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1.
Int J Syst Evol Microbiol ; 59(Pt 11): 2916-20, 2009 Nov.
Article in English | MEDLINE | ID: mdl-19625415

ABSTRACT

A novel obligately organotrophic, facultatively microaerophilic spirillum, designated strain D-427(T), was isolated from sulfidic sludge of a municipal wastewater-treatment plant. Cells were Gram-negative, large and highly motile due to bipolar tufts of flagella covered with mucous sheaths. Coccoid cells were sometimes formed. Strain D-427(T) grew optimally at pH 7.5-7.8 and 28 degrees C in the presence of 2 % O(2) in the gas phase. The organism showed oxidase and very low catalase activity. The isolate grew chemo-organotrophically with a limited number of organic acids as substrates. The DNA G+C content was 38.0 mol% (T(m)). Phylogenetic analysis of the 16S rRNA gene sequence placed strain D-427(T) in the genus Spirillum within the class Betaproteobacteria. The 16S rRNA gene sequence similarity between strain D-427(T) and Spirillum volutans ATCC 19554(T), the type strain of the single species of the genus, was 98.6 %. The low level of DNA-DNA hybridization and different phenotypic properties indicate that strain D-427(T) is clearly distinguishable from Spirillum volutans. No strain of S. volutans is available from any established culture collection or from the authors who described this species. Therefore, on the basis of phenotypic and genotypic data and the fact that the type and single species of the genus Spirillum cannot be included in any scientific study, since the type strain has been lost, we propose to assign strain D-427(T) as a novel species of the genus Spirillum, Spirillum winogradskyi sp. nov. (type strain D-427(T) =DSM 12756(T) =VKM B-2518(T)), and we request that the Judicial Commission place the name Spirillum volutans on the list of rejected names if a suitable type strain is not found or a neotype is not proposed within 2 years following the publication of this paper. An emended description of the genus Spirillum is also provided.


Subject(s)
Sewage/microbiology , Spirillum/classification , Spirillum/isolation & purification , DNA, Bacterial/genetics , DNA, Ribosomal/genetics , Molecular Sequence Data , Phylogeny , RNA, Ribosomal, 16S/genetics , Spirillum/genetics
2.
Int J Syst Evol Microbiol ; 58(Pt 5): 1194-7, 2008 May.
Article in English | MEDLINE | ID: mdl-18450712

ABSTRACT

The precise taxonomic position of Roseivirga seohaensis strain SW-152T, formerly [Marinicola] seohaensis, was established. On the basis of data from DNA-DNA reassociation experiments and phenotypic analysis, it is proposed that this strain should be considered as a later heterotypic synonym of Roseivirga ehrenbergii KMM 6017T Nedashkovskaya et al. 2005. Emended descriptions for Roseivirga ehrenbergii and for the genus Roseivirga are also given.


Subject(s)
Cytophagaceae/classification , Bacterial Typing Techniques , Base Composition , Cytophagaceae/genetics , Cytophagaceae/physiology , DNA, Bacterial/analysis , DNA, Bacterial/genetics , DNA, Bacterial/isolation & purification , Genes, rRNA , Genomics , Nucleic Acid Hybridization , Phenotype , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Species Specificity
3.
Int J Syst Evol Microbiol ; 57(Pt 11): 2655-2659, 2007 Nov.
Article in English | MEDLINE | ID: mdl-17978235

ABSTRACT

Two marine, heterotrophic, aerobic, pigmented and gliding bacteria, isolated from the sea urchin Strongylocentrotus intermedius were subjected to a polyphasic taxonomy study. The 16S rRNA gene sequence analysis revealed that strains KMM 6032T and KMM 6047 formed a distinct branch within the genus Arenibacter, a member of the family Flavobacteriaceae. The level of sequence similarity between the novel isolates and members of the genus Arenibacter was 94.5-98.9%. The DNA G+C content was 39-40 mol%. The dominant fatty acids were iso-C15:1, iso-C15:0, C15:0, C15:1omega6c, iso-C15:0 3-OH, iso-C17:1omega9c, iso-C17:0 3-OH and summed feature 3 (comprising iso-C15:0 2-OH and/or C16:1omega7c). The results of DNA-DNA hybridization experiments supported by phenotypic data indicated that the isolates represent a novel species within the genus Arenibacter, for which the name Arenibacter echinorum sp. nov. is proposed. The type strain is KMM 6032T (=KCTC 22013T=LMG 22574T).


