Microvirga indica sp. nov., an arsenite-oxidizing Alphaproteobacterium, isolated from metal industry waste soil

Microvirga terricola sp. nov. and Microvirga solisilvae sp. nov, isolated from forest soil

Two Gram-staining-negative, aerobic and rod-shaped strains, designated c23x22^T and sex2^T, were isolated from forest soil collected from Chebaling National Nature Reserve in Guangdong Province and Limu Mountain National Forest Park in Hainan Province, P. R. China, respectively. Phylogenetic analyses based on 16S rRNA gene sequences revealed that they belonged to the genus Microvirga, and strain c23 x22^T was most closely related to 'Microvirga alba' KCTC 72385, while strain sex2^T showed close relationship with Microvirga guangxiensis CGMCC 1.7666^T. The average nucleotide identity and digital DNA-DNA hybridization values between strains c23 x22^T and sex2^T and their close relatives, 'M. alba' KCTC 72385 and M. guangxiensis CGMCC 1.7666^T, were all below the threshold values for species delimitation. The predominant quinones of the two novel strains were ubiquinone 10, and the major fatty acids contained C_19:0 cyclo ω8c and summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c). Their predominant polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The phenotypic, genotypic and chemotaxonomic analyses clearly supported that strains c23 x 22^T and sex2^T represent two novel species of the genus Microvirga, for which the name Microvirga terricola sp. nov. (type strain c23 x 22^T = GDMCC 1.1700^T = KCTC 62432^T) and Microvirga solisilvae sp. nov. (type strain sex2^T = GDMCC 1.1651^T = KACC 21311^T) are proposed, respectively.

Microvirga puerhi sp. nov., isolated from Puerh tea garden soil

Strain WGZ8^T was isolated from a soil sample of Puerh tea garden in Pu'er city, Southwest China. The isolate was rod-shaped, Gram-stain negative, facultative anaerobic, non-motile. Growth occurred within 0-3.0% (w/v) NaCl (optimal concentration, 0-1.0%), pH 5.0-11.0 (optimal pH, 7.0) and 10-40 °C (optimal temperature, 28 °C). 16S rRNA gene sequence-based phylogenetic and phylogenomic analysis revealed that WGZ8^T belonged to the genus Microvirga. Its major cellular fatty acids were C_19:0 cyclo ω8c, C_16:0, C_18:1ω7c and/or C_18:1ω6c. The profile of polar lipids included phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol and phosphatidylglycerol. The only respiratory quinone was detected as ubiquinone 10 (Q-10). The genome size of strain WGZ8^T was 5.17 MB, and the content of DNA G + C was 61 mol%. Based on the results of digital DNA-DNA hybridization and phenotypic results, strain WGZ8^T could be concluded as a novel species of the genus Microvirga, for which the name Microvirga puerhi sp. nov. is proposed. The type strain is WGZ8^T (= CGMCC 1.19171 ^T = JCM 35317 ^T).

Microvirga roseola sp. nov. and Microvirga lenta sp. nov., isolated from Taklamakan Desert soil

Two Gram-negative, rod-shaped, non-spore-forming bacteria, designated SM9T and SM2T, were isolated from Taklamakan Desert soil samples. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strains SM9T and SM2T had the highest sequence similarity to the type strains Microvirga indica BCRC 80972T and Microvirga soli NBRC 112417T with similarity values of 98.2 and 97.7 %, respectively, and Microvirga was among the predominant genera in the desert soil. The draft genomes of these two strains were 4.56 Mbp (SM9T) and 5.08 Mbp (SM2T) long with 65.1 mol% (SM9T) and 63.5 mol% (SM2T) G+C content. To adapt to the desert environment, these two strains possessed pathways for the synthesis of stress metabolite trehalose. The major fatty acids (>5 %) included C18 : 1 ω9c in SM2T, but C16 : 0, C18 : 0 and C19 : 0 cyclo ω8c in SM9T, while the major menaquinone was ubiquinone 10 in both strains. The major polar lipids of SM9T and SM2T were phosphatidylglycerol, phosphatidylethanolamine and phospholipid. The average nucleotide identity and digital DNA–DNA hybridization results further indicated that strains SM9T and SM2T were distinguished from phylogenetically related species and represented two novel species within the genus Microvirga , for which the names Microvirga roseola sp. nov. (type strain SM2T=KCTC 72792T=CGMCC 1.17776T) and Microvirga lenta sp. nov. (type strain SM9T=KCTC 82729T=CCTCC AB 2021131T) are proposed.

