Microbial Diversity

Aharon Oren, The Hebrew University of Jerusalem, Jerusalem, Israel

Published online: December 2009

DOI: 10.1002/9780470015902.a0020376

Prokaryotic and eukaryotic microorganisms dominate life on Earth with respect to the numbers of individuals and biomass. Yet, the number of species of macroorganisms described as well as the estimated numbers of yet to be described species exceeds those of the microorganisms by an order of magnitude. Such numbers give an incomplete picture of the diversity in the microbial world. Only two modes of life are found in higher plants and animals: oxygenic photosynthesis and aerobic respiration. In the microbial world a great variety of processes occur, aerobic as well as anaerobic, phototrophic (oxygenic and anoxygenic), respiratory (with oxygen or other electron acceptors), fermentative and chemoautotrophic (using reduced inorganic compounds as energy sources). Also phylogenetically the microbial world is by far the most diverse. Most branches in the small ribosomal subunit ribonucleic acid (RNA)-based phylogenetic tree contain only microorganisms, whereas higher plants and animals only form short lineages in the eukaryotic branch.

Key concepts

  • The microbial world encompasses most of the phylogenetic diversity on Earth, as all Bacteria, all Archaea and most lineages of the Eukarya are microorganisms.
  • The morphological diversity in the microbial world is much smaller than that of the higher plants and animals.
  • With respect to numbers of individual microorganisms and biomass the microbial world is far more important than the world of macroorganisms, but the numbers of species of microorganisms described to date and the predicted numbers of yet undescribed species are about an order of magnitude lower than those of the macroorganisms.
  • Based on their modes of energy generation and the variety of organic and inorganic compounds used as energy source and/or nutrients, the microbial world and especially the world of the prokaryotes, has many more possibilities than are realized by macroscopic animals and plants.
  • Sequencing of microbial DNA isolated from natural environments (environmental genomics, metagenomics) has revealed the existence of a tremendous variety of yet uncultured microorganisms, showing that the true microbial diversity in nature is much higher than currently recognized on the basis of organisms studied in culture.

Keywords: prokaryotes; Archaea; Bacteria; eukaryotes; phylogeny; metabolic diversity

