Giant Virus Found in Sewage Blurs the Line Between Life and Non-Life

By Jeffrey Marlow | April 20, 2017 12:00 pm
An artist's rendition of the newly discovered Klosneuvirus (Image: NIH / Ella Maru studio)

An artist’s rendition of the newly discovered Klosneuvirus (Image: NIH / Ella Maru studio)

In most biology textbooks, there’s a clear separation between the three domains of cellular organisms – Bacteria, Archaea, and Eukaryotes – and viruses. This fault line is also typically accepted as the divider between life and non-life: since viruses rely on host machinery to enact metabolic transformations and to replicate, they are not self-sufficient, and generally not considered living entities.

But several discoveries of giant viruses over the last decade have blurred this distinction. Some viruses are even larger and contain more genes than typical microbes like E. coli. Ultra-small bacteria detected in filtered groundwater from Rifle, Colorado are moving the goalposts from the opposite end, leading to a virus-microbe continuum in which distinguishing one from the other isn’t so straightforward. Among the alluring interpretations: giant viruses could be indicative of a fourth domain of life.

A recent study led by Frederik Schulz at the Department of Energy’s Joint Genome Institute blurs the virus-microbe line even further. While assembling a metagenome from sewage sludge in Klosterneuburg, Austria, Schulz found several genes that all mapped back to the same unknown virus, genes that until now have only been associated with free-living cells.

The particle – named Klosneuvirus – is still a virus, given its other genes and outer coat, but its 1.57 million-base genome allows a greater degree of autonomy than many of its viral relatives. Most notably, they have a relatively complete complement of protein-making machinery, which would reduce the dependence on host cells to do their bidding. For example, most viruses lack aminoacyl tRNA synthetase enzymes, which shuttle amino acids onto transfer RNA molecules; these in turn make their way to the ribosome, dropping off their cargo to build proteins from the chains of amino acids. While some previously discovered giant viruses have seven of the 20 aminoacyl tRNA synthetases, Klosneuvirus has 19, making it almost entirely independent of host involvement in protein synthesis. (It’s also worth noting that autonomy is not a requirement for cellular life, either: many microbes are “auxotrophic,” meaning they depend on external input of organics – often amino acids – in order to survive.)

So could this sophisticated, rule-breaking giant virus indeed be a sign of the mythical fourth domain? To find out, the team compared Klosneuvirus’s aminoacyl tRNA synthetase sequences with other forms of the enzymes across the tree of life. The results were all over the place, with each synthetase showing closest similarity to a different organism (mostly algae). In the ever hyperbolic language of scientific journalese, Schulz notes that “these findings are incompatible with the fourth domain hypothesis…and instead imply piecemeal acquisition of these genes by giant viruses.” The synthetases don’t seem to have evolved together, from the same branch point and within the same organism; rather, they were scooped up by an opportunisitc virus and incorporated into an increasingly mature metabolic network.

As suggested by previous revelations of giant viruses, Klosneuvirus is likely just the beginning of a more thorough reconfiguration of the tree of life. After the intriguing result from the sewage treatment plant in Austria, Schulz looked for genomes of similar viruses, lurking in previously obtained metagenomes from around the world. He found three more – enough to propose a new subfamily, the Klosneuvirinae – the latest links in the chain connecting viruses and the three domains of cellular life.

CATEGORIZED UNDER: environment, living world, top posts
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  • Maia

    A continuum is what we seem to find wherever we deeply look…we stop looking too soon many time, and conclude there are only the yes and no categories, eg non-living and living. Humans are the ones dividing reality up into segments and labeling them, while reality is a rainbow of degrees.

  • Mitchell Porter

    I feel skeptical. It sounds like these “giant viruses” haven’t been *seen*, but only inferred by sequence assembly from a metagenome. In paleontology they sometimes “discover” fictitious organisms by spuriously connecting bones from different skeletons jumbled together in the same dig; how do we know giant viruses aren’t an artefact of horizontal gene transfer in a microbial ecology?

