Characterization of Chemolithoautotrophic Growth Herbaspirillum sp. Isolated from Volcanic Environment in Miyake-Jima Island, Japan

2013 ◽  
Vol 668 ◽  
pp. 924-927
Author(s):  
Hong Sheng Lu ◽  
Long Qing Shi
Keyword(s):  
Mineral Salt Medium ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Position ◽  
Accession Number ◽  
Herbaspirillum Seropedicae ◽  
16S Rdna Gene ◽  
Cellular Fatty Acids ◽  
Phenotypic Tests

A chemolithoautotrophic growth bacterium KP1-50T was isolated from 22-year-old volcanic deposits of Miyake-jima island (Japan) in this study. Its chemolithoautotrophic growth was tested using mineral salt medium (MS) medium under the atmosphere of H2, O2 and CO2. Phenotypic tests were mainly done with API 20NE kit system (bioMérieux). Phylogenetic position was determined by constructing the system tree. Chemolithoautotrophic growth of strain KP1-50T was proved by its growth curve with OD660 value of 0.5. The phylogenetic analysis based on 16S rDNA gene sequences indicated that sequence similarity between this strain and Herbaspirillum seropedicae LMG 6513T was 97%. The major cellular fatty acids are C16:0(31.3%), C16:1w7c/C15:0 2-OH iso (26.5%), C18:1 iso/trans (22.7%). The DNA G+C content of strain KP1-50T was 58mol%. DNA-DNA relatedness between strain KP1-50T and H.seropedicae LMG6513T, H.putei NBRC102406T and H.rubrisubalbicans NBRC102523T were 14.7%, 22.7% and 12.5% respectively. Strain KP1-50T seemed to be a novel species of the genus Herbaspicrillum, its accession number was AB366195 and the name of Herbaspirillum chemorialis sp. nov. was proposed.

scholarly journals Antricoccus suffuscus gen. nov., sp. nov., isolated from a natural cave

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4410-4416 ◽  
Author(s):  
Soon Dong Lee
Keyword(s):  
Type Strain ◽  
New Genus ◽  
Novel Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Diamino Acid ◽  
Unknown Phospholipid

A novel actinobacterium, designated strain C4-31T, was isolated from soil collected from a cave. Cells were aerobic, Gram-reaction-positive, oxidase-negative, catalase-positive and non-motile cocci. Comparison of 16S rRNA gene sequences showed that the organism occupied a distinct phylogenetic position within the suborder Frankineae, with sequence similarity values of less than 93.2 % to members of this suborder. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major menaquinone was MK-9(H4). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, an unknown aminophospholipid and an unknown phospholipid. The major fatty acids were iso-C16 : 0, C17 : 1ω6c and C16 : 0. The G+C content of the DNA was 62.8 mol%. On the basis of morphological and chemotaxonomic data as well as phylogenetic evidence, strain C4-31T ( = KCTC 39556T = DSM 100065T) is considered to represent the type strain of a novel species of a new genus in the suborder Frankineae, for which the name Antricoccus suffuscus gen. nov., sp. nov. is proposed.

scholarly journals Paenibacillus hunanensis sp. nov., isolated from rice seeds

2010 ◽  
Vol 60 (6) ◽  
pp. 1266-1270 ◽  
Author(s):  
Yang Liu ◽  
Lin Liu ◽  
Fubin Qiu ◽  
Peter Schumann ◽  
Yu Shi ◽  
...  
Keyword(s):  
Type Strain ◽  
Hybrid Rice ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Gram Stain ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
Cellular Fatty Acids

Four Gram-stain-positive, aerobic or facultatively anaerobic, motile, endospore-forming, rod-shaped bacteria, designated strains FeL05T, FeL11, Fek19 and Fek21, were isolated from seeds of hybrid rice (Oryza sativa L. Jinyou 611), and their taxonomic positions were determined using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that the four strains were members of the genus Paenibacillus. They showed 95.4 % sequence similarity or less with strains of other Paenibacillus species. The G+C content of strain FeL05T was found to be 53.3 mol%. Its predominant respiratory quinone was MK-7. The predominant cellular fatty acids were anteiso-C15 : 0 (61.7 %), C16 : 0 (10.9 %), iso-C16 : 0 (7.0 %), anteiso-C17 : 0 (6.7 %) and iso-C15 : 0 (5.2 %). On the basis of its phenotypic properties and phylogenetic distinctiveness, strain FeL05T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus hunanensis sp. nov. is proposed. The type strain is strain FeL05T (=ACCC 10718T =CGMCC 1.8907T =DSM 22170T).

