scholarly journals Thermococcus celericrescens sp. nov., a fast-growing and cell-fusing hyperthermophilic archaeon from a deep-sea hydrothermal vent

2007 ◽  
Vol 57 (3) ◽  
pp. 437-443 ◽  
Author(s):  
Tomohiko Kuwabara ◽  
Masaomi Minaba ◽  
Noriko Ogi ◽  
Masahiro Kamekura
Keyword(s):  
Surface Layer ◽  
Hydrothermal Vent ◽  
Genomic Dna ◽  
Cell Envelope ◽  
Optimal Growth ◽  
Exponential Phase ◽  
Cell Multiplication ◽  
Rrna Gene ◽  
Hyperthermophilic Archaeon ◽  
Fast Growing

A fast-growing and cell-fusing hyperthermophilic archaeon was isolated from a hydrothermal vent at Suiyo Seamount, Izu-Bonin Arc, Western Pacific Ocean. Strain TS2T is an irregular, motile coccus that is generally 0.7–1.5 μm in diameter and possesses a polar tuft of flagella. In the mid-exponential phase of growth, cells that appeared black under phase-contrast microscopy fused at room temperature in the presence of a DNA-intercalating dye, as previously observed in Thermococcus coalescens. Cell fusion was not observed in later growth phases. Transmission electron microscopy revealed that the cells in the mid-exponential phase had a 5 nm-thick, electron-dense cell envelope that appeared to associate loosely with the cytoplasmic membrane. As the growth stage progressed, a surface layer developed on the membrane under the envelope and the envelope eventually peeled off. These observations suggest that the surface layer prevents the fusion of cells. Cells of strain TS2T grew at 50–85 °C, pH 5.6–8.3 and at NaCl concentrations of 1.0 to 4.5 %, with optimal growth occurring at 80 °C, pH 7.0 and 3.0 % NaCl. Under optimal growth conditions, strain TS2T grew very fast with an apparent doubling time of 20 min. It is suggested that the biosynthesis of the surface layer cannot catch up with cell multiplication in the mid-exponential phase and thus cells without the surface layer are generated. Strain TS2T was an anaerobic chemo-organotroph that grew on either yeast extract or tryptone as the sole growth substrate. The genomic DNA G+C content was 54.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the isolate belongs to the genus Thermococcus. However, no significant DNA–DNA hybridization was observed between the genomic DNA of strain TS2T and phylogenetically related Thermococcus species. On the basis of this evidence, strain TS2T is proposed to represent a novel species, Thermococcus celericrescens sp. nov., a name chosen to reflect the fast growth of the strain. The type strain is TS2T (=NBRC 101555T=JCM 13640T=DSM 17994T).

scholarly journals Thermococcus coalescens sp. nov., a cell-fusing hyperthermophilic archaeon from Suiyo Seamount

2005 ◽  
Vol 55 (6) ◽  
pp. 2507-2514 ◽  
Author(s):  
Tomohiko Kuwabara ◽  
Masaomi Minaba ◽  
Yukihiro Iwayama ◽  
Isao Inouye ◽  
Miwako Nakashima ◽  
...  
Keyword(s):  
Cell Fusion ◽  
Genomic Dna ◽  
Cell Envelope ◽  
16S Rrna Gene Sequencing ◽  
Exponential Phase ◽  
Rrna Gene ◽  
Hyperthermophilic Archaeon ◽  
Intercalating Dye ◽  
A Cell ◽  
Rrna Gene Sequencing

A cell-fusing hyperthermophilic archaeon was isolated from hydrothermal fluid obtained from Suiyo Seamount of the Izu-Bonin Arc. The isolate, TS1T, is an irregular coccus, usually 0·5–2 μm in diameter and motile with a polar tuft of flagella. Cells in the exponential phase of growth fused at room temperature in the presence of DNA-intercalating dye to become as large as 5 μm in diameter. Fused cells showed dark spots that moved along in the cytoplasm. Large cells with a similar appearance were also observed upon culture at 87 °C, suggesting the occurrence of similar cell fusions during growth. Transmission electron microscopy revealed that cells in the exponential phase possessed a thin and electron-lucent cell envelope that could be lost subsequently during culture. The fragile cell envelope must be related to cell fusion. The cells grew at 57–90 °C, pH 5·2–8·7 and at NaCl concentrations of 1·5–4·5 %, with the optima being 87 °C, pH 6·5 and 2·5 % NaCl. The isolate was an anaerobic chemo-organotroph that grew on either yeast extract or tryptone as the sole growth substrate. The genomic DNA G+C content was 53·9 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the isolate was closely related to Thermococcus species. However, no significant DNA–DNA hybridization was observed between genomic DNA of strain TS1T and phylogenetically related Thermococcus species. We propose that isolate TS1T represents a novel species, Thermococcus coalescens sp. nov., with the name reflecting the cell fusion activity observed in the strain. The type strain is TS1T (=JCM 12540T=DSM 16538T).

