Recent research indicates that our oceans can play a crucial role in tackling significant issues like the lack of antimicrobial medications, solutions for plastic waste, and innovative enzymes for genome editing.
Over the last two decades, scientists have successfully gathered a vast array of microbial genomes from oceanic sources. However, applying this valuable information in biotechnology and medicine has proven to be challenging.
This latest study, conducted by BGI Research in China in partnership with Shandong University, Xiamen University, the Ocean University of China (OUC), the University of Copenhagen in Denmark, and the University of East Anglia (UEA) in the UK, examined nearly 43,200 genomes of micro-organisms (including bacteria and archaea) obtained from marine samples, revealing a remarkable diversity comprised of 138 distinct groups.
The researchers gained new insights into the evolution of genome sizes and how oceanic microbes maintain a balance between CRISPR-Cas systems—integral to their immune defense—and antibiotic resistance genes. Many of these genes are triggered by antibiotics, enabling microbes to endure.
Both CRISPR-Cas systems and antibiotic resistance genes form part of bacterial immune systems. Using computational techniques, the team identified a novel CRISPR-Cas9 system and ten antimicrobial peptides, which are also essential components of the immune systems in various organisms.
Antimicrobials—such as antibiotics, antivirals, antifungals, and antiparasitics—are medications utilized to prevent and manage infections in humans, animals, and plants. Nevertheless, the World Health Organization warns that increasing resistance due to the excessive use of certain drugs jeopardizes effective prevention and treatment across a growing range of infections, highlighting the necessity for new alternatives.
In their publication in the journal Nature, the researchers also discovered three enzymes capable of degrading a prevalent marine plastic pollutant, polyethylene terephthalate (PET), which represents a significant environmental and health concern.
Laboratory tests validated the results obtained from ocean metagenomics, showcasing their promising applicability. Lead author Thomas Mock, a Professor of Marine Microbiology at UEA’s School of Environmental Sciences, remarked that this research elevates the field of ocean metagenomics to a “new level.”
“This study underscores the potential of large-scale metagenomic sequencing of ocean microbiomes to enhance our understanding of marine microbial diversity, its evolution, and to discover new ways to leverage this knowledge in biotechnology and medicine,” explained Prof. Mock.
“The relationships between marine microbes and their surroundings are foundational to global processes like carbon fixation and nutrient recycling. Consequently, these dynamics are vital for making Earth habitable, as the oceans are the planet’s largest and most critical ecosystem.
“Elements such as salinity, temperature fluctuations, light availability, and pressure variations—from the ocean’s surface to its deepest trenches and from the poles to the tropics—create unique selection pressures that drive the adaptation and co-evolution of oceanic microbes.
“Building upon these insights, our study employs the collection of marine microbial genomes sourced from metagenomes as a key asset for genome mining and bioprospecting, facilitating the discovery of new genetic tools and bioactive substances.”
The data encompasses a wide range of marine ecosystems globally, from poles to poles and from the surface to the ocean’s depths. This study significantly enhances the understanding of marine microbiomes by creating a new publicly accessible database featuring approximately 24,200 species-level genomes.
“While previous research has shed light on the role of marine ecosystems in preserving biological diversity, our work extends these findings and opens up new avenues for sustainable exploration and use of the oceans, which is timely given the global challenges humanity faces,” stated Prof. Mock.
“Progressing this research through deep learning-based genome mining of ocean microbiomes, paired with biochemical and biophysical lab experiments, holds great promise for addressing pressing global issues like the shortage of antimicrobials and ocean pollution.
“This approach emphasizes the vital role of marine microbiomes in enhancing human health and fostering environmental sustainability.”