scholarly journals Frateuria terrea sp. nov., isolated from forest soil, and emended description of the genus Frateuria

2011 ◽  
Vol 61 (2) ◽  
pp. 443-447 ◽  
Author(s):  
Jia-Yue Zhang ◽  
Xing-Yu Liu ◽  
Shuang-Jiang Liu
Keyword(s):  
Forest Soil ◽  
Novel Species ◽  
Sequence Similarity ◽  
Changbai Mountains ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Cellular Fatty Acids ◽  
Emended Description ◽  
Negative Growth

A bacterial strain, designated VA24T, was isolated from forest soil of the Changbai Mountains, Heilongjiang province, China. Cells of strain VA24T were Gram-reaction-negative, aerobic, non-spore-forming, long rods, 0.3–0.5×2.0–3.0 μm in size and were motile by means of a subpolar flagellum. Strain VA24T was oxidase-positive and catalase-negative. Growth occurred at 21–36 °C, pH 5–10 and in 0–2 % (w/v) NaCl but did not occur at 37 °C. The predominant respiratory quinone was Q-8, the major polar lipids were phosphatidylethanolamine and phosphatidylmonomethylethanolamine and the major cellular fatty acids were iso-C15 : 0 (14.9 %), iso-C17 : 1 ω9c (14.1 %), iso-C17 : 0 (10.8 %) and iso-C16 : 0 (10.3 %). The DNA G+C content was 67.4 mol% (T m). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain VA24T was closely related to Frateuria aurantia IFO 13300T with 96.9 % sequence similarity. DNA–DNA relatedness of strain VA24T to F. aurantia DSM 6220T was 15.8 %. Based on its phenotypic and genotypic features, strain VA24T represents a novel species of the genus Frateuria, for which the name Frateuria terrea sp. nov. is proposed. The type strain is VA24T (=CGMCC 1.7053T =NBRC 104236T).

scholarly journals Geobacillus lituanicus sp. nov.

2004 ◽  
Vol 54 (6) ◽  
pp. 1991-1995 ◽  
Author(s):  
Nomeda Kuisiene ◽  
Juozas Raugalas ◽  
Donaldas Chitavichius
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequence Analysis ◽  
Pcr Rflp ◽  
Group 5

Obligately thermophilic, aerobic, proteolytic, endospore-forming strain N-3T was isolated from a high-temperature oilfield in Lithuania. 16S rRNA gene sequence analysis placed this strain in genetic group 5 of the endospore formers. Geobacillus thermoleovorans appeared to be the closest phylogenetic neighbour (99·4 % sequence similarity). The G+C content of strain N-3T was 52·5 mol% and matched the range established for the genus Geobacillus. Studies of DNA–DNA relatedness and morphological and physiological analyses enabled strain N-3T to be described as a member of the genus Geobacillus, but could not assign this strain to any other known species of this genus. Results of this polyphasic study allowed characterization of strain N-3T as a novel species in the genus Geobacillus – Geobacillus lituanicus sp. nov. This species can be distinguished from G. thermoleovorans and Geobacillus stearothermophilus on the basis of 16S rRNA gene PCR-RFLP assays with the restriction endonucleases AluI, HaeIII and TaqI. The type strain of the novel species is N-3T (=DSM 15325T=VKM B-2294T).

Chitinophaga cymbidii sp. nov., isolated from Cymbidium goeringii roots

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1800-1804 ◽  
Author(s):  
Lubin Li ◽  
Lei Sun ◽  
Nan Shi ◽  
Lin Liu ◽  
Huijuan Guo ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Cellular Fatty Acids ◽  
Link Type ◽  
Gram Staining ◽  
Cymbidium Goeringii

Two Gram-staining-negative, aerobic, non-spore-forming rod-shaped, non-motile bacteria, designated strains R156-2T and T58-2 were isolated from the roots of Cymbidium goeringii. The colonies were yellow-pigmented. On the basis of 16S rRNA gene sequence similarity, strains R156-2T and T58-2 were shown to be members of the genus Chitinophaga . Strains R156-2T and T58-2 showed the greatest level of sequence similarity with Chitinophaga niabensis (96.0–96.3 %). The major menaquinone was MK-7. The main cellular fatty acids were iso-C15 : 0, C16 : 1ω5c and iso-C17 : 0 3-OH. Phenotypic and genotypic analyses indicated that strains R156-2T and T58-2 could not be assigned to any recognized species. Therefore, strains R156-2T and T58-2 represent a novel species of the genus Chitinophaga , for which the name Chitinophaga cymbidii sp. nov. is proposed. The type strain is R156-2T ( = ACCC 05363T = KCTC 23738T). The DNA G+C content of this strain is 51.9 mol%.

