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. In this study, 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 homogeneous liquid medium. The guiding hypothesis was that the initial species richness would influence the tendency for the selected consortia to stabilize and maintain a relatively constant community structure over time. We also hypothesized that long-term, substrate-driven growth would result in consortia with reduced species richness 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 from that in 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 than in liquid environments. IMPORTANCE The 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. In this study, 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.

Balanced stochastic versus deterministic assembly processes benefit diverse yet uneven ecosystem functions in representative agroecosystems

“…Our result is in agreement with previous findings that determinism favours particular microorganisms that function at high levels in optimized environments (e.g., fertility or redox status) (Jangid et al ., 2013; Knelman and Nemergut, 2014; Graham et al ., 2016a; Graham and Stegen, 2017). When the impact of environment to microbial communities is severe, the ecosystem functions of those communities are formed in selection‐only conditions (high determinism), leading to high rates of functions but limited numbers of functions (Langenheder and Lindstrom, 2019; Zegeye et al ., 2019). For example, in P‐deficient agricultural soils, the agroecosystem imposed strong stresses on microorganisms, and consequently, only those with similar functional traits or environmental preferences could survive (Feng et al ., 2017).…”

Visualizing Microbial Community Dynamics via a Controllable Soil Environment

“…We tested 14%, 24%, and 34% soil moisture regimes (gravimetric moisture content). The 24% moisture regime was selected to represent the field capacity of the soil used in this study (23), whereas the 14% and 34% moisture regimes were introduced to probe the effects of drought and added moisture, respectively, on soil microbial processes. After incubating soil under the abovementioned moisture conditions for 7 days, ITO-coated glass slides fabricated with chitin islands were placed on the windows and incubated for 3 days, while keeping the respective moisture level consistent in each of the SoilBoxes.…”

“…Here, the SoilBoxes were filled with live soil collected in October 2017, from a field site operated by Washington State University, located in Prosser, WA, USA (46°15=04ЉN and 119°43=43ЉW) (23). This soil represents a Warden silt loam, characterized as a coarse-silty, mixed, superactive, and mesic Xeric Haplocambid.…”

Dilution-to-Stimulation/Extinction Method: a Combination Enrichment Strategy To Develop a Minimal and Versatile Lignocellulolytic Bacterial Consortium

“…2D ) suggested that a selective process, determined by the lignocellulose input in the culture flasks, drives community assembly. In this regard, Zegeye et al ( 38 ) reported that substrate-driven soil community succession is mainly deterministic. Moreover, reductions of diversity and enrichment of Sphingobacteriales and Enterobacteriales species were evident at T6 ( Fig.…”