Remediation of aniline-contaminated aquifer by combining in-well Rhizobium borbori and circulated groundwater electrolysis

Aniline has become a common groundwater contaminant due to its wide use as a raw material in agriculture and pharmaceutical products. The current technologies for in situ remediation of aniline in groundwater are limited by the strains deficient in bacterial species, limited oxygen supply, excessive waste gas load and cost. Accordingly, we conducted a laboratory sand tank experiment to remediate groundwater contaminated with aniline by combining circulated groundwater electrolysis and in-well Rhizobium borbori, which was isolated from activated sludge. The results of the experiment indicated that the optimum concentration of aniline for Rhizobium borbori is about 5 mg/L, beyond which the maximum cell density and the highest specific growth rate decreases as the aniline concentration increases. The optimized duration for immobilizing the Rhizobium borbori into the bioreactor is 4-5 days. Though the Rhizobium borbori was strongly inhibited by the high-concentration of aniline, the immobilized bioreactor in the 350 mg/L aniline solution successfully formed biofilm. The aniline volatilization had limited influence on the observation of bioremediation performance, and the combination of circulated groundwater and in-well Rhizobium borbori supplied a steady dose of oxygen to the bioreactor efficiently degrading the entire region between the injection and extraction well. In addition, a numerical model for the sand tank remediation experiment was used to estimate the yield coefficient of oxygen to be 0.484 g/g, which indicates the presence of ammonia nitrogen as by-products; accordingly, a smaller wellbore size as well a higher circulation flow rate and intensity of current are recommended to improve the water quality. Despite the positive outcomes and potential of the newly developed technology to degrade subsurface aniline, parallel experiments should be conducted to estimate the environmental risk of the by-products and explore the controlling mechanisms of each component in this comprehensive system.

Phylogenomic reappraisal of the family Rhizobiaceae at the genus and species levels, including the description of Ectorhizobium quercum gen. nov., sp. nov

The family Rhizobiaceae contains 19 validly described genera including the rhizobia groups, many of which are important nitrogen-fixing bacteria. Early classification of Rhizobiaceae relied heavily on the poorly resolved 16S rRNA genes and resulted in several taxonomic conflicts. Although several recent studies illustrated the taxonomic status of many members in the family Rhizobiaceae, several para- and polyphyletic genera still needed to be elucidated. The rapidly increasing number of genomes in Rhizobiaceae has allowed for a revision of the taxonomic identities of members in Rhizobiaceae. In this study, we performed analyses of genome-based phylogeny and phylogenomic metrics to review the relationships of 155-type strains within the family Rhizobiaceae. The UBCG and concatenated protein phylogenetic trees, constructed based on 92 core genes and concatenated alignment of 170 single-copy orthologous proteins, demonstrated that the taxonomic inconsistencies should be assigned to eight novel genera, and 22 species should be recombined. All these reclassifications were also confirmed by pairwise cpAAI values, which separated genera within the family Rhizobiaceae with a demarcation threshold of ~86%. In addition, along with the phenotypic and chemotaxonomic analyses, a novel strain BDR2-2T belonging to a novel genus of the family Rhizobiaceae was also confirmed, for which the name Ectorhizobium quercum gen. nov., sp. nov. was proposed. The type strain is BDR2-2T (=CFCC 16492T = LMG 31717T).

Stable-isotope probing coupled with high-throughput sequencing reveals bacterial taxa capable of degrading aniline at three contaminated sites with contrasting pH

The biodegradation of aniline is an important process related to the attenuation of aniline pollution at contaminated sites. Aniline contamination could occur in various pH (i.e., acidic, neutral, and alkaline) environments. However, little is known about preferred pH conditions of diverse aniline degraders at different sites. This study investigated the active aniline degraders present under contrasting pH environments using three aniline-contaminated cultures, namely, acidic sludge (ACID-S, pH 3.1), neutral river sediment (NEUS, pH 6.6), and alkaline paddy soil (ALKP, pH 8.7). Here, DNA-based stable isotope probing coupled with high-throughput sequencing revealed that aniline degradation was associated with Armatimonadetes sp., Tepidisphaerales sp., and Rhizobiaceae sp. in ACID-S; Thauera sp., Zoogloea sp., and Acidovorax sp. in NEUS; Delftia sp., Thauera sp., and Nocardioides sp. in ALKP. All the putative aniline-degrading bacteria identified were present in the "core" microbiome of these three cultures; however, only an appropriate pH may facilitate their ability to metabolize aniline. In addition, the biotic interactions between putative aniline-degrading bacteria and non-direct degraders showed different characteristics in three cultures, suggesting aniline-degrading bacteria employ diverse survival strategies in different pH environments. These findings expand our current knowledge regarding the diversity of aniline degraders and the environments they inhabit, and provide guidance related to the bioremediation of aniline contaminated sites with complex pH environments.

