Dr. Bik's appeal for Eukaryotes

I attended Dr. Holly Bik's lecture this afternoon titled "Eukaryotes are microbes, too." The talk was focused around the importance and difficulties of including eukaryotes in sequencing analysis in order to more accurately measure biodiversity. Her research involved nematodes, of which there are 1-100 million different species (only 4,000 of which have been genetically described). She also stated that there can be anywhere from 100,000 to 84,000,000 nematodes in one square meter of land. That's quite the statement, but I'm not surprised by these numbers. Nematodes are so small they can make their way into our tap water, along with amoebae, algae, and other microbes.
The methods behind her research involve what we discussed in class. She takes a land sample (dirt), extracts the DNA, performs PCR (polymerase chain reaction) to amplify the rRNA of the ribosomes, sequences the results, and performs a community analysis. She stated that the latter step was by far the most difficult to perform, simply because there are no efficient tools (programs, scripts, services, etc) that makes this easy. She screens for 16s rRNA; it's easy in prokaryotes because there's only one copy, but in eukaryotes there can be 10s to 10,000s of copies of the ribosomal rRNA, making it difficult to sequence. Coming up with a phylogeny tree for these newly discovered eukaryotic species can be extremely difficult for this reason. She aims to use OTU (operational taxonomic units) clouds (or clustering) to help view the similarities and diferences between different species from a land sample. While she currently uses Phylosift, which uses a probability distribution over a reference phylogeny, in order to come up with maps of genetic similarity, she hopes to soon come up with an application/program that allows one to select for what they want to see in one of these OTU maps, as per her Kayak.com example with airplane flights.
I really enjoyed Dr. Bik's presentation on eukaryotes today. She was very confident in the material she presented, and seemed very clearly passionate about her work.