Abstract
This chapter is intended to be a brief introduction to the concepts and practices embraced by microbial systematics, the scientific study of the kinds and diversity of microorganisms and their relationships. The subject is generally divided into three related disciplines, the taxonomic trinity recognised by Cowan (1955), namely, classification, nomenclature and identification. Classification and identification are core scientific disciplines that are relevant to both pure and applied microbiologists. Nomenclature is central to all facets of the microbial sciences as microbiologists need to know what organisms they are working with before they can pass on information about them within and outwith the scientific community. In other words, the name of an organism is the key to its literature, an entry to what is known about it.
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References
Alm, R.A. & Manning, P.A. (1990). Biotype-specific probe for Vibrio cholerae serogroup 01. Journal of Clinical Microbiology 28, 823–824.
Benson, D.A., Boguski, M.S., Lipman, D.J., Ostell, J. & Ouellette, B.F. (1998). GenBank. Nucleic Acids Research 26, 1–7.
Bousfield, I.J. (1993). Bacterial nomenclature and its role in systematics. In Handbook of New Bacterial Systematics, pp. 317–338. London, Academic Press Ltd.
Boysen, M., Skouboe, P., Frisvad, J. & Rossen, L. (1996). Reclassification of the Penicillium roqueforti group into three species on the basis of molecular genetic and biochemical profiles. Microbiology 142, 541–549.
Brandt, K.K., Patel, B.K.C. & Ingvorsen, K. (1999). Desulfocella halophila gen. nov., sp. nov., a halophilic, fatty-acid oxidising, sulfate-reducing bacterium isolated from sediments of the Great Salt Lake. International Journal of Systematic Bacteriology 49, 193–200.
Bridge, P.D., Holderness, M., Paterson, R.R.M. & Rutherford, M. (1995). Multidisciplinary characterization of fungal plant pathogens. Bulletin OEPP/EPPO Bulletin 25, 125–131.
Bull, A.T., Goodfellow, M. & Slater, J.H. (1992). Biodiversity as a source of innovation in biotechnology. Annual Review of Microbiology 42, 219–257.
Caetano-Anollés, G. & Gresshoff, P.M., eds. (1997). DNA Markers: Protocols, Applications and Overviews. New York, Wiley
Canhos, V.P., Manfio, G.P. & Blaine, L.D. (1993). Software tools and databases for bacterial systematics and their dissemination via global networks. Antonie van Leeuwenhoek 64, 205–229.
Cavalier-Smith, T. (1992). Origins of secondary metabolism. Ciba Foundation Symposium 171, 64–80.
Cavalier-Smith, T. (1993). Kingdom Protozoa and its 18 phyla. Microbiological Reviews 57, 953–994.
Chatton, E. (1937). Titres et travaux scientifiques (1906–1937) de Edouard Chatton. Sette, Italy, E. Sottano.
Colwell, R.R. (1970). Polyphasic taxonomy of bacteria. In Culture Collections of Microorganisms, pp. 421–436. Edited by H. Iizuka & T. Hasegawa. Tokyo, University of Tokyo Press.
Coombs, G.H., Vickerman, K., Sleigh, M.A. & Warren, A., eds. (1998). Evolutionary Relationships among Protozoa. Dordrecht, Kluwer Academic Publishers.
Cowan, S.T. (1955). The principles of microbial classification. Introduction: the philosophy of classification. Journal of General Microbiology 12, 314–319.
De Jonckheere, J.F. (1998). Relationships between ameoboflagellates. In: Evolutionary Relationships among Protozoa, pp. 181–194. Edited by G.H. Coombs, K. Vickerman, M.A. Sleigh & A. Warren. Dordrecht, Kluwer Academic Publishers.
Eardly, B.D., Wang, F.S. & van Berkum, P. (1996). Corresponding 16S rRNA gene segments in Rhizobiaceae and Aeromonas yield discordant phylogenies. Plant and Soil 186, 69–74.
Foissner, W. (1998). The karyorelictids (Protozoa:Ciliophora), a unique and enigmatic assemblage of marine, intestinal ciliates: a review emphasizing ciliary patterns and evolution. In Evolutionary Relationships among Protozoa, pp. 304–325. Edited by G.H. Coombs, K. Vickerman, M.A. Sleigh & A. Warren. London, Chapman and Hall.
Fox, G.E., Pechman, K.G. & Woese, C.R. (1977). Comparative cataloguing of 16S ribosomal ribonucleic molecular approach to prokaryotic systematics. International Journal of Systematic Bacteriology 27, 44–57.
