Ancient Microbes Spring to Life After 100 Million Years Under the Seafloor

Ancient Microbes Spring to Life After 100 Million Years Under the Seafloor
Magnified image showing microbes revived from 101.5-million-year-old sediment. (Image: JAMSTEC)

Scientists have revived microbes found deep beneath the seafloor in 100-million-year-old sediment, dramatically expanding our view of where life exists on Earth and for how long.

An international team of scientists led by geomicrobiologist Yuki Morono from the Japan Agency for Marine-Earth Science and Technology has revived microbes pulled from energy-poor seafloor sediments dated to 101.5 million years ago. Under laboratory conditions, these microbes sprung back to life, munching on food and multiplying. After enduring low-energy conditions for millions of years, these microbes — a type of bacteria — still managed to “retain their metabolic potential,” according to the new research, which was published today in Nature Communications.

“Once again, this new study extends our view of the habitable biosphere on Earth and the ability of microbes to survive under suboptimal conditions,” Virginia Edgcomb, a geologist from the Woods Hole Oceanographic Institution who wasn’t involved in the new study, said in an email. “It also extends our view of where viable microbial life contributes to carbon and other nutrient turnover in the deep biosphere.”

Previously, scientists said they had recovered and revived bacterial spores from 250-million-year-old salt crystals found in the Permian Salado Formation in New Mexico, but some experts disagreed with this conclusion, saying the samples were contaminated, among other issues. In 1995, scientists revived a bacterial spore from a bee preserved in amber dated to between 25 million and 40 million years old.

The microbes revived in the new study are from the oldest marine sediment samples ever studied, explained Morono in an email. Also, the researchers “directly saw microbial revival through incorporation of added nutrients,” and a large fraction of the microbes “were not spore-forming microbes,” he added. In this case, the awakened microbes immediately went about their microbial business, consuming food and engaging in cellular division. Bacterial spores, on the other hand, must transition back to a reproductive state.


The sediment samples containing the microbes were extracted 10 years ago at the abyssal plain in the South Pacific Gyre. These samples were pulled from depths reaching 75 metres beneath the seafloor and dated to 13 million to 101.5 million years old. Some oxygen was detected in these deep layers, but virtually no organic materials like carbon (i.e. food for microbes).

This part of the ocean contains some of the clearest water in the world, owing to low concentrations of sea surface phytoplankton, which normally sink and supply food to sub-seafloor microbes. Because marine snow, as it’s called, is so light in this region, the formation of the seafloor sediment is exceptionally slow, forming at a paltry rate of around 1 to 2 meters every million years. The main purpose of the new study was to see if life could live in such a nutrient-starved environment, and if so, for how long these microbes could survive with practically no food.

Map showing locations of sampling sites. (Image: Y. Morono et al., 2020) Map showing locations of sampling sites. (Image: Y. Morono et al., 2020)

Back at the lab, these microbes were incubated and given a steady diet of isotope-labelled substrates comprised of carbon and nitrogen. An extremely important aspect of the study was to track the microbial consumption of these added foods, hence the stable isotope-labelled substrates.

Within this cosy laboratory setting, the microbes, including those pulled from the oldest sediment samples, responded almost immediately. Over the course of 68 days, the researchers watched in amazement as populations increased in size by more than four orders of magnitude. Upwards of 99% of the microbes found within the samples sprung back to life, in a result that even shocked the scientists.

Deep beneath the seafloor, “nutrients are very limited,” so the microbes were “almost at the state of ‘fasting,’” said Morono. “So it is surprising and biologically challenging that a large fraction of microbes could be revived from a very long time of burial or entrapment in extremely low nutrient/energy conditions.”

Using DNA and RNA gene profiling, the researchers identified the microbes as aerobic, or oxygen-loving, bacteria. The authors also ruled out potential contamination, saying there’s virtually no permeability between the thick seafloor layers.

Sediment sample. (Image: JAMSTEC) Sediment sample. (Image: JAMSTEC)

Jennifer Biddle, an associate professor from the School of Marine Science and Policy at the University of Delaware, saw no issues with contamination.

“In fact, were I given a precious sample of Martian material with which I could conclusively prove evidence of life on another planet, I would give it to Yuki Morono,” said Biddle, who wasn’t involved with the new research.

These microbes “were likely buried” within the South Pacific Gyre sediments, and “they or their descendants have persisted there since that time,” said Edgcomb. Either these microbes were in a state of suspended animation, or the “original cells were able to divide occasionally since they were buried, and they are looking at the nth [indeterminate] generation of the original cells,” she said. Edgcomb said open questions remain as to “how long different types of microorganisms can survive in a quiescent state without dividing.”

Reviving ancient microbes sounds a bit scary, given what we don’t know about ancient germs. When asked about the risks and any safety precautions that were put in place for the experiment, Morono said “subseafloor sediment is regarded as at low risk for health, since no infecting host, like a human, exists in this environment.” However, “we have been handling the microbes at all times in the clean room” and all specimens were kept in a lab — a biosafety level 1 environment — for the whole time.

Edgcomb didn’t have issues with safety, saying: “As a marine microbial ecologist, I don’t see any safety concerns in the experiments they conducted.”

As to how these microbes were able to stay in a state of hibernation for so long, Morono said he’s not sure, but he hopes the new findings will “stimulate discussions on this topic” and ultimately an identification of the survival mechanisms required for the microbes to stay dormant across such vast geological timescales.

“What is really surprising about this study is that this sediment has oxygen in it. As we all strive to have diets full of antioxidants, we know oxygen is an agent of degradation, so having long-term survival in it is impressive,” said Biddle. “However, we don’t know what the cell is actually seeing in the sediment; there may be small cages of low-oxygen habitat that enhance survival.”

The new study also reinforces the importance of organic carbon as a food source for microbes living beneath the seafloor — a regrettable finding, as far as Biddle was concerned.

“It’s a bit disappointing, considering that we are finding out time and time again that the subsurface is reliant on the surface for its food,” said Biddle. “I still await the self-reliant subsurface sedimentary microbe!”