This strange microbe can mark one of the great leaps of life

A strange microbe with tentacles discovered at the bottom of the Pacific Ocean can help explain the origins of complex life on this planet and solve one of the deepest mysteries in biology, scientists reported Wednesday.

Two billion years ago, simple cells gave rise to much more complex cells. Biologists have struggled for decades to learn how it happened.

Scientists have long known that there must have been predecessors along the evolutionary path. But judging by the fossil record, complex cells simply appeared out of nowhere.

The new species, called Prometheoarchaeum, turns out to be a form of transition, helping to explain the origins of all animals, plants, fungi and, of course, humans. The research was reported in the journal Nature.

“It is actually quite good, it will have a great impact on science,” said Christa Schleper, a microbiologist at the University of Vienna who was not involved in the new study.

Our cells are full of containers. They store DNA in a nucleus, for example, and generate fuel in compartments called mitochondria. They destroy old proteins inside small cleaning machines called lysosomes.

Our cells also build a filament skeleton, built from Lego type building blocks. By extending some filaments and separating others, cells can change their shape and even move on surfaces.

The species that share these complex cells are known as eukaryotes, and they all descend from a common ancestor that lived approximately two billion years ago.

Before that, the world only harbored bacteria and a group of small, simple organisms called archaea. Bacteria and archaea have no nuclei, lysosomes, mitochondria or skeletons.

Evolutionary biologists have long wondered how eukaryotes could have evolved from such simple precursors.

In the late twentieth century, researchers discovered that mitochondria were free-living bacteria at some time in the past. They were somehow dragged into another cell, providing new fuel for their host.

In 2015, Thijs Ettema of Uppsala University in Sweden and his colleagues discovered DNA fragments in sediments recovered from the Arctic Ocean. The fragments contained genes from a kind of archaea that seemed to be closely related to eukaryotes.

Dr. Ettema and his colleagues called them Archaea de Asgard. (Asgard is the home of the Norse gods.) The DNA of these mysterious microbes appeared in a river in North Carolina, hot springs in New Zealand and other places in the world.

Asgard’s archaea are based on a series of genes that had previously only been found in eukaryotes. It was possible that these microbes used these genes for the same purposes, or for something else.

“Until you have an organism, you can’t be really sure,” said Dr. Schleper.

Masaru K. Nobu, a microbiologist at the National Institute of Advanced Industrial Science and Technology in Tsukuba, Japan, and his colleagues managed to grow these organisms in a laboratory. The effort took more than a decade.

Microbes, which are adapted to life on the cold seabed, have a slow motion existence. Prometheoarchaeum can take up to 25 days to divide. On the contrary, E. coli is divided once every 20 minutes.

The project began in 2006, when researchers lifted sediments from the Pacific Ocean soil. Initially, they hoped to isolate the microbes that eat methane, which could be used to clean wastewater.

In the laboratory, the researchers imitated the conditions on the seabed by placing the sediment in a chamber without oxygen. They pumped methane and extracted deadly residual gases that could kill resident microbes.

The mud contained many types of microbes. But by 2015, researchers had isolated a new species of intriguing arches. And when Dr. Ettema and his colleagues announced the discovery of Asgard’s DNA, the Japanese researchers were surprised. His new live microbe belonged to that group.

Then, the researchers conducted a more thorough investigation to understand the new species and link it with the evolution of eukaryotes.

The researchers named the microbe Prometheoarchaeum syntrophicum, in honor of Prometheus, the Greek god who set fire to humans, after molding them with clay.

“The twelve years of microbiology that were needed to get to the point where you can see with a microscope are incredible,” said James McInerney, an evolutionary biologist at the University of Nottingham who was not involved in the research.

Under the microscope, Prometheoarchaeum proved to be a strange beast. The microbe begins as a small sphere, but over the course of the months, long branched tentacles sprout and release a flotilla of membrane-covered bubbles.

It was even weirder when researchers examined the inside of the cell. Dr. Schleper and other researchers expected Asgard’s archaea to use their eukaryotic-like proteins to build some eukaryotic-like structures within their cells. But that was not what the Japanese team found.

“Inside, there is no structure, only DNA and proteins,” said Dr. Nobu.

This finding suggests that the proteins that eukaryotes used to build complex cells began to do other things, and only later were they assigned new jobs.

Dr. Nobu and his colleagues are now trying to discover what those original works were. It’s possible, he said, that Prometheoarchaeum creates its tentacles with genes that eukaryotes then used to build cell skeletons.

Dr. Schleper wanted to see more evidence for this idea. “There are very nice arms in other arches,” he observed. But those other species do not use proteins so similar to ours.

Before the discovery of Prometheoarchaeum, some researchers suspected that eukaryotic ancestors lived as predators, swallowing smaller microbes. They could have swallowed the first mitochondria in this way.

But Prometheoarchaeum does not fit that description. Dr. Nobu’s team often found the microbe stuck to the sides of bacteria or other archaea.

Instead of hunting prey, Prometheoarchaeum seems to make a living by sipping floating protein fragments. Your partners feed on your waste. They, in turn, provide vitamins and other essential compounds to Prometheoarchaeum.

Dr. Nobu speculated that a kind of Asgard arches on the seabed dragged the bacteria into a web of tentacles, attracting them to an even more intimate association. Ultimately, the bacterium was swallowed, which evolved into the mitochondria feeding each complex cell.

Dr. McInerney was skeptical that Prometheoarchaeum could provide a clear picture of how our ancestors took mitochondria two billion years ago. “This is a living organism today in 2020,” he said.

While Dr. Nobu’s team continues to study Prometheoarchaeum, they are also hunting their relatives in the seafloor mud. These microbes may be even closer to our own ancestry, and may offer even more unexpected clues.

“We hope this helps us understand each other better,” said Dr. Nobu.

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