Microbial Interactions Drive the Complete Catabolism of the Antibiotic Sulfamethoxazole in Activated Sludge Microbiomes

Microbial communities are believed to outperform monocultures in the complete catabolism of organic pollutants via reduced metabolic burden and increased robustness to environmental challenges; however, the interaction mechanism in functional microbiomes remains poorly understood. Here, three functionally differentiated activated sludge microbiomes (S1: complete catabolism of sulfamethoxazole (SMX); S2: complete catabolism of the phenyl part of SMX ([phenyl]-SMX) with stable accumulation of its heterocyclic product 3-amino-5-methylisoxazole (3A5MI); A: complete catabolism of 3A5MI rather than [phenyl]-SMX) were enriched. Combining time-series cultivation-independent microbial community analysis, DNA-stable isotope probing, molecular ecological network analysis, and cultivation-dependent function verification, we identified key players involved in the SMX degradation process. Paenarthrobacter and Nocardioides were primary degraders for the initial cleavage of the sulfonamide functional group (-C-S-N- bond) and 3A5MI degradation, respectively. Complete catabolism of SMX was achieved by their cross-feeding. The co-culture of Nocardioides, Acidovorax, and Sphingobium demonstrated that the nondegraders Acidovorax and Sphingobium were involved in the enhancement of 3A5MI degradation. Moreover, we unraveled the internal labor division patterns and connections among the active members centered on the two primary degraders. Overall, the proposed methodology is promisingly applicable and would help generate mechanistic, predictive, and operational understanding of the collaborative biodegradation of various contaminants. This study provides useful information for synthetic activated sludge microbiomes with optimized environmental functions.

Allorhizobium terrae sp. nov., isolated from paddy soil, and reclassification of Rhizobium oryziradicis (Zhao et al. 2017) as Allorhizobium oryziradicis comb. nov

A polyphasic taxonomic approach was used to characterize a nitrogen-fixing bacterium, designated strain CC-HIH110^T, isolated from paddy soil in Taiwan. Cells of strain CC-HIH110^T were Gram-stain-negative, rod-shaped, motile with polar flagella, catalase-positive and oxidase-positive. Optimal growth occurred at 30 °С, pH 7 and 1 % NaCl. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-HIH110^T associated with Rhizobium oryziradicis (98.4 % sequence identity), Allorhizobium vitis (97.8 %), Allorhizobium taibaishanense (97.7 %) and Allorhizobium undicola (96.0 %), and lower sequence similarity to other species. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain CC-HIH110^T and the type strains of other closely related species were 71.5-88.6 % and 19.6-35.5 %, respectively. Strain CC-HIH110^T contained C_16 : 0 3-OH, C_14 : 0 3-OH/iso C_16 : 1 I and C_18 : 1 ω7c/C_{18  : 1} ω6c as the predominant fatty acids. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, three unknown aminophospholipids, two unknown phospholipids and an unknown lipid. The major polyamine was homospermidine. The DNA G+C content was 55.0 mol% and the predominant quinone was ubiquinone (Q-10). Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, ANI and dDDH analyses, strain CC-HIH110^T is proposed to represent a novel Allorhizobium species, for which the name Allorhizobium terrae sp. nov. (type strain CC-HIH110^T=BCRC 80932^T=JCM 31228^T). In addition, Rhizobium oryziradicis is reclassified as Allorhizobium oryziradicis (type strain N19^T=ACCC 19962^T=KCTC 52413^T) comb. nov.

