Up to now, the oldest rocks known to contain living bacteria—microorganisms that were alive since the rock were formed—were sediments from about 100 million years ago. Now, a group of researchers from South Africa, Japan, and Germany report finding living bacteria in rocks 20 times older than that: over two billion years ago. And those bacteria were alive, and presumably dividing.
This finding, published in Microbial Ecology, suggests that if there was once life on Mars, one might be able to find its remnants by examining rock samples the way these researchers did.
The paper can be accessed by clicking on the screenshot below. You can also find a pdf here and a short New Scientist article about the discovery here.
The details: the researchers drilled into 2-billion-year old igneous “mafic rocks” in the Bushveld Igneous Complex of South Africa, described by Wikipedia as “the largest layered igneous intrusion within the Earth’s crust“. Drilling down 15 meters using a special drilling fluid to lubricate and cool the drill bit, they extracted a 30-cm (about 12-inch) core of rock with a diameter of 8.5 cm (3.3 inches). They then carefully cut into this core, making sure not to contaminate it with modern bacteria.
Here’s a photo of part of the Bushveld intrusion showing the igneous rock (see caption for details:
Remember that igneous rock is formed when other rock is melted by extreme heat and then cooled. As this rock cooled, there were cracks in it that were filled with clay during the process, and, when the rock was solid, the clay was impervious to further intrusions. In other words, the clay in the rock cracks were 2 billion years old. But was the clay and its inhabitant bacteria that old? (See below.)
What they found. To test whether what they saw in the cracks (bacteria!) were really original, 2-billion-year-old bacteria rather than organisms that had entered the rock after formation or were contaminants during the drilling or handling, the authors dissolved tiny fluorescent microspheres in the drilling fluid, spheres smaller than bacteria. Tests showed that although the microspheres were visible in the fluid sample, they were not seen within the rock (of course the researchers took great care to not contaminate the rock either during extraction or when it was cut and examined). Here is their schematic of how the cores were extracted and handled (figure from the paper). Note the flaming to kill anything living on the outside of the core (click all figures and photos to enlarge them):
Here is a fluorescent sample of drilling fluid (on the left), showing many microspheres, and a sample of the rock showing DNA-stained bacteria on the right, which appear as green rods. The scale is the same, so you can see that the microspheres are smaller than the bacteria:
The presence of living organisms (at one time) in the cracks was also confirmed by finding “amides I and II,” which, say the authors “are diagnostic for proteins in microbial cells.” The New Scientist paper adds that the cell walls of the bacteria (if they are indeed “bacteria”!) were intact, which, says author Chen Ly, is “a sign that the cells were alive and active”.
What did the bacteria eat? The paper’s authors say that “indigenous microbes are immobile and survive in the veins by metabolizing inorganic and/or organic energy available around clay minerals.” They do add that there is doubt about the ages of the clay cracks, as they might actually have been formed much more recently than two billion years. Both the paper and the NS blurb are careful not to say that the bacteria have actually been in the rocks for two billion years, but that seems to be the tacit assumption.
Here are two photos from the paper of one of the bacteria-containing cracks. The color indicates, say the authors, spectra from silicate minerals and microbial cells
The upshot and implications: These are by far the oldest rocks even seen to contain indigenous (rather than externally-derived) living organisms, presumably bacteria. It’s not 100% clear that the organisms are themselves 2 billion years old, but the assumption here is that they are. New Scientist floats the idea that we should do this kind of analysis to look for life on other planets, most notably Mars:
This discovery may also have important implications for the search for life on other planets. “The rocks in the Bushveld Igneous Complex are very similar to Martian rocks, especially in terms of age,” says Suzuki, so it is possible that microorganisms could be persisting beneath the surface of Mars. He believes that applying the same technique to differentiate between contaminant and indigenous microbes in Martian rock samples could help detect life on the Red Planet.
