scholarly journals Oleibacter marinus gen. nov., sp. nov., a bacterium that degrades petroleum aliphatic hydrocarbons in a tropical marine environment

2011 ◽  
Vol 61 (2) ◽  
pp. 375-380 ◽  
Author(s):  
Maki Teramoto ◽  
Motoyuki Ohuchi ◽  
Ariani Hatmanti ◽  
Yeti Darmayati ◽  
Yantyati Widyastuti ◽  
...  
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Aliphatic Hydrocarbons ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Distinct Cluster ◽  
Novel Genus And Species

Three Gram-negative, motile, mesophilic, aerobic, rod-shaped bacterial strains, designated 2O1T, 1O14 and 1O18, were isolated from Indonesian seawater after enrichment with crude oil and a continuous supply of supplemented seawater. The strains exhibited high n-alkane-degrading activity, which indicated that the strains were important degraders of petroleum aliphatic hydrocarbons in tropical marine environments. Phylogenetic analyses based on 16S rRNA gene sequences of members of the Gammaproteobacteria showed that the isolates formed a coherent and distinct cluster in a stable lineage containing Oceanobacter kriegii IFO 15467T (96.4–96.5 % 16S rRNA gene sequence similarity) and Thalassolituus oleivorans MIL-1T. DNA G +C content was 53.0–53.1 mol%. The major fatty acids were C16 : 0, C16 : 1 ω7 and C18 : 1 ω9 and the hydroxy fatty acids were C12 : 0 3-OH and C10 : 0 3-OH. The polar lipids were phosphatidylglycerol, a ninhydrin-positive phospholipid(s) and glycolipids. The major quinone was Q-9 (97–99 %), which distinguished the isolates from Oceanobacter kriegii NBRC 15467T (Q-8; 91 %). On the basis of phenotypic, genotypic and chemotaxonomic data, including DNA–DNA hybridization, the isolates represent a novel genus and species, for which the name Oleibacter marinus gen. nov., sp. nov. is proposed. The type strain of Oleibacter marinus is 2O1T (=NBRC 105760T =BTCC B-675T).

scholarly journals Acetanaerobacterium elongatum gen. nov., sp. nov., from paper mill waste water

2004 ◽  
Vol 54 (6) ◽  
pp. 2257-2262 ◽  
Author(s):  
Shuangya Chen ◽  
Xiuzhu Dong
Keyword(s):  
Waste Water ◽  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Paper Mill ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Novel Genus And Species ◽  
Branched Chain

Two mesophilic anaerobic bacterial strains (Z7T and Z1) were isolated from waste water sludge of the Xinanzhang paper mill, Beijing, China. The strains were Gram-positive, non-spore-forming and motile. Cells were thin rods (0·2–0·4×4·0–8·0 μm). Growth of the strains was observed at 20–42 °C and pH 5·0–7·5. Both strains hydrolysed gelatin and aesculin and fermented several kinds of mono-, di- and oligosaccharides. The fermentation end products formed from glucose were acetate, ethanol, hydrogen and carbon dioxide. The predominant cellular fatty acids were the branched-chain fatty acids isoC15 : 0 (42·83 %) and isoC14 : 0 (32·11 %). The DNA G+C contents of strains Z7T and Z1 were 50·4 and 48·6 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolates represent a new phyletic sublineage within the Clostridium leptum rRNA cluster, with <91 % 16S rRNA gene sequence similarity to currently described species. On the basis of polyphasic evidence from this study, Acetanaerobacterium elongatum gen. nov., sp. nov., a novel genus and species, is proposed, with strain Z7T (=JCM 12359T=AS 1.5012T) as the type strain.

scholarly journals Demequina aestuarii gen. nov., sp. nov., a novel actinomycete of the suborder Micrococcineae, and reclassification of Cellulomonas fermentans Bagnara et al. 1985 as Actinotalea fermentans gen. nov., comb. nov.

