Phylogenetic Clustering and Overdispersion in Bacterial Communities

Abstract

Abstract. Very little is known about the structure of microbial communities, despite their abundance and importance to ecosystem processes. Recent work suggests that bacterial biodiversity might exhibit patterns similar to those of plants and animals. However, relative to our knowledge about the diversity of macro-organisms, we know little about patterns of relatedness in free-living bacterial communities, and relatively few studies have quantitatively examined community structure in a phylogenetic framework. Here we apply phylogenetic tools to bacterial diversity data to determine whether bacterial communities are phylogenetically structured. We find that bacterial communities tend to contain lower taxonomic diversity and are more likely to be phylogenetically clustered than expected by chance. Such phylogenetic clustering may indicate the importance of habitat filtering (where a group of closely related species shares a trait, or suite of traits, that allow them to persist in a given habitat) in the assembly of bacterial communities. Microbial communities are especially accessible for phylogenetic analysis and thus have the potential to figure prominently in the integration of evolutionary biology and community ecology.

Reproducibility of Vibrionaceae population structure in coastal bacterioplankton

“…At fine-graded spatial and phylogenetic scales, communities appear assembled according to niche partitioning while decreasing resolution changes interpretation of community assembly mechanisms first to neutrality and finally to habitat filtering (Cavender-Bares et al, 2009). The latter predicts that communities contain more closely related species than expected by chance (phylogenetic clustering) because their close relationship ensures that they share many traits that might enhance their survival in a given environment (Horner-Devine and Bohannan, 2006). These considerations are relevant for microbial communities since they are typically sampled at the 'bucket' scale, corresponding more to ecosystem rather than to habitat scales, and with phylogenetic markers (for example, 16S rRNA genes) that have relatively coarse genotypic resolution.…”

Microbial community structure across the tree of life in the extreme Río Tinto

“…Modern-day ecologists have adopted phylogenetic methods to explore this question (Martin, 2002). Most of these studies have concentrated on multicellular life, with the exception of a few studies that are microbial in focus (Horner-Devine and Bohannan, 2006;Bryant et al, 2008). Methods developed by Webb et al (2002) provide a method to use phylogenetic structuring in microbial communities to quantify the drivers of community assembly.…”

River organic matter shapes microbial communities in the sediment of the Rhône prodelta

“…The significant segregation patterns could mean that competitive interactions between OTUs drives community assembly but it could also be a result of non-overlapping niches (habitat checkerboard) or historical effect (see, for example, Diamond, 1975;Gotelli et al, 1997;Horner-Devine et al, 2007). Phylogenetic clustering patterns can give deeper insight into the underlying ecological processes (Webb et al, 2002;Horner-Devine and Bohannan, 2006) especially when performed on each sample separately. Although very few of our samples were significantly phylogenetically clustered or dispersed, we did observe more phylogenetic clustering in deep samples in August, suggesting that the community was shaped by habitat filtering, a process that is arguably the most predominant process in shaping microbial communities (Horner-Devine and Bohannan, 2006;Pontarp et al, 2012;Wang et al, 2012), although it can depend on OTU definitions (Koeppel and Wu, 2014).…”

“…Phylogenetic clustering patterns can give deeper insight into the underlying ecological processes (Webb et al, 2002;Horner-Devine and Bohannan, 2006) especially when performed on each sample separately. Although very few of our samples were significantly phylogenetically clustered or dispersed, we did observe more phylogenetic clustering in deep samples in August, suggesting that the community was shaped by habitat filtering, a process that is arguably the most predominant process in shaping microbial communities (Horner-Devine and Bohannan, 2006;Pontarp et al, 2012;Wang et al, 2012), although it can depend on OTU definitions (Koeppel and Wu, 2014). Thus, with less perturbation, the community probably became more specialized toward specific environmental conditions.…”