Horizontal gene transfer and recombination shape mesorhizobial populations in the gene center of the host plantsAstragalus luteolusandAstragalus ernestiiin Sichuan, China

Diverse Mesorhizobium bacteria nodulate native Astragalus and Oxytropis in arctic and subarctic areas in Eurasia

Rhizobia nodulating native Astragalus and Oxytropis spp. in Northern Europe are not well-studied. In this study, we isolated bacteria from nodules of four Astragalus spp. and two Oxytropis spp. from the arctic and subarctic regions of Sweden and Russia. The phylogenetic analyses were performed by using sequences of three housekeeping genes (16S rRNA, rpoB and recA) and two accessory genes (nodC and nifH). The results of our multilocus sequence analysis (MLSA) of the three housekeeping genes tree showed that all the 13 isolates belonged to the genus Mesorhizobium and were positioned in six clades. Our concatenated housekeeping gene tree also suggested that the isolates nodulating Astragalus inopinatus, Astragalus frigidus, Astragalus alpinus ssp. alpinus and Oxytropis revoluta might be designated as four new Mesorhizobium species. The 13 isolates were grouped in three clades in the nodC and nifH trees. ¹⁵N analysis suggested that the legumes in association with these isolates were actively fixing nitrogen.

Genetic diversity and distribution of rhizobia associated with the medicinal legumes Astragalus spp. and Hedysarum polybotrys in agricultural soils

With the increasing cultivation of medicinal legumes in agricultural fields, the rhizobia associated with these plants are facing new stresses, mainly from fertilization and irrigation. In this study, investigations on the nodulation of three cultivated medicinal legumes, Astragalus mongholicus, Astragalus membranaceus and Hedysarum polybotrys were performed. Bacterial isolates from root nodules of these legumes were subjected to genetic diversity and multilocus sequence analyses. In addition, the distribution of nodule bacteria related to soil factors and host plants was studied. A total 367 bacterial isolates were obtained and 13 genospecies were identified. The predominant microsymbionts were identified as Mesorhizobium septentrionale, Mesorhizobium temperatum, Mesorhizobium tianshanense, Mesorhizobium ciceri and Mesorhizobium muleiense. M. septentrionale was found in most root nodules especially from legumes grown in the barren soils (with low available nitrogen and low organic carbon contents), while M. temperatum was predominant in nodules where the plants were grown in the nitrogen-rich fields. A. mongholicus tended to be associated with M. septentrionale, M. temperatum and M. ciceri in different soils, while A. membranaceus and H. polybotrys tended to be associated with M. tianshanense and M. septentrionale, respectively. This study showed that soil fertility may be the main determinant for the distribution of rhizobia associated with these cultured legume plants.

Diversity and phylogeny of rhizobia associated with Desmodium spp. in Panxi, Sichuan, China

Thirty-four rhizobial isolates were obtained from root nodules of four wild Desmodium species growing in Panxi, Sichuan, China. According to the combined ARDRA and IGS-RFLP (CACAI) cluster analysis, Rhizobium, Pararhizobium and Mesorhizobium isolates outnumbered Bradyrhizobium isolates. In general, the isolates representing the same species from the same site clustered together. Furthermore, the four Desmodium species were all nodulated by more than one rhizobial species. AFLP and phenotypic analyses showed that the 34 isolates represented at least 32 distinct strains. None of the strains were found from more than one site or host, indicating a high degree of rhizobial diversity in Panxi. In the multilocus sequence analysis, the isolates were assigned to Pararhizobium giardinii, Bradyrhizobium japonicum, Mesorhizobium septentrionale, and to undescribed species of the genera Rhizobium, Bradyrhizobium and Agrobacterium.

Recombination and horizontal transfer of nodulation and ACC deaminase (acdS) genes within Alpha- and Betaproteobacteria nodulating legumes of the Cape Fynbos biome

The goal of this work is to study the evolution and the degree of horizontal gene transfer (HGT) within rhizobial genera of both Alphaproteobacteria (Mesorhizobium, Rhizobium) and Betaproteobacteria (Burkholderia), originating from South African Fynbos legumes. By using a phylogenetic approach and comparing multiple chromosomal and symbiosis genes, we revealed conclusive evidence of high degrees of horizontal transfer of nodulation genes among closely related species of both groups of rhizobia, but also among species with distant genetic backgrounds (Rhizobium and Mesorhizobium), underscoring the importance of lateral transfer of symbiosis traits as an important evolutionary force among rhizobia of the Cape Fynbos biome. The extensive exchange of symbiosis genes in the Fynbos is in contrast with a lack of significant events of HGT among Burkholderia symbionts from the South American Cerrado and Caatinga biome. Furthermore, homologous recombination among selected housekeeping genes had a substantial impact on sequence evolution within Burkholderia and Mesorhizobium. Finally, phylogenetic analyses of the non-symbiosis acdS gene in Mesorhizobium, a gene often located on symbiosis islands, revealed distinct relationships compared to the chromosomal and symbiosis genes, suggesting a different evolutionary history and independent events of gene transfer. The observed events of HGT and incongruence between different genes necessitate caution in interpreting topologies from individual data types.

