Rhizobium sophorae sp. nov. and Rhizobium sophoriradicis sp. nov., nitrogen-fixing rhizobial symbionts of the medicinal legume Sophora flavescens

Abstract

Five bacterial strains representing 45 isolates originated from root nodules of the medicinal legume Sophora flavescens were defined as two novel groups in the genus Rhizobium based on their phylogenetic relationships estimated from 16S rRNA genes and the housekeeping genes recA, glnII and atpD. These groups were distantly related to Rhizobium leguminosarum USDA 2370 T (95.6 % similarity for group I) and Rhizobium phaseoli ATCC 14482 T (93.4 % similarity for group II) in multilocus sequence analysis. In DNA-DNA hybridization experiments, the reference strains CCBAU 03386 T (group I) and CCBAU 03470 T (group II) showed levels of relatedness of 17.9-57.8 and 11.0-42.9 %, respectively, with the type strains of related species. Both strains CCBAU 03386 T and CCBAU 03470 T contained ubiquinone 10 (Q-10) as the major respiratory quinone and possessed 16 : 0, 18 : 0, 19 : 0 cyclo v8c, summed feature 8 and summed feature 2 as major fatty acids, but did not contain 20 : 3 v6,8,12c. Phenotypic features distinguishing both groups from all closely related species of the genus Rhizobium were found. Therefore, two novel species, Rhizobium sophorae sp. nov. for group I (type strain CCBAU 03386 T 5E5 T 5LMG 27901 T 5HAMBI 3615 T) and Rhizobium sophoriradicis sp. nov. for group II (type strain CCBAU 03470 T 5C-5-1 T 5LMG 27898 T 5HAMBI 3510 T), are proposed. Both groups were able to nodulate Phaseolus vulgaris and their hosts of origin (Sophora flavescens) effectively and their nodulation gene nodC was phylogenetically located in the symbiovar phaseoli. Rhizobia isolated from the medicinal legume Sophora flavescens have not been surveyed previously, although the genetic diversity of rhizobia associated with another wild species in the same genus, Sophora alopecuroides, have been extensively studied. Rhizobia isolated from Sophora alopecuroides were classified into five genera and nine genospecies, with Mesorhizobium alhagi and Mesorhizobium gobiense as the main groups, and Agrobacterium tumefaciens, Mesorhizobium amorphae, Phyllobacterium trifolii, Rhizobium giardinii, Rhizobium indigoferae, Ensifer fredii (former Sinorhizobium fredii) and Ensifer meliloti (former Sinorhizobium meliloti) as the minor groups (Zhao et al., 2010). At the time of writing, 76 species have been classified and described in the genus Rhizobium (Euzéby, 1997; Parte, 2014), including recently described species

Rhizobium anhuiense sp. nov., isolated from effective nodules of Vicia faba and Pisum sativum

“…The ML tree of the 16S rRNA gene sequences (1318 nt) showed that the four isolates had identical 16S rRNA genes, which had the same sequence as those of R. leguminosarum USDA 2370 T , R. laguerreae FB206 T , Rhizobium indigoferae CCBAU 71042 T and Rhizobium sophorae CCBAU 03386 T , a novel species described recently (Jiao et al, 2015) (, Table S2). The similarities between the isolates and type strains of species of the genus Rhizobium varied from 95.6 to 100 %.…”

Cicer canariense, an endemic legume to the Canary Islands, is nodulated in mainland Spain by fast-growing strains from symbiovar trifolii phylogenetically related to Rhizobium leguminosarum

“…The analysis of the recA and atpD housekeeping genes allows the differentiation of rhizobia at the species level and they are available for most described species able to nodulate legumes to date [14,40,41]. The similarity values for the recA and atpD genes among the isolated strains ranged from 98.7% to 97.1% and 98.8% to 90.1%, respectively.…”

Brevibacterium metallicus sp. nov., an endophytic bacterium isolated from roots of Prosopis laegivata grown at the edge of a mine tailing in Mexico

“…Cell motility was assayed by development of turbidity in test tube containing semisolid TSA medium (0.4 % agar), after 2 days of incubation at 28 °C (Cowan and Steel 1965). Cell dimension and appearance were observed by using a Hitachi S-3400 scanning electron microscope (SEM), and the sample was prepared using the protocol of Jiao et al (2015). Bacterial growth was tested at 28 °C on LB agar, nutrient agar (NA), International Streptomyces Project (ISP) 1 medium (Pridham and Gottlieb 1948), ISP 4 medium (Shirling and Gottlieb 1966), Czapek's agar and ISP 5 medium (Pridham and Lyons 1961).…”