2007 ◽  
Vol 57 (1) ◽  
pp. 151-156 ◽  
Author(s):  
Hana Yi ◽  
Peter Schumann ◽  
Jongsik Chun
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Novel Genus ◽  
Novel Genus And Species

An actinobacterial strain containing demethylmenaquinone DMK-9(H4) as the diagnostic isoprenoid quinone was isolated from a tidal flat sediment sample, from South Korea. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain JC2054T represents a distinct phyletic line within the suborder Micrococcineae of the order Actinomycetales. The closest phylogenetic neighbour was Cellulomonas fermentans, with 94.7 % 16S rRNA gene sequence similarity. The novel isolate was strictly aerobic and slightly halophilic, with optimum growth occurring in 2–4 % (w/v) NaCl. Cells were non-motile, non-sporulating and rod-shaped. The peptidoglycan type was of the A-type of cross-linkage. l-ornithine was the diamino acid and d-glutamate represented the N-terminus of the interpeptide bridge. The predominant fatty acids were anteiso-branched and straight-chain fatty acids. The major polar lipids were phosphatidylinositol, diphosphatidylglycerol and an unknown phospholipid. The menaquinone composition of C. fermentans was determined to be MK-10(H4), MK-9(H4) and MK-8(H4) in the ratio 56 : 2 : 1. On the basis of the polyphasic evidence presented in this study, it is proposed that strain JC2054T should be classified as representing a novel genus and species of the suborder Micrococcineae, with the name Demequina aestuarii gen. nov., sp. nov. The type strain is JC2054T (=IMSNU 14027T=KCTC 9919T=JCM 12123T). In addition, it was clear from the phylogenetic analysis and chemotaxonomic data that C. fermentans does not belong to the genus Cellulomonas or any other recognized genera. Therefore, C. fermentans should be reclassified as representing a novel genus, for which the name Actinotalea fermentans gen. nov., comb. nov. is proposed, with strain DSM 3133T (=ATCC 43279T=CFBP 4259T=CIP 103003T=NBRC 15517T=JCM 9966T=LMG 16154T) as the type strain.

scholarly journals Pedobacter lentus sp. nov. and Pedobacter terricola sp. nov., isolated from soil

2007 ◽  
Vol 57 (9) ◽  
pp. 2089-2095 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Sooyeon Park ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Type Strains

Two Gram-negative, non-motile, pleomorphic bacterial strains, DS-40T and DS-45T, were isolated from a soil sample collected from Dokdo, Korea, and their exact taxonomic positions were investigated by using a polyphasic approach. Strains DS-40T and DS-45T grew optimally at 25 °C and pH 6.5–7.5 in the presence of 0–1.0 % (w/v) NaCl. They contained MK-7 as the predominant menaquinone and possessed iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH) as the major fatty acids. The DNA G+C contents of strains DS-40T and DS-45T were 36.0 and 36.8 mol%, respectively. Strains DS-40T and DS-45T shared a 16S rRNA gene sequence similarity of 96.7 % and demonstrated a mean DNA–DNA relatedness level of 12 %. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strains DS-40T and DS-45T were most closely phylogenetically affiliated with the genus Pedobacter of the family Sphingobacteriaceae. Strains DS-40T and DS-45T exhibited 16S rRNA gene sequence similarity values of 91.4–93.7 and 89.9–91.6 % with respect to the type strains of Pedobacter and Sphingobacterium species, respectively. Phenotypic and chemotaxonomic properties, together with the phylogenetic data, support the assignment of strains DS-40T and DS-45T as two distinct species within the genus Pedobacter. On the basis of phenotypic, phylogenetic and genetic data, strains DS-40T and DS-45T represent two novel species of the genus Pedobacter, for which the names Pedobacter lentus sp. nov. and Pedobacter terricola sp. nov. are proposed, respectively. The respective type strains are DS-40T (=KCTC 12875T=JCM 14593T) and DS-45T (=KCTC 12876T=JCM 14594T).

scholarly journals Sporacetigenium mesophilum gen. nov., sp. nov., isolated from an anaerobic digester treating municipal solid waste and sewage

2006 ◽  
Vol 56 (4) ◽  
pp. 721-725 ◽  
Author(s):  
Shuangya Chen ◽  
Lei Song ◽  
Xiuzhu Dong
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Municipal Solid Waste ◽  
Solid Waste ◽  
Sequence Similarity ◽  
Anaerobic Digester ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Fermentation Products ◽  
Novel Genus And Species