Georhizobium profundi gen. nov., sp. nov., a piezotolerant bacterium isolated from a deep-sea sediment sample of the New Britain Trench

A novel alphaproteobacterium, strain WS11T, was isolated from a deep-sea sediment sample collected from the New Britain Trench. The full-length 16S rRNA gene of strain WS11T had the highest sequence similarity of 97.6 % to Rhizobium subbaraonis JC85T, followed by Mycoplana ramosa DSM 7292T (96.9 %) and Rhizobium azooxidifex Po 20/26T (96.8 %). Phylogenetic analysis of concatenated 16S rRNA, atpD and recA gene sequences showed that strain WS11T was deeply separated from the species within the family Rhizobiaceae. Phylogenomic analysis based on the whole-genome protein sequences showed that strain WS11T formed an independent monophyletic branch in the family Rhizobiaceae, paralleled with the species in the families Brucellaceae and Phyllobacteriaceae within the order Rhizobiales. Cells were Gram-stain-negative, oxidase- and catalase-positive, and aerobic short rods (1.5-2.4×0.9-1.0 µm). Growth was observed at salinities ranging from 0 to 5% (optimum, 1 %), from pH 6.5 to 9 (optimum, pH 7) and at temperatures between 20 and 30 °C (optimum, 28 °C). Strain WS11T was piezotolerant, growing optimally at 0.1 MPa (range 0.1-70 MPa). The main fatty acid was summed feature 8 (C18 : 1 ω7c/C18  : 1 ω 6c). The sole respiratory quinone was ubiquinone-10 (Q-10). The predominant polar lipids were phosphatidylcholine, two unidentified aminophospholipids and an unidentified phospholipid. The genome size was about 4.36 Mbp and the G+C content was 62.3 mol%. The combined genotypic and phenotypic data show that strain WS11T represents a novel species of a novel genus in the family Rhizobiaceae, for which the name Georhizobium profundi gen. nov., sp. nov. is proposed (type strain WS11T=MCCC 1K03498T=KCTC 62439T).

The diversity of hydrogen-producing bacteria and methanogens within an in situ coal seam

BACKGROUND

Biogenic and biogenic-thermogenic coalbed methane (CBM) are important energy reserves for unconventional natural gas. Thus, to investigate biogenic gas formation mechanisms, a series of fresh coal samples from several representative areas of China were analyzed to detect hydrogen-producing bacteria and methanogens in an in situ coal seam. Complete microbial DNA sequences were extracted from enrichment cultures grown on coal using the Miseq high-throughput sequencing technique to study the diversity of microbial communities. The species present and differences between the dominant hydrogen-producing bacteria and methanogens in the coal seam are then considered based on environmental factors.

RESULTS

Sequences in the Archaea domain were classified into four phyla and included members from Euryarchaeota, Thaumarchaeota, Woesearchaeota, and Pacearchaeota. The Bacteria domain included members of the phyla: Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Acidobacteria, Verrucomicrobia, Planctomycetes, Chloroflexi, and Nitrospirae. The hydrogen-producing bacteria was dominated by the genera: Clostridium, Enterobacter, Klebsiella, Citrobacter, and Bacillus; the methanogens included the genera: Methanorix, Methanosarcina, Methanoculleus, Methanobrevibacter, Methanobacterium, Methanofollis, and Methanomassiliicoccus.

CONCLUSION

Traces of hydrogen-producing bacteria and methanogens were detected in both biogenic and non-biogenic CBM areas. The diversity and abundance of bacteria in the biogenic CBM areas are relatively higher than in the areas without biogenic CBM. The community structure and distribution characteristics depend on coal rank, trace metal elements, temperature, depth and groundwater dynamic conditions. Biogenic gas was mainly composed of hydrogen and methane, the difference and diversity were caused by microbe-specific fermentation of substrates; as well as by the environmental conditions. This discovery is a significant contribution to extreme microbiology, and thus lays the foundation for research on biogenic CBM.

Rhizobium albus sp. nov., Isolated from Lake Water in Xiamen, Fujian Province of China

A Gram-stain-negative, aerobic bacterial strain, designated Y21^T, was isolated from surface lake water in Xiamen, Fujian Province of China. Growth was observed at temperatures from 4 to 37 °C, at salinities from 0 to 7.0 % and at pH from 6.0 to 10.0. Optimum growth was observed at 28 °C, at pH 7.0 and with 1.5-2.0 % (w/v) NaCl. The highest similarity of 16S rRNA gene sequence between strain Y21^T and the other strains was 96.9 %. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the strain was a member of the genus Rhizobium, forming a distinct lineage with R. subbaraonis KCTC 23614^T. The dominant fatty acids were summed feature 8 (comprising C_18:1 ω7c and/or C_18:1 ω6c), C_18:1 ω7c 11-methyl, which accounted for 78.1 %. The G+C content of the chromosomal DNA was 60.9 mol%. The predominant respiratory quinone was ubiquinone-10. The polar lipids of strain Y21^T were found to consist of five unidentified phospholipids and three unidentified aminolipids. According to its morphology, physiology, fatty acid composition and 16S rRNA sequence data, strain Y21^T should be regarded as a new species of the genus Rhizobium, for which Rhizobium albus sp. nov. is proposed (type strain Y21^T = MCCC 1F01210^T = KCTC 42252^T).

