California Sea Grant College Program

Monitoring the bacterial flora in coastal marine waters by conventional techniques has been difficult as most of the bacteria do not readily grow on culture plates and their morphologies are virtually identical in the microscope. Molecular techniques, particularly characterizing bacteria using polymerase chain reaction (PCR) amplification of their small subunit ribosomal RNA (SSU rRNA) genes, has dramatically improved the ability to identify bacteria from environmental samples. Identification of bacteria by PCR amplification is specific and very sensitive. However, it is exactly these properties of PCR amplification which make it difficult to determine the amount of each individual bacterial species in the population.