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Giant marine virus found

Researchers discover yet another virus with a large, complex genome, suggesting they may be fairly common

By | October 25, 2010

With a genome of more than 700 kilobases, a newly discovered virus marks the first giant virus known to infect a marine organism, and the second largest virus ever recorded.
Image: Wikimedia commons
The discovery, published this week in Proceedings of the National Academy of Sciences (PNAS), adds to the growing list of giant DNA viruses and suggests that these viruses, which appear to obtain much of their large genomes from their hosts and other microorganisms, may be more commonplace than scientists once believed. "It's really interesting, and a completely different way of seeing viruses," said microbiologist linkurl:Didier Raoult;http://www.antimicrobe.org/authors/didier_raoult.asp of the University of the Mediterranean in Marseille, France, who was not involved in the research. "It's a completely new field that is emerging." These viruses "are probably playing a big role in the genetic diversity of organisms in the ocean as well," said microbiologist linkurl:James Van Etten;http://www.unl.edu/virologycenter/faculty/vanetten.shtml of the University of Nebraska, who also did not participate in the study. Not only can viruses take up genetic material from their hosts and other organisms, but they can donate genes, as well, he said. "If you're teaching a beginning virology course now, it'd be pretty hard to ignore... that there are these very large DNA viruses in nature," said Van Etten, who edited the PNAS paper. Over the past decade or so, scientists have slowly begun identifying viruses that defied the conventional idea that they were tiny infectious agents with highly streamlined genomes. In 2004, researchers discovered and sequenced the 1.2 million-base pair genome of the largest known virus to date, the mimivirus (although still dwarfed by sequenced multicellular organisms, whose genomes usually exceed 100 million base pairs). This virus, and most of the other recently discovered giant viruses, has been found in amoebae, which are sometimes referred to as "melting pots" because of all the microorganisms they ingest. Inside the amoebae, these viruses and bacteria may exchange their DNA and grow their genomes. The new giant virus, dubbed CroV, is the first to be isolated from a marine organism -- a microzooplankton called Cafeteria roenbergensis. They are major consumers of heterotrophic bacteria and phytoplankton, and thus critical to maintaining the delicate balance of marine food webs. Once thought not to exist in marine environments, scientists now realize that there are some 50 million viruses in every milliliter of seawater. Every day, marine viruses kill about 20 percent of the ocean's microorganisms, which produce about half the oxygen on the planet. "These [viruses] are major players in the global ecosystem," said study author and marine virologist linkurl:Curtis Suttle;http://www.eos.ubc.ca/about/faculty/C.Suttle.html of the University of British Columbia. Like amoebae, C. roenbergensis harbor many microorganisms simultaneously, making them "a good place to exchange genes," Raoult said. "When you live in a phagocytic protist, such as this one, you meet a number of microorganisms, and then you can exchange genes and get a bigger genome." Indeed, of the 500 protein-coding genes Suttle and his colleagues found when they sequenced the virus's genome, about half were similar to those in eukaryotes, bacteria, archaea, and other giant viruses. Those with known function included genes that code for translation factors, DNA repair enzymes, ubiquitin pathway components, and tRNAs. "We're finding suites of genes that you would really never expect to find in viral life, but would expect to find in cellular organisms," Suttle said. "It is exciting to verify that [these large viruses] are out there," Van Etten said. There are likely many more, he added; "it's just a matter of people looking." Editor's Note: A linkurl:2005 paper in Science;http://www.sciencemag.org/cgi/content/short/309/5737/1090 also found a large DNA virus in marine microalga. The Cafeteria roenbergensis virus discovered by Suttle and colleagues is in fact the largest marine virus found to date, with a genome nearly twice the size of any other sequenced marine virus. There is no official definition of "giant virus," and conservative researchers would only include the Mimivirus and Mimi-like viruses (such as CroV), according to coauthor linkurl:Matthias Fischer.;http://www.ocgy.ubc.ca/%7Esuttle/?p=matthias As a result, some would indeed call this the first "giant" virus found in a marine organism.
**__Related stories:__***linkurl:New giant virus discovered;http://www.the-scientist.com/blog/display/56208/
[7th December 2009]*linkurl:A virus's virus;http://www.the-scientist.com/blog/display/54915/
[6th August 2008]

