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The management of yellow-eyed penguins on the Otago Peninsula could be affected for the next six years, as a result of flooding across Dunedin this week.
Yellow-eyed Penguin Trust general manager Sue Murray said flooding from a nearby stream destroyed about 80% of the plants being matured at the trust's Company Bay nursery.
More than 6000 plants, with an estimated value of more than $40,000, had been lost, she said.
''Very small seedlings right through to 6-year-old plants have been destroyed.
''We don't even know what damage is within the buildings and the glasshouses - they're under just so much silt that at this stage we can't tell.
''The whole infrastructure of the plant nursery has been destroyed.''
The plants were to have been planted along the peninsula coastline to provide shelter for nesting and moulting penguins.
Without the plants, breeding patterns of the yellow-eyed penguins would be disrupted.
It could interrupt management of the species for up to six years, she said.
''It's certainly going to have long-term effects.''
The trust was now waiting for insurance assessors to investigate the damage.
''Until then, we're in limbo. We've just had to shut the door.''