Rhizobium vignae sp. nov., a symbiotic bacterium isolated from multiple legume species

Abstract

A group of rhizobial strains isolated from nodules of multiple legume species grown in different geographical regions of China had identical 16S rRNA genes. Phylogenetic analysis based on the 16S rRNA gene sequences showed that the novel strains formed a subclade in the genus Rhizobium together with Rhizobium galegae, Rhizobium huautlense and Rhizobium alkalisoli, with 99.8 % gene sequence similarity between the strains. The DNA-DNA relatedness values between the representative strain CCBAU 05176 T and R. galegae ATCC 43677 T , R. huautlense S02 T and R. alkalisoli CCBAU 01393 T were 22.6 %, 8.9 % and 15.9 %, respectively. The novel strains were distinguished from recognized species of the genus Rhizobium by using a polyphasic approach, including PCR-based restriction fragment length polymorphism analysis (RFLP) of the 16S-23S intergenic spacer (IGS), phenotypic and physiological tests, sequence comparisons of housekeeping genes and cellular fatty acid profiles. Therefore, it is suggested that this group of strains represents a novel species for which the name Rhizobium vignae sp. nov. is proposed. The type strain is CCBAU 05176 T (5HAMBI 3039 T 5LMG 25447 T ).Rhizobia are Gram-negative rod-shaped bacteria that induce the formation of nodules on the roots or stems of leguminous plants. Within the nodules, they convert atmospheric nitrogen to ammonia and then provide organic nitrogenous compounds such as glutamine or ureides to the plant. In the past two decades, the description of novel taxa of root-and stem-nodule bacteria has been accelerated by the adoption of a polyphasic taxonomic approach (Vandamme et al., 1996) to characterize new isolates from various leguminous plants. The genus Rhizobium, proposed for a group of fast-growing, nodule-forming rhizobia, was firstly described by Frank (1889) and at the time of writing contained 34 species, including the recently described species In previous studies, seven strains of root-nodule bacteria isolated from Vigna radiata (Zhang et al., 2006), Astragalus dahuricus, Astragalus oxyglottis (Zhao et al., 2008) and Desmodium microphyllum (Gu et al., 2007) grown in different regions of China were classified into the genus Rhizobium and were demonstrated to be closely related to Rhizobium galegae by using amplified rDNA restriction analysis (ARDRA). The nodulation ability of the strains on their hosts of origin was confirmed in each of the previous studies. In the present study, the taxonomic status of these strains was clarified by analysis of the 16S-23S rRNA intergenic spacer (IGS-RFLP) and housekeeping gene (atpD, recA and glnII) sequences, cellular fatty acid profiles, DNA-DNA relatedness and the determination of phenotypic characteristics.Seven novel strains (Table 1) and the reference strains were purified and cultured using a standard procedure on yeast mannitol agar (YMA) medium (Vincent, 1970). They were maintained on YMA at 4 u C for temporary storage and in 20 % (w/v) glycerol at 280 u C for long-term storage.Total DNA from each strain was prepared as descri...

Host-dependent symbiotic efficiency of Rhizobium leguminosarum bv. trifolii strains isolated from nodules of Trifolium rubens

“…trifolii WSM2304. Strain Trb30 was most closely related to R. vignae CCBAU05176 T and N. galegae LMG6214 T with 97 and 96% similarity, respectively (Ren et al 2011 ; Österman et al 2015 ). Rhizobium sp.…”

Rhizobium tarimense sp. nov., isolated from soil in the ancient Khiyik River

“…The first description of the genus Rhizobium as root and/or stem-nodule bacteria, was from Frank (1889). Currently, this genus is an evolutionary lineage within the family Rhizobiaceae of the Alphaproteobacteria (Lee et al , 2005), and contains more than 50 species at the time of writing including the latest described species: Rhizobium soli (Yoon et al , 2010), Rhizobium vignae (Ren et al , 2011) and Rhizobium vallis (Wang et al , 2011). Members of the genus Rhizobium have generally been isolated from nodules in leguminous plants (Peng et al , 2008; Wei et al , 2003).…”

IS‐pro: high‐throughput molecular fingerprinting of the intestinal microbiota

“…Here, we present IS-pro, a novel 16S-23S rDNA interspace (IS)-region-based profiling method. We have chosen the IS region above the 16S region, as the 16S sequence, despite having hypervariable and extremely informative regions, shows little variation in length and is sometimes not divergent enough to give good separation in close relationships, e.g., species of the same genus (11)(12)(13)(14). The 16S-23S rDNA IS region, in contrast, is extremely variable in size and sequence, even within closely related taxonomic groups (15), making it more suitable for analysis of complex communities.…”