scholarly journals Thermosipho atlanticus sp. nov., a novel member of the Thermotogales isolated from a Mid-Atlantic Ridge hydrothermal vent

2004 ◽  
Vol 54 (6) ◽  
pp. 1953-1957 ◽  
Author(s):  
Laurent Urios ◽  
Valérie Cueff-Gauchard ◽  
Patricia Pignet ◽  
Anne Postec ◽  
Marie-Laure Fardeau ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Yeast Extract ◽  
Hydrothermal Vent ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Fermentation Products ◽  
Mid Atlantic Ridge

A novel anaerobic, thermophilic and heterotrophic bacterium, designated strain DV1140T, was isolated from a deep-sea hydrothermal vent sample from the Mid-Atlantic Ridge. The cells were non-motile straight rods, 1·8 μm long and 0·4 μm wide, surrounded by an outer sheath-like structure (toga). They grew at 45–80 °C (optimum 65 °C), pH 5·0–9·0 (optimum pH 6·0) and at sea salt concentrations of 20–60 g l−1 (optimum 30 g l−1). Strain DV1140T was able to ferment yeast extract, peptone, brain heart infusion, gelatin, starch, galactose, arabinose, glucose, trehalose and cellobiose. The fermentation products identified on glucose in the presence of yeast extract and peptone were acetate, isovalerate and hydrogen. The G+C content of the genomic DNA was 33 mol%. Phylogenetic analysis of the 16S rRNA gene sequence (GenBank accession number AJ577471) located the strain within the genus Thermosipho in the bacterial domain. On the basis of 16S rRNA gene sequence comparisons, and physiological and biochemical characteristics, the isolate represents a novel species, for which the name Thermosipho atlanticus sp. nov. is proposed. The type strain is DV1140T (=CIP 108053T=DSM 15807T).

Anaerosalibacter bizertensis gen. nov., sp. nov., a halotolerant bacterium isolated from sludge

2012 ◽  
Vol 62 (Pt_10) ◽  
pp. 2469-2474 ◽  
Author(s):  
Raja Rezgui ◽  
Abderrazak Maaroufi ◽  
Marie-Laure Fardeau ◽  
Zouhaier Ben Ali Gam ◽  
Jean-Luc Cayol ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Yeast Extract ◽  
Type Species ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

A strictly anaerobic, halotolerant and thermotolerant strain, designated C5BELT, was isolated in north Tunisia from storage tanks holding waste generated by the recycling of discarded motor oils. Cells of strain C5BELT were Gram-stain-positive, motile by laterally inserted flagella, straight, and spore-forming. Their two major fatty acids were iso-C15 : 0 and iso-C15 : 0 dimethyl acetal. Growth was observed at temperatures of 25–55 °C (optimum, 40 °C) and at pH 6–9 (optimum, pH 7.5). The salinity range for growth was 0–100 g l−1 NaCl (optimum, 5 g l−1). Yeast extract was required for growth. Strain C5BELT was heterotrophic, able to use glucose, pyruvate, succinate, yeast extract, bio-trypticase and peptone, but unable to grow on Casamino acids. Sulfate, thiosulfate, sulfite, elemental sulfur, fumarate, nitrate and nitrite were not reduced. The DNA G+C content of strain C5BELT was 31.1 mol%. 16S rRNA gene sequence analysis indicated that strain C5BELT was a member of the family Clostridiaceae , class Clostridia , phylum Firmicutes and was most closely related to Sporanaerobacter acetigenes Lup33T ( = DSM 13106T) (92.4 % similarity). On the basis of 16S rRNA gene sequence comparisons and physiological characteristics, strain C5BELT can be classified as a novel species in a new genus, for which the name Anaerosalibacter bizertensis gen. nov., sp. nov. is proposed. The type strain of the type species is C5BELT ( = DSM 23801T = JCM 17239T).

