Bradyrhizobium daqingense sp. nov., isolated from soybean nodules

Abstract

Thirteen slow-growing rhizobial strains isolated from root nodules of soybean (Glycine max L.) grown in Daqing city in China were classified in the genus Bradyrhizobium based on 16S rRNA gene sequence analysis. Multilocus sequence analysis of IGS, atpD, glnII and recA genes revealed that the isolates represented a novel clade in this genus. DNA-DNA relatedness lower than 42.5 % between the representative strain CCBAU 15774 T and the type strains of the closely related species Bradyrhizobium liaoningense USDA 3622 T , Bradyrhizobium yuanmingense CCBAU 10071 T and Bradyrhizobium betae LMG 21987 T , further confirmed that this group represented a novel species. CCBAU 15774 T shared seven cellular fatty acids with the three above-mentioned species, but the fatty acids 15 : 0 iso and summed feature 5 (18 : 2v6,9c and/or 18 : 0 anteiso) were unique for this strain. The respiratory quinone in CCBAU 15774 T was ubiquinone-10 and the cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, cardiolipin and unknown aminolipid, polar lipid and phospholipid. In addition, some phenotypic features could be used to differentiate the novel group from the related species. On basis of these results, we propose the name Bradyrhizobium daqingense sp. nov., with CCBAU 15774 T (5LMG 26137 T 5HAMBI 3184 T 5CGMCC 1.10947 T ) as the type strain. The DNA G+C content of the type strain is 61.2 mol% (T m ).

Genetic Divergence of Bradyrhizobium Strains Nodulating Soybeans as Revealed by Multilocus Sequence Analysis of Genes Inside and Outside the Symbiosis Island

“…The 272 Bradyrhizobium strains used in this study (see Table S1 and Fig. S1 in the supplemental material) were previously collected from soybean nodules in four ecoregions of China (South China, Huanghuaihai, Northeast China, and Xinjiang) (2,3,6,8,10,33). These strains were grown in TY medium at 28°C.…”

“…It has been recurrently reported that Bradyrhizobium japonicum, Bradyrhizobium elkanii, Bradyrhizobium liaoningense, Bradyrhizobium yuanmingense, and Sinorhizobium fredii could nodulate soybeans (2)(3)(4)(5). Recently, Bradyrhizobium huanghuaihaiense, Bradyrhizobium daqingense, Sinorhizobium sojae, and several unnamed species were also found to be effective microsymbionts of soybeans (2,3,(6)(7)(8). Strain USDA110 represents a widely distributed type formerly known as B. japonicum Ia, but it has recently been proposed as a member of the new species Bradyrhizobium diazoefficiens (9).…”

“…In contrast to the highly conserved rrs sequences in Bradyrhizobium, sequence analyses of housekeeping genes (atpD, recA, glnII, gyrB, rpoB, dnaK, etc.) have been found to be very useful in this scenario, especially when these genes were concatenated (5,6,8,(14)(15)(16). Although the phylogeny of the concatenated housekeeping genes was usually considered to represent the species tree, these housekeeping loci showed high rates of intergenic recombination and a limited gap between interspecies and intraspecies sequence similarities (15,16).…”

Rhizobia Indigenous to the Okavango Region in Sub-Saharan Africa: Diversity, Adaptations, and Host Specificity

“…Concordantly, the Namibian bradyrhizobia were phylogenetically and physiologically more diverse, with the bulk being related to B. yuanmingense and B. daqingense. While B. daqingense was described just recently (58) and information is limited, B. yuanmingense seems to be widespread in the subtropics and tropics and was found, e.g., in China (59), India and Mexico (23), Peru (60), Botswana (61), and South Africa (10). Moreover, the Namibian isolates were very diverse even within the groups, as could be seen in the BOX-PCR fingerprinting.…”

Diversity and distribution of soybean-nodulating bradyrhizobia isolated from major soybean-growing regions in Myanmar

“…Rhizobiaare highly diverse and classified into several genera and species. The slow-growing, soybean-nodulating rhizobia are B. japonicum (Jordan, 1982), B. elkanii (Kuykendall et al, 1992), B. liaoningense (Xu et al, 1995), B. huanghuaihaiense (Zhang et al, 2012), B. daqingense (Wang et al, 2013), B. diazoefficiens (Delamuta et al, 2013) and B. ottawaense (Yu et al, 2014). The fast-growing bradyrhizobia are classified into twoSinorhizobium (Ensifer) species: S. fredii (Chen et al, 1998)and S. soyae (Li et al, 2011b).…”