scholarly journals Nereida ignava gen. nov., sp. nov., a novel aerobic marine α-proteobacterium that is closely related to uncultured Prionitis (alga) gall symbionts

2005 ◽  
Vol 55 (2) ◽  
pp. 631-636 ◽  
Author(s):  
M. J. Pujalte ◽  
M. C. Macián ◽  
D. R. Arahal ◽  
W. Ludwig ◽  
K. H. Schleifer ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Sea Water ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Good Growth ◽  
Strictly Aerobic ◽  
Phylogenetic Distance ◽  
Novel Genus And Species

A Gram-negative, slightly halophilic, non-pigmented, strictly aerobic, chemo-organotrophic bacterium was isolated from Mediterranean sea water off the Spanish coast near Valencia. This strain was poorly reactive, being unable to grow in most carbon sources analysed in minimal medium. However, good growth was observed when more complex media and longer incubation times were used. Phylogenetic analysis based on an almost complete 16S rRNA gene sequence placed strain 2SM4T within the Roseobacter group, in the vicinity of uncultured bacteria described as gall symbionts of several species of the red alga Prionitis. Sequence similarity values between strain 2SM4T and the closest neighbouring species were below 95·0 %. The cellular fatty acid composition of the Mediterranean strain confirmed its position within the ‘Alphaproteobacteria’, sharing 18 : 1ω7c as the major cellular fatty acid. The phylogenetic distance from any taxon with a validly published name and also a number of distinguishing features support the designation of strain 2SM4T as representing a novel genus and species, for which the name Nereida ignava gen. nov., sp. nov. is proposed. The type strain is 2SM4T (=CECT 5292T=DSM 16309T=CIP 108404T=CCUG 49433T).

scholarly journals Kordia algicida gen. nov., sp. nov., an algicidal bacterium isolated from red tide

2004 ◽  
Vol 54 (3) ◽  
pp. 675-680 ◽  
Author(s):  
Jae Hak Sohn ◽  
Jung-Hyun Lee ◽  
Hana Yi ◽  
Jongsik Chun ◽  
Kyung Sook Bae ◽  
...  
Keyword(s):  
Sea Water ◽  
Sequence Similarity ◽  
Red Tide ◽  
Carbon Sources ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Phenotypic Characters ◽  
Algicidal Bacterium ◽  
Rdna Sequences ◽  
The Family

A bacterium (named OT-1T) that showed algicidal activity was isolated from sea water of Masan Bay, Korea, during an outbreak of red tide. Phylogenetic analysis based on 16S rDNA sequences showed that the isolate formed a distinct phyletic lineage within the family Flavobacteriaceae of the Cytophaga–Flavobacterium–Bacteroides group. No species with a validly published name showed ⩾93 % 16S rRNA gene sequence similarity to strain OT-1T. The isolate had major amounts of iso-branched and 3-hydroxy iso-branched fatty acids and menaquinone 6 and a DNA G+C content of 34 mol%; these chemotaxonomic characters also supported the placement of the organism in the family Flavobacteriaceae. The strain was Gram-negative, yellow-pigmented, non-motile, non-gliding, flexirubin-negative, strictly aerobic, catalase-negative, oxidase-positive and halophilic. Na+, Ca2+ and Mg2+ ions were obligately required for growth. The strain utilized various sugars as sole carbon sources and degraded gelatin, skimmed milk and starch. Several phenotypic characters can be used to differentiate the test strain from phylogenetically related marine bacterial genera. On the basis of polyphasic evidence, it is proposed that strain OT-1T should be assigned to the family Flavobacteriaceae as Kordia algicida gen. nov., sp. nov. The type strain is OT-1T (=KCTC 8814PT=NBRC 1000336T).

scholarly journals Hoeflea phototrophica sp. nov., a novel marine aerobic alphaproteobacterium that forms bacteriochlorophyll a

2006 ◽  
Vol 56 (4) ◽  
pp. 821-826 ◽  
Author(s):  
Hanno Biebl ◽  
Brian J. Tindall ◽  
Rüdiger Pukall ◽  
Heinrich Lünsdorf ◽  
Martin Allgaier ◽  
...  
Keyword(s):  
Sea Water ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Photosynthetic Pigment ◽  
Carbon Sources ◽  
Rrna Gene ◽  
Good Growth ◽  
Reaction Centre ◽  
The Novel ◽  
Poor Growth