Two mesophilic, anaerobic bacterial strains (ZLJ115T and L4-2) were isolated from the sludge of an anaerobic digester treating municipal solid waste and sewage in Fujian province, China. The strains were Gram-positive, spore-forming, motile rods (0·9–1·0×3·6–7·3 μm). Growth of the strains was observed at 20–42 °C and pH 6·0–9·5. Both strains fermented several mono- and disaccharides. The main fermentation products from glucose were acetate, ethanol, hydrogen and carbon dioxide. Optimal hydrogen production by the new isolates was observed at pH 8·8 and 39 °C, and 1·4 mol H2 was detected from fermentation of 1 mol glucose. The DNA G+C contents of strains ZLJ115T and L4-2 were 53·9 and 54·3 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolates represented a novel phyletic sublineage within cluster XI of the clostridia, clustering with four thermophilic species, with <93·8 % 16S rRNA gene sequence similarity to previously described species. Phenotypically, the new isolates were distinguished from their phylogenetic relatives by growing mesophilically and by fermenting a variety of pentoses, as well as their higher genome DNA G+C content. On the basis of polyphasic evidence from this study, a novel genus and species are proposed, Sporacetigenium mesophilum gen. nov., sp. nov.; strain ZLJ115T (=DSM 16796T=AS 1.5019T) is the type strain of Sporacetigenium mesophilum.

scholarly journals Phycicoccus jejuensis gen. nov., sp. nov., an actinomycete isolated from seaweed

2006 ◽  
Vol 56 (10) ◽  
pp. 2369-2373 ◽  
Author(s):  
Soon Dong Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Mycolic Acids ◽  
The Family ◽  
Novel Genus And Species ◽  
The Republic

A marine actinomycete strain, designated KSW2-15T, was isolated from a dried seaweed sample collected from a sandy beach on the coast of Jeju in the Republic of Korea. The organism produced non-motile, non-endospore-forming, Gram-positive, coccoid cells. The colonies were circular, translucent and yellow in colour with entire margins. meso-Diaminopimelic acid was present as the diamino acid of the peptidoglycan. The acyl type of the muramic acid was acetyl. Mycolic acids were not present. The predominant menaquinone was MK-8(H4). The polar lipids were phosphatidylethanolamine, phosphatidylinositol and diphosphatidylglycerol. The major cellular fatty acids were of the saturated, unsaturated and iso-branched methyl types. The DNA G+C content was 74 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain KSW2-15T formed a loose association with ‘Candidatus Nostocoida limicola’, within the radiation of the family Intrasporangiaceae of the suborder Micrococcineae. The organism showed the highest levels of sequence similarity with ‘Candidatus Nostocoida limicola’ (96.1 %), Terrabacter tumescens (96.1 %) and Terrabacter terrae (96.0 %). The levels of 16S rRNA gene sequence similarity between the isolate and members of other genera of the family Intrasporangiaceae were in the range 92.1–95.5 %. On the basis of the polyphasic evidence, the isolate should be classified within a novel genus and species, for which the name Phycicoccus jejuensis gen. nov., sp. nov. is proposed. The type strain of Phycicoccus jejuensis is strain KSW2-15T (=KCCM 42315T=NRRL B-24460T).

scholarly journals Maribacter dokdonensis sp. nov., isolated from sea water off a Korean island, Dokdo

2005 ◽  
Vol 55 (5) ◽  
pp. 2051-2055 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Soo-Young Lee ◽  
Choong-Hwan Lee ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sea Water ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Dna Relatedness

