View More View Less
  • 1 DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH Mascheroder Weg 1b, 38124 Braunschweig, Germany
Restricted access

Purchase article

USD  $25.00

1 year subscription (Individual Only)

USD  $784.00

This communication will summarize recent estimations on prokaryotic cell numbers, technical aspects of the exploration of the hidden diversity of the as-yet-uncultured prokaryotes and their function in the environment, recognition of novel major lines of descent, elucidation of novel metabolic pathways and attempts to improve the definition of the taxon species. These are some of recent highlights that will reflect only incompletely recent advances of microbiologist and other aspects of diversity at the genomic level, including the tremendous influence of whole genome sequences on the development of DNA macro- and microarrays for rapid identification of genes and specimen, the annotation of gene sequences to gene function by proteomics and the recognition of the extent of lateral gene transfer in the evolution of the genome, hence of contemporary organisms. As an example of modern trends in systematics three new families will be described for recently described genera, namely Thermoleophilaceae, Solirubrobacteraceae and Conexibacteraceae, which are phylogenetically positioned among environmental clone sequences at the root of the class Actinobacteria.

  • Maynard Smith, J., Feil, E. S., Smith, N. H.: Population structure and evolutionary dynamics of pathogenic bacteria. Bioessays 22, 1115-1122 (2000).

    'Population structure and evolutionary dynamics of pathogenic bacteria ' () 22 Bioessays : 1115 -1122.

    • Search Google Scholar
  • Istock, C. A., Bell, J. A., Ferguson, N., Istock, N. L.: Bacterial species and evolution: theoretical and practical perspectives. J Indust Microbiol 17, 137-150 (1996).

    'Bacterial species and evolution: theoretical and practical perspectives ' () 17 J Indust Microbiol : 137 -150.

    • Search Google Scholar
  • Achtman, M.: Microevolution during epidemic spread of Neisseria meningitidis Electrophoresis 19, 593-596 (1998).

    'Microevolution during epidemic spread of Neisseria meningitidis ' () 19 Electrophoresis : 593 -596.

    • Search Google Scholar
  • Stackebrandt, E., Frederiksen, W., Garrity, G. M., Grimont, P. A. D., Kämpfer, P., Maiden, M. C. J., Nesme, X., Rossello-Mora, R., Swings, J., Trüper, H. G., Vauterin, L., Ward, A. C., Whitman, W. B.: Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52, 1043-1052 (2002).

    'Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology ' () 52 Int J Syst Evol Microbiol : 1043 -1052.

    • Search Google Scholar
  • Merkel, G. J., Stapleton, S. S., Perry, J. J.: Isolation and peptidoglycan of Gram-negative hydrocarbon-utilizing thermophilic bacteria. J Gen Microbiol 109, 141-148 (1978a).

    'Isolation and peptidoglycan of Gram-negative hydrocarbon-utilizing thermophilic bacteria ' () 109 J Gen Microbiol : 141 -148.

    • Search Google Scholar
  • Merkel, G. J., Underwood, W. H., Perry, J. J.: Isolation of thermophilic bacteria capable of growth solely in long-chain hydrocarbons. FEMS Microbiol Lett 3, 81-83 (1978b).

    'Isolation of thermophilic bacteria capable of growth solely in long-chain hydrocarbons ' () 3 FEMS Microbiol Lett : 81 -83.

    • Search Google Scholar
  • Suzuki, K., Collins, M. D., Iijima, E., Komagata, K.: Chemotaxonomic characterization of a radiotolerant bacterium Arthrobacter radiotolerans: description of Rubrobacter radiotolerans gen. nov. comb. nov. FEMS Microbiol Lett 52, 33-40 (1988).

    'Chemotaxonomic characterization of a radiotolerant bacterium Arthrobacter radiotolerans: description of Rubrobacter radiotolerans gen. nov. comb. nov ' () 52 FEMS Microbiol Lett : 33 -40.

    • Search Google Scholar
  • Lan, R., Reeves, P. R.: When does a clone deserve a name? A perspective on bacterial species based on population genetics. Trends Microbiol 9, 419-424 (2001).

    'When does a clone deserve a name? A perspective on bacterial species based on population genetics ' () 9 Trends Microbiol : 419 -424.