Description and genome analysis of Microvirga antarctica sp. nov., a novel pink-pigmented psychrotolerant bacterium isolated from Antarctic soil

A novel pink-pigmented bacterium, designated strain 3D7^T, was isolated during an investigation of potential psychrotolerant species from Antarctic soil. Cells of the isolate were observed to be rod-shaped (0.7-0.9 × 1.0-2.2 µm), Gram-stain negative and non-motile. It was able to grow at 4-32  °C, pH 7.0-10.0 and in the presence of 0-3% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 3D7^T belongs to the genus Microvirga and was most closely related to 'Microvirga brassicacearum' CDVBN77^T (98.3%), Microvirga subterranea DSM 14364 ^T (96.8%), Microvirga guangxiensis 25B^T (96.5%) and Microvirga aerophila DSM 21344 ^T (96.5%). The predominant quinone was ubiquinone 10 (Q-10), and the major fatty acids were summed feature 8 (C_18:1ω7c and/or C_18:1ω6c) and C_19:0 cyclo ω8c. The predominant polar lipids were phosphatidylcholine and phosphatidylethanolamine. The genomic DNA G + C content of strain 3D7^T was 63.5 mol%. Its genome sequence showed genes encoding phosphatases and lipases. Genetic machinery related to carbohydrate-active enzymes and secondary metabolites were also observed. The average nucleotide identity and digital DNA-DNA hybridization values based on whole genome sequences of strain 3D7^T and its closely related species were below the threshold range for species determination. Phenotypic, chemotaxonomic, phylogenetic and genomic analyses suggested that strain 3D7^T represents a novel species of the genus Microvirga, for which the name Microvirga antarctica sp. nov. is proposed. The type strain is 3D7^T (= CGMCC 1.13821^T = KCTC 72465^T).

Microvirga pudoricolor sp. nov., and Microvirga alba sp. nov., isolated from soil in South Korea

Two novel Gram-stain-negative, aerobic, rod-shaped, circular, convex, light-pink and white-colored bacterial strains BT291^T and BT350^T were isolated from soil collected in Uijeongbu city (37° 44' 55″ N, 127° 2' 20″ E) and Jeju island (33° 22' 48″ N, 126° 31' 48″ E), respectively, South Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that each of the strains BT291^T and BT350^T belong to a distinct lineages within the genus Microvirga (family Methylobacteriaceae, order Rhizobiales, class Alpha Proteobacteria, phylum Proteobacteria, kingdom Bacteria). The 16S rRNA gene sequence similarity between the two strains BT291^T and BT350^T was 97.4%. The two strains were found to have the same quinone system, with Q-10 as the major respiratory quinone. The major polar lipids of strains BT291^T and BT350^T were phosphatidylethanolamine (PE), diphosphatydilglycerol (DPG), phosphatidylcholine (PC) and phosphatidylglycerol (PG). The major cellular fatty acids of strain BT291^T were C_18:1 ω7c (58.2%) and cyclo-C_19:0 ω8c (25.7%). The major cellular fatty acids of strain BT350^T were C_18:1 ω7c (38.5%) and cyclo-C_19:0 ω8c (27.7%). Based on the polyphasic analysis (phylogenetic, chemotaxonomic and biochemical), strains BT291^T and BT350^T can be suggested as two novel bacterial species within the genus Microvirga and the proposed names are Microvirga pudoricolor and Microvirga alba, respectively. The type strain of Microvirga pudoricolor is BT291^T (= KCTC 72368^T = NBRC 114845^T) and the type strain of Microvirga alba is BT350^T (= KCTC 72385^T = NBRC 114848^T).

Microvirga arsenatis sp. nov., an arsenate reduction bacterium isolated from Tibet hot spring sediments

