scholarly journals Vibrio marisflavi sp. nov., isolated from seawater

2011 ◽  
Vol 61 (3) ◽  
pp. 568-573 ◽  
Author(s):  
Hong Wang ◽  
Jiwen Liu ◽  
Yan Wang ◽  
Xiao-Hua Zhang
Keyword(s):  
Gene Sequence ◽  
Water Mass ◽  
Cold Water ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
The Yellow Sea ◽  
Arginine Dihydrolase ◽  
Pr China ◽  
Curved Rods ◽  
Sequence Similarities

A Gram-reaction-negative, facultatively anaerobic bacterial strain, designated WH134T, was isolated from a seawater sample collected at a depth of 10 m near the Yellow Sea Cold Water Mass (YSCWM), 3 ° 59.970′ N 12 ° 0.157′ E, PR China. Cells of strain WH134T were slightly curved rods, motile by means of a polar flagellum and positive for poly-β-hydroxybutyrate (PHB) accumulation. The strain was able to grow in 1–6 % (w/v) NaCl, at pH 5–10 and 16–37 °C but not at 4 or 40 °C. The major cellular fatty acids were summed feature 3 C16  : 1 ω7c and/or iso-C15 : 0 2-OH, C16 : 0, C18 : 1 ω7c, C18 : 0 and C14 : 0. The DNA G+C content was 42.5 mol%. Phylogenetic analyses based on 16S rRNA, gyrB, topA, recA, ftsZ, mreB, gapA and rpoA gene sequences revealed that strain WH134T belongs to the genus Vibrio and showed gene sequence similarities of 96.6, 75.7, 74.6, 83.6, 78.9, 82.9, 86.0 and 89.4 % , respectively, to Vibrio rumoiensis S-1T. The possession of a flagellum, activity of arginine dihydrolase and lysine decarboxylase and inability to utilize citrate, however, differentiated strain WH134T from V. rumoiensis DSM 19141T. On the basis of the phenotypic, chemotaxonomic and phylogenetic evidence, strain WH134T represents a novel species of the genus Vibrio, for which the name Vibrio marisflavi sp. nov. is proposed. The type strain is WH134T (=CGMCC 1.8994T =LMG 25284T =DSM 23086T).

scholarly journals Taxonomy, ontogeny and molecular phylogeny of Anteholosticha marimonilata spec. nov. (Ciliophora, Hypotrichida) from the Yellow Sea, China

2011 ◽  
Vol 61 (8) ◽  
pp. 2000-2014 ◽  
Author(s):  
Yuan Xu ◽  
Jie Huang ◽  
Xiaozhong Hu ◽  
Khaled A. S. Al-Rasheid ◽  
Weibo Song ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Yellow Sea ◽  
Gene Sequence ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Sequence Information ◽  
Rrna Gene Sequence ◽  
Cortical Granules

The morphology, morphogenesis and molecular phylogeny of the marine ciliated protozoan Anteholosticha marimonilata spec. nov., isolated from mollusc-farming waters of the Yellow Sea, Qingdao, PR China, were investigated using microscopic observations of live and protargol-impregnated specimens and by small subunit rRNA gene sequence analysis. The novel species could be distinguished by the following features: an elongated elliptical body, in vivo size 80–160 µm × 30–50 µm; an adoral zone consisting of about 36 membranelles; three frontal, one parabuccal, one buccal, two frontoterminal and usually two pretransverse ventral cirri; 10–13 transverse cirri; a midventral complex composed of 12–17 pairs of cirri only, terminating in posterior 1/5; four or five dorsal kineties; two types of colourless cortical granules; four to nine moniliform macronuclear nodules and one to three micronuclei, and a contractile vacuole positioned at mid-body. Hitherto, the ontogenesis of the genus Anteholosticha has been regarded as rather diverse, which was confirmed by the morphogenetic processes of this novel species. The most noteworthy feature of A. marimonilata was that the proter retained almost the entire parental adoral zone except for a few proximal membranelles that were renewed in situ. The SSU rRNA gene sequence information clearly discriminated this isolate from its congeners. Molecular phylogenetic analyses demonstrated, with high statistical support, that A. marimonilata branched as a sister lineage to the Nothoholosticha–Pseudokeronopsis clade and hence belongs to the core part of the order Urostylida.

