Phaseolus vulgaris (common bean) is nodulated by diverse Rhizobium species. Although Ecuador is recognized as one of the centers of bean diversification, its native rhizobial diversity and geographic distribution remains poorly characterized. We isolated 46 native Rhizobium strains from root nodules across four Andean provinces (Imbabura, Pichincha, Chimborazo, and Loja). Partial sequencing of the recA gene delineated nine strain clusters (R1–R9) within two major phylogenetic groups: (i) Rhizobium ecuadorense/Rhizobium leguminosarum/Rhizobium etli/Rhizobium phaseoli and (ii) R. tropici. Multilocus sequence analysis (MLSA) of the housekeeping genes recA, glnII, dnaK genes from 19 representative isolates showed four phylogenetic clusters (C1–C4). Cluster C1 (R. ecuadorense–related) predominated in northern Ecuador; C2 formed a distinct Chimborazo cluster; C3 appeared sporadically in Imbabura and Chimborazo; and C4 (R. tropici–related) was confined to Loja’s Amotape–Huancabamba Zone and displayed unique phenotypes. In greenhouse assays on two local bean varieties, all isolates formed nodules in both varieties; several isolates induced significantly higher nodule counts than the commercial inoculant UMR1899 (Rhizobium tropici IIB CIAT 899T). These results suggest geographic variation among Ecuadorian Rhizobium populations and identify locally predominant groups for further evaluation as bioinoculants.

Periplasmic transport channels to accelerate the proton motive force for efficient groundwater bioelectrocatalytic Cr(VI) reduction.

Soil salinity poses a major challenge to the legume-rhizobia symbiosis development, thereby affecting sustainable agriculture. Selecting NaCl-tolerant strains and enhancing the native strains' fitness under salt stress are essential steps for the restoration of marginal areas. In this work, 49 Sinorhizobium meliloti strains, the rhizobial species forming symbiotic nitrogen-fixing associations with alfalfa-including 21 de novo-sequenced field isolates-were subjected to a thorough invitro screening for salt tolerance at progressively higher NaCl concentrations. Field isolates showed genome-based geographical clustering but contrasting salt tolerance abilities. Indeed, genome-wide association (GWA) analysis on the strains' whole-genome sequencing data indicated several loci associated with the variability in salt tolerance. Candidate genes were involved in various processes including cell wall organisation, LPS biosynthesis, quorum sensing, and carbohydrate transport and metabolism. The relationship with carbohydrate metabolism was further confirmed by Phenotype Microarray analysis which indicated salt-tolerant strains having enhanced capacity in carbon source usage. These findings reveal synergistic pathways underlying salt tolerance and suggest candidate traits (e.g., quorum sensing, carbohydrate synthesis and modification) for developing bioinoculants to enhance legume performance in saline soils.

Phaseolus vulgaris (common bean) is nodulated by diverse Rhizobium species. Although Ecuador is recognized as one of the centers of bean diversification, its native rhizobial diversity and geographic distribution remains poorly characterized. We isolated 46 native Rhizobium strains from root nodules across four Andean provinces (Imbabura, Pichincha, Chimborazo, and Loja). Partial sequencing of the recA gene delineated nine strain clusters (R1-R9) within two major phylogenetic groups: (i) Rhizobium ecuadorense/Rhizobium leguminosarum/Rhizobium etli/Rhizobium phaseoli and (ii) R. tropici. Multilocus sequence analysis (MLSA) of the housekeeping genes recA, glnII, dnaK genes from 19 representative isolates showed four phylogenetic clusters (C1-C4). Cluster C1 (R. ecuadorense-related) predominated in northern Ecuador; C2 formed a distinct Chimborazo cluster; C3 appeared sporadically in Imbabura and Chimborazo; and C4 (R. tropici-related) was confined to Loja's Amotape-Huancabamba Zone and displayed unique phenotypes. In greenhouse assays on two local bean varieties, all isolates formed nodules in both varieties; several isolates induced significantly higher nodule counts than the commercial inoculant UMR1899 (Rhizobium tropici IIB CIAT 899T). These results suggest geographic variation among Ecuadorian Rhizobium populations and identify locally predominant groups for further evaluation as bioinoculants.

