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Abstract

Plants make intimate associations with a plethora of microorganisms that harm or help the plant to counteract biotic and abiotic stresses. These plant inhabitants make microbial assemblages in various organs. Different taxa have been characterized in various plants based on culturable and unculturable approaches. They have been visualized further inside roots, stems, leaves, but also within flowers, fruits and seeds. Some of them derive from the soil, while others have been described as coming from sources such as the phyllosphere, the anthosphere, or the carposphere. Transmission by Human or insects, for some of them, have also been revealed.

Analyses of the microbiota of the plant holobionts have revealed not only niches and sources of microbial colonization but also how microbial cells have been adapted to the plant systems and some of their genomic contents. In-depth analyses have recently revealed the sources and niches of colonization, for beneficial, commensal and detrimental microorganisms, but also the assemblies within plant organs, their effects on plants, the mechanisms involved, and how we could use the knowledge on routes of colonization to preadapt beneficial strains to their environment for a sustainable agriculture. 

Stéphane Compant is Project leader/Scientist working on plant-microbe interactions in Austria. He is Section Editor of Biocontrol, Plant and Soil, Oeno One and Frontiers in Plant Sciences. He is also member of Cost Action on endophytes for biotechnology, co-chair of microbial ecology of Cost Action on grapevine trunk diseases, and member of EIP-AGRI.