Genetic diversity and community structure of bacterial glycoside hydrolases family 48 genes in soil and compost

Glycoside hydrolases belonging to family 48 (GH48) are one of the most important cellulases responsible for the synergistic degradation of crystalline cellulose (CC) to glucose. Microbial DNA was extracted from soils and compost followed by PCR amplification to detect bacterial GH48 genes. Amplified fragments were cloned to develop DNA libraries to determine the diversity and community structure of bacterial genes responsible for cellulose degradation using GH48 genes. Soil bacterial communities were predominantly based upon unidentified GH48 genes (66%). When identification was possible, community composition analysis of soil samples showed 4 known bacterial phyla with Proteobacteria (23%), Actinobacteria (9%), Firmicutes (1%), and Bacteroidetes (1%). Phylogenetic analysis of unidentified clones showed 2% of clones clustered with a reference sequence from the Chloroflexota genus Herpetosiphon sp. Compost GH48 sequences were predominantly comprised of 3 different bacterial phyla belonging to Firmicutes (72%), Actinobacteria (16%), Myxococcota (5%) with 7% of sequences not matching any known bacteria. The most abundant microbial species in soil with GH48 genes was the Proteobacteria species Massilia violaceinigra (13%) while in compost the Firmicutes species Bacillus licheniformis showed the highest percentage (70%). Soil communities showed a higher genetic diversity than compost predominantly composed of unknown genetic sequences showing the potential to isolate and characterize new cellulases from soil. The contribution of different bacterial phyla, genera, and species to the synergistic CC degradation by GH48 genes demonstrated the importance of diverse bacterial communities to optimize carbon recycling in the environment.