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Plants, like all eukaryotic organisms have evolved in a milieu with the preceding prokaryote organisms, and as such have developed to live in concert as well as used the preceding organisms if they provided a competitive advantage. In the few short years of the microbiome we have seen the discovery of a number of features that our (human) microbiome contributes to our health. Would we expect less from the plant microbiome? That is unknown but there are likely more beneficial relationships with plant hosts than now recognized. We have used metagenomics to investigate the plant microbiome in several ways. First, we have used shotgun sequencing of the close rhizosphere of three biofuel crops: corn, switchgrass and Miscanthus to examine its composition at the organism and gene levels. Both show that the corn system is more variable among replicates and different for the two grasses but the later two are different from each other. We have also used a new gene targeted assembly tool, Xander, to assemble genes of interest that is more sensitive than general assembly to describe the N-cycle genes and their likely host bacteria. Second, we have used gene-targeted metagenomics (amplicon sequencing) to assess the nitrogen reductase (<i>nifH</i>) gene in different plant parts. Finally, we have used metatranscriptomics of the rhizosphere of the biofuel crops it investigate which populations and genes are active in this niche.