scholarly journals Costertonia aggregata gen. nov., sp. nov., a mesophilic marine bacterium of the family Flavobacteriaceae, isolated from a mature biofilm

2006 ◽  
Vol 56 (6) ◽  
pp. 1349-1353 ◽  
Author(s):  
Kae Kyoung Kwon ◽  
Yoo Kyung Lee ◽  
Hong Kum Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Bacterium ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
The Sea Of Japan ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
The Family

A marine bacterium, strain KOPRI 13342T, was isolated from a mature marine biofilm, including various marine algae, covering a rock-bed of the East Sea, Korea (also known as the Sea of Japan). Colonies of the isolate were orange-coloured on marine agar 2216. The isolate showed relatively high 16S rRNA gene sequence similarities to members of the genera Maribacter (91.2–92.4 % similarity), Zobellia (90.7–91.5 %) and Muricauda (90.7–91.4 %). Phylogenetic analysis based on the nearly complete 16S rRNA gene sequence revealed that the isolate formed a phyletic lineage with members of the genus Muricauda. Cells were aerobic, motile, Gram-negative rods and they produced non-diffusible carotenoid pigments. Optimal growth was observed at pH 7.5–8.0 and 26–32 °C and required the presence of 3 % (w/v) sea salt. The strain required Ca2+ and K+ ions in addition to NaCl for growth. The dominant fatty acids were i-15 : 0, i-15 : 1ω10, 15 : 0 and 16 : 1ω9. The major respiratory quinone was MK-6. The DNA G+C content was 35.8 mol%. On the basis of this polyphasic taxonomic evidence, strain KOPRI 13342T should be classified as a representative of a novel species in a new genus in the family Flavobacteriaceae; the name Costertonia aggregata gen. nov., sp. nov. is proposed. The type strain of Costertonia aggregata is KOPRI 13342T (=KCCM 42265T=JCM 13411T).

scholarly journals Sediminicola luteus gen. nov., sp. nov., a novel member of the family Flavobacteriaceae

2006 ◽  
Vol 56 (4) ◽  
pp. 841-845 ◽  
Author(s):  
Shams Tabrez Khan ◽  
Yasuyoshi Nakagawa ◽  
Shigeaki Harayama
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Golden Yellow ◽  
The Family

The taxonomic position of four Gram-negative, rod-shaped, golden-yellow-coloured bacteria isolated from marine sediments was determined. Analysis of the almost complete 16S rRNA gene sequences indicated that these isolates belong to the family Flavobacteriaceae. An unclassified bacterium, NBRC 15975, was found to be the closest relative, showing 16S rRNA gene sequence similarity of 93 %; other related genera shared only 87·9–90·5 % similarity. In contrast, the four isolates shared high levels of 16S rRNA gene sequence similarity (99·3–99·7 %) and high DNA–DNA reassociation values (93–104 %). The isolates could be differentiated phenotypically from other genera by the abilities to reduce nitrate and to degrade gelatin, casein and starch. The only respiratory quinone was MK-6, and the major fatty acids were iso-C15 : 0, iso-C15 : 1, anteiso-C15 : 0, iso-C17 : 1 ω9c and iso-C17 : 0 3-OH. The DNA G+C content was 38–40 mol%. Differentiating phenotypic characteristics and large phylogenetic distances between the isolates and previously published genera indicated that the isolates constitute a novel genus, for which the name Sediminicola gen. nov. is proposed. The type species is Sediminicola luteus sp. nov. (type strain CNI-3T=NBRC 100966T=LMG 23246T).

scholarly journals Shewanella corallii sp. nov., a marine bacterium isolated from a Red Sea coral

2010 ◽  
Vol 60 (10) ◽  
pp. 2293-2297 ◽  
Author(s):  
Maya Shnit-Orland ◽  
Alex Sivan ◽  
Ariel Kushmaro
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Bacterium ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons ◽  
The Family

A marine bacterial strain, designated fav-2-10-05T, was isolated from the mucus layer of a coral of the genus Favia, collected from the coral reef in the Gulf of Eilat, Israel (29.5 ° N 34.9 ° E). On the basis of 16S rRNA gene sequence comparisons, strain fav-2-10-05T was affiliated with the family Shewanellaceae. The closest relatives of strain fav-2-10-05T were Shewanella marisflavi SW-117T (96.0 % 16S rRNA gene sequence similarity) and Shewanella haliotis DW-1T (95.9 %). Strain fav-2-10-05T was Gram-negative, rod-shaped and motile by means of a single polar flagellum and formed yellow–brownish colonies within 2 days of incubation at 26 °C. Strain fav-2-10-05T demonstrated antibacterial activity against indicator strains and grew in the presence of 0.5–8.0 % (w/v) NaCl and at 10–37 °C. The major fatty acids were C17 : 1 ω8c (21.6 %), iso-C15 : 0 (18.6 %), C15 : 0 (9.1 %) and iso-C13 : 0 (8.9 %). The DNA G+C content was 49.1 mol%. The phylogenetic and phenotypic analyses of strain fav-2-10-05T suggested that it belongs to a novel species of the genus Shewanella, for which the name Shewanella corallii sp. nov. is proposed. The type strain is fav-2-10-05T (=LMG 24563T =DSM 21332T).