scholarly journals Spirochaeta perfilievii sp. nov., an oxygen-tolerant, sulfide-oxidizing, sulfur- and thiosulfate-reducing spirochaete isolated from a saline spring

2011 ◽  
Vol 61 (1) ◽  
pp. 110-117 ◽  
Author(s):  
Galina Dubinina ◽  
Margarita Grabovich ◽  
Natalia Leshcheva ◽  
Frederick A. Rainey ◽  
Ekaterina Gavrish
Keyword(s):  
Gene Sequence ◽  
Elemental Sulfur ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Gene Sequence Analysis ◽  
Optimum Ph ◽  
Saline Spring

A novel strain of fermenting, aerotolerant, chemo-organoheterotrophic spirochaete designated PT was isolated from a sulfur ‘Thiodendron’ mat in a saline spring at the Staraya Russa resort (Novgorod Region, Russia). Cells of strain PT exhibited a helical shape. The spirochaete required sulfide in the growth medium and was able to oxidize it non-enzymically to elemental sulfur via the interaction of H2O2 with sulfide and deposit it in the periplasmic space. Growth occurred at 4–32 °C (optimum at 28–30 °C), pH 6.0–8.5 (optimum pH 7.0–7.5), and in 0.1–1 M NaCl (optimum 0.35 M). The isolate used several sugars and polysaccharides as carbon or energy sources but did not use peptides, amino acids, organic acids or alcohols. The products of glucose fermentation were formate, acetate, ethanol, pyruvate, CO2 and H2. The genomic DNA G+C content was 41.7 mol%. 16S rRNA gene sequence analysis showed that strain PT fell within a group of species in the genus Spirochaeta, including Spirochaeta litoralis, S. isovalerica and S. cellobiosiphila, with which it shared less then 89 % sequence similarity. On the basis of its morphology, physiology and other phenotypic properties, as well as its phylogenetic position, the new isolate is considered to represent a novel species of the genus Spirochaeta, for which the name Spirochaeta perfilievii sp. nov. is proposed. The type strain is PT (=DSM 19205T =VKM B-2514T).

scholarly journals Duganella violaceinigra sp. nov., a novel mesophilic bacterium isolated from forest soil

2004 ◽  
Vol 54 (5) ◽  
pp. 1811-1814 ◽  
Author(s):  
Wen-Jun Li ◽  
Yu-Qin Zhang ◽  
Dong-Jin Park ◽  
Chang-Tian Li ◽  
Li-Hua Xu ◽  
...  
Keyword(s):  
Forest Soil ◽  
Yunnan Province ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Rrna Gene Sequence ◽  
Cellular Fatty Acids ◽  
Mesophilic Bacterium

A mesophilic bacterium, designated strain YIM 31327T, was isolated from a forest soil sample collected from Yunnan Province, China, and was then investigated using a polyphasic approach. The strain grew optimally at 28–30 °C and pH 7·2. The cells were Gram-negative, short, rod-shaped, motile and non-spore-forming with flagella. The major ubiquinone was Q-8 and the cellular fatty acids were C16 : 0 and C12 : 0. The DNA G+C content of strain YIM 31327T was 62·8 mol%. Phylogenetic analysis revealed that strain YIM 31327T was a member of the β-Proteobacteria, being most closely related to Duganella zoogloeoides, with which it exhibited less than 96 % 16S rRNA gene sequence similarity. On the basis of the phenotypic and genotypic differences between strain YIM 31327T and D. zoogloeoides, a novel species, Duganella violaceinigra sp. nov., is proposed, with YIM 31327T (=CIP 108077T=KCTC 12193T) as the type strain.

scholarly journals Arcobacter defluvii sp. nov., isolated from sewage samples

2011 ◽  
Vol 61 (9) ◽  
pp. 2155-2161 ◽  
Author(s):  
Luis Collado ◽  
Arturo Levican ◽  
Jessica Perez ◽  
Maria José Figueras
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Sequence Similarity ◽  
Housekeeping Genes ◽  
Specific Pattern ◽  
Phenotypic Characterization ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Taxonomic Approach

