Genomic Potential for Polysaccharide Deconstruction in Bacteria

Abstract

Glycoside hydrolases are important enzymes that support bacterial growth by enabling the degradation of polysaccharides (e.g., starch, cellulose, xylan, and chitin) in the environment. Presently, little is known about the overall phylogenetic distribution of the genomic potential to degrade these polysaccharides in bacteria. However, knowing the phylogenetic breadth of these traits may help us predict the overall polysaccharide processing in environmental microbial communities. In order to address this, we identified and analyzed the distribution of 392,166 enzyme genes derived from 53 glycoside hydrolase families in 8,133 sequenced bacterial genomes. Enzymes for oligosaccharides and starch/glycogen were observed in most taxonomic groups, whereas glycoside hydrolases for structural polymers (i.e., cellulose, xylan, and chitin) were observed in clusters of relatives at taxonomic levels ranging from species to genus as determined by consenTRAIT. The potential for starch and glycogen processing, as well as oligosaccharide processing, was observed in 85% of the strains, whereas 65% possessed enzymes to degrade some structural polysaccharides (i.e., cellulose, xylan, or chitin). Potential degraders targeting one, two, and three structural polysaccharides accounted for 22.6, 32.9, and 9.3% of genomes analyzed, respectively. Finally, potential degraders targeting multiple structural polysaccharides displayed increased potential for oligosaccharide deconstruction. This study provides a framework for linking the potential for polymer deconstruction with phylogeny in complex microbial assemblages.

Long-Term Warming Alters Carbohydrate Degradation Potential in Temperate Forest Soils

“…In line with previous studies (79), we found that carbohydrate degradation was phylogenetically conserved. Due to cultivation bias (82), phylogenetic correction is required to conclude increased probability of carbohydrate degradation ability (83), although many previous papers comparing the physiological capacity of bacteria isolated from different environments or under different conditions in the laboratory have failed to consider the potential need to correct for phylogenetic autocorrelation in their analysis (84–86).…”

“…This is consistent with a global trend toward increased relative abundance of this phylum under warming (74), including in metagenomes of a decade-long prairie warming experiment (12). Although members of the Actinobacteria show considerable variability in their ability to degrade carbohydrates (79), the genomes of Actinobacteria in our metagenomes were on average enriched in glycoside hydrolases responsible for cellulose, starch, and xylan degradation compared to other phyla based on a CAZyme-to-RNA polymerase subunit B standardization (see Fig. S5 in the supplemental material).…”

Evidence for Ecological Flexibility in the Cosmopolitan Genus Curtobacterium

“…This characterization is supported by a comprehensive analysis into the distribution of GHs across all bacteria, which showed that Actinobacteria has the highest genomic potential for being cellulose degraders (Berlemont and Martiny, 2015). Therefore, we concentrated on these GH proteins, as they are responsible for the breakdown of large carbohydrates that may prove advantageous in decomposition of plant debris.…”

“…Therefore, we concentrated on these GH proteins, as they are responsible for the breakdown of large carbohydrates that may prove advantageous in decomposition of plant debris. For instance, an increase in diversity and abundance of GHs with the potential for cellulose utilization generally corresponds to better cellulose degradation (Fontes and Gilbert, 2010; Wilson, 2011; Berlemont and Martiny, 2015). Previously, Curtobacterium isolates collected from a neutral garden soil were shown to rapidly degrade cellulose fibers (Lednická et al, 2000).…”

Characterization of three plant biomass-degrading microbial consortia by metagenomics- and metasecretomics-based approaches

“…Annotation was performed via Hidden Markov Models based on CAZy family domains (v3) (downloaded from dbCAN site) (http://csbl.bmb.uga.edu/dbCAN/) (Yin et al 2012) using an e value cutoff of 1e-15. Bacterial glycosyl hydrolase (GH) families involved in polysaccharide deconstruction were selected according to Berlemont and Martiny (2015). To evaluate the RA of reads per selected GH family, the counts were normalized to hits, or unique matches, per million reads, thereby accounting for differences in metagenome sizes (Cardenas et al 2015).…”