scholarly journals Idiomarina maris sp. nov., a marine bacterium isolated from sediment

2012 ◽  
Vol 62 (2) ◽  
pp. 370-375 ◽  
Author(s):  
Yan-Jiao Zhang ◽  
Xi-Ying Zhang ◽  
Hui-Lin Zhao ◽  
Ming-Yang Zhou ◽  
Hui-Juan Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Bacterium ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Major Respiratory Quinone

A protease-producing marine bacterium, designated CF12-14T, was isolated from sediment of the South China Sea. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain CF12-14T formed a separate lineage within the genus Idiomarina (Gammaproteobacteria). The isolate showed the highest 16S rRNA gene sequence similarity with Idiomarina salinarum ISL-52T (94.7 %), Idiomarina seosinensis CL-SP19T (94.6 %) and other members of the genus Idiomarina (91.9–94.6 %). Cells were Gram-negative, aerobic, flagellated, straight or slightly curved, and often formed buds and prosthecae. Strain CF12-14T grew at 4–42 °C (optimum 30–35 °C) and with 0.1–15 % (w/v) NaCl (optimum 2–3 %). The isolate reduced nitrate to nitrite and hydrolysed DNA, but did not produce acids from sugars. The predominant cellular fatty acids were iso-C15 : 0 (27.4 %), iso-C17 : 0 (16.0 %) and iso-C17 : 1ω9c (15.8 %). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major respiratory quinone was ubiquinone 8. The DNA G+C content was 50.4 mol%. The phylogenetic, phenotypic and chemotaxonomic data supported the conclusion that CF12-14T represents a novel species of the genus Idiomarina, for which the name Idiomarina maris sp. nov. is proposed. The type strain is CF12-14T ( = CCTCC AB 208166T = KACC 13974T).

Altererythrobacter epoxidivorans gen. nov., sp. nov., an epoxide hydrolase-active, mesophilic marine bacterium isolated from cold-seep sediment, and reclassification of Erythrobacter luteolus Yoon et al. 2005 as Altererythrobacter luteolus comb. nov.

2007 ◽  
Vol 57 (10) ◽  
pp. 2207-2211 ◽  
Author(s):  
Kae Kyoung Kwon ◽  
Jung-Hee Woo ◽  
Sung-Hyun Yang ◽  
Ji-Hyun Kang ◽  
Sung Gyun Kang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Marine Bacterium ◽  
Gene Sequence ◽  
Cold Seep ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
The Family

A novel marine bacterium, strain JCS350T, was isolated from marine sediment samples collected from a cold-seep area. The 16S rRNA gene sequence of the isolate showed high similarity to that of Erythrobacter luteolus SW-109T (95.9 % sequence similarity). Lower 16S rRNA gene sequence similarities were shown to other members of the genus Erythrobacter (94.6–95.4 %) and members of the genus Porphyrobacter (94.5–95.2 %). Phylogenetic analysis with all members of the family Erythrobacteraceae and several members of the family Sphingomonadaceae revealed that the isolate formed a phyletic line with [Erythrobacter] luteolus that was distinct from other members of the family Erythrobacteraceae. The dominant fatty acids of strain JCS350T were 18 : 1ω7c, 16 : 1ω7c and cyclopropane 17 : 0. The major respiratory quinone was ubiquinone 10. The DNA G+C content was 54.5 mol%. The isolate did not contain bacteriochlorophyll a. Optimal growth required the presence of 2 % (w/v) NaCl with either 0.18 % CaCl2 or 0.59 % MgCl2, at pH 6.5 and at 35 °C. On the basis of the evidence of this polyphasic taxonomic study, strain JCS350T should be classified in a novel genus and species in the family Erythrobacteraceae, for which the name Altererythrobacter epoxidivorans gen. nov., sp. nov. is proposed. The misclassified species [Erythrobacter] luteolus is transferred to the new genus as Altererythrobacter luteolus comb. nov. The type strain of Altererythrobacter epoxidivorans is JCS350T (=KCCM 42314T =JCM 13815T) and the type strain of Altererythrobacter luteolus is SW-109T (=KCTC 12311T =JCM 12599T).

scholarly journals Hydromonas duriensis gen. nov., sp. nov., isolated from freshwater

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4134-4139 ◽  
Author(s):  
Ivone Vaz-Moreira ◽  
Carlos Narciso-da-Rocha ◽  
Evie De Brandt ◽  
Peter Vandamme ◽  
A. C. Silva Ferreira ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
The Family ◽  
Major Respiratory Quinone

