scholarly journals Classification of isolates from locations in Austria and Yellowstone National Park as Geobacillus tepidamans sp. nov.

2004 ◽  
Vol 54 (6) ◽  
pp. 2361-2368 ◽  
Author(s):  
Christina Schäffer ◽  
William L. Franck ◽  
Andrea Scheberl ◽  
Paul Kosma ◽  
Timothy R. McDermott ◽  
...  
Keyword(s):  
Yellowstone National Park ◽  
Type Strain ◽  
National Park ◽  
Cellular Fatty Acid ◽  
Culture Collection ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Moderately Thermophilic ◽  
Biochemical Analyses ◽  
Heated Soil

Two moderately thermophilic, Gram-positive, spore-forming bacteria were isolated from different geographical locations and sources; strain GS5-97T from a beet sugar factory in Leopoldsdorf, Lower Austria, and strain YNP10 from a geothermally heated soil, Yellowstone National Park, USA. The sequences of their 16S rRNA genes were found to be 99·8 % identical, and DNA–DNA hybridization experiments revealed that strains GS5-97T and YNP10 share 89·9 mol% similarity to each other, but only 34·3 and 39·2 mol% similarity, respectively, to Geobacillus caldoxylosilyticus DSM 12041T, which is their closest related type strain. A polyphasic analysis showed that these two isolates were more similar to each other than to other characterized geobacilli. Their DNA G+C content was 43·2 and 42·4 mol%, respectively, and they were identical with respect to many phenotypic features (e.g. Topt 55 °C; pHopt 7·0). Both strains clearly displayed best growth when cultured aerobically. They differed slightly in their cellular fatty acid profiles and polar lipid pattern, and genotypically they could also be distinguished based on randomly amplified polymorphic DNA fingerprints and internal transcribed spacer analysis. Freeze-etching experiments revealed oblique surface layer (S-layer) lattices in both strains, and biochemical analyses of the purified S-layer proteins indicated the occurrence of glycosylation. Based on the properties of these organisms relative to those currently documented for the genus Geobacillus and for the various sister genera in the Bacillus radiation, a novel species is proposed, Geobacillus tepidamans sp. nov., with GS5-97T (=ATCC BAA-942T=DSM 16325T) as the type strain. Strain YNP10 has been deposited in the American Type Culture Collection as ATCC BAA-943.

scholarly journals Isolation, Characterization, and Ecology of Sulfur-Respiring Crenarchaea Inhabiting Acid-Sulfate-Chloride-Containing Geothermal Springs in Yellowstone National Park

2007 ◽  
Vol 73 (20) ◽  
pp. 6669-6677 ◽  
Author(s):  
Eric S. Boyd ◽  
Robert A. Jackson ◽  
Gem Encarnacion ◽  
James A. Zahn ◽  
Trevor Beard ◽  
...  
Keyword(s):  
Yellowstone National Park ◽  
National Park ◽  
Hot Springs ◽  
Lipid Fraction ◽  
Carbon Sources ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Pcr Analysis ◽  
Geothermal Springs ◽  
Physiological Characterization

ABSTRACT Elemental sulfur (S0) is associated with many geochemically diverse hot springs, yet little is known about the phylogeny, physiology, and ecology of the organisms involved in its cycling. Here we report the isolation, characterization, and ecology of two novel, S0-reducing Crenarchaea from an acid geothermal spring referred to as Dragon Spring. Isolate 18U65 grows optimally at 70 to 72°C and at pH 2.5 to 3.0, while isolate 18D70 grows optimally at 81°C and pH 3.0. Both isolates are chemoorganotrophs, dependent on complex peptide-containing carbon sources, S0, and anaerobic conditions for respiration-dependent growth. Glycerol dialkyl glycerol tetraethers (GDGTs) containing four to six cyclopentyl rings were present in the lipid fraction of isolates 18U65 and 18D70. Physiological characterization suggests that the isolates are adapted to the physicochemical conditions of Dragon Spring and can utilize the natural organic matter in the spring as a carbon and energy source. Quantitative PCR analysis of 16S rRNA genes associated with the S0 flocs recovered from several acid geothermal springs using isolate-specific primers indicates that these two populations together represent 17 to 37% of the floc-associated DNA. The physiological characteristics of isolates 18U65 and 18D70 are consistent with their potential widespread distribution and putative role in the cycling of sulfur in acid geothermal springs throughout the Yellowstone National Park geothermal complex. Based on phenotypic and genetic characterization, the designations Caldisphaera draconis sp. nov. and Acidilobus sulfurireducens sp. nov. are proposed for isolates 18U65 and 18D70, respectively.

scholarly journals Ureibacillus composti sp. nov. and Ureibacillus thermophilus sp. nov., isolated from livestock-manure composts

2007 ◽  
Vol 57 (12) ◽  
pp. 2908-2911 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Seon-Young Lee ◽  
Byung-Yong Kim ◽  
Hyung-Jun Noh ◽  
Peter Schumann ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Sequence Similarity ◽  
Cellular Fatty Acid ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Strains ◽  
Phylogenetic Affiliation ◽  
Dna Reassociation ◽  
Compost Facility

Two Gram-negative, rod-shaped, thermophilic bacterial strains, HC145T and HC148T, were isolated from a compost sample from a compost facility in Ichon, Korea. Sequencing of the 16S rRNA genes of HC145T and HC148T and comparative analyses of the resulting sequences clearly showed that these strains had a phylogenetic affiliation to the genus Ureibacillus. The level of 16S rRNA similarity between the two novel strains was 98.4 % and the levels of sequence similarity between them and existing Ureibacillus species were 97.8–98.1 (HC145T) and 97.4–98.7 % (HC148T). The DNA–DNA reassociation values between the two strains and the type strains of Ureibacillus species ranged from 38 to 51 %. The polar lipid profiles for both isolates consisted of phosphatidylglycerol, diphosphatidylglycerol, phospholipids and glycolipids of unknown composition. The major quinones were MK-8, MK-9 and MK-7, the peptidoglycan type was l-Lys←d-Asp and the main cellular fatty acid was iso-C16 : 0. The DNA G+C contents of strains HC145T and HC148T were 42.4 and 38.5 mol%, respectively. On the basis of the data from this polyphasic study, strains HC145T and HC148T represent members of the genus Ureibacillus, for which the names Ureibacillus composti sp. nov. and Ureibacillus thermophilus sp. nov., respectively, are proposed. The type strain of U. composti is HC145T (=KACC 11361T =DSM 17951T) and the type strain of U. thermophilus is HC148T (=KACC 11362T =DSM 17952T).

scholarly journals Legionella Species Diversity in an Acidic Biofilm Community in Yellowstone National Park

2005 ◽  
Vol 71 (1) ◽  
pp. 507-511 ◽  
Author(s):  
Kathy B. Sheehan ◽  
Joan M. Henson ◽  
Michael J. Ferris
Keyword(s):  
Yellowstone National Park ◽  
National Park ◽  
Pcr Amplification ◽  
18S Rrna Gene ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Thermal Gradients ◽  
Legionella Species ◽  
Legionella Micdadei

ABSTRACT Legionella species are frequently detected in aquatic environments, but their occurrence in extreme, acidic, geothermal habitats has not been explored with cultivation-independent methods. We investigated a predominately eukaryotic algal mat community in a pH 2.7 geothermal stream in Yellowstone National Park for the presence of Legionella and potential host amoebae. Our analyses, using PCR amplification with Legionella-specific primers targeting 16S rRNA genes, detected four known Legionella species, as well as Legionella sequences from species that are not represented in sequence databases, in mat samples and cultivated isolates. The nonrandom occurrence of sequences detected at lower (30�C) and higher (35 to 38�C) temperatures suggests that natural thermal gradients in the stream influence Legionella species distributions in this mat community. We detected only one sequence, Legionella micdadei, from cultivated isolates. We cultured and sequenced partial 18S rRNA gene regions from two potential hosts, Acanthamoeba and Euglena species.

scholarly journals Acinetobacter portensis sp. nov. and Acinetobacter guerrae sp. nov., isolated from raw meat

2020 ◽  
Vol 70 (8) ◽  
pp. 4544-4554 ◽  
Author(s):  
Ana Carvalheira ◽  
Lucia Gonzales-Siles ◽  
Francisco Salvà-Serra ◽  
Åsa Lindgren ◽  
Liselott Svensson-Stadler ◽  
...  
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Taxonomic Status ◽  
Cellular Fatty Acid ◽  
16S Rrna Genes ◽  
Whole Genome Sequence ◽  
Rrna Genes ◽  
Whole Genome ◽  
Content Type ◽  
Link Type

The taxonomic status of six strains of Acinetobacter obtained from meat samples, collected from supermarkets in Porto, Portugal, was investigated using polyphasic analysis. Partial rpoB sequence similarities lower than 95 % to other Acinetobacter species with validly published names led to the hypothesis that these strains represented novel species. This was confirmed based on comparative multilocus sequence analysis, which included the gyrB, recA and 16S rRNA genes, revealing that these strains represented two coherent lineages that were distinct from each other and from all known species. The names Acinetobacter portensis sp. nov. (comprising four strains) and Acinetobacter guerrae sp. nov. (comprising two strains) are proposed for these novel species. The species status of these two groups was confirmed by low (below 95 %) whole-genome sequence average nucleotide identity values and low (below 70 %) digital DNA–DNA hybridization similarities between the whole-genome sequences of the proposed type strains of each novel species and the representatives of the known Acinetobacter species. Phylogenomic treeing from core genome analysis supported these results. The coherence of each new species lineage was supported by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry differentiation of the species at the protein level, by cellular fatty acid profiles, and by unique and differential combinations of metabolic and physiological properties shared by each novel species. The type strain of A. portensis sp. nov. is AC 877T (=CCUG 68672T=CCM 8789T) and the type strain of A. guerrae sp. nov. is AC 1271T (=CCUG 68674T=CCM 8791T).

scholarly journals Microbial Composition of Near-Boiling Silica-Depositing Thermal Springs throughout Yellowstone National Park

2002 ◽  
Vol 68 (10) ◽  
pp. 5123-5135 ◽  
Author(s):  
Carrine E. Blank ◽  
Sherry L. Cady ◽  
Norman R. Pace
Keyword(s):  
Yellowstone National Park ◽  
National Park ◽  
Hydrogen Oxidation ◽  
Large Subunit ◽  
Microbial Community Composition ◽  
Pcr Amplification ◽  
Small Subunit ◽  
Rrna Genes ◽  
Small Subunit Rrna ◽  
Microbial Composition

ABSTRACT The extent of hyperthermophilic microbial diversity associated with siliceous sinter (geyserite) was characterized in seven near-boiling silica-depositing springs throughout Yellowstone National Park using environmental PCR amplification of small-subunit rRNA genes (SSU rDNA), large-subunit rDNA, and the internal transcribed spacer (ITS). We found that Thermocrinis ruber, a member of the order Aquificales, is ubiquitous, an indication that primary production in these springs is driven by hydrogen oxidation. Several other lineages with no known close relatives were identified that branch among the hyperthermophilic bacteria. Although they all branch deep in the bacterial tree, the precise phylogenetic placement of many of these lineages is unresolved at this time. While some springs contained a fair amount of phylogenetic diversity, others did not. Within the same spring, communities in the subaqueous environment were not appreciably different than those in the splash zone at the edge of the pool, although a greater number of phylotypes was found along the pool's edge. Also, microbial community composition appeared to have little correlation with the type of sinter morphology. The number of cell morphotypes identified by fluorescence in situ hybridization and scanning electron microscopy was greater than the number of phylotypes in SSU clone libraries. Despite little variation in Thermocrinis ruber SSU sequences, abundant variation was found in the hypervariable ITS region. The distribution of ITS sequence types appeared to be correlated with distinct morphotypes of Thermocrinis ruber in different pools. Therefore, species- or subspecies-level divergences are present but not detectable in highly conserved SSU sequences.

scholarly journals Reclassification of Trichlorobacter thiogenes as Geobacter thiogenes comb. nov.

2007 ◽  
Vol 57 (3) ◽  
pp. 463-466 ◽  
Author(s):  
Kelly P. Nevin ◽  
Dawn E. Holmes ◽  
Trevor L. Woodard ◽  
Sean F. Covalla ◽  
Derek R. Lovley
Keyword(s):  
Type Strain ◽  
Original Description ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Phylogenetic Position ◽  
Temperature Optimum ◽  
Ph Optimum ◽  
Donor And Acceptor ◽  
The Family ◽  
Electron Donor And Acceptor