Within a collection of marine strains that were shown to contain the photosynthesis reaction-centre genes pufL and pufM, a novel group of alphaproteobacteria was found and was characterized phenotypically. The 16S rRNA gene sequence data suggested that the strains belonged to the order Rhizobiales and were closest (98·5 % sequence similarity) to the recently described species Hoeflea marina. The cells contained bacteriochlorophyll a and a carotenoid, presumably spheroidenone, in small to medium amounts. Cells of the novel strains were small rods and were motile by means of single polarly inserted flagella. Good growth occurred in complex media with 0·5–7·0 % sea salts, at 25–33 °C (optimum, 31 °C) and at pH values in the range 6–9. With the exception of acetate and malate, organic carbon sources tested supported poor growth or no growth at all. Growth factors were required; these were provided by small amounts of yeast extract, but not by standard vitamin solutions. Growth occurred under aerobic to microaerobic conditions, but not under anaerobic conditions, either in the dark or light. Nitrate was not reduced. Photosynthetic pigments were formed at low to medium salt concentrations, but not at the salt concentration of sea water (3·5 %). On the basis of smaller cell size, different substrate utilization profile and photosynthetic pigment content, the novel strains can be classified as representatives of a second species of Hoeflea, for which the name Hoeflea phototrophica sp. nov. is proposed. The type strain of Hoeflea phototrophica sp. nov. is DFL-43T (=DSM 17068T=NCIMB 14078T).

scholarly journals Glaciecola polaris sp. nov., a novel budding and prosthecate bacterium from the Arctic Ocean, and emended description of the genus Glaciecola

2004 ◽  
Vol 54 (5) ◽  
pp. 1765-1771 ◽  
Author(s):  
Stefanie Van Trappen ◽  
Tjhing-Lok Tan ◽  
Jifang Yang ◽  
Joris Mergaert ◽  
Jean Swings
Keyword(s):  
Fatty Acid ◽  
Sea Water ◽  
Novel Species ◽  
Sequence Similarity ◽  
The Other ◽  
The Arctic ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Phenotypic Properties ◽  
Emended Description

Four strains of cold-adapted, strictly aerobic and facultative oligotrophic bacteria were isolated from polar seas and investigated using a polyphasic taxonomic approach. Two strains (LMG 21857T and LMG 21854) derive from Arctic sea water whereas the other two strains (LMG 21855 and LMG 21858) were isolated from Antarctic sea water. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains belong to the γ-subclass of the Proteobacteria and are related to the genus Glaciecola, with 98·0–99·7 % sequence similarity to Glaciecola mesophila and 94·2–95·3 % sequence similarity to Glaciecola punicea, their nearest phylogenetic neighbours. Two strains (LMG 21855 and LMG 21858) were identified as G. mesophila, whereas DNA–DNA hybridization results and differences in phenotypic characteristics showed that the other two strains (LMG 21857T and LMG 21854) constitute a novel species within the genus Glaciecola, with a DNA G+C content of 44·0 mol%. The isolates are Gram-negative, chemoheterotrophic, motile, rod-shaped cells that are psychrotolerant and moderately halophilic. Buds can be produced on mother cells and on prosthecae. Branch formation of prosthecae occurs. Whole-cell fatty acid profiles of the isolates are very similar and include C16 : 0 and C16 : 1 ω7c as the major fatty acid components. On the basis of genotypic and phenotypic properties, a novel species of the genus Glaciecola is described, for which the name Glaciecola polaris sp. nov. is proposed, with isolate LMG 21857T (=CIP 108324T=ARK 150T) as the type strain. An emended description of the genus Glaciecola is presented.

scholarly journals Neptuniibacter caesariensis gen. nov., sp. nov., a novel marine genome-sequenced gammaproteobacterium

2007 ◽  
Vol 57 (5) ◽  
pp. 1000-1006 ◽  
Author(s):  
David R. Arahal ◽  
Itziar Lekunberri ◽  
José M. González ◽  
Javier Pascual ◽  
María J. Pujalte ◽  
...  
Keyword(s):  
Eastern Mediterranean ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Carbon Sources ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Polar Lipid Profile ◽  
Novel Genus And Species ◽  
Bacterium Strain