  • Lars Franssen

    Viruses pick up genetic material all the time. If they are giant, they obviously have more space in their protein shell to keep new genes. Having a few aminoacyl-tRNA synthetases doesn’t make for a very exciting metabolism in my eyes, nor does it make up for the other criteria of life still lacking. And even if they have 19 out of 20, how do they autonomously synthetise proteins? Auxotrophy is all very well, but you need to differentiate a little. We, after all, need to import 8 aminoacids, ourselves. But we can at least incorporate all 20 into proteins without help.

    • Maia

      “doesn’t make for a very exciting metabolism”? “at least”? “Without help?”
      Humans get continual help doing every single thing we do! A human is an ecosystem participating in an even more mind-boggling Ecosystem.

  • GORT

    We don’t need to use a giant virus as an argument for a 4th branch of life. Instead, we should recognize that our definition of life is too restrictive, and that the 4th branch has existed all along. In my opinion, a virus is simply a parasite, and just because it lacks certain functionality that would allow it to meet our narrow definition of life doesn’t mean that it isn’t alive.

    Questions:
    – If a virus isn’t alive, what is it?
    – If a virus isn’t alive, why can it be killed? Or, what does it mean to kill a virus if it isn’t alive to begin with?
    – What, other than life, contains genetic material that can be used to manipulate an environment to its own benefit?
    – What if viruses are required for life to exist? The ability to transfer genetic material is a fundamental requirement for creating the tremendous diversity we see today.
    – What would life be like on Earth if there were no viruses?

    With unknown millions of distinct types, it could be that viruses represent the most diverse branch of life. Perhaps the real problem is simply that humans tend to get stuck in the “threesies”. 😉

    [==*==]

  • OWilson

    A virus is as alive as an hibernating bear. Or a 100 year old grain of wheat.

    Given the proper wake up call, it recognizes its surroundings, and utilizes them to replicate and multiply.

    Sorta like a human :)

    The real question is what makes it different from a pebble, and why?

    • Maia

      Love the first three sentences of your comment. The last one might be turned into: what makes a human (or a marigold) different from a pebble, and why?

  • Craig Monk

    Hears another pathogen mind bender. PRION. It is not alive and yet it is the cause of Chronic Wasting Disease, Mad Cow, and rare progressive neurodegenerative disorders that affect both humans and animals like Creutzfeldt-Jakob disease. There are even studies that show Alzheimers is caused by “prion.”
    Rather than “kill” scientist talk in terms of “deactivating”.

    Prion, supposedly, can be deactivated at a temperature of 270 F at 21 psi for 90 minutes.

    Because prion is resilient, I do not trust any studies at this point.

    Consider that one way prion is passed on is though feces and urine. Now consider that biosolids regulations from the EPA only require a temperature of 131 F to achieve Class A biosolids. Biosolids
    is the contaminate derived from cleaning sewage the EPA calls “safe” and the regulation were derived from data collected in the 70s and 80s and is unchanged to date.

    Since the US EPA allows biosolids to be wholesale distributed on farms and forests, exposing livestock and vegetation, do you feel “safe”?
    1. One more “safety” feature of biosolids is : EPA’s 40 CFR 261.30(d) and 261.33 (4), every US industry connected to a sewer can discharge any amount of hazardous and acute hazardous waste into sewage treatment plants. There are over 80,000 chemicals in commerce and growing even today.
    2. When the sewage industry tells you “pre-treatment of these industrial chemical are strictly regulated”, read the EPA’s Office of Inspector General’s Report No.14-P-0363- 09/2014 Just Google the
    number to see how insane the statement CFR 261.30 above is.

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The Extremo Files

The Extremo Files traces the science that is pushing the boundaries of biology, from the deep sea to outer space to the brave new world of synthetic biology.

About Jeffrey Marlow

Jeffrey Marlow is a geobiologist exploring the limits of life, from the role of microbes in global elemental cycles to the possibility of life beyond Earth and the brave new world of synthetic biology. He received his PhD from the California Institute of Technology and is currently a Postdoctoral Scholar at Harvard University, where he studies the inner workings of methane-metabolizing organisms.

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