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A new branch of life found in a pond in Melbourne: Pandoravirus promises future surprises

The pandora virus is a brand new form of life, and it’s a bit like a knitted potato. No one can imagine a knitted potato. Klara Kim

A recent paper in Science has announced the discovery of an organism that is going to require a reappraisal of our assumptions about viruses, evolution and the history of life. The authors named the organism Pandoravirus, in memory of the Greek myth about Pandora, who also unleashed something surprising with far-reaching consequences.

The publication by a group of French scientists describes a new kind of virus, which sounds like a little thing, but isn’t in this case for many reasons. The first reason is that these viruses are enormous. Not only are they bigger than Megavirus, the largest virus known, they contain more DNA and the genes they carry are sufficiently different from anything previously sequenced to qualify as a fundamentally new type of life.

We are literally going to have to rewrite the textbooks.

One aspect of this story that personally excites me is that of the two species described, one was found in a pond at my University. I am familiar with the ponds of La Trobe University in Melbourne, because I spent a year wading in them with a dip net collecting chironomids (a type of aquatic midge). This means that I have personally met the species Pandoravirus dulcis, at least biochemically. We just hadn’t been introduced until now.

Should I be worried about having contact with a really big virus? Does this mean I might get a big disease? No, because these viruses infect aquatic amoebas that live in muddy sediments. There is no evidence that they attack humans. Although, given how little we know about Pandoraviruses, we cannot rule out anything with confidence.

In an article about the discovery, a virologist is quoted as saying, “It’s like finding a sasquatch!” Except that it isn’t, because people have been actually looking for sasquatch, while until recently, nobody was looking for giant viruses.

These organisms were large enough to be seen using a light microscope, but unrecognised because everybody “knew” that you can’t see viruses with a microscope. They were hiding in plain sight.

Of course, it is impossible to tell if a cell is a virus just by looking at it. French scientists Jean-Michel Claverie, Chantal Abergel and their colleagues deserve credit for not only deciding to look for something that was considered more unlikely than a sasquatch, but for developing methods that allowed them to recognise what they had found.

In 2003, these scientists found a virus large enough to be seen by microscope. They named it Mimivirus, for “microbe mimicking virus”. It was so big it even had its own parasites, called virophages. Mimivirus also had far more genes than expected for a virus. As a comparison, the Aids virus has 10 genes and the influenza virus has 13; Mimivirus had up to 900 genes! For the first time it made sense to search for large viruses.

The French scientists began by inoculating Acanthamoeba with water samples collected from around the world and then watching for patterns of cell death that indicated a viral infection. In other words, when the amoebas began to explode, the scientists took a closer look. In 2011 they found a virus larger than any seen before and named it Megavirus.

Pandoravirus are massive at one micrometre: almost twice as big as Megavirus. The larger species, Pandoravirus salinus, was found at the mouth of a river in Chile, and the smaller species, P. dulcis, was found in Melbourne. This does not mean that these organisms are rare. Indeed, the discovery of two closely related organisms in distant locations suggests that they are probably quite common and have a worldwide distribution.

When the researchers examined the Pandoravirus DNA they found multiple surprises. Pandoravirus have far more genes than any other virus: up to 2556 protein coding sequences in P. salinas and 1502 genes in P. dulcis. Although they share 14 of the 31 genes usually found in large viruses, 93% of their genes resemble nothing known. (They even have introns!) And yet Pandoravirus still meet the criteria for being a virus: they do not have any genes for protein translation and they do not reproduce by binary fission.

In fact, the description of their reproductive cycle is fascinating. The particles disappear when they first enter the amoeba’s cell, but then thousands of viruses inside an envelope are assembled in a “a manner similar to knitting”. This is hard to explain, but imagine a bag full of potatoes where the potatoes are assembled along with the bag. I think this is extraordinary. Who knits potatoes?

These organisms will surely live up to their name, which the authors chose for “the surprises expected from their future study”. One of those surprises will be the ability to look at the evolution of viruses. Looking for large viruses is a way of looking back in time.

A virus is a cell without enough components to even be considered alive, technically. In some circles, at least, they are considered inert particles, more chemistry than biology. The typical virus contains only few genes and cannot reproduce without using the machinery of a host cell. There must have been a time when their ancestors had a full set of genes and lived independently. Pandoravirus is a window into that world.

