There are actually two ways to analyze environmental DNA. Some of you are familiar with this technique being used in the Chicago area to analyze for the presence of two Asian carp species. In that case, they selected a single gene, a sequence of DNA bases, that they knew was specific for each of the two carp species: the silver carp and the bighead carp. They went out and actually would collect just pure water and sample the water, and from that, extract DNA. They would collect the DNA that was filtered onto a mesh, and from the mesh, they could amplify it many times over and run it through a sequencer.
You can almost view it as sausages in a chain. What you need to do is determine the identity of each one of the sausages in that chain. Each sausage could be one of four different DNA bases. This is Biology 101. What we do, one by one, is cleave off the end one, determine what it is, and then we continue along the chain until we're finished. From that, you can determine what the sequence of DNA is.
They would be targeting two species and the DNA from those two species from raw water samples. That's a little bit different from what we are doing. In our case, we're actually collecting net samples, the way we've traditionally done, but instead of counting them under a microscope, we take all of the organisms.
It kind of looks like one of those toys you had as a kid—I forget what they're called—the little globes that you shake and see the snow flying around. That's what the plankton typically looks like, the snow in those little globes. So instead of trying to identify what every species is in that snowstorm, we take all the stuff and put it together, then we mash it all up. We don't try to identify the species. All we want to do is extract the DNA from those species. What you end up with is maybe 500 or 600 different species all combined together.