scholarly journals Desulfuromonas carbonis sp. nov., an Fe(III)-, S0- and Mn(IV)-reducing bacterium isolated from an active coalbed methane gas well

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1686-1693 ◽  
Author(s):  
Thuy T. An ◽  
Flynn W. Picardal
Keyword(s):  
Coalbed Methane ◽  
Iron Reduction ◽  
Sequence Similarity ◽  
Coal Bed ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Gas Well ◽  
Content Type ◽  
Methane Gas ◽  
Link Type

A novel, mesophilic, obligately anaerobic, acetate-oxidizing, dissimilatory iron-, sulfur-, and manganese-reducing bacterium, designated strain ICBMT, was obtained from an active, coalbed methane gas well in Indiana, USA. Strain ICBMT was a Gram-stain-negative, non-spore-forming, rod-shaped, non-motile bacterium that was rich in c-type cytochromes and formed red colonies in solid medium. Strain ICBMT conserved energy to support growth from the oxidation of acetate, propionate, pyruvate, malate, fumarate, succinate and dl-lactate, concomitant with dissimilatory iron reduction. Strain ICBMT fermented fumarate yielding succinate and acetate. Strain ICBMT was able to grow in the temperature range of 10 °C to 37 °C, NaCl concentration range of 0 to 1.2 M, and pH range of 6.5 to 8.0. The physiological characteristics of strain ICBMT indicated that it belongs to the Desulfuromonas cluster. The G+C content of its genomic DNA was 61.2 mol%. The predominant cellular fatty acids were C16 : 0 (39.3 %), C16 : 1ω7c and/or iso-C15 : 0 2-OH (36.6 %). The closest cultured phylogenetic relative of strain ICBMT was Desulfuromonas michiganensis BB1T with only 95 % 16S rRNA gene sequence similarity. This confirmed that strain ICBMT is affiliated with the genus Desulfuromonas . On the basis of phenotypic and genotypic differences between strain ICBMT and other taxa of the genus Desulfuromonas , strain ICBMT represents a novel species for which the name Desulfuromonas carbonis sp. nov. is proposed (type strain ICBMT = DSM 29759T = JCM 30471T). Strain ICBMT is the first Fe(III)-, S0-, and Mn(IV)-reducing bacterium that was isolated from a coal bed.

scholarly journals Methanosarcina spelaei sp. nov., a methanogenic archaeon isolated from a floating biofilm of a subsurface sulphurous lake

2014 ◽  
Vol 64 (Pt_10) ◽  
pp. 3478-3484 ◽  
Author(s):  
Lars Ganzert ◽  
Janosch Schirmack ◽  
Mashal Alawi ◽  
Kai Mangelsdorf ◽  
Wolfgang Sand ◽  
...  
Keyword(s):  
Type Species ◽  
Dimethyl Sulfide ◽  
Membrane Lipids ◽  
Sequence Similarity ◽  
Optimal Growth ◽  
Methanosarcina Barkeri ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Content Type ◽  
Link Type

A novel methanogenic archaeon, strain MC-15T, was isolated from a floating biofilm on a sulphurous subsurface lake in Movile Cave (Mangalia, Romania). Cells were non-motile sarcina-like cocci with a diameter of 2–4 µm, occurring in aggregates. The strain was able to grow autotrophically on H2/CO2. Additionally, acetate, methanol, monomethylamine, dimethylamine and trimethylamine were utilized, but not formate or dimethyl sulfide. Trypticase peptone and yeast extract were not required for growth. Optimal growth was observed at 33 °C, pH 6.5 and a salt concentration of 0.05 M NaCl. The predominant membrane lipids of MC-15T were archaeol and hydroxyarchaeol phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylinositol as well as hydroxyarchaeol phosphatidylserine and archaeol glycosaminyl phosphatidylinositol. The closely related species, Methanosarcina vacuolata and Methanosarcina horonobensis, had a similar composition of major membrane lipids to strain MC-15T. The 16S rRNA gene sequence of strain MC-15T was similar to those of Methanosarcina vacuolata DSM 1232T (sequence similarity 99.3 %), Methanosarcina horonobensis HB-1T (98.8 %), Methanosarcina barkeri DSM 800T (98.7 %) and Methanosarcina siciliae T4/MT (98.4 %). DNA–DNA hybridization revealed 43.3 % relatedness between strain MC-15T and Methanosarcina vacuolata DSM 1232T. The G+C content of the genomic DNA was 39.0 mol%. Based on physiological, phenotypic and genotypic differences, strain MC-15T represents a novel species of the genus Methanosarcina , for which the name Methanosarcina spelaei sp. nov. is proposed. The type strain is MC-15T ( = DSM 26047T = JCM 18469T).

