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Chapter 6 Notes

Diversification of Bacteria and Archaea. I: Phylogeny and Biology


General Resources

The best introduction to microbes and their diversity is in the textbook series, Brock Biology of Microorganisms.

There are also a number of excellent web resources, including websites and some textbooks that are available online.

  • An excellent web resource is Microbeworld presented by American Society for Microbiology. There are discussions of different types of microbes, a history of microbial studies, resources for educators, and much more.

  • Another good web resource can be found here.

  • The National Center for Biotechnology Information (NCBI) provides online access to a number of textbooks. One microbiology textbook they have, which contains lots of information related to this chapter, is Medical Microbiology, 4th edition, edited by Samuel Baron (1996).

  • The Department of Bacteriology at the University of Wisconsin-Madison provides a microbiology web textbook.

Introduction to the Bacteria and Archaea

Bacteria Share Many Key Features

The microbiology textbooks and web sites mentioned above are the best places to look for general information. For more detail on specific topics introduced in this section, some good reviews are as follows.

The Archaea, although Unique in Many Ways, Share Some Features with Bacteria and Others with Eukaryotes

A classic paper that compares bacteria and archaea is by Zillig (1991).

Not all archaea are extremophiles. This is made clear in a paper by DeLong (1998).

Several notable reviews of archaeal histones, chromatin, and transcription are Bell and Jackson (2001), White and Bell (2002), and Reeve (2003).

Cell membranes and wall polymers in Archaea are discussed by Kandler and König (1998).

Archaea are extremely diverse in both size and shape. Two papers on unusual archaea are Kessel and Cohen (1982), who describe square-celled halophiles, and Huber et al. (2002), who examine nanosized organisms.

Phylogenetic Diversification of Bacteria and Archaea

The Only Reliable Way to Infer the Phylogenetic History of Bacteria and Archaea Is by Molecular Systematics

An excellent overview of the changes in prokaryotic systematics and phylogeny is by Woese (2000).

A key paper in the reclassification of Deinococcus is the 16s rRNA study done by Weisburg et al. (1989).

Differences between the Rickettsia and Chlamydia lineages are discussed by Zomorodipour and Andersson (1999).

Bacteria and Archaea Have Been Split into Many Distinct Subdivisions

The best reference books for details about the bacterial and archaeal groups are The Prokaryotes (Dworkin 2006) and Bergey’s Manual of Systematic Bacteriology (Garrity 2001).

Molecular Approaches Allow Microbes to be Studied in the Environment

The great plate count anomaly is discussed in Staley and Konopka (1985).

Two good reviews on uncultured microorganisms and the positive impact of molecular phylogenetic studies on understanding microbial diversity are Hugenholtz et al. (1998a) and Rappe and Giovannoni (2003).

rRNA sequencing before the advent of PCR sequencing is described in Lane et al. (1985).

PCR sequencing of rRNA is reviewed in Hugenholtz et al. (1998a).

The best example of finding novel phyla using a molecular phylogenetic survey is described in Hugenholtz et al. (1998b). They surveyed Obsidian Pool, a hot spring in Yellowstone National Park.

Genome Sequencing Allows the Biology of Uncultured Microbes to be Predicted

The term metagenomics was coined by Handelsman et al. (1998); see also Handelsman (2004).

An excellent overview of metagenomics is the book The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet (Committee on Metagenomics 2007), which can be read online at no charge.

Phylogenetic anchors and rhodopsin are discussed by Béjà et al. (2000, 2001).

A good review of environmental shotgun sequencing is Eisen (2007). The first papers in this field were Tyson et al. (2004) and Venter et al. (2004).

Biological Diversification of Bacteria and Archaea

Many Bacteria and Archaea Thrive in Extreme Environments

A good review of microbial extremophiles is in Rothschild and Mancinelli (2001).

A discussion of the challenges in inferring the growth temperature of LUCA is in Galtier et al. (1999).

