Tuesday, May 14, 2013
"Eukaryotes are Microbes, too"
In her lecture “Eukaryotes are microbes, too,” Dr. Bik addressed the issue of the difficulty that comes with trying to include eukaryotes in measurements of biodiversity. She began her presentation with some facts about nematode diversity in deep-sea environments. There are between 1-100 million species of nematode species, with an abundance of 100,000-84 million per meter squared. She also mentioned that in some places, nematodes can be found in the tap water that we drink (gross!). She then went on to describe her methods of collecting her data, which we have seen a few time in class before. She takes samples, extracts the environmental DNA, amplifies the rRNA, does high throughput sequencing, and finally community analysis. She mentioned that this last step (community analysis) was by far the most difficult due to the lack of software capable of doing this. She mentioned that another difficulty in this data collection is that rRNA is not just present in one copy in eukaryotes (as it is in prokaryotes), therefore you can’t quantify species based on the rRNA extracted. Moreover, there are variant copies of rRNA in eukaryotes.
She states that because of this, she visualizes the biodiversity of eukaryotes with their rRNA by using OTUs (operational taxonomic units) as clouds, which shows that the more closely the data points are clustered, the more biologically similar they are. She then addressed some limitations of this method. For example, this approach is dependent on reference databases and the eukaryote sequence databases are patchy and sparsely sampled leading to ambiguous taxonomy. Her proposed solution to this is to use explicitly phylogenetic approaches. In this approach, sequences are used with reference to phylogenetic tree to find their places on the tree (by the best matched). She currently uses a program called Phylosift, which gives taxonomy assignments based on probability distribution over reference phylogeny.
She finished her presentation by talking about her hopes of creating a program where you can filter your results by using advanced settings, as is done on kayak.com when booking flights and hotels. Overall, I really enjoyed Dr.Bik’s lecture and think that her program idea is very creative and could be extremely helpful to many biologists.