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Systematic and Evolution of Microorganisms: General Concepts

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Environmental Microbiology: Fundamentals and Applications

Abstract

The diversity of metabolic activities is a characteristic of the microbial world. This enormous diversity needs to be structured in order to be understood, and as a result, taxonomy and systematics are constantly changing since the beginning of the history of microbiology and particularly today with the introduction in the last 20 years of phylogeny as the core of systematics. The history of concepts in systematics and classification is presented. Classification is the science of ordering microorganism groups (taxa) based on their interrelationships. Taxonomy is the discipline that defines the principles and laws of classification. Nomenclature is the science of defining and naming the taxonomic categories (species, genera, families, orders, classes, divisions, phyla, kingdoms, domains), according to their hierarchical rank. In this way, different schools of classification and bacterial systematics were developed in the twentieth century. Today, there is an international consensus based on the classification of the Bergey’s Manual revisited with the concepts of phylogeny. Through this classification, the concept of the prokaryotic world organization has evolved. From the idea of a kingdom of prokaryotes, the concept of three domains in the organization of life supported by phylogenetic trees is fully accepted today. Among these three domains, two are prokaryotic: Bacteria and Archaea. In this chapter, the role of horizontal gene transfers in the evolution of life is discussed. The origin of eukaryotes with the primary, secondary, and tertiary endosymbioses is also presented. This allows to improve or to transform the concept of the tree of life from phylogeny to full genome study.

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Notes

  1. 1.

    Viruses are functionally inactive when they are outside their host. However, a virus, as parasite of the archaea Acidianus convivator, was discovered in hydrothermal vents of Pozzuoli (Italy) and was able to generate outside of the host, a double tail protein (800 amino acids). It was named ATV (Acidianus two-tailed virus) (Häring et al. 2005).

  2. 2.

    http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View.ShowTOC&rid=icnb.TOC&depth=2)

  3. 3.

    For prokaryotes, including Cyanobacteria and Planctomycetes, only the “International Code of Bacterial Nomenclature” should have the authority. Discussions are underway to harmonize the nomenclature of Cyanobacteria and Planctomycetes with the “International Code of Botanical Nomenclature.”

  4. 4.

    The name of Linnaeus is often translated as “Linné.” This goes back to the tradition that was, until the eighteenth century, to change its name according to the languages and countries. This is also the choice of the Royal Swedish Museum of Natural History (www2.nrm.se/fbo/hist/linnaeus/linnaeus.html.se) website that talks about Carl von Linné, which is the French form he chose himself when he was knighted in 1762 by the King of Sweden. However, the name that appears on the cover of the book Species Plantarum, chosen as the starting point of the nomenclature, is “Caroli Linnaei” the declined Latin form of Carolus Linnaeus.

  5. 5.

    The confusion between Turbinaria “plants” and “animals” is all the more disturbing given that they can coexist in the same coral reef ecosystem and even live one on the other.

  6. 6.

    For example, Paranema (Dujardin 1841) is a valid name for a colorless Euglena species according to zoologists. For botanists, the valid name of the same species is Pseudoparanema (Christen 1962) as Paranema (Don 1825) is a fern and has the priority.

  7. 7.

    Chlorarachniobionta are amoebae equipped with chloroplasts.

  8. 8.

    The use of steranes, as biomarkers of eukaryotes, is disputed (cf. Chap. 4).

  9. 9.

    In this chapter, we use the term symbiosis in its original and modern sense as relations between two taxonomically different organisms, and not in the sense of coexistence with mutual benefits, a meaning to which this has gradually derivated and continues to be accepted by current authors (cf. Chap. 10). Symbiosis therefore includes exploitation (predation, parasitism), competition, commensalism, amensalism, mutualism (mutually beneficial interaction), and helotism (servitude).

  10. 10.

    The abundance of these chloroplasts gives a green color to Elysia viridis. Note that viridis means “green” in Latin.

