The Dinosaur Microbiome

nick longrich hat and bone
Dinosaur Bone in Dinosaur Provincial Park, with Estwing and Stetson

Life lives pretty much everywhere. In fact one of the most astonishing biological discoveries of the past century has been the discovery that the biosphere extends much further than we realized- into hot springs and hydrothermal vents, below Antarctic ice sheets… and miles underground. We tend to think of the subterranean world as being the realm of geologists, but in fact it’s the largest ecosystem on the planet- extending deep below the surface of the earth and the floor of the ocean.

 

So what does this have to do with paleontology? In recent years, we’ve seen some startling claims published about organic material preserved inside dinosaur bones- protein and protein-derived materials, DNA, even cells and tissues like blood vessels. Contamination is always an issue with these kinds of studies. Techniques designed to detect small amounts of DNA or protein from 75 million years ago must be incredibly sensitive- that also means that they’re sensitive to picking up biological material from you, the bacteria on your hands, a specimen in the lab, or what you had for lunch. As a result, rigorous protocols have been put in place to deal with contamination. But what if the contamination starts before the bone has even left the ground?

IMG_4334
Spotting a bone. Note the bright orange stuff- it’s a species of lichen.

Doing fieldwork in Dinosaur Provincial Park, in Alberta, I was always struck by the fact that a bright orange lichen sometimes grew on the bone- it was common enough you could actually use it to help find the bones in the field, like they were sprayed with dayglo orange paint. The lichen seemed to like the bone for some reason. For one thing, the bone was stable, whereas the muds and sandstones eroded away, so the lichen couldn’t grow there. It also had lots of moisture inside its spongy internal structure. And it was full of minerals, which a growing lichen needs. Living things actually used bone as a microhabitat. What’s more, when you peeled back the rock to expose the bone, you’d sometimes find sagebrush wrapped around it, probably feeding off the minerals. Which raises the question- why would we assume that bone is sterile? Why wouldn’t it be shot through with microbes- just the way the rocks around it are?

IMG_4331.JPG
Orange lichen growing on a dinosaur bone

In a new study, my colleagues and I (to be honest, almost entirely my colleagues) have been able to isolate DNA and amino acids from a dinosaur bone, dug up from Dinosaur Provincial Park in Alberta, in what must be one of the strangest dinosaur digs ever undertaken- since we weren’t hunting dinosaurs at all, but microbes living inside them. We excavated a bonebed of the dinosaur Centrosaurus, sterilizing tools with bleach, alcohol, and a blowtorch to prevent the introduction of contaminating bacteria, wrapping the bones in sterilized aluminum foil as soon as they were exposed, and then freezing them for later analysis in the lab. What we were able to show is that the organic material in these bones not ancient.
The DNA comes from bacteria. The most common thing is called Euzebya which is (don’t ask me why) found in odd places like Etruscan tombs and the skin of sea cucumbers. What’s more, the bacteria in the bone are at high densities- about ten times that of the surround rock. Bacteria don’t just work their way into the bone, they actively prefer living there.

longrich Centrosaur hook.JPG
The hook off of a Centrosaurus frill. This bone isn’t dead, but home to a community of microbes. 

 

 

The amino acids also show biological activity, since they’re mostly left handed. If you remember intro biology, the chemistry of all living things has a handedness. The individual amino acids that make up proteins can be in either a left-handed form, or a mirror-image, right-handed form. Living things exclusively make and use left-handed amino acids, but after they die, the amino acids slowly flip their symmetry back and forth, to convert to a 50:50 mixture of left- and right-handed forms- a process called racemization. Racemization takes thousands, not millions of years. So if we have amino acids from dinosaurs living millions of years ago, they should be fully racemized, a 50:50 ratio of left and right handed amino acids. But since the amino acids we found are mostly of the left-handed variety, that means the biological material is mostly very recent, not from the Cretaceous.

We also carbon-dated the material. Our atmosphere is full of trace amounts of carbon 14, a highly radioactive element with a half-life of around 6,000 years- that is, half of it undergoes radioactive decay and breaks down every 6,000 years. When plants and other organisms use C02 to build things, they (and anything they eat) incorporate that c 14. After death, they stop taking in new carbon 14, and the amount left halves every 6000 years or so. The upshot is that we can figure out how old stuff is by the amount of C 14 remaining- up until a limit of 50,000 years, at which point its basically all gone. Since dinosaur bones are more than 50,000 years old, any carbon 14 from the dinosaur era incorporated into DNA and proteins would have long ago disappeared. But we found a lot of carbon 14- meaning most or all of the material we isolated wasn’t from dinosaurs, but from recently living things.

