Microbulbifer chitinilyticus sp. nov. and Microbulbifer okinawensis sp. nov., chitin-degrading bacteria isolated from mangrove forests

2011 ◽  
Vol 61 (9) ◽  
pp. 2215-2220 ◽  
Author(s):  
Atsushi Baba ◽  
Masayuki Miyazaki ◽  
Takahiko Nagahama ◽  
Yuichi Nogi
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Threshold Level ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Mangrove Forests ◽  
The Novel ◽  
Separate Species ◽  
Gene Sequence Analysis ◽  
Degrading Bacteria

Three chitin-degrading strains representing two novel species were isolated from mangrove forests in Okinawa, Japan. The isolates, ABABA23T, ABABA211 and ABABA212T, were Gram-negative, non-spore-forming, strictly aerobic chemo-organotrophs. The novel strains produced Q-8 as the major isoprenoid quinone component. The predominant fatty acids were iso-C15 : 0 and C16 : 0. On the basis of 16S rRNA gene sequence analysis, the isolates were closely affiliated with members of the genus Microbulbifer. The DNA G+C contents of strains ABABA23T and ABABA212T were 57.8 and 60.2 mol%, respectively. DNA–DNA relatedness values between these two strains and Microbulbifer reference strains were significantly lower than 70 %, the generally accepted threshold level below which strains are considered to belong to separate species. Based on differences in taxonomic characteristics, the three isolates represent two novel species of the genus Microbulbifer, for which the names Microbulbifer chitinilyticus sp. nov. (type strain, ABABA212T = JCM 16148T = NCIMB 14577T) and Microbulbifer okinawensis sp. nov. (type strain, ABABA23T = JCM 16147T = NCIMB 14576T; reference strain, ABABA211) are proposed.

scholarly journals Lysobacter niabensis sp. nov. and Lysobacter niastensis sp. nov., isolated from greenhouse soils in Korea

2007 ◽  
Vol 57 (3) ◽  
pp. 548-551 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Byung-Yong Kim ◽  
Min-Kyeong Kim ◽  
Seung-Hee Yoo ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Bacterial Strains ◽  
Lysobacter Enzymogenes ◽  
Gene Sequence Analysis ◽  
Greenhouse Soils

Two bacterial strains, designated GH34-4T and GH41-7T, were isolated from greenhouse soil cultivated with cucumber. The bacteria were strictly aerobic, Gram-negative, rod-shaped and oxidase- and catalase-positive. 16S rRNA gene sequence analysis indicated that these strains belong to the genus Lysobacter within the Gammaproteobacteria. Strain GH34-4T showed highest sequence similarity to Lysobacter yangpyeongensis GH19-3T (97.5 %) and Lysobacter koreensis Dae16T (96.4 %), and strain GH41-7T showed highest sequence similarity to Lysobacter antibioticus DSM 2044T (97.5 %), Lysobacter enzymogenes DSM 2043T (97.5 %) and Lysobacter gummosus ATCC 29489T (97.4 %). Levels of DNA–DNA relatedness indicated that strains GH34-4T and GH41-7T represented species clearly different from L. yangpyeongensis, L. antibioticus, L. enzymogenes and L. gummosus. The major cellular fatty acids of strains GH34-4T and GH41-7T were iso-C16 : 0, iso-C15 : 0 and iso-C17 : 1 ω9c, and the major isoprenoid quinone was Q-8. The DNA G+C contents of GH34-4T and GH41-7T were 62.5 and 66.6 mol%, respectively. On the basis of the polyphasic taxonomic data presented, it is evident that each of these strains represents a novel species of the genus Lysobacter, for which the names Lysobacter niabensis sp. nov. (type strain GH34-4T=KACC 11587T=DSM 18244T) and Lysobacter niastensis sp. nov. (type strain GH41-7T=KACC 11588T=DSM 18481T) are proposed.

scholarly journals Amycolatopsis decaplanina sp. nov., a novel member of the genus with unusual morphology

