completely disappear because many microorganisms would
survive and reinitiate evolutionary branches.
The emergence of new pathogens always surprises, either
as a new genus Legionella in 1976 or as a particularly
virulent new strain of a well-known species such as E. coli
strain O157: H7 in 1985. Many environments are still poorly
known, and probably only 1–10 % of prokaryotes have been
described as of 2012. We must therefore expect many
discoveries of new species in partly known environments
including manmade and natural extreme environments, in
particular, the deep subsurface environment and possibly in
extraterrestrial environments that are being explored by
metagenomic approaches (cf. Chap. 18). Moreover, it is
clear that with many emerging pathogens and the accumulation of xenobiotic compounds in various environmental
pollutants that cause the rapid evolution of new pathways
of biodegradation, the world of prokaryotic microorganisms
is in constant evolution. Consequently, their taxonomy cannot be frozen, and microbial taxonomists must describe a
fluid world, with rapid modifications.
Websites http://www.bacterio.cict.fr/classificationgenera.html. This
site is managed by Jean Euze ´by of the ENV Toulouse; it maintains
bacterial taxonomy entries based on the publications validly made in
journals of bacterial taxonomy.
http://www.ncbi.nlm.nih.gov/sites/entrez?db¼taxonomy. This site
is managed by the American NCBI. It is complementary to the first;
however, it incorporates several nonvalid taxa.
References
Albers SV, Meyer BH (2011) The archaeal cell envelope. Nat Rev
Microbiol 9:414–426
Bailly X, Olivieri I, De Mita S, Cleyet-Marel J-C, Bena G (2006)
Recombination and selection shape the molecular diversity pattern
of nitrogen-fixing Sinorhizobium sp. associated to Medicago. Mol
Ecol 15:2719–2734
Bapteste E, Brochier C, Boucher Y (2005) Higher level classification of
the Archaea: evolution of methanogenesis and methanogens.
Archaea 1:353–363
Barns SM, Delwiche CF, Palmer JD, Pace NR (1996) Perspectives on
archaeal diversity, thermophily and monophyly from environmental
rRNA sequences. Proc Natl Acad Sci U S A 93:9188–9193
Beja O et al (2000) Bacterial rhodopsin: evidence for a new type of
phototrophy in the sea. Science 289:1902–1906
Boone DR, Castenholz RW (2001) Bergey’s manual of systematic
bacteriology, vol 1, 2nd edn. Springer, New York
Brenner DJ, Krieg NR, Staley JT (2005) Bergey’s manual of systematic
bacteriology: the proteobacteria, vol 2, 2nd edn. Springer, New
York
Brochier C, Gribaldo S, Zivanovic Y, Confalonieri F, Forterre P (2005)
Nanoarchaea: representatives of a novel archaeal phylum or a fastevolving euryarchaeal lineage related to Thermococcales. Genome
Biol 6:R42
Brochier-Aramanet C, Boussau B, Gribaldo S, Forterre P (2008)
Mesophilic Crenarchaeota: proposal for a third archaeal phylum,
the Thaumarchaeota. Nat Rev Microbiol 6:245–252
Brochier-Armanet C, Forterre P, Gribaldo S (2011) Phylogeny and
evolution of the Archaea: one hundred genomes later. Curr Opin
Microbiol 14:274–281
Brochier-Armanet C, Gribaldo S, Forterre P (2012) Spotlight on the
Thaumarchaeota. ISME J 6:227–230
Cilia V, Lafay B, Christen R (1996) Sequence heterogeneities among
16S ribosomal RNA sequences, and their effect on phylogenetic
analyses at the species level. Mol Biol Evol 13:451–461
Cohan FM (2001) Bacterial species and speciation. Syst Biol
50:513–524
Costechareyre D, Bertolla F, Nesme X (2009) Homologous recombination in Agrobacterium: potential implications for the genomic
species concept in bacteria. Mol Biol Evol 26:167–176
Cox MM, Battista JR (2005) Deinococcus radiodurans the consummate survivor. Nat Rev Microbiol 3:882–892
Daubin V, Gouy M, Perriere G (2001) Bacterial molecular phylogeny
using supertree approach. Genome Inform Ser Workshop
12:155–164
de Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA,
Schleifer KH, Whitman WD (2008) Bergey’s manual of systematic
bacteriology: the firmicutes, vol 3, 2nd edn. Springer, New York
Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E
(2006) The prokaryotes – a handbook on the biology of bacteria, vol
3, 3rd edn. Springer, New York
Dybvig K, Voelker LL (1996) Molecular biology of mycoplasmas.
