Collage working group Plant Microbiosis.

Junior Research Group Plant Microbiosis

Dr Matthew T. Agler
Collage working group Plant Microbiosis.
Image: Arbeitsgruppe Plant Microbiosis
Matthew Agler, Ph.D.
Junior research group leader Plant Microbiosis
Portrait Dr. Matthew Agler.
+49 3641 9-49980
Hellfeldsches Haus
Neugasse 23
07743 Jena
Rhodococcus sp. isolate colonizing vasculature of A. thaliana roots Rhodococcus sp. isolate colonizing vasculature of A. thaliana roots Image: Matthew Agler


In plants, microorganisms function together with host genetics and the abiotic environment to help regulate processes like plant growth, flowering, stress resistance and the outcomes of disease and herbivory. Therefore, from both a basic research and applied agriculture point of view, it is critical to understand how plant-associated microbial communities form and their implications. Until now, most of our knowledge of plant-microbe interactions comes from molecular and evolutionary studies of binary plant-microbe model systems. At the microscopic level, however, plants are living ecosystems simultaneously colonized by diverse prokaryotes and eukaryotes. Recent research has revealed that besides interacting with the host, plant-associated microbes interact with each other, playing important roles in shaping microbial community structures.

Little is known about what types of microbe-microbe interactions occur in plants and how they affect the structure and functions of plant-associated microbiota. Even less is known about whether these interactions are conserved and have played important roles in the evolution of microorganisms and host plants. This knowledge gap severely limits our understanding of host-associated microbiota in the wild and in agricultural systems. The research group “Plant Microbiosis” studies microbe-microbe interactions to help answer these questions and to bridge the gap between ecological (microbiome diversity) and evolutionary (plant-microbe interactions) understandings of plant-associated microbiota.

Further information may be found on the website of the research group "Plant Microbiosis":

CV – Matthew Agler

Zeitraum Station
2017 Group Leader Junior Research Group, Plant Microbiosis, Institute of Microbiology, Friedrich Schiller University Jena
2017 Faculty member, Jena School for Microbial Communication
2017 Faculty member, International Leibniz Research School
2012 – 2017 Posdoctoral Researcher, MPI for Plant Breeding Research, Cologne, Germany
2012 PhD, Cornell University
2006 BS, University of Illinois in Urbana-Champaign




Agler, M.T., Mari, A., Dombrowski, N., Hacquard, S., and Kemen, E.M. (2016) New insights in host-associated microbial diversity with broad and accurate taxonomic resolution. Available on: BioRxiv, doi:



Kroll, S**., Agler, M.T.** and Kemen, E.M. (2017) Genomic dissection of host-microbe and microbe-microbe interactions for advanced plant breeding. (2017). Current Opinions in Plant Biology. Vol 36, 71-78. doi:

Dombrowski, N., Schlaeppi, K., Agler, M., Hacquard, S., Kemen, E., Garrido Oter, R., Wunder J., Coupland, G., and Schulze-Lefert, P. (2017) Root microbiota dynamics of perennial Arabis alpina is dependent on soil residence time but independent of flowering time. ISME Journal, Vol 11, 43-55. doi:10.1038/ismej.2016.109


Ruhe, J., Agler, M.T., Placzek, A., Finkemeier, I., and Kemen, E.M. (2016) Obligate biotroph pathogens defend their niche against competing microbes by keeping host defense at a functional level. Frontiers in Plant Science. In press. doi:

Agler, M.T., Ruhe, J., Kroll, S., Morhenn, C., Kim, S-T., Weigel, D., and Kemen, E.M. (2016) Microbial hub taxa link host and abiotic factors to plant microbiome variation. PLOS Biology. 14(1):e1002352. doi:


Kemen, A.**, Agler, M.T.**, and Kemen, E.M. (2014) Evolution and biodiversity of obligate biotrophic parasitism. New Phytologist, (Tansley Review). Vol 206, 1207–1228. doi:, *: Co-first authors

Zhang W., Werner J. J., Agler M. T. and Angenent L. T. (2014). Substrate type drives variation in reactor microbiomes of anaerobic digesters. Bioresource Technology, Vol 151, pp. 397-401.

Agler, M.T., Spirito, C.M., Usack, J.G., Werner, J.J., and Angenent, L.T. (2014). Development of a highly specific and productive process for n-caproic acid production: applying lessons from methanogenic microbiomes. Water Science and Technology, Vol 69, No. 1, pp. 62-68.

2012 und früher

Heger, S., Bluhm, K., Agler, M.T., Maletz, S., Schäffer, A., Seiler, T-B., Angenent, L.T., and Holler, H. (2012). Biotests for hazard assessment of biofuel fermentation. Energy and Environmental Science, Vol.5, pp. 9778-9788.

Agler, M.T., Spirito, C.M., Usack, J.G., Werner, J.J., and Angenent, L.T. (2012). Chain elongation with microbiomes: upgrading dilute ethanol to medium-chain carboxylates. Energy and Environmental Science, Vol. 5, pp 8189-8192.

Agler, M.T., Werner, J.J., Iten, L.B., Dekker, A., Cotta, M.A., Dien, B.S., and Angenent, L.T. (2012) Shaping reactor microbiomes to produce the fuel precursor n-butyrate from pretreated cellulosic waste. Environmental Science and Technology , Vol 46, No. 18, pp. 10229-10238.

Agler M. T., Wrenn B. A., Zinder S. H. and Angenent L. T. (2011). Waste to bioproduct conversion with undefined mixed cultures: the carboxylate platform. Trends in Biotechnology, Vol. 29, No. 2, pp. 70-78 (Review). – Listed among the top cited articles of Trends in Biotechnology since 2010 (as of December 2015)

Agler, M.T., Aydinkaya, Z., Cummings, T.A., Beers, A.R., Angnenent, L.T. (2010). Anaerobic digestion of brewery primary sludge to enhance bioenergy generation: A comparison between low- and high-rate solids treatment and different temperatures. Bioresource Technology, 101, pp. 5842-5851.

Agler, M.T., Garcia, M.L., Lee, E.S., Schlicher, M., Angenent, L.T. (2008). Thermophilic Anaerobic Digestion to Increase the Net Energy Balance of Corn Grain Ethanol. Environmental Science and Technology, 42(17): p6723-6729.

Bocher, B.T., Agler, M.T., Garcia, M.L., Beers, A.R., Angenent, L.T. (2008) Anaerobic digestion of secondary residuals from an anaerobic bioreactor at a brewery to enhance bioenergy generation. Journal of Industrial Microbiology and Biotechnology. 35(5): p321-329.

Microbiology Campus (JSMC/Micro) Microbiology Campus (JSMC/Micro) Image: Matthew Agler
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