Tal­mu­dic Ques­tion #23

I am filled with shame.
My amaz­ing wiseass pow­ers have let me down. I thought for sure I'd be able to find at least ONE men­tion of a methanogenic bac­terium some­where.
FAIL.
In my de­fense, I hadn't even looked at methano­gen­e­sis or methano/methylotrophy un­til this came up, which also means you're all in­vited to point and laugh at the ad­mit­ted ig­no­rance which may be ev­i­dent in the rest of my an­swer here...
My best guess (and that's all it is) is that it's sort of a case of evo­lu­tion­ary des­per­a­tion that some ar­chaea de­vel­oped the ca­pa­bil­ity. The ca­pa­bil­ity seems to have de­vel­oped from some func­tions com­mon to both some ar­chaea and some eu­bac­te­ria but only some ar­chaea ended up man­ag­ing to hang on in a fringe en­vi­ron­ment long enough for the pop­u­la­tion to de­velop the abil­ity.
In gen­eral, it seems like ar­chaea are largely shoved out into the en­vi­ron­men­tal mar­gins these days, while bac­te­ria dom­i­nate around what we freak­ish eu­kary­otes think of as "nor­mal" en­vi­ron­men­tal con­di­tions. It is a vir­tual cer­tainty that bac­te­ria and ar­chaea de­rive from a com­mon an­ces­tor. I've also of­ten seen it sug­gested that the sort of ex­treme en­vi­ron­ments still dom­i­nated by ar­chaea (specif­i­cally high tem­per­a­ture and pos­si­bly high-pres­sure en­vi­ron­ments) rep­re­sent a likely orig­i­nal en­vi­ron­ment in which cel­lu­lar life first arose.
The methane-pro­duc­ing and methane-"eating" bio­chem­i­cal path­ways seem to over­lap quite a bit — sev­eral of the same en­zymes are ap­par­ently in­volved in both processes, and it seems like sev­eral of them can have more than one "pur­pose". Though I've seen sug­ges­tions that the shared en­zymes' genes were the re­sult of hor­i­zon­tal gene trans­fer, my (again, ad­mit­tedly in­ex­pert and from a mere un­der­grad­u­ate) opin­ion is that it is more likely that the shared genes were present in some form in the last com­mon an­ces­tor of both mod­ern-day ar­chaea and eu­bac­te­ria.
I stum­bled on an in­ter­est­ing paper[1] as I was pok­ing around that re­ports ver­sions of sev­eral of these genes were found in the com­par­a­tively bizarre bac­te­r­ial phy­lum of Planc­to­mycetes. Fas­ci­nat­ingly, the gene se­quences in the Planc­to­mycetes ex­am­ined ap­pear (it is re­ported) to be about equally evo­lu­tion­ar­ily dis­tant from both the known methane-eat­ing pro­teobac­te­ria and the methane-belch­ing ar­chaea. Makes me won­der if per­haps the Planc­to­mycetes might har­bor the largest re­main­ing col­lec­tion (in one group of or­gan­isms) of ge­netic fea­tures pos­sessed by the last com­mon an­ces­tor of the eu­bac­te­ria and ar­chaea — I haven't got the back­ground to make any kind of judge­ment on whether there's even grounds to spec­u­late about that, but the pos­si­bil­ity is re­ally spiffy any­way, as far as I'm con­cerned.
In any case, here's my per­haps-laugh­ably spec­u­la­tive hy­poth­e­sis:
We start with the Last Com­mon An­ces­tor, who had what I'd guess were genes in­volved in detox­i­fy­ing "C‑1" or­ganic mol­e­cules (which might have more than one car­bon, but no car­bon-car­bon bonds e.g. di­methyl ether) like formalde­hyde. At some point, we get an evo­lu­tion­ary split. Eu­bac­te­ria de­velop fea­tures that let them go nuts out­side of the orig­i­nal hot en­vi­ron­ment, while ar­chaea ini­tially end up largely re­tain­ing the higher-tem­per­a­ture sur­vival ca­pa­bil­i­ties and are more firmly es­tab­lished there. In the process of all of this, eu­bac­te­ria per­haps tended to lose much of their for­mer ca­pa­bil­i­ties through evo­lu­tion­ary at­ro­phy (genes that are no longer used are al­lowed to break over time through nat­ural mu­ta­tion and even­tu­ally end up spliced out al­to­gether in many cases). Ar­chaea do even­tu­ally move out from hot/high-pres­sure en­vi­ron­ments, but seem to be out-com­peted in more mod­er­ate en­vi­ron­ments. Still they man­age to make their way out to niches that the eu­bac­te­ria for what­ever rea­son don't bother with, like places with ex­tremely high os­motic pres­sure (e.g. sat­u­rated brines, like the north­ern end of the Great Salt Lake in Utah). Even­tu­ally, some pop­u­la­tions of ar­chaea end up in places where there isn't much to dump left­over elec­trons from me­tab­o­lism onto ex­cept for car­bon diox­ide, and which per­haps is too hot, or too high a pres­sure, or what­ever for ex­ist­ing eu­bac­te­ria to tol­er­ate. The ar­chaeal pop­u­la­tion man­ages to hang on long enough for some mem­bers to de­velop mu­tant en­zymes which can har­ness the fee­ble elec­tron-suck­ing power of sin­gle-car­bon mol­e­cules and are able to eke out a mea­ger liv­ing. Even­tu­ally they make their way back out of this tiny niche into other ar­eas which are not as ex­treme, but now the pop­u­la­tions have the abil­ity to con­tinue their meta­bolic ac­tiv­ity by methane pro­duc­tion in des­per­ate, elec­tron-ac­cep­tor-poor en­vi­ron­ments where noth­ing else sur­vives. Both ar­chaea and eu­bac­te­ria ap­pear to have de­vel­oped methan­otro­phy, if I re­mem­ber what I was look­ing at over the week­end cor­rectly, so maybe this was spurred on around the pe­riph­ery of methanogenic ar­chaeal pop­u­la­tions by all the new methane be­ing pro­duced.