scholarly journals Thermosipho globiformans sp. nov., an anaerobic thermophilic bacterium that transforms into multicellular spheroids with a defect in peptidoglycan formation

2011 ◽  
Vol 61 (7) ◽  
pp. 1622-1627 ◽  
Author(s):  
Tomohiko Kuwabara ◽  
Akitomo Kawasaki ◽  
Ikuko Uda ◽  
Akihiko Sugai
Keyword(s):  
Outer Membrane ◽  
Yeast Extract ◽  
Genomic Dna ◽  
Optimal Growth ◽  
Thermophilic Bacterium ◽  
Exponential Phase ◽  
Binary Fission ◽  
Rrna Gene ◽  
Multicellular Spheroids ◽  
Phase Transmission

An anaerobic rod-shaped thermophile was isolated from a hydrothermal vent at Suiyo Seamount, Izu-Bonin Arc, western Pacific Ocean, and was named strain MN14T. The rods were Gram-negative-staining, non-motile without flagella, 2–4 µm long and 0.5 µm wide, and divided by binary fission in the mid-exponential phase. The cells were surrounded by a sheath-like structure (toga) and occurred singly or in chains. Spheroids containing multiple cells were observed not only in the stationary phase, as previously observed for species of the order Thermotogales, but also from the early exponential phase. Transmission electron microscopy revealed that the peptidoglycan in rods partly disintegrated in the early growth phases and that the outer membrane of the spheroids was not completely lined with peptidoglycan. These findings suggested that the spheroids were formed from rods by the disintegration of peptidoglycan and subsequent inflation of the outer membrane. The spheroids eventually generated tiny cells in the periplasmic space, indicating a viviparous mode of proliferation in addition to binary fission. Strain MN14T grew at 40–75 °C, pH 5.0–8.2 and with 0.25–5.20 % (w/v) NaCl, with optimal growth occurring at 68 °C, pH 6.8 and with 2.5 % NaCl. The shortest doubling time was 24 min, assuming that the strain propagated only by binary fission. Elemental sulfur enhanced growth, but was not essential. Thiosulfate was not an electron acceptor for growth. The strain was a chemo-organotroph that grew on yeast extract as the sole growth substrate. Tryptone and starch supported its growth in the presence of yeast extract. The G+C content of the genomic DNA was 31.7 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that this strain belonged to the genus Thermosipho. No significant DNA–DNA hybridization was observed between the genomic DNA of strain MN14T and phylogenetically related species of the genus Thermosipho. Based on this evidence, strain MN14T is proposed to represent a novel species, named Thermosipho globiformans sp. nov. The species epithet globiformans reflects the formation of multicellular and reproductive spheroids by the novel strain. The type strain of this species is MN14T ( = JCM 15059T = DSM 19918T).

scholarly journals Release of Compact Nucleoids with Characteristic Shapes from Escherichia coli

2001 ◽  
Vol 183 (17) ◽  
pp. 5041-5049 ◽  
Author(s):  
Steven B. Zimmerman ◽  
Lizabeth D. Murphy
Keyword(s):  
Escherichia Coli ◽  
Genomic Dna ◽  
Phase Contrast ◽  
Cell Envelope ◽  
Simple Procedure ◽  
Sodium Dodecyl ◽  
Cell Lysis ◽  
Exponential Phase ◽  
Stable Form ◽  
General Shape

ABSTRACT The genomic DNA of bacteria is contained in one or a few compact bodies known as nucleoids. We describe a simple procedure that retains the general shape and compaction of nucleoids from Escherichia coli upon cell lysis and nucleoid release from the cell envelope. The procedure is a modification of that used for the preparation of spermidine nucleoids (nucleoids released in the presence of spermidine) (T. Kornberg, A. Lockwood, and A. Worcel, Proc. Natl. Acad. Sci. USA 71:3189–3193, 1974). Polylysine is added to prevent the normal decompaction of nucleoids which occurs upon cell lysis. Nucleoids retained their characteristic shapes in lysates of exponential-phase cells or in lysates of cells treated with chloramphenicol or nalidixate to alter nucleoid morphology. The notably unstable nucleoids of rifampin-treated cells were obtained in compact, stable form in such lysates. Nucleoids released in the presence of polylysine were easily processed and provided well-defined DNA fluorescence and phase-contrast images. Uniform populations of nucleoids retaining characteristic shapes could be isolated after formaldehyde fixation and heating with sodium dodecyl sulfate.