scholarly journals Paludibaculum fermentans gen. nov., sp. nov., a facultative anaerobe capable of dissimilatory iron reduction from subdivision 3 of the Acidobacteria

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2857-2864 ◽  
Author(s):  
Irina S. Kulichevskaya ◽  
Natalia E. Suzina ◽  
W. Irene C. Rijpstra ◽  
Jaap S. Sinninghe Damsté ◽  
Svetlana N. Dedysh
Keyword(s):  
Type Species ◽  
Iron Reduction ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Anoxic Conditions ◽  
Link Type ◽  
Dissimilatory Iron Reduction ◽  
Novel Genus And Species ◽  
Northern Russia

A facultatively anaerobic, non-pigmented, non-spore-forming bacterium was isolated from a littoral wetland of a boreal lake located on Valaam Island, northern Russia, and designated strain P105T. Cells of this isolate were Gram-negative, non-motile rods coated by S-layers with p2 lattice symmetry. Sugars were the preferred growth substrates. Under anoxic conditions, strain P105T was capable of fermentation and dissimilatory Fe(III) reduction. End products of fermentation were acetate, propionate and H2. Strain P105T was a mildly acidophilic, mesophilic organism, capable of growth at pH 4.0–7.2 (optimum pH 5.5–6.0) and at 4–35 °C (optimum at 20–28 °C). The major fatty acids were iso-C15 : 0 and C16 : 1ω7c; the cells also contained significant amounts of 13,16-dimethyl octacosanedioic acid (isodiabolic acid). The major polar lipids were phosphocholine and phosphoethanolamine; the quinone was MK-8. The G+C content of the DNA was 60.5 mol%. 16S rRNA gene sequence analysis showed that strain P105T belongs to subdivision 3 of the Acidobacteria and is only distantly related (90 % sequence similarity) to the only currently characterized member of this subdivision, Bryobacter aggregatus . The novel isolate differs from Bryobacter aggregatus in its cell morphology and ability to grow under anoxic conditions and in the presence of iron- and nitrate-reducing capabilities as well as quinone and polar lipid compositions. These differences suggest that strain P105T represents a novel genus and species, for which the name Paludibaculum fermentans gen. nov., sp. nov., is proposed. The type strain of Paludibaculum fermentans is P105T ( = DSM 26340T = VKM B-2878T).

scholarly journals Bacillus luteus sp. nov., isolated from soil

2014 ◽  
Vol 64 (Pt_5) ◽  
pp. 1580-1586 ◽  
Author(s):  
Y. Subhash ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Bacterial Strains ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type

Two bacterial strains (JC167T and JC168) were isolated from a soil sample collected from Mandpam, Tamilnadu, India. Colonies of both strains were orange and cells Gram-stain-positive. Cells were small rods, and formed terminal endospores of ellipsoidal to oval shape. Both strains were positive for catalase, oxidase and hydrolysis of starch/gelatin, and negative for chitin hydrolysis, H2S production, indole production and nitrate reduction activity. Major fatty acids of both strains (>5 %) were anteiso-C15 : 0, iso-C16 : 0, iso-C15 : 0, anteiso-C17 : 0, iso-C14 : 0 and C16 : 0 with minor (<5 but >1 %) amounts of iso-C17 : 0, anteiso-C17 : 0 B/iso-C17 : 0 I and C16 : 1ω11c. Diphosphatydilglycerol, phosphatidylethanolamine and phosphatidylglycerol were the major polar lipids of both strains. Cell wall amino acids were l-alanine, d-alanine, d-glutamic acid and meso-diaminopimelic acid. β-Carotene and five unidentified carotenoids were present in both strains. Mean genomic DNA G+C content was 53.4±1 mol% and the two strains were closely related (mean DNA–DNA hybridization >90 %). 16S rRNA gene sequence comparisons of both strains indicated that they represent species of the genus Bacillus within the family Bacillaceae of the phylum Firmicutes . Both strains had a sequence similarity of 97.6 % with Bacillus saliphilus 6AGT and <96.8 % with other members of the genus Bacillus . Sequence similarity between strain JC167T and 168 was 100 %. Strain JC167T showed 25.8±1 % reassociation (based on DNA–DNA hybridization) with B. saliphilus DSM 15402T ( = 6AGT). Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of strain JC167T as a representative of a novel species of the genus Bacillus , for which the name Bacillus luteus sp. nov. is proposed. The type strain is JC167T ( = KCTC 33100T = LMG 27257T).

