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Bacteria and me: Cell walls, classification, phylogeny and the hidden microbes. Syst Appl Microbiol 2017; 40:321-328. [PMID: 28760568 DOI: 10.1016/j.syapm.2017.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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2
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Waite DW, Vanwonterghem I, Rinke C, Parks DH, Zhang Y, Takai K, Sievert SM, Simon J, Campbell BJ, Hanson TE, Woyke T, Klotz MG, Hugenholtz P. Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.). Front Microbiol 2017; 8:682. [PMID: 28484436 PMCID: PMC5401914 DOI: 10.3389/fmicb.2017.00682] [Citation(s) in RCA: 224] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 04/04/2017] [Indexed: 12/25/2022] Open
Abstract
The Epsilonproteobacteria is the fifth validly described class of the phylum Proteobacteria, known primarily for clinical relevance and for chemolithotrophy in various terrestrial and marine environments, including deep-sea hydrothermal vents. As 16S rRNA gene repositories have expanded and protein marker analysis become more common, the phylogenetic placement of this class has become less certain. A number of recent analyses of the bacterial tree of life using both 16S rRNA and concatenated marker gene analyses have failed to recover the Epsilonproteobacteria as monophyletic with all other classes of Proteobacteria. In order to address this issue, we investigated the phylogenetic placement of this class in the bacterial domain using 16S and 23S rRNA genes, as well as 120 single-copy marker proteins. Single- and concatenated-marker trees were created using a data set of 4,170 bacterial representatives, including 98 Epsilonproteobacteria. Phylogenies were inferred under a variety of tree building methods, with sequential jackknifing of outgroup phyla to ensure robustness of phylogenetic affiliations under differing combinations of bacterial genomes. Based on the assessment of nearly 300 phylogenetic tree topologies, we conclude that the continued inclusion of Epsilonproteobacteria within the Proteobacteria is not warranted, and that this group should be reassigned to a novel phylum for which we propose the name Epsilonbacteraeota (phyl. nov.). We further recommend the reclassification of the order Desulfurellales (Deltaproteobacteria) to a novel class within this phylum and a number of subordinate changes to ensure consistency with the genome-based phylogeny. Phylogenomic analysis of 658 genomes belonging to the newly proposed Epsilonbacteraeota suggests that the ancestor of this phylum was an autotrophic, motile, thermophilic chemolithotroph that likely assimilated nitrogen from ammonium taken up from the environment or generated from environmental nitrate and nitrite by employing a variety of functional redox modules. The emergence of chemoorganoheterotrophic lifestyles in several Epsilonbacteraeota families is the result of multiple independent losses of various ancestral chemolithoautotrophic pathways. Our proposed reclassification of this group resolves an important anomaly in bacterial systematics and ensures that the taxonomy of Proteobacteria remains robust, specifically as genome-based taxonomies become more common.
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Affiliation(s)
- David W. Waite
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St LuciaQLD, Australia
| | - Inka Vanwonterghem
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St LuciaQLD, Australia
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St LuciaQLD, Australia
| | - Donovan H. Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St LuciaQLD, Australia
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, KingstonRI, USA
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and TechnologyYokosuka, Japan
| | - Stefan M. Sievert
- Department of Biology, Woods Hole Oceanographic Institution, Woods HoleMA, USA
| | - Jörg Simon
- Microbial Energy Conversion and Biotechnology, Department of Biology, Technische Universität DarmstadtDarmstadt, Germany
| | - Barbara J. Campbell
- Department of Biological Sciences, Life Science Facility, Clemson University, ClemsonSC, USA
| | - Thomas E. Hanson
- School of Marine Science and Policy, College of Earth, Ocean, and Environment, Delaware Biotechnology Institute, University of Delaware, NewarkDE, USA
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut CreekCA, USA
| | - Martin G. Klotz
- Department of Biology and School of Earth and Environmental Sciences, Queens College of the City University of New York, New YorkNY, USA
- State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen UniversityXiamen, China
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St LuciaQLD, Australia
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Wang JY, Wang R, Zhang YM, Liu HC, Chen WF, Wang ET, Sui XH, Chen WX. Bradyrhizobium daqingense sp. nov., isolated from soybean nodules. Int J Syst Evol Microbiol 2013; 63:616-624. [PMID: 22544787 DOI: 10.1099/ijs.0.034280-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thirteen slow-growing rhizobial strains isolated from root nodules of soybean (Glycine max L.) grown in Daqing city in China were classified in the genus Bradyrhizobium based on 16S rRNA gene sequence analysis. Multilocus sequence analysis of IGS, atpD, glnII and recA genes revealed that the isolates represented a novel clade in this genus. DNA-DNA relatedness lower than 42.5 % between the representative strain CCBAU 15774(T) and the type strains of the closely related species Bradyrhizobium liaoningense USDA 3622(T), Bradyrhizobium yuanmingense CCBAU 10071(T) and Bradyrhizobium betae LMG 21987(T), further confirmed that this group represented a novel species. CCBAU 15774(T) shared seven cellular fatty acids with the three above-mentioned species, but the fatty acids 15 : 0 iso and summed feature 5 (18 : 2ω6,9c and/or 18 : 0 anteiso) were unique for this strain. The respiratory quinone in CCBAU 15774(T) was ubiquinone-10 and the cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, cardiolipin and unknown aminolipid, polar lipid and phospholipid. In addition, some phenotypic features could be used to differentiate the novel group from the related species. On basis of these results, we propose the name Bradyrhizobium daqingense sp. nov., with CCBAU 15774(T) ( = LMG 26137(T) = HAMBI 3184(T) = CGMCC 1.10947(T)) as the type strain. The DNA G+C content of the type strain is 61.2 mol% (T(m)).
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Affiliation(s)
- Jing Yu Wang
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Rui Wang
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Yan Ming Zhang
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Hong Can Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Wen Feng Chen
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México DF, Mexico
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Xin Hua Sui
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
| | - Wen Xin Chen
- State Key Laboratory for Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, PR China
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Proposal that the arsenite-oxidizing organisms Thiomonas cuprina and ‘Thiomonas arsenivorans’ be reclassified as strains of Thiomonas delicata, and emended description of Thiomonas delicata. Int J Syst Evol Microbiol 2011; 61:2816-2821. [DOI: 10.1099/ijs.0.023408-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The three As(III)-oxidizing members of the class Betaproteobacteria Thiomonas delicata, Thiomonas cuprina and ‘Thiomonas arsenivorans’ were isolated from mining sites in geographically distinct areas, namely Japan, Germany and France, respectively. They are all able to oxidize As(III) but only ‘T. arsenivorans’ and T. cuprina show efficient autotrophic growth with As(III) and are able to grow on a sole carbon source. These two organisms are also motile, whereas T. delicata is not. Only T. cuprina can grow autotrophically on chalcopyrite. The three strains share >99 % gene sequence similarity with each other based on their 16S rRNA genes and 16S–23S ITS regions. DNA–DNA hybridization results are above, or close to, the threshold value of 70 % recommended for the definition of bacterial species. The three taxa show very similar fatty acid profiles with differences only in five minor fatty acid components. They possess phylogenetic and chemotaxonomic similarities supporting the reclassification of these taxa as a single species. We propose that ‘T. arsenivorans’ and T. cuprina be reassigned as strains of T. delicata (type strain DSM 17897T).
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Yilmaz P, Kottmann R, Pruesse E, Quast C, Glöckner FO. Analysis of 23S rRNA genes in metagenomes – A case study from the Global Ocean Sampling Expedition. Syst Appl Microbiol 2011; 34:462-9. [DOI: 10.1016/j.syapm.2011.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 04/04/2011] [Accepted: 04/04/2011] [Indexed: 12/19/2022]
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Salman V, Amann R, Girnth AC, Polerecky L, Bailey JV, Høgslund S, Jessen G, Pantoja S, Schulz-Vogt HN. A single-cell sequencing approach to the classification of large, vacuolated sulfur bacteria. Syst Appl Microbiol 2011; 34:243-59. [PMID: 21498017 DOI: 10.1016/j.syapm.2011.02.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 02/20/2011] [Accepted: 02/21/2011] [Indexed: 10/18/2022]
Abstract
The colorless, large sulfur bacteria are well known because of their intriguing appearance, size and abundance in sulfidic settings. Since their discovery in 1803 these bacteria have been classified according to their conspicuous morphology. However, in microbiology the use of morphological criteria alone to predict phylogenetic relatedness has frequently proven to be misleading. Recent sequencing of a number of 16S rRNA genes of large sulfur bacteria revealed frequent inconsistencies between the morphologically determined taxonomy of genera and the genetically derived classification. Nevertheless, newly described bacteria were classified based on their morphological properties, leading to polyphyletic taxa. We performed sequencing of 16S rRNA genes and internal transcribed spacer (ITS) regions, together with detailed morphological analysis of hand-picked individuals of novel non-filamentous as well as known filamentous large sulfur bacteria, including the hitherto only partially sequenced species Thiomargarita namibiensis, Thioploca araucae and Thioploca chileae. Based on 128 nearly full-length 16S rRNA-ITS sequences, we propose the retention of the family Beggiatoaceae for the genera closely related to Beggiatoa, as opposed to the recently suggested fusion of all colorless sulfur bacteria into one family, the Thiotrichaceae. Furthermore, we propose the addition of nine Candidatus species along with seven new Candidatus genera to the family Beggiatoaceae. The extended family Beggiatoaceae thus remains monophyletic and is phylogenetically clearly separated from other related families.
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Affiliation(s)
- Verena Salman
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
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Watsuji TO, Nakagawa S, Tsuchida S, Toki T, Hirota A, Tsunogai U, Takai K. Diversity and Function of Epibiotic Microbial Communities on the Galatheid Crab, Shinkaia crosnieri. Microbes Environ 2010; 25:288-94. [DOI: 10.1264/jsme2.me10135] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Tomo-o Watsuji
- Subsurface Geobiology Advanced Research Team (SUGAR), Extremobiosphere Research Program (XBR)
| | - Satoshi Nakagawa
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University
| | - Shinji Tsuchida
- Deep Sea Ecosphere Research Team, Marine Biodiversity Research Program, JAMSTEC
| | | | - Akinari Hirota
- Department of Earth and Planetary System Science, Faculty of Science, Hokkaido University
| | - Urumu Tsunogai
- Department of Earth and Planetary System Science, Faculty of Science, Hokkaido University
| | - Ken Takai
- Subsurface Geobiology Advanced Research Team (SUGAR), Extremobiosphere Research Program (XBR)
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Zhao JS, Manno D, Hawari J. Psychrilyobacter atlanticus gen. nov., sp. nov., a marine member of the phylum Fusobacteria that produces H2 and degrades nitramine explosives under low temperature conditions. Int J Syst Evol Microbiol 2009; 59:491-7. [PMID: 19244428 DOI: 10.1099/ijs.0.65263-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative and obligately anaerobic marine bacterium, strain HAW-EB21(T), was isolated in a previous study from marine sediment from the Atlantic Ocean, near Halifax Harbor, Canada, and found to have the potential to degrade both hexahydro-1,3,5-trinitro-1,3,5-triazine and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine. In the present study, phylogenetic analyses showed that strain HAW-EB21(T) was only distantly related to the genera Propionigenium and Ilyobacter with 6.6-7.5 % and 8.2-10.5 % dissimilarity as measured by 16S rRNA and 23S rRNA gene sequence analyses, respectively. Strain HAW-EB21(T) displayed unique properties in being psychrotrophic (18.5 degrees C optimum) and unable to utilize any of the carbon substrates (succinate, l-tartrate, 3-hydroxybutyrate, quinate or shikimate) used for isolating members of the genera Propionigenium and Ilyobacter. Strain HAW-EB21(T) utilized glucose, fructose, maltose, N-acetyl-d-glucosamine, citrate, pyruvate, fumarate and Casitone as carbon sources and produced H(2) and acetate as the major fermentation products. Cells grown at 10 degrees C produced C(15 : 1) (30 %), C(16 : 1)omega7 (15 %) and C(16 : 0) (16 %) as major membrane fatty acids. The novel strain had a genomic DNA G+C content of 28.1 mol%, lower than the values of the genera Ilyobacter and Propionigenium. Based on the present results, the novel isolate is suggested to be a member of a new genus for which the name Psychrilyobacter atlanticus gen. nov., sp. nov. is proposed. The type strain of the type species is HAW-EB21(T) (=DSM 19335(T)=JCM 14977(T)).
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Affiliation(s)
- Jian-Shen Zhao
- Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount Ave, Montreal, Quebec H4P 2R2, Canada.
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Reassessment of the phylogenetic relationships of Thiomonas cuprina. Int J Syst Evol Microbiol 2007; 57:2720-2724. [DOI: 10.1099/ijs.0.65537-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The published sequence of the 16S rRNA gene of Thiomonas cuprina strain Hö5 (=DSM 5495T) (GenBank accession no. U67162) was found to be erroneous. The 16S rRNA genes from the type strain held by the DSMZ since 1990 (DSM 5495T =NBRC 102145T) and strain Hö5 maintained frozen in the Universität Regensburg for 23 years (=NBRC 102094) were sequenced and found to be identical, but to show no significant similarity to the U67162 sequence. This also casts some doubt on the previously published 5S and 23S rRNA gene sequences (GenBank accession nos U67171 and X75567). The correct 16S rRNA gene sequence showed 99.8 % identity to those from Thiomonas delicata NBRC 14566T and ‘Thiomonas arsenivorans’ DSM 16361. The properties of these three species are re-evaluated, and emended descriptions are provided for the genus Thiomonas and the species Thiomonas cuprina.
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Søgaard M, Hansen DS, Fiandaca MJ, Stender H, Schønheyder HC. Peptide nucleic acid fluorescence in situ hybridization for rapid detection of Klebsiella pneumoniae from positive blood cultures. J Med Microbiol 2007; 56:914-917. [PMID: 17577055 DOI: 10.1099/jmm.0.46829-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This study evaluated a novel peptide nucleic acid (PNA) probe targeting a region of the 23S rRNA gene of Klebsiella pneumoniae by fluorescence in situ hybridization (FISH). Analytical performance was determined using 39 reference strains and other well-characterized strains of Klebsiella spp. and Enterobacter aerogenes. The probe was found to be specific for the K. pneumoniae complex (K. pneumoniae including Klebsiella ozaenae and Klebsiella variicola). The diagnostic accuracy was evaluated with 264 blood cultures containing Gram-negative rods. Using conventional identification as the reference, performance specifications were as follows: sensitivity 98.8 %, specificity 99.5 %, positive predictive value 98.8 % and negative predictive value 99.5 %. Discrepancies were resolved by PNA FISH retest and phenotypic tests. In conclusion, the K. pneumoniae probe provided an accurate diagnosis within 3 h and may supplement other methods for direct identification of Gram-negative bacteria.
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Affiliation(s)
- Mette Søgaard
- Department of Clinical Epidemiology, Aalborg Hospital, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Microbiology, Aalborg Hospital, Aarhus University Hospital, Postbox 365, 9100 Aalborg, Denmark
| | - Dennis S Hansen
- Department of Clinical Microbiology, Hillerød Sygehus, Denmark
- The International Escherichia and Klebsiella Reference Center (WHO), Statens Serum Institut, Copenhagen, Denmark
| | | | | | - Henrik C Schønheyder
- Department of Clinical Microbiology, Aalborg Hospital, Aarhus University Hospital, Postbox 365, 9100 Aalborg, Denmark
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Martens M, Weidner S, Linke B, de Vos P, Gillis M, Willems A. A prototype taxonomic microarray targeting the rpsA housekeeping gene permits species identification within the rhizobial genus Ensifer. Syst Appl Microbiol 2007; 30:390-400. [PMID: 17291704 DOI: 10.1016/j.syapm.2007.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Indexed: 10/23/2022]
Abstract
To develop a reliable tool for the identification and classification of the different Ensifer species, without the need for sequencing, a prototype DNA microarray that targets the rpsA housekeeping gene was designed and tested. Internal segments of the rpsA gene from 34 reference strains, representing the different Ensifer species, were sequenced and the sequences were used to select 44 diagnostic oligonucleotides that served as probes for the identification microarray. Both, genomic DNA and specific rpsA PCR-products were tested as a target in hybridisation experiments. Experimental conditions were optimised and the diagnostic oligonucleotides were validated. Hybridisation results with the rpsA PCR-products showed reliable identification of the reference strains to species and genomovar level. Our data indicate that a microarray targeting housekeeping genes is a promising, accurate and relatively simple genotyping technique that would also be applicable for the identification and characterization of other bacterial groups of interest.