scholarly journals Pseudomonas coleopterorum sp. nov., a cellulase-producing bacterium isolated from the bark beetle Hylesinus fraxini

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 2852-2858 ◽  
Author(s):  
Esther Menéndez ◽  
Martha H. Ramírez-Bahena ◽  
Anna Fabryová ◽  
José M. Igual ◽  
Oldrich Benada ◽  
...  
Keyword(s):  
Bark Beetle ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Arginine Dihydrolase

We isolated a strain coded Esc2AmT during a study focused on the microbial diversity of adult specimens of the bark beetle Hylesinus fraxini. Its 16S rRNA gene sequence had 99.4 % similarity with respect to its closest relative, Pseudomonas rhizosphaerae IH5T. The analysis of partial sequences of the housekeeping genes rpoB, rpoD and gyrB confirmed that strain Esc2AmT formed a cluster with P. rhizosphaerae IH5T clearly separated from the remaining species of the genus Pseudomonas. Strain Esc2AmT had polar flagella and could grow at temperatures from 4 °C to 30 °C. The respiratory quinone was Q9 and the main fatty acids were C16 : 0, C18 : 1ω7c and/or C18 : 1ω6c in summed feature 8 and C16 : 1ω7c and/or C16 : 1ω6c in summed feature 3. DNA–DNA hybridization results showed 51 % relatedness with respect to P. rhizosphaerae IH5T. Oxidase, catalase and urease-positive, the arginine dihydrolase system was present but nitrate reduction and β-galactosidase production were negative. Aesculin hydrolysis was positive. Based on the results from the genotypic, phenotypic and chemotaxonomic analyses, we propose the classification of strain Esc2AmT as representing a novel species of the genus Pseudomonas, for which we propose the name Pseudomonas coleopterorum sp. nov. The type strain is Esc2AmT ( = LMG 28558T = CECT 8695T).

scholarly journals Paenibacillus ripae sp. nov., isolated from bank side soil

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4757-4762 ◽  
Author(s):  
Ying Sun ◽  
Zhaohui Guo ◽  
Qi Zhao ◽  
Qiyu Gao ◽  
QinJian Xie ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Gene Sequence Analysis ◽  
Optimum Ph ◽  
Pr China ◽  
Diamino Acid

A Gram-stain-variable, rod-shaped, non-motile and endospore-forming bacterium, designated strain HZ1T, was isolated from a sample of bank side soil from Hangzhou city, Zhejiang province, PR China. On the basis of 16S rRNA gene sequence analysis, strain HZ1T was closely related to members of the genus Paenibacillus, sharing the highest levels of sequence similarity with Paenibacillus agarexedens DSM 1327T (94.4 %), Paenibacillus sputi KIT00200-70066-1T (94.4 %). Growth occurred at 15–42 °C (optimum 30–37 °C), pH 5.0–9.5 (optimum pH 7.0–8.0) and NaCl concentrations of up to 6.0 % (w/v) were tolerated (optimum 0.5 %). The dominant respiratory quinone was MK-7 and the DNA G+C content was 40.1 mol%. The major fatty acids were anteiso-C15 : 0 and iso-C16 : 0. The major polar lipids of strain HZ1T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and several unknown lipids. The diagnostic diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. Based on its phenotypic and chemotaxonomic characteristics and phylogenetic data, strain HZ1T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus ripae sp. nov. (type strain HZ1T = CCTCC AB 2014276T = LMG 28639T) is proposed.

scholarly journals Spirosoma aerolatum sp. nov., isolated from a motor car air conditioning system

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4003-4007 ◽  
Author(s):  
Dong-Uk Kim ◽  
Hyosun Lee ◽  
Song-Gun Kim ◽  
Jae-Hyung Ahn ◽  
So Yoon Park ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Polar Lipids ◽  
Rrna Gene ◽  
Gram Stain ◽  
Rrna Gene Sequence ◽  
Air Conditioning System ◽  
Optimum Ph ◽  
Sequence Similarities

