EXTRACTION AND ENZYMATIC CHARACTERIZATION OF FORAMINIFERAL DNA

The Foraminifera have remained an enigmatic group for molecular biologists, and the origins of this geologically important group remain unclear. Here we report techniques developed to isolate and purify foraminiferal DNA. We also outline techniques for polymerase chain reaction (PCR) amplification, cloning and nucleotide sequencing of prepared foraminiferal DNA. Detailed protocols for all of the major techniques are discussed. Using these techniques we have been able to obtain the complete DNA sequences for the nuclear small-subunit (18s) ribosomal RNA coding region for six benthic foraminifera from three suborders. Preliminary phylogenetic tests indicate that the sequences collected are representative of the foraminifera and not their symbionts or food organisms. We believe that the techniques herein form a reliable method for the investigation of foraminiferal DNA sequences. We also discuss the problems which might be caused by foraminiferal endosymbioses and the caveats of using PCR techniques.