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).

Rhizobium gei sp. nov., a bacterial endophyte of Geum aleppicum

A bacterial strain, designated as ZFJT-2T, was isolated from the stem of Geum aleppicum Jacq. collected from Taibai Mountain in Shaanxi Province, north-west China. Cells of strain ZFJT-2T were Gram-stain-negative, strictly aerobic, rod-shaped and motile by means of a single polar flagellum. The major fatty acids were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0, 11-methyl C18 : 1ω7c and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), and the DNA G+C content was 58.3 mol% (HPLC). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ZFJT-2T was a member of the genus Rhizobium and was most closely related to Rhizobium giardinii KACC 10720T (98.6 % similarity) and Rhizobium herbae CCBAU 83011T (98.5 %). The low levels of sequence similarity found between the atpD, recA and glnII gene sequences of strain ZFJT-2T and those of recognized species of the genus Rhizobium (no more than 94.4, 87.2 and 89.5 %, respectively) indicated that it may represent a separate species of the genus Rhizobium. The DNA-DNA relatedness values for strain ZFJT-2T with respect to R. giardinii KACC 10720T and R. herbae CCBAU 83011T were 17.6 and 41.9 %, respectively. On the basis of phenotypic, phylogenetic and genotypic data, strain ZFJT-2T is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium gei sp. nov. is proposed. The type strain is ZFJT-2T (=CCTCC AB 2013015T=KCTC 32301T=LMG 27603T).

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).

Rhizobium helianthi sp. nov., isolated from the rhizosphere of sunflower

A Gram-stain-negative, non-spore-forming, rod-shaped and aerobic bacterium, designated Xi19T, was isolated from a soil sample collected from the rhizosphere of sunflower (Helianthus annuus) in Wuyuan county of Inner Mongolia, China and was characterized taxonomically by using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel isolate was related to species of the genus Rhizobium, sharing the greatest 16S rRNA gene sequence similarity with Rhizobium rhizoryzae J3-AN59T (98.4 %), followed by Rhizobium pseudoryzae J3-A127T (97.4 %). There were low similarities ( < 91 %) between the atpD, recA and glnII gene sequences of the novel strain and those of members of the genus Rhizobium. DNA-DNA hybridization values between strain Xi19T and the most related strain Rhizobium rhizoryzae J3-AN59T were low. The major cellular fatty acids of strain Xi19T were C16 : 0, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C19 : 0 cyclo ω8c. Q-10 was identified as the predominant ubiquinone and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The DNA G+C content of strain Xi19T was 60.2 mol%. On the basis of physiological and biochemical characteristics, coupled with genotypic data obtained in this work, strain Xi19T represents a novel species of the genus Rhizobium, for which the name Rhizobium helianthi is proposed. The type strain is Xi19T ( = CGMCC 1.12192T = KCTC 23879T).

Rhizobium pakistanensis sp. nov., isolated from groundnut (Arachis hypogaea) nodules grown in rainfed Pothwar, Pakistan

