Comparative Genome Analysis of the Lignocellulose Degrading Bacteria so4 and w15.

Two bacterial strains, denoted so4 and w15, isolated from wheat straw (WS)-degrading microbial consortia, were found to grow synergistically in media containing WS as the single carbon and energy source. They were identified as so4 and w15 based on 16S rRNA gene sequencing and comparison to the respective and type strains. In order to identify the mechanisms driving the synergistic interactions, we analyzed the draft genomes of the two strains and further characterized their metabolic potential. The latter analyses revealed that the strains had largely complementary substrate utilization patterns, with only 22 out of 190 compounds shared. The analyses further indicated so4 to primarily consume amino acids and simple sugars, with laminarin as a key exception. In contrast, w15 showed ample capacity to transform complex polysaccharides, including intermediates of starch degradation. Sequence analyses revealed so4 to have a genome of 4,883,214 bp, with a G + C content of 52.5%, 4,554 protein-encoding genes and 86 RNA genes. w15 has a genome of 6,678,278 bp, with a G + C content of 39.7%, 5,999 protein-encoding genes and 76 RNA genes. Genes for motility apparatuses (flagella, chemotaxis) were present in the genome of so4, but absent from that of w15. In the genome of w15, 348 genes had regions matching CAZy family enzymes and/or carbohydrate-binding modules (CBMs), with 193 glycosyl hydrolase (GH) and 50 CBM domains. Remarkably, 22 domains matched enzymes of glycoside hydrolase family GH43, suggesting a strong investment in the degradation of arabinoxylan. In contrast, 130 CAZy family genes were found in so4, with 61 GH and 12 CBM domains identified. Collectively, our results, based on both metabolic potential and genome analyses, revealed the two strains to harbor complementary catabolic armories, with w15 primarily attacking the WS hemicellulose and so4 the cellobiose derived from cellulose, next to emerging oligo- or monosaccharides. Finally, so4 may secrete secondary metabolites that w15 can consume, and detoxify the system by reducing the levels of (toxic) by-products.