A study employing a polyphasic taxonomic approach was undertaken to clarify the position of 12 isolates recovered from sewage samples. These isolates were recognized as a potential novel species because a new and specific pattern was produced with the 16S rRNA-RFLP Arcobacter identification method. The sequences of the 16S rRNA gene not only supported the classification of these novel strains as members of the genus Arcobacter, but also showed that they formed a separate phylogenetic line. Strain SW28-11T, chosen as the representative of these strains, showed 16S rRNA gene sequence similarity of 95.6 % with the closest related species Arcobacter nitrofigilis. The phylogenetic position of the novel strains was further confirmed by analysis of the housekeeping genes hsp60, rpoB and, for the first time, gyrB. The latter proved to be an excellent additional gene for establishing the phylogeny of this genus. These data, together with phenotypic characterization, revealed that this group of isolates represent a novel species of the genus Arcobacter. The name Arcobacter defluvii sp. nov., is proposed, with the type strain SW28-11T ( = CECT 7697T = LMG 25694T).

Novosphingobium barchaimii sp. nov., isolated from hexachlorocyclohexane-contaminated soil

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 667-672 ◽  
Author(s):  
Neha Niharika ◽  
Hana Moskalikova ◽  
Jasvinder Kaur ◽  
Miroslava Sedlackova ◽  
Ales Hampl ◽  
...  
Keyword(s):  
Contaminated Soil ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Physiological Tests

A yellow-pigmented bacterial strain, designated LL02T, was isolated from hexachlorocyclohexane-contaminated soil from Spolana Neratovice, a former Czech producer of lindane. A neighbour-joining tree based on 16S rRNA gene sequences showed that strain LL02T occupied a distinct phylogenetic position in the genus Novosphingobium and showed the highest sequence similarity with Novosphingobium resinovorum NCIMB 8767T (98.59 %). DNA–DNA relatedness between strain LL02T and its closest phylogenetic neighbours was <70 %, which indicated that strain LL02T represented a novel species of the genus Novosphingobium . The DNA G+C content of strain LL02T was 67.72±0 mol%. The major respiratory quinone was ubiquinone Q-10. The polar lipid profile of the isolate corresponded to those reported for other members of the genus Novosphingobium (phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylmonomethylethanolamine and sphingoglycolipids), thus supporting its classification in the genus. Spermidine was the major polyamine. The major fatty acids were summed feature 3 (consisting of C16 : 1ω7c and/or C16 : 1ω6c; 40.13 %), summed feature 8 (consisting of C18 : 1ω7c and/or C18 : 1ω6c; 31.09 %) and C14 : 0 2-OH (23.16 %). The results obtained from DNA–DNA hybridization and biochemical and physiological tests clearly distinguished the isolate from its closest phylogenetic neighbours. Thus, strain LL02T represents a novel species of the genus Novosphingobium , for which the name Novosphingobium barchaimii sp. nov. is proposed. The type strain is LL02T ( = CCM 7980T  = DSM 25411T).

scholarly journals Hymenobacter psychrophilus sp. nov., a psychrophilic bacterium isolated from soil

2011 ◽  
Vol 61 (4) ◽  
pp. 859-863 ◽  
Author(s):  
De-Chao Zhang ◽  
Hans-Jürgen Busse ◽  
Hong-Can Liu ◽  
Yu-Guang Zhou ◽  
Franz Schinner ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Good Growth ◽  
Psychrophilic Bacterium ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Polar Lipid Profile ◽  
Cellular Fatty Acids

A non-motile, rod-shaped, red-pigmented bacterium, designated strain BZ33rT, was isolated from soil of an industrial site. Cells stained Gram-negative and were aerobic and psychrophilic, showing good growth at 1–20 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BZ33rT was related to members of the genus Hymenobacter and had highest sequence similarity with Hymenobacter aerophilus DSM 13606T (97.5 %). The predominant cellular fatty acids were anteiso-C15 : 0 (20.3 %), summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH; 20.2 %), iso-C15 : 0 (20.0 %), summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B; 8.2 %) and C16 : 1ω5c (7.9 %). Strain BZ33rT had MK-7 as the major menaquinone. The polyamine pattern contained sym-homospermidine as the major compound with moderate amounts of spermidine. Phosphatidylethanolamine, three unknown aminophospholipids, two unknown aminolipids, two unknown glycolipids and five unknown polar lipids were present in the polar lipid profile. The G+C content of the DNA was 61.6 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, strain BZ33rT is considered to represent a novel species of the genus Hymenobacter, for which the name Hymenobacter psychrophilus sp. nov. is proposed. The type strain is BZ33rT ( = DSM 22290T  = CGMCC 1.8975T  = LMG 25548T).

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