Ancient viruses discovered in coral symbionts’ DNA

Newswise — HOUSTON – (June 1, 2023) –A group of marine biologists from various countries has made a remarkable finding, uncovering the traces of ancient RNA viruses integrated into the DNA of symbiotic organisms residing within coral reefs.

In a groundbreaking revelation, it has been revealed that the RNA fragments derived from viruses had infected the symbiotic organisms as far back as 160 million years. The astonishing discovery, highlighted in a recent open-access publication in the journal Communications Biology by Nature, holds immense potential for enhancing our understanding of the ongoing battle against viral infections in corals and their associated organisms. This finding has taken scientists by surprise since the integration of RNA viruses into the DNA of their host organisms is an uncommon phenomenon.

Through the study, it has been revealed that endogenous viral elements (EVEs) are prevalent in the genetic makeup of coral symbionts. These symbionts, known as dinoflagellates, are single-celled algae residing within corals, imparting vibrant colors to their hosts. The identification of EVEs reinforces recent findings that viruses, not limited to retroviruses, have the ability to incorporate fragments of their genetic material into the genomes of their host organisms.

"Then how did it happen?" inquired Adrienne Correa, one of the co-authors of the study from Rice University. She further explained, "While it might seem accidental, researchers are increasingly discovering that such occurrences are more common than previously thought. These 'accidents' have been identified in various hosts, ranging from bats and ants to plants and algae."

The presence of an RNA virus within coral symbionts came as an unexpected revelation.

"I found this project particularly intriguing," expressed Alex Veglia, the lead author of the study and a graduate student in Correa's research team. Veglia continued, "Based on our current understanding, there is truly no logical explanation for the presence of this virus within the genome of the symbionts."

The research, funded by the Tara Ocean Foundation and the National Science Foundation, was spearheaded by Correa, Veglia, along with two scientists from Oregon State University: postdoctoral scholar Kalia Bistolas and marine ecologist Rebecca Vega Thurber. By unraveling crucial insights, this study offers valuable clues for scientists to enhance their comprehension of the ecological and economic ramifications of viruses on reef well-being.

During their investigation, the researchers did not detect any endogenous viral elements (EVEs) derived from RNA viruses in the samples of filtered seawater or within the genomes of dinoflagellate-free stony corals, hydrocorals, or jellyfish. However, EVEs were found extensively in coral symbionts gathered from numerous coral reef locations. This indicates that the pathogenic viruses were, and likely still are, selective in their choice of target hosts.

Correa, an assistant professor of biosciences, emphasized the vast diversity of viruses that exist on our planet. She explained, "While we have extensive knowledge about certain viruses, the majority of viruses remain uncharacterized. We may be able to detect their presence, but we are still unaware of their host organisms."

Correa highlighted the various methods by which viruses, including retroviruses, can replicate through host infections. She stated, "One intriguing aspect of our study is that this RNA virus is not classified as a retrovirus. Considering this, one wouldn't anticipate it to integrate into the host's DNA."

Correa remarked, "Over the past several years, we have observed a multitude of viruses within coral colonies, but it has been challenging to definitively determine their specific targets." She further stated, "Therefore, this discovery provides us with the most reliable and conclusive data regarding the actual host of a virus associated with coral colonies. With this knowledge in hand, we can now delve into understanding why the symbiont retains that DNA or a portion of the genome. The question arises: Why hasn't it been lost over time?"

The revelation that the endogenous viral elements (EVEs) have been preserved over millions of years implies that they might hold some advantageous role for the coral symbionts. It also suggests the existence of a mechanism that actively promotes the genomic integration of EVEs.

Veglia expressed the multitude of possibilities for further exploration, such as investigating whether these elements serve as antiviral mechanisms within dinoflagellates and assessing their potential impact on reef health, particularly in the context of rising ocean temperatures.

Veglia raised important questions related to the potential influence of rising seawater temperatures on the presence of endogenous viral elements (EVEs) within Symbiodiniaceae species. He pondered whether the presence of EVEs in their genomes enhances their ability to combat infections caused by present-day RNA viruses. These queries emphasize the need for further research to unravel the intricate connections between EVEs, symbiont genomes, and the response to viral infections under changing environmental conditions.

"In another study, we demonstrated that there is a rise in RNA viral infections during episodes of thermal stress in corals. Hence, there are numerous interconnected factors at play. The current discovery provides another valuable piece to complete the puzzle," Veglia explained. The intricate relationship between thermal stress, viral infections, and coral health requires comprehensive examination to gain a holistic understanding of the dynamics involved.

Correa cautioned against making assumptions about the virus having a negative impact, but she also noted that there is evidence suggesting its increased productivity under conditions of temperature stress. This highlights the complexity of the situation and the need for further investigation to better understand the potential effects of the virus on coral health.

Thurber holds the distinguished position of Emile F. Pernot Professor in the Department of Microbiology at Oregon State University.

The study included more than 20 co-authors from the University of Konstanz, Germany; the Institute of Microbiology and Swiss Institute of Bioinformatics, Zürich; the University of Perpignan, France; the Scientific Center of Monaco; the Université Paris-Saclay, Evry, France; the Tara Ocean Foundation, Paris; the University of Maine; Sorbonne University, France; the University of Tsukuba, Japan; Paris Science and Letters University, France; the University of Paris-Saclay; the Weizmann Institute of Science, Rehovot, Israel; Côte d’Azur University, Nice, France; the European Bioinformatics Institute, University of Cambridge, England; Ohio State University; and the National University of Ireland, Galway.

National Science Foundation support was provided by three grants (2145472, 2025457, 1907184).

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Peer-reviewed paper:

“Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes” | Communications Biology | DOI: 10.1038/s42003-023-04917-9

Authors: Alex J. Veglia, Kalia S.I. Bistolas, Christian R, Voolstra, Benjamin C. C. Hume, Hans-Joachim Ruscheweyh, Serge Planes, Denis Allemand, Emilie Boissin, Patrick Wincker, Julie Poulain, Clémentine Moulin, Guillaume Bourdin, Guillaume Iwankow, Sarah Romac, Sylvain Agostini, Bernard Banaigs, Emmanuel Boss, Chris Bowler, Colomban de Varga, Eric Douville, Michel Flores, Didier Forcioli, Paola Furla, Pierre Galand, Eric Gilson, Fabien Lombard, Stéphane Pesant, Stéphanie Reynaud, Matthew B. Sullivan, Shinichi Sunagawa, Olivier Thomas, Romain Troublé, Didier Zoccola, Adrienne M.S. Correa, and Rebecca L. Vega Thurber

https://doi.org/10.1038/s42003-023-04917-9