But they quote one critic who asks the same questions I do above, and insists that the bacteria aren’t as old as the rocks. (For one thing, bacteria couldn’t survive in an igneous rock when it was very hot during formation.)
“This study adds to the view that the deep subsurface is an important environment for microbial life,” says Manuel Reinhardt at the University of Göttingen, Germany. “But the microorganisms themselves are not 2 billion years old. They colonised the rocks after formation of cracks; the timing still needs to be investigated.”
Questions that remain:
1.) Are the bacteria themselves two billion years old? I’m not sure how they would investigate this if the clay could have entered the rock and then been sealed into the cracks a long time after the igneous rock was formed.
2.) If the bacteria that old, were they dividing during that period? I don’t see any mention of seeing dividing cells, and the authors say that the cells were effectively trapped in the clay. If so, could they still divide, or are we seeing the original bacteria, perhaps two billion years old and still kicking? This raises another question:
3.) Were the bacteria “alive” during this period? If they were really metabolizing over this period, then yes, they were alive. But if their metabolism was completely shut down, what do we mean by saying they were alive? The NS piece says that the presence of cell walls means that the bacteria were “alive and active”, but is that really true?
4.) Finally, if these things had stainable DNA, can it be sequenced? It would be interesting to get the DNA sequences of these bacteria, which they’d presumably have to do by culturing them. Although we now have methods to get the DNA sequence of a single bacterium by sequencing its RNA transcripts (see this report), you’d have to pry the bacteria out of the clay to do that. And if you can get the sequence, does it resemble that of any living bacteria, or are these ancient forms very different from today’s microbes? (If they do resemble modern bacteria—for evolution would be very slow when cell division takes millions of years—then perhaps we could culture them.)
The biggest question, of course, is #1 above. I’m hoping that these things really are two billion years old, for what we’d then have is a very, very ancient bacterial culture. But I’m very dubious that we’ll find bacteria in Martian rocks.
h/t: Matthew Cobb, for alerting me to the relevant. tweet
Astonishing!
Thanks for pointing this out!
Well that is really cool. But it seems more likely that the bacteria are descended from bacteria that infiltrated into the cracks. The only way I know to assess their age is with radioisotopes, but that seems very difficult.
I am just a lay observer who tries to read some well-vetted authors’ trade publications, but I think it was Nick Lane and the late Tommy Gold who got me thinking about underground, not the Earth’s surface as a default location for first life.
+1
I read a highly abbreviated report of this the other day, but yours is the most detailed I’ve yet read, which spurred me on to read the original article.
To me the big question is whether the bacteria represent a 2 billion-year-old colony or not. Since the bacteria were not present in the original igneous rock, they must have gotten into the rock at some point more recently than at the time of the rock’s formation. How can that happen? It happens when cracks form in the rock that allow groundwater in. The bacteria come in with the groundwater. Depending on the permeability of the rock, groundwater may even be able to get in without the formation of cracks—if there are tiny spaces between mineral grains through which liquids can percolate. (Mafic plutonic rocks are pretty low permeability, so I would expect that the bacteria originally got into the rocks via cracks.)
Now, cracks can form in many ways. They can form during the original cooling of the melt, or they can form later as the result of other disturbances: heating/cooling events, mountain-building events, or simply erosion (which reduces the pressures holding the underlying rocks together, allowing them to fracture when they become unloaded).
Two billion years is a very long time, so there could have been many generations of fracturing and reforming of the rocks and many opportunities for bacteria to enter. The challenge for the researchers is to rule out such later events. Clues in the rocks—e.g., cross-cutting relationships among cracks—can help them figure things out.
+1
Zeolites come to mind
The precise structure of the “rock” becomes critical to understand for this – as Dawkins sort of pointed out once, a rock has lots of space in it for similarly small moieties to as you say percolate.
Another thought is prebiotic fiber like inulin – lettuce – in the gut forms a substrate for bacteria to grow well – perhaps as the case here, structurally.
