scholarly journals Desulfovibrio gilichinskyi sp. nov., a cold-adapted sulfate-reducing bacterium from a Yamal Peninsula cryopeg

2019 ◽  
Vol 69 (4) ◽  
pp. 1081-1086 ◽  
Author(s):  
Yana Ryzhmanova ◽  
Tatyana Abashina ◽  
Daria Petrova ◽  
Viktoria Shcherbakova
Keyword(s):  
Type Species ◽  
Yamal Peninsula ◽  
Rrna Gene ◽  
Content Type ◽  
Sulfate Reducing ◽  
Link Type ◽  
Subzero Temperatures ◽  
Visible Growth ◽  
Bacterium Strain ◽  
Gene Similarity

A psychrotolerant non-spore-forming sulfate-reducing bacterium, strain K3ST, was isolated from a Yamal Peninsula cryopeg within permafrost. Strain K3ST grew at subzero temperatures and required Na+ for growth. The new bacterium was able to use lactate, formate, pyruvate, fumarate, alanine, ethanol and molecular hydrogen as electron donors in the presence of sulfate, and used sulfate, sulfite, thiosulfate and elemental sulfur as electron acceptors in the presence of lactate. Fe(III)-citrate and Fe(III)-EDTA were reduced without visible growth. Major polar lipids were рhosphatidylserine, рhosphatidylethanolamine, phospholipids, cardiolipin and aminolipid; major cellular fatty acids were C16 : 1ω7, C16 : 0 and C18 : 1ω7; and the predominant isoprenoid quinone was MK-6 (H2). The genomic DNA G+C content was found to be 42.33 mol%. Phylogenetic analysis showed that the closest relative of the new isolate was Desulfovibrio ferrireducens strain 61T with 97.1 % 16S rRNA gene similarity. In addition, the ANI value between strain K3ST and D. ferrireducens 61T was 82.1 %. On the basis of the genomic and polyphasic taxonomy data of strain K3ST, we conclude that the strain is a representative of a novel species Desulfovibrio gilichinskyi sp. nov. (=VKM B-2877T=DSM 100341T).

Eikenella glucosivorans sp. nov., isolated from a human throat swab, and emendation of the genus Eikenella to include saccharolytic species

2021 ◽  
Vol 71 (9) ◽  
Author(s):  
Silvio Hering ◽  
Moritz K. Jansson ◽  
Michael E. J. Buhl
Keyword(s):  
Type Species ◽  
Throat Swab ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Routine Care ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain

A novel species within the genus Eikenella is described, based on the phenotypical, biochemical and genetic characterization of a strain of a facultatively anaerobic, Gram-negative rod-shaped bacterium. Strain S3360T was isolated from the throat swab of a patient sampled during routine care at a hospital. Phylogenetic analyses (full-length 16S rRNA gene and whole-genome sequences) placed the strain in the genus Eikenella , separate from all recognized species but with the closest relationship to Eikenella longinqua (NML 02-A-017T). Eikenella is one of the genera in the HACEK group known to be responsible for rare cases of endocarditis in humans. Until the recent descriptions of Eikenella exigua , Eikenella halliae and Eikenella longinqua , Eikenella corrodens had been the only validly published species in this genus since its description as Bacteroides corrodens in 1958. Unlike these species, strain S3360T is able to metabolize carbohydrates (glucose). The average nucleotide identities of strain S3360T with E. longinqua (NML 02-A-017T) and E. corrodens (NCTC 10596T), the type species of the genus, were 90.5 and 84.7 %, respectively, and the corresponding genome-to-genome distance values were 41.3 and 29.0 %, respectively. The DNA G+C content of strain S3360T was 58.4 mol%. Based on the phenotypical, biochemical and genetic findings, strain S3360T is considered to represent a novel species within the genus Eikenella , for which the name Eikenella glucosivorans sp. nov. is proposed. The type strain is S3360T (DSM 110714T=CCOS 1935T=CCUG 74293T). In addition, an emendation of the genus Eikenella is proposed to include species which are saccharolytic.

