In 2009, a team of international scientists working for the Tara Ocean Foundation set out on a mission to study uncharted marine biodiversity (1). For three and a half years, the researchers collected more than 1,000 oceanic samples across the world. Their latest findings, published in Nature, report two biosynthetic pathways that could produce potential new drugs (2).
Characterizing the biodiversity of the ocean is an immense task. “There are about 1 million microbial cells per milliliter of seawater. With 70 to 71 percent of the planet being covered by seawater, it's beyond comprehension the number of organisms we're talking about,” said Lucas Paoli, a microbiologist at the Pasteur Institute and the lead author of the study.
In the past, scientists have attempted to chart this expansive ocean microbiome by culturing marine microbes in the lab to access their genetic material. However, this process is not always successful. “[Some organisms] need a unique environment, such as salinity, pressure, and light, to be able to grow,” said Sam Afoullouss, a deep-sea natural product chemist at the University of South Florida who was not involved in the study.
Instead, Paoli’s team took a metagenomics approach, piecing together each organism’s genome from DNA fragments recovered from the seawater. Extracting microbial DNA directly from the environment was “a really, really good strategy,” according to Afoullouss. “If you’re doing metagenomics, you don’t need to worry about culturing them.”
The team combined their own dataset with those collected from prior oceanographical surveys (3,4). They relied on computational methods to understand how the complex mixture of DNA fragments fit together to form thousands of different organisms’ genomes. “Imagine having 1000 sets of puzzles. Some of them are the same; some of them are different. You open all the boxes and mix everything in a bag. That’s what we have initially,” Paoli said.
The result was a library of more than 26,000 draft genomes or genome segments. The researchers compared these segments to available reference genomes and identified 2,700 completely new species. “There is an extremely large microbial diversity that was not previously known, and with our approach, we were able to access a large part of this unknown diversity of the ocean microbiome,” said Paoli.
Within those new species, the researchers focused on identifying novel genes that encode biologically useful enzymes. “In bacteria, genes that encode functions involved in the same biosynthetic pathway often sit together in the genome,” said Chris Bowler, a marine biologist at Harvard Radcliffe Institute and The French National Centre for Scientific Research and the scientific director of the Tara Ocean Foundation. The metagenomic analysis identified around 40,000 biosynthetic gene clusters — groups of genes that encode potential natural product synthesis pathways. Many of these genes originated from a lineage of bacteria they called Candidatus eudoremicrobiaceaebium after the Greek sea nymph Eudore, for its “bountiful catches and fine gifts from the ocean,” said Paoli.
The researchers used computational methods to predict the molecules the biosynthetic gene clusters would produce in the ocean, which could be different from the compounds they yield in the lab. “Microbes will change what they produce based on their environment,” Afoullous said.
To validate their predictions, the researchers introduced two biosynthetic gene clusters into Escherichia coli and observed that these genes produced the same molecule in bacteria as they are expected to under the sea. In this way, the team discovered two pathways that give rise to molecules with therapeutic promise.
One was the phospeptin pathway, which generates a unique peptide structure consisting of many phosphate groups. The peptide inhibits neutrophil elastase, a protease enzyme that neutrophils secrete during inflammation to destroy bacteria. Paoli thinks that this peptide could serve as a new chemical scaffold for drugs to treat autoimmune diseases such as cystic fibrosis that show irregular protease activities.
The team also described the pythonamide pathway, which encodes an enzyme that catalyzes the addition of methyl groups to the backbone of peptides. “This modification is something that pharmaceutical industries have been after for a while because it's been known to produce very potent natural products,” said Paoli. The chemical reaction is extremely challenging to achieve in the lab, and as far as Paoli knows, this is only the second enzyme ever identified with this capability.
While the scientists made significant progress towards characterizing the oceanic biodiversity that can give rise to therapeutic natural products, the work is not exhaustive. Since the expedition prioritized collecting from the surface portion of the sea, the scientists do not have samples from deeper waters, oceanic floors, or coasts. The Tara Ocean Foundation is planning its next expedition sometime this year, which may uncover other classes of biologically relevant molecules at the land-sea interface.
“In this new project, we're going to be staying close to the coast. We will have even more potential, I think, to identify new antibiotic strategies to overcome the problem of antibiotic resistance,” said Bowler.
References
- Sunagawa, S. et al.Tara Oceans: towards global ocean ecosystems biology. Nat Rev Microbiol 18, 428–445 (2020).
- Paoli, L. et al. Biosynthetic potential of the global ocean microbiome. Nature 607, 111–118 (2022).
- Acinas, S.G. et al. Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. Commun Biol 4, 604 (2021).
- Biller, S. et al. Marine microbial metagenomes sampled across space and time. Sci Data 5, 180176 (2018).
