151
|
Abstract
A Gram-negative, non-motile, rod- or oval-shaped Sulfitobacter-like bacterial strain, SW-265T, was isolated from seawater at Hwajinpo, Korea, and was subjected to a polyphasic taxonomic study. Strain SW-265T grew optimally at pH 7.0–8.0 and 30 °C in the presence of 2 % (w/v) NaCl. It contained Q-10 as the predominant ubiquinone and C18 : 1
ω7c as the major fatty acid. The DNA G+C content was 57.8 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain SW-265T fell within the cluster comprising Sulfitobacter species. The levels of 16S rRNA gene sequence similarity between strain SW-265T and the type strains of Sulfitobacter species ranged from 97.1 to 98.7 %. DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain SW-265T differs from recognized Sulfitobacter species. On the basis of the phenotypic, phylogenetic and genetic data, strain SW-265T represents a novel species of the genus Sulfitobacter, for which the name Sulfitobacter marinus sp. nov. is proposed. The type strain is SW-265T (=KCTC 12738T=JCM 13602T).
Collapse
MESH Headings
- Bacterial Typing Techniques
- Base Composition
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Fatty Acids/chemistry
- Genes, rRNA/genetics
- Hydrogen-Ion Concentration
- Korea
- Molecular Sequence Data
- Movement
- Phylogeny
- Quinones/analysis
- Quinones/chemistry
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Rhodobacteraceae/classification
- Rhodobacteraceae/cytology
- Rhodobacteraceae/isolation & purification
- Rhodobacteraceae/physiology
- Seawater/microbiology
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Temperature
- Water Microbiology
Collapse
Affiliation(s)
- Jung-Hoon Yoon
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - So-Jung Kang
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| | - Tae-Kwang Oh
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), PO Box 115, Yusong, Taejon, Korea
| |
Collapse
|
152
|
Ying JY, Liu ZP, Wang BJ, Dai X, Yang SS, Liu SJ. Salegentibacter catena sp. nov., isolated from sediment of the South China Sea, and emended description of the genus Salegentibacter. Int J Syst Evol Microbiol 2007; 57:219-222. [PMID: 17267953 DOI: 10.1099/ijs.0.64658-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel marine bacterial strain, HY1T, was isolated from sediment of the South China Sea. The strain was aerobic and heterotrophic and formed saffron yellow-pigmented colonies on marine agar 2216. Cells were non-motile, Gram-negative rods, frequently occurring in chains. blastn searches revealed that the 16S rRNA gene sequence of strain HY1T showed high similarity with those of members of the genera Gillisia (91.7–93.8 %) and Salegentibacter (92.6–93.5 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain clustered with members of both Salegentibacter and Gillisia and phylogenetic trees constructed using three different methods (neighbour-joining, maximum-parsimony and minimum-evolution) indicated that strain HY1T clustered more frequently with members of the genus Salegentibacter. The DNA G+C content of strain HY1T was 44.4 mol% and its major cellular fatty acids (⩾5 % of the total fatty acids) were iso-15 : 1 (5.0 %), iso-15 : 0 (6.8 %), anteiso-15 : 0 (6.4 %), 15 : 0 (10.4 %), iso-16 : 0 (13.5 %), summed feature 3 (comprising iso-15 : 0 2-OH and/or 16 : 1ω7c; 6.3 %), iso-17 : 0 3-OH (5.2 %) and 17 : 0 2-OH (5.0 %). Cells contained menaquinone 6. Based on the phylogenetic and phenotypic analyses, strain HY1T should be classified as representing a novel species within the genus Salegentibacter, for which the name Salegentibacter catena sp. nov. is proposed. The type strain is HY1T (=CGMCC 1.6101T=JCM 14015T). Based on this study and on previously described Salegentibacter species, an emended description of the genus Salegentibacter is given.
Collapse
MESH Headings
- Aerobiosis
- Bacterial Typing Techniques
- Base Composition
- Base Sequence
- China
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Fatty Acids/chemistry
- Flavobacteriaceae/classification
- Flavobacteriaceae/cytology
- Flavobacteriaceae/isolation & purification
- Flavobacteriaceae/physiology
- Genes, rRNA/genetics
- Geologic Sediments/microbiology
- Locomotion
- Molecular Sequence Data
- Phylogeny
- Pigments, Biological/biosynthesis
- Quinones/analysis
- Quinones/chemistry
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Seawater/microbiology
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Water Microbiology
Collapse
Affiliation(s)
- Jiao-Yan Ying
- College of Biological Sciences, China Agricultural University, Beijing 100094, P. R. China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, P. R. China
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, P. R. China
| | - Bao-Jun Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, P. R. China
| | - Xin Dai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, P. R. China
| | - Su-Sheng Yang
- College of Biological Sciences, China Agricultural University, Beijing 100094, P. R. China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, P. R. China
| |
Collapse
|
153
|
Abstract
A Gram-negative bacterium, designated strain EMB117T, was isolated from a municipal wastewater treatment plant and characterized by polyphasic taxonomy. The cells were non-spore-forming rods that showed gliding motility. Optimal growth occurred at 25–30 °C and pH 7.0–8.0. Strain EMB117T contained phosphatidylethanolamine as the predominant polar lipid, and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH and summed feature 3 (C16 : 1
ω7c and/or iso-C15 : 0 2-OH). The G+C content of the genomic DNA was 33.5 mol% and the major isoprenoid quinone was MK-6. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain EMB117T belonged to the genus Flavobacterium and was most closely related to Flavobacterium johnsoniae DSM 425T (97.8 % sequence similarity). The DNA–DNA relatedness between strain EMB117T and F. johnsoniae ATCC 17061T was about 18 %. On the basis of the phenotypic, chemotaxonomic and molecular data, strain EMB117T represents a novel species within the genus Flavobacterium, for which the name Flavobacterium defluvii sp. nov. is proposed. The type strain is EMB117T (=KCTC 12612T=DSM 17963T).
Collapse
Affiliation(s)
- Minjeong Park
- Division of Applied Life Science, EB-NCRC, PMBBRC, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Seung Hyun Ryu
- Division of Applied Life Science, EB-NCRC, PMBBRC, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Thu-Huong Thi Vu
- Division of Applied Life Science, EB-NCRC, PMBBRC, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Hyeon-Su Ro
- Department of Microbiology and Research Institute of Life Science, Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Pil-Yong Yun
- Jeju Hi-Tech Industry Development Institute, 4-8 Ara-1 dong, Jeju 690-121, Republic of Korea
| | - Che Ok Jeon
- Division of Applied Life Science, EB-NCRC, PMBBRC, Gyeongsang National University, Jinju 660-701, Republic of Korea
| |
Collapse
|
154
|
Scheirlinck I, Van der Meulen R, Van Schoor A, Cleenwerck I, Huys G, Vandamme P, De Vuyst L, Vancanneyt M. Lactobacillus namurensis sp. nov., isolated from a traditional Belgian sourdough. Int J Syst Evol Microbiol 2007; 57:223-227. [PMID: 17267954 DOI: 10.1099/ijs.0.64607-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A biodiversity study on lactic acid bacteria (LAB) occurring in traditional Belgian sourdoughs resulted in the isolation of two Lactobacillus isolates, LMG 23583T and LMG 23584, that could not be assigned to any recognized LAB species. The two isolates were initially investigated by means of phenylalanyl-tRNA synthase (pheS) gene sequence analysis and were found to occupy a separate position relative to recognized Lactobacillus species present in the pheS database. Subsequently, their phylogenetic affiliation was determined by 16S rRNA gene sequence analysis, indicating that the two isolates belong to the Lactobacillus buchneri species group with Lactobacillus zymae, Lactobacillus acidifarinae and Lactobacillus spicheri as closest relatives. Whole-cell protein analysis (SDS-PAGE) and amplified fragment length polymorphism fingerprinting of whole genomes confirmed their separate taxonomic status. DNA–DNA hybridization experiments, DNA G+C content, growth characteristics and biochemical features demonstrated that the two isolates represent a novel Lactobacillus species, for which the name Lactobacillus namurensis sp. nov. is proposed. The type strain is LMG 23583T (=CCUG 52843T).
Collapse
MESH Headings
- Bacterial Proteins/analysis
- Bacterial Typing Techniques
- Base Composition
- Belgium
- DNA Fingerprinting
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Electrophoresis, Polyacrylamide Gel
- Flour/microbiology
- Food Microbiology
- Genes, rRNA/genetics
- Lactobacillus/classification
- Lactobacillus/genetics
- Lactobacillus/isolation & purification
- Lactobacillus/physiology
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phenylalanine-tRNA Ligase/genetics
- Phylogeny
- Polymorphism, Restriction Fragment Length
- Proteome/analysis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
Collapse
Affiliation(s)
- Ilse Scheirlinck
- BCCM/LMG Bacteria Collection, Department of Biochemistry, Physiology and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
- Laboratory of Microbiology, Department of Biochemistry, Physiology and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Roel Van der Meulen
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Applied Biological Sciences and Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Ann Van Schoor
- BCCM/LMG Bacteria Collection, Department of Biochemistry, Physiology and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
- Laboratory of Microbiology, Department of Biochemistry, Physiology and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Ilse Cleenwerck
- BCCM/LMG Bacteria Collection, Department of Biochemistry, Physiology and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Geert Huys
- Laboratory of Microbiology, Department of Biochemistry, Physiology and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry, Physiology and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Department of Applied Biological Sciences and Engineering, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Marc Vancanneyt
- BCCM/LMG Bacteria Collection, Department of Biochemistry, Physiology and Microbiology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium
| |
Collapse
|
155
|
Kublanov IV, Prokofeva MI, Kostrikina NA, Kolganova TV, Tourova TP, Wiegel J, Bonch-Osmolovskaya EA. Thermoanaerobacterium aciditolerans sp. nov., a moderate thermoacidophile from a Kamchatka hot spring. Int J Syst Evol Microbiol 2007; 57:260-264. [PMID: 17267961 DOI: 10.1099/ijs.0.64633-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An anaerobic, moderately thermoacidophilic bacterium, strain 761-119T, was isolated from an acidic hot spring in the Orange Field of the Uzon Caldera (Kamchatka, far-eastern Russia). Cells were spore-forming, Gram-positive rods, possessing one polar flagellum. Growth of strain 761-119Twas observed between 37 and 68 °C and in the pH20 °Crange 3.2–7.1. No growth was observed within 5 days of incubation at or below 35 °C and at or above 70 °C, as well as at or below pH20 °C2.8 and at or above pH20 °C7.5. The optimal temperature and pH20 °Cfor growth were 55 °C and pH20 °C5.7, respectively. A wide range of carbohydrates and polysaccharides were fermented, as well as peptides and proteinaceous substrates. The main products of glucose fermentation were acetate, ethanol, lactate, H2and CO2. The DNA G+C content was 34 (±0.5) mol%. 16S rRNA gene sequence analysis indicated that strain 761-119Tbelonged to the genusThermoanaerobacterium. The level of 16S rRNA gene sequence similarity with otherThermoanaerobacteriumspecies was 86.5–97.8 %, with the only moderately acidophilic member of this genus,Thermoanaerobacterium aotearoense, being one of its closest relatives. DNA–DNA hybridization withT. aotearoenseshowed 33 % relatedness. Thus, morphological (one polar flagellum) and physiological characteristics (lower pH limit of growth at pH20 °C3.2 compared withT. aotearoense) and 16S rRNA gene sequence analyses revealed that strain 761-119Trepresents a novel species in the genusThermoanaerobacterium, for which the nameThermoanaerobacterium aciditoleranssp. nov. is proposed, with the type strain 761-119T(=DSM 16487T=VKM B-2363T).