scholarly journals Skermanella aerolata sp. nov., isolated from air, and emended description of the genus Skermanella

2007 ◽  
Vol 57 (7) ◽  
pp. 1539-1542 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Byung-Yong Kim ◽  
Seung-Beom Hong ◽  
Jae-Ho Joa ◽  
Sang-Sik Nam ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Type Strain ◽  
Novel Species ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
16S Rrna Gene Sequences ◽  
Emended Description ◽  
Air Sample ◽  
Sequence Similarities

A light-pink-coloured bacterium, designated strain 5416T-32T, was isolated from an air sample in Korea. Cells of the strain were strictly aerobic, Gram-negative, motile (single polar or subpolar flagellum) and rod-shaped. Optimal growth occurred at 25–30 °C and at pH 6.0–7.0. The major quinones were Q-10 and Q-8. The major fatty acids were C18 : 1 ω7c (53.8 %) and C16 : 0 (15.9 %). The G+C content of the genomic DNA was 65.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 5416T-32T was most closely related to Skermanella parooensis, with a similarity of 96.2 %, but relatively low sequence similarities (<92 %) were found with respect to other species with validly published names held in GenBank. Phenotypic and genotypic analyses indicated that strain 5416T-32T could not be assigned to any recognized species. Therefore strain 5416T-32T represents a novel species of the genus Skermanella, for which the name Skermanella aerolata sp. nov. is proposed. The type strain is 5416T-32T (=KACC 11604T=DSM 18479T).

scholarly journals Fervidobacterium changbaicum sp. nov., a novel thermophilic anaerobic bacterium isolated from a hot spring of the Changbai Mountains, China

2007 ◽  
Vol 57 (10) ◽  
pp. 2333-2336 ◽  
Author(s):  
Jingang Cai ◽  
Yanping Wang ◽  
Dongbo Liu ◽  
Yan Zeng ◽  
Yanfen Xue ◽  
...  
Keyword(s):  
Hot Spring ◽  
Cell Envelope ◽  
Carbon Sources ◽  
Optimal Growth ◽  
Changbai Mountains ◽  
Rrna Gene ◽  
High Concentration ◽  
Gene Sequence Analysis ◽  
Wide Range ◽  
Bacterium Strain

A thermophilic, obligately anaerobic, rod-shaped bacterium (strain CBS-1T) was isolated from a hot spring mixture of water and mud of the Changbai Mountains, China. Strain CBS-1T was found to be non-sporulating, Gram-negative, with optimal growth at 75–80 °C. It grew on a wide range of carbon sources, including glucose, lactose, maltose, starch, sorbitol and pyruvate amongst others. The DNA G+C content of strain CBS-1T was 31.9 mol%. The 16S rRNA gene sequence analysis indicated that the strain was a member of the genus Fervidobacterium. The high concentration of C16 : 0 (52.2 %) in the fatty acid profile of the cell envelope supported its inclusion as a member of the genus Fervidobacterium. On the basis of the low values of DNA–DNA hybridization (25.8 and 20.5 %) and phenotypic features, strain CBS-1T represents a novel species of the genus Fervidobacterium, for which the name Fervidobacterium changbaicum sp. nov. is proposed. The type strain is CBS-1T (=DSM 17883T=JCM 13353T).

scholarly journals Recurrent Bacteremia Caused by a “Flexispira”-Like Organism in a Patient with X-Linked (Bruton’s) Agammaglobulinemia

1999 ◽  
Vol 37 (8) ◽  
pp. 2439-2445 ◽  
Author(s):  
Susan Weir ◽  
Brenda Cuccherini ◽  
Anne M. Whitney ◽  
Marsha L. Ray ◽  
John P. MacGregor ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Dna Hybridization ◽  
Genomic Dna ◽  
Gene Sequence ◽  
Optimal Growth ◽  
Rrna Gene ◽  
New Taxon ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis

Helicobacter spp., except for Helicobacter cinaedi, have only rarely been reported in cases of septicemia. A patient with X-linked (Bruton’s) agammaglobulinemia was found to have persistent sepsis with a Helicobacter-like organism despite multiple courses of antibiotics. His periods of sepsis were associated with leg swelling thought to be consistent with cellulitis. The organism was fastidious and required a microaerophilic environment containing H2 for growth. Optimal growth was observed at 35 to 37°C on sheep blood, CDC anaerobe, and Bordet-Gengou agars. Serial subcultures every 4 to 5 days were required to maintain viability. The organism was strongly urease positive and showed highest relatedness toHelicobacter-like organisms with the vernacular name “Flexispira rappini” by 16S rRNA gene sequence analysis. Genomic DNA hybridization studies, however, found 24 to 37% relatedness to “F. rappini” and even less to otherHelicobacter spp. Although the organism phenotypically resembles “Flexispira” and Helicobacter, it is thought to represent a new taxon. The patient’s infection was eventually cleared with a prolonged (5-month) course of intravenous imipenem and gentamicin.

