Culturing a plant microbiome community at the cross‐Rhodes

Plants live in close association with microbial communities consisting of a variety of bacteria and fungi. Individual members of thismicrobiota can contribute to plant growth anddevelopment, plant productivity and phytoremediation (Weyens et al., 2009). These microbes prosper in close proximity of plant roots (the rhizosphere), on root and leaf surfaces (the rhizoplane and phyllosphere (Lindow & Brandl, 2003), respectively) as well as within plant tissue as leaf or root endophytes (Hardoim et al., 2008). Interactions of plants with their associated microbes span a broad continuum of symbioses from mutualistic through commensalistic, including parasitic at the extreme. Moreover, soil bacteria influence each other in complex networks, which influence plant fitness directly or indirectly as described for disease suppressive soils (Berendsen et al., 2012). Thus far, molecular genetic research has focused mainly on binary microbial interactions of plants with individual pathogens or symbioticmutualists that cause macroscopically visible plant phenotypes such as disease symptoms for pathogenic bacteria or plant growth promotion for mycorrhizal fungi and nitrogen fixing bacteria. However, a large portion of the plant-associated microbial diversity has not been isolated as pure cultures and underlying first principles of how plants establish and interact with their associated microbiota as a whole remain largely elusive: Which factors influence plant–microbe interactions at the community level? How do plants discriminate friends from foes? How do beneficial microbes escape the sophisticated plant innate immune system? Can the low heritability of plant growth be accounted for by environmental interactions with large microbial assemblies? Now, with new tools like next-generation DNA sequencing it is possible to take a deep census of the plant microbiota in a culture-independent manner and use this as a springboard for more detailed analyses of both the host and microbiota contributions to an extended plant phenotype (Dawkins, 1978). This is typically achieved by massive sequencing of bacterial 16S rRNA genes or of internal transcribed spacer regions between rRNA genes of fungi or by untargeted metagenomic sequencing of a microhabitat. Importantly, new technologies raise new challenges including analysis of huge amounts of data and the need to establish best practice standards for an emerging research field (Knight et al., 2012). To do so, while trying to bridge the gaps between phyllosphere and rhizosphere research, as well as between plant and soil science, was the remit of the 28th New Phytologist Symposiumon functions and ecology of the plantmicrobiomeheld inRhodes, Greece inMay 2012. This symposiumbrought together researchers working in genetics/genomics, soil science, microbiology, computational biology, and plant and microbial physiology. Over 130 participants from these highly diverse disciplinary backgrounds presented 94 posters and 27 talks over five sessions: Rhizosphere microbiology and biochemical cycling; Soil microbial communities; Phyllosphere and endophytic microbial communities; Genetic control and selection of plant microbiomes; and Characterization and ecology of plant microbiota. An important feature of the meeting was the inclusion of both structured discussions and the ever critical informal discussions, which were made easier by the lovely location, which provided ample opportunity for participants to discuss and debate the issues raised in individual presentations. Here, we present some of the emerging and unresolved issues that formed the basis of many lively debates.