How ‘viral dark matter’ can help mitigate climate change: Study identifies over 1,200 RNA viruses linked to carbon flux

A deep dive into the 5,500 species of marine RNA viruses recently identified by scientists has revealed that several of them could help drive carbon absorbed from the atmosphere into permanent storage at the ocean floor.

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

Beyond mapping a source of fundamental ecological data, the research is leading to a better understanding of the outsized role these tiny particles play in the ocean ecosystem.

“The results are important for developing models and predicting what’s happening with carbon in the right direction and at the right magnitude,” said Ahmed Zayed, microbiology researcher at Ohio State University and co-first author. of the study.

The question of magnitude is a serious consideration when considering the vastness of the ocean.

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

“As humans put more carbon into the atmosphere, we depend on the massive buffering capacity of the ocean to slow climate change. We are increasingly aware that we may need to adjust the pump to the atmosphere. ‘ocean scale,'” Sullivan said.

“We would be interested in viruses that could adapt to more digestible carbon, which allows the system to grow, produce bigger and bigger cells and sink. And if it sinks, we still gain a few hundreds or a thousand years of the worst effects of climate change.

“I think society is basically relying on this kind of technological solution, but it’s a complex fundamental scientific problem to solve.”

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 aboard 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 learning about the mysterious organisms that live there and do most of the work of absorbing half of the human-generated carbon in the ocean. atmosphere and producing half of the oxygen we breathe. .

Although these marine viral species do not pose a threat to human health, they behave like all viruses, each infecting another organism and using its cellular machinery to reproduce. Although the outcome may still be considered bad for the host, the activities of a virus may generate benefits for the environment, such as helping to dissipate a harmful algal bloom.

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

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

Statistical analysis of 44,000 sequences revealed structural patterns of the viral community which the team used to distribute RNA virus communities across four ecological zones: arctic, antarctic, temperate epipelagic, and tropical (closest to surface, where photosynthesis occurs) and temperate and tropical mesopelagic (200-1,000 meters deep). These zones closely match the zone assignments for the nearly 200,000 species of marine DNA virus that the researchers had previously identified.

There were a few surprises. While biodiversity tends to expand in warmer regions near the equator and fall near colder poles, Zayed said a network-based analysis of ecological interactions showed that species diversity RNA virus was higher than expected in the Arctic and Antarctic.

“When it comes to diversity, viruses don’t care about temperature,” he said. “There were more apparent interactions between viruses and cell life in the polar zones. This tells us that the great diversity we see in the polar zones is essentially due to the fact that we have more viral species competing for the same host. We see fewer host species 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 viruses in the context of marine plankton, then making predictions based on how the amounts of viruses and hosts “co-vary” because their abundance depends on each other. The third strategy was to find evidence for the integration of RNA viruses into cellular genomes.

“The viruses we study don’t insert into the host genome, but many do by accident. When this happens, it’s a clue to the host because if you find a viral signal in the host genome, it’s because at some point the virus was inside the cell,” Dominguez-Huerta said.

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

The analysis also led to the unexpected discovery of 72 discernible and functionally different helper metabolic genes (AMGs) interspersed among 95 RNA viruses, which provided some of the best clues about the types of organisms these viruses infect and on the metabolic processes they are trying to reprogram. in order to maximize the “manufacturing” of viruses in the ocean.

Further network-based analysis identified 1,243 RNA virus species linked to carbon export and, very conservatively, 11 were thought to be involved in promoting carbon export to the bottom of the lattice. Of these, two viruses related to hosts of the algal family were selected as the most promising targets for monitoring.

“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 the Center of Microbiome. Ohio Science. .

“I envision our use of AMGs and these viruses that are expected to infect particular hosts to compose these metabolic maps to the carbon that we need. It’s through this metabolic activity that we probably have to act.”

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

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

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

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