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Although plant pathologists and microbiologists have been investigating the impact of soil microbial communities for several decades, we still have an incomplete picture of how microbial diversity affects crop yield, disease severity, and ecosystem function. As new sequencing technologies have become cheaper and more accessible it provides an opportunity to investigate the interactions between soil microbial communities, plant hosts, and the soil environment at greater spatial and temporal scales. While the power and depth of data generated from soil ecosystems is unprecedented, using these new sequencing technologies in the absence of generally acknowledged standards may prove counterproductive. In this talk I will address these issues within the larger context of soilborne and root diseases in agricultural and forest ecosystems, and discuss some of the key aspects of meta ‘-omics’ analyses and how they can be used to provide a more comprehensive picture of the complex interactions of soilborne pathogens with their biotic and abiotic environments. Finally, I will present examples of how these new sequencing technologies can be integrated into traditional plant pathology research to investigate many of the unanswered questions associated with how soil microbial communities effect plant production and how we can harness the diversity of these communities for improved crop production and ecological function.<p><p>Keywords: