scholarly journals Umboniibacter marinipuniceus gen. nov., sp. nov., a marine gammaproteobacterium isolated from the mollusc Umbonium costatum from the Sea of Japan

2010 ◽  
Vol 60 (3) ◽  
pp. 603-609 ◽  
Author(s):  
Lyudmila A. Romanenko ◽  
Naoto Tanaka ◽  
Galina M. Frolova
Keyword(s):  
Sea Of Japan ◽  
Sequence Similarity ◽  
Fatty Acid Analysis ◽  
Phenotypic Characterization ◽  
The Sea Of Japan ◽  
Rrna Gene ◽  
Phylogenetic Distance ◽  
The Novel ◽  
Bacterial Strains ◽  
Separate Branch

Two bacterial strains, KMM 3891T and KMM 3892, were isolated from internal tissues of the marine mollusc Umbonium costatum collected from the Sea of Japan. The novel isolates were Gram-negative, aerobic, faint pink–reddish-pigmented, rod-shaped, non-motile, stenohaline and psychrotolerant bacteria that were unable to degrade most tested complex polysaccharides. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Fatty acid analysis revealed C17 : 1 ω6c, C17 : 0, C16 : 0 and C16 : 1 ω7c as the dominant components. The major isoprenoid quinone was Q-7. The DNA G+C content of strain KMM 3891T was 51.7 mol%. According to phylogenetic analysis of 16S rRNA gene sequences, strains KMM 3891T and KMM 3892 were positioned within the Gammaproteobacteria as a separate branch, sharing <93 % sequence similarity to their phylogenetic relatives including Saccharophagus degradans, Microbulbifer species, Endozoicomonas elysicola, Simiduia agarivorans and Teredinibacter turnerae. Based on phenotypic characterization and phylogenetic distance, the novel marine isolates KMM 3891T and KMM 3892 represent a new genus and species, for which the name Umboniibacter marinipuniceus gen. nov., sp. nov. is proposed. The type strain of Umboniibacter marinipuniceus is KMM 3891T (=NRIC 0753T =JCM 15738T).

scholarly journals Arenicella xantha gen. nov., sp. nov., a gammaproteobacterium isolated from a marine sandy sediment

2010 ◽  
Vol 60 (8) ◽  
pp. 1832-1836 ◽  
Author(s):  
Lyudmila A. Romanenko ◽  
Naoto Tanaka ◽  
Galina M. Frolova ◽  
Valery V. Mikhailov
Keyword(s):  
Sequence Similarity ◽  
Phospholipid Fatty Acid ◽  
Fatty Acid Analysis ◽  
The Sea Of Japan ◽  
Rrna Gene ◽  
Sandy Sediment ◽  
Phylogenetic Distance ◽  
Separate Branch ◽  
Novel Genus And Species ◽  
Bacterium Strain

A Gram-negative, aerobic, yellow-pigmented, rod-shaped, non-motile bacterium, strain KMM 3895T, was isolated from a marine sandy sample collected offshore from the Sea of Japan. Phylogenetic analysis based on the 16S rRNA gene sequence placed strain KMM 3895T in the class Gammaproteobacteria, forming a separate branch, sharing 89.5 % sequence similarity with Nitrincola lacisaponensis 4CAT and 88–87 % similarity with the other members of the cluster, including members of Kangiella, Spongiibacter, Alcanivorax and Microbulbifer. The major isoprenoid quinone was Q-8. Polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, aminophospholipid and an unknown phospholipid. Fatty acid analysis revealed C16 : 1 ω7, iso-C16 : 0, iso-C18 : 0 and C18 : 1 ω7 as dominant components. The DNA G+C content was determined to be 48.1 mol%. Based on its unique phenotypic characteristics and phylogenetic distance, the marine coastal sediment isolate KMM 3895T should be classified as a representative of a novel genus and species, for which the name Arenicella xantha gen. nov., sp. nov. is proposed. The type strain of Arenicella xantha is KMM 3895T (=NRIC 0759T =JCM 16153T).

scholarly journals Aestuariibacter litoralis sp. nov., isolated from a sandy sediment of the Sea of Japan