Diverse nodule bacteria were associated with Astragalus species in arid region of northwestern China

The legume species of Astragalus as traditional Chinese medicine source and environmental protection plants showed an extensive distribution in the arid region of northwestern China. However, few rhizobia associating with Astragalus have been investigated in this region so far. In this study, 78 endophytic bacteria were isolated from root nodules of 12 Astragalus species and characterized by the PCR-RFLP of 16S rRNA gene and symbiotic genes together with the phylogenetic analysis. Results showed that the majority (53%) of isolates are non-nodulating Agrobacterium sp. and the rest are Mesorhizobium genomic species (41%), Ensifer spp. and Rhizobium gallicum (6%), respectively. Mesorhizobium genomic species are broadly distributed in the Astragalus symbioses and most of them share similar symbiotic genes. It seems that horizontal gene transfer occurred frequently among different genomic species independent of their original hosts and sites. Astragalus adsurgens is nodulated by a widely range of rhizobial species in the nodulation test, revealing that it could play an important role in diversification of Astragalus symbionts and that might be a reason for its wide adaptation to diverse environments.

Mesorhizobium sangaii sp. nov., isolated from the root nodules of Astragalus luteolus and Astragalus ernestii

Our previous published data indicated that the two rhizobial strains SCAU7T and SCAU27, which were isolated from the root nodules of Astragalus luteolus and Astragalus ernestii respectively, in Sichuan Province, China, might be novel species of the genus Mesorhizobium . Their exact taxonomic position was determined in the present study by using polyphasic approaches. Comparative analysis of nearly full-length 16S rRNA gene sequences showed that these strains belonged to the genus Mesorhizobium , with Mesorhizobium ciceri USDA 3383T, Mesorhizobium loti NZP 2213T, Mesorhizobium shangrilense CCBAU 65327T and Mesorhizobium australicum WSM2073T as the closest neighbours (>99 % 16S rRNA gene sequence similarity). Phylogenies of the housekeeping genes atpD and recA confirmed their distinct position, showing low similarity with respect to those of M. loti LMG 6125T (96.5 % and 92.3 % similarity respectively), M. ciceri USDA 3383T (96.8 % and 93.3 % similarity, respectively), M. shangrilense CCBAU 65327T (96.5 % and 92.7 % similarity, respectively) and M. australicum WSM2073T (95.4 % and 90.6 % similarity, respectively). The DNA–DNA relatedness values between strain SCAU7T and strain SCAU27 were 83.0 %, showing that they belong to the same species. The DNA–DNA relatedness values of SCAU7T with M. loti NZP 2213T, M. ciceri USDA 3383T and M. shangrilense CCBAU 65327T were 41.1 %, 48.8 % and 23.4 %, respectively, clearly indicating that strain SCAU7T represents a novel species. A series of phenotypic and genotypic tests and comparison of cellular fatty acids indicated that the novel group of isolates was distinct from previously described species. Therefore, we propose that strains SCAU7T and SCAU27 represent a novel species of the genus Mesorhizobium , Mesorhizobium sangaii sp. nov., with strain SCAU7T ( = HAMBI 3318T = ACCC 13218T) as the type strain.

Polyphasic characterization of rhizobia isolated from Leucaena leucocephala from Panxi, China

Leucaena leucocephala was introduced into Panxi, Sichuan, China, in the 1980s and 1990s for afforestation and preventing water loss and soil erosion in this area. The co-introduction of rhizobial symbionts of introduced plants has drawn attention since they may influence local soil communities. We studied the phylogenetic position of the L. leucocephala isolates and assessed if the rhizobia were introduced together with the host to Panxi, Sichuan, China. The glnII and atpD genes of fifteen representative isolates were sequenced and analyzed, and applied multilocus sequence analyses in which the housekeeping genes recA, glnII and atpD were included. Furthermore, we estimated the within species diversity directly with 23S rDNA and IGS RFLP and indirectly through phenotypic analysis of forty L. leucocephala isolates. The isolates represented seven species and 38 diversified strains in the genera Ensifer, Mesorhizobium, Bradyrhizobium and Rhizobium. The within species diversity of the Ensifer isolates was large, proposing a potential to occupy novel niches. There was not conclusive evidence to show that any of the strains would have been co-introduced with L. leucocephala. On the contrary, we came to a conclusion that the possible introduction should not be inferred from sequence data alone.

Diversity of endophytic bacteria within nodules of the Sphaerophysa salsula in different regions of Loess Plateau in China

A total of 115 endophytic bacteria were isolated from root nodules of the wild legume Sphaerophysa salsula grown in two ecological regions of Loess Plateau in China. The genetic diversity and phylogeny of the strains were revealed by restriction fragment length polymorphism and sequencing of 16S rRNA gene and enterobacterial repetitive intergenic consensus-PCR. Their symbiotic capacity was checked by nodulation tests and analysis of nifH gene sequence. This is the first systematic study on endophytic bacteria associated with S. salsula root nodules. Fifty of the strains found were symbiotic bacteria belonging to eight putative species in the genera Mesorhizobium, Rhizobium and Sinorhizobium, harboring similar nifH genes; Mesorhizobium gobiense was the main group and 65 strains were nonsymbiotic bacteria related to 17 species in the genera Paracoccus, Sphingomonas, Inquilinus, Pseudomonas, Serratia, Mycobacterium, Nocardia, Streptomyces, Paenibacillus, Brevibacillus, Staphylococcus, Lysinibacillus and Bacillus, which were universally coexistent with symbiotic bacteria in the nodules. Differing from other similar studies, the present study is the first time that symbiotic and nonsymbiotic bacteria have been simultaneously isolated from the same root nodules, offering the possibility to accurately reveal the correlation between these two kinds of bacteria. These results provide valuable information about the interactions among the symbiotic bacteria, nonsymbiotic bacteria and their habitats.