Search

Background and aims: Seed associated microbial communities are an important part of the plant microbiota. However, for legumes, seed microbiota and their life cycle including colonization and vertical transmission to nodule remain largely unknown. Here we explored the sources of seed microbes and tested the hypothesis that the plant microbiota is partially inherited through vertical transmission. Methods: Nodules, rhizosphere soil and seeds were collected from Sophora davidii grown in fields, and from inoculation test with fermentation broth of nodule endophytes. Additionally, structure of seed microbial communities and vertical transmission of seed microbes across one plant generations were assessed through amplicon sequencing of bacterial 16S rRNA gene. Results: A total of 4074 endophytic OTUs were detected from S. davidii seeds, in which 233 shared with rhizosphere and nodules were defined as core microbiota of this plant, including various rhizobia. The core microbiota of S. davidii seeds was vertically transmitted to the nodules of upcoming generation of plants. Moreover, Firmicutes was the dominant phylum in S. davidii seeds. Notably, the dominant bacteria changed from Mesorhizobium in the field nodules to Sinorhizobium in the passage nodules in pot culture with inoculation. Conclusions: Diverse microbial community habited in S. davidii seeds, including various rhizobia. The core microbiota could be transmitted from seeds to nodules, including the rhizobial endophytes, which made S. davidii plants potential to nodulated with distinct rhizobia in different environments, as revealed by the changed of dominant genus from Mesorhizobium to Sinorhizobium in an artificial condition. This study gives empirical evidence for the source, colonization and vertical transmission routes of S. davidii seed bacterial communities. [ABSTRACT FROM AUTHOR] more...

Aims: To estimate the relative abundance, diversity and distribution of rhizobia associated with Vicia villosa Roth in soils of Northwest China. Method: Rhizobia were trapped with V. villosa Roth plants from soils at seven sites and identified into genotypes by PCR-RFLP of IGS genes. They were further characterized by phylogenetic analyses of 16S rRNA, housekeeping genes (atpD, recA, glnII) and symbiotic genes (nodC). Soil physicochemical characteristics were recorded and Canonical Correlation Analysis was performed to correlate soil features and the distribution of IGS genotypes. Results: 253 rhizobial strains were obtained from soils with pH 7.1–7.9. They were discriminated into 27 IGS types and further affiliated by phylogenetic analyses of 16S rRNA and multilocus sequence analysis (MLSA) into two clusters in Rhizobium. One corresponds to Rhizobium sophorae covering 228 strains in 25 IGS types and the other includes a novel genospecies containing two IGS types only detected in Shanxi Province, with higher soil pH and intermediate available phosphate and potassium contents. Representative strains of the novel genospecies show a specific phylogenetic nodC lineage, which may reflect differences in symbiosis properties. Furthermore, the Shanxi site was the less IGS diversified, based on Shannon diversity indices varying from 0.96 to 2.19 along the sampled area. Conclusions: As the first study on diversity of rhizobia nodulating V. villosa Roth in China, R. sophorae and a novel Rhizobium genospecies with specific symbiotic genes were identified; and biogeographic patterns were found, mainly directed by soil pH, organic matter and soil salinity, including available phosphorus salts. [ABSTRACT FROM AUTHOR] more...

Aims: This study investigated the role of long-distance signaling in the compositional response of Phaseolus vulgaris rhizomicrobiome to a changing soil environment. Methods: P. vulgaris seedlings were grown in Jiangxi and Shaanxi soils under two different planting patterns, 'Mix' (P. vulgaris planted with split roots in two types of soil simultaneously) and 'Double' (P. vulgaris planted with split roots in double pots supplied with the same type of soil type). The rhizomicrobiomes were analyzed by high-throughput sequencing of the bacterial 16S rRNA gene and fungal internal transcribed spacer region. Results: There were significant differences in the biotic and abiotic properties between two kinds of soil. The alpha- and beta-diversity of the rhizomicrobiomes were significantly influenced by soil type and planting pattern. Soil type explained the majority of the variation in the rhizomicrobiome composition. The compositional difference between the Jiangxi and Shaanxi rhizomicrobiomes was significantly reduced in the 'Mix' treatment compared with the 'Double' treatment. Conclusions: In split-root experiment, the separated roots shared a common aerial part and communicated via long-distance signaling pathways. Hence, this study demonstrated that the long-distance signaling pathways in P. vulgaris regulated and harmonized the rhizomicrobiome composition as the roots sensed two different soil environments. [ABSTRACT FROM AUTHOR] more...