    • Search Google Scholar
  • Palys, T., Berger, E., Mitrica, I., Nakamura, L. K., Cohan, F. M.: Protein-coding genes as molecular markers for ecologically distinct populations: the case of two Bacillus species. Int J Syst Evol Microbiol 50, 1021-1028 (2000).

    'Protein-coding genes as molecular markers for ecologically distinct populations: the case of two Bacillus species ' () 50 Int J Syst Evol Microbiol : 1021 -1028.

    • Search Google Scholar
  • Torsvik, V., Øvreås, L., Thingstad, T. F.: Prokaryotic diversity-magnitude, dynamics, and controlling factors. Science 296, 1064-1066 (2002).

    'Prokaryotic diversity-magnitude, dynamics, and controlling factors ' () 296 Science : 1064 -1066.

    • Search Google Scholar
  • Whitman, W. B., Coleman, D. C., Wiebe, W. J.: Prokaryotes: the unseen majority. PNAS USA 95, 6578-6583 (1998).

    'Prokaryotes: the unseen majority ' () 95 PNAS USA : 6578 -6583.

  • Bull, A. T., Ward, A. C., Goodfellow, M.: Search and discovery strategies for biotechnology: the paradigm shift. Microbiol Molec Biol Rev 64, 573-606 (2000).

    'Search and discovery strategies for biotechnology: the paradigm shift ' () 64 Microbiol Molec Biol Rev : 573 -606.

    • Search Google Scholar
  • Dykhuizen, D. E.: Santa Rosalia revisited: Why are there so many species of bacteria? Antonie van Leeuwenhoek J Microbiol 73, 25-33 (1998).

    'Santa Rosalia revisited: Why are there so many species of bacteria? ' () 73 Antonie van Leeuwenhoek J Microbiol : 25 -33.

    • Search Google Scholar
  • Kaeberlein, T., Lewis, K., Epstein, S. S.: Isolating "uncultivable" microorganisms in pure culture in a simulated natural environment. Science 296, 1127-1129 (2002).

    'Isolating "uncultivable" microorganisms in pure culture in a simulated natural environment ' () 296 Science : 1127 -1129.

    • Search Google Scholar
  • Pace, N. R., Stahl, D. A., Lane, D. J., Olson, G. J.: The analysis of natural microbial populations by ribosomal RNA sequences. Adv Microbial Ecol 9, 1-5 (1986).

    'The analysis of natural microbial populations by ribosomal RNA sequences ' () 9 Adv Microbial Ecol : 1 -5.

    • Search Google Scholar
  • Nogales, B., Moore, E. R., Lobet-Brossa, E., Rosello-Mora, R., Amann, R., Timmis, K. N.: Combined use of 16S ribosomal DNA and 16S rRNA to study bacterial community of polychlorinated biphenyl-polluted soil. Appl Environ Microbiol 67, 1874-1884 (2001).

    'Combined use of 16S ribosomal DNA and 16S rRNA to study bacterial community of polychlorinated biphenyl-polluted soil ' () 67 Appl Environ Microbiol : 1874 -1884.

    • Search Google Scholar
  • Brambilla, E., Hippe, H., Hagelstein, A., Tindall, B. J., Stackebrandt, E.: 16S rDNA diversity of cultured and uncultured prokaryotes of a mat sample from Lake Fryxell, McMurdo Dry Valleys, Antartica. Extremophiles 5, 22-33 (2001).

    '16S rDNA diversity of cultured and uncultured prokaryotes of a mat sample from Lake Fryxell, McMurdo Dry Valleys, Antartica ' () 5 Extremophiles : 22 -33.

    • Search Google Scholar
  • Axelrood, P. E., Chow, M. L., Radomski, C. C., McDermott, J. M., Davies, J.: Molecular characterization of bacterial diversity from British Columbia forest soil subjected to disturbance. Can J Microbiol 48, 655-674 (2002).

    'Molecular characterization of bacterial diversity from British Columbia forest soil subjected to disturbance ' () 48 Can J Microbiol : 655 -674.

    • Search Google Scholar
  • Yoshinsaka, T., Yano, K., Yamaguchi, H.: Isolation of highly radioresistant bacterium, Arthrobacter radiotolerans nov. sp. Agric Biol Chem 37, 2269-2275 (1973).

    'Isolation of highly radioresistant bacterium, Arthrobacter radiotolerans nov. sp ' () 37 Agric Biol Chem : 2269 -2275.

    • Search Google Scholar
  • Fell, N., Liss, P.: Can Algae Cool the Planet? New Scientist 21, 14 (1993).

    'Can Algae Cool the Planet? ' () 21 New Scientist : 14.

  • Carreto, L., Moore, E., Nobre, M. F., Wait, R., Riley, P. W., Sharp, R. J., da Costa, M. S.: Rubrobacter xylanophilus sp. nov., a new thermophilic species from a thermally polluted effluent. Int J Syst Bacteriol 46, 460-465 (1996).

    'Rubrobacter xylanophilus sp. nov., a new thermophilic species from a thermally polluted effluent ' () 46 Int J Syst Bacteriol : 460 -465.

    • Search Google Scholar
  • Choi, B.-K., Paster, B., Dewhirst, F. E., Göbel, U. B.: Diversity of cultivable and uncultivable oral spirochetes from a patient with severe destructive periodinitis. Infect Immun 62, 1889-1895 (1994).

    'Diversity of cultivable and uncultivable oral spirochetes from a patient with severe destructive periodinitis ' () 62 Infect Immun : 1889 -1895.

    • Search Google Scholar
  • Tiedje, J. M., Asuming-Brempong, S., Nüsslein, K., Marsh, T. L., Flynn, S. J.: Opening the black box of soil microbial diversity. Appl Soil Ecol 13, 109-122 (1999).

    'Opening the black box of soil microbial diversity ' () 13 Appl Soil Ecol : 109 -122.

  • Farelly, V., Rainey, F. A., Stackebrandt, E.: Effect of genomic size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl Environ Microbiol 61, 2798-2801 (1995).

    'Effect of genomic size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species ' () 61 Appl Environ Microbiol : 2798 -2801.

    • Search Google Scholar
  • Von Wintzingerode, F., Göbel, U., Stackebrandt, E.: Determination of microbial diversity in enviromental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21, 213-229 (1997).

    'Determination of microbial diversity in enviromental samples: pitfalls of PCR-based rRNA analysis ' () 21 FEMS Microbiol Rev : 213 -229.

    • Search Google Scholar
  • Strous, M., Fuerst, J. A., Kramer, E. H. M., Logemann, S., Muyzer, G., van de Pas-Schoonen, K. T., Webb, R. I., Kuenen, J. G., Jetten, M. S. M.: Missing lithotroph identified as new planctomycete. Nature 400, 446-449 (1999).

    'Missing lithotroph identified as new planctomycete ' () 400 Nature : 446 -449.

  • Schmidt, M., Twachtmann, U., Klein, M., Strous, M., Juretschko, S., Jetten, M., Metzger, J. W., Schleifer, H. K. H., Wagner, M.: Molecular evidence for the genus level diversity of bacteria capable of catalyzing anaerobic ammonium oxidation. Syst Appl Microbiol 23, 93-106 (2000).

    'Molecular evidence for the genus level diversity of bacteria capable of catalyzing anaerobic ammonium oxidation ' () 23 Syst Appl Microbiol : 93 -106.

    • Search Google Scholar
  • Kypers, M. M. M., Sliekers, A. O., Lavik, G., Schmidt, M., Jørgensen, B. B., Kuenen, J. G., Sinninghe Damsté, J. S., Strous, M., Jetten, M. S. M.: Anaerobic ammonium oxidation by anammox bacteria in the Black Sea. Nature 422, 608-611 (2003).

    'Anaerobic ammonium oxidation by anammox bacteria in the Black Sea ' () 422 Nature : 608 -611.

    • Search Google Scholar
  • Jansen, M.: Microbial demethylation of dimethylsulfoniopropionate and methylthiopropionate. PhD Thesis, Rijksuniversiteit Groningen, The Netherlands (2000).

  • Orphan, V. J., House, C. H., Hinrichs, K.-U., McKeegan, K. D., De Long, E. F.: Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments. Proc Natl Acad Sci USA 99, 7663-7668 (2002).

    'Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments ' () 99 Proc Natl Acad Sci USA : 7663 -7668.

    • Search Google Scholar
  • Sørensen, K. B., Finster, K., Ramsing, N. B.: Thermodynamic and kinetic requirements in anaerobic methane oxidizing consortia exclude hydrogen, acetate, and methanol as possible electron shuttles. Microb Ecol 42, 1-10 (2001).

    'Thermodynamic and kinetic requirements in anaerobic methane oxidizing consortia exclude hydrogen, acetate, and methanol as possible electron shuttles ' () 42 Microb Ecol : 1 -10.

    • Search Google Scholar
  • Dunn, J. J., McCorkle, S. R., Praissman, L. A., Hind, G., van der Lelie, D., Bahou, W. F. et al.: Genomic signature tags (GSTs): a system for profiling genomic DNA. Genome Res 12, 1756-1765 (2002).

    'Genomic signature tags (GSTs): a system for profiling genomic DNA ' () 12 Genome Res : 1756 -1765.

    • Search Google Scholar
  • Borneman, J., Skrotch, P. W., O'Sullivan, K. M., Palus, J. A., Rumjanek, N. G. et al.: Molecular microbial diversity of an agricultural soil in Wisconsin. Appl Environ Microbiol 62, 1935-1943 (1996).

    'Molecular microbial diversity of an agricultural soil in Wisconsin ' () 62 Appl Environ Microbiol : 1935 -1943.

    • Search Google Scholar
  • Liesack, W., Stackebrandt, E.: Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment. J Bacteriol 174, 5072-5078 (1992).

    'Occurrence of novel groups of the domain Bacteria as revealed by analysis of genetic material isolated from an Australian terrestrial environment ' () 174 J Bacteriol : 5072 -5078.

    • Search Google Scholar
  • Rheims, H., Spröer, C., Rainey, F. A., Stackebrandt, E.: Molecular biological evidence for the occurrence on uncultured members of the actinomycete line of descent in different environments and geographical locations. Microbiol (UK) 142, 2863-2870 (1996).

    'Molecular biological evidence for the occurrence on uncultured members of the actinomycete line of descent in different environments and geographical locations ' () 142 Microbiol (UK) : 2863 -2870.

    • Search Google Scholar
  • Felske, A., Rheims, H., Wolterink, A., Stackebrandt, E., Akkermans, A. D. L.: Ribosome analysis reveals prominent activity of an uncultured member of the class Actinobacteria in grassland soils. Microbiol (UK) 143, 2983-2989 (1997).

    'Ribosome analysis reveals prominent activity of an uncultured member of the class Actinobacteria in grassland soils ' () 143 Microbiol (UK) : 2983 -2989.

    • Search Google Scholar
  • Gremion, F., Chatzinotas, A., Harms, H.: Comparative 16S rDNA and 16S rRNA sequence analysis indicates that Actinobacteria might be a dominant part of metabolically active bacteria in heavy metal-contaminated bulk and rhizosphere soil. Env Microbiol 5, 896-907 (2003).

    'Comparative 16S rDNA and 16S rRNA sequence analysis indicates that Actinobacteria might be a dominant part of metabolically active bacteria in heavy metal-contaminated bulk and rhizosphere soil ' () 5 Env Microbiol : 896 -907.

    • Search Google Scholar
  • Rheims, H., Stackebrandt, E.: Application of nested PCR for the detection of as yet uncultured organisms of the class Actinobacteria in environmental samples. Molec Ecol 1, 137-143 (1998).

    'Application of nested PCR for the detection of as yet uncultured organisms of the class Actinobacteria in environmental samples ' () 1 Molec Ecol : 137 -143.

    • Search Google Scholar
  • Rheims, H., Felske, A., Seufert, S., Stackebrandt, E.: Molecular monitoring of an uncultured group of the class Actinobacteria in two terrestrial environments. J Microbial Meth 36, 65-75 (1998).

    'Molecular monitoring of an uncultured group of the class Actinobacteria in two terrestrial environments ' () 36 J Microbial Meth : 65 -75.

    • Search Google Scholar
  • Rheims, H., Frühiling, A., Schumann, P., Rohde, M., Stackebrandt, E.: Description of Bacillus silvestris sp. nov., a new member of the genus Bacillus, containing lysine in its cell wall. Int J Syst Bacteriol 49, 795-802 (1999).

    'Description of Bacillus silvestris sp. nov., a new member of the genus Bacillus, containing lysine in its cell wall ' () 49 Int J Syst Bacteriol : 795 -802.

    • Search Google Scholar
  • Rheims, H., Schumann, P., Rohde, M., Stackebrandt, E.: Verrucosispora gifhornensis gen. nov. spec. nov, a new member of the actinobacterial family Micromonosporaceae. Int J Syst Bact 48, 1119-1127 (1998).

    'Verrucosispora gifhornensis gen. nov. spec. nov, a new member of the actinobacterial family Micromonosporaceae ' () 48 Int J Syst Bact : 1119 -1127.

    • Search Google Scholar
  • Yakimov, M. M., Lünsgorf, H., Golyshin, P. N.: Thermoleophilum album and Thermoleophilum minutum are culturable representatives of group 2 of the Rubrobacteridae (Actinobacteria). Int J Syst Evol Microbiol 53, 377-380 (2003).

    'Thermoleophilum album and Thermoleophilum minutum are culturable representatives of group 2 of the Rubrobacteridae (Actinobacteria) ' () 53 Int J Syst Evol Microbiol : 377 -380.

    • Search Google Scholar
  • Stackebrandt, E., Rainey, F. A., Ward-Rainey, N. L.: Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 47, 479-491 (1997).

    'Proposal for a new hierarchic classification system, Actinobacteria classis nov. ' () 47 Int J Syst Bacteriol : 479 -491.

    • Search Google Scholar
  • Zarilla, K. A., Perry, J. J.: Thermoleophilum album, gen. nov. and sp. nov., a bacterium obligate for thermophily and n-alkane substrates. Arch Microbiol 137, 286-290 (1984).

    'Thermoleophilum album, gen. nov. and sp. nov., a bacterium obligate for thermophily and n-alkane substrates ' () 137 Arch Microbiol : 286 -290.

    • Search Google Scholar
  • Gupta, R. S.: Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among Archaebacteria, Eubacteria, and Eukaryotes. Microb Mol Biol Rev 62, 1425-1491 (1998).

    'Protein phylogenies and signature sequences: a reappraisal of evolutionary relationships among Archaebacteria, Eubacteria, and Eukaryotes ' () 62 Microb Mol Biol Rev : 1425 -1491.

    • Search Google Scholar
  • Maiden, M. C. J., Bygraves, J. A., Feil, E., Morelli, G., Russel, J. E., Urwin, R., Zhang, Q., Zhou, J., Zurth, K., Caugant, D. A., Feavers, I. M., Achtman, M., Spratt, B. G.: Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic organisms. Proc Natl Acad Sci USA 95, 3140-3145 (1998).

    'Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic organisms ' () 95 Proc Natl Acad Sci USA : 3140 -3145.

    • Search Google Scholar
  • Eisen, J. A.: The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species. J Mol Evol 41, 1105-1123 (1995).

    'The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species ' () 41 J Mol Evol : 1105 -1123.

    • Search Google Scholar
  • Singleton, D. R., Furlong, M. A., Peacock, A. D., White, D. C., Coleman, D. C., Whitman, W. B.: Solirubrobacter pauli gen. nov., sp. nov., a mesophilic bacterium within the Rubrobacteridae related to common soil clones. Int J Syst Evol Microbiol 53, 485-490 (2002).

    'Solirubrobacter pauli gen. nov., sp. nov., a mesophilic bacterium within the Rubrobacteridae related to common soil clones ' () 53 Int J Syst Evol Microbiol : 485 -490.

    • Search Google Scholar
  • Monciardini, P., Cavaletti, L., Schumann, P., Rohde, M., Donadio, S.: Conexibacter woesei gen. nov., sp. nov., a novel representative of a deep evolutionary line of descent within the class Actinobacteria. Int J Syst Evol Microbiol 53, 569-576 (2003).

    'Conexibacter woesei gen. nov., sp. nov., a novel representative of a deep evolutionary line of descent within the class Actinobacteria ' () 53 Int J Syst Evol Microbiol : 569 -576.

    • Search Google Scholar

Monthly Content Usage

Abstract Views Full Text Views PDF Downloads
Jun 2020 0 2 3
Jul 2020 4 0 0
Aug 2020 6 0 0
Sep 2020 1 0 0
Oct 2020 27 0 0
Nov 2020 2 1 1
Dec 2020 0 0 0