Mass Extinctions, Ancient Viruses May Hold Clues to Life’s Origins

Apr 03, 2009 By Lisa Zyga feature
Crenarchaeal viruses come in diverse morphologies, as shown by these silhouettes. According to a new model, because these viruses live in hot, acidic environments, they may have been immune to the mass extinctions throughout Earth’s history, which explains why they have almost nothing in common with today’s more modern organisms. Image credit: Jalasvuori and Bamford.

(PhysOrg.com) -- Mass extinctions occur repeatedly, though irregularly, throughout Earth’s history, and occasionally these extinctions have been devastating to life on our planet - or have they? Extinction events have sometimes accelerated the evolution of life on earth by eliminating old dominating species and making room for new ones. A new study takes this idea a step further, showing that life may have never achieved the complexity necessary for the development of advanced multi-cellular organisms without recurring extinction events.

In their study, Matti Jalasvuori and Jaana K.H. Bamford of the University of Jyväskylä in Jyväskylä, Finland, have developed a model that helps to explain how life evolved from its origins to the complex cellular systems we see today. Their model is based on a type of virus in the archaeal kingdom called Crenarchaeota, which thrives in extremely hot, acidic environments like those found on the bottom of the ocean, where the infiltrate hosts called acidophilic hyperthermophiles. Because crenarchaeal viruses share almost no similarities with other viruses or , they likely originated very early in Earth’s history.

"On a personal note, I find it exciting to think that very early life on Earth might have had a wide variety of peculiar viruses," Jalasvuori told PhysOrg.com. "We may ask whether their presence is a natural consequence of the processes that led to the origin of the first cells."

In addition to having few similarities with other organisms, crenarchaeal viruses are unexpectedly diverse among themselves, as well. Their diverse morphologies include spheres, light bulbs, bottles, tulips, polyhedrons with tails, and more. In an attempt to explain the origins of these differences, Jalasvuori and Bamford propose that mass extinctions caused by meteorites and volcanoes might have wiped out many cellular organisms, but the hyperthermophiles at the bottom of the ocean would have survived, along with their parasitic viruses.

As the scientists explain, both meteorite impacts and volcanic eruptions can warm the Earth. Meteorites boil the oceans and heat the atmosphere, as well as vaporize sulfoxides in rocks upon impact, leading to poisonous acidic rain. Similarly, volcanism in the form of flood basalts increases carbon dioxide levels, causing atmospheric warming and acid rain. While meteorites and volcanoes are considered the two main causes of extinctions, the “snowball Earth” scenario, in which Earth is covered in ice, may have been another extinction mechanism.

While these events may have led to the extinction of the majority of bacterial and archaeal cells living in cool and neutral-pH environments, the naturally acidic and geothermally heated environments of the crenarchaeal viruses and their hosts would not have been greatly affected. The hyperthermophiles are already used to hot acidic conditions, and geothermal heat would protect them from snowball Earth conditions. The scientists propose, then, that crenarchaeal viruses have simply maintained their originally diverse morphologies, whereas viruses of non-hyperthermophile hosts (including other crenarchaeal viruses) have not. In this view, crenarchaeal viruses in geothermally heated areas would have formed from the primordial gene pool.

As previous research has shown, the battle between viruses and the cells they try to infect is thought to be a major force in driving evolution. Under pressure from viruses, cells continually develop mutations to avoid infections, but these mutations usually aren’t useful in other ways (except coincidentally).

However, as the new model shows, when an extinction event occurs that kills off many of the cells in an environment, the number of viruses also decreases for lack of hosts. The viruses’ main weapon is having a variety of host recognition proteins (HRPs) that know which cells to attack. But fewer viruses means fewer HRPs, so that surviving cells that are immune to the few remaining viruses now have a chance to evolve in an environment free of virus interference. Under virus-free conditions, cells can inherit mutations that are likely to be more useful in the long run, rather than simply defensive strategies. In this way, extinction events speed up the development of new biological functions that might otherwise be unlikely to emerge. Without extinction events, viruses might control all of Earth’s evolution.