Pontibacter ruber sp. nov. and Pontibacter deserti sp. nov., isolated from the desert

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 1006-1011 ◽  
Author(s):  
Y. Subhash ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Major Polar Lipid ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Hydrolysed Casein

Two strains of bacteria, JC213T and JC215T, were isolated from desert soil. Colonies were red to pink and cells Gram-stain-negative. Both strains were oxidase- and catalase-positive and hydrolysed casein. In both strains, phosphatidylethanolamine was the major polar lipid, iso-C15 : 0 was the major fatty acid and the bacteriohopane derivative, BHD1, was the major hopanoid. The genomic DNA G+C contents of strains JC213T and JC215T were 52.7 and 46.3 mol%, respectively. 16S rRNA gene sequence comparisons indicated that both strains belong to the genus Pontibacter within the family Cytophagaceae and the phylum Bacteroidetes . Strain JC213T showed the highest sequence similarity to Pontibacter populi HLY7-15T (96.6 %) and with other species of the genus Pontibacter sequence similarity was less than 96 %. Strain JC215T exhibited highest sequence similarity with Pontibacter lucknowensis DM9T (95.1 %) and shared 95 % or less sequence similarity with other species of the genus Pontibacter . The sequence similarity between strains JC213T and JC215T was 95.8 %. Distinct morphological, physiological and genotypic differences from previously described taxa support JC213T and JC215T being representatives of two novel species of the genus Pontibacter , for which the names Pontibacter ruber sp. nov. and Pontibacter deserti sp. nov. are proposed and the type strains are JC213T ( = KCTC 32442T = LMG 27669T) and JC215T ( = KCTC 32443T = LMG 27670T), respectively.

Metallibacterium scheffleri gen. nov., sp. nov., an alkalinizing gammaproteobacterium isolated from an acidic biofilm

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1499-1504 ◽  
Author(s):  
Sibylle Ziegler ◽  
Barbara Waidner ◽  
Takashi Itoh ◽  
Peter Schumann ◽  
Stefan Spring ◽  
...  
Keyword(s):  
Type Species ◽  
Iron Reduction ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Growth Optimum ◽  
Acid Tolerant ◽  
Type Strains ◽  
Physiological And Biochemical

A Gram-stain-negative, non-motile, facultatively anaerobic, acid-tolerant rod, designated strain DKE6T, was isolated from an acidic biofilm (pH 2.5) harvested in the pyrite mine Drei Kronen und Ehrt in Germany. The isolate grew optimally at pH 5.5, between 25 and 30 °C and only with casein as the carbon and energy source; although a variety of sugars were tested as growth substrates, none supported growth of the isolate. During casein consumption, strain DKE6T produced ammonium, which led to an alkalinization of the medium. This is a possible strategy to raise the pH in the direct vicinity of the cell and hence modulate the pH towards the growth optimum. The predominant fatty acids (>5 %) were iso-C11 : 0 3-OH, iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1ω9c. The DNA G+C content was 66.6 %. Strain DKE6T was not able to oxidize iron or thiosulfate. Iron reduction was detected. The isolate showed 93.3 % 16S rRNA gene sequence similarity to the most closely related cultivable strain, Dokdonella koreensis DS-123T, but <93.2 % sequence similarity with other type strains of closely related type species of the Gammaproteobacteria . On the basis of physiological and biochemical data, the isolate is considered to represent a novel species of a new genus in the class Gammaproteobacteria , for which we propose the name Metallibacterium scheffleri gen. nov., sp. nov. The type strain of the type species is DKE6T ( = DSM 24874T = JCM 17596T).

Salinimicrobium sediminis sp. nov., isolated from a deep-sea sediment

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 984-988 ◽  
Author(s):  
Y. Subhash ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Major Polar Lipid ◽  
Sequence Comparisons ◽  
Content Type ◽  
Deep Sea Sediment ◽  
Link Type