2004 ◽  
Vol 54 (1) ◽  
pp. 235-239 ◽  
Author(s):  
Joachim Wink ◽  
Julia Gandhi ◽  
Reiner M. Kroppenstedt ◽  
Gerhard Seibert ◽  
Bettina Sträubler ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Glycopeptide Antibiotic ◽  
Rrna Gene Sequence ◽  
Amycolatopsis Orientalis ◽  
Physiological Properties ◽  
Gene Sequence Analysis

Strain DSM 44594T, which produces the glycopeptide antibiotic decaplanin, is a member of the genus Amycolatopsis based on 16S rRNA gene sequence analysis and chemotaxonomic properties. It is the first member of this genus that is reported to form pseudosporangia, which resemble those of members of the genus Kibdelosporangium. Phylogenetically, the novel taxon is related to Amycolatopsis orientalis, Amycolatopsis lurida, Amycolatopsis azurea, Amycolatopsis japonica and Amycolatopsis keratiniphila. Morphological, cultural and physiological properties, the production of a unique glycolipid and DNA–DNA similarity of <55 % with phylogenetically related strains reveal that strain DSM 44594T represents a novel species of the genus, for which the name Amycolatopsis decaplanina sp. nov. (type strain, FH 1845T=DSM 44594T=NRRL B-24209T) is proposed.

scholarly journals Chelativorans multitrophicus gen. nov., sp. nov. and Chelativorans oligotrophicus sp. nov., aerobic EDTA-degrading bacteria

2010 ◽  
Vol 60 (5) ◽  
pp. 1044-1051 ◽  
Author(s):  
Nina V. Doronina ◽  
Elena N. Kaparullina ◽  
Yuri A. Trotsenko ◽  
Bernd Nörtemann ◽  
Margarete Bucheli-Witschel ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
The Novel ◽  
Phenotypic Properties ◽  
Mesorhizobium Loti ◽  
Degrading Bacteria

Two previously isolated strains (DSM 9103T and LPM-4T) able to grow with EDTA (facultatively and obligately, respectively) as the source of carbon, nitrogen and energy were investigated in order to clarify their taxonomic positions. The strains were strictly aerobic, Gram-negative, asporogenous and non-motile rods that required biotin for growth. Reproduction occurred by binary fission. The strains were mesophilic and neutrophilic. Their major fatty acids were summed feature 7 (consisting of C18 : 1 ω7c, C18 : 1 ω9t and/or C18 : 1 ω12t) and C19 : 0 cyclo ω8c. The polyamine pattern revealed homospermidine as a major polyamine. Predominant polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylmonomethylethanolamine and diphosphatidylglycerol. Mesorhizobium-specific ornithine lipid was absent. The predominant isoprenoid quinone was Q-10. The DNA G+C values were 60.8 and 63.1 mol% (T m) for strains LPM-4T and DSM 9103T, respectively. The level of 16S rRNA gene sequence similarity between these EDTA-utilizers was 99.3 % while the DNA–DNA hybridization value was only 37 %. Both strains were phylogenetically related to members of the genera Aminobacter and Mesorhizobium (95–97 % sequence similarity). However, DNA–DNA hybridization values between the novel EDTA-degrading strains and Aminobacter aminovorans DSM 7048T and Mesorhizobium loti DSM 2626T were low (10–11 %). Based on their genomic and phenotypic properties, the new alphaproteobacterial strains are assigned to a novel genus, Chelativorans gen. nov., with the names Chelativorans multitrophicus sp. nov. (type strain DSM 9103T=VKM B-2394T) and Chelativorans oligotrophicus sp. nov. (type strain LPM-4T=VKM B-2395T=DSM 19276T).

scholarly journals Zobellella aerophila sp. nov., isolated from seashore sand, and emended description of the genus Zobellella

