Rhizobium Species Research Articles

Assessment of Experimental and Predicted Toxicity of Pesticides and Heavy Metals Binary Mixtures to Rhizobium Species

Assessment of Experimental and Predicted Toxicity of Pesticides and Heavy Metals Binary Mixtures to Rhizobium Species

Studies on isolation, identification and characterization of Rhizobium species from Nallamalla Forest area of Mahabub Nagar district, Telangana State

Studies on isolation, identification and characterization of Rhizobium species from Nallamalla Forest area of Mahabub Nagar district, Telangana State

Genomics of the "tumorigenes" clade of the family Rhizobiaceae and description of Rhizobium rhododendri sp. nov.

Tumorigenic members of the family Rhizobiaceae, known as agrobacteria, are responsible for crown and cane gall diseases of various crops worldwide. Tumorigenic agrobacteria are commonly found in the genera Agrobacterium, Allorhizobium, and Rhizobium. In this study, we analyzed a distinct "tumorigenes" clade of the genus Rhizobium, which includes the tumorigenic species Rhizobium tumorigenes, as well as strains causing crown gall disease on rhododendron. Here, high-quality, closed genomes of representatives of the "tumorigenes" clade were generated, followed by comparative genomic and phylogenomic analyses. Additionally, the phenotypic characteristics of representatives of the "tumorigenes" clade were analyzed. Our results showed that the tumorigenic strains isolated from rhododendron represent a novel species of the genus Rhizobium for which the name Rhizobium rhododendri sp. nov. is proposed. This species also includes additional strains originating from blueberry and Himalayan blackberry in the United States, whose genome sequences were retrieved from GenBank. Both R. tumorigenes and R. rhododendri contain multipartite genomes, including a chromosome, putative chromids, and megaplasmids. Synteny and phylogenetic analyses indicated that a large putative chromid of R. rhododendri resulted from the cointegration of an ancestral megaplasmid and two putative chromids, following its divergence from R. tumorigenes. Moreover, gene clusters specific for both species of the "tumorigenes" clade were identified, and their biological functions and roles in the ecological diversification of R. rhododendri and R. tumorigenes were predicted and discussed.

Nitrogen-Fixing Symbiotic Paraburkholderia Species: Current Knowledge and Future Perspectives

A century after the discovery of rhizobia, the first Beta-proteobacteria species (beta-rhizobia) were isolated from legume nodules in South Africa and South America. Since then, numerous species belonging to the Burkholderiaceae family have been isolated. The presence of a highly branching lineage of nodulation genes in beta-rhizobia suggests a long symbiotic history. In this review, we focus on the beta-rhizobial genus Paraburkholderia, which includes two main groups: the South American mimosoid-nodulating Paraburkholderia and the South African predominantly papilionoid-nodulating Paraburkholderia. Here, we discuss the latest knowledge on Paraburkholderia nitrogen-fixing symbionts in each step of the symbiosis, from their survival in the soil, through the first contact with the legumes until the formation of an efficient nitrogen-fixing symbiosis in root nodules. Special attention is given to the strain P. phymatum STM815T that exhibits extraordinary features, such as the ability to: (i) enter into symbiosis with more than 50 legume species, including the agriculturally important common bean, (ii) outcompete other rhizobial species for nodulation of several legumes, and (iii) endure stressful soil conditions (e.g., high salt concentration and low pH) and high temperatures.

CHARACTERIZATION OF RHIZOBIUM ISOLATES AS BIOCONTROL AGENTS AGAINST FUSARIUM SOLANI AND MACROPHOMINA PHASEOLINA

This study recovered 15 Rhizobium and Bradyrhizobium isolates from nodules of different legume plants (Faba bean, Pea, Soybean, and Clover) grown in nine Egyptian governorates representing the delta region (Menoufia, Gharbia, Suez, Qalubia, Cairo, Sharkia, Behirah, Kafr El-sheikh, and Ismailia). The infectivity test proceeded with all isolates retaining and infecting their hosts, demonstrating that they are Rhizobium cultures. Molecular identification based on 16S rRNA gene sequencing revealed that the isolates belonged to two species of Rhizobium, namely Rhizobium leguminosarum (RL1, RL2, RL3, RL4, RL5, RL6, RL7, RL8, RL9, RL10, RL11, RL12, and RL13) and Bradyrhizobium japonicum (BJ1 and BJ2). Moreover, PCR based on specific primers was employed to detect nifH gene in the genomes of tested isolates. Most of the isolates exhibited sensitivity toward antibiotics, and were able to produce HCN. The isolates of RL4, RL6, RL9, and RL10 were positive for chitinase activity and exhibited clear zones ranging from weak to sturdy. The antagonism evaluation of Rhizobium isolates against Fusarium solani and Macrophomina phaseolina ensued under in vitro conditions. The isolates RL6 and RL9 of R. leguminosarum were the most effective, suppressing more than 50% growth of M. phaseolina. Similarly, the isolates RL4, RL6, RL9, and RL10 revealed the most effective and inhibited more than 50% growth of F. solani. Interestingly, the isolates RL6 and RL9, which exhibited high levels of suppression against M. phaseolina, also displayed high levels of suppression against F. solani.