Aims: To identify the rhizobia nodulating Vicia sativa in Northwestern China and to estimate their geographic distribution. Methods: Rhizobia trapped with V. sativa plants from soils at six sites in the northwest of China were classified into genotypes by PCR-based restriction fragment length polymorphism (RFLP) of 16S–23S rRNA intergenic spacer (IGS) and 16S rRNA genes, and phylogenetic analyses of housekeeping (16S rRNA, recA, atpD) and symbiotic genes were performed for the representative strains. Soil physicochemical characteristics were recorded and canonical correlation analysis was performed to examine the correlations between soil features and distribution of rhizobial genotypes. Results: A total of 202 rhizobial isolates were discriminated by RFLP analyses into 15 IGS types and a single 16S rRNA type, which were identified as Rhizobium by 16S rRNA gene phylogeny and as four clusters by multilocus sequence analysis (MLSA). Cluster 1 covering 86 strains and 7 IGS types prevalent in all sites was identified as Rhizobium laguerreae; cluster 2 was R. sophorae with 18 strains in 2 IGS types found in the site Q-GD. Each of cluster 3 and cluster 4 contained three IGS types representing two novel Rhizobium genospecies specific to Gansu Province and Shanxi Province, respectively. Four nodC phylogenetic clades were defined among the isolates. Conclusions: R. sophorae, R. laguerreae, and two novel Rhizobium genospecies with diverse symbiotic genotypes are associated with Vicia sativa L. in Northwest China. Their biogeographic patterns are mainly directed by soil pH and salinity. This is the first study on the diversity of rhizobia nodulating Vicia sativa in China. [ABSTRACT FROM AUTHOR] more...

Aims: To identify the rhizobia nodulating Astragalus sinicus in the acid soils at Xinyang, China and to estimate the effects of fertilization strategies on the rhizobial community.Methods: Soil samples were collected from treatments submitted to different fertilization strategies (chemical fertilizers, A. sinicus green manure, various input levels). Nodules obtained from the A. sinicus trapping plants grown in the soil samples were used for rhizobial isolation. The isolates were grouped into PCR-RFLP genotypes based on analyses of 16S rRNA gene and IGS, and representatives for each genotype were further subjected to phylogenetic analyses of housekeeping genes (16S rRNA gene, atpD, glnII, and rpoB), as well as symbiotic genes (nodC and nifH). Soil physicochemical characteristics were also estimated and redundancy analysis was performed to examine the relations between soil features and distribution of rhizobial genotypes across different fertilization treatments.Results: A total of 257 rhizobial isolates were obtained and discriminated into 12 IGS types in a single 16S rRNA type by RFLP analyses. Further 16S rRNA gene sequence-based phylogeny and multilocus sequence analysis (MLSA) distinguished a minor group (10 strains, 4 IGS types) affiliated to Mesorhizobium huakuii and a main group (247 strains, 8 IGS types) to Mesorhizobium jarvisii, for which a novel symbiovar, sv. astragali, was described. The long-term input of A. sinicus green manure increased rhizobial diversity and modified rhizobial community structures, via the increase of organic matter and decrease of soil pH, available phosphate, available potassium, and total salt.Conclusions: M. jarvisii sv. nov. astragali was the predominant microsymbiont of A. sinicus in the tested acidic soils. The long-term input of green manure modified the soil features, enhancing the genetic diversity of rhizobia associated with A. sinicus and alternating the rhizobial community structure. [ABSTRACT FROM AUTHOR] more...

Aims: To describe the chickpea rhizobial diversity in Gansu Province of China, so far uninvestigated. Methods: Nodule bacteria were isolated from chickpea grown in Gansu and characterized by phylogenetic analysis of 16S rRNA gene, housekeeping genes ( atpD, recA, and glnII), and symbiotic genes ( nodC and nifH). The genetic differentiation and gene flow among the chickpea microsymbionts were estimated and considered in view of soil characteristics. Results: A total of nineteen new isolates originating from alkaline-saline (pH 7.9-8.1) soils in Gansu formed two clades by housekeeping gene analyses; clade I (16 isolates) was identified as Mesorhizobium muleiense (97.7-98.7 % of similarities with the type strain CCBAU 83963) and clade II (3 isolates) formed a separate group within Mesorhizobium branch, displaying 97.0 and 96.6 % similarities with the most related type strains M. temperatum SDW 018 and M. muleiense CCBAU 83963, respectively. Their symbiotic genes ( nodC and nifH) were highly similar (>98.0 %) with those described for chickpea microsymbionts in literature, i.e., M. muleiense, M. ciceri, and M. mediterraneum. The genetic differentiation and gene flow between the chickpea rhizobial groups supported our conclusions for species affiliation. Conclusions: M. muleiense and a novel Mesorhizobium genospecies, sharing similar symbiotic genes, are distributed in the alkaline-saline soils of Gansu and may be considered as the main and specific chickpea symbionts in the Northwest of China. [ABSTRACT FROM AUTHOR] more...