Rhizobium petrolearium sp. nov., isolated from oil-contaminated soil

Phenanthrene-Degrading and Nickel-Resistant Neorhizobium Strain Isolated from Hydrocarbon-Contaminated Rhizosphere of Medicago sativa L

Pollutant degradation and heavy-metal resistance may be important features of the rhizobia, making them promising agents for environment cleanup biotechnology. The degradation of phenanthrene, a three-ring polycyclic aromatic hydrocarbon (PAH), by the rhizobial strain Rsf11 isolated from the oil-polluted rhizosphere of alfalfa and the influence of nickel ions on this process were studied. On the basis of whole-genome and polyphasic taxonomy, the bacterium Rsf11 represent a novel species of the genus Neorhizobium, so the name Neorhizobium phenanthreniclasticum sp. nov. was proposed. Analysis of phenanthrene degradation by the Rsf1 strain revealed 1-hydroxy-2-naphthoic acid as the key intermediate and the activity of two enzymes apparently involved in PAH degradation. It was also shown that the nickel resistance of Rsf11 was connected with the extracellular adsorption of metal by EPS. The joint presence of phenanthrene and nickel in the medium reduced the degradation of PAH by the microorganism, apparently due to the inhibition of microbial growth but not due to the inhibition of the activity of the PAH degradation enzymes. Genes potentially involved in PAH catabolism and nickel resistance were discovered in the microorganism studied. N. phenanthreniclasticum strain Rsf11 can be considered as a promising candidate for use in the bioremediation of mixed PAH-heavy-metal contamination.

Neorhizobium turbinariae sp. nov., a coral-beneficial bacterium isolated from Turbinaria peltata

Coral reef ecosystems are facing decline due to climate change, overfishing, habitat destruction and pollution. Bacteria play an essential role in maintaining the stability of coral reef ecosystems, influencing the well-being and fitness of coral hosts. The exploitation of coral probiotics has become an urgent issue. A short-rod shaped aerobic bacterium, designated NTR19T, was isolated in a healthy coral Turbinaria peltata from Daya Bay, Shenzhen, PR China. Its cells were Gram-negative, motile with a polar flagellum. The activities of catalase and oxidase were positive. Strain NTR19T grew at 10-41 °C (optimum, 28 °C), with NaCl concentrations of 0-4 % (w/v; optimum, 0.5 %) and at pH 5.0-9.5 (optimum, pH 7.0-7.5). The predominant fatty acids (>10 %) were summed feature 8 (57.6 %), C19 : 0 cyclo ω8c (12.6 %) and C16 : 0 (12.0 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phospholipid and phosphatidylcholine. The major respiratory quinone was Q-10. The draft genome was 4.68 Mbp with 61.2 mol% DNA G+C content. In total, 4477 coding sequences were annotated and there were 64 RNA genes. The average nucleotide identity (ANI) and average amino acid identity (AAI) values between strain NTR19T and the related Neorhizobium species were 78.23-79.70% and 80.26-80.50 %, respectively. This strain encoded many proteins for the activities of catalase and oxidase in the genome. Strain NTR19T was clearly distinct from its closest neighbours Rhizobium oryzicola ACCC 05753T and Neorhizobium petrolearium ACCC 11238T with the 16S rRNA gene sequence similarity values of 96.86 and 96.36 %, respectively. The results of phylogenetic analysis, as well as ANI and AAI values, revealed that strain NTR19T belongs to Neorhizobium and was distinct from other species of this genus. The physiological, biochemical and chemotaxonomic characteristics also supported the species novelty of strain NTR19T. Thus, strain NTR19T is considered to be classified as a novel species in the genus Neorhizobium, for which the name Neorhizobium turbinariae sp. nov. is proposed. The type strain is NTR19T (=JCM 35342T=MCCC 1K07226T).

Genomics for the characterization of the mechanisms of microbial strains in degrading petroleum pollutants

Four petroleum-tolerant bacteria, namely, Pseudomonas hibiscicola, Enterobacter hormaechei, Rhizobium pusense and Pseudomonas japonica were isolated. These strains showed excellent performance in the remediation of petroleum contamination with degradation percentages of 26.13%, 26.47%, 32.27%, and 18.74% for petroleum hydrocarbons, 29.63%, 70.11%, 88.38%, and 67.03% for n-docosane, and 61.00%, 96.36%, 98.00%, and 67.01% for fluorene. Accordingly, the strain of Rhizobium pusense was used to further study its underlying degradation mechanism. N-docosane could be metabolised through the pathway of subterminal oxidation by Rhizobium pusense, while the main pathway for fluorene metabolism is the meta-cleavage. R. pusense contains 10 genes that are involved in the synthetic of biosurfactants and 71 genes that are involved in the metabolism of petroleum hydrocarbons and organic pollutants, such as hydrocarbons, toluene, xylene, ethylbenzene and naphthalene. This study was the first to determine that concerning the metabolism ability and metabolic genes of R. pusense for petroleum pollutant degradation, which is important for understanding the bioremediation mechanism of petroleum pollution.