Photobacterium arenosum sp. nov., isolated from marine sediment sand

2021 ◽  
Vol 71 (10) ◽  
Author(s):  
Veeraya Weerawongwiwat ◽  
Seokmin Yoon ◽  
Jong-Hwa Kim ◽  
Jung-Hoon Yoon ◽  
Jung Sook Lee ◽  
...  
Keyword(s):  
Marine Sediment ◽  
Type Species ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Protein Coding ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain ◽  
The Republic ◽  
The 16S Rrna Gene

A Gram-stain-negative, aerobic, motile, short rod-shaped, catalase-negative and oxidase-positive bacterium, strain CAU 1568T, was isolated from marine sediment sand sampled at Sido Island in the Republic of Korea. The optimum conditions for growth were at 25–30 °C, at pH 6.5–8.5 and with 0–4.0 % (w/v) NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain CAU 1568T was a member of the genus Photobacterium with high similarity to Photobacterium salinisoli JCM 30852T (97.7 %), Photobacterium halotolerans KACC 17089T (97.3 %) and Photobacterium galatheae LMG F28894T (97.3 %). The predominant cellular fatty acids were C16 : 0, summed feature 3 (C16 : 1  ω6c and/or C16 : 1  ω7c) and summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), with Q-8 as the major of isoprenoid quinone. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerols, phosphatidylcholine, phosphatidylethanolamine, phospholipid, two aminophospholipids and three unidentified lipids. The whole genome size of strain CAU 1568T was 4.8 Mb with 50.1 mol% G+C content; including 38 contigs and 4233 protein-coding genes. These taxonomic data support CAU 1568T as representing a novel Photobacterium species, for which the name Photobacterium arenosum sp. nov. is proposed. The type strain of this novel species is CAU 1568T (=KCTC 82404T=MCCC 1K05668T).

Xenorhabdus lircayensis sp. nov., the symbiotic bacterium associated with the entomopathogenic nematode Steinernema unicornum

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Carlos Castaneda-Alvarez ◽  
Simona Prodan ◽  
Alan Zamorano ◽  
Ernesto San-Blas ◽  
Erwin Aballay
Keyword(s):  
New Species ◽  
Type Species ◽  
Entomopathogenic Nematode ◽  
Phylogenetic Reconstruction ◽  
Symbiotic Bacterium ◽  
Rrna Gene ◽  
Species List ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain

Xenorhabdus is a symbiotic group of bacteria associated with entomopathogenic nematodes of the family Steinernematidae. Although the described Steirnernema species list is extensive, not all their symbiotic bacteria have been identified. One single motile, Gram-negative and non-spore-forming rod-shaped symbiotic bacterium, strain VLST, was isolated from the entomopathogenic nematode Steinernema unicornum. Analyses of the 16S rRNA gene determined that the VLST isolate belongs to the genus Xenorhabdus , and its closest related species is Xenorhabdus szentirmaii DSM 16338T (98.2 %). Deeper analyses using the whole genome for phylogenetic reconstruction indicate that VLST exhibits a unique clade in the genus. Genomic comparisons considering digital DNA–DNA hybridization (dDDH) values confirms this result, showing that the VLST values are distant enough from the 70 % threshold suggested for new species, sharing 30.7, 30.5 and 30.3 % dDDH with Xenorhabdus khoisanae MCB, Xenorhabdus koppenhoeferi DSM 18168T and Xenorhabdus miraniensis DSM 18168T, respectively, as the closest species. Detailed physiological, biochemical and chemotaxonomic tests of the VLST isolate reveal consistent differences from previously described Xenorhabdus species. Phylogenetic, physiological, biochemical and chemotaxonomic approaches show that VLST represents a new species of the genus Xenorhabdus , for which the name Xenorhabdus lircayensis sp. nov. (type strain VLST=CCCT 20.04T=DSM 111583T) is proposed.