A Gram-stain-negative, yellow-pigmented bacterial strain, designated PR1012KT, was isolated from a motor car evaporator core collected in Korea. Cells of the strain were facultatively anaerobic, non-spore-forming and rod-shaped. The strain grew at 10–40 °C (optimum, 25 °C), at pH 6.5–8.0 (optimum, pH 7.0–8.0) and in the presence of 0–1 % (w/v) NaCl. Phylogenetically, the strain was closely related to members of the genus Spirosoma (97.50–90.74 % 16S rRNA gene sequence similarities) and showed highest sequence similarity to Spirosoma panaciterrae DSM 21099T (97.50 %). Its predominant fatty acids included summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 1ω5c, iso-C15 : 0 and summed feature 4 (iso-C17 : 1 I and/or anteiso B) and it had MK-7 as the major menaquinone. The polar lipids present included phosphatidylethanolamine, one unknown aminophospholipid, two unknown aminolipids and five unknown polar lipids. The DNA G+C content of this strain was 54 mol%. Based on phenotypic, genotypic and chemotaxonomic data, strain PR1012KT represents a novel species in the genus Spirosoma, for which the name Spirosoma aerolatum sp. nov. is proposed. The type strain is PR1012KT ( = KACC 17939T = NBRC 110794T).

Redescription and SSU rRNA gene-based phylogeny of an anaerobic ciliate, Plagiopyla ovata Kahl, 1931 (Ciliophora, Plagiopylea)

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Ran Li ◽  
Wenbao Zhuang ◽  
Congcong Wang ◽  
Hamed El-Serehy ◽  
Saleh A. Al-Farraj ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Gene Trees ◽  
Ssu Rrna Gene ◽  
Anaerobic Ciliate ◽  
Pr China

The morphology and molecular phylogeny of Plagiopyla ovata Kahl, 1931, a poorly known anaerobic ciliate, were investigated based on a population isolated from sand samples collected from the Yellow Sea coast at Qingdao, PR China. Details of the oral ciliature are documented for the first time to our knowledge and an improved species diagnosis is given. The small subunit ribosomal RNA (SSU rRNA) gene was newly sequenced and phylogenetic analyses revealed that P. ovata clusters within the monophyletic family Plagiopylidae. However, evolutionary relationships within both the family Plagiopylidae and the genus Plagiopyla remain obscure owing to undersampling, the lack of sequence data from known species and low nodal support or unstable topologies in gene trees. A key to the identification of the species of the genus Plagiopyla with validly published names is also supplied.

scholarly journals Methanobacterium aggregans sp. nov., a hydrogenotrophic methanogenic archaeon isolated from an anaerobic digester

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1975-1980 ◽  
Author(s):  
Tobias Kern ◽  
Mary Linge ◽  
Michael Rother
Keyword(s):  
16S Rrna ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Optimal Growth ◽  
Maximum Growth ◽  
Maximum Growth Rate ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Curved Rods

A novel, strictly anaerobic, hydrogenotrophic methanogen, strain E09F.3T, was isolated from a commercial biogas plant in Germany. Cells of E09F.3T were Gram-stain-negative, non-motile, slightly curved rods, long chains of which formed large aggregates consisting of intertwined bundles of chains. Cells utilized H2+CO2 and, to a lesser extent, formate as substrates for growth and methanogenesis. The optimal growth temperature was around 40 °C; maximum growth rate was obtained at pH around 7.0 with approximately 6.8 mM NaCl. The DNA G+C content of strain E09F.3T was 39.1 mol%. Phylogenetic analyses based on 16S rRNA and mcrA gene sequences placed strain E09F.3T within the genus Methanobacterium. On the basis of 16S rRNA gene sequence similarity, strain E09F.3T was closely related to Methanobacterium congolense CT but morphological, physiological and genomic characteristics indicated that strain E09F.3T represents a novel species. The name Methanobacterium aggregans sp. nov. is proposed for this novel species, with strain E09F.3T ( = DSM 29428T = JCM 30569T) as the type strain.

scholarly journals Thermovibrio ammonificans sp. nov., a thermophilic, chemolithotrophic, nitrate-ammonifying bacterium from deep-sea hydrothermal vents

2004 ◽  
Vol 54 (1) ◽  
pp. 175-181 ◽  
Author(s):  
Costantino Vetriani ◽  
Mark D. Speck ◽  
Susan V. Ellor ◽  
Richard A. Lutz ◽  
Valentin Starovoytov
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vents ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
East Pacific ◽  
Casamino Acids ◽  
The 16S Rrna Gene