Two Gram-negative, non-spore-forming, slightly halophilic gliding bacterial strains, DSW-8T and DSW-9, were isolated from sea water off a Korean island, Dokdo, of the East Sea, Korea, and their taxonomic position was investigated by a polyphasic study. The two strains grew optimally at 30 °C and in the presence of 2–3 % (w/v) NaCl. Strains DSW-8T and DSW-9 were characterized chemotaxonomically as containing MK-6 as the predominant menaquinone and iso-C17 : 0 3-OH, iso-C15 : 0 and iso-C15 : 1 as the major fatty acids. Major polar lipids were phosphatidylethanolamine, two unidentified phospholipids, an unidentified glycolipid and an amino group-containing lipid that was ninhydrin-positive. Their DNA G+C contents were 36·1 and 35·9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strains DSW-8T and DSW-9 fell within the genus Maribacter of the family Flavobacteriaceae. Strains DSW-8T and DSW-9 exhibited no difference in their 16S rRNA gene sequences and possessed a mean DNA–DNA relatedness level of 89 %. Strains DSW-8T and DSW-9 exhibited 16S rRNA gene sequence similarity levels of 96·9–98·0 % to the type strains of the four recognized Maribacter species, but their low level of DNA–DNA relatedness with these species demonstrated that they constitute a distinct Maribacter species. On the basis of phenotypic and phylogenetic data and genetic distinctiveness, strains DSW-8T (=KCTC 12393T=DSM 17201T) and DSW-9 were classified in the genus Maribacter as members of a novel species, for which the name Maribacter dokdonensis sp. nov. is proposed.

scholarly journals Rhizobium vallis sp. nov., isolated from nodules of three leguminous species

2011 ◽  
Vol 61 (11) ◽  
pp. 2582-2588 ◽  
Author(s):  
Fang Wang ◽  
En Tao Wang ◽  
Li Juan Wu ◽  
Xin Hua Sui ◽  
Ying Li ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Root Nodules ◽  
Phylogenetic Analyses ◽  
Housekeeping Genes ◽  
Phenotypic Characterization ◽  
Rrna Gene ◽  
Bacterial Strains

Four bacterial strains isolated from root nodules of Phaseolus vulgaris, Mimosa pudica and Indigofera spicata plants grown in the Yunnan province of China were identified as a lineage within the genus Rhizobium according to the analysis of 16S rRNA gene sequences, sharing most similarity with Rhizobium lusitanum P1-7T (99.1 % sequence similarity) and Rhizobium rhizogenes IAM 13570T (99.0 %). These strains also formed a distinctive group from the reference strains for defined species of the genus Rhizobium in a polyphasic approach, including the phylogenetic analyses of the 16S rRNA gene and housekeeping genes (recA, atpD, glnII), DNA–DNA hybridization, BOX-PCR fingerprinting, phenotypic characterization, SDS-PAGE of whole-cell proteins, and cellular fatty acid profiles. All the data obtained in this study suggested that these strains represent a novel species of the genus Rhizobium, for which the name Rhizobium vallis sp. nov. is proposed. The DNA G+C content (mol%) of this species varied between 60.9 and 61.2 (T m). The type strain of R. vallis sp. nov. is CCBAU 65647T ( = LMG 25295T  = HAMBI 3073T), which has a DNA G+C content of 60.9 mol% and forms effective nodules on Phaseolus vulgaris.

scholarly journals Humicoccus flavidus gen. nov., sp. nov., isolated from soil

2007 ◽  
Vol 57 (1) ◽  
pp. 56-59 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Seo-Youn Jung ◽  
Tae-Kwang Oh
Keyword(s):  
Fatty Acids ◽  
Cell Wall ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Diamino Acid

A Gram-positive, non-motile, spherical, non-spore-forming bacterial strain, DS-52T, was isolated from soil from Dokdo, Korea, and its taxonomic position was investigated by using a polyphasic approach. It grew optimally at 25 °C and pH 6.0–7.0. Strain DS-52T had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, and galactose, mannose, xylose and rhamnose as whole-cell sugars. It contained MK-8(H4) and MK-9(H4) as the predominant menaquinones and anteiso-C15 : 0, iso-C15 : 0 and C17 : 0 as major fatty acids. Major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidyldimethylethanolamine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DS-52T is most closely related to the genus Nakamurella of the suborder Frankineae. Strain DS-52T exhibited 16S rRNA gene sequence similarity values of 96.5 % to Nakamurella multipartita JCM 9543T and 92.0–93.9 % to other members of the suborder Frankineae. The diagnostic diamino acid type and polar lipid profile of strain DS-52T were the same as those of the genus Nakamurella. However, strain DS-52T could be clearly distinguished from the genus Nakamurella by differences in predominant menaquinones, major fatty acids and cell-wall sugars. Accordingly, based on combined phenotypic, chemotaxonomic and phylogenetic data, strain DS-52T (=KCTC 19127T=CIP 108919T) is proposed as the type strain of a novel species in a new genus, Humicoccus flavidus gen. nov., sp. nov.

