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How ‘viral dark matter’ may help mitigate climate change

climate change

Credit: Pixabay/CC0 public domain

A deep dive into the 5,500 marine RNA virus species scientists have recently identified has found that several can help move carbon absorbed from the atmosphere to permanent storage on the ocean floor.

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

In addition to mapping out a source of fundamental ecological data, the research leads to a better understanding of the outsized role these tiny particles play in the ocean ecosystem.

“The findings are important for modeling and predicting what happens to carbon in the right direction and size,” said Ahmed Zayed, a research scientist in microbiology at Ohio State University and co-first author of the study. research.

The question of size is a serious consideration when the vastness of the ocean is taken into account.

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

“As humans put more carbon into the atmosphere, we depend on the ocean’s vast buffering capacity to slow climate change. We are becoming more aware that we may need to tailor the pump to the scale of the ocean,” said Sullivan.

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

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

The study appears online today in Science

These RNA viruses were detected in plankton samples collected by the Tara Oceans Consortiuman ongoing global survey 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 getting to know the mysterious organisms that live there and do most of the work by absorbing half of the human-generated carbon in the atmosphere and half of it. of the oxygen we breathe.

While these marine viral species pose no threat to human health, they behave like all viruses do, each infecting a different organism and using its cellular machinery to make copies of itself. While the outcome can always be considered bad for the host, the activities of a virus can provide environmental benefits, for example by helping to expel a harmful algal bloom.

The trick to determining where they fit in the ecosystem is developing computer techniques that can extract information about RNA viral functions and hosts from fragments of genomes that, by genomics standards, are small to begin with.

“We’ll 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 structural patterns of virus communities that the team used to map RNA virus communities to four ecological zones: Arctic, Antarctic, temperate and tropical epipelagic (closest to the surface, where photosynthesis occurs), and temperate and tropical. mesopelagic (200-1000 meters deep). These zones closely match zone assignments for the nearly 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 decline near the colder poles, Zayed said a network-based ecological interaction analysis showed that the diversity of RNA viral species was greater than expected in the Arctic and Antarctic waters.

“When it comes to diversity, viruses don’t care about temperature,” he said. “There were more apparent interactions between viruses and cellular life in polar regions. That tells us that the great diversity we’re looking at in polar regions is actually because 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 the viruses in the context of marine plankton, and then making predictions based on how amounts of viruses and hosts “co-vary” because their abundances depend on each other. The third strategy was to find evidence of integration of RNA viruses into cellular genomes.

“The viruses we study don’t add themselves to the host genome, but many get integrated into the genome by mistake. When it happens, it’s a clue about the host, because if you find a virus signal in a host genome, it’s because the virus was in the cell at one point,” Dominguez-Huerta said.

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

The analysis also yielded the unexpected discovery of 72 observable functionally distinct supportive metabolic genes (AMGs) spread across 95 RNA viruses, providing some of the best clues about what types of organisms these viruses infect and what metabolic processes they are trying to reprogram in order to maximize the “manufacture” of viruses in the ocean.

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

“Modelling is getting to the point where we can pull genes out of these large-scale genomic studies and paint metabolic maps,” said Sullivan, also a professor of civil, environmental, and geodetic engineering and founder of Ohio State’s Center of Microbiome Science. †

“I imagine that our use of AMGs and these viruses that are predicted to infect certain hosts will actually dial those metabolic maps in the direction of the carbon we need. It’s through that metabolic activity that we probably need to intervene.” .”

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


Researchers identified more than 5,500 new viruses in the ocean, including a missing link in viral evolution


More information:
Guillermo Dominguez-Huerta et al, Diversity and Ecological Footprint of Global Ocean RNA Viruses, Science (2022). DOI: 10.1126/science.abn6358www.science.org/doi/10.1126/science.abn6358

Provided by Ohio State University


Quote: How ‘viral dark matter’ could help mitigate climate change (2022, June 9,), retrieved June 10, 2022 from https://phys.org/news/2022-06-viral-dark-mitigate-climate.html

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