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Affiliation(s)
- Miet Martens
- Laboratorium voor Microbiologie (WE10), Universiteit Gent, B-9000 Ghent, Belgium
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12
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Jin DZ, Wen SY, Chen SH, Lin F, Wang SQ. Detection and identification of intestinal pathogens in clinical specimens using DNA microarrays. Mol Cell Probes 2006; 20:337-47. [PMID: 16730943 DOI: 10.1016/j.mcp.2006.03.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2006] [Revised: 03/26/2006] [Accepted: 03/30/2006] [Indexed: 11/26/2022]
Abstract
The detection and identification of intestinal pathogens is critical for clinical patient diagnosis and antimicrobial therapy. No currently available assays with DNA microarrays can simultaneously detect and identify multiple intestinal pathogens, because there is no appropriate method for choosing target probes. To solve the problem we have experimented for facilitating screening of specific probes and developed a rapid (<3h) and reliable assay for simultaneous detection of intestinal pathogens using two universal PCR primers to amplify two variable regions of bacterial 16S and 23S ribosomal DNA (rDNA) genes, and then applied to DNA microarrays, hybridization between probes and amplicons occurred. Through this idea for screening of probes the assay was successful in discriminating 15 genera or species of intestinal pathogens. The limit of detection was approximately 10(3)CFU/mL for one species of pathogen and 10(5)CFU/mL for six species pathogens existing simultaneously in stool. When this assay was applied directly to identify 99 clinical specimens, 80(80.8%) were correctly analyzed, including four with mixed pathogens; 8(8.08%) received negative results due to no corresponding probes in this array and 11(11.11%) belonging to our targets were misidentified due to low-level pathogens and other factors. This approach is also convenient to obtain specific and proper probes while establishing assays for the applications in other aspects using DNA microarrays. In addition, the more species may be added to this system easily and endlessly by screening of candidate target probes in order to increase the power of simultaneous detection.
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Affiliation(s)
- Da-Zhi Jin
- Beijing Institute of Radiation Medicine, No. 27 Taiping Road, Beijing, China
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13
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Simms EL, Taylor DL, Povich J, Shefferson RP, Sachs JL, Urbina M, Tausczik Y. An empirical test of partner choice mechanisms in a wild legume-rhizobium interaction. Proc Biol Sci 2006; 273:77-81. [PMID: 16519238 PMCID: PMC1560009 DOI: 10.1098/rspb.2005.3292] [Citation(s) in RCA: 138] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mutualisms can be viewed as biological markets in which partners of different species exchange goods and services to their mutual benefit. Trade between partners with conflicting interests requires mechanisms to prevent exploitation. Partner choice theory proposes that individuals might foil exploiters by preferentially directing benefits to cooperative partners. Here, we test this theory in a wild legumerhizobium symbiosis. Rhizobial bacteria inhabit legume root nodules and convert atmospheric dinitrogen (N2) to a plant available form in exchange for photosynthates. Biological market theory suits this interaction because individual plants exchange resources with multiple rhizobia. Several authors have argued that microbial cooperation could be maintained if plants preferentially allocated resources to nodules harbouring cooperative rhizobial strains. It is well known that crop legumes nodulate non-fixing rhizobia, but allocate few resources to those nodules. However, this hypothesis has not been tested in wild legumes which encounter partners exhibiting natural, continuous variation in symbiotic benefit. Our greenhouse experiment with a wild legume, Lupinus arboreus, showed that although plants frequently hosted less cooperative strains, the nodules occupied by these strains were smaller. Our survey of wild-grown plants showed that larger nodules house more Bradyrhizobia, indicating that plants may prevent the spread of exploitation by favouring better cooperators.
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Affiliation(s)
- Ellen L Simms
- Department of Integrative Biology, University of California, 3060 Valley Life Sciences Building #3140, Berkeley, CA 94720, USA.
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14
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Hunt DE, Klepac-Ceraj V, Acinas SG, Gautier C, Bertilsson S, Polz MF. Evaluation of 23S rRNA PCR primers for use in phylogenetic studies of bacterial diversity. Appl Environ Microbiol 2006; 72:2221-5. [PMID: 16517676 PMCID: PMC1393206 DOI: 10.1128/aem.72.3.2221-2225.2006] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2005] [Accepted: 12/19/2005] [Indexed: 11/20/2022] Open
Abstract
The availability of a diverse set of 23S rRNA gene sequences enabled evaluation of the specificity of 39 previously published and 4 newly designed primers specific for bacteria. An extensive clone library constructed using an optimized primer pair resulted in similar gene richness but slightly differing coverage of some phylogenetic groups, compared to a 16S rRNA gene library from the same environmental sample.
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Affiliation(s)
- Dana E Hunt
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 48-421, 77 Massachusetts Ave., Cambridge, MA 02139, USA
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Trujillo ME, Willems A, Abril A, Planchuelo AM, Rivas R, Ludeña D, Mateos PF, Martínez-Molina E, Velázquez E. Nodulation of Lupinus albus by strains of Ochrobactrum lupini sp. nov. Appl Environ Microbiol 2005; 71:1318-27. [PMID: 15746334 PMCID: PMC1065145 DOI: 10.1128/aem.71.3.1318-1327.2005] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The nodulation of legumes has for more than a century been considered an exclusive capacity of a group of microorganisms commonly known as rhizobia and belonging to the alpha-Proteobacteria. However, in the last 3 years four nonrhizobial species, belonging to alpha and beta subclasses of the Proteobacteria, have been described as legume-nodulating bacteria. In the present study, two fast-growing strains, LUP21 and LUP23, were isolated from nodules of Lupinus honoratus. The phylogenetic analysis based on the 16S and 23S rRNA gene sequences showed that the isolates belong to the genus Ochrobactrum. The strains were able to reinfect Lupinus plants. A plasmid profile analysis showed the presence of three plasmids. The nodD and nifH genes were located on these plasmids, and their sequences were obtained. These sequences showed a close resemblance to the nodD and nifH genes of rhizobial species, suggesting that the nodD and nifH genes carried by strain LUP21T were acquired by horizontal gene transfer. A polyphasic study including phenotypic, chemotaxonomic, and molecular features of the strains isolated in this study showed that they belong to a new species of the genus Ochrobactrum for which we propose the name Ochrobactrum lupini sp. nov. Strain LUP21T (LMG 20667T) is the type strain.