Thermicanus aegyptius gen. nov., sp. nov., Isolated from Oxic Soil, a Fermentative Microaerophile That Grows Commensally with the Thermophilic Acetogen Moorella thermoacetica

1999 ◽  
Vol 65 (11) ◽  
pp. 5124-5133 ◽  
Author(s):  
Anita S. Gößner ◽  
Richard Devereux ◽  
Nadja Ohnemüller ◽  
Georg Acker ◽  
Erko Stackebrandt ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Fermentation Products ◽  
Moorella Thermoacetica ◽  
Anoxic Conditions

ABSTRACT A thermophilic, fermentative microaerophile (ET-5b) and a thermophilic acetogen (ET-5a) were coisolated from oxic soil obtained from Egypt. The 16S rRNA gene sequence of ET-5a was 99.8% similar to that of the classic acetogen Moorella thermoacetica. Further analyses confirmed that ET-5a was a new strain of M. thermoacetica. For ET-5b, the nearest 16S rRNA gene sequence similarity value to known genera was approximately 88%. ET-5b was found to be a motile rod with a genomic G+C content of 50.3 mol%. Cells were weakly gram positive and lacked spores. Growth was optimal at 55 to 60°C and pH 6.5 to 7.0. ET-5b grew under both oxic and anoxic conditions, but growth was erratic under atmospheric concentrations of O2. Utilizable substrates included oligosaccharides and monosaccharides. Acetate, formate, and succinate supported growth only under oxic conditions. Saccharides yielded succinate, lactate, ethanol, acetate, formate, and H2 under anoxic conditions; fermentation products were also formed under oxic conditions. A new genus is proposed, the type strain beingThermicanus aegyptius ET-5b gen. nov., sp. nov. (DSMZ 12793). M. thermoacetica ET-5a (DSMZ 12797) grew commensally with T. aegyptius ET-5b on oligosaccharides via the interspecies transfer of H2 formate, and lactate. In support of this interaction, uptake hydrogenase and formate dehydrogenase specific activities were fundamentally greater inM. thermoacetica ET-5a than in T. aegyptiusET-5b. These results demonstrate that (i) soils subject to high temperatures harbor uncharacterized thermophilic microaerophiles, (ii) the classic acetogen M. thermoacetica resides in such soils, and (iii) trophic links between such soil bacteria might contribute to their in situ activities.

scholarly journals Desulfosalsimonas propionicica gen. nov., sp. nov., a halophilic, sulfate-reducing member of the family Desulfobacteraceae isolated from a salt-lake sediment

2010 ◽  
Vol 60 (5) ◽  
pp. 1060-1065 ◽  
Author(s):  
Kasper Urup Kjeldsen ◽  
Trine Fredlund Jakobsen ◽  
Jens Glastrup ◽  
Kjeld Ingvorsen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Yeast Extract ◽  
Gene Sequence ◽  
Salt Lake ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sulfate Reducing ◽  
The Family

A novel halophilic Gram-negative sulfate-reducing bacterium affiliated with the deltaproteobacterial family Desulfobacteraceae, strain PropAT, was isolated from the extreme hypersaline sediment of the northern arm of Great Salt Lake, Utah, USA. Comparative 16S rRNA gene sequence analysis showed that strain PropAT is the first cultured representative of a clade of phylotypes that have been retrieved from a range of geographically and ecologically distinct hypersaline environments. Strain PropAT shared ≤90 % 16S rRNA gene sequence identity with cultured strains within the family Desulfobacteraceae. Cells of strain PropAT were rod-shaped and sometimes motile. The strain required NaCl for growth and grew at salinities up to 200 g NaCl l−1 (optimum 60 g l−1). Growth was observed at 15–40 °C, optimum growth occurred at about 40 °C, while growth was absent at 10 and 45 °C. The pH range for growth was pH 6.0–8.3. Yeast extract (0.1 g l−1) was required for growth. C2–4 alcohols, C3–4 carboxylic acids, yeast extract and H2/acetate supported growth with sulfate as electron acceptor. Sulfate, thiosulfate and sulfite served as electron acceptors, but not elemental sulfur, nitrate or fumarate. The DNA G+C content of strain PropAT was 54.1 mol%. Based on the genotypic and physiological properties, we propose that strain PropAT represents a novel species within a novel genus, Desulfosalsimonas propionicica gen. nov., sp. nov. The type strain of Desulfosalsimonas propionicica is PropAT (=DSM 17721T =VKM B-2385T).

