Largest DNA database of marine microbes to track the impact of global warming on ocean health

You may have heard of the human genome, but have you come across the ocean genome?

While the former maps the full set of genes that occur in humans, the latter does the same across marine flora and fauna.

The King Abdullah University of Science and Technology (KAUST) in Saudi Arabia has just released the Global Ocean Gene Catalog 1.0. It contains more than 317 million gene clusters and is the largest open-source catalogue of marine microbes to date, based on samples from across the world’s ocean.

Next-generation genome sequencing techniques have enabled this type of metagenomic analysis – the study of genomics across different organisms in a sample.

Ocean microbes were the earliest life forms on our planet, and they are involved in the cycles of climate-relevant elements such as nitrogen, sulphur and carbon.

The authors of the study, published in Frontiers in Science, point out that these microorganisms can therefore provide a baseline for tracking the impact of global warming, pollution and other influences on the health of our ocean. What is more, the study of ocean microbes can help in the discovery of new genes that could be used in medicine, energy, food and many other areas.

The ocean is the largest habitat on our planet. It covers nearly three-quarters of its surface. Sea life began with single-celled organisms, and today’s microbial diversity reflects a whole array of functions and metabolic pathways to source energy and process organic matter.

The KAUST study shows the distributions of microbes across different ocean realms and depth zones, and their functions.

Bacteria – which form the largest group of organisms in the study’s sample – are most prevalent in the lower reaches of the ocean and on the ocean floor – the benthic realm. Viruses and Eukaryota reach their highest levels in the pelagic realm – or open ocean.

Fungi represented more than half of the gene clusters in the middle reaches of the pelagic realm, highlighting their importance to microbial diversity and functionality.

The upper reaches of the ocean also had an abundance of genes involved in carbon-related pathways and sulphur processing. Genes found in the benthic realm were focused on carbon fixation, while those in the dark ocean – beyond 1,000m where no light reaches – related to nitrate and citrate reductions.

To date, marine metagenomics – “the study of the pooled genetic information contained in an environmental sample” – has largely focused on the pelagic realm, which is open ocean.

The benthic realm, the seafloor, is less well documented. Given that the ocean floor is highly threatened, developing a baseline understanding of those microbial communities will be critical, the researchers say.

Studying this realm, besides building a deeper understanding of how these habitats and organisms function, also brings the possibility of discovering many more genes and functions, they add. This is important because many benthic habitats are at risk.

For example, up to 90% of coral reefs could be lost by 2050, scientists predict – even if global warming can be slowed. As biodiversity hotspots, they support a quarter of marine species and provide food and livelihoods as well as protection from flooding. Climate change and rising sea temperatures are only one threat – overfishing and pollution are other known contributors to coral decline.

The benthic realm may also be threatened by deep-sea mining – an activity likely to increase because of the abundance of metals found in our ocean, needed for use in electronics and electrification.

And with 95% of ocean plastics ending up in the deep sea, microbe communities in those far reaches may also have their habitats and functions disrupted, the study suggests.

The study’s findings indicate the ocean genome is dynamic and responds to human-induced changes. Impacts include developments such as the proliferation of antibiotic resistance in marine bacteria, which can be a result of human activity – for example, wastewater discharge in coastal areas.

Understanding these dynamics will be critical to maintaining biodiversity and marine habitats.This is the focus of the World Economic Forum’s Ocean Action Agenda, which works to create a healthy, thriving ocean by protecting and restoring it while enhancing the resilience of coastal and ocean-dependent communities.