scholarly journals Nitrosophilus alvini gen. nov., sp. nov., a hydrogen-oxidizing chemolithoautotroph isolated from a deep-sea hydrothermal vent in the East Pacific Rise, inferred by a genome-based taxonomy of the phylum “Campylobacterota”

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0241366
Author(s):  
Taiki Shiotani ◽  
Sayaka Mino ◽  
Wakana Sato ◽  
Sayo Nishikawa ◽  
Masanori Yonezawa ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Deep Sea ◽  
Hydrothermal Vent ◽  
Elemental Sulfur ◽  
East Pacific Rise ◽  
Rrna Gene ◽  
Sulfur Source ◽  
East Pacific ◽  
A Genome

A novel bacterium, strain EPR55-1T, was isolated from a deep-sea hydrothermal vent on the East Pacific Rise. The cells were motile rods. Growth was observed at temperatures between 50 and 60°C (optimum, 60°C), at pH values between 5.4 and 8.6 (optimum, pH 6.6) and in the presence of 2.4–3.2% (w/v) NaCl (optimum, 2.4%). The isolate used molecular hydrogen as its sole electron donor, carbon dioxide as its sole carbon source, ammonium as its sole nitrogen source, and thiosulfate, sulfite (0.01 to 0.001%, w/v) or elemental sulfur as its sole sulfur source. Nitrate, nitrous oxide (33%, v/v), thiosulfate, molecular oxygen (0.1%, v/v) or elemental sulfur could serve as the sole electron acceptor to support growth. Phylogenetic analyses based on both 16S rRNA gene sequences and whole genome sequences indicated that strain EPR55-1T belonged to the family Nitratiruptoraceae of the class “Campylobacteria”, but it had the distinct phylogenetic relationship with the genus Nitratiruptor. On the basis of the physiological and molecular characteristics of the isolate, the name Nitrosophilus alvini gen. nov. sp. nov. is proposed, with EPR55-1T as the type strain (= JCM 32893T = KCTC 15925T). In addition, it is shown that “Nitratiruptor labii” should be transferred to the genus Nitrtosophilus; the name Nitrosophilus labii comb. nov. (JCM 34002T = DSM 111345T) is proposed for this organism. Furthermore, 16S rRNA gene-based and genome-based analyses showed that Cetia pacifica is phylogenetically associated with Caminibacter species. We therefore propose the reclassification of Cetia pacifica as Caminibacter pacificus comb. nov. (DSM 27783T = JCM 19563T). Additionally, AAI thresholds for genus classification and the reclassification of subordinate taxa within “Campylobacteria” are also evaluated, based on the analyses using publicly available genomes of all the campylobacterial species.

scholarly journals Hippea jasoniae sp. nov. and Hippea alviniae sp. nov., thermoacidophilic members of the class Deltaproteobacteria isolated from deep-sea hydrothermal vent deposits

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1252-1258 ◽  
Author(s):  
Gilberto E. Flores ◽  
Ryan C. Hunter ◽  
Yitai Liu ◽  
Anchelique Mets ◽  
Stefan Schouten ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Deep Sea ◽  
Hydrothermal Vent ◽  
Type Strain ◽  
Type Species ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

Thirteen novel, obligately anaerobic, thermoacidophilic bacteria were isolated from deep-sea hydrothermal vent sites. Four of the strains, designated EP5-rT, KM1, Mar08-272rT and Mar08-368r, were selected for metabolic and physiological characterization. With the exception of strain EP5-rT, all strains were short rods that grew between 40 and 72 °C, with optimal growth at 60–65 °C. Strain EP5-rT was more ovoid in shape and grew between 45 and 75 °C, with optimum growth at 60 °C. The pH range for growth of all the isolates was between pH 3.5 and 5.5 (optimum pH 4.5 to 5.0). Strain Mar08-272rT could only grow up to pH 5.0. Elemental sulfur was required for heterotrophic growth on acetate, succinate, Casamino acids and yeast extract. Strains EP5-rT, Mar08-272rT and Mar08-368r could also use fumarate, while strains EP5-rT, KM1 and Mar08-272rT could also use propionate. All isolates were able to grow chemolithotrophically on H2, CO2, sulfur and vitamins. Phylogenetic analysis of 16S rRNA gene sequences placed all isolates within the family Desulfurellaceae of the class Deltaproteobacteria , with the closest cultured relative being Hippea maritima MH2 T (~95–98 % gene sequence similarity). Phylogenetic analysis also identified several isolates with at least one intervening sequence within the 16S rRNA gene. The genomic DNA G+C contents of strains EP5-rT, KM1, Mar08-272rT and Mar08-368r were 37.1, 42.0, 35.6 and 37.9 mol%, respectively. The new isolates differed most significantly from H. maritima MH2 T in their phylogenetic placement and in that they were obligate thermoacidophiles. Based on these phylogenetic and phenotypic properties, the following two novel species are proposed: Hippea jasoniae sp. nov. (type strain Mar08-272rT = DSM 24585T = OCM 985T) and Hippea alviniae sp. nov. (type strain EP5-rT = DSM 24586T = OCM 986T).

