Fulvic Acid Promotes Legume-Rhizobium Symbiosis by Stimulating Endogenous Flavonoids Synthesis and Secretion.

Fulvic acid (FA) promotes symbiosis between legumes and rhizobia. To elucidate from the aspect of symbiosis, the effects of root irrigation of water-soluble humic materials (WSHM) or foliar spraying of its highly active component, FA, on soybean root exudates and on rhizosphere microorganisms were investigated. As a result, WSHM/FA treatments significantly altered root exudate metabolite composition, and isoflavonoids were identified as key contributors in both treatments compared to the control. Increased expression of genes related to the isoflavonoid biosynthesis were validated by RT-qPCR in both treatments, which notably elevated the synthesis of symbiotic signals genistein, daidzin, coumestrol, and biochanin A. Moreover, the WSHM/FA treatments induced a change in rhizosphere microbial community, coupled with an increase in the relative abundance of rhizobia. Our findings showed that WSHM/FA promotes symbiosis by stimulating the endogenous flavonoid synthesis and leads to rhizobia accumulation in the rhizosphere. This study provides new insights into mechanisms underlying the FA-mediated promotion of symbiosis.

Soluble humic acid suppresses plant immunity and ethylene to promote soybean nodulation.

Symbiotic nitrogen fixation (SNF) is a crucial process for nitrogen geochemical cycling and plant-microbe interactions. Water-soluble humic acid (WSHM), an active component of soil humus, has been shown to promote SNF in the legume-rhizobial symbiosis, but its molecular mechanism remains largely unknown. To reveal the SNF-promoting mechanism, we conducted transcriptomic analysis on soybean treated with WSHM. Our findings revealed that up- and downregulated differentially expressed genes (DEGs) were mainly involved in plant cell-wall/membrane formation and plant defence/immunity in the early stage, while the late stage was marked by the flavonoid synthesis and ethylene biosynthetic process. Further study on representative DEGs showed that WSHM could inhibit GmBAK1d-mediated immunity and BR signalling, thereby promoting rhizobial colonisation, infection, and nodulation, while not favoring pathogenic bacteria colonisation on the host plant. Additionally, we also found that the ethylene pathway is necessary for promoting the soybean nodulation by WSHM. This study not only provides a significant advance in our understanding of the molecular mechanism of WSHM in promoting SNF, but also provides evidence of the beneficial interactions among the biostimulator, host plant, and soil microbes, which have not been previously reported.

Selective regulation of endophytic bacteria and gene expression in soybean by water-soluble humic materials.

BACKGROUND: As part of the plant microbiome, endophytic bacteria play an essential role in plant growth and resistance to stress. Water-soluble humic materials (WSHM) is widely used in sustainable agriculture as a natural and non-polluting plant growth regulator to promote the growth of plants and beneficial bacteria. However, the mechanisms of WSHM to promote plant growth and the evidence for commensal endophytic bacteria interaction with their host remain largely unknown. Here, 16S rRNA gene sequencing, transcriptomic analysis, and culture-based methods were used to reveal the underlying mechanisms. RESULTS: WSHM reduced the alpha diversity of soybean endophytic bacteria, but increased the bacterial interactions and further selectively enriched the potentially beneficial bacteria. Meanwhile, WSHM regulated the expression of various genes related to the MAPK signaling pathway, plant-pathogen interaction, hormone signal transduction, and synthetic pathways in soybean root. Omics integration analysis showed that Sphingobium was the genus closest to the significantly changed genes in WSHM treatment. The inoculation of endophytic Sphingobium sp. TBBS4 isolated from soybean significantly improved soybean nodulation and growth by increasing della gene expression and reducing ethylene release. CONCLUSION: All the results revealed that WSHM promotes soybean nodulation and growth by selectively regulating soybean gene expression and regulating the endophytic bacterial community, Sphingobium was the key bacterium involved in plant-microbe interaction. These findings refined our understanding of the mechanism of WSHM promoting soybean nodulation and growth and provided novel evidence for plant-endophyte interaction.

