New Insights Into Soil Microbial Interactions By Reducing Complexity Of Soil Microbiomes

Abstract:

Recent advances in sequencing and bioinformatics have enabled exploration of soil community DNA (metagenomes) and community RNA (metatranscriptomes) for potential functions carried out by interacting members of soil microbiomes. Soil complexity, both with respect to heterogeneity of the soil habitat, and with respect to a high abundance and diversity of soil microorganisms, still poses a challenge to understanding specifics of species interactions that underly a given measured response. For example, soil respiration is the result of coordinated metabolism of soil organic matter by interacting soil microorganisms, including interactions across microbial trophic levels; i.e. bacteria, archaea, fungi, protists and viruses. To reduce soil complexity to a tractable level we carried out two complementary approaches: 1) we enriched sub-communities of the soil microbiome into reduced complexity 'functional modules' and 2) we derived a model soil consortium (MSC-1) consisting of a tractable number (~20) of interacting species. Using the functional module approach, we were able to define functional subsets of the soil microbiome that carried out metabolic steps involved in metabolism of simple and complex carbon substrates. Functional modules had reproducible and predictable taxonomic compositions and gene expression profiles and enriched for rare taxa not found at significant levels in bulk soil controls. When using the model soil microbiome approach, we could delineate specific interactions between species during metabolism of a complex carbon substrate; i.e. chitin. Network analyses revealed keystone species that were central to community interactions. Finally, the contributions of soil viruses were predicted in metagenomes and metatranscriptomes by focusing on viral contigs. For example, we found that soil DNA and RNA viruses were shaped by differences in soil moisture. Together these findings help to piece together previously unknown links between soil microorganisms that have relevance for global biogeochemical cycling and their responses to climate change.