Fox, G.E., Wisotzkey, J.D. & Jurtshuk, Jr. P. (1992). How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. International Journal of Systematic Bacteriology 42, 166–170.
Fry, N.R., Saunders, N.A., Warwick, S. & Embley, T.M. (1991). The use of 16S ribosomal RNA analyses to investigate the phylogeny of the family Legionellaceae. Journal of General Microbiology 137, 1215–1222.
Gilmour, J.S.L. (1940). Taxonomy and philosophy. In The New Systematics, pp. 461–474. Oxford, Clarendon Press.
Goodacre, R., Timmins, E.M., Burton, R., Kaderbhai, N., Woodward, A.M., Kell, D.B. & Rooney, P.J. (1998). Rapid identification of urinary tract infection bacteria using hyperspectral whole-organism fingerprinting and artificial neural networks. Microbiology 144, 1157–1170.
Goodfellow, M. & Dickinson, C.H. (1985). Delineation and description of microbial populations using numerical methods. In Computer-Assisted Bacterial Systematics, pp. 165–225. Edited by M. Goodfellow, D. Jones & EG. Priest. London, Academic Press.
Goodfellow, M. & Magee, J.G. (1998). Taxonomy of mycobacteria. In Mycobacteria. I. Basic Aspects, pp. 1-71. Edited by P.R.J. Gangadharam & P.A. Jenkins. New York, Chapman & Hall.
Goodfellow, M. & O’Donnell, A.G. (1993). The roots of bacterial systematics. In Handbook of New Bacterial Systematics, pp. 3-54. Edited by M. Goodfellow & A.G. O’Donnell. London, Academic Press Ltd.
Goodfellow, M. & O’Donnell, A.G. eds. (1994). Chemical Methods in Prokaryotic Systematics. Chichester, John Wiley & Sons.
Goodfellow, M., Chun, J., Atalan, E. & Sanglier, J-J. (1994). Curie point pyrolysis mass spectrometry and its application to bacterial systematics. In Bacterial Diversity and Systematics, pp. 87–104. Edited by EG. Priest, A. Ramos-Cormenzana & B.J. Tindall. New York, Plenum Press.
Goodfellow, M., Freeman, R. & Sisson, P.R. (1997a). Curie-point pyrolysis mass spectrometry as a tool in clinical microbiology. Zentralblatt für Bakteriologie 285, 133–156.
Goodfellow, M., Manfio, G.P. & Chun, J. (1997b). Towards a practical species concept for cultivable bacteria. In Species: The Units of Biodiversity, pp. 25–59. Edited by M.E Claridge, H.A. Dawah & M.R. Wilson. London, Chapman & Hall.
Goodfellow, M., Alderson, G. & Chun, J. (1998). Rhodococcal systematics: problems and developments. Antonie van Leeuwenhoek 74, 1–18.
Greuter, W., Barrie, F.R., Burdet, H.M., Chaloner, W.G., Demoulin, V., Hawksworth, D.L., Jfragensen, P.M., Nicholson, D.H., Silva, D.C., Trehane, P. & McNeil, J. (1994). International Code of Botanical Nomenclature. Renum Vegetable 131, 1–389.
Gupta, R.S. (1998). Protein phytogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria and eukaryotes. Microbiology and Molecular Biology Reviews 62, 1435–1491.
Gürtler, V. & Stanisich, V.A. (1996). New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142, 3–16.
Hillis, D.M., Allard, W. & Miyamoto, M.M. (1993). Analysis of DNA sequence data: phylogenetic inference. Methods of Enzymology 224, 456–487.
Isik, K., Chun, J., Hah, Y.C. & Goodfellow, M. (1999). Nocardia salmonicida nom. rev., a fish pathogen. International Journal of Systematic Bacteriology 49, 833–837.
James, A.L. (1994). Enzymes in taxonomy and diagnostic bacteriology. In Chemical Methods in Prokaryotic Systematics, pp. 471–492. Edited by M. Goodfellow & A.G. O’Donnell. Chichester, John Wiley & Sons Ltd.
Kim, S.B. & Goodfellow, M. (1999). Reclassification of Amycolatopsis rugosa Lechevalier et al. 1986 as Prauserella rugosa gen. nov., comb. nov. International Journal of Systematic Bacteriology 49, 507–512.
Kim, B., Sahin, N., Minnikin, D.E., Zakrzewska-Czerwinska, J., Mordarski, M. & Goodfellow, M. (1999). Classification of thermophilic streptomycetes, including the description of Streptomyces thermoalkalitolerans sp. nov. International Journal of Systematic Bacteriology 49, 7–17.
