The most common organism in the oceans harbors a virus in its DNA

University of Washington

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IMAGE: The viruses, colored orange, attached to a membrane vesicle from the SAR11 marine bacteria, colored gray, that was the subject of this study. view more  Credit: Morris et al./Nature Microbiology

The most common organism in the oceans, and possibly on the entire planet, is a family of single-celled marine bacteria called SAR11. These drifting organisms look like tiny jelly beans and have evolved to outcompete other bacteria for scarce resources in the oceans.

We now know that this group of organisms thrives despite — or perhaps because of — the ability to host viruses in their DNA. A study published in May in Nature Microbiology could lead to new understanding of viral survival strategies.

University of Washington oceanographers discovered that the bacteria that dominate seawater, known as Pelagibacter or SAR11, hosts a unique virus. The virus is of a type that spends most of its time dormant in the host’s DNA but occasionally erupts to infect other cells, potentially carrying some of its host’s genetic material along with it.

“Many bacteria have viruses that exist in their genomes. But people had not found them in the ocean’s most abundant organisms,” said co-lead author Robert Morris, a UW associate professor of oceanography. “We suspect it’s probably common, or more common than we thought — we just had never seen it.”

This virus’ two-pronged survival strategy differs from similar ones found in other organisms. The virus lurks in the host’s DNA and gets copied as cells divide, but for reasons still poorly understood, it also replicates and is released from other cells.

The new study shows that as many as 3% of the SAR11 cells can have the virus multiply and split, or lyse, the cell — a much higher percentage than for most viruses that inhabit a host’s genome. This produces a large number of free viruses and could be key to its survival.

“There are 10 times more viruses in the ocean than there are bacteria,” Morris said. “Understanding how those large numbers are maintained is important. How does a virus survive? If you kill your host, how do you find another host before you degrade?”

The study could prompt basic research that could help clarify host-virus interactions in other settings.

“If you study a system in bacteria, that is easier to manipulate, then you can sort out the basic mechanisms,” Morris said. “It’s not too much of a stretch to say it could eventually help in biomedical applications.”

The UW oceanography group had published a previous paper in 2019 looking at how marine phytoplankton, including SAR11, use sulfur. That allowed the researchers to cultivate two new strains of the ocean-dwelling organism and analyze one strain, NP1, with the latest genetic techniques.

Co-lead author Kelsy Cain collected samples off the coast of Oregon during a July 2017 research cruise. She diluted the seawater several times and then used a sulfur-containing substance to grow the samples in the lab — a difficult process, for organisms that prefer to exist in seawater.

The team then sequenced this strain’s DNA at the UW PacBio sequencing center in Seattle.

“In the past we got a full genome, first try,” Morris said. “This one didn’t do that, and it was confusing because it’s a very small genome.”

The researchers found that a virus was complicating the task of sequencing the genome. Then they discovered a virus wasn’t just in that single strain.

“When we went to grow the NP2 control culture, lo and behold, there was another virus. It was surprising how you couldn’t get away from a virus,” said Cain, who graduated in 2019 with a UW bachelor’s in oceanography and now works in a UW research lab.

Cain’s experiments showed that the virus’ switch to replicating and bursting cells is more active when the cells are deprived of nutrients, lysing up to 30% of the host cells. The authors believe that bacterial genes that hitch a ride with the viruses could help other SAR11 maintain their competitive advantage in nutrient-poor conditions.

“We want to understand how that has contributed to the evolution and ecology of life in the oceans,” Morris said.

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Other co-authors are postdoctoral researcher Kelli Hvorecny and associate professor Justin Kollman in the UW Department of Biochemistry. The study was funded by the National Science Foundation and the National Institutes of Health’s National Institute of Allergy and Infectious Disease.

From EurekAlert!

17 thoughts on “The most common organism in the oceans harbors a virus in its DNA

  1. Not sure why these guys are calling these “viruses” and not phages. Phage is the more correct term for the viruses that infect, replicate, and lyse bacteria. Most phages are DNA based.

    This is nothing novel in bacteria and phages. Basic bacteriology and their phages 101. Phages have long been recognized (since the 1950’s) in many bacteria as having a two modes, and usually some stressor switches on the lysogenic action of the phage to release itself (destroying the host bacteria in the process) to find new bacteria to infect. It is a symbiotic relationship in most case (maybe all) in that the virus brings to the bacteria new ways to acquire food-energy from it environment and thus help the bacteria replicate itself. Mutualism.

    • I too don’t see what’s new. If the researchers can show some mutualistic effect regarding sulfur metabolism, then they’d have something.

      Not just prokaryotes but we eukaryotes have viruses in our DNA.

    • Im fascinated by Phage therapies and wondered why the hell anyone isnt finding the phage that will knock Covid around
      they DO kill other viruses as well as bacterias( knocked off smallpox in petri dishes, unplanned)
      and the hunting Covid in sewers would also find the phages as thats how the polish n russians used to locate theirs for disease fighting.

    • If I’m reading this right (and always remembering that this is a press release) – the “novel” part is finding a phage in this particular bacterium.

      A rather minor accomplishment, if done in a somewhat new way (DNA analysis rather than observation). But everything “virus” is viral in these days.

      • Good observation about press releases. Just because it’s written up by the sophomore high school interns who write the EurekAlert! press releases, doesn’t automatically mean that the study is a steaming pile.

    • So how does the virus bring new ways to acquire food to the bacteria? I would love to hear more about that, or if you could provide a link to something that discusses it.

      I know almost nothing about this, but speculating I would think that all of a virus’s DNA or RNA is normally dedicated to the replication of the virus, and that there would be nothing extraneous in a virus that was not normally used on every cycle of replication.

      Or so I would intuitively imagine.

      As I was reading the article I was trying to imagine what a virus could possibly bring to a bacteria, that is something that would make it more than just a parasite, and the only two speculations I came up with is it might play some kind of vague sexual role, or perhaps the substance of the virus itself brings resources the bacteria needs. Of course for the latter to work the bacteria would need to have a chance to deactivate the virus and consume it.

    • At the very least we must PANIC!

      Then stop all economic activity in or on or under the oceans.

      Then stop burning fossil fuels, we need more socialism.

  2. As the goal of the phage DNA is to be replicated, it makes sense that, under favorable bacterial growth conditions, it would be laying dormant and replicated with the bacteria. And, also logically, when conditions are bad and bacterial replication slows or ceases, the virus simply packs up (literally) moves on. Bacteria do the same thing by forming spores when conditions are no longer favorable for normal growth. Plants seed in an effort to leave the area which has become unfavorable. Nothing new here and not a surprise that viruses are everywhere. The greater surprise is that the researchers were surprised by viral interference.

  3. The study of viruses in the ocean is quite new and exciting with new discoveries being made every single day at a guess.

    According to Forest Rohwer in part, without viruses, the oceans would soon become cesspools of uncontrolled bacterial growth. The real area of interest for me at this time is that it is emerging that ‘viromes’, or communities of viruses are just as important as the communities of bacteria that inhabit a gastrointestinal tract, and that some work together and so on.

    From: https://www.youtube.com/watch?v=WZxUCEpsppQ
    “Virions and Provirus, Oxygen and Algae: Forest Rohwer Talks Research on Viromes”
    24 views
    •Apr 30, 2020″

    Also of interest to me recently is the virus protein that forms the boundary of a mammalian placenta that prevent the immune systems from seeing each other in effect.

    From: http://isciencemag.co.uk/features/the-syncytin-gene-viruses-responsible-for-human-life/
    “Many individuals think of viruses as harmful organisms that invade, infect and even kill. But the reality is very different as a virus has now been credited with making human life possible.”

    • While long known study of marine diseases in general have indeed greatly increased leading to new revelations. They increased after the Anthropocene somewhat suggested by Harvell, C. D. et al. 1999. Emerging marine diseases–climate links and anthropogenic factors. Science. 285:1505-1510. Not the worst paper around, perhaps this one that didn’t do much homework–[Williams, E. H., Jr. and L. Bunkley-Williams. 1990. Recurring mass mortalities of Caribbean herrings: implications for the study of major marine ecological disturbances. J. of Aquatic Animal. Health. 2:230-236.] corrected by Lafferty, K. D., et al. 2004. Are diseases increasing in the ocean? Annual Review of Ecology, Evolution and Systematics. 35:31-54.

      These tiny critters are a problem in obscure diseases as possible confounding causes. There were famous nearly century old cases of mass mortalities of sponges in Florida, eelgrass in the northern hemisphere, among others. And for those of you that like crabs–Yudin, A. I. and W. H. Clark, Jr. 1979. A description of rhabdovirus-like particles in the mandibular gland of the blue crab, Callinectes sapidus. J. Invertebrate Pathology. 33:133-147.

  4. If bacteria are exchanging DNA by means of viral transport, does that mean that viruses are effectively carrying out the sexual function for this bacterium? If we reduce sex to the essential of mixing up DNA. These SAR11 bacteri seem to be outsourcing at least a part of their “sexual” mixing of DNA to viruses.

    • Viruses are just one Mobile Genetic Element through which bacteria engage in “sex”. Others are plasmids and transposons, which facilitate Horizontal Gene Transfer, and not just genes, but sequences not coding for proteins.

      Of course archaea and eukaryotes also exchange genetic material by these means, besides in the latter (our) case, also sexual reproduction.

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