Sustainable agricultural production is frequently related with the use of agrochemicals, particularly pesticides, which are effective in combating plant infections and pests. Herbicides, a type of pesticide used to control weeds, can have a variety of effects on the growth of beneficial microbial populations in soil. The purpose of this paper was to investigate the effects of three pesticides on the growth of Rhizobium sp. strains. In this experiment, the growth of three bacterial strains (Rhizobium (Sinorhizobium) meliloti RM1, Rhizobium trifolii RT2, and RT3) was measured in the presence of three herbicides (Lumax 537.5, Agrodimark, and Siran 40 SC), which were added after impregnation of paper discs plated on Muller Hinton Agar. In this experiment, the recommended and doubled doses of each herbicide were employed. Resistance, susceptibility - increased exposure, and susceptibility - standard dosage were assessed following inhibition zone diameter measurement. Our findings demonstrated that the diameter of the inhibitory zone varies with herbicide type, dose, and rhizobial species. The findings revealed that treatments with increasing herbicide concentrations produced a larger inhibition zone diameter. The useof Lumax 537.5 SE led to higher inhibition zone diameter compared with other herbicides. In general, Rhizobium trifolii was more sensitive to Lumax 537.5 SE and Agrodimark than Rhizobium (Sinorhizobium) meliloti. This work may have scientific and applicative relevance for plant farmers, improving their knowledge of soil microbiology and pesticide application.

This article explores the use of biofertilizers over the traditional use of chemical fertilizers due to their potential benefits in sustainable agriculture. Studies on overuse of chemical fertilizers and chemical pesticides shows that these chemicals are major cause of cancer and other lethal diseases which are also discussed here. Biofertilizers have become an eco-friendly alternative of chemical fertilizers and comprises a variety of microorganisms such as fungi and bacteria, and symbiotic associations like mycorrhiza which aids in maintaining soil integrity and fertility. Current article thoroughly explains about the selection and production of biofertilizers. The selection of correct species of soil bacteria is important as the bacteria associates with the plant which could impact the yield of the crop. Recent modification in biofertilizer formulations is one of the applications of genetic engineering which aims to improve its efficacy, stability and shelf life in order to adapt to diverse environmental conditions. Additionally, genetically modified bacterial strains improve bacterial competitiveness and shelf life. These strains mainly include the species of Rhizobium, Azospirillum and Alcaligenes faecalis. By doing the thorough examination of current researches, case studies and practical application, the article highlights the ecological, socio-economical and agricultural advantages of biofertilizers. Ultimately, this article highlights the potential of biofertilizers and how they contribute to the health of farmers and support sustainable agricultural practices.

The species Rhizobium panacihumi was isolated from ginseng-cultivated soil in Gochang-gun (South Korea) and only encompassed the type strain DCY116T (=KCTC 62017T=JCM 32251T), which was phylogenetically related to Rhizobium yantingense. Although the species R. yantingense was later reclassified as Endobacterium yantingense, the species R. panacihumi was not transferred to the genus Endobacterium, which currently encompasses the species Endobacterium cereale and E. yantingense. The 16S rRNA phylogenetic analysis showed that strain DCY116T clustered with the type strains of these two species. The phylogenomic analysis of the whole genome of the type strain R. panacihumi KCTC 62017T, which was obtained in this study, confirmed that E. cereale RZME27T and E. yantingense CCTCC AB 2014007T are the closest relatives of R. panacihumi KCTC 62017T. The calculated average nucleotide identity and digital DNA-DNA hybridization values between the genome of this strain and those of E. cereale RZME27T and E. yantingense CCTCC AB 2014007,T together with the results of the phylogenomic analysis, support the reclassification of the species R. panacihumi as Endobacterium panacihumi comb. nov. and the emendation of the genus Endobacterium.

Endophytic Rhizobium species represent promising bioinoculants for enhancing crop performance and nutritional profiles. This study investigated the impact of Rhizobium sp. CRRU65 inoculation on blackberry (Rubus sp.) plants, with emphasis on fruit phytochemical composition and cross-kingdom bioactivity. Inoculated plants exhibited a significant increase in yield and elevated levels of phenolic compounds, notably sanguiin H6 and cyanidin-3-O-glucoside, as quantified by HPLC-DAD-MS. Antioxidant functionality was evaluated using Caenorhabditis elegans under oxidative stress. Extracts from inoculated fruits significantly improved nematode survival, accompanied by transcriptional upregulation of skn-1 and hsp-16, genes involved in stress response and proteostasis. These findings demonstrate that Rhizobium sp. CRRU65 enhances not only agronomic traits but also the nutraceutical quality of blackberry fruits, with beneficial effects extending across biological kingdoms. This work underscores the potential of endophytic bacteria to contribute to sustainable agriculture and functional food innovation through molecular and physiological modulation in both plants and animal models.

