Selection, succession and stabilization of soil microbial consortia

Abstract

Soil microorganisms play fundamental roles in cycling of soil carbon, nitrogen and other nutrients, yet we have a poor understanding of how soil microbiomes are shaped by their nutritional and physical environment. Here we investigated the successional dynamics of a soil microbiome during 21-weeks of enrichment on chitin and its monomer, N-acetylglucosamine. We examined succession of the soil communities in a physically heterogeneous soil matrix as well as a highly mixed liquid medium. The guiding hypothesis was that the initial species richness would influence the tendency for the selected consortia to stabilize and maintain relatively constant community structure over time. We also hypothesized that long term, substrate-driven growth would result in consortia with reduced species richness as compared to the parent microbiome and that this process would be deterministic with relatively little variation between replicates. We found that the initial species richness does influence the long-term community stability in both liquid media and soil and that lower initial richness results in a more rapid convergence to stability. Despite use of the same soil inoculum and access to the same major substrate, the resulting community composition differed greatly in soil compared to liquid medium. Hence, distinct selective pressures in soils relative to homogenous liquid media exist and can control community succession dynamics. This difference is likely related to the fact that soil microbiomes are more likely to thrive, with fewer compositional changes, in a soil matrix compared to liquid environments.IMPORTANCEThe soil microbiome carries out important ecosystem functions, but interactions between soil microbial communities have been difficult to study due to the high microbial diversity and complexity of the soil habitat. Here we successfully obtained stable consortia with reduced complexity that contained species found in the original source soil. These consortia and the methods used to obtain them can be a valuable resource for exploration of specific mechanisms underlying soil microbial community ecology. The results of this study also provide new experimental context to better inform how soil microbial communities are shaped by new environments and how a combination of initial taxonomic structure and physical environment influences stability.

Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules

“…First, in the interests of controllability and throughput, all enrichments were conducted in liquid (rather than soil) media. Due to the relative homogeneity of this media type, liquid cultures are predisposed to enrich for one or a few OTUs (10,35), are potentially biased against rare taxa due to the use of soil dilutions (5), and will evoke different community profiles than would be obtained in soil (29,50). We observed domination by fast-growing microbes under certain substrates in liquid cultures, but these findings do not equate to these microbes being the only ones capable of metabolizing the substrates.…”

“…Opportunistic growth by Pseudomonas was the cause of this trend in numerous modules enriched with simple substrates. As an r-selected organism, Pseudomonas grows rapidly in liquid cultures containing labile carbon substrates (12,29), outcompeting less opportunistic microbes. Thus, the results observed here are consistent with its life strategy (30).…”

“…We observed domination by fast-growing microbes under certain substrates in liquid cultures, but these findings do not equate to these microbes being the only ones capable of metabolizing the substrates. In contrast, in soils, various factors (e.g., inaccessibility of substrates due to irregular spatial distribution or physical protection mechanisms [51]) will invoke competitive or synergistic interactions and, by extension, a more diverse community, even with the same substrate (29). However, where applicable we included native bulk soil as a point of comparison to partially address this issue.…”

“…Functional module sample generation. Soil used in these experiments was the same as described in a previous study (29). Briefly, the soil was collected in October 2017 from an experimental field site (Washington State University Irrigated Agriculture Research and Extension Center located in Prosser, WA), and then 4 mm sieved to remove soil aggregates, rocks, and extraneous plant matter before long-term storage (0.5 to 1.5 years) at 4°C.…”

Evaluation of Pig Dung for Electricity Generation Using Microbial Fuel Cell

“…There was a decline in the population of the microbial community between the initial and final isolation. This is possible as a result of microbial adaptation, succession and evolution which are likely to have taken place in the anode chamber of the MFC within the 40 days period of current and voltage generation, this naturally occurs in response to environmental changes dictating the survival, elimination or evolution of the members in the microbial community (Zegeye et al, 2019). All the identified bacteria at the phylum level can be classified into three which include the phylum Firmicute, the phylum Proteobacteria and the phylum Actinobacteria.…”