Determinism of microbial community assembly by drastic environmental change.

Akifumi Nishida,Masayuki Yamamura,Mayuko Nakagawa,Hein Min Tun

doi:10.1371/journal.pone.0260591

Akifumi Nishida, Masayuki Yamamura + Show 2 more

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https://doi.org/10.1371/journal.pone.0260591

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Abstract

Microbial community assembly is shaped by deterministic and stochastic processes, but the relationship between these processes and the environment is not understood. Here we describe a rule for the determinism and stochasticity of microbial community assembly affected by the environment using in silico, in situ, and ex situ experiments. The in silico experiment with a simple mathematical model showed that the existence of essential symbiotic microorganisms caused stochastic microbial community assembly, unless the community was exposed to a non-adapted nutritional concentration. Then, a deterministic assembly occurred due to the low number of microorganisms adapted to the environment. In the in situ experiment in the middle of a river, the microbial community composition was relatively deterministic after the drastic environmental change caused by the treated wastewater contamination, as analyzed by 16S rRNA gene sequencing. Furthermore, by culturing microbial communities collected from the upstream natural area and downstream urban area of the river in test tubes with varying carbon source concentrations, the upstream community assembly became deterministic with high carbon concentrations while the downstream community assembly became deterministic with low carbon concentrations. These results suggest that large environmental changes, which are different from the original environment, result in a deterministic microbial community assembly.

Highlights

Microbial communities in the human gut, floral nectars, and bioreactors are shaped by deterministic and stochastic processes, which result in different microbial communities even in the same environment [1]
We supposed the existence of essential-microbial species for each microbial species that generated stochasticity of microbial community assembly based on the different initial microbial abundances (Fig 3A)
We investigated the possible factors controlling stochasticity of microbial community assembly with an in silico experiment that enabled the regulation of simple virtual microbial communities for comprehensive understanding, an in situ experiment observing original bacterial communities at various sites, and an ex situ experiment comparing bacterial communities assembled in artificial environments

Summary

Introduction

Microbial communities in the human gut, floral nectars, and bioreactors are shaped by deterministic and stochastic processes, which result in different microbial communities even in the same environment [1]. The deterministic convergence and stochastic variation among microbial community replicates have been studied with various systems, such as bottom-up synthetic microbial communities with a few microbial species and microbial communities cultivated from the natural environment. Previous research has used the bottom-up synthetic microbial communities to study population density fluctuations around replicateaverage dynamics in three microbial species communities [2], stochastic assembly in the host by two bacterial species [3], priority effects among four yeast species [4], and high-order. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

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