The Abbott government's first budget in May resulted in a $111 million cut to CSIRO funding over four years. That came on the back of a tough period for the agency, which last financial year shed 513 positions following a Labor government-enforced efficiency drive, a recruitment freeze implemented by the newly installed government and falling external revenue. Staff had also weathered a sizeable restructure of the 88-year-old organisation.

What impact has this had – how many jobs have been lost that we know of?

As a direct consequence of the $111 million budget cut, the organisation will lose 489 researchers and support staff by mid-next year. Another 300 positions will be cut after an internal restructure. The federal budget included a one-off, $32.2 million fund specifically to cover redundancy costs. The union estimates CSIRO is set to shrink by about 20 per cent over two years.

As well as reducing staff numbers, a number of CSIRO sites will close or be consolidated to minimise costs. New South Wales' Griffith laboratory, where 10 staff work, will close while the 130 staff at Melbourne's Aspendale laboratory will be relocated to Clayton. Meanwhile, the CSIRO farm known as Arding in Armidale, NSW, was sold in June.

What specific areas have been affected – and which, if any, leading scientists have been made redundant or left the organisation?

In August, management confirmed eight infectious disease researchers at the Australian Animal Health Laboratory in Geelong, the country's only facility for researching live samples of deadly diseases such as Ebola, would lose their jobs.

Eight staff have left the Aspendale laboratory, which focuses on marine and atmospheric research, since the budget was handed down in May. Those leaving Aspendale include senior scientist Paul Fraser, who has taken a voluntary redundancy. Dr Fraser, head of oceans and atmosphere, has been honoured by NASA and also helped establish one of the world's two most important climate research centres at Cape Grim in Tasmania.

Water research also appears to have been targeted. The office of water science research and the national water commission will be abolished, while the sustainable rural water use and infrastructure program's budget has had a $400 million trim.

At CSIRO's largest Victorian site, in Clayton, 15 staff have left or are in the process of leaving. The laboratory, home to research areas including advanced materials, nanotechnology, energy, mining and minerals work, had already lost staff under Labor's efficiency drive. Among them was organic chemist San Thang, who was made redundant in September. It came as Dr Thang and two colleagues were nominated as frontrunners for the illustrious Nobel Prize in chemistry. Dr Thang has been made an honorary fellow – an unpaid position allowing him to both continue his work and to supervise PhD students.

In addition to the budget cuts, CSIRO also lost about $4 million indirectly when the government folded the Australian Climate Change Science Program into the new National Environmental Science Program. The union has expressed concern that this will undermine the organisation's ability to provide government with accurate, world-class climate advice. The budget papers state the move will allow for "greater cohesion between environmental and climate science research" as well as providing "administrative efficiencies".

What do scientists and their union say will be the impact of the cuts?

Not a profession known for being loud-mouthed protesters, the most public reaction to the budget cuts was during the national day of action in June. However, some staff have spoken off the record about the impact the cuts will have on their work. Among the primary concerns are that they will hamper Australia's ability to collaborate internationally and remain scientifically competitive.

For some researchers who kept their jobs, life in a leaner organisation now includes chores such as cleaning laboratories, writing promotional material, sorting mail and refilling photocopiers.

How does the government explain the reduction in funding – and what is its model for the future?

Incoming CSIRO chief executive Larry Marshall has said he is well aware that the organisation had weathered a "sea change in funding", and stressed that staff morale would be a priority for him when he takes over in January.

However, Dr Marshall said CSIRO would have to work within the financial boundaries imposed on it, adding that "fiscal constraints ... make you focus". He told Fairfax Media upon his appointment in October that there was "an edge in knowing that the money isn't always going to be there".

An entrepreneur and venture capitalist, Sydney-born Dr Marshall has said the CSIRO will boost its collaboration with industry. It's a direction backed by Innovation Minister Ian Macfarlane, whose portfolio takes in science. Mr Macfarlane has praised Dr Marshall's commercial background, noting that his arrival comes at a time when the agency was embarking on a "significant new phase" in which the CSIRO would play an increasingly important role in the economy. Dr Marshall takes over from Dr Megan Clark, who stands down this month after six years at the helm.

Are there particular areas of science the government is investing in? If so, why those areas?

The May budget delivered CSIRO's newly commissioned research ship, the RV Investigator, $17.4 million for its first year of operation, rising to $18.1 million and $20.6 million in following years. Based in Hobart, the 10-storey ship can accommodate up to 40 scientists whose work will range from sampling the atmosphere above the ship to studying marine life and surveying the seafloor eight kilometres below. Its first voyage will be an 11-day trip in March to the sub-Antarctic Southern Ocean, to place three scientific buoys. The funding will enable the ship to operate 180 days a year, although it has the capacity to run 300 days a year.

Antarctic research received a budget boost, with $24 million allocated for a new partnership between CSIRO, the University of Tasmania and the Australian Antarctic Division. A further $68 million towards covering the cost of Australia's presence in the Antarctic was also granted, with the money to be spent on rising shipping and fuel costs, station operations and the air link between Hobart and Antarctica.

What do experts say it means for the future of CSIRO?

Both minister Macfarlane and incoming chief executive Dr Marshall have expressed an eagerness to boost collaboration with the private sector as a way of speeding up the time it takes for CSIRO research to reach the market and to generate income from royalties faster.

In the 2012-2013 financial year, the CSIRO generated $37.5 million in licence fees and royalties. Much of that income was directed to the research budget and this appears to be a favoured business model.

More than 200 companies collaborate with CSIRO. Outside funding accounts for about 40 per cent of the organisation's research budget, with the agency liaising with companies in a range of fields, from resources and agriculture to health and energy.