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The origin of breathing: how bacteria learnt to use oxygen

The views expressed are those of the author and are not necessarily those of Scientific American.

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Thursday 26th July saw the launch of, a new English language science blog network., the brand-new home for Nature Network bloggers, forms part of the SciLogs international collection of blogs which already exist in GermanSpanish and Dutch. To celebrate this addition to the NPG science blogging family, some of the NPG blogs are publishing posts focusing on “Beginnings”.

Participating in this cross-network blogging festival is’s Soapbox Science blogScitable’s Student Voices blog and bloggers from, SciLogs.deScitable and Scientific American’s Blog Network. Join us as we explore the diverse interpretations of beginnings – from scientific examples such as stem cells to first time experiences such as publishing your first paper. You can also follow and contribute to the conversations on social media by using the #BeginScights hashtag.

The first signs of life on earth appeared about 4.5 Ga (1 Ga is an American billion, ie. 109 years) ago. It’s not yet completely certain exactly how this life arose; hot volcanic mineral springs have been suggested, as have the more traditional lightning-struck primordial soups and (rather wonderfully) radioactive beaches. At any rate something happened which lead to a little membrane-bound ball with internal nucleic acids which, crucially, could replicate…

I've never been convinced by the lightening explanation myself, but it would have been a wonderfully dramatic moment!

And then it was all over really, bar the evolution.

The atmosphere back then was very different, little oxygen and an abundance of carbon dioxide with plenty of methane being released into the atmosphere once the first life forms started eking out an entropy-defying existence. In order to get energy to power cellular processes you need to set up redox pathways, which involve cycles of electron donors and acceptors. The main electron donors around at the time were H2, H2S and CH4 and the main acceptor probably nitrogenous. Water, the electron donor used for photosynthesis, was around in abundance, but none of the little proto-life-blobs quite had the energy required to split it (or the physical proteins required back then either) so it mostly stayed unused.

Carbon dioxide levels went down, methane levels went up and the planet warmed up a little due to global warming. Things stayed like that for a billion years or so (1 Ga) and then something quite special happened, something that would have mindblowingly devastating affects on the life surrounding it.

Photosynthesis. The process by which carbon dioxide is fixed into usable sugars by the splitting of a water molecule. The process of photosynthesis produces oxygen, which is highly dangerous for cells; it can screw up the internal redox potential, create dangerous free-radicals and precipitate ions out into soluble forms. This means that from the point of view of every other organism the newly-evolved photosynthetic blobs were floating around spewing toxic gas into the atmosphere.

Floating green blobs of DEATH. Image from wikimedia commons.

The arrival of this new resource (oxygen) lead to a change in the way organisms respired as well. Up until what is sometimes called the Great Oxidation Event most respiration was anoxic, probably similar to anaerobic respiration, or fermentation,  in anaerobic bacteria around today. This process, while enough t0 keep life going, is around sixteen times less efficient than aerobic respiration. The proto-bacteria that managed to use the oxygen would therefore have gained a major energy boost.

This energy boost allowed the oxygen-using bacteria to go forth and multiply, leaving the anoxic bacteria clinging to the few environmental niches where no oxygen could penetrate. Some of these oxygen-using bacteria were swallowed up by larger cells who then used them as specialised intracellular breathing compartments. The bacteria became mitochondria, and the cells with mitochondria grew bigger and formed more intracellular compartments. They became eukaryotic cells, the kind of cells that all multicellular animals are made from.

So even now, when you breath, it’s ancient bacteria inside your cells that process the oxygen. The only part of the human cell that does oxidative-respiration is the mitochondria. Sure, the human part of the cell can produce small amounts of energy in the cytoplasm, but then the whole process is shuttled into the mitochondria in order to get the massive oxygen energy boost.

One biochemical trick that evolved around two billion years ago to take advantage of oxygen is still being used for respiration by all multicellular life on earth.

This post was largely taken from a previous one, over at my old blog.

S.E. Gould About the Author: A biochemist with a love of microbiology, the Lab Rat enjoys exploring, reading about and writing about bacteria. Having finally managed to tear herself away from university, she now works for a small company in Cambridge where she turns data into manageable words and awesome graphs. Follow on Twitter @labratting.

The views expressed are those of the author and are not necessarily those of Scientific American.

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  1. 1. Torbjörn Larsson, OM 6:39 pm 07/29/2012

    I’m rather tickled (in an “I have said so too” way) by the early date for life signs claimed here, seeing that there are such alluring hints if not conclusive evidence among the scant data. [Disclaimer: studies astrobiology on and off when I have time.]

    I know you didn’t mean to conflate the two, but anoxic photosynthesis is likely older than the oxygen producing one. Early stromatolites have signs of photophily. In fact it may have been necessary for free-living cells, as they don’t show much evidence for early differentiation.