2010 ◽  
Vol 60 (2) ◽  
pp. 317-320 ◽  
Author(s):  
Naoto Tanaka ◽  
Lyudmila A. Romanenko ◽  
Galina M. Frolova ◽  
Valery V. Mikhailov
Keyword(s):  
Sea Of Japan ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Fatty Acid Analysis ◽  
The Sea Of Japan ◽  
Rrna Gene ◽  
Sandy Sediment ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

The phenotypic and phylogenetic characteristics of an aerobic, Gram-negative, motile, non-pigmented Alteromonas-like bacterium (designated strain KMM 3894T), isolated from a sandy sediment sample collected offshore of the Sea of Japan, were investigated. Comparative 16S rRNA gene sequence analysis revealed that strain KMM 3894T belonged to the genus Aestuariibacter and was most closely related to Aestuariibacter halophilus JC2043T (95.5 % sequence similarity). Fatty acid analysis showed C16 : 1 ω7c, C18 : 1 ω7c, and C16 : 0 as the dominant components. Strain KMM 3894T could be differentiated from recognized species of the genus Aestuariibacter by its ability to grow at 4 °C and at 30 °C, the optimum temperature for growth, and its inability to utilize most carbohydrates. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain KMM 3894T is considered to represent a novel species of the genus Aestuariibacter, for which the name Aestuariibacter litoralis sp. nov. is proposed. The type strain is KMM 3894T (=NRIC 0754T=JCM 15896T).

scholarly journals Litoreibacter albidus gen. nov., sp. nov. and Litoreibacter janthinus sp. nov., members of the class Alphaproteobacteria isolated from the seashore

2011 ◽  
Vol 61 (1) ◽  
pp. 148-154 ◽  
Author(s):  
Lyudmila A. Romanenko ◽  
Naoto Tanaka ◽  
Galina M. Frolova ◽  
Vassilii I. Svetashev ◽  
Valery V. Mikhailov
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Fatty Acid Analysis ◽  
The Sea Of Japan ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Phylogenetic Distance ◽  
Hybridization Data

Two Gram-negative, strictly aerobic, non-motile bacteria designated strains KMM 3851T and KMM 3842T were respectively isolated from a marine snail specimen (Umbonium costatum) and from surrounding sediments collected simultaneously from the shore of the Sea of Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains KMM 3851T and KMM 3842T were affiliated with the Roseobacter lineage of the class Alphaproteobacteria as a separate phylogenetic line adjacent to the members of the genus Thalassobacter. These novel isolates shared 98.5 % 16S rRNA gene sequence similarity and 15 % DNA–DNA relatedness. The major isoprenoid quinone of both strains was Q-10 and polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and aminophospholipids. In addition, strain KMM 3851T contained two unknown lipids, whereas strain KMM 3842T contained diphosphatidylglycerol. Fatty acid analysis revealed C18 : 1 ω7c and C16 : 0 as major components and small amounts of C18 : 2. The DNA G+C contents were 60.4 mol% (KMM 3851T) and 58.5 mol% (KMM 3842T). Based on distinctive phenotypic characteristics, DNA–DNA hybridization data and phylogenetic distance, strains KMM 3851T and KMM 3842T should be classified as representatives of two novel species in a new genus, Litoreibacter gen. nov., with the type species Litoreibacter albidus sp. nov. (type strain KMM 3851T =NRIC 0773T =JCM 16493T) and a second species Litoreibacter janthinus sp. nov. (type strain KMM 3842T =NRIC 0772T =JCM 16492T).

scholarly journals Marinicella litoralis gen. nov., sp. nov., a gammaproteobacterium isolated from coastal seawater

2010 ◽  
Vol 60 (7) ◽  
pp. 1613-1619 ◽  
Author(s):  
Lyudmila A. Romanenko ◽  
Naoto Tanaka ◽  
Galina M. Frolova ◽  
Valery V. Mikhailov
Keyword(s):  
Sequence Similarity ◽  
Fatty Acid Analysis ◽  
The Sea Of Japan ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Coastal Seawater ◽  
Separate Branch ◽  
Marine Isolate ◽  
Novel Genus And Species ◽  
Bacterium Strain