Subject(s)
Flavobacteriaceae/classification , Flavobacteriaceae/isolation & purification , Strongylocentrotus/microbiology , Animals , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/analysis , DNA, Ribosomal/analysis , Fatty Acids/analysis , Flavobacteriaceae/genetics , Flavobacteriaceae/physiology , Genes, rRNA , Molecular Sequence Data , Nucleic Acid Hybridization , Phenotype , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Species Specificity
4.
Microbiology (Reading) ; 152(Pt 10): 3013-3023, 2006 Oct.
Article in English | MEDLINE | ID: mdl-17005982

ABSTRACT

Unexpectedly high culturable diversity of moderately and extremely halophilic obligately chemolithoautotrophic sulfur-oxidizing bacteria (SOB) was discovered in the sediments of various hypersaline habitats, including chloride-sulfate lakes in Mongolia, Russia and Ukraine, a sea saltern in Slovenia and a deep-sea salt brine from the Mediterranean. Six different groups of halophilic SOB, including four new genera, all belonging to the Gammaproteobacteria, were found. Two groups of moderately halophilic strictly aerobic SOB dominated at 2 M NaCl, including representatives of the genus Halothiobacillus (in fully aerobic conditions) and Thiomicrospira (in micro-oxic conditions). Under denitrifying conditions at 2 M NaCl, a group of moderately halophilic and facultatively anaerobic SOB was selected, capable of complete denitrification of nitrate. The group represents a new genus with closest relatives among as yet undescribed marine thiodenitrifying isolates. With thiocyanate as a substrate, an enrichment culture at 2 M NaCl yielded a pure culture of moderately halophilic SOB capable of aerobic growth with thiocyanate and thiosulfate at up to 4 M NaCl. Furthermore, this bacterium also grew anaerobically using nitrite as electron acceptor. It formed a new lineage distantly related to the genus Thiomicrospira. Enrichments at 4 M NaCl resulted in the domination of two different, previously unknown, groups of extremely halophilic SOB. Under oxic conditions, they were represented by strictly aerobic spiral-shaped bacteria, related to the Ectothiorhodospiraceae, while under denitrifying conditions a group of facultatively anaerobic nitrate-reducing bacteria with long rod-shaped cells was selected, distantly related to the genus Acidithiobacillus.


Subject(s)
Biodiversity , Gammaproteobacteria/classification , Gammaproteobacteria/isolation & purification , Geologic Sediments/microbiology , Sulfur/metabolism , Water Microbiology , Aerobiosis , Anaerobiosis , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Gammaproteobacteria/growth & development , Gammaproteobacteria/metabolism , Mediterranean Sea , Microscopy , Molecular Sequence Data , Mongolia , Nitrates/metabolism , Nitrites/metabolism , Oxidation-Reduction , Phylogeny , RNA, Ribosomal, 16S/genetics , Russia , Sequence Analysis, DNA , Sequence Homology, Nucleic Acid , Slovenia , Sodium Chloride , Thiocyanates/metabolism , Ukraine
5.
Int J Syst Evol Microbiol ; 56(Pt 5): 953-958, 2006 May.
Article in English | MEDLINE | ID: mdl-16627637

ABSTRACT

The taxonomic position of three novel marine, heterotrophic, pigmented and agarolytic bacteria with gliding motility, isolated from the sea urchin Strongylocentrotus intermedius, was investigated. 16S rRNA gene sequence analysis revealed that strains KMM 6166, KMM 6172T and KMM 6173 are members of the phylum Bacteroidetes; their nearest neighbours were Belliella baltica and Hongiella marincola (similarities of 94.5 and 93.6 %, respectively). The DNA G+C content of the strains was 44-45 mol%. The predominant fatty acids were C15 : 0 iso, C16:1omega5c, C17:1 iso omega9c, C17:0 iso 3-OH and summed feature 3 (C16:1omega7c and/or C15:0 iso 2-OH). The major respiratory quinone was MK-7. Results of molecular experiments supported by phenotypic and chemotaxonomic data enabled the isolates to be classified as representatives of a novel species in a new genus, for which the name Echinicola pacifica gen. nov., sp. nov. is proposed. Echinicola pacifica is the type species of the genus Echinicola, and its type strain is KMM 6172T (=KCTC 12368T=LMG 23350T).


