Diversity and Biogeography of Rhizobia Isolated from Root Nodules of Glycine max Grown in Hebei Province, China

Liu

Chen

et al. 2011

Appl Environ Microbiol

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145

105

As the putative center of origin for soybean and the second largest region of soybean production in China, the North China Plain covers temperate and subtropical regions with diverse soil characteristics. However, the soybean rhizobia in this plain have not been sufficiently studied. To investigate the biodiversity and biogeography of soybean rhizobia in this plain, a total of 309 isolates of symbiotic bacteria from the soybean nodules collected from 16 sampling sites were studied by molecular characterization. These isolates were classified into 10 genospecies belonging to the genera Sinorhizobium and Bradyrhizobium, including four novel groups, with S. fredii (68.28%) as the dominant group. The phylogeny of symbiotic genes nodC and nifH defined four lineages among the isolates associated with Sinorhizobium fredii, Bradyrhizobium elkanii, B. japonicum, and B. yuanmingense, demonstrating the different origins of symbiotic genes and their coevolution with the chromosome. The possible lateral transfer of symbiotic genes was detected in several cases. The association between soil factors (available N, P, and K and pH) and the distribution of genospecies suggest clear biogeographic patterns: Sinorhizobium spp. were superdominant in sampling sites with alkaline-saline soils, while Bradyrhizobium spp. were more abundant in neutral soils. This study clarified the biodiversity and biogeography of soybean rhizobia in the North China Plain.

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confidence: 99%

Biodiversity and Biogeography of Rhizobia Associated with Soybean Plants Grown in the North China Plain

Liu

Chen

et al. 2011

Appl Environ Microbiol

Self Cite

145

105

“…Previously, B. japonicum, B. elkanii, B. liaoningense, B. yuanmingense, Ensifer fredii and Ensifer sojae (Han et al, 2009;Li et al, 2011a;Man et al, 2008;Wang et al, 2009;Xu et al, 1995) have been isolated from root nodules of soybean grown in different regions of China. Clear biogeographic patterns have been revealed in the soybean rhizobia and soil types seemed to be the main determinant of the biogeography of these bacteria (Han et al, 2009;Li et al, 2011b;Man et al, 2008;Zhang et al, 2011).…”

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confidence: 99%

Bradyrhizobium daqingense sp. nov., isolated from soybean nodules

Wang

International Journal of Systematic and Evolutionary Microbiology

et al. 2013

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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 ).

“…Ninety percent of their production comes from the United States, Brazil, Argentina, China, and India (FAO, 2007(FAO, to 2011. One of the key features of soybean is its ability to form symbiotic nitrogen-fixing nodules with diverse rhizobial species (2,3), implying its important role in sustainable agriculture. It has been recurrently reported that Bradyrhizobium japonicum, Bradyrhizobium elkanii, Bradyrhizobium liaoningense, Bradyrhizobium yuanmingense, and Sinorhizobium fredii could nodulate soybeans (2)(3)(4)(5).…”

mentioning

confidence: 99%

“…One of the key features of soybean is its ability to form symbiotic nitrogen-fixing nodules with diverse rhizobial species (2,3), implying its important role in sustainable agriculture. 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).…”

mentioning

confidence: 99%

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

Guo

Wang

et al. 2014

Appl Environ Microbiol

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The genus Bradyrhizobium has been considered to be a taxonomically difficult group. In this study, phylogenetics and evolutionary genetics analyses were used to investigate divergence levels among Bradyrhizobium strains nodulating soybeans in China. Eleven genospecies were identified by sequence analysis of three phylogenetic and taxonomic markers (SMc00019, thrA, and truA). This was also supported by analyses of eight genes outside the symbiosis island ("off-island" genes; SMc00019, thrA, truA, fabB, glyA, phyR, exoN, and hsfA). However, seven genes inside the symbiosis island ("island" genes; nifA, nifH, nodC, nodV, fixA, trpD, and rhcC2) showed contrasting lower levels of nucleotide diversity and recombination rates than did off-island genes. Island genes had significantly incongruent gene phylogenies compared to the species tree. Four phylogenetic clusters were observed in island genes, and the epidemic cluster IV (harbored by Bradyrhizobium japonicum, Bradyrhizobium diazoefficiens, Bradyrhizobium huanghuaihaiense, Bradyrhizobium liaoningense, Bradyrhizobium daqingense, Bradyrhizobium sp. I, Bradyrhizobium sp. III, and Bradyrhizobium sp. IV) was not found in Bradyrhizobium yuanmingense, Bradyrhizobium sp. II, or Bradyrhizobium elkanii. The gene flow level of island genes among genospecies is discussed in the context of the divergence level of off-island genes. Soybeans (Glycine max L.) were first domesticated in China and then introduced into different parts of the planet (1), now with an annual harvest area of 100 million hectares around the world (FAO, 2011). Ninety percent of their production comes from the United States, Brazil, Argentina, China, and India (FAO, 2007(FAO, to 2011. One of the key features of soybean is its ability to form symbiotic nitrogen-fixing nodules with diverse rhizobial species (2, 3), implying its important role in sustainable agriculture. It has been recurrently reported that Bradyrhizobium japonicum, Bradyrhizobium elkanii, Bradyrhizobium liaoningense, Bradyrhizobium yuanmingense, and Sinorhizobium fredii could nodulate soybeans (2-5). Recently, Bradyrhizobium huanghuaihaiense, Bradyrhizobium daqingense, Sinorhizobium sojae, and several unnamed species were also found to be effective microsymbionts of soybeans (2, 3, 6-8). 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).Recent studies not only suggested differences in the biogeographic distribution of rhizobial species nodulating soybeans but also demonstrated a biased selection of rhizobial species by different genotypes of soybeans (2,4,10,11). Consistent with these findings, comparative genomics of rhizobia revealed that the phyletic distribution of rhizobial functional genes involved in environmental adaptations and symbiotic interactions generally agrees with the phylogeny of rhizobial species (7). Therefore, it is important to distinguish different rhizobial species and even subdivis...