A Gram-negative, white, non-motile, rod shaped bacterial strain BN-19(T) was isolated from a root nodule of groundnut (Arachis hypogaea) in Pakistan. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain BN-19(T) formed a subclade in the genus Rhizobium together with Rhizobium alkalisoli CCBAU 01393(T), Rhizobium vignae CCBAU 05176(T), Rhizobium huautlense SO2(T) and Rhizobium tarimense PL-41(T) with sequence similarities of 97.5, 97.3, 97.2 and 97.1 % respectively. Sequence analysis of housekeeping genes atpD, glnII and recA (with sequence similarities of ≤92 %) confirmed the unique position of BN-19(T) in the genus Rhizobium. DNA-DNA relatedness between the strain BN-19(T) and R. alkalisoli CCBAU 01393(T), R. vignae CCBAU 05176(T), R. huautlense SO2(T) and R. tarimense PL-41(T) were 20.6, 22.5, 15.9 and 20.5 % respectively, further confirming that BN-19(T) represents a novel species in the genus Rhizobium. The DNA G + C content was 60.1 mol%. The dominant fatty acids of strain BN-19(T) were C19:0 cyclo ω8c, summed feature 2 (C14:0 3OH and/or C16:1 iso I) and summed feature 8 (C18:1 ω7c). Some phenotypic features also differentiate the strain BN-19(T) from the related species. On the basis of these results, strain BN-19(T) is considered to represent a novel species in the genus Rhizobium, for which the name Rhizobium pakistanensis sp. nov. is proposed. The type strain is BN-19(T) (=LMG 27895(T) = CCBAU 101086(T)).

Rhizobium populi sp. nov., an endophytic bacterium isolated from Populus euphratica

An endophytic bacterium, designated K-38T, was isolated from the storage liquid in the stems of Populus euphratica trees at the ancient Ugan River in Xinjiang, PR China. Strain K-38T was found to be rod-shaped, Gram-stain-negative, aerobic, non-motile and non-spore-forming. Strain K-38T grew at temperatures of 25–37 °C (optimum, 28 °C), at pH 6.0–9.0 (optimum, pH 7.5) and in the presence of 0–3 % (w/v) NaCl with 1 % as the optimum concentration for growth. According to phylogenetic analysis based on 16S rRNA gene sequences, strain K-38T was assigned to the genus Rhizobium with highest 16S rRNA gene sequence similarity of 97.2 % to Rhizobium rosettiformans W3T, followed by Rhizobium nepotum 39/7T (96.5 %) and Rhizobium borbori DN316T (96.2 %). Phylogenetic analysis of strain K-38T based on the protein coding genes recA, atpD and nifH confirmed (similarities were less than 90 %) it to be a representative of a distinctly delineated species of the genus Rhizobium . The DNA G+C content was determined to be 63.5 mol%. DNA–DNA relatedness between K-38T and R. rosettiformans W3T was 48.4 %, indicating genetic separation of strain K-38T from the latter strain. The major components of the cellular fatty acids in strain K-38T were revealed to be summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c; 57.2 %), C16 : 0 (13.6 %) and summed feature 2 (comprising C12 : 0 aldehyde, C14 : 0 3-OH/iso-C16 : 1 I and/or unknown ECL 10.928; 11.0 %). Polar lipids of strain K-38T include phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminophospholipids and two unidentified phospholipids. Q-10 was the major quinone in strain K-38T. Based on phenotypic, chemotaxonomic and phylogenetic properties, strain K-38T represents a novel species of the genus Rhizobium , for which the name Rhizobium populi sp. nov. is proposed. The type strain is K-38T ( = CCTCC AB 2013068T = NRRL B-59990T = JCM 19159T).

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 paknamense sp. nov., isolated from lesser duckweeds (Lemna aequinoctialis)

A Gram-stain-negative, rod-shaped bacterium was isolated and designated strain L6-8T during a study of endophytic bacterial communities in lesser duckweed (Lemna aequinoctialis). Cells of strain L6-8T were motile with peritrichous flagella. The analysis of the nearly complete 16S rRNA gene sequence indicated that strain L6-8T was phylogenetically related to species of the genus Rhizobium . Its closest relatives were Rhizobium borbori DN316T (97.6 %), Rhizobium oryzae Alt 505T (97.3 %) and Rhizobium pseudoryzae J3-A127T (97.0 %). The sequence similarity analysis of housekeeping genes recA, glnII, atpD and gyrB showed low levels of sequence similarity (<91.5 %) between strain L6-8T and other species of the genus Rhizobium with validly published names. The pH range for growth was 4.0–9.0 (optimum 6.0–7.0), and the temperature range for growth was 20–45 °C (optimum 30 °C). Strain L6-8T tolerated NaCl up to 2 % (w/v) (optimum 1 % NaCl). The predominant components of cellular fatty acids were C19 : 0 cyclo ω8c (31.32 %), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 25.39 %) and C16 : 0 (12.03 %). The DNA G+C content of strain L6-8T was 60.4 mol% (T m). nodC and nifH were not amplified in strain L6-8T. DNA–DNA relatedness between strain L6-8T and R. borbori DN316T, R. oryzae Alt505T and R. pseudoryzae J3-A127T was between 11.2 and 18.3 %. Based on the sequence similarity analyses, phenotypic, biochemical and physiological characteristics and DNA–DNA hybridization, strain L6-8T could be readily distinguished from its closest relatives and represents a novel species of the genus Rhizobium , for which the name Rhizobium paknamense sp. nov. is proposed. The type strain is L6-8T ( = NBRC 109338T = BCC 55142T).

