Characterization of microbial communities using randomly amplified polymorphic DNA (RAPD)

Similarity among a number of aquatic microbial communities was examined usi ng randomly amplified polymorphic DNA (RAPD), a common polymerase chain rea ction (PCR)-based DNA fingerprinting technique. After amplification of whol e-community DNA extracts, the PCR products were resolved by agarose gel ele ctrophoresis and the band patterns compared to determine percent similarity . Twelve different primers were used to amplify approximately 100 fragments (total) from each DNA sample; the bands were scored as present or absent a nd the similarity between each sample was determined using Jaccard's coeffi cient. From this information, dendrograms were constructed and a bootstrapp ing procedure was used to assess how well supported the tree topologies wer e. Principal component analyses were also conducted as a means of visualizi ng the relationships among samples. Results obtained for two different expe rimental systems (a pair of tidal creeks and several wells in a shallow gro undwater aquifer) correlated well with the temporal and spatial variations in environmental regime at the sites confirming that arbitrarily primed PCR -based DNA fingerprinting techniques such as RAPD are useful means of discr iminating among microbial communities and estimating community relatedness. Moreover, this approach has several advantages over other DNA-based proced ures for whole-community analysis; it is less laborious and uses smaller qu antities of DNA, making it amenable to sample-intensive monitoring, and it does not depend on culturing or the use of selective PCR primers. (C) 1999 Elsevier Science B.V. All rights reserved.