Vogesella lacus sp. nov., isolated from a soft-shell turtle culture pond

Vogesella aquatica sp. nov. and Vogesella margarita sp. nov., isolated from rivers in Southwest China

Eight Gram-stain-negative, aerobic, short rod-shaped and motile strains (DC21WT, LYT5WT, LYT10W, LYT16W, LYT22W, LYT23W, LYT24W and SH7W) were isolated from rivers in Southwest China. Comparisons based on the 16S rRNA gene sequences showed that strain DC21WT shared the highest 16S rRNA gene sequence similarity (99.6 %) with Vogesella mureinivorans 389T, strain LYT5WT shared 99.2 % with Vogesella fluminis Npb-07T, and the other isolated strains took Vogesella indigofera DSM 3303T as their most similar strain, respectively. The phylogenetic trees reconstructed based on the 16S rRNA gene sequences also supported that strains V. mureinivorans 389T, V. fluminis Npb-07T and V. indigofera DSM 3303T were the closest neighbours of the isolated strains. The phylogenomic tree showed similar phylogenetic relationships among these strains. The calculated OrthoANIu and digital DNA-DNA hybridization values among strains DC21WT, LYT5WT and other related strains were less than 93.7 and 53.7 %, respectively. The calculated OrthoANIu and digital DNA-DNA hybridization values among strains LYT10W, LYT16W, LYT22W, LYT23W, LYT24W, SH7W and V. indigofera DSM 3303T ranged from 94.8 to 97.2 % and from 59.8 to 74.9 %, respectively. Although these values were located in the transition region of species demarcation, their similar phenotypic, biochemical and genotypic characteristics supported that these six strains should be assigned to the species V. indigofera. Comparative genomic analyses showed that only V. indigofera DSM 3303T harboured 19 genes encoding the Type VI secretion system. Combining above descriptions, strains DC21WT and LYT5WT should represent two independent novel species of the genus Vogesella, for which the names Vogesella aquatica sp. nov. (type strain DC21WT=GDMCC 1.3220T=KCTC 92556T) and Vogesella margarita sp. nov. (type strains LYT5WT=GDMCC 1.3213T=KCTC 92549T) are proposed, respectively.

Vogesella perlucida-induced bacteremia in an advanced-age patient: first case report

Background

Vogesella species are common aquatic, Gram-negative rod-shaped bacteria, originally described in 1997. Vogesella perlucida was first isolated from spring water in 2008. Furthermore, bacterial pathogenicity of Vogesella perlucida has never been reported. Here, we report the first case of rare Vogesella perlucida-induced bacteremia in an advanced-age patient with many basic diseases and history of dexamethasone abuse.

Case presentation

A 71-year-old female was admitted with inflamed upper and lower limbs, rubefaction, pain and fever (about 40 °C). She had been injured in a fall at a vegetable market and then touched river snails with her injury hands. A few days later, soft tissue infection of the patient developed and worsened. Non-pigmented colonies were isolated from blood cultures of the patient. Initially, Vogesella perlucida was wrongly identified as Sphingomonas paucimobilis by Vitek-2 system with GN card. Besides, we failed to obtain an acceptable identification by the MALDI-TOF analysis. Finally, the isolated strain was identified as Vogesella perlucida by 16S rRNA gene sequences. In addition, the patient recovered well after a continuous treatment of levofloxacin for 12 days.

Conclusion

Traditional microbiological testing system may be inadequate in the diagnosis of rare pathogenic bacteria. Applications of molecular diagnostics techniques have great advantages in clinical microbiology laboratory. By using 16S rRNA gene sequence analysis, we report the the first case of rare Vogesella perlucida-induced bacteremia.

