title: Genomic identification of nitrogen-fixing Klebsiella variicola, K. pneumoniae and K. quasipneumoniae.
abstract: It was difficult to differentiate Klebsiella pneumoniae, K. quasipneumoniae and K. variicola by biochemical and phenotypic tests. Genomics increase the resolution and credibility of taxonomy for closely-related species. Here, we obtained the complete genome sequence of the K. variicola type strain DSM 15968(T) (=F2R9(T)). The genome of the type strain is a circular chromosome of 5,521,203 bp with 57.56% GC content. From 540 Klebsiella strains whose genomes had been publicly available as at 3 March 2015, we identified 21 strains belonging to K. variicola and 8 strains belonging to K. quasipneumoniae based on the genome average nucleotide identities (ANI). All the K. variicola strains, one K. pneumoniae strain and five K. quasipneumoniae strains contained nitrogen-fixing genes. A phylogenomic analysis showed clear species demarcations for these nitrogen-fixing bacteria. In accordance with the key biochemical characteristics of K. variicola, the idnO gene encoding 5-keto-D-gluconate 5-reductase for utilization of 5-keto-D-gluconate and the sorCDFBAME operon for catabolism of L-sorbose were present whereas the rbtRDKT operon for catabolism of adonitol was absent in the genomes of K. variicola strains. Therefore, the genomic analyses supported the ANI-based species delineation; the genome sequence of the K. variicola type strain provides the reference genome for genomic identification of K. variicola, which is a nitrogen-fixing species.
authors.affiliation: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
authors.forename: Mingyue
authors.initials: M
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
authors.forename: Yuanyuan
authors.initials: Y
authors.lastname: Li
authors.affiliation: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
authors.forename: Shuying
authors.initials: S
authors.lastname: Li
authors.affiliation: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
authors.forename: Lie
authors.initials: L
authors.lastname: Tang
authors.affiliation: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
authors.forename: Jingwu
authors.initials: J
authors.lastname: Zheng
authors.affiliation: State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
authors.forename: Qianli
authors.initials: Q
authors.lastname: An
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D001483:Base Sequence; D002874:Chromosome Mapping; D004269:DNA, Bacterial / Q000235:genetics; D016680:Genome, Bacterial; D005942:Gluconates / Q000378:metabolism; D007709:Klebsiella / Q000235:genetics* / Q000378:metabolism*; D007711:Klebsiella pneumoniae / Q000235:genetics / Q000378:metabolism; D009584:Nitrogen / Q000378:metabolism; D009586:Nitrogen Fixation; D009591:Nitrogenase / Q000235:genetics / Q000378:metabolism; D009876:Operon; D010088:Oxidoreductases / Q000235:genetics; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D005942:Gluconates; D010088:Oxidoreductases; C093584:gluconate 5-dehydrogenase; D009591:Nitrogenase; D009584:Nitrogen; C030691:gluconic acid
keywords: Average nucleotide identity; Klebsiella pneumoniae; Klebsiella quasipneumoniae; Klebsiella variicola; Nitrogen fixation