A thermophilic, anaerobic, chemolithoautotrophic bacterium was isolated from the walls of an active deep-sea hydrothermal vent chimney on the East Pacific Rise at 9° 50′ N. Cells of the organism were Gram-negative, motile rods that were about 1·0 μm in length and 0·6 μm in width. Growth occurred between 60 and 80 °C (optimum at 75 °C), 0·5 and 4·5 % (w/v) NaCl (optimum at 2 %) and pH 5 and 7 (optimum at 5·5). Generation time under optimal conditions was 1·57 h. Growth occurred under chemolithoautotrophic conditions in the presence of H2 and CO2, with nitrate or sulfur as the electron acceptor and with concomitant formation of ammonium or hydrogen sulfide, respectively. Thiosulfate, sulfite and oxygen were not used as electron acceptors. Acetate, formate, lactate and yeast extract inhibited growth. No chemoorganoheterotrophic growth was observed on peptone, tryptone or Casamino acids. The genomic DNA G+C content was 54·6 mol%. Phylogenetic analyses of the 16S rRNA gene sequence indicated that the organism was a member of the domain Bacteria and formed a deep branch within the phylum Aquificae, with Thermovibrio ruber as its closest relative (94·4 % sequence similarity). On the basis of phylogenetic, physiological and genetic considerations, it is proposed that the organism represents a novel species within the newly described genus Thermovibrio. The type strain is Thermovibrio ammonificans HB-1T (=DSM 15698T=JCM 12110T).

scholarly journals Dyadobacter hamtensis sp. nov., from Hamta glacier, located in the Himalayas, India

2005 ◽  
Vol 55 (5) ◽  
pp. 2113-2117 ◽  
Author(s):  
P. Chaturvedi ◽  
G. S. N. Reddy ◽  
S. Shivaji
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Characteristics ◽  
Mountain Ranges ◽  
Himalayan Mountain

Strain HHS 11T was isolated from a water sample collected from the snout of Hamta glacier located in the Himalayan mountain ranges of India. Phenotypic, chemotaxonomic and phylogenetic analyses established the affiliation of the isolate to the genus Dyadobacter. HHS 11T possessed 96 and 95 % 16S rRNA gene sequence similarity with respect to Dyadobacter crusticola and Dyadobacter fermentans, respectively. Furthermore, strain HHS 11T differs from D. crusticola and D. fermentans in a number of phenotypic characteristics. These data suggest that strain HHS 11T represents a novel species of the genus Dyadobacter, for which the name Dyadobacter hamtensis sp. nov. is proposed. The type strain is HHS 11T (=JCM 12919T=MTCC 7023T).

scholarly journals Treponema berlinense sp. nov. and Treponema porcinum sp. nov., novel spirochaetes isolated from porcine faeces

2005 ◽  
Vol 55 (4) ◽  
pp. 1675-1680 ◽  
Author(s):  
Marcel Nordhoff ◽  
David Taras ◽  
Moritz Macha ◽  
Karsten Tedin ◽  
Hans-Jürgen Busse ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Gene Sequence Analysis ◽  
Sequence Similarities

Limit-dilution procedures were used to isolate seven, helically coiled bacterial strains from faeces of swine that constituted two unidentified taxa. Comparative 16S rRNA gene sequence analysis showed highest similarity values with species of the genus Treponema indicating that the isolates are members of this genus. Strain 7CPL208T, as well as five further isolates, and 14V28T displayed the highest 16S rRNA gene sequence similarities with Treponema pectinovorum ATCC 33768T (92·3 %) and Treponema parvum OMZ 833T (89·9 %), respectively. Polar lipid profiles distinguished 7CPL208T and 14V28T from each other as well as from related species. Based on their phenotypic and genotypic distinctiveness, strains 7CPL208T and 14V28T are suggested to represent two novel species of the genus Treponema, for which the names Treponema berlinense sp. nov. and Treponema porcinum sp. nov. are proposed. The type strain for Treponema berlinense is 7CPL208T (=ATCC BAA-909T=CIP 108244T=JCM 12341T) and for Treponema porcinum 14V28T (=ATCC BAA-908T=CIP 108245T=JCM 12342T).

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