Oil Spill Brainstorm

• Josh, May 31: I think that some of our methods and ideas could be easily adapted for investigating the effects of the Gulf of Mexico oil spill on marine microbes. There is a lot funding available to do this -- see http://www.nsf.gov/pubs/2010/nsf10060/nsf10060.jsp . What do you think?
• Katie, June 1: I'm not sure our work qualifies in terms of having an urgency component - but maybe. It looks like one applies through the usual programs but with different deadlines. So, when you talk to program officers this week you could ask if the application would qualify as a RAPID proposal.
• Tom, June 1: I think this could be interesting, especially from a standpoint of natural remediation. In addition to what Katie mentioned, we'd probably have to collaborate with someone that can obtain samples for us - an expensive endeavour.
• Sam, June 2: I'd be interested to hear how you think we could make our methods seem urgently relevant. I think it would be cool to work on the oil spill, if it makes sense and we can find collaborators with samples.
• Tom, June 2: A quick, poorly thought out idea:
  • Can we use the read classification (gene family) pipeline to identify the presence of genomes in the area of the spill that are putatively capable of degrading oil. If so, it may warrent attempts to attenuate the activity of the cells with such genes through various bioremediation operations.
  • Alternatively, metagenomics and 16S analyses could provide insight into how the microbial community and function shifts during an oil spill. Would be great to find a t0 point, maybe an uncontaminated area in the gulf would do.
• Josh, June 2: Yes, that sounds intriguing. In addition, we could also potentially use the ecological methods to map the impact on the microbial community of the oil spill, or understand how currents/diffusion processes affect the impact. Apparently, the deep sea effects of oil are pretty much unknown. See http://www.nytimes.com/2010/06/02/us/02coral.html?ref=us . Might worth looking into the effects on deep-sea microbes; e.g., to attempt to use them as indicator taxa.
• Katie, June 2: You guys could start a wiki page to brain storm on this.
• Sam, June 2: Sounds like we should get Venter on board to do some deep-sea sampling closer to and further from the oil spill. :) One thing I was thinking about was this talk that we saw by B. Jesse Shapiro at CSHL-- oh wait, just got Katie's email about a wiki page. I started one here and I'll put our ideas there.
• Sam, June 2: Maybe this is too far out there, but I was thinking about this talk we saw by B. Jesse Shapiro from MIT at the CSHL Biology of Genomes meeting where he took coastal samples and separated out different "eco-types" using filters that filtered out particles of varying sizes. He looked at what sequences came up for specific gene families, if I remember right, and looked at the differences that came up for different filtered populations. If someone were already doing sampling like that or interested in doing sampling like that, it might give a way to see if the impact of the oil spill is different on different microbial eco-types. Combining this with a time-series would be the most interesting thing, but as Tom points out, it may be possible to use an uncontaminated area in the gulf as a background (is there one left?).
  • One reason why this is cool is that it might also give a clue as to what is going on at the level of the host ecosystems for the microbial eco-types.