Annu Rev Microbiol 50:25–57
Elkins JG et al (2008) Akorarchaeal genome reveals insights into the
evolution of the Archaea. Proc Natl Acad Sci U S A 105:8102–8107
Fleischmann RD et al (1995) Whole-genome random sequencing and
assembly of Haemophilus influenzae Rd. Science 269:496–512
Forterre P, Brochier C, Philippe H (2002) Evolution of the Archaea.
Theor Popul Biol 61:409–422
Fox GE et al (1980) The phylogeny of prokaryotes. Science
209:457–463
Fraser C, Alm EJ, Polz MF, Spratt BG, Hanage WP (2009) The
bacterial species challenge: making sense of genetic and ecological
diversity. Science 323:741–746
Gevers D et al (2005) Opinion: re-evaluating prokaryotic species. Nat
Rev Microbiol 3:733–739
Goodfellow M, Ka ¨mpfer P, Busse HJ, Trujillo ME, Suzuki K-I, Ludwig
W, Whitman WB (2012) Bergey’s manual of systematic bacteriology: the actinobacteria, vol 5, 2nd edn. Springer, New York
Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P,
Tiedje JM (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol
Microbiol 57:81–91
Gribaldo S, Brochier-Armanet C (2006) The origin and evolution of
Archaea: a state of the art. Philos Trans R Soc Lond B Biol Sci
361:1007–1022
Grimont PA (1988) Use of DNA reassociation in bacterial classification. Can J Microbiol 34:541–546
Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO
(2002) A new phylum of Archaea represented by a nanosized
hyperthermophilic symbiont. Nature 417:63–67
Imhoff JF, Caumette P (2004) Recommended standards for the description of new species of anoxygenic phototrophic bacteria. Int J Syst
Evol Microbiol 54:1415–1421
Ko ¨nneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB,
Stahl DA (2005) Isolation of an autotrophic ammonia-oxidizing
marine archaeon. Nature 437:543–546
Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL,
Ludwig W, Whitman WB (2011) Bergey’s manual of systematic
bacteriology: the Bacteroidetes, Spirochaetes, Tenericutes
(Mollicutes),
Acidobacteria,
Fibrobacteres,
Fusobacteria,
Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia,
Chlamydiae, and Planctomycete, vol 4, 2nd edn. Springer, New York
6 Taxonomy and Phylogeny of Prokaryotes
189
survive and reinitiate evolutionary branches.
The emergence of new pathogens always surprises, either
as a new genus Legionella in 1976 or as a particularly
virulent new strain of a well-known species such as E. coli
strain O157: H7 in 1985. Many environments are still poorly
known, and probably only 1–10 % of prokaryotes have been
described as of 2012. We must therefore expect many
discoveries of new species in partly known environments
including manmade and natural extreme environments, in
particular, the deep subsurface environment and possibly in
extraterrestrial environments that are being explored by
metagenomic approaches (cf. Chap. 18). Moreover, it is
clear that with many emerging pathogens and the accumulation of xenobiotic compounds in various environmental
pollutants that cause the rapid evolution of new pathways
of biodegradation, the world of prokaryotic microorganisms
is in constant evolution. Consequently, their taxonomy cannot be frozen, and microbial taxonomists must describe a
fluid world, with rapid modifications.
Websites http://www.bacterio.cict.fr/classificationgenera.html. This
site is managed by Jean Euze ´by of the ENV Toulouse; it maintains
bacterial taxonomy entries based on the publications validly made in
journals of bacterial taxonomy.
http://www.ncbi.nlm.nih.gov/sites/entrez?db¼taxonomy. This site
is managed by the American NCBI. It is complementary to the first;
however, it incorporates several nonvalid taxa.
References
Albers SV, Meyer BH (2011) The archaeal cell envelope. Nat Rev
Microbiol 9:414–426
Bailly X, Olivieri I, De Mita S, Cleyet-Marel J-C, Bena G (2006)
Recombination and selection shape the molecular diversity pattern
of nitrogen-fixing Sinorhizobium sp. associated to Medicago. Mol
Ecol 15:2719–2734
Bapteste E, Brochier C, Boucher Y (2005) Higher level classification of
the Archaea: evolution of methanogenesis and methanogens.