Acidovorax antarcticus sp. nov., isolated from a soil sample of Collins Glacier front, Antarctica

2021 ◽  
Author(s):  
Qiang Xu ◽  
Xiaoya Peng ◽  
Yanhong Wang ◽  
Lu Lu ◽  
Yongping Zhang ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
Fildes Peninsula ◽  
Content Type ◽  
Link Type ◽  
Glacier Front ◽  
Bacterium Strain ◽  
Sequence Similarities

A Gram-stain-negative, rod-shaped, and aerobic bacterium, strain 16-35-5T, was isolated from Collins Glacier front soil from the Fildes Peninsula, Antarctica. The bacterium grew optimally at 28 °C, pH 7.0 and in the presence of 0–4.0 % (w/v) NaCl. On the basis of the results of 16S rRNA gene sequence phylogenetic analyses, it was concluded that 16-35-5T represented a member of the genus Acidovorax and had the highest sequence similarities with Acidovorax anthurii CFBP 3232T (96.48 %). The genome of 16-35-5T is 4.2 Mb long with a DNA G+C content of 66.3 mol%. Average nucleotide identity (ANI) value between the genomes of 16-35-5T and Acidovorax wautersii DSM 27981T, was 85.29 %. Strain 16-35-5T had ubiquinone-8 (Q-8) as the respiratory ubiquinone. The polar lipids of 16-35-5T were consisted of phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The main fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 25.2 %), summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c, 12.9 %), C16 : 0 (35.2 %), and C17 : 0 cyclo (19.0 %). On the basis of the evidence presented in this study, 16-35-5T should be classified as representing a novel species of the genus Acidovorax , for which the name Acidovorax antarcticus sp. nov., is proposed, with the type strain 16-35-5T (=CCTCC AB 2019325T=KCTC 72915T).

Celerinatantimonas yamalensis sp. nov., a cold-adapted diazotrophic bacterium from a cold permafrost brine

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4421-4427 ◽  
Author(s):  
Viktoria Shcherbakova ◽  
Nataliya Chuvilskaya ◽  
Elizaveta Rivkina ◽  
Nikita Demidov ◽  
Victoria Uchaeva ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Novel Species ◽  
Carbon Sources ◽  
Yamal Peninsula ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain ◽  
The Yamal Peninsula

A facultatively anaerobic nitrogen-fixing bacterium, strain C7T, was isolated from a permafrost cryopeg on the Yamal Peninsula, Russia. Comparative analysis of 16S rRNA gene sequences revealed that this bacterium was closely related to Celerinatantimonas diazotrophica S-G2-2T with a similarity of 95.5 %. Strain C7T differed from Celerinatantimonas diazotrophica in its ability to hydrolyse gelatin and inability to use d-mannose, melibiose, l-rhamnose, myo-inositol, lactose, lactulose, d-mannitol, trehalose, dl-lactate, glycogen or l-proline as sole carbon sources. In addition, strain C7T grew over a temperature range of 0–34 °C with optimum growth at 18–22 °C. The whole-cell fatty acid profile included C16 : 0, C16 : 1ω7, C18 : 1ω7, C17 cyclo and summed feature 2 [comprising C12 : 0 aldehyde and/or unknown fatty acid 10.913 (MIDI designation) and/or iso-C16 : 1/C14 : 0 3-OH]. The DNA G+C content was 44.7 mol%. Strain C7T is thus considered to represent a novel species, for which the name Celerinatantimonas yamalensis sp. nov. is proposed. The type strain is C7T ( = VKM B-2511T = DSM 21888T).

scholarly journals Alicyclobacillus cellulosilyticus sp. nov., a thermophilic, cellulolytic bacterium isolated from steamed Japanese cedar chips from a lumbermill

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2257-2263 ◽  
Author(s):  
Masataka Kusube ◽  
Asami Sugihara ◽  
Yoshito Moriwaki ◽  
Takahiro Ueoka ◽  
Yasuhiro Shimane ◽  
...  
Keyword(s):  
Type Species ◽  
Japanese Cedar ◽  
Thermophilic Bacterium ◽  
Rrna Gene ◽  
Cellulolytic Bacterium ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Alicyclobacillus Acidocaldarius ◽  
Bacterium Strain

