Scoop a cup of water out of the Atlantic Ocean, the Pacific Ocean, or any sea in between, and you’re sure to get more than just salty water. The sample will be teeming with algae, bacteria, and millions of viruses. Most of the viruses are phages; they infect bacteria and control how the bacteria grow and interact with their surroundings, making them a key player in the ocean’s nutrient cycles. But phages have been studied far less than bacteria, and getting a handle on the ocean’s viruses has been a slower-going process than characterizing the other life thriving in the waves. Now, scientists report in a PNAS Early Edition paper the discovery of twelve new genera of ocean-dwelling phages. The new phages were found in both deep and surface waters; both shoreline and open oceans.
“I was dumbfounded that there were twelve new genera,” says Matthew Sullivan of the University of Arizona, who led the new work. “And now that we have this initial data, we can start to look at different ecological patterns in different places where these phages are abundant.”
There’s no single gene that all viruses share, which makes it difficult to isolate all the viruses from a seawater sample. So Sullivan and his colleagues instead decided to isolate one particular aquatic bacteria, Cellulophaga baltica, from water collected out of the strait of Oresund between Sweden and Denmark. Cellulophaga had not been analyzed to see what phages it contained in the past, and is known to be common in not only the ocean, but soils, glacial ice, and even the human body.
Once the team had the bacteria, they cultured and grew it in the lab, then sequenced the genetic material it contained. Inside, they found 31 sequences that resembled viruses. Further analysis of the viral genomes revealed that the phages fell into 12 diverse groups, none of which had been identified before.
“When we normally talk about viral groups, they share at least half their genomes with each other,” says Sullivan. “But these viral genomes share less than three percent of their genomes with known viruses.”
This divergence from usual viruses likely suggests that the new phages have different ways of interacting with bacteria than have been characterized and studied before, he says. Already, initial characterizations of the viruses by Sullivan’s team revealed uncommon genes involved in metabolism and larger genome sizes than expected.
To see how ubiquitous the 12 phage groups were in the world’s oceans, Sullivan used the genetic data on the viruses to search through Cellulophaga from other sources. 94% of the bacteria, from diverse waters, contained the newly discovered phages.
“There’s an incredible amount more to be explored,” says Sullivan. “This is just one glimpse into the rare biosphere of the ocean.”
The techniques used by the scientists can now be applied to other aquatic bacteria to further dive into what phages they host. And each identified phage can be used to develop new virus-bacteria pairs to recreate and study in the lab to shed light on their biology. As more phages are added to the library of the ocean’s viruses, Sullivan says, scientists will begin to get a better idea of the role that they play in controlling the biology and chemistry of the deep seas.