A Gram-negative, aerobic, greyish–yellowish-pigmented, stenohaline, rod-shaped, non-motile bacterium, strain KMM 3900T, was isolated from a coastal seawater sample collected from the Sea of Japan. Based on phylogenetic analysis, strain KMM 3900T was positioned within the Gammaproteobacteria on a separate branch adjacent to members of the genera Reinekea and Kangiella, sharing less than 88 % 16S rRNA gene sequence similarity with all recognized species of the Gammaproteobacteria. The major isoprenoid quinone was Q-8. Polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unknown phospholipids. Fatty acid analysis revealed iso-C15 : 0, C16 : 1 ω7c and C16 : 0 as the dominant components. The DNA G+C content was 43.8 mol%. Based on its unique phenotypic characteristics and phylogenetic remoteness, marine isolate KMM 3900T is considered to represent a novel genus and species, for which the name Marinicella litoralis gen. nov., sp. nov. is proposed. The type strain of Marinicella litoralis is KMM 3900T (=NRIC 0758T =JCM 16154T).

scholarly journals Desulfoplanes formicivorans gen. nov., sp. nov., a novel sulfate-reducing bacterium isolated from a blackish meromictic lake, and emended description of the family Desulfomicrobiaceae

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1902-1907 ◽  
Author(s):  
Miho Watanabe ◽  
Hisaya Kojima ◽  
Manabu Fukui
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Meromictic Lake ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
The Novel ◽  
Sulfate Reducing ◽  
The Family ◽  
The 16S Rrna Gene

A novel sulfate-reducing bacterium, designated strain Pf12BT, was isolated from sediment of meromictic Lake Harutori in Japan. Cells were vibroid (1.0 × 3.0–4.0 μm), motile and Gram-stain-negative. For growth, the optimum pH was 7.0–7.5 and the optimum temperature was 42–45 °C. Strain Pf12BT used sulfate, thiosulfate and sulfite as electron acceptors. The G+C content of the genomic DNA was 55.4 mol%. Major cellular fatty acids were C16 : 0 and C18 : 0. The strain was desulfoviridin-positive. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belonged to the order Desulfovibrionales in the class Deltaproteobacteria. The closest relative was Desulfomicrobium baculatum DSM 4028T with which it shared 91  % 16S rRNA gene sequence similarity. On the basis of phylogenetic and phenotypic characterization, a novel species of a new genus belonging to the family Desulfomicrobiaceae is proposed, Desulfoplanes formicivorans gen. nov., sp. nov. The type strain of Desulfoplanes formicivorans is Pf12BT ( = NBRC 110391T = DSM 28890T).

scholarly journals Paenibacillus sabinae sp. nov., a nitrogen-fixing species isolated from the rhizosphere soils of shrubs

2007 ◽  
Vol 57 (1) ◽  
pp. 6-11 ◽  
Author(s):  
Yuchao Ma ◽  
Zhiqiang Xia ◽  
Xuming Liu ◽  
Sanfeng Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Significant Feature ◽  
Rrna Gene ◽  
The Novel ◽  
Nitrogen Fixing ◽  
Bacterial Strains ◽  
Rhizosphere Soils

Five novel endospore-forming, nitrogen-fixing bacterial strains were isolated from the rhizosphere soils of plants of the species Sabina squamata, Weigela florida and Zanthoxylum simulans. A phylogenetic analysis based on 16S rRNA gene sequences revealed that the five strains formed a distinct cluster within the genus Paenibacillus. These novel strains showed the highest levels (96.2–98.2 %) of 16S rRNA gene sequence similarity with Paenibacillus azotofixans. However, the DNA–DNA relatedness between these novel strains and P. azotofixans was 12.9–29.5 %. The DNA G+C contents of the five strains were found to be 51.9–52.9 mol%. Phenotypic analyses showed that a significant feature of the novel strains (differentiating them from P. azotofixans and other Paenibacillus species) is that all of them were unable to produce acid and gas from various carbohydrates such as glucose, sucrose, lactose and fructose. Anteiso-branched C15 : 0 was the major fatty acid present in the novel type strain. On the basis of these data, the five novel strains represent a novel species of the genus Paenibacillus, for which the name Paenibacillus sabinae sp. nov. is proposed. The type strain is T27T (=CCBAU 10202T=DSM 17841T).

scholarly journals Hydrotalea flava gen. nov., sp. nov., a new member of the phylum Bacteroidetes and allocation of the genera Chitinophaga, Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Hydrotalea to the family Chitinophagaceae fam. nov.