Figure 1. The universal small-subunit rRNA sequence-based phylogenetic tree. Branches that contain macroorganisms (fungi, algae, higher plants and animals) are highlighted orange; all other branches consist entirely of microorganisms.
close
 References
    Angert ER, Clements KD and Pace NR (1993) The largest bacterium. Nature 362: 239–241.
    Cavalier-Smith T (1993) Kingdom Protozoa and its 18 phyla. Microbiological Reviews 57: 953–994.
    Cavalier-Smith T (2003) Protist phylogeny and the high-level classification of Protozoa. European Journal of Protistology 39: 338–348.
    DeLong EF (1998) Everything in moderation: Archaea as “nonextremophiles”. Current Opinion in Genetics and Development 8: 649–654.
    DeLong EF and Pace NR (2001) Environmental diversity of Bacteria and Archaea. Systematic Biology 50: 480–478.
    Doolittle WF (1999) Phylogenetic classification and the universal tree. Science 284: 2124–2128.
    Dykhuizen DE (1998) Santa Rosalia revisited: why are there so many species of bacteria? Antonie van Leeuwenhoek 73: 25–33.
    Ellis LBM, Hershberger CD and Wackett LP (1999) The University of Minnesota Biocatalysis/Biodegradation Database: specialized metabolism for functional genomics. Nucleic Acids Research 27: 373–376 [http://umbbd.ahc.umn.edu].
    Finlay BJ (1998) The global diversity of protozoa and other small species. International Journal of Parasitology 28: 29–48.
    Finlay BJ (2004) Protist taxonomy: an ecological perspective. Philosophical Transactions of the Royal Society of London. Part B 359: 599–610.
    Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiology and Molecular Biology Reviews 68: 669–685.
    Huber H, Hohn MJ, Rachel R et al. (2002) A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417: 63–67.
    Hugenholtz P, Goebel BM and Pace NR (1998) Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. Journal of Bacteriology 180: 4765–4774.
    book Kelly DP and Wood AP (2006) "The chemolithotrophic prokaryotes". In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH and Stackebrandt E (eds) The Prokaryotes. A Handbook on the Biology of Bacteria: Ecophysiology and Biochemistry, vol. 2, pp. 441–456. New York: Springer.
    Könneke M, Bernhard AE, de la Torre JR et al. (2005) Isolation of an autotrophic nitrifying marine archaeon. Nature 437: 543–546.
    book Lee JJ, Leedale GF and Bradbury P (eds) (2002) An Illustrated Guide to the Protozoa, 2nd edn (dated 2000). Lawrence, KS: Society for Protozoologists.
    book Ludwig W and Klenk H-P (2001) "Overview: a phylogenetic backbone and taxonomic framework for prokaryotic systematics". In: Boone DR and Castenholz RW (eds) Garrity GM (ed in chief) Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. I, pp. 49–65. New York: Springer.
    Maidak BL, Cole JR, Lilburn TG et al. (2001) The RDP-II (Ribosomal Database Project). Nucleic Acids Research 29: 173–174.
    May RM (1988) How many species are there on Earth? Science 241: 1441–1449.
    Meng J, Wang F, Wang F et al. (2009) An uncultivated crenarchaeota contains functional bacterochlorophyll a synthase. ISME Journal 3: 106–116.
    Moodie AD and Ingledew WJ (1990) Microbial anaerobic respiration. Advances in Microbial Physiology 31: 225–269.
    Moreira D and López-García P (2002) The molecular ecology of microbial eukaryotes unveils a hidden world. Trends in Microbiology 10: 31–38.
    book Oren A (2002) "Metabolic diversity in prokaryotes and eukaryotes". In: Contrafatto G (ed.) Encyclopedia of Life Support Systems, (http://www.eolss.net). Oxford: EOLSS Publishers.
    Oren A (2004) Prokaryote diversity and taxonomy: present status and future challenges. Philosophical Transactions of the Royal Society of London. Part B 359: 623–638.
    Pace NR (1997) A molecular view of microbial diversity and the biosphere. Science 276: 734–740.
    Rosselló-Mora R and Amann R (2001) The species concept for prokaryotes. FEMS Microbiology Reviews 25: 39–67.
    book Schlegel HG and Bowien B (eds) (1989) Autotrophic Bacteria. Madison: Science Tech Publishers.
    book Schmitz R, Daniel R, Deppenmeier U and Gottschalk G (2006) "The anaerobic way of life". In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH and Stackebrandt E (eds) The Prokaryotes. A Handbook on the Biology of Bacteria: Ecophysiology and Biochemistry, vol. 2, pp. 86–101. New York: Springer.
    Schulz HN, Brinkhoff T, Ferdelman TG et al. (1999) Dense populations of a giant sulfur bacterium in Namibian shelf sediments. Science 284: 493–495.
    Stackebrandt E and Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiology Today 33: 152–155.
    Stackebrandt E and Goebel BM (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.
    Treusch AH, Leininger S, Kletzin A et al. (2005) Novel genes for nitrite reductase and Amo-related proteins indicate a role of uncultivated mesophilic crenarchaeota in nitrogen cycling. Environmental Microbiology 7: 1985–1995.
    Walsby AE (1980) A square bacterium. Nature 283: 69–71.
    Whitman WB, Coleman DC and Wiebe WJ (1998) Prokaryotes: the unseen majority. Proceedings of the National Academy of Sciences of the USA 95: 6578–6583.
    Williams DM and Embley TM (1996) Microbial diversity: domains and kingdoms. Annual Review of Ecology and Systematics 27: 569–595.
    Woese CR (1987) Bacteral evoloution. Microbiological Reviews 51: 221–271.
    Woese CR and Fox GE (1977) Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proceedings of the National Academy of Sciences of the USA 74: 5088–5090.
    Woese CR, Kandler O and Wheelis ML (1990) Towards a natural system of organisms: proposal of the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences of the USA 87: 4576–4579.
    book Zinder SH and Dworkin M (2006) "Morphological and physiological diversity". In: Dworkin M, Falkow S, Rosenberg E, Schleifer KH and Stackebrandt E (eds) The Prokaryotes. A Handbook on the Biology of Bacteria: Ecophysiology and Biochemistry, vol. 1, pp. 185–220. New York: Springer.
 Further Reading
    book Dworkin M, Falkow S, Rosenberg E, Schleifer KH and Stackebrandt E (eds) (2006) The Prokaryotes. A Handbook on the Biology of Bacteria: Ecophysiology and Biochemistry, 3rd edn. New York: Springer.
    book Lengeler JW, Drews G and Schlegel HG (1999) Biology of the Prokaryotes. Stuttgart: Thieme.
    book Madigan MT, Martinko JM, Dunlap PV and Clark DP (2009) Brock Biology of Microorganisms, 12th edn. San Francisco: Pearson/Benjamin Cummings.
    book Staley JT and Reysenbach A-L (eds) (2002) Biodiversity of Microbial Life. Foundation of Earth's Biosphere. New York: Wiley-Liss.

Related Sub-Topics:

Classification | Diversity of Life | Reconstruction of Phylogeny | Evolution of Species | Biodiversity | Microbial Evolution and Taxonomy | General Microbiology
Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

Article Title: Microbial Diversity
 
How to Cite close
Oren, Aharon(Dec 2009) Microbial Diversity. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0020376]