Subject(s)
Cytophagaceae/classification , Cytophagaceae/isolation & purification , Strongylocentrotus/microbiology , Animals , Bacterial Typing Techniques , Base Composition , Cytophagaceae/chemistry , Cytophagaceae/physiology , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Fatty Acids/analysis , Fatty Acids/isolation & purification , Genes, rRNA/genetics , Molecular Sequence Data , Phylogeny , Quinones/analysis , Quinones/isolation & purification , RNA, Bacterial/genetics , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
6.
Int J Syst Evol Microbiol ; 56(Pt 4): 797-800, 2006 Apr.
Article in English | MEDLINE | ID: mdl-16585697

ABSTRACT

A novel anaerobic, thermophilic, CO-utilizing bacterium, strain KarT, was isolated from a hot spring of Karymskoe Lake, Kamchatka Peninsula. The cells of the novel isolate were Gram-positive, spore-forming, short rods. The bacterium grew chemolithoautotrophically on CO, producing equimolar quantities of H2 and CO2 (according to the equation CO + H2O --> CO2 + H2), and in the absence of CO, under N2 in the gas phase, chemoorganoheterotrophically with yeast extract, sucrose or pyruvate. Growth was observed in the temperature range 50-70 degrees C, with an optimum at 60 degrees C, and in the pH range 6.2-8.0, with an optimum at pH 6.8. The micro-organism did not grow on solid media; it was able to grow only in semi-solid medium containing 0.5 % agar. The generation time under optimal conditions for chemolithoautotrophic growth was 1 h. The G+C content of the DNA was 46.5+/-1 mol%. Growth was completely inhibited by penicillin, novobiocin, streptomycin, kanamycin and neomycin. Analysis of the 16S rRNA gene sequence showed that the isolate should be assigned to the genus Carboxydocella. On the basis of the results of DNA-DNA hybridization and morphological and physiological analyses, strain KarT represents a novel species of the genus Carboxydocella, for which the name Carboxydocella sporoproducens sp. nov. is proposed. The type strain is KarT (=DSM 16521T = VKM B-2358T).


Subject(s)
Bacteria, Anaerobic/classification , Carbon Monoxide/metabolism , Gram-Positive Rods/classification , Hot Springs/microbiology , Hydrogen/metabolism , Bacteria, Anaerobic/genetics , Bacteria, Anaerobic/isolation & purification , Bacteria, Anaerobic/metabolism , Gram-Positive Rods/genetics , Gram-Positive Rods/isolation & purification , Gram-Positive Rods/metabolism , Hot Temperature , Molecular Sequence Data , Phylogeny , RNA, Bacterial/genetics , RNA, Ribosomal, 16S/genetics , Russia
7.
Int J Syst Evol Microbiol ; 56(Pt 4): 883-887, 2006 Apr.
Article in English | MEDLINE | ID: mdl-16585710

ABSTRACT

A sponge-associated strain, KMM 7019T, was investigated in a polyphasic taxonomic study. The bacterium was strictly aerobic, heterotrophic, Gram-negative, yellow-pigmented, motile by gliding and oxidase-, catalase-, beta-galactosidase- and alkaline phosphatase-positive. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain KMM 7019T is closely related to members of the genus Salegentibacter, namely Salegentibacter holothuriorum, Salegentibacter mishustinae and Salegentibacter salegens (97.7-98 % sequence similarities). The DNA-DNA relatedness between the strain studied and Salegentibacter species ranged from 27 to 31 %, clearly demonstrating that KMM 7019T belongs to a novel species of the genus Salegentibacter, for which the name Salegentibacter agarivorans sp. nov. is proposed. The type strain is KMM 7019T (=KCTC 12560T = LMG 23205T).


Subject(s)
Flavobacteriaceae/classification , Flavobacteriaceae/isolation & purification , Porifera/microbiology , Seawater/microbiology , Animals , Flavobacteriaceae/chemistry , Flavobacteriaceae/genetics , Molecular Sequence Data , Nucleic Acid Hybridization , Phylogeny , RNA, Ribosomal, 16S/analysis , RNA, Ribosomal, 16S/genetics
8.
Int J Syst Evol Microbiol ; 56(Pt 3): 569-576, 2006 Mar.
Article in English | MEDLINE | ID: mdl-16514029

ABSTRACT

Five Gram-negative, motile, spiral-shaped strains were isolated from a sulfide spring (D-412T), active sludge of wastewater (D-419T, D-420, D-424) and industrial wastewater (D-416). Comparative 16S rRNA gene sequence analysis showed that the isolates belong to the family Comamonadaceae, within the class Betaproteobacteria, but fall into a distinct cluster. On the basis of phenotypic, chemotaxonomic and phylogenetic data, a new genus, Giesbergeria gen. nov., is proposed, including five species. The type species of the genus is Giesbergeria voronezhensis sp. nov. (type strain D-419T = DSM 12825T = CIP 107340T = VKM B-2350T) and other novel members of the genus are Giesbergeria kuznetsovii sp. nov. (type strain D-412T = DSM 12827T = VKM B-2352T), Giesbergeria giesbergeri comb. nov. (basonym Aquaspirillum giesbergeri), Giesbergeria sinuosa comb. nov. (basonym Aquaspirillum sinuosum) and Giesbergeria anulus comb. nov. (basonym Aquaspirillum anulus). Using the same criteria, isolate D-416 (= DSM 12826) was identified as a strain of [Aquaspirillum] metamorphum. Strain D-416, the type strain of [A.] metamorphum and the type strain of [Aquaspirillum] psychrophilum form a distinct cluster within the family Comamonadaceae (97-97.2% 16S rRNA gene sequence similarity) and share phenotypic and chemotaxonomic properties. Therefore, it is proposed that these strains are reclassified as members of a new genus, Simplicispira gen. nov., as Simplicispira metamorpha comb. nov. (the type species) and Simplicispira psychrophila comb. nov., respectively.


