How ‘Viral Dark Matter’ May Help Mitigate Climate Change

Study identifies 1,200+ RNA viruses with connections to carbon flux

Peer-Reviewed Publication

OHIO STATE UNIVERSITY

COLUMBUS, Ohio – A deep dive into the 5,500 marine RNA virus species scientists recently identified has found that several may help drive carbon absorbed from the atmosphere to permanent storage on the ocean floor.

The analysis also suggests that a small portion of these newly identified species had “stolen” genes from organisms they infected, helping researchers identify their presumed hosts and functions in marine processes.

Beyond mapping a fount of foundational ecological data, the research is leading to a fuller understanding of the outsize role these tiny particles play in the ocean ecosystem.

“The findings are important for model development and predicting what is happening with carbon in the correct direction and at the correct magnitude,” said Ahmed Zayed, a research scientist in microbiology at The Ohio State University and co-first author of the study.

The question of magnitude is a serious consideration when taking into account the vastness of the ocean.

Lead author Matthew Sullivan, professor of microbiology at Ohio State, envisions identifying viruses that, when engineered on a massive scale, could function as controllable “knobs” on a biological pump that affects how carbon in the ocean is stored.

“As humans put more carbon into the atmosphere, we’re dependent on the massive buffering capacity of the ocean to slow climate change. We’re growing more and more aware that we might need to tune the pump at the scale of the ocean,” Sullivan said.

“We’d be interested in viruses that could tune toward a more digestible carbon, which allows the system to grow, produce bigger and bigger cells, and sink. And if it sinks, we gain another few hundred or a thousand years from the worst effects of climate change.

“I think society is basically counting on that kind of technological fix, but it’s a complex foundational science problem to tease apart.”

The study appears online today (June 9, 2022) in Science.

These RNA viruses were detected in plankton samples collected by the Tara Oceans Consortium, an ongoing global study onboard the schooner Tara of the impact of climate change on the ocean. The international effort aims to reliably predict how the ocean will respond to climate change by getting acquainted with the mysterious organisms that live there and do most of the work of absorbing half the human-generated carbon in the atmosphere and producing half of the oxygen we breathe.

Though these marine viral species don’t pose a threat to human health, they behave as all viruses do, each infecting another organism and using its cellular machinery to make copies of itself. Though the outcome could always be considered bad for the host, a virus’s activities may generate benefits for the environment – for example, helping dissipate a harmful algal bloom.

The trick to defining where they fit into the ecosystem has been developing computational techniques that can coax information about RNA viral functions and hosts from fragments of genomes that are, by genomics standards, small to begin with.

“We let the data be our guide,” said co-first author Guillermo Dominguez-Huerta, a former postdoctoral researcher in Sullivan’s lab.

Statistical analysis of 44,000 sequences revealed virus community structural patterns the team used to assign RNA virus communities into four ecological zones: Arctic, Antarctic, Temperate and Tropical Epipelagic (closest to the surface, where photosynthesis occurs), and Temperate and Tropical Mesopelagic (200-1,000 meters deep). These zones closely match zone assignments for the almost 200,000 marine DNA virus species the researchers had previously identified.

There were some surprises. While biodiversity tends to broaden in warmer regions near the equator and drop close to the colder poles, Zayed said a network-based ecological interaction analysis showed the diversity of RNA viral species was higher than expected in the Arctic and Antarctic.

“When it comes to diversity, viruses don’t care about the temperature,” he said. “There were more apparent interactions between viruses and cellular life in polar areas. That tells us the high diversity we’re looking at in polar areas is basically because we have more viral species competing for the same host. We see fewer species of hosts but more viral species infecting the same hosts.”

The team used several methodological approaches to identify likely hosts, first inferring the host based on the classification of the viruses in the context of marine plankton and then making predictions based on how quantities of viruses and hosts “co-vary” because their abundances depend on each other. The third strategy consisted of finding evidence of integration of RNA viruses in cellular genomes.

“The viruses we’re studying don’t insert themselves into the host genome, but many get integrated into the genome by accident. When it happens, it’s a clue about the host because if you find a virus signal within a host genome, it’s because at some point the virus was inside the cell,” Dominguez-Huerta said.

While most dsDNA viruses had been found to infect bacteria and archaea, which are abundant in the ocean, this new analysis found that RNA viruses mostly infect fungi and microbial eukaryotes and, to a lesser extent, invertebrates. Only a tiny fraction of the marine RNA viruses infect bacteria.

The analysis also yielded the unanticipated discovery of 72 discernible functionally different auxiliary metabolic genes (AMGs) sprinkled among 95 RNA viruses, which provided some of the best clues as to what kinds of organisms these viruses infect and what metabolic processes they’re trying to reprogram in order to maximize the “fabrication” of viruses in the ocean.