"I find the idea that viruses face extinctions along with their hosts important," said Jalasvuori. "It is widely believed that viruses, in a sense, control the evolution of their hosts and kill the evolutionary winners. Therefore, right after extinction level events, such as massive meteorite impacts, there would be very few viruses to bring the success-story of the winner to an end. Some of the novel evolutionary innovations observed today might have emerged for the first time in the genomes of these winners."

Nevertheless, the hot, acidic environments in which ancient species live is not necessarily a hindrance to evolution, and may in fact be essential to life’s origins. Without such regions, emerging life might not have survived meteorite bombardments and volcanic eruptions that repeatedly wipe out species "farther from the nest." Yet, as Jalasvuori and Bamford note, their proposal is only a model, and more research is required to see how well the model fits with data and laboratory studies. Overall, the study shows that the diversity of crenarchaeal viruses in geothermally heated areas requires further attention, since the details could help scientists better understand the origins of life.

"We have experiments taking place within laboratory microcosmoses, in which we attempt to determine the impact of viruses on the evolution of different aspects of their hosts," said Jalasvuori. "These cosmoses give us the control over the factors that could have an effect on the evolution of the hosts and thus we should be able to see more precisely the adaptive traits that are caused by viruses and those that are not."

More information: Jalasvuori, Matti and Bamford, Jaana K.H. "Did the Ancient Crenarchael Viruses from the Dawn of Life Survive Exceptionally Well the Eons of Meteorite Bombardment?" Astrobiology, Volume 9, Number 1, 2009. © Mary Ann Liebert, Inc. DOI: 10.1089/ast.2007.0189.

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All rights reserved. This material may not be published, broadcast, rewritten or redistributed in whole or part without the express written permission of PhysOrg.com.

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tkjtkj
4.5 / 5 (4) Apr 03, 2009
Good article, yet it suffers from some misperceptions:

Viruses are not alive. They are merely particles/collections of DNA/RNA that are 'spilled out ' by truely living organisms and are either then ingested (much as a paramecium will 'ingest' strings of free-floating DNA) and by default should be considered to be 'information data packets' that have come to exist because they have evolutionary advantage to the organisms which are able to use the nucleic acid's data.

We see this throughout the cellular world: bacteria taking in DNA whose data convey ability to resist antibiotics, eg..

That early existing organisms evolved a way to manufacture (xerox?) multiple copies of a DNA string (precursor virus?) and even to have such particles protected by very resiliant 'envelopes' is not surprising.

When we add the fact that increasing temperatures (re: oceanic vents) can drasticlly increase the velocity of chemical evolution (and consequently, later, biological evolution) we are not surprised.

In fact, I have made the case that the essential condition for development of life is not 'water' but is, in fact, 'heat'. This means that we often are looking at the wrong 'time scale' when we offer some figure representing 'velocity of evolution'. An environment at a temperature much higher than temps we are 'used to' will foster extremely rapid chemical reaction rates, ie: extremely fast evolution velocity. Millions of years might not be necessary to pass in order for great flowerings of bio-diversity can appear.

This concept also forces us to consider that on other worlds, where the laws of physics are still working, oceans of methane, eg, can exist on frigid planets, where 'hot vents' can supply the reaction velocities necessary for life forms based upon a 'hot methane' environment.

I do hope that NASA and those who contribute ideas for future planetary exploration do consider these ideas.

tkjtkj@gmail.com
TJ_alberta
5 / 5 (1) Apr 04, 2009
Valid point tkjtki. I think an external energy source has always been assumed necessary to get the chemical reactions going so why not heat, as you suggest.



It will be interesting to see these viral DNAs sequenced. The sequencing might answer the question: are they really archaic or just adapted to hot acidic conditions and their highly specialized hosts.