Efficient pollutants removal and microbial flexibility under high-salt gradient of an oilfield wastewater treatment system

The treatment of hypersaline oilfield wastewater (HSOW) is a challenge due to its complex composition and low biodegradability, especially in coastal areas. In this study, an HSOW treatment system of gas flotation and biochemistry technology combined with constructed wetland (CW) was investigated. The combined treatment system could efficiently remove COD, NH₄⁺-N and oil under high salinity (1.36-2.21 × 10⁴ mg/L), with average removal rates of 98.5%, 99.9% and 96%, respectively. Meanwhile, different salinity shaped particular community structures and functions. The abundance of Marivita, Parvibaculum, etc. was highly correlated with salinity. Co-occurrence network resulted that the microorganisms were highly interconnected, and formed a functional group of petroleum degrading. Pseudomonas, Rosevarius, Alternaria, etc. were the key genera. Moreover, functional prospected revealed that high salinity reduced the energy metabolism activity. This study will optimize the combined process and provide the basis for further extraction of high-efficiency degradation strains for HSOW enhanced treatment.

Rhizobium setariae sp. nov., an Indole-3-Acetic Acid-Producing Bacterium Isolated from Green Foxtail, Setaria viridis

A Gram-negative, indole-3-acetic acid-producing, aerobic, motile strain, designated as KVB221^T, was isolated from a green foxtail plant, Setaria viridis, from a park near the coast of Haeundae Beach, Busan, Republic of Korea. The 16S rRNA gene analysis revealed strain KVB221^T to be a member of the genus Rhizobium, from which Rhizobium alvei TNR-22^T (97.2%), Rhizobium daejeonense L61^T (96.9%), and Rhizobium ipomoeae shin9-1^T (95.7%) were selected for comparative analysis. Growth of the strain was observed at 10-50 °C (optimum 25-30 °C), at pH 5-10 (optimum pH 7), and in the presence of 0-8% NaCl (optimum 0%). The strain was observed to produce 36.3 ± 0.8 μg/ml of indole following 5 days of incubation. The major fatty acids are comprised of C_16:0, C_19:0 cyclo ω8c, C_18:1 ω7c, and the unresolved group summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c), while major polar lipids are identified as phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and phosphatidylmonomethylethanolamine (PME). The predominant quinone is Q-10 and the DNA G+C content of the strain is 59.3%. Based on publicly available genome data between strain KVB221^T and its closely related strains, the average nucleotide identity and in silico DNA-DNA hybridization values ranged from 72.7 to 73.1 and 19.7 to 20.4%, respectively. Based on the chemotaxonomic, phenotypic, and genomic comparisons reported here, we propose Rhizobium setariae sp. nov. as a novel species belonging to the genus Rhizobium. The type strain is KVB221^T (= KACC 21713^T = NBRC 114644^T).

Taxonomy of Rhizobiaceae revisited: proposal of a new framework for genus delimitation

The alphaproteobacterial family Rhizobiaceae is highly diverse, with 168 species with validly published names classified into 17 genera with validly published names. Most named genera in this family are delineated based on genomic relatedness and phylogenetic relationships, but some historically named genera show inconsistent distribution and phylogenetic breadth. The most problematic is Rhizobium , which is notorious for being highly paraphyletic, as most newly described species in the family are assigned to this genus without consideration of their proximity to existing genera, or the need to create novel genera. Moreover, many Rhizobiaceae genera lack synapomorphic traits that would give them biological and ecological significance. We propose a common framework for genus delimitation within the family Rhizobiaceae , wherein genera are defined as monophyletic groups in a core-genome gene phylogeny, that are separated from related species using a pairwise core-proteome average amino acid identity (cpAAI) threshold of approximately 86 %. We further propose that additional genomic or phenotypic evidence can justify division of species into separate genera even if they share greater than 86 % cpAAI. Applying this framework, we propose to reclassify Rhizobium rhizosphaerae and Rhizobium oryzae into Xaviernesmea gen. nov. Data is also provided to support the formation of Peteryoungia aggregata comb. nov., Endobacterium yantingense comb. nov., Neorhizobium petrolearium comb. nov., Pararhizobium arenae comb. nov., Pseudorhizobium tarimense comb. nov. and Mycoplana azooxidifex comb. nov. Lastly, we present arguments that the unification of the genera Ensifer and Sinorhizobium in Opinion 84 of the Judicial Commission is no longer justified by current genomic and phenotypic data. Despite pairwise cpAAI values for all Ensifer species and all Sinorhizobium species being >86 %, additional genomic and phenotypic data suggest that they significantly differ in their biology and ecology. We therefore propose emended descriptions of Ensifer and Sinorhizobium , which we argue should be considered as separate genera.

Rhizobium flavescens sp. nov., Isolated from a Chlorothalonil-Contaminated Soil

A Gram-negative, facultative anaerobic, non-lagellated and rod-shaped bacterium FML-4^T was isolated from a chlorothalonil-contaminated soil in Nanjing, China. Phylogenetic analyses of 16S rRNA genes revealed that the strain FML-4^T shared the highest sequence similarity of 97.1% with Ciceribacter thiooxidans KCTC 52231^T, followed by Rhizobium rosettiformans CCM 7583^T (97.0%) and R. daejeonense KCTC 12121^T (96.8%). Although the sequence similarities of the housekeeping genes thrC, rceA, glnII, and atpD between strain FML-4^T and C. thiooxidans KCTC 52231^T were 83.8%, 88.7%, 86.2%, and 92.0%, respectively, strain FML-4^T formed a monophyletic clade in the cluster of Rhizobium species. Importantly, the feature gene of the genus Rhizobium, nifH gene (encoding the dinitrogenase reductase), was detected in strain FML-4^T but not in C. thiooxidans KCTC 52231^T. In addition, strain FML-4^T contained the summed feature 8 (C_18:1ω7c and/or C_18:1ω6c), C_19:0 cyclo ω8c and C_16:0 as the major fatty acids. Genome sequencing of strain FML-4^T revealed a genome size of 7.3 Mbp and a G+C content of 63.0 mol%. Based on the results obtained by phylogenetic and chemotaxonomic analyses, phenotypic characterization, average nucleotide identity (ANI, similarity 77.3-75.4%), and digital DNA-DNA hybridization (dDDH, similarity 24.5-22.3%), it was concluded that strain FML-4^T represented a novel species of the genus Rhizobium, for which the name Rhizobium flavescens sp. nov. was proposed (type strain FML-4^T = CCTCC AB 2019354^T = KCTC 62839^T).

