Selective Isolation of a Eucalyptus spp. Woodchip Bacterial Community and Its Taxonomic and Metabolic Profiling

Abstract

Taxonomic and metabolic profiles of bacterial inhabitants of Eucalyptus spp. woodchips from storage piles were analysed using whole genome shotgun metagenomics sequencing. The majority of the bacterial species present in the metagenome from the Eucalyptus spp. woodchips are found within four bacterial phyla: Proteobacteria (77%), Bacteroidetes (15%), Acidobacteria (3%) and Actinobacteria (2%). The most abundant species in the metagenome were Burkholderia spp. (25%; Proteobacteria) and Chryseobacterium spp. (37%; Bacteroidetes). Other species prevalent in this bacterial metagenome are Rhodanobacter spp. (7%), Klebsiella spp. (6%) and Pseudomonas spp. (5%). Both PhyloSift and Metagenome Rapid Annotation Subsystem Technology tools to estimate taxonomic diversity showed that the phylum Proteobacteria was the predominant group among the bacteria in the bacterial metagenome from the Eucalyptus spp. woodchips, followed by Bacteroidetes, Acidobacteria and Actinobacteria. Functional analysis revealed that clustering-based subsystem and carbohydrate metabolism which are key to degradation of the lignocellulose were the most abundant SEED subsystems representing 14% and 11% of the bacterial metagenome, respectively. Approximately 8% of the sequences were grouped under “miscellaneous functions” and 3% under metabolism of aromatic compounds. One thousand two hundred forty-seven potential contigs encoding biomass-degrading enzymes including glycoside hydrolases (GH, 525 contigs), glycosyl transferases (GT, 452 contigs) carbohydrate binding modules (CBM, 149 contigs), carbohydrate esterases (CE, 70 contigs), polysaccharide lyases (PL, 16 contigs) and auxiliary activity (AA, 35 contigs) were identified. Both taxonomic and functional classifications suggest that the bacterial inhabitants of the Eucalyptus spp. woodchips present a broader metabolic potential than the degradation of plant biomass.