2011 ◽  
Vol 61 (10) ◽  
pp. 2491-2495 ◽  
Author(s):  
Hana Yi ◽  
Jaekyeong Song ◽  
Jang-Cheon Cho ◽  
Jongsik Chun
Keyword(s):  
Type Strain ◽  
Nitrite Reduction ◽  
Rrna Gene ◽  
Sand Sample ◽  
Strictly Aerobic ◽  
The Novel ◽  
Carbohydrate Utilization ◽  
Gene Sequence Analysis ◽  
Lipid Pattern ◽  
Seashore Sand

A strictly aerobic, nitrate-reducing, motile, rod-shaped member of the class Gammaproteobacteria, designated strain JC2671T, was isolated from a seashore sand sample from Dokdo, Korea. The isolate reduced nitrate to nitrite, but not to nitrogen, and required NaCl for growth. 16S rRNA gene sequence analysis indicated that the isolate belonged to the genus Zobellella within the order Alteromonadales with sequence similarities of 96.0–97.6 % to strains of Zobellella species with validly published names. However, in DNA–DNA hybridization studies, a low genomic relatedness (43 %) between strain JC2671T and the type strain of Zobellella denitrificans indicated that the isolate represented a novel genomic species. The polar lipid pattern (phosphatidylethanolamine and phosphatidylglycerol), predominant cellular fatty acids [C16 : 0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c)] and the DNA G+C content (59 mol%) of the novel strain were consistent with its assignment to the genus Zobellella. In contrast, a number of phenotypic characteristics, namely a requirement of NaCl for growth, the inability to grow under facultatively anaerobic conditions, the absence of nitrite reduction and differences in carbohydrate utilization and enzymic activities, clearly distinguished the novel isolate from other species of the genus Zobellella. Data from this polyphasic study indicate that strain JC2671T represents a novel species in the genus Zobellella, for which the name Zobellella aerophila sp. nov. is proposed. The type strain is JC2671T ( = KACC 15081T  = JCM 17110T). The description of the genus Zobellella has been emended accordingly.

scholarly journals Castellaniella gen. nov., to accommodate the phylogenetic lineage of Alcaligenes defragrans, and proposal of Castellaniella defragrans gen. nov., comb. nov. and Castellaniella denitrificans sp. nov.

2006 ◽  
Vol 56 (4) ◽  
pp. 815-819 ◽  
Author(s):  
P. Kämpfer ◽  
K. Denger ◽  
A. M. Cook ◽  
S.-T. Lee ◽  
U. Jäckel ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Alcaligenes Faecalis ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Data ◽  
Gene Sequence Analysis ◽  
Distinct Genus

Comparative 16S rRNA gene sequence analysis indicates that two distinct sublineages exist within the genus Alcaligenes: the Alcaligenes faecalis lineage, comprising Alcaligenes aquatilis and A. faecalis (with the three subspecies A. faecalis subsp. faecalis, A. faecalis subsp. parafaecalis and A. faecalis subsp. phenolicus), and the Alcaligenes defragrans lineage, comprising A. defragrans. This phylogenetic discrimination is supported by phenotypic and chemotaxonomic differences. It is proposed that the A. defragrans lineage constitutes a distinct genus, for which the name Castellaniella gen. nov. is proposed. The type strain for Castellaniella defragrans gen. nov., comb. nov. is 54PinT (=CCUG 39790T=CIP 105602T=DSM 12141T). Finally, on the basis of data from the literature and new DNA–DNA hybridization and phenotypic data, the novel species Castellaniella denitrificans sp. nov. (type strain NKNTAUT=DSM 11046T=CCUG 39541T) is proposed for two strains previously identified as strains of A. defragrans.

Three novel species of the genus Catellatospora, Catellatospora chokoriensis sp. nov., Catellatospora coxensis sp. nov. and Catellatospora bangladeshensis sp. nov., and transfer of Catellatospora citrea subsp. methionotrophica Asano and Kawamoto 1988 to Catellatospora methionotrophica sp. nov., comb. nov.