A Gram-stain-negative, rod-shaped, strictly aerobic bacterium strain SG148T, within the family Rhizobiaceae, was isolated from rice leaves collected in Fujian Province, China. Phylogenetic analysis utilizing 16S rRNA gene sequences revealed that strain SG148T displayed a high sequence similarity of 95.2-95.8% to the strains of closely related species of Shinella and Rhizobium. The highest digital DNA-DNA hybridization (dDDH), core-proteome average amino acid identity (cpAAI), and average nucleotide identity (ANI) values between strain SG148T and related strains were estimated as 20.7%, 79.3%, and 73.7%, respectively. The predominant respiratory quinones in strain SG148T were identified as Q-9 and Q-10, while major polar lipids included diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, and phosphatidylethanolamine. Additionally, strain SG148T was capable of phosphate-solubilizing and siderophore-producing carrier, significantly promoting rice seedling growth. The DNA G + C content was determined to be 56.1%. Given its distinct phylogenetic and phenotypic characteristics, strain SG148T is considered to represent a novel genus, for which the name Oryzifoliimicrobium ureilyticus gen. nov., sp. nov. is proposed. The type strain is SG148T (= MCCC 1K08901T = KCTC 8337T).

The present study was carried out with plant pathogenic microorganisms were isolated from the infected roots of Vigna mungo plant, collected from Thanajavur district, Tamil Nadu, India. The identified fungal colonies were confirmed as Aspergillus flavus and Fusarium solani. In this study plant growth promoting rhizobacterial strains were successfully isolated from the Vigna mungo rhizosphere soil. The isolated organisms were confirmed as Rhizobium meliloti. The isolated organisms were used for indole acetic acid production the isolated organism were produced high level. The seed germination test were analysed in agar plates. The Vigna mungo seeds were treated with isolated Rhizobial species and placed on agar surface the seed germination was counted 90% percentage seeds were germinated in this results. Analysis the Morphometric and Biochemical parameters, After 10 days of growth, germination percentage, root length, shoot length, fresh weight and dry weight were measured and calculated. Biochemical compound such as chlorophyll, total protein and total carbhohydrate were analysed. The biochemical contents such as chlorophyll, protein and carbohydrates content were notied in decreased amountthe in treatment T6 (Aspergillus flavus and Fusarium solani) containing pot, when compared with control treatment (without microorganisms).

Abstract Common bean (Phaseolus vulgaris L.) can fix atmospheric nitrogen (N) through symbiosis with Rhizobia species. This trait is often underutilized by growers and overlooked by breeders due to the laborious and costly evaluation techniques involved. There is a critical need for the development of new screening tools to enhance nitrogen fixation efficiency. Remote sensing techniques utilizing unmanned aerial systems offer a potential solution to this challenge, providing a high‐throughput phenotyping method for trait evaluation. In this study, we investigated the use of vegetation indices and machine learning (ML) methods in estimating symbiotic nitrogen fixation (SNF). Forty‐two black bean breeding lines from the Dry Bean Breeding Program at Michigan State University were grown and compared under both high and low N conditions. A random forest model developed to predict percent nitrogen derived from the atmosphere (%Ndfa) using remote sensing (RS) data resulted in an average accuracy of R2 = 0.86. A 3‐year evaluation of these trials in Michigan demonstrated how seed yield under unfertilized conditions could be used as an indirect indicator of SNF ability. Two accurate prediction models for yield were developed using stepwise general linear modeling (StepwiseGLM) and Bayesian regularized artificial neural network (BRNeural Network) (stepwise general linear model r = 0.64; Bayesian regularized neural network r = 0.65). These results suggest that seed yield and RS data coupled with ML offer a promising tool to efficiently implement indirect selection for SNF in common bean.

Inoculation with Rhizobium can improve not only host yield and quality but also host adaptability to stress. The match between inoculated strains and hosts and resistance to stress are the key factors determining the inoculation effect. Four types of Desmodium, Pleurolobus gangeticus, Puhuaea sequax, Grona heterocarpos, and Polhillides velutina, were used to capture Rhizobium strains in soil, and the phylogenetic classification and salt and acid—alkaline resistances of the strains were determined through isolation, identification, and different salt and pH treatments. The phylogenetic classification of the 62 rhizobial strains was determined by 16S rDNA analysis. After comparison, the strains were grouped into 10 groups with known strains of rhizobia, including 14 strains of fast-growing rhizobia grouped with Rhizobium tropici and Rhizobium oryzicola and 48 strains of slow-growing rhizobia. The salt tolerance and acid—base adaptability of 52 strains were qualitatively and quantitatively determined in this study, and salt stress was found to have varying effects on the growth of different strains. Some strains grew normally on media with NaCl concentrations of 0.4 and 0.35 mol/L and had strong salt tolerance. The plants grew normally on media with pH 5–9. This study provides theoretical support for the classification of Desmodium and provides efficient Rhizobium strains for the cultivation and application of Desmodium.

