SOP 4.1. Taxonomic identification by light microscopy

A rapid taxonomic identification is important for estimating potential risks to animal and human health caused by cyanobacteria in waters used for recreation, drinking and irrigation. Light microscopy provides a rapid means for preliminary identification and quantitative estimation of potentially toxic cyanobacteria based on their morphology (morphotypes). However, the final species assignment should rely on a polyphasic characterization of cultured strains (or population isolates) consisting of several different molecular methods, and (whenever possible) the determination of ultrastructural, physiological, biochemical, and ecological characteristics. In this chapter, we describe the major steps essential for cyanobacterial taxa identification. These include examination by light microscopy, genetic characterization by single or multiple loci sequence analyses, and by molecular typing. The value of taxonomic and molecular databases is explained. Finally, the usefulness of a polyphasic approach is highlighted by examples. Although analyses of genes known to be involved in toxin synthesis can be helpful for the identification of potentially toxic strains (or population isolates), reliable health risk assessments require confirmation by analytical measurement of the respective cyanotoxins.