Vogesella urethralis sp. nov., isolated from human urine, and emended descriptions of Vogesella perlucida and Vogesella mureinivorans

A novel Vogesella strain, YM-1^T, was recovered from human urine in PR China in 2017. Cells of strain YM-1^T were Gram-stain-negative, rod-shaped, aerobic, motile, non-spore-forming and poly-β-hydroxybutyrate-accumulating. The strain contained C_16:1ω6c/C _16:1ω7c, C_16:0 and C_18:0ω7c as major fatty acids; phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unidentified phospholipid as major polar lipids; and ubiquinone-8 as the predominant respiratory quinone. Comparison of 16S rRNA gene sequences indicated that this strain had highest similarities to Vogesella perlucida DS-28^T (98.8 %) and Vogesella mureinivorans 389^T (98.1 %). The results of phylogenetic analysis based on the 16S rRNA gene sequences revealed that the novel strain was clustered and well separated with V. perlucida DS-28^T and V. mureinivorans 389^T within the genus Vogesella. The average nucleotide identity (ANI) and amino acid identity (AAI) analyses showed that this strain was not identified as V. perlucida DS-28^T or V. mureinivorans 389^T, with values well below the threshold limit for species demarcation (ANI <88.1 %, AAI <88.6 %). Based on the above results, strain YM-1^T is proposed to be a novel species of the genus Vogesella with the name Vogesella urethralis sp. nov. (YM-1^T=NBRC 113779=CGMCC 1.17135).

Effects of Physiochemical Factors on Prokaryotic Biodiversity in Malaysian Circumneutral Hot Springs

Malaysia has a great number of hot springs, especially along the flank of the Banjaran Titiwangsa mountain range. Biological studies of the Malaysian hot springs are rare because of the lack of comprehensive information on their microbial communities. In this study, we report a cultivation-independent census to describe microbial communities in six hot springs. The Ulu Slim (US), Sungai Klah (SK), Dusun Tua (DT), Sungai Serai (SS), Semenyih (SE), and Ayer Hangat (AH) hot springs exhibit circumneutral pH with temperatures ranging from 43°C to 90°C. Genomic DNA was extracted from environmental samples and the V3–V4 hypervariable regions of 16S rRNA genes were amplified, sequenced, and analyzed. High-throughput sequencing analysis showed that microbial richness was high in all samples as indicated by the detection of 6,334–26,244 operational taxonomy units. In total, 59, 61, 72, 73, 65, and 52 bacterial phyla were identified in the US, SK, DT, SS, SE, and AH hot springs, respectively. Generally, Firmicutes and Proteobacteria dominated the bacterial communities in all hot springs. Archaeal communities mainly consisted of Crenarchaeota, Euryarchaeota, and Parvarchaeota. In beta diversity analysis, the hot spring microbial memberships were clustered primarily on the basis of temperature and salinity. Canonical correlation analysis to assess the relationship between the microbial communities and physicochemical variables revealed that diversity patterns were best explained by a combination of physicochemical variables, rather than by individual abiotic variables such as temperature and salinity.

Vogesella amnigena sp. nov., isolated from a freshwater river

A bacterial strain, designated Npb-02T, was isolated from a freshwater river in Taiwan and characterized in a taxonomic study using a polyphasic approach. Cells of strain Npb-02T were Gram-stain-negative, aerobic, poly-β-hydroxybutyrate-accumulating, rod-shaped and non-motile. Growth occurred at 15–40 °C (optimum 25–30 °C), at pH 7.0–8.0 (optimum pH 7.0) and with 0–1 % NaCl (optimum 0.5 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Npb-02T belonged to the genus Vogesella and was most closely related to Vogesella perlucida DS-28T with sequence similarity of 98.3 %. Strain Npb-02T contained summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as the major fatty acids. The major respiratory quinone was Q-8.The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminophospholipid and an uncharacterized phospholipid. The genomic DNA G+C content of strain Npb-02T was 64.1 mol%. The DNA–DNA hybridization values for strain Npb-02T with Vogesella perlucida DS-28T, Vogesella mureinivorans 389T and Vogesella lacus GR13T were less than 25 %. On the basis of phylogenetic inference and phenotypic data, strain Npb-02T represents a novel species of the genus Vogesella, for which the name Vogesella amnigena sp. nov. is proposed. The type strain is Npb-02T ( = BCRC 80887T = LMG 28419T = KCTC 42195T).

