Disturbance-Diversity Relationships of Microbial Communities Change Based on Growth Substrate

Abstract

Disturbance events can impact ecological community dynamics. Understanding how communities respond to disturbances, and how those responses can vary, is a challenge in microbial ecology. In this study, we grew a previously enriched specialized microbial community on either cellulose or glucose as a sole carbon source, and subjected them to one of five different disturbance regimes of varying frequencies ranging from low to high. Using 16S rRNA gene amplicon sequencing, we show that community structure is largely driven by substrate, but disturbance frequency affects community composition and successional dynamics. When grown on cellulose, bacteria in the genera Cellvibrio, Lacunisphaera, and Asticaccacaulis are the most abundant microbes. However, Lacunisphaera is only abundant in the lower disturbance frequency treatments, while Asticaccaulis is more abundant in the highest disturbance frequency treatment. When grown on glucose, the most abundant microbes are two Pseudomonas sequence variants, and a Cohnella sequence variant that is only abundant in the highest disturbance frequency treatment. Communities grown on cellulose exhibited a greater range of diversity (0.67-1.99 Shannon diversity and 1.38-5.25 Inverse Simpson diversity) that peak at the intermediate disturbance frequency treatment, or 1 disturbance every 3 days. Communities grown on glucose, however, ranged from 0.49-1.43 Shannon diversity and 1.37- 3.52 Inverse Simpson with peak diversity at the greatest disturbance frequency treatment. These results demonstrate that the dynamics of a microbial community can vary depending on substrate and the disturbance frequency, and may potentially explain the variety of diversity-disturbance relationships observed in microbial ecosystems.

Figure 1.

A. Image of A. colombica refuse dump. These piles are predominantly composed of partially degraded plant biomass, removed from the bottom of fungus gardens by worker ants. B. Experimental setup. The cellulose-enriched community was used as the starter inoculum for the growth of microbial communities exposed to ten treatments. Samples were grown in either cellulose or glucose M63 minimal media, then subjected to one of five disturbance regimes. At the end of their respective disturbance regime, communities were used to inoculated 7–10 tubes (containing their respective substrate) and those tubes were destructively sampled every day for seven days.

Figure 2.

Line graph of community composition based on relative abundance of the 16S rRNA gene amplicon sequence of the 6 most abundant ASVs and their assigned genus. Plots are facetted by disturbance frequency (1/n days).

Figure 3.

A. NMDS plot of community composition. Dissimilarity matrix was calculated using Bray-Curtis dissimilarity. Communities grown in cellulose are shown as circles, and communities grown in glucose are shown as triangles. Disturbance frequency is marked by color. B. Table of ANOSIM and ADONIS tests of recorded factors that may contribute to variance.

Figure 4.

Community diversity varies across substrate and disturbance frequency. Shannon diversity and Inverse Simpson diversity (Y-axis) change across disturbance frequency (X-axis) and vary by substrate.