A new approach to analyze genotypes of colony-forming cyanobacteria from environmental samples.

Several studies have shown the efficiency of sequences as rRNA-ITS, cpcBA, rbcLX and other housekeeping genes to study taxonomy [1, 2, 3], population, community structure of cyanobacteria, or for Multi Locus Sequence Analysis [4].
Recently, the genotypic analysis of single colonies and single filaments directly isolated from the environment has been carried out by other authors. It appears that different genotypes of Microcystis are present in one population in one lake. Besides, succession of toxic and non-toxic genotypes may have a critical influence on toxin concentrations during the blooms [5]. Genotypic analysis of colony-forming cyanobacteria requires enough DNA. So far, the genotypes of environmental single colonies of Microcystis were characterized on the basis of one or two PCR [6]. As the DNA content of one single colony only allows for a few PCR reactions, we have developed a new approach using Whole Genome Amplification with Phi29 polymerase to allow for the Multi Locus Sequences Typing analysis of a single colony or filament. For the first time, we were able to amplify and sequence more than one locus of the genome of a single colony of Microcystis. In addition, we have obtained the first sequences of rpoC1, rbcLX and rRNA-ITS from a single colony of the genus Woronichinia ( identified by microscopy). This approach allows to work with a small amount of DNA, and represents a concrete answer to the lack of data on non-cultivable cyanobacteria.
This research is supported by the Belgian Science policy under the science for a sustainable development (SSD) and Fonds de la Recherche Scientifique-FNRS with a FRIA fellowship.
References:
[1] Otsuka S, et al (1999) FEMS Microbiology Letters 172 15-21
[2] Gugger M, et al (2002) Int J Syst Evol Microbiol 52 1867-1880
[3] Haverkamp T, et al (2008) Environmental Microbiology 10(1) 174-188
[4] Lodders N, et al (2005) Environmental Microbiology 7 (3) 434-442
[5] Kardinaal E, and Visser P (2005) In Harmfuf cyanobacteria, Springer Dordrecht pp 41-64
[6] Janse I, et al (2004) Appl Environm Microbiol 70 (7) 3979–3987