Convergent gene pair dSH3 and irr regulate Pi and Fe homeostasis in Bradyrhizobium diazoefficiens USDA110 and symbiotic nitrogen fixation efficiency.

The nitrogen-fixing bacteroids inhabit inside legume root nodules must manage finely the utilization of P and Fe, the two most critical elements, due to their antagonistic interactions. While the balance mechanism for them remains unclear. A double SH3 domain-containing protein (dSH3) in the Bradyrhizobium diazoefficiens USDA110 was found to inhibit the alkaline phosphatase activity, thereby reducing P supply from organophosphates. The dSH3 gene is adjacent to the irr gene, which encodes the iron response repressor and regulates Fe homeostasis under Fe-limited conditions. Their transcription directions converge to a common intergenic sequence (IGS) region, forming a convergent transcription. Extending the IGS region through Tn5 transposon or pVO155 plasmid insertion significantly down-regulated expression of this gene pair, leading to a remarkable accumulation of P and an inability to grow under Fe-limited conditions. Inoculation of soybean with either of the insertion mutants resulted in N2-fixing failure. However, the IGS-deleted mutant showed no visible changes in N2-fixing efficiency on soybean compared to that inoculated with wild type. These findings reveal a novel regulative strategy in the IGS region and its flanking convergent gene pair for antagonistic utilization of P and Fe in rhizobia and coordination of N2-fixing efficiency.

Diverse Bradyrhizobium spp. with Similar Symbiosis Genes Nodulate Peanut in Different Regions of China: Characterization of Symbiovar sv. Arachis.

A total of 219 rhizobial strains isolated from peanut grown in soils from six peanut croplands in Zhengyang county, Henan Province, were typed by PCR-RFLP of IGS sequences. Their phylogenetic relationships were refined on representative strains using sequence analyses of 16S rRNA genes, housekeeping genes (atpD, recA, glnII) and symbiosis genes (nodA, nodC and nifH). The 219 rhizobial isolates were classified into 13 IGS types, and twenty representatives were defined within eight Bradyrhizobium genospecies: B. guangdongense covering 5 IGS types (75.2% of total isolates), B. guangzhouense (2 IGS types, 2.7% total isolates), B. zhengyangense (1 IGS type, 11.3% total isolates) and five novel genospecies (5 IGS types, 0.9 to 3.2% total isolates). All representative strains had identical nodA, nodC and nifH sequences except for one nifH sequence. With this one exception, these sequences were identical to those of the type strains of Bradyrhizobium species and several Bradyrhizobium genospecies isolated from peanut in different regions of China. The nodC sequences of all strains showed < 67% similarity to the closest strains on the Genbank database indicating that they are representative of a novel Bradyrhiobium symbiovar. This study has shown that (1) diverse Bradyrhizobium spp. with similar symbiosis genes nodulate peanut in different regions of China. (2) Horizontal transfer of genes involved in nodulating peanut is common between Bradyrhizobium species in soils used to grow the crop in China. (3) The strains studied here are representative of a novel Bradyrhizobium symbiovar that nodulates peanut in China. We propose the name sv. arachis for this novel symbiovar indicating that the strains were isolated from Arachis hypogaea. Results here have practical implications in relation to the selection of rhizobial inoculants for peanut in China.

The Effect of Different Rhizobial Symbionts on the Composition and Diversity of Rhizosphere Microorganisms of Chickpea in Different Soils.