Two novel Gram-stain negative, moderately thermophilic, aerobic, rod-shaped strains, designated 3D203^T and 3D207, were isolated from hot spring sediment samples collected from Tibet, western China. Phylogenetic analyses based on 16S rRNA gene sequence similarities showed that two isolates belonged to the genus Microvirga and were most closely related to Microvirga makkahensis SV1470^T (98.5% and 98.4%, respectively) and two strains had 99.8% similarity to each other. The average nucleotide identity (ANI) based on whole genome sequences of two strains and M. makkahensis SV1470^T was 80.8% and 80.78%, respectively. Optimum growth was observed at 45 °C, pH 7.0 and 0.5% NaCl. They both could tolerate to high concentration arsenic. Ubiquinone 10 (Q10) was their predominant quinone. The differences of strains 3D203^T and 3D207 were phosphatidyl dimethyl ethanolamine, phosphatidyl-N-methylethanolamine, phosphatidylglycerol, unidentified glycolipids and unidentified lipids. The major fatty acids (> 5%) were identified C_18:1ω7c and/or C_18:1ω6c, C_18:0 and C_16:0. The genomic DNA G + C contents of strain 3D203^T and 3D207 based on whole genome sequences were 64.8% and 64.7%, respectively. Phenotypic, chemotaxonomic, phylogenetic and genomic analyses suggested that two strains represent a novel species of the genus Microvirga, for which the name Microvirga arsenatis sp. nov. is proposed. The type strain is 3D203^T (= CGMCC 1.17691^T = KCTC 72653^T).

Isolation and Identification of Microvirga thermotolerans HR1, a Novel Thermo-Tolerant Bacterium, and Comparative Genomics among Microvirga Species

Members of the Microvirga genus are metabolically versatile and widely distributed in Nature. However, knowledge of the bacteria that belong to this genus is currently limited to biochemical characteristics. Herein, a novel thermo-tolerant bacterium named Microvirga thermotolerans HR1 was isolated and identified. Based on the 16S rRNA gene sequence analysis, the strain HR1 belonged to the genus Microvirga and was highly similar to Microvirga sp. 17 mud 1-3. The strain could grow at temperatures ranging from 15 to 50 °C with a growth optimum at 40 °C. It exhibited tolerance to pH range of 6.0–8.0 and salt concentrations up to 0.5% (w/v). It contained ubiquinone 10 as the predominant quinone and added group 8 as the main fatty acids. Analysis of 11 whole genomes of Microvirga species revealed that Microvirga segregated into two main distinct clades (soil and root nodule) as affected by the isolation source. Members of the soil clade had a high ratio of heat- or radiation-resistant genes, whereas members of the root nodule clade were characterized by a significantly higher abundance of genes involved in symbiotic nitrogen fixation or nodule formation. The taxonomic clustering of Microvirga strains indicated strong functional differentiation and niche-specific adaption.

Rhizobia population was favoured during in situ phytoremediation of vanadium-titanium magnetite mine tailings dam using Pongamia pinnata

Mine tailings contain toxic metals and can lead to serious pollution of soil environment. Phytoremediation using legumes has been regarded as an eco-friendly way for the rehabilitation of tailings-laden lands but little is known about the changes of microbial structure during the process. In the present study, we monitored the dynamic change of microbiota in the rhizosphere of Pongamia pinnata during a 2-year on-site remediation of vanadium-titanium magnetite tailings. After remediation, overall soil health conditions were significantly improved as increased available N and P contents and enzyme activities were discovered. There was also an increase of microbial carbon and nitrogen contents. The Illumina sequencing technique revealed that the abundance of taxa under Proteobacteria was increased and rhizobia-related OTUs were preferentially enriched. A significant difference was discovered for sample groups before and after remediation. Rhizobium and Nordella were identified as the keystone taxa at genus rank. The functional prediction indicated that nitrogen fixation was enhanced, corresponding well with qPCR results which showed a significant increase of nifH gene copy numbers by the 2nd year. Our findings for the first time elucidated that legume phytoremediation can effectively cause microbial communities to shift in favour of rhizobia in heavy metal contaminated soil.

Genome Insights into the Novel Species Microvirga brassicacearum, a Rapeseed Endophyte with Biotechnological Potential

Plants harbor a diversity of microorganisms constituting the plant microbiome. Many bioinoculants for agricultural crops have been isolated from plants. Nevertheless, plants are an underexplored niche for the isolation of microorganisms with other biotechnological applications. As a part of a collection of canola endophytes, we isolated strain CDVBN77^T. Its genome sequence shows not only plant growth-promoting (PGP) mechanisms, but also genetic machinery to produce secondary metabolites, with potential applications in the pharmaceutical industry, and to synthesize hydrolytic enzymes, with potential applications in biomass degradation industries. Phylogenetic analysis of the 16S rRNA gene of strain CDVBN77^T shows that it belongs to the genus Microvirga, its closest related species being M. aerophila DSM 21344^T (97.64% similarity) and M. flavescens c27j1^T (97.50% similarity). It contains ubiquinone 10 as the predominant quinone, C19:0 cycloω8c and summed feature 8 as the major fatty acids, and phosphatidylcholine and phosphatidylethanolamine as the most abundant polar lipids. Its genomic DNA G+C content is 62.3 (mol %). Based on phylogenetic, chemotaxonomic, and phenotypic analyses, we suggest the classification of strain CDVBN77^T within a new species of the genus Microvirga and propose the name Microvirga brassicacearum sp. nov. (type strain CDVBN77^T = CECT 9905^T = LMG 31419^T).

