Biologia 66/2: 238—243, 2011 Section Botany DOI: 10.2478/s11756-011-0003-8 Rapid differentiation of phenotypically and genotypically similar Synechococcus elongatus strains by PCR fingerprinting. Gangatharan Muralitharan 1 & Nooruddin Thajuddin 1 Department of Microbiology, School of Life Sciences, Bharathidasan University, Palkalaiperur, Tiruchirappalli 620 024, Tamilnadu, India; e-mail: gmuralitharan2002@yahoo.co.in Abstract: PCR amplification techniques viz., repetitive DNA element PCR (REP-PCR), short tandemly repeated repeti- tive PCR (STRR-PCR) and arbitrarily primed PCR (RAPD-PCR) were used for the taxonomic discrimination among the strains of the unicellular cyanobacterium Synechococcus elongatus collected across the coastal regions of the Indian subcon- tinent. These strains showed similar phenotypic and genotypic characteristics. Data obtained from genomic fingerprinting were used to perform cluster analysis and demonstrated ability to differentiate strains at intra-specific level. Polymorphisms of different PCR amplification products can serve as strain-specific molecular fingerprints. In comparison with the STRR and RAPD, the REP primer set generates fingerprints of lower complexity, but still the phenogram clearly differentiated the strains. In conclusion, described PCR fingerprinting methods can be considered as promising tools for the differentiation at the strain level of cyanobacteria from the same species. Key words: Synechococcus elongatus; genetic diversity; PCR-fingerprinting; RAPD-PCR; REP-PCR; STRR-PCR Abbreviations: BDU, Bharathidasan University; NFMC, National Facility for Marine Cyanobacteria; PCR, polymerase chain reaction; RAPD, randomly amplified polymorphic DNA; REP, repetitive extragenic palindromic sequences; STRR, short tandom repetitive repeats. Introduction The genus Synechococcus is a provisional taxon includ- ing unicellular coccoid to rod-shaped microorganisms lacking structured sheaths, occupy an important posi- tion at the base of the marine food web: they are among the most abundant members of the picoplankton in the open ocean, and their contribution to primary produc- tion has been estimated to be 5 to 30 % (Waterbury et al. 1986). Marine Synechococcus species possess a num- ber of unique biological properties not found in any other cyanobacterial group. These include the ability of some strains to swim by a novel mechanism (Water- bury et al. 1985), the ability to acquire major nutrients and trace metals at the submicromolar concentrations found in the oligotrophic ocean, and the ability to syn- thesize unique photosynthetic pigments (Alberte et al. 1984; Ong & Glazer 1987). The Synechococcus group has been divided into six clusters based mainly on the habitat (marine or freshwater) and the mole percentage G+C content of DNA, named the Cyanobacterium clus- ter, the Cyanobium cluster, the Synechococcus cluster, and marine clusters A, B, and C (Waterbury & Rippka 1989). Genetic diversity in marine cluster A Synechococ- cus strains has been examined in a few strains using 16S rDNA sequences (Urbach et al. 1998) and more exten- sively using rpoC1 sequences (Toledo & Palenik 1997; Toledo et al. 1999). Using rpoC1, a collection of strains from the California Current could be divided into two lineages consistent with their high or low phycouro- bilin amounts. However, each of these lineages was dis- tinct from the typical laboratory model high- and low phycourobilin strains (WH 8130 and WH 7803, respec- tively) suggesting that pigment content alone may not resolve the multiple ecotypes of marine cluster A Syne- chococcus. Motility, however, does appear to be corre- lated with phylogeny, as all motile isolates characterized to date are closely related (Toledo et al. 1999). Another recently described clade consists of strains whose mem- bers are capable of altering their pigment content in re- sponse to light quality in an acclimation process known as chromatic adaptation (Palenik 2001). The marine clusters A, B, and C have recently been reclassified. Marine clusters A and B are now combined into two subclusters within Synechococcus cluster 5 (Herdman et al. 2001). It has thus been suggested that since these organisms are phylogenetically diverse they should be reclassified into several independent taxonomic units (Honda et al. 1999; Robertson et al. 2001). For a variety of reasons, precise identification of cyanobacteria by classical bacteriological criteria is dif- ficult (Castenholz & Waterbury 1989; Rippka et al. 1979), but a number of different PCR based strategies for the genetic characterization of strains, or environ- mental samples are now available (Laloui et al. 2002). c 2011 Institute of Botany, Slovak Academy of Sciences Unauthenticated Download Date | 7/30/18 4:02 AM