BACKGROUND: Chickpea (Cicer arietinum L.) is currently the third most important legume crop in the world. It could form root nodules with its symbiotic rhizobia in soils and perform bio-nitrogen fixation. Mesorhizobium ciceri is a prevalent species in the world, except China, where Mesorhizobium muleiense is the main species associated with chickpea. There were significant differences in the competitive ability between M. ciceri and M. muleiense in sterilized and unsterilized soils collected from Xinjiang, China, where chickpea has been grown long term. In unsterilized soils, M. muleiense was more competitive than M. ciceri, while in sterilized soils, the opposite was the case. In addition, the competitive ability of M. ciceri in soils of new areas of chickpea cultivation was significantly higher than that of M. muleiense. It was speculated that there might be some biological factors in Xinjiang soils of China that could differentially affect the competitive nodulation of these two chickpea rhizobia. To address this question, we compared the composition and diversity of microorganisms in the rhizosphere of chickpea inoculated separately with the above two rhizobial species in soils from old and new chickpea-producing regions. RESULTS: Chickpea rhizosphere microbial diversity and composition varied in different areas and were affected significantly due to rhizobial inoculation. In general, eight dominant phyla with 34 dominant genera and 10 dominant phyla with 47 dominant genera were detected in the rhizosphere of chickpea grown in soils of Xinjiang and of the new zones, respectively, with the inoculated rhizobia. Proteobacteria and Actinobacteria were dominant at the phylum level in the rhizosphere of all soils. Pseudomonas appeared significantly enriched after inoculation with M. muleiense in soils from Xinjiang, a phenomenon not found in the new areas of chickpea cultivation, demonstrating that Pseudomonas might be the key biological factor affecting the competitive colonization of M. muleiense and M. ciceri there. CONCLUSIONS: Different chickpea rhizobial inoculations of M. muleiense and M. ciceri affected the rhizosphere microbial composition in different sampling soils from different chickpea planting areas. Through high throughput sequencing and statistical analysis, it could be found that Pseudomonas might be the key microorganism influencing the competitive nodulation of different chickpea rhizobia in different soils, as it is the dominant non-rhizobia community in Xinjiang rhizosphere soils, but not in other areas.

Comparative analysis of the effects of conventional and biodegradable plastic mulching films on soil-peanut ecology and soil pollution.

In agricultural production, biodegradable plastic mulching film (Bio-PMF) has the potential to replace conventional plastic mulching film (CPMF) due to its degradability, but their impacts on soil-crop ecology are controversial. In this study, from 2019 to 2021, effects of CPMF and Bio-PMF on the soil-crop ecology and soil pollution were evaluated on a peanut farm. Compared to the Bio-PMF, an overall improvement in the soil-peanut ecology under the CPMF was observed, including an increase of 10.77 ± 4.8% in peanut yield, an amelioration of four soil physicochemical properties (total P and available P in the flowering stage, total P and temperature in the mature stage), an increase of rhizobacterial relative abundances in class level (Bacteroidia, Blastocatellia, Thermoleophilia and Vicinamibacteria in the flowering stage, Nitrospira and Bacilli in the mature stage) and genus level (RB41 and Bacillus in the flowering stage, Bacillus and Dongia in the mature stage), and an enhancement of soil nitrogen metabolism abilities (ureolysis, nitrification and aerobic ammonia in the flowering stage, nitrate reduction and nitrite ammonification in the mature stage). These preserved soil nutrients and temperature, reshaped rhizobacterial communities, and enhanced soil nitrogen metabolism abilities in the mature stage were obviously correlated with peanut yield under CPMF. However, such remarkable relations were not existed under Bio-PMF. In addition, compared with Bio-PMF, CPMF significantly increased the contents of dimethyl phthalate (DMP), diethyl phthalate (DEP), dibutyl phthalate (DBP) and microplastics (MPs) in soil by 79.93, 44.55, 138.72 and 14.1%, respectively. Thus, CPMF improved soil-peanut ecology and caused serious soil pollution, while Bio-PMF introduced little pollutants into the soil and had little impact on soil-peanut ecology. Based on these, the degradation ability of CPMF or the ecological improvement capacity of Bio-PMF should be improved to obtain the environmentally and soil-crop ecology friendly plastic film in the future.

Distinct lignocellulolytic enzymes produced by Trichoderma harzianum in response to different pretreated substrates.