Collapse
Affiliation(s)
- I V Kublanov
- Institute of Microbiology, Russian Academy of Sciences, Prospekt 60-Letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - M I Prokofeva
- Institute of Microbiology, Russian Academy of Sciences, Prospekt 60-Letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - N A Kostrikina
- Institute of Microbiology, Russian Academy of Sciences, Prospekt 60-Letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - T V Kolganova
- Bioengineering Center, Russian Academy of Sciences, Prospect 60-Letiya Oktyabrya 7/1, 117312 Moscow, Russia
| | - T P Tourova
- Institute of Microbiology, Russian Academy of Sciences, Prospekt 60-Letiya Oktyabrya 7/2, Moscow 117312, Russia
| | - J Wiegel
- Department of Microbiology, University of Georgia, Athens, GA, USA
| | - E A Bonch-Osmolovskaya
- Institute of Microbiology, Russian Academy of Sciences, Prospekt 60-Letiya Oktyabrya 7/2, Moscow 117312, Russia
| |
Collapse
|
156
|
Yang SH, Lee JH, Ryu JS, Kato C, Kim SJ. Shewanella donghaensis sp. nov., a psychrophilic, piezosensitive bacterium producing high levels of polyunsaturated fatty acid, isolated from deep-sea sediments. Int J Syst Evol Microbiol 2007; 57:208-212. [PMID: 17267951 DOI: 10.1099/ijs.0.64469-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, motile, rod-shaped, psychrophilic bacterium, LT17T, was isolated from deep-sea sediments (3300 m depth) of the East Sea (Sea of Japan). Optimal growth of LT17T requires the presence of 2.5 % (w/v) NaCl, a pH of 7.0–7.5 and a temperature of 17 °C. The isolate grows optimally under a hydrostatic pressure of 10 MPa and growth is possible between 0.1 and <30 MPa. The novel strain is positive in tests for catalase, oxidase, lipase, β-glucosidase and gelatinase activities and reduces nitrate to nitrate. The predominant cellular fatty acids are iso-C13 : 0, iso-C15 : 0, C16 : 0, C16 : 1ω7 and C20 : 5ω3. The DNA G+C content of strain LT17T is 38.8 mol%. Phylogenetic analysis of 16S rRNA gene sequences places this bacterium in the class Gammaproteobacteria, within the genus Shewanella. The closest relatives of strain LT17T are Shewanella japonica (97.8 % gene sequence similarity), Shewanella pacifica (97.5 %), Shewanella olleyana (96.8 %), Shewanella frigidimarina (96.5 %) and Shewanella gelidimarina (95.4 %). The DNA–DNA hybridization levels between the novel isolate and its closest known phylogenetic relatives, S. japonica and S. pacifica, are lower than 14 %. On the basis of this polyphasic evidence, strain LT17T represents a novel species of the genus Shewanella, for which the name Shewanella donghaensis sp. nov. is proposed. The type strain is LT17T (=KCTC 10635BPT=JCM 12524T).
Collapse
MESH Headings
- Bacterial Proteins/analysis
- Bacterial Typing Techniques
- Base Composition
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Enzymes/analysis
- Fatty Acids/analysis
- Fatty Acids, Unsaturated/biosynthesis
- Genes, rRNA/genetics
- Geologic Sediments/microbiology
- Hydrogen-Ion Concentration
- Hydrostatic Pressure
- Japan
- Molecular Sequence Data
- Movement
- Nucleic Acid Hybridization
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Saline Solution, Hypertonic
- Seawater/microbiology
- Sequence Analysis, DNA
- Shewanella/classification
- Shewanella/cytology
- Shewanella/isolation & purification
- Shewanella/metabolism
- Temperature
- Water Microbiology
Collapse
Affiliation(s)
- Sung-Hyun Yang
- Marine Biotechnology Research Centre, Korea Ocean Research & Development Institute, PO Box 29, Ansan 425-600, Republic of Korea
| | - Jung-Hyun Lee
- Marine Biotechnology Research Centre, Korea Ocean Research & Development Institute, PO Box 29, Ansan 425-600, Republic of Korea
| | - Ji-Sun Ryu
- Marine Biotechnology Research Centre, Korea Ocean Research & Development Institute, PO Box 29, Ansan 425-600, Republic of Korea
| | - Chiaki Kato
- Research Program for Marine Biology and Ecology, Extremobiosphere Research Center, JAMSTEC, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Sang-Jin Kim
- Marine Biotechnology Research Centre, Korea Ocean Research & Development Institute, PO Box 29, Ansan 425-600, Republic of Korea
| |
Collapse
|
157
|
Ghosh A, Bhardwaj M, Satyanarayana T, Khurana M, Mayilraj S, Jain RK. Bacillus lehensis sp. nov., an alkalitolerant bacterium isolated from soil. Int J Syst Evol Microbiol 2007; 57:238-242. [PMID: 17267957 DOI: 10.1099/ijs.0.64617-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-positive, endospore-forming, alkalitolerant bacterial strain, designated MLB2T, was isolated from soil from Leh, India, and was subjected to a polyphasic taxonomic study. The strain exhibited phenotypic properties that included chemotaxonomic characteristics consistent with its classification in the genusBacillus. Growth was observed at pH 7.0–11.0, but not at pH 6.0. The DNA G+C content was 41.4 mol%. The highest level of 16S rRNA gene sequence similarity was withBacillus oshimensisJCM 12663T(98.8 %). However, DNA–DNA hybridization experiments indicated low levels of genomic relatedness with the type strains ofB. oshimensis(62 %),Bacillus patagoniensis(55 %),Bacillus clausii(51 %) andBacillus gibsonii(34 %), the species with which strain MLB2Tformed a coherent cluster (based on the results of the phylogenetic analysis). On the basis of the phenotypic characteristics and genotypic distinctiveness of strain MLB2T, it should be classified within a novel species ofBacillus, for which the nameBacillus lehensissp. nov. is proposed. The type strain is MLB2T(=MTCC 7633T=JCM 13820T).
Collapse
MESH Headings
- Alkalies/pharmacology
- Anti-Bacterial Agents/pharmacology
- Bacillus/classification
- Bacillus/cytology
- Bacillus/isolation & purification
- Bacillus/physiology
- Bacterial Typing Techniques
- Base Composition
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Drug Resistance, Bacterial
- Genes, rRNA/genetics
- Hydrogen-Ion Concentration
- India
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Soil Microbiology
Collapse
Affiliation(s)
- A Ghosh
- Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - M Bhardwaj
- Microbiology, University of Delhi, South Campus, Benito Juarez Road, New Delhi 110021, India
| | - T Satyanarayana
- Microbiology, University of Delhi, South Campus, Benito Juarez Road, New Delhi 110021, India
| | - M Khurana
- Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - S Mayilraj
- Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| | - R K Jain
- Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Sector-39A, Chandigarh 160036, India
| |
Collapse
|
158
|
Bjerregaard B, Pedersen HG, Jakobsen AS, Rickords LF, Lai L, Cheong HT, Samuel M, Prather RS, Strejcek F, Rasmussen ZR, Laurincik J, Niemann H, Maddox-Hyttel P, Thomsen PD. Activation of ribosomal RNA genes in porcine embryos produced in vitro or by somatic cell nuclear transfer. Mol Reprod Dev 2007; 74:35-41. [PMID: 16941707 DOI: 10.1002/mrd.20594] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The onset of ribosomal RNA (rRNA) synthesis occurs during the second half of the third cell cycle, that is, at the four-cell stage, in porcine embryos developed in vivo. In the present study the onset of rRNA synthesis was investigated in porcine embryos produced in vitro (IVP) or by somatic cell nuclear transfer (SCNT) using fluorescence in situ hybridization (FISH) with an rDNA probe and subsequent visualization of the nucleolar proteins by silver staining. In the 205 IVP embryos investigated, all two-cell embryos (n = 34) were categorized as transcriptionally inactive. At the late four-cell stage (n = 45), 38% of the embryos contained 1-3 nuclei with signs of rRNA transcription, indicating an asynchronous transcription initiation. This pattern continued in the following stages, as 78% (n = 47), 47% (n = 42) and 83% (n = 37) of the embryos revealed a mixture of transcriptionally inactive and active cells at the eight-cell, 16-cell and blastocyst stage, respectively. In the 143 SCNT embryos investigated, all two-cell embryos (n = 34) and early four-cell embryos (n = 12) were also transcriptionally inactive. At the late four-cell stage (n = 33) and at the eight-cell stage (n = 24) there were equal proportions of transcriptionally active and inactive embryos and essentially all embryos that developed to the 16-cell stage (n = 21) and further to the blastocyst stage (n = 19) contained only transcriptionally active cells. In conclusion, porcine embryos produced in vitro had an asynchronous pattern of rRNA transcription initiation when compared to SCNT and in vivo developed porcine embryos.
Collapse
Affiliation(s)
- Bolette Bjerregaard
- Department of Animal and Veterinary Basic Sciences, The Royal Veterinary and Agricultural University, Frederiksberg C, Denmark
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
159
|
Agatha S, Strüder-Kypke MC. Phylogeny of the order Choreotrichida (Ciliophora, Spirotricha, Oligotrichea) as inferred from morphology, ultrastructure, ontogenesis, and SSrRNA gene sequences. Eur J Protistol 2007; 43:37-63. [PMID: 17166704 PMCID: PMC2850171 DOI: 10.1016/j.ejop.2006.10.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2006] [Revised: 10/25/2006] [Accepted: 10/27/2006] [Indexed: 10/23/2022]
Abstract
The phylogeny within the order Choreotrichida is reconstructed using (i) morphologic, ontogenetic, and ultrastructural evidence for the cladistic approach and (ii) the small subunit ribosomal RNA (SSrRNA) gene sequences, including the new sequence of Rimostrombidium lacustris. The morphologic cladograms and the gene trees converge rather well for the Choreotrichida, demonstrating that hyaline and agglutinated loricae do not characterize distinct lineages, i.e., both lorica types can be associated with the most highly developed ciliary pattern. The position of Rimostrombidium lacustris within the family Strobilidiidae is corroborated by the genealogical analyses. The diagnosis of the genus Tintinnidium is improved, adding cytological features, and the genus is divided into two subgenera based on the structure of the somatic kineties. The diagnosis of the family Lohmanniellidae and the genus Lohmanniella are improved, and Rimostrombidium glacicolum Petz, Song and Wilbert, 1995 is affiliated.
Collapse
Affiliation(s)
- Sabine Agatha
- Department of Organismal Biology, University of Salzburg, Hellbrunnerstrasse 34, A-5020 Salzburg, Austria.
| | | |
Collapse
|
160
|
Bereschenko LA, Stams AJM, Heilig GHJ, Euverink GJW, Nederlof MM, Van Loosdrecht MCM. Investigation of microbial communities on reverse osmosis membranes used for process water production. Water Sci Technol 2007; 55:181-90. [PMID: 17546985 DOI: 10.2166/wst.2007.257] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
In the present study, the diversity and the phylogenetic affiliation of bacteria in a biofouling layer on reverse osmosis (RO) membranes were determined. Fresh surface water was used as a feed in a membrane-based water purification process. Total DNA was extracted from attached cells from feed spacer, RO membrane and product spacer. Universal primers were used to amplify the bacterial 16S rRNA genes. The biofilm community was analysed by 16S rRNA-gene-targeted denaturing gradient gel electrophoresis (DGGE) and the phylogenetic affiliation was determined by sequence analyses of individual 16S rDNA clones. Using this approach, we found that five distinct bacterial genotypes (Sphingomonas, Beta proteobacterium, Flavobacterium, Nitrosomonas and Sphingobacterium) were dominant genera on surfaces of fouled RO membranes. Moreover, the finding that all five "key players" could be recovered from the cartridge filters of this RO system, which cartridge filters are positioned before the RO membrane, together with literature information where these bacteria are normally encountered, suggests that these microorganisms originate from the feed water rather than from the RO system itself, and represent the fresh water bacteria present in the feed water, despite the fact that the feed water passes an ultrafiltration (UF) membrane (pore size approximately 40 nm), which is able to remove microorganisms to a large extent.
Collapse
Affiliation(s)
- L A Bereschenko
- Wetsus, Centre for Sustainable Water Technology, 8900 CC, Leeuwarden.
| | | | | | | | | | | |
Collapse
|
161
|
Lauro FM, Chastain RA, Blankenship LE, Yayanos AA, Bartlett DH. The unique 16S rRNA genes of piezophiles reflect both phylogeny and adaptation. Appl Environ Microbiol 2006; 73:838-45. [PMID: 17158629 PMCID: PMC1800765 DOI: 10.1128/aem.01726-06] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the ocean's most extreme depths, pressures of 70 to 110 megapascals prevent the growth of all but the most hyperpiezophilic (pressure-loving) organisms. The physiological adaptations required for growth under these conditions are considered to be substantial. Efforts to determine specific adaptations permitting growth at extreme pressures have thus far focused on relatively few gamma-proteobacteria, in part due to the technical difficulties of obtaining piezophilic bacteria in pure culture. Here, we present the molecular phylogenies of several new piezophiles of widely differing geographic origins. Included are results from an analysis of the first deep-trench bacterial isolates recovered from the southern hemisphere (9.9-km depth) and of the first gram-positive piezophilic strains. These new data allowed both phylogenetic and structural 16S rRNA comparisons among deep-ocean trench piezophiles and closely related strains not adapted to high pressure. Our results suggest that (i) the Circumpolar Deep Water acts as repository for hyperpiezophiles and drives their dissemination to deep trenches in the Pacific Ocean and (ii) the occurrence of elongated helices in the 16S rRNA genes increases with the extent of adaptation to growth at elevated pressure. These helix changes are believed to improve ribosome function under deep-sea conditions.