Comments

Avatar of: Michael Shapira

Michael Shapira

Posts: 3

October 26, 2010

Every once in a while you come across an estimate for the contribution of a biological feature/process, something that looks like a back of the envelope calculation. These are always interesting, as they demonstrate in a very straightforward way the importance of that feature. However, how can we know how reliable it is? It is not expected to be very accurate - after all, these are typically rough estimates, but it would be nice to know what is the basis for such a calculation and who did it.\n
Avatar of: Michael Shapira

Michael Shapira

Posts: 3

October 26, 2010

Of course, the example referred to is\n"...there are some 50 million viruses in every milliliter of seawater. Every day, marine viruses kill about 20 percent of the ocean's microorganisms, which produce about half the oxygen on the planet."
Avatar of: Ed Rybicki

Ed Rybicki

Posts: 82

October 26, 2010

Hard to know what the previous comment refers to: WHICH calculation? The figures for numbers of viruses per ml of seawater are pretty solid; I've been following this sort of thing a while now, and there are enough samplings that one can be pretty sure that there are 50 million virions per ml - give or take 40 million odd, I am sure, depending on WHICH ml you are looking at - which are doing serious damage to the oceans' micro- and other organisms, and hastening the carbon cycle. And contributing a significant amount of oxygen to our atmosphere, by adding to the efficiency of photosynthesis in cyano (blue-green) bacteria.\n\nGreat things, viruses!
Avatar of: Ed Rybicki

Ed Rybicki

Posts: 82

October 26, 2010

Ummmm...well, at 700 kb it may be the biggest, but it is NOT the first: that distinction belongs to "...The genus Coccolithovirus [which] is a recently discovered group of viruses that infect the globally important marine calcifying microalga Emiliania huxleyi" - the exemplar of which has a 407 kb genome, and was described in Science on 12 August 2005 (Complete Genome Sequence and Lytic Phase Transcription Profile of a Coccolithovirus; William H. Wilson et al., Science Vol. 309. no. 5737, pp. 1090 - 1092; DOI: 10.1126/science.1113109).
Avatar of: Mike Waldrep

Mike Waldrep

Posts: 155

October 26, 2010

Interesting!
Avatar of: Jef Akst

Jef Akst

Posts: 28

October 26, 2010

Thanks for your comment and this citation, Ed. We are looking into this issue further and will post an update as soon as possible.\n\nThanks for reading!\n~Jef Akst, Associate Editor, The Scientist
Avatar of: Jonas Moses

