If a microbiologist is studying bacteria that bioremediate, or break down, toxic wastes and wants to know which specific genes are active when that bacterium is degrading, say, PCBs, he would likely use a tool called the DNA microarray.
Microarrays enable scientists to monitor the activities of hundreds or thousands of genes at once. All microarrays (also called DNA chips or gene chips) work on the basic principle that complementary nucleotide sequences in DNA (and RNA) match up like the two halves of a piece of Velcro coming together.
Scientists also use molecular tools to extract and compare bits of a particular kind of RNA from samples in order to determine if previously known or new microbes are present in a particular environment. This technique is widely used as a biomarker and for microbial ecology studies. It uses a particular kind of RNA known as 16S ribosomal RNA, or 16S rRNA.
The advent of PCR has led to an explosion of microbial gene sequencing in recent years. PCR spells out the entire sequence of the nucleotide bases (the As, Gs, Cs, and Ts) in a DNA molecule that code for a specific protein. Scientists also use sequencing to spell out from start to end every single nucleotide in an organism’s DNA — its entire genome.
Not all microorganisms can be grown in culture. In fact, microbiologists have figured out how to grow very few species in the lab, less than 1% of all the microbial species in the world.
PCR allows scientists to extract and analyze bits of microbial DNA from samples, meaning they don’t need to find and grow whole cells.
PCR is an essential element in DNA fingerprinting and in the sequencing of genes and entire genomes.