A Gram-negative, slightly halophilic, strictly aerobic, motile chemoorganotrophic bacterium, strain MED92T, was isolated from a surface water sample from the eastern Mediterranean Sea. Phylogenetic analysis based on its 16S rRNA gene sequence, retrieved from the whole-genome sequence, demonstrated that this isolate is unique, showing <93 % sequence similarity to species of the families Oceanospirillaceae and Alteromonadaceae. The polar lipid profile of the novel strain consisted of phosphatidylethanolamine, phosphatidylglycerol, an unknown aminophospholipid and diphosphatidylglycerol. Major fatty acids are 16 : 1ω7c/15 iso 2-OH (41.2 % relative amount), 18 : 1ω7c (35.9 %), 16 : 0 (16.1 %), 10 : 0 3-OH (5.0 %) and 18 : 0 (1.0 %). Preferred carbon sources are organic acids and amino acids. The DNA G+C content is 46.6 mol%. Based on a phenotypic, chemotaxonomic and phylogenetic analyses, it is proposed that this marine bacterium represents a novel genus and species, for which the name Neptuniibacter caesariensis gen. nov., sp. nov. is proposed. The type strain is MED92T (=CECT 7075T=CCUG 52065T).

scholarly journals Serinicoccus marinus gen. nov., sp. nov., a novel actinomycete with l-ornithine and l-serine in the peptidoglycan

2004 ◽  
Vol 54 (5) ◽  
pp. 1585-1589 ◽  
Author(s):  
Hana Yi ◽  
Peter Schumann ◽  
Kyounghee Sohn ◽  
Jongsik Chun
Keyword(s):  
Sea Water ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Marine Isolate ◽  
Glycan Chain ◽  
Novel Genus And Species ◽  
Phyletic Line ◽  
Diamino Acid

A Gram-positive bacterial strain containing l-ornithine as the diagnostic diamino acid was isolated from a sea-water-sample from the East Sea, Korea. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain JC1078T represents a phyletic line within the suborder Micrococcineae of the order Actinomycetales, adjacent to the genus Ornithinimicrobium. The highest sequence similarity values to the isolate were observed against Ornithinimicrobium humiphilum (94·3 %) and Kytococcus sedentarius (94·1 %). The strain was strictly aerobic and moderately halophilic with optimal growth at 2–3 % (w/v) NaCl. Cells were non-motile, non-sporulating and coccoid-shaped. The cell wall contains l-ornithine, glutamic acid, alanine, glycine and serine. The major menaquinone was MK-8(H4). The predominant cellular fatty acids were of the iso- and anteiso-methyl-branched types. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and an unknown glycolipid. The acyl type of the glycan chain of peptidoglycan is acetyl. The DNA G+C content was 72 mol%. The combination of physiological, biochemical and chemotaxonomical data clearly separated the marine isolate from other members of the suborder Micrococcineae. On the basis of polyphasic evidence, it is proposed to classify strain JC1078T in a novel genus and species, for which the name Serinicoccus marinus gen. nov., sp. nov. is proposed. The type strain is JC1078T (=IMSNU 14026T=KCTC 9980T=DSM 15273T).

scholarly journals Alteromonas stellipolaris sp. nov., a novel, budding, prosthecate bacterium from Antarctic seas, and emended description of the genus Alteromonas

2004 ◽  
Vol 54 (4) ◽  
pp. 1157-1163 ◽  
Author(s):  
Stefanie Van Trappen ◽  
Tjhing-Lok Tan ◽  
Jifang Yang ◽  
Joris Mergaert ◽  
Jean Swings
Keyword(s):  
Fatty Acid ◽  
Sea Water ◽  
Novel Species ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Emended Description ◽  
Mother And Daughter ◽  
Taxonomic Approach