scholarly journals Pyrococcus yayanosii sp. nov., an obligate piezophilic hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent

2011 ◽  
Vol 61 (12) ◽  
pp. 2827-2881 ◽  
Author(s):  
Jean-Louis Birrien ◽  
Xiang Zeng ◽  
Mohamed Jebbar ◽  
Marie-Anne Cambon-Bonavita ◽  
Joël Quérellou ◽  
...  
Keyword(s):  
Hydrothermal Vent ◽  
Ribosomal Proteins ◽  
Culture Collection ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
16S Rrna Gene Sequences ◽  
Hyperthermophilic Archaeon ◽  
Physiological Properties ◽  
Mid Atlantic Ridge ◽  
Pyrococcus Yayanosii

An obligate piezophilic anaerobic hyperthermophilic archaeon, designated strain CH1T, was isolated from a hydrothermal vent site named ‘Ashadze’, which is located on the Mid-Atlantic Ridge at a depth of 4100 m. Enrichment and isolation of the strain were carried out at 95 °C under a hydrostatic pressure of 42 MPa. Cells of strain CH1T were highly motile irregular cocci with a diameter of ~1–1.5 µm. Growth was recorded at 80–108 °C (optimum 98 °C) and at pressures of 20–120 MPa (optimum 52 MPa). No growth was observed under atmospheric pressures at 60–110 °C. Growth was observed at pH 6.0–9.5 (optimum 7.5–8.0) and in 2.5–5.5 % (w/v) NaCl (optimum 3.5 %). Strain CH1T was strictly anaerobic and grew on complex proteinaceous substrates, such as yeast extract, Peptone, and casein, as well as on sucrose, starch, chitin, pyruvate, acetate and glycerol without electron acceptors. The G+C content of the genomic DNA was 49.0±0.5 mol%. Analysis of 16S rRNA gene sequences revealed that strain CH1T belongs to the genus Pyrococcus. Based on its physiological properties and similarity levels between ribosomal proteins, strain CH1T represents a novel species, for which the name Pyrococcus yayanosii sp. nov. is proposed. The type strain is CH1T ( = JCM 16557). This strain is also available by request from the Souchothèque de Bretagne (catalogue LMBE) culture collection (collection no. 3310).

Methyloceanibacter caenitepidi gen. nov., sp. nov., a facultatively methylotrophic bacterium isolated from marine sediments near a hydrothermal vent

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 462-468 ◽  
Author(s):  
Mio Takeuchi ◽  
Taiki Katayama ◽  
Takao Yamagishi ◽  
Satoshi Hanada ◽  
Hideyuki Tamaki ◽  
...  
Keyword(s):  
Hydrothermal Vent ◽  
Optimal Growth ◽  
Cellular Fatty Acid ◽  
Methylotrophic Bacterium ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Content Type ◽  
Moderately Thermophilic ◽  
Gram Staining ◽  
Novel Genus And Species

A moderately thermophilic, methanol-oxidizing bacterium (strain Gela4T) was isolated from methane-utilizing mixed-culture originating from marine sediment near a hydrothermal vent. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain Gela4T was closely related to members of the genus ‘Methyloligella’ (94.7 % similarity) within the class Alphaproteobacteria . Strain Gela4T was a Gram‐staining‐negative and aerobic organism. Cells were rod-shaped and non-motile. The temperature range for growth of strain Gela4T was 19–43 °C (optimal growth at 35 °C). Strain Gela4T tolerated up to 9 % NaCl with an optimum at 1 %. The organism was a facultative methylotroph that could utilize methanol, methylamine, trimethylamine and a variety of multi-carbon compounds. The major cellular fatty acid and major respiratory quinone were C18 : 1ω7c and ubiquinone-10, respectively. The predominant phospholipids were phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 63.9 mol%. On the basis of the morphological, physiological, biochemical and genetic information, a novel genus and species, Methyloceanibacter caenitepidi is proposed, with Gela4T ( = NBRC 109540T = DSM 27242T) as the type strain.

scholarly journals Ecofriendly Synthesis of Silver Nanoparticles by Terrabacter humi sp. nov. and Their Antibacterial Application against Antibiotic-Resistant Pathogens

