More on Microbial Sequencing

(Continued from “On Microbial Sequencing“). Well, it’s really been a great meeting. The biology of pathogens, parasites and symbionts is amazing. Historically, the microbes that chiefly interested us were one of those three: those that causes disease in humans, animals (focus on domesticated animals), plants (again, mostly domesticated). However, as we are (alas, too slowly) learning about our planet, the changes that take place, we learn how embedded many microbes are to the ability of Earth to sustain life. A drastic example is the dreaded “methane pulse”. Methane (CH4) is a greenhouse gas which has heat retention capability 23 times of that of CO2.  Soil methanogens are the chief producers of methane. There is an estimated 75x 109 tons of methane trapped in a frozen peat bog in West Siberia which constitutes 25% of the estimated methane trapped in soil and ice-age permafrost worldwide. This permafrost is melting, releasing methane, which in turn contributes to global warming in a vicious cycle. The Nature paper, and an article in TerraNature.

On a positive side, microbes also constitute the largest methane sink: those would be methanotrophs, “methane eaters” (see my previous post about Tom Schmidt lab’s work).  If we understand how these operate, perhaps we can halt the vicious cycle of methane release -> warming that leads to more methane release.

Bioinformatics is a critical component in all this. Environmental genomics is the research tool that is used to help diagnose these problem and document the flux in bacterial population.
I was delighted to see how many new algorithms and tools were emerging from those studies, some of that software being developed in the wet labs, rather than in “speciality” dry labs. Bioinformatics is becoming a lab skill, and that is a good thing.  What was even more encouraging is that the software was being developed with a forethought towards software sustainability and community use. Regarding software sustainability, one of the gripes people had (yeah, me too) is that there is a strong bias in Federal funding towards funding the development of new tools, as opposed to sustaining existing ones. Well, Lita Proctor and Ann-Lichens Park were actually very informative on the places we can apply to for software maintenace. We’ll see.  JAFA, one of my pet projects, is in a severe state of disrepair, and I plan on applying for funding for that soon enough.

Regarding software community use, thought was taken in proper licensing of some of the software mentioned. Being “license mindful”, and understanding the need for correct licensing is no longer the realm of Stalman-and-Torvalds-quoting nerds.

Share and Enjoy:
  • Fark
  • Digg
  • Technorati
  • StumbleUpon
  • Facebook
  • Reddit
  • Twitter
  • FriendFeed
  • PDF
  • email
  • Print
  • Google Bookmarks

Comments are closed.