Whatever the outcome it seems clear that intensive study of extremophiles can contribute both to biology here and exobiology.
smiffy
3 / 5 (3) Apr 04, 2009
I find the the basic premise of this article very difficult to accept. Viruses can only exist in close association with their hosts. The chances that a species could be exposed to a near extinction event where all instances of virus carriers are eliminated, yet leaving just a very few organisms that happen to be virus-free, must be very very slim. And how long would it be before a virus from a similar species jumped the species gap to re-infect?

Also I don't go much on the idea that a cell's mutations are usually confined to fighting off viruses. Why not fight off viruses and develop useful mutations at the same time? Why should one exclude or even inhibit the other?
KVie
5 / 5 (1) Apr 04, 2009
Well, smiffy, I guess the point was that there are only few hosts left after a near-extinction event, and when the survivors start to recolonize the habitat there would be only few different types of viruses to infect them. Thus the survivors don't actually need to be virus free.. Think humans for example: it would require much less effort from our immune system if there was only, lets say, herpes virus infecting us, instead of the great variety of different viruses (influenza, ebola, nipah, HIV etc) that can each cause great damage to our bodies. If most humans would die, then perhaps we could also get rid of most of our viruses (..for a while).

It might just be easier for the hosts to cope with only few different viruses. And natural selection perhaps can favor totally different traits in such hosts.
smiffy
2 / 5 (1) Apr 04, 2009
I take your point about the remaining organisms having to suffer fewer viruses.

But firstly I would have thought that events that wipe out nearly all of a certain species but stop just short of annihilating them all, are relatively rare. I don't know what the mathematics would be, but to have a virus-destroying effect the species would have to be reduced to a few thousand in number? And to suffer such adverse conditions would possibly mean that the remaining few would have reduced immune system response and be all the more vulnerable to viral infection, and therefore be bearing a relatively higher level of infection.

Secondly, in being reduced in number the species will also be losing genetic diversity and will therefore have a more restricted gene pool on which to draw for future evolution. This will have the opposite effect to what the researchers are claiming.

Thirdly, and more speculatively, can we be sure that viruses themselves are not acting as a horizontal gene transfer vector, responsible for increased genetic change in their hosts?

The thinking behind the article seems to be 'What doesn't kill me makes me stronger'. A discredited philosophy I think. The benefits conferred on a species' evolutionary success by having fewer viruses would be more than offset by the disadvantages of a greatly reduced population, and a reduced gene pool for the survivors.

Three further points about the article -
The research was on extremophiles and these were safely cosseted from the environmental stress that would provide near-extinction events. So the statements on this seem to be speculations outside the scope of their investigation.
It is widely believed that viruses, in a sense, control the evolution of their hosts and kill the evolutionary winners.
I'm not a biologist so I can't comment on where the wide belief comes from but I would have thought viruses are more likely to kill the struggling evolutionary *losers* and therefore help accelerate evolution.

I still don't know what the relevance is to the origin of life that the title claims. Seems to be a typical weekend hyped-up title by PhysOrg to get people clicking.
el_gramador
not rated yet Apr 04, 2009
@ smiffy: The title does discuss what it talks about. It talks about Mass Extinctions, and discusses an ancient virus that may hold clues. It does well in that sense, but fails to grab attention, for me anyway, with the lack of any real interesting discussion.

As for the idea that viruses can't be living, consider this: If HIV, a virus, is only a collection of proteins encasing DNA and cannot be considered alive, then how does it react to constantly changing environments? If not by receptors on the surface of the protein case, then how does it know how to attack and defend. In a very simple sense it is a bag of life, though not necessarily the most useful or helpful. Along with the fact that organisms tend towards preservation of helpful traits at the time when it is most suited (they keep their genes when they are useful).
KVie
not rated yet Apr 05, 2009
smiffy: I understand your point about extinction-events, but I guess it would be more unlikely that most organisms survived them (e.g. massive meteorite impacts) but then only few species would be destroyed completely. When the asteroid wiped out dinosaurs, I am quite sure that also mammals faced big losses in their numbers. However, mammals just didn't all die.
Moreover, I don't see why the death of your fellow family members would reduce your capability to fight off virus infections (unless they die due to lack of food, in which case you would be starving also)..