Rhizobium tarimense sp. nov., isolated from soil in the ancient Khiyik River

A Gram-negative, non-motile, pale-yellow, rod-shaped bacterial strain, PL-41T, was isolated from Populus euphratica forest soil at the ancient Khiyik River valley in Xinjiang Uyghur Autonomous Region, People's Republic of China. Strain PL-41T grew optimally at 30 °C and pH 7.0–8.0. The major quinone was Q-10. The predominant cellular fatty acids of strain PL-41T were summed feature 8 (comprising C18 : 1ω7c and C18 : 1ω6c), C16 : 0 and C19 : 0 cyclo ω8c. Polar lipids of strain PL-41T include two unidentified aminophospholipids (APL1, 2), two unidentified phospholipids (PL1, 2), phosphatidylcholine and three unidentified lipids (L1–3). Strain PL-41T showed 16S rRNA gene sequence similarity of 97.0–97.5 % to the type strains of recognized species of the genus Rhizobium . Phylogenetic analysis of strain PL-41T based on the sequences of housekeeping genes recA and atpD confirmed (similarities are less than 90 %) its position as a distinct species of the genus Rhizobium . The DNA G+C content was 57.8 mol%. DNA–DNA relatedness between strain PL-41T and the type strains of Rhizobium huautlense S02T, Rhizobium alkalisoli CCBAU 01393T, Rhizobium vignae CCBAU 05176T and Rhizobium loessense CCBAU 7190BT were 33.4, 22.6, 25.5 and 45.1 %, respectively, indicating that strain PL-41T was distinct from them genetically. Strain PL-41T also can be differentiated from these four phylogenetically related species of the genus Rhizobium by various phenotypic properties. On the basis of phenotypic properties, phylogenetic distinctiveness and genetic data, strain PL-41T is considered to represent a novel species of the genus Rhizobium , for which the name Rhizobium tarimense sp. nov. is proposed. The type strain is PL-41T ( = CCTCC AB 2011011T = NRRL B-59556T).

Rapid and accurate species and genomic species identification and exhaustive population diversity assessment of Agrobacterium spp. using recA-based PCR

Agrobacteria are common soil bacteria that interact with plants as commensals, plant growth promoting rhizobacteria or alternatively as pathogens. Indigenous agrobacterial populations are composites, generally with several species and/or genomic species and several strains per species. We thus developed a recA-based PCR approach to accurately identify and specifically detect agrobacteria at various taxonomic levels. Specific primers were designed for all species and/or genomic species of Agrobacterium presently known, including 11 genomic species of the Agrobacterium tumefaciens complex (G1-G9, G13 and G14, among which only G2, G4, G8 and G14 still received a Latin epithet: pusense, radiobacter, fabrum and nepotum, respectively), A. larrymoorei, A. rubi, R. skierniewicense, A. sp. 1650, and A. vitis, and for the close relative Allorhizobium undicola. Specific primers were also designed for superior taxa, Agrobacterium spp. and Rhizobiaceace. Primer specificities were assessed with target and non-target pure culture DNAs as well as with DNAs extracted from composite agrobacterial communities. In addition, we showed that the amplicon cloning-sequencing approach used with Agrobacterium-specific or Rhizobiaceae-specific primers is a way to assess the agrobacterial diversity of an indigenous agrobacterial population. Hence, the agrobacterium-specific primers designed in the present study enabled the first accurate and rapid identification of all species and/or genomic species of Agrobacterium, as well as their direct detection in environmental samples.