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Affiliation(s)
- Martha E Trujillo
- Departamento de Microbiología y Genética, Lab. 209, Edificio Departamental de Biología, Campus M, Unamuno, 37007 Salamanca, Spain
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16
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Peplies J, Glöckner FO, Amann R, Ludwig W. Comparative sequence analysis and oligonucleotide probe design based on 23S rRNA genes of Alphaproteobacteria from North Sea bacterioplankton. Syst Appl Microbiol 2004; 27:573-80. [PMID: 15490559 DOI: 10.1078/0723202041748172] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Almost complete 23S rRNA gene sequences were obtained from 11 Alphaproteobacteria isolated from marine surface water of the German Bight. Five of the strains belong to the "marine alpha" group, a phylogenetic cluster which encompasses members of the genus Roseobacter and closely related bacteria. Phylogenetic sequence analysis based on 52 published as well as unpublished complete 23S rDNA sequences from Alphaproteobacteria including the newly obtained was in general consistent with the 16S rRNA gene sequence-derived phylogeny. 16S and 23S rRNA based phylogenies both showed a distinct cluster for strains associated with the "marine alpha" group. The suitability of both markers for the design of oligonucleotide probes targeting selected groups of Alphaproteobacteria was systematically evaluated and compared in silico. Six clusters of sequences covering different phylogenetic levels as well as two strains were selected in a case study. To compensate for the quantitative difference in the two data sets, the 16S rRNA dataset was truncated to sequences with an equivalent in the 23S rRNA data set. Our results show, that the overall number of phylogenetically redundant probes available could be more than doubled by extending probe design to the 23S rRNA. For small clusters of high sequence similarity and single strains, up to 8 times more discriminating binding sites were provided by the 23S rRNA.
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MESH Headings
- Alphaproteobacteria/classification
- Alphaproteobacteria/genetics
- Alphaproteobacteria/isolation & purification
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- Genes, rRNA
- Germany
- Molecular Sequence Data
- North Sea
- Oligonucleotide Probes/genetics
- Phylogeny
- Plankton
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 23S/genetics
- Roseobacter/classification
- Seawater/microbiology
- Sensitivity and Specificity
- Sequence Analysis, DNA
- Water Microbiology
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Affiliation(s)
- Jörg Peplies
- Max Planck Institute for Marine Microbiology, Department of Molecular Ecology, Bremen, Germany
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17
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Tsang JSH. Molecular biology of the Burkholderia cepacia complex. ADVANCES IN APPLIED MICROBIOLOGY 2004; 54:71-91. [PMID: 15251276 DOI: 10.1016/s0065-2164(04)54002-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Jimmy S H Tsang
- Molecular Microbiology Laboratory, Department of Botany, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, China
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18
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Mitterer G, Huber M, Leidinger E, Kirisits C, Lubitz W, Mueller MW, Schmidt WM. Microarray-based identification of bacteria in clinical samples by solid-phase PCR amplification of 23S ribosomal DNA sequences. J Clin Microbiol 2004; 42:1048-57. [PMID: 15004052 PMCID: PMC356827 DOI: 10.1128/jcm.42.3.1048-1057.2004] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The rapid identification of the bacteria in clinical samples is important for patient management and antimicrobial therapy. We describe a DNA microarray-based PCR approach for the quick detection and identification of bacteria from cervical swab specimens from mares. This on-chip PCR method combines the amplification of a variable region of bacterial 23S ribosomal DNA and the simultaneous sequence-specific detection on a solid phase. The solid phase contains bacterial species-specific primers covalently bound to a glass support. During the solid-phase amplification reaction the polymerase elongates perfectly matched primers and incorporates biotin-labeled nucleotides. The reaction products are visualized by streptavidin-cyanine 5 staining, followed by fluorescence scanning. This procedure successfully identified from pure cultures 22 bacteria that are common causes of abortion and sterility in mares. Using the on-chip PCR method, we also tested 21 cervical swab specimens from mares for the presence of pathogenic bacteria and compared the results with those of conventional bacteriological culture methods. Our method correctly identified the bacteria in 12 cervical swab samples, 8 of which contained more than one bacterial species. Due to the higher sensitivity of the on-chip PCR, this method identified bacteria in five cervical swab samples which were not detected by the conventional identification procedure. Our results show that this method will have great potential to be incorporated into the routine microbiology laboratory.
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MESH Headings
- Abortion, Veterinary/microbiology
- Animals
- Bacteria/genetics
- Bacteria/isolation & purification
- Base Sequence
- DNA Primers
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/genetics
- DNA, Ribosomal/isolation & purification
- Female
- Horses
- Oligonucleotide Array Sequence Analysis
- Polymerase Chain Reaction/methods
- Pregnancy
- Pregnancy Complications, Infectious/microbiology
- Pregnancy Complications, Infectious/veterinary
- RNA, Bacterial/genetics
- RNA, Bacterial/isolation & purification
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/isolation & purification
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Affiliation(s)
- Georg Mitterer
- Institute of Microbiology & Genetics, University of Vienna, 1030 Vienna, Austria
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19
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Jarabo-Lorenzo A, Pérez-Galdona R, Donate-Correa J, Rivas R, Velázquez E, Hernández M, Temprano F, Martínez-Molina E, Ruiz-Argüeso T, León-Barrios M. Genetic diversity of bradyrhizobial populations from diverse geographic origins that nodulate Lupinus spp. and Ornithopus spp. Syst Appl Microbiol 2004; 26:611-23. [PMID: 14666990 DOI: 10.1078/072320203770865927] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The genetic diversity of 45 bradyrhizobial isolates that nodulate several Lupinus and Ornithopus species in different geographic locations was investigated by 16S rDNA PCR-RFLP and sequence analysis, 16S-23S rDNA intergenic spacer (IGS) PCR-RFLP analysis, and ERIC-PCR genomic fingerprinting. Reference strains of Bradyrhizobium japonicum, B. liaoningense and B. elkanii and some Canarian isolates from endemic woody legumes in the tribe Genisteae were also included. The 16S rDNA-RFLP analysis resolved 9 genotypes of lupin isolates, a group of fourteen isolates presented restriction-genotypes identical or very similar to B. japonicum, while another two main groups of isolates (69%) presented genotypes that clearly separated them from the reference species of soybean. 16S rDNA sequencing of representative strains largely agreed with restriction analysis, except for a group of six isolates, and showed that all the lupin isolates are relatives of B. japonicum, but different lineages were observed. The 16S-23S IGS-RFLP analysis showed a high resolution level, resolving 19 distinct genotypes among 30 strains analysed, and so demonstrating the heterogeneity of the 16S-RFLP groups. ERIC-PCR fingerprint analysis showed an enormous genetic diversity producing a different pattern for each but two of the isolates. Phylogeny of nodC gene was independent from the 16S rRNA phylogeny, and showed a tight relationship in the symbiotic region of the lupin isolates with isolates from Canarian genistoid woody legumes, and in concordance, cross-nodulation was found. We conclude that Lupinus is a promiscuous host legume that is nodulated by rhizobia with very different chromosomal genotypes, which could even belong to several species of Bradyrhizobium. No correlation among genomic background, original host plant and geographic location was found, so, different chromosomal genotypes could be detected at a single site and in a same plant species, on the contrary, an identical genotype was detected in very different geographical locations and plants.
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20
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Yeates C, Saunders AM, Crocetti GR, Blackall LL. Limitations of the widely used GAM42a and BET42a probes targeting bacteria in the Gammaproteobacteria radiation. MICROBIOLOGY (READING, ENGLAND) 2003; 149:1239-1247. [PMID: 12724385 DOI: 10.1099/mic.0.26112-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The 23S rRNA-targeted probes GAM42a and BET42a provided equivocal results with the uncultured gammaproteobacterium 'Candidatus Competibacter phosphatis' where some cells bound GAM42a and other cells bound BET42a in fluorescence in situ hybridization (FISH) experiments. Probes GAM42a and BET42a span positions 1027-1043 in the 23S rRNA and differ from each other by one nucleotide at position 1033. Clone libraries were prepared from PCR products spanning the 16S rRNA genes, intergenic spacer region and 23S rRNA genes from two mixed cultures enriched in 'Candidatus C. phosphatis'. With individual clone inserts, the 16S rDNA portion was used to confirm the source organism as 'Candidatus C. phosphatis' and the 23S rDNA portion was used to determine the sequence of the GAM42a/BET42a probe target region. Of the 19 clones sequenced, 8 had the GAM42a probe target (T at position 1033) and 11 had G at position 1033, the only mismatch with GAM42a. However, none of the clones had the BET42a probe target (A at 1033). Non-canonical base-pairing between the 23S rRNA of 'Candidatus C. phosphatis' with G at position 1033 and GAM42a (G-A) or BET42a (G-T) is likely to explain the probing anomalies. A probe (GAM42_C1033) was optimized for use in FISH, targeting cells with G at position 1033, and was found to highlight not only some 'Candidatus C. phosphatis' cells, but also other bacteria. This demonstrates that there are bacteria in addition to 'Candidatus C. phosphatis' with the GAM42_C1033 probe target and not the BET42a or GAM42a probe target.
