This scanner has a few bugs, and we’re glad about it

How many insect specimens do you think are in the Australian National Insect Collection? A few hundred thousand? A million?

Actually, at the moment, it has about 12 million specimens, and it’s growing by about 100,000 a year. Like many natural history collections around the globe, the ANIC holds thousands of holotypes – each the single specimen of a species that is used to define its characteristic features.

There are all sorts of uses for these specimens, and a lot of people outside the world of entomology have very good reasons for looking at them very closely. But they’re fragile things, and many of them are tiny, so they can’t really leave their cases. And photographs don’t capture all the detail that’s sometimes needed.

So how to make the necessary information available to the people who can use it, while keeping the precious specimens safe and available for research work? Digital 3D colour modelling is ideal, but there have been some major barriers to doing that effectively. The system most used at present – Micro Computed Tomography (Micro CT) can create amazingly accurate models. But it doesn’t capture the object’s natural colour, which is vital information for species identification. It can take many hours. It’s X-ray based, so it needs special safety equipment. The machines also cost around $100,000, and they’re not portable.

Well, there had to be a better way, didn’t there?

So Matt Adcock and his colleagues did some lateral thinking, and came up with InsectScan 3D. This re-imagines 3D image-gathering in a way that doesn’t need custom-made or high-cost equipment (some of it actually came from the local hardware megastore), and the image is in full colour. The entire system uses standard components, and costs less than $8000 for the hardware and software. The digital 3D models come out in a file size small enough to be sent by email and used in web pages. And to make it even better, we can 3D print them.

3D scanned images, printed in 3D. Image by Eleanor Gates-Stuart

3D scanned images, printed in 3D. Image by Eleanor Gates-Stuart

The process uses multiple photographs of the subject, mounted on a disc marked with a pattern of dots. Using a standard DSLR camera and a 2-axis turntable, the insect is photographed at different angles and focus depths. These are then plotted by a computer, using the dot pattern to gauge the angle from which the picture was taken.

In some cases the 3D image is more useful than conventional microscopy. Obviously, the actual specimen provides all the information, but it has to be examined under a microscope for features like the mouth area and hair surface on the head. Out-of-focus effect and other physical restrictions makes using a microscope to view the actual specimen more difficult than viewing the 3D model.

The possibilities for this system are varied. Entomologists and taxonomists already have a massive backlog of insect types which have not yet been digitised in any form, and this system can provide what they’ve been asking for: a network of automated instruments that can clear the backlog by quickly and accurately creating 3D images of type specimens.

Schools and universities can use 3D models of insects as rich education materials, so students can interact with insects without endangering the fragile specimens.

But the most interesting use could be in quarantine and biosecurity. Invasive insects and the diseases they carry are an ever-present threat to Australia‘s environment, its agricultural industries and the health of the population. With this affordable, portable and accurate scanning technology, quarantine officers could carry a 3D gallery of invasive insects with them on inspections to help identify pests. Suspect specimens could be scanned in 3D and sent straight to an expert entomologist for examination. High resolution image libraries will mean we can quickly extract, analyse and share rich information, supporting biodiversity discovery, species identification, quarantine control, and unlocking the value of our biological collections.

Sounds pretty good, doesn’t it? This technology is a finalist in the Smart 100 innovation awards, and there’s a people’s choice category. If you like it as much as we do, we’d really like you to vote for it. All you need to do is click the ‘Share on Facebook’ (or Twitter, or any of the others) button and that’s a vote.

Farming carbon can be a win for wildlife, if the price is right

Koalas are one of the threatened species that could benefit from carbon farming. christopher charles/Flickr, CC BY-NC-SA

Koalas are one of the threatened species that could benefit from carbon farming. christopher charles/Flickr, CC BY-NC-SA

Megan Evans, Australian National University; Anna Renwick, The University of Queensland; Josie Carwardine, CSIRO, and Tara Martin, CSIRO

Climate change and the loss of biodiversity are two of the greatest environmental issues of our time. Is it possible to address both of those problems at once?

In Australia, farmers and landholders will this week be able to apply for payments through the Federal government’s A$2.55 billion Emissions Reduction Fund. Bidders can request funding for projects that reduce emissions using agreed methods, which include approaches relevant to the transport, waste and mining sectors, as well as the land sector: for example, by managing or restoring forests.

Forests hold carbon in vegetation and soils and provide important habitat for native wildlife. Restoring forests in areas where they have been cleared in the past could be good for the climate, good for biodiversity, and generate additional income for landholders.

How well the Emissions Reduction Fund can achieve these benefits will depend on three things: the right approach, the right price, and the right location.

Farming carbon

There are a range of approaches available for restoring forests, and they vary in how quickly carbon can be sequestered, cost, and suitability for wildlife.

