Scientists uncovered enigmatic viral "fingerprints" concealed in an ancient collection of bacteria that may have aided in the evolution of all complex life on Earth, from fungus to plants to humans.
These microorganisms, known as Asgard archaea after the Norse mythological dwelling of the gods, live in the freezing sediments deep in the ocean and in boiling hot springs, and existed on Earth before the first eukaryotic cells, which contain their DNA inside a nucleus.
Viruses invading Asgard archaea may have impacted how such living forms originally evolved, and may even have given rise to some of the first precursors to the nucleus, according to some experts. However, no Asgard-infecting viruses had been identified till today.
Scientists have uncovered a swarm of viruses that may infect the ancient archaea in a trio of papers published Monday (June 27) in the journal Nature Microbiology.
"These are the first studies investigating Asgard archaeal viruses; there was nothing known before," said Susanne Erdmann, group leader of the archaeal virology research group at the Max Planck Institute for Marine Microbiology in Bremen, Germany, who was not involved in the study.
This line of study might one day disclose if and how viruses played a role in the origin of eukaryotic cells on Earth, Erdmann told Live Science in an email.
Dusting for viral 'fingerprints'
The current study looked for signs of viral infection contained in the DNA of Asgard archaea. This implanted evidence takes the form of "CRISPR spacers," which are small fragments of viral DNA.
Most people associate CRISPR with the well-known gene-editing tool that allows scientists to easily manipulate genetic sequences, according to Ian Rambo, a former doctoral student at the University of Texas at Austin Marine Science Institute and first author of one of the Nature Microbiology studies. However, he told Live Science that this gene-editing technology was initially adopted from the natural defensive systems of bacteria and archaea.
CRISPR stands for "clusters of regularly interspaced short palindromic repeats" and refers to a region of DNA composed of short, repeating sequences with "spacers" placed between each repetition. Bacteria and archaea steal these spacers from viruses that infect them, and as a result, the cells save a memory bank of viral DNA that lets them detect the viruses if they attack again.
"It's an adaptive immune system that remembers these previous infections," explained Rambo, who is now a postdoctoral fellow at the USDA's Agricultural Research Service.
Rambo and his colleagues looked for such DNA spacers in Asgard archaea specimens taken from sediments around hydrothermal vents in the Guaymas Basin of the Gulf of California, which connects Baja California and mainland Mexico.
The researchers compared the spacers they discovered to larger sections of viral DNA collected from the deep oceans.
"It is fairly easy to sequence viruses from deep-sea sediments … but the challenge is to recognize which hosts these viruses infect," said Mart Krupovic, head of the Archaeal Virology Unit at the Institut Pasteur in Paris and co-author of the other two research. "CRISPR spacer matching is the most convenient and most convincing and reliable approach to assign the host."
Rambo's team eventually discovered six viruses that infect two species of Asgard archaea, which they dubbed Lokiarchaeota and Helarchaeota after the Norse deity Loki and goddess Hel, respectively. The new viruses were named after Norse legendary animals such as the huge wolf Fenrir and the dragon Nidhogg.
Similarly, Krupovic and his colleagues identified two viruses dubbed Huginn and Muninn after the two ravens that act as scouts for the Norse deity Odin in one research; these viruses were detected in an Asgard genome taken from a hot spring in Yellowstone National Park.
Krupovic and his colleagues discovered viruses in deep-sea sediments collected from the Shimokita Peninsula, the northeastern tip of the Japanese island of Honsh, as well as two additional Pacific and one Indian Ocean locations.
They discovered three family-level groupings of viruses in these samples, which they named after the three Norns - Wyrd, Verdandi, and Skuld - who are magical entities in Norse mythology who determine the fates of gods and mortals.
Using the viral DNA, the researchers were able to deduce what sorts of proteins the individual genes code for, and hence how the viruses may appear and operate.
Krupovic and his colleagues discovered that viruses named after the Norn Verdandi had tails that protrude from their outer shells, or capsids, while viruses named after Wyrd are likely lemon-shaped.
Rambo's team also discovered evidence that Nidhogg viruses may hijack crucial proteins in their host cells, allowing them to replicate themselves. (Viruses that infect eukaryotic cells operate in a similar manner.)
Ultimately, the researchers were only able to determine the roles of some of the viruses' genes; the great majority of the genes' functions remain unclear, according to Erdmann. Furthermore, because CRISPR does not operate against all viruses, she believes that many more Asgard-infecting viruses have yet to be identified.
Growing Asgard archaea in the lab and isolating any viruses found within their cells would be one technique to find these hidden viruses.
"However, culturing Asgard archaea has been proven very difficult," Erdmann said.
Only one scientific group has successfully cultivated Asgard archaea to yet, and it took them 12 years. This is due in part to the fact that archaeal cells require weeks to multiply. (By comparison, the bacteria Escherichia coli, according to Science News, takes roughly 20 minutes.)
CRISPR spacer matching is probably the most effective approach to locate new viruses until more Asgards can be generated in the lab, according to Krupovic. And when more viruses are discovered, their function in the evolution of eukaryotes, including humans, may become clearer, according to Rambo.
This article was originally published by Live Science. Read the original article here.
