Tuesday, July 14, 2009

Deep subseafloor microbiology talk at #UCDavis raises questions about the definition of life

Wildly interesting talk here at Davis yesterday by Bo Barker Jorgensen Prof. Dr. Bo Barker Jørgensen

He talked about deep subseafloor microbiology and how many/most of the microbes there grow VERY VERY slowly or not at all.

His talk was part of a series here on "Major Issues in Modern Biology Seminar Series" funded by the Tracy and Ruth Storer Lectureship in the Life Sciences endowment

He did a great job of presenting the evidence for and possibly against whether these organisms that live in the deep subseafloor are alive and whether or not they grow really slowly (with doubling times of hundreds of years). He refers to these organisms as the "starving majority" because their main challenge appears to be getting energy.

The way they do much of their work is to take cores (from ships) of the deep subseafloor and to then characterize the microbes in the cores. They have found, for example, high #s of microbes (mostly bacteria and archaea) as far as 1000m down in the cores.

Among the things he discussed were
  • Paper by Whitman on estimating the number of prokaryotes (his word, not mine) in different places on the planet. This paper suggested most of the prokaryotes are in the subsurface (terrestrial and seafloor)
  • Paper by him in Science reviewing the starving majority.
  • Paper by Biddle et al on rRNA surveys of sedimentary subsurface that suggested that most of the microbes were archaea
  • Paper by Schippers et al (on which Jorgensen is the sr. author) that used qPCR and suggested that most of the microbes were bacteria
  • Paper by Biddle et al on metagenomics of subsurface microbes
  • Paper by Lipp et al in 2008 that looked at membrane lipids to estimate the amount of cellular carbon in the deep subsurface.
  • Various papers that suggest that radioactivity could be the indirect energy source fo these communities (note they are not proposing these are radiation-utilizaing microbes but rather that radiation can lead to the production of H2 which in turn is an energy source).
  • Various papers that suggest that the archaea found in these environments are phylgoenetically very novel
  • He did not mention it but he was a cuauthor on a cool PLOS Biology paper on giant bacteria.
  • At the dinner he discussed briefly one of my favorite topics - nano wires and mentioned one of my favorite scientists - Yury Gorby who is studying these nanowires. Nanowires appear to be mechanisms by which microbes can move electrons around and scanege for electrons
Anyway - the talk gave me lots to think about in terms of slowly growing organisms and how to determine if something was living or not.


  1. Thank you for this post!
    I have a question: would you have any reference on those "phylogenetically very novel" sub-sea floor archaea?

  2. I was also at the talk and I thought I would list a couple of my thoughts:

    1)Should we consider this a living environment or rather a graveyard?

    2)If we consider the sub-floor environment a graveyard and we sample the diversity of organisms at different depths are we essentially looking at a history of evolution of organisms over time?

    3)Keeping in mind that these diverse species are not even growing (and arguably not even alive), the only thing these organisms are probably good at is staying dormant. Gives a new view on survival of the fittest!

  3. Bastien - Dont have refs ...

    Morgan --- unclear if it is a graveyard or not --- worth studying still before deciding

    If it is a graveyard it very well could be a window into past

    They may be good at staying dormant or they may just work slowly --- not sure what to call dormant, dead or slow

    Regardless - another kjey question is - are they able to get activated?

    Also - can their DNA serve as a genetic reservoir?

  4. Thank you! I'll pubmed, then...

  5. Is there any evidence that the DNA is damaged in these organism? dC to dU changes, etc (as per the Neandertal DNA fragment sequence signatures)?

  6. Excellent question The Other Jim. That was in fact the same question I asked him in his after dinner talk and that is how we ended the whole dinner. He said he did not know and asked if I would think about looking into that ...

  7. Sounds quite interesting. Detecting the signatures may be harder with amplification-sequencing, as strongest signature is closer to broken ends of a DNA fragment.

    Still - may shed some light on whether these are dead, or just waiting.


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