    Protein fold family phylogenies have been penetrating down to the RNA/protein world and the DNA LUCA, who racks up ~ 20 % of time each on a fold clock proxy. The diversification into domains comes after ~ 40 % of proxy time. ["The evolution and functional repertoire of translation proteins following the origin of life", Goldman et al, Bio Dir 2010; and similar work]

    Phylometabolic methods tests some of that. They test that, on a trophic level, a root autotrophic CO2 fixating robust metabolism was present at the UCA stage. It is doubled, implying that early control of metabolism and growth (which would act as a parasitic drain on the autocatalytic metabolic cores) would have been less well evolved.

    Crucially, diversification comes first with oxygen and energy stress, most likely due to an oxygenated atmosphere. ["The Emergence and Early Evolution of Biological Carbon-Fixation, Braakman et al, PLoS Comp Bio 2012]

    So presumably cells from the RNA world to the DNA UCA ecology could have lived in the deep by something similar to todays purple bacteria photosynthesis. Using low light levels, so the then high UV (no ozone) at the ocean surface was no problem. Having many similar core mechanisms, implying it is easy to evolve.

    Either cells evolved to produce poisonous oxygen waste (oops) or glaciations led to oxygen liberation by UV photolysis [there is some paper on that, I hear], but perhaps eventually too much oxygen initiated the diversification. (The glaciation first hypothesis would in effect reverse the usual oxygenating photosynthesis – oxygenated atmosphere – glaciation scheme.)

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  2. 2. PGibbs 12:28 am 07/30/2012

    Did I hear it right? Anoxic? Anaerobic respiration? Fermentation? Life did began with beer! We knew it all along. The elixir of life, indeed!

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  3. 3. 1:18 am 07/30/2012

    Typing mistake in the last sentence
    oxgyen —> oxygen

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  4. 4. thinkyhead 3:59 am 07/30/2012

    If you ever need a proofreader, I’m fast and efficient, and I can help with grammar too. So for instance, your readers wouldn’t see “lead” when you meant “led” or “affect” when you meant “effect.” Little details like these can go a long way towards making your writing appear smarter and more professional, and it will avoid peeving your sharper readers.

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  5. 5. S.E. Gould in reply to S.E. Gould 4:41 am 07/30/2012

    @Torbjorn: Thanks for the extra information. I didn’t mention anoxic photosynthesis in this article because, unfortunately, there is never enough room to put everything into one blog post! Anoxic photosynthesis will be another post for another day. Thanks for the links to the papers!

    @PGibbs: Life did indeed begin with something of a soupy brown fermenting mess. Would not attempt drinking it though!

    @curry and thinky: Thanks for the heads-up for the mistakes. Proofreading is something I need more practice at, but the odd little mistake I think adds to the flavour of the blog and reinforces the message that I am not an infallible god of science, but a person who occasionally writes too fast, thinks too slow, or has a grammar-fail. It is a personal blog after all, that aims to share a love and excitement of science rather than dictating unquestionable truths. Also yes, sometimes I am lazy :p

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  6. 6. rickbb 8:21 am 07/30/2012

    “learnt”, really? Is that really a word now? My high skool teecher was wrong, I two could have been a righter if only I’d learnt how.


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  7. 7. S.E. Gould in reply to S.E. Gould 9:11 am 07/30/2012

    Learnt is indeed a word, it is the past tense of the verb “learn” in British English.

    Just because something does not exist in American-English does not mean it isn’t a word. I know I sometimes make the odd mistake but this is not one of them.

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  8. 8. m 10:01 am 07/30/2012

    For cells to be as they are today, they must have been open layers in the past, that loosely tangled “A’s” and “B’s”, and new A and Bs joined when separated from the first in the slime. A+B.


    It is plausible the first “slime” covered “rocks” got broken and the slime formed the membrane enclosing some basic structure inside…really really tight, like a bubble.

    When this inside structure worked in one this new cell found a place when it drifted and attached and was integrated into another blob.

    The cell functioned but the membrane still allowed the chemicals A or B through, swelled, popped and the bubble reformed on 2 cells. Because bubbles like to reform into smaller bubbles.

    And so the cell was born.

    Be interesting if we can make the original slime and see it then form into a squished cell.

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  9. 9. em_allways_right 10:50 am 07/30/2012

    I believe that “learnt” is considered slang in the U.S. (but not in Britain). Since you are writing for an “American” (U.S.) publication you should have used “learned” in your title.

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  10. 10. S.E. Gould in reply to S.E. Gould 11:06 am 07/30/2012

    @m: Thanks for the comment. The current materials that form membranes (phospholipids) are already capable of forming little balls naturally in water. Chemical passage through the membrane is certainly important, but until you had materials that replicated in an organised fashion (like RNA) I don’t think you could call it a “cell”. The ability to create not just copies, but reliably similar copies of oneself is what started to drive the evolution of life.