And for the second part: You are right that the amount of genes in the pool decrease. However, evolution is not all about picking genes from the gene pool. Extinctions are known to sometimes speed up evolution, so therefore the reduction of different genes seem not have had that much of an effect during Cambrian explosion, for example. Instead, the reduction of the amount of competing organisms perhaps gave room for new (genetic) innovations to evolve.

And about the relatedness to origin of life: since the simplest cell is a rather complex organism, it could not have emerged out of nothing. These (perhaps) ancient viruses may therefore be somehow related to this chain of events that led to the origin of the first cell.

smiffy
5 / 5 (1) Apr 05, 2009
KVie: I think that there is a distinction to be made between mass extinction events in general and the kind of extinction event the article focuses on - which I've called a near extinction event ( or what might be more accurately called a dam' near-extinction event since I'm assuming that to get a reduction in population of a species that significantly eliminates the viruses associated with that species would mean that only a few thousand members remain. That assumption is a guess and may well be wrong.)
I don't doubt that any kind of calamitous event to befall an ecosystem, resulting in a massive drop in population, offers great opportunities for those lucky enough to survive, and that this will mean that the subsequent course of evolution is markedly changed from what it would have been. For instance the Black Death allegedly killed off about a third of the population in Britain, but also could be said to have liberated the lower classes from poverty and servitude, as post-plague demand for their labour soared. However that is far from a near-extinction event - to get such an extreme outcome the whole population must suffer badly from the heavily fatal environmental conditions. (Unless the deaths were caused, say, by a specific virus, that the few surivors were simply lucky enough to be resistant to) The environmental stress would also weaken the very few survivors physically, and these survivors, also weakened both in terms of numbers and in terms of their gene pool, might well have to compete with those species that didn't suffer so much - such as species who, say, lost 'only' 0-90% of their populations. I know where I'd be placing my bets.

As far as the title relevance is concerned I must simply disagree with both you and el_gramador. Viruses are parasites relying on their host's replicative machinery in order to reproduce, and must have therefore evolved after the first cell. They couldn't have had an influence on the origin of cells.

What is good about the research paper is the highlighting of the great range and variety of the extremophiles' vruses. This is what you might expect in a species which lives in a hyperthermal vent on the deep ocean floor. Here is an environment where there is a great deal of stability which implies that nearly all the environmental pressures are from predators and parasites. The extremophile's evolution would be to address threats predominately from that quarter. The viruses would likewise also have to match their hosts, giving rise to their diversity. Possibly this is how the researchers came up with idea that viruses can preoccupy the evolution of a species and somehow inhibit that species' evolution in general. I think that the extremophiles didn't evolve in a more 'general' way because their environment simply didn't demand it.
A_Paradox
not rated yet Apr 07, 2009
I think I agree with just about everybody here. It seems we are talking as much as 4 billion years of evolution in what may well have been the original "gene pool"; 4 km down in the smoker tubes and environs at the ocean spreading centres. If we think of organisms as coalitions of genes cooperating to their mutual advantage, there were no species until sexual reproduction started. Prior to that there were only quasi species - which is what viruses are - but it somehow evolved that some quasi species made much bigger organisms than others. Obviously that had to be for there to be enough genes to provide the recipes and guidance enabling growth in size and self-duplication.

I assume viruses were just one way of some kinds of genes getting themselves reproduced, like the plasmids that bacteria can absorb and emit. It may be, for example, that virus coatings provided a means whereby different kinds of protective skins evolved, enabling adhesion to different kinds of newly condensing rocks and minerals at different locations along the mid-ocean spreading centres.

Perhaps it is simply the case that the periodic fluctuations in population numbers and geographic spread caused when virus parasites, added a degree of destabilisation in the otherwise too cosy smoker tubes. Once sexual reproduction arrived the variation and useful 'chaos' caused by virus was no longer necessary but because viruses [the successful ones anyway :-] always evolve dialectically with their host species, they have been with us ever since.

