We're primarily funded by the NSF to study the trophic dynamics of foraminifera in the Antarctic. In English, that means that we are trying to see whether changes in food supply over the course of the year causes changes in the foram population. Since forams are major players in the Antarctic benthic ecosystem, changes in their populations should have effects on other organisms as well. (Forams are excellent indicators of climate change too.)
The traditional method involves identifying individual organisms--kind of like foram birdwatching. Forams are sorted out of bulk bottom sediments by sieving and individualized hand-picking. (The title bar shows a diver vacuuming sediment from the Explorers Cove seafloor.) This is very quantitative, but it takes a lot of time. The other disadvantage is that it can easily miss small or delicate forams, such as juveniles or soft-bodied allogromiids.
Luckily, forams are also genetically distinctive. Of special usefulness is some modifications to the gene for the small ribosomal subunit, which has made it possible to design foram-specific PCR primers. (For a description, check out Jan Pawlowski's molecular systematics article.) These can be used to hunt for foram DNA directly in the sediment, without identifying the cell bodies first. The gene is variable enough to allow us to distinguish different species (see the "Lineup" page for details.)
Using these methods, we've found a number of novel genetic sequences that clearly belong to foraminifera. These are a kind of "genetic fingerprint". We can use this sequence to design probes to identify the organisms from which the genetic signal came.
We are actively working to develop an extensive library of whole-sediment and organismal DNA extracts from a large variety of unusual benthic environments. (As of November 2002, we have 70 whole-sediment DNA extracts from three continents and three oceans, and the number is growing weekly.) We feel that this will be a valuable resource for understanding the diversity of small organisms in these environments.