Differences in resource use lead to coexistence of seed-transmitted microbial populations

G. Torres-Cortés, B. J. Garcia, S. Compant, S. Rezki, P. Jones, A. Préveaux, M. Briand, A. Roulet, O. Bouchez, D. Jacobson, M. Barret

Research output: Contribution to journalArticlepeer-review

19 Scopus citations

Abstract

Seeds are involved in the vertical transmission of microorganisms in plants and act as reservoirs for the plant microbiome. They could serve as carriers of pathogens, making the study of microbial interactions on seeds important in the emergence of plant diseases. We studied the influence of biological disturbances caused by seed transmission of two phytopathogenic agents, Alternaria brassicicola Abra43 (Abra43) and Xanthomonas campestris pv. campestris 8004 (Xcc8004), on the structure and function of radish seed microbial assemblages, as well as the nutritional overlap between Xcc8004 and the seed microbiome, to find seed microbial residents capable of outcompeting this pathogen. According to taxonomic and functional inference performed on metagenomics reads, no shift in structure and function of the seed microbiome was observed following Abra43 and Xcc8004 transmission. This lack of impact derives from a limited overlap in nutritional resources between Xcc8004 and the major bacterial populations of radish seeds. However, two native seed-associated bacterial strains belonging to Stenotrophomonas rhizophila displayed a high overlap with Xcc8004 regarding the use of resources; they might therefore limit its transmission. The strategy we used may serve as a foundation for the selection of seed indigenous bacterial strains that could limit seed transmission of pathogens.

Original languageEnglish
Article number6648
JournalScientific Reports
Volume9
Issue number1
DOIs
StatePublished - Dec 1 2019

Funding

The authors wish to thank Guillaume Chesneau for his help with bacterial competition assays, Laurent Noel for providing the strain pTac::GUS-GFP, the FNAMS for running field experiments, the ANAN platform (SFR QuaSav) for amplicon sequencing and BGI for sequencing the bacterial genomes. We would also like to thank BBRIC network for all the bioinformatic support. This research was supported by the grant awarded by the Region des Pays de la Loire (metaSEED, 2013 10080); RFI Objectif V\u00E9g\u00E9tal (DynaSeedBiome) and the AgreenSkills + fellowship programme, which has received funding from the EU\u2019s Seventh Framework Programme under grant agreement n\u00B0 FP7-609398. This research used resources from the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725. This research was also supported by the Plant-Microbe Interfaces Scientific Focus Area in the Genomic Science Program, the Office of Biological and Environmental Research (BER) in the U.S. Department of Energy Office of Science, and by the Department of Energy, Laboratory Directed Research and Development funding (ProjectID 8321).

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