Deep-Sea Viruses Destroy Archaea

Viruses are responsible for the majority of archaea deaths on the deep ocean floors, scientists show.

By | October 12, 2016

WIKIMEDIA, LARS LENTZIn the microbial populations of deep-sea sediments, archaea suffer viral infections about twice as often as bacteria, despite the latter being more abundant, according to a study published in Science Advances today (October 12). Given the enormous scale of deep-sea ecosystems, the results indicate that archaea-virus relationships could be a major contributor to global biogeochemical cycles.

“[This] appears to be a careful and thorough study that has significant implications for microbial communities across all oceanic basins,” microbiologist Steven Wilhelm of the University of Tennessee, Knoxville, who was not involved in the work, wrote in an email to The Scientist. “[It] implies that certain microbial populations are much more susceptible to virus activity in these deep ocean regions,” he added.

Deep-sea ecosystems cover more than 65 percent of the world’s surface and comprise more than 90 percent of the global biosphere, but how they work is still somewhat of a mystery, said marine biologist and ecologist Roberto Danovaro of the Marche Polytechnic University in Ancona, Italy. One thing that is clear: just like in the rest of the world’s biosphere, viruses are by far the most abundant biological entities in the deep ocean.

The main hosts for these viruses are prokaryotes (bacteria and archaea), explained Danovaro. Indeed, he and his colleagues have previously shown that nearly all prokaryotic death in deep-sea sediments is due to viral infection. And, because of the scale of these ecosystems, the team has estimated that this viral killing of prokaryotes is responsible for the global release of between 0.37 and 0.63 gigatons of carbon per year.

On land and in the shallows, in general bacteria are considerably more abundant than archaea, explained Danovaro, “But in the deep, [archaea] become much more abundant,” he said. In the deep-sea samples analyzed in the present study, for example, Danovaro’s team showed that archaea comprised up to 32 percent (average 12 percent) of the prokaryotes. Given that archaea likely have a larger influence on these ecosystems than others, Danovaro’s team examined viral killing of archaea in particular.

Using nearly 500 sediment samples from deep-sea regions across the globe, the team analyzed extracellular DNA—as a proxy for virus-induced cell lysis—and determined that while between 1 percent and 2.2 percent of bacteria were lysed by viral infection per day, for archaea the lysis rate was double (2.3 percent to 4.3 percent). Thus, although archaea are less abundant than bacteria in these ecosystems, they are considerably more susceptible to viral infection, the researchers reported.

“If there is a lot of mortality due to viruses, then the growth rates of the cells have to offset this,” explained Wilhelm.

Sure enough, the team calculated that the turnover times of archaea in their samples were 12 to 22 days, compared with 31 to 52 days for the bacteria. Extrapolating from their results, the team estimated that viral lysis of archaea alone could contribute between 15 percent and 30 percent of the total carbon released from virus-killed prokaryotes in this ecosystem.

The authors concluded that viruses play a crucial role in the lifecycle of deep-sea archaea and, in turn, the global cycling of carbon as well as other chemicals and nutrients.

The results are “an important contribution to our understanding of marine archaea and their viruses with respect to both biogeochemical cycling and ecological interactions,” ecologist and evolutionary biologist Julie Huber of the Marine Biological Laboratory at Woods Hole, Massachusetts, who did not participate in the research, wrote in an email to The Scientist. “While marine sediments remain more well-studied then many other subseafloor habitats, this is essential data that will serve as an important comparison point as more studies are done on archaea-virus interactions in a variety of marine habitats,” she added.

R. Danovaro et al., “Virus-mediated archaeal hecatomb in the deep seafloor,” Science Advances, doi:10.1126/sciadv.1600492, 2016.

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Avatar of: JonRichfield

JonRichfield

Posts: 131

October 15, 2016

This is not about the subject matter, but about the presentation. I beg The Scientist to eschew the expression "scientists show", and abandon it to the uncomprehending tabloids. How about something more like "sediment samples show" or "microbiologists conclude" (or whatever the line of work was. Some verbs less hackneyed than "show" might also be nice, though that may be less important.)

October 17, 2016

Hmmnn.  Maybe. Ruth Williams' summary of this work might describe evidence for LYSIS (as measured by the presence of soluble bacterial or archaeal DNA), but nowhere does it describe any evidence for viruses as the cause of this lysis. Yes, bacterial species are known to be susceptible to viral (bacteriophage) lysis, but there are also other causes of bacterial lysis, including mechanical lysis (e.g., the French-Press-like effect of bringing ocean sediment samples up from the ocean floor to a boat). It would not be unreasonable to hypothesize that bacteria might be more resistant to decompression-induced (or other nonviral) lysis than archaea, due to differences in cell size, wall thicknesses, or other physical, chemical or anatomical distinctions. 

In order to claim that the lysis is due to viruses, it is necessary to actually show that there are in fact lysogenic viruses associated with these prokaryotic cells. This article was totally silent about any search for virus-specific genes, or any other evidence of these putative "viruses." Nor did the article mention any experiments to control for the possibility of mechanical lysis.

Did the original research paper present additional information that addressed these issues, which Ruth Williams simply failed to present here (perhaps in the misguided attempt at brevity)? Did the original research paper include crucial additional data to either determine the actual presence of viruses or to rule out other, non-viral causes of lysis? If not, this is a poorly-controlled and scientifically unconvincing piece of work, from which one cannot conclude anything at all about deep-sea bacteriophages or archaeophages. If yes, if the original researchers actually did the right experiments, then Ms. Williams should be chided for failing to mention that crucial controls were in fact performed. 

"The Scientist" should not merely entertain or intrigue non-scientist readers with golly-gee stuff; it should also strive to educate non-scientists about the way science -- good science, valid science -- is done. The skills of logic and critical thinking, and the need to test ideas rigorously,  which form the basis of scientific methodology, are skills that are well worth learning because they are transferable to all human endeavors. 

 

Avatar of: JohnnyMorales

JohnnyMorales

Posts: 28

Replied to a comment from RetiredInBoyntonBeach made on October 17, 2016

January 10, 2017

Well the article does reference this, but only in passing.

In the middle of the piece you will read "he and his colleagues have previously shown that nearly all prokaryotic death in deep-sea sediments is due to viral infection."

If they met the standards that you expect than it would have been in those studies where actual viral lysis was demonstrated.

Overall though I agree with your sentiment. It all sounds too assumptive.

Avatar of: JonRichfield

JonRichfield

Posts: 131

Replied to a comment from RetiredInBoyntonBeach made on October 17, 2016

January 20, 2017

Well said, and well taken.

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