scholarly journals Sulfurimonas paralvinellae sp. nov., a novel mesophilic, hydrogen- and sulfur-oxidizing chemolithoautotroph within the Epsilonproteobacteria isolated from a deep-sea hydrothermal vent polychaete nest, reclassification of Thiomicrospira denitrificans as Sulfurimonas denitrificans comb. nov. and emended description of the genus Sulfurimonas

2006 ◽  
Vol 56 (8) ◽  
pp. 1725-1733 ◽  
Author(s):  
Ken Takai ◽  
Masae Suzuki ◽  
Satoshi Nakagawa ◽  
Masayuki Miyazaki ◽  
Yohey Suzuki ◽  
...  
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Type Strain ◽  
Elemental Sulfur ◽  
Okinawa Trough ◽  
Rrna Gene ◽  
Sulfur Source ◽  
The Novel ◽  
Emended Description ◽  
Thiomicrospira Denitrificans

A novel mesophilic bacterium, strain GO25T, was isolated from a nest of hydrothermal vent polychaetes, Paralvinella sp., at the Iheya North field in the Mid-Okinawa Trough. Cells were motile short rods with a single polar flagellum. Growth was observed between 4 and 35 °C (optimum 30 °C; 13–16 h doubling time) and between pH 5.4 and 8.6 (optimum pH 6.1). The isolate was a facultatively anaerobic chemolithoautotroph capable of growth using molecular hydrogen, elemental sulfur or thiosulfate as the sole energy source, carbon dioxide as the sole carbon source, ammonium or nitrate as the sole nitrogen source and elemental sulfur, thiosulfate or yeast extract as the sole sulfur source. Strain GO25T represents the first deep-sea epsilonproteobacterium capable of growth by both hydrogen and sulfur oxidation. Nitrate or molecular oxygen (up to 10 % partial pressure) could serve as the sole electron acceptor to support growth. Metabolic products of nitrate reduction shifted in response to the electron donor provided. The G+C content of genomic DNA was 37.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel isolate belonged to the genus Sulfurimonas and was most closely related to Sulfurimonas autotrophica OK10T (96.3 % sequence similarity). DNA–DNA hybridization demonstrated that the novel isolate could be differentiated genotypically from Sulfurimonas autotrophica OK10T. On the basis of the physiological and molecular properties of the novel isolate, the name Sulfurimonas paralvinellae sp. nov. is proposed, with strain GO25T (=JCM 13212T=DSM 17229T) as the type strain. Thiomicrospira denitrificans DSM 1251T (=ATCC 33889T) is phylogenetically associated with Sulfurimonas autotrophica OK10T and Sulfurimonas paralvinellae GO25T. Based on the phylogenetic relationship between Thiomicrospira denitrificans DSM 1251T, Sulfurimonas autotrophica OK10T and Sulfurimonas paralvinellae GO25T, we propose the reclassification of Thiomicrospira denitrificans as Sulfurimonas denitrificans comb. nov. (type strain DSM 1251T=ATCC 33889T). In addition, an emended description of the genus Sulfurimonas is proposed.

scholarly journals Brevirhabdus pacifica gen. nov., sp. nov., isolated from deep-sea sediment in a hydrothermal vent field

