Symbol of Easter and scourge of Mr McGregor, the rabbit may be the cute hero of children’s books but its rapid reproduction has traditionally made it a pest for farmers and gardeners.

Now, however, with British rabbit populations are being decimated by disease, the humble bunny is being hailed as an “ecosystem engineer” and landowners encouraged to create innovative “rabbit hotels” to revive its numbers.

The hotels – piles of branches artfully arranged near existing rabbit warrens – provide safety from burgeoning predators, and new places for female rabbits to burrow and give birth to their kits.

The brash piles are the key technique in a new “toolkit” successfully trialled in five locations as part of Shifting Sands, a four-year National Heritage lottery-funded project to restore rare species in the East Anglian Brecks.

Rabbit numbers decreased by 88% in the east Midlands and 83% in Scotland between 1996 and 2018. They fell 43% across the whole of the UK over the decade to 2018, with the latest scientific survey recording no sign of the declines slowing.

“Rabbits are in a lot of trouble,” said Pip Mountjoy, Shifting Sands project manager at Natural England. “They are actually an endangered species in their native region on the Iberian peninsula. It’s surprising for people that rabbits are important in some ecosystems. We think of them as a pest but in Britain they are a keystone species – they act as landscape managers and a lot of other species rely on them.”

Shifting Sands is part of the Back from the Brink species-rescue effort.

The European rabbit is not native to the UK but was brought here by the Normans. For nearly nine centuries they were intensively farmed for meat on the Brecks. In this unique dry, sandy biodiversity hotspot, their grazing helped rare plants and invertebrates thrive.

Rabbits are selective grazers, and keep vigorous grasses in check, thereby assisting more delicate wildflowers. The animal’s earth-scratching and burrowing helps seeds germinate and creates what ecologists call “mini mosaic habitat” – patches of warm, bare earth which are havens for rare flowers and invertebrates, as well as the common lizards and adders that bask there.

Rare plants assisted by rabbit grazing include purple milk vetch, rare spring sedge, spring speedwell, and prostrate perennial knawel, which is found nowhere in the world outside Breckland.

The caterpillars of the declining lunar yellow underwing moth are found close to rabbit burrows and even endangered birds are helped: rabbits unearth lots of flints from the sandy soil which provide perfect camouflage for the stone curlew, which lays its flint-coloured eggs on the ground.

Myxomatosis introduced into Britain in the 1950s was allowed to spread and reduce rabbit populations by 99%. While many crop-growers were pleased, the rapid loss of wild rabbits and their grazing contributed to the extinction of the large blue butterfly in 1979 (since reintroduced) and near-loss of other species that require warm, closely cropped grassland.

Rabbit populations revived when individuals developed resistance to myxomatosis but a new virus, rabbit haemorrhagic disease virus type 2 (RHDV2), has caused a second crash in Britain’s rabbit population since it emerged in commercial rabbit farms in northern France in 2010.

Diana Bell, professor of conservation biology at the University of East Anglia, a partner in the Shifting Sands project, has studied the impact of RHDV2 on the large rabbit warrens on her university campus.

“This virus has decimated rabbit populations – they’ve just crashed everywhere, and the virus keeps coming back,” she said. “It’s become endemic like myxomatosis. Even now we still don’t see baby rabbits by the side of the road as we used to.”

The virus can kill rabbits at a young age, and a typical sight are baby rabbits, or kits, sat motionless at the entrance to a hole. The earlier variant, RHD1, caused bleeding from the nose but this virus often has no visible signs. When dead animals are subject to postmortem, major haemorrhaging has been found in their livers and organs. Myxomatosis still kills rabbits as well.

“When you’ve got two completely different viruses attacking them at different stages in different ways I don’t think we will ever see rabbits back in the numbers they once were,” said Bell.

Under her guidance, the Shifting Sands project has trialled techniques to boost rabbit populations where family groups are clinging on. “Rabbit habitat enhancement plots” – or rabbit hotels – are built to provide refuges for rabbits to hide from aerial predators such as buzzards and create “stepping stones” to help them hop through the landscape.

But the rabbit hotels have another function. Bell’s research has revealed that rabbits live in matriarchal family groups, with a dominant female assisted by daughters, nieces, aunties, grandmothers and great-grandmothers. The dominant female prevents other females from having kits – sometimes even dragging a rival’s babies above ground to die – because too many young around a warren attracts predators including foxes, badgers, stoats and polecats.

The hotels provide space where subordinate females can safely have babies, so helping rabbits breed like rabbits again.

Monthly monitoring by volunteers from Natural England and Suffolk and Norfolk wildlife trusts found 41% of the brash piles contained rabbit burrows – which usually leads to breeding – and 91% contained scrapes – evidence of use by rabbits.

The Shifting Sands project also used diggers to create artificial banks for rabbits to burrow and breed, as originally deployed by the warreners who bred rabbits in the Brecks. But researchers found the brash piles were more effective and cheaper to construct.

The findings have gone into a toolkit, which is now being given to other landowners to boost rabbit populations.

“We’re hoping this toolkit can be used across the UK because it’s a national problem,” said Mountjoy.

Even though the rabbit is still classified as a costly, invasive pest by some studies, Mountjoy said it had not been difficult to persuade landowners to learn to love it, with one of 10 project partners being the Elveden Estate, a major vegetable grower.

“It’s definitely true that a rabbit on cropland or a golfing green is a pest,” said Mountjoy, “but the landowners are overwhelmingly on board. We’ve had a really positive response.”

Private landowners and conservation charities who own lowland heaths and grassland that are designated sites of special scientific interest are often required to maintain “open, disturbed conditions” on the site.

“You can either get mechanical disturbance with a digger and pay for it or you can get it for free with rabbits, so landowners and rabbits aren’t at odds in the way that you might imagine,” said Mountjoy.

Where Peter Rabbit-style vegetable theft has proved problematic, non-lethal deterrents such as rabbit-proof fencing can be used, according to Mountjoy, although she said rabbit populations were so low in many locations now that they simply were not the problem they once were.

She added: “There’s little we can do to tackle the virus but these works will provide a lifeline to populations and help them deal with the threats that are coming in from all directions.”