Fingerprinting aquatic virus communities

Ruth-Anne Sandaa, Steven M. Short, and Declan C. Schroeder

Full Citation: Sandaa, R.-A., S. M. Short, and D. C. Schroeder. 2010. Fingerprinting aquatic virus communities, p. 9-18. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Manual of Aquatic Viral Ecology. ASLO. [DOI 10.4319/mave.2010.978-0-9845591-0-7.9]

ABSTRACT: To circumvent the limitations of cultivation-based studies of complex microbial communities, molecular fingerprinting techniques such as pulsed field gel electrophoresis (PFGE) and denaturing gradient gel electrophoresis (DGGE) have been used to examine their richness, diversity, and dynamics. PFGE is based on the electrophoretic separation of extremely large DNA, raising the upper size limit from 50 kb (standard agarose separation) to well over 10 Mb. This technique has been used to separate aquatic virus genomes ranging in size from tens to hundreds of kilo base pairs (kb); aquatic virus genomes range from 15 to 630 kb, with the majority between 20 and 80 kb. DGGE, on the other hand, is based on the electrophoretic separation of PCR- amplified gene fragments of similar sizes, but differing in base composition or sequence. In this chapter, we provide a brief overview of each of these methods and their application to the study of aquatic viruses. We describe some of the common equipment, reagents, and procedures involved, and conclude by briefly considering some of the strengths and weaknesses of each method.