The use of morphological characters for the classification of cyanobacteria has often led to ambiguous strain assignment. In the past two decades, the availability of sequences, such as those of the 16S rRNA, nif, cpc and rpoC1 genes, and the use of metagenomics, has steadily increased and has made the reconstruction of evolutionary relationships of some cyanobacterial groups possible in addition to improving strain assignment. Conserved indels (insertions/deletions) are present in all cyanobacterial RpoB (β subunit of RNA polymerase) sequences presently available in public databases. These indels are located in the Rpb2_6 domain of RpoB, which is involved in DNA binding and DNA-directed RNA polymerase activity. They are variable in length (6–44 aa) and sequence, and form part of what appears to be a longer signature sequence (43–81 aa). Indeed, a number of these sequences turn out to be distinctive among several strains of a given genus and even among strains of a given species. These signature sequences can thus be used to identify cyanobacteria at a subgenus level and can be useful molecular markers to establish the taxonomic positions of cyanobacterial isolates in laboratory cultures, and/or to assess cyanobacterial biodiversity in space and time in natural ecosystems.
BoutteC.,
GrubisicS.,
BalthasartP.,
WilmotteA.2006; Testing of primers for the study of cyanobacterial molecular diversity by DGGE. J Microbiol Methods 65:542–550[CrossRef]
CaseR. J.,
BoucherY.,
DahllofI.,
HolmstromC.,
DoolittleW. F.,
KjellebergS.2007; Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl Environ Microbiol 73:278–288[CrossRef]
DorigoU.,
VolatierL.,
HumbertJ. F.2005; Molecular approaches to the assessment of biodiversity in aquatic microbial communities. Water Res 39:2207–2218[CrossRef]
GuptaR. S.1997; Protein phylogenies and signature sequences: evolutionary relationships within prokaryotes and between prokaryotes and eukaryotes. Antonie van Leeuwenhoek 72:49–61[CrossRef]
GuptaR. S.1998; Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol Mol Biol Rev 62:1435–1491
GuptaR. S.2009; Protein signatures (molecular synapomorphies) that are distinctive characteristics of the major cyanobacterial clades. Int J Syst Evol Microbiol 59:2510–2526[CrossRef]
HondaD.,
YokotaA.,
SugiyamaJ.1999; Detection of seven major evolutionary lineages in cyanobacteria based on the 16S rRNA gene sequence analysis with new sequences of five marine Synechococcus strains. J Mol Evol 48:723–739[CrossRef]
HongS. K.,
KimB. J.,
YunY. J.,
LeeK. H.,
KimE. C.,
ParkE. M.,
ParkY. G.,
BaiG. H.,
KookY. H.2004; Identification of Mycobacterium tuberculosis by PCR-linked reverse hybridization using specific rpoB oligonucleotide probes. J Microbiol Methods 59:71–79[CrossRef]
IshidaT.,
WatanabeM. M.,
SugiyamaJ.,
YokotaA.2001; Evidence for polyphyletic origin of the members of the orders of Oscillatoriales and Pleurocapsales as determined by 16S rDNA analysis. FEMS Microbiol Lett 201:79–82[CrossRef]
ItemanI.,
RippkaR.,
Tandeau de MarsacN.,
HerdmanM.2002; rDNA analyses of planktonic heterocystous cyanobacteria, including members of the genera Anabaenopsis and Cyanospira
. Microbiology 148:481–496
KuznedelovK.,
KorzhevaN.,
MustaevA.,
SeverinovK.2002; Structure-based analysis of RNA polymerase function: the largest subunit's rudder contributes critically to elongation complex stability and is not involved in the maintenance of RNA–DNA hybrid length. EMBO J 21:1369–1378[CrossRef]
LapageS. P.,
SneathP. H. A.,
LesselE. F.,
SkermanV. B. D.,
SeeligerH. P. R.,
ClarckW. A.1992International Code of Nomenclature of Bacteria (1990 revision) Washington, D.C: American Society for Microbiology;
RajaniemiP.,
HrouzekP.,
KastovskaK.,
WillameR.,
RantalaA.,
HoffmannL.,
KomarekJ.,
SivonenK.2005; Phylogenetic and morphological evaluation of the genera Anabaena, Aphanizomenon, Trichormus and Nostoc (Nostocales, Cyanobacteria. Int J Syst Evol Microbiol 55:11–26[CrossRef]
RasmussenB.,
FletcherI. R.,
BrocksJ. J.,
KilburnM. R.2008; Reassessing the first appearance of eukaryotes and cyanobacteria. Nature 455:1101–1104[CrossRef]
StanierR. Y.,
SistromW. R.,
HansenT. A.,
WhittonB. A.,
CastenholzR. W.,
PfennigN.,
GorlenkoV. N.,
KondratievaE. N.,
EimhjellenK. E.other authors1978; Proposal to place the nomenclature of the cyanobacteria (blue-green algae) under the rules of the International Code of Nomenclature of Bacteria. Int J Syst Bacteriol 28:335–336[CrossRef]
SudaS.,
WatanabeM. M.,
OtsukaS.,
MahakahantA.,
YongmanitchaiW.,
NopartnarapornN.,
LiuY.,
DayJ. G.2002; Taxonomic revision of water-bloom-forming species of oscillatorioid cyanobacteria. Int J Syst Evol Microbiol 52:1577–1595[CrossRef]
TanabeY.,
KasaiF.,
WatanabeM. M.2007; Multilocus sequence typing (MLST) reveals high genetic diversity and clonal population structure of the toxic cyanobacterium Microcystis aeruginosa
. Microbiology 153:3695–3703[CrossRef]
TrüperH. G.1986; International Committee on Systematic Bacteriology Subcommittee on the Taxonomy of Phototrophic Bacteria. Minutes of the Discussion Workshop: Taxonomy of Cyanobacteria17 to 19 June 1985; Paris, France. Int J Syst Bacteriol 36:114–115[CrossRef]
TurnerS.,
PryerK. M.,
MiaoV. P. W.,
PalmerJ. D.1999; Investigating deep phylogenetic relationships among cyanobacteria and plastids by small subunit rRNA sequence analysis. J Eukaryot Microbiol 46:327–338[CrossRef]
VolokhovD. V.,
NeverovA. A.,
GeorgeJ.,
KongH.,
LiuS. X.,
AndersonC.,
DavidsonM. K.,
ChizhikovV.2007; Genetic analysis of housekeeping genes of members of the genus Acholeplasma : Phylogeny and complementary molecular markers to the 16S rRNA gene. Mol Phylogenet Evol 44:699–710[CrossRef]
WilmotteA.,
HerdmanM.2001; Phylogenetic relationships among the cyanobacteria based on 16S rRNA sequences. In Bergey's Manual of Systematic Bacteriology, 2nd edn. vol 1 pp 487–493 Edited by
BooneD. R.,
CastenholzR. W.
New York: Springer;
ZhangJ.,
MaddenT. L.1997; PowerBLAST: a new network blast application for interactive or automated sequence analysis and annotation. Genome Res 7:649–656