One thing is clear: scientists aren’t going to run out of new, deep-sea species to find any time soon. In a recent three-year study in the Pacific Ocean, remotely operated vehicles (ROVs) photographed nearly 350,000 animals: fish, octopuses, corals, anemones, shrimp, squid, sponges, and sculpted, living mud balls called xenophyophores… the list goes on. Only one in five were known species. Not all the images were clear enough to identify, but most were organisms nobody had seen before.

Whenever scientists look in the deep ocean they’re pretty much guaranteed to find something new and unexpected. “It’s always an incredible adventure,” says Prof Randi Rotjan from Boston University, who just returned from co-leading a month-long expedition to the Phoenix archipelago in the central Pacific Ocean.

Their mission on the Schmidt Ocean Institute’s RV Falkor involved studying the ecosystems on seamounts. With the ROV SuBastian, the team conducted 21 dives and clocked up 250 hours underwater, gathering samples and high definition video of corals, sponges and other intricate life forms.

Standard techniques for studying deep-sea species involve a combination of visual recognition and collecting specimens for detailed analysis. Environmental DNA (eDNA), which looks for DNA-containing cells and mucus shed by organisms in large samples of water, is becoming a quicker and cheaper way of finding out which species are in the vicinity.

Archives of genetic sequences from deep-sea species are gradually being built. One day it should be possible to know whether a giant squid or a Greenland shark or any other mysterious deep-sea denizen just swam by out of sight, from the DNA they left behind.

When Rotjan’s team have finished analysing their findings, they will undoubtedly be adding entries to the World Register of Deep-Sea Species, which in mid-2021 listed 26,599 species, a number that’s rising all the time. “It’s not just a catalogue of what’s there, but why they’re there, who they’re interacting with and what they’re doing,” says Rotjan.

An aspect of deep-sea ecology that Rotjan is studying is the immune systems of corals that can live for thousands of years. She wants to understand how they heal from attacks by coral-eating predators, or corallivores. This could offer new insights into how innate immunity evolved among some of the earliest, multicellular animals on Earth. It could even have applications in medicine, because we share ancient ancestors with corals.

Expeditions such as Rotjan’s hold immense potential to inspire the public about the deep. Footage of deep-diving whale sharks and a pair of exquisite glass octopuses sparked enormous responses online. For Rotjan, these glimpses of deep-sea ecosystems are crucial reminders that we share the world with so much hidden life. “What we really need, as stewards of this planet, is to protect our neighbours,” she says.

Will we ever build a deep-sea base?

Technically speaking, there is nowhere in the abyss that’s entirely off limits to humans. A growing roll call of brave and curious people have paid brief visits to the ocean’s greatest depths. Earlier this year, Nicole Yamase became the first Pacific Islander, the third woman and the youngest person to descend into the Challenger Deep in the Mariana Trench, the ocean’s deepest point at close to 11 kilometres down.

But going down and staying down is a different undertaking. The people who have so far spent the longest time deep underwater are commercial divers who carry out construction work on oil and gas installations. They spend weeks inside pressurised capsules on ships and oil rigs, commuting each day inside a diving bell to their work site 100 metres or more below. Their bodies stay saturated with diving gases the entire time, until they are slowly decompressed at the end of each mission.

Scientists have also adopted saturation diving as a means of spending more time at greater depths. A pioneer of this was French underwater filmmaker, Jacques-Yves Cousteau, who in the 1960s built a starfish-shaped underwater base in the Red Sea called Conshelf II. His grandson, Fabien Cousteau, is now planning a next generation, deep-sea facility called Proteus.

“In order for us to understand something as complex, something as mysterious, something as foreign as the ocean world, one has to spend a lot of time down there,” Cousteau said, when we spoke about Proteus on the Catch Our Drift podcast.

Dubbed the first International Space Station for the ocean, Proteus will be a larger and more adaptable version of previous underwater habitats including Aquarius in Florida – the only one still in operation and where in 2014 Cousteau spent a record-breaking 31 days living underwater.

Eventually, Cousteau hopes there will be a network of Proteus bases through the ocean, to be used by scientists and filmmakers, as well as astronauts training for the rigours of space. The first base will accommodate a team of 12 aquanauts and is due to be installed in a marine protected area off the island of Curaçao. It will be in around 18 metres of water, so not exactly the abyss, but still proof of concept for groups of people living and working underwater.

Proteus will even house the world’s first underwater greenhouses to grow fresh food for the crew and a broadcast studio to help communicate the wonders of the deep. “We want people to be able to dream, to be able to connect with the ocean,” said Cousteau.

Will the climate crisis change the deep sea?

