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The trust, which cares for 250,000 hectares of land, 780 miles of coastline and 220 gardens and parks, said approximately 71 per cent of the places it looks after could be at medium or high risk by 2060.
The National Trust shut Inner Farne for the rest of the season to try to help next year's seabirds.
More than 7,000 birds have died this year at five of the trust’s sites in England, Wales and Northern Ireland
The "heartbreaking" disease is posing a considerable threat to the UK's wild birds, with concern over breeding populations and hundreds of dead birds washing up on beaches.
Twenty-one dead Common Terns were lifted from Cockle Island during the recent breeding season.