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Is This Spindly Fossil a 3-Billion-Year-Old Eukaryote?

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


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One of the planet's former dominant species? A proposed microfossil from Western Australian Quartzite. To preserve the detail in this image in the space I have, I cropped the image and moved the scale bar, but preserved its proportion to the image. Any resemblance to a dreidel is purely coincidental. I think. Image by Christopher H. House; Pennsylvania State University. Click for source.

“Surprisingly Large and Complex” 3 Billion Year Old Fossil ID’d as ex-Plankton

Eukaryotes may not be the most abundant organisms on earth (that would be viruses, if you count them as alive), or the most ancient (bacteria and archaea are surely Eldest), but they have given Earth its most structurally entertaining passengers. Pterodactyls, anglerfish, slime molds, kelp, monkey puzzle trees, sloths, shih-tzus, and Humongous Funguses are all descendants of the first cells to package their DNA in a tidy compartment called a nucleus.

Of course, it’s not simply the nucleus that made the difference — it also has something to do with the Super-Friends-like team of specialized cell compartments called organelles that cohabit the eukaryotic cell. Whatever the reasons, Domain Eukaryota has been an unqualified Earth success.

This success has understandably inspired a lot of curiosity on the part of biologists about how and when the eukaryotes evolved. It’s looking increasingly likely that life appeared on Earth almost as soon as it could — perhaps just a few hundred million years after the planet formed, well over 4 billion years ago. This life probably resembled today’s bacteria and archaea (collectively known as prokaryotes). But whence the eukaryotes? Guesses of their age range from 1 billion to 3.5 billion years. But finding the bodies to substantiate these claims has proved difficult, given the range of unfortunate fates that rocks of a certain age may suffer, few of which result in the deposit of any incriminating fossils at the business end of a microscope.

Another World, Another Time

Enter the suspiciously organic-looking, spindle-shaped structure pictured above. In a recent article in Geology, scientists describe it as “surprisingly large and complex”. There are many others like it, and they range from 20 to 60 micrometers in diameter — about the size of many fungal spores, at least twice as big as a red blood cell, and dozens of times larger than most bacteria. In addition to their prickly spindles, they also possess flanges and net-like internal structures. But here’s the kicker: the rock they’re embedded in is about 3 billion years old.

Imagining what Earth was like 3 billion years ago is *tremendously* fun for a bio-nerd (what did the land look like then? What were the seas filled with? What color was the sky and the ocean? Would it have smelled funny? Would we have recognized it as Earth?), so finding any evidence of what the old homeplace and its occupants actually looked like waaaaaaaay back when is understandably exciting.

What makes it more exciting is this: if it turns out that this microfossil really is an ex-organism, its size and complexity suggest it could be among the first eukaryotes (this is not suggested in the Geology paper, though it has been in others) . If so, it would push eukaryotic origins back to well over 3 billion years. Old, to be sure, but still within the realm of possibility.

It’s worth nothing, however, that giant bacteria are not unknown. The current record holder is Thiomargarita namibiensis, which measures hundreds of micrometers in diameter. Bacterial resting structures like spores or cysts can also reach prodigious size. Such defensive structures may have been useful on an early Earth subject to intermittent cosmic blows capable of generating “nearly planet-sterilizing heat”, the authos of a paper in Astrobiology have suggested.

But how can we be sure these really are expired cells and not some sort of faux fossils made of organic schmutz accumulated around or within mineral crystals? That is precisely what the the team of scientists from Pennsylvania State, NASA’s Johnson Space Center, and Nagoya University who published in Geology last week set out to discover.

CSI: Carbon

To do so, they turned to carbon isotopes, although not the carbon isotopes you may be thinking of. Isotopes are chemical element variants containing different numbers of sub-atomic particles. Carbon, with 6 protons in its nucleus, can also have 6, 7, or 8 neutrons: carbon-12, -13, and -14 respectively. Only carbon-14 is radioactive, and once incorporated from the atmosphere into wood or rock, decays steadily. Carbon dating uses these isotopes as a proxy for age. But with a trifling half-life of about 5,730 years, carbon-14 is long, long gone in 3-billion year old rocks.