Collapse
Affiliation(s)
- Federico M Lauro
- Center for Marine Biotechnology and Biomedicine, Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0202, USA
| | | | | | | | | |
Collapse
|
162
|
Fiala I. The phylogeny of Myxosporea (Myxozoa) based on small subunit ribosomal RNA gene analysis. Int J Parasitol 2006; 36:1521-34. [PMID: 16904677 DOI: 10.1016/j.ijpara.2006.06.016] [Citation(s) in RCA: 367] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2006] [Revised: 06/27/2006] [Accepted: 06/30/2006] [Indexed: 10/24/2022]
Abstract
The phylogeny of the Myxosporea was studied using the small-subunit ribosomal RNA gene sequences. Maximum parsimony and Bayesian inference were used to determine myxosporean phylogenetic relationships. The analysis included 120 myxosporean sequences retrieved from GenBank and 21 newly obtained sequences of myxosporeans representing nine genera. Members of the genera Palliatus and Auerbachia were sequenced for the first time. The phylogenetic analysis supported a split of myxosporeans into two main lineages separating most of freshwater species from marine ones as described by previous authors. In addition to the two main lineages, a third lineage consisting of three species was found (Sphaerospora truttae, Sphaerospora elegans and Leptotheca ranae) and additional exceptions to the marine/freshwater myxosporean split were recognised (Sphaeromyxa hellandi, Sphaeromyxa longa and Myxidium coryphaenoideum). All three myxosporean lineages were characterised by specific lengths of SSU rDNA sequences. The lineage of marine myxosporeans split into five well-defined clades. They consisted of species with a similar site of infection and spore morphology and were referred as the Parvicapsula clade, the Enteromyxum clade, the Ceratomyxa clade, the marine Myxidium clade and the Kudoa clade, respectively. The inner topology of the freshwater clade was more complex but the trend to branch according to site of infection was observed in this clade as well. Due to the number of sequences available, a histozoic (Myxobolus clade) predominated. Interestingly, five morphologically different species infecting urinary bladder clustered within the histozoic (Myxobolus) clade. The phylogenetic trees derived from this study differ in a number of respects from the current taxonomy of the myxosporeans, which suggests that several currently utilised characters may be homoplasious or that reliance on a single gene tree may not adequately reflect the phylogeny of the group.
Collapse
Affiliation(s)
- Ivan Fiala
- Institute of Parasitology and Faculty of Biological Sciences, Academy of Sciences of the Czech Republic, University of South Bohemia, Branisovská 31, 370 05 Ceské Budejovice, Czech Republic.
| |
Collapse
|
163
|
Gong YC, Yu YH, Villalobo E, Zhu FY, Miao W. Reevaluation of the phylogenetic relationship between mobilid and sessilid peritrichs (Ciliophora, Oligohymenophorea) based on small subunit rRNA genes sequences. J Eukaryot Microbiol 2006; 53:397-403. [PMID: 16968459 DOI: 10.1111/j.1550-7408.2006.00121.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Based on morphological characters, peritrich ciliates (Class Olygohymenophorea, Subclass Peritrichia) have been subdivided into the Orders Sessilida and Mobilida. Molecular phylogenetic studies on peritrichs have been restricted to members of the Order Sessilida. In order to shed more light into the evolutionary relationships within peritrichs, the complete small subunit rRNA (SSU rRNA) sequences of four mobilid species, Trichodina nobilis, Trichodina heterodentata, Trichodina reticulata, and Trichodinella myakkae were used to construct phylogenetic trees using maximum parsimony, neighbor joining, and Bayesian analyses. Whatever phylogenetic method used, the peritrichs did not constitute a monophyletic group: mobilid and sessilid species did not cluster together. Similarity in morphology but difference in molecular data led us to suggest that the oral structures of peritrichs are the result of evolutionary convergence. In addition, Trichodina reticulata, a Trichodina species with granules in the center of the adhesive disc, branched separately from its congeners, Trichodina nobilis and Trichodina heterodentata, trichodinids without such granules. This indicates that granules in the adhesive disc might be a phylogenetic character of high importance within the Family Trichodinidae.
Collapse
Affiliation(s)
- Ying-Chun Gong
- Laboratory of Taxonomy and Ecology of Protozoa, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan 430072, China
| | | | | | | | | |
Collapse
|
164
|
Valenza G, Burgemeister S, Girschick H, Schoen C, Veihelmann S, Moter A, Haban V, Vogel U, Schlagenhauf U. Analysis of the periodontal microbiota in childhood-type hypophosphatasia. Int J Med Microbiol 2006; 296:493-500. [PMID: 16875876 DOI: 10.1016/j.ijmm.2006.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2006] [Revised: 05/16/2006] [Accepted: 05/29/2006] [Indexed: 11/21/2022] Open
Abstract
Seven patients with childhood-type hypophosphatasia and healthy control subjects were analysed for microbiological and clinical evidence of periodontitis. The bacterial composition of the subgingival plaque was analysed by 16S rRNA gene cloning and sequencing, DNA-DNA hybridisation with specific probes, and specific PCR. With the exception of the genus Veillonella and the species Eikenella corrodens, no differences between the cohorts in the composition of bacterial orders, families, genera, and species were observed. Accordingly, patients showed only slightly more bleeding on probing (BOP), and slightly higher periodontal probing depth (PPD) values than controls. Although this pilot study did not have the power to assess the prevalence of periodontitis in HP, we suggest that most paediatric patients suffering from HP harbour a subgingival microbiota, which is comparable to that of the healthy population.
Collapse
MESH Headings
- Adolescent
- Adult
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- Child
- Cohort Studies
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Dental Plaque/microbiology
- Genes, rRNA/genetics
- Humans
- Hypophosphatasia/complications
- Male
- Molecular Sequence Data
- Nucleic Acid Hybridization
- Periodontal Index
- Periodontal Pocket/pathology
- Periodontitis/microbiology
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
Collapse
Affiliation(s)
- Giuseppe Valenza
- Institute for Hygiene and Microbiology, University of Würzburg, Josef-Schneider-Strasse 2/E1, D-97080 Würzburg, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
165
|
Abstract
Marine actinomycetes belonging to the genus Salinispora were cultured from marine sediments collected at six geographically distinct locations. Detailed phylogenetic analyses of both 16S rRNA and gyrB gene sequences reveal that this genus is comprised of three distinct but closely related clades corresponding to the species Salinispora tropica, Salinispora arenicola and a third species for which the name 'Salinispora pacifica' is proposed. Salinispora arenicola was cultured from all locations sampled and provides clear evidence for the cosmopolitan distribution of an individual bacterial species. The co-occurrence of S. arenicola with S. tropica and S. pacifica suggests that ecological differentiation as opposed to geographical isolation is driving speciation within the genus. All Salinispora strains cultured to date share greater than 99% 16S rRNA gene sequence identity and thus comprise what has been described as a microdiverse ribotype cluster. The description of this cluster as a new genus, containing multiple species, provides clear evidence that fine-scale 16S rDNA sequence analysis can be used to delineate among closely related species and that more conservative operational taxonomic unit values may significantly underestimate global species diversity.
Collapse
Affiliation(s)
- Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, CA, USA.
| | | |
Collapse
|
166
|
Fischer JM, Keely SP, Stringer JR. Evolutionary Rate of Ribosomal DNA in Pneumocystis Species is Normal Despite the Extraordinarily Low Copy-Number of rDNA Genes. J Eukaryot Microbiol 2006; 53 Suppl 1:S156-8. [PMID: 17169042 DOI: 10.1111/j.1550-7408.2006.00213.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jared M Fischer
- University of Cincinnati, Department of Molecular Genetics, Biochemistry and Microbiology, Cincinnati, Ohio 45267-0524, USA
| | | | | |
Collapse
|
167
|
Clark CG, Kaffashian F, Tawari B, Windsor JJ, Twigg-Flesner A, Davies-Morel MCG, Blessmann J, Ebert F, Peschel B, Van AL, Jackson CJ, Macfarlane L, Tannich E. New insights into the phylogeny of Entamoeba species provided by analysis of four new small-subunit rRNA genes. Int J Syst Evol Microbiol 2006; 56:2235-2239. [PMID: 16957127 DOI: 10.1099/ijs.0.64208-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sequences of small-subunit rRNA genes have been obtained for four new isolates of Entamoeba. Phylogenetic analyses give new insights into the evolution of these organisms. A novel Entamoeba from pigs in Vietnam that produces uninucleate cysts proved to be unrelated to other uninucleated cyst-producing species. Revival of the name Entamoeba suis for this organism is proposed. Instead of being related to Entamoeba polecki, it shares a recent common ancestor with the non-encysting Entamoeba gingivalis in a lineage that is basal to the tetranucleate cyst-producing clade. This suggests that species producing cysts with four nuclei are descended from an ancestor that produced cysts with a single nucleus. An Entamoeba from a horse was isolated in culture. No cysts were observed in the original stool sample but the sequence is placed unequivocally within the clade of tetranucleate cyst-producing species with no other sequences being specifically related. Revival of the name Entamoeba equi for this organism is proposed. The Entamoeba ecuadoriensis sequence was found to be the most closely related to Entamoeba histolytica and Entamoeba dispar, as predicted, despite the organism having been an environmental isolate originally assigned to Entamoeba moshkovskii. Finally, a partial E. polecki gene sequence from a pig proved to be virtually identical to that of Entamoeba struthionis from an ostrich, suggesting that the latter name is a synonym.
Collapse
Affiliation(s)
- C Graham Clark
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Farrokh Kaffashian
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Blessing Tawari
- Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Jeffrey J Windsor
- National Public Health Service for Wales Aberystwyth, Bronglais Hospital, Aberystwyth, Ceredigion SY23 1ER, UK
| | - Anke Twigg-Flesner
- Institute of Rural Sciences, University of Wales, Aberystwyth, Ceredigion SY23 3AL, UK
| | - Mina C G Davies-Morel
- Institute of Rural Sciences, University of Wales, Aberystwyth, Ceredigion SY23 3AL, UK
| | - Joerg Blessmann
- Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, D-20359 Hamburg, Germany
| | - Frank Ebert
- Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, D-20359 Hamburg, Germany
| | - Babett Peschel
- Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, D-20359 Hamburg, Germany
| | - An Le Van
- Medical College, University of Hué, Hué, Vietnam
| | - Colin J Jackson
- Institute of Rural Sciences, University of Wales, Aberystwyth, Ceredigion SY23 3AL, UK
| | - Lorna Macfarlane
- National Public Health Service for Wales Aberystwyth, Bronglais Hospital, Aberystwyth, Ceredigion SY23 1ER, UK
| | - Egbert Tannich
- Department of Molecular Parasitology, Bernhard Nocht Institute for Tropical Medicine, D-20359 Hamburg, Germany
| |
Collapse
|
168
|
Dombrink-Kurtzman MA. The sequence of the isoepoxydon dehydrogenase gene of the patulin biosynthetic pathway in Penicillium species. Antonie van Leeuwenhoek 2006; 91:179-89. [PMID: 17043910 DOI: 10.1007/s10482-006-9109-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2006] [Accepted: 07/20/2006] [Indexed: 10/24/2022]
Abstract
Interest in species of the genus Penicillium is related to their ability to produce the mycotoxin patulin and to cause spoilage of fruit products worldwide. The sequence of the isoepoxydon dehydrogenase (idh) gene, a gene in the patulin biosynthetic pathway, was determined for 28 strains representing 12 different Penicillium species known to produce the mycotoxin patulin. Isolates of Penicillium carneum, Penicillium clavigerum, Penicillium concentricum, Penicillium coprobium, Penicillium dipodomyicola, Penicillium expansum, Penicillium gladioli, Penicillium glandicola, Penicillium griseofulvum, Penicillium paneum, Penicillium sclerotigenum and Penicillium vulpinum were compared. Primer pairs for DNA amplification and sequencing were designed from the P. griseofulvum idh gene (GenBank AF006680). The two introns present were removed from the nucleotide sequences, which were translated to produce the IDH sequences of the 12 species for comparison. Phylogenetic relationships among the species were determined from rDNA (ITS1, 5.8 S, ITS2 and partial sequence of 28S rDNA) and from the idh nucleotide sequences minus the two introns. Maximum parsimony analysis showed trees based on rDNA and idh sequences to be congruent. It is anticipated that the genetic information obtained in the present study will aid in the design of probes, specific for patulin biosynthetic pathway genes, to identify the presence of these mycotoxigenic fungi.
