DNA From the Ocean’s ‘Twilight Zone’ Could Lead to New Lifesaving Drugs, Scientists Say

Researchers catalogued the genes of more than 300 million groups of marine bacteria, viruses and fungi in hopes that the database could lead to breakthroughs in medicine, energy and agriculture

dark coral, fish and distant manta rays underwater
Scientists produced the most complete catalog of marine microbe DNA yet, including data from the deeper zones of the oceans. Rowan Coe via Getty Images

As of Tuesday, scientists around the world have an exciting new tool at their disposal: the largest-ever collection of marine microbe genomes, organized in an online database.

The catalog, described in the journal Frontiers in Science, is an open-source digital library of genetic codes from the ocean’s organisms—and scientists say it may open doors to drug development or innovations in energy and agriculture.

“Genes and proteins derived from marine microbes have endless potential applications,” study co-author Carlos Duarte, a marine ecologist at the King Abdullah University of Science and Technology (KAUST) in Saudi Arabia, says to Nature News’ Carissa Wong. “We can probe for new antibiotics; we can find new enzymes for food production. If they know what they’re searching for, researchers can use our platform to find the needle in the haystack that can address a specific problem.”

To build the database, researchers analyzed thousands of marine samples collected over the last 15 years, from all five oceans and the Mediterranean Sea. The samples were sourced from a variety of past expeditions and studies, such as the global Tara Oceans expedition that ran from 2009 to 2013. The DNA represented bacteria, fungi and viruses from a variety of geographies and oceanic depths.

In the past, barriers to DNA sequencing presented a major roadblock for scientists—even when the genetic samples were collected and in hand, their efforts could be foiled by cost, time or the condition of the DNA. As of 2022, 303 million unique marine microbial genes had been sequenced.

The team’s breakthrough came via sequencing and technological advances. Improvements in the speed and accuracy of supercomputing, as well as developments in artificial intelligence and shotgun DNA sequencing, allowed the team to analyze more than 2,100 metagenomes, or bulk quantities of genetic material. All told, they sequenced approximately 317 million unique groups of microbial genes to create the most complete catalog yet.

map of the sampled locations across the world; most are pelagic, upper ocean areas, with some deeper in the twilight zone or dark ocean
The team gathered samples, taken at varying depths, from oceans across the world. Laiolo et al., Frontiers in Science, 2024, under CC BY 4.0 DEED

In particular, the study took a close look at life accustomed to the extreme conditions of the oceanic “twilight zone.” Stretching between 650 and 3,300 feet below the surface—just out of range for sunlight—this region is home to some of Earth’s most unique creatures, with adaptations driven by such a harsh habitat.

Within the twilight zone, researchers were surprised to discover that more than half of the unique gene clusters found belonged to fungi.

“There have been some indications of [fungi abundance at this level] before, so this is another piece of the puzzle,” lead author Elisa Laiolo, a marine biologist at KAUST, says to the Guardian’s Sophie Kevany.

Drugs like penicillin, for example, were developed from fungi. And the ones found in the deep ocean have evolved rare traits that could be useful to scientists developing medicines. “That could potentially lead to the discovery of new species with unique biochemical properties,” Fabio Favoretto, a marine ecologist at the Scripps Institution of Oceanography who was not involved in the research, tells the Guardian. “We might find something like [penicillin] from these ocean fungi.”

Examining marine microbes also shed light on viruses’ role in increasing genetic diversity, which they do by moving genes between organisms.

various fungi in 40 petri dishes
Morphological diversity of fungi collected from a marine sponge species, Ircinia variabilis. CC BY 4.0 DEED

The study suggests avenues for future research—for example, the scientists identified a wide gap in knowledge about the deep sea and ocean floor. They also point out that their catalog can serve as a baseline for the diversity of marine microbes, which could allow future researchers to gauge the impact of human activities—such as deep-sea mining or burning fossil fuels—on these organisms, per Nature News.

For the catalog to truly be effective, the team says, countries and scientists need to prioritize the dissemination of knowledge. The 2023 “high seas treaty,” which nearly 200 countries signed, maintains that a marine gene is owned by the country that discovers it, though its benefits must be shared. Still, the agreement was unclear on how that would work.

“Such uncertainty must be resolved now we have reached the point where genetic and artificial intelligence technologies could unlock unprecedented innovation and progress in blue biotechnology,” Duarte says in a statement.

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