2020 ◽  
Vol 21 (24) ◽  
pp. 9746
Author(s):  
Shahina Akter ◽  
Sun-Young Lee ◽  
Muhammad Zubair Siddiqi ◽  
Sri Renukadevi Balusamy ◽  
Md. Ashrafudoulla ◽  
...  
Keyword(s):  
Silver Nanoparticles ◽  
Spherical Shape ◽  
Optimal Growth ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Drug Resistant ◽  
Protein Coding ◽  
A Genome ◽  
The Fourier Transform

It is essential to develop and discover alternative eco-friendly antibacterial agents due to the emergence of multi-drug-resistant microorganisms. In this study, we isolated and characterized a novel bacterium named Terrabacter humi MAHUQ-38T, utilized for the eco-friendly synthesis of silver nanoparticles (AgNPs) and the synthesized AgNPs were used to control multi-drug-resistant microorganisms. The novel strain was Gram stain positive, strictly aerobic, milky white colored, rod shaped and non-motile. The optimal growth temperature, pH and NaCl concentration were 30 °C, 6.5 and 0%, respectively. Based on 16S rRNA gene sequence, strain MAHUQ-38T belongs to the genus Terrabacter and is most closely related to several Terrabacter type strains (98.2%–98.8%). Terrabacter humi MAHUQ-38T had a genome of 5,156,829 bp long (19 contigs) with 4555 protein-coding genes, 48 tRNA and 5 rRNA genes. The culture supernatant of strain MAHUQ-38T was used for the eco-friendly and facile synthesis of AgNPs. The transmission electron microscopy (TEM) image showed the spherical shape of AgNPs with a size of 6 to 24 nm, and the Fourier transform infrared (FTIR) analysis revealed the functional groups responsible for the synthesis of AgNPs. The synthesized AgNPs exhibited strong anti-bacterial activity against multi-drug-resistant pathogens, Escherichia coli and Pseudomonas aeruginosa. Minimal inhibitory/bactericidal concentrations against E. coli and P. aeruginosa were 6.25/50 and 12.5/50 μg/mL, respectively. The AgNPs altered the cell morphology and damaged the cell membrane of pathogens. This study encourages the use of Terrabacter humi for the ecofriendly synthesis of AgNPs to control multi-drug-resistant microorganisms.

scholarly journals Growth and Phylogenetic Properties of Novel Bacteria Belonging to the Epsilon Subdivision of the Proteobacteria Enriched fromAlvinella pompejana and Deep-Sea Hydrothermal Vents

2001 ◽  
Vol 67 (10) ◽  
pp. 4566-4572 ◽  
Author(s):  
Barbara J. Campbell ◽  
Christian Jeanthon ◽  
Joel E. Kostka ◽  
George W. Luther ◽  
S. Craig Cary
Keyword(s):  
Deep Sea ◽  
Hydrothermal Vent ◽  
Hydrothermal Vents ◽  
Heterotrophic Bacteria ◽  
Geographic Location ◽  
Optimal Growth ◽  
Small Subunit ◽  
Ribosomal Gene ◽  
Moderately Thermophilic ◽  
Novel Bacteria

ABSTRACT Recent molecular characterizations of microbial communities from deep-sea hydrothermal sites indicate the predominance of bacteria belonging to the epsilon subdivision of Proteobacteria(epsilon Proteobacteria). Here, we report the first enrichments and characterizations of four epsilonProteobacteria that are directly associated withAlvinella pompejana, a deep sea hydrothermal vent polychete, or with hydrothermal vent chimney samples. These novel bacteria were moderately thermophilic sulfur-reducing heterotrophs growing on formate as the energy and carbon source. In addition, two of them (Am-H and Ex-18.2) could grow on sulfur lithoautrotrophically using hydrogen as the electron donor. Optimal growth temperatures of the bacteria ranged from 41 to 45°C. Phylogenetic analysis of the small-subunit ribosomal gene of the two heterotrophic bacteria demonstrated 95% similarity to Sulfurospirillum arcachonense, an epsilon Proteobacteria isolated from an oxidized marine surface sediment. The autotrophic bacteria grouped within a deeply branching clade of the epsilonProteobacteria, to date composed only of uncultured bacteria detected in a sample from a hydrothermal vent along the mid-Atlantic ridge. A molecular survey of various hydrothermal vent environments demonstrated the presence of two of these bacteria (Am-N and Am-H) in more than one geographic location and habitat. These results suggest that certain epsilonProteobacteria likely fill important niches in the environmental habitats of deep-sea hydrothermal vents, where they contribute to overall carbon and sulfur cycling at moderate thermophilic temperatures.

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