Validation of the detection of Alexandrium species using specific RNA probes tested in a microarray format: Calibration of signal using variability of RNA content with environmental conditions

• Published in: Harmful algae 2014-07, Vol.37, p.17-27
• Main Authors: Taylor, Joe D., Kegel, Jessica U., Lewis, Jane M., Medlin, Linda K.
• Format: Article
• Language: English
• Subjects: Alexandrium; Alexandrium minutum; Alexandrium ostenfeldii; Alexandrium tamarense; Algae; Animal and plant ecology; Animal, plant and microbial ecology; Applied ecology; Autoecology; Biological and medical sciences; Ecotoxicology, biological effects of pollution; Fundamental and applied biological sciences. Psychology; Microarray; MIDTAL; Phylochip; Plant cytology, morphology, systematics, chorology and evolution; Plants and fungi; RNA content; rRNA probes; Thallophyta; Toxic algae
• ISSN: 1568-9883; 1878-1470
• DOI: 10.1016/j.hal.2014.05.001

•Species specific probes were designed or adapted for use in a microarray for Alexandrium spp.•Alexandrium spp. all showed adaptability to environmental stress conditions.•RNA content in the cells of Alexandrium spp. showed little variation under all treatments.•The microarray will enable detection of A. ostenfeldii, A. minutum cells in natural samples and enable distinction between Group I and Group III Alexandrium tamarense. The dinoflagellate genus Alexandrium contains several toxin producing species and strains, which can cause major economic losses to the shell fish industry. It is therefore important to be able to detect these toxin producers and also distinguish toxic strains from some of the morphologically identical non-toxic strains. To facilitate this DNA probes to be used in a microarray format were designed in silico or developed from existing published probes. These probes targeted either the 18S or 28S ribosomal ribonucleic acid (rRNA) gene in Alexandrium tamarense Group I, Group III and Group IV, Alexandrium ostenfeldii and Alexandrium minutum. Three strains of A. tamarense Group I, A. tamarense Group III, A. minutum and two strains of A. ostenfeldii were grown at optimal conditions and transferred into new environmental conditions changing either the light intensity, salinity, temperature or nutrient concentrations, to check if any of these environmental conditions induced changes in the cellular ribonucleic acid (RNA) concentration or growth rate. The aim of this experiment was the calibration of several species-specific probes for the quantification of the toxic Alexandrium strains. Growth rates were highly variable but only elevated or lowered salinity significantly lowered growth rate for A. tamarense Group I and Group III; differences in RNA content were not significant for the majority of the treatments. Only light intensity seemed to affect significantly the RNA content in A. tamarense Group I and Group III, but this was still within the same range as for the other treatments meaning that a back calibration from RNA to cell numbers was possible. The designed probes allow the production of quantitative information for Alexandrium species for the microarray chip.