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3645-3651 ◽  
Author(s):  
Yue-Hong Wu ◽  
Lin Xu ◽  
Peng Zhou ◽  
Chun-Sheng Wang ◽  
Aharon Oren ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Deep Sea ◽  
Hydrothermal Vent ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Deep Sea Sediment ◽  
The Family ◽  
Hydrothermal Vent Field

A Gram-stain-negative, motile, aerobic bacterial strain, designated 22DY15T, was isolated from a deep-sea sediment sample collected from a hydrothermal vent field located in the East Pacific Rise. The isolate was a short rod with a single flagellum and was positive for catalase and oxidase activities. Q-10 was the predominant respiratory quinone. The major polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphoglycolipid, one aminolipid and three unidentified phospholipids. The principal fatty acid (>70 %) was C18 : 1ω7c. The genomic DNA G+C content was 64.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 22DY15T represents a distinct lineage within the family Rhodobacteraceae. The closest relatives were species of the genera Aliiroseovarius (93.3–96.0 % 16S rRNA gene sequence similarity), Sulfitobacter (94.0–96.0 %) and Loktanella (92.0–95.9 %). Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain 22DY15T could be differentiated from its most closely related genera. Therefore, it is proposed that strain 22DY15T represents a novel species in a new genus of the family Rhodobacteraceae, for which the name Brevirhabdus pacifica gen. nov., sp. nov. is proposed. The type strain of the type species is 22DY15T ( = JCM 19489T = DSM 27767T = CGMCC 1.12416T = MCCC 1K00276T).

Desulfomarina profundi gen. nov., sp. nov., a novel mesophilic, hydrogen-oxidizing, sulphate-reducing chemolithoautotroph isolated from a deep-sea hydrothermal vent chimney

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Yurina Hashimoto ◽  
Akihiro Tame ◽  
Shigeki Sawayama ◽  
Junichi Miyazaki ◽  
Ken Takai ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Deep Sea ◽  
Hydrothermal Vent ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Casamino Acids ◽  
The 16S Rrna Gene

A novel mesophilic, strictly anaerobic, chemolithoautotrophic sulphate-reducing bacterium, designated strain KT2T, was isolated from a deep-sea hydrothermal vent chimney at the Suiyo Seamount in the Izu-Bonin Arc. Strain KT2T grew at 25–40 °C (optimum 35 °C) and pH 5.5–7.0 (optimum 6.6) in the presence of 25–45 g l−1 NaCl (optimum 30 g l−1). Growth occurred with molecular hydrogen as the electron donor and sulphate, thiosulphate, and sulphite as the electron acceptors. The isolate utilized CO2 as the sole carbon source for chemolithoautotrophic growth on H2. Glycerol, succinate, fumarate, malate, glutamate, or casamino acids could serve as an alternative electron donor in the presence of CO2. Malate, citrate, glutamate, and casamino acids were used as fermentative substrates for weak growth. The G+C content of genomic DNA was 46.1 %. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain KT2T is a member of the family Desulfobulbaceae , showing a sequence similarity of 94.3 % with Desulforhopalus singaporensis . Phylogenomic analysis based on concatenated 156 single-copy marker genes confirmed the same topology as the 16S rRNA gene phylogeny. The ANI and AAI values between strain KT2T and related genera of the family Desulfobulbaceae were 65.6–68.6 % and 53.1–62.9 %. Based on the genomic, molecular, and physiological characteristics, strain KT2T represents a novel genus and species within the family Desulfobulbaceae , for which the name Desulfomarina profundi gen. nov., sp. nov. is proposed, with KT2T (=JCM 34118T = DSM 111364T) as the type strain.

scholarly journals The mutL Gene as a Genome-Wide Taxonomic Marker for High Resolution Discrimination of Lactiplantibacillus plantarum and Its Closely Related Taxa

2021 ◽  
Vol 9 (8) ◽  
pp. 1570
Author(s):  
Chien-Hsun Huang ◽  
Chih-Chieh Chen ◽  
Yu-Chun Lin ◽  
Chia-Hsuan Chen ◽  
Ai-Yun Lee ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Target Genes ◽  
Marker Genes ◽  
Rrna Gene ◽  
Accurate Identification ◽  
Discrimination Power ◽  
Sequence Identity ◽  
Genome Wide ◽  
A Genome

