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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  Citrobacter freundii  so4 and  Sphingobacterium multivorum  w15 based on 16S rRNA gene sequencing and comparison to the respective  C. freundii  and  S. multivorum  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  C. freundii  so4 to primarily consume amino acids and simple sugars, with laminarin as a key exception. In contrast,  S. multivorum  w15 showed ample capacity to transform complex polysaccharides, including intermediates of starch degradation. Sequence analyses revealed  C. freundii  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.  S. multivorum  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  C. freundii  so4, but absent from that of  S. multivorum  w15. In the genome of  S. multivorum  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  C. freundii  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  S. multivorum  w15 primarily attacking the WS hemicellulose and  C. freundii  so4 the cellobiose derived from cellulose, next to emerging oligo- or monosaccharides. Finally,  C. freundii  so4 may secrete secondary metabolites that  S. multivorum  w15 can consume, and detoxify the system by reducing the levels of (toxic) by-products.

Comparative Genome Analysis of the Lignocellulose Degrading Bacteria Citrobacter freundii so4 and Sphingobacterium multivorum w15