Soil microbial communities are among the most complex and diverse on the planet. This has led to difficulties in deciphering the metabolic roles carried out by members of the soil microbiome and how key metabolic functions that they carry out are impacted by environmental change. I will discuss different approaches that we have developed to tackle the complexity of the soil microbiome and to determine the collective phenotypes of the community members; i.e. the metaphenome. Starting from deep metagenome sequence analyses we have begun to mine the data for features of interest, including soil viruses and their metabolic potential. In addition, we have dissected the complex metagenome into functional modules to parse out the soil biogeochemistry into tractable units. Finally, we have worked with low complexity model soil microbiomes to determine specific interspecies interactions. Together these examples illustrate how advances in omics technologies, computational biology and mathematics are helping to better define the soil metaphenome.
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