Of Aer­obes and Anaer­obes

Note­wor­thy

When first in­tro­duced to mi­crobes, we quickly learn to di­vide them into aer­obes and anaer­obes. Then we qual­ify those ti­tles with mod­i­fiers to yield such classes as fac­ul­ta­tive anaer­obes (can grow with­out oxy­gen but can respire it to great ben­e­fit), ob­lig­ate aer­obes (those ab­solutely de­pend­ing on oxy­gen res­pi­ra­tion) and strict anaer­obes (these will die in the pres­ence of oxy­gen). But then, just as quickly, we learn that there are al­ways ex­cep­tions to the rules. When it comes to growth in the pres­ence of oxy­gen, well, things de­pend...

Bio­geo­log­i­cal time­line show­ing the evo­lu­tion of mi­cro­bial me­tab­o­lisms in par­al­lel with the rise in at­mos­pheric oxy­gen con­cen­tra­tions. Source

Take, for ex­am­ple, the long-held tenet that Bac­teroides frag­ilis was a strict anaer­obe. That idea was de­bunked over two decades ago, when Baughn and Malamy showed B. frag­ilis could grow aer­o­bi­cally at sub-mi­cro­mo­lar (hun­dreds of nanomo­lar) oxy­gen con­cen­tra­tion, ac­tu­ally ben­e­fit­ting from oxy­gen me­tab­o­lism. As a new de­scrip­tor for such bac­te­ria, the nanaer­obe was coined. In the en­su­ing twenty years the con­cept of strict anaer­obes con­tin­ued to erode as more and more mi­crobes ca­pa­ble of tol­er­at­ing and me­tab­o­liz­ing oxy­gen grew as the con­cen­tra­tions of oxy­gen that were tested got lower. Turns out, the new rule may some­day be that there are no strict anaer­obes; it's just a mat­ter of how sen­si­tive our meth­ods are in de­tect­ing low oxy­gen con­cen­tra­tions. Cur­rently, the limit of de­tec­tion is 3 nanomo­lar. So, there's still a lot of room to test be­tween 3 nanomo­lar to zero oxy­gen, if only we de­velop meth­ods with such sen­si­tiv­ity. A 2022 re­view on this sub­ject, by Jas­mine Berg and col­leagues, is very much worth the read to get a sense of "how low can they go" in terms of oxy­gen con­cen­tra­tion.

Oxy­gen me­tab­o­lism is, of course, not only of great in­ter­est for un­der­stand­ing present day mi­cro­bial phys­i­ol­ogy and ecol­ogy. Earth's nat­ural his­tory was greatly al­tered by the ac­cu­mu­la­tion of at­mos­pheric oxy­gen over half a bil­lion years (from 2.5 to 2.0 bil­lion years ago) in what is known as the Great Oxy­gena­tion Event or GOE, the con­se­quence of the evo­lu­tion of oxy­genic pho­to­syn­the­sis. (The length of that "event" gives great per­spec­tive on the du­ra­tion of our own cur­rent events!) Which means that for ~1.5 bil­lion years of life on Earth the at­mos­phere had prac­ti­cally no oxy­gen. But ap­par­ently it must have had at least some. A re­cent pa­per, based on mol­e­c­u­lar clocks, ma­chine learn­ing and phy­lo­ge­netic rec­on­cil­i­a­tion, con­cludes that aer­o­bic mi­crobes (prob­a­bly nanaer­obes) likely emerged be­fore the GOE. Thus, "oxy­gen tol­er­ance may have been a pre­req­ui­site for, rather than a con­se­quence of, the evo­lu­tion of oxy­genic pho­to­syn­the­sis."

("Note­wor­thy" is the new for­mat for STC's Thurs­day posts. Please read our Jan 20, 2025 post out­lin­ing this and other changes in our blog.)

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