They may seem inhospitable to us, but organisms manage to find ways to survive and even thrive in Earth’s most extreme environments. Deep beneath the ocean floor, for example, scientists have found an abundance of different microbes, including bacteria, archaea—ancient single-celled organisms constituting one of the three major domains of life—and fungi. Now, to add to the collection of surprising microbes discovered here, scientists have identified a remarkable new virus that seems to infect archaea living beneath the sea floor.
Interestingly, this previously unknown virus was found to possess a system that selectively targets and mutates one of its own genes, which could be helping the virus adapt to defense mechanisms evolved by its host. Furthermore, this capacity for mutation was actually found to be shared by archaea themselves. These intriguing findings have been published in Nature Communications.
Viruses don’t possess the necessary machinery to self-replicate, meaning that they are dependent on other cells to copy themselves. Those found beneath the ocean floor must therefore be infecting and exploiting other life forms co-inhabiting these hostile environments in order to continue their existence. Since archaea are well-adapted and dominant in these environments, scientists were keen to find out more about the viruses that infect them.
To do this, researchers from the National Science Foundation used a submersible to collect sediment samples from one system in the marine subsurface: a deep-ocean methane seep. Archaea that live here are known as methanotrophs, meaning that they can use methane as their sole carbon and energy source.
The samples were then returned to the lab and fed methane to encourage the methanotrophic archaea to grow. After analyzing the organisms present, the scientists discovered a virus that didn’t match any documented viruses listed in global databases, but appeared to be parasitizing the archaea. Further investigation revealed that its genome partially matched viruses identified in methane seeps off Norway and California, suggesting that this kind of virus has a global distribution in these systems.
Interestingly, genomic analyses also revealed the presence of a small genetic element, called a diversity-generating retroelement, which speeds up mutation in one of the virus’ own genes. This is a valuable weapon for the parasite since it allows the virus to rapidly diversify its proteins, which is a crucial ability since its hosts will also continually be evolving defense mechanisms to protect themselves from infection.
Having identified this system in an archaea-infecting virus, the researchers reasoned that it likely also exists in archaea, so they began scouring archaeal genomes to find out. Eventually, they discovered a similar system in two archaeal species found in the terrestrial subsurface. But unlike the viral system, which only targeted a single gene, these archaeal systems were found to mutate at least four different genes. This find was particularly exciting since these mechanisms had never been found to target more than two genes in any other organism investigated so far.
According to the researchers, these systems could be key to the survival of archaea in these extreme environments. “The cell is choosing to modify certain proteins,” lead researcher David Valentine said in a news release. “While we don’t yet know what these proteins are being used for, learning about the process can tell us something about the environment in which these organisms thrive.”
[Via National Science Foundation, Nature Communications and Discovery News]