Evaluation of rhizoremediation and methane emission in diesel-contaminated soil cultivated with tall fescue (Festuca arundinacea)

Rhizoremediation, CH₄ emission, and bacterial community dynamics were evaluated in diesel-contaminated soil cultivated with tall fescue via a pot experiment. At the beginning of the experiment, total petroleum hydrocarbons (TPHs) removal efficiency was 30.2% in tall fescue-cultivated soil, which was significantly higher than that of unplanted soil (19.4%). However, when compost was added as a soil amendment, TPHs removal efficiency increased to 39.2% in tall fescue-cultivated soil. Interestingly, potential CH₄ emissions were more affected by the initial diesel concentration than by compost addition or tall fescue planting. Specifically, the potential CH₄ emission was approximately 3.8 times higher in the treatment with the highest initial diesel concentration (T-WC38) than that of the treatment with the lowest initial diesel concentration (T-WC5). Functional gene analysis revealed that TPHs removal had a linear correlation with the alkB/16S gene ratio, whereas potential CH₄ emission had a linear correlation with pmoA gene copy numbers. Initial diesel concentrations in soil also affected bacterial community structures and the genera Rhizobium, Halothiobacillus, and Geobacter were found to be positively linked to diesel-contaminated soil rhizoremediation. Therefore, this study provides useful insights into the development of strategies to enhance rhizoremediation efficiency and CH₄ emission mitigation in diesel-contaminated soils.

Rhizodegradation of PAHs differentially altered by C3 and C4 plants

Pyrosequencing of 16S ribosomal RNA (rRNA) was employed to characterize bacterial communities colonizing the rhizosphere of plants with C3 and C4 photosynthetic pathways grown in soil contaminated with polycyclic aromatic hydrocarbons (PAHs) after 60 and 120 days. The results of this study exhibited a clear difference in bacterial diversity between the rhizosphere and non-rhizosphere samples and between the rhizospheres of the C3 and C4 plants after 120 days. In both C3 and C4 rhizospheres, an incremental change in PAHs degrading bacterial genera was observed in the 120th day samples compared to the 60th day ones. Among the PAHs degrading bacterial genera, Pseudomonas showed good resistance to PAHs in the 120th day rhizosphere of both C3 and C4 plants. Conversely, the genus Sphingomonas showed sensitivity to PAHs in the 120th day rhizosphere soils of C3 plants only. Also, a significant increase in the PAHs degrading genera was observed at 120th day in the C4 rhizosphere in comparison to the C3 rhizosphere, which was reflected in a reduced PAHs concentration measured in the soil remediated with C4 plants rather than C3 plants. These results suggest that the rhizoremediation of PAHs was primarily governed by the plant photosystems, which led to differences in root secretions that caused the variation in bacterial diversity seen in the rhizospheres. This study is the first report to demonstrate the greater effectiveness of C4 plants in enhancing the PAHs degrading bacterial community than C3 plants.

Isolation, Identification and Characterization of Endophytic Bacterium Rhizobium oryzihabitans sp. nov., from Rice Root with Biotechnological Potential in Agriculture

A flagellate, rod–shaped bacterium designated strain M15^T was isolated from rice roots. Phylogenetic analysis based on the sequences of the 16S rRNA, housekeeping genes and genomes showed that the isolate belonged to the genus Rhizobium, with the highest 16S rRNA similarity to Rhizobium radiobacter LMG140^T (99.64%) and Rhizobium pusense NRCPB10^T (99.36%), respectively. The complete genome of the strain M15^T has a 59.28% G+C content, and the highest average nucleotide identity (ANI) and DNA-DNA relatedness (DDH) values were obtained with R. radiobacter LMG140^T (88.11%, 54.80%), R. pusense NRCPB10^T (86.00%, 53.00%) and R. nepotum 39/7^T (88.80%, 49.80%), respectively. Plant growth-promoting characteristics tests showed that the strain M15^T produced siderophore, 1–aminocyclopropane–1–carboxylate (ACC) deaminase and indole-3-acetic acid (IAA) and also produced some secondary metabolites according to the analysis of the comparative genomes. Based on the data mentioned above, we proposed that the strain M15^T represented a novel species of the genus Rhizobium, named Rhizobium oryzihabitans sp. nov. The type strain is M15^T (=JCM 32903^T  = ACCC 60121^T), and the strain M15^T can be a novel biofertilizer Rhizobium to reduce the use of synthetic fertilizers for plant growth promotion.