2006 ◽  
Vol 56 (2) ◽  
pp. 393-400 ◽  
Author(s):  
Ismet Ara ◽  
Takuji Kudo
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Physiological Data ◽  
Rrna Gene ◽  
The Novel ◽  
Biochemical Tests ◽  
Separate Species ◽  
Nearest Neighbours ◽  
Agar Media

Three Gram-positive, aerobic, non-motile, mesophilic strains, designated 2-25(1)T, 2-29(17)T and 2-70(23)T, were isolated from sandy soil from Chokoria, Cox's Bazar, Bangladesh. The organisms produce short chains of non-motile spores that emerge singly or in tufts from vegetative hyphae on the surface of agar media. A comparative phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolates formed a distinct clade within the evolutionary radiation of the family Micromonosporaceae and clustered with members of the genus Catellatospora. The nearest neighbours were Catellatospora citrea subsp. citrea and C. citrea subsp. methionotrophica. Chemotaxonomic data, such as the presence of meso- and 3-hydroxy-diaminopimelic acids, N-glycolyl type muramic acid, arabinose and xylose and glucose in whole-cell hydrolysates, phosphatidylethanolamine as a diagnostic phospholipid, a tetrahydrogenated menaquinone with 9 isoprene units as a major menaquinone and fatty acid profiles predominated by iso-branched hexadecanoic acid and iso-branched pentadecanoic acid, supported the affiliation of the novel isolates to the genus Catellatospora. The results of DNA–DNA hybridization and physiological and biochemical tests allowed the novel isolates to be differentiated genotypically and phenotypically from the three recognized Catellatospora species. The three isolates therefore represent novel species for which the names Catellatospora chokoriensis sp. nov. [type strain 2-25(1)T=JCM 12950T=DSM 44900T], Catellatospora coxensis sp. nov. [type strain 2-29(17)T=JCM 12951T=DSM 44901T] and Catellatospora bangladeshensis sp. nov. [type strain 2-70(23)T=JCM 12949T=DSM 44899T], are proposed. DNA–DNA hybridization tests with C. citrea subsp. citrea and C. citrea subsp. methionotrophica, in combination with chemotaxonomic and physiological data, demonstrated that C. citrea subsp. methionotrophica should be elevated to a separate species for which the name Catellatospora methionotrophica sp. nov., comb. nov. is proposed (type strain JCM 7543T=DSM 44098T).

scholarly journals Prevotella saccharolytica sp. nov., isolated from the human oral cavity

2010 ◽  
Vol 60 (10) ◽  
pp. 2458-2461 ◽  
Author(s):  
Julia Downes ◽  
Anne C. R. Tanner ◽  
Floyd E. Dewhirst ◽  
William G. Wade
Keyword(s):  
Oral Cavity ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Long Chain Fatty Acids ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Human Oral Cavity ◽  
Gene Sequence Analysis

Two strains of anaerobic, Gram-stain-negative bacilli isolated from the human oral cavity (D033B-12-2T and D080A-01) were subjected to a comprehensive range of phenotypic and genotypic tests and were found to be distinct from any previously described species. 16S rRNA gene sequence analysis revealed that the strains were related most closely to the type strain of Prevotella marshii (93.5 % sequence identity). The novel strains were saccharolytic and produced acetic acid and succinic acid as end products of fermentation. The principal cellular long-chain fatty acids were C16 : 0, iso-C14 : 0, C14 : 0, anteiso-C15 : 0, iso-C16 : 0 and C16 : 0 3-OH. The G+C content of the DNA of strain D033B-12-2T was 44 mol%. Strains D033B-12-2T and D080A-01 are considered to represent a single novel species of the genus Prevotella, for which the name Prevotella saccharolytica sp. nov. is proposed. The type strain is D033B-12-2T (=DSM 22473T =CCUG 57944T).

scholarly journals Nocardioides aestuarii sp. nov., isolated from tidal flat sediment