2011 ◽  
Vol 61 (3) ◽  
pp. 518-523 ◽  
Author(s):  
P. Kämpfer ◽  
N. Lodders ◽  
E. Falsen
Keyword(s):  
New Genus ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Fatty Acid Profiles ◽  
Bacterial Strains ◽  
16S Rrna Gene Sequences ◽  
Biochemical Tests ◽  
The Family

Three bacterial strains, designated CCUG 51397T, CCUG 53736 and CCUG 53920, isolated from water samples taken at different locations in southern Sweden were studied to determine their taxonomic position using a polyphasic approach. Comparative analysis of 16S rRNA gene sequences showed that these bacteria had <93 % sequence similarity to all described species of the genera Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Chitinophaga. The three organisms grouped most closely with Sediminibacterium salmoneum NJ-44T but showed only 92.5 % sequence similarity to this strain, the only recognized species of this genus. The fatty acid profiles showed large amounts of iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G with smaller amounts of iso-C15 : 0 3-OH, iso-C16 : 0 3-OH and other fatty acids, which differentiated the novel strains from related genera. Biochemical tests performed on strains CCUG 51397T, CCUG 53736 and CCUG 53920 also gave different results from those of Sediminibacterium salmoneum NJ-44T and other related genera. Based on this evidence, strains CCUG 51397T, CCUG 53736 and CCUG 53920 represent a novel species of a new genus, for which the name Hydrotalea flava gen. nov., sp. nov. is proposed. The type strain of Hydrotalea flava is CCUG 51397T (=CCM 7760T). A formal allocation of the genera Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Chitinophaga to the family Chitinophagaceae fam. nov. is also proposed.

scholarly journals Arcanobacterium bialowiezense sp. nov. and Arcanobacterium bonasi sp. nov., isolated from the prepuce of European bison bulls (Bison bonasus) suffering from balanoposthitis, and emended description of the genus Arcanobacterium Collins et al. 1983

2006 ◽  
Vol 56 (4) ◽  
pp. 861-866 ◽  
Author(s):  
Alexandra Lehnen ◽  
Hans-Jürgen Busse ◽  
Kai Frölich ◽  
Malgorzata Krasinska ◽  
Peter Kämpfer ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
European Bison ◽  
Rrna Gene ◽  
The Novel ◽  
Bison Bonasus ◽  
Bacterial Strains ◽  
Separate Species ◽  
Arcanobacterium Pyogenes

A taxonomic study was performed on 13 bacterial strains isolated from preputial swabs of European bison (Bison bonasus) bulls suffering from balanoposthitis. The isolates were Gram-positive, non-motile, facultatively anaerobic, diphtheroid-shaped cells. Based on biochemical profiles and BOX-PCR-generated genomic fingerprints, the isolates were grouped into two clusters represented by four and nine strains, respectively. Strains 1(W3/01)T and 2(W106/04)T, selected as representatives of the two clusters, shared 97·2 % 16S rRNA gene sequence similarity. The highest gene sequence similarities found (95·5–96·4 %) were to Arcanobacterium pyogenes DSM 20630T and Arcanobacterium bernardiae DSM 9152T, demonstrating that the novel strains are members of the genus Arcanobacterium, but are not members of a recognized species. The polar lipid profiles of the two novel strains displayed the major characteristics also found in A. pyogenes DSM 20630T and Arcanobacterium haemolyticum DSM 20595T. Detection of a quinone system with MK-10(H4) as the predominant compound confirmed phylogenetic relatedness of the novel strains to A. pyogenes and separated them from the type species of the genus, A. haemolyticum, which contains MK-9(H4) as the predominant quinone. Results from DNA–DNA hybridizations clearly demonstrated that strains 1(W3/01)T and 2(W106/04)T represent separate species. Based on these data, two novel species of the genus Arcanobacterium are described, for which the names Arcanobacterium bialowiezense sp. nov. [type strain 1(W3/01)T=DSM 17162T=NCTC 13354T] and Arcanobacterium bonasi sp. nov. [type strain 2(W106/04)T=DSM 17163T=NCTC 13355T] are proposed.