Rhizobium terrae sp. nov., Isolated from an Oil-Contaminated Soil in China

A Gram-stain-negative, facultative aerobic, non-spore-forming, non-motile, non-flagellated, rod-shaped bacterium, designated strain NAU-18^T was isolated from an oil-contaminated soil in China. Strain NAU-18^T could grow at 10-42 °C (optimum, 30 °C), at pH 5.0-8.0 (optimum, 7.0) and in the presence of 0-2.0% (w/v) NaCl (optimum, 0.5% NaCl in R2A). The predominant fatty acids were C_18:1ω7c (71.2%) and Summed feature 2 (5.1%), representing 76.3% of the total fatty acids. The major respiratory quinones were Q9 and Q10. The DNA G + C content of strain NAU-18^T was 61.4 mol% based on its draft genome sequence. Genome annotation of strain NAU-18^T predicted the presence of 6668 genes, of which 6588 are coding proteins and 80 are RNA genes. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain NAU-18^T was a member of the genus Rhizobium and showed 96.93% (with 93.2% coverage) and 96.81% (with 100% coverage) identities with those of Neorhizobium alkalisoli CCBAU 01393^T and Rhizobium oryzicola ZYY136^T, respectively. In the phylogenetic analysis, strain NAU-18^T and R. oryzicola ZYY136^T are consistently placed in the same branch. Strain NAU-18^T represents a novel species within the genus Rhizobium, for which the name Rhizobium terrae sp. nov. is proposed, with the type strain NAU-18^T (=KCTC 62418^T = CCTCC AB 2018075^T).

Rhizobium chutanense sp. nov., isolated from root nodules of Phaseolus vulgaris in China

Two Gram-stain-negative, rod-shaped bacterial strains (C5T and C16), isolated from root nodules of Phaseolus vulgaris L. in Jiangxi Province, PR China, were characterized by using a polyphasic taxonomical approach. The phylogenetic analysis of the 16S rRNA gene and three concatenated housekeeping genes (recA-glnII-atpD) revealed that C5T and C16 were members of the genus Rhizobium, yet were distinct from known species. The case for strain C5T representing a novel species was supported by genomic results. Pairwise digital DNA-DNA hybridization and average nucleotide identity values were much lower than the proposed and generally accepted species boundaries. The genome-based phylogenetic tree reconstructed by using the up-to-date bacterial core gene set consisting of 92 genes showed that the strains formed a monophyletic branch, further supporting this result. The symbiotic genes of nodC and nifH were identified in both strains; each could nodulate Phaseolus vulgaris and Glycine max but not Leucaena leucocephala, Pisum sativum or Medicago sativa plants. Major cellular fatty acids of C5T were summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c; 58.8 %), C18 : 1 ω7c 11-methyl (14.2 %) and C18 : 0 (8.1 %). The DNA G+C content of C5T was 61.4 mol%. Based on these genomic, chemotaxonomic and phenotypic characteristics, we propose a novel species: Rhizobium chutanense sp. nov. The type strain is C5T (=CCTCC AB 2018143T=LMG 30777T).

Rhizobium album sp. nov., isolated from a propanil-contaminated soil

A novel Gram-stain negative, facultatively anaerobic, non-spore-forming, motile and rod-shaped bacterium (NS-104^T) was isolated from a propanil-contaminated soil in Nanjing, China. Growth occurred at pH 5.0-9.0 (optimum 6.0), 16-37 °C (optimum 30 °C) and in the presence of 0-2.0% (w/v) NaCl (optimum, without NaCl). Strain NS-104^T showed high 16S rRNA gene sequence identity to Rhizobium azooxidifex DSM 100211^T (96.7%). The phylogenetic analysis of the 16S rRNA gene as well as the housekeeping genes recA, atpD and glnA demonstrated that strain NS-104^T belongs to the genus Rhizobium. Strain NS-104^T did not form nodules on six different legumes, and the nodD, nodC and nifH genes were neither amplified by PCR nor found in the draft genome of strain NS-104^T. The sole respiratory quinone was ubiquinone Q-10. The polar lipid profile included the major amounts phosphatidylmonomethylethanolamine, phosphatidylglycerol and moderate amounts of phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol and unidentified aminolipids. The major cellular fatty acids were C_18:1ω7c (39.6%), C_19:0 cyclo ω8c (29.8%) and C_16:0 (11.5%). The G + C content of strain NS-104^T was 61.9 mol%. Strain NS-104^T therefore represents a new species, for which the name Rhizobium album sp. nov. is proposed, with the type strain NS-104^T (= KCTC 62327^T = CCTCC AB 2017250^T).

Rhizobium wenxiniae sp. nov., an endophytic bacterium isolated from maize root

A novel Gram-stain-negative, aerobic, rod-shaped strain designated 166T was isolated from surface-sterilized root tissue of maize planted in the Fangshan District of Beijing, PR China. The 16S rRNA gene sequence analysis indicated that strain 166T belongs to the genus Rhizobium and is closely related to Rhizobium cellulosilyticum ALA10B2T and Rhizobium yantingense H66T with sequence similarities of 98.8 and 98.3 %, respectively. According to atpD and recA sequence analysis, the highest sequence similarity between strain 166T and R. cellulosilyticum ALA10B2T is 93.8 and 84.7 %, respectively. However, the new isolate exhibited relatively low levels of DNA-DNA relatedness with respect to R. cellulosilyticum DSM 18291T (20.8±2.3 %) and Rhizobium yantingense CCTCC AB 2014007T (47.2±1.4 %). The DNA G+C content of strain 166T was 59.8 mol%. The main polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, an unidentified aminophospholipid and an unidentified aminolipid. The major fatty acids of strain 166T were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The results of the physiological and biochemical tests and minor differences in the fatty acid profiles allowed a clear phenotypic differentiation of strain 166T from the type strains of closely related species, R. cellulosilyticum DSM 18291T and R. yantingense CCTCC AB 2014007T. Strain 166T represents a novel species within the genus Rhizobium, for which the name Rhizobium wenxiniae sp. nov. is proposed, with the type strain 166T (=CGMCC 1.15279T=DSM 100734T).

