Phylogenetic and gene trees of Synechococcus: choice of the right marker to evaluate the population diversity in the Tucuruí Hydroelectric Power Station Reservoir in Brazilian Amazonia

• Published in: Journal of plankton research 2012-03, Vol.34 (3), p.245-257
• Main Authors: Dall'agnol, Leonardo T., Ghilardi-Junior, Rubens, Mcculloch, John A., Schneider, Horácio, Schneider, Maria P. C., Silva, Artur
• Format: Article
• Language: English
• Subjects: Animal and plant ecology; Animal, plant and microbial ecology; Biological and medical sciences; Fundamental and applied biological sciences. Psychology; General aspects; Synechococcus; Synecology
• ISSN: 0142-7873; 1464-3774
• DOI: 10.1093/plankt/fbr109

The genus Synechococcus is widespread in aquatic environments and is known to be abundant in the Tucuruí Hydroelectric Power Station (HPS) reservoir, in eastern Brazilian Amazonia. However, little is known about this man-made water body's planktonic community. The diversity and phylogeny of the Synechococcus group present in the Tucuruí HPS reservoir were analysed using a culture-independent approach, by amplifying three different loci: the rpoC1 gene, the 16S-23S rRNA-internal transcribed spacer (ITS) and the cpcBA-IGS operon and comparing them to the 16S rRNA gene. The phenograms inferred independently using the three markers indicate the presence of at least six Synechococcus groups in the reservoir. The results also demonstrate a high level of microdiversity in the reservoir. The rpoC1 gene was unable to resolve the most recent branches and is therefore not suggested for studies at the Cyanobacteria genus level. The ITS sequences obtained permitted the modelling of the secondary structure of the RNA of the segment containing the two transfer RNAs and a variable stem region, which was a useful complementary tool in diversity studies of the group. The cpcBA genes have good phylogenetic signal and resolution throughout several taxonomic levels, allowing for correlation between the sequence and pigmentation physiology. However, the choice of molecular markers for phylogenetic analysis of cyanobacteria should be made carefully to maximize the phylogenetic signal.