Reclassification of the species Trichlorobacter thiogenes as Geobacter thiogenes comb. nov. is proposed on the basis of physiological traits and phylogenetic position. Characteristics additional to those provided in the original description revealed that the type strain (strain K1T=ATCC BAA-34T=JCM 14045T) has the ability to use Fe(III) as an electron acceptor for acetate oxidation and has an electron donor and acceptor profile typical of a Geobacter species, contains abundant c-type cytochromes, and has a temperature optimum of 30 °C and a pH optimum near pH 7.0; traits typical of members of the genus Geobacter. Phylogenetic analysis of nifD, recA, gyrB, rpoB, fusA and 16S rRNA genes further indicated that T. thiogenes falls within the Geobacter cluster of the family Geobacteraceae. Based on extensive phylogenetic evidence and the fact that T. thiogenes has the hallmark physiological characteristics of a Geobacter species, Trichlorobacter thiogenes should be reclassified as a member of the genus Geobacter.

scholarly journals Draft Genome Sequence of the Photoheterotrophic Chloracidobacterium thermophilum Strain OC1 Found in a Mat at Ojo Caliente

2016 ◽  
Vol 4 (1) ◽  
Author(s):  
Patrick C. Hallenbeck ◽  
Melanie Grogger ◽  
Megan Mraz ◽  
Donald Veverka
Keyword(s):  
New Mexico ◽  
Genome Sequence ◽  
Yellowstone National Park ◽  
Type Strain ◽  
National Park ◽  
Hot Spring ◽  
Enrichment Culture ◽  
Draft Genome ◽  
High Degree ◽  
First Time

Metagenomics of an enrichment culture from a New Mexico hot spring allowed the description of a draft genome of a Chloracidobacterium thermophilum strain for the first time outside Yellowstone National Park with a surprisingly high degree of identity with the type strain.

scholarly journals Description of Anaerobaculum hydrogeniformans sp. nov., an anaerobe that produces hydrogen from glucose, and emended description of the genus Anaerobaculum

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 832-838 ◽  
Author(s):  
Matthew W. Maune ◽  
Ralph S. Tanner
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Content Type ◽  
Moderately Thermophilic ◽  
Link Type ◽  
Production Water ◽  
Emended Description ◽  
Casamino Acids

A novel anaerobic, moderately thermophilic, NaCl-requiring fermentative bacterium, strain OS1T, was isolated from oil production water collected from Alaska, USA. Cells were Gram-negative, non-motile, non-spore-forming rods (1.7–2.7 × 0.4–0.5 µm). The G+C content of the genomic DNA of strain OS1T was 46.6 mol%. The optimum temperature, pH and NaCl concentration for growth of strain OS1T were 55 °C, pH 7 and 10 g l−1, respectively. The bacterium fermented d-fructose, d-glucose, maltose, d-mannose, α-ketoglutarate, l-glutamate, malonate, pyruvate, l-tartrate, l-asparagine, Casamino acids, l-cysteine, l-histidine, l-leucine, l-phenylalanine, l-serine, l-threonine, l-valine, inositol, inulin, tryptone and yeast extract. When grown on d-glucose, 3.86 mol hydrogen and 1.4 mol acetate were produced per mol substrate. Thiosulfate, sulfur and l-cystine were reduced to sulfide, and crotonate was reduced to butyrate with glucose as the electron donor. 16S rRNA gene sequence analysis indicated that strain OS1T was related to Anaerobaculum thermoterrenum (99.7 % similarity to the type strain), a member of the phylum Synergistetes . DNA–DNA hybridization between strain OS1T and A. thermoterrenum DSM 13490T yielded 68 % relatedness. Unlike A. thermoterrenum , strain OS1T fermented malonate, maltose, tryptone, l-leucine and l-phenylalanine, but not citrate, fumarate, lactate, l-malate, glycerol, pectin or starch. The major cellular fatty acid of strain OS1T was iso-C15 : 0 (91 % of the total). Strain OS1T also contained iso-C13 : 0 3-OH (3 %), which was absent from A. thermoterrenum , and iso-C13 : 0 (2 %), which was absent from Anaerobaculum mobile . On the basis of these results, strain OS1T represents a novel species of the genus Anaerobaculum , for which the name Anaerobaculum hydrogeniformans sp. nov. is proposed. The type strain is OS1T ( = DSM 22491T  = ATCC BAA-1850T). An emended description of the genus Anaerobaculum is also given.

scholarly journals Mycoplasma anserisalpingitidis sp. nov., isolated from European domestic geese (Anser anser domesticus) with reproductive pathology

