Researchers Discover the Largest Virus in the Oceans Yet
Researchers Discover the Largest Virus in the Oceans Yet

Researchers Discover the Largest Virus in the Oceans Yet

The ChoanoVirus genome codes for rhodopsin, perhaps giving its choanoflagellate host extra energy-harvesting capabilities.

Kerry Grens
Kerry Grens
Mar 1, 2020

ABOVE: Choanoflagellates (pictured here in a multicellular state) are eukaryotes that feed on bacteria in the ocean. © THIBAUT BRUNET, KING LAB

A few years ago, Alexandra Worden was watching as an $800,000 medical-grade fluorescence activated single-cell sorter dangled from a crane, about to be loaded onto a research vessel—and hoping the crane operator appreciated just how delicate the equipment was. The marine microbial ecologist and her colleagues were about to set sail on the Atlantic Ocean to collect unicellular eukaryotes and sequester them individually for single-cell whole-genome sequencing. The trip was part of a survey that also included expeditions on the Pacific Ocean to find archaea, bacteria, and other organisms associated with these microbes. Worden and her collaborators wanted to avoid bringing the seawater samples back to the lab, which would risk distorting the biodiversity of the sample—“some guys just don’t make it,” says Worden, especially when it can take days to steam back to shore. So instead, they’d decided to bring the lab to the field.

With the crane operation well-executed and the instrument safely on board, the crew set off on its journey. The researchers gathered seawater, fluorescently stained cells for a food vacuole to label those organisms that were actively eating, and fed samples to the cell sorter to sift out the fluorescent cells from the rest. The vast majority of cells selected turned out to be choanoflagellates, predatory eukaryotes that feed on bacteria. The team then began looking for bacteria and archaea among the choanoflagellates, but in doing the sequencing to identify prokaryote genomes, “we weren’t getting a big signal,” says Worden, a professor at GEOMAR, the Helmholtz Centre for Ocean Research in Kiel, Germany, and a senior scientist at the Monterey Bay Aquarium Research Institute (MBARI) in California.  

After the expedition, postdoc David Needham decided to mine frozen samples for the presence of viruses. He hit pay dirt. What he found was the largest known virus to inhabit the ocean, and only the second discovered that infects predatory protists. “By looking for the usual [microbial] candidates, we initially missed that there was quite a beautiful virus to be assembled,” says Worden.

BUG CATCHER: Researchers collect seawater from the side of a ship as part of a survey of marine unicellular eukaryotes and the organisms associated with them.
© alexandra Worden

At 875 kilobases, the so-called ChoanoVirus’s genome is impressive in size, and the proteins it codes for are particularly exciting to the researchers. Among hundreds of protein sequences, Worden’s team identified three for rhodopsins—light-processing receptors found in certain cellular membranes of many living organisms, including humans, who require rhodo-psin in the retina for sight. The viral genome also codes for the components of a pathway that synthesizes a molecule called β-carotene along with the enzyme that processes it into retinal, the pigment that does the actual light sensing within the rhodopsin protein. By contrast, humans and indeed most eukaryotes make only part of the rhodopsin machinery and have to obtain β-carotene from external sources to make retinal.

To find out what these viral rhodopsins were possibly doing inside the choanoflagellate hosts, the researchers expressed the viral sequences in E. coli and found that light triggered the proteins to start pumping protons. The likely scenario is that the virus is actually helping the cell harvest energy from the sun—“something you would never expect in a predatory cell,” says Worden. “Here was a virus bringing an entirely new function, something that didn’t exist in the host organism.”

That some organisms use rhodopsins to generate chemical energy from light is not a new discovery. Decades ago, scientists reported that halophilic archaea make use of rhodopsins for just that. And in 2000, Worden’s coauthor Ed DeLong, then at MBARI and now at the University of Hawai‘i at Manoa, and colleagues described marine bacteria that also use rhodopsins to capture light energy. Since then, marine biologists have uncovered this form of metabolism in a wide range of microbial species in the ocean, according to Laura Gómez-Consarnau of the University of Southern California. Last year, she and her colleagues quantified the abundance of rhodopsins in seawater samples and estimated that, in some parts of the ocean, the energy harvested from sunlight by rhodopsins is more than that captured by chlorophyll. 

See “Oceanic Bacteria Trap Vast Amount of Light Without Chlorophyll

The latest paper is the first to show a virus apparently giving a predatory unicellular organism that functionality. Gómez-Consarnau says she suspects choanoflagellates turn to the rhodopsin mechanism to get energy when organic matter is scarce, or perhaps to help speed up their metabolisms. 

“This hypothesis challenges us to try to understand the infectious process beyond the pathogenic consequences for the host,” Jose Luis López, who studies marine rhodopsins at the University of Buenos Aires but was not involved in the work, writes in an email to The Scientist. Rather than infecting their hosts and lysing the cells to spread more virus, perhaps ChoanoViruses and others provide some survival benefit. The concept has gained traction in human virology, says Joaquín Martínez Martínez, a senior research scientist at the Bigelow Laboratory for Ocean Sciences in Maine who was not involved in the study, but it’s rather new on the marine side, where viruses have received far less scientific attention.

See “Viruses Mediate Interactions Between Bacteria and Sponges: Study

“So far we mostly have circumstantial evidence” of a symbiotic relationship between marine viruses and hosts, says Martínez Martínez, who studies these interactions. Part of the trouble is that many of these organisms are not cultured, making lab experiments on them impossible—at least for now, until more subjects are cultivated in the lab. “Papers like this are very important to keep building on circumstantial evidence with more actual data.”

Kerry Grens is a senior editor and the news director of The Scientist. Email her at kgrens@the-scientist.com.