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 hostassociated 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.lateral gene transfer | biofilm | ecological model M etagenomic analysis of environmental microbial communities has revealed an enormous and previously unknown microbial diversity, and expanded our knowledge of their function in a variety of environments (1-5). Much still remains unknown, however, such as the principles underlying the assembly and structure of complex microbial communities, an issue of long-standing concern to the field of microbial ecology. To this aim, several recent studies have supported the "neutral hypothesis" (6-8), a largely stochastic model for community assembly, which assumes that species are ecologically equivalent and that community structure is determined by random processes (9, 10). However, there is also evidence that niche or deterministic processes play a role in community structure (11, 12); thus, both niche and neutral processes are likely to affect the assembly of complex microbial communities.Support for these models is based on species abundance distributions, and critical functional aspects, such as the assumption of ecological equivalence, have for the most part not been tested. In this study, we examine the encoded functions of an algalassociated bacterial community and link patterns of function to patterns of community assembly. Following the results of an earlier study (13), we investigate these communities in the context of the lottery hypothesis, a model for community "assembly" derived from studies of eukaryotic communities, such as coral reef fish (14). This hypothesis incorporates both neutral and functional aspects and arg...

The microbiome of North Sea copepods

“…The colonisation process itself could be most likely explained by the competitive lottery model as already proposed for the colonisation of algal surfaces (Burke et al 2011b). In this context, we suggest to investigate the link between community structure and function using metagenomic sequence analysis (Burke et al 2011a) in future studies. From the phylogenetic analysis, it can be emphasis that chitin degradation seems to be a common trait of the bacterial community associated with copepods.…”

Global biogeography of Prochlorococcus genome diversity in the surface ocean

“…Questions regarding the relationship between phylogeny and functional gene diversity are critical to understanding the ecological and evolutionary mechanisms structuring microbial populations (Martiny et al, 2009c;Burke et al, 2011;Raes et al, 2011;Wiedenbeck and Cohan, 2011;Brown et al, 2014;Dupont et al, 2014). Increasing amounts of evidence suggest that using the whole genome rather than simply a single-gene classification is often needed to define microbial lineages and, more importantly, determine its role in the environment (Brown et al, 2014).…”

Evaluating community–environment relationships along fine to broad taxonomic resolutions reveals evolutionary forces underlying community assembly

“…Conversely, breaking down broader taxa into finer units may result in more noise than information, as the distributions and abundances of those ecologically equivalent units exhibit a high degree of randomness caused by neutral-stochastic processes instead of nichedeterministic processes (Lozupone et al, 2012;Prosser, 2012;DeLong, 2014). Actually, previous studies have indicated that despite the considerable variability in species-level composition, prokaryotic communities in a given habitat usually have stable phylum-level composition as well as similar functional attributes (Fierer et al, 2007;Lauber et al, 2009;Burke et al, 2011;Fan et al, 2012;Lozupone et al, 2012); these findings further support the view that there is ecological coherence in deep prokaryotic branches (Philippot et al, 2009(Philippot et al, , 2010) and potentially many fine-level taxa are functionally redundant and fulfill the same ecological role (Lozupone et al, 2012;Prosser, 2012;DeLong, 2014).…”