2020 ◽  
Vol 70 (4) ◽  
pp. 2369-2381 ◽  
Author(s):  
Dmitriy V. Volokhov ◽  
Dénes Grózner ◽  
Miklós Gyuranecz ◽  
Naola Ferguson-Noel ◽  
Yamei Gao ◽  
...  
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type

In 1983, Mycoplasma sp. strain 1220 was isolated in Hungary from the phallus lymph of a gander with phallus inflammation. Between 1983 and 2017, Mycoplasma sp. 1220 was also identified and isolated from the respiratory tract, liver, ovary, testis, peritoneum and cloaca of diseased geese in several countries. Seventeen studied strains produced acid from glucose and fructose but did not hydrolyse arginine or urea, and all grew under aerobic, microaerophilic and anaerobic conditions at 35 to 37 ˚C in either SP4 or pleuropneumonia-like organism medium supplemented with glucose and serum. Colonies on agar showed a typical fried-egg appearance and transmission electron microscopy revealed a typical mycoplasma cellular morphology. Molecular characterization included analysis of the following genetic loci: 16S rRNA, 23S rRNA, 16S–23S rRNA ITS, rpoB, rpoC, rpoD, uvrA, parC, topA, dnaE, fusA and pyk. The genome was sequenced for type strain 1220T. The 16S rRNA gene sequences of studied strains of Mycoplasma sp. 1220 shared 99.02–99.19 % nucleotide similarity with M. anatis strains but demonstrated ≤95.00–96.70 % nucleotide similarity to the 16S rRNA genes of other species of the genus Mycoplasma . Phylogenetic, average nucleotide and amino acid identity analyses revealed that the novel species was most closely related to Mycoplasma anatis . Based on the genetic data, we propose a novel species of the genus Mycoplasma , for which the name Mycoplasma anserisalpingitidis sp. nov. is proposed with the type strain 1220T (=ATCC BAA-2147T=NCTC 13513T=DSM 23982T). The G+C content is 26.70 mol%, genome size is 959110 bp.

scholarly journals Methylomagnum ishizawai gen. nov., sp. nov., a mesophilic type I methanotroph isolated from rice rhizosphere

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3527-3534 ◽  
Author(s):  
Ashraf Khalifa ◽  
Chol Gyu Lee ◽  
Takuya Ogiso ◽  
Chihoko Ueno ◽  
Dayéri Dianou ◽  
...  
Keyword(s):  
Type Strain ◽  
Carbon Assimilation ◽  
Membrane System ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Type I ◽  
Intracytoplasmic Membrane ◽  
Respiratory Quinone ◽  
Rice Rhizosphere ◽  
The Family

An aerobic, methane-oxidizing bacterium (strain RS11D-PrT) was isolated from rice rhizosphere. Cells of strain RS11D-PrT were Gram-stain-negative, motile rods with a single polar flagellum and contained an intracytoplasmic membrane system typical of type I methanotrophs. The strain utilized methane and methanol as sole carbon and energy sources. It could grow at 20–37 °C (optimum 31–33 °C), at pH 6.8–7.4 (range 5.5–9.0) and with 0–0.2 % (w/v) NaCl (there was no growth at above 0.5 % NaCl). pmoA and mmoX genes were present. The ribulose monophosphate and/or ribulose bisphosphate pathways were used for carbon assimilation. Results of sequence analysis of 16S rRNA genes showed that strain RS11D-PrT is related closely to the genera Methylococcus, Methylocaldum, Methyloparacoccus and Methylogaea in the family Methylococcaceae. The similarity was low (94.6 %) between strain RS11D-PrT and the most closely related type strain (Methyloparacoccus murrellii R-49797T). The DNA G+C content was 64.1 mol%. Results of phylogenetic analysis of the pmoA gene and chemotaxonomic data regarding the major cellular fatty acids (C16 : 1ω7c, C16 : 0 and C14 : 0) and the major respiratory quinone (MQ-8) also indicated the affiliation of strain RS11D-PrT to the Methylococcus–Methylocaldum–Methyloparacoccus–Methylogaea clade. On the basis of phenotypic, genotypic and phylogenetic characteristics, strain RS11D-PrT is considered to represent a novel genus and species within the family Methylococcaceae, for which the name Methylomagnum ishizawai gen. nov., sp. nov. is proposed. The type strain is RS11D-PrT ( = JCM 18894T = NBRC 109438T = DSM 29768T = KCTC 4681T).

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