  11. 11.

    The reader will probably be surprised by the fact that the current CO2 concentration was considered, in this chapter, as a historic minimum, while its increase, due to human activities, is so disturbing. Fig. 5.16, which shows the evolution of CO2 in geological time, does not highlight, due to the scale, the current increase.

  12. 12.

    Some authors (e.g., Embley and Martin 2006) hypothesized that in Chromalveolata a single secondary endosymbiotic event is the origin of photosynthesis; it would have occurred in the common ancestor of Chromalveolata. This hypothesis has been criticized by other authors (e.g., Bodyl et al. 2009; Burki et al. 2012).

  13. 13.

    Some authors propose that the apicoplast of Apicomplexa is from a Viridiplantae (green pathway).

  14. 14.

    No single character can be considered characteristic of all organisms that tradition has gathered under the name of “plants.” Similarly, no any combination of characters could define the set of “plants.”

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Authors and Affiliations

  1. Institut Méditerranéen d’Océanologie (MIO), UM 110, CNRS 7294 IRD 235, Université de Toulon, Aix-Marseille Université, Campus de Luminy, 13288, Marseille Cedex 9, France

    Charles-François Boudouresque & Jean-Claude Bertrand

  2. Institut des Sciences Analytiques et de Physico-chimie pour l’Environnement et les Matériaux (IPREM), UMR CNRS 5254, Université de Pau et des Pays de l’Adour, B.P. 1155, 64013, Pau Cedex, France

    Pierre Caumette

  3. Microbial Ecology Center, UMR CNRS 5557 / USC INRA 1364, Université Lyon 1, 69622, Villeurbanne, France

    Philippe Normand

  4. Laboratoire Microorganismes: Génome et Environnement (LMGE), UMR CNRS 6023, Université Blaise Pascal, Clermont Université, B.P. 80026, 63171, Aubère Cedex, France

    Télesphore Sime-Ngando

Authors
  1. Charles-François Boudouresque
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  2. Pierre Caumette
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  3. Jean-Claude Bertrand
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  4. Philippe Normand
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  5. Télesphore Sime-Ngando
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Corresponding authors

Correspondence to Charles-François Boudouresque or Pierre Caumette .

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Editors and Affiliations

  1. Université de Toulon, Aix-Marseille Université, Institut Méditerranéen d’Océanologie (MIO), UM 110, CNRS 7294 IRD 235, Cedex 9, Marseille, France

    Jean-Claude Bertrand

  2. Université de Pau et des Pays de l’Adour, Institut des Sciences Analytiques et de Physico-chimie pour l’Environnement et les Matériaux (IPREM), UM 110, CNRS 5254, Pau Cedex, France

    Pierre Caumette

  3. Observatoire Océanologique de Banyuls, Laboratoire de Biodiversité et Biotechnologie Microbiennes (LBBM), Sorbonne Universités, UPMC Univ, Paris 06, USR CNRS 3579, Banyuls-sur-Mer, France

    Philippe Lebaron

  4. Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE), UMR-CNRS-IRD 7263, Aix-Marseille Université, Cedex 20, Marseille, France

    Robert Matheron

  5. Microbial Ecology Center, UMR CNRS 5557/USC INRA 1364, Villeubanne, France

    Philippe Normand

  6. Laboratoire Microorganismes: Génome et Environnement (LMGE), UMR CNRS 6023, Université Blaise Pascal, Clermont Université, Aubère Cedex, France

    Télesphore Sime-Ngando

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Boudouresque, CF., Caumette, P., Bertrand, JC., Normand, P., Sime-Ngando, T. (2015). Systematic and Evolution of Microorganisms: General Concepts. In: Bertrand, JC., Caumette, P., Lebaron, P., Matheron, R., Normand, P., Sime-Ngando, T. (eds) Environmental Microbiology: Fundamentals and Applications. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9118-2_5

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