Further network-based analysis identified 1,243 RNA virus species connected to carbon export and, very conservatively, 11 were implied to be involved in promoting carbon export to the bottom of the sea. Of those, two viruses linked to hosts in the algae family were selected as the most promising targets for follow-up.

“Modeling is getting to the point where we can take bags of genes from these large-scale genomic surveys and paint metabolic maps,” said Sullivan, also a professor of civil, environmental and geodetic engineering and founding director of Ohio State’s Center of Microbiome Science.

“I’m envisioning our use of AMGs and these viruses that are predicted to infect particular hosts to actually dial up those metabolic maps toward the carbon we need. It’s through that metabolic activity that we probably need to act.”

Sullivan, Dominguez-Huerta and Zayed are also team members in the EMERGE Biology Integration Institute at Ohio State.

This research was supported by the National Science Foundation, the Gordon and Betty Moore Foundation, the Ohio Supercomputer Center, Ohio State’s Center of Microbiome Science, a Ramon-Areces Foundation Postdoctoral Fellowship, Laulima Government Solutions/NIAID and France Génomique. The work was also made possible by the unprecedented sampling and science of the Tara Oceans Consortium, the nonprofit Tara Ocean Foundation and its partners.

Additional co-authors on the paper include James Wainaina, Jiarong Guo, Funing Tian, Akbar Adjie Pratama, Benjamin Bolduc, Mohamed Mohssen and Olivier Zablocki, all of Sullivan’s lab; Jens Kuhn of the National Institute of Allergy and Infectious Diseases; Alexander Culley of the Université Laval; Erwan Delage, Damien Eveillard and Samuel Chaffron of the Nantes Université; Lionel Guidi of the Sorbonne Université; Hiroyuki Ogata of Kyoto University; Chris Bowler of the Ecole Normale Supérieure; Eric Karsenti of the the Ecole Normale Supérieure and Directors’ Research European Molecular Biology Laboratory; and Eric Pelletier, Adriana Alberti, Jean-Marc Aury, Quentin Carradec, Corinne da Silva, Karine Labadie, Julie Poulain and Patrick Wincker of Genoscope.

#

Contacts:

Ahmed Zayed, Zayed.10@osu.edu
Guillermo Dominguez-Huerta, Dominguezhuerta.1@osu.edu
Matthew Sullivan, Sullivan.948@osu.edu (Sullivan is traveling June 6-18 with limited ability to respond to emails or conduct phone interviews.)

Written by Emily Caldwell, Caldwell.151@osu.edu; 614-292-8152


JOURNAL

Science

DOI

10.1126/science.abn6358 

ARTICLE TITLE

Diversity and ecological footprint of Global Ocean RNA viruses

ARTICLE PUBLICATION DATE

10-Jun-2022

From EurekAlert!

1.9 8 votes
Article Rating
43 Comments
Oldest
Newest Most Voted
Inline Feedbacks
View all comments
RoHa
June 9, 2022 10:01 pm

OT, but a useful line from Russel Brand.

“The trouble with following the science is that science follows the money.”

Scissor
Reply to  RoHa
June 10, 2022 5:27 am

Soros is making good use of his money and even got some face work done.

https://nypost.com/2022/06/08/how-george-soros-is-remaking-americas-justice-system/

markl
Reply to  Scissor
June 10, 2022 2:09 pm

They just recalled one of his backed prosecutors in San Fransisco. Even SF couldn’t handle the lack of consequences for criminals. People are realizing that “Progressive justice” means let the perpetrators off the hook at the expense of the victims and they don’t like it. I still don’t understand how being lenient on criminals helps anybody but criminals. Does anyone understand the logic behind it?

Steve Case
June 9, 2022 10:11 pm

Lead author Matthew Sullivan, professor of microbiology at Ohio State, envisions identifying viruses that, when engineered on a massive scale, could function as controllable “knobs” on a biological pump that affects how carbon in the ocean is stored.
__________________________________________________________

Oh WOW! Let’s engineer some viruses!!! What could possibly go wrong????

Deano
Reply to  Steve Case
June 9, 2022 10:56 pm

Yeah – Absolutely terrifying.. Just curious if they are “teaming” with the Wuhan bio-weapons factory on this effort to program viruses for the oceans…

Randle Dewees
Reply to  Steve Case
June 10, 2022 5:25 am

Yeah, let’s play God, again.

Frank from NoVA
Reply to  Steve Case
June 10, 2022 7:28 am

The carbon equivalent of Vonnegut’s ‘Ice-9’?.

Phil R
Reply to  Steve Case
June 10, 2022 8:35 am

Though the outcome could always be considered bad for the host, a virus’s activities may generate benefits for the environment…

Wait, back up. Let’s not brush over the first part of this sentence so cavalierly.

paul
Reply to  Steve Case
June 10, 2022 5:38 pm

you beat me to it ? These mad men are worse than Frankinstine

PCman999
June 9, 2022 10:24 pm

It’s really sad that so much effort and money is going into tackling the CO2 boogeyman instead of real problems, even real environmental problems that have nothing to do with CO2.

