Want to see what we collect?

Mould spores. We collect them

Mould spores. We collect them

We collect things. Lots of things.

You might have heard about our major collections – the National Wildlife Collection, National Fish Collection, National Insect Collection, National Herbarium. You might even have heard of the Cape Grim Air Archive. But what about the National Soil Archive? Let alone the Fungus Collection or the Algae Collection.

The National Soil Archive contains more than 70 000 soil samples from nearly ten thousand sites across Australia. They’re not just bits of dirt picked up from anywhere. Not only are the samples representative of soil types throughout Australia, they’re a time capsule of sorts as well. Quite a lot of the samples date from the early 1920s, before widespread pesticide use.

Having these old samples gives us an historical record of soil carbon, so they’re an important resource for our work on climate change. They also provide an interactive key to Australian soil classification, which is a handy tool for landcare advisors, agronomists, environmental consultants, ecologists, foresters, geomorphologists, land use planners and catchment managers, and they form the backbone of our SoilMapp tool. Who’d have thought?

And there are actually three different fungi collections. There’s the Wood-Inhabiting Fungi Collection, which is self-explanatory. Then there’s the WA-based Mycology Herbarium, which deals with fungi as parts of ecosystem biodiversity. Blue-fungi-on-wood

The third is a little more off-putting. It’s the FRR Culture Collection. It’s a comprehensive archive of filamentous fungi and yeasts of the kinds associated with processed food spoilage. To put it simply, the national mould collection is a real thing. It’s not in a student share house fridge, but carefully stored and catalogued at CSIRO.

We mustn’t forget the algae. We have a comprehensive collection – the Australian National Algae Culture Collection – stored in Hobart: more than 1000 strains of over 300 species. It’s an important resource for two reasons. The first is that the nutrient value of algae is of growing scientific interest. The second is – and this volvox-aureus-green-alga_32106_1might come as a surprise – it’s aligned with CSIRO’s Microalgae Supply Service. This provides microalgal strains for ‘starter cultures’. They go to industry, research organisations and universities in more than 50 countries. We also supply starter cultures to the Australian aquaculture industry: microalgae are the essential first foods for larval and juvenile animals. They’re also the basis of our Novacq™ prawn food additive.

We think the contents of our cupboards are pretty interesting. They’re certainly unusual.


The ankle bone’s connected to the … 3D-printed titanium implant

3D printed titanium heel implant

The 3D-printed titanium heel implant

Surgery has come a long way since the days when it consisted of either cutting things out or cutting them off. But there are still conditions where amputation is the only alternative.

One of them, until recently, was bone cancer.

Len Chandler was facing the prospect of having his leg off below the knee when he was diagnosed with cancer of the calcaneus (heel bone). Until his surgeon, Professor Peter Choong from Melbourne’s St Vincent’s Hospital, