Deepwater microbe found in Japan sheds light on primordial evolutionary milestone

A microorganism collected in the mud of the deep sea off the coast of Japan has helped scientists discover the mystery of one of the evolutionary events of the basin for life on Earth: the transition of simple cells that colonized the planet to complex cell life: fungi, plants and animals including people.

The researchers said Wednesday that they were able to study the biology of the microorganism, recovered from depths of approximately 1.5 miles (2.5 km), after convincing it to grow in the laboratory. They called it Prometheoarchaeum syntrophicum, referring to the Greek mythological figure Prometheus who created humanity from clay and stole the fire of the gods.

The spherical cell of Prometheoarchaeum, with a diameter of approximately 500 nanometers, or one hundredth of a centimeter, has long, often branched, tentacle-shaped appendages on its outer surface.

It is part of a group called Archaea, relatively simple unicellular organisms that lack internal structures like a nucleus. Scientists have long wondered about the evolutionary change of such simple bacteria-like cells to the first rudimentary fungi, plants and animals, a group called eukaryotes, perhaps 2 billion years ago.

Based on a thorough laboratory study of Prometheoarchaeum and observations of their mutually beneficial symbiotic relationship with a companion bacteria, the researchers offered an explanation.

They proposed that appendages such as those of Prometheoarchaeum entangle a transient bacterium, which was then swallowed and eventually evolved into an organelle – internal structure – called mitochondria that is the source of a cell’s energy and crucial for respiration and energy production.

The solar system, including Earth, was formed 4.5 billion years ago. The first life on Earth, simple marine microbes, appeared about 4 billion years ago. The subsequent advent of the eukaryotes set in motion evolutionary paths that led to an unbridled set of organisms during eons such as palm trees, blue whales, T. rex, hummingbirds, clownfish, shiitake mushrooms, lobsters, daisies, woolly mammoths and Marilyn Monroe.

“How we originate, as eukaryotes, is a fundamental question related to how we, as humans, arise,” said microbiologist Masaru Nobu, of the National Institute of Advanced Industrial Science and Technology of Japan, one of the leaders of the study published in the Nature magazine.

Prometheoarchaeum is a member of a subgroup called Asgard archaea, named after the abode of the gods in Norse mythology. Other members of this subgroup were recovered from the frozen seabed near a hydrothermal ventilation system called Loki Castle, named after a Norse mythological figure, between Greenland and Norway.

Research on Prometheoarchaeum, Nobu said, indicates that Asgard archaea are the closest living relatives to the first eukaryotes.

The researchers used a submersible research vessel to collect mud containing Prometheoarchaeum from the Omine Ridge in Japan in 2006. They studied it in the laboratory in a process of several years and watched as it slowly proliferated after incubating the samples in a container infused with methane gas to simulate the deep-sea marine sediment environment in which it resides.

“We were able to obtain the first complete genome from this group of archaea and conclusively demonstrate that these archaea possess many genes that were thought to be found only in eukaryotes,” said Nobu.

It was discovered that Prometheoarchaeum depended on its companion bacteria.

“The organism” eats “amino acids through symbiosis with a partner,” said Nobu. “This is because the body cannot fully digest amino acids by itself, gain energy if byproducts have accumulated, nor build its own cell without outside help.”

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