scholarly journals Fervidicella metallireducens gen. nov., sp. nov., a thermophilic, anaerobic bacterium from geothermal waters

2010 ◽  
Vol 60 (6) ◽  
pp. 1394-1400 ◽  
Author(s):  
Christopher D. Ogg ◽  
Bharat K. C. Patel
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Yeast Extract ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence ◽  
Casamino Acids ◽  
Gene Similarity

A strictly anaerobic, thermophilic bacterium, designated strain AeBT, was isolated from microbial mats colonizing a run-off channel formed by free-flowing thermal water from a bore well (registered number 17263) of the Great Artesian Basin, Australia. Cells of strain AeBT were slightly curved rods (2.5–6.0×1.0 μm) that stained Gram-negative and formed spherical terminal to subterminal spores. The strain grew optimally in tryptone–yeast extract–Casamino acids medium at 50 °C (range 37–55 °C) and pH 7 (range pH 5–9). Strain AeBT grew poorly on yeast extract (0.2 %) and tryptone (0.2 %) as sole carbon sources, which were obligately required for growth on other energy sources. Growth of strain AeBT increased in the presence of various carbohydrates and amino acids, but not organic acids. End products detected from glucose fermentation were ethanol, acetate, CO2 and H2. In the presence of 0.2 % yeast extract, iron(III), manganese(IV), vanadium(V) and cobalt(III) were reduced, but not sulfate, thiosulfate, sulfite, elemental sulfur, nitrate or nitrite. Iron(III) was also reduced in the presence of tryptone, peptone, Casamino acids and amyl media (Research Achievement), but not starch, xylan, chitin, glycerol, ethanol, pyruvate, benzoate, lactate, acetate, propionate, succinate, glycine, serine, lysine, threonine, arginine, glutamate, valine, leucine, histidine, alanine, aspartate, isoleucine or methionine. Growth was inhibited by chloramphenicol, streptomycin, tetracycline, penicillin, ampicillin and NaCl concentrations >2 %. The DNA G+C content was 35.4±1 mol%, as determined by the thermal denaturation method. 16S rRNA gene sequence analysis indicated that strain AeBT is a member of the family Clostridiaceae, class Clostridia, phylum ‘Firmicutes’, and is positioned approximately equidistantly between the genera Sarcina, Anaerobacter, Caloramator and Clostridium (16S rRNA gene similarity values of 87.8–90.9 %). On the basis of 16S rRNA gene sequence comparisons and physiological characteristics, strain AeBT is considered to represent a novel species in a new genus, for which the name Fervidicella metallireducens gen. nov., sp. nov. is proposed; the type strain is AeBT (=JCM 15555T=KCTC 5667T).

scholarly journals Geosporobacter subterraneus gen. nov., sp. nov., a spore-forming bacterium isolated from a deep subsurface aquifer

2007 ◽  
Vol 57 (8) ◽  
pp. 1757-1761 ◽  
Author(s):  
Nihel Klouche ◽  
Marie-Laure Fardeau ◽  
Jean-François Lascourrèges ◽  
Jean-Luc Cayol ◽  
Hocine Hacene ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Rrna Gene Sequence ◽  
Sequence Comparisons ◽  
Deep Aquifer ◽  
Fermentation Products