Subject(s)
Comamonadaceae/classification , Sewage/microbiology , Comamonadaceae/cytology , Comamonadaceae/genetics , Comamonadaceae/physiology , DNA, Ribosomal/chemistry , Industrial Waste , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
9.
Int J Syst Evol Microbiol ; 56(Pt 3): 583-586, 2006 Mar.
Article in English | MEDLINE | ID: mdl-16514031

ABSTRACT

A yellow-pigmented, non-motile, Gram-negative bacterium, designated Fg 69T, was isolated from a sediment sample collected in Chazhma Bay (Sea of Japan). The novel organism grew at 10-35 degrees C, was neutrophilic and required 3-10% NaCl for optimal growth. Strain Fg 69T was able to degrade starch and to hydrolyse gelatin and Tween 80 weakly but not casein or agar. Predominant cellular fatty acids comprised n-C15 and n-C16 branched-chain and straight-chain saturated and unsaturated fatty acids, including iso-C(15:0) (5%), anteiso-C(15:0) (11%), C(15:0) (9%), iso-C(15:1) (5%), iso-C(16:0) (8%), C(16:0) (5%) and C(16:1)omega7 (5%) and iso- and anteiso-branched 2-OH and 3-OH C(15:0) to C(17:0) fatty acids (26 % in total). The G + C content of the DNA was 40.4 mol%. 16S rRNA gene sequence data indicated that strain Fg 69T belonged to the genus Salegentibacter but was distinct from recognized Salegentibacter species (94-95 % sequence similarity). Based on these results, a novel species, Salegentibacter flavus sp. nov., is proposed. The type strain is Fg 69T (= KMM 6000T = CIP 107843T).


Subject(s)
Flavobacteriaceae/classification , Geologic Sediments/microbiology , DNA, Ribosomal/chemistry , Fatty Acids/analysis , Flavobacteriaceae/chemistry , Flavobacteriaceae/genetics , Phenotype , Phylogeny , RNA, Ribosomal, 16S , Sequence Analysis, DNA
10.
Extremophiles ; 10(3): 213-20, 2006 Jun.
Article in English | MEDLINE | ID: mdl-16491340

ABSTRACT

Four new isolates were obtained from denitrifying enrichments with various electron donors using sediment samples from hypersaline soda lakes. Based on 16S rRNA gene analysis and DNA-DNA hybridization results, they were all identified as members of the Gammaproteobacteria closely associated with the Alkalispirillum-Alkalilimnicola group. Two isolates were obtained from samples enriched with nitrate as electron acceptor and H2 or polysulfide as electron donors, and another two strains were obtained with N2O as the electron acceptor and sulfide or acetate as electron donors. All four new isolates, together with the type strains of the genera Alkalispirillum and Alkalilimnicola originally described as obligate aerobes, were capable of anaerobic growth with acetate using either nitrate or N2O as electron acceptors. Their denitrification pathway, however, was disrupted at the level of nitrite. RuBisCO form I gene was detected and sequenced in the new isolates and in Alkalilimnicola halodurans but not in Alkalispirillum mobile. These data, together with the evidence of Oremland et al. (Appl Environ Microbiol 68:4795-4802, 2002) on the potential of Alkalilimnicola sp. MLHE-1 for autotrophic growth with arsenite as electron donor and nitrate as electron acceptor, demonstrate much higher metabolic diversity of this specific group of haloalkaliphilic Gammaproteobacteria than was originally anticipated.


Subject(s)
Carbonates , Ectothiorhodospiraceae/classification , Ectothiorhodospiraceae/metabolism , Fresh Water/chemistry , Fresh Water/microbiology , DNA, Bacterial/genetics , Ectothiorhodospiraceae/genetics , Ectothiorhodospiraceae/isolation & purification , Microscopy, Electron , Molecular Sequence Data , Phylogeny , Ribulose-Bisphosphate Carboxylase/genetics , Ribulose-Bisphosphate Carboxylase/metabolism
11.
Int J Syst Evol Microbiol ; 56(Pt 1): 155-60, 2006 Jan.
Article in English | MEDLINE | ID: mdl-16403881

ABSTRACT

The taxonomic position of three novel, marine, heterotrophic, aerobic, pigmented, gliding bacteria, isolated from the green alga Ulva fenestrata in the Sea of Japan, was determined. 16S rRNA gene sequence analysis revealed that the strains belong to the genus Arenibacter. The results of DNA-DNA hybridization experiments supported by phenotypic and chemotaxonomic data showed that the isolates represent a novel species of the genus Arenibacter, for which the name Arenibacter palladensis sp. nov. is proposed. The type strain is KMM 3961T (= LMG 21972T = CIP 108849T).