Competitiveness and Phylogenetic Relationship of Rhizobial Strains with Different Symbiotic Efficiency in Trifolium repens: Conversion of Parasitic into Non-Parasitic Rhizobia by Natural Symbiotic Gene Transfer

In Uruguayan soils, populations of native and naturalized rhizobia nodulate white clover. These populations include efficient rhizobia but also parasitic strains, which compete for nodule occupancy and hinder optimal nitrogen fixation by the grassland. Nodulation competitiveness assays using gusA-tagged strains proved a high nodule occupancy by the inoculant strain U204, but this was lower than the strains with intermediate efficiencies, U268 and U1116. Clover biomass production only decreased when the parasitic strain UP3 was in a 99:1 ratio with U204, but not when UP3 was at equal or lower numbers than U204. Based on phylogenetic analyses, strains with different efficiencies did not cluster together, and U1116 grouped with the parasitic strains. Our results suggest symbiotic gene transfer from an effective strain to U1116, thereby improving its symbiotic efficiency. Genome sequencing of U268 and U204 strains allowed us to assign them to species Rhizobium redzepovicii, the first report of this species nodulating clover, and Rhizobium leguminosarun, respectively. We also report the presence of hrrP- and sapA-like genes in the genomes of WSM597, U204, and U268 strains, which are related to symbiotic efficiency in rhizobia. Interestingly, we report here chromosomally located hrrP-like genes.

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.

Members of Ensifer and Rhizobium genera are new bacterial endosymbionts nodulating Pisum sativum (L.).

A total of 84 Pisum sativum legume nodulating bacteria (LNB) were isolated from seven geographical sites from southern Tunisia. Phylogenetic analyses based on partial sequences of 16S rRNA gene and the housekeeping genes glnII, and recA grouped strains into six clusters, four of which belonged to the genus Rhizobium and two to the Ensifer genus. Among Rhizobium clusters, 41 strains were affiliated to Rhizobium leguminosarum, two strains to R. pisi, two strains to R. etli, and interestingly two strains belonged to previously undescribed Rhizobium species. The remaining two strains were closely related to Ensifer medicae (two strains) and Ensifer meliloti (two strains). A symbiotic nodC gene-based phylogeny and host specificity test showed that all Rhizobium strains nodulating pea belonged to the symbiovar viciae, whereas the Ensifer strains were associated with the symbiovar meliloti never described to date. All strains under investigation differed in the number of induced root nodules and the effectiveness of atmospheric nitrogen fixation. The R. leguminosarum PsZA23, R. leguminosarum PsGBL42, and E. medicae PsTA22a, forming the most effective symbiosis with the plant host, are potential candidates for inoculation programs.

Isolation, Screening, and Molecular Characterization of Rhizosphere Derived Potential Biofertilizer from Different Crops Land for Sustainable Agriculture and Environment

Overpopulation in world has created immense pressure on agricultural land to increase crops production by using excess chemical fertilizers, pesticides, and plant growth regulators. Nowadays, biofertilizer is one of the best concerns of research interest for sustainable development in agriculture and environment. About 30 soil bacteria were isolated from three different locations in Bangladesh by growing on nitrogen-free selective media and primarily had been categorized based on colony features. However, to short out the biofertilizer and biocontrol potential bacteria several assay had been conducted including nitrogen-fixing assay, ammonia production assay, phosphate solubilizing assay, IAA production assay, siderophores production assay, amylase production assay, biocontrol assay, and seed germination bioassay. Different species of Rhizobium, Bacillus, Paraburkholderia, Priestia, Arthrobacter, Pseudarthrobacter, Rhodanobacter, Flavobacterium, Mucilaginibacter, and Sphingomonas were identified by analyzing 16S rRNA gene partial sequence analysis by BLASTn that revealed many of these act as biofertilizer. Moreover, the antibiotic resistance tests of biofertilizer potential isolates and all others intensive data analysis in respect of biofertilizer functionality revealed that Paraburkholderia sacchari is the best while Priestia megaterium, Bacillus zanthoxyli, Arthrobacter globiformis, and Bacillus wiedmanni have also the potentiality to be biofertilizer. The outcome will help the researchers and industries to develop biofertilizer for crops plant.