Kim, W-S., Gardan, L., Rhum, S-L. & Geider, K. (1999). Erwinia pyrifoliae sp. nov., a novel pathogen that affects Asian pear trees (Pyrus pyrifolia Nakai). International Journal of Systematic Bacteriology 49, 899–906.
Kurtzman, C.P. (1992). rRNA sequence comparisons for assessing phylogenetic relationships among yeasts. International Journal of Systematic Bacteriology 42, 1–6.
Labeda, D.P. (1998). DNA relatedness among the Streptomyces fulvissimus and Streptomyces griseoviridis phenotypic cluster groups. International Journal of Systematic Bacteriology 48, 829–832.
Lapage, S.P., Sneath, P.H.A., Lessel, E.F., Skerman, V.B.D., Seeliger, H.P.R. & Clark, W.A. (1975). International Code of Nomenclature of Bacteria, 1975 Revision. Washington, D.C., American Society for Microbiology.
Larsen, T.O. & Frisvad, J.C. (1995). Characterisation of volatile metabolites from 47 Penicillium taxa. Mycological Research 99, 1153–1166.
Ludwig, W., Neumaier, J., Klugbauer, N., Brockmann, E., Roller, C., Jilg, S., Reetz, K., Schachtner, I., Ludvigsen, A., Bachleitner, M., Fischer, U. & Schleifer, K.H. (1993). Phylogenetic relationships of bacteria based on comparative sequence analysis of elongation factor Tu and ATP-synthase β-subunit genes. International Journal of Systematic Bacteriology 64, 285–305.
MacAdoo, T.O. (1993). Nomenclatural literacy. In Handbook of New Bacterial Systematics, pp. 339–358. Edited by M. Goodfellow & A.G. O’Donnell. London, Academic Press.
Magee, J.T. (1993). Whole-organisms fingerprinting. In Handbook of New Bacterial Systematics, pp. 383–427. Edited by M. Goodfellow & A.G. O’Donnell. London, Academic Press Ltd.
Magee, J.T. (1998). Taxonomy and nomenclature of bacteria. In Topley and Wilson’s, Microbiology and Microbial Infections, Volume 2, Systematic Bacteriology, pp. 45–64. Edited by A. Balows & B.I. Duerden. London, Arnold.
Maidak, B.L., Olsen, G.J., Larsen, N., Overbeek, R., McCaughey, MJ. & Woese, C.R. (1997). The Ribosomal Database Project (RDP). Nucleic Acids Research 5, 109–111.
Margulis, L. & Guerro, R. (1991). Kingdoms in turmoil. New Scientist 129, 46–50.
Martinez-Murcia, A.J., Benlloch, S. & Collins, M.D. (1992). Phylogenetic interrelationships of members of the genera Aeromonas and Plesiomonas as determined by 16S ribosomal DNA sequencing: Lack of congruence with results of DNA:DNA hybridisation. International Journal of Systematic Bacteriology 42, 412–421.
Mayr, E. (1990). A natural system of organisms. Nature 348, 491.
Mayr, E. (1998). Two empires or three. Proceedings of the National Academy of Science, USA 95, 9720–9723.
Moore, W.E.C. & Moore, L.V.D., eds. (1989). Index of the Bacterial and Yeast Nomenclatural Changes Published in the International Journal of Systematic Bacteriology since the 1980 Approved Lists of Bacterial Names (1 January 1980 to 1 January 1989). Washington, D.C., American Society for Microbiology.
Mordue, J.E.M., Banniza, S., Bridge, P.D., Rutherford, M.A. & Holderness, M. (1996). Integrated biochemical, cultural and numerical methods. In: Rhizoctonia species: Taxonomy, Molecular Biology, Ecology, Pathology and Disease Control. pp. 87–98. Edited by B. Sneh, S. Jabaji-Hare, S. Neate & G. Dijst. London, Kluwer Academic Publishers.
Murray, R.G.E., Brenner, D.J., Colwell, R.R., De Vos, P., Goodfellow, M., Grimont, P.A.D., Pfennig, N., Stackebrandt, E. & Zavarzin, G.A. (1990). Report of the ad hoc committee on approaches to taxonomy within the Proteobacteria. International Journal of Systematic Bacteriology 40, 213–215.
Naumann, D., Helm, D. & Schultz, C. (1994). Characterization and identification of micro-organisms by FT-IR spectroscopy and FT-IR microscopy. In Bacterial Diversity and Systematics, pp. 67–85. Edited by F.G. Priest, A. Ramos-Cormenzana & B.J. Tindall. New York, Plenum Press.
Nielsen, P., Fritze, D. & Priest, F.G. (1995). Phenetic diversity of alkaliphilic Bacillus strains: proposal for nine new species. Microbiology 141, 1745–1761.