Rhizobium arenae sp. nov., isolated from the sand of Desert Mu Us, China

A Gram-strain-negative, rod-shaped, motile bacterium, designated MIM27T, was isolated from the sand of the Mu Us Desert, PR China. The strain could grow at 4-45 °C (optimum, 37 °C), at pH 6.6-9.0 (optimum, 8.0) and in the presence of 0-3 % (w/v) NaCl (optimum, 0 % in RNA liquid medium). The results of phylogenetic analysis of 16S rRNA gene sequences indicated that the strain represented a member of the genus Rhizobium, with the highest similarity (96.5 %) to Rhizobium pakistanense BN-19T. The results of analysis of the sequences of the nitrogen fixation gene nifH and three housekeeping genes, recA, atpD and glnII, also indicated that MIM27T was most closely related to the species of the genus Rhizobiumwith validly published names but the similarities were low (≤90.7 %). MIM27T did not form nodules on Pisum sativum, Vicia faba, Astragalus sinicus and Phaseolus vulgaris. The major respiratory quinone of MIM27T was Q-10. The genomic DNA G+C content was 59.8 mol%. Major fatty acids of MIM27T were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C18 : 1ω7c 11-methyl, C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 2 (C12 : 0 aldehyde and/or unknown ECL 10.9525). On the basis of the physiological, chemotaxonomic and phenotypic data, MIM27T is suggested to represent a novel species of the genus Rhizobium, for which the name Rhizobium arenae sp. nov. is proposed. The type strain is MIM27T (=KCTC 52299T=MCCC 1K03215T).

Rhizobium oryziradicis sp. nov., isolated from rice roots

Two Gram-stain-negative, aerobic, rod-shaped endophytic bacterial strains, N19T and N11-2, were isolated from fresh rice (Oryza sativa) roots during investigation of the rice endophytic bacterial diversity. The 16S rRNA gene sequence results indicated that the similarity between strains N19T and N11-2 was 100 %. Both of them belong to the genus Rhizobium, with close similarity to Rhizobium taibaishanense CCNWSX 0483T (97.7 %), followed by Rhizobium vitis NCPPB 3554T (97.5 %). The sequence similarities of the housekeeping genes recA, gyrB and glnA between the novel isolates and members of the established species of the genus Rhizobium were less than 87 %. The DNA-DNA hybridization rates between strains N19T and N11-2 were 87.9 % using the initial renaturation rate method. Based on draft genome sequences, strain N19T showed 18.2 % and 19.6 % DNA-DNA hybridization values to R. taibaishanense CCNWSX 0483T and R. vitis S4, which demonstrated that these new isolates represent a novel species in the genus Rhizobium. The main cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The DNA G+C content of strain N19T was 58.7 mol% (Tm). The polar lipid profile of N19T consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unknown lipid, two unknown aminolipids and an unidentified aminophospholipid. According to physiological and biochemical characteristics and genotypic data, strains N19T and N11-2 are considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium oryziradicis sp. nov. is proposed, with N19T (=ACCC 19962T=KCTC 52413T) as the type strain.

Isolation and characterization of Rhizobium sp. strain YS-1r that degrades lignin in plant biomass

AIMS

The aim of this work was to isolate novel lignin-degrading organisms.

METHODS AND RESULTS

Several pure cultures of bacteria that degrade lignin were isolated from bacterial consortia developed from decaying biomass. Among the isolates, Rhizobium sp. strain YS-1r (closest relative of Rhizobium petrolearium strain SL-1) was explored for its lignin-degrading ability. Microcosm studies showed that strain YS-1r was able to degrade a variety of lignin monomers, dimers and also native lignin in switchgrass and alfalfa. The isolate demonstrated lignin peroxidase (LiP) activity when grown on alkali lignin, p-anisoin, switchgrass or alfalfa, and only negligible activity was measured in glucose-grown cells suggesting inducible nature of the LiP activity. Analysis of the strain YS-1r genome revealed the presence of a variety of genes that code for various lignin-oxidizing, H₂ O₂ -producing as well as polysaccharide-hydrolysing enzymes.

CONCLUSIONS

This study shows both the genomic and physiological capability of bacteria in the genus Rhizobium to metabolize lignin and lignin-like compounds. This is the first detailed report on the lignocellulose-degrading ability of a Rhizobium species and thus this study expands the role of alpha-proteobacteria in the degradation of lignin.

SIGNIFICANCE AND IMPACT OF THE STUDY

The organism's ability to degrade lignin is significant since Rhizobia are widespread in soil, water and plant rhizospheres and some fix atmospheric nitrogen and also have the ability to degrade aromatic hydrocarbons.