Vogesella facilis sp. nov., isolated from a freshwater river, and emended description of the genus Vogesella

A bacterial strain, designated TTM-24T, was isolated from a freshwater river in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain TTM-24T were Gram-stain-negative, facultatively anaerobic, poly-β-hydroxybutyrate-accumulating, motile by a single polar flagellum, rod-shaped, with rods surrounded by a thick capsule and forming white-coloured colonies. Growth occurred at 15-37 °C (optimum, 25 °C), at pH 6.0-8.0 (optimum, pH 7.0) and with 0-1 % NaCl (optimum, 0.5 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TTM-24T belonged to the genus Vogesella and was most closely related to 'Vogesella amnigena' Npb-02 with sequence similarity of 97.1 %. Strain TTM-24T contained summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 0 as the major fatty acids. The major respiratory quinone was Q-8. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminophospholipid and two uncharacterized phospholipids. The genomic DNA G+C content of strain TTM-24T was 67.4 mol%. The DNA-DNA hybridization value for strain TTM-24T with 'V. amnigena' Npb-02 was less than 45 %. On the basis of the phylogenetic inference and phenotypic data, strain TTM-24T should be classified as a novel species, for which the name Vogesella facilis sp. nov. is proposed. The type strain is TTM-24T ( = BCRC 80912T = KCTC 42742T = LMG 29003T).

Description of Vogesella oryzae sp. nov., isolated from the rhizosphere of saline tolerant pokkali rice

Three strains, namely L3B39(T), L3D16, and L1E9, were obtained while studying the cultivable rhizosphere bacteria of saline tolerant pokkali rice, at Kerala, India. The novel strains were negative for many plant growth promoting plate assays such as phytohormone and siderophore production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase and growth in nitrogen free agar medium but found to utilize malic acid, citrate, D-glucose, L-arabinose, and D-maltose, important components of the plant root exudates, indicating that they are normal plant rhizosphere residents without yet known benefits to the plant. The 16S rRNA gene analysis placed these strains in the genus Vogesella, forming a separate branch independent of the previously described type strains of this genus in all tree making algorithms applied. Vogesella perlucida DS-28(T) was the type strain with highest 16S rRNA sequence similarity (97.59%). DNA-DNA hybridization values among these novel strains were above 85% andthat with Vogesella perlucida LMG 24214(T) was below 50%. Phenotypically, the novel strains can be differentiated from Vogesella perlucida LMG 24214(T) by many characters such as NaCl tolerance, growth temperature, and utilization of L-arabinose, D-maltose, and citrate. These novel strains contain C16:1ω6c/C16:1ω7c and C16:0 as major fatty acids, ubiquinone Q-8 as the major respiratory quinone, and phosphatidylethanolamine and phosphatidylglycerol as major polar lipids. Based on the results obtained from the polyphasic taxonomic approach we conclude that the strains belong to a novel Vogesella species for which the name Vogesella oryzae sp.nov. is proposed. The type strain is L3B39(T) (= LMG 28272(T)=DSM 28780(T)).

Rivicola pingtungensis gen. nov., sp. nov., a new member of the family Neisseriaceae isolated from a freshwater river