Collapse
MESH Headings
- Amino Acid Sequence
- Biosynthetic Pathways/genetics
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Fungal/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Fungal Proteins/genetics
- Genes, rRNA/genetics
- Introns/genetics
- Molecular Sequence Data
- Oxidoreductases/genetics
- Patulin/biosynthesis
- Penicillium/enzymology
- Penicillium/genetics
- Phylogeny
- RNA, Fungal/genetics
- RNA, Ribosomal, 28S/genetics
- Sequence Alignment
- Sequence Analysis, DNA
Collapse
Affiliation(s)
- Mary Ann Dombrink-Kurtzman
- Mycotoxin Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, United States Department of Agriculture, Peoria, IL 61604-3902, USA.
| |
Collapse
|
169
|
López-Cortés A, Fardeau ML, Fauque G, Joulian C, Ollivier B. Reclassification of the sulfate- and nitrate-reducing bacterium Desulfovibrio vulgaris subsp. oxamicus as Desulfovibrio oxamicus sp. nov., comb. nov. Int J Syst Evol Microbiol 2006; 56:1495-1499. [PMID: 16825618 DOI: 10.1099/ijs.0.64074-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Desulfovibrio vulgaris subsp. oxamicus (type strain, DSM 1925(T)) was found to use nitrate as a terminal electron acceptor, the latter being reduced to ammonium. Phylogenetic studies indicated that strain DSM 1925(T) was distantly related to the type strain of Desulfovibrio vulgaris (95.4 % similarity of the small-subunit rRNA gene) and had as its closest phylogenetic relatives two other nitrate- and sulfate-reducing bacteria, namely Desulfovibrio termitidis (99.4 % similarity) and Desulfovibrio longreachensis (98.4 % similarity). Additional experiments were conducted to characterize better strain DSM 1925(T). This strain incompletely oxidized lactate and ethanol to acetate. It also oxidized butanol, pyruvate and citrate, but not glucose, fructose, acetate, propionate, butyrate, methanol, glycerol or peptone. The optimum temperature for growth was 37 degrees C (range 16-50 degrees C) and the optimum NaCl concentration for growth was 0.1 % (range 0-5 %). Because of significant genotypic and phenotypic differences from Desulfovibrio termitidis and Desulfovibrio longreachensis, reclassification of Desulfovibrio vulgaris subsp. oxamicus as Desulfovibrio oxamicus sp. nov., comb. nov., is proposed. The type strain is strain Monticello 2(T) (=DSM 1925(T)=NCIMB 9442(T)=ATCC 33405(T)).
Collapse
MESH Headings
- Carbohydrate Metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Desulfovibrio/classification
- Desulfovibrio/genetics
- Desulfovibrio/metabolism
- Desulfovibrio/physiology
- Desulfovibrio vulgaris/classification
- Desulfovibrio vulgaris/genetics
- Desulfovibrio vulgaris/metabolism
- Desulfovibrio vulgaris/physiology
- Genes, rRNA/genetics
- Growth Inhibitors/pharmacology
- Molecular Sequence Data
- Nitrates/metabolism
- Oxidation-Reduction
- Peptones/metabolism
- Phylogeny
- Quaternary Ammonium Compounds/metabolism
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Sodium Chloride/pharmacology
- Sulfates/metabolism
Collapse
Affiliation(s)
- Alejandro López-Cortés
- Laboratorio de Ecología Microbiana Molecular, Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Mar Bermejo 195, Playa Palo Santa Rita, La Paz, Baja California Sur, 23090, Mexico
| | - Marie-Laure Fardeau
- Laboratoire de Microbiologie IRD, Universités de Provence et de la Méditerranée, 163 avenue de Luminy, ESIL-GBMA, Case 925, 13288 Marseille Cedex 9, France
| | - Guy Fauque
- Laboratoire de Microbiologie, Géochimie et Ecologie Marines, UMR CNRS 6117, Campus de Luminy, Case 901, 13288 Marseille Cedex 9, France
- Laboratoire de Microbiologie IRD, Universités de Provence et de la Méditerranée, 163 avenue de Luminy, ESIL-GBMA, Case 925, 13288 Marseille Cedex 9, France
| | - Catherine Joulian
- BRGM, Environment and Process Division, Biotechnology Unit, 2, avenue Claude Guillemin, 45060 Orléans Cedex 2, France
| | - Bernard Ollivier
- Laboratoire de Microbiologie IRD, Universités de Provence et de la Méditerranée, 163 avenue de Luminy, ESIL-GBMA, Case 925, 13288 Marseille Cedex 9, France
| |
Collapse
|
170
|
Van den Bulck K, Decostere A, Baele M, Vandamme P, Mast J, Ducatelle R, Haesebrouck F. Helicobacter cynogastricus sp. nov., isolated from the canine gastric mucosa. Int J Syst Evol Microbiol 2006; 56:1559-1564. [PMID: 16825630 DOI: 10.1099/ijs.0.63860-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, microaerophilic helical rod, isolated from the gastric mucosa of a dog and designated strain JKM4(T), was subjected to a polyphasic taxonomic study. The tightly coiled organism, measuring 10-18 mum long and up to 1 mum wide, was motile by means of multiple sheathed flagella located at both ends of the cell and by a periplasmic fibril running along the external side of the helix. Strain JKM4(T) grew preferably on biphasic culture plates or on very moist agar. Coccoid forms predominated in cultures older than 4 days as well as in growth obtained on dry agar plates. The strain grew at 30 and 37 degrees C, but not at 25 or 42 degrees C and exhibited urease, oxidase and catalase activities. On the basis of 16S rRNA gene sequence analysis, the novel isolate was identified as a member of the genus Helicobacter and showed > 97 % similarity to Helicobacter felis, Helicobacter bizzozeronii and Helicobacter salomonis, three species previously isolated from the canine gastric mucosa. Protein profiling of strain JKM4(T) using SDS-PAGE revealed a pattern different from those of other Helicobacter species of mammalian gastric origin and from Helicobacter canis. Additionally, the urease gene sequence of strain JKM4(T) was different from those of urease genes of H. felis, H. bizzozeronii, H. salomonis and "Candidatus Helicobacter heilmannii". It is thus proposed that strain JKM4(T) (=LMG 23188(T)) represents a novel species within this genus, Helicobacter cynogastricus sp. nov.
Collapse
MESH Headings
- Animals
- Bacterial Proteins/analysis
- Bacterial Proteins/isolation & purification
- Catalase/analysis
- Cluster Analysis
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Dog Diseases/microbiology
- Dogs
- Electrophoresis, Polyacrylamide Gel
- Flagella/physiology
- Gastric Mucosa/microbiology
- Genes, rRNA/genetics
- Helicobacter/classification
- Helicobacter/cytology
- Helicobacter/isolation & purification
- Helicobacter/physiology
- Helicobacter Infections/microbiology
- Helicobacter Infections/veterinary
- Molecular Sequence Data
- Movement
- Oxidoreductases/analysis
- Phylogeny
- Proteome/analysis
- Proteome/isolation & purification
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Temperature
- Urease/analysis
- Urease/genetics
Collapse
Affiliation(s)
- K Van den Bulck
- Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
| | - A Decostere
- Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
| | - M Baele
- Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
| | - P Vandamme
- Department of Biochemistry, Physiology and Microbiology, Faculty of Sciences, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - J Mast
- CODA-CERVA-VAR, Groeselenberg 99, B-1180 Brussels, Belgium
| | - R Ducatelle
- Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
| | - F Haesebrouck
- Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
| |
Collapse
|
171
|
Henry S, Bru D, Stres B, Hallet S, Philippot L. Quantitative detection of the nosZ gene, encoding nitrous oxide reductase, and comparison of the abundances of 16S rRNA, narG, nirK, and nosZ genes in soils. Appl Environ Microbiol 2006; 72:5181-9. [PMID: 16885263 PMCID: PMC1538733 DOI: 10.1128/aem.00231-06] [Citation(s) in RCA: 432] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nitrous oxide (N2O) is an important greenhouse gas in the troposphere controlling ozone concentration in the stratosphere through nitric oxide production. In order to quantify bacteria capable of N2O reduction, we developed a SYBR green quantitative real-time PCR assay targeting the nosZ gene encoding the catalytic subunit of the nitrous oxide reductase. Two independent sets of nosZ primers flanking the nosZ fragment previously used in diversity studies were designed and tested (K. Kloos, A. Mergel, C. Rösch, and H. Bothe, Aust. J. Plant Physiol. 28:991-998, 2001). The utility of these real-time PCR assays was demonstrated by quantifying the nosZ gene present in six different soils. Detection limits were between 10(1) and 10(2) target molecules per reaction for all assays. Sequence analysis of 128 cloned quantitative PCR products confirmed the specificity of the designed primers. The abundance of nosZ genes ranged from 10(5) to 10(7) target copies g(-1) of dry soil, whereas genes for 16S rRNA were found at 10(8) to 10(9) target copies g(-1) of dry soil. The abundance of narG and nirK genes was within the upper and lower limits of the 16S rRNA and nosZ gene copy numbers. The two sets of nosZ primers gave similar gene copy numbers for all tested soils. The maximum abundance of nosZ and nirK relative to 16S rRNA was 5 to 6%, confirming the low proportion of denitrifiers to total bacteria in soils.
Collapse
Affiliation(s)
- S Henry
- INRA-University of Burgundy, Microbiology and Soil Geochemistry, CMSE, 17 rue Sully, B.P. 86510, 21065 Dijon Cedex, France
| | | | | | | | | |
Collapse
|
172
|
Saha P, Chakrabarti T. Emticicia oligotrophica gen. nov., sp. nov., a new member of the family 'Flexibacteraceae', phylum Bacteroidetes. Int J Syst Evol Microbiol 2006; 56:991-995. [PMID: 16627643 DOI: 10.1099/ijs.0.64086-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aquatic bacterium, strain GPTSA100-15T, was isolated on nutritionally poor medium TSBA100 (tryptic soy broth diluted 100 times and solidified with 1.5 % agarose) and characterized using a polyphasic approach. The isolate was unable to grow on commonly used nutritionally rich media such as tryptic soy agar, nutrient agar and Luria-Bertani agar. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was affiliated with the family 'Flexibacteraceae' in the phylum Bacteroidetes. Phylogenetically, it showed closest similarity (94.0 %) with an uncultured bacterial clone, HP1A92, detected in a sludge microbial community. Among the culturable bacteria, the isolate had highest 16S rRNA gene sequence similarity with Leadbetterella byssophila 4M15T (87.8 %). Sequence similarities with other members of the phylum Bacteroidetes were less than 85 %. The fatty acid profile of the isolate grown on TSBA100 indicated that the major fatty acid was iso-C15:0, which is also present in many members of the family 'Flexibacteraceae'. Cells of strain GPTSA100-15T are Gram-negative, strictly aerobic rods. The DNA G+C content of the isolate is 36.9 mol%. Results of phenotypic, chemotaxonomic and phylogenetic analyses clearly indicate that strain GPTSA100-15T represents a new genus within the family 'Flexibacteraceae'; the name Emticicia gen. nov. is proposed for the genus, with Emticicia oligotrophica sp. nov. as the type species. The type strain of Emticicia oligotrophica is GPTSA100-15T (=MTCC 6937T=DSM 17448T).
Collapse
Affiliation(s)
- P Saha
- Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Sector 39A, Chandigarh 160 036, India
| | - T Chakrabarti
- Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Sector 39A, Chandigarh 160 036, India
| |
Collapse
|
173
|
Sato Y, Nishihara H, Yoshida M, Watanabe M, Rondal JD, Concepcion RN, Ohta H. Cupriavidus pinatubonensis sp. nov. and Cupriavidus laharis sp. nov., novel hydrogen-oxidizing, facultatively chemolithotrophic bacteria isolated from volcanic mudflow deposits from Mt. Pinatubo in the Philippines. Int J Syst Evol Microbiol 2006; 56:973-978. [PMID: 16627640 DOI: 10.1099/ijs.0.63922-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Taxonomic studies were performed on ten hydrogen-oxidizing, facultatively chemolithotrophic bacteria that were isolated from volcanic mudflow deposits derived from the eruption of Mt. Pinatubo in the Philippines in 1991. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these isolates belonged to the genus Cupriavidus of the Betaproteobacteria; sequence similarity values with their nearest phylogenetic neighbour, Cupriavidus basilensis, were 97.1-98.3 %. In addition to phylogenetic analysis, results of whole-cell protein profiles and biochemical tests revealed that these strains were members of two distinct species. DNA-DNA hybridizations and whole-cell protein profiles enabled these isolates to be differentiated from related Cupriavidus species with validly published names. The isolates were aerobic, Gram-negative, non-sporulating, peritrichously flagellated rods. Their G+C contents ranged from 65.2 to 65.9 mol% and their major isoprenoid quinone was ubiquinone Q-8. On the basis of these results, two novel species are proposed, Cupriavidus pinatubonensis sp. nov. [nine strains, with 1245T (=CIP 108725T=PNCM 10346T) as the type strain] and Cupriavidus laharis sp. nov. [one strain, the type strain 1263aT (=CIP 108726T=PNCM 10347T)]. It is also suggested that Ralstonia sp. LMG 1197 (=JMP 134) should be included in the species C. pinatubonensis.