Instead, the scientists relied on the ratio of the two non-radioactive forms of carbon: carbon-12 and carbon-13. The carbon-capturing enzymes of light-harvesting microbes prefer grabbing carbon dioxide containing carbon-12. So we would expect that if the putative fossils are enriched in carbon-12 with respect to the rock around them, then odds are they are not some sort of artifacts made from the surrounding organic debris. In that case, we’d expect the carbon ratios to be similar.

The team sampled bits of rock (presumably, very carefully) from inside and outside the suspicious shapes. And they found that, indeed, rock bits extracted from inside the putative fossils were depleted in carbon-13 with respect to the surrounding rock. They further suggest that the organisms were free-floating plankton, because the spindles’ uniformly low levels of carbon-13 would not be expected in an environment where carbon dioxide — and thus the organisms’ ability to be choosy about their source of carbon — was limited. They could not, however, rule out the possibility that the organisms were making or eating methane, since those organisms have a range of carbon-13 to carbon-12 ratios.

Similar fossils have been found before, they said, in the ~3.4 billion year old Strelley Pool rock formation, also of Australia, and the ~3.4 billion year old Onverwacht rock group of South Africa. If these structures are indeed related, the scientists suggest the spindle-shaped organisms could “represent the remains of a cosmopolitan biological experiment that appears to have lasted for several hundred million years.” In other words, Earth’s seas were filled with these microbes for hundreds of times longer than humans have been on the planet. And then, after a good long run, they went extinct or evolved into something else.

And Then Again . . . Maybe Not

Also this week, scientists reported a new calculation in the Proceedings of the National Academy of Sciences of the age of mitochondria and chloroplasts — two eukaryotic organelles that began as free-living bacteria, got swallowed by the proto-eukaryotic cell, and somehow escaped digestion. They would become cell partners called “endosymbionts” that would fuel (quite literally) the eukaryotic rise to power.

The University of Washington team of Patrick Shih and Nicholas Matzke based their analysis on duplicated subunits of an important protein called ATP synthase and another called “elongation factor thermo unstable“. They took advantage of the idea that gene duplications and endosymbiosis that occur in a common ancestor can act as calibration points for gene clocks in their various descendants. According to their calculations, the two endosymbioses appear to have happened relatively recently: around 1.2 billion years ago for the mitochondrion, and 900 million years ago for the green chloroplast.

That could cast doubt that the spindle-shaped organism is a eukaryote. Or maybe not. Who knows how long it took to go from 100% prokaryote to the eukaryote that was the last common ancestor of the Domain today? With so many moving parts, the eukaryotic cell could have spent millennia in a transitional state (a proto-eukaryote?) before it became the full-fledged super-organism that would be the ancestor of the planet’s entire over-1 mm crowd.

References
House C.H., Oehler D.Z., Sugitani K. & Mimura K. (2013). Carbon isotopic analyses of ca. 3.0 Ga microstructures imply planktonic autotrophs inhabited Earth’s early oceans, Geology, 41 (6) 651-654. DOI:

Shih P.M. & Matzke N.J. Primary endosymbiosis events date to the later Proterozoic with cross-calibrated phylogenetic dating of duplicated ATPase proteins, Proceedings of the National Academy of Sciences, DOI:

Oehler D.Z., Robert F., Walter M.R., Sugitani K., Meibom A., Mostefaoui S. & Gibson E.K. (2010). Diversity in the Archean Biosphere: New Insights from NanoSIMS, Astrobiology, 10 (4) 413-424. DOI:

Jennifer Frazer About the Author: Jennifer Frazer is a AAAS Science Journalism Award-winning science writer. She has degrees in biology, plant pathology/mycology, and science writing, and has spent many happy hours studying life in situ. Follow on Twitter @JenniferFrazer.

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





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  1. 1. phalaris 2:20 pm 06/27/2013

    Highly interesting. But don’t forget the fate of poor Schopf, and the insistent critics of evidence of early life (including of isotope ratios).

    http://sandwalk.blogspot.de/2009/09/did-life-arise-35-billion-years-ago.html

    Link to this

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