Microbial communities can be characterized using certain tests that look at the DNA molecules of the microbes. DNA, as you might already know, is the genetic material of the cell. It contains instructions, in the form of genes, which provide the blueprint for creating the organism. Studying specific genes is a good way for scientists to learn about microbial communities. For example, we can look at a gene called the 16S rRNA gene. The 16S rRNA gene tells us about the relationships of microbes, and that is why it is called a "phylogenetic" marker gene. "Phylogenetic" is derived from Greek words meaning the origin of a tribe or a family. There were other marker genes used in this study, too, including genes coding for special proteins called enzymes—specifically enzymes that are important in using sulfur for energy.
By studying the DNA of these microbes using several different methods, which will be described below, we were able to study three things: how many microbes were present in the samples taken from the groundwater, how those microbes grew over time in each microcosm, and how those microbes were related to each other and to other microbes that we know about.

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