Collapse
Affiliation(s)
- Yoshinori Sato
- Department of Bioresource Science, Ibaraki University College of Agriculture, Ami-machi, Ibaraki 300-0393, Japan
| | - Hirofumi Nishihara
- Department of Bioresource Science, Ibaraki University College of Agriculture, Ami-machi, Ibaraki 300-0393, Japan
| | - Masao Yoshida
- Department of Bioresource Science, Ibaraki University College of Agriculture, Ami-machi, Ibaraki 300-0393, Japan
| | - Makiko Watanabe
- Department of Environmental Science and Technology, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Nagatsuda, Midori-ku, Yokohama 226-8503, Japan
| | - Jose D Rondal
- Soils Research and Development Centre, Bureau of Soils and Water Management, Diliman, Quezon City, Philippines
| | - Rogelio N Concepcion
- Soils Research and Development Centre, Bureau of Soils and Water Management, Diliman, Quezon City, Philippines
| | - Hiroyuki Ohta
- Department of Bioresource Science, Ibaraki University College of Agriculture, Ami-machi, Ibaraki 300-0393, Japan
| |
Collapse
|
174
|
Mayilraj S, Krishnamurthi S, Saha P, Saini HS. Rhodococcus kroppenstedtii sp. nov., a novel actinobacterium isolated from a cold desert of the Himalayas, India. Int J Syst Evol Microbiol 2006; 56:979-982. [PMID: 16627641 DOI: 10.1099/ijs.0.63831-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic position of an actinomycete, strain K07-23T, isolated from a cold desert of the Himalayas, India, was established by a polyphasic approach. The strain exhibited phenotypic characters that were typical of the genus Rhodococcus. 16S rRNA gene sequence (1467 bases) comparisons confirmed that strain K07-23T belongs to the genus Rhodococcus. 16S rRNA sequence similarity studies showed that the isolate is very closely related to Nocardia corynebacterioides DSM 20151T (98.6 %), which has been recently reclassified as Rhodococcus corynebacterioides. It showed 94.4-96.6 % sequence similarity with other species of the genus Rhodococcus. However, genomic relatedness between strain K07-23T and R. corynebacterioides as revealed by DNA-DNA hybridization was low (62 %). Based on polyphasic analysis, strain K07-23T could be clearly distinguished from other species. It is proposed that strain K07-23T (=MTCC 6634T=DSM 44908T=JCM 13011T) represents a novel species of Rhodococcus, Rhodococcus kroppenstedtii sp. nov.
Collapse
Affiliation(s)
- S Mayilraj
- Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Chandigarh 160 036, India
| | - S Krishnamurthi
- Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Chandigarh 160 036, India
| | - P Saha
- Microbial Type Culture Collection and Gene Bank (MTCC), Institute of Microbial Technology, Chandigarh 160 036, India
| | - H S Saini
- Department of Microbiology, Guru Nanak Dev University (GNDU), Amritsar 143 005, India
| |
Collapse
|
175
|
Nowlan B, Dodia MS, Singh SP, Patel BKC. Bacillus okhensis sp. nov., a halotolerant and alkalitolerant bacterium from an Indian saltpan. Int J Syst Evol Microbiol 2006; 56:1073-1077. [PMID: 16627657 DOI: 10.1099/ijs.0.63861-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A strictly aerobic, rod-shaped bacterium (0.6-0.8 x2-3 microm), designated strain Kh10-101T, was isolated from a saltpan (22 degrees 15' N, 69 degrees 1' E) in the vicinity of Port Okha, India. The creamish pigmented colonies of strain Kh10-101T were round, flat and translucent with irregular margins and a smooth surface. The strain possessed up to three subpolar flagella, and was motile by a corkscrew motion. The strain grew optimally at 37 degrees C (temperature growth range 25-40 degrees C) in a complex glucose-containing medium with 5 % NaCl (NaCl growth range 0-10 %) at pH 9 (pH growth range pH 7-10), indicating that it was a mesophilic halotolerant alkaliphile. The strain was sensitive to lincomycin, meticillin, cefuroxime and cephalexin, but resistant to gentamicin, tetracycline and cotrimazine. Spores were not detected and cells were heat sensitive. The isolate metabolized a range of carbohydrates and hydrolysed casein, gelatin and starch. Growth was not observed on aromatic compounds, Tween 40 or Tween 80. Nitrate was not reduced and catalase was produced. Electron microscopic examination of thin sections revealed a single thick Gram-positive cell wall. The DNA G+C content was 41+/-1 mol%. Phylogenetic analyses of the 16S rRNA gene sequence revealed that strain Kh10-101T was a member of the sixth rRNA group of the genus Bacillus, which includes alkalitolerant, alkaliphilic and halotolerant species. The halotolerant obligate alkaliphile Bacillus krulwichiae is the closest relative of strain Kh10-101T (96 % similarity) but a number of phenotypic differences suggest that strain Kh10-101T (=JCM 13040T=ATCC BAA-1137T) should be designated the type strain of a new species, for which the name Bacillus okhensis sp. nov. is proposed.
Collapse
MESH Headings
- Aerobiosis
- Anti-Bacterial Agents/pharmacology
- Bacillus/classification
- Bacillus/cytology
- Bacillus/isolation & purification
- Bacillus/physiology
- Bacterial Typing Techniques
- Base Composition
- Carbohydrate Metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Drug Resistance, Multiple, Bacterial
- Flagella/ultrastructure
- Genes, rRNA/genetics
- Growth Inhibitors/pharmacology
- Hydrogen-Ion Concentration
- India
- Microbial Sensitivity Tests
- Molecular Sequence Data
- Movement
- Phylogeny
- Pigments, Biological/biosynthesis
- Proteins/metabolism
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sodium Chloride/pharmacology
- Soil Microbiology
- Temperature
Collapse
Affiliation(s)
- Bianca Nowlan
- Microbial Gene Research and Resources Facility, School of Biomolecular and Biomedical Sciences, Griffith University, Brisbane, Australia 4111
| | - Mital S Dodia
- Department of Biosciences, Saurashtra University, Rajkot, India 360005
| | - Satya P Singh
- Department of Biosciences, Saurashtra University, Rajkot, India 360005
| | - B K C Patel
- Microbial Gene Research and Resources Facility, School of Biomolecular and Biomedical Sciences, Griffith University, Brisbane, Australia 4111
| |
Collapse
|
176
|
Abstract
About half of the rRNA gene units (rDNA units) of Drosophila melanogaster are inserted by the retrotransposable elements R1 and R2. Because transcripts to R1 and R2 were difficult to detect on blots and electron microscopic observations of rRNA synthesis suggested that only uninserted rDNA units were transcribed, it has long been postulated that inserted rDNA units are in a repressed (inactive) chromatin structure. Studies described here suggest that inserted and uninserted units are equally accessible to DNase I and micrococcal nuclease and contain similar levels of histone H3 and H4 acetylation and H3K9 methylation. These studies have low sensitivity, because psoralen cross-linking suggested few (estimated <10%) of the rDNA units of any type are transcriptionally active. Nuclear run-on experiments revealed that R1-inserted and R2-inserted units are activated for transcription at about 1/5 and 1/10, respectively, the rate of uninserted units. Most transcription complexes of the inserted units terminate within the elements, thus explaining why previous molecular and electron microscopic methods indicated inserted units are seldom transcribed. The accumulating data suggest that all units within small regions of the rDNA loci are activated for transcription, with most control over R1 and R2 activity involving steps downstream of transcription initiation.
Collapse
Affiliation(s)
- Junqiang Ye
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | | |
Collapse
|
177
|
Leininger S, Urich T, Schloter M, Schwark L, Qi J, Nicol GW, Prosser JI, Schuster SC, Schleper C. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 2006; 442:806-9. [PMID: 16915287 DOI: 10.1038/nature04983] [Citation(s) in RCA: 1128] [Impact Index Per Article: 62.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2006] [Accepted: 06/19/2006] [Indexed: 01/03/2023]
Abstract
Ammonia oxidation is the first step in nitrification, a key process in the global nitrogen cycle that results in the formation of nitrate through microbial activity. The increase in nitrate availability in soils is important for plant nutrition, but it also has considerable impact on groundwater pollution owing to leaching. Here we show that archaeal ammonia oxidizers are more abundant in soils than their well-known bacterial counterparts. We investigated the abundance of the gene encoding a subunit of the key enzyme ammonia monooxygenase (amoA) in 12 pristine and agricultural soils of three climatic zones. amoA gene copies of Crenarchaeota (Archaea) were up to 3,000-fold more abundant than bacterial amoA genes. High amounts of crenarchaeota-specific lipids, including crenarchaeol, correlated with the abundance of archaeal amoA gene copies. Furthermore, reverse transcription quantitative PCR studies and complementary DNA analysis using novel cloning-independent pyrosequencing technology demonstrated the activity of the archaea in situ and supported the numerical dominance of archaeal over bacterial ammonia oxidizers. Our results indicate that crenarchaeota may be the most abundant ammonia-oxidizing organisms in soil ecosystems on Earth.
Collapse
Affiliation(s)
- S Leininger
- Department of Biology, University of Bergen, Jahnebakken 5, N-5020 Bergen, Norway
| | | | | | | | | | | | | | | | | |
Collapse
|
178
|
Oakes ML, Johzuka K, Vu L, Eliason K, Nomura M. Expression of rRNA genes and nucleolus formation at ectopic chromosomal sites in the yeast Saccharomyces cerevisiae. Mol Cell Biol 2006; 26:6223-38. [PMID: 16880531 PMCID: PMC1592796 DOI: 10.1128/mcb.02324-05] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We constructed yeast strains in which rRNA gene repeats are integrated at ectopic sites in the presence or absence of the native nucleolus. At all three ectopic sites analyzed, near centromere CEN5, near the telomere of chromosome VI-R, and in middle of chromosome V-R (mid-V-R), a functional nucleolus was formed, and no difference in the expression of rRNA genes was observed. When two ribosomal DNA (rDNA) arrays are present, one native and the other ectopic, there is codominance in polymerase I (Pol I) transcription. We also examined the expression of a single rDNA repeat integrated into ectopic loci in strains with or without the native RDN1 locus. In a strain with reduced rRNA gene copies at RDN1 (approximately 40 copies), the expression of a single rRNA gene copy near the telomere was significantly reduced relative to the other ectopic sites, suggesting a less-efficient recruitment of the Pol I machinery from the RDN1 locus. In addition, we found a single rRNA gene at mid-V-R was as active as that within the 40-copy RDN1. Combined with the results of activity analysis of a single versus two tandem copies at CEN5, we conclude that tandem repetition is not required for efficient rRNA gene transcription.
Collapse
Affiliation(s)
- Melanie L Oakes
- Department of Biological Chemistry, University of California at Irvine, 240D Medical Sciences I, Irvine, CA 92697-1700, USA
| | | | | | | | | |
Collapse
|
179
|
Lynn DH, Strüder-Kypke MC. Species of Tetrahymena Identical by Small Subunit rRNA Gene Sequences are Discriminated by Mitochondrial Cytochrome c Oxidase I Gene Sequences. J Eukaryot Microbiol 2006; 53:385-7. [PMID: 16968457 DOI: 10.1111/j.1550-7408.2006.00116.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mitochondrial cytochrome c oxidase 1 (CO1) genes of two isolates of each of the seven mating types of Tetrahymena thermophila were sequenced and found to differ by < 1% in nucleotide sequence and to be identical by putative protein sequence. As this gene was highly conserved in this species, the CO1 gene sequence was determined for four pairs of Tetrahymena species identical in their small subunit rRNA gene sequences. The following pairs of species showed from 1% to 12% divergence at the nucleotide level, enabling discrimination of all these species: (1) Tetrahymena pyriformis strain T and Tetrahymena setosa strain HZ-1; (2) Tetrahymena canadensis strain UM1215 and Tetrahymena rostrata strain ID-3; (3) Tetrahymena pigmentosa strain UM1285 and Tetrahymena hyperangularis strain EN112; and (4) Tetrahymena tropicalis strain TC-105 and Tetrahymena mobilis. However, because of the synonymous nature of the majority of substitutions, the pairs of species were identical based on the putative protein sequence.
Collapse
Affiliation(s)
- Denis H Lynn
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | | |
Collapse
|
180
|
Abstract
Specimens of Rhizoplaca chrysoleuca from Mount Wuling can be divided into two distinct groups based on obvious differences in morphological characters. Here we investigated 26 specimens of R. chrysoleuca from Mount Wuling, 10 specimens of this species from other areas and seven specimens of other Rhizoplaca species by analyzing morphology, chemistry and genetics. Nine chemotypes were detected among the specimens of R. chrysoleuca from Mount Wuling, and five of them were reported for the first time. Based on the ITS phylogenetic analysis, the chemotypes and the insertion distribution patterns in SSU rDNA, the samples of R. chrysoleuca from Mount Wuling were grouped in two distinct clades corresponding to two phenotypic groups and no gene flow was detected between these two groups. Our results establish all individuals of Rhizoplaca chrysoleuca are conspecific although some populations have been isolated on Mount Wuling, indicating that they are in the process of speciation. Our study also reveals that the relationships between genotypes and chemotypes are complicated and should be avoided, and we instead recommend using single individuals or few individuals from the same site to represent the population or whole species in systematics study. The results also indicate that Rhizoplaca chrysoleuca might provide a good model for studying the speciation of saxicolous lichenized fungi.