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Affiliation(s)
- Christine Yeates
- Advanced Wastewater Management Centre, The University of Queensland, St Lucia, 4072, Australia
| | - Aaron M Saunders
- Advanced Wastewater Management Centre, The University of Queensland, St Lucia, 4072, Australia
| | - Gregory R Crocetti
- Advanced Wastewater Management Centre, The University of Queensland, St Lucia, 4072, Australia
| | - Linda L Blackall
- Advanced Wastewater Management Centre, The University of Queensland, St Lucia, 4072, Australia
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21
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Qian J, Parker MA. Contrasting nifD and ribosomal gene relationships among Mesorhizobium from Lotus oroboides in northern Mexico. Syst Appl Microbiol 2002; 25:68-73. [PMID: 12086191 DOI: 10.1078/0723-2020-00095] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
PCR screens for length variation in a 5' portion of 23S ribosomal RNA and in the 3' end of the 16S rRNA-23S rRNA internal transcribed spacer (ITS) region indicated that nodule bacteria from a Mexican population of Lotus oroboides were diverse on a local scale. Three 23S rRNA length variants and five ITS length variants were detected among the 22 isolates. Sequencing of nearly full-length 16S rRNA genes in three isolates indicated that they fell into the genus Mesorhizobium, but comprised two distinct groups. Two isolates were closely related to M. loti LMG 6125T, while the other isolate clustered with an assemblage of Mesorhizobium taxa that included M. amorphae, M. plurifarium and M. huakuii. However, a phylogenetic tree based on 715 bp of the nitrogenase alpha-subunit (nifD) gene was significantly discordant with the relationships inferred from rRNA sequences. Two isolates that were nearly identical for 16S rRNA had nifD genes that varied at 2% of sites, and one of these nifD sequences was identical to that of another isolate with a strongly divergent 16S rRNA gene. A plasmid screen followed by Southern hybridization indicated that only one of these strains harbored a plasmid-borne nifD gene. These results imply that gene transfer events have altered the distribution of nifD sequences among lineages within this natural population of Mesorhizobium strains.
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Affiliation(s)
- Jinghui Qian
- Department of Biological Sciences, State University of New York Binghamton, 13902-6000, USA
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22
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Parker MA. Case of localized recombination in 23S rRNA genes from divergent bradyrhizobium lineages associated with neotropical legumes. Appl Environ Microbiol 2001; 67:2076-82. [PMID: 11319084 PMCID: PMC92839 DOI: 10.1128/aem.67.5.2076-2082.2001] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2000] [Accepted: 02/28/2001] [Indexed: 11/20/2022] Open
Abstract
Enzyme electrophoresis and rRNA sequencing were used to analyze relationships of Bradyrhizobium sp. nodule bacteria from four papilionoid legumes (Clitoria javitensis, Erythrina costaricensis, Rhynchosia pyramidalis, and Desmodium axillare) growing on Barro Colorado Island (BCI), Panama. Bacteria with identical multilocus allele profiles were commonly found in association with two or more legume genera. Among the 16 multilocus genotypes (electrophoretic types [ETs]) detected, six ETs formed a closely related cluster that included isolates from all four legume taxa. Bacteria from two other BCI legumes (Platypodium and Machaerium) sampled in a previous study were also identical to certain ETs in this group. Isolates from different legume genera that had the same ET had identical nucleotide sequences for both a 5' portion of the 23S rRNA and the nearly full-length 16S rRNA genes. These results suggest that Bradyrhizobium genotypes with low host specificity may be prevalent in this tropical forest. Parsimony analysis of 16S rRNA sequence variation indicated that most isolates were related to Bradyrhizobium japonicum USDA 110, although one ET sampled from C. javitensis had a 16S rRNA gene highly similar to that of Bradyrhizobium elkanii USDA 76. However, this isolate displayed a mosaic structure within the 5' 23S rRNA region: one 84-bp segment was identical to that of BCI isolate Pe1-3 (a close relative of B. japonicum USDA 110, based on 16S rRNA data), while an adjacent 288-bp segment matched that of B. elkanii USDA 76. This mosaic structure is one of the first observations suggesting recombination in nature between Bradyrhizobium isolates related to B. japonicum versus B. elkanii.
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Affiliation(s)
- M A Parker
- Department of Biological Sciences, State University of New York, Binghamton, NY 13902-6000, USA.
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23
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García-Martínez J, Rodríguez-Valera F. Microdiversity of uncultured marine prokaryotes: the SAR11 cluster and the marine Archaea of Group I. Mol Ecol 2000; 9:935-48. [PMID: 10886656 DOI: 10.1046/j.1365-294x.2000.00953.x] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The SAR11 cluster and the Group I of marine Archaea represent probably the best two examples of uncultured marine prokaryotes of widespread occurrence. To study their microdiversity and distribution, a total of 81 and 48 clones, respectively, were sequenced from Mediterranean and Antarctic waters at different locations and depths. The DNA regions chosen for the analysis were the last third, approximately, of the 16S rRNA gene and the 16S-23S intergenic spacer (also known as internal transcribed spacer [ITS]). There was a high concordance in both, even with the extremely variable ITS, where potential probes have been proposed for the identification and isolation of these micro-organisms. In terms of community structure, our results show that although depth-related factors seem to be predominant in the final associations of the clones, geography also plays a significant role. A major group of surface-associated sequences was found in both SAR11 and marine Archaea. In both cases this group was relatively homogeneous containing little diversity in terms of sequence, while sequences retrieved from deep samples and some surface clones contained much more heterogeneity. As a whole, both groups of prokaryotes seem to fall within the limits of well-defined taxonomic units.
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Affiliation(s)
- J García-Martínez
- División de Microbiología, Universidad Miguel Hernández, Campus de San Juan, 03550 San Juan, Alicante, Spain
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24
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Bohnert J, Hübner B, Botzenhart K. Rapid identification of Enterobacteriaceae using a novel 23S rRNA-targeted oligonucleotide probe. Int J Hyg Environ Health 2000; 203:77-82. [PMID: 10956593 DOI: 10.1078/s1438-4639(04)70011-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The aim of this study was to rapidly identify bacteria of the family of Enterobacteriaceae using fluorescent in situ hybridization (FISH). A comparative sequence analysis was carried out and a 23S rRNA signature sequence for Enterobacteriaceae was identified. A 23S rRNA-targeted oligonucleotide probe (EBAC1790) was constructed and subsequently tested against 40 reference strains. Nearly all of the Enterobacteriaceae used in this study yielded positive results with EBAC1790, except for Edwardsiella tarda (ATCC 15947). None of the non-Enterobacteriaceae reference strains gave positive signals with the probe. The possibility of a rapid detection of Enterobacteriaceae in groundwater was demonstrated using colony hybridization.
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Affiliation(s)
- J Bohnert
- Abteilung für Allgemeine Hygiene und Umwelthygiene, Eberhard-Karls-Universität Tübingen, Germany.
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25
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Anthony RM, Brown TJ, French GL. Rapid diagnosis of bacteremia by universal amplification of 23S ribosomal DNA followed by hybridization to an oligonucleotide array. J Clin Microbiol 2000; 38:781-8. [PMID: 10655385 PMCID: PMC86203 DOI: 10.1128/jcm.38.2.781-788.2000] [Citation(s) in RCA: 145] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/1999] [Accepted: 10/29/1999] [Indexed: 11/20/2022] Open
Abstract
The rapid identification of bacteria in blood cultures and other clinical specimens is important for patient management and antimicrobial therapy. We describe a rapid (<4 h) detection and identification system that uses universal PCR primers to amplify a variable region of bacterial 23S ribosomal DNA, followed by reverse hybridization of the products to a panel of oligonucleotides. This procedure was successful in discriminating a range of bacteria in pure cultures. When this procedure was applied directly to 158 unselected positive blood culture broths on the day when growth was detected, 125 (79.7%) were correctly identified, including 4 with mixed cultures. Nine (7.2%) yielded bacteria for which no oligonucleotide targets were present in the oligonucleotide panel, and 16 culture-positive broths (10.3%) produced no PCR product. In seven of the remaining eight broths, streptococci were identified but not subsequently grown, and one isolate of Staphylococcus aureus was misidentified as a coagulase-negative staphylococcus. The accuracy, range, and discriminatory power of the assay can be continually extended by adding further oligonucleotides to the panel without significantly increasing complexity or cost.
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Affiliation(s)
- R M Anthony
- Department of Microbiology, King's College St. Thomas' Campus, St. Thomas' Hospital, London SE1 7EH, United Kingdom
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26
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Parker MA. Relationships of bradyrhizobia from the legumes Apios americana and Desmodium glutinosum. Appl Environ Microbiol 1999; 65:4914-20. [PMID: 10543803 PMCID: PMC91661 DOI: 10.1128/aem.65.11.4914-4920.1999] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/1999] [Accepted: 08/24/1999] [Indexed: 11/20/2022] Open
Abstract
Multilocus enzyme electrophoresis, partial 23S rRNA sequences, and nearly full-length 16S rRNA sequences all indicated high genetic similarity among root-nodule bacteria associated with Apios americana, Desmodium glutinosum, and Amphicarpaea bracteata, three common herbaceous legumes whose native geographic ranges in eastern North America overlap extensively. A total of 19 distinct multilocus genotypes (electrophoretic types [ETs]) were found among the 35 A. americana and 33 D. glutinosum isolates analyzed. Twelve of these ETs (representing 78% of all isolates) were either identical to ETs previously observed in A. bracteata populations, or differed at only one locus. Within both 23S and 16S rRNA genes, several isolates from A. americana and D. glutinosum were either identical to A. bracteata isolates or showed only single nucleotide differences. Growth rates and nitrogenase activities of A. bracteata plants inoculated with isolates from D. glutinosum were equivalent to levels found with native A. bracteata bacterial isolates, but none of the three A. americana isolates tested had high symbiotic effectiveness on A. bracteata. Phylogenetic analysis of both 23S and 16S rRNA sequences indicated that both A. americana and D. glutinosum harbored rare bacterial genotypes similar to Bradyrhizobium japonicum USDA 110. However, the predominant root nodule bacteria on both legumes were closely related to Bradyrhizobium elkanii.
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Affiliation(s)
- M A Parker
- Department of Biological Sciences, State University of New York, Binghamton, New York 13902, USA.
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27
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Sterner JP, Parker MA. Diversity and relationships of Bradyrhizobia from Amphicarpaea bracteata based on partial nod and ribosomal sequences. Syst Appl Microbiol 1999; 22:387-92. [PMID: 10553291 DOI: 10.1016/s0723-2020(99)80047-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Partial sequences of three nod genes (nodC, nodD1, and nodA 5' flanking region) and of 16S and 23S rDNA were obtained from isolates of Bradyrhizobium sp. associated with the native North American legume Amphicarpaea bracteata. Isolates from Amphicarpaea had identical sequences in the three nod gene regions, but differed from all other Bradyrhizobium taxa at > 10% of nucleotide sites. Parsimony analysis of all nod gene segments indicated a phylogenetic relationship of these bacteria to B. elkanii, with B. japonicum diverging prior to the diversification of these taxa. All Bradyrhizobium isolates from Amphicarpaea were also identical to B. elkanii in the size of the intervening sequence (IVS) in the 5' region of the 23S rRNA gene, while B. japonicum had an IVS length variant with 29 additional nucleotides. Parsimony analysis of both 16S and 23S partial rDNA sequences grouped Bradyrhizobium sp. isolates from Amphicarpaea into a clade together with B. elkanii, consistent with the relationships inferred from nod sequences.
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Affiliation(s)
- J P Sterner
- Department of Biological Sciences, State University of New York, Binghamton, USA
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28
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Bauernfeind A, Schneider I, Jungwirth R, Roller C. Discrimination of Burkholderia multivorans and Burkholderia vietnamiensis from Burkholderia cepacia genomovars I, III, and IV by PCR. J Clin Microbiol 1999; 37:1335-9. [PMID: 10203482 PMCID: PMC84768 DOI: 10.1128/jcm.37.5.1335-1339.1999] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present a PCR procedure for identification of Burkholderia cepacia, Burkholderia multivorans, and Burkholderia vietnamiensis. 16S and 23S ribosomal DNAs (rDNAs) of B. multivorans and B. vietnamiensis were sequenced and aligned with published sequences for definition of species-specific 18-mer oligonucleotide primers. Specific antisense 16S rDNA primers (for B. cepacia, 5'-AGC ACT CCC RCC TCT CAG-3'; for B. multivorans, 5'-AGC ACT CCC GAA TCT CTT-3') and 23S rDNA primers (for B. vietnamiensis, 5'-TCC TAC CAT GCG TGC AA-3') were paired with a general sense primer of 16S rDNAs (5'-AGR GTT YGA TYM TGG CTC AG-3') or with a sense primer of 23S rDNA (5'-CCT TTG GGT CAT CCT GGA-3'). PCR with these primers under optimized conditions is appropriate to specifically and rapidly identify B. multivorans, B. vietnamiensis, and B. cepacia (genomovars I, III, and IV are not discriminated). In comparison with the polyphasic taxonomic analyses presently necessary for species and genomovar identification within the B. cepacia complex, our procedure is more rapid and easier to perform and may contribute to clarifying the clinical significance of individual members of the complex in cystic fibrosis.
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29
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Antón AI, Martínez-Murcia AJ, Rodríguez-Valera F. Intraspecific diversity of the 23S rRNA gene and the spacer region downstream in Escherichia coli. J Bacteriol 1999; 181:2703-9. [PMID: 10217757 PMCID: PMC93708 DOI: 10.1128/jb.181.9.2703-2709.1999] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The molecular microevolution of the 23S rRNA gene (rrl) plus the spacer downstream has been studied by sequencing of different operons from some representative strains of the Escherichia coli ECOR collection. The rrl gene was fully sequenced in six strains showing a total of 67 polymorphic sites, a level of variation per nucleotide similar to that found for the 16S rRNA gene (rrs) in a previous study. The size of the gene was highly conserved (2902 to 2905 nucleotides). Most polymorphic sites were clustered in five secondary-structure helices. Those regions in a large number of operons were sequenced, and several variations were found. Sequences of the same helix from two different strains were often widely divergent, and no intermediate forms existed. Intercistronic variability was detected, although it seemed to be lower than for the rrs gene. The presence of two characteristic sequences was determined by PCR analysis throughout all of the strains of the ECOR collection, and some correlations with the multilocus enzyme electrophoresis clusters were detected. The mode of variation of the rrl gene seems to be quite similar to that of the rrs gene. Homogenization of the gene families and transfer of sequences from different clonal lines could explain this pattern of variation detected; perhaps these factors are more relevant to evolution than single mutation. The spacer region between the 23S and 5S rRNA genes exhibited a highly polymorphic region, particularly at the 3' end.
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MESH Headings
- Bacterial Typing Techniques
- Base Sequence
- Biological Specimen Banks
- DNA, Ribosomal/classification
- DNA, Ribosomal/genetics
- Escherichia coli/classification
- Escherichia coli/genetics
- Evolution, Molecular
- Gene Transfer Techniques
- Genes, Bacterial
- Genetic Variation
- Molecular Sequence Data
- Nucleic Acid Conformation
- Nucleic Acid Probes
- Operon
- RNA, Ribosomal, 23S/classification
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 5S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Species Specificity
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Affiliation(s)
- A I Antón
- Unidad de Microbiología, Centro de Biología Molecular y Celular, Universidad Miguel Hernández, Campus de San Juan, 03550 San Juan, Alicante, Spain
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30
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Baker SC, Ferguson SJ, Ludwig B, Page MD, Richter OM, van Spanning RJ. Molecular genetics of the genus Paracoccus: metabolically versatile bacteria with bioenergetic flexibility. Microbiol Mol Biol Rev 1998; 62:1046-78. [PMID: 9841665 PMCID: PMC98939 DOI: 10.1128/mmbr.62.4.1046-1078.1998] [Citation(s) in RCA: 151] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Paracoccus denitrificans and its near relative Paracoccus versutus (formerly known as Thiobacilllus versutus) have been attracting increasing attention because the aerobic respiratory system of P. denitrificans has long been regarded as a model for that of the mitochondrion, with which there are many components (e.g., cytochrome aa3 oxidase) in common. Members of the genus exhibit a great range of metabolic flexibility, particularly with respect to processes involving respiration. Prominent examples of flexibility are the use in denitrification of nitrate, nitrite, nitrous oxide, and nitric oxide as alternative electron acceptors to oxygen and the ability to use C1 compounds (e.g., methanol and methylamine) as electron donors to the respiratory chains. The proteins required for these respiratory processes are not constitutive, and the underlying complex regulatory systems that regulate their expression are beginning to be unraveled. There has been uncertainty about whether transcription in a member of the alpha-3 Proteobacteria such as P. denitrificans involves a conventional sigma70-type RNA polymerase, especially since canonical -35 and -10 DNA binding sites have not been readily identified. In this review, we argue that many genes, in particular those encoding constitutive proteins, may be under the control of a sigma70 RNA polymerase very closely related to that of Rhodobacter capsulatus. While the main focus is on the structure and regulation of genes coding for products involved in respiratory processes in Paracoccus, the current state of knowledge of the components of such respiratory pathways, and their biogenesis, is also reviewed.
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Affiliation(s)
- S C Baker
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom.
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31
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Dodd HN, Pemberton JM. Construction of a physical and preliminary genetic map of Aeromonas hydrophila JMP636. MICROBIOLOGY (READING, ENGLAND) 1998; 144 ( Pt 11):3087-3096. [PMID: 9846744 DOI: 10.1099/00221287-144-11-3087] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A physical and preliminary genetic map of the Aeromonas hydrophila JMP636 chromosome has been constructed. The topology of the genome was predicted to be circular as chromosomal DNA did not migrate from the origin during PFGE unless linearized by S1 nuclease. Cleavage of the chromosome with PacI and PmeI produced 23 and 14 fragments, respectively, and enabled calculation of the genome size at 4.5 Mb. Digestion of the chromosome with I-CeuI produced 10 fragments, indicating that 10 rrl (23S) genes were likely to be present. Hybridizations between DNA fragments generated with PacI, PmeI and I-CeuI were used to initially determine the relationship between these segments. To accurately map genes previously characterized from JMP636, the suicide vector pJP5603 was modified to introduce restriction sites for PacI and PmeI, producing pJP9540. Following cloning of genes into this vector and recombinational insertion into the JMP636 chromosome, PacI and PmeI cleavage determined the location of genes within macrorestriction fragments with the additional bands produced forming hybridization probes. From the data generated, it was possible to form a physical map comprising all the fragments produced by PacI and PmeI, and assign the contig of I-CeuI fragments on this map. The preliminary genetic map defines the location of six loci for degradative enzymes previously characterized from JMP636, while the locations of the 10 sets of ribosomal genes were assigned with less accuracy from hybridization data.
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Affiliation(s)
- Helen N Dodd
- Department of Microbiology QueenslandAustralia 4072 University
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32
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Wullings BA, Van Beuningen AR, Janse JD, Akkermans AD. Detection of Ralstonia solanacearum, which causes brown rot of potato, by fluorescent in situ hybridization with 23S rRNA-targeted probes. Appl Environ Microbiol 1998; 64:4546-54. [PMID: 9797321 PMCID: PMC106683 DOI: 10.1128/aem.64.11.4546-4554.1998] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During the past few years, Ralstonia (Pseudomonas) solanacearum race 3, biovar 2, was repeatedly found in potatoes in Western Europe. To detect this bacterium in potato tissue samples, we developed a method based on fluorescent in situ hybridization (FISH). The nearly complete genes encoding 23S rRNA of five R. solanacearum strains and one Ralstonia pickettii strain were PCR amplified, sequenced, and analyzed by sequence alignment. This resulted in the construction of an unrooted tree and supported previous conclusions based on 16S rRNA sequence comparison in which R. solanacearum strains are subdivided into two clusters. Based on the alignments, two specific probes, RSOLA and RSOLB, were designed for R. solanacearum and the closely related Ralstonia syzygii and blood disease bacterium. The specificity of the probes was demonstrated by dot blot hybridization with RNA extracted from 88 bacterial strains. Probe RSOLB was successfully applied in FISH detection with pure cultures and potato tissue samples, showing a strong fluorescent signal. Unexpectedly, probe RSOLA gave a less intense signal with target cells. Potato samples are currently screened by indirect immunofluorescence (IIF). By simultaneously applying IIF and the developed specific FISH, two independent targets for identification of R. solanacearum are combined, resulting in a rapid (1-day), accurate identification of the undesired pathogen. The significance of the method was validated by detecting the pathogen in soil and water samples and root tissue of the weed host Solanum dulcamara (bittersweet) in contaminated areas.
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Affiliation(s)
- B A Wullings
- Laboratory of Microbiology, Department of Biomolecular Sciences, Wageningen Agricultural University, Wageningen, The Netherlands
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33
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Kang Y, Carlson R, Tharpe W, Schell MA. Characterization of genes involved in biosynthesis of a novel antibiotic from Burkholderia cepacia BC11 and their role in biological control of Rhizoctonia solani. Appl Environ Microbiol 1998; 64:3939-47. [PMID: 9758823 PMCID: PMC106582 DOI: 10.1128/aem.64.10.3939-3947.1998] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genetic manipulation of fluorescent pseudomonads has provided major insight into their production of antifungal molecules and their role in biological control of plant disease. Burkholderia cepacia also produces antifungal activities, but its biological control activity is much less well characterized, in part due to difficulties in applying genetic tools. Here we report genetic and biochemical characterization of a soil isolate of B. cepacia relating to its production of an unusual antibiotic that is very active against a variety of soil fungi. Purification and preliminary structural analyses suggest that this antibiotic (called AFC-BC11) is a novel lipopeptide associated largely with the cell membrane. Analysis of conditions for optimal production of AFC-BC11 indicated stringent environmental regulation of its synthesis. Furthermore, we show that production of AFC-BC11 is largely responsible for the ability of B. cepacia BC11 to effectively control the damping-off of cotton caused by the fungal pathogen Rhizoctonia solani in a gnotobiotic system. Using Tn5 mutagenesis, we identified, cloned, and characterized a region of the genome of strain BC11 that is required for production of this antifungal metabolite. DNA sequence analysis suggested that this region encodes proteins directly involved in the production of a nonribosomally synthesized lipopeptide.
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Affiliation(s)
- Y Kang
- Department of Microbiology, University of Georgia, Athens, Georgia 30602, USA
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34
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Bauernfeind A, Schneider I, Jungwirth R, Roller C. Discrimination of Burkholderia gladioli from other Burkholderia species detectable in cystic fibrosis patients by PCR. J Clin Microbiol 1998; 36:2748-51. [PMID: 9705429 PMCID: PMC105199 DOI: 10.1128/jcm.36.9.2748-2751.1998] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A procedure for molecular identification of Burkholderia gladioli is described. Specific 16S and 23S rRNA gene signature sequences were defined as primers for PCR. The method allows rapid and specific discrimination of B. gladioli from related species (B. cepacia, B. multivorans, B. vietnamiensis, B. mallei, B. pseudomallei, Ralstonia pickettii, and R. eutropha) and should contribute to the clarification of its role as a human pathogen, e.g., in cystic fibrosis.
