This Archaeon Makes Scientists Question the Tree of Life

Shin Jie Yong

It’s named after Prometheus, the supreme trickster Greek god —and it’s one of the 2019 scientific breakthroughs.
Image from Pixabay

The three-domain tree of life divides lifeforms into 3 domains: Bacteria, archaea, eukarya. Most eukaryotes are multicellular organisms consisting of many cells. Whereas bacteria and archaea are unicellular as they’re only made up of one cell.

Archaea are different from bacteria in terms of their cell wall structure and their enzymes that are more similar to eukaryotes. Archaea can’t be killed by antibiotics and usually thrive in extreme conditions such as >100°C.

According to this widely accepted model, these three domains of life shared a hypothetical last universal common ancestor (LUCA) that existed ~4 billion years ago. Both archaea and eukaryotes, thus, arise from a common ancestor.
Source: Open-access publication. Citation: Fournier GP and Poole AM (2018)

Proponents of a two-domain tree of life, however, say that eukaryotes diverged from a subgroup of archaea — that archaeon is an ancestor of eukaryotes. The debates heated and eventually settled down.

But a recent 2019 scientific breakthrough revives it. Scientists are now reconsidering the two-domain tree of life.

The Trickster Asgardian

Earning its place as a runner-up in 2019 scientific breakthroughs, microbiologists at the Japan Agency for Marine-Earth Science and Technology isolated an archaeon from the Pacific Ocean floor and successfully grew it in a lab bioreactor. Fine-tuning laboratory conditions to mimic the environment of the ocean floor was an arduous task; it took them 12 years.

“This is a monumental paper that reflects a tremendous amount of work and perseverance,” says Professor Thijs Ettema, an evolutionary microbiologist at the Wageningen University, who was unaffiliated with the research. “It’s a major step forward in understanding this important lineage.”

The Japanese named the archaeon species as Candidatus Prometheoarchaeum syntrophicum, under the Asgard superphylum.
“File: Prometheus I .jpg” by Weltkanon is licensed under CC BY-SA 4.0

Asgard is the home of gods of Norse mythology. Prometheus — which the Asgard archaeon is named after — is a titan Greek god who sculpted humans out of clay, and a supreme trickster that stole fire from Zeus to give it to humans.

In this way, Prometheoarchaeum is a trickster microbe that makes scientists reconsider the tree of life, from a three-domain into two-domain.

“The genus name is an analogy [of the] involvement of Prometheus in the origin of humans from sediments and the acquisition of an unprecedented oxygen-driven energy-harnessing ability,” the Japanese wrote in Nature, 2020.

[Author’s own interpretation: Prometheus as Prometheoarchaeum; sediments as clay or the ocean floor; oxygen-driven energy-harnessing like how fire combustion requires oxygen].

How the Archaeon Behaves

Prometheoarchaeum appears sphere-like under the microscope. It needs methane to grow, as well as other microbes (i.e., the archaeon Methanogenium or bacterium Halodesulfovibrio) that consume hydrogen. Prometheoarchaeum secretes hydrogen as waste, and hydrogen stunts its growth.

Once environmental conditions are met, Prometheoarchaeum grows but rather slow. It takes 20 days to double in numbers, compared to bacteria that usually take less than an hour. “It’s one of the slowest-dividing organisms I know of,” remarks Professor Ettema.

After waiting for months, they witnessed an intriguing phenomenon. The spherical Prometheoarchaeum protrudes long tentacles outward to engulf surrounding proteins as food (see photo). The predator, Prometheoarchaeum may have swallowed the first mitochondria this way. As the Japanese put it,

“The [Prometheoarchaeum] host may have further interacted with a facultatively aerobic organotrophic partner that could scavenge toxic oxygen (the future mitochondrion).”

This provides real-life evidence for a previous hypothesis that an archaeon can reach out, encircle, and eat a microscopic host that possesses mitochondria, an organelle that converts oxygen to energy. They called it the,

“Entangle–engulf–endogenize (also known as E³) model.”

Oxygen was toxic to many primitive lifeforms. As oxygen levels rise in early Earth, Prometheoarchaeum with mitochondria, thus, holds a survival advantage, marking the start of eukaryotic life — i.e., eukaryogenesis.
Figure: Membrane-protrusions of Prometheoarchaeum. Source: Imachi et al. (2020).

Genomic analyses also back this up, showing that Prometheoarchaeum and other archaea are more closely related to eukaryotes than bacteria. As the Japanese microbiologists, yet computationally skilled, stated,

“We confirmed the presence of 80 eukaryotic signature proteins, which are also observed in related Asgard archaea.”

Current Understanding

Professor James McInerney, a computational evolutionary microbiologist at the University of Nottingham, remains skeptical that Prometheoarchaeum reflects what happened 2 billion years ago. “This is an organism alive today in 2020,” the professor said.

“It is important to emphasize that the vast amount of time (roughly 2 billion years) that separates this modern-day organism from the organism that evolved into the last eukaryotic common ancestor (LECA) leaves many uncertainties,” the Japanese admitted. “Although we can make reasoned assumptions on the events that may have occurred during the course of evolution.”

The pictures are “intriguing” but inconclusive, critiques Rohit Ghai, a microbiologist at the Czech Academy of Sciences. I’m unsure what he meant by inconclusive, but perhaps it doesn’t prove that Prometheoarchaeum can actually ingest a mitochondrion.

The Japanese researchers themselves say that their study provides a hypothetical model for eukaryogenesis, certainly not a direct proof or fact. As they concluded,

“On the basis of the available data obtained from cultivation and genomics, and reasoned interpretations of the existing literature, we propose a hypothetical model for eukaryogenesis, termed the entangle–engulf–endogenize (also known as E³) model.”

This article was originally published in Microbial Instincts with minor modifications.

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