Diversity of common bean rhizobia in blackland of northeastern China and their symbiotic compatibility with two host varieties.

The common bean (Phaseolus vulgaris L.) is an important crop in the world that forms root nodules with diverse rhizobia. Aiming to learn the rhizobial communities associated with the common bean in the black soil of Northeast China, 79 rhizobia were isolated from root nodules of two host varieties (Cuican and Jiadouwang) grown in two sites of blackland and were characterized by comparative sequence analyses of 16S rRNA, recA, atpD, nodC, and nifH genes, and whole genome. As a result, Rhizobium indigoferae, R. anhuiense, and R. croatiense as minor groups and three dominant novel Rhizobium species were identified based on their average nucleotide identity and DNA-DNA hybridization values to the type strains of relative species. This community composition of rhizobia associated with the common bean in the tested black soils was unique. Despite their different species affiliations, all of them were identified into the symbiovar phaseoli according to the phylogenies of symbiotic genes, nodC and nifH. While the phylogenetic discrepancies found in nodC, nifH evidenced that the evolutions of nodulation (nod) and nitrogen fixation (nif ) genes were partially independent. In addition, only one dominant rhizobial species was shared by the two common bean varieties grown in the two soil samples, implying that both the plant variety and the soil characteristics affected the compatibility between rhizobia and their hosts. These findings further enlarged the spectrum of common bean-nodulating rhizobia and added more information about the interactions among the soil factors, rhizobial species, and host plants in the symbiosis.

Morphological, Physiological and Biohchemical Identification of Nitrogen Fixing Mesorhizobium in Chickpea

Chickpea is the world’s second most important legume, and it can be nodulated with a variety of rhizobial species to generate root nodules. The current study investigated the isolation, cultural, and biochemical characterization of several strains of root nodulating bacteria from different locations of Yavatmal districts. The serial dilution approach was used for isolation. Bacterium Mesorhizobium is a gram- negative, aerobic, non-spore producing, motile rods with circular, convex, whitish pink, and glistering colonies with an entire edge. The biochemical characterization of five different strains of bacteria revealed that the catalase, methyl red, urease, and triple sugar iron and citrate utilization test yielded positive results. Based on morphological, biochemical, and physiological characters most of the characteristics were found like the Mesorhizobium spp. The physical and biochemical properties of five different isolates of bacteria were analyzed to determine their taxonomic position, and the authentication test revealed that the strain of rhizobium bacteria is Mesorhizobium spp.

Phyto-interactive impact of green synthesized iron oxide nanoparticles and Rhizobium pusense on morpho-physiological and yield components of greengram

The iron oxide nanoparticles (IONPs) prepared by green synthesis method using Syzigium cumini leaf extract was characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). The XRD confirmed the crystalline structure of green synthesized NPs measuring around 33 nm while SEM revealed its nearly spherical shape. Rhizobium species recovered from greengram nodules, identified by 16s rRNA gene sequencing as Rhizobium pusense produced 30% more exopolysaccharides (EPS) in basal medium treated with 1000 μg IONPs/ml. Compositional variation in EPS was observed by Fourier-transform infrared spectroscopy (FTIR). There was no reduction in rhizobial viability and no damage to bacterial membrane was observed under SEM and confocal laser scanning microscopy (CLSM), respectively. Effects of IONPs and R. pusense, used alone and in combination on the growth and development of greengram plants varied considerably. Plants grown with IONPs and R. pusence, used alone and in combination, showed a significant increase in seed germination rate, length and dry biomass of plant organs and seed components compared to controls. The IONPs in the presence of rhizobial strain further increased seed germination, plant growth, seed protein and pigments. Greater protein content (442 mg/g) was observed in seeds at 250 mg/kg of IONPs compared to control. Plants raised with mixture of IONPs plus R. pusense had maximum chlorophyll content (39.2 mg/g FW) while proline content decreased by 53% relative to controls. This study confirms that the green synthesis of IONPs from S. cumini leaf possess useful plant growth promoting effects and could be developed as a nano-biofertilizer for optimizing legume production.