Jonas Moses

Posts: 26

October 26, 2010

"We're finding suites of genes that you would really never expect to find in viral life, but would expect to find in cellular organisms," Suttle said.\n\n"...viral life...?\n\nThis statement was culled from the last few sentences in the article, written by Jeff Akst. I feel compelled to point out to Mr. Akst that he failed, in fundamental way, to call out another scientist on a serious flaw in the way people think about viruses: There is no single piece of evidence that suggests viruses are living things, or can be considered organisms. As recently as today, I had this same conversation with a medical scientist. Viruses plainly do not meet the classical definition of what constitutes "life": they do not respire, do not undergo sexual or asexual reproduction and do not metabolize.\n\nWe must, in the name of Science (a capital "S,"with intention) and the Scientific Method, put a stop to sloppy reporting of medical and Life Sciences facts. When trained, educated scientists not only mis-speak facts but allow the perpetuation of non-scientific statements and ideas, the entire lay public is done a huge disservice. Please, let us identify the opinions, the factoids, the hypotheses, the dogma, the "truths" for what they are. When we report on them, we must label them appropriately. We must clearly separate statements of fact from all other statements, opinions or observations. \n\nI am horrified at the absolute drivel that passes for statement of scientific or medical fact - especially in the Media, and prominently as regards cancer and infectious diseases. On a daily basis, one or another scientist or physician is being interviewed and makes a patently wrong and misleading statement, such as "this virus is very smart...it has cleverly mutated so as to be resistant to current drug therapies." \n\nEven a young child can be made to understand that something non-living, which does not have a brain, which has no cognitive abilities and is incapable of acting even on primitive thought or genetic memory, cannot possibly modify itself to "outsmart" a drug... There is a world - a universe (!) - of difference between drug-resistant strains of bacterium (living organisms) and non-living DNA/RNA strands (viruses).\n\nThe ridiculous personification of a simple chain of DNA or RNA is outrageous, ans unacceptable. Yet, when prominent scientists spout such nonsense on television, on the radio or in the print media, millions of lay citizens accept these as statements of fact, and then not only do not question these "fact"...they repeat this junk science to others and also take action in how they live their own lives, based upon what they have heard.\n\nMr. Akst, time and again you have quoted the misstatements of other scientists, either ignorant of their falsehood (a forgivable, occasional sin, which simply means you did not do your homework) or (in so-doing) blatantly failing to editorialize on statements you must certainly know to be incorrect.\n\nI have made this observation on many occasions - in my lectures, in my television series, in radio interviews and in my scientific writings:\n\n"...we must also acknowledge that there can be no sacred cows, no immutable dogma or doctrine. For, as soon as we cease to question hypotheses and conventional wisdom, we have lost the ability to engage in the most fundamental processes of discovery ? the Scientific Method. When we begin to elevate our paradigms to the status of deities, then we have also made of our science a religion."\n\nCorollary to this idea is how we report on medical and scientific theories, paradigms, dogma and conventional wisdom. All too often - indeed, with alarming regularity - the medical and scientific communities state theories/hypotheses and dogma as facts. Facts exist in a vacuum, in the absence of a human observer. A blending of all electromagnetic wavelengths in the visible spectrum produces white light. That is a physical fact. How white the light looks to one observer versus another, is not fact...for it is relative to the observer's ability to perceive light and color and to process and articulate this information. This is the reporting of perception, not fact.\n\nMr. Akst, I implore you, as one earnest scientific reporter to another: please stick with reporting the facts. Leave the "truths," "factoids," "opinions," "conventional wisdoms" and "dogma" to Fox News.\n\nRespectfully submitted, \n\nDr. Jonas Moses\n
Avatar of: CURTIS SUTTLE

CURTIS SUTTLE

Posts: 1

October 26, 2010

Thanks for your interest in the topic. The question of whether viruses are alive is a topic of some debate and complexity. For excellent, and balanced perspectives, I encourage a look at:\n\nhttp://www.uvm.edu/~biology/Classes/011/alive.pdf\nhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC2837877/\n\n
Avatar of: thanit intaphan

thanit intaphan

Posts: 4

October 26, 2010

In 2004, researchers discovered and sequenced the 1.2 million-base pair genome of the largest known virus to date, the mimivirus\n\n---but why mimivirus has around 900 protein-coding genes?? read this from Virus's virus\n\nsorry my question is kind of weird but i really want to know it.
Avatar of: thanit intaphan

thanit intaphan

Posts: 4

October 26, 2010

well , i can`t say that virus is really a dead thing. but i can't say it is a living thing either.\ni think they kind of between the two major. \n\nseriously we can't say it a non-living thing. in my part i voted for virus is a living thing. \n1. it contain DNA \n2.it maintain order inside their body.\n3.living thing develop and respond . virus can mutate and fight immune system\n4.it reproduce (even thought it needs host)\n5.virus have traits that evolved over time . see HIV virus was an evolution form Simian virus!!\n\ni don't know a lot about virus but i think it is one kind of living thing...\n\nif you are saying it is non living thing how can we explain why it contain DNA , reproduce , and have evolution?? look at rock ,river , sand! they are non-living thing. they don't have any revolution and can't respond to the signal either. but virus can. how can we say it is non-living thing though.\n\ni think if we can't not put it in living or non-living group. why don`t we put it in another group though. saying it is living or non-living can`t give us any real answer.\n\nsorry if i said something wrong.
Avatar of: Philip Harriman