An arsenate-reducing and alkane-metabolizing novel bacterium, Rhizobium arsenicireducens sp. nov., isolated from arsenic-rich groundwater

A novel arsenic (As)-resistant, arsenate-respiring, alkane-metabolizing bacterium KAs 5-22^T, isolated from As-rich groundwater of West Bengal was characterized by physiological and genomic properties. Cells of strain KAs 5-22^T were Gram-stain-negative, rod-shaped, motile, and facultative anaerobic. Growth occurred at optimum of pH 6.0-7.0, temperature 30 °C. 16S rRNA gene affiliated the strain KAs 5-22^T to the genus Rhizobium showing maximum similarity (98.4 %) with the type strain of Rhizobium naphthalenivorans TSY03b^T followed by (98.0 % similarity) Rhizobium selenitireducens B1^T. The genomic G + C content was 59.4 mol%, and DNA-DNA relatedness with its closest phylogenetic neighbors was 50.2 %. Chemotaxonomy indicated UQ-10 as the major quinone; phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol as major polar lipids; C_16:0, C_17:0, 2-OH C_10:0, 3-OH C_16:0, and unresolved C_18:1 ɷ7C/ɷ9C as predominant fatty acids. The cells were found to reduce O₂, As⁵⁺, NO₃^-, SO₄^2- and Fe³⁺ as alternate electron acceptors. The strain's ability to metabolize dodecane or other alkanes as sole carbon source using As⁵⁺ as terminal electron acceptor was supported by the presence of genes encoding benzyl succinate synthase (bssA like) and molybdopterin-binding site (mopB) of As⁵⁺ respiratory reductase (arrA). Differential phenotypic, chemotaxonomic, genotypic as well as physiological properties revealed that the strain KAs 5-22^T is separated from its nearest recognized Rhizobium species. On the basis of the data presented, strain KAs 5-22^T is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium arsenicireducens sp. nov. is proposed as type strain (=LMG 28795^T=MTCC 12115^T).

Diverse Bacteria with Lignin Degrading Potentials Isolated from Two Ranks of Coal

Taking natural coal as a “seed bank” of bacterial strains able to degrade lignin that is with molecular structure similar to coal components, we isolated 393 and 483 bacterial strains from a meager lean coal sample from Hancheng coalbed and a brown coal sample from Bayannaoer coalbed, respectively, by using different media. Statistical analysis showed that isolates were significantly more site-specific than medium-specific. Of the 876 strains belonging to 27 genera in Actinobacteria, Firmicutes, and Proteobacteria, 612 were positive for lignin degradation function, including 218 strains belonging to 35 species in Hancheng and 394 strains belonging to 19 species in Zhongqi. Among them, the dominant lignin-degrading strains were Thauera (Hancheng), Arthrobacter (Zhongqi) and Rhizobium (both). The genes encoding the laccases- or laccase-like multicopper oxidases, key enzymes in lignin production and degradation, were detected in three genera including Massila for the first time, which was in high expression by real time PCR (qRT-PCR) detection, confirming coal as a good seed bank.

Distinct Mineral Weathering Behaviors of the Novel Mineral-Weathering Strains Rhizobium yantingense H66 and Rhizobium etli CFN42

Bacteria play important roles in mineral weathering, soil formation, and element cycling. However, little is known about the interaction between silicate minerals and rhizobia. In this study, Rhizobium yantingense H66 (a novel mineral-weathering rhizobium) and Rhizobium etli CFN42 were compared with respect to potash feldspar weathering, mineral surface adsorption, and metabolic activity during the mineral weathering process. Strain H66 showed significantly higher Si, Al, and K mobilization from the mineral and higher ratios of cell numbers on the mineral surface to total cell numbers than strain CFN42. Although the two strains produced gluconic acid, strain H66 also produced acetic, malic, and succinic acids during mineral weathering in low- and high-glucose media. Notably, higher Si, Al, and K releases, higher ratios of cell numbers on the mineral surface to total cell numbers, and a higher production of organic acids by strain H66 were observed in the low-glucose medium than in the high-glucose medium. Scanning electron microscope analyses of the mineral surfaces and redundancy analysis showed stronger positive correlations between the mineral surface cell adsorption and mineral weathering, indicated by the dissolved Al and K concentrations. The results showed that the two rhizobia behaved differently with respect to mineral weathering. The results suggested that Rhizobium yantingense H66 promoted potash feldspar weathering through increased adsorption of cells to the mineral surface and through differences in glucose metabolism at low and high nutrient concentrations, especially at low nutrient concentrations.

IMPORTANCE

This study reported the potash feldspar weathering, the cell adsorption capacity of the mineral surfaces, and the metabolic differences between the novel mineral-weathering Rhizobium yantingense H66 and Rhizobium etli CFN42 under different nutritional conditions. The results showed that Rhizobium yantingense H66 had a greater ability to weather the mineral in low- and high-glucose media, especially in the low-glucose medium. Furthermore, Rhizobium yantingense H66 promoted mineral weathering through the increased adsorption of cells to the mineral surface and through increased organic acid production. Our results allow us to better comprehend the roles of different rhizobia in silicate mineral weathering, element cycling, and soil formation in various soil environments, providing more insight into the geomicrobial contributions of rhizobia to these processes.