Isolation and characterization of Rhizobium spp. and Bradyrhizobium spp. from legume nodules

Rhizobia topic has been re-focused in recent years because of new findings on their traits not only as nitrogen-fixing bacteria but also as plant growth-promoting rhizobacteria. When combing rhizobial strains with novel biological carriers (e.g., biochar) for inoculant production, it brings great potential for improving soil health in long-term. Appreciating this trend, this study is designed to isolate and characterize local rhizobial strains from legume fields using the conventional method with some modifications to increase efficiency in rhizobial identification. As a result, 17 rhizobial strains were isolated and classified biochemically that genetic identification outcome confirmed 10 strains belong to 07 different Rhizobium species as R. mayense, R. paknamense, R. pusense, R. miluonense, R. tropici, R. phaseoli, and R. multihospitium while the rest belong to 06 various Bradyrhizobium species as B. elkanii, B. centrosematis, B. guangxiense, B. liaoningense, B. yuanmingense, and B. arachidis. Thermal and saline tolerant tests together with seed germination tests also performed on these rhizobial strains to gain data on their responses to abiotic stresses. By comparing rice and mung bean GI values, we can assess the effectiveness of each rhizobial strains to help seeds at their early germination.

A Promiscuity Locus Confers Lotus burttii Nodulation with Rhizobia from Five Different Genera.

Legumes acquire access to atmospheric nitrogen through nitrogen fixation by rhizobia in root nodules. Rhizobia are soil-dwelling bacteria and there is a tremendous diversity of rhizobial species in different habitats. From the legume perspective, host range is a compromise between the ability to colonize new habitats, in which the preferred symbiotic partner may be absent, and guarding against infection by suboptimal nitrogen fixers. Here, we investigate natural variation in rhizobial host range across Lotus species. We find that Lotus burttii is considerably more promiscuous than Lotus japonicus, represented by the Gifu accession, in its interactions with rhizobia. This promiscuity allows Lotus burttii to form nodules with Mesorhizobium, Rhizobium, Sinorhizobium, Bradyrhizobium, and Allorhizobium species that represent five distinct genera. Using recombinant inbred lines, we have mapped the Gifu/burttii promiscuity quantitative trait loci (QTL) to the same genetic locus regardless of rhizobial genus, suggesting a general genetic mechanism for symbiont-range expansion. The Gifu/burttii QTL now provides an opportunity for genetic and mechanistic understanding of promiscuous legume-rhizobia interactions. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Microbial pathogenesis and the evasion strategies from the legume plant protective immunity

AbstractPlants are stringent sources for the global food supply, and among them, legumes are considered to be the special ones since they have the specific capability to develop a symbiotic relationship with certain soil microorganisms (i.e., the rhizobial community) which deliberately fix the atmospheric nitrogen that is required for the further cellular synthesis. Biological nitrogen fixation (BNF) by the legume plants is essential for viable agricultural production and to decrease the use of synthetic nitrogen fertilizer in the agricultural fields. However, being the indigenous soil habitants, almost all plants are constantly encountering soil bacteria, viruses, fungi, nematodes, and so on, which may instigate an array of plant diseases conferring the global food security risk. Assimilation of plant nutrients is largely driven by the specific symbiotic interaction between rhizobial species and the leguminous plant roots through the formation of root nodules. Hence, in order to improve the crop yield and to ensure a sustainable supply of plant proteins and other nutrients, the protective immunity of the legume plants against the plant pathogens needs to be understood well because legumes comprise the maximum portion of all plants for serving as the human food and livestock feed. Present review emphasized on the bacterial pathogens and the virulent genes that are detrimental to plants including legumes. The evasion strategy of these harmful microorganisms from the plants' protective immunity is also discussed.

Rhizobium alarense sp. nov. and Rhizobium halophilum sp. nov. isolated from the nodule and rhizosphere of Lotus japonicus.