An overview of microbial adaptations to growth at extreme temperature is Saunders et al. (2003).

The role of specific amino acid changes in these microbial adaptations to temperature is examined in a number of papers, including Haney et al. (1999), Kreil and Ouzonis (2001), and Nakashima et al. (2003).

Adaptations of halophiles are discussed in Oren (2008) and Paul et al. (2008).

Bacteria and Archaea Have Evolved an Enormous Variety in Biochemical Reactions

A good review on the discovery of a fifth pathway of carbon fixation is by Thauer (2007).

Bryant and Frigaard (2006) provide a good review of phototrophy.

Bacteria and Archaea Have Diverse Types of Interactions with Other Species: Mutualism, Parasitism, and Sociality

Among the many reviews of symbiosis involving microorganisms are Moran and Baumann (2000) and Moran (2006).

A good description of the photoautotroph Prochloron can be found on MicrobeWiki.

Chemoautotrophs are reviewed in Stewart et al. (2005).

An example of a study of nutritional symbionts is Wu et al. (2006).

A good review of microbial symbiosis in the human intestine is Ley et al. (2006).

Cavicchioli et al. (2003) muse over whether pathogenic Archaea may exist.

For a review of genomic insights into virulence, see Raskin et al. (2006).

A discussion of the evolution of virulence factors can be found in Brown et al. (2006).

Pathogenicity islands are reviewed in Hacker and Kaper (2000).

Symbiosis islands are described in Sullivan and Ronson (1998).

A comparison of symbiosis and pathogenicity is in Hentschel et al. (2000).

A good review of quorum sensing by the people who first described it is Waters and Bassler (2005).


Baron S., ed. 1996. Medical microbiology, 4th ed. The University of Texas Medical Branch at Galveston. Freely available from The National Center for Biotechnology Information (NCBI) online at http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mmed.TOC&depth=2.

Béjà O., Aravind L., Koonin E.V., Suzuki M.T., Hadd A., Nguyen L.P., Jovanovich S.B., Gates C.M., Feldman R.A., Spudich J.L., et al. 2000. Bacterial rhodopsin: Evidence for a new type of phototrophy in the sea. Science 289: 1902–1906.

Béjà O., Spudich E.N., Spudich J.L., Leclerc M., and DeLong E.F. 2001. Proteorhodopsin phototrophy in the ocean. Nature 411: 786–789.

Bell S.D. and Jackson S.P. 2001. Mechanism and regulation of transcription in Archaea. Curr. Opin. Microbiol. 4: 208–213.

Brown N.F., Wickham M.E., Coombes B.K., and Finlay B.B. 2006. Crossing the line: Selection and evolution of virulence traits. PLoS Pathog. 2: e42. doi:10.1371/journal.ppat.0020042.

Bryant D.A. and Frigaard N.-U. 2006. Prokaryotic photosynthesis and phototrophy illuminated. Trends Microbiol. 14: 488–496.

Cavicchioli R., Curmi P.M., Saunders N., and Thomas T. 2003. Pathogenic archaea: Do they exist? Bioessays 25: 1119–1128.

Committee on Metagenomics: Challenges and Functional Applications, National Research Council. 2007. The new science of metagenomics: Revealing the secrets of our microbial planet. The National Academies Press, Washington, D.C. Freely available from National Academy of Sciences online at http://books.nap.edu/catalog.php?record_id=11902.

DeLong E.F. 1998. Everything in moderation: Archaea as “non-extremophiles.” Curr. Opin. Genet. Dev. 8: 649–654.

Dworkin M., editor-in-chief. 2006. The prokaryotes, 3rd ed. (ed. S. Falkow, E. Rosenberg, K.-H., Schleifer, E. Stackebrandt). Springer-Verlag, New York. First published in 1981.

Eisen J.A. 2007. Environmental shotgun sequencing: Its potential and challenges for studying the hidden world of microbes. PLoS Biol. 5: e82.

