Bacterial community assembly based on functional genes rather than species

Abstract

The principles underlying the assembly and structure of complex microbial communities are an issue of long-standing concern to the field of microbial ecology. We previously analyzed the community membership of bacterial communities associated with the green macroalga Ulva australis, and proposed a competitive lottery model for colonization of the algal surface in an attempt to explain the surprising lack of similarity in species composition across different algal samples. Here we extend the previous study by investigating the link between community structure and function in these communities, using metagenomic sequence analysis. Despite the high phylogenetic variability in microbial species composition on different U. australis (only 15% similarity between samples), similarity in functional composition was high (70%), and a core of functional genes present across all algal-associated communities was identified that were consistent with the ecology of surface- and host-associated bacteria. These functions were distributed widely across a variety of taxa or phylogenetic groups. This observation of similarity in habitat (niche) use with respect to functional genes, but not species, together with the relative ease with which bacteria share genetic material, suggests that the key level at which to address the assembly and structure of bacterial communities may not be "species" (by means of rRNA taxonomy), but rather the more functional level of genes.

Fig. 1.

MDS plots based on Bray-Curtis similarity of functional gene profiles based on COG and SEED annotations of U. australis and planktonic seawater metagenomes. (A) MDS plots for all samples, including UA4, UA6, SW4, SW6, SW8, and SW10, which contained an order-of-magnitude less sequencing than the remaining samples. (B) MDS plots with low coverage samples removed. Samples from each of the respective environments cluster together based on their functional profile.

Fig. 2.

COG (A) and SEED subsystems (B), which comprise the characteristic functions of the U. australis community, by comparison with planktonic seawater, with SD across the six algal and eight seawater samples analyzed. COGs and SEED subsystems are presented in the order of their contribution to difference (highest to lowest, Top to Bottom) as assessed by SIMPER analysis.