The highlights, deliverables and performance of our National Research Facilities and National Biological Collections.
CSIRO hosts National Research Infrastructure on behalf of the broader scientific community to assist in delivering research. There are two types of National Research Infrastructure: National Research Facilities and National Biological Collections.
Objectives and deliverables
National Research Facilities
We operate a range of specialised laboratories, scientific and testing equipment and other research facilities. These are available for use by Australian and international researchers and not restricted to CSIRO staff. The three major National Research Facilities, classified as landmark facilities, are:
- The Australian Animal Health Laboratory (AAHL)
- The Australia Telescope National Facility (ATNF)
- The Marine National Facility (MNF).
AAHL is located in Geelong, Victoria and is a national centre of excellence in disease diagnosis, research and policy advice in animal health and human diseases of animal origin (zoonoses). AAHL helps protect Australia’s billion dollar livestock and aquaculture industries and the general public from exotic and emerging infectious diseases.
ATNF comprises radio telescopes at three observatories near the towns of Parkes, Coonabarabran and Narrabri in NSW. The Facility offers a powerful view of the Southern Hemisphere radio spectrum and supports world-leading research by Australian and international astronomers. A fourth telescope, the next-generation Australian Square Kilometre Array Pathfinder (ASKAP), is currently being developed at the Murchison Radio-astronomy Observatory in Western Australia.
The MNF supports research across Australia’s vast ocean territory and adjoining oceans. It supports Australian marine researchers and their international collaborators to carry out world-class research that addresses national challenges in fisheries management, geological resources, regional and global climate, coastal and offshore developments and marine operations.
National Biological Collections
National Biological Collections are similarly available to all researchers and are storehouses of information on Australia’s biodiversity. They support a significant part of the country’s taxonomic, genetic, bio-geographical and ecological research and are a vital resource for conservation and research. CSIRO is the custodian of four National Biological Collections:
- Australian National Fish Collection (ANFC), specialising in marine fishes
- Australian National Herbarium (ANH), specialising in our native plants and weeds
- Australian National Insect Collection (ANIC), specialising in terrestrial invertebrates
- Australian National Wildlife Collection (ANWC), specialising in land vertebrates.
We also manage over 20 smaller collections of interest that contribute to the discovery, inventory, understanding and conservation of Australia’s biological diversity.
This year, our National Research Infrastructure Program continued to perform well. An assessment of the Program’s six key performance indicators (KPIs) identified in the Portfolio Budget Statements, showed we have largely met expectations and targets. Table 2.11 provides an overview of the evidence for each KPI with a more detailed analysis following.
|Key performance indicator||Target (and performance assessment)||Performance|
|Utilisation of the National Research Infrastructure||Maintain or Increase||We maintained the availability levels and supported an increase in the use of the National Research Infrastructure under its custodianship. More than 76 per cent of major facility ATNF time was allocated to astronomical observations in 2013–14, recording an increasing trend since 2010–11.|
|Maintenance and operation of National Research Infrastructure||Meet International Standards||Compliance with relevant Australian and International Standards was achieved. The new Biosecure Immunology Laboratory will provide more specialised world-class facilities for researchers to harness a host’s successful immune mechanisms to develop new treatments for highly infectious viruses.|
|Coverage of National Biological Collections||Maintain or Increase||The National Biological Collections provide approximately 70 per cent coverage of Australian species (and up to 99 percent in some areas). Coverage levels were maintained across all collections with the Australian National Fish collection increasing by one per cent from 2012–13.|
|Proportion of National Biological Collections digitised and available to the public||Maintain or Increase||The proportion of the National Biological Collections digitised was maintained. The Australian National Herbarium increased collection digitisation by four per cent from 2012–13.|
|Response to national events||Timely Response||In 2013, AAHL was actively involved in the Avian Influenza outbreak in NSW, confirming the two cases and characterised the virus as being the H7N2 subtype, similar to those recently identified in some wild bird populations.|
|Scientific contributions in support of research||Demonstrated high-quality contributions||Our National Research Infrastructure Program continues to provide significant support and opportunities for collaboration with Australian and international scientific communities. For example, in late-2013 an international team including CSIRO reported in Nature the isolation of a very close relative of the Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) from horseshoe bats in China, confirming them as the origin of the virus responsible for the 2002–03 pandemic. The discovery was made possible by using the world renowned bat virus isolation methodology developed at AAHL by CSIRO’s Bat Virology Group. Similarly a team of scientists from the University of California Berkley and CSIRO reported in 2014 in Nature Communications significant insights into the evolution of Australian biodiversity using data from the Australian National Herbarium.|
Blue shading: indicates positive progress for the year and the target has been achieved.
