Rhizobium tubonense sp. nov., isolated from root nodules of Oxytropis glabra

Abstract

Four rhizobial strains, designated CCBAU 85046 T , CCBAU 85051, CCBAU 85048 and CCBAU 85049, isolated from root nodules of Oxytropis glabra grown in Tibet, China, were previously defined, using amplified 16S rRNA gene restriction analysis, as a novel group within the genus Rhizobium. To clarify their taxonomic position, these strains were further analysed and compared with reference strains of related bacteria using a polyphasic approach. The 16S rRNA gene analysis showed that the four isolates formed a distinct phylogenetic lineage in the genus Rhizobium. The isolates showed highest sequence similarity (97.8 %) to Rhizobium indigoferae CCBAU 71042 T . Phenotypic and physiological tests, DNA-DNA hybridization, phylogenetic analyses of housekeeping genes recA, atpD and glnII and fatty acid profiles also indicated that these four strains constitute a novel group distinct from recognized species of the genus Rhizobium. , CCBAU 85048, CCBAU 85049 and CCBAU 85051 as a novel group belonging to the genus Rhizobium based on restriction fragment length polymorphism analysis of amplified 16S rRNA genes. To clarify the taxonomic status of this group, in the present study the four strains were further characterized and compared with reference strains by using a polyphasic approach.The four test strains and reference strains for species of the genus Rhizobium were obtained from the corresponding culture collection centres and maintained on YMA medium (Vincent, 1970) at 4 u C for temporary storage. Genomic DNA was extracted from the strains according to the protocol of Terefework et al. (2001) and was used as a template in the amplification of different genes or specific Abbreviation: IGS, intergenic spacer.The GenBank/EMBL/DDBJ accession numbers for the partial 16S rRNA, 16S-23S rRNA intergenic spacer, atpD, recA and glnII gene sequences of strain CCBAU 85046 T are EU256434, EU288745, EU288670, EU288696 and DQ985380, respectively. The GenBank/ EMBL/DDBJ accession numbers for the 16S rRNA gene sequences of strains CCBAU 85051, CCBAU 85048 and CCBAU 85049 are GU938296, GU938297 and GU938298, respectively. DNA fragments. The 16S rRNA gene of each of the four strains was amplified using primers fD1 and rD1 as described previously (Weisburg et al., 1991) and sequenced directly (van Berkum et al., 1996). The 16S rRNA gene sequences of type strains of species of the genus Rhizobium were obtained from the GenBank database. All sequences were aligned using the CLUSTAL W program in MEGA 4.0 software (Tamura et al., 2007). Phylogenetic distances were calculated according to the model of Jukes & Cantor (1969). Phylogenetic trees were reconstructed using the neighbour-joining (Saitou & Nei, 1987) and maximumlikelihood (Felsenstein, 1985) methods with bootstrap values based on 1000 replicates. The topology of the maximum-likelihood tree (not shown) was similar to that of the neighbour-joining tree (Fig. 1). In the phylogenetic tree ( Fig. 1 T , which showed sequence similarities ranging between 97.6 and 96.9 %.Since the 16S-23S intergeni...

Rhizobium lemnae sp. nov., a bacterial endophyte of Lemna aequinoctialis

“…Similarly, the phylogenetic relationship between the type strain of Rhizobium tubonense and other recognized species of the genus Rhizobium based on the 16S rRNA gene was not in accordance with those obtained from analyses of the recA, atpD and glnII genes (Zhang et al, 2011a).…”

“…For example, phylogenetic analysis of the 16S rRNA gene indicated that Rhizobium subbaraonis JC85 T was closely related to Rhizobium borbori DN316 T , whereas phylogenetic analyses of the glnA and recA genes showed that R. subbaraonis JC85 T formed a cluster with Rhizobium huautlense LMG 18254 T and Rhizobium halophytocola YC6881 T (Ramana et al , 2013). Similarly, the phylogenetic relationship between the type strain of Rhizobium tubonense and other recognized species of the genus Rhizobium based on the 16S rRNA gene was not in accordance with those obtained from analyses of the recA , atpD and glnII genes (Zhang et al , 2011a).…”

Rhizobium vallis sp. nov., isolated from nodules of three leguminous species

“…The genus Rhizobium (Frank, 1889) was the first and only rhizobial genus described for a century, before the genus Bradyrhizobium was reported (Jordan, 1982). Since then, a series of taxonomic changes have been made in the genus Rhizobium and at the time of writing it contains 47 species, including the recently described species Rhizobium soli (Yoon et al , 2010), Rhizobium borbori (Zhang et al , 2011b), Rhizobium vignae (Ren et al , 2011) and Rhizobium tubonense (Zhang et al , 2011a).…”

Rhizobium puerariae sp. nov., an endophytic bacterium from the root nodules of the medicinal plant Pueraria candollei var. candollei

“…These microbes have been isolated from various sources, with the majority being associated with fabaceous plants (Ló pez-Ló pez et al, 2012;Mnasri et al, 2014;Ren et al, 2011a, b;Rincó n-Rosales et al, 2013;Yao et al, 2012;Zhang et al, 2011b), although some are from non-fabaceous plants (Berge et al, 2009;Kittiwongwattana & Thawai, 2013Peng et al, 2008;Puławska et al, 2012;Zhang et al, 2014) and non-plant sources (Parag et al, 2013;Quan et al, 2005;Zhang et al, 2011a). At the time of writing, the genus Rhizobium comprises 70 recognized species.…”