For example, fast-growing monocultures such as blue gum plantations can sequester carbon very rapidly, but don’t provide ideal habitat for wildlife. Planting a diversity of native trees and shrubs using an approach called environmental plantings is far more wildlife-friendly, but the costs are higher, and carbon is not stored as quickly.

A third possible approach is to assist the natural regeneration of vegetation. This can be done by fencing off cattle or by ceasing on-farm practises such as burning or disturbance with machinery. Assisted natural regeneration is the cheapest of these three possible methods, and is also good for biodiversity: our recent paper found that it could be a great option for restoring forests in agricultural landscapes across Queensland and northern New South Wales.

Brigalow woodlands allowed to regrow for 3-10 years. Image: John Dwyer

Regenerated brigalow woodlands after 50 years. Image: John Dwyer

Location, location, location

Across Australia, there are a number of places where growing carbon could be a more profitable option than the current land use. Some of these places are more important for biodiversity than others.

The mulga lands of western Queensland may be worth more as carbon farms than other uses. Image: Don Butler

If we’re interested in getting some wins for biodiversity while growing carbon forests, we need to think carefully about the possible opportunities and trade-offs, as the best places for sequestering carbon are not always the most beneficial for biodiversity, and vice versa.

In our recent paper, we found that it is possible to identify where growing forests could provide win-wins for both carbon and biodiversity.

For example, the top 25% of priority areas for environmental plantings could sequester 132 million tonnes of CO2 equivalent annually, which is almost a quarter of Australia’s annual emissions (excluding those caused by land-use change).

Relative priority areas for restoring 139 threatened ecosystems to 30% of original extent using environmental plantings, where carbon is stored at $20/tonne. Pink areas are higher priority, green is lower priority

These high-priority areas for environmental plantings could restore some of the most threatened ecosystems in Australia. There are 139 ecosystem types across the country that have lost more than 70% of their original extent. If it were possible to restore these ecosystems up to 30% of their original extent, they will have a better chance of surviving in the long term.

Restoring parts of the landscape with these ecosystems is a high priority for biodiversity – not only are the ecosystems rare, but many of the birds and animals that depend on these ecosystems are those that are most threatened. For example the brigalow woodlands of south east Queensland, of which less than 10% remain, are home to nationally threatened koalas and a host of other wildlife.

The right price

It will generally be more expensive to grow carbon forests that also provide benefits for biodiversity. This is because the places most profitable for land uses such as agriculture are often where the most threatened species and ecosystems are located.

In our analysis, we found that with a price on carbon equivalent to A$5 per tonne, it would not be profitable to restore threatened ecosystems up to 30% of their original extent. This means that without additional funding from another source, there is limited opportunity to achieve wins for biodiversity if the price on carbon is low.

However, a higher price of A$20 per tonne, reflecting Australia’s 2011-2013 carbon price, could allow up to half of the heavily cleared vegetation types to be restored up to 30% without any additional funding for biodiversity itself. At this A$20 price, we also found that it made more economic sense to farm carbon than the existing land use, in over 1.2 million hectares in Queensland.

This week’s Emissions Reduction Fund auction will be a good first test of how the current approach to carbon farming can provide the dual benefit of restoring habitat for native wildlife and addressing climate change. Our analysis shows that Australia’s climate policies could have a very significant impact on biodiversity – if we think carefully about the right approach, price, and location.

The Conversation

This article was originally published on The Conversation.
Read the original article.

The future of biodiversity is in our hands

Australia’s Biodiversity series – Part 12: Conclusions

When talking about the fate of biodiversity it’s easy to get bogged down in doom and gloom—we know that it’s in decline, that human populations and demand for resources continue to grow, and therefore the pressure we’re putting on other species is increasing, and that big gaps remain in our understanding of the biodiversity that’s out there.

Australia is developing a vast capacity for monitoring the natural environment through the Terrestrial Ecosystem Research Network. Image: Gregory Heath.

Australia is developing a vast capacity for monitoring the natural environment through the Terrestrial Ecosystem Research Network. Image: Gregory Heath.

But there are solutions. Since the concept of biodiversity first emerged in the 1980s, the science dedicated to understanding our natural systems has come a long way. With the emergence of new technologies it has become possible to find out far more about the species we share the planet with, and we can do it with far more efficiency.

It’s these big challenges and scientific solutions that we focused on in our book, Biodiversity: Science and Solutions for Australia. In the twelfth and final video in our Australia’s Biodiversity series, the book’s editors, Dr Steve Morton, Dr Mark Lonsdale and Dr Andy Sheppard, engage in a panel discussion about the future of biodiversity science in Australia:

You might like to read the concluding chapter of CSIRO’s Biodiversity Book to find out more about the scientific solutions that could help us address the big threats to Australia’s biodiversity.