Philip Harriman

Posts: 5

October 26, 2010

I'm replying to the comment by a Dr. Jonas Moses. Reasonable people can disagree over whether or not viruses are "alive". I remember first debating this in the Virology Department at UC Berkeley when I was a graduate student there in the 1960s. They do reproduce, mutate, and evolve. They even have sex; two different viruses infecting the same call can swap genes, and viruses with a combination of genes from the two parental viruses can emerge. Al Hershey shared a Nobel Prize, in part, for discovering this. From the Nobel award ceremony: "The realization that bacteriophage after all is a respectable representative of all living matter was slow in coming. Today, however, the general applicability of the principles you established is beyond doubt and the full impact of your achievements is finally felt. You have been awarded this year's Nobel prize in physiology and medicine for your discoveries concerning virus replication and genetics..." Having become acquainted with the concept of "fuzzy sets" and "fuzzy logic" I now think of viruses as "half alive". They share some properties with what we think of as alive, but other properties with inanimate macromolecules.\nPhil Harriman, PhD \n
Avatar of: DENNIS HOLLENBERG

DENNIS HOLLENBERG

Posts: 26

October 26, 2010

Like many single-celled and multicellular parasites, viruses require hosts' organic processes to reproduce (think of Sacculina spp.). Like spores and pollen, viruses don't metabolize; maybe we should view them as 'spores' of pathological cells. Nature's living variations transcend humans' parochial criteria, among which are viruses.\n\n@Moses: We have no universal definition of life, nor do we have a discipline-spanning theory of life (because we perform science as discrete businesses serving disparate markets rather than as the orthogonal and cooperative pursuit of knowledge per se that the promotional brochures would have you believe). Perhaps such facts tell you something about the human-centric view of nature.
Avatar of: MICHAEL ALLEN

MICHAEL ALLEN

Posts: 1

October 27, 2010

I really think this a rather over the top response to Curtis Suttle's quote on "viral life". I have no desire to get into a debate over what is or is not alive. [Although, I'm of the opinion that viruses are undead?.. work that one out]. I think you have missed the point and have taken the phrase out of context. We often use the word "life" in our dealings with research e.g. life cycle, half-life etc, which is not associated with respiration, sexual reproduction, metabolism. I do not think for one moment that a radio-active atom has a life, but I know it has a half-life. My car is not alive, but I know it will reach the end of its working life in a few years. The phrase "viral life" in the quote has yet another meaning, here (I believe) Curtis is referring to the realm/domain/area associated with viruses. This is a common usage of the word 'life' e.g. we all have a work life and a personal life, 'life' in this regard being used to separate work from play activities. Using "viral life" in this context is perfectly acceptable in my opinion; Curtis is merely referring to a domain ("viral life") separate from bacteria, archaea and eukaryotic domains, not making bold statements about the status of life on earth. \n\n\n
Avatar of: WILBER BAKER

WILBER BAKER

Posts: 1

October 27, 2010

Posts on this topic remind me of a brief, but memorable, exchange between two faculty members during a senior colloquium in the spring of 1956 when I was a student at Grinnell College. Although our knowledge base has increased by orders of magnitude, the debate remains essentially unchanged.
Avatar of: Jonas Moses

