157 Examining Phytoplankton Communities with Environmental PCR

Recent advances in biotechnology have taken much of the guesswork out of many molecular biological procedures, and promote a high rate of success even for relative beginners. In designing the laboratory component of my Phycology course, I have taken advantage of these improved methods to develop a semester‐long, molecular‐based class project, using “environmental PCR” to examine phytoplankton diversity. Students learn a number of common molecular techniques within the context of dynamic and unrehearsed phycological research. This provides a greater appreciation of the general utility of molecular technology, and its application to algal systems in particular. A series of easy to follow protocols are linked together, allowing students to PCR amplify sequences from mixed environmental samples, clone the resulting fragments to separate individual sequences, screen the clones by restriction enzyme digests and sequence clones with clearly different restriction patterns. The resulting sequences then are used in BLAST searches of GenBank to determine the nearest available match among sequences annotated previously. The techniques allow both qualitative and quantitative estimates of the organisms present, as well as comparative analyses of the diversity observed through direct visual observations versus those recovered by PCR. Each step of the procedure can be accomplished in the duration of a typical 3 hour lab period, and most involve intervals of incubation that permit adequate time for other lab exercises, such as a survey algal diversity, on which traditional phycological laboratories are based.