And if you’ve been inspired to get more involved in the management of our biodiversity, there’s a lot you can do—even from your computer. Visit the Atlas of Living Australia to find out about volunteer opportunities.

You can find all the videos from our biodiversity series on our YouTube channel.

Mining and biodiversity: are they getting along?

Australia’s Biodiversity series – Part 11: Mining

Dolphin poking its head out of the water in the foreground and a ship in the background

Dolphin conservation is carried out to offset impacts of infrastructure development in Darwin Harbour. Image: Carol Palmer

Many people worry about the environmental impacts of mining, but as a society we have a growing demand for its products. Most Australian’s consider it worthwhile and a valuable industry for the nation’s prosperity, as our recent national survey indicates.

The direct impacts of mining on biodiversity are relatively limited compared with other major land uses—less than 1% of the Australian land area is used for mining, while 62%  is used for agriculture for example.

The greatest threats to biodiversity from mining come from the cumulative impacts of the infrastructure required for mining operations—roads, ports, pipelines, shipping etc. Science can help to assess any potential implications for biodiversity from mining development so that impacts can be better managed and rehabilitation and offsetting efforts can be more effective.

In the eleventh video of our Australia’s Biodiversity series, Dr Alan Andersen talks about the main impacts of mining on biodiversity and how these can be appropriately managed through processes like strategic regional assessments, use of bioindicators in rehabilitation, and biodiversity offsets:

To find out more about mining and biodiversity in Australia, you might like to read the corresponding chapter of CSIRO’s Biodiversity Book.

Last week’s video looked at the biodiversity in our inland water systems and how our approach to water management impacts ecosystem health. You can review it and the other videos in the series on our YouTube channel.

Water: we need it to live, and so does our wildlife

Australia’s Biodiversity series – Part 10: Inland waters

Even though it is one of the world’s most arid continents, Australia’s inland waters support a rich diversity of life.

Rivers, streams, wetlands, floodplains, lakes, underground aquifers—we’ve got them all and they all support native species.

A large brown and yellow frog

The New Holland water-holding frog. 94% of our frog species are found only in certain ecosystems – the highest rate of endemism among Australia’s vertebrate species. Image: Danial Stratford.

Biodiversity is enhanced by the wide variation in rainfall across the continent and the change in climate from the tropical north to the temperate southern regions. Life in Australia’s inland water ecosystems has had to adapt to the ‘boom and bust’ that comes from periods of both extreme dry and extreme wet.

Human development has had a dramatic impact on these ecosystems, particularly in the Murray Darling Basin and other areas in the southeast, as we use water for our cities and towns and for irrigated agriculture. These water uses are obviously of great benefit to the Australian population but the use of the water and the infrastructure associated with it can disrupt the natural flows of water and nutrients through inland water ecosystems, which native plants and animals depend on.

In the tenth video of our Australia’s Biodiversity series, Dr Carmel Pollino talks about Australia’s unique inland water ecosystems and how water can best be managed for the benefit of biodiversity and our communities:

To find out more about the biodiversity in our inland water ecosystems, you might like to read the corresponding chapter of CSIRO’s Biodiversity Book.

Last week’s video looked at the new ways science is attempting to understand the unknown biodiversity in our oceans. You can review it and the other videos in the series on our YouTube channel.

What’s in your porcini packet? You may find a new species … or three

By Nai Tran-Dinh, CSIRO and David Midgley, CSIRO

Mycologists – scientists who study fungi – estimate there are up to five million species of fungi on Earth. Of these, only about 2%, or 100,000 species, have been formally described. So where are the other 98% of fungi hiding?

At least three, it seems, were hiding in a supermarket packet of dried porcini mushrooms from China. Mycologists Bryn Dentinger and Laura Suz from the Royal Botanic Gardens in Kew, UK, used DNA sequencing to identify three new species in a packet of dried porcini mushrooms purchased from a supermarket, and report their findings in the journal PeerJ today.

The internal transcribed spacer (ITS) is a DNA region commonly used to identify fungi. (In fact, it’s been called the “universal DNA barcode marker for fungi”.) In their PeerJ paper, Dentinger and Suz compared previously published ITS sequences for porcini and discovered significant differences in three of their packet of dried mushrooms, enough to mark them as new species.

Their work also highlighted the use of modern DNA sequencing technologies for identifying species in food, and for monitoring foods for quality and adherence to international regulations, such as the Convention on Biological Diversity.

Fungi really are fascinating

Like an apple, a mushroom is the fruit of the fungus. It’s not the apple tree.


