Ancient microbes come to life after 100 million years under the seabed

Enlarged image showing revived microbes from sediments 101.5 million years old.

Enlarged image showing revived microbes from sediments 101.5 million years old.

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

An international team of scientists led by geomicrobiologist Yuki Morono of the Japan Earth and Sea Science and Technology Agency has revived low-energy microbes extracted from seafloor sediments dating back 101.5 million years ago. . Under laboratory conditions, these microbes came back to life, chewing 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 investigation, which was published today in Nature Communications.

“Once again, this new study expands our view of Earth’s habitable biosphere and the ability of microbes to survive in suboptimal conditions,” said Virginia Edgcomb, a geologist at the Woods Hole Oceanographic Institution who was not involved in the new study. in an email “It also expands our vision of where viable microbial life contributes to the turnover of carbon and other nutrients in the deep biosphere.”

Scientists previously said they had recovered and revived 250 million-year-old bacterial spores of salt crystals found in the Permian Salt Formation in New Mexico, but some experts in disagreement With this conclusion, say that the samples were contaminated, among other issues. In 1995 scientists revived A bacterial spore of a bee preserved in amber that dates back 25 to 40 million years.

The revived microbes in the new study come from the oldest marine sediment samples ever studied, Morono explained in an email. Furthermore, the researchers “directly saw microbial reactivation by incorporating added nutrients,” and a large fraction of the microbes “were not spore-forming microbes,” he added. In this case, the awake microbes immediately went about their microbial business, consumed food, and participated in cell division. Bacterial spores, on the other hand, must transition return to a reproductive state.

Illustration for article titled Ancient microbes come to life after 100 million years below the seabed


Sediment samples containing the microbes were collected 10 years ago in the abyssal plain in the South Pacific turn. These samples were drawn from depths reaching 75 meters (245 feet) below the sea floor and date from 13 million to 101.5 million years. Some oxygen was detected in these deep layers, but there are virtually no organic materials like carbon (i.e., food for microbes).

This part of the ocean contains some of the cleanest water in the world, due to the low concentrations of phytoplankton on the sea surface, which normally sink and supply food to microbes on the sea floor. Because marine snow, as it is called, is so light in this region, the formation of seabed sediment is exceptionally slow, forming at a negligible rate of about 3 to 6 feet (1 to 2 meters) per million of years. The main goal of the new study was to see if life could live in such a nutrient-deprived environment, and if so, for how long these microbes could survive with virtually no food.

Map showing the locations of the sampling sites.

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

Back in the laboratory, these microbes were incubated and given a constant diet of isotopes labeled substrates composed of carbon and nitrogen. An extremely important aspect of the study was to trace the microbial consumption of these added foods, hence the stable substrates labeled with isotopes.

Within this cozy laboratory environment, microbes, including those extracted from the oldest sediment samples, responded almost immediately. Over the course of 68 days, the researchers stared in amazement as populations increased in size by more than four orders of magnitude. More than 99% of the microbes found within the samples came back to life, in a result that even shocked scientists.

In the depths of the seabed, “nutrients are very limited,” so the microbes were “almost in the ‘fast’ state,” Morono said. “Therefore, it is surprising and biologically challenging that a large fraction of microbes can be revived from a very long burial or entrapment time under extremely low nutrient / energy conditions.”

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

Sediment sample.

Sediment sample.

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

“In fact, if I were 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 was not involved in the new research.

These microbes “were probably buried” within the Gyre sediments of the South Pacific, and “they or their descendants have persisted there since then,” Edgcomb said. Either these microbes were in a state of suspended animation, or the “original cells may occasionally divide since they were buried, and are looking at the umpteenth [indeterminate] generation of the original cells, “he said. Edgcomb said there are open questions about” how long different types of microorganisms can survive in an inactive state without dividing. “

Reliving the old Microbes are a little scary, given what we don’t know about ancient germs. When asked about the risks and safety precautions established for the experiment, Morono said that “the subsoil sediment is considered to be of low risk to health, since there is no infecting host, such as a human being, in this environment ” However, “we have been manipulating microbes at all times in the clean room” and all samples were kept in a laboratory, a biosafety level 1 environment, throughout.

Edgcomb had no safety issues and said, “As a marine microbial ecologist, I don’t see any safety issues in the experiments they conducted.”

As for how these microbes were able to remain in hibernation for so long, Morono said he is not sure, but hopes that the new findings “will stimulate discussions on this topic” and, ultimately, an identification of survival mechanisms. necessary for microbes. remain dormant on such vast geological time scales.

“The really surprising thing about this study is that this sediment contains oxygen. Since we all strive to have diets full of antioxidants, we know that oxygen is a breakdown agent, so having long-term survival is impressive, ”Biddle said. “However, we don’t know what the cell is actually seeing in the sediment; there may be small cages of low oxygen habitat that improve survival. “

The new study also reinforces the importance of organic carbon as a food source for microbes that live below the seabed, an unfortunate finding, when it comes to Biddle.

“It’s a little disappointing, considering that we’re discovering over and over again that the subsoil depends on the surface for its food,” Biddle said. “I’m still waiting for the self-sufficient subsurface sediment microbe!”