    @em_allways: This is not an American publication, it is a personal science blog hosted on an American site. I appreciate that there are differences in the languages but I simply do not have time to go through every word I type every single week and check whether or not Americans use it. Learnt is an acceptable, commonly used, and grammatically correct word and I make no apologies for using it in my title.

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  11. 11. curiouswavefunction 1:40 pm 07/30/2012

    @em_allways: Actually Sci Am is now controlled by Nature Publishing Group, a British outfit whose headquarters are in London. This might imply that Lab Rat is one of the very people using correct English here. Sounds silly? Yes it is, hopefully you get the drift…

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  12. 12. Bill_Crofut 11:05 am 08/3/2012

    Re: “The atmosphere back then was very different, little oxygen and an abundance of carbon dioxide with plenty of methane being released into the atmosphere once the first life forms started eking out an entropy-defying existence.”

    A pair of geologists, in a critique of the Urey/Miller experiment, expressed their disagreement 3 decades ago:

    Geological evidence often presented in favor of an early anoxic atmosphere is both contentious and ambiguous. The features that should be present in the geological record had there been such an atmosphere seem to be missing….Ever since the work of Oparin…and the success of the experiments conducted by Miller…the dogma has arisen that Earth’s early atmosphere was anoxic, probably highly reducing…Conjecture and speculation, based on a knowledge of the chemistry of living matter, gave to them the composition of their starting materials, and it would have been surprising if they had not achieved the results they did.

    [Harry Clemmey and Nick Badham. 1982. Oxygen in the Precambrian Atmosphere: An Evaluation of the geological Evidence. GEOLOGY, March, p. 141]

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  13. 13. S.E. Gould in reply to S.E. Gould 11:49 am 08/3/2012

    @Bill: Thanks for the link, that looks like really interesting research. I’m not a geologist myself, but the evolution of bacterial respiration does seem to imply that anoxic respiration arose before oxidative phosphorylation. Whether the actual environment had oxygen or not at that point is clearly still the subject of study!

    A lot of the biochemist-geology work does seem to start from the composition of living organisms and their systems and extrapolate from that. I wouldn’t be surprised if the geological evidence didn’t quite match up. It’s really quite exciting that all this evidence from so many different disciplines can be used to start to piece together the information.

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  14. 14. shalamabobbi 2:44 am 12/22/2014

    As for the reducing atmosphere, this is marked by several things. The sudden appearance of iron oxide deposits and other compounds that only form in the presence of elemental oxygen are common examples. However, the most accurate “clock” we have for this is the shift in sulphur isoforms to those found in sulphur-oxygen compounds almost exclusively. Using these methods we can tell that the Earth had a non-oxidative atmosphere until as little as 3.5 billion years ago.

    You might be wondering why natural nuclear reactors at Oklo developed in uranium deposits only two billion years ago, when uranium-235 had already been depleted to less than 4% of uranium. Wouldn’t fission reactors have been even more likely to develop earlier in Earth’s history, when the uranium-235 levels were even higher? Remember that a high isotopic abundance of uranium-235 is just one of four conditions required for a natural nuclear reactor to develop. Another important condition is that uranium be concentrated. It turns out, no significant concentrations of uranium developed on Earth prior to about two billion years ago. The reason for this is simple: oxygen.

    In most rocks on Earth, uranium is present only in trace quantities (parts per million or parts per billion). Uranium is generally concentrated by hydrothermal circulation, which picks up uranium and concentrates it in a new hydrothermal deposit. In order for this hydrothermal circulation to concentrate uranium, that uranium must be soluble (able to be picked up in water). However, uranium solubility is a little tricky. When uranium is in its reduced form (U4+), uranium tends to form very stable compounds that are not easily brought into solution. However, when uranium is in its oxidized form (U6+), uranium easily forms soluble complexes. There was very little oxygen in Earth’s very early atmosphere. So, it would have been very difficult to concentrate a significant amount of uranium since there was no oxygen to transform uranium into its soluble forms.

    However, starting around 2.4 billion years ago, there was an event called the “Great Oxidation Event” during which the levels of oxygen in the atmosphere rose significantly, from <1% to ≥15%. This significant rise in atmospheric oxygen was a result of photosynthetic cyanobacteria producing oxygen. For awhile, the oxygen produced by these bacteria was taken up by minerals which became oxidized. However, when these minerals became saturated in oxygen, this oxygen began to accumulate in the atmosphere. This increase of atmospheric oxygen allowed uranium to become mobile and to be concentrated through hydrothermal circulation.

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