Collapse
MESH Headings
- Ascomycota/chemistry
- Ascomycota/classification
- Ascomycota/genetics
- Benzofurans/analysis
- Chromatography, Thin Layer
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Fungal/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal/isolation & purification
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- DNA, Ribosomal Spacer/isolation & purification
- Genes, rRNA/genetics
- Genetic Variation
- Hydroxybenzoates/analysis
- Introns/genetics
- Molecular Sequence Data
- Phylogeny
- RNA, Fungal/genetics
- RNA, Ribosomal/genetics
- Salicylates/analysis
- Sequence Analysis, DNA
Collapse
Affiliation(s)
- Qi-Ming Zhou
- Systematic Mycology & Lichenology Laboratory, Institute of Microbiology, Academia Sinica, Beijing, PR China
| | | | | | | |
Collapse
|
181
|
Lages-Silva E, Ramírez LE, Pedrosa AL, Crema E, da Cunha Galvão LM, Pena SDJ, Macedo AM, Chiari E. Variability of kinetoplast DNA gene signatures of Trypanosoma cruzi II strains from patients with different clinical forms of Chagas' disease in Brazil. J Clin Microbiol 2006; 44:2167-71. [PMID: 16757616 PMCID: PMC1489452 DOI: 10.1128/jcm.02124-05] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The clinical course of Chagas' disease varies widely among different patients and geographic regions. For reasons that are not completely understood but involve host and parasite factors, some patients never develop the disease while others present cardiac and/or gastrointestinal symptoms. Many studies have been conducted in order to correlate the genetic variability of the parasites with the clinical forms of the disease, but no conclusive data have been obtained. Our research aims at characterizing the genetic profiles of Trypanosoma cruzi isolates recently obtained from 70 chagasic patients who either showed pathological lesions with symptoms of various intensities or were asymptomatic. All patients came from an area where Chagas' disease is endemic in southeast Brazil where vectorial transmission has been controlled and different clinical forms of the disease can be found. The molecular characterization of parasites evaluated the polymorphisms of the 3' region of the 24Salpha rRNA gene and the variability of kinetoplast DNA (kDNA) minicircles of T. cruzi populations by low-stringency single specific primer PCR. Data presented here provide a strong correlation between T. cruzi II and human infection in this region. However, a high degree of variability was observed within T. cruzi II, as demonstrated by intense kDNA polymorphism among all clinical forms and also within each of them, irrespective of the intensity of pathological processes.
Collapse
Affiliation(s)
- Eliane Lages-Silva
- Departamento de Ciências Biológicas, Universidade Federal do Triângulo Mineiro, Uberaba, Brazil.
| | | | | | | | | | | | | | | |
Collapse
|
182
|
Abstract
When microbes are subjected to temporal changes in nutrient availability, growth rate and substrate affinity can contribute to competitive fitness and thereby affect microbial community structure. This hypothesis was tested using planktonic bacterial communities exposed to nutrient additions at 1-, 3-, 7-, or 14-day intervals. Growth rates after nutrient addition were inversely proportional to the pulse interval and declined from 0.5 h(-1) to 0.15 h(-1) as the pulse interval increased from 1 to 14 days. The dynamics of community structure were monitored by 16S rRNA gene PCR-denaturing gradient gel electrophoresis. At pulse intervals of more than 1 day, the community composition continued to change over 130 days. Although replicate systems exposed to the same pulse interval were physiologically similar, their community compositions could exhibit as much dissimilarity (Dice similarity coefficients of <0.5) as did systems operated at different intervals. Bacteria were cultivated from the systems to determine if the physiological characteristics of individual members were consistent with the measured performance of the systems. The isolates fell into three bacterial divisions, Bacteroidetes, Proteobacteria, and Actinobacteria. In agreement with community results, bacteria isolated from systems pulsed every day with nutrients had higher growth rates and ectoaminopeptidase specific activities than isolates from systems pulsed every 14 days. However, the latter isolates did not survive starvation longer than those provided with nutrients every day. The present study demonstrates the dynamic nature of microbial communities exposed to even simple and regular environmental discontinuities when a substantial pool of species that can catabolize the limiting substrate is present.
Collapse
Affiliation(s)
- Militza Carrero-Colón
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907-2054, USA
| | | | | |
Collapse
|
183
|
Habura A, Goldstein ST, Parfrey LW, Bowser SS. Phylogeny and ultrastructure of Miliammina fusca: evidence for secondary loss of calcification in a Miliolid Foraminifer. J Eukaryot Microbiol 2006; 53:204-10. [PMID: 16677344 DOI: 10.1111/j.1550-7408.2006.00096.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The classification of the Foraminifera, a widely distributed group of largely marine protists, has traditionally been based on morphological characters. The most important of these are the composition and structure of the shell or "test." Here, we use both phylogenetic analysis of the genes for small subunit rRNA and beta-tubulin and ultrastructural analysis to document a reversion in wall type from more derived calcareous tests to an agglutinated test. These data indicate that the genus Miliammina, and possibly other members of the Rzehakinidae, should be placed in the Order Miliolida as opposed to their current assignment in Order Textulariida. We also address the effects this reversion may have had on the ability of rzehakinacids to effectively colonize marginal marine environments. Finally, the hypothesis that some multilocular agglutinated foraminiferans descended from calcareous lineages has implications for interpretation of the foraminiferal fossil record.
Collapse
MESH Headings
- Animals
- DNA, Protozoan/chemistry
- DNA, Protozoan/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Eukaryota/classification
- Eukaryota/ultrastructure
- Genes, rRNA/genetics
- Microscopy, Electron, Scanning
- Microscopy, Electron, Transmission
- Molecular Sequence Data
- Phylogeny
- Protozoan Proteins/genetics
- Sequence Analysis, DNA
- Tubulin/genetics
- Water Microbiology
Collapse
Affiliation(s)
- Andrea Habura
- Division of Molecular Medicine, Wadsworth Center, PO Box 509, Albany, New York 12201, USA.
| | | | | | | |
Collapse
|
184
|
Abstract
The bacterial community composition in soil and rhizosphere taken from arable field sites, differing in soil parent material and soil texture, was analyzed using terminal restriction fragment length polymorphism (T-RFLP) of 16S rRNA genes. Nine sandy to silty soils from North-East Germany could clearly be distinguished from each other, with a relatively low heterogeneity in the community structure within the field replicates. There was a relationship between the soil parent material, i.e. different glacial and aeolian sediments, and the clustering of the profiles from different sites. A site-specific grouping of T-RFLP profiles was also found for the rhizosphere samples of the same field sites that were planted with potatoes. The branching of the rhizosphere profiles corresponded partly with the soil parent material, whereas the effect of the plant genotype was negligible. Selected terminal restriction fragments differing in their relative abundance within the nine soils were analyzed based on the cloning of the 16S rRNA genes of one soil sample. A high phylogenetic diversity observed to include Acidobacteria, Betaproteobacteria, Bacteroidetes, Verrucomicrobia, and Gemmatimonadetes. The assignment of three out of the seven selected terminal restriction fragments to members of Acidobacteria suggested that this group seems to participate frequently in the shifting of community structures that result from soil property changes.
Collapse
Affiliation(s)
- Andreas Ulrich
- Leibniz-Zentrum für Agrarlandschaftsforschung, Institut für Landschaftsstoffdynamik, Müncheberg, Germany.
| | | |
Collapse
|
185
|
Gill JJ, Sabour PM, Gong J, Yu H, Leslie KE, Griffiths MW. Characterization of bacterial populations recovered from the teat canals of lactating dairy and beef cattle by 16S rRNA gene sequence analysis. FEMS Microbiol Ecol 2006; 56:471-81. [PMID: 16689878 DOI: 10.1111/j.1574-6941.2006.00091.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Bovine mastitis is of major concern to the dairy industry worldwide. The bovine teat canal is the primary route through which pathogens enter the mammary gland. The microflora of the teat canals of dairy and beef cattle was investigated by analysis of 16S rRNA gene sequences. The goal was to examine the global difference between dairy cattle, which are sanitized on a regular basis, and beef cattle, which receive little sanitary management. A diverse population of 16S rRNA gene sequences was recovered from both the dairy and the beef herd samples, with diversity higher in the beef sample. Analysis revealed the presence of 90 operational taxonomic units (OTUs) among 156 sequences, with 45 OTUs in the dairy sample and 53 OTUs in the beef sample. Only eight OTUs were common to both samples. Members of the classes Clostridia and Bacilli dominated both samples, followed by Actinobacteria and Proteobacteria. The dairy sample contained a cluster (20/80 clones) of Staphylococcaceae members, seven of which were identifiable as coagulase-negative Staphylococcus species. The beef sample was dominated by members of the genus Clostridia, many of which have not been previously cultured. The results suggest that the microorganisms present in the bovine teat canal are more diverse than previously described.
Collapse
Affiliation(s)
- Jason J Gill
- Department of Food Science, University of Guelph, Guelph, Ontario, Canada
| | | | | | | | | | | |
Collapse
|
186
|
Mahmood S, Freitag TE, Prosser JI. Comparison of PCR primer-based strategies for characterization of ammonia oxidizer communities in environmental samples. FEMS Microbiol Ecol 2006; 56:482-93. [PMID: 16689879 DOI: 10.1111/j.1574-6941.2006.00080.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
PCR-based techniques are commonly used to characterize microbial communities, but are subject to bias that is difficult to assess. This study aimed to evaluate bias of several PCR primer-based strategies used to study diversity of autotrophic ammonia oxidizers. 16S rRNA genes from soil- or sediment-DNA were amplified using primers considered either selective or specific for betaproteobacterial ammonia oxidizers. Five approaches were assessed: (a) amplification with primers betaAMO143f-betaAMO1315r; (b) amplification with primers CTO189f-CTO654r; (c) nested amplification with betaAMO143f-betaAMO1315r followed by CTO189f-CTO654r primers; (d) nested amplification with betaAMO143f-betaAMO1315r and CTO189f-Pf1053r primers; (e) nested amplification with 27f-1492r and CTO189f-CTO654r primers. Amplification products were characterized by denaturing gradient gel electrophoresis (DGGE) analysis after further amplification with 357f-GC-518r primers. DGGE profiles of soil communities were heterogeneous and depended on the approach followed. Ammonia oxidizer diversity was higher using approaches (b), (c) and (e) than using (a) and (d), where sequences of the most prominent bands showed similarities to nonammonia oxidizers. Profiles from marine sediments were more consistent, regardless of the approach adopted, and sequence analysis of excised bands indicated that these consisted of ammonia oxidizers only. The study demonstrates the importance of choice of primer, of screening for sequences of nontarget organisms and use of several approaches when characterizing microbial communities in natural environments.
Collapse
Affiliation(s)
- Shahid Mahmood
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, UK
| | | | | |
Collapse
|
187
|
Li L, Song W, Warren A, Wang Y, Ma H, Hu X, Chen Z. Phylogenetic position of the marine ciliate, Cardiostomatella vermiforme (Kahl, 1928) Corliss, 1960 inferred from the complete SSrRNA gene sequence, with establishment of a new order Loxocephalida n. ord. (Ciliophora, Oligohymenophorea). Eur J Protistol 2006; 42:107-14. [PMID: 17070756 DOI: 10.1016/j.ejop.2006.01.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2005] [Revised: 12/27/2005] [Accepted: 01/27/2006] [Indexed: 11/18/2022]
Abstract
The small subunit rRNA (SSrRNA) gene was sequenced for Cardiostomatella vermiforme, a large marine ciliate the systematic position of which is uncertain but which has been regarded as a scuticociliate for about forty years. The present work indicates that this organism, together with a closely related species, Dexiotrichides pangi, always form a separate assemblage as a sister group to the scuticociliates sensu stricto. The fact that the clade comprising Cardiostomatella and Dexiotrichides branches between the typical scuticociliates and Hymenostomatia, and shares a series of morphological and morphogenetical characters with both, supports the conclusion that it belongs to an intermediate group between the two. We suggest that this group represents a new order, Loxocephalida n. ord. within the subclass Scuticociliatia, which possibly contains all taxa within the families Loxocephalidae and Cinetochilidae and with Loxocephalidae as the type family.
