Development and evaluation of specific 16S rDNA primers for marine Cytophaga-Flavobacteria cluster

Through multiple alignment analysis of 16S rDNA sequences from all known genera of Cytophaga-Flavobacteria (CF) cluster, a new primer pair specifically targeting this cluster was developed, greatly facilitating their diversity and function's exploration in marine ecosystems. Compared with previously reported primers, the new primer pair could theoretically retrieve broader CF diversity without decreasing specificity. The effectiveness for field samples was further evaluated by testing the community DNA samples from various marine environments using the optimal polymerase chain reaction (PCR) conditions established in this work. The results showed its robustness and high specificity for amplifying CF cluster's 16S rDNA fragments from complex marine environments. © 2006 The Authors.