A robust symbiotic relationship between soybean and rhizobia can enhance the yield and quality of soybeans by reducing nitrogen fertilizer input, thereby contributing to sustainable agriculture. However, the genetic interplay between soybean cultivars and the rhizobial species colonizing their roots under natural conditions is yet to be sufficiently assessed. In this study, we build on previous observations that have revealed a significant variation in the prevalence of rhizobial species associated with the soybean cultivars "Peking" and "Tamahomare." Using recombinant inbred lines derived from a cross between Peking and Tamahomare, we performed quantitative trait loci (QTL) analysis of the proportion of Rhizobium species present in the root nodules of these cultivars and accordingly identified a major QTL on chromosome 18, accounting for 42% of the phenotypic variation, which was subsequently localized to a 240-kb region. RNA-seq analysis indicated that a single gene harboring nucleotide binding site-leucine-rich repeat domains exhibited markedly different expression within the QTL region in the parent cultivars. As this locus is distinct from the chromosomal regions containing known nodule-related genes, such as Rj and rj, we speculate that it represents a novel gene involved in the symbiosis between rhizobia and soybeans. Further research on the function and role of this new gene could potentially contribute to enhancing soybean yield, and hence sustainable agriculture, under low-nitrogen fertilization conditions.

Viruses, including bacteriophages, influence bacterial life and contribute to soil structure modification. Their genomes primarily exist in DNA form. Therefore, it is essential to understand the diversity of DNA viruses in agricultural soils, which serve as habitats for beneficial bacteria such as Rhizobium and Azotobacter species. These viruses play a significant role in microbial dynamics by regulating bacterial populations, facilitating gene transfer, and impacting nutrient cycling within the soil ecosystem. This study aims to identify useful random amplified polymorphic DNA (RAPD) markers for detecting DNA virus diversity in soil. Twenty-five primers were tested using the PCR method with 50 soil samples collected from 44 locations where bean cultivation is prevalent in six geographical regions of Turkey. The soil samples were meticulously filtered using a 0.22-µm filter and the filtered samples were checked for eukaryotic and prokaryotic contamination markers. All primers' PCR amplification efficiency and the useful primers' polymorphism information content values were calculated. Binary data were obtained using Phoretix1D software and a dendrogram illustrating the DNA virus diversity of the soil samples was created. Principal coordinates analysis of the samples was performed using GenAlEx software. PCR and dendrogram analysis revealed the primers that effectively distinguished and compared DNA virus diversity in soils.

In this study, we sequenced the genome of Mesorhizobium sp. strain AaZ16, a nitrogen-fixing rhizobial species isolated from the root nodules of Astragalus armatus growing wild in a lead- and zinc-rich mine tailings in the High Atlas, Morocco. This study reveals the genomic characteristics of the root microsymbiont.

The endophytic microflora of Crotalaria constitute a heterogeneous community of beneficial microorganisms that colonize healthy tissues of the host plant without causing any apparent harm. The microflora play a crucial role in promoting plant growth, nutrient gain, and resilience to various biotic and abiotic stresses. This review highlights the range of endophytic microorganisms that reside in Crotalaria tissues, providing insights on the methods of detection and the role played by endophytes in promoting host plant growth. Diverse groups of endophytes ranging from bacteria, fungi, and actinomycetes colonize internal organs of Crotalaria species. Key findings indicate that Crotalaria-associated endophytes, including species of Bradyrhizobium, Rhizobium, Burkholderia, and Methylobacterium, exhibit plant growth-promoting traits such as nitrogen fixation, phytohormone production, phosphate solubilization, and resistance to abiotic stresses. Additionally, some endophytes produce metabolites that serve as biocontrol agents, protecting Crotalaria against phytopathogens. This review offers valuable insights for future exploitation of endophytic microflora of Crotalaria in enhancing crop productivity and stress tolerance.

