Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules

Abstract

<jats:title>ABSTRACT</jats:title> <jats:p>The soil microbiome represents one of the most complex microbial communities on the planet, encompassing thousands of taxa and metabolic pathways, rendering holistic analyses computationally intensive and difficult. Here, we developed an alternative approach in which the complex soil microbiome was broken into components (“functional modules”), based on metabolic capacities, for individual characterization. We hypothesized that reproducible, low-complexity communities that represent functional modules could be obtained through targeted enrichments and that, in combination, they would encompass a large extent of the soil microbiome diversity. Enrichments were performed on a starting soil inoculum with defined media based on specific carbon substrates, antibiotics, alternative electron acceptors under anaerobic conditions, or alternative growing conditions reflective of common field stresses. The resultant communities were evaluated through 16S rRNA amplicon sequencing. Less permissive modules (anaerobic conditions, complex polysaccharides, and certain stresses) resulted in more distinct community profiles with higher richness and more variability between replicates, whereas modules with simple substrates were dominated by fewer species and were more reproducible. Collectively, approximately 27% of unique taxa present in the liquid soil extract control were found across functional modules. Taxa that were underrepresented or undetected in the source soil were also enriched across the modules. Metatranscriptomic analyses were carried out on a subset of the modules to investigate differences in functional gene expression. These results demonstrate that by dissecting the soil microbiome into discrete components it is possible to obtain a more comprehensive view of the soil microbiome and its biochemical potential than would be possible using more holistic analyses.</jats:p> <jats:p><jats:bold>IMPORTANCE</jats:bold> The taxonomic and functional diversity inherent to the soil microbiome complicate assessments of the metabolic potential carried out by the community members. An alternative approach is to break down the soil microbiome into reduced-complexity subsets based on metabolic capacities (functional modules) prior to sequencing and analysis. Here, we demonstrate that this approach successfully identified specific phylogenetic and biochemical traits of the soil microbiome that otherwise remained hidden from a more top-down analysis.</jats:p>

Resource-diversity relationships in bacterial communities reflect the network structure of microbial metabolism

“…This is still largely unresolved because, traditionally, different facets of resource availability have been tackled separately, with theory focusing on the effects of the number of resources on species coexistence, e.g. (4)(5)(6)(7), and experiments concentrating on the impact of resource identity on community composition and function (8)(9)(10)). Yet, understanding how the identity and number of available resources shape microbial diversity is key to anticipating the response of ecosystem to alterations in the environment, including global climate change and evolving human diets (11).…”

Disentangling soil microbiome functions by perturbation

“…This example highlights that targeted perturbation of a specific function in a soil microbial community presents a powerful tool to reveal complex soil ecosystem services. In addition, a totally different approach to study soil microbiome functions was presented recently by Naylor and colleagues ( 2020a ) where a soil microbiome was enriched in functions by using different nutritional and growth conditions. This work presents an intriguing set of different ‘functional modules’ and their implications for the bacterial community.…”

Predicting Microbiome Metabolism and Interactions through Integrating Multidisciplinary Principles

“…A recent study deconstructed the soil microbiome into functional modules through targeted enrichment of desired metabolic traits. It allows for investigating a community with significantly less complexity and drawing mechanistic conclusions ( 25 ). Another promising approach is to culture the “unculturable” organism in a microbiome using microfluidic droplets as localized, nanoliter-sized bioreactors.…”