The current taxonomy of the Lactiplantibacillus plantarum group comprises of 17 closely related species that are indistinguishable from each other by using commonly used 16S rRNA gene sequencing. In this study, a whole-genome-based analysis was carried out for exploring the highly distinguished target genes whose interspecific sequence identity is significantly less than those of 16S rRNA or conventional housekeeping genes. In silico analyses of 774 core genes by the cano-wgMLST_BacCompare analytics platform indicated that csbB, morA, murI, mutL, ntpJ, rutB, trmK, ydaF, and yhhX genes were the most promising candidates. Subsequently, the mutL gene was selected, and the discrimination power was further evaluated using Sanger sequencing. Among the type strains, mutL exhibited a clearly superior sequence identity (61.6–85.6%; average: 66.6%) to the 16S rRNA gene (96.7–100%; average: 98.4%) and the conventional phylogenetic marker genes (e.g., dnaJ, dnaK, pheS, recA, and rpoA), respectively, which could be used to separat tested strains into various species clusters. Consequently, species-specific primers were developed for fast and accurate identification of L. pentosus, L. argentoratensis, L. plantarum, and L. paraplantarum. During this study, one strain (BCRC 06B0048, L. pentosus) exhibited not only relatively low mutL sequence identities (97.0%) but also a low digital DNA–DNA hybridization value (78.1%) with the type strain DSM 20314T, signifying that it exhibits potential for reclassification as a novel subspecies. Our data demonstrate that mutL can be a genome-wide target for identifying and classifying the L. plantarum group species and for differentiating novel taxa from known species.

Nonomuraea montanisoli sp. nov., isolated from mountain forest soil

2021 ◽  
Author(s):  
Suchart Chanama ◽  
Chanwit Suriyachadkun ◽  
Manee Chanama
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Related Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Mountain Forest ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
A Genome

A novel actinomycete, strain SMC 257T, was isolated from a soil sample collected from mountain forest, Nan Province, Thailand. Strain SMC 257T formed tightly closed spiral spore chains on aerial mycelia. A polyphasic approach was used for the taxonomic study of this strain. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SMC 257T belonged to the genus Nonomuraea , and the closest phylogenetically related species were Nonomuraea roseoviolacea subsp. carminata JCM 9946T (98.9 % 16S rRNA gene sequence similarity), Nonomuraea rhodomycinica TBRC 6557T (98.4 %), and Nonomuraea roseoviolacea subsp. roseoviolacea JCM 3145T (98.3 %). Genome sequencing revealed a genome size of 9.76 Mbp and a G+C content of 72.3 mol%. The genome average nucleotide identity (ANI) and the digital DNA–DNA hybridization (dDDH) values that distinguished this novel strain from its closest related species were species boundary of 95–96 % and 70 %, respectively. The cell wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars were glucose, ribose, madurose and mannose. The major menaquinone was MK-9(H4). The polar lipid profile consisted of phosphatidylethanolamine, hydroxyphosphatidylethanolamine, lysophosphatidylethanolamine, diphosphatidylglycerol, N-phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The predominant cellular fatty acids were C17 : 0 10-methyl and iso-C16 : 0. Based on comparative analysis of phenotypic, chemotaxonomic and genotypic data, strain SMC 257T is considered to represent a novel species of the genus Nonomuraea , for which the name Nonomuraea montanisoli is proposed. The type strain is SMC 257T (=TBRC 13065T=NBRC 114772T).

scholarly journals Hansschlegelia quercus sp. nov., a novel methylotrophic bacterium isolated from oak buds

2020 ◽  
Vol 70 (8) ◽  
pp. 4646-4652 ◽  
Author(s):  
Nadezhda V. Agafonova ◽  
Elena N. Kaparullina ◽  
Denis S. Grouzdev ◽  
Nina V. Doronina
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Methylotrophic Bacterium ◽  
Rrna Gene ◽  
Methylotrophic Bacteria ◽  
Content Type ◽  
Link Type ◽  
A Genome

