Lassalle F et al (2011) Genomic species are ecological species as
revealed by comparative genomics in Agrobacterium tumefaciens.
Genome Biol Evol 3:762–781
Leigh JA, Albers SV, Atomi H, Allers T (2011) Model organisms for
genetics in the domain Archaea: methanogens, halophiles,
Thermococcales and Sulfolobales. FEMS Microbiol Rev 35:577–608
Linnaeus C (1753) Species plantarum. Stockholm. Holmiae: Impensis
Laurentii Salvii
Lopez-Garcia P, Moreira D (2008) Tracking microbial biodiversity
through molecular and genomic ecology. Res Microbiol 159:67–73
Mayr E (1942) Systematics and the origin of species from the viewpoint
of a zoologist. Columbia University Press, New York
Mougel C, Thioulouse J, Perriere G, Nesme X (2002) A mathematical
method for determining genome divergence and species delineation
using AFLP. Int J Syst Evol Microbiol 52:573–586
Murray RG, Stackebrandt E (1995) Taxonomic note: implementation
of the provisional status Candidatus for incompletely described
procaryotes. Int J Syst Bacteriol 45:186–187
Narasingarao P, Podell S, Ugalde JA, Brochier-Armanet C, Emerson
JB, Brocks JJ, Heidelberg KB, Banfield JF, Allen EE (2011) De
novo metagenomic assembly reveals abundant novel major lineage
of Archaea in hypersaline microbial communities. ISME J 6:81–93
Normand P, Lalonde M (1982) Evaluation of Frankia strains isolated
from provenances of two Alnus species. J Can Microbiol
28:1133–1142
Ochman H, Elwyn S, Moran NA (1999) Calibrating bacterial evolution.
Proc Natl Acad Sci U S A 96:12638–12643
Paul K, Nonoh JO, Mikulski L, Brune A (2012) “Methanoplasmatales”,
Thermoplasmatales-related archaea in termite guts and other
environments, are the seventh order of methanogens. Appl Environ
Microbiol 78:8245–8253
Pester M, Schleper C, Wagner M (2011) The Thaumarchaeota: an
emerging view of their phylogeny and ecophysiology. Curr Opin
Microbiol 14:300–306
Podar M, Makarova KS, Graham DE, Wolf YI, Koonin EV, Reysenbach
AL (2013) Insights into archaeal evolution and symbiosis from the
genomes of a nanoarchaeon and its inferred crenarchaeal host from
Obsidian Pool, Yellowstone National Park. Biol direct, Apr 22; 8-9.
doi:10.1186/1745-6150-8-9
Polzin KM, McKay LL (1991) Identification, DNA sequence, and
distribution of IS981, a new, high-copynumber insertion sequence
in lactococci. Appl Environ Microbiol 57:734–743
Rainey FA, Ward-Rainey NL, Janssen PH, Hippe H, Stackebrandt E
(1996) Clostridium paradoxum DSM 7308T contains multiple 16S
rRNA genes with heterogeneous intervening sequences. Microbiology 142:2087–2095
Saitou N, Nei M (1987) The neighbor-joining method: a new method
for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Schleper C, Jurgens G, Jonuscheit M (2005) Genomic studies of uncultivated Archaea. Nat Rev Microbiol 3:479–488
Stacey G, Bottomley PJ, van Baalen C, Tabita FR (1979) Control of
heterocyst and nitrogenase synthesis in Cyanobacteria. J Bacteriol
137:321–326
Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited:
tarnished gold standards. Microbiol Today 33:152–155
Stackebrandt E, Goebel B (1994) Taxonomic note: a place for DNA-DNA
reassociation and 16S rRNA sequence analysis in the present species
definition in bacteriology. Int J Syst Bacteriol 44:846–849
Stackebrandt E, Liesack W, Goebel BM (1993) Bacterial diversity in a
soil sample from a subtropical Australian environment as determined by 16S rDNA analysis. FASEB J 7:232–236
Stackebrandt E et al (2002) Report of the ad hoc committee for the reevaluation of the species definition in bacteriology. Int J Syst Evol
Microbiol 52:1043–1047
Thompson FL, Iida T, Swings J (2004) Biodiversity of vibrios.
Microbiol Mol Biol Rev 68:403–431
Treusch AH, Leininger S, Kletzin A, Schuster SC, Klenk HP, Schleper
C (2005) Novel genes for nitrite reductase and Amo-related proteins
indicate a role of uncultivated mesophilic crenarchaeota in nitrogen
cycling. Environ Microbiol 7:1985–1995
Wayne LG et al (1987) International Committee on Systematic
Bacteriology. Report of the ad hoc committee on reconciliation
of approaches to bacterial systematics. Int J Syst Bacteriol
37:463–464
Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271
Woese CR (2007) The birth of the Archaea: a personal retrospective.
In: Garrett RA, Klenk HP (eds) Archaea: evolution, physiology, and
molecular biology. Blackwell publishing, Oxford, pp 1–15
Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic
domain: the primary kingdoms. Proc Natl Acad Sci U S A
74:5088–5090
Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system
of organisms: proposal for the domains Archaea, Bacteria, and
Eucarya. Proc Natl Acad Sci U S A 87:4576–4579
Yap WH, Zhang Z, Wang Y (1999) Distinct types of rRNA operons
exist in the genome of the actinomycete Thermomonospora
chromogena and evidence for horizontal transfer of an entire
rRNA operon. J Bacteriol 181:5201–5209
190
P. Caumette et al.
revealed by comparative genomics in Agrobacterium tumefaciens.