Strain JC207T was isolated from a deep (265 m) sea sediment, and appeared as dark yellow colonies on agar plates with cells staining Gram-negative. Catalase, oxidase and caseinase were positive, while chitinase, gelatinase and amylase were negative. Major (>5 %) fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 1ω9c, iso-C16 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH, iso-C14 : 0 and iso-C15 : 1G. Strain JC207T contained phosphatidylethanolamine as the major polar lipid, with minor amounts of five unidentified lipids. A bacterial hopane derivative, diplopterol and adenosylhopane were the major hopanoids. Genomic DNA G+C content was 47.5 mol%. 16S rRNA gene sequence comparisons indicated that strain JC207T represented a member of the genus Salinimicrobium within the family Flavobacteriaceae of the phylum Bacteroidetes . Strain JC207T had sequence similarity with Salinimicrobium terrae YIM-C338T (98 %), Salinimicrobium xinjiangense BH206T (97.6 %) and other members of the genus Salinimicrobium (<96.8 %). However, strain JC207T showed an average of 23.6±4 and 37±4 relatedness (based on DNA–DNA hybridization) with Salinimicrobium terrae CGMCC 1.6308T ( = YIM-C338T) and Salinimicrobium xinjiangense KCTC 12883T ( = BH206T), respectively. Morphological, physiological and genotypic differences from the previously described taxa support the classification of strain JC207T as a representative of a novel species in the genus Salinimicrobium , for which the name Salinimicrobium sediminis sp. nov. is proposed. The type strain is JC207T ( = KCTC 32444T = CGMCC 1.12641T).

Listeria weihenstephanensis sp. nov., isolated from the water plant Lemna trisulca taken from a freshwater pond

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 641-647 ◽  
Author(s):  
Evi Lang Halter ◽  
Klaus Neuhaus ◽  
Siegfried Scherer
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Position ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Content Type ◽  
Link Type ◽  
Freshwater Pond ◽  
Water Plant

The phylogenetic position and phenotypic characteristics of two non-spore-forming bacilli similar to members of the genus Listeria were studied. The Gram-reaction-positive, slightly motile, facultatively anaerobic strains were isolated from the water plant Lemna trisulca sampled from a freshwater pond in Bavaria, Germany. Although no identification was possible employing the API Listeria test (bioMérieux), 16S rRNA sequence analysis confirmed a close phylogenetic similarity to Listeria rocourtiae DSM 22097T (99.0 % sequence similarity) and a more distant relationship to other Listeria species (96.0 % to Listeria monocytogenes DSM 20600T and 95.0 % similarity to Listeria grayi DSM 20601T). DNA–DNA hybridization analysis between the isolates and Listeria rocourtiae DSM 22097T yielded a similarity of 22.5 %. Analysis of partial sequences of sigB, prs, recA and HSP60 were studied and compared with those of other members of the genus Listeria and Brochothrix thermosphacta DSM 20171T supporting the relationships indicated by 16S rRNA gene sequences. The studied isolates were non-haemolytic and were not associated with cases of human or animal disease. While the results demonstrate that the strains belong to the genus Listeria , phenotypic and genotypic differences from Listeria rocourtiae DSM 22097T suggest that the strains represent a novel species for which the name Listeria weihenstephanensis sp. nov. is proposed; the type strain is WS 4560T ( = DSM 24698T = LMG 26374T), with WS 4615 ( = DSM 24699 = LMG 26375) as a second strain of the species.

Falsirhodobacter halotolerans gen. nov., sp. nov., isolated from dry soils of a solar saltern

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2132-2137 ◽  
Author(s):  
Y. Subhash ◽  
L. Tushar ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
Sequence Similarity ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Bacterial Strains ◽  
Unidentified Phospholipid ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
The 16S Rrna Gene

Two bacterial strains (JA744T and JA745) were isolated from dry soil samples collected from solar salterns at Humma, Odisha, India. Both strains were Gram-stain-negative, catalase- and oxidase-positive, motile rods. Major fatty acids in both strains included C18 : 1ω7c, C18 : 0 and C16 : 0, while minor amounts of C10 : 0 3-OH, C12 : 0, C12 : 0 3-OH, C14 : 0 and C16 : 0 were also present. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, an unidentified glycolipid, five unidentified lipids, an unidentified aminolipid and an unidentified phospholipid made up the polar lipids of both strains. Both strains had bacteriohopane derivatives (BHD1,2) and diploptene as major hopanoids. Mean genomic DNA G+C content was 75±1 mol% and the two strains were closely related (mean DNA–DNA hybridization >90 %). Phylogenetic analysis based on the 16S rRNA gene sequence showed that the two strains clustered with species of the genus Rhodobacter belonging to the family Rhodobacteraceae of the class Alphaproteobacteria . The highest sequence similarity was observed with Rhodobacter sphaeroides ATH2.4.1T (96 %) and other members of the genera Rhodobacter and Pseudorhodobacter (<96 %). However, the two strains were positioned distinctly outside the group formed by the other genera of the family Rhodobacteraceae . Distinct morphological, physiological and genotypic differences from previously described taxa support the classification of these isolates as representatives of a novel species in a new genus, for which the name Falsirhodobacter halotolerans gen. nov., sp. nov. is proposed. The type strain of Falsirhodobacter halotolerans is JA744T ( = KCTC 32158T  = NBRC 108897T).