Growth of the common bean plant Phaseolus vulgaris is tightly linked to its symbiotic relationship with diverse rhizobial species, particularly Rhizobium phaseoli, an alphaproteobacterium that forms root nodules and provides high levels of nitrogen to the plant. Molecular cross-talk is known to happen through plant-derived metabolites, but only flavonoids have been identified as nodulation signals, which act through the activation of the NodD Transcription Factor (TF). The identification of signals that mediate nodulation via TFs can aid in the rational design of biofertilizers that promote plant-bacteria symbiosis. Here, we identified 57 TFs in the R. phaseoli genome through sequence conservation from Escherichia coli, and predicted a transcriptional regulatory network comprising 16 TFs, and 1,371 target genes. We identified the regulatory interactions relevant to nodulation via transcriptome analysis, and hypothesize that PuuR is a TF involved in nodulation, potentially acting via its known binding metabolite putrescine. Sequence and structural evidence predict a model where putrescine acts as a signaling metabolite in nodulation via the TF PuuR, and the regulation of the nodI gene.

Abstract This research was conducted to isolate, authenticate, and assess the symbiotic effectiveness of cowpea nodulating rhizobia isolated from Centrosema pubescens and Mucuna pruriens at different locations in Ile-Ife, Nigeria with two varieties of cowpea (Ife BPC and Ife Brown). Thirteen Rhizobium and three Bradyrhizobium species were isolated and all of them significantly enhanced nodulation with Ife brown and Ife BPC cowpeas having 50% and 81.25% effective nodules formation, respectively. The inoculation of the cowpea with Bradyrhizobium sp (C7) increased the yields significantly with Ife brown recording 73.92 g, while Ife BPC had 58.14 g. The symbiotic relationship between the rhizobia species and the two varieties of cowpea increased the soil fertility with nitrogen concentration in the soil increasing to 84.28 mg/g for Ife brown and 55.89 mg/g for Ife BPC. All the sixteen rhizobia isolates were resistant to Carbendazim 12% + Mancozeb 63% W/P; 2,3 Dichlorovinyl dimethyl phosphate; Chlorpyriphos; Atrazine and 2,3 Dimethylamine. In contrast, four Rhizobium sp. were sensitive to Glyphosate at 14.4 mg/ml, while paraquat had inhibitory effect on 14 out of the 16 rhizobial species at 2.76 mg/ml. This study concluded that the rhizobia isolates improved the cowpea yield and also enriched the soil compared to the Nitrogen, Phoshorus and potassium (NPK) fertilized soil.

It is known that Glycine max and G. soja, entering into symbiotic relations with different rhizobia species, form nodules of determinate type. In such nodules, bacteroids are low differentiated and only slightly differ from free-living bacteria. Recently, it has been shown that in G. soja nodules when inoculated with Bradyrhizobium liaoningense strain RCAM04656, bacteroids were significantly larger than free-living bacteria. In this study, decreased temperature (21°C) was found to increase variation in the length of bacteroids in both G. max and G. soja nodules, with individual bacteroids increasing in size more than 15-fold over bacteria. At the optimal temperature (28°/24°C), the size of bacteroids varied to a lesser extent.

This investigation is associated with the microbial diversity of different agroforestry systems. The study interpreted the changes of bacterial population during the duration of the experiments. This study was analyzed by CRBD (Complete Randomized Block Design) with 5 treatments (i.e. agroforestry systems) and 4 replications. The research was conducted on cropping systems at JNKVV, Jabalpur, and the Forest Research Farm during the Rabi season of 2021-22 and 2022-23. Soil collection was carried out at a depth of Rhizosphere soil (0 to 15 cm) in different agroforestry systems; later on, the soil was tested through the use of serial dilution methods. The bacterial population influence to the decomposition of leaf litter and straw material in the soil.The result revealed that the Rhizobium species population was found in maximum T1-D. sissoo- wheat (66.28 and 66.96 X 107 cfu g-1) in the respective years of 2021-22 and 2022-23, followed by the sequence of population of Rhizobium spp. had T3 (M. pinnata-Wheat) > T2 (G. arborea-Mustard) > T5 (M. indica-linseed) > T4 (A. nilotica-wheat) estimated under agroforestry systems. The Azospirillum species population increases year to year under the agroforestry system. the population sequence under agroforestry system had T1 (D. sissoo-wheat) >T3 (M. pinnata-wheat) > T2 (G. arborea-mustard) > T5 (M. indica-linseed) > T4 (A. nilotica-wheat) obtained under agroforestry systems. The overall conclusion of this investigation is that the bacterial population is obtained under maximum in the D. sissoo with wheat-based agroforestry systems.