2004 ◽  
Vol 54 (6) ◽  
pp. 2151-2154 ◽  
Author(s):  
Hana Yi ◽  
Jongsik Chun
Keyword(s):  
Fatty Acids ◽  
Tidal Flat ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Rrna Gene Sequence ◽  
Cellular Fatty Acids ◽  
Gene Sequence Analysis

A strictly aerobic, non-motile, rod-shaped actinomycete, designated strain JC2056T, was isolated from a sediment sample of getbol, the tidal flat of Korea. Results of 16S rRNA gene sequence analysis indicated that the isolate belonged to the genus Nocardioides, with the highest similarity being to Nocardioides luteus KCTC 9575T (95·7 %). The major menaquinone was MK-8(H4), and predominant cellular fatty acids were iso-16 : 0 and iso-16 : 1 H. The DNA G+C content was 70 mol%. Based on the morphological, physiological, biochemical and chemotaxonomical data presented in this study, strain JC2056T should be classified as a novel species, for which the name Nocardioides aestuarii sp. nov. is proposed; the type strain is JC2056T (=IMSNU 14029T=KCTC 9921T=JCM 12125T).

scholarly journals Proposal of Algoriphagus vanfongensis sp. nov., transfer of members of the genera Hongiella Yi and Chun 2004 emend. Nedashkovskaya et al. 2004 and Chimaereicella Tiago et al. 2006 to the genus Algoriphagus, and emended description of the genus Algoriphagus Bowman et al. 2003 emend. Nedashkovskaya et al. 2004

2007 ◽  
Vol 57 (9) ◽  
pp. 1988-1994 ◽  
Author(s):  
Olga I. Nedashkovskaya ◽  
Seung Bum Kim ◽  
Kae Kyoung Kwon ◽  
Dong Sung Shin ◽  
Xuseong Luo ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
Emended Description ◽  
Genotypic Characteristics ◽  
Sequence Similarities

A taxonomic study of a novel marine, heterotrophic, non-gliding, halotolerant and light-pink-pigmented bacterium was carried out using a polyphasic approach. 16S rRNA gene sequence analysis revealed that strain KMM 6241T is a member of the phylum Bacteroidetes. Strain KMM 6241T formed a cluster with the genera Algoriphagus, Chimaereicella and Hongiella with sequence similarities of 94.0–98.2 %. Hongiella ornithinivorans was the closest relative of the novel isolate. Comparative analysis of phenotypic, chemotaxonomic and genotypic characteristics of strain KMM 6241T and representatives of the genera Algoriphagus, Chimaereicella and Hongiella revealed many similar features. Consequently, phylogenetic evidence supported by phenotypic and genotypic similarities support the transfer of members of the genera Chimaereicella and Hongiella to the genus Algoriphagus and the establishment of a novel species, Algoriphagus vanfongensis sp. nov., with strain KMM 6241T (=DSM 17529T=KCTC 12716T) as the type strain.

scholarly journals Mesonia mobilis sp. nov., isolated from seawater, and emended description of the genus Mesonia

2006 ◽  
Vol 56 (10) ◽  
pp. 2433-2436 ◽  
Author(s):  
Olga I. Nedashkovskaya ◽  
Seung Bum Kim ◽  
Natalia V. Zhukova ◽  
Jangryul Kwak ◽  
Valery V. Mikhailov ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
Emended Description

The taxonomic position of a novel marine, heterotrophic, strictly aerobic, gliding and yellow-pigmented bacterium, designated strain KMM 6059T, was determined. 16S rRNA gene sequence analysis revealed that this strain represents a member of the genus Mesonia. Phenotypic and chemotaxonomic data showed that the isolate represents a novel species of the genus Mesonia, for which the name Mesonia mobilis sp. nov. is proposed. The type strain is KMM 6059T (=KCTC 12708T=LMG 23670T). An emended description of the genus Mesonia based on the new data is also given.

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