I've been try­ing to turn that into a co­her­ent and in­ter­est­ing story off and on all week­end, and this is the best I've man­aged to do so far. I haven't had much back­ground in this area so help­ful com­ments are ap­pre­ci­ated. I did skim over every­thing pretty quickly and I'd be sur­prised if I didn't at least miss a few things if not out­right mis­in­ter­pret some­thing...
In­ci­den­tally, it ap­pears that ASM's "Mi­crobe" mag­a­zine has an overview of the sub­ject avail­able on­line, too.[2]
[1] Chis­toser­dova, L., C. Jenk­ins, M. Ka­lyuzh­naya, C. J. Marx, A. Lapidus, J. A. Vorholt, J. T. Sta­ley, and M. E. Lid­strom: "The enig­matic planc­to­mycetes may hold a key to the ori­gins of methano­gen­e­sis and methy­lotro­phy." 2004; Mol. Biol. Evol. 21:1234–1241.
[2] Lud­mila Chis­toser­dova, Ma­rina G. Ka­lyuzh­naya, and Mary E. Lid­strom: "C1-Trans­fer Mod­ules: from Ge­nomics to Ecol­ogy" http://www.asm.org/microbe/index.asp?bid=38603 (re­trieved 20071105)

Af­ter read­ing SMC's in­ter­est­ing story and pok­ing around a bit (read, pro­cras­ti­nat­ing) I think I can maybe add to his hy­poth­e­sis. The phy­lo­ge­netic re­stric­tion of methano­gen­e­sis sug­gests an an­cient ori­gin and re­stric­tion (duh!). So, we can think a bit about the Ar­chaeal at­mos­phere, and a hot, wet, re­duc­ing, anoxic world. This seems like a world in which H2 is a pretty ro­bust elec­tron source, so bac­te­ria that can get those will have some suc­cess. I'm not sure about CO2 lev­els in ge­o­log­i­cally an­cient at­mos­pheres, wa­ters, and sed­i­ments, but lets as­sume there was some- This niche seems rea­son­able to fill at or near the out­set.
So, the ques­tion be­comes what kept these or­gan­isms from di­ver­si­fy­ing their me­tab­o­lism over evo­lu­tion­ary time (i.e. why are they still methanogens fix­ing CO2 and get­ting e from H2 when there are so many other meta­bolic path­ways out there?).
Here's my goofy idea — maybe the in­ter­me­di­ates of methanogenic elec­tron trans­fer and car­bon as­sim­i­la­tion poi­son other meta­bolic path­ways. Or, al­ter­na­tively, other es­sen­tial parts of the methanogenic cell are in­com­pat­i­ble with other chemotrophic en­ergy? This seems a stretch. Al­ter­na­tively, maybe we just aren't good enough in­ves­ti­gat­ing methanogens to know all their meta­bolic ca­pa­bil­i­ties.
The flip side is why hasn't any­one else de­vel­oped methano­gen­e­sis (which was ac­tu­ally the ques­tion!). I have to think that this sug­gests that the in­ter­me­di­ates of methano­gen­e­sis poi­son other meta­bolic strate­gies in some way (note, not a bio­chemist!!), mak­ing it an all or noth­ing propo­si­tion. It was noted by SMC that methy­lotro­phy and methano­gen­e­sis share some in­ter­me­di­ate steps, so maybe those ones are ok, but some crit­i­cal step is in­ac­ces­si­ble to an or­gan­ism us­ing ROC for en­ergy and cell car­bon? An added mys­tery is that there are lots of H2 uti­liz­ing CO2 fix­ing eu­bac­te­ria, but they don't make methane (at least, if they do no one is talk­ing about it!).