Jonas Moses

Posts: 26

October 27, 2010

Dr. Suttle, thank you for directing me to the article by Luis Villareal. While his work is highly readable, in it he only serves to illustrate my point:\n\n"Of course, evolutionary biologists do not deny that viruses have had some role in evolution. But by viewing viruses as inanimate, these investigators place them in the same category\nof influences as, say, climate change. Such external influences select among individuals having varied, genetically controlled traits; those individuals most able to survive and thrive when faced with these challenges go on to reproduce most successfully and hence spread their genes to future generations. But viruses directly exchange genetic information with living\norganisms?that is, within the web of life itself. A possible surprise to most physicians, and perhaps to most evolutionary biologists as well, is that most known viruses are persistent\nand innocuous, not pathogenic. They take up residence in cells, where they may remain dormant for long periods or take advantage of the cells? replication apparatus to reproduce at a slow and steady rate. These viruses have developed many\nclever ways to avoid detection by the host immune system?essentially every step in the immune process can be altered or controlled by various genes found in one virus or another."\n\nI call attention, here again, to Villareal's statement that, "...these viruses have developed many clever ways to avoid detection by the host immune system..."\n\nWhether or not you believe that viruses are living organisms, precursors of life, seeds/spores, or chemistry sets in a protein bag...there is one thing that is certain: viruses are not sentient - they cannot be clever, devious, evil or malevolent. Perhaps you feel that I am over-stating the obvious, here? \n\nTo all those who chose to make commentary on my first posting: you have missed the point of what I said. You attack my take on viral theory, which has little to do with why I opted to post a response to this article.\n\nYes, you are all correct. I am by no means a virus expert, not a world-class cell biologist, not a guru on infectious diseases; I am only a learner...and not yet learned. Very well, fine. I am no one of consequence. Also fine. All of you are the experts; I concede you that. Factually, I know little about anything, save that I am able to recognize that what we state, publish, broadcast as scientific fact - when it is anything but - is irresponsible reporting. \n\nConsider that not everyone who reads what you write, listens to your lectures, sees you being interviewed on television or hears you on the radio is as well-versed in your science as are your colleagues and you. Indeed, and perhaps surprising to you - the vast majority of your audiences are not members of your scientific and medical communities, they are from among the general lay public. Herein lies the crux of my message...what all of you failed to note and acknowledge. We all have a responsibility to this larger audience to take care with our reporting of facts, versus the reporting of our opinions, hypotheses, dogma, and conjecture.\n\nAs regards what is fact, fiction, hyperbole or hypotheses concerning viruses: this is virtually irrelevant to my main concern and sole reason for posting a comment here, in the first place. It is interesting, if unsurprising to me, that none of you - who readily attacked my perspectives on viruses - even took note of (or if you did notice, chose to address) the far more significant and challenging issue of how we differentiate between fact, hypothesis and opinion when we report on Medicine, the Sciences and Technology issues. \n\nSincere thanks to all of you for seeking to further educate me on viral theory. Perhaps you, collectively, would also consider taking the lead in championing the cause of reporting on scientific/medical fact, when you report on Science and Medicine?\n\nRespectfully submitted, \n\nDr. Jonas Moses\n\n[An aside: Dr. Suttle, I would be most interested in sharing a conversation, offline, regarding your scientific views. Please let me know how we might connect? Thank you.]
Avatar of: thanit intaphan

thanit intaphan

Posts: 4

October 28, 2010

sorry doctor Jonarh\n\ni was probably miss understood your point of view in your first comment. i'm really apologize for that. but as what i had read. i really feel that science issue write with easy understanding words. even its mean you have to said virus are clever. it is easier to understand that way. it was how my Biology teacher though me. i think it is easy to understand and remember them. like sometime i imagine that an antigen is like a police man though.\ni'm not a scientist. only a high school student and i found it very hard to read any science issue that write down very hard and i alway gave up half way. ^-^
Avatar of: Steven Pace

Steven Pace

Posts: 22

November 7, 2010

The common definition of life can be like porn, "I don't know, but I know it when I see it". For a scientific definition of life, we can, and probably should have several. Life in my opinion, could be as simple as a single self replicating protein. If a definition is useful in a particular context, than use it; like any other tool.
Avatar of: anonymous poster

anonymous poster

Posts: 13

February 15, 2011

Perhaps viruses should be viewed as one modality of the assortment of genetic systems found in what everyone agrees are living cells. Viruses infect and lyse cells, sometimes, but also integrate, transduce, or bleb off new encapsulated virions without killing the host cell. They may be a horizontal genetic transfer mechanism that sometimes gets out of hand. And what of jumping genes, transposons, insertion sequences, viroids, prions, yadda yadda--it's a jungle in there! I've read articles describing multicellular animals as multigenomic composite organisms; perhaps we have further levels to become aware of under the category of "alive".

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