Microvirga calopogonii sp. nov., a novel alphaproteobacterium isolated from a root nodule of Calopogonium mucunoides in Southwest China

In this study, a Gram-negative, rod-shaped, and non-spore-forming bacterium, which was designated as strain CCBUA 65841^T, was isolated from a root nodule of Calopogonium mucunoides grown in Yunan Province of China. The sequence alignment results of 16S rRNA and four housekeeping genes (including gyrB, recA, dnaK and rpoB) indicated the isolated strain is a member of the genus Microvirga, closely related to Microvirga lotononidis WSM3557^T. In addition, results of genome average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) had revealed the lower values (ANI ≤ 88.72%, dDDH ≤ 39.5%) between strain CCABU 65841^T and other related Microvirga species. The genome of the novel strain exhibits a G + C content of 64.48% and contains 7296 protein-coding genes and 93 RNA genes. The major polar lipids were found to be phosphatidylcholine and phosphatidylethanolamine. The predominant cellar fatty acids were identified to be C16:0, C18:0, C19:0 _cyclo ω8c, summed feature 2, summed feature 3 and summed feature 8. Moreover, menaquinone 8 (MK-8) was detected to be the predominant quinone. Based on the phylogenetic and phenotypic dissimilarity, a novel species Microvirga calopogonii sp. nov. is proposed with the type strain CCABU 65841^T (= LMG 25488 ^T = HAMBI 3033^T).

Microvirga flavescens sp. nov., a novel bacterium isolated from forest soil and emended description of the genus Microvirga

An aerobic, Gram-stain-negative, motile and rod-shaped bacterium, designated c27j1^T, was isolated from a forest soil sample from the Chebaling National Nature Reserve in Guangdong Province, China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain c27j1^T belongs to the genus Microvirga and was most closely related to Microvirga aerophila DSM 21344^T (97.7 %) and Microvirga subterranea DSM 14364^T (96.7 %). The average nucleotide identity and digital DNA-DNA hybridization values based on whole genome sequences of strain c27j1 ^T and M. aerophila DSM 21344^T were 77.2 and 22.4 %, respectively. It contained ubiquinone 10 as the predominant quinone, and C19 : 0 cycloω8c and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as the major fatty acids. The polar lipids consisted of phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine and two unidentified glycolipids. The genomic DNA G+C content based on the whole genome sequence was 62.2 mol%. Phenotypic, chemotaxonomic, phylogenetic and genomic analyses suggested that strain c27j1^T should represent a novel species of the genus Microvirga, for which the name Microvirgaflavescens sp. nov. is proposed. The type strain is c27j1^T (=GDMCC 1.1356^T=KCTC 62433^T). The description of the genus Microvirga is also emended, including the major fatty acids, genome size and DNA G+C content.

Assessment of arsenic oxidation potential of Microvirga indica S-MI1b sp. nov. in heavy metal polluted environment

Arsenic oxidizing α-proteobacterial strain Microvirga indica S-MI1b sp. nov. was isolated from metal industry soil and has the ability to oxidize 15 mM of arsenite [As(III)] completely in 39 h. The strain S-MI1b resists to different heavy metals and it oxidizes arsenite in presence of Li, Pb, Hg, Sb(III), Cd, Cr(VI), Ni, and exhibited growth inhibitory effect in presence of Hg, Cu, and Cd at higher concentration. The morphology of Microvirga indica S-MI1b changed in presence of heavy metals however there was no accumulation of As(III) in the cells. The study showed that Microvirga indica S-MI1b can oxidize arsenite at broad pH ranges from 4.0 to 9.0 with optimum at pH 7.0. The kinetic studies of arsenite oxidation by strain S-MI1b signified that it has greater affinity towards As(III). The arsenite oxidase activity of cells grown in presence of Li and Cr(VI) supported the cell culture studies. This is first report on biotransformation of arsenite by Microvirga genus and also arsenite oxidation in presence of heavy metals.