Genuine, caring environmentalists are being played and preyed on to milk the system and their sympathies for every buck they can squeeze out, and then dump everything to jump on the next bandwagon.

Ed Hanley
Reply to  PCman999
June 9, 2022 11:38 pm

CO2 is the only molecule that can be vilified, bought and sold, and taxed. The fact that it is the keystone to life on this planet is completely irrelevant to the ruling class.

IanE
Reply to  Ed Hanley
June 10, 2022 1:24 am

True, but they will be after our O2 next!

Scissor
Reply to  Ed Hanley
June 10, 2022 4:31 am

Klaus Schwab calls CO2, “kahbun” and say we must de-kahbunize ze world.

H. D. Hoese
Reply to  Ed Hanley
June 10, 2022 5:49 am

It’s not just carbon, also nitrogen. The late Scott Nixon was a real scholar who studied it, called nitrogen in another paper “demonized.” His conclusion–

“…. Carlos Duarte pointed out that those who believe that reducing nutrient inputs will return coastal ecosystems to some pristine state have forgotten that the ‘baseline’ has been changing. Like Peter Pan, he said, they want to return to ‘Neverland’ where time stands still and nothing ever changes. The scientific community, of course, does not make decisions about policy. However, I do suggest that all of us, scientists, regulators, politicians, and even the activists need to consider coastal marine eutrophication and oligotrophication as the fundamental ecological processes they are. They are not simple ‘pollution problems’ but major ecological changes that must be viewed through the macroscope.” Open Access

Nixon, S. W. 2009. Eutrophication and the macroscope. Hydrobiologia . 629:5–19. DOI 10.1007/s10750-009-9759-z

Disputin
Reply to  Ed Hanley
June 10, 2022 6:48 am

What about ethyl alcohol?

TonyL
June 9, 2022 10:59 pm

YouReekAlert: Skip it.
Done.

Dead On Arrival.
It has been known that there are vast numbers of viruses in seawater. Most of them attack bacteria, of which there are also vast numbers in seawater. Both are known to be insignificant compared to the phytoplankton, zooplankton, algae especially diatoms, and a whole host of everything else.
All of which has been known since forever.

H.R.
Reply to  TonyL
June 10, 2022 6:22 am

I think they are saying that they can engineer these viruses so when phytoplankton is infected, it can no longer fart.

Something like that. It’s a little short on details in the press release.

TonyL
Reply to  H.R.
June 10, 2022 7:02 am

It’s a little short on details in the press release.
Thank goodness for that.

Mark Freeman
Reply to  H.R.
June 10, 2022 4:15 pm

Plankton farts oxygen. We need to manufacture a virus to stop oxygen pollution because 2/3 of the CO2 molecule is oxygen. Stop it and CO2 emissions stop.

AndyHce
June 9, 2022 11:23 pm

If there are any people that need to stick strictly to models it is kooks wanting to re-engineer the oceans.

Ed Hanley
June 9, 2022 11:35 pm

“As humans put more carbon into the atmosphere, we’re dependent on the massive buffering capacity of the ocean to slow climate change. We’re growing more and more aware that we might need to tune the pump at the scale of the ocean,” Sullivan said.

“Tune the pump” is a tricky way of saying, “GAIN OF FUNCTION.” What could go wrong? (And if anything does go wrong “at the scale of the ocean,” hopes of fixing it would be pretty close to zero.)


H.R.
Reply to  Ed Hanley
June 10, 2022 6:28 am

No worries, Ed. They are “Scientists so they know what they are doing… we hope. 😲

4E Douglas
June 10, 2022 12:48 am

“Mad science means you never have to worry about: What’s the worst possible outcome?”

June 10, 2022 12:58 am

“Climate change’? Ther’s no such thing. There’s possible net warming of the surface due to increases of man-made heat sinks on the surface, which otherwise tends to be reversed by the cooling effect of carbon dioxide’s dislocation of molecules (nitrogen and oxygen) that have greater heat energy.

How Was This Missed?

Hugh victory for scientific truth, and empirical proof for scientific fraud…

The revised Second Law of Thermodynamics, where ‘back radiation’ (the foundation upon which ‘climate change’ stands) is present in the Earth’s Energy Budget…

https://www.nasa.gov/feature/langley/what-is-earth-s-energy-budget-five-questions-with-a-guy-who-knows

…and missing is the ‘back radiation’ for the incoming radiation (77.1 Wm2) that’s directly absorbed by the atmosphere. Opps!