Olsen, G.J. & Woese, C.R. (1993). Ribosomal RNA: A key to phylogeny. FASEB Journal 7, 113–123.
Palleroni, N.J. (1993). Pseudomonas classification. A new case history in the taxonomy of Gram-negative bacteria. Antonie van Leeuwenhoek 64, 231–251.
Philippe, H. (1998). Molecular phylogeny of kinetoplastids. In Evolutionary Relationships among Protozoa, pp. 195–212. Edited by G.H. Coombs, K. Vickerman, M.A. Sleigh & A. Warren. Dordrecht, Kluwer Academic Publishers.
Priest, F.G. & Austin, B., eds. (1993). Modern Bacterial Taxonomy. London, Chapman and Hall.
Prosser, J.I. (1994). Molecular marker systems for detection of genetically engineered micro-organisms in the environment. Microbiology 140, 5–17.
Ride, W.D.L., Sabrosky, C.W., Bernardi, G. & Melville, R.V., eds. (1985). International Code of Zoological Nomencalture. Berkeley and Los Angeles, University of California Press.
Rosa, C.A., Lachance, M-A., Starmer, W.T., Barker, J.S.F., Bowles, J.M. & Schlag-Edler, B. (1999). Kodamaea nitidulidarum, Candida restingae and Kodamaea anthophila, three new related yeast species from ephemeral flowers. International Journal of Systematic Bacteriology 49, 309–318.
Rossello, R., Garcia-Valdéz, J., Lalucat, J. & Ursing, J. (1991). Genotypic and phenotypic diversity of Pseudomonas stutze ri. Systematic and Applied Microbiology 8, 124–127.
Sackin, M.J. & Jones, D. (1993). Computer-assisted classification. In Handbook of New Bacterial Systematics, pp. 281–313. London, Academic Press Ltd.
Simpson, G.G. (1961). Principles of Animal Taxonomy. New York, Columbia University Press.
Skerman, V.B.D., McGowan, V. & Sneath, P.H.A. (1980). Approved lists of bacterial names. International Journal of Systematic Bacteriology 30, 225–420.
Sneath, P.H.A. (1957a). Some thoughts on bacterial classification. Journal of General Microbiology 17, 184–200.
Sneath, P.H.A. (1957b). The applications of computers to taxonomy. Journal of General Microbiology 17, 201–226.
Sneath, P.H.A. (1986). Nomenclature of bacteria. In Biological Nomenclature Today IUBS Monograph Series No. 2, pp. 38–48. Edited by W.D.L. Ride and T. Younes. Eynsham, IRL Press.
Sneath, P.H.A. (1988). The phenetic and cladistic approaches. In Prospects in Systematics, pp. 252–273. Edited by D.L. Hawksworth. Oxford, Clarendon Press.
Sneath, P.H.A. (1989). Predictivity in taxonomy and the probability of a tree. Plant Systematics and Evolution 167, 43–57.
Sneath, P.H.A., ed. (1992). International Code of Nomenclature of Bacteria, 1990 Revision. Washington, D.C., American Society for Microbiology.
Sneath, P.H.A. (1993). Evidence from Aeromonas for genetic crossing-over in ribosomal sequences. International Journal of Systematic Bacteriology 43, 626–629.
Sokal, R.R. (1985). The principles of numerical taxonomy: Twenty-five years later. In Computer-Assisted Bacterial Systematics, pp. 1–20. Edited by M. Goodfellow, D. Jones & F.G. Priest. London, Academic Press Ltd.
Stackebrandt, E. & Goebel, B.M. (1994). Taxonomic note: a place for DNA:DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. International Journal of Systematic Bacteriology 44, 846–849.
Stackebrandt, E., Tindall, B., Ludwig, W. & Goodfellow, M. (1999). Diversity and systematics. In Biology of the Prokaryotes, pp. 674–720. Edited by J.W. Lengeler, G. Drews & H.G. Schlegel. Stuttgart, Thieme.
Stanier, R.Y. & van Niel, C.B. (1941). The main outlines of bacterial classification. Journal of Bacteriology 42, 437–466.
Stead, D.E., Sellwood, J.E., Wilson, J. & Viney, I. (1992). Evaluation of a commercial microbial identi fication system based on fatty acid profiles for rapid, accurate identification of plant pathogenic bacteria. Journal of Applied Bacteriology 72, 315–321.
Stroesser, G., Tuli, M.A., Lopez, R. & Sterk, P. (1999). The EMBL nucleotide sequence database. Nucleic Acids Research 27, 18–24.
