Comparison of terminal-restriction fragment length polymorphism (T-RFLP) analysis and sequencing of 16S rDNA clones in marine sediments

Abstract

Terminal-restriction fragment length polymorphism (T-RFLP) analysis has been optimized by using in vitro model community composed of genomic DNAs of known bacterial strains and has been applied to assess the bacterial community structure in marine sediments. The results of T-RFLP analysis were compared with that of cloning and sequencing 16S rDNA clones from the same sediments. Sequence analysis of 16S rDNA clones (72) of the pristine sediment revealed a diverse collection of lineages, largely of the class Proteobacteria (6% alpha subdivision, 46% gamma subdivision, 13% delta subdivision, and 3% epsilon subdivision), Nitrospina (8%), high G+C gram positive (8%), Verrucomicrobia (7%), and Planctomycetes (6%). In the contaminated sediments, 17 (59%) of the 16S rDNA clones (29) were related to Campylobacter and symbiont of Rimicaris exoculata belonging to epsilon subdivision of Prteobacteria. The results obtained indicated that T-RFLP analysis is a rapid and precise technique for comparative bacterial community analysis.