Two strains (TRM95111T and TRM95001T) of Gram-stain-negative, aerobic, rod-shaped microbes were isolated from the nodule and rhizosphere of Lotus japonicus grown in the campus of Tarim University in Alar, Xinjiang, China. Strain TRM95111T and strain TRM95001T shared 93.1% 16S rRNA gene sequences similarity with each other and had 98.2 and 97.9% 16S rRNA gene sequence similarity to the closest species Rhizobium subbaraois JC85T and R. halotolerans AB21T by EzBioCloud blast, respectively. Phylogenetic analyses based on 16S rRNA gene sequences, housekeeping gene sequences and core-proteome average amino acid identity (cpAAI) showed that two strains belonged to the genus Rhizobium. The value of digital DNA-DNA hybridization (dDDH) between strain TRM95111T and the closest strain R. subbaraonis JC85T was 21.8%, respectively. The dDDH value between strain TRM95001T and the closest strains R. tarimense PL-41T was 27.1%. Whole-genome average nucleotide identity (ANI) values of the strain TRM95111T were 75.6-79.3% and strain TRM95001T were 79.2-83.8%, compared to their closely related strains. The G + C content values of strain TRM95111T and TRM95001T were 65.1 and 60.7mol%, respectively. Two isolates contained predominant quinone of Q-10 and the major fatty acids was C18:1ω7c and they were sensitive to 1μg of amikacin and kanamycin. The polar lipids of strain TRM95111T included unidentified aminophospho lipids (APL1-3), unidentified phospholipids (PL1-2), phosphatidylcholine (PC), unidentified lipids (L1-5) and phospholipids of unknown structure containing glucosamine (NPG), compared to the polar lipids of strain TRM95001T including unidentified aminophospho lipids (APL1-3), unidentified phospholipids (PL1-2), phosphatidylcholine (PC), unidentified lipids (L2-5), hydroxy phosphatidyl ethanolamine (OH-PE) and phospholipids of unknown structure containing glucosamine (NPG). Nodulation tests showed that two strains could induce nodules formation in L. japonicus. Based on the genomic, phenotypic and phylogenetic analyses, strain TRM95111T and strain TRM95001T are suggested to represent two new species of the genus Rhizobium, whose names are proposed as Rhizobium alarense sp. nov. and Rhizobium halophilum sp. nov. The type strains are TRM95111T (=CCTCC AB 2021116T =JCM34826T) and TRM950011T (=CCTCC AB 2021095T =JCM34967T), respectively.

Plant Growth Promoting and Abiotic Stress Tolerant Chickpea (Cicer arietinum L.) Rhizobial Isolates from Some Areas of South Wollo Zone, Ethiopia

Chickpea (Cicer arietinum L) is an important pulse crop prized for its high protein content and is grown as a food source worldwide, including Ethiopia. However, the yield of chickpea is low due to low soil fertility and the ever-changing abiotic stresses. Therefore, this study aimed at isolation, characterization, and selection of chickpea rhizobia effective in their nitrogen fixation and abiotic stress tolerance potential. As a result, 150 nodule samples were collected from three districts of chickpea-producing areas in South Wollo. The nodules were crushed, and the rhizobia were isolated and characterized by using standard microbiological procedures. Based on the presumptive tests conducted, 103 (68.7%) of the rhizobial isolates were tentatively categorized as Rhizobium species. Regarding phosphate solubilization, only 48 (46.7%) solubilized phosphate with a solubilization index ranging from 2.1 to 2.7 mm. Twenty-four (50%) of the isolates were found to be hydrogen cyanide producers. Among the rhizobial isolates tested under greenhouse conditions, 37 (77.1%) of them induced nodulation on their host plant (chickpea). Their symbiotic effectiveness evaluation test confirmed that 16(47.1%), 6(17.6%), 26.47%, and 3(8.8%) were highly effective, effective, low effective, and ineffective, respectively. Of the authenticated rhizobial isolates, 12 (35.5%) of them, including WuCR-15, 16, 17, 18, 19, 20, 23, 30, 31, 32, 36, 38, and 48, accumulated higher shoot dry matter than the positive control. Isolates WuCR- 11, 17, and 36 showed resistance to low and high extreme abiotic stresses of pH, temperature, and salt. Consequently, rhizobial isolates, WuCR- 11, 17, and 36, which were effective and competent in all the tested parameters, were recommended as good rhizobial candidates for applications under greenhouse and field conditions.