So (stream of con­cious­ness alert!) maybe that ex­plains it — in eu­bac­te­ria, an al­ter­na­tive set of tools de­vel­oped for the same pur­pose (get­ting e and car­bon), mak­ing methano­gen­e­sis less at­trac­tive

The ques­tion is very sim­i­lar to the ques­tion that caused me to write a gutwrench­ing pa­per not too long ago. The pa­per was [1]:
The ques­tion was: How is it pos­si­ble that methanogens re­quire help from chemios­mo­sis in or­der to gen­er­ate a pro­ton gra­di­ent? Re­lated: why don't they make ac­etate from H2 and CO2?
One thing leads to an­other and it doesn't take long be­fore one is star­ing at the bio­chem­i­cal sim­i­lar­i­ties in the methyl syn­the­sis branch of the acetyl-CoA path­way be­tween ace­to­gens and methanogens and the dif­fer­ences in their pro­ton pump­ing mech­a­nisms (in the ab­sence of shared pro­teins be­fore we get to CODH/ACS). As far as I can tell (and I might be wrong, but give me a fair shake and read the pa­per first, please), there is ho­mol­ogy (yes, sim­i­lar via com­mon de­scent) be­tween the syn­the­sis of methane and ac­etate at some hy­drother­mal vents and the chem­istry of the acetyl-CoA path­way as it is man­i­fest in ace­to­gens and methanogens. That might sound nutty, but in the ab­sence of a bet­ter sug­ges­tion for the main re­ac­tion that got life go­ing, I'd say CO2 re­duc­tion with elec­trons from H2 is a pretty good null hy­poth­e­sis. Se­pen­tiniza­tion is a nice key word here, be­cause it is the source of (n.b.) ge­o­log­i­cal H2 and methane (and other re­duced C1 com­pounds) at vents even to­day. Why should that have been dif­fer­ent at life's ori­gin? I sup­pose that het­erotrophic ori­gins first fans will scoff, but that's fine, as long as they can of­fer a bet­ter sug­ges­tion for a ther­mo­dy­nam­i­cally favourable core re­ac­tion (main waste prod­uct) at lifes ori­gin that does not re­quire mir­a­cles. So I'd say ac­etate first be­cause its ki­net­i­cally easy, methane later, be­cause its harder to make. But when I say methane later, I mean methano­gen­e­sis as the core ph­syi­ol­ogy of the com­mon an­ces­tor of archeabac­te­ria, that de­scended from a Last Com­mon An­ces­tor that was not free liv­ing. Those who start with a free-liv­ing Last Com­mon An­ces­tor might want to let us know what its lifestyle was sup­posed to have been. Early evo­lu­tion is a mis­er­able topic, but I didn't pose the ques­tion of this dis­cus­sion.
Afetr all: the abil­ity to har­ness a nat­u­rally pre-ex­ist­ing pro­ton gra­di­ent (at the vent–ocean in­ter­face) via an AT­Pase has to be older than the abil­ity to gen­er­ate a pro­ton gra­di­ent with chem­istry that is spec­i­fied by genes. And if we look around, that tends to fit with what we see in the or­gan­i­sa­tion of mod­ern mi­cro­bial phys­i­ol­ogy.
So my an­swer is: They never learned how, and those that might have made steps in that di­rec­tion (via LGT or what­ever) found them­selves un­able to com­pete with pre­ex­ist­ing well-honed ar­chaeal com­peti­tors that could do it bet­ter on the mol­e­cule for mol­e­cule suc­strate com­pe­ti­tion ba­sis. The pro­ton pump­ing mech­a­nisms that en­able ace­to­gens and methanogens to work seem to be their own spe­cific so­lu­tions to the prob­lem of how to pump your own pro­tons and thus make the tran­si­tion to the free-liv­ing state. Sound crazy? Ar­tic­u­late a bet­ter sug­ges­tion than in [1].
[1] Mar­tin W, Rus­sell MJ: On the ori­gin of bio­chem­istry at an al­ka­line hy­drother­mal vent. Phil. Trans Roy. Soc. Lond. B 367:1187–1925 (2007).

(re­gard­ing David Lipson's com­ment) If tetraether lipids are es­sen­tial to life in ex­treme en­vi­ro­ments (his com­ment) then how and why do eu­bac­te­ria sur­vive in ex­treme en­vi­ron­ments. A Tal­mu­dic ques­tion — but only if you be­lieve that tetraethers are the en­try pass­word to the ex­treme. If not, no Tal­mud needed there (but it al­ways helps, I ad­mit, as some­one who can­not read He­brew.)