Little red buds poke through the bark of burnt eucalyptus trees in the Blue Mountains. It's been just over a month since the Gospers Mountain fire tore through , but regeneration has begun.

The early signs of recovery are positive, but ecologists are preparing for "a lot of loss" as they begin the challenges of conserving, managing and studying bushfire affected ecosystems.

The director of the Centre for Integrative Ecology at Deakin University, professor Don Driscoll, said one of the key challenges will be managing unburnt pockets of land.

Ecologists will spend the next few months conserving, managing and studying bushfire affected ecosystems. Nick Moir

"It will be critical to protect those areas from further fire for coming years and manage the animals that might be using those areas as a refuge," he said.

"The real concern is that animals, including feral horses, deer, cats, pigs, might all concentrate in the unburnt areas and that will impact the ecological value. It will decrease the ecological value of the areas because feral herbivores will take away resources from native animals.

"Managing ecosystems on this scale is a massive challenge, everybody in the ecological community is shocked at the scale of what’s happened."

Environmental change biology professor David Bowman at the University of Tasmania said the fires are an opportunity to learn about how ecosystems regenerate, but there is a “limited window” of about 18 months to collect data.

"We have an opportunity to learn about how nature works here because we’ve had these fires," Professor Bowman said. "We're still learning about fire intensity and the impact of fire.

"Without serious investment and serious prioritisation, then it's 100 per cent certain that many, many environments impacted by fires won't have anybody with serious scientific training doing any discovery of what happened in those fires."

He said many areas, including the Mount Kosciuszko National Park, could suffer from regeneration failure, with entire populations of vegetation unable to recover.

A specialist team of remote area firefighters have helped to save the prehistoric Wollemi Pines from this season’s bushfires.

But scientists at the Royal Botanic Gardens Sydney and Australian Botanic Garden Mount Annan have been preparing for this possibility for more than 10 years by collecting seed of threatened species. They will use the seeds to propagate plants in fire-affected areas.

Chief botanist at the Botanic Gardens and Centennial Parklands Brett Summerell said some of Australia's flora is resilient to fire and has adapted to recover.

For example, eucalyptus trees store their buds under protective bark to produce foliage quickly, while wattles and banksia seeds are stimulated to germinate by fire.

"If the fire is too hot then there is almost a sterilisation effect with very low recovery – I expect we will see a mosaic of effects across the landscape," he said.

"For ecosystems like rainforests which have burnt where the species and communities are not fire adapted, the recovery, if it happens at all, will be very long term."

The Blue Mountains Botanic Garden Mount Tomah estimates about a quarter of its living collection was impacted.

"Unfortunately, the majority of the 180 hectares of conservation forest surrounding the formal garden areas was also burnt," said Denise Ora, the executive director of Botanic Gardens and Centennial Parklands.

"This diverse wilderness is comprised of patches of rainforest with numerous species of fern, eucalypt woodlands, small swampland and a complex heathland dominated by banksias, persoonia and mountain devils."

The garden reopened to visitors on Monday but many parts, including the popular Gondwana Forest walk, remain closed due to safety concerns.