Collagen is the structural backbone of animal bodies. It weaves through skin, muscle, organs and connective tissue, giving even the squishiest organisms a measure of internal scaffolding. In the absence of enzymes capable of cutting it apart, collagen is remarkably stubborn. Philip Vixseboxse, lead author of the study, who completed the work as a PhD candidate in Cambridge’s Department of Earth Sciences, compares it to modern plastic: a biopolymer that simply sits there until something evolves the biochemical machinery to digest it. Once an organism dies, however, and collagen-degrading enzymes known as collagenases are present, that scaffolding can be dismantled rapidly, collapsing the tissues long before sediment can entomb them in a form capable of surviving hundreds of millions of years.

The contrast between eras is what makes the new findings so compelling. During the late Ediacaran Period, between roughly 579 and 539 million years ago, Earth hosted its first known communities of complex animal life. None of these organisms possessed hard parts, yet at sites around the world their fossils are preserved with extraordinary fidelity — in some places entire ecosystems, complete with the soft anatomy of animals that would otherwise have left nothing behind. For decades, researchers have wrestled with how this was possible. Proposed explanations have included unusual ocean chemistry, distinctive tissue compositions in Ediacaran animals, and the presence of a pervasive microbial mat or slime layer that blanketed the seafloor and sealed remains beneath it. Each of these mechanisms can account for preservation at particular localities, but none of them works universally, and the debate has remained unresolved.

To test whether biology itself might hold the answer, Vixseboxse and his colleagues turned to genomics. They traced the evolutionary history of collagenase genes across 700 bacterial genomes and mapped those genes onto a time-dated tree of life, allowing them to reconstruct when and in which microbial groups the ability to degrade collagen first appeared and then spread. The results revealed that collagenases are far older than animals themselves. Crucially, however, the earliest collagenases belonged exclusively to anaerobic microbes — organisms that cannot tolerate oxygen. In the oxygenated waters of the Ediacaran oceans, that limitation mattered enormously.

The logic of the preservation window follows directly from that biochemical constraint. When an Ediacaran animal died and sank into the sediment, aerobic decay processes would consume the oxygen in the surrounding sediments relatively quickly. Once that oxygen was gone, the anaerobic collagen-degrading microbes could go to work — but only slowly, and only after a substantial delay. In the interim, the animal’s collagen-rich tissues remained intact, giving mineralisation and impression-forming processes time to operate. In effect, the microbial community of the Ediacaran seafloor imposed a built-in lag between death and destruction, and that lag was exactly what fragile, soft-bodied animals needed to enter the fossil record. The ‘bags of goo’ of the Ediacaran were, paradoxically, protected by the very limitations of the microbes that would eventually consume them.

That protection did not last. As the team’s genomic timeline shows, around the transition between the Ediacaran and Cambrian Periods, collagenase genes began to spread far more widely through the microbial world. Through horizontal gene transfer, the enzymes moved into a much broader range of bacterial groups, including aerobic bacteria — the oxygen-using microbes that drive much of the decay we observe today. Once collagen degradation became possible in oxygenated environments, the protective lag disappeared. Tissues could begin breaking down immediately after death, in oxygen-rich settings, dramatically shortening the window in which fossilisation could occur. This shift, the researchers note, coincides with a pronounced decline in the abundance and quality of soft-tissue fossils in the rock record.

‘Around this critical time where these soft-bodied animals stopped fossilising, we start seeing the appearance of collagenases in aerobic bacteria, meaning the ability to break down collagen-bearing tissues could start to spread into new environments as animal diversity accelerated,’ said Vixseboxse. ‘Now that collagen could be degraded, you needed ever-faster fossilisation processes to outpace decay, which is likely why we start to see a big drop in the abundance and quality of the fossil record, in terms of the preservation of soft tissue.’ The timing is significant because the Cambrian was also the period in which animal diversity exploded, filling the oceans with new body plans and, implicitly, with vastly more collagen — a fresh and abundant food resource for any microbe equipped to exploit it.

The new model does not mean that soft tissues vanished from the fossil record entirely after the Ediacaran. Exceptional circumstances can still deliver exquisite preservation in younger rocks, and palaeontologists have documented many such Lagerstätten, from the Burgess Shale to Chengjiang. The key variable, according to the study, is speed. An animal buried almost instantaneously — beneath an avalanche of sediment triggered by a storm or a slump, for example — can be sealed away from oxygen and decay agents before its collagen is dismantled. But such rapid burial is inherently rare, which is why soft-tissue fossils from the Cambrian onward are celebrated exceptions rather than the norm. The baseline probability of preservation collapsed once aerobic collagen degradation became widespread.

‘These results suggest there may be an overarching biological mechanism that has shaped the fossil record of soft tissues across Earth’s history,’ said co-author Professor Alex Liu, also of the Cambridge Department of Earth Sciences. ‘The acquisition of key enzymes by microbes to exploit a growing food resource may have decreased the preservation potential of soft tissues.’ Framed this way, the gaps in the fossil record are not simply an artefact of incomplete sampling or unlucky geology. They reflect an evolutionary arms race of sorts: as animals diversified and flooded the environment with collagen, microbes evolved the tools to exploit it, and in doing so they rewrote the rules of what could survive the passage of deep time.

The study, published in the journal Current Biology, also carries a provocative modern echo. Vixseboxse points out that plastic behaves in the environment much as collagen once did — a persistent biopolymer that accumulates because nothing has yet evolved to break it down efficiently. ‘Bacteria had no reason to efficiently degrade collagen when it didn’t exist,’ he said. ‘But once collagen became more abundant, and provided a new food source for these microbes, collagenases proliferated. Perhaps someday, microbes will exploit similar enzymes to break down the increasing abundance of plastic polymers we are putting into the environment, but that will be long after we’re gone.’ The research was supported in part by the Leverhulme Trust, the Natural Environment Research Council and the Biotechnology and Biological Sciences Research Council, part of UK Research and Innovation. If the analogy holds, the same evolutionary logic that erased the soft-bodied Ediacaran world may one day reshape the Anthropocene’s most durable litter — a reminder that in biology, no polymer stays indigestible forever.

Subject of Research: Evolution of microbial collagenase enzymes and its impact on the preservation of soft-bodied animals in the fossil record

Article Title: Rise of collagen-eating microbes may help explain gaps in the fossil record

Article References: Rise of collagen-eating microbes may help explain gaps in the fossil record. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: fossil record, collagen, collagenase, Ediacaran, Cambrian, soft-tissue preservation, microbial evolution, palaeontology, taphonomy, bacteria, University of Cambridge, Current Biology