Rhizobium marinum sp. nov., a malachite-green-tolerant bacterium isolated from seawater

A motile, Gram-stain-negative, non-pigmented bacterial strain, designated MGL06T, was isolated from seawater of the South China Sea on selection medium containing 0.1 % (w/v) malachite green. Strain MGL06T showed highest 16S rRNA gene sequence similarity to Rhizobium vignae CCBAU 05176T (97.2 %), and shared 93.2–96.9 % with the type strains of other recognized Rhizobium species. Phylogenetic analyses based on 16S rRNA and housekeeping gene sequences showed that strain MGL06T belonged to the genus Rhizobium. Mean levels of DNA–DNA relatedness between strain MGL06T and R. vignae CCBAU 05176T, Rhizobium huautlense S02T and Rhizobium alkalisoli CCBAU 01393T were 20 ± 3, 18 ± 2 and 14 ± 3 %, respectively, indicating that strain MGL06T was distinct from them genetically. Strain MGL06T did not form nodules on three different legumes, and the nodD and nifH genes were also not detected by PCR or based on the draft genome sequence. Strain MGL06T contained Q-10 as the predominant ubiquinone. The major fatty acid was C18 : 1ω7c/C18 : 1ω6c with minor amounts of C19 : 0 cyclo ω8c, C16 : 0 and C18 : 1ω7c 11-methyl. Polar lipids of strain MGL06T included unknown glycolipids, phosphatidylcholine, aminolipid, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, an unknown polar lipid and aminophospholipid. Based on its phenotypic and genotypic data, strain MGL06T represents a novel species of the genus Rhizobium, for which the name Rhizobium marinum sp. nov. is proposed. The type strain is MGL06T ( = MCCC 1A00836T = JCM 30155T).

The coupling of the plant and microbial catabolisms of phenanthrene in the rhizosphere of Medicago sativa

We studied the catabolism of the polycyclic aromatic hydrocarbon phenanthrene by four rhizobacterial strains and the possibility of enzymatic oxidation of this compound and its microbial metabolites by the root exudates of alfalfa (Medicago sativa L.) in order to detect the possible coupling of the plant and microbial metabolisms under the rhizospheric degradation of the organic pollutant. A comparative study of phenanthrene degradation pathways in the PAH-degrading rhizobacteria Ensifer meliloti, Pseudomonas kunmingensis, Rhizobium petrolearium, and Stenotrophomonas sp. allowed us to identify the key metabolites from the microbial transformation of phenanthrene, including 9,10-phenanthrenequinone, 2-carboxybenzaldehyde, and 1-hydroxy-2-naphthoic, salicylic, and o-phthalic acids. Sterile alfalfa plants were grown in the presence and absence of phenanthrene (0.03 g kg(-1)) in quartz sand under controlled environmental conditions to obtain plant root exudates. The root exudates were collected, concentrated by ultrafiltration, and the activity of oxidoreductases was detected spectrophotometrically by the oxidation rate for various substrates. The most marked activity was that of peroxidase, whereas the presence of oxidase and tyrosinase was detected on the verge of the assay sensitivity. Using alfalfa root exudates as a crude enzyme preparation, we found that in the presence of the synthetic mediator, the plant peroxidase could oxidize phenanthrene and its microbial metabolites. The results indicate the possibility of active participation of plants in the rhizospheric degradation of polycyclic aromatic hydrocarbons and their microbial metabolites, which makes it possible to speak about the coupling of the plant and microbial catabolisms of these contaminants in the rhizosphere.

Rhizobium oryzicola sp. nov., potential plant-growth-promoting endophytic bacteria isolated from rice roots

Bacterial strains ZYY136(T) and ZYY9 were isolated from surface-sterilized rice roots from a long-term experiment of rice-rice--Astragalus sinicus rotation. The 16S rRNA gene sequences of strains ZYY136(T) and ZYY9 showed the highest similarity, of 97.0%, to Rhizobium tarimense PL-41(T). Sequence analysis of the housekeeping genes recA, thrC and atpD clearly differentiated the isolates from currently described species of the genus Rhizobium. The DNA-DNA relatedness value between ZYY136(T) and ZYY9 was 82.3%, and ZYY136(T) showed 34.0% DNA-DNA relatedness with the most closely related type strain, R. tarimense PL-41(T). The DNA G+C content of strain ZYY136(T) was 58.1 mol%. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and C16 : 0 3-OH. Strains ZYY136(T) and ZYY9 could be differentiated from the previously defined species of the genus Rhizobium by several phenotypic characteristics. Therefore, we conclude that strains ZYY136(T) and ZYY9 represent a novel species of the genus Rhizobium, for which the name Rhizobium oryzicola sp. nov. is proposed (type strain ZYY136(T) = ACCC 05753(T) = KCTC 32088(T)).

Isolation and characterization of an early colonizing Rhizobium sp. R8 from a household toilet bowl

The bacterial community structure was compared between the third days', one week', and three weeks' biofilm samples from the surface of a household toilet bowl. It was found that the PCR-DGGE band pattern of 16S rRNA gene was dramatically changed after the third day and was not further changed until three weeks. This result suggests that there are early and late colonizing bacterial groups. One of the early colonizers isolated from the third days' sample was Rhizobium sp. R8, a closest relative to Rhizobium giardinii, which exhibited the highest biofilm formation activity in an artificial urine condition. R8 produced extracellular polysaccharides containing galactose, glucose, and mannose at the molar ratio of 8:1:1, which were probably responsible for the biofilm formation. Its excelled biofilm formation and urease activities together with the lack of nodulation and nitrogen fixing genes in R8 suggest that this strain has been specifically adapted to urine condition in a toilet bowl.

