Off the north-west coast of Scotland, 3,300ft (1,000m) under the sea, life is thriving amidst an otherwise drab and muddy ocean floor.

This is thanks to a cold-water coral system called the Darwin Mounds. Unlike their tropical counterparts, these corals do not need sunlight to survive. Instead they sit in the dark, waiting for food to pass by.

As they are so deep, these corals are not easily visible. In fact, until 1998, no one even knew this group of corals existed. They are also extremely fragile: easily damaged and even destroyed by the deep-sea fishing trawlers that drag their nets along the ocean floor. The reef structures, which can take thousands of years to grow, can be killed in mere moments.

The fragile corals, which can take thousands of years to grow, can be killed in mere moments

"If all the 'parent' coral colonies are damaged, they will not easily produce offspring, and it becomes very difficult to have new coral colonies establishing," says Veerle Huvenne of the National Oceanography Centre (NOC) in the UK.

This is why they need to be protected. But although the Darwin Mounds are now well recognised, there are believed to be many more cold-water corals off the UK coast that remain undiscovered. How can an area deep under the sea be protected if nobody knows it is there in the first place?

The corals are important as more than oddities: they provide the ideal place for small sea life. There are numerous niches, crevices and holes where animals can hide, explains Huvenne. They are "little islands of high biodiversity". In fact, one mound can be home to as many as 1,300 different types of marine life.

Coral reefs are also places where mothers rear their young fish. "We saw cold-water coral reefs teeming with pregnant fish – ready to span," Huvenne says of one expedition.

Corals also offer glimpses into the past. By drilling into coral mounds, the lowest parts of which are the most ancient, scientists can get an idea of the sea's condition when the corals were first growing.

For instance, the Darwin Mounds have existed for about 10,000 years, ever since the end of the last ice age. That means they could tell us how the sea has changed since then.

"During glacial times, the water masses, temperatures and primary productivity at surface were very different to what it is now. It's only when Earth started warming again that we could have these coral reefs in this area," says Huvenne.

As important as they are, cold-water corals are not especially rare. They are found in waters from Norway to northern Africa. But their depth means they can go undetected for years.

Their depth means they can go undetected for years

The existence of deep-water corals in UK waters will have been known to fishermen since at least the 1700s. But for decades, no one knew just how many existed in the seas surrounding the UK. Then in 1998, the National Oceanography Centre's (NOC) Brian Bett led a large-scale environmental survey.

"I was sent a fax of a hand-written sketch saying 'there's something interesting over there,'" recalls Bett. Armed with the clue, he dropped a camera down into the waters below the area.

In doing so, he discovered the Darwin Mounds: the UK's largest cold-water corals. They are spread over a total area of 39 square miles (100 sq km). The corals that made them belong to the species Lophelia pertusa, which is the main coral in British waters that forms reefs.

Two years later, Bett came back for a more extensive survey – and to his horror he found that some of the corals had experienced significant damage. Deep-sea trawlers were to blame: there were tell-tale linear grooves on the sea bed from where their nets had scraped over it. To prevent further damage, the UK Government, acting through the Joint Nature Conservation Committee, used the evidence collected by NOC scientists to arrange for the site to become a marine protected area.

But Bett knew a deep-sea fishing ban would also need to be enforced. "There's no point in having a protected area without a ban on bottom fishing," he says. It took more than three years to enact.

To understand whether the corals had recovered from this damage, Bett, Huvenne and other colleagues returned to the site in 2011. They finally published their findings in the journal Biological Conservation in August 2016.

Over the course of more than a decade, the parts of the coral that had been damaged showed no signs of recovery

The news was not great. Over the course of a decade, the parts of the Darwin Mounds that had already been damaged showed no recovery whatsoever. "There was no sign of regrowth and recolonisation [of sea life] of the corals," says Bett.

These deep-water corals are extremely slow-growing, so they may take hundreds of years to rebuild their reefs. This is why they are referred as a "vulnerable marine ecosystem".

Fortunately, the areas unaffected by trawlers looked healthy and life was abundant. "The encouraging side is we don't see much violation of the protected area. We found one or two fresh trawl marks, but not many at all," Bett says. "By and large, the fishing industry has been respecting the protected area."

This shows, says Huvenne, that protecting marine areas does work. She is now urging what is known as the "precautionary principle" when considering any future deep-sea fishing.

It's like if you want to make a holiday home in the middle of a forest: you have to apply for a permit. That needs to happen in the ocean too

"Unless you have evidence your activity is not going to harm, it would be better not to start trawling or affecting the seabed until you have made a full assessment," she says. "It's a bit like if you want to make a holiday home in the middle of a forest. You also have to apply for a permit – you can't just go in and put a house there. That needs to happen in the ocean too."

The UK government is also in the process of designating a larger number of areas that require protection. But this is a lengthy process and "the world moves quickly," says Huvenne. "We run after the facts."

It is precisely because corals are home to so many fish that their surrounding waters are ideal targets for fisheries. This, conservationists argue, is why all corals should be protected. But so too should unexplored waters, where other diversity might exist and offer still more of the ocean's secrets.

Because of their protected status, for now the UK's deep-sea corals are in a "fairly good condition", says Andrew Davies of Bangor University in Wales.

This may change due to the effects of climate change, including ocean acidification and warming. "I do not believe that we can save all the corals," Davies says. "I believe that there are some regions of the oceans that would be impacted less by climate change than others."

One study found that L. pertusa corals in the northern Atlantic Ocean could "acclimatise to increased levels of carbon dioxide (CO2)". However, the same research also showed that CO2 could still weaken the corals.

One obstacle to understanding what challenges corals face is that not all of them have been surveyed. "Corals cover a vast area throughout the north Atlantic," says Davies. Visiting all the known – and unknown – sites takes time and money.

An expedition in August 2016 showed just how important it is to be able to explore new areas within the ocean. Led by Kerry Howell of Plymouth University, researchers set out to discover how corals from different populations in the north-east Atlantic Ocean are connected.

"We found a whole load of new reefs," says Howell. "Some are pretty stunning." It is now clear to her that there are many more out there. Models can help predict where they are hiding.

Because these corals happened to be in protected areas, their diversity and beauty was largely unaffected. If other areas of the ocean are protected in similar ways, deep-water corals will still have a chance of combatting the numerous stresses they face – and could exist for thousands of years to come. 

Nerc-funded Deep Links Project images courtesy of: Plymouth University, the University of Oxford, JNCC, BGS, Deep Links Project. 

This story is a part of BBC Britain – a series focused on exploring this extraordinary island, one story at a time. Readers outside of the UK can see every BBC Britain story by heading to the Britain homepage; you also can see our latest stories by following us on Facebook and Twitter.