on A.thaliana under controlled conditions. Sequencing genomes and performing selection analyses on the driver node Dioszegia revealed a significant intensification of the selective pressure compared to other closely related basidiomycete fungi. We therefore hypothesize that from a regulatory perspective of host fitness, driver nodes play an essential evolutionary role. Our results for unrevealed microbial cues and their predictability to shift communities from a healthy to a detrimental pathogenic state.

Eric Kemen completed his PhD in biology at the University of Konstanz in 2007 before he moved to the Sainsbury Laboratory in Norwich UK, where he joined the group of Jonathan Jones, working on plant pathogen genomics. In 2012, Eric Kemen became a research group leader at the MPI for Plant Breeding Research in Cologne, focusing with his group on microbe-microbe and plant-microbe interactions. An important finding was the discovery of ‘microbial hubs’ that link microbial communities to the host genotype. In 2017 the Kemen Group moved to the University of Tuebingen where Eric Kemen started as a full professor heading the department of Microbial Interactions in Plant Ecosystems. Goal of the Kemen group is to combine computational modelling with ecology and host/microbe genetics. 

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Related publications:

Karasov TL, Almario J, Friedemann C, Ding W, Giolai M, Heavens D, Kersten S, Lundberg DS, Neumann M, Regalado J, Neher RA, Kemen E, Weigel D (2018). Arabidopsis thaliana and Pseudomonas Pathogens Exhibit Stable Associations over Evolutionary Timescales. Cell Host & Microbe 24, 168-179

Kroll S, Agler MT, Kemen E (2017) Genomic dissection of host-microbe and microbe-microbe interactions for advanced plant breeding. Curr Opin Plant Biol 36: 71-78

Agler MT, Ruhe J, Kroll S, Morhenn C, Kim S, Weigel D, Kemen E (2016) Microbial hub taxa link host and abiotic factors to plant microbiome variation. PLoS Biol 14(1): e1002352

Kemen A, Agler MT, Kemen E (2015) Host-microbe and microbe-microbe interactions in the evolution of obligate plant parasitism. New Phytologist DOI: 10.1111/nph.13284

Kemen E, Kemen A, Ehlers A, Voegele R, Mendgen K (2013) A novel structural effector from rust fungi is capable of fibril formation. Plant J 75(5): 767-780