Soil aggregate microbial communities: Towards understanding microbiome interactions at biologically relevant scales

Soils contain a tangle of minerals, water, nutrients, gases, plant roots, decaying organic matter, and microorganisms which work together to cycle nutrients and support terrestrial plant growth. Most soil microorganisms live in periodically interconnected communities closely associated with soil aggregates, i.e. small ( Here, we review the current state of knowledge regarding soil aggregate microbial communities and identify areas of opportunity to study soil ecosystems at a scale relevant to individual cells. We present a framework for understanding aggregate communities as “microbial villages” that are periodically connected through wetting events, allowing for the transfer of genetic material, metabolites, and viruses. We describe both top-down (whole community) and bottom-up (reductionist) strategies for studying these communities. Understanding this requires combining “model system” approaches (e.g. developing mock community artificial aggregates), field observations of natural communities, and broader study of community interactions to include understudied community members like viruses. Initial studies suggest that aggregate-based approaches are a critical next-step for developing a predictive understanding of how geochemical and community interactions govern microbial community structure and nutrient cycling in soil.