It is also likely to lead to a reappraisal of the main branches of the tree of life. The three Domains (bacteria, archaea and eukaryotes) may soon become four. There are few discoveries that can claim to require such a substantial rethink about the nature of life.

And to think it came from some mud that I have literally washed from between my toes!

Join the conversation

21 Comments sorted by

  1. Dale Bloom

    Analyst

    Fascinating, and thanks for this article.

    I have sometimes wondered if the term “evolution” simply means “change”.

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    1. Susan Lawler

      Head of Department, Department of Environmental Management & Ecology at La Trobe University

      In reply to Dale Bloom

      Organic evolution is a bit more precise than mere change.

      It is about adapting to survive in a particular environment.

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    2. Dale Bloom

      Analyst

      In reply to Susan Lawler

      Many people may believe that existing species are better than past species because of something termed “evolution”.

      To me, dinosaurs would have been quite sophisticated to have existed so long, and possibly the same with the pandoravirus.

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    3. Susan Lawler

      Head of Department, Department of Environmental Management & Ecology at La Trobe University

      In reply to Dale Bloom

      Organisms that survive are not more or less sophisticated, although they may be better adapted. Usuallay and the ones that survive longer do so becuase their environment was stable during that time.

      I suppose the inside of an Acanthamoeba hasn't changed much over the eons...

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  2. Peter Ormonde
    Peter Ormonde is a Friend of The Conversation.

    Farmer

    "....found in a pond at my University." Talk about a brush with fame.

    Lovely article.

    Truly weird bits of gear viruses - absolute efficiency, crisp minimalism and outstanding engineering ...a unique fusion of form and function... like tiny diabolic dysons. For an economist quite fascinating really.

    Have a look at a few. Some of them look like lunar landers under a decent microscope ... not surprising really given the design principles and constraints involved. Could be Fred Houyle…

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    1. Rotha Jago

      concerned citizen

      In reply to Peter Ormonde

      Makes me wonder about the environment in the pond.
      I have seen a lot of strange life forms since Glyphosate has been
      used so universally here in the tropics.

      The widespread distribution of a substance which breaks the Shikimate Pathway, in the presence of warmth and nutrients, is bound to result in something not seen before.

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    2. Dianna Arthur

      Environmentalist

      In reply to Peter Ormonde

      Great article, Susan Lawler and terrific links Mr O.

      Am still recovering from a rather nasty bout of flu and the thought of giant potato viruses equipped with lunar landing gear... best not think too much about it.

      As for life status of viruses in general - could they simply be "life, Jim, but not as we know it"?

      I am willing to place bets that we discover viruses xeno-terra, before any other alien thing.

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    3. Peter Ormonde
      Peter Ormonde is a Friend of The Conversation.

      Farmer

      In reply to Dianna Arthur

      Yes it's a difficult thing isn't it Ms A - deciding which is more extraordinary - the prospect of extraterrestrial life (which the stats would strongly suggest) or the prospect that there is none and this little blue planet (with brown streaks) is in fact unique. Life alone.

      Which makes even amoebas and their zeppelin sized virus mates rather precious doesn't it?

      I wonder if they sneeze these amoebas? Be shocking that I'd imagine. What does being sneakily infected by a shipping container worth of genetic pathogen do to one? Like a nasty outbreak of elephants in the bladder? Does one try a couple of codral and soldier on lugging your new best friend on a trolly of some sort?

      The more you look at it this whole Nature business is deeply unnatural.

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    4. Dianna Arthur

      Environmentalist

      In reply to Peter Ormonde

      "The more you look at it this whole Nature business is deeply unnatural. "

      If not utterly godforsaken.

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    5. Susan Lawler

      Head of Department, Department of Environmental Management & Ecology at La Trobe University

      In reply to Dianna Arthur

      Interesting speculation, but since viruses can only live in other living cells, they cannot exist alone out there. At least, not as we now know them...

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    6. Peter Ormonde
      Peter Ormonde is a Friend of The Conversation.