Rhizobium halophytocola sp. nov., isolated from the root of a coastal dune plant

During a study of endophytic bacteria from coastal dune plants, a bacterial strain, designated YC6881T, was isolated from the root of Rosa rugosa collected from the coastal dune areas of Namhae Island, Korea. The bacterium was found to be Gram-staining-negative, motile, halophilic and heterotrophic with a single polar flagellum. Strain YC6881T grew at temperatures of 4–37 °C (optimum, 28–32 °C), at pH 6.0–9.0 (optimum, pH 7.0–8.0), and at NaCl concentrations in the range of 0–7.5 % (w/v) (optimum, 4–5 % NaCl). Strain YC6881T was catalase- and oxidase-positive and negative for nitrate reduction. According to phylogenetic analysis using 16S rRNA gene sequences, strain YC6881T belonged to the genus Rhizobium and showed the highest 16S rRNA gene sequence similarity of 96.9 % to Rhizobium rosettiformans , followed by Rhizobium borbori (96.3 %), Rhizobium radiobacter (96.1 %), Rhizobium daejeonense (95.9 %), Rhizobium larrymoorei (95.6 %) and Rhizobium giardinii (95.4 %). Phylogenetic analysis of strain YC6881T by recA, atpD, glnII and 16S–23S intergenic spacer (IGS) sequences all confirmed the phylogenetic arrangements obtained by using 16S rRNA gene sequences. Cross-nodulation tests showed that strain YC6881T was a symbiotic bacterium that nodulated Vigna unguiculata and Pisum sativum. The major components of the cellular fatty acids were C18 : 1ω7c (53.7 %), C19 : 0 cyclo ω8c (12.6 %) and C12 : 0 (8.1 %). The DNA G+C content was 52.8 mol%. Phenotypic and physiological tests with respect to carbon source utilization, antibiotic resistance, growth conditions, phylogenetic analyses of housekeeping genes recA, atpD and glnII, and fatty acid composition could be used to discriminate strain YC6881T from other species of the genus Rhizobium in the same sublineage. Based on the results obtained in this study, strain YC6881T is considered to represent a novel species of the genus Rhizobium , for which the name Rhizobium halophytocola sp. nov. is proposed. The type strain is YC6881T ( = KACC 13775T = DSM 21600T).

MALDI-TOF mass spectrometry is a fast and reliable platform for identification and ecological studies of species from family Rhizobiaceae

Family Rhizobiaceae includes fast growing bacteria currently arranged into three genera, Rhizobium, Ensifer and Shinella, that contain pathogenic, symbiotic and saprophytic species. The identification of these species is not possible on the basis of physiological or biochemical traits and should be based on sequencing of several genes. Therefore alternative methods are necessary for rapid and reliable identification of members from family Rhizobiaceae. In this work we evaluated the suitability of Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) for this purpose. Firstly, we evaluated the capability of this methodology to differentiate among species of family Rhizobiaceae including those closely related and then we extended the database of MALDI Biotyper 2.0 including the type strains of 56 species from genera Rhizobium, Ensifer and Shinella. Secondly, we evaluated the identification potential of this methodology by using several strains isolated from different sources previously identified on the basis of their rrs, recA and atpD gene sequences. The 100% of these strains were correctly identified showing that MALDI-TOF MS is an excellent tool for identification of fast growing rhizobia applicable to large populations of isolates in ecological and taxonomic studies.

Rhizobium vallis sp. nov., isolated from nodules of three leguminous species

Four bacterial strains isolated from root nodules of Phaseolus vulgaris, Mimosa pudica and Indigofera spicata plants grown in the Yunnan province of China were identified as a lineage within the genus Rhizobium according to the analysis of 16S rRNA gene sequences, sharing most similarity with Rhizobium lusitanum P1-7(T) (99.1 % sequence similarity) and Rhizobium rhizogenes IAM 13570(T) (99.0 %). These strains also formed a distinctive group from the reference strains for defined species of the genus Rhizobium in a polyphasic approach, including the phylogenetic analyses of the 16S rRNA gene and housekeeping genes (recA, atpD, glnII), DNA-DNA hybridization, BOX-PCR fingerprinting, phenotypic characterization, SDS-PAGE of whole-cell proteins, and cellular fatty acid profiles. All the data obtained in this study suggested that these strains represent a novel species of the genus Rhizobium, for which the name Rhizobium vallis sp. nov. is proposed. The DNA G+C content (mol%) of this species varied between 60.9 and 61.2 (T(m)). The type strain of R. vallis sp. nov. is CCBAU 65647(T) ( = LMG 25295(T) =HAMBI 3073(T)), which has a DNA G+C content of 60.9 mol% and forms effective nodules on Phaseolus vulgaris.