Archaea 1:353–363
Barns SM, Delwiche CF, Palmer JD, Pace NR (1996) Perspectives on
archaeal diversity, thermophily and monophyly from environmental
rRNA sequences. Proc Natl Acad Sci U S A 93:9188–9193
Beja O et al (2000) Bacterial rhodopsin: evidence for a new type of
phototrophy in the sea. Science 289:1902–1906
Boone DR, Castenholz RW (2001) Bergey’s manual of systematic
bacteriology, vol 1, 2nd edn. Springer, New York
Brenner DJ, Krieg NR, Staley JT (2005) Bergey’s manual of systematic
bacteriology: the proteobacteria, vol 2, 2nd edn. Springer, New
York
Brochier C, Gribaldo S, Zivanovic Y, Confalonieri F, Forterre P (2005)
Nanoarchaea: representatives of a novel archaeal phylum or a fastevolving euryarchaeal lineage related to Thermococcales. Genome
Biol 6:R42
Brochier-Aramanet C, Boussau B, Gribaldo S, Forterre P (2008)
Mesophilic Crenarchaeota: proposal for a third archaeal phylum,
the Thaumarchaeota. Nat Rev Microbiol 6:245–252
Brochier-Armanet C, Forterre P, Gribaldo S (2011) Phylogeny and
evolution of the Archaea: one hundred genomes later. Curr Opin
Microbiol 14:274–281
Brochier-Armanet C, Gribaldo S, Forterre P (2012) Spotlight on the
Thaumarchaeota. ISME J 6:227–230
Cilia V, Lafay B, Christen R (1996) Sequence heterogeneities among
16S ribosomal RNA sequences, and their effect on phylogenetic
analyses at the species level. Mol Biol Evol 13:451–461
Cohan FM (2001) Bacterial species and speciation. Syst Biol
50:513–524
Costechareyre D, Bertolla F, Nesme X (2009) Homologous recombination in Agrobacterium: potential implications for the genomic
species concept in bacteria. Mol Biol Evol 26:167–176
Cox MM, Battista JR (2005) Deinococcus radiodurans the consummate survivor. Nat Rev Microbiol 3:882–892
Daubin V, Gouy M, Perriere G (2001) Bacterial molecular phylogeny
using supertree approach. Genome Inform Ser Workshop
12:155–164
de Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA,
Schleifer KH, Whitman WD (2008) Bergey’s manual of systematic
bacteriology: the firmicutes, vol 3, 2nd edn. Springer, New York
Dworkin M, Falkow S, Rosenberg E, Schleifer KH, Stackebrandt E
(2006) The prokaryotes – a handbook on the biology of bacteria, vol
3, 3rd edn. Springer, New York
Dybvig K, Voelker LL (1996) Molecular biology of mycoplasmas.
Annu Rev Microbiol 50:25–57
Elkins JG et al (2008) Akorarchaeal genome reveals insights into the
evolution of the Archaea. Proc Natl Acad Sci U S A 105:8102–8107
Fleischmann RD et al (1995) Whole-genome random sequencing and
assembly of Haemophilus influenzae Rd. Science 269:496–512
Forterre P, Brochier C, Philippe H (2002) Evolution of the Archaea.
Theor Popul Biol 61:409–422
Fox GE et al (1980) The phylogeny of prokaryotes. Science
209:457–463
Fraser C, Alm EJ, Polz MF, Spratt BG, Hanage WP (2009) The
bacterial species challenge: making sense of genetic and ecological
diversity. Science 323:741–746
Gevers D et al (2005) Opinion: re-evaluating prokaryotic species. Nat
Rev Microbiol 3:733–739
Goodfellow M, Ka ¨mpfer P, Busse HJ, Trujillo ME, Suzuki K-I, Ludwig
W, Whitman WB (2012) Bergey’s manual of systematic bacteriology: the actinobacteria, vol 5, 2nd edn. Springer, New York
Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P,
Tiedje JM (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol
Microbiol 57:81–91
Gribaldo S, Brochier-Armanet C (2006) The origin and evolution of
Archaea: a state of the art. Philos Trans R Soc Lond B Biol Sci
361:1007–1022
Grimont PA (1988) Use of DNA reassociation in bacterial classification. Can J Microbiol 34:541–546
Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO
(2002) A new phylum of Archaea represented by a nanosized
hyperthermophilic symbiont. Nature 417:63–67
Imhoff JF, Caumette P (2004) Recommended standards for the description of new species of anoxygenic phototrophic bacteria. Int J Syst
Evol Microbiol 54:1415–1421
Ko ¨nneke M, Bernhard AE, de la Torre JR, Walker CB, Waterbury JB,
Stahl DA (2005) Isolation of an autotrophic ammonia-oxidizing
marine archaeon. Nature 437:543–546
Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ, Ward NL,
Ludwig W, Whitman WB (2011) Bergey’s manual of systematic
bacteriology: the Bacteroidetes, Spirochaetes, Tenericutes
(Mollicutes),
Acidobacteria,
Fibrobacteres,
Fusobacteria,
Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia,
Chlamydiae, and Planctomycete, vol 4, 2nd edn. Springer, New York
6 Taxonomy and Phylogeny of Prokaryotes
189