Subject(s)
Bacteroidetes/classification , Seawater , Ulva/microbiology , Aerobiosis , Bacteroidetes/genetics , Bacteroidetes/isolation & purification , Japan , Molecular Sequence Data , RNA, Bacterial/genetics , RNA, Ribosomal, 16S/genetics , Sequence Homology, Nucleic Acid , Species Specificity
12.
Int J Syst Evol Microbiol ; 56(Pt 1): 161-7, 2006 Jan.
Article in English | MEDLINE | ID: mdl-16403882

ABSTRACT

Two marine, heterotrophic, aerobic, yellow-pigmented, agarolytic bacterial strains that are motile by means of gliding were isolated from the green alga Acrosiphonia sonderi and from sea water. Comparative 16S rRNA gene sequence analysis revealed an affiliation between the strains studied and the genus Formosa, a member of the family Flavobacteriaceae. The level of sequence similarity between strain KMM 3901T and Formosa algae KMM 3553T was 99.1 %. The results of DNA-DNA hybridization experiments and phenotypic analysis indicated that the strains represent a novel species of the genus Formosa, for which the name Formosa agariphila sp. nov. is proposed, with KMM 3901T (= KCTC 12365T = LMG 23005T = DSM 15362T) as the type strain. The description of the genus Formosa is emended with newly obtained data.


Subject(s)
Chlorophyta/microbiology , Flavobacteriaceae/classification , Chlorophyta/genetics , Flavobacteriaceae/isolation & purification , Flavobacteriaceae/physiology , Korea , Molecular Sequence Data , Oceans and Seas , RNA, Bacterial/genetics , RNA, Ribosomal, 16S/genetics , Sequence Homology, Nucleic Acid , Species Specificity
13.
Int J Syst Evol Microbiol ; 55(Pt 6): 2391-2394, 2005 Nov.
Article in English | MEDLINE | ID: mdl-16280502

ABSTRACT

The taxonomic position of a novel marine, heterotrophic, aerobic, pigmented, non-motile bacterium isolated from sea water was determined. 16S rRNA gene sequence analysis revealed that strain KMM 6143T is a member of the genus Cyclobacterium. The results of DNA-DNA hybridization experiments supported by phenotypic and chemotaxonomic data showed that the isolate represents a novel species of the genus Cyclobacterium, for which the name Cyclobacterium amurskyense sp. nov. is proposed. The type strain is KMM 6143T (=KCTC 12363T=LMG 23026T).


Subject(s)
Cytophagaceae/isolation & purification , RNA, Ribosomal, 16S/analysis , Seawater/microbiology , Cytophagaceae/genetics , DNA, Ribosomal/analysis , Marine Biology , Molecular Sequence Data , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA
14.
Curr Microbiol ; 51(6): 408-12, 2005 Dec.
Article in English | MEDLINE | ID: mdl-16235024

ABSTRACT

A novel heterotrophic, yellow pigmented, aerobic, Gram-negative, nonmotile, oxidase- and catalase-positive bacterium KMM 3,938(T) was isolated from sea water collected in the Sea of Japan, Russia. The strain grew at mesophilic temperature range, and required the presence of NaCl for growth. 16S rRNA gene sequence analysis revealed that strain KMM 3,938(T) is a member of the family Flavobacteriaceae. The predominant fatty acids were C13:0 iso, C14:0 iso, C15:0 iso, C15:0, C15:1Delta6, 3OH-C15:0:3 iso, and 3OH-C15:0. The G + C content of the DNA of KMM 3938(T) was 32.4 mol%. On the basis of phenotypic, chemotaxonomic, genotypic, and phylogenetic characteristics, the novel bacterium was assigned to the genus Polaribacter as Polaribacter butkevichii sp. nov. The type strain is KMM 3938(T )(= KCTC 12100(T) = CCUG 48005(T)).