scholarly journals Reclassification of [Cytophaga] marinoflava Reichenbach 1989 as Leeuwenhoekiella marinoflava gen. nov., comb. nov. and description of Leeuwenhoekiella aequorea sp. nov.

2005 ◽  
Vol 55 (3) ◽  
pp. 1033-1038 ◽  
Author(s):  
Olga I. Nedashkovskaya ◽  
Marc Vancanneyt ◽  
P. Dawyndt ◽  
Katrien Engelbeen ◽  
Katrien Vandemeulebroecke ◽  
...  
Keyword(s):  
Sea Water ◽  
Sequence Similarity ◽  
Single Species ◽  
Gliding Motility ◽  
The Sea Of Japan ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Peter The Great ◽  
Nearest Neighbours ◽  
Gene Sequence Analysis

Five heterotrophic, aerobic, halotolerant and pigmented bacterial strains with gliding motility were isolated from Antarctic sea water; one other isolate was collected from the sea urchin Strongylocentrotus intermedius in the Gulf of Peter the Great in the Sea of Japan. 16S rRNA gene sequence analysis indicated that the strains are members of the family Flavobacteriaceae, the nearest neighbour (with 97·1 % sequence similarity) being the misclassified species [Cytophaga] marinoflava. DNA–DNA hybridization experiments and chemotaxonomic and phenotypic analyses demonstrated that the six novel isolates represent a single species distinct from [C.] marinoflava. On the basis of its separate phylogenetic lineage (the nearest neighbours show 92 % sequence similarity), [C.] marinoflava is reclassified as Leeuwenhoekiella marinoflava gen. nov., comb. nov. A second species of this new genus, Leeuwenhoekiella aequorea sp. nov., is proposed for the six novel isolates, with strain LMG 22550T (=CCUG 50091T) as the type strain.

scholarly journals Tamlana sedimentorum sp. nov., isolated from shallow sand sediments of the Sea of Japan

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2891-2896 ◽  
Author(s):  
Lyudmila A. Romanenko ◽  
Naoto Tanaka ◽  
Valeriya V. Kurilenko ◽  
Vassilii I. Svetashev
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sea Of Japan ◽  
The Sea Of Japan ◽  
Rrna Gene ◽  
Phylogenetic Distance ◽  
Content Type ◽  
Link Type ◽  
Marine Sand ◽  
The 16S Rrna Gene

An aerobic, Gram-stain-negative, saffron-pigmented, non-motile bacterial strain KMM 9545T, was isolated from a marine sand sediment sample obtained from the Sea of Japan seashore and characterized in a taxonomic study using a polyphasic approach. The 16S rRNA gene sequence of strain KMM 9545T showed a high level of similarity to species of the genus Gaetbulibacter (95.1–96.2 %), the type strains of species of the genus Tamlana (94.9–96.1 %) and members of the genus Algibacter (94.8–96.1 %). Phylogenetic analysis based on the 16S rRNA gene sequences positioned strain KMM 9545T as a distinct lineage in the cluster comprising species of the genus Tamlana . Strain KMM 9545T grew at temperatures between 5–36 °C and in the presence of 2–4 % (w/v) NaCl. It contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C15 : 1, iso-C17 : 1 3-OH, iso-C15 : 0 3-OH and iso-C15 : 0 2-OH as the major fatty acids. The genomic DNA G+C content was 31.3 mol%. On the basis of the phenotypic characteristics and phylogenetic distance, it can be concluded that strain KMM 9545T represents a novel species of the genus Tamlana , for which the name Tamlana sedimentorum sp. nov. is proposed. The type strain is KMM 9545T ( = NRIC 0921T = JCM 19808T).

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