Dispersing misconceptions and identifying opportunities for the use of 'omics' in soil microbial ecology

In this Opinion article, James Prosser considers the conceptual limitations of metagenomics and metatranscriptomics in contributing to our understanding of soil microbial ecology, and also explores potential opportunities for using these techniques to address specific ecological questions. Technological advances are enabling the sequencing of environmental DNA and RNA at increasing depth and with decreasing costs. Metagenomic and transcriptomic analysis of soil microbial communities and the assembly of 'population genomes' from soil DNA are therefore now feasible. Although the value of such 'omic' approaches is limited by the associated technical and bioinformatic difficulties, even if these obstacles were eliminated and 'perfect' metagenomes and metatranscriptomes were available, important conceptual challenges remain. This Opinion article considers these conceptual challenges in the context of the current use of omics in soil microbiology, but the main arguments presented are also relevant to the application of omics to marine, freshwater, gut or other environments.