Collapse
Affiliation(s)
- Lifang Li
- Laboratory of Protozoology, KLM, Ocean University of China, Qingdao 266003, PR China
| | | | | | | | | | | | | |
Collapse
|
188
|
Shivaji S, Chaturvedi P, Suresh K, Reddy GSN, Dutt CBS, Wainwright M, Narlikar JV, Bhargava PM. Bacillus aerius sp. nov., Bacillus aerophilus sp. nov., Bacillus stratosphericus sp. nov. and Bacillus altitudinis sp. nov., isolated from cryogenic tubes used for collecting air samples from high altitudes. Int J Syst Evol Microbiol 2006; 56:1465-1473. [PMID: 16825614 DOI: 10.1099/ijs.0.64029-0] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four novel bacterial strains were isolated from cryogenic tubes used to collect air samples at altitudes of 24, 28 and 41 km. The four strains, 24KT, 28KT, 41KF2aT and 41KF2bT, were identified as members of the genus Bacillus. Phylogenetic analysis based on 16S rRNA gene sequences indicated that three of the strains, 24KT, 28KT and 41KF2aT, are very similar to one another (>98 % sequence similarity) and show a similarity of 98–99 % with Bacillus licheniformis and 98 % with Bacillus sonorensis. DNA–DNA hybridization studies showed that strains 24KT, 28KT and 41KF2aT exhibit <70 % similarity with each other and with B. licheniformis and B. sonorensis. Differences in phenotypic and chemotaxonomic characteristics between the novel strains and B. licheniformis and B. sonorensis further confirmed that these three isolates are representatives of three separate novel species. Strain 41KF2bT showed 100 % 16S rRNA gene sequence similarity to Bacillus pumilus, but differed from its nearest phylogenetic neighbour in a number of phenotypic and chemotaxonomic characteristics and showed only 55 % DNA–DNA relatedness. Therefore, the four isolates represent four novel species for which the names Bacillus aerius sp. nov. (type strain, 24KT=MTCC 7303T=JCM 13348T), Bacillus aerophilus sp. nov. (type strain, 28KT=MTCC 7304T=JCM 13347T), Bacillus stratosphericus sp. nov. (type strain, 41KF2aT=MTCC 7305T=JCM 13349T) and Bacillus altitudinis sp. nov. (type strain, 41KF2bT=MTCC 7306T=JCM 13350T) are proposed.
Collapse
Affiliation(s)
- S Shivaji
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
| | - P Chaturvedi
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
| | - K Suresh
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
| | - G S N Reddy
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
| | - C B S Dutt
- Indian Space Research Organization, Antariksha Bhavan, New BEL Road, Bangalore 500 094, India
| | - M Wainwright
- Department of Molecular Biology and Biotechnology, University of Sheffield, Fifth Court, Western Bank, Sheffield S10 2TN, UK
| | - J V Narlikar
- Inter-University Centre for Astronomy and Astrophysics, Post Bag No. 4, Ganeshkhind, Pune 411 007, India
| | - P M Bhargava
- Anveshna Consultancy Services, Furqan Cottage, Street No. 3, Tarnaka, Hyderabad 500 017, India
| |
Collapse
|
189
|
Im WT, Kim SH, Kim MK, Ten LN, Lee ST. Pleomorphomonas koreensis sp. nov., a nitrogen-fixing species in the order Rhizobiales. Int J Syst Evol Microbiol 2006; 56:1663-1666. [PMID: 16825646 DOI: 10.1099/ijs.0.63499-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, non-motile, non-spore-forming, rod-shaped bacterium (strain Y9T) was isolated from a contaminated culture of the phototrophic bacterium Rhodopseudomonas palustris, and was investigated using a polyphasic taxonomic approach. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain Y9T belonged to the order Rhizobiales in the Alphaproteobacteria. Comparison of phylogenetic data indicated that it was most closely related to Pleomorphomonas oryzae (98.5 % similarity of 16S rRNA gene sequence), and the phylogenetic distance from any other species of the order Rhizobiales with a validly published name was greater than 7.5 % (i.e. less than 92.5 % similarity). The predominant ubiquinone was Q-10 and the major fatty acids were C18 : 1, C16 : 0, C19 : 0 cyclo ω8c and C18 : 0. The G+C content of genomic DNA of strain Y9T was 65.1 mol%. The results of DNA–DNA hybridization in combination with chemotaxonomic and physiological data demonstrated that strain Y9T represents a novel species within the genus Pleomorphomonas, for which the name Pleomorphomonas koreensis sp. nov. is proposed. The type strain is Y9T (=KCTC 12246T=NBRC 100803T)
Collapse
MESH Headings
- Alphaproteobacteria/classification
- Alphaproteobacteria/genetics
- Alphaproteobacteria/isolation & purification
- Alphaproteobacteria/metabolism
- Bacterial Typing Techniques
- Base Composition
- Carbohydrate Metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Fatty Acids/chemistry
- Genes, rRNA/genetics
- Molecular Sequence Data
- Nitrogen Fixation
- Nucleic Acid Hybridization
- Phylogeny
- Quinones/analysis
- Quinones/chemistry
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
Collapse
Affiliation(s)
- Wan-Taek Im
- Environmental and Molecular Microbiology Laboratory, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, South Korea
| | - Seong-Hye Kim
- Environmental and Molecular Microbiology Laboratory, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, South Korea
| | - Myung Kyum Kim
- Environmental and Molecular Microbiology Laboratory, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, South Korea
| | - Leonid N Ten
- National University of Uzbekistan, Students town, Tashkent, 700-174, Uzbekistan
| | - Sung-Taik Lee
- Environmental and Molecular Microbiology Laboratory, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejeon 305-701, South Korea
| |
Collapse
|
190
|
Sakamoto M, Benno Y. Reclassification of Bacteroides distasonis, Bacteroides goldsteinii and Bacteroides merdae as Parabacteroides distasonis gen. nov., comb. nov., Parabacteroides goldsteinii comb. nov. and Parabacteroides merdae comb. nov. Int J Syst Evol Microbiol 2006; 56:1599-1605. [PMID: 16825636 DOI: 10.1099/ijs.0.64192-0] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The characteristics of three Bacteroides species, Bacteroides distasonis, Bacteroides goldsteinii and Bacteroides merdae, were examined. 16S rRNA gene sequence analysis showed that B. distasonis, B. goldsteinii and B. merdae should not be classified as species within the genus Bacteroides. Although B. distasonis, B. goldsteinii and B. merdae were phylogenetically related to Tannerella forsythensis, the ratios of anteiso-C15 : 0 to iso-C15 : 0 in whole-cell methanolysates of the three species were different from that of T. forsythensis. In addition, whereas the major menaquinones of T. forsythensis were MK-10 and MK-11, the major menaquinones of B. distasonis, B. goldsteinii and B. merdae were MK-9 and MK-10. The three species were phenotypically similar to Bacteroides sensu stricto, but phylogenetically distinct. Furthermore, B. distasonis, B. goldsteinii and B. merdae could be differentiated from Bacteroides sensu stricto (predominant menaquinones: MK-10 and MK-11) by the menaquinone composition. This is an important chemotaxonomic characteristic of the three species. On the basis of these data, a novel genus, Parabacteroides gen. nov., is proposed for B. distasonis, B. goldsteinii and B. merdae, with three species, Parabacteroides distasonis gen. nov., comb. nov. (the type species), Parabacteroides goldsteinii comb. nov. and Parabacteroides merdae comb. nov. The type strains of P. distasonis, P. goldsteinii and P. merdae are JCM 5825T (=CCUG 4941T=DSM 20701T=ATCC 8503T), JCM 13446T (=CCUG 48944T) and JCM 9497T (=CCUG 38734T=ATCC 43184T), respectively.
Collapse
MESH Headings
- Bacterial Typing Techniques
- Bacteroides/chemistry
- Bacteroides/classification
- Bacteroides/genetics
- Bacteroides/physiology
- Bacteroidetes/chemistry
- Bacteroidetes/classification
- Bacteroidetes/genetics
- Bacteroidetes/metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Fatty Acids/chemistry
- Genes, rRNA/genetics
- Molecular Sequence Data
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Vitamin K 2/analysis
- Vitamin K 2/chemistry
Collapse
Affiliation(s)
- Mitsuo Sakamoto
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
| | - Yoshimi Benno
- Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Center, Wako, Saitama 351-0198, Japan
| |
Collapse
|
191
|
Oakes ML, Siddiqi I, French SL, Vu L, Sato M, Aris JP, Beyer AL, Nomura M. Role of histone deacetylase Rpd3 in regulating rRNA gene transcription and nucleolar structure in yeast. Mol Cell Biol 2006; 26:3889-901. [PMID: 16648483 PMCID: PMC1489006 DOI: 10.1128/mcb.26.10.3889-3901.2006] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The 35S rRNA genes at the RDN1 locus in Saccharomyces cerevisiae can be transcribed by RNA polymerase (Pol) II in addition to Pol I, but Pol II transcription is usually silenced. The deletion of RRN9 encoding an essential subunit of the Pol I transcription factor, upstream activation factor, is known to abolish Pol I transcription and derepress Pol II transcription of rRNA genes, giving rise to polymerase switched (PSW) variants. We found that deletion of histone deacetylase gene RPD3 inhibits the appearance of PSW variants in rrn9 deletion mutants. This inhibition can be explained by the observed specific inhibition of Pol II transcription of rRNA genes by the rpd3Delta mutation. We propose that Rpd3 plays a role in the maintenance of an rRNA gene chromatin structure(s) that allows Pol II transcription of rRNA genes, which may explain the apparently paradoxical previous observation that rpd3 mutations increase, rather than decrease, silencing of reporter Pol II genes inserted in rRNA genes. We have additionally demonstrated that Rpd3 is not required for inhibition of Pol I transcription by rapamycin, supporting the model that Tor-dependent repression of the active form of rRNA genes during entry into stationary phase is Rpd3 independent.
Collapse
Affiliation(s)
- Melanie L Oakes
- Department of Biological Chemistry, University of California--Irvine, 240D Medical Sciences I, Irvine, California 92697-1700, USA
| | | | | | | | | | | | | | | |
Collapse
|
192
|
Abstract
Numerous studies have demonstrated that DNA replication initiates within the 30 kB non-transcribed spacer (NTS) region of the human ribosomal RNA gene (rDNA). Using a series of closely spaced primer pairs to measure nascent leading strand abundance in mid and late S phase cells isolated by centrifugal elutriation, we find evidence for one highly preferred initiation site and two less utilized sites within a 6 kb region of the NTS. The initiation sites colocalize with significant DNA unwinding elements (DUEs), matrix attachment regions (MARs), and ARS-like sequences. An intrinsic DNA bending site was localized by circular permutation analysis to within several hundred base pairs of one initiation site. While DUE and MAR elements occur elsewhere throughout the 43 kb rDNA sequence, the close association of DUE and MAR elements occurs only near replication initiation sites, a juxtaposition also seen in other well-studied mammalian replication initiation sites. The utilization of rDNA initiation sites close to DUE and MAR elements in mid and late S phase, but not in very early S phase as previously shown, suggests that in rRNA genes, contributions from these sequence-associated properties may be more significant to initiation sites associated with transcriptionally inactive genes, than to initiation sites associated with transcriptionally active genes.
Collapse
Affiliation(s)
- Frederick D Coffman
- Department of Pathology and Laboratory Medicine, UMDNJ-New Jersey Medical School, Newark, New Jersey 07103, USA.
| | | | | | | |
Collapse
|
193
|
Poli A, Esposito E, Lama L, Orlando P, Nicolaus G, de Appolonia F, Gambacorta A, Nicolaus B. Anoxybacillus amylolyticus sp. nov., a thermophilic amylase producing bacterium isolated from Mount Rittmann (Antarctica). Syst Appl Microbiol 2006; 29:300-7. [PMID: 16682297 DOI: 10.1016/j.syapm.2005.10.003] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2005] [Indexed: 11/23/2022]
Abstract
A new thermophilic spore-forming strain MR3CT was isolated from geothermal soil located on Mount Rittmann in Antarctica. Strain MR3CT was Gram-positive, rod-shaped, occurring in pairs or filamentous. Growth was observed between 45 and 65 degrees C (optimum 61 degrees C) and at pH 5.0-6.5 (optimum pH 5.6). It was capable of utilizing galactose, trehalose, maltose and sucrose. The microorganism produced an exopolysaccharide and synthesized an extracellular constitutive amylolytic activity. The G + C content of DNA was 43.5 mol%. On the basis of 16S rRNA gene sequence similarity, strain MR3CT was shown to be related most closely to Anoxybacillus species. Chemotaxonomic data (major isoprenoid quinone-menaquinone-7; major fatty acid-iso-C15:0 and iso-C17:0) supported the affiliation of strain MR3C1T to the genus Anoxybacillus. The results of DNA-DNA hybridization, physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain MR3CT from the validly published Anoxybacillus species. MR3CT therefore represents a new species, for which the name Anoxybacillus amylolyticus sp. nov., is proposed, with the type strain MR3CT (= ATCC BAA-872T = DSM 15939T = CIP 108338T).
