Microdiversity of extracellular enzyme genes among sequenced prokaryotic genomes

Abstract

Understanding the relationship between prokaryotic traits and phylogeny is important for predicting and modeling ecological processes. Microbial extracellular enzymes have a pivotal role in nutrient cycling and the decomposition of organic matter, yet little is known about the phylogenetic distribution of genes encoding these enzymes. In this study, we analyzed 3058 annotated prokaryotic genomes to determine which taxa have the genetic potential to produce alkaline phosphatase, chitinase and b-N-acetyl-glucosaminidase enzymes. We then evaluated the relationship between the genetic potential for enzyme production and 16S rRNA phylogeny using the consenTRAIT algorithm, which calculated the phylogenetic depth and corresponding 16S rRNA sequence identity of clades of potential enzyme producers. Nearly half (49.2%) of the genomes analyzed were found to be capable of extracellular enzyme production, and these were non-randomly distributed across most prokaryotic phyla. On average, clades of potential enzymeproducing organisms had a maximum phylogenetic depth of 0.008004-0.009780, though individual clades varied broadly in both size and depth. These values correspond to a minimum 16S rRNA sequence identity of 98.04-98.40%. The distribution pattern we found is an indication of microdiversity, the occurrence of ecologically or physiologically distinct populations within phylogenetically related groups. Additionally, we found positive correlations among the genes encoding different extracellular enzymes. Our results suggest that the capacity to produce extracellular enzymes varies at relatively fine-scale phylogenetic resolution. This variation is consistent with other traits that require a small number of genes and provides insight into the relationship between taxonomy and traits that may be useful for predicting ecological function.

Microbial regulation of the soil carbon cycle: evidence from gene–enzyme relationships

“…However, the functional potential of the microbial community will be driven by the selection of active taxa within different lineages. Functional attributes are embedded in the genomic blueprint and the capacity to produce extracellular enzymes varies at relatively fine-scale phylogenetic resolution (Philippot et al, 2010;Trivedi et al, 2013;Zimmerman et al, 2013). Because the composition of microbial community does not correlate strongly with the enzyme activity, functional genes and processes may offer a better predictive framework for investigating the ecological consequences of microbial traits conserved at higher phylogenetic resolutions than inferring function based on phylogenetic marker genes.…”

Functional distinctness in the exoproteomes of marine Synechococcus

“…Furthermore, extracellular enzymes with a simple genetic structure are known to be rapidly gained and lost through evolution (Zimmerman et al ., 2013), facilitating the acquisition of functional distinctness via this extracellular fraction. Horizontal gene transfer of large genetic islands may facilitate the acquisition of these simple functions, but also of more complex operons or genes encoding for giant proteins such as those detected here (Dufresne et al ., 2008).…”

Fungal Traits That Drive Ecosystem Dynamics on Land

“…In bacteria, phylogeny is sometimes correlated with functional traits (215) and habitat preferences (207,216,217), but not always (218). For bacteria, decomposition-related traits, such as cellulase production and organic C use, vary primarily at the species and subspecies levels (219,220). Horizontal gene transfer is common within prokaryotes (221), and it may contribute to this pattern.…”