Maybe a simpler, younger rock should be tested the same way – a sedimentary rock made without heat (and pressure?) in which numerous bacteria were encased during formation – not by later infiltration. If microbes just millions of years old could be found in such rock then it isn’t so hard to accept ones billions of years old.
Maybe the clay-filled fissures are a key environment though and being otherwise trapped in rock doesn’t cut it, survival- and evolution-wise.
I have to believe that the particular bacteria seen are descendants of bacteria isolated in the fissures billions of years ago. But if they are cells that old I think putting them in a skin cream would be a winner.
Thank you for the sober skepticism.
I have to say that my immediate reaction is of scepticism but for the sake of argument let’s suppose that the claim is true – that there is a population of archaea that is either 2 billion years or is descended from that population, and here is the clincher: that population has been isolated from “mainstream” evolution during that period. The consequences are huge: the biochemistry of the archaea would be seriously different from today’s. I am not sure when the TCA cycle first evolved but it must have been around then – both oxidative and reductive cycles – and it would have been before the Great Oxidation Event.
There would be serious differences in the biochemistry. Maybe Bill Martin’s deep sea vents might give a clue.
Archaea aren’t bacteria, and I read that “it is now generally accepted that Archaea evolved from bacteria and not the other way around as originally thought for a very long time.”
(Source: https://pmc.ncbi.nlm.nih.gov/articles/PMC8066391/)
To add to the questions: if the bacteria are 2 billion years old, and were alive for that time, where did the energy they needed to metabolize come from? They probably didn’t need a whole lot, but 2 billion years is a damn long time to survive on essentially nothing.
I’m skeptical too. If these bacteria were even a billion years old and actively metabolizing, wouldn’t they hollow out the rock by consuming its minerals? What is their carbon source to make the deoxyribose of DNA and proteins, carbonate? It seems highly unlikely that these rocks are an impermeable time capsule without water seepage bringing in necessary materials for life (like the undersea hydrothermal vent niche).
I wish publications like this wouldn’t get published until the researchers at least established the bacteria were quite old or different from many modern bacteria (or those sampled from the exterior of the rocks or soil) even if by some sequencing. I’ve read countless hype articles about microfossil-looking structures on Mars (not) or arsenate used in place of phosphate in a few places to make DNA strands (so what?), etc.
Maybe the only story here is: 2 billion year old rocks contain bacteria from the immediate area that aren’t old, in which case, this work is not publication worthy and a waste of everyone’s time
The original article doesn’t mention finding cell walls and doesn’t make any finding that the bacteria were “alive.” I can’t therefore make anything of the statement in the New Scientist story that the researchers determined this. SYBR Green I, which they used to stain the bacteria to see them under fluorescence microscopy, is a DNA stain. It intercalates into the spaces between the flat planar DNA bases, much like the potentially more dangerous (because mutagenic) ethidium bromide that many of us used earlier in our scientific efforts.
Point being that the technique does not stain cell-wall material and their electron microscopy didn’t detect any bacterial ultrastructure of any kind. (The EM was of the mineral elements.) I also can’t accept the assertion made by NS that persistence of cell wall material (if detected) would prove that the organism was alive. That doesn’t follow. Plasma membranes rapidly become disordered and disintegrate when ATP is no longer being produced but cell-wall material such as peptidoglycan persists around dead bacteria until something comes along to chew it up for recycling. Continuing incorporation of precursors into the anatomic structure of a cell wall — something that can be shown with radiolabeling — is one of the metabolic tests that would prove that someone is alive in there.
It is most interesting that DNA arranged in shapes consistent with bacterial cells has been found in these old rocks. But I remain skeptical of the New Scientist‘s claims.
I don’t buy the argument that they have to culture the bacteria to gain sequnece information. 16s rRNA sequences should be amplifiable and the geomic DNA could be amplified by strand-displacement DNA polymerases. Isn’t this what is actually done in meta-genomic environmental studies?