Seven novel, cold-adapted, strictly aerobic, facultatively oligotrophic strains, isolated from Antarctic sea water, were investigated by using a polyphasic taxonomic approach. The isolates were Gram-negative, chemoheterotrophic, motile, rod-shaped cells that were psychrotolerant and moderately halophilic. Buds were produced on mother and daughter cells and on prosthecae. Prostheca formation was peritrichous and prosthecae could be branched. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains belong to the γ-Proteobacteria and are related to the genus Alteromonas, with 98·3 % sequence similarity to Alteromonas macleodii and 98·0 % to Alteromonas marina, their nearest phylogenetic neighbours. Whole-cell fatty acid profiles of the isolates were very similar and included C16 : 0, C16 : 1 ω7c, C17 : 1 ω8c and C18 : 1 ω8c as the major fatty acid components. These results support the affiliation of these isolates to the genus Alteromonas. DNA–DNA hybridization results and differences in phenotypic characteristics show that the strains represent a novel species with a DNA G+C content of 43–45 mol%. The name Alteromonas stellipolaris sp. nov. is proposed for this novel species; the type strain is ANT 69aT (=LMG 21861T=DSM 15691T). An emended description of the genus Alteromonas is given.

scholarly journals Oceanithermus desulfurans sp. nov., a novel thermophilic, sulfur-reducing bacterium isolated from a sulfide chimney in Suiyo Seamount

2004 ◽  
Vol 54 (5) ◽  
pp. 1561-1566 ◽  
Author(s):  
Koji Mori ◽  
Takeshi Kakegawa ◽  
Yowsuke Higashi ◽  
Ko-ichi Nakamura ◽  
Akihiko Maruyama ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Growth Conditions ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Good Growth ◽  
Chain Link ◽  
Circular Structure ◽  
Hybridization Test ◽  
A Chain ◽  
Cellular Fatty Acid Profile

A novel thermophilic, microaerophilic, sulfur-reducing bacterium designated strain St55BT was isolated from a sulfide chimney in the hydrothermal field of Suiyo Seamount (Izu-Bonin Arc, Western Pacific). Cells of the isolate were rod-shaped and tended to form a chain-link circular structure (a rotund body) at exponential phase under good growth conditions. The isolate was a chemoheterotroph requiring yeast extract for growth. Although strain St55BT used oxygen as an electron acceptor, it could not form colonies in an oxygen concentration of more than 5 % (v/v). The isolate also used nitrate, nitrite or elemental sulfur in the absence of oxygen. A phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was closely related to Oceanithermus profundus, belonging to the phylum ‘Deinococcus–Thermus’ (sequence similarity 99·5 %). However, strain St55BT differed from O. profundus in terms of usage of electron donors, cellular fatty acid profile and DNA G+C content. In addition, a DNA–DNA hybridization test indicated low relatedness between the isolate and O. profundus. For the reasons given above, the name Oceanithermus desulfurans sp. nov. is proposed for strain St55BT (=NBRC 100063T=DSM 15757T).

scholarly journals Paucibacter toxinivorans gen. nov., sp. nov., a bacterium that degrades cyclic cyanobacterial hepatotoxins microcystins and nodularin

2005 ◽  
Vol 55 (4) ◽  
pp. 1563-1568 ◽  
Author(s):  
Jarkko Rapala ◽  
Katri A. Berg ◽  
Christina Lyra ◽  
R. Maarit Niemi ◽  
Werner Manz ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Fatty Acid ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence

Thirteen bacterial isolates from lake sediment, capable of degrading cyanobacterial hepatotoxins microcystins and nodularin, were characterized by phenotypic, genetic and genomic approaches. Cells of these isolates were Gram-negative, motile by means of a single polar flagellum, oxidase-positive, weakly catalase-positive and rod-shaped. According to phenotypic characteristics (carbon utilization, fatty acid and enzyme activity profiles), the G+C content of the genomic DNA (66·1–68·0 mol%) and 16S rRNA gene sequence analysis (98·9–100 % similarity) the strains formed a single microdiverse genospecies that was most closely related to Roseateles depolymerans (95·7–96·3 % 16S rRNA gene sequence similarity). The isolates assimilated only a few carbon sources. Of the 96 carbon sources tested, Tween 40 was the only one used by all strains. The strains were able to mineralize phosphorus from organic compounds, and they had strong leucine arylamidase and chymotrypsin activities. The cellular fatty acids identified from all strains were C16 : 0 (9·8–19 %) and C17 : 1 ω7c (<1–5·8 %). The other predominant fatty acids comprised three groups: summed feature 3 (<1–2·2 %), which included C14 : 0 3-OH and C16 : 1 iso I, summed feature 4 (54–62 %), which included C16 : 1 ω7c and C15 : 0 iso OH, and summed feature 7 (8·5–28 %), which included ω7c, ω9c and ω12t forms of C18 : 1. A more detailed analysis of two strains indicated that C16 : 1 ω7c was the main fatty acid. The phylogenetic and phenotypic features separating our strains from recognized bacteria support the creation of a novel genus and species, for which the name Paucibacter toxinivorans gen. nov., sp. nov. is proposed. The type strain is 2C20T (=DSM 16998T=HAMBI 2767T=VYH 193597T).