Subject(s)
Flavobacteriaceae/classification , Seawater/microbiology , Aerobiosis , Base Composition , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Fatty Acids/analysis , Flavobacteriaceae/cytology , Flavobacteriaceae/isolation & purification , Flavobacteriaceae/physiology , Gentian Violet , Growth Substances/pharmacology , Locomotion , Oxidoreductases/analysis , Peroxidase/analysis , Phenazines , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Sequence Homology, Nucleic Acid , Sodium Chloride/pharmacology , Temperature , Water Microbiology
15.
Int J Syst Evol Microbiol ; 55(Pt 5): 1797-1800, 2005 Sep.
Article in English | MEDLINE | ID: mdl-16166668

ABSTRACT

A novel strictly aerobic, heterotrophic, pink-pigmented, non-motile, Gram-negative, oxidase-, catalase-, beta-galactosidase- and alkaline phosphatase-positive marine bacterium, designated strain KMM 6058(T), was isolated from the sea urchin Strongylocentrotus intermedius and studied using a polyphasic taxonomic approach. The G+C content of the DNA of the isolate was 41.3 mol%. The predominant fatty acids were i15:1, i15:0, a15:0 and i17:0 3-OH. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain KMM 6058(T) formed a monophyletic clade with Roseivirga ehrenbergii, with 99% similarity. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, the novel bacterium should be assigned to the genus Roseivirga as Roseivirga echinicomitans sp. nov. The type strain is KMM 6058(T) (=KCTC 12370(T)=LMG 22587(T)).


Subject(s)
Cytophagaceae/classification , Cytophagaceae/isolation & purification , Seawater/microbiology , Strongylocentrotus/microbiology , Animals , Base Composition , Cytophagaceae/chemistry , Cytophagaceae/genetics , DNA, Bacterial/analysis , Fatty Acids/analysis , Genes, rRNA , Genotype , Molecular Sequence Data , Phenotype , Phylogeny , RNA, Ribosomal, 16S/genetics
16.
Int J Syst Evol Microbiol ; 55(Pt 5): 2159-2165, 2005 Sep.
Article in English | MEDLINE | ID: mdl-16166725

ABSTRACT

A moderately thermophilic, anaerobic, chemolithoheterotrophic, sulfate-reducing bacterium, strain CO-1-SRB(T), was isolated from sludge from an anaerobic bioreactor treating paper mill wastewater. Cells were Gram-positive, motile, spore-forming rods. The temperature range for growth was 30-68 degrees C, with an optimum at 55 degrees C. The NaCl concentration range for growth was 0-17 g l(-1); there was no change in growth rate until the NaCl concentration reached 8 g l(-1). The pH range for growth was 6.0-8.0, with an optimum of 6.8-7.2. The bacterium could grow with 100% CO in the gas phase. With sulfate, CO was converted to H(2) and CO(2) and part of the H(2) was used for sulfate reduction; without sulfate, CO was completely converted to H(2) and CO(2). With sulfate, strain CO-1-SRB(T) utilized H(2)/CO(2), pyruvate, glucose, fructose, maltose, lactate, serine, alanine, ethanol and glycerol. The strain fermented pyruvate, lactate, glucose and fructose. Yeast extract was necessary for growth. Sulfate, thiosulfate and sulfite were used as electron acceptors, whereas elemental sulfur and nitrate were not. A phylogenetic analysis of 16S rRNA gene sequences placed strain CO-1-SRB(T) in the genus Desulfotomaculum, closely resembling Desulfotomaculum nigrificans DSM 574(T) and Desulfotomaculum sp. RHT-3 (99 and 100% similarity, respectively). However, the latter strains were completely inhibited above 20 and 50% CO in the gas phase, respectively, and were unable to ferment CO, lactate or glucose in the absence of sulfate. DNA-DNA hybridization of strain CO-1-SRB(T) with D. nigrificans and Desulfotomaculum sp. RHT-3 showed 53 and 60% relatedness, respectively. On the basis of phylogenetic and physiological features, it is suggested that strain CO-1-SRB(T) represents a novel species within the genus Desulfotomaculum, for which the name Desulfotomaculum carboxydivorans is proposed. This is the first description of a sulfate-reducing micro-organism that is capable of growth under an atmosphere of pure CO with and without sulfate. The type strain is CO-1-SRB(T) (=DSM 14880(T)=VKM B-2319(T)).