I think the meteorites, super volcanoes, interstellar dust clouds, evolution of Earth's inner chemistry, evolution of the crust, etc, are all just by the by. We happened eventually but almost didn't. It could have been dinosaurs burning all the fossil hydrocarbons, or maybe elephants might eventually have gotten around to burning each other at the stake. If we stuff it all up totally this time, it may well be something totally different that comes away from the smokers after a few hundred million years. Won't we look stupid - just another bunch of curious fossils in the rocks, another 'great extinction'.

We must lift our game.
A_Paradox
3 / 5 (2) Apr 07, 2009
I just thought: 4km down in the spreading centres would be pretty safe from supernovae also.
jeffsaunders
1 / 5 (1) Apr 08, 2009
ditto
Avitar
1 / 5 (1) Apr 09, 2009
It was not too many years after Darwin hijacked the Creationist Science (where humans are the creators) of Animal Husbandry that it was identified that without eliminating the existing populations evolution would not operate fast enough to account for observed conditions. Observations on the original volcanic islands on which Darwin made his observations argues that evolution must be driven by "regional" mass extinctions from super volcanoes and continent size meteor strikes.

This field of study is very promising. The distribution of mutations in the crenarchaeal viruses and their hosts across the ocean floors should provide important information in the relative frequency and the types of regional mass extinctions. A strike of intermediate size meteor has to cause content size regional extinctions with much higher frequency than the worldwide events but likely leaves detectable persistent footprint in the genetics of the regional populations of the crenarchaeal viruses and their hosts in the regions most affected.

I am speaking of a persistence of much shorter timeframe of earth history than Matti Jalasvuori and Jaana K.H. Bamford seem to be focused on.
denijane
not rated yet Apr 10, 2009
A lovely article! I find it fascinating how the worst kind of event, can actually lead to something good-but it's what always happens in history. The spiral always goes upwards.

As for whether viruses are alive, I think that is a nonsense discussion. We don't know what life is yet-because we've seen it in only one form. Who knows what else the Universe came up with. And you have to admit viruses are quite well adapted to survive and thrive. Only bacteria beats them into that.
smiffy
5 / 5 (1) Apr 10, 2009
I find it fascinating how the worst kind of event, can actually lead to something good-but it's what always happens in history
Everything in history leads to us. That's why we see it as leading to 'something good'.

Even if there were a spiral, where it goes no-one knows.
jeffsaunders
not rated yet Apr 16, 2009
Had a discussion about life just the other day with my brother. It came to a not very satisfactory conclusion because our definition of life is completely different.

He was suggesting life as a state of matter almost where I say there is not border line between life and non-life.

He was saying a person is alive and well then they are not. therefore something must turn non-living substance into living.

I say there is no such thing. A person is a colony not an individual. A person is not alive one minute and dead the next. Instead they are alive and dead at the same time depending where you look and even after catastrophic event a person dies gradually and may outlast the brain activity in many parts by considerable time.

Consciousness, likewise is not on then off, but exists in full range from active to not active and the point where a person stops functioning in a conscious way is not necessarily a point of death, just look at coma patients.

When a person/colony has a major defect in critical piece of infrastructure it may lie down and die officially. But, again, a person may be a single unit legally but that does not mean we are in truth single entities. A breakdown in a towns sewer system if not repaired, will spell the death of the town, just like a breakdown in our kidneys will spell the death of a person if it is not repaired.

Like a town, a person has need of infrastructure as well as skilled sub units devoted to various tasks.
We have the equivalent of transport, electricity, water and waste management systems as well as numerous other sub systems like law and order etc.

buddhamaster
not rated yet Apr 24, 2009
Given enough time to transpire (3.5 to 4.5 billion years), every possible chemical/molecular combination and condition would have frequently occurred in numerous locations for primordial life to emerge from matter is possible. Time is the essence. In the presence matter and of course heat, the energy to make the chemical reaction possible, it is just a matter of time. The rest is only details. The successful seeding of life could very likely be terrestial or extra-terrestial.

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