Genome Insight and Description of Previously Uncultured N2-Fixing Bacterium Rhizobium terricola sp. nov., Isolated from Forest Rhizospheric Soil by Using Modified Culture Method

A bacterial strain S-51T was isolated from rhizospheric forest soil at Kyonggi University during the study of previously uncultured bacterium. The phylogenetic analysis was based on 16S rRNA gene sequences that indicated that strain S-51T belonged to the genus Rhizobium within the family Rhizobiaceae. The closest members of strain S-51T were Rhizobium naphthalenivorans TSY03bT (98.2% sequence similarity) and Rhizobium selenitireducens ATCC BAA-1503T (98.1%). The sequence similarities of other members were <97.7%. The sole respiratory quinone was Q-10 and the major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, and unidentified glycolipid. The principal fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c), cyclo-C19:0ω8c, and C18:0. The DNA G+C content was 63.1 mol%. The genome was 4930044 bp long and contained N2-fixing genes, such as fixF, ntrC, and ptsN, in addition to respiratory nitrate reductase genes, such as narC, narG, narH, narI, and narJ. The average nucleotide identity (ANIu), average amino acid identity (AAI), and digital DNA-DNA hybridization (dDDH) relatedness between strain S-51T and phylogenetically related species were ≤82.6, ≤83.6 and ≤25.3%, respectively, much lower than the species delineation thresholds. Based on the polyphasic taxonomic study, strain S-51T represents a new species in the genus Rhizobium, for which the name Rhizobium terricola is proposed. The type strain is S-51T (=KACC 19117T = KEMB 9005-539T = NBRC 112711T).

Rhizobium quercicola sp. nov., isolated from the leaf of Quercus variablis in China.

Strain DKSPLA3T, a novel Gram-negative, catalase-positive, oxidase-positive, non-spore-forming, aerobic, non-nitrogen-fixing, non-motile bacterium was isolated from Quercus variablis leaf, in Zunyi, Guizhou, China. Growth occurred at 4-37°C (optimum 28°C), pH 4.0-9.0 (optimum pH 7.0) and up to 4.0% (w/v) NaCl (optimum under 2.0%, w/v). Phylogeny based on 16S rRNA gene indicated that strain DKSPLA3T was a novel species in the genus Rhizobium, which was supported by average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values. The predominant fatty acids of strain DKSPLA3T were C16:0, C18:1 ω7c and/or C18:1 ω6c and C18:1 ω7c 11-methyl. The major respiratory quinone was Q-10. Major polar lipids were diphosphatidyl glycerol (DPG), phosphatidyl glycerol (PG), phosphatidylethanolamine (PE), phosphatidylmonomethylethanolamine (PME), phosphatidylcholine (PC), two unidentified phospholipids (PL) and nine unidentified lipids (L). The genomic G + C content was 64.47mol%. Based on the phenotypic, phylogenetic and genotypic data, DKSPLA3T should be classified as a novel species in the genus Rhizobium, for which the name Rhizobium quercicola sp. nov. (KCTC 82843T = CFCC 16,707T) is proposed.

Two New Rhizobiales Species Isolated from Root Nodules of Common Sainfoin (Onobrychis viciifolia) Show Different Plant Colonization Strategies.

ABSTRACTRoot nodules of legume plants are primarily inhabited by rhizobial nitrogen-fixing bacteria. Here, we propose two new Rhizobiales species isolated from root nodules of common sainfoin (Onobrychis viciifolia), as shown by core-gene phylogeny, overall genome relatedness indices, and pan-genome analysis. Mesorhizobium onobrychidis sp. nov. actively induces nodules and achieves atmospheric nitrogen and carbon dioxide fixation. This species appears to be depleted in motility genes and is enriched in genes for direct effects on plant growth performance. Its genome reveals functional and plant growth-promoting signatures, like a large unique chromosomal genomic island with high density of symbiotic genetic traits. Onobrychidicola muellerharveyae gen. nov. sp. nov. is described as a type species of the new genus Onobrychidicola in Rhizobiaceae. This species comprises unique genetic features and plant growth-promoting traits (PGPTs), which strongly indicate its function in biotic stress reduction and motility. We applied a newly developed bioinformatics approach for in silico prediction of PGPTs (PGPT-Pred), which supports the different lifestyles of the two new species and the plant growth-promoting performance of M. onobrychidis in the greenhouse trial.IMPORTANCE The intensive use of chemical fertilizers has a variety of negative effects on the environment. Increased utilization of biological nitrogen fixation (BNF) is one way to mitigate those negative impacts. In order to optimize BNF, suitable candidates for different legume species are required. Despite intensive search for new rhizobial bacteria associated with legumes, no new rhizobia have recently been identified from sainfoin (Onobrychis viciifolia). Here, we report on the discovery of two new rhizobial species associated with sainfoin, which are of high importance for the host and may help to increase sustainability in agricultural practices. We employed the combination of in silico prediction and in planta experiments, which is an effective way to detect promising plant growth-promoting bacteria.