SUMMARY: The use of primers based on the Hipl sequence as a typing technique for cyanobacteria has been investigated. The discovery of short repetitive sequence structures in bacterial DNA during the last decade has led t o the development of PCR-based methods for typing, i.e. distinguishing and identifying, bacterial species and strains. An octameric palindromic sequence known as Hipl has been shown t o be present in the chromosomal DNA of many species of cyanobacteria as a highly repetitious interspersed sequence. PCR primers were constructed that extended the Hipl sequence at the 3` end by two bases. Five of the 16 possible extended primers were tested. Each of the five primers produced a different set of products when used t o prime PCR from cyanobacterial genomic DNA. Each primer produced a distinct set of products for each of the 15 cyanobacterial species tested. The ability of Hipl-based PCR to resolve taxonomic differences was assessed by analysis of independent isolates of Anabaena flos-aquae and Nostoc ellipsosporum obtained from the CCAP (Culture Collection of Algae and Protozoa, IFE, Cumbria, UK). A PCR-based RFLP analysis of products amplified from the 235-165 rDNA intergenic region was used to characterize the isolates and to compare with the Hipl typing data. The RFLP and Hipl typing yielded similar results and both techniques were able to distinguish different strains. On the basis of these results it is suggested that the Hipl PCR technique may assist in distinguishing cyanobacterial species and strains.
AllenM.B.,
ArnonD.I.1955; Studies on nitrogen-fixing blue green algae. I. Growth and nitrogen fixation by Anabaena cylindrica Lemm.. Plant Physiol 30:366–372
ArbeitR.D.,
AuthurM.,
DunnR.D.,
KimC.,
SelanderR.K.,
GoldsteinR.1990; Resolution of recent evolutionary divergence among Escherichia coli from related lineages: the application of pulsed field gel electrophoresis to molecular epidemiology.. J Infect Dis 161:230–235
BeesleyB.E.,
SmithR.J.,
TempleS.J.,
LeaP.J.1994; Cloning and nucleotide sequence of the gene encoding dinitro- genase reductase (nifH) from the cyanobacterium Nostoc 6720.. Biochim Biophys Acta 1219:548–550
BolchC.J.S.,
BlackburnS.I.,
NeilanB.A.,
GreweP.M.1996; Genetic characterisation of strains of cyanobacteria using PCR- RFLP of the cpcBA intergenic spacer and flanking regions.. J Phycol 32:445–451
BritschgiT.B.,
GiovannoniS.J.1991; Phylogenetic analysis of a natural marine bacterioplankton population by ribosomal RNA gene cloning and sequencing.. Appl Environ Microbiol 57:1707–1713
CastenholzR.W.,
ManhartJ.R.,
MccourtR.M.,
WoodA.M.,
LeathamT.1992; Species usage, concept, and evolution in the cyanobacteria (blue-green algae).. J Phycol 28:737–745
EvansE.H.,
FouldsI.,
CarrN.G.1976; Environmental conditions and morphological variation in the blue green alga Chloroglea fritschii.. J Gen Microbiol 92:147–155
FerrisM.J.,
MuyzerG.,
WardD.M.1996; Denaturing gradient gel electrophoresis profiles of 16S ribosomal RNA - defined populations inhabiting a hot-spring microbial mat community.. Appl Environ Microbiol 62:340–346
FreyP.,
SmithJ.J.,
AlbarL.,
PriorP.,
SaddlerG.S.,
Trigalet-demeryD.,
TrigaletA.1996; Bacteriocin typing of Burk- holderia (Pseudomonas) solanacearum race-1 of the French West Indies and correlation with the genomic variation of the pathogen.. Appl Environ Microbiol 62:473–479
GiesendorfB.A.J.,
Van BelkumA.,
KoekenA.,
StegemanH.,
HenkensM.H.C.,
Van der PlasJ.,
GoosensH.,
NeistersH.G.M.,
QuintW.G.V.1993; Development of species specific DNA probes for Campylobacter jejuni, Campylobacter coli and Campylobacter lari by polymerase chain reaction fingerprinting.. J Clin Microbiol 31:1541–1546
GillingsM.,
HolleyM.1997; Repetitive element PCR fingerprinting (rep-PCR) using enterobacterial repetitive intergenic consensus (ERIC) primers is not necessarily directed at ERIC primers.. Lett Appl Microbiol 25:17–21