Utilisation of the National Research Infrastructure
Australian Animal Health Laboratory
As a crucial part of Australia’s biosecurity infrastructure, maintaining the integrity of AAHL’s high-containment facility and ensuring our preparedness in the event of an outbreak, requires continuous monitoring. AAHL has therefore remained operational 24 hours a day, 365 days a year since the official opening in 1985, and every year welcomes over 2000 visitors, many of them visiting scientists. The combination of our scientific capability and the benefits of the AAHL Facility place us in a strong position, nationally and internationally, to harness this potential in the form of new research partnerships and funding. We are also experiencing increased interest since many of our Facility’s laboratories became available as a national resource, thanks to operational funding support from the National Collaborative Research Infrastructure Strategy (NCRIS). In 2013–14, as part of the NCRIS agreement, we started offering specialised biosecurity and biosafety training to international organisations and we expect this area to grow significantly in the coming years.
Australia Telescope National Facility
The ATNF’s telescopes continue to be oversubscribed (see Table 2.12). Observing time is determined on the scientific merit of the observing proposals submitted for assessment. As in previous years, international astronomers received half the total observing time, with CSIRO and other Australian researchers sharing the remainder. Over 75 per cent of the time was allocated for astronomical observations on the Australia Telescope Compact Array and Parkes telescope, with telescope maintenance, reconfigurations and changes accounting for about 20 per cent. Time lost during scheduled observations due to equipment failure remained below five per cent, comparable with other observatories. Over 120 papers using ATNF data were published in refereed journals in 2013, including six in Science and Nature.
Observing time at the Mopra telescope near Coonabarabran is primarily dedicated to researchers from the National Astronomical Observatory of Japan, the University of NSW and the University of Adelaide, as the telescope now operates under a new model funded by these groups. However, some observing time is made available to the general astronomical community as National Facility time.
|Access to National Research Infrastructure||2009–10||2010–11||2011–12||2012–13||2013–14|
|Australia Telescope National Facility2|
|Time allocated to observations (%)||75.3||72.4||73.6||76.7||76.8|
|Time lost to equipment failure (%)||2.9||3.1||2.7||2.7||3.3|
|Time allocated to CSIRO staff (%)||24||24||22||22||19|
|Time allocated to other Australian researchers (%)||23||25||21||28||30.3|
|Time allocated to international researchers (%)||53||51||57||50||50.7|
Marine National Facility
With the MNF in transition to the new vessel Investigator, the Facility provided 109 days of ship time before the decommissioning of the Southern Surveyor in late 2013. Participants included 24 scientists from 11 Australian research institutions, including the Antarctic Climate and Ecosystems Cooperative Research Centre, Bureau of Meteorology, James Cook University, Australian National University, University of NSW, University of Tasmania, University of Technology Sydney, University of Western Australia, Australian Institute of Marine Science, University of Sydney and CSIRO. One international collaborating scientist from the United States also took part in a voyage during this period.
Supporting the development of the next generation of marine researchers, the MNF enabled eight students to experience scientific work at sea as part of the Next Wave program. This program provides a unique opportunity for students and early-career researchers to experience the working environment on a blue-water research vessel and will continue to expand with the commissioning of Investigator.
Maintenance and operation of National Research Infrastructure
Australian Animal Health Laboratory
In May 2014, we officially opened a new Biosecure Immunology Laboratory. Located inside AAHL’s biologically secure area, this new laboratory enables researchers to compare the immune responses of different animal species, including humans, with the most pathogenic infectious agents. Our researchers at AAHL are already world-renowned for their work with zoonotic agents – those that can pass from animals to people – but this new laboratory will provide more specialised techniques, at a cellular level, to help pinpoint the immune mechanisms by which animals fight infections. Understanding how pathogens affect different hosts, for example, how pigs or poultry protect themselves from influenza, will allow our immunologists to harness a host’s successful immune mechanisms to develop new treatments for highly infectious viruses such as influenza and Middle Eastern Respiratory Syndrome.
This year, we also initiated a working group to evaluate the extent of works required for an AAHL modernisation project. As the Facility has now been in operation for 30 years, ‘mid-life’ upgrades are essential to ensure the Facility is best equipped to meet future research and regulatory requirements.
To ensure best practice in aspects of biocontainment and to uphold the quality and integrity of our research, AAHL continues with its aim to maintain or exceed the many regulatory requirements as certified by the Department of Agriculture, the Office of the Gene Technology Regulator and the Department of Health’s Security Sensitive Biological Agent legislation, while also ensuring all relevant ISO accreditation.
