Phylogenetic distribution of potential cellulases in bacteria

Abstract

Many microorganisms contain cellulases that are important for plant cell wall degradation and overall soil ecosystem functioning. At present, we have extensive biochemical knowledge of cellulases but little is known about the phylogenetic distribution of these enzymes. To address this, we analyzed the distribution of 21,985 genes encoding proteins related to cellulose utilization in 5,123 sequenced bacterial genomes. First, we identified the distribution of glycoside hydrolases involved in cellulose utilization and synthesis at different taxonomic levels, from the phylum to the strain. Cellulose degradation/utilization capabilities appeared in nearly all major groups and resulted in strains displaying various enzyme gene combinations. Potential cellulose degraders, having both cellulases and β-glucosidases, constituted 24% of all genomes whereas potential opportunistic strains, having β-glucosidases only, accounted for 56%. Finally, 20% of the bacteria have no relevant enzymes and do not rely on cellulose utilization. The latter group was primarily connected to specific bacterial lifestyles like autotrophy and parasitism. Cellulose degraders, as well as opportunists, have multiple enzymes with similar functions. However, the potential degraders systematically harbor about twice more β-glucosidases than their potential opportunistic relatives. Although scattered, the distribution of functional types, in bacterial lineages, is not random but mostly follows a Brownian motion evolution model. Degraders form clusters of relatives at the species level, whereas opportunists are clustered at the genus level. This information can form a mechanistic basis for the linking of changes in microbial community composition to soil ecosystem processes.

Fig 1

Phylum-specific average glycoside hydrolase gene content (expressed as genes/genome). The number of analyzed genomes from each phylum is indicated in brackets beside the phylum names.

Fig 2

Distribution of cellulose utilization strategies in fully sequenced genomes of the eight most abundant phyla. The fractions include bacteria having no GH relevant for cellulose utilization (black), potential opportunists (red), and potential cellulose degraders (green). A and B values represent the average β-glucosidase content (∼standard deviation [SD]) in opportunists versus potential cellulose degraders.

Fig 3

Strain-specific glycoside hydrolase distribution in bacteria. The consensus phylogenetic tree was based on a 16S rRNA alignment retrieved from the SILVA database (32) and constructed using Phylip (distance matrix F84, neighbor joining, 100 bootstraps) (34). The outer circles show the absence (white) or the presence of one copy (red) or multiple copies (blue) of genes from a considered GH family in each genome.

Fig 4

Comparison of the clustering of Actinobacteria based on GH content (left) and 16S rRNA phylogeny (right). The consensus phylogenetic tree was based on a 16S rRNA alignment retrieved from the SILVA database and constructed using Phylip (distance matrix F84, neighbor joining, 100 bootstraps). GH clustering was based on a Bray-Curtis dissimilarity index measured for the pairwise comparison of the glycoside hydrolase families involved in cellulose degradation of each sequenced genome (1 gene, blue; 2 genes, red; >2 genes, green). The gray lines connect identical strains in the displayed clustering.

Fig 5

Abundance of putative β-glucosidases and cellulases in specific bacterial subpopulations, based on the presence of lifestyle-specific genetic markers, and in some Actinobacteria subgroups. The subpopulations were compared to the “Others” bacteria using the Welch t test (*, P < 1.10⁻¹⁶).