The above‐ground surfaces of plants (the phyllosphere) harbour a diverse variety of microorganisms, and this phyllosphere microbiome interacts with the host plant affecting its health and function. Phyllosphere microorganisms, predominantly bacteria and fungi, can act as mutualists promoting plant growth and tolerance of environmental stressors, commensals using the leaf habitat for their own growth and reproduction, or as antagonistic pathogens. Although much of the literature has focused on plant–pathogen interactions and disease mechanisms, we expand this discussion to the structural and functional dynamics of the whole phyllosphere community, rather than single‐species populations. We highlight the particular challenges posed to microorganisms living on the leaf surface, describe the structure of the phyllosphere microbiome, and discuss how these microbial constituents interact with the plant with respect to stress tolerance, growth promotion, nutrient acquisition, and disease resistance. Lastly, we pose new directions for the field made possible by advances in sequencing and computational technologies.

Freshwater mussels are a species-rich group of aquatic invertebrates that are among the most endangered groups of fauna worldwide. As filter-feeders that are constantly exposed to new microbial inoculants, mussels represent an ideal system to investigate the effects of species or the environment on gut microbiome composition. In this study, we examined if host species or site exerts a greater influence on microbiome composition. Individuals of four co-occurring freshwater mussel species, Cyclonaias asperata, Fusconaia cerina, Lampsilis ornata, and Obovaria unicolor were collected from six sites along a 50 km stretch of the Sipsey River in Alabama, USA. High throughput 16S rRNA gene sequencing revealed that mussel gut bacterial microbiota were distinct from bacteria on seston suspended in the water column, and that the composition of the gut microbiota was influenced by both host species and site. Despite species and environmental variation, the most frequently detected sequences within the mussel microbiota were identified as members of the Clostridiales. Sequences identified as the nitrogen-fixing taxon Methylocystis sp. were also abundant in all mussel species, and sequences of both bacterial taxa were more abundant in mussels than in water. Site physicochemical conditions explained almost 45% of variation in seston bacterial communities but less than 8% of variation in the mussel bacterial microbiome. Together, these findings suggest selective retention of bacterial taxa by the freshwater mussel host, and that both species and the environment are important in determining mussel gut microbiome composition.

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