Plants, both above- and belowground, offer diverse habitats for microbial colonization and growth. Plant-microbe interactions lie at the heart of plant performance and ecology. Plants provide various growth substrates and physical habitats for microbes on both sides of the air-soil interface, and numerous plant-associated niches have been exploited by specific microbial species, either by specializing on the distinct environmental conditions available, or entering into commensal, mutualistic, or parasitic interactions with plants. This chapter seeks to examine the state of the art with respect to our ability to characterize the structure, function and interactions of plant-associated microbial communities, with a particular focus on the role of molecular biological methods and environmental genomics strategies in promoting this field. We will pay particular attention to bacterial and fungal colonization of above and belowground plant surfaces (phyllosphere and rhizosphere, respectively), as well as in planta (endosphere) interactions of endophytic, parasitic and symbiotic microorganisms. Of particular importance to advancing this research field are emerging methodologies, including novel '-omics' approaches, that seek to link microbial identity to in situ functioning, and holistic approaches that capture the complexities involved in multiple plant-microbe interactions
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