The follow NASA graph of the ‘Earth’s Energy Budget’ follows the Second Law of Thermodynamics* before that law was updated…

https://www.nasa.gov/pdf/62319main_ICS_Energy.pdf
————————
* The reason NASA couldn’t have ‘back radiation’ for that 77.1Wm2 is because any ‘back radiation’ would constitute Sunlight being emitted downwards by the atmosphere. In other words, planets would also be a source of Sunlight without the need for an exothermic event (e.g., lightening, vegetation fires, and burning a candle). Stars and other hot bodies would have to share their monopoly on creating Sunlight!

Let’s Explain…

The 77.1 Wm2 absorbed by the atmosphere is UV radiation. When the electrons that absorb that radiation return to their normal energy levels by emitting the absorbed radiation, a portion of the energy is lost in the process, whereby the energy emitted is now less than that absorbed. In this particular scenario, the energy emitted would be Sunlight, because Sunlight is the next lower energy level on the electromagnetic spectrum.

Last edited 23 days ago by Dean M Jackson
TonyL
Reply to  Dean M Jackson
June 10, 2022 4:12 am

“In this particular scenario, the energy emitted would be Sunlight, because Sunlight is the next lower energy level on the electromagnetic spectrum.”
Ummm…..
That is a fluorescent molecule you are describing there. I am pretty sure there are no fluorescent compounds as constituents of the atmosphere.

fretslider
June 10, 2022 1:05 am

“Modeling is getting to the point where we can…”

Get any desired result

Peter Barrett
June 10, 2022 4:29 am

“The viruses we’re studying don’t insert themselves into the host genome, but many get integrated into the genome by accident.”
We were assured, a short while ago, by many worthy and eminent virologists that viral RNA would never do this.

TonyL
Reply to  Peter Barrett
June 10, 2022 5:02 am

many worthy and eminent virologists
many worthy and eminent virologists seem to have never heard of the enzyme Reverse Transcriptase.
Biochemistry : The transcriptase enzyme generates RNA from DNA. This is a fundamental process.

Now, Reverse Transcriptase, Hmmm… I wonder what that might do????
No, never mind, could not be important no matter what it does.
:worthy and eminent virologists: Perhaps worthy and eminent like the ones who created the Wuhan Flu.

whiten
Reply to  Peter Barrett
June 10, 2022 5:14 am

Viruses are simply genetic code packets, which exist for only one purpose;

To become part of the operational code of life.
Becoming part of DNA.
Even when success rate very very very low.

cheers

whiten
Reply to  whiten
June 10, 2022 8:45 am

I am sorry, really, but;

Still maybe not appropriate, but;

nice music there for likes of me;

“Alice Cooper – Feed My Frankenstein (Official Video)”

whiten
Reply to  whiten
June 10, 2022 9:28 am

Still;

Coolio – Gangsta’s Paradise (feat. L.V.) [Official Music Video]

Leonard Weinstein
June 10, 2022 4:40 am

We are likely approaching the end of the Holocene (based on all the previous interglacial durations), and likely headed for a glacial period of severe cooling with natural lowering of CO2 levels, the forcing of additional CO2 removal could drop Earth below a CO2 level able to sustain much plant life (below 180 ppm). How stupid is this?

whiten
Reply to  Leonard Weinstein
June 10, 2022 7:43 am

We at this point in time, are the first civilized human lot, living within the ‘line” between the Interglacial and the Glacial period.

bluecat57
June 10, 2022 4:55 am

Easy. By killing billions of humans.
Where’s my Nobel?

sniffybigtoe
June 10, 2022 6:14 am

So the answer to, “How can a microbiologist get some of that sweet, sweet climate change money?”, has been discovered?

LdB
Reply to  sniffybigtoe
June 10, 2022 7:37 pm

If you can’t beat the greentards then join them and get that snout in the trough.

ResourceGuy
June 10, 2022 6:44 am

I would suggest a large grant to the Wuhan virology lab and include the study of imported seafood as the CCP intones.

H.R.
Reply to  ResourceGuy
June 10, 2022 7:20 am

But what about pangolins?

MARTIN BRUMBY
June 10, 2022 9:03 am

Models?
Two dozen co-authors?
Go forth and multiply….

Josh Scandlen
June 10, 2022 9:15 am

Not sure where the dark matter comes into this, at least the dark matter in space that physicists refer to.

But I’d still ask, “dont you need to prove dark matter exists first”?

Fran
June 10, 2022 9:53 am

Please no attempts to “engineer” viruses to deal with non-existent “carbon” problem.

Bob
June 10, 2022 9:11 pm

More gibberish.

June 11, 2022 10:47 am

What a colossal waste of time and money. CO2 IS PLANT FOOD and should not be purposely sequestered. In addition, the idea that a virus can affect climate is a joke. But, they all want in on the money gravy train. It was only a matter of time before the virologists put in for their “share” of the climate governmental booty swollen from the people./

%d bloggers like this: