It has been 30 years since the last new class of antibiotic was introduced to the market. All the existing drugs are essentially variations on a theme: they kill bacteria, in similar ways. Some burst cells walls, others block DNA replication.

But the bacteria are swiftly evolving to survive those chemical attacks – and as they survive, they become virulent superbugs. Without new antibiotics, by 2050 the death toll from drug-resistant infections is projected to reach 10 million people a year, making the coronavirus pandemic seem almost quaint.

This is why scientists at Plymouth University have been searching the cold, dark abyss of the north Atlantic – where they have found sponges that contain powerful molecules capable of killing those superbugs.

Kerry Howell, professor of deep-sea ecology, and her colleagues have been carefully collecting specimens of these plant-like animals, bringing them back to the lab and testing pulverised extracts against stubborn, disease-causing bacteria. Among the deep-sea molecules, they are finding promising bactericidal novelties.

“We don’t actually know exactly what they are yet,” says Prof Mat Upton, a microbiologist who leads the laboratory side of the biodiscovery programme at Plymouth. “We’ve got compounds that kill bacteria that we want to try to kill, and we have a pretty good idea that they are new compounds. It is early, but things are progressing through the pipeline.”

The hit rate for finding powerful and useful new compounds is proving to be especially high among animals of the deep sea. Hundreds of biologically active compounds have been found at the bottom of the ocean, some already in widespread use. Enzymes found in bacteria living around hydrothermal vents are even being used in tests for the Covid virus.

Yet novel antibiotics and an untold variety of beneficial molecules could easily be wiped out if ecosystems around vents and elsewhere on the ocean floor were to be destroyed by deep-sea mining, which could go ahead in less than two years. Even after 40 years of scientific research since hydrothermal vents were first found, a tremendous amount is still being discovered about these extreme ecosystems, which thrive in scorching, toxic waters pouring through cracks in the deep seabed, miles underwater.

Howell says: “Part of the big concern that all deep-sea ecologists have is that we know just how little is known about these areas and we are desperately trying to play catch-up with the [deep-sea mining] industry. To my mind, that’s the wrong way round. We ought to be finding out about these places before we even consider mining them.”

One of the potential targets for deep-sea mining is the south-east Atlantic abyss, where Howell is planning her next expedition, along with South African colleagues. “It’s one of the least-explored parts of our planet. There’s really very little data,” she says .

They will visit a vast underwater mountain range, the Walvis Ridge, which stretches almost 2,000 miles between the island of Tristan da Cunha and Namibia. Deep-sea miners are eyeing up seamounts such as these for their outer crusts, which are rich in metals, including cobalt.

Howell’s team also plans to study the south Atlantic’s abyssal plain, which is dotted with metallic rocky nodules similar to those in the central Pacific’s Clarion Clipperton zone, now attracting feverish interest among deep-sea miners.

“We’re trying to find out more about these areas, the species that live there and also what else they do for humans, one aspect of which is their potential biomedical value,” says Howell.

Their voyage, which has been delayed by the coronavirus pandemic, is part of a five-year research programme, One Ocean Hub, that is seeking ways to share various benefits of the oceans equitably, encompassing environmental, socioeconomic and cultural values.

One aim of the collaboration between dozens of organisations worldwide is to juxtapose the oceans’ easily monetised values, such as seabed mining, with the less tangible benefits, such as carbon sequestration and the hidden stash of potential new medicines.

Natural capital economists will run models to predict how the deep sea’s wildlife, mineral riches and hidden benefits interact, and how using one could put others at risk.

“What we’re interested in doing is making society aware of those trade-offs and those competing uses,” says Howell. “We obviously get a lot of benefits from the ocean that we don’t necessarily appreciate.”

Studies have found that up to three-quarters of deep-sea sponges and corals contain potentially useful compounds. These animals can look like trees, flowers or shrubs, and sometimes like balls of cheese on sticks. “They can’t run away and they need to find ways of protecting themselves – and often it’s chemical,” says Rosemary Dorrington, professor of microbiology at Rhodes University in Grahamstown, South Africa, and a research partner at One Ocean Hub.

Many of these chemical defences are made by communities of microbes living inside the corals and sponges, which Dorrington likens to the human gut microbiome. “There can be up to 1,000 different species of bacteria in one sponge,” she says.

Unlike mining, expeditions such as Howell’s should cause little impact on deep-sea ecosystems. Robotic submersibles developed for the offshore oil and gas industry have become the remote eyes and hands for scientists working in the deep. And only a single specimen of each species is needed. “In the old days, you’d need kilograms of something to extract milligrams of a compound. Now we can detect those compounds in parts per million,” Dorrington says.

In contrast to the search for medicines – where only a single specimen needs to be plucked from the seabed, using deep-diving submersibles originally developed for the oil industry – the likely footprint of deep-sea mining operations will be immense. Mining robots would be dispatched to scrape the tops off enormous seamounts, to gather nodules over hundreds of square miles and to demolish hydrothermal vent chimneys.

Animals living around vents may be especially vulnerable to mining, because many have small geographical ranges.

Bizarre snails with feet covered in armoured scales were recently classified as endangered on the International Union for the Conservation of Nature’s red list. Two out of only three known populations live on vent fields in the Indian Ocean that have been allocated mineral exploration permits, allowing mining corporations to prospect and conduct testing.

Besides destroying habitats and species, Dorrington worries that mining operations, working on far vaster scale than scientific research, could contaminate fragile, living communities – including microbes – that have taken millions of years to evolve.

“It would be exactly the same as if we went to Mars,” she says. “We would need to be considering what we’re taking with us.”

• Helen Scales is author of The Brilliant Abyss, available at the Guardian Bookshop