Galtier N., Tourasse N., and Gouy M. 1999. A nonhyperthermophilic common ancestor to extant life forms. Science 283: 220–221.

Garrity G.M., editor-in-chief. 2001. Bergey’s manual of systematic bacteriology, 2nd ed. (see http://www.springer.com/series/4157 for the 5th-vol. editors). First published in 1984.

Hacker J. and Kaper J.B. 2000. Pathogenicity islands and the evolution of microbes. Annu. Rev. Microbiol. 54: 641–679.

Handelsman J. 2004. Metagenomics: Application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 68: 669–685. Author correction published 2005 in Microbiol. Mol. Biol. Rev. 69: 195.

Handelsman J., Rondon M.R., Brady S.F., Clardy J., and Goodman R.M. 1998. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem. Biol. 5: R245–R249.

Haney P.J., Badger J.H., Buldak G.L., Reich C.I., Woese C.R., and Olsen G.J. 1999. Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species. Proc. Natl. Acad. Sci. 96: 3578–3583.

Hentschel U., Steinert M., and Hacker J. 2000. Common molecular mechanisms of symbiosis and pathogenesis. Trends Microbiol. 8: 226–231.

Huber H., Hohn M.J., Rachel R., Fuchs T., Wimmer V.C., and Stetter K.O. 2002. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417: 63–67.

Hugenholtz P., Goebel B.M., and Pace N.R. 1998a. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180: 4765–4774.

Hugenholtz P., Pitulle C., Hershberger K.L., and Pace N.R. 1998b. Novel division level bacterial diversity in a Yellowstone hot spring. J. Bacteriol. 180: 366–376.

Kandler O. and König H. 1998. Cell wall polymers in Archaea (Archaebacteria). Cell. Mol. Life Sci. 54: 305–308.

Kessel M. and Cohen Y. 1982. Ultrastructure of square bacteria from a brine pool in Southern Sinai. J. Bacteriol. 150: 851–860.

Kreil D.P. and Ouzounis C.A. 2001. Identification of thermophilic species by the amino acid compositions deduced from their genomes. Nucleic Acids Res. 29: 1608–1615.

Lane D.J., Pace B., Olsen G.J., Stahl D.A., Sogin M.L., and Pace N.R. 1985. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc. Natl. Acad. Sci. 82: 6955–6959.

Ley R.E., Peterson D.A., and Gordon J.I. 2006. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 124: 837–848.

Macnab R.M. 2003. How bacteria assemble flagella. Annu. Rev. Microbiol. 57: 77–100.

Moran N.A. 2006. Symbiosis. Curr. Biol. 16: R866–R871.

Moran N.A. and Baumann P. 2000. Bacterial endosymbionts in animals. Curr. Opin. Microbiol. 3: 270–275.

Nakashima H., Fukuchi S., and Nishikawa K. 2003. Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures. J. Biochem. 133: 507–513.

Oren A. 2008. Microbial life at high salt concentrations: Phylogenetic and metabolic diversity. Saline Systems 4: 2.

Paul S., Bag S.K., Das S., Harvill E.T., and Dutta C. 2008. Molecular signature of hypersaline adaptation: Insights from genome and proteome composition of halophilic prokaryotes. Genome Biol. 9: R70.

Rappe M.S. and Giovannoni S.J. 2003. The uncultured microbial majority. Annu. Rev. Microbiol. 57: 369–394.

Raskin D., Seshadri R., Pukatzki S., and Mekalanos J. 2006. Bacterial genomics and pathogen evolution. Cell 124: 703–714.

Reeve J.N. 2003. Archaeal chromatin and transcription. Mol Microbiol. 48: 587–598.

Rothschild L.J. and Mancinelli R.L. 2001. Life in extreme environments. Nature 409: 1092–1101.

