Did microbes cause the Great Dying?

In one of my very first posts almost a decade ago, I wrote about the end-Permian extinction 250 million years ago, which was the greatest mass extinction thus far. In that post I covered research that had ruled out an asteroid impact and found evidence of global warming, possibly due to volcanos, as a cause. Now, a recent paper in PNAS proposes that a horizontal gene transfer event from bacteria to archaea may have been the main cause for the increase of methane and CO2. This paper is one of the best papers I have read in a long time, combining geological field work, mathematical modeling, biochemistry, metabolism, and evolutionary phylogenetic analysis to make a compelling argument for their hypothesis.

Their case hinges on several pieces of evidence. The first comes from well-dated carbon isotopic records from China.  The data shows a steep plunge in the isotopic ratio (i.e ratio between the less abundant but heavier carbon 13 and the lighter more abundant carbon 12) in the inorganic carbonate reservoir with a moderate increase in the organic reservoir. In the earth’s carbon cycle, the organic reservoir comes from the conversion of atmospheric CO2 into carbohydrates via photosynthesis, which prefers carbon 12 to carbon 13. Organic carbon is returned to inorganic form through oxidation by animals eating photosynthetic organisms or by the burning of stored carbon like trees or coal. A steep drop in the isotopic ratio means that there was an extra surge of carbon 12 into the inorganic reservoir. Using a mathematical model, the authors show that in order to explain the steep drop, the inorganic reservoir must have grown superexponentially (faster than exponential). This requires some runaway positive feedback loop that is difficult to explain by geological processes such as volcanic activity, but is something that life is really good at.

The increased methane would have been oxidized to CO2 by other microbes, which would have lowered the oxygen concentration. This would allow for more efficient fermentation and thus more acetate fuel for the archaea to make more methane. The authors showed in another simple mathematical model how this positive feedback loop could lead to superexponential growth. Methane and CO2 are both greenhouse gases and their increase would have caused significant global warming. Anaerobic methane oxidation could also lead to the release of poisonous hydrogen sulfide.

They then considered what microbe could have been responsible. They realized that during the late Permian, a lot of organic material was being deposited in the sediment. The organic reservoir (i.e. fossil fuels, methane hydrates, soil organic matter, peat, etc) was much larger back then than today, as if someone or something used it up at some point. One of the end products of fermentation of this matter would be acetate and that is something archaea like to eat and convert to methane. There are two types of archaea that can do this and one is much more efficient than the other at high acetate concentrations. This increased efficiency was also shown recently to have arisen by a horizontal gene transfer event from a bacterium. A phylogenetic analysis of all known archaea showed that the progenitor of the efficient methanogenic one likely arose 250 million years ago.

The final piece of evidence is that the archaea need nickel to make methane. The authors then looked at the nickel concentrations in their Chinese geological samples and found a sharp increase in nickel immediately before the steep drop in the isotopic ratio. They postulate that the source of the nickel was the massive Siberian volcano eruptions at that time (and previously proposed as the cause of the increased methane and CO2).

This scenario required the unlikely coincidence of several events –  lots of excess organic fuel, low oxygen (and sulfate), increased nickel, and a horizontal gene transfer event. If any of these were missing, the Great Dying may not have taken place. However, given that there have been only 5 mass extinctions, although we may be currently inducing the 6th, low probability events may be required for such calamitous events. This paper should also give us some pause about introducing genetically modified organisms into the environment. While most will probably be harmless, you never know when one will be the match that lights the fire.



2 thoughts on “Did microbes cause the Great Dying?

  1. i’ve been reading updates on the ‘golden rice’ issue. one side (eg v. shiva) says alternatives exist to GM rice (ie vegetables); the other side says golden rice can be stored, and then one gets into the issue of culture/tradition (people eat alot of rice) and also whether vegetables or other things can really deliver the vitamin requirement. (there is also the issue of whether golden rice actually delivers what it promises). (Lewontin discussed this long ago in a book or articles on science and politics). It seems a precautionary principle or modification thereof could be considered—consider the alternatives. One could also maybe make this part of the NSF or other granting process—-if we are going to funs one idea, then we also have to fund the others, and possibly they could be enjoined. (this goes back to groups like MADD and various rehab/detox programs—-its not (to me) a big deal to help people ‘get clean’ if the second you let them out the only place they have to go is a corner with 4 liquor stores on it—it looks like a scam often since its a revolving door.
    (as an aside but on the same theme, i remember talking to an extended family member who said tkaing the kids to see the ‘hunger games’ was a good idea because it was the only place they could get moral lessons (and this is a teacher). i gather the child of someone associated with that movie just killed 6 people, so perhaps he saw the movie too.
    i’d also add that i’ve known quite a few people in various forms of rehab, who were coached by therapists (who sound like they had some sort of community college certificate in counseling including biology of addiction). they learned ‘my condition is genetic’—so they were told ‘have self-control, but also you don’t have any self-control because of the genes’.
    well, i guess we have to keep the student debt business in operation for the sake of picketty’s (‘r,g’) theory (see Richard Goodwin or Paul Samuelson in PNAS around 1972—lotka volterra model of class struggle, mixed in with E Kerner (‘gibbs ensemble, biological ensemble’ now being ‘updated’). Chemsitry departments need to train people for jobs such as the designer drug market (eg K2 which was an issue around my area) since they don’t do econophysics or high fructose corn syrup or bitcoins.


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