Australia Telescope National Facility
Our Australia Telescope Compact Array marked its 25th year of operation in September 2013. The telescope has had several upgrades, gaining the ability to observe at a greater range of frequencies, particularly higher frequencies and greater sensitivity to faint signals. The latest upgrade, completed this year, has made the telescope four times more sensitive. It also greatly increased the bandwidth at higher frequencies (4–12 GHz), allowing astronomers to detect previously unreachable spectral lines and gain considerably more information about the movement of gas within galaxies and of whole galaxies themselves.
During the year, systems were put in place to allow astronomers to control the Parkes radio telescope from a remote location, eliminating the need for an operator to be present in the telescope tower. The default location for using the telescope is now the new Science Operations Centre at ATNF headquarters in Sydney. Once qualified in its use, astronomers can operate the telescope from their home institutions.
All 36 ASKAP antennas are in place at the Murchison Radio-astronomy Observatory and six have been outfitted with widefield phased array feeds – in essence, ‘radio cameras’ for imaging the sky. This year we took major steps towards bringing the telescope into operation: these included the detection of the 21-centimetre spectral line of hydrogen from known astronomical sources and the creation of a test image covering ten square degrees of sky – a region 50 times larger than the full Moon. These achievements show the new hardware, firmware and software systems are all working well and that the novel aspects of ASKAP’s design will let it outperform a conventional telescope.
Marine National Facility
The MNF operates under the direction of an independent Steering Committee. To date, the MNF’s capability has been delivered by the 66-metre Southern Surveyor and a suite of unique scientific equipment providing over 28 years of marine data. CSIRO is commissioning a new state-of-the-art MNF research vessel Investigator to replace Southern Surveyor. Investigator is nearing completion and due to arrive in Hobart during September 2014. Investigator will carry out voyages from the tropics to the Antarctic ice edge, carry up to 40 scientists and have the capability to spend up to 300 days per year at sea on voyages up to 60 days in duration.
Investigator hosts an extensive suite of state of the art scientific research equipment and is one of a handful of research vessels in the world designed for very quiet operation, with the ability to undertake acoustic mapping and sampling to the deepest parts of our oceans. With greatly increased atmospheric research capabilities, Investigator’s weather radar can study detailed cloud formation processes in a 150-kilometre radius up to 20-kilometres above the ship. Interest in the new vessel remains high with progress being reported to the public through a – CSIRO blog . In May 2014 the Australian Government reaffirmed a commitment to the MNF, allocating $65.7 million over the next four years to operate Investigator for 180 days per year.
Coverage of National Biological Collections
The National Biological Collections provide approximately 70 per cent coverage of Australian species (and up to 99 per cent, see Figure 2.11), although in the national context the collections have focused on building strength in particular areas.
Pie chart showing what percentage of Australian species are in the National Biological Collections.
Coverage of Australian species in the collections include:
- 70 per cent in Australian National Insect Collection
- 99 per cent in Australian National Wildlife Collection (birds)
- 55 per cent in Australian National Wildlife Collection (other vertebrates)
- 60 per cent Australian National Fish Collection
- 70 per cent Australian National Herbarium.
The National Biological Collections cover approximately 70 per cent of species overall.
These collections are a vital resource for the provision of accurate and reliable information on species identification for biosecurity, conservation and the development of sustainable land and marine management systems. The collections contribute to a range of national and international initiatives such as the Global Biodiversity Information Facility and the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Sciences through staff participation and data provision.
They also contribute significantly to on-ground national biodiversity research initiatives such as Bush Blitz (Australian Biological Resources Study), the Biomes of Australian Soil Environments project (Bioplatforms Australia) and the High Rainfall Zone Biodiversity Project (Grains Research and Development Corporation).
In each case the collections make a crucial contribution, providing unique biodiversity reference datasets that represent the highest quality, comprehensive, up-to-date, geocoded, biologically accurate, digitised inventories of Australian biodiversity assets.
The collections continue to be widely accessed by a range of users. Continued access to collections’ data via web portals – such as the Atlas of Living Australia (ALA)3, Australia’s Virtual Herbarium4 and the Online Zoological Collections of Australian Museums5– and the increasing amount of data available as the National Collections are digitised, has seen sustained demand for access to specimens by external researchers (see Table 2.13).
