A low-density oligonucleotide array study for parallel detection of harmful algal species using hybridization of...

A low-density oligonucleotide array approach based on the hybridization of consensus PCR products of LSU rDNA was developed in order to simultaneously detect various harmful algae. A set of oligonucleotide probes for the hybridization of specific LSU rDNA D2 regions was developed for the identification of 10 representative harmful microalgae. Each probe was spotted onto a streptoavidin-coated glass slide by pipetting. Universal primers were designed within the conserved regions adjacent to the D2 regions of all harmful algae and used to PCR amplify the complete D2 regions. The PCR products were hybridized to the oligonucleotides arrayed on the slide. The array produced unique hybridization patterns for each species of harmful algae and allowed us to differentiate the closely related species. Furthermore, we were able to simultaneously detect several predominant HAB species from a mixture of culture strains and from a natural sample. These results show that DNA microarray can be a new technical platform for parallel discrimination of harmful algae and has great potential to alter the manner in which researchers monitor these microorganisms.