Climate change is already reaching down into the deep ocean. A 2020 study confirmed the average global temperature between the surface and 2,000 metres has been rising year on year. The increase may seem small — in 2019, it was 0.075°C above the average between 1981 and 2010 — but due to the volume of water, the heat absorbed is equivalent to the energy of 3.6 billion atomic bombs exploding.

And there are greater changes on the way. By the end of the century, it’s predicted temperatures in the twilight and midnight zones, down to 1,000 and 4,000 metres respectively, will rise to 8°C. This will come as a hot shock for deep-sea organisms that are adapted to around 4°C.

Other climate impacts will accompany the rising temperatures. Ocean acidification is expected to hit hardest between 200 and 3,000 metres down, where deep-sea corals will find it increasingly difficult to make their exoskeletons. Warming seawater will lose its ability to hold oxygen. In the northeast Pacific, off Vancouver Island, oxygen levels down to 3,000 metres have already declined by 15 per cent over the last 60 years.

Human impacts are likely to reduce the ability of the deep to buffer against rising carbon concentrations and temperature.

A recent study estimates that trawling disrupts seabed carbon stores and causes emissions similar to the aviation industry. There are also plans to fish the open waters of the twilight zone for lanternfish, thought to be the world’s most abundant vertebrates. Each night, huge shoals of the fish migrate from the twilight zone to feed in the shallows, before fleeing back to the deep at dawn, bringing masses of carbon with them. Hunting these fish in large numbers could cut off a critical pathway of carbon into deeper waters.

Plans to begin mining the abyss likewise come with worrying predictions. Mining could disturb seabed carbon stores, potentially on a larger scale than trawling. Contaminated wastewater extracted from the mined slurry could be disposed of by pumping it into the twilight zone, where it would choke gelatinous midwater animals such as jellyfish and siphonophores, all of which are important in the drawdown of carbon into the deep.

A great unanswered mystery is whether seabed mining would help solve the climate crisis by providing metals to make green technologies like electric car batteries, or make the situation a great deal worse.

Read more about the oceans:

• There are five oceans now, not four. A marine biologist explains why that matters…
• The secrets of the immortal jellyfish, Earth’s longest-living animal

What does the seabed look like?

It’s been said many times that we know more about the surface of the Moon than the bottom of the sea. This is true, at least in terms of the maps we have, but it’s a fact that’s gradually changing.

The entire surface of the Moon has been mapped to a resolution of seven metres. Compare that to the best complete maps of the seabed, which are created using satellites that measure bulges in the sea surface and only show features that are at least five kilometres across.

It’s worth bearing in mind that the area of the Moon is about 10 times smaller than the Earth’s seabed, and with no ocean getting in the way it’s a good deal easier to see what’s going on up there. Even so, scientists and engineers are finding new, better ways of mapping the bottom of the sea.

The Nippon Foundation-GEBCO Seabed 2030 project aims to map the entire seafloor by the end of the decade through data donated by governments, researchers, industry and private individuals. The plan is to obtain a depth reading for every 800 x 800m pixel of the deep seabed. For areas shallower than 1,500 metres, that goes down to one reading per 100 x 100m pixel.

Better seafloor maps will serve all sorts of purposes. They will help us navigate, they will aid in the laying of telecommunications cables, and they will improve our understanding of how seabed topography influences currents and the mixing of water, allowing us to make better climate change predictions.

In 2021, Seabed 2030 passed the 20 per cent mark, so there’s still a long way to go. A new generation of Uncrewed Surface Vessels (USVs) could help meet the challenge, including a fleet based on the design that won the 2019 ocean-mapping XPRIZE. The Sea-Kit Maxlimer deploys and recovers an autonomous submersible that echo sounds the depths. It also recently hit the headlines when it navigated across the North Sea, carrying oysters and beer from Belgium to England – a first for a commercial, robotic ship.

As well as plans for a global map, portions of the abyss are also being charted in greater detail, to make maps of giant underwater mountains. When Rotjan was co-leading the recent expedition to the Pacific on the RV Falkor, her team studied 14 seamounts, including 10 that were previously unvisited. They used an array of the ship’s onboard sensors, including a multibeam echo sounding system, to interrogate the seabed. As the data flowed in, three-dimensional maps were drawn and the scientists started planning where to dive.

When studies of those seamounts are published, the scientists will have a chance to name them. There’s a formal process for naming seamounts and there are rules to stick to. You can’t, for instance, name them after a living person. Rotjan and her team have some thoughtful and fun ideas drawn from history and popular culture, but for now they’re keeping them under wraps.

• This article first appeared in issue 368 of BBC Science Focus Magazine – find out how to subscribe here

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