A novel, strictly anaerobic, chemo-organotrophic bacterium, designated strain VNs68T, was isolated from a well that collected water from a deep aquifer at a depth of 800 m in the Paris Basin, France. Cells were thin, non-motile, Gram-positive rods forming terminal endospores (3.0–5.0×0.5 μm). Strain VNs68T grew at temperatures between 30 and 55 °C (optimum 42 °C) and at pH 5.6–8.4 (optimum pH 7.3). It did not require salt for growth but tolerated up to 40 g NaCl l−1. Strain VNs68T was an obligate heterotroph fermenting carbohydrates such as glucose, xylose, fructose, ribose and cellobiose. Casamino acids and amino acids (arginine, serine, lysine, alanine, aspartate, asparagine, isoleucine, histidine) were also fermented. The main fermentation products from glucose were acetate with H2 and CO2. Sulfate, sulfite, thiosulfate, elemental sulfur, nitrate and nitrite were not used as electron acceptors. The G+C content of the genomic DNA was 42.2 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain VNs68T was affiliated to cluster XI, order Clostridiales, domain Bacteria. On the basis of 16S rRNA gene sequence comparisons and physiological characteristics, strain VNs68T is considered to represent a novel species of a new genus, for which the name Geosporobacter subterraneus gen. nov., sp. nov. is proposed. The type strain of Geosporobacter subterraneus is VNs68T (=DSM 17957T =JCM 14037T).

scholarly journals Streptomonospora litoralis sp. nov., a halophilic thiopeptides producer isolated from sand collected at Cuxhaven beach

2021 ◽  
Author(s):  
Shadi Khodamoradi ◽  
Richard L. Hahnke ◽  
Yvonne Mast ◽  
Peter Schumann ◽  
Peter Kämpfer ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Bioinformatic Analysis ◽  
Biosynthetic Gene Cluster ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Polar Lipid Profile

AbstractStrain M2T was isolated from the beach of Cuxhaven, Wadden Sea, Germany, in course of a program to attain new producers of bioactive natural products. Strain M2T produces litoralimycin and sulfomycin-type thiopeptides. Bioinformatic analysis revealed a potential biosynthetic gene cluster encoding for the M2T thiopeptides. The strain is Gram-stain-positive, rod shaped, non-motile, spore forming, showing a yellow colony color and forms extensively branched substrate mycelium and aerial hyphae. Inferred from the 16S rRNA gene phylogeny strain M2T affiliates with the genus Streptomonospora. It shows 96.6% 16S rRNA gene sequence similarity to the type species Streptomonospora salina DSM 44593 T and forms a distinct branch with Streptomonospora sediminis DSM 45723 T with 97.0% 16S rRNA gene sequence similarity. Genome-based phylogenetic analysis revealed that M2T is closely related to Streptomonospora alba YIM 90003 T with a digital DNA-DNA hybridisation (dDDH) value of 26.6%. The predominant menaquinones of M2T are MK-10(H6), MK-10(H8), and MK-11(H6) (> 10%). Major cellular fatty acids are iso-C16:0, anteiso C17:0 and C18:0 10-methyl. The polar lipid profile consisted of diphosphatidylglycerol phosphatidyl glycerol, phosphatidylinositol, phosphatidylcholine, phosphatidylethanolamine, three glycolipids, two unknown phospholipids, and two unknown lipids. The genome size of type strain M2T is 5,878,427 bp with 72.1 mol % G + C content. Based on the results obtained from phylogenetic and chemotaxonomic studies, strain M2T (= DSM 106425 T = NCCB 100650 T) is considered to represent a novel species within the genus Streptomonospora for which the name Streptomonospora litoralis sp. nov. is proposed.

scholarly journals Faecalicoccus acidiformans gen. nov., sp. nov., isolated from the chicken caecum, and reclassification of Streptococcus pleomorphus (Barnes et al. 1977), Eubacterium biforme (Eggerth 1935) and Eubacterium cylindroides (Cato et al. 1974) as Faecalicoccus pleomorphus comb. nov., Holdemanella biformis gen. nov., comb. nov. and Faecalitalea cylindroides gen. nov., comb. nov., respectively, within the family Erysipelotrichaceae

