PNNL

Abstract

The soil microbiome is central to the cycling of carbon and other nutrients and to the promotion of plant growth. However, despite its importance, analysis of the soil microbiome is difficult due its sheer complexity, the number of species, and their possible interactions. Here, we reduced this complexity by developing model microbial consortia that are simpler and more amenable to experimental analysis but still represent important microbial functions of the native soil ecosystem. We collected samples from a native grassland soil and enriched for communities on agar plates containing chitin as the main carbon source. Chitin was chosen because it is an abundant carbon and nitrogen polymer in our model soil type/system that often requires the coordinated action of several microorganisms for complete metabolic degradation. Using this approach, we derived model soil consortia that had tractable complexity (20-50 OTUs) and contained a number of diverse phyla representative of the native soil, including Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria and Verrucomicrobia. We demonstrated that the resulting consortia could be stored as glycerol or lyophilized stocks at -80° C and revived while retaining community composition, greatly increasing their use as tools for the research community at large. Focusing on one of the consortia that was particularly stable, we studied population interactions using both pairwise co-cultivation in liquid media and during growth in soil under several perturbations. Co-abundance analyses highlighted interspecies interactions and helped to define keystone species, including Rhodococcus and Rhizobiales taxa. These experiments demonstrate the success of an approach based on naturally enriching a community of interacting species that can be stored, revived, and shared. Within this consortium, Rhodococcus and Rhizobiales act as critical players that likely participate in positive interactions with other constituent species. The knowledge gained from developing these communities and querying their interactions will be critical to a better understanding of interspecies interactions within the soil microbiome and the role these interactions play in cycling abundant nutrient sources within the soil environment.