A bacterial strain, designated Npb-03(T), was isolated from a freshwater river in Taiwan and was characterized using a polyphasic taxonomic approach. The cells were Gram-reaction-negative, straight rod-shaped, non-motile, non-spore-forming and facultatively anaerobic. Growth occurred at 10-37 °C (optimum, 30-35 °C), at pH 6.0-8.0 (optimum, pH 6.0-7.0) and with 0-1.0% NaCl (optimum, 0%). The predominant fatty acids were summed feature 3 (comprising C(16 : 1)ω7c and/or C(16 : 1)ω6c) and C(16 : 0). The major isoprenoid quinone was Q-8 and the DNA G+C content was 64.1 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminolipid and three uncharacterized phospholipids. The major polyamines were putrescine, 2-hydroxyputrescine, cadaverine and spermidine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Npb-03(T) forms a distinct lineage with respect to closely related genera within the family Neisseriaceae of the class Betaproteobacteria, most closely related to the genera Aquaspirillum, Laribacter, Leeia and Microvirgula, and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera are less than 93%. On the basis of the genotypic and phenotypic data, strain Npb-03(T) represents a novel genus and species of the family Neisseriaceae, for which the name Rivicola pingtungensis gen. nov., sp. nov. is proposed. The type strain is Npb-03(T) ( = BCRC 80376(T) = LMG 26668(T) = KCTC 23712(T)).

Vanadate and acetate biostimulation of contaminated sediments decreases diversity, selects for specific taxa, and decreases aqueous V5+ concentration

Vanadium is a commercially important metal that is released into the environment by fossil fuel combustion and mining. Despite its prevalence as a contaminant, the potential for vanadium bioremediation has not been widely studied. Injection of acetate (as a carbon source) directly into an aquifer to biostimulate contaminated sediments in Colorado, United States, resulted in prolonged removal of aqueous vanadium for a period of at least two years. To further investigate this process, we simultaneously added acetate and vanadate (V(5+)) to columns that were packed with aquifer sediment and inserted into groundwater wells installed on the Colorado River floodplain. This allowed evaluation of the microbial response to amendments in columns that received an influx of natural groundwater. Our results demonstrate the removal of up to 99% of the added V(5+)(aq) and suggest microbial mediation. Most probable number measurements demonstrate up to a 50-fold increase in numbers of V(5+)-reducing cells in vanadium-amended columns compared to controls. 16S rRNA gene sequencing indicates decreased diversity and selection for specific taxa in columns that received vanadate compared to those that did not. Overall, our results demonstrate that acetate amendment can be an effective strategy for V removal, and that V bioremediation may be a viable technology.

Vogesella fluminis sp. nov., isolated from a freshwater river, and emended description of the genus Vogesella

A bacterial strain designated Npb-07(T) was isolated from a freshwater river in Taiwan and characterized using a polyphasic taxonomic approach. Strain Npb-07(T) was Gram-negative, aerobic, rod-shaped and motile by means of a single polar flagellum. Growth occurred at 10-37 °C (optimum, 20-30 °C), at pH 6.0-9.0 (optimum, pH 6.0-7.0) and with 0-1 % NaCl (optimum, 0.5 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Npb-07(T) belonged to the genus Vogesella and its most closely related neighbour was Vogesella indigofera ATCC 19706(T) with sequence similarity of 98.4 %. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c, 44.4 %) and C16 : 0 (31.9 %). The major respiratory quinone was Q-8. The DNA G+C content of the genomic DNA was 65.3 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two uncharacterized aminophospholipids and an uncharacterized phospholipid. The DNA-DNA relatedness of strain Npb-07(T) with respect to V. indigofera ATCC 19706(T) was less than 70 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Npb-07(T) represents a novel species in the genus Vogesella, for which the name Vogesella fluminis sp. nov. is proposed. The type strain is Npb-07(T) ( = LMG 26669(T) = BCRC 80377(T) = KCTC 23713(T)).