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3877-3884 ◽  
Author(s):  
Celine De Maesschalck ◽  
Filip Van Immerseel ◽  
Venessa Eeckhaut ◽  
Siegrid De Baere ◽  
Margo Cnockaert ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Strains LMG 27428T and LMG 27427 were isolated from the caecal content of a chicken and produced butyric, lactic and formic acids as major metabolic end products. The genomic DNA G+C contents of strains LMG 27428T and LMG 27427 were 40.4 and 38.8 mol%. On the basis of 16S rRNA gene sequence similarity, both strains were most closely related to the generically misclassified Streptococcus pleomorphus ATCC 29734T. Strain LMG 27428T could be distinguished from S. pleomorphus ATCC 29734T based on production of more lactic acid and less formic acid in M2GSC medium, a higher DNA G+C content and the absence of activities of acid phosphatase and leucine, arginine, leucyl glycine, pyroglutamic acid, glycine and histidine arylamidases, while strain LMG 27428 was biochemically indistinguishable from S. pleomorphus ATCC 29734T. The novel genus Faecalicoccus gen. nov. within the family Erysipelotrichaceae is proposed to accommodate strains LMG 27428T and LMG 27427. Strain LMG 27428T ( = DSM 26963T) is the type strain of Faecalicoccus acidiformans sp. nov., and strain LMG 27427 ( = DSM 26962) is a strain of Faecalicoccus pleomorphus comb. nov. (type strain LMG 17756T = ATCC 29734T = DSM 20574T). Furthermore, the nearest phylogenetic neighbours of the genus Faecalicoccus are the generically misclassified Eubacterium cylindroides DSM 3983T (94.4 % 16S rRNA gene sequence similarity to strain LMG 27428T) and Eubacterium biforme DSM 3989T (92.7 % 16S rRNA gene sequence similarity to strain LMG 27428T). We present genotypic and phenotypic data that allow the differentiation of each of these taxa and propose to reclassify these generically misnamed species of the genus Eubacterium formally as Faecalitalea cylindroides gen. nov., comb. nov. and Holdemanella biformis gen. nov., comb. nov., respectively. The type strain of Faecalitalea cylindroides is DSM 3983T = ATCC 27803T = JCM 10261T and that of Holdemanella biformis is DSM 3989T = ATCC 27806T = CCUG 28091T.

scholarly journals 16S rRNA Gene Sequence Analysis ofPhotobacterium damselae and Nested PCR Method for Rapid Detection of the Causative Agent of Fish Pasteurellosis

1999 ◽  
Vol 65 (7) ◽  
pp. 2942-2946 ◽  
Author(s):  
Carlos R. Osorio ◽  
Matthew D. Collins ◽  
Alicia E. Toranzo ◽  
Juan L. Barja ◽  
Jesús L. Romalde
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Causative Agent ◽  
Nested Pcr ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Photobacterium Damselae

ABSTRACT The causative agent of fish pasteurellosis, the organism formerly known as Pasteurella piscicida, has been reclassified asPhotobacterium damselae subsp. piscicida on the basis of 16S rRNA gene sequence comparisons and chromosomal DNA-DNA hybridization data; thus, this organism belongs to the same species asPhotobacterium damselae subsp. damselae(formerly Vibrio damselae). Since reassignment of P. damselae subsp. piscicida was based on only two strains, one objective of the present work was to confirm the taxonomic position of this fish pathogen by sequencing the 16S rRNA genes of 26 strains having different geographic and host origins. In addition, a nested PCR protocol for detection of P. damselae based on 16S rRNA was developed. This PCR protocol was validated by testing 35 target and 24 nontarget pure cultures, and the detection limits obtained ranged from 1 pg to 10 fg of DNA (200 to 20 cells). A similar level of sensitivity was observed when the PCR protocol was applied to fish tissues spiked with bacteria. The PCR approach described in this paper allows detection of the pathogen in mixed plate cultures obtained from asymptomatic fish suspected to be carriers of P. damselae subsp. piscicida, in which growth of this bacterium cannot be visualized. Our results indicate that the selective primers which we designed represent a powerful tool for sensitive and specific detection of fish pasteurellosis.

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