scholarly journals Characterization of uncultured giant rod-shaped magnetotactic Gammaproteobacteria from a freshwater pond in Kanazawa, Japan

Microbiology ◽  
2014 ◽  
Vol 160 (10) ◽  
pp. 2226-2234 ◽  
Author(s):  
Azuma Taoka ◽  
Junya Kondo ◽  
Zachery Oestreicher ◽  
Yoshihiro Fukumori
Keyword(s):  
New Genus ◽  
Gene Sequence ◽  
Rrna Gene ◽  
Comprehensive Understanding ◽  
Dense Granules ◽  
Freshwater Pond ◽  
Bacterium Strain ◽  
And Function ◽  
The 16S Rrna Gene

Magnetotactic bacteria (MTB) are widespread aquatic bacteria, and are a phylogenetically, physiologically and morphologically heterogeneous group, but they all have the ability to orientate and move along the geomagnetic field using intracellular magnetic organelles called magnetosomes. Isolation and cultivation of novel MTB are necessary for a comprehensive understanding of magnetosome formation and function in divergent MTB. In this study, we enriched a giant rod-shaped magnetotactic bacterium (strain GRS-1) from a freshwater pond in Kanazawa, Japan. Cells of strain GRS-1 were unusually large (~13×~8 µm). They swam in a helical trajectory towards the south pole of a bar magnet by means of a polar bundle of flagella. Another striking feature of GRS-1 was the presence of two distinct intracellular biomineralized structures: large electron-dense granules composed of calcium and long chains of magnetosomes that surround the large calcium granules. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that this strain belongs to the Gammaproteobacteria and represents a new genus of MTB.

A thermophilic, hydrogenogenic and carboxydotrophic bacterium, Calderihabitans maritimus gen. nov., sp. nov., from a marine sediment core of an undersea caldera

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3602-3608 ◽  
Author(s):  
Yasuko Yoneda ◽  
Takashi Yoshida ◽  
Hisato Yasuda ◽  
Chiaki Imada ◽  
Yoshihiko Sako
Keyword(s):  
Sediment Core ◽  
Marine Bacterium ◽  
New Genus ◽  
Gene Sequence ◽  
Ferric Iron ◽  
Core Sample ◽  
Rrna Gene ◽  
Content Type ◽  
Bacterium Strain ◽  
The 16S Rrna Gene

A hydrogenogenic, carboxydotrophic marine bacterium, strain KKC1T, was isolated from a sediment core sample taken from a submerged marine caldera. Cells were non-motile, Gram-stain-negative, 1.0–3.0 µm straight rods, often observed with round endospores. Strain KKC1T grew at 55–68 °C, pH 5.2–9.2 and 0.8–14 % (w/v) salinity. Optimum growth occurred at 65 °C, pH 7.0–7.5 and 2.46 % salinity with a doubling time of 3.7 h. The isolate grew chemolithotrophically, producing H2 from carbon monoxide (CO) oxidation with reduction of various electron acceptors, e.g. sulfite, thiosulfate, fumarate, ferric iron and AQDS (9,10-anthraquinone 2,6-disulfonate). KKC1T grew heterotrophically on pyruvate, lactate, fumarate, glucose, fructose and mannose with thiosulfate as an electron acceptor. When grown mixotrophically on CO and pyruvate, C16 : 0 constituted almost half of the total cellular fatty acids. The DNA G+C content was 50.6 mol%. The 16S rRNA gene sequence of KKC1T was most closely related to those of members of the genus Moorella with similarity ranging from 91 to 89 %. Based on physiological and phylogenetic novelty, we propose the isolate as a representative of a new genus and novel species with the name Calderihabitans maritimus gen. nov., sp. nov.; the type strain of the type species is KKC1T ( = DSM 26464T = NBRC 109353T).

scholarly journals Kistimonas asteriae gen. nov., sp. nov., a gammaproteobacterium isolated from Asterias amurensis

2010 ◽  
Vol 60 (4) ◽  
pp. 938-943 ◽  
Author(s):  
Eun Ju Choi ◽  
Hak Cheol Kwon ◽  
Young Chang Sohn ◽  
Hyun Ok Yang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Asterias Amurensis ◽  
Light Yellow ◽  
Bacterium Strain ◽  
The 16S Rrna Gene