An aerobic, Gram-stain-negative rod, designated strain A2P5T, was isolated from the Douro river, in Porto, Portugal. Cells were catalase- and oxidase-positive. Growth occurred at 15–30 °C, at pH 6–8 and in the presence of 1 % (w/v) NaCl. The major respiratory quinone was Q8, the genomic DNA had a G+C content of 47 ± 1 mol%, and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol were amongst the major polar lipids. On the basis of 16S rRNA gene sequence analysis, strain A2P5T was observed to be a member of the family Burkholderiaceae, but could not be identified as a member of any validly named genus. The low levels of 16S rRNA gene sequence similarity to other recognized taxa ( < 91 %), together with the comparative analysis of phenotypic and chemotaxonomic characteristics, supported the proposal of a novel species of a new genus within the family Burkholderiaceae. The name Hydromonas duriensis gen. nov., sp. nov. is proposed. The type strain of Hydromonas duriensis is A2P5T ( = LMG 28428T = CCUG 66137T).

scholarly journals Crenobacter luteus gen. nov., sp. nov., isolated from a hot spring

2015 ◽  
Vol 65 (Pt_1) ◽  
pp. 214-219 ◽  
Author(s):  
Lei Dong ◽  
Hong Ming ◽  
En-Min Zhou ◽  
Yi-Rui Yin ◽  
Lan Liu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Hot Spring ◽  
Polar Lipids ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
The Family

A slightly thermophilic, Gram-staining-negative and strictly aerobic bacteria, designated strain YIM 78141T, was isolated from a sediment sample collected at Hehua hot spring, Tengchong, Yunnan province, south-west China. Cells of the strain were short-rod-shaped and colonies were yellowish and circular. The strain grew at pH 6.0–10.0 (optimum, pH 8.0–9.0) and 10–55 °C (optimum, 40–50 °C). Phylogenetic analyses based on 16S rRNA gene sequence comparison demonstrated that strain YIM 78141T belongs to the family Neisseriaceae , and strain YIM 78141T also showed low levels of 16S rRNA gene sequence similarity (below 93.4 %) with all other genera in this family. The only quinone was ubiquinone 8 and the genomic DNA G+C content was 67.3 mol%. Major fatty acids (>5 %) were C12 : 0, C16 : 0, C18 : 1ω7c and summed feature 3. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phospholipids of unknown structure containing aminoglycophospholipid and three unidentified polar lipids. On the basis of the morphological, physiological and biochemical characteristics as well as genotypic data, this strain should be classified as a representative of a novel genus and species of the family Neisseriaceae , for which the name Crenobacter luteus gen. nov., sp. nov. is proposed. The type strain is YIM 78141T ( = BCRC 80650T = KCTC 32558T = DSM 27258T).

scholarly journals Effusibacillus dendaii sp. nov. isolated from farm soil

2021 ◽  
Author(s):  
Tomoyuki Konishi ◽  
Tomohiko Tamura ◽  
Toru Tobita ◽  
Saori Sakai ◽  
Namio Matsuda ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Respiratory Quinone ◽  
Genome Analyses

Abstract Gram-positive, rod-shaped, spore-forming, thermophilic, acidophilic bacterium, designated strain skT53T, was isolated from farm soil in Tokyo, Japan. The strain grew aerobically at 37–55°C (optimum 50°C) and pH 4.0–6.0 (optimum 5.0). Phylogenetic analysis of the 16S rRNA gene sequence showed that the isolate was most closely related to the type strain of Effusibacillus consociatus (94.3% similarity). The G + C content of the genomic DNA was 48.22 mol%. MK-7 was the predominant respiratory quinone. The major fatty acids were anteiso-C15:0, iso-C15:0, iso-C16:0 and C18:3ω6c. The results of phenotypic and chemotaxonomic, 16S rRNA gene sequence similarity, and whole genome analyses support strain skT53T as representing a novel species of Effusibacillus dendaii sp. nov. is proposed. The type strain is strain skT53T (= NBRC 114101T = TBRC 11241T).

