A deep dive into the diversity of the 5,500 species of marine RNA viruses that scientists recently identified found that several can help bring carbon absorbed from the atmosphere to permanent storage on the ocean floor. The results of the analysis, which was conducted by a team from Ohio State University, also suggest that a small portion of these newly identified species had genes “stolen” from the organisms they infected, helping researchers identify their hosts. Putative hosts and roles in marine processes.
Beyond mapping a source of fundamental ecological data, the research could give scientists a more complete understanding of the outsized role these viruses play in the ocean ecosystem. “The findings are important for model development and prediction of what happens to carbon in the right direction and at the right magnitude,” said Ahmed Zayed, PhD, a microbiology research scientist at The Ohio State University and co-author of the study. team study. report published in Science.
The question of magnitude is a serious consideration when considering the vastness of the ocean. Lead author Matthew Sullivan, a microbiology professor at Ohio State, plans to identify viruses that, when engineered on a large scale, could function as controllable “knobs” on a biological pump that affect how carbon is stored in the ocean. “As humans deposit more carbon into the atmosphere, we rely on the enormous buffering capacity of the ocean to slow climate change,” Sullivan said. “We are increasingly aware that we might need to tune the pump to the scale of the ocean. We would be interested in viruses that could tune to more digestible carbon, allowing the system to grow, produce ever larger cells, and sink. And if it sinks, we gain another hundreds or thousands of years from the worst effects of climate change. I think society basically has that kind of technological fix, but it’s a complex fundamental scientific problem to unravel.”
Zayed, Sullivan, and colleagues describe their study in a paper titled “Diversity and Ecological Footprint of Global Ocean RNA Viruses.”
The oceans are dominated by communities of plankton that are essential to supporting life on Earth, the authors explained. “Plankton are at the base of the food web of marine and terrestrial organisms and drive planetary biogeochemical cycles.” Marine plankton are also critical to the biological carbon pump, the team continued, “…because their activity determines whether dissolved carbon dioxide is assimilated into biomass that can be sequestered in the deep ocean or recycled in surface waters.” and probably released into the atmosphere.
Plankton are susceptible to virus infection, the team noted, and it is increasingly recognized that DNA viruses influence marine microbes and microbe-mediated biogeochemical cycling. However, little is known about the diversity, ecology, and ecosystem functions of marine RNA viruses globally. “Although the literature increasingly presents RNA viruses as a likely major force behind the biogeochemistry, empirical data is difficult to obtain,” the researchers continued. “Recent experimental work has emerged to assess how DNA viruses affect small-scale ocean carbon export. We seek to complement these efforts through global ocean assessment of RNA viruses using previously developed machine learning and ecosystem modeling approaches to assess in silico whether RNA viruses could affect carbon export from the ocean.” .
For their study, the team focused their analyzes on RNA viruses 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. One goal of this international effort is to reliably predict how the ocean will respond to climate change by becoming familiar with the organisms that live there and do most of the work of absorbing half of the human-made carbon in the 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 make copies of itself. Although the result could always be considered bad for the host, the activities of a virus can have benefits for the environment, for example by helping to dissipate a harmful algal bloom. The trick to defining where they fit in the ecosystem has been the development of computational techniques that can glean insights into viral RNA and host functions from fragments of genomes that, by genomic standards, are small to begin with. “We let the data be our guide,” said co-author Guillermo Dominguez-Huerta, PhD, a former postdoctoral researcher in Sullivan’s lab.
The team’s statistical analysis of 44,000 sequences revealed virus community structural patterns that the team used to assign RNA virus communities into four ecological zones, determined largely by depth and, to a lesser extent, latitudinal shift: Epipelagic arctic, antarctic, temperate and tropical (closer to the surface, where photosynthesis occurs), and the 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 viruses that the researchers had previously identified.
There were some surprises. While biodiversity tends to expand in warmer regions near the equator and dip near cooler poles, Zayed said a network-based ecological interaction analysis showed that the diversity of RNA viral species was higher than expected in the Arctic and Antarctica. “When it comes to diversity, viruses don’t care about temperature,” he said. “There were more apparent interactions between viruses and cellular life in the polar areas. That tells us that the great diversity we’re seeing in the polar areas is basically 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 potential hosts, first inferring the host based on virus classification in the context of marine plankton and then making predictions based on how the numbers of viruses and hosts “co-vary” because their abundance depends on each other. The third strategy was to find evidence of integration of RNA viruses in cell genomes. While most dsDNA viruses were found to 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 fraction of marine RNA viruses infect bacteria.
“Although these results only provide broad predictions of host taxonomic range, as in silico host inferences for RNA viruses are not well established, they did indicate infection of diverse organisms of ecological interest, predominantly protists and fungi, and to a lesser extent. measure, invertebrate metazoans. ”, the researchers noted. “…several of these
Hosts, including certain invertebrate metazoans and, in particular, protists and fungi, are also recognized as critical contributors to the biological carbon pump. Although host prediction is challenging, these findings support previous work at smaller scales indicating that RNA viruses are central ecological players in the oceans.”
Domínguez-Huerta said: “The viruses we are studying do not insert into the host genome, but many integrate into the genome by accident. When it happens, it’s a clue about the host because if you find a virus signal within the host genome, it’s because at some point the virus was inside the cell.”
The analysis also yielded the unexpected discovery of 72 discernible functionally different helper metabolic genes (AMGs) scattered among 95 RNA viruses, providing some of the best clues about what types of organisms these viruses infect and what processes metabolic are trying to reprogram. to maximize the “manufacture” of viruses in the ocean. “Functionally, the 72AMG types were diverse, with only four instances overlapping with the previously reported 12 AMGs in RNA virus genomes,” the team reported.
Further network-based analysis identified 1,243 RNA virus species related to carbon export and, very conservatively, 11 were assumed to be involved in promoting carbon export to the deep sea. Of these, two host-linked viruses from the algae family were selected as the most promising targets for follow-up. “Modeling is getting to the point where we can take gene bags from these large-scale genomic studies and paint metabolic maps,” said Sullivan, also a professor of civil, environmental and geodetic engineering and founding director of the State Microbiome Science Center. from Ohio. .
“The influence of RNA viruses on ecosystems appears to be large, as the predicted hosts are ecologically important,” the authors concluded. “In addition, the appearance of metabolic helper genes indicates that RNA viruses cause reprogramming of various host metabolisms, including photosynthesis and the carbon cycle, and that the abundance of RNA viruses predicts carbon export in the ocean. .. Together, these findings provide a roadmap for studying RNA viruses in nature, as well as evidence that RNA viruses play an important role in the ocean ecosystem.”
Sullivan further noted, “I’m envisioning our use of AMG and these viruses that are predicted to infect particular hosts to mark those metabolic maps to carbon that we need. It is through that metabolic activity that we should probably act.”
Sullivan, Dominguez-Huerta and Zayed are also team members at the EMERGE Biology Integration Institute at Ohio State.
Source: www.genengnews.com