Interactions between the individual collections have continued. A project evaluating collection management software, with a view to improving and integrating data management across the collections, as well as providing more secure long-term data management, has progressed significantly and is nearing completion.
|Use of National Biological Collections||2009–10||2010–11||2011–12||2012–13||2013–14|
|Number of specimens dispatched||29,300||25,925||15,548||13,660||30,514|
|Outward going loans||147||193||157||153||222|
|Tissue samples sent||3,800||4,447||3,819||2,415||8,461|
|Tissue sample grants||44||40||43||74||34|
|Number of visitors hosted||186||336||267||238||233|
|Total visitor research days||713||551||800||1,066||799|
|Number of tours hosted||57||70||52||67||79|
|Total number of visitors on tours||597||1,266||363||586||584|
Proportion of National Biological Collections digitised
The proportion of specimen level material digitised in the four collections ranges from five to 100 per cent, see Figure 2.12.
Digitisation activity in the ANIC is focused on databasing and imaging the most scientifically valuable specimens and is value-adding to research projects by making taxonomic and phylogenetic information available online. Imaging of whole insect drawers has continued. Images and data are delivered to and accessible through the Atlas of Living Australia (ALA).
The holdings of the Australian National Wildlife Collection (ANWC) are almost completely digitised. Four thousand files of bird vocalisations from the Sound Library are available for download from the ALA.
Pie chart showing approximate number of digitised specimens from Australia's major collections.
Specimens digitised from each collection include:
- 5 per cent of the Australian National Insect Collection
- 92 per cent of the Australian National Wildlife Collection (excluding sound collection)
- 100 per cent of the Australian National Fish Collection
- 80 per cent of the Australian National Herbarium.
The Australian National Fish Collection (ANFC) specimen data is 100 per cent digitised. Approximately 65 per cent of these data are available publicly through the Online Zoological Collections of Australian Museums and the ALA.
The majority of ANH Australian specimen records are digitised, available through Australia’s Virtual Herbarium and the ALA. A pilot project examining the feasibility of digitising ANH specimens from Papua New Guinea has also been undertaken, with promising results. Imaging of type collections continues as part of a joint initiative across Australian herbaria funded by the Mellon Foundation.
New digitisation technologies are expanding the ways in which data from the collections can be utilised. The Australian National Insect Collection (ANIC) was involved in a collaborative project with CSIRO Computational Informatics and the ALA, to create true-colour 3D models of insects. These 3D models represent high-quality visualisations of physical specimens and are a novel solution to quickly extract, analyse and share the rich information in our biological collections. The technology used in creating these scans won the 2014 ACT iAward in the Research and Development category and will be heading to the National iAwards Competition in Melbourne in August 2014.
Demonstrated response to national events
Australian Animal Health Laboratory
In October 2013, AAHL’s Diagnostic, Surveillance and Response scientists were actively involved in the Avian Influenza outbreak in NSW. As the National Reference Laboratory for Avian Influenza, AAHL was instrumental in confirming the two cases on chicken farms near Young and characterised the virus as being the H7N2 subtype, similar to those recently identified in some wild bird populations. NSW Department of Primary Industries worked successfully to contain the outbreak minimising the potential impact.
For the past year, the United States has been fighting an outbreak of the viral disease, Porcine Epidemic Diarrhoea (PED). Unlike foot-and-mouth disease, it is not a trade-restricting disease, but rather a production-related disease and particularly fatal in piglets. As part of AAHL’s work in disease preparedness and in response to the potential threat posed by PED to the Australian pork industry, our diagnostic scientists developed the capability to test for PED, thus ensuring a rapid response should the disease reach our shores. This is all part of our ongoing national responsibility to protect Australia’s livestock industry from disease.
Scientific contributions in support of research
Every year excellent science is being conducted with the support of our National Research Infrastructure. Here are just some highlights of the high-quality scientific contributions made by the National Facilities and Collections in 2013–14.
Australian Animal Health Laboratory
As reported in Nature, an international research team including CSIRO, isolated a close relative of the Severe Acute Respiratory Syndrome coronavirus (SARS–CoV) from horseshoe bats in China, confirming the bat as the origin of the virus responsible for the 2002–03 pandemic. The discovery was made possible by using the world-renowned bat virus isolation methodology developed at AAHL by CSIRO’s Bat Virology Group. The SARS virus killed 774 people of the 8094 people infected. It is hoped the results will help governments design more effective prevention strategies for SARS and similar epidemics.
This year, our Biosecurity Flagship’s Hendra virus research team worked at the highest containment levels at AAHL to demonstrate 12-month duration of immunity of the Equivac® vaccine. This research could not have been performed anywhere else in the world.
Australia Telescope National Facility
An international team of astronomers used telescopes including our Parkes telescope and Australia Telescope Compact Array to identify a small star that switches between emitting x-rays and emitting radio waves. The star is a pulsar, the leftover core of a ‘regular’ star that has exploded. Its unusual behaviour appears to be caused by matter falling onto it from a companion star. Published in the journal Nature, this is the first direct evidence of one kind of pulsar turning into another and helps us better understand how pulsars change over time.