In order to optimize the composition of enzyme cocktail for improving the hydrolytic efficiency of lignocellulose, different substrates were tested as inducers for producing lignocellulolytic enzymes by Trichoderma harzianum EM0925 in this study. As results, ultrafine grinding or steam explosion pretreated substrates can induce T. harzianum EM0925 to secret holo lignocellulolytic enzymes; acid treated substrate can induce cellobiohydrolase; while alkali or sodium chlorite treated substrates can induce ß-xylosidase specifically. Furthermore, the combination of enzyme cocktails with different hydrolysis characteristics can further improve the hydrolysis efficiency, since 100% yields of glucose and xylose were obtained simultaneously from ultrafine grinding treated corn stover at low enzyme dosage (1.2 mg proteins/g substrate). This study for the first time demonstrated an effective solution that specific-pretreated substrates can be used as inducers for specific enzyme production by T. harzianum, which provided new idea and potential strategy for the construction of highly-efficient lignocellulolytic enzyme cocktails.

Chelativorans petroleitrophicus sp. nov., a paraffin oil-degrading bacterium isolated from a mixture of oil-based drill cuttings and paddy soil.

We isolated a paraffin oil-degrading bacterial strain from a mixture of oil-based drill cutting and paddy soil, and characterized the strain using a polyphasic approach. The Gram-positive, aerobic, rod-shaped and non-spore-forming strain (SCAU 2101T) grew optimally at 50 °C, pH 7.0 and 0.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence indicated that the strain represented a distinct clade in the genus Chelativorans, neighbouring Chelativorans intermedius LMG 28482T (97.1 %). The genome size and DNA G+C content of the strain were 3 969 430 bp and 63.1 mol%, respectively. Whole genome based phylogenomic analyses showed that the average nucleotide identity and digital DNA-DNA hybridization values between strain SCAU 2101T and C. intermedius LMG 28482T were 77.5 and 21.2 %, respectively. The major respiratory quinone was Q-10. The dominant fatty acids were C19 : 0 cyclo ω8c (50.6 %), summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c; 22.5 %) and C18 : 0 (13.8 %). The polar lipids of the strain included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, phosphatidylcholine and diphosphatidylglycerol. Based on the results, strain SCAU 2101T was considered to represent a novel species in the genus Chelativorans, for which the name Chelativorans petroleitrophicus sp. nov. is proposed. The type strain is SCAU 2101T (= CCTCC AB 2021125T=KCTC 92067T).

Production of 5-aminolevulinic acid from hydrolysates of cassava residue and fish waste by engineered Bacillus cereus PT1.

The economical production of 5-aminolevulinic acid (ALA) has recently received increasing attention for its extensive use in agriculture. In this study, a strain of Bacillus cereus PT1 could initially produce ALA at a titre of 251.72 mg/L by using a hydrolysate mixture of low-cost cassava residue and fish waste. The integration of endogenous hemA encoding glutamyl-tRNA reductase led to a 39.30% increase in ALA production. Moreover, improving cell permeability by deletion of the LytR-CpsA-Psr (LCP) family gene tagU led to a further increase of 59.73% in ALA production. Finally, the engineered strain B. cereus PT1-hemA-ΔtagU produced 2.62 g/L of ALA from the previously mentioned hydrolysate mixture in a 7-L bioreactor. In a pot experiment, foliar spray of the ALA produced by B. cereus PT1-hemA-ΔtagU from the hydrolysates increased salt tolerance of cucumber by improving chlorophyll content and catalase activity, while decreasing malondialdehyde content. Overall, this study demonstrated an economic way to produce ALA using a microbial platform and evidenced the potential of ALA in agricultural application.

Impacts of maize hybrids with different nitrogen use efficiency on root-associated microbiota based on distinct rhizosphere soil metabolites.