A novel marine bacterium, strain KMD 001T, was isolated from the starfish Asterias amurensis, which inhabits the East Sea of Korea. Strain KMD 001T was aerobic, light-yellow pigmented and Gram-stain-negative. Analyses of the 16S rRNA gene sequence revealed that strain KMD 001T represents a novel lineage within the class Gammaproteobacteria. Strain KMD 001T is closely related to the genera Endozoicomonas and Zooshikella, which belong to the family Hahellaceae and to the order Oceanospirillales. The 16S rRNA gene sequence of strain KMD 001T shows similarities of approximately 91.8–94.6 % with the above-mentioned genera. The DNA G+C content of KMD 001T is 47.6 mol%. It contains Q-9 as the major isoprenoid quinone. The predominant fatty acids were determined to be anteiso-C15 : 0, iso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. Strain KMD 001T should be assigned to a novel bacterial genus within the class Gammaproteobacteria based on its phylogenetic, chemotaxonomic and phenotypic characteristics. The name Kistimonas asteriae gen. nov., sp. nov. is proposed. The type strain is KMD 001T (=KCCM 90076T =JCM 15607T).

scholarly journals Agromyces arachidissp. nov. Isolated from a Peanut (Arachis hypogaea) Crop Field

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Chandandeep Kaur ◽  
Anil Kumar Pinnaka ◽  
Nitin Kumar Singh ◽  
Monu Bala ◽  
Shanmugam Mayilraj
Keyword(s):  
Arachis Hypogaea ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Crop Field ◽  
Bacterium Strain ◽  
The 16S Rrna Gene

A Gram-positive, yellowish bacterium strain AK-1Twas isolated from soil sample collected from peanut (Arachis hypogaea) crop field and studied by using a polyphasic approach. The organism had morphological and chemotaxonomic properties consistent with its classification in the genusAgromyces. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain AK-1Twas closely related toAgromyces aurantiacus(98.6%) followed byAgromyces soli(98.3%),Agromyces tropicus(97.6%),Agromyces ulmi(97.3%),Agromyces flavus(97.2%), andAgromyces italicus(97.0%), whereas the sequence similarity values with respect to the otherAgromycesspecies with validly published names were between 95.3 and 96.7 %. However, the DNA-DNA hybridization values obtained between strain AK-1Tand other related strains were well below the threshold that is required for the proposal of a novel species. The DNAG+Ccontent of the strain is 71.8 mol%. The above data in combination with the phenotypic distinctiveness of AK-1Tclearly indicate that the strain represents a novel species, for which the nameAgromyces arachidissp. nov. is proposed. The type strain is AK-1T(=MTCC 10524T= JCM 19251T).

scholarly journals Coraliomargarita akajimensis gen. nov., sp. nov., a novel member of the phylum ‘Verrucomicrobia’ isolated from seawater in Japan

2007 ◽  
Vol 57 (5) ◽  
pp. 959-963 ◽  
Author(s):  
Jaewoo Yoon ◽  
Mina Yasumoto-Hirose ◽  
Atsuko Katsuta ◽  
Hiroshi Sekiguchi ◽  
Satoru Matsuda ◽  
...  
Keyword(s):  
Cell Wall ◽  
New Genus ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Hard Coral ◽  
The 16S Rrna Gene

An obligately aerobic, Gram-negative, non-spore-forming, non-motile, spherical bacterium, designated strain 04OKA010-24T, was isolated from seawater surrounding the hard coral Galaxea fascicularis L., collected at Majanohama, Akajima, Japan, and was subjected to a polyphasic taxonomic study. Phylogenetic analyses based on the 16S rRNA gene sequence indicated that the new strain represented a member of the phylum ‘Verrucomicrobia’ and shared 84–95 % sequence similarity with cultivated strains of ‘Verrucomicrobia’ subdivision 4. Amino acid analysis of the cell-wall hydrolysate indicated the absence of muramic acid and diaminopimelic acid, which suggested that the strain did not contain peptidoglycan in the cell wall. The G+C content of the DNA was 53.9 mol%. MK-7 was the major menaquinone and C14 : 0, C18 : 1 ω9c and C18 : 0 were the major fatty acids. On the basis of these data, it was concluded that strain 04OKA010-24T represents a novel species in a new genus in subdivision 4 of the phylum ‘Verrucomicrobia’, for which the name Coraliomargarita akajimensis gen. nov., sp. nov. is proposed. The type strain of Coraliomargarita akajimensis is 04OKA010-24T (=MBIC06463T=IAM 15411T=KCTC 12865T).

scholarly journals Proposal of Umezawaea gen. nov., a new genus of the Actinosynnemataceae related to Saccharothrix, and transfer of Saccharothrix tangerinus Kinoshita et al. 2000 as Umezawaea tangerina gen. nov., comb. nov.