A thermophilic bacterium, strain SueokaT, was isolated from steamed Japanese cedar chips from a lumber mill in Gobo, Japan. The strain was able to grow on carboxymethyl cellulose at 60 °C, was Gram-stain-negative, and grew between 40.0 and 67.5 °C (optimum at 55 °C) and between pH 3.5 and 6.5 (optimum at pH 4.8). Comparative analysis of 16S rRNA gene sequences revealed 91.9 , 90.9 , and 90.8 % similarity to Alicyclobacillus macrosporangiidus T , Alicyclobacillus pomorum T , and Alicyclobacillus acidocaldarius T , respectively. The major quinone was MK-7 and the predominant cellular fatty acids were ω-cyclohexane C19 : 0 and ω-cyclohexane C17 : 0. The DNA G+C content was 60.8 mol%. Based on the results of this study, strain SueokaT is a novel species of the genus Alicyclobacillus , and the namehttp://dx.doi.org/10.1601/nm.5071 Alicyclobacillus cellulosilyticus sp. nov. (type strain SueokaT = JCM 18487T = KCTC 33007T) is proposed.

scholarly journals Reclassification of Desulfobacterium anilini as Desulfatiglans anilini comb. nov. within Desulfatiglans gen. nov., and description of a 4-chlorophenol-degrading sulfate-reducing bacterium, Desulfatiglans parachlorophenolica sp. nov.

2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3081-3086 ◽  
Author(s):  
Daisuke Suzuki ◽  
Zhiling Li ◽  
Xinxin Cui ◽  
Chunfung Zhang ◽  
Arata Katayama
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Electron Acceptors ◽  
Electron Donors ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Content Type ◽  
Sulfate Reducing ◽  
Link Type

A strictly anaerobic, mesophilic, sulfate-reducing bacterial strain (DST), isolated from river sediment contaminated with volatile organic compounds, was characterized phenotypically and phylogenetically. Cells were Gram-reaction-negative, non-motile short rods. For growth, optimum NaCl concentration was 0.9 g l−1, optimum temperature was 30 °C and optimum pH was 7.2. Strain DST utilized phenol, benzoate, 4-hydroxybenzoate, 4-methylphenol, 4-chlorophenol, acetate, butyrate and pyruvate as electron donors for sulfate reduction. Electron donors were completely oxidized. Strain DST did not utilize sulfite, thiosulfate or nitrate as electron acceptors. The genomic DNA G+C content of strain DST was 58.9 mol%. Major cellular fatty acids were iso-C14 : 0, anteiso-C15 : 0 and C18 : 1ω7c. Phylogenetic analyses based on the 16S rRNA gene indicated its closest relatives were strains of Desulfobacterium anilini (about 98–99 % sequence similarity) but the DNA–DNA hybridization value with Desulfobacterium anilini Ani1T was around 40 %. Although strain DST and its relatives shared most phenotypic and chemotaxonomic characteristics, the utilization of 4-chlorophenol, the range of electron acceptors and the optimum growth conditions differed. Strain DST is closely related to strains of Desulfobacterium anilini , but constitutes a different species within the genus. Based on phylogeny, phenotypic characteristics and chemotaxonomic characteristics, strain DST and Desulfobacterium anilini were clearly different from strains of other species of the genus Desulfobacterium . We thus propose the reclassification of Desulfobacterium anilini within a new genus, Desulfatiglans gen. nov., as Desulfatiglans anilini comb. nov. We also propose Desulfatiglans parachlorophenolica sp. nov. to accommodate strain DST. The type strain is DST ( = JCM 19179T = DSM 27197T).

scholarly journals Chitinimonas viridis sp. nov., isolated from a mesotrophic artificial lake

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1123-1126 ◽  
Author(s):  
Yochan Joung ◽  
Beom-Il Lee ◽  
Heeyoung Kang ◽  
Haneul Kim ◽  
Kiseong Joh
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Artificial Lake ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Bacterium Strain