Rhizobium yantingense sp. nov., a mineral-weathering bacterium

A Gram-stain-negative, rod-shaped bacterial strain, H66(T), was isolated from the surfaces of weathered rock (purple siltstone) found in Yanting, Sichuan Province, PR China. Cells of strain H66(T) were motile with peritrichous flagella. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain H66(T) belongs to the genus Rhizobium. It is closely related to Rhizobium huautlense SO2(T) (98.1 %), Rhizobium alkalisoli CCBAU 01393(T) (98.0 %) and Rhizobium cellulosilyticum ALA10B2(T) (98.0 %). Analysis of the housekeeping genes, recA, glnII and atpD, showed low levels of sequence similarity (<92.0 %) between strain H66(T) and other recognized species of the genus Rhizobium. The predominant components of the cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The G+C content of strain H66(T) was 60.3 mol%. Strain H66(T) is suggested to be a novel species of the genus Rhizobium based on the low levels of DNA-DNA relatedness (ranging from 14.3 % to 40.0 %) with type strains of species of the genus Rhizobium and on its unique phenotypic characteristics. The namehttp://dx.doi.org/10.1601/nm.1279Rhizobium yantingense sp. nov. is proposed for this novel species. The type strain is H66(T) ( = CCTCC AB 2014007(T) = LMG 28229(T)).

Rhizobium flavum sp. nov., a triazophos-degrading bacterium isolated from soil under the long-term application of triazophos

A Gram-stain-negative, non-motile, pale yellow, rod-shaped bacterial strain, YW14T, was isolated from soil and its taxonomic position was investigated by a polyphasic study. Strain YW14T did not form nodules on three different legumes, and the nodD and nifH genes were not detected by PCR. Strain YW14T contained Q-10 as the predominant ubiquinone. The major cellular fatty acid was C18 : 1ω7c. Phylogenetic analyses based on 16S rRNA gene sequences and seven housekeeping gene sequences (recA, atpD, glnII, gyrB, rpoB, dnaK and thrC) showed that strain YW14T belonged to the genus Rhizobium . Strain YW14T showed 16S rRNA gene sequence similarity of 93.4–97.3 % to the type strains of recognized species of the genus Rhizobium . DNA–DNA relatedness between strain YW14T and the type strains of Rhizobium sullae IS123T and Rhizobium yanglingense CCBAU 71623T was 19.6–25.7 %, indicating that strain YW14T was distinct from them genetically. Strain YW14T could also be differentiated from these phylogenetically related species of the genus Rhizobium by various phenotypic properties. On the basis of phenotypic properties, phylogenetic distinctiveness and genetic data, strain YW14T is considered to represent a novel species of the genus Rhizobium , for which the name Rhizobium flavum sp. nov. is proposed. The type strain is YW14T ( = KACC 17222T = CCTCC AB2013042T).

Rhizobium rhizoryzae sp. nov., isolated from rice roots

Two strains (J3-AN59(T) and J3-N84) of Gram-stain-negative, aerobic and rod-shaped bacteria were isolated from the roots of fresh rice plants. The 16S rRNA gene sequence similarity results showed that the similarity between strains J3-AN59(T) and J3-N84 was 100 %. Both strains were phylogenetically related to members of the genus Rhizobium, and they were most closely related to Rhizobium tarimense ACCC 06128(T) (97.43 %). Similarities in the sequences of housekeeping genes between strains J3-AN59(T) and J3-N84 and those of recognized species of the genus Rhizobium were less than 90 %. The polar lipid profiles of both strains were predominantly composed of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and an unknown aminophospholipid. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The DNA G+C contents of J3-AN59(T) and J3-N84 were 55.7 and 57.1 mol%, respectively. The DNA-DNA relatedness value between J3-AN59(T) and J3-N84 was 89 %, and strain J3-AN59(T) showed 9 % DNA-DNA relatedness to R. tarimense ACCC 06128(T), the most closely related strain. Based on this evidence, we found that J3-AN59(T) and J3-N84 represent a novel species in the genus Rhizobium and we propose the name Rhizobium rhizoryzae sp. nov. The type strain is J3-AN59(T) ( = ACCC 05916(T) = KCTC 23652(T)).

Rhizobium subbaraonis sp. nov., an endolithic bacterium isolated from beach sand

Two strains (JC85(T) and JC108) of Gram-stain-negative, motile bacteria were isolated from endolithic beach sand samples on an oligotrophic medium. Based on the 16S rRNA gene sequence analysis, both strains were identified as belonging to the genus Rhizobium. Strain JC108 had 16S rRNA gene sequence similarity of 100 % with Rhizobium pusense NRCPB10(T) and formed a cluster with this strain. Strain JC85(T) had 96.9 % 16S rRNA gene sequence similarity and was 18 % related (based on DNA-DNA hybridization) to Rhizobium borbori DN316(T). With other strains of the genus Rhizobium, the 16S rRNA gene sequence similarity was less than 96.3 %. Strain JC85(T) could tolerate up to 3 % salinity, fix N(2), was resistant to ampicillin (10 µg) and was positive for catalase and oxidase. The major fatty acid was C(18 : 1)ω7c (69 %) with minor amounts of C(19 : 0) cyclo ω8c (8.9 %), C(16 : 0) (6.9 %), C(12 : 0) (5.7 %) and C(19 : 1)ω7c/C(19 : 1)ω6c (2.2 %). Polar lipids of strain JC85(T) include two unidentified aminophospholipids (APL1,2), two unidentified phospholipids (PL1,2), phosphatidylcholine and four unidentified lipids (L1-4). Q-10 is the major quinone of strain JC85(T). Based on polyphasic taxonomic analysis, strain JC85(T) represents a novel species for which, the name Rhizobium subbaraonis JC85(T) is proposed. The type strain is JC85(T) ( = DSM 24765(T) = KCTC 23614(T)).