2007 ◽  
Vol 57 (12) ◽  
pp. 2758-2761 ◽  
Author(s):  
D. P. Labeda ◽  
R. M. Kroppenstedt
Keyword(s):  
Type Strain ◽  
Type Species ◽  
New Genus ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Aerial Mycelium ◽  
Detailed Examination ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
The 16S Rrna Gene

In the course of phylogenetic analyses of the taxa within the suborder Pseudonocardineae, it was observed that Saccharothrix tangerinus MK27-91F2T was misplaced in the genus Saccharothrix. After a detailed examination of nucleotide signatures in the 16S rRNA gene sequence along with the morphological and chemotaxonomic characteristics of this strain, which are different from those of all species of Saccharothrix as well as the other genera within the suborder, it was concluded that this strain represents a new genus, for which the name Umezawaea gen. nov. is proposed. Pseudosporangia are produced on the aerial mycelium, the whole-cell sugar pattern consists of galactose, mannose and ribose, phosphatidylethanolamine, phosphatidylinositol and lyso-phosphatidylethanolamine are the predominant phospholipids and MK-9(H4) is the predominant menaquinone. The type species of the proposed new genus is Umezawaea tangerina gen. nov., comb. nov., with the type strain MK27-91F2T (=NRRL B-24463T =DSM 44720T =FERM P-16053T =JCM 10302T =NBRC 16184T).

scholarly journals Thermostable Chitosanase from Bacillus sp. Strain CK4: Cloning and Expression of the Gene and Characterization of the Enzyme

2000 ◽  
Vol 66 (9) ◽  
pp. 3727-3734 ◽  
Author(s):  
Ho-Geun Yoon ◽  
Hee-Yun Kim ◽  
Young-Hee Lim ◽  
Hye-Kyung Kim ◽  
Dong-Hoon Shin ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Specific Activity ◽  
High Specific Activity ◽  
Industrial Applications ◽  
Cloning And Expression ◽  
Rrna Gene ◽  
Phenotypic Analysis ◽  
Reading Frame ◽  
The 16S Rrna Gene

ABSTRACT A thermostable chitosanase gene from the environmental isolateBacillus sp. strain CK4, which was identified on the basis of phylogenetic analysis of the 16S rRNA gene sequence and phenotypic analysis, was cloned, and its complete DNA sequence was determined. The thermostable chitosanase gene was composed of an 822-bp open reading frame which encodes a protein of 242 amino acids and a signal peptide corresponding to a 30-kDa enzyme. The deduced amino acid sequence of the chitosanase from Bacillus sp. strain CK4 exhibits 76.6, 15.3, and 14.2% similarities to those from Bacillus subtilis, Bacillus ehemensis, and Bacillus circulans, respectively. C-terminal homology analysis shows thatBacillus sp. strain CK4 belongs to cluster III withB. subtilis. The gene was similar in size to that of the mesophile B. subtilis but showed a higher preference for codons ending in G or C. The enzyme contains 2 additional cysteine residues at positions 49 and 211. The recombinant chitosanase has been purified to homogeneity by using only two steps with column chromatography. The half-life of the enzyme was 90 min at 80�C, which indicates its usefulness for industrial applications. The enzyme had a useful reactivity and a high specific activity for producing functional oligosaccharides as well, with trimers through hexamers as the major products.

scholarly journals Kocuria himachalensis sp. nov., an actinobacterium isolated from the Indian Himalayas

2006 ◽  
Vol 56 (8) ◽  
pp. 1971-1975 ◽  
Author(s):  
S. Mayilraj ◽  
R. M. Kroppenstedt ◽  
K. Suresh ◽  
H. S. Saini
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Cold Desert ◽  
Bacterium Strain ◽  
Kocuria Rosea ◽  
The 16S Rrna Gene ◽  
Genomic Relatedness ◽  
Indian Himalayas

A reddish orange bacterium, strain K07-05T, was isolated from soil during a study of the bacterial diversity of a cold desert of the Indian Himalayas and was studied by using a polyphasic approach. The organism had morphological and chemotaxonomic properties consistent with its classification in the genus Kocuria. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain K07-05T was closely related to Kocuria rosea DSM 20447T and Kocuria polaris MTCC 3702T (98.1 and 97.8 % sequence similarity, respectively), whereas the sequence similarity values with respect to the other Kocuria species with validly published names were between 96.4 and 94.2 %. However, the genomic relatedness, as shown by DNA–DNA hybridization, of strain K07-05T and K. polaris MTCC 3702T is 49.5 % and that with K. rosea MTCC 2522T is 24.0 %. The DNA G+C content of the strain is 75.3 mol%. The above data in combination with the phenotypic distinctiveness of K07-05T clearly indicate that the strain represents a novel species, for which the name Kocuria himachalensis sp. nov. is proposed. The type strain is K07-05T (=MTCC 7020T=DSM 44905T=JCM 13326T).

scholarly journals Negativibacillus massiliensis gen. nov., sp. nov., a New Bacterial Genus Isolated from a Human Left Colon Sample