Novel aerobic, restricted facultatively methylotrophic bacteria were isolated from buds of English oak (Quercus robur L.; strain DubT) and northern red oak (Quercus rubra L.; strain KrD). The isolates were Gram-negative, asporogenous, motile short rods that multiplied by binary fisson. They utilized methanol, methylamine and a few polycarbon compounds as carbon and energy sources. Optimal growth occurred at 25 °C and pH 7.5. The dominant phospholipids were phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol and phoshatidylglycerol. The major cellular fatty acids of cells were C18 : 1 ω7c, 11-methyl C18 : 1 ω7c and C16 : 0. The major ubiquinone was Q-10. Analysis of 16S rRNA gene sequences showed that the strains were closely related to the members of the genus Hansschlegelia : Hansschlegelia zhihuaiae S113T(97.5–98.0 %), Hansschlegelia plantiphila S1T (97.4–97.6 %) and Hansschlegelia beijingensis PG04T(97.0–97.2 %). The 16S rRNA gene sequence similarity between strains DubT and KrD was 99.7 %, and the DNA–DNA hybridization (DDH) result between the strains was 85 %. The ANI and the DDH values between strain DubT and H. zhihuaiae S113T were 80.1 and 21.5  %, respectively. Genome sequencing of the strain DubT revealed a genome size of 3.57 Mbp and a G+C content of 67.0 mol%. Based on the results of the phenotypic, chemotaxonomic and genotypic analyses, it is proposed that the isolates be assigned to the genus Hansschlegelia as Hansschlegelia quercus sp. nov. with the type strain DubT (=VKM B-3284T=CCUG 73648T=JCM 33463T).

scholarly journals Sulfurimonas xiamenensis sp. nov. and Sulfurimonas lithotrophica sp. nov., hydrogen- and sulfur-oxidizing chemolithoautotrophs within the Epsilonproteobacteria isolated from coastal sediments, and an emended description of the genus Sulfurimonas

2020 ◽  
Vol 70 (4) ◽  
pp. 2657-2663 ◽  
Author(s):  
Shasha Wang ◽  
Lijing Jiang ◽  
Xuewen Liu ◽  
Suping Yang ◽  
Zongze Shao
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Elemental Sulfur ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Emended Description

Strains 1-1NT and GYSZ_1T were isolated from marine sediments collected from the coast of Xiamen, PR China. Cells of the two strains were Gram-stain-negative, rod-shaped or slightly curved. Strain 1-1NT was non-motile, whereas strain GYSZ_1T was motile by means of one polar flagellum. The temperature, pH and salinity concentration ranges for growth of 1-1NT were 10–45 °C (optimum 30 °C), pH 5.5–8.0 (optimum 7.0) and 0–90 g l−1 NaCl (optimum 50 g l−1), while the growth of GYSZ_1T occurred at 4–45 °C (optimum 33 °C), pH 5.0–8.5 (optimum 6.5) and 5–90 g l−1 NaCl (optimum 20 g l−1). The two novel isolates were obligate chemolithoautotrophs capable of growth using hydrogen, thiosulfate, sulfide or elemental sulfur as the sole energy source, and nitrate, elemental sulfur or molecular oxygen as an electron acceptor. The major fatty acids of 1-1NT were C16 : 1ω7c, C16 : 0, C18 : 1ω7c and C18 : 0, while the predominant fatty acids of strain GYSZ_1T were C16 : 1ω7c, C16 : 0, C18 : 1ω7c and C14 : 0 3-OH. The DNA G+C contents of 1-1NT and GYSZ_1T were 34.5 mol% and 33.2 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that 1-1NT and GYSZ_1T represented members of the genus Sulfurimonas , with the highest sequence similarities to Sulfurimonas crateris SN118T (97.4 %) and Sulfurimonas denitrificans DSM 1251T (94.7 %), respectively. However, 1-1NT and GYSZ_1T shared 95.5 % similarity of 16S rRNA gene sequences, representing different species of the genus Sulfurimonas . On the basis of the physiological properties and the results of phylogenetic analyses, including average nucleotide identity and in silico DNA–DNA hybridization values, strains 1-1NT and GYSZ_1T represent two novel species within the genus Sulfurimonas , for which the names Sulfurimonas xiamenensis sp. nov. and Sulfurimonas lithotrophica sp. nov. are proposed, with the type strains 1-1NT (=MCCC 1A14514T=KCTC 15851T) and GYSZ_1T (=MCCC 1A14739T=KCTC 15853T), respectively. Our results also justify an emended description of the genus Sulfurimonas .

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