Sandarakinotalea sediminis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae

2006 ◽  
Vol 56 (5) ◽  
pp. 959-963 ◽  
Author(s):  
Shams Tabrez Khan ◽  
Yasuyoshi Nakagawa ◽  
Shigeaki Harayama
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Heterotrophic Bacteria ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
The Family

Four Gram-negative, orange-coloured, aerobic, heterotrophic bacteria were isolated from sediment samples collected on the Pacific coast of Japan near the cities of Toyohashi and Katsuura. 16S rRNA gene sequence analysis indicated that these strains form a distinct lineage within the family Flavobacteriaceae. The four isolates shared 99.9–100 % 16S rRNA gene sequence similarity with each other and showed 88–90.9 % similarity with their neighbours in the family Flavobacteriaceae. The four strains also shared high DNA–DNA reassociation values of 67–99 % with each other. All the strains grew at 37 °C but not at 4 °C, and degraded gelatin, starch and DNA. The major fatty acids were i-C15 : 0, a-C15 : 0, i-C16 : 0 and i-C17 : 0 3-OH. However, two common fatty acids of members of the Flavobacteriaceae, i-C15 : 1 and a-C15 : 1, were absent in these strains. The DNA G+C contents of the four strains were in the range 35–37 mol%. On the basis of the polyphasic evidence, it was concluded that these strains should be classified as a novel genus and a novel species in the family Flavobacteriaceae, for which the name Sandarakinotalea sediminis gen. nov., sp. nov. is proposed. The type strain of Sandarakinotalea sediminis is CKA-5T (=NBRC 100970T=LMG 23247T).

scholarly journals Thermasporomyces composti gen. nov., sp. nov., a thermophilic actinomycete isolated from compost

2011 ◽  
Vol 61 (1) ◽  
pp. 86-90 ◽  
Author(s):  
Shuhei Yabe ◽  
Yoshifumi Aiba ◽  
Yasuteru Sakai ◽  
Masaru Hazaka ◽  
Akira Yokota
Keyword(s):  
Cell Wall ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Optimum Growth ◽  
Rrna Gene Sequence ◽  
The Family

A thermophilic, Gram-positive bacterium that formed a branched vegetative mycelium was isolated from compost. The strain, designated I3T, grew at temperatures between 35 and 62 °C, with optimum growth at 50–55 °C. No growth was observed below 29 °C or above 65 °C. The pH range for growth was 5.7–10.0, the pH for optimum growth was 7.0 and no growth was observed below pH 5.6 or above pH 10.8. The DNA G+C content of strain I3T was 69.2 mol%. The major fatty acids found were C15 : 0 iso (14.2 %), C15 : 0 anteiso (12.1 %), C17 : 0 iso (16.3 %) and C17 : 0 anteiso (21.7 %). The major menaquinones were MK-9(H4), MK-10(H4) and MK-11(H4). The cell wall contained glutamic acid, glycine, alanine and ll-diaminopimelic acid in a molar ratio of 1.0 : 3.9 : 0.6 : 0.5. The polar lipids consisted of ninhydrin-positive phosphoglycolipids, phosphatidylglycerol, diphosphatidylglycerol and an unknown glycolipid. The cell-wall sugars were rhamnose and arabinose. 16S rRNA gene sequence analysis assigned this actinomycete to the family Nocardioidaceae, but its 16S rRNA gene sequence shared no more than 95.5 % similarity with those of other members of the family. The chemotaxonomic and phenotypic characteristics of strain I3T differed in some respects from those of members of the genus Actinopolymorpha, the most closely related genus. Therefore, strain I3T represents a novel species in a new genus of the family Nocardioidaceae, for which the name Thermasporomyces composti gen. nov., sp. nov. is proposed. The type strain of the type species is I3T (=JCM 16421T=DSM 22891T).

scholarly journals Candidimonas nitroreducens gen. nov., sp. nov. and Candidimonas humi sp. nov., isolated from sewage sludge compost

2011 ◽  
Vol 61 (9) ◽  
pp. 2238-2246 ◽  
Author(s):  
Ivone Vaz-Moreira ◽  
Vânia Figueira ◽  
Ana R. Lopes ◽  
Evie De Brandt ◽  
Peter Vandamme ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sludge Compost ◽  
The Family

Two bacterial strains (SC-089T and SC-092T) isolated from sewage sludge compost were characterized by using a polyphasic approach. The isolates were Gram-negative short rods, catalase- and oxidase-positive, and showed good growth at 30 °C, at pH 7 and with 1 % (w/v) NaCl. Ubiquinone 8 was the major respiratory quinone, and phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol were amongst the major polar lipids. On the basis of 16S rRNA gene sequence analysis, the strains were observed to be members of the family Alcaligenaceae, but could not be identified as members of any validly described genus. The low levels of 16S rRNA gene sequence similarity to other recognized taxa, together with comparative analysis of phenotypic traits and chemotaxonomic markers, supported the proposal of a new genus within the family Alcaligenaceae, for which the name Candidimonas gen. nov. is proposed. Strains SC-089T and SC-092T, which shared 99.1 % 16S rRNA gene sequence similarity, could be differentiated at the phenotypic level, and DNA–DNA hybridization results supported their identification as representing distinct species. The names proposed for these novel species are Candidimonas nitroreducens sp. nov. (type strain, SC-089T = LMG 24812T = CCUG 55806T) and Candidimonas humi sp. nov. (type strain, SC-092T = LMG 24813T = CCUG 55807T).

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