Why reading entire ocean food webs with marine macrogenomics matters

Zooming out on ocean life

Imagine tracking just one car on a satnav while trying to manage an entire city's traffic. Single-species genetics works like that lone car, watching one animal while missing the wider gridlock. Today, researchers are shifting toward marine macrogenomics, studying whole communities of genomes at once.

By reading genetic data across entire food webs, this approach tracks how ecosystems shift over space and time. It links environmental DNA, museum records, and whole-genome sequencing into a broad view of ocean health. Looking at solitary species overlooks trophic cascades, where the collapse of one creature triggers the fall of its neighbours.

The hidden record in sea mud

The puzzle is predicting how oceans will alter as temperatures climb. Under a high-emission scenario, nearly half of 33,000 modelled marine species will lose 50% of their core habitat area by 2100. To forecast that kind of reshuffling, scientists need to know how communities coped with past shifts.

They found answers buried deep on the seabed. By extracting sedimentary ancient DNA, or sedaDNA, teams traced major community shifts from 20,000 years ago back to 2 million years before the present. These muddy layers capture ancient ecosystems, showing how whole food webs formed and dissolved during historic climate swings.

Researchers then feed this ancient and modern data into computer simulations, alongside joint species distribution modelling. These tools calculate a fitness offset, which measures the gap between an organism's current adaptive genes and future climate conditions. Spotting where this gap is widest warns scientists of genome erosion, the dangerous loss of genetic variation that leaves populations fragile.

A lopsided map of the sea

Yet our genetic map of the ocean has massive blind spots. Out of about 230,000 described marine eukaryote species, genomic datasets exist for just over 9,000, roughly 4%. That means 96% of known complex ocean life remains unsequenced.

The data we do have is skewed. Fish and invertebrates are the only groups with over 100 species possessing at least 50 whole-genome sequencing libraries. Most samples come from the Northern Hemisphere, while the Arctic and Indian Oceans remain undersampled. Combining studies with different data standards also demands huge amounts of computing power.

What we still do not know

Our traffic map analogy works well for tracking connected movement across a network. It stops working, however, because cars cannot reproduce or adapt their engines when conditions alter. Living ocean species change their biology, and we still do not know if they can adapt fast enough to keep pace with rapid contemporary warming.

Scientists also do not know how to weigh individual species when building ecosystem-wide genetic scores. A top predator might alter a habitat far more than an abundant plankton species. Finally, future marine communities may not reach a stable equilibrium, as climate disruption is projected to persist for centuries.