The KMAP Ocean Gene Catalog 1.0 is the largest database of marine microbes to date. Credit: The KMAP Ocean Gene Catalog 1.0 is the largest database of marine microbes to date
The ocean is the largest habitat on the planet, but much of its biodiversity is still unknown. A study published in Frontiers of science marks a significant advance, providing the largest and most comprehensive database of marine microbes to date, based on their biological function, location and habitat type.
“The KMAP Global Ocean Gene Catalog 1.0 is a step toward understanding the full diversity of the ocean, containing more than 317 million gene clusters from marine organisms around the world,” said lead author Elisa Laiolo from King Abdullah University of Science and Technology (KAUST). in Saudi Arabia. “The catalog focuses on marine microbes, which have a tremendous impact on human life through their influence on the health of the oceans and the Earth’s climate.”
“The catalog is available free of charge through the KAUST Metagenomic Analysis Platform (KMAP),” added the study’s lead author, KAUST faculty member Professor Carlos Duarte. “Scientists can access the catalog remotely to study how different ocean ecosystems work, track the impact of pollution and global warming, and research biotechnology applications such as new antibiotics or new ways to break down plastics: the possibilities are infinite.”
A feat of technological innovation and scientific collaboration
Researchers have been mapping marine biodiversity for hundreds of years, but have faced many challenges creating a comprehensive atlas of ocean life. The first is that most marine organisms cannot be studied in the laboratory. The advent of DNA sequencing technologies has overcome this problem by making it possible to identify organisms directly from water and ocean sediments.
The global genome constitutes a major resource for science and society. Credit: Laiolo et al/Frontiers
“As each species has its own set of genes, we can identify which organisms are in an ocean sample by analyzing its genetic material,” Laiolo explained. “Two technological advances have made this possible on a large scale.
“The first is the enormous increase in speed and decrease in cost of DNA sequencing technologies. This has allowed researchers to sequence all of the genetic material from thousands of ocean samples.”
“The second is the development of massive computing power and AI technologies, which make it possible to analyze these millions of sequences.”
The team used KMAP to analyze DNA sequences from 2,102 ocean samples collected at different depths and locations around the world. This advanced computing infrastructure identified 317.5 million gene groups, more than half of which could be classified according to organism type and gene function. By matching this information with sample location and habitat type, the resulting catalog provides unprecedented insight into which microbes live, where and what they do.
“This achievement reflects the critical importance of open science,” Duarte said. “The construction of the catalog was only possible thanks to ambitious global sailing expeditions during which the samples were collected and the sharing of DNA from the samples in the open access European Nucleotide Archive. We continue these collaborative efforts by making the catalog available free of charge.”
A wealth of scientific and industrial applications
The catalog has already revealed a difference in microbial activity in the water column and ocean floor, as well as a surprising number of fungi living in the mesopelagic “twilight” zone. This and other insights will help scientists understand how microbes living in different habitats shape ecosystems, contribute to ocean health, and influence climate.
The catalog also serves as a reference for tracking the effect of human impacts such as pollution and global warming on marine life. And it offers a wealth of genetic material that researchers can analyze to find new genes that could be used for drug development, energy and agriculture.
Benthic and pelagic genes encode different biological functions. Credit: Laiolo et al/Frontiers
Towards a global ocean genome
The KMAP Ocean Gene Catalog 1.0 is a first step toward developing a global ocean genome atlas, which will document every gene in every marine species in the world, from bacteria and fungi to plants and animals.
“Our analysis highlights the need to continue sampling the oceans, focusing on understudied areas, such as the ocean floor and ocean floor. Additionally, as the ocean is constantly changing, both due to human activity and natural processes, the catalog will need to be continually updated,” Laiolo said.
Duarte cautions that despite its obvious benefits, the future of the catalog is uncertain. A major obstacle lies in the status of international legislation on the sharing of benefits arising from discoveries made in international waters.
“While the 2023 High Seas Treaty offers some solutions, it could inadvertently hinder research by reducing investment incentives for businesses and governments. “Such uncertainty must be resolved now that we have reached the point where genetic and artificial intelligence technologies could unlock innovation and progress in blue biotechnology,” he concluded.
More information:
Elisa Laiolo et al, Metagenomic survey towards an atlas of the taxonomic and metabolic foundations of the global ocean genome, Frontiers of science (2024). DOI: 10.3389/fsci.2023.1038696
Quote: Largest-ever study of ocean DNA creates comprehensive catalog of marine microbes (January 16, 2024) retrieved January 16, 2024 from
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