A Gram-staining-negative, rod-shaped bacterium, strain HMD2169T, was isolated from a mesotrophic artificial lake in Korea. Strain HMD2169T grew in the presence of 0–3.0 % (w/v) NaCl, at pH 5–10 and at 20–37 °C. The predominant quinone of strain HMD2169T was ubiquinone (UQ)-8. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, two unidentified aminolipids and two unidentified lipids. The DNA G+C content was 59.8 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HMD2169T was a representative of a lineage within the genus Chitinimonas . Strain HMD2169T was closely related to Chitinimonas taiwanensis (95.8 % sequence similarity) and Chitinimonas koreensis (94.6 %). On the basis of the evidence presented in this study, strain HMD2169T is a representative of a novel species of the genus Chitinimonas , for which the name Chitinimonas viridis sp. nov. is proposed with the type strain HMD2169T ( = KCTC 22839T = CECT 7703T).

Methylobacterium oxalidis sp. nov., isolated from leaves of Oxalis corniculata

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1647-1652 ◽  
Author(s):  
Akio Tani ◽  
Nurettin Sahin ◽  
Kazuhide Kimbara
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Methylotrophic Bacterium ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain ◽  
Sequence Similarities

A pink-pigmented, facultatively methylotrophic bacterium, strain 35aT, was isolated from the leaves of Oxalis corniculata. Cells of strain 35aT were Gram-reaction-negative, motile, non-spore-forming rods. The highest 16S rRNA gene pairwise sequence similarities for strain 35aT were found with the strains of Methylobacterium iners 5317S-33T (96.7 %), ‘Methylobacterium soli’ YIM 48816 (96.6 %) and Methylobacterium jeotgali S2R03-9T (96.3 %). 16S rRNA gene sequence similarities with the type strains of all other recognized species of the genus Methylobacterium were below 96 %. Major cellular fatty acids were C18 : 1ω7c, C18 : 0 and C16 : 0. The results of DNA–DNA hybridization experiments, analysis of cpn60 gene sequences, fatty acid profiles, whole-cell MALDI-TOF/MS spectral pattern analysis, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 35aT from its nearest phylogenetic neighbours. Strain 35aT is therefore considered to represent a novel species within the genus Methylobacterium , for which the name Methylobacterium oxalidis sp. nov. is proposed. The type strain is 35aT ( = DSM 24028T = NBRC 107715T).

Methylobacterium haplocladii sp. nov. and Methylobacterium brachythecii sp. nov., isolated from bryophytes

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3287-3292 ◽  
Author(s):  
Akio Tani ◽  
Nurettin Sahin
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Methylotrophic Bacteria ◽  
Content Type ◽  
Link Type ◽  
Gene Similarity

Pink-pigmented, facultatively methylotrophic bacteria, strains 87eT and 99bT, were isolated from the bryophytes Haplocladium microphyllum and Brachythecium plumosum, respectively. The cells of both strains were Gram-reaction-negative, motile, non-spore-forming rods. On the basis of 16S rRNA gene sequence similarity, strains 87eT and 99bT were found to be related to Methylobacterium organophilum ATCC 27886T (97.1 % and 97.7 %, respectively). Strains 87eT and 99bT showed highest 16S rRNA gene similarity to Methylobacterium gnaphalii 23eT (98.3 and 99.0 %, respectively). The phylogenetic similarities to all other species of the genus Methylobacterium with validly published names were less than 97 %. Major cellular fatty acids of both strains were C18 : 1ω7c and C18 : 0. The results of DNA–DNA hybridization, phylogenetic analyses based on 16S rRNA and cpn60 gene sequences, fatty acid profiles, whole-cell matrix-assisted, laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS) analysis, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strains 87eT and 99bT from their phylogenetically closest relatives. We propose that strains 87eT and 99bT represent novel species within the genus Methylobacterium , for which the names Methylobacterium haplocladii sp. nov. (type strain 87eT = DSM 24195T = NBRC 107714T) and Methylobacterium brachythecii sp. nov. (type strain 99bT = DSM 24105T = NBRC 107710T) are proposed.

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