Scientists have gained important new insights into the Hauraki Gulf's resident Bryde's whales – by analysing their poo.

About 50 critically threatened Bryde's whales are estimated to live year-round within the Hauraki Gulf, mixing with another 150 seasonal visitors; one of the few resident populations of this species in the world.

These 15m-long whales have a varied diet of small, schooling fish and zooplankton and forage almost entirely during the day, stopping to rest at night.

As they need to get all their daily energy requirements from their resident region, they are particularly responsive to prey movements and anything that might influence their prey.

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In a new study, University of Auckland researchers spent more than two years collecting poo and zooplankton samples from the Gulf, then used a DNA "barcode" approach to identify different types of prey found in the whale poo.

"We were surprised how strong the whales' prey preferences were," said Associate Professor Rochelle Constantine, of the university's School of Biological Sciences.

"We had thought they ate a sort of multi-species 'plankton soup' commonly found in the gulf but they favoured a few specific types of plankton, typically found in patches."

The research team identified 1235 types of zooplankton but the whales preferred only a very few of them; mostly krill-like shrimps, gelatinous salps, and small crustaceans called copepods.

"We are now going to work out how the whales they find these prey patches, but what we don't yet know is whether they use smell - no one knows whether baleen whales have a sense of smell."

This study was novel, Constantine said, because new genetic techniques were used to analyse both the whale poo and the potential food available at the same time.

"Many species of whales target a single prey species but Bryde's whales' diet is more complicated than that," she said.

Associate Professor Rochelle Constantine collects samples from the Hauraki Gulf. Photo / Supplied
Associate Professor Rochelle Constantine collects samples from the Hauraki Gulf. Photo / Supplied

"It's important to discover which type of plankton these whales are eating because we know climate change is affecting plankton productivity.

"If the type of prey the whales eat becomes scarce in the gulf, then the whales may move away. This has happened elsewhere in the world."

Over the past few years, the 2015-2016 La Nina event and the 2018 oceanic "warm blob" saw a major shift in whale distribution to the outer regions of the gulf, as sea surface temperatures up to 3C above average made it too warm for plankton.

While the whales used to forage more on fish, zooplankton were their primary prey now – and although the reason for the shift was unknown, it might have been down to changes in habitat, disease events or fishing.

It was possible the whales had moved to ensure they didn't overheat – yet they had been observed in tropical waters and had a thin blubber layer, so were well suited to warm-temperate waters.

Study co-author Dr Emma Carroll said zooplankton communities were more diverse in cooler months than warmer months but that didn't change the whales' diet.

"They were not eating what was seasonally available but had a clear preference for only a few types of zooplankton and occasionally fish."

While collecting samples of whale poo took some time, the team is grateful for the valuable help they got from some study collaborators.

"Auckland Whale and Dolphin Safari crews collected many of the samples and that's been really helpful, apparently poop-scooping was a bit of a novelty for the passengers," Constantine said.

The team used techniques and data from other studies to carry out the genetic analysis, including a terrestrial eDNA study by Professor Richard Newcomb from Plant and Food Research and the University of Auckland, and Dr John Zeldis's group at NIWA who are carrying out a long-term study of zooplankton communities.

The research was funded by the University of Auckland and the Hauraki Gulf Marine Mammal Fund, Department of Conservation.