Incredible virus detection provides clues as to the origin of complex lives

The origin of life artist concept

“Origin of Life” artist’s concept.

The first discovery of a virus that infects a group of microbes that can include the ancestors of all complex life has been found, researchers at the University of Texas at Austin (UT Austin) report in Natural microbiology. The incredible discovery provides tempting clues about the origins of complex life and suggests new directions for examining the hypothesis that viruses were crucial to the evolution of humans and other complex life forms.

There is a well-supported hypothesis that all complex life forms such as humans, starfish and trees – which have cells with a nucleus and are called eukaryotes – originated when archaea and bacteria joined together to form a hybrid organism. Recent research suggests that the first eukaryotes are direct descendants of the so-called Asgard archaea. The latest research, by Ian Rambo (a former doctoral student at UT Austin) and other members of Brett Baker’s laboratory, sheds light on how viruses may also have played a role in this billion – year – old history.

Virus that infects ASGARD archaea

Comparison of all known virus genomes. These viruses with similar genomes are grouped together, including those that infect bacteria (left), eukaryotes (right and bottom center). The viruses that infect Asgard archaea are unique from those described earlier. Credit: University of Texas at Austin

“This study opens a door to better understand the origins of eukaryotes and understand the role of viruses in the ecology and evolution of the Asgard archaea,” said Rambo. “There is a hypothesis that viruses may have contributed to the emergence of complex cell life.”

Alvin submersible

Researchers from UT Austin used the Alvin submersible to collect sediment samples and microbes from 2,000 m (6,600 feet) deep in the Gulf of California. Credit: Brett Baker

Rambo refers to a hotly debated hypothesis called viral eukaryogenesis. This suggests that, in addition to bacteria and archaea, viruses may have contributed a genetic component to the development of eukaryotes. Although this latest discovery does not resolve that debate, it does provide some interesting clues.

The newly discovered viruses that infect the living Asgard archaea have some features similar to viruses that infect eukaryotes, including the ability to copy their own[{” attribute=””>DNA and hijack protein modification systems of their hosts. The fact that these recovered Asgard viruses display characteristics of both viruses that infect eukaryotes and prokaryotes, which have cells without a nucleus, makes them unique since they are not exactly like those that infect other archaea or complex life forms.

“The most exciting thing is they are completely new types of viruses that are different from those that we’ve seen before in archaea and eukaryotes, infecting our microbial relatives,” said Baker, associate professor of marine science and integrative biology and corresponding author of the study.

The Asgard archaea, which probably evolved more than 2 billion years ago and whose descendants are still living, have been discovered in deep-sea sediments and hot springs around the world, but so far only one strain has been successfully grown in the lab. To identify them, scientists collect their genetic material from the environment and then piece together their genomes. In this latest study, the researchers scanned the Asgard genomes for repeating DNA regions known as CRISPR arrays, which contain small pieces of viral DNA that can be precisely matched to viruses that previously infected these microbes. These genetic “fingerprints” allowed them to identify these stealthy viral invaders that infect organisms with key roles in the complex origin story of eukaryotes.

Alvin Submersible in Gulf of California

Researchers from UT Austin used the Alvin submersible to collect sediment samples and microbes from 2000m (6600 feet) deep in the Gulf of California. Credit: Brett Baker

“We are now starting to understand the implication and role that viruses could have had in the eukaryogenesis puzzle,” said Valerie De Anda, a research associate at UT Austin and co-author of the study.

Reference: “Genomes of six viruses that infect Asgard archaea from deep-sea sediments” 27 June 2022, Nature Microbiology.
DOI: 10.1038/s41564-022-01150-8

The other co-authors of the study are Pedro Leão, a postdoctoral research fellow at UT Austin, and Marguerite Langwig, formerly a master’s student at UT Austin and currently a doctoral candidate at the University of Wisconsin-Madison. This work was supported by the Moore and Simons Foundations.