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Affiliation(s)
- A Bauernfeind
- Department of Experimental Medical Microbiology and Cystic Fibrosis, Max von Pettenkofer Institute, D-80336 Munich, Germany.
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35
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Bauernfeind A, Roller C, Meyer D, Jungwirth R, Schneider I. Molecular procedure for rapid detection of Burkholderia mallei and Burkholderia pseudomallei. J Clin Microbiol 1998; 36:2737-41. [PMID: 9705426 PMCID: PMC105196 DOI: 10.1128/jcm.36.9.2737-2741.1998] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A PCR procedure for the discrimination of Burkholderia mallei and Burkholderia pseudomallei was developed. It is based on the nucleotide difference T 2143 C (T versus C at position 2143) between B. mallei and B. pseudomallei detected in the 23S rDNA sequences. In comparison with conventional methods the procedure allows more rapid identification at reduced risk for infection of laboratory personnel.
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Affiliation(s)
- A Bauernfeind
- Max von Pettenkofer Institut, D-80336 Munich, Germany.
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36
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Ludwig W, Strunk O, Klugbauer S, Klugbauer N, Weizenegger M, Neumaier J, Bachleitner M, Schleifer KH. Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 1998; 19:554-68. [PMID: 9588802 DOI: 10.1002/elps.1150190416] [Citation(s) in RCA: 612] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Comparative sequence analysis of small subunit rRNA is currently one of the most important methods for the elucidation of bacterial phylogeny as well as bacterial identification. Phylogenetic investigations targeting alternative phylogenetic markers such as large subunit rRNA, elongation factors, and ATPases have shown that 16S rRNA-based trees reflect the history of the corresponding organisms globally. However, in comparison with three to four billion years of evolution the phylogenetic information content of these markers is limited. Consequently, the limited resolution power of the marker molecules allows only a spot check of the evolutionary history of microorganisms. This is often indicated by locally different topologies of trees based on different markers, data sets or the application of different treeing approaches. Sequence peculiarities as well as methods and parameters for data analysis were studied with respect to their effects on the results of phylogenetic investigations. It is shown that only careful data analysis starting with a proper alignment, followed by the analysis of positional variability, rates and character of change, testing various data selections, applying alternative treeing methods and, finally, performing confidence tests, allows reasonable utilization of the limited phylogenetic information.
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Affiliation(s)
- W Ludwig
- Lehrstuhl für Mikrobiologie, Technische Universität München, Germany.
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Hanada S, Shigematsu T, Shibuya K, Eguchi M, Hasegawa T, Suda F, Kamagata Y, Kanagawa T, Kurane R. Phylogenetic analysis of trichloroethylene-degrading bacteria newly isolated from soil polluted with this contaminant. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s0922-338x(99)80003-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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38
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Paoli GC, Soyer F, Shively J, Tabita FR. Rhodobacter capsulatus genes encoding form I ribulose-1,5-bisphosphate carboxylase/oxygenase (cbbLS) and neighbouring genes were acquired by a horizontal gene transfer. MICROBIOLOGY (READING, ENGLAND) 1998; 144 ( Pt 1):219-227. [PMID: 9467914 DOI: 10.1099/00221287-144-1-219] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Analysis of the nucleotide sequence of the form I ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) genes (cbbL and cbbS) of the non-sulfur purple bacterium Rhodobacter capsulatus indicated that the deduced amino acid sequence of the large subunit was not closely homologous to the large subunit from related organisms. Indeed, phylogenetic analysis suggested that the large subunit protein (CbbL) more closely resembled the enzyme from alpha/beta/gamma purple bacteria and cyanobacteria and is within a 'green-like' radiation of the RubisCO phylogenetic tree, well separated from CbbL of the related organism Rhodobacter sphaeroides. A cbbQ gene was discovered downstream of cbbS in Rh. capsulatus, a gene arrangement which also appears to be limited to certain organisms containing a 'green-like' RubisCO. Upstream, and divergently transcribed from cbbLSQ, is a gene (cbbRI) that encodes a LysR-type transcriptional activator. Phylogenetic analysis of the deduced amino acid sequence of CbbRI also suggests that this protein is quite distinct from the Rh. sphaeroides CbbR protein, and is even distinct from the previously described CbbRII protein, the gene of which is upstream and divergently transcribed from the cbbII operon of Rh. capsulatus. Interestingly, Rh. capsulatus CbbRI is more closely related to CbbR from bacteria whose RubisCO falls within the 'green-like' radiation of the CbbL tree. These studies suggest that the cbbRI-cbbL-cbbS-cbbQ genes were acquired by Rh. capsulatus via horizontal gene transfer from a bacterial species containing a 'green-like' RubisCO.
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Affiliation(s)
- George C Paoli
- The Department of Microbiology and Plant Molecular Biology/Biotechnology Program, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210-1292, USA
| | - Ferda Soyer
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - Jessup Shively
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
| | - F Robert Tabita
- The Department of Microbiology and Plant Molecular Biology/Biotechnology Program, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210-1292, USA
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Hurtado A, Clewley JP, Linton D, Owen RJ, Stanley J. Sequence similarities between large subunit ribosomal RNA gene intervening sequences from different Helicobacter species. Gene X 1997; 194:69-75. [PMID: 9266674 DOI: 10.1016/s0378-1119(97)00158-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
When the 23S rRNA genes from several Helicobacter species were amplified by PCR and compared with similar amplicons derived from H. pylori, they were seen to be enlarged in size. Sequencing of these enlarged genes from H. mustelae, H. canis (two strains) and H. muridarum identified insertions of novel sequence (intervening sequences, IVSs) sized between 93 and 377 bp located at nt 545, in place of an 8-nt sequence in the conventionally sized H. pylori gene. These IVSs were not present elsewhere in the genome. All strains with such IVSs lacked intact 23S rRNA which was replaced by two fragment whose sizes were consistent with cleavage at either side of the particular IVS. The predicted secondary structures of the four IVSs were characterised by base pairing at the 5' and 3' ends to form a stem. The four IVSs exhibited significant sequence inter-relationships. Further relationships were also observed between them and similar elements in both small and large subunit rRNA genes of other Helicobacter and Campylobacter species. Alignment of each IVS with the other such elements identified blocks of related sequence consistent with insertion/deletion events, indicating possible evolutionary relationships.
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Affiliation(s)
- A Hurtado
- Laboratory of Enteric Pathogens, Central Public Health Laboratory, London, UK
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Polyphasic Characterization of the Genus Leptothrix: New Descriptions of Leptothrix mobilis sp. nov. and Leptothrix discophora sp. nov. nom. rev. and Emended Description of Leptothrix cholodnii emend. Syst Appl Microbiol 1996. [DOI: 10.1016/s0723-2020(96)80036-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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41
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Moreira D, Amils R. PCR-mediated detection of the chemolithotrophic bacterium Thiobacillus cuprinus using 23S rDNA- and 16S/23S intergenic spacer region-targeted oligonucleotide primers. FEMS Microbiol Lett 1996; 142:289-93. [PMID: 8810512 DOI: 10.1111/j.1574-6968.1996.tb08445.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Bioleaching is carried out by chemolithotrophic microorganisms, most of them belonging to the genera Thiobacillus and Leptospirillum. The role of the mixotrophic species T. cuprinus in this process is controversial, since its ecological study applying classical detection techniques to natural or industrial environments is very difficult. For this reason, we have developed an alternative method based on PCR-mediated detection using specific oligonucleotide primers that target variable regions of the 23S rRNA coding gene and of the 16S/23S intergenic spacer region. Specificity and sensitivity of PCR amplifications performed with both kinds of primers were studied.
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Affiliation(s)
- D Moreira
- Centro de Biología Molecular, Universidad Autónoma de Madrid, Cantoblanco, Madrid, Spain,
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