Genome Biol Evol 3:762–781
Leigh JA, Albers SV, Atomi H, Allers T (2011) Model organisms for
genetics in the domain Archaea: methanogens, halophiles,
Thermococcales and Sulfolobales. FEMS Microbiol Rev 35:577–608
Linnaeus C (1753) Species plantarum. Stockholm. Holmiae: Impensis
Laurentii Salvii
Lopez-Garcia P, Moreira D (2008) Tracking microbial biodiversity
through molecular and genomic ecology. Res Microbiol 159:67–73
Mayr E (1942) Systematics and the origin of species from the viewpoint
of a zoologist. Columbia University Press, New York
Mougel C, Thioulouse J, Perriere G, Nesme X (2002) A mathematical
method for determining genome divergence and species delineation
using AFLP. Int J Syst Evol Microbiol 52:573–586
Murray RG, Stackebrandt E (1995) Taxonomic note: implementation
of the provisional status Candidatus for incompletely described
procaryotes. Int J Syst Bacteriol 45:186–187
Narasingarao P, Podell S, Ugalde JA, Brochier-Armanet C, Emerson
JB, Brocks JJ, Heidelberg KB, Banfield JF, Allen EE (2011) De
novo metagenomic assembly reveals abundant novel major lineage
of Archaea in hypersaline microbial communities. ISME J 6:81–93
Normand P, Lalonde M (1982) Evaluation of Frankia strains isolated
from provenances of two Alnus species. J Can Microbiol
28:1133–1142
Ochman H, Elwyn S, Moran NA (1999) Calibrating bacterial evolution.
Proc Natl Acad Sci U S A 96:12638–12643
Paul K, Nonoh JO, Mikulski L, Brune A (2012) “Methanoplasmatales”,
Thermoplasmatales-related archaea in termite guts and other
environments, are the seventh order of methanogens. Appl Environ
Microbiol 78:8245–8253
Pester M, Schleper C, Wagner M (2011) The Thaumarchaeota: an
emerging view of their phylogeny and ecophysiology. Curr Opin
Microbiol 14:300–306
Podar M, Makarova KS, Graham DE, Wolf YI, Koonin EV, Reysenbach
AL (2013) Insights into archaeal evolution and symbiosis from the
genomes of a nanoarchaeon and its inferred crenarchaeal host from
Obsidian Pool, Yellowstone National Park. Biol direct, Apr 22; 8-9.
doi:10.1186/1745-6150-8-9
Polzin KM, McKay LL (1991) Identification, DNA sequence, and
distribution of IS981, a new, high-copynumber insertion sequence
in lactococci. Appl Environ Microbiol 57:734–743
Rainey FA, Ward-Rainey NL, Janssen PH, Hippe H, Stackebrandt E
(1996) Clostridium paradoxum DSM 7308T contains multiple 16S
rRNA genes with heterogeneous intervening sequences. Microbiology 142:2087–2095
Saitou N, Nei M (1987) The neighbor-joining method: a new method
for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Schleper C, Jurgens G, Jonuscheit M (2005) Genomic studies of uncultivated Archaea. Nat Rev Microbiol 3:479–488
Stacey G, Bottomley PJ, van Baalen C, Tabita FR (1979) Control of
heterocyst and nitrogenase synthesis in Cyanobacteria. J Bacteriol
137:321–326
Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited:
tarnished gold standards. Microbiol Today 33:152–155
Stackebrandt E, Goebel B (1994) Taxonomic note: a place for DNA-DNA
reassociation and 16S rRNA sequence analysis in the present species
definition in bacteriology. Int J Syst Bacteriol 44:846–849
Stackebrandt E, Liesack W, Goebel BM (1993) Bacterial diversity in a
soil sample from a subtropical Australian environment as determined by 16S rDNA analysis. FASEB J 7:232–236
Stackebrandt E et al (2002) Report of the ad hoc committee for the reevaluation of the species definition in bacteriology. Int J Syst Evol
Microbiol 52:1043–1047
Thompson FL, Iida T, Swings J (2004) Biodiversity of vibrios.
Microbiol Mol Biol Rev 68:403–431
Treusch AH, Leininger S, Kletzin A, Schuster SC, Klenk HP, Schleper
C (2005) Novel genes for nitrite reductase and Amo-related proteins
indicate a role of uncultivated mesophilic crenarchaeota in nitrogen
cycling. Environ Microbiol 7:1985–1995
Wayne LG et al (1987) International Committee on Systematic
Bacteriology. Report of the ad hoc committee on reconciliation
of approaches to bacterial systematics. Int J Syst Bacteriol
37:463–464
Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271
Woese CR (2007) The birth of the Archaea: a personal retrospective.
In: Garrett RA, Klenk HP (eds) Archaea: evolution, physiology, and
molecular biology. Blackwell publishing, Oxford, pp 1–15
Woese CR, Fox GE (1977) Phylogenetic structure of the prokaryotic
domain: the primary kingdoms. Proc Natl Acad Sci U S A
74:5088–5090
Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system
of organisms: proposal for the domains Archaea, Bacteria, and
Eucarya. Proc Natl Acad Sci U S A 87:4576–4579
Yap WH, Zhang Z, Wang Y (1999) Distinct types of rRNA operons
exist in the genome of the actinomycete Thermomonospora
chromogena and evidence for horizontal transfer of an entire
rRNA operon. J Bacteriol 181:5201–5209
190
P. Caumette et al.