Dr Kimberley Clayfield, Executive Manager for Space Sciences and Technology in CSIRO, become the first Australian to receive the Lawrence Sperry Award from the American Institute of Aeronautics and Astronautics. CSIRO Fellow and first Director of ATNF, Professor Ron Ekers, received the 2014 Grote Reber Medal for his lifetime of achievements in radio astronomy.
Marine National Facility
Prior to decommissioning, four Southern Surveyor voyages retrieved moorings that are providing valuable data for improving regional and global climate models and our understanding of the marine environment. Moorings from the Southern Ocean are providing insights into the major role of this ocean as a carbon sink, while moorings from the east Australian Current are being used to measure changes in this major current system and future impacts on Australia’s eastern marine environment.
Also, researchers on a transit voyage from Broome to Brisbane surveyed the microbial oceanography of northern Australia, obtained detailed maps of the Great Barrier Reef shelf edge to determine the submerged geographic limits of the world’s longest fossil (currently at 1000-kilometres) and measured greenhouse gases in the marine atmosphere which highlighted the influence of terrestrial burning.
Australian National Insect Collection
During 2013–14, ANIC researchers working with scientists from other organisations – such as the Beijing Genomics Institute, British Natural History Museum and the Chinese Academy of Sciences – collaborated on a large project aimed at analysing the evolution of all insects worldwide, using very large molecular genetic datasets derived from next generation sequencing. ANIC scientists also published two major works on beetles, the largest group of insects in Australia and the world: Australian Beetles, a major work covering all beetle families in Australia, and the first of two volumes on the economically and environmentally important Australian Longhorn Beetles.
Australian National Wildlife Collection
This year saw significant developments in studies by the ANWC on the relationship of the faunas of Australia and our near neighbour Papua New Guinea (PNG). Extensive field work, particularly in southern PNG, is building new collections suitable for modern molecular studies, while laboratory work has helped unravel the evolutionary connections between wetland and savanna birds of southern PNG and northern Australia. Specimens from this project are also being used in several other international collaborative projects.
For example, the Helmeted Friarbird (pictured) is one of the key species of interest driving current ANWC field work in PNG. Inclusion of the PNG populations of this species in genetic analyses will contribute to a more complete understanding of genetic and evolutionary connectivity between Australia and PNG.
The Helmeted Friarbird is a key species of interest for ANIC in Papua New Guinea6.
Australian National Fish Collection
The ANFC continued to deliver high quality taxonomic research on Australia’s fish fauna through a number of projects undertaken within our Wealth from Oceans Flagship. We continued our engagement with external clients, such as the Australian Centre for International Agricultural Research (ACIAR) and Bay of Bengal Large Marine Ecosystem project, undertaking taxonomic research and/or training in Indonesia, Papua New Guinea, Maldives, Myanmar and Thailand. The recently completed ACIAR-funded Indonesian fisheries project culminated in a book published in late 2013, Market Fishes of Indonesia. The ANFC has also commenced a collaborative project with Bioplatforms Australia. This project will use tissue samples from the ANFC to develop a reference data set for use in DNA-based identification of Australian fishes of commercial and biodiversity significance.
Participants in just one of the successful training workshops held in Papua New Guinea as part of an ongoing four-year ACIAR project led by CSIRO.
Australian National Herbarium
As part of the Norfolk Island Quarantine Survey, managed by the Federal Department of Agriculture, the ANH undertook surveys of the weed flora of Norfolk Island. The surveys documented biosecurity risks for the island, covering plants and insects as well as plant and animal diseases. Over the course of the surveys more than 400 specimens of weeds and other introduced plants were collected by the ANH, greatly increasing knowledge of the flora of Norfolk Island and identifying potential biosecurity risks.
Working with partners across universities, state and federal research sectors and Bioplatforms Australia, ANH staff are leading the Biomes of Australian Soil Environments project. Over the last 24 months this project has taken over 500 soil samples across Australia, and used next-generation DNA sequencing to characterise the microbial community and model it against soil, vegetation and climate parameters. This data represents a baseline against which to measure effects of human activity on microbial community structure and soil biological function, and how such changes influence ecosystem productivity and resilience.
- Figures are determined for ATNF observing semesters so that, for example, the 2013–14 figures apply to the period 1 April 2013 to 31 March 2014.
- More information can be found in the ATNF’s Annual Report.
- See: Atlas of Living Australia
- See: Australia's Virtual Herbarium
- See: Online Zoological Collections of Australian Museums
- Image: ALA Occurrence record - Philemon (Philemon) buceroides | Helmeted Friarbird