Saunders N.F., Thomas T., Curmi P.M., Mattick J.S., Kuczek E., Slade R., Davis J., Franzmann P.D., Boone D., Rusterholtz K., et al. 2003. Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. Genome Res. 13: 1580–1588.

Schulz H.N. and Jorgensen B.B. 2001. Big bacteria. Annu. Rev. Microbiol. 55: 105–137.

Staley J.T. and Konopka A. 1985. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu. Rev. Microbiol. 39: 321–346.

Stewart F.J., Newton I.L., and Cavanaugh C.M. 2005. Chemosynthetic endosymbioses: Adaptations to oxic-anoxic interfaces. Trends Microbiol. 13: 439–448.

Sullivan J.T. and Ronson C.W. 1998. Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. Proc. Natl. Acad. Sci. U. S. A. 95: 5145–5149.

Szurmant H. and Ordal G.W. 2004. Diversity in chemotaxis mechanisms among the bacteria and archaea. Microbiol. Mol. Biol. Rev. 68: 301–319.

Thauer R.K. 2007. Microbiology. A fifth pathway of carbon fixation. Science 318: 1732–1733.

Thomas C.M. 2000. Paradigms of plasmid organization. Mol. Microbiol. 37: 485–491.

Thomas N.A., Bardy S.L., and Jarrell K.F. 2001. The archaeal flagellum: A different kind of prokaryotic motility structure. FEMS Microbiol. Rev. 25: 147–174.

Tyson G.W., Chapman J., Hugenholtz P., Allen E.E., Ram R.J., Richardson P.M., Solovyev V.V., Rubin E.M., Rokhsar D.S., and Banfield J.F. 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37–43.

Venter J.C., Remington K., Heidelberg J.F., Halpern A.L., Rusch D., Eisen J.A., Wu D., Paulsen I., Nelson K.E., Nelson W., et al. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66–74.

Wadhams G.H. and Armitage J.P. 2004. Making sense of it all: Bacterial chemotaxis. Nat. Rev. Mol. Cell Biol. 5: 1024–1037.

Waters C.M. and Bassler B.L. 2005. Quorum sensing: Cell-to-cell communication in bacteria. Annu. Rev. Cell Dev. Biol. 21: 319–346.

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White M.F. and Bell S.D. 2002. Holding it together: Chromatin in the Archaea. Trends Genet. 18: 621–626.

Woese C.R. 2000. Prokaryote systematics: The evolution of a science. In The prokaryotes (ed.-in-chief M. Dworkin; ed. S. Falkow, E.Rosenberg, K.-H.Schleifer, E. Stackebrandt), Vol. 3, pp. 2–18. Springer-Verlag, New York.

Wu D., Daugherty S.C., Van Aken S.E., Pai G.H., Watkins K.L., Khouri H., Tallon L.J., Zaborsky J.M., Dunbar H.E., Tran P.L., et al. 2006. Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters. PLoS Biol. 4: e188.

Zillig W. 1991. Comparative biochemistry of Archaea and Bacteria. Curr. Opin. Genet. Dev. 1: 544–551.

Zomorodipour A. and Andersson S.G. 1999. Obligate intracellular parasites: Rickettsia prowazekii and Chlamydia trachomatis. FEBS Lett. 452: 11–15.

WWW Resources

http://www.biology.ed.ac.uk/research/groups/jdeacon/microbes/. The Microbial World. Microorganisms and microbial activities. Produced by Jim Deacon, Institute of Cell and Molecular Biology, The University of Edinburgh.

http://www.microbeworld.org/ American Society for Microbiology. Washington, D.C.

http://microbewiki.kenyon.edu/index.php/Prochloron A Microbial Biorealm page on the genus Prochloron. Kenyon College Department of Biology, Gambier, Ohio 43022.

http://www.microbiologytext.com/index.php?module=Book&func=toc&book_id=4. Through the microscope: A look at all things small, by T. Paustian and G. Roberts, University of Wisconsin-Madison.


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