All this points in the same direction- the bones are in a very real sense alive. They host a thriving bacterial community, a microbiome, and the amino acids and proteins we isolated were primarily recent. Some of the material is a bit older- there are some right-handed amino acids, and the carbon 14 ratios are a bit lower than you’d expect on a modern living thing- so it does seem that there are some older organics in there. But whether they are thousands of years old, or millions, we don’t know.

What does this mean for dinosaur DNA and proteins? Well, it’s too soon to say, but it’s one more reason for skepticism. Currently, the record for the preservation of DNA is a genome extracted from a 750,000 year old horse. DNA has a relatively short half-life, about half the DNA breaks down every 500 years, so it’s thought to become unreadable after about 1.5 million years even under optimal conditions. It’s extremely unlikely we can get Jurassic DNA from 150 million years ago, or even DNA from the much younger T. rex, which went extinct a mere 66 million years ago.
Proteins appear to be more robust than DNA, however, protein also tends to break down over time, with water molecules breaking apart the bonds between amino acids. The oldest confirmed proteins are about five times older than the oldest DNA: protein sequences from ostrich eggshell have been recovered going back almost 4 million years. Which is not to say that organics can’t survive from dinosaurs- we’ve been able to isolate pigments, for example- but we need to be a little skeptical. How and whether things like cells and vessels can survive that long isn’t entirely clear.

Clearly some organics do survive- actually a lot of stuff. Sporopollenin, for example, is a biopolymer that makes up the wall of pollens and it is an incredibly robust molecule. It’s nigh-invulnerable, to the point that you can dissolve rock in concentrated acids and all that remains are little 75 million year old pollen grains from the Cretaceous. So we can get pollen grains from dinosaur age sediments. We can also recover organic-walled fossils like dinoflagellates.

Personally, I’m mostly a morphologist- I don’t have the expertise to critically evaluate finer points of debates about organic chemistry. But I can say that extraordinary claims require extraordinary evidence. The claims of DNA and protein isolated from dinosaurs are far, far older than anything else. Importantly, these finds have been difficult to replicate. And there’s a lot of contamination down there. That some kind of heavily altered protein- basically fossil protein– might remain seems more plausible. I’m not saying it doesn’t exist. I don’t know. But there’s a lot of other stuff down in the subsurface community- not just bacteria, but archaeans, eukaryotes, multicellular organisms like fungi, nematodes. Before we identify ancient traces, we need to be able to rule out contamination, and contamination is going to be everywhere. But by getting a better handle on what that contamination looks like, we can at least do a better job telling the contamination from the original organics.

But  I also think the microbiome is fascinating in its own right, not just an annoying contaminant. It’s interesting to think about what it says about the evolution of life on our planet. It’s bizarre to think, but dinosaurs didn’t stop interacting with the environment when they died, they just did so in a different kind of way. After that Centrosaurus died, it was food for scavengers- tyrannosaurs, dromaeosaurs, pterosaurs, beetles and flies. Then the skeleton was buried underground, and bacteria continued to eat away at the proteins. After thousands of years, it was part of the subsurface microbiome. Then the Western Interior Seaway rolled in, and it was part of a deeper microbiome existing under the bottom of the ocean. Then it rolled back out again after the dinosaurs died out, thousands of feet of sediments were piled up, and the Centrosaurus bone was part of a deep biome, far underground. At last, the glaciers came through, ground the land down, and an ancient glacial lake burst, gouging out the badlands that would become Dinosaur Provincial Park. From the time that Centrosaurus died up until now, it has seen a succession of microbial communities- on a Cretaceous floodplain, then underneath it, then under a sea, then under a glacier, and at last, just below the prairies of Alberta. It’s amazing to think that the life of the past still affects the life of today- as Faulkner put it, the past isn’t dead, it isn’t even past.

nick longrich - more lichen bone
A piece of fossil wood hosts a diverse community of lichens. 

There’s a good writeup of the paper here in the Atlantic by Ed Yong.

The original paper is here: Saitta, E.T., Liang, R., Lau, M.C., Brown, C.M., Longrich, N.R., Kaye, T.G., Novak, B.J., Salzberg, S.L., Norell, M.A., Abbott, G.D. and Dickinson, M.R., 2019. Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities. eLife8, p.e46205.

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