Typical porcini (Boletus edulis var. clavipes) in its natural habitat. This is not one of the newly discovered species (which are only known from the dried remains in the packet).
Bryn Dentinger

Most of the fungus grows below the ground, in a vast network of root-like tubes called hyphae. How vast, you might ask? Well, in a case known as the “humongous fungus”, a single clone (individual) of the honey mushroom (Armillaria ostoyae) has been shown to cover more than 900 hectares in Malheur National Forest in Oregon, USA. Estimates place the age of this gigantic fungal network at more than 2,000 years.

In Australia, some of our fungi are a little more modest in size, though perhaps bigger than you might guess. Nicole Sawyer and John Cairney at the University of Western Sydney have estimated the size of individuals of the Australian Elegant Blue Webcap (Cortinarius rotundisporus) at more than 30m in diameter – about the size of tennis court.

Despite the impressive size of some species, new species of fungi don’t get the same recognition as a new species of mammal, bird or reptile. But discoveries of novel species are the new norm in modern mycology – a change being driven by advances in our ability to sequence DNA.

It’s very important to better understand fungi, as they underpin the terrestrial biology of Earth. They associate with the vast majority of plants in a symbiosis called mycorrhiza.

Living both within plant roots, and out in the soil, they gather nutrients for the plant, and protect it against diseases and water stress, enhancing plant growth in exchange for sugars the plant produces via photosynthesis.

Without their fungal assistants, plants as we know them would not exist. Other fungi are vital decomposers and return nutrients stored in organic matter to the soil. While the most fungi are beneficial, some fungi are devastating plant pathogens, while a small number of fungi can cause disease in humans such as ringworm, trichosporonosis or aspergillosis.

Close human relationships

Humans have also recruited an array of fungi to their cause. Products produced by fungi are used in medicine – many antibiotics come from fungi – and the production of a range of food products including soy sauce, blue cheese, bread, beer and wine.

New porcini dried

Some of the new porcini species reported in PeerJ today.
Bryn Dentinger

Numerous new fungi related to Malassezia (a yeast that causes dandruff in humans) have been found in marine subsurface sediments in the South China Sea by Chinese researchers from Zhongshan (Sun Yatsen) University, while scientists from the Woods Hole Oceanographic Institution in the US found the same Malassezia-like species from the Peru Trench in the Pacific Ocean.

The work in the Peru Trench used environmental RNA sequencing to guarantee that sequences observed were from environmental samples, and not contaminants from human skin.

Recent advances in modern DNA sequencing technology routinely yield millions of DNA fragments (reads) that can be quickly and accurately identified using classification tools. One such tool is the recently released Warcup ITS fungal identification set developed by CSIRO scientists in collaboration with the Ribosomal Database Project (RDP) and partners from the Western Illinois University and the Los Alamos National Laboratory in the US.

The Warcup ITS dataset allows identification, to species level, of thousands of ITS sequences within minutes.

The use of modern DNA technologies and classification tools may allow development of bioactive compounds for medicine, enhanced agricultural productivity, environmental damage repair, industrial applications such as biofuels and enzymes, along with food identification and potentially new food sources … sometimes in places you’d least expect.

The Conversation

The authors do not work for, consult to, own shares in or receive funding from any company or organisation that would benefit from this article. They also have no relevant affiliations.

This article was originally published on The Conversation.
Read the original article.

A sea full of mysteries to be solved

Australia’s Biodiversity series – Part 9: Seas and coasts

Life originated in the oceans 3–5 billion years ago and even today 20 of the 33 animal phyla (the highest groupings within the animal kingdom) remain confined to the sea. That means that most life under the sea is like nothing we find on land.

An elephant seal with an electronic tag on its head

Sea creatures can also help us explore the oceans. Sea mammals can take sensors to parts of the ocean we’d never be able to go ourselves, like under Antarctic sea ice. Image: Chris Oosthuizen

Worldwide there are big gaps in our understanding of the oceans and the life within them. Our exploration of Australia’s marine biodiversity has been limited mostly to the margins of the continent, on the continental shelf and the upper continental slope. Even near the continent, some 50–70% of the species we’ve found in recent surveys have never before been seen by scientists.

New technology and equipment, like autonomous robotic vehicles and electronic tagging, as well as our brand new marine research vessel, RV Investigator, is allowing us to explore in ways we’ve never explored before and so we can begin to address those knowledge gaps.

In the ninth video of our Australia’s Biodiversity series, Dr Alan Butler and Dr Nic Bax talk about the unique habitats of the sea, the challenges it poses to exploration, and new tools and technologies helping us discover and manage the biodiversity it holds:

To find out more about discovering biodiversity in the ocean, you might like to read the corresponding chapter of CSIRO’s Biodiversity Book.

Last week’s video looked at the relationship between our cities and biodiversity. You can review it and the other videos in the series on our YouTube channel.


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