scholarly journals Streptococcus moroccensis sp. nov. and Streptococcus rifensis sp. nov., isolated from raw camel milk

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2480-2485 ◽  
Author(s):  
Zaina Kadri ◽  
Mohamed Amar ◽  
Mouna Ouadghiri ◽  
Margo Cnockaert ◽  
Maarten Aerts ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Camel Milk ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Biochemical Tests ◽  
Content Type ◽  
Link Type

Two catalase- and oxidase-negative Streptococcus -like strains, LMG 27682T and LMG 27684T, were isolated from raw camel milk in Morocco. Comparative 16S rRNA gene sequencing assigned these bacteria to the genus Streptococcus with Streptococcus rupicaprae 2777-2-07T as their closest phylogenetic neighbour (95.9 % and 95.7 % similarity, respectively). 16S rRNA gene sequence similarity between the two strains was 96.7 %. Although strains LMG 27682T and LMG 27684T shared a DNA–DNA hybridization value that corresponded to the threshold level for species delineation (68 %), the two strains could be distinguished by multiple biochemical tests, sequence analysis of the phenylalanyl-tRNA synthase (pheS), RNA polymerase (rpoA) and ATP synthase (atpA) genes and by their MALDI-TOF MS profiles. On the basis of these considerable phenotypic and genotypic differences, we propose to classify both strains as novel species of the genus Streptococcus , for which the names Streptococcus moroccensis sp. nov. (type strain, LMG 27682T = CCMM B831T) and Streptococcus rifensis sp. nov. (type strain, LMG 27684T = CCMM B833T) are proposed.

scholarly journals Sphingopyxis contaminans sp. nov., isolated from a contaminated Petri dish

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2238-2243 ◽  
Author(s):  
Y. Subhash ◽  
Ch. Sasikala ◽  
Ch. V. Ramana
Keyword(s):  
Type Species ◽  
Sequence Similarity ◽  
Petri Dish ◽  
Rrna Gene ◽  
Genotypic Differences ◽  
Yellow Colour ◽  
Content Type ◽  
Link Type ◽  
The Family

Strain JC216T was isolated from a contaminated Petri dish. Colonies were of pale yellow colour and cells were Gram-stain-negative, oxidase-positive and catalase-positive. Chitin, starch and gelatin were not hydrolysed. Strain JC216T contained C18 : 1ω7c/C18 : 1ω6c, C16 : 1ω7c/C16 : 1ω6c, C14 : 0 2-OH and C16 : 0 as the major (≥8 %) fatty acids with minor amounts of C12 : 0, C15 : 0 2-OH, C16 : 0 2-OH, C16  : 1 2-OH, C17 : 1ω6c, C17 : 1ω8c and C17 : 1ω9c. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and sphingoglycolipid were the major polar lipids. Minor amounts of unidentified amino lipids and unidentified lipids were also detected. The major hopanoids identified were bacterial hopane derivatives and diplopterol. Minor amounts of diploptene and an unidentified hopanoid were also present. Spermidine was the major polyamine with minor amounts of sym-homospermidine and putrescine. N-Acetylglucosamine and fructose were identified as major cell-wall sugars along with minor amounts of mannose and galactose. The genomic DNA G+C content was 55 mol%. Comparisons of the16S rRNA gene sequence indicated that strain JC216T represents a member of the genus Sphingopyxis in the family Sphingomonadaceae within the class Alphaproteobacteria . Strain JC216T had a sequence similarity of 97.28 % with Sphingopyxis wooponensis 03SU3-PT and <96.71 % with other members of the family Sphingomonadaceae . Furthermore, strain JC216T had 33±1 % relatedness (based on DNA–DNA hybridization) with S. wooponensis KCTC 23340T ( = 03SU3-PT). Distinct morphological, physiological and genotypic differences from the previously described taxa support the classification of strain JC216T as a representative of a novel species in the genus Sphingopyxis , for which the name Sphingopyxis contaminans sp. nov. is proposed. The type strain is JC216T ( = KCTC 32445T = LMG 27671T).

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