GuptaA.,
MorbyA.P.,
TurnerJ.S.,
WhittonB.A.,
RobinsonN.J.1993; Deletion within the metallothionein locus of cadmium tolerant Synechococcus PCC6301 involving a highly iterated palindrome (Hipl).. Mol Microbiol 7:189–195
HultonC.S.J.,
HigginsC.F.,
SharpP.M.1991; ERIC sequences - a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium, and other enterobacteria.. Mol Microbiol 5:825–834
LipmanL.J.A.,
DenijsA.,
LamT.J.G.M.,
RostJ.A.,
VandijkL.S.,
ChukkenY.H.,
GaastraW.1996; Genotyping by PCR, of Staphylococcus aureus strains isolated from mammary glands of cows.. Vet Microbiol 38:51–55
LottiF.,
GiovannettiL.,
MargheriM.G,
VenturaS.,
MaterassiR.1996; Diversity of DNA methylation pattern and total DNA restriction pattern in symbiotic Nostoc.. World J Microbiol Biotechnol 12:38–42
LuW.,
EvansE.H.,
McCollS.M.,
SaundersV.A.1997; Identification of cyanobacteria by polymorphisms of PCR- amplified ribosomal DNA spacer region.. FEMS Microbiol Lett 153:141–149
MahenthiralingamE.,
CampbellM.E.,
FosterJ.,
LamJ.S.,
SpeertD.P.1996; Random Amplified Polymorphic DNA typing of Pseudomonas aeruginosa isolates recovered from patients with cystic fibrosis.. J Clin Microbiol 34:1129–1135
MullinsT.D.,
BritschgiT.B.,
KrestR.L.,
GiovanniS.J.1995; General comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities.. Limnol Oceanogr 40:148–158
NeilanB.A.1996; Identification and phylogenetic analysis of toxigenic cyanobacteria by multiplex randomly amplified polymorphic DNA PCR.. Appl Environ Microbiol 61:2286–2291
NeilanB.A.,
JacobsD.,
GoodmanA.E.1995; Genetic diversity and phylogeny of cyanobacteria determined by DNA polymorphisms within the phycocyanin locus.. Appl Environ Microbiol 61:3875–3883
NelissenB.,
De BaereR.,
WilmotteA.,
De WachterR.1996; Phylogenetic relationships of nonaxenic filamentous cyano- bacterial strains based on 16S rRNA sequence analysis.. J Mol Evol 42:194–200
RasmussenU.,
SvenningM.M.1998; Fingerprinting of cyanobacteria based on PCR with primers derived from short and long tandemly repeated repetitive sequences.. Appl Environ Microbiol 64:265–272
RobinsonN.J.,
RobinsonP.J.,
GuptaA.,
BleasbyA.J.,
WhittonB.A.,
MorbyA.P.1995; Singular overrepresentation of an octameric palindrome, Hipl, in DNA from many cyanobacteria.. Nucleic Acids Res 23:729–735
RouhiainenL.,
SivonenK.,
BuikemaW.J.,
HaselkornR.1995; Characterisation of toxin-producing cyanobacteria by using an oligonucleotide probe containing a tandemly repeated heptamer.. J Bacteriol 177:6021–6026
SchmidtT.M.,
DelongE.F.,
PaceN.R.1991; Analysis of a marine picoplankton community by 16S ribosomal RNA gene cloning and sequencing.. J Bacteriol 73:4371–4378
TenoverF.C.,
ArbeitR.D.,
GoeringR.V.,
MickelsenP.A.,
MurrayB.E.,
PershingD.H.,
SwaminathanB.1995; Interpreting chromosomal DNA restriction patterns produced by pulsed field gel electrophoresis: criteria for bacterial strain typing.. J Clin Microbiol 33:2233–2239
TompkinsJ.,
DeVilleM.M.,
DayJ.G.,
TurnerM. F.1995Culture Collection of Algae and Protozoa, Catalogue of Strains. Ambleside, Cumbria, UK: Culture Collection of Algae and Protozoa;
VersalovicJ.,
KoeuthT.,
LupskiJ.R.1991; Distribution of repetitive DNA sequences in Eubacteria and application to fingerprinting of bacterial genomes.. Nucleic Acids Res 19:6823–6831
VilaJ.,
MarcosM.A.,
Jimemez de AntaM.T.1996; A comparative study of different PCR-based DNA fingerprinting techniques for typing of the Acinetobacter calcoaceticus-A. baumannii complex.. J Med Microbiol 44:482–489
WilmotteA.,
Van der AuweraG.,
De WachterR.1993; Structure of the 16S ribosomal RNA of the thermophilic cyanobacterium Chlorogloeopsis HTF (‘ Mastigocladus laminosus ’) strain PCC7518 and phylogenetic analysis.. FEBS Lett 317:96–100