Silvimonas terrae gen. nov., sp. nov., a novel chitin-degrading facultative anaerobe belonging to the ‘Betaproteobacteria’

Abstract

Silvimonas terrae gen. nov., sp. nov., a novel chitindegrading facultative anaerobe belonging to the 'Betaproteobacteria' During the course of a study on the culturable aerobic and facultatively anaerobic bacterial community of forest soil and rice fields near Daejeon, South Korea, a large number of novel bacterial strains were isolated. One of these isolates, strain KM-45 T , was identified as belonging to the family Neisseriaceae in the 'Betaproteobacteria' lineage and was the subject of further taxonomic investigation. We report on its taxonomic position, including genotypic, chemotaxonomic and classical phenotypic characteristics, in order to establish its phylogenetic affiliation, and propose that strain KM-45 T should be placed in a novel genus and species, for which the name Silvimonas terrae gen. nov., sp. nov. is proposed. Strain KM-45T was isolated from forest soil collected near the Korea Advanced Institute of Science and Technology (KAIST) in Daejeon, South Korea. The soil was homogenized by using an Ace Homogenizer (Nihonseiki Kaisha Ltd). The suspension was spread on R2A agar plates (Difco) after being diluted serially with 50 mM phosphate buffer (pH 7?0). The plates were incubated at 30 u C for 2 weeks. Single colonies on the plates were purified by transferring them onto new plates and incubating again under the same conditions. The isolate was cultured routinely on R2A agar at 30 uC and maintained as a glycerol suspension (20 %, w/v) at 270 u C.Extraction of genomic DNA was performed by using a commercial genomic DNA extraction kit (Core Biosystem), and PCR-mediated amplification of the 16S rRNA gene and sequencing of the purified PCR product were carried out according to the methods given by Kim et al. (2005). The full-length 16S rRNA gene sequences were compiled by using SeqMan software (DNASTAR). 16S rRNA gene sequences of related taxa were obtained from GenBank. Multiple alignments were performed by using the CLUSTAL_X program (Thompson et al., 1997). Gaps were edited in the BIOEDIT program (Hall, 1999). Evolutionary distances were calculated by using the Kimura twoparameter model (Kimura, 1983). Phylogenetic trees were constructed by using the neighbour-joining (Saitou & Nei, 1987) and maximum-parsimony (Fitch, 1971) methods, using the MEGA3 program (Kumar et al., 2004) with bootstrap values based on 1000 replications (Felsenstein, 1985).A nearly complete 16S rRNA gene sequence of strain T was obtained (1491 bp). Preliminary comparison against the 16S rRNA gene sequences in GenBank indicated that strain T belonged to the order 'Neisseriales' of the 'Betaproteobacteria'. On the basis of 16S rRNA geneThe GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain T is AB194302.

Chitiniphilus shinanonensis gen. nov., sp. nov., a novel chitin-degrading bacterium belonging to Betaproteobacteria

“…T (Yang et al, 2005), Andreprevotia chitinolytica JS11-7 T (Weon et al, 2007), Chitinibacter tainanensis BCRC17254 T (Chern et al, 2004), Deefgea rivuli WB3.4-79 T (Stackebrandt et al, 2007), and Iodobacter fl uviatilis ATCC33051 T (Logan, 1989). The closest genus, Formivibrio citricus DSM6150 T (93.8% identity) is distant enough to warrant placing the strain SAY3 T in a new genus.…”

Silvimonas iriomotensis sp. nov. and Silvimonas amylolytica sp. nov., new members of the class Betaproteobacteria isolated from the subtropical zone in Japan

“…Both strains ir6-1 T and ir6-4 T formed convex colonies, as described for the genus Silvimonas by Yang et al (2005). Cellular morphology was observed under light and transmission electron microscopes.…”

“…The emended description is based on data from Yang et al (2005) and this study. Cells are Gram-negative, rod-shaped (0.8-2.0 mm by 0.3-0.8 mm) and facultatively anaerobic.…”

“…Cells are Gram-stain-negative, facultatively anaerobic, motile rods that are 0.8-1.3 mm long and 0.4-0.5 mm (Yang et al, 2005). DData from Yang et al (2005).…”

“…Two isolates were phylogenetically related to the genus Silvimonas in the class Betaproteobacteria. The genus Silvimonas belongs to the family Neisseriaceae and accommodates only one species, Silvimonas terrae, until now (Yang et al, 2005). S. terrae was isolated from forest soil in Korea in 2005 and is a Gram-negative, rod-shaped and facultatively anaerobic bacterium.…”