Vogesella alkaliphila sp. nov., isolated from an alkaline soil, and emended description of the genus Vogesella

Strain JC141(T) was isolated from an alkaline soil (pH 8.8) at Mau, Uttar Pradesh, India. Colonies were blue with a metallic sheen; cells stained Gram-negative, and were oxidase- and catalase-positive, but chitinase-negative. Major fatty acids were C16:1ω7c/C16:1ω6c, C16:0 and C18:0 with minor amounts of C10:0, C10:0 3-OH, C12:0, C14:0 and C18:1ω7c. Strain JC141(T) contained phosphatidylethanolamine and phosphatidylglycerol as major polar lipids, with minor amounts of diphosphatidylglycerol, unidentified aminolipids (AL1-3) and unidentified lipids (L1-4). A bacterial hopane derivative (BHD1) was the major hopanoid. Genomic DNA G+C content was 62.5 mol%. 16S rRNA gene sequence comparisons indicated that strain JC141(T) represents a member of the genus Vogesella within the family Neisseriaceae of the class Betaproteobacteria. Strain JC141(T) had a 16S rRNA gene sequence similarity of 98% with Vogesella indigofera ATCC 19706(T) and <96.5% with other members of the genus Vogesella. However, strain JC141(T) showed 45.8% relatedness (based on DNA-DNA hybridization) with V. indigofera LMG 6867(T) (=ATCC 19706(T)). Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain JC141(T) as a representative of a novel species in the genus Vogesella, for which the name Vogesella alkaliphila sp. nov. is proposed. The type strain is JC141(T) (=KCTC 32041(T)=LMG 27066(T)). An emended description of the genus Vogesella is also proposed.

Purification and characterization of a fish scale-degrading enzyme from a newly identified Vogesella sp

The objective of the present study is to purify and characterize the fish scale-degrading enzyme from Vogesella sp.7307-1, which was newly identified and isolated from fish scales. The enzyme from Vogesella sp.7307-1 was assayed with casein and confirmed as a protease. Crude protease was extracted, isolated, and purified 35.7-fold with 19.6% recovery using 20-80% saturation of ammonium sulfate fractionation, Q FF ion exchange chromatography, and Superdex 200 gelfiltration. The molecular weight of the purified enzyme was 119 kDa. The Km and Vmax were 0.067 mM and 425.5 U/mg-min, respectively using azo-casein as substrate. The optimum pH of the purified enzyme was 7.5, and the optimum temperature was 50 °C. The enzyme was stable at temperatures below 55 °C and pH range 7.5 to 9.0. The enzyme activity of the purified protease was completely inhibited by EDTA (ethylene diamine teraacetates), indicating the enzyme was a metalloprotease. Hydrolysates from fish scales treated with protease 7307-1 were found having low molecular weight peptides (<1 kDa). The protease 7307-1 is a promising enzyme for preparing smaller peptides from fish scales.

Vogesella mureinivorans sp. nov., a peptidoglycan-degrading bacterium from lake water

A novel, non-pigmented, rod-shaped, Gram-negative strain was isolated from mesotrophic lake water in Zealand, Denmark. Phylogenetic analysis of the 16S rRNA gene sequence of the bacterium, designated strain 389(T), indicated that the strain belonged to the genus Vogesella and formed a monophyletic group with Vogesella perlucida DS-28(T) (99.1 % nucleotide similarity); it was less related to Vogesella indigofera ATCC 19706(T) (96.9 % similarity) and Vogesella lacus LMG 24504(T) (96.8 % similarity). Hybridization of DNA from strain 389(T) and V. perlucida demonstrated a reassociation of 50.6 ± 9.6 %. The DNA G+C content of strain 389(T) was 61.2 mol%. The fatty acid profile of the strain differed from those of the other strains representing the genus Vogesella by a high content of C₁₆:₁ω7c and/or iso-C₁₅:₀ 2-OH (71.6 %) and a lower content of C₁₆: ₀. Strain 389(T) was capable of degrading peptidoglycan and had chitinase and lysozyme activities, possibly associated with the degradation of peptidoglycan, and had capacity for degradation of several other polymer compounds. Based on phenotypic and genotypic characteristics, strain 389(T) represents a novel species, for which we propose the name Vogesella mureinivorans sp. nov. The type strain is 389(T) (=DSM 21247(T) =LMG 25302(T)).