Subject(s)
Carbon Monoxide/metabolism , Desulfotomaculum/classification , Desulfotomaculum/growth & development , Sewage/microbiology , Sulfates/metabolism , Anaerobiosis , Bioreactors , DNA, Bacterial/analysis , DNA, Ribosomal/analysis , Desulfotomaculum/genetics , Desulfotomaculum/isolation & purification , Genes, rRNA , Molecular Sequence Data , Oxidation-Reduction , Paper , Phenotype , Phylogeny , RNA, Ribosomal, 16S/genetics , Refuse Disposal/methods , Sequence Analysis, DNA , Sulfur-Reducing Bacteria/classification , Sulfur-Reducing Bacteria/genetics , Sulfur-Reducing Bacteria/isolation & purification
17.
Int J Syst Evol Microbiol ; 55(Pt 5): 2203-2207, 2005 Sep.
Article in English | MEDLINE | ID: mdl-16166733

ABSTRACT

One whitish and four pinkish strains of Gram-negative, non-motile, aerobic bacteria were isolated from sea-water and sediment samples collected in Chazhma Bay (Sea of Japan, Pacific Ocean). Analysis of 16S rRNA gene sequences revealed that these strains belonged to the 'Alphaproteobacteria', having highest sequence similarity of about 94-97% with species of the genus Loktanella. None of the strains degraded gelatin, casein, chitin, agar, DNA or starch and they had limited ability to utilize carbon sources. The four pinkish strains, Fg36(T), Fg1, Fg116 and Fg117, degraded Tween 80. Sea-water strain R10SW5(T) grew at 3-6% NaCl and a temperature range of 8-35 degrees C, whilst strains Fg36(T), Fg1, Fg116 and Fg117 grew at NaCl concentrations of 1-12% and a temperature range of 4-35 degrees C. Phosphatidylglycerol (58/79%), diphosphatidylglycerol (11/6%) and phosphatidylcholine (28/22%) were the major phospholipids. The predominant fatty acids were 16:0 (12.2/8.6%) and 18:1omega7 (76.6/68.4%). The DNA G+C content of strain R10SW5(T) was 59.1 mol% and those of the four pinkish strains ranged from 60.5 to 61.8 mol%. Based on the results of phenotypic, genotypic, chemotaxonomic and phylogenetic investigation, two novel species, Loktanella agnita sp. nov. and Loktanella rosea sp. nov., are proposed. The type strains are R10SW5(T) (=KMM 3788(T)=CIP 107883(T)) and Fg36(T) (=KMM 6003(T)=CIP 107851(T)=LMG 22534(T)), respectively.


Subject(s)
Geologic Sediments/microbiology , Rhodobacteraceae/classification , Seawater/microbiology , DNA, Bacterial/analysis , DNA, Ribosomal/analysis , Genes, rRNA , Genotype , Molecular Sequence Data , Pacific Ocean , Phenotype , Phylogeny , RNA, Ribosomal, 16S/genetics , Rhodobacteraceae/chemistry , Rhodobacteraceae/genetics , Rhodobacteraceae/isolation & purification , Sequence Analysis, DNA , Species Specificity
18.
J Gen Appl Microbiol ; 51(2): 65-71, 2005 Apr.
Article in English | MEDLINE | ID: mdl-15942867

ABSTRACT

Two Pseudomonas-like yellow-orange-pigmented non-fluorescent denitrifying strains KMM 235 and KMM 1447T were isolated from marine ascidian specimens and investigated by a polyphasic approach to clarify their taxonomic status. On the basis of 16S rDNA gene sequence data the new isolates clustered with the Pseudomonas stutzeri species group with sequence similarities of >98%. The results of DNA-DNA hybridization and biochemical characterization showed genetic and phenotypic distinction between strains KMM 235 and KMM 1447T and from the other validly described Pseudomonas species. Strain KMM 235 was found to be closely related to the type strain of Pseudomonas stutzeri in their phenotypic and genetic characteristics and represented, probably, a new P. stutzeri genomovar. It is proposed that strain KMM 1447T be classified as a new species of the genus Pseudomonas, Pseudomonas xanthomarina sp. nov., with the type strain KMM 1447T (=JCM 12468T=NRIC 0617T=CCUG 46543T).


Subject(s)
Pseudomonas/isolation & purification , Urochordata/microbiology , Animals , Base Sequence , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , Fatty Acids/analysis , Nucleic Acid Hybridization , Phylogeny , Pseudomonas/classification , Pseudomonas/genetics , Pseudomonas/metabolism , RNA, Ribosomal, 16S/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Alignment , Sequence Analysis, DNA
19.
Int J Syst Evol Microbiol ; 55(Pt 3): 1001-1006, 2005 May.
Article in English | MEDLINE | ID: mdl-15879225