2021 ◽  
Vol 12 (1) ◽  
pp. 29-42
Author(s):  
Camille Valles ◽  
Morgane Mailhe ◽  
Davide Ricaboni ◽  
Nicholas Armstrong ◽  
Stéphane Alibar ◽  
...  
Keyword(s):  
New Genus ◽  
Gene Sequence ◽  
Healthy Woman ◽  
Optimal Growth ◽  
Left Colon ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Gram Stain ◽  
Rrna Gene Sequence ◽  
The 16S Rrna Gene

A new genus, a member of the Ruminococcaceae family, was isolated from the left colon of a healthy woman. Strain Marseille P3213 was a non-motile, spore-forming, Gram-stain negative, rod-shaped bacterium. This strictly anaerobic species reached optimal growth after an incubation of 72 h at 37 °C. The 16S rRNA gene sequence of this strain shared a 93.52% similarity level with Harryflintia acetispora strain V20-281a, its closest phylogenetic neighbor with standing in the nomenclature. Its genome had a size of 2.87 Mb, with a 45.81% G + C content. We hereby propose the creation of Negativibacillus massiliensis strain P3213T as the 43rd genus within the Ruminococcaceae family.

Ferriphaselus amnicola gen. nov., sp. nov., a neutrophilic, stalk-forming, iron-oxidizing bacterium isolated from an iron-rich groundwater seep

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 921-925 ◽  
Author(s):  
Shingo Kato ◽  
Sean Krepski ◽  
Clara Chan ◽  
Takashi Itoh ◽  
Moriya Ohkuma
Keyword(s):  
New Genus ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Content Type ◽  
Taxonomic Analysis ◽  
Iron Oxidizing Bacteria ◽  
Gene Sequence Analysis ◽  
Total Dna ◽  
Bacterium Strain

A neutrophilic, stalk-forming, iron-oxidizing bacterium, strain OYT1T, which was isolated from a groundwater seep in Ohyato Park, Tokyo, Japan, was subjected to taxonomic analysis. OYT1T was a motile, bean-shaped, Gram-negative bacterium that was able to grow at 8–30 °C (optimally at 25–30 °C) and at pH 5.6–7.3 (optimally at pH 6.1–6.5). The strain grew microaerobically and autotrophically. Major cellular fatty acids detected were C16 : 1ω7c/C16 : 1ω6c and C16 : 0. The total DNA G+C content was 57.6 mol%. 16S rRNA gene sequence analysis revealed that strain OYT1T was affiliated with the class Betaproteobacteria and clustered with iron-oxidizing bacteria isolated from groundwater seeps and wetlands and with uncultured clones detected in freshwater iron-rich environments. Based on the phenotypic and phylogenetic characteristics of strain OYT1T, we propose that the strain represents a novel species in a new genus, for which the name Ferriphaselus amnicola gen. nov., sp. nov. is proposed; the type strain of Ferriphaselus amnicola is OYT1T ( = JCM 18545T = DSM 26810T).

scholarly journals Perexilibacter aurantiacus gen. nov., sp. nov., a novel member of the family ‘Flammeovirgaceae’ isolated from sediment

2007 ◽  
Vol 57 (5) ◽  
pp. 964-968 ◽  
Author(s):  
Jaewoo Yoon ◽  
Shu Ishikawa ◽  
Hiroaki Kasai ◽  
Akira Yokota
Keyword(s):  
New Genus ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
The Family ◽  
Republic Of Palau ◽  
The 16S Rrna Gene

A strictly aerobic, Gram-negative, gliding, dull-orange-pigmented, rod-shaped bacterium, designated strain Shu-F-UV2-2T, was isolated from sediment (Carp Island, Republic of Palau) and was the focus of a polyphasic taxonomic study. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the novel isolate was affiliated to the family ‘Flammeovirgaceae’ of the phylum Bacteroidetes and that it showed highest sequence similarity (85.5 %) to Flammeovirga yaeyamensis NBRC 100898T. The novel isolate could be differentiated phenotypically and physiologically from recognized members of the family ‘Flammeovirgaceae’. The G+C content of the DNA was 43.0 mol%, MK-7 was the major menaquinone and iso-C15 : 0, C16 : 1 ω7c and C16 : 1 ω5c were the major fatty acids. On the basis of this polyphasic evidence, it was concluded that strain Shu-F-UV2-2T represents a novel species in a new genus of the family ‘Flammeovirgaceae’, for which the name Perexilibacter aurantiacus gen. nov., sp. nov. is proposed. The type strain is Shu-F-UV2-2T (=MBIC06993T=IAM 15413T=KCTC 12867T).

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