Suh, S-O. & Nakase, T. (1995). Phylogenetic analysis of the ballistosporous anamorphic genera Udeniomyces and Bullera, and related basidiomycetous yeasts, based on 18S rDNA sequence. Microbiology 141, 901–906.
Suzuki, T., Muroga, Y., Takahama, M., Shiba, T. & Nishimura, Y. (1999). Roseovivax halodurans gen. nov., sp. nov. and Roseovivax halotolerans sp. nov., aerobic bacteriochlorophyll-containing bacterium isolated from a saline lake. International Journal of Systematic Bacteriology 49, 629–634.
Takashima, M. & Nakase, T. (1998). Bullera penniseticola sp. nov. and Kockovaella sacchari sp. nov., two new yeast species isolated from plants in Thailand. International Journal of Systematic Bacteriology 48, 1025–1030.
Tateno, Y., Fukami-Kobayashe, K., Miyazaki, S., Sugawara, H. & Gojobori, T. (1998). DNA Data Bank of Japan at work on genome sequence data. Nucleic Acids Research 26, 16–20.
Towner, K.J. & Cockayne, A. (1993). Molecular Methods for Microbial Identification and Typing. London, Chapman & Hall.
Ursing, J.B., Rosselló-Mora, R.A., Garcia-Valdés, E. & Lalucat, J. (1995). Taxonomic note: a pragmatic approach to the nomenclature of phenotypically similar genomic groups. International Journal of Systematic Bacteriology 45, 604.
Van Belkum, A., Scherer, S., Loek, van A. & Verbrugh, H. (1998). Short-sequence DNA repeats in prokaryotic domains. Microbiology and Molecular Biology Reviews 62, 275–293.
Vandamme, P., Pot, B., Gillis, M., De Vos, P., Kersters, K. & Swings, J. (1996). Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiological Reviews 60, 407–438.
Vauterin, L., Swings, J. & Kersters, K. (1993). Protein electrophoresis and classification. In Handbook of New Bacterial Systematics, pp. 251–280. London, Academic Press Ltd.
Wayne, L.G., Brenner, D.J., Colwell, R.R., Grimont, P.A.D., Kandier, P., Krichevsky, M.I., Moore, L.H., Moore, W.E.C., Murray, R.G.E., Stackebrandt, E., Starr, M.P. & Trüper, H.G. (1987). Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. International Journal of Systematic Bacteriology 37, 463–464.
Wayne, L.G., Good, R.C., Böttger, E.C., Butler, R., Dorsch, M., Ezaki, T., Gross, W., Jones, V., Kilburn, J., Kirschner, P., Krichevsky, M.I., Ridell, M., Shinnick, T.M., Springer, B., Stackebrandt, E., Târnok, Z., Tasaka, H., Vincent, V., Warren, N.G., Knott, C.A. & Johnson, R. (1996). Semantide-and chemotaxonomy-based analyses of some problematic phenotypic clusters of slowly growing mycobacteria, a cooperative study of the International Working Group on Mycobacterial Taxonomy. International Journal of Systematic Bacteriology 46, 280–297.
White, D., Sharp, R.J. & Priest, F.G. (1993). A polyphasic taxonomic study of thermophilic bacilli from a wide geographic area. Antonie van Leeuwenhoek 64, 357–386.
Williams, S.T., Goodfellow, M. & Alderson, G. (1989). Genus Streptomyces Waksman and Henrici 1943, 339AL. In Bergey’s Manual of Systematic Bacteriology, Volume 4, pp. 2452–2492. Baltimore, Williams and Wilkins.
Woese, C.R. (1987). Bacterial evolution. Microbiological Reviews 51, 221–271.
Woese, C.R. & Fox, G.E. (1977). Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences, USA 74, 5088–5090.
Woese, C.R., Kandier, O. & Wheelis, M.L. (1990). Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences, USA 87, 4576–4579.
Yamamoto, S. & Harayama, S. (1996). Phylogenetic analysis of Acinetobacter strains based on the nucleotide sequences of gyr B genes and on the amino acid sequences of their products. International Journal of Systematic Bacteriology 46, 506–511.
Yassin, A.F., Rainey, F.A., Burghardt, J., Brzezinka, H., Schmitt, S., Seifert, P., Zimmermann, O., Mauch, H., Gierth, D., Lux, I. & Schaal, K.P. (1997). Tsukamurella tyrinosolvens sp. nov. International Journal of Systematic Bacteriology 47, 607–614.
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Goodfellow, M. (2000). Microbial Systematics: Background and Uses. In: Priest, F.G., Goodfellow, M. (eds) Applied Microbial Systematics. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-4020-1_1
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