Scientists Collect Entirely New Type of Virus From Marianas Trench Ocean Abyss

Scientists have discovered a novel marine virus that lives at an astonishing depth of 8,900 meters (roughly 5.5 miles) under the ocean surface, making it the deepest known isolated phage ever found in the global seas, reports a new study. The rare find could shed light on the microbial ecosystems that lurk in the deepest reaches of the ocean, known as the “hadal” zone, which play critical roles in the global climate and carbon cycle.

The virus was identified in sediments hauled up from the Mariana Trench, a vast formation in the Pacific Ocean that hosts the deepest abysses on Earth. It belongs to an entirely new family of so-called “siphoviruses,” known as Suviridae, that only infect bacteria and cannot use humans as a host. 

Viruses that live and replicate in bacterial hosts are known as bacteriophages, and they are a ubiquitous presence in every ecosystem on Earth—including the Mariana Trench. Scientists have previously discovered bacteriophages at depths of up to 8,636 ​meters in the trench, though the nature of these viruses is still largely unknown.

Now, scientists led by Min Wang, a researcher at the Ocean University of China in Qingdao, report the discovery of a new bacteriophage in trench samples captured at a depth of 8,900 meters, which is about 260 meters (800 feet) deeper than the previous record-holder. Scientists report that the phage, which is known as vBHmeYH4907, is “the deepest known phage isolated to date” and that “it represents a novel abundant viral family in the ocean,” according to a study published on Wednesday in Microbiology Spectrum.

“We are marine virologists, and our research team’s primary focus lies in investigating the community structure, diversity, distribution patterns, regulatory mechanisms, and ecological roles of viruses and their hosts in various marine habitats, such as polar regions and the deep sea,” Wang and two of her co-authors, Yue Su and Yantao Liang, said in an email to Motherboard

“Host bacteria was isolated from the sediments of the Mariana Trench by our collaborator Yu-Zhong Zhang’s team,” the researchers continued. “Their research team has been exploring microbial life in various extreme environments, including the Mariana Trench, while we are primarily focused on viruses. Considering the unique nature of the trench, the likelihood of isolating viruses using conventional infection methods is pretty low. So we decided to use the induction method”—which is a special method of phage detection—”to isolate phages by referring to previous studies.”

This approach yielded fascinating results, as the team discovered a new phage that infects a bacterial species in the Halomonas family of bacteria, which has adapted to a variety of deep hadal environments that ranges from the Antarctic seafloor to deep-sea hydrothermal vents. 

These bacteria are “widely used in synthetic biology because members of Halomonas are well known for their capacity to break down petroleum hydrocarbons, flourish in environments with high salt concentrations and alkaline pH, and high tolerance to contamination,” the team said in the study. “It is also abundant in the Mariana Trench, suggesting that it may play an essential role in hadal environments. Despite its significance, very little is known about the viruses that infect Halomonas, with only two phages published in the National Center for Biotechnology Information (NCBI) dataset so far.”

Now, the team has upped the count to three with the identification of vBHmeYH4907. The researchers were able to conduct a genomic analysis of the phage, which demonstrated that it has a “lysogenic” life strategy in which it incorporates its own genome into the host genome, infecting it from inside the cell. With the help of a transmission electron microscope, the team was even able to make out the phage’s “icosahedron head” with an average diameter of 65 nanometers, and its “long, non-contractible tail” which measured about 183 nanometers, according to the study. For reference, a sheet of paper is about 100,000 nanometers thick.

“Genomic analysis showed that vBHmeYH4907 was evolutionarily distant from other reference viruses and widely distributed in the ocean with high abundance, which further demonstrated the lysogenic life strategy of hadal phage and the necessity of isolating prophages from their hosts,” the researchers told Motherboard. “Besides, the temperate phage vBHmeYH4907 is highly homologous to its host, which provides a theoretical basis for an in-depth analysis of the survival strategy of viruses in extremely harsh environments and their co-evolution with their hosts.” 

The discovery opens a new and unprecedented window into the largely unexplored microbial universe that dominates the hadal seafloor. The bacteria and viruses that live in these otherworldly realms may be small in size, but their cumulative effect on our world packs a big punch. Indeed, deep sea viruses are described as “essential regulators of global ecology” in the study because they influence the flow of carbons through the oceans, and in turn, have an impact on climate change, making it crucial to understand their evolution and life cycles. 

And while the discovery of a virus from the deep ocean might seem scary at first, these microbes are more likely to benefit human health than to cause harm.

“The host of this bacteriophage is a bacterium, which is a type of prokaryotic organism,” Su, Wang, and Liang said. “Currently, the isolation of bacteriophages and the enrichment of bacteriophage gene libraries are more beneficial to human health. They help protect humans from bacterial infections, especially in today’s era of antibiotic use and the proliferation of antibiotic-resistant bacteria. At the same time, current research suggests that there is no precedent for bacteriophages infecting eukaryotic organisms”—a group that includes humans.

To better understand these enigmatic ecosystems, the researchers plan to continue examining their microbial inhabitants with advanced instruments.

“Metagenomic studies in the Marianas Trench have shown that viruses in the hadal may prefer a lysogenic viral approach to adapt to the hadal environment, and our study has also shown that the temperate phage vBHmeYH4907 has a higher abundance in the hadal, which may validate the speculation of a higher abundance of temperate phages in the hadal environment,” the researchers said in their email. 

“In the future, we will isolate more phages from the abyss to test this hypothesis and explore the co-evolutionary relationship between temperate virus and host,” they concluded. “Subsequently, we aim to delve into the molecular mechanisms underlying the interaction between hadal trench viruses and their hosts. For instance, investigating the impact on a host’s physiological and biochemical processes after knocking out the specific viral segments from its genome.”

Update: This article has been updated to include comments from study authors Yue Su, Min Wang, and Yantao Liang.