Plant genotypes shape root-associated microbiota that affect plant nutrient acquisition and productivity. It is unclear how maize hybrids modify root-associated microbiota and their functions and relationship with nitrogen use efficiency (NUE) by regulating rhizosphere soil metabolites. Here, two N-efficient (NE) (ZD958, DMY3) and two N-inefficient (NIE) maize hybrids (YD9953, LY99) were used to investigate this issue under low N (60 kg N ha-1 , LN) and high N (180 kg N ha-1 , HN) field conditions. NE hybrids had higher yield than NIE hybrids under LN but not HN. NE and NIE hybrids recruited only distinct root-associated bacterial microbiota in LN. The bacterial network stability was stronger in NE than NIE hybrids. Compared with NIE hybrids, NE hybrids recruited more bacterial taxa that have been described as plant growth-promoting rhizobacteria (PGPR), and less related to denitrification and N competition; this resulted in low N2 O emission and high rhizosphere NO3 - -N accumulation. NE and NIE hybrids had distinct rhizosphere soil metabolite patterns, and their specific metabolites were closely related to microbiota and specific genera under LN. Our findings reveal the relationships among plant NUE, rhizosphere soil metabolites, root-associated microbiota, and soil nutrient cycling, and this information is informative for breeding NE crops.

Nodule-associated diazotrophic community succession is driven by developmental phases combined with microhabitat of Sophora davidii.

Nodule-associated nitrogen-fixing microorganisms (diazotrophs) residing in legume root nodules, and they have the potential to enhance legume survival. However, the succession characteristics and mechanisms of leguminous diazotrophic communities remain largely unexplored. We performed a high-throughput nifH amplicon sequencing with samples of root nodules and soil in the three developmental phases (young nodules, active nodules and senescent nodules) of the Sophora davidii (Franch.) Skeels root nodules, aiming to investigate the dynamics of nodule-endophytic diazotrophs during three developmental phases of root nodules. The results demonstrated the presence of diverse diazotrophic bacteria and successional community shifting dominated by Mesorhizobium and Bradyrhizobium inside the nodule according to the nodule development. The relative abundance decreased for Mesorhizobium, while decreased first and then increased for Bradyrhizobium in nodule development from young to active to senescent. Additionally, strains M. amorphae BT-30 and B. diazoefficiens B-26 were isolated and selected to test the interaction between them in co-cultured conditions. Under co-culture conditions: B. diazoefficiens B-26 significantly inhibited the growth of M. amorphae BT-30. Intriguingly, growth of B. diazoefficiens B-26 was significantly promoted by co'culture with M. amorphae BT-30 and could utilize some carbon and nitrogen sources that M. amorphae BT-30 could not. Additionally, the composition of microbial community varied in root nodules, in rhizosphere and in bulk soil. Collectively, our study highlights that developmental phases of nodules and the host microhabitat were the key driving factors for the succession of nodule-associated diazotrophic community.

Volatile Organic Compounds of Streptomyces sp. TOR3209 Stimulated Tobacco Growth by Up-Regulating the Expression of Genes Related to Plant Growth and Development.

To investigate the mechanism underlying the plant growth-promoting (PGP) effects of strain Streptomyces sp. TOR3209, PGP traits responsible for indoleacetic acid production, siderophore production, and phosphate solubilization were tested by culturing the strain TOR3209 in the corresponding media. The effects of volatile organic compounds (VOCs) produced by the strain TOR3209 on plant growth were observed by co-culturing this strain with tobacco seedlings in I-plates. Meanwhile, the effects of VOCs on tobacco gene expression were estimated by performing a transcriptome analysis, and VOCs were identified by the solid-phase micro-extraction (SPME) method. The results showed positive reactions for the three tested PGP traits in the culture of strain TOR3209, while the tobacco seedlings co-cultured with strain TOR3209 revealed an increase in the fresh weight by up to 100% when compared to that of the control plants, demonstrating that the production VOCs was also a PGP trait. In transcriptome analysis, plants co-cultured with strain TOR3209 presented the highest up-regulated expression of the genes involved in plant growth and development processes, implying that the bacterial VOCs played a role as a regulator of plant gene expression. Among the VOCs produced by the strain TOR3209, two antifungal molecules, 2,4-bis(1,1-dimethylethyl)-phenol and hexanedioic acid dibutyl ester, were found as the main compounds. Conclusively, up-regulation in the expression of growth- and development-related genes via VOCs production is an important PGP mechanism in strain TOR3209. Further efforts to explore the effective VOCs and investigate the effects of the two main VOCs in the future are recommended.

Bradyrhizobium aeschynomenes sp. nov., a root and stem nodule microsymbiont of Aeschynomene indica.

Aeschynomene indica has a distinctive symbiosis with Bradyrhizobium in which nodulation is Nod factor-independent. In this study, we characterised three Gram-negative and rod-shaped strains (83002T, 81013 and 83012) isolated from root nodules of Aeschynomene indica in Shandong Peninsula. The major cellular fatty acids of isolates were C16:0, C18:0, C18:1 ω7c 11-methyl, summed feature 3 and summed feature 8. The major polar lipids were phosphatidylethanolamine (PE), aminolipids (AL) and phosphatidylcholine (PC). Phylogenetic analysis based on the 16S rRNA locus showed that they belonged to the Bradyrhizobium genus, and shared the highest similarity to the type strains Bradyrhizobium oligotrophicum S58T and Bradyrhizobium denitrificans LMG 8443T. As expected, analysis of concatenated sequences of six housekeeping genes (atpD, recA, glnII, dnaK, gyrB, and rpoB) and nifH gene proposed that these three strains formed a distinct clade within the genus Bradyrhizobium. The highest average nucleotide identity and DNA-DNA hybridization values of the three strains in comparison to the closest Bradyrhizobium species were 87.5% and 65.3%, respectively, which are far below the threshold of species delineation, and thus confirmed the three strains as a new species. The genome size of strain 83002T is 7.52 Mbp, and the DNA G+C content is 65.42 mol%. Strain 83002T (=KCTC 82266T=MCCC 1K04775T) was chosen as the type strain of the new species, for which the name Bradyrhizobium aeschynomenes sp. nov. was proposed.

Effects of mycorrhiza and hyphae on the response of soil microbial community to warming in eastern Tibetan Plateau.

The effects of mycorrhiza and its external hyphae on the response of soil microbes to global warming remain unclear. This study investigates the role of mycorrhiza and its hyphae in regulating soil microbial community under warming by examining the microbial biomass and composition in the ingrowth cores of arbuscular mycorrhiza (AM) plant, Fargesia nitida, and ectomycorrhiza (ECM) plant, Picea asperata, with/without mycorrhiza/hyphae and experimental warming. The results showed that warming significantly increased the biomass of all soil microbes (by 19.89%-137.48%) and altered the microbial composition in both plant plots without mycorrhiza/hyphae. However, this effect was weakened in the presence of mycorrhiza or hyphae. In F. nitida plots, warming did not significantly affect biomass and composition of most soil microbial groups when mycorrhiza or hyphae were present. In P. asperata plots, warming significantly increased the total and ECM fungi (ECMF) biomass in the presence of hyphae (p < 0.05) and the total, Gn, and AM fungi (AMF) biomass in the presence of mycorrhiza (p < 0.05). Meanwhile, the response of enzyme activities to warming was also altered with mycorrhiza or hyphae. Additionally, soil microbial community composition was mainly influenced by soil available phosphorus (avaP), while enzyme activities depended on soil avaP, dissolved organic carbon (DOC), and nitrate concentrations. Our results indicate that mycorrhiza and its hyphae are essential in regulating the response of microbes to warming.

Bacillus amyloliquefaciens as an excellent agent for biofertilizer and biocontrol in agriculture: An overview for its mechanisms.

Bacillus amyloliquefaciens (BA) is one of the most promising bacteria for plant growth promotion (PGP) without harmful side effects. As an excellent agent for biofertilizer and biocontrol in agriculture, the PGP mechanisms of BA have been studied extensively. However, these studies have been rarely summarized, although it could hinder a better understanding of BA strains' potential mechanisms and application in agriculture and other fields. Hence, we reviewed in this work the PGP mechanisms of BA and the current limits of BA application in agriculture. First, BA can improve soil nutrient availability, including improving nitrogen supply, solubilizing phosphate and potassium, and producing siderophores. Second, BA can change the soil microbial community and improve the availability of minerals and plant growth conditions. Third, BA can secrete hormones and volatile organic compounds (VOCs) associated with plant cell growth and root development and further improve nutrient uptake by plants. Fourth, BA can enhance plant resistance against biotic stresses from soil pathogens through competition of niches and nutrients, producing substances such as cyclic lipopeptides, polyketides, and VOCs to antagonize pathogens directly, and induction of system resistance of the plants. Similarly, inoculation with BA can promote plant growth by inducing systematic tolerance to abiotic stresses by leading to genetic, chemical, and physical changes in the host plant. We further suggested that, in future studies, more attention should be paid to nutrient uptake mechanisms of plants with advanced techniques in different soil conditions and fields.

Diversification of Sinorhizobium populations associated with Medicago polymorpha and Medicago lupulina in purple soil of China.

The double selection of environment adaptation and host specificity forced the diversification of rhizobia in nature. In the tropical region of China, Medicago polymorpha and Medicago lupulina are widely distributed, particularly in purple soil. However, the local distribution and diversity of rhizobia associated with these legumes has not been systematically investigated. To this end, root nodules of M. polymorpha and M. lupulina grown in purple soil at seven locations in Yunnan Province of China were collected for rhizobial isolation. The obtained rhizobia were characterized by RFLP of 16S-23S rRNA intergenic spacer, BOXAIR fingerprinting, and phylogeny of housekeeping and symbiosis genes. As result, a total of 91 rhizobial strains were classified into species Sinorhizobium medicae and S. meliloti, while three nodC gene types were identified among them. S. medicae containing nodC of type I was dominant in farmlands associated with M. polymorpha; while S. meliloti harboring nodC of type III was dominant in wild land nodulated by M. lupulina. For both rhizobial species, greater genetic diversity was detected in the populations isolated from their preferred host plant. A high level of genetic differentiation was observed between the two Sinorhizobium species, and gene flow was evident within the populations of the same species derived from different soil types, indicating that rhizobial evolution is likely associated with the soil features. To examine the effects of environmental features on rhizobial distribution, soil physicochemical traits and rhizobial genotypes were applied for constrained analysis of principle coordinates, which demonstrated that soil features like pH, nitrogen and sodium were the principle factors governing the rhizobial geographical distribution. Altogether, both S. medicae and S. meliloti strains could naturally nodulate with M. polymorpha and M. lupulina, but the rhizobium-legume symbiosis compatibility determined by both the host species and soil factors was also highlighted.

Rhizobium sophorae is the dominant rhizobial symbiont of Vicia faba L. In North China.

Faba bean (Vicia faba L.) is a major introduced grain-legume crop cultivated in China. In this study, rhizobia that nodulated faba bean grown in soils from three sites in North China (Hebei Province) were isolated and characterized. Firstly, isolates were categorized into genotypes by ribosomal IGS PCR-RFLP analysis, then representatives of the different IGS genotypes were further identified by phylogenetic analyses of 16S rRNA, housekeeping (atpD, recA) and nodulation (nodC) gene sequences. Rhizobial distribution based on the IGS genotype was related to the different soil physicochemical features by redundancy analysis. IGS typing and phylogenetic analyses of 16S rRNA and concatenated housekeeping gene sequences affiliated the 103 rhizobial strains isolated into four Rhizobium species/genospecies. A total of 69 strains of 3 IGS types were assigned to R. sophorae, 20 isolates of 5 IGS types to R. changzhiense and 9 isolates of 3 IGS types to R. indicum. The representative strain of the five remaining isolates (1 IGS type) was clearly separated from all Rhizobium type strains and was most closely related to defined genospecies according to the recently described R. leguminosarum species complex. Rhizobium sophorae strains (67% of total isolates) were common in all sites and shared an identical nodC sequence typical of faba bean symbionts belonging to symbiovar viciae. In this first study of rhizobia nodulating faba bean in Hebei Province, China, R. sophorae was found to be the dominant symbiont in contrast to other countries.