Collapse
MESH Headings
- Amylases/biosynthesis
- Antarctic Regions
- Base Composition
- Carbohydrate Metabolism
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Fatty Acids/isolation & purification
- Genes, rRNA/genetics
- Gram-Positive Bacteria/classification
- Gram-Positive Bacteria/cytology
- Gram-Positive Bacteria/isolation & purification
- Gram-Positive Bacteria/physiology
- Hydrogen-Ion Concentration
- Microscopy, Electron, Scanning
- Molecular Sequence Data
- Phylogeny
- Polysaccharides, Bacterial/biosynthesis
- Quinones/analysis
- Quinones/isolation & purification
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Soil Microbiology
- Temperature
- Terpenes/analysis
Collapse
Affiliation(s)
- Annarita Poli
- Istituto di Chimica Biomolecolare (ICB), CNR, Via Campi Flegrei 34, 80078 Pozzuoli (Napoli), Italy.
| | | | | | | | | | | | | | | |
Collapse
|
194
|
Abstract
In grazed, grassland soils, sheep urine generates heterogeneity in ammonia concentrations, with potential impact on ammonia oxidizer community structure and soil N cycling. The influence of different levels of synthetic sheep urine on ammonia oxidizers was studied in grassland soil microcosms. 'Total' and active ammonia oxidizers were distinguished by comparing denaturing gradient gel electrophoresis (DGGE) profiles following PCR and RT-PCR amplification of 16S rRNA gene fragments, targeting DNA and RNA, respectively. The RNA-based approach indicated earlier, more reproducible and finer scale qualitative shifts in ammonia oxidizing communities than DNA-based analysis, but led to amplification of a small number of nonammonia oxidizer sequences. Qualitative changes in RNA-derived DGGE profiles were related to changes in nitrate accumulation. Sequence analysis of excised DGGE bands revealed that ammonia oxidizing communities in synthetic sheep urine-treated soils consisted mainly of Nitrosospira clusters 2, 3 and 4. Nitrosospira cluster 2 increased in relative abundance in microcosms treated with all levels of synthetic sheep urine. Low levels additionally led to increased relative abundance of Nitrosospira cluster 4 and medium and high levels increased relative abundance of cluster 3. Synthetic sheep urine is therefore likely to influence the spatial distribution and composition of ammonia oxidizer communities, with consequent effects on nitrate accumulation.
Collapse
Affiliation(s)
- Shahid Mahmood
- School of Medical Sciences, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, UK
| | | |
Collapse
|
195
|
Zaballos M, López-López A, Ovreas L, Bartual SG, D'Auria G, Alba JC, Legault B, Pushker R, Daae FL, Rodríguez-Valera F. Comparison of prokaryotic diversity at offshore oceanic locations reveals a different microbiota in the Mediterranean Sea. FEMS Microbiol Ecol 2006; 56:389-405. [PMID: 16689872 DOI: 10.1111/j.1574-6941.2006.00060.x] [Citation(s) in RCA: 484] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The bacterial and archaeal assemblages at two offshore sites located in polar (Greenland Sea; depth: 50 and 2000 m) and Mediterranean (Ionian Sea; depth 50 and 3000 m) waters were studied by PCR amplification and sequencing of the last 450-500 bp of the 16S rRNA gene. A total of 1621 sequences, together with alignable 16S rRNA gene fragments from the Sargasso Sea metagenome database, were analysed to ascertain variations associated with geographical location and depth. The Ionian 50 m sample appeared to be the most diverse and also had remarkable differences in terms of the prokaryotic groups retrieved; surprisingly, however, many similarities were found at the level of large-scale diversity between the Sargasso database fragments and the Greenland 50 m sample. Most sequences with more than 97% sequence similarity, a value often taken as indicative of species delimitation, were only found at a single location/depth; nevertheless, a few examples of cosmopolitan sequences were found in all samples. Depth was also an important factor and, although both deep-water samples had overall similarities, there were important differences that could be due to the warmer waters at depth of the Mediterranean Sea.
Collapse
Affiliation(s)
- Milagros Zaballos
- División de Microbiología and Evolutionary Genomics Group, Universidad Miguel Hernández, San Juan de Alicante, Spain
| | | | | | | | | | | | | | | | | | | |
Collapse
|
196
|
Dinglasan-Panlilio MJ, Dworatzek S, Mabury S, Edwards E. Microbial oxidation of 1,2-dichloroethane under anoxic conditions with nitrate as electron acceptor in mixed and pure cultures. FEMS Microbiol Ecol 2006; 56:355-64. [PMID: 16689868 DOI: 10.1111/j.1574-6941.2006.00077.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Many organisms have been found to readily oxidize the prevalent contaminant 1,2-dichloroethane (1,2-DCA) to CO2 under aerobic conditions. Some organisms have also been isolated that can reduce 1,2-DCA to ethene via dihaloelimination under anaerobic, fermentative conditions. However, none have been described that can metabolize 1,2-DCA under anoxic, nitrate-reducing conditions. In microcosms prepared from aquifer material and groundwater samples from a contaminated site in eastern Louisiana, USA, 1,2-DCA was observed to degrade with nitrate as the terminal electron acceptor. Nitrate-dependent enrichment cultures were developed from these microcosms that sustained rapid 1,2-DCA degradation rates of up to 500 microM day(-1). This degradation was tightly coupled to complete reduction of nitrate via nitrite to nitrogen gas. A novel 1,2-DCA-degrading organism belonging to the Betaproteobacteria (affiliated with the genus Thauera) was isolated from this enrichment culture. However, degradation rates were much slower in cultures of the isolate than observed in the parent mixed culture. Complete mineralization of 1,2-DCA to CO2 was linked to cell growth and to nitrate reduction in both enrichment and isolated cultures. Monochloroacetate, a putative metabolite of 1,2-DCA degradation, could also be mineralized by these cultures.
Collapse
|
197
|
Musat N, Werner U, Knittel K, Kolb S, Dodenhof T, van Beusekom JEE, de Beer D, Dubilier N, Amann R. Microbial community structure of sandy intertidal sediments in the North Sea, Sylt-Rømø Basin, Wadden Sea. Syst Appl Microbiol 2006; 29:333-48. [PMID: 16431068 DOI: 10.1016/j.syapm.2005.12.006] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2005] [Indexed: 11/18/2022]
Abstract
Molecular biological methods were used to investigate the microbial diversity and community structure in intertidal sandy sediments near the island of Sylt (Wadden Sea) at a site which was characterized for transport and mineralization rates in a parallel study (D. de Beer, F. Wenzhöfer, T. Ferdelman, S.E. Boehme, M. Huettel, J.E.E. van Beusekom, M.E. Böttcher, N. Musat, N. Dubilier, Transport and mineralization rates in North Sea sandy intertidal sediments, Sylt-Romo Basin, Wadden Sea, Limnol. Oceanogr. 50 (2005) 113-127). Comparative 16S rRNA sequence analysis revealed a high bacterial diversity. Most sequences retrieved by PCR with a general bacterial primer set were affiliated with Bacteroidetes, Gammaproteobacteria, Deltaproteobacteria and the Pirellula cluster of Planctomycetales. Fluorescence in situ hybridization (FISH) and slot-blot hybridization with group-specific rRNA-targeted oligonucleotide probes were used to characterize the microbial community structure over depth (0-12 cm) and seasons (March, July, October). We found high abundances of bacteria with total cell numbers up to 3 x 10(9) cells ml(-1) and a clear seasonal variation, with higher values in July and October versus March. The microbial community was dominated by members of the Planctomycetes, the Cytophaga/Flavobacterium group, Gammaproteobacteria, and bacteria of the Desulfosarcina/Desulfococcus group. The high abundance (1.5 x 10(7)-1.8 x 10(8) cells ml(-1) accounting for 3-19% of all cells) of presumably aerobic heterotrophic polymer-degrading planctomycetes is in line with the high permeability, deep oxygen penetration, and the high rates of aerobic mineralization of algal biomass measured in the sandy sediments by de Beer et al. (2005). The high and stable abundance of members of the Desulfosarcina/Desulfococcus group, both over depth and season, suggests that these bacteria may play a more important role than previously assumed based on low sulfate reduction rates in parallel cores (de Beer et al., 2005).
Collapse
MESH Headings
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- Biodiversity
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Ecosystem
- Genes, rRNA/genetics
- Geologic Sediments/microbiology
- In Situ Hybridization, Fluorescence
- Microscopy, Fluorescence
- Molecular Sequence Data
- North Sea
- Nucleic Acid Hybridization
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Seasons
- Sequence Analysis, DNA
- Temperature
- Water Microbiology
Collapse
Affiliation(s)
- Niculina Musat
- Max Planck Institute for Marine Microbiology, Celsiusstr. 1, D-28359 Bremen, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
198
|
Xu P, Li WJ, Tang SK, Jiang Y, Gao HY, Xu LH, Jiang CL. Nocardia lijiangensis sp. nov., a novel actinomycete strain isolated from soil in China. Syst Appl Microbiol 2006; 29:308-14. [PMID: 16337766 DOI: 10.1016/j.syapm.2005.11.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2005] [Indexed: 11/21/2022]
Abstract
A novel actinomycete strain YIM 33378T was isolated from a soil sample collected from Lijiang, Yunnan Province, China. Based on the results of phenotypic and genotypic characteristics, strain YIM 33378T should be assigned to a new species of the genus Nocardia, for which the name Nocardia lijiangensis sp. nov. is proposed. The type strain is YIM 33378T (= CCTCC AA 204005T = KCTC 19028T). The GenBank accession number for the sequence reported in this paper is AY779043.
Collapse
MESH Headings
- Bacterial Typing Techniques
- Base Composition
- China
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Fatty Acids/analysis
- Fatty Acids/isolation & purification
- Genes, rRNA/genetics
- Microscopy, Electron, Scanning
- Molecular Sequence Data
- Nocardia/classification
- Nocardia/isolation & purification
- Nocardia/physiology
- Nocardia/ultrastructure
- Phylogeny
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Soil Microbiology
Collapse
Affiliation(s)
- Ping Xu
- Key Laboratory for Microbial Resources of Ministry of Education, Yunnan Institute of Microbiology and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan University, Kunming, Yunnan, 650091, PR China
| | | | | | | | | | | | | |
Collapse
|
199
|
Hall DB, Wade JT, Struhl K. An HMG protein, Hmo1, associates with promoters of many ribosomal protein genes and throughout the rRNA gene locus in Saccharomyces cerevisiae. Mol Cell Biol 2006; 26:3672-9. [PMID: 16612005 PMCID: PMC1447432 DOI: 10.1128/mcb.26.9.3672-3679.2006] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HMG proteins are architectural proteins that bind to DNA with low sequence specificity, but little is known about their genomic location and biological functions. Saccharomyces cerevisiae encodes 10 HMG proteins, including Hmo1, which is important for maximal transcription of rRNA. Here we use chromatin immunoprecipitation coupled with microarray analysis to determine the genome-wide association of Hmo1. Unexpectedly, Hmo1 binds strongly to the promoters of most ribosomal protein (RP) genes and to a number of other specific genomic locations. Hmo1 binding to RP promoters requires Rap1 and (to a lesser extent) Fhl1, proteins that also associate with RP promoters. Hmo1, like Fhl1 and Ifh1, typically associates with an IFHL motif in RP promoters, but deletion of the IFHL motif has a very modest effect on Hmo1 binding. Surprisingly, loss of Hmo1 abolishes binding of Fhl1 and Ifh1 to RP promoters but does not significantly affect the level of transcriptional activity. These results suggest that Hmo1 is required for the assembly of transcription factor complexes containing Fhl1 and Ifh1 at RP promoters and that proteins other than Fhl1 and Ifh1 also play an important role in RP transcription. Lastly, like mammalian UBF, Hmo1 associates at many locations throughout the rRNA gene locus, and it is important for processing of rRNA in addition to its role in rRNA transcription. We speculate that Hmo1 has a role in coordinating the transcription of rRNA and RP genes.
Collapse
Affiliation(s)
- Daniel B Hall
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | | | | |
Collapse
|
200
|
Park JH, Guk SM, Han ET, Shin EH, Kim JL, Chai JY. Genotype analysis of Cryptosporidium spp. prevalent in a rural village in Hwasun-gun, Republic of Korea. Korean J Parasitol 2006; 44:27-33. [PMID: 16514279 PMCID: PMC2532641 DOI: 10.3347/kjp.2006.44.1.27] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Two species of Cryptosporidium are known to infect man; C. hominis which shows anthroponotic transmission between humans, and C. parvum which shows zoonotic transmission between animals or between animals and man. In this study, we focused on identifying genotypes of Cryptosporidium prevalent among inhabitants and domestic animals (cattle and goats), to elucidate transmittal routes in a known endemic area in Hwasun-gun, Jeollanam-do, Republic of Korea. The existence of Cryptosporidium oocysts was confirmed using a modified Ziehl-Neelsen stain. Human infections were found in 7 (25.9%) of 27 people examined. Cattle cryptosporidiosis cases constituted 7 (41.2%) of 17 examined, and goat cases 3 (42.9%) of 7 examined. Species characterizations were performed on the small subunit of the rRNA gene using both PCR-RFLP and sequence analysis. Most of the human isolates were mixtures of C. hominis and C. parvum genotypes and similar PCR-RFLP patterns were observed in cattle and goat isolates. However, sequence analyses identified only C. hominis in all isolates examined. The natural infection of cattle and goats with C. hominis is a new and unique finding in the present study. It is suggested that human cryptosporidiosis in the studied area is caused by mixtures of C. hominis and C. parvum oocysts originating from both inhabitants and domestic animals.
Collapse
Affiliation(s)
- Jae-Hwan Park
- Department of Parasitology and Tropical Medicine, Seoul National University College of Medicine, and Institute of Endemic Diseases, Seoul National University Medical Research Center, Seoul, Korea
| | | | | | | | | | | |
Collapse
|