      Farmer

      In reply to Susan Lawler

      Depends more on what we mean by "live" really.... true they can on reproduce via a host but rest of the time they're just rather boring and celibate... not living, but not exactly dead either... potential.

      Anyway - aside from moving Canberra offshore - it's been revealed that your Pandora virus is an alien space menace... you read it here first folks ...http://english.ruvr.ru/2013_07_31/Pandora-virus-covert-threat-from-space-7084/

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    7. Michael Wilbur-Ham (MWH)

      Writer (ex telecommunications engineer)

      In reply to Susan Lawler

      Susan,

      We cannot live without other species either.

      Without the food and oxygen provided by plants we would die.

      So if a virus only needs other species to reproduce,
      and we need other species just to live,
      then perhaps a virus is more alive than us? :)

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    8. Susan Lawler

      Head of Department, Department of Environmental Management & Ecology at La Trobe University

      In reply to Peter Ormonde

      Thanks for the link Peter, just priceless. I like the way they say it was "discovered accidentally". I see no reason to speculate that it's origin is extra terrestrial or to worry much about danger to people, but now that the Russians are worried we have to talk about it.

      If Pandoravirus made people sick we would have discovered it long before now.

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    9. Dianna Arthur

      Environmentalist

      In reply to Susan Lawler

      Susan

      A life support system for alien viruses could be as simple as the right chemical cocktail and/or collection of bacteria within a protective layer of rock, after all I suspect that viruses are among the most adaptable forms of self-replicating organisms.

      As for a Pandoravirus epidemic - we are still at a loss to explain so many potato shaped people compared to previous generations ;)

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    10. Peter Ormonde
      Peter Ormonde is a Friend of The Conversation.

      Farmer

      In reply to Dianna Arthur

      The really clever thing about viruses though Ms A is that they don't feel under much of an obligation to reproduce ... they can just hang about doing absolutely nothing for yonks ... just sitting there - not getting any older - no hurry, no biological clock ticking, no thoughts of romance at all ... then the right amoeba or bug or environmental opportunity turns up and away they go like rabbits!!!!

      It's an interesting notion isn't it - that you can have a whole strain of evolutionary success predicated…

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    11. Dianna Arthur

      Environmentalist

      In reply to Peter Ormonde

      "lean and mean and live forever....Economic rationalism in extremis"

      Absolutely. Those neo-capitalists had to get their ideas from somewhere, I mean these people are not among the world's visionaries - it woz virus mind control.

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    12. Peter Ormonde
      Peter Ormonde is a Friend of The Conversation.

      Farmer

      In reply to Dianna Arthur

      Are we creeping to some new explanation of the girthy issues surrounding the likes of Nathan Tinkler, poet laureate Gina or our own Nelson Mandela - Clive Palmer? All larger than life characters in every way possible.

      Where are our slim magnates - our svelte captains of industry?

      But could it all be viral - the behaviour, the size the self-interest - the whole package? Is it possible that we humans have some hitherto unnoticed blimps of tailor-made spud knitting machinery hunting us down like specials at the supermarket?

      There's just gotta be a cure Ms A.

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    13. Dianna Arthur

      Environmentalist

      In reply to Peter Ormonde

      Svelte captains of industry? Possibly Rupert? He looks more preserved in vinegar than plumped by potato virus. Definitely explains Gina - how she managed to march in protest defies normal human powers.

      You may well owe Nelson Mandela an apology. Mr Palmer has been contaminated by a potato virus variant known and unknown as Rumsfeld neuronal clotting virus.

      Am working on a cure...

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    14. Dianna Arthur

      Environmentalist

      In reply to Peter Ormonde

      Oh dear, I think I have to back to the drawing board.

      "Igor, stop that dissection right now...."

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    15. Dale Bloom

      Analyst

      In reply to Susan Lawler

      A smaller size can make it easier and quicker for the cell to reproduce, and more nutrient can be absorbed through the cell membrane due to the larger surface area to volume ratio (SA:V) of a smaller cell.

      http://www.mhhe.com/biosci/esp/2001_gbio/folder_structure/ce/m2/s1/

      Viruses don’t absorb nutrient, but there is a question of why large sized viruses exist at all, as they would have to find a host cell large enough to reproduce the virus inside the host cell.

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