Photosynthetic and phylogenetic primers for detection of anoxygenic phototrophs in natural environments

Primer sets were designed to target specific 16S ribosomal DNA (rDNA) seque nces of photosynthetic bacteria, including the green sulfur bacteria, the g reen nonsulfur bacteria, and the members of the Heliobacteriaceae (a gram-p ositive phylum). Due to the phylogenetic diversity of purple sulfur and pur ple nonsulfur phototrophs, the 16S rDNA gene was not an appropriate target for phylogenetic rDNA primers. Thus, a primer set was designed that targets the pufM gene, encoding the h I subunit of the photosynthetic reaction cen ter, which is universally distributed among purple phototrophic bacteria, T he pufM primer set amplified DNAs not only from purple sulfur and purple no nsulfur phototrophs but also from Chloroflexus species, which also produce a reaction center like that of the purple bacteria. Although the purple bac terial reaction center structurally resembles green plant photosystem II, t he pufM primers did not amplify cyanobacterial DNA, further indicating thei r specificity for purple anoxyphototrophs, This combination of phyrogenetic - and photosynthesis-specific primers covers all groups of known anoxygenic phototrophs and as such shows promise as a molecular tool for the rapid as sessment of natural samples in ecological studies of these organisms.