Physiological and genomic analyses of cobalamin (vitamin B 12 )-auxotrophy of Lysobacter auxotrophicus sp. nov., a methionine-auxotrophic chitinolytic bacterium isolated from chitin-treated soil.

A novel bacterium , designated 5-21a ^T , isolated from chitin-treated upland soil, exhibits methionine (Met) auxotrophy and chitinolytic activity. A physiological experiment revealed the cobalamin (synonym, vitamin B ₁₂ )(Cbl)-auxotrophic property of strain 5-21a ^T . The newly determined complete genomic sequence indicated that strain 5-21a ^T possesses only the putative gene for Cbl-dependent Met synthase (MetH) and lacks that for the Cbl-independent one (MetE), which implies the requirement of Cbl for Met-synthesis in strain 5-21a ^T . The set of genes for the upstream (corrin ring synthesis) pathway of Cbl synthesis is absent in the genome of strain 5-21a ^T , which explains the Cbl-auxotrophy of 5-21a ^T . This strain was characterized via a polyphasic approach to determine its taxonomic position. The nucleotide sequences of two copies of the 16S rRNA gene of strain 5-21a ^T indicated the highest similarities to Lysobacter soli DCY21 ^T (99.8 and 99.9 %) and Lysobacter panacisoli CJ29 ^T (98.7 and 98.8 %, respectively), whose Cbl-auxotrophic properties were revealed in this study. The principal respiratory quinone was Q-8. The predominant cellular fatty acids were iso-C _15:0 , iso-C _16:0 and iso-C _17:1 ω 9 c . The complete genome sequence of strain 5-21a ^T revealed that the genome size was 4 155 451 bp long and the G+C content was 67.87 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain 5-21a ^T and its most closely phylogenetic relative L. soli DCY21 ^T were 88.8 and 36.5%, respectively. Based on genomic, chemotaxonomic, phenotypic and phylogenetic data, strain 5-21a ^T represents a novel species in the genus Lysobacter , for which the name Lyobacter auxotrophicus sp. nov. is proposed. The type strain is 5-21a ^T (=NBRC 115507 ^T =LMG 32660 ^T ).