Characterization of two aerobic ultramicrobacteria isolated from urban soil and a description of Oxalicibacterium solurbis sp. nov

• Published in: FEMS microbiology letters Vol. 307; no. 1; pp. 25 - 29
• Main Authors: Sahin, Nurettin, Gonzalez, Juan M, Iizuka, Takashi, Hill, Janet E
• Format: Journal Article
• Language: English
• Published: Oxford, UK Oxford, UK : Blackwell Publishing Ltd 01-06-2010; Blackwell Publishing Ltd; Oxford University Press
• Subjects: Bacterial Proteins - genetics; Bacterial Typing Techniques; Biochemical tests; Cluster Analysis; Deoxyribonucleic acid; Differentiation; DNA; DNA, Bacterial - chemistry; DNA, Bacterial - genetics; DNA, Ribosomal - chemistry; DNA, Ribosomal - genetics; Fatty acids; Fatty Acids - analysis; Gene sequencing; Herminiimonas; Hybridization; Microbiology; Molecular Chaperones - genetics; Molecular Sequence Data; New species; Nucleic Acid Hybridization; Nucleotide sequence; Nucleotides; Oxalicibacterium solurbis; Oxalobacteraceae; Oxalobacteraceae - classification; Oxalobacteraceae - genetics; Oxalobacteraceae - isolation & purification; Oxalobacteraceae - physiology; Phylogeny; Physiology; RNA, Ribosomal, 16S - genetics; rRNA 16S; Sequence Analysis, DNA; Soil Microbiology; Soils; Strains (organisms); ultramicrobacteria; ultramicrobacteria
• ISSN: 0378-1097; 1574-6968
• DOI: 10.1111/j.1574-6968.2010.01954.x

Two strains of aerobic, non-spore-forming, Gram-negative, rod-shaped bacteria (ND5 and MY14T), previously isolated from urban soil using the membrane-filter enrichment technique, were characterized. Analysis of their 16S rRNA gene sequence grouped strains ND5 and MY14T within the family Oxalobacteraceae (Betaproteobacteria). The highest pairwise sequence similarities for strain ND5 were found with members of the genus Herminiimonas, namely with Herminiimonas saxobsidens NS11T (99.8%) and Herminiimonas glaciei UMB49T (99.6%). Although some fatty acid profiles, physiological and biochemical differences exist between strain ND5 and the respective Herminiimonas-type strains, DNA-DNA hybridization experiments confirm that strain ND5 is a member of the H. glaciei genospecies. Taxonomical analyses revealed a wider range of variability within this genus than considered previously. The highest pairwise nucleotide similarity for strain MY14T was found with Oxalicibacterium flavum (96.8%). Phylogenetic analyses based on 16S rRNA and cpn60 gene sequences, DNA-DNA hybridization, fatty acid profiles, physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain MY14T from other Oxalicibacterium species representing a new species, for which the name Oxalicibacterium solurbis sp. nov. (type strain MY14T=NBRC 102665T,=CCM 7664T) is proposed.