ABSTRACT

A novel alkaliphilic, sulfate-reducing bacterium was isolated from a syntrophic acetate-decomposing community enriched from samples of the soda lake Khadin, Tuva, Russia; the isolate was designated strain Z-7999(T). Cells of strain Z-7999(T) were vibrioid, Gram-negative, 0.4-0.5 x 1.0-2.5 microm and motile by means of a polar flagellum. The temperature range for growth was 15-40 degrees C, with an optimum of 35-38 degrees C. The pH range for growth was 6.7-10.3, with an optimum of pH 8.0-9.0. The NaCl concentration range for growth was 1-80 g l(-1). The novel isolate was obligately anaerobic, was alkaliphilic with a broad pH range and had an obligate requirement for carbonate ions in the growth medium. In the presence of sulfate as electron acceptor, it grew with hydrogen, formate and lactate. It was not able to ferment sugars, organic acids, amino acids or peptides. During growth on formate, strain Z-7999(T) reduced sulfite and thiosulfate to sulfide. It was able to grow lithoheterotrophically with sulfate and formate when acetate was added as a carbon source for biosynthesis of biomass. The G + C content of the genomic DNA of strain Z-7999(T) was 56.5 mol%. Results of comparative 16S rRNA gene sequence analyses revealed that strain Z-7999(T) was part of the delta-Proteobacteria and clustered with other members of the genus Desulfonatronum (similarity values of 95.2 and 95.3 % to Desulfonatronum lacustre and Desulfonatronum thiodismutans, respectively). DNA-DNA hybridization with D. lacustre was 37 %. On the basis of physiological and phylogenetic data, it is proposed that strain Z-7999(T) (= DSM 16749(T) = VKM B-2329(T)) should be placed in the genus Desulfonatronum as a representative of a novel species, Desulfonatronum cooperativum sp. nov.


Subject(s)
Acetic Acid/metabolism , Deltaproteobacteria/classification , Deltaproteobacteria/isolation & purification , Hydrogen/metabolism , Sulfates/metabolism , Water Microbiology , Amino Acids/metabolism , Base Composition , Carbohydrate Metabolism , Carboxylic Acids/metabolism , Culture Media , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Deltaproteobacteria/cytology , Deltaproteobacteria/physiology , Flagella/physiology , Formates/metabolism , Genes, rRNA , Gram-Negative Anaerobic Bacteria/classification , Gram-Negative Anaerobic Bacteria/isolation & purification , Gram-Negative Anaerobic Bacteria/metabolism , Gram-Negative Anaerobic Bacteria/physiology , Hydrogen-Ion Concentration , Molecular Sequence Data , Movement , Nucleic Acid Hybridization , Oxidation-Reduction , Phylogeny , Proteins/metabolism , RNA, Bacterial/genetics , RNA, Ribosomal, 16S/genetics , Russia , Sequence Analysis, DNA , Sulfur Compounds/metabolism , Temperature
20.
Int J Syst Evol Microbiol ; 55(Pt 3): 1065-1068, 2005 May.
Article in English | MEDLINE | ID: mdl-15879234

ABSTRACT

On the basis of phenotypic, genotypic characteristics and analysis of 16S rRNA gene sequences, a novel species belonging to the genus Alteromonas is described. A non-pigmented, motile, Gram-negative bacterium designated R10SW13(T) was isolated from sea water samples collected in Chazhma Bay (Sea of Japan, Pacific Ocean). The novel organism mainly grew between 4 degrees C and 37 degrees C, was neutrophilic and slightly halophilic, tolerating up to 10 % NaCl. Strain R10SW13(T) was haemolytic and was able to degrade starch and Tween 80 and to degrade gelatin and agar weakly, but did not degrade casein. Phosphatidylethanolamine (44.3 +/- 0.9 %) and phosphatidylglycerol (55.7 +/ -0.9 %) were the predominant phospholipids. The major fatty acids formed were typical for the genus Alteromonas, including 16 : 0, 16 : 1omega-7 and 18 : 1omega-7. The G + C content of the DNA was 43.4 mol%. DNA-DNA hybridization experiments showed 38-53 % binding with the DNAs of type strains of phylogenetically related species of the genus Alteromonas, namely: Alteromonas macleodii, Alteromonas marina, Alteromonas stellipolaris, Alteromonas litorea, 'Alteromonas macleodii subsp. fijiensis' and 'Alteromonas infernus'. Based on these results, a novel species, Alteromonas addita sp. nov., is proposed, with strain R10SW13(T) (=KMM 3600(T) = KCTC 12195(T) = LMG 22532(T)) as the type strain.


Subject(s)
Alteromonas/classification , Alteromonas/isolation & purification , Seawater/microbiology , Agar/metabolism , Alteromonas/cytology , Base Composition , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Fatty Acids/analysis , Gelatin/metabolism , Genes, rRNA , Gentian Violet , Growth Inhibitors/pharmacology , Hemolysis , Hydrogen-Ion Concentration , Japan , Molecular Sequence Data , Movement , Nucleic Acid Hybridization , Pacific Ocean , Phenazines , Phospholipids/analysis , Phylogeny , Pigments, Biological , Polysorbates/metabolism , RNA, Bacterial/genetics , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Sodium Chloride/pharmacology , Temperature , Water Microbiology
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