scholarly journals Prevotella copri sp. nov. and Prevotella stercorea sp. nov., isolated from human faeces

2007 ◽  
Vol 57 (5) ◽  
pp. 941-946 ◽  
Author(s):  
Hidenori Hayashi ◽  
Kensaku Shibata ◽  
Mitsuo Sakamoto ◽  
Shinichi Tomita ◽  
Yoshimi Benno
Keyword(s):  
Fatty Acid ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Fatty Acid Profiles ◽  
Phenotypic Characteristics ◽  
Human Faeces ◽  
Gene Sequence Analysis ◽  
Type Strains ◽  
Fatty Acid Compositions

Six strains (CB7T, CB18, CB23, CB26, CB28 and CB35T) were isolated from human faeces. Based on phylogenetic analysis, phenotypic characteristics, cellular fatty acid profiles and menaquinone profiles, these strains could be included within the genus Prevotella and made up two clusters. 16S rRNA gene sequence analysis indicated that five strains were most closely related to Prevotella veroralis, sharing about 92 % sequence similarity; the remaining strain was most closely related to Prevotella shahii, sharing about 90 % sequence similarity. All six strains were obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative rods. The cellular fatty acid compositions of the six strains differed significantly from those of other Prevotella species. Five strains (CB7T, CB18, CB23, CB26 and CB28) contained dimethyl acetals and the major menaquinones of these strains were MK-11, MK-12 and MK-13. The major menaquinones of CB35T were MK-12 and MK-13. Based on phenotypic and phylogenetic findings, two novel species, Prevotella copri sp. nov. and Prevotella stercorea sp. nov., are proposed, representing the two different strain clusters. The DNA G+C contents of strains CB7T and CB35T were 45.3 and 48.2 mol%, respectively. The type strains of P. copri and P. stercorea are CB7T (=JCM 13464T=DSM 18205T) and CB35T (=JCM 13469T=DSM 18206T), respectively.

Bacillus gottheilii sp. nov., isolated from a pharmaceutical manufacturing site

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 867-872 ◽  
Author(s):  
Herbert Seiler ◽  
Mareike Wenning ◽  
Verena Schmidt ◽  
Siegfried Scherer
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Acid Type

A novel Gram-staining-positive, rod-shaped, motile, strictly aerobic, endospore-forming bacterium, designated WCC 4585T, was isolated from a pharmaceutical production line. The organism grew optimally at 30 °C, at pH 8 and in the presence of 0.5 % (w/v) NaCl. Oval endospores were formed subterminally and terminally in swollen sporangia. The cell-wall diamino acid was meso-diaminopimelic acid (type A1γ) and the genomic DNA G+C content was 38.7 mol%. The major menaquinone was MK-7. The cellular fatty acid profile contained major amounts of iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0, and the cellular phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and aminophospholipid. The isolate was most closely related to Bacillus oceanisediminis H2T, Bacillus infantis SMC 4352-1T, Bacillus firmus NCIMB 9366T, Bacillus circulans ATCC 4513T and Bacillus horneckiae DSM 23495T with which it shared less than 98.0 % 16S rRNA gene sequence similarity. DNA–DNA relatedness values between strain WCC 4585T and five type strains of related species were ≤27 % and sequence similarity values based on groEL sequences were ≤88.7 %. On the basis of the characteristics presented, strain WCC 4585T is proposed to represent a novel species, Bacillus gottheilii sp. nov. The type strain is WCC 4585T( = DSM 23668T = CCUG 59876T = LMG 25856T).

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