scholarly journals Puniceicoccus vermicola gen. nov., sp. nov., a novel marine bacterium, and description of Puniceicoccaceae fam. nov., Puniceicoccales ord. nov., Opitutaceae fam. nov., Opitutales ord. nov. and Opitutae classis nov. in the phylum ‘Verrucomicrobia’

2007 ◽  
Vol 57 (3) ◽  
pp. 532-537 ◽  
Author(s):  
Yoe-Jin Choo ◽  
Kiyoung Lee ◽  
Jaeho Song ◽  
Jang-Cheon Cho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Novel Genus ◽  
Marine Isolate ◽  
Novel Genus And Species

A Gram-negative, chemoheterotrophic, facultatively anaerobic coccus, designated IMCC1545T, was isolated from the digestive tract of a marine clamworm, Periserrula leucophryna, inhabiting a tidal flat of the Yellow Sea. Cells of strain IMCC1545T are non-motile, dividing by binary fission. The predominant fatty acids are anteiso-C15 : 0 and C18 : 0. The respiratory quinone is menaquinone-7 and the DNA G+C content is 52.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences using three treeing algorithms revealed that the strain formed a novel genus-level lineage within the phylum ‘Verrucomicrobia’. The most closely related named organisms to strain IMCC1545T are ‘Fucophilus fucoidanolyticus’ SI-1234 (86.5 % 16S rRNA gene sequence similarity), Alterococcus agarolyticus ADT3T (81.8 %) and Opitutus terrae PB90-1T (80.3 %), which belong to subdivision 4 of the ‘Verrucomicrobia’. Subdivision 4 of the ‘Verrucomicrobia’ (here named Opitutae classis nov.) was divided into two clades, a clade containing strain IMCC1545T and a clade containing Opitutus terrae. From the taxonomic data obtained in this study, it is proposed that the new marine isolate be placed into a novel genus and species named Puniceicoccus vermicola gen. nov., sp. nov. (the type strain of Puniceicoccus vermicola is IMCC1545T=KCCM 42343T=NBRC 101964T) within Puniceicoccaceae fam. nov and Puniceicoccales ord. nov in the class Opitutae. The family Opitutaceae fam. nov. and order Opitutales ord. nov. are also formally proposed.

Ethanoligenens harbinense gen. nov., sp. nov., isolated from molasses wastewater

2006 ◽  
Vol 56 (4) ◽  
pp. 755-760 ◽  
Author(s):  
Defeng Xing ◽  
Nanqi Ren ◽  
Qiubo Li ◽  
Ming Lin ◽  
Aijie Wang ◽  
...  
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Continuous Stirred Tank Reactor ◽  
Bacterial Strains ◽  
Molasses Wastewater ◽  
Aggregative Growth

Two strictly anaerobic bacterial strains (YUAN-3T and X-29) were isolated from anaerobic activated sludge of molasses wastewater in a continuous stirred-tank reactor. The strains were Gram-positive, non-spore-forming, mesophilic and motile. Cells were regular rods (0·4–0·8×1·5–8·0 μm) and occurred singly, in pairs and sometimes in chains of up to eight. Autoaggregative and autofluorescent growth of strain YUAN-3T and non-aggregative growth of strain X-29 were observed at 20–44 °C and pH 3·5–9·0. Both strains hydrolysed gelatin and aesculin and fermented several kinds of mono-, di- and oligosaccharides. Fermentation end products formed from glucose were acetate, ethanol, hydrogen and carbon dioxide. The predominant cellular fatty acids were the branched-chain fatty acids iso-C16 : 0 (44·18 %) and iso-C12 : 0 (26·67 %). The DNA G+C contents of strains YUAN-3T and X-29 were 47·8 and 49·0 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolates represent a novel phyletic sublineage within the Clostridium cellulosi rRNA cluster, with <92 % 16S rRNA gene sequence similarity to currently known species. On the basis of polyphasic evidence from this study, it is proposed that the unknown bacterium should be classified in a new genus as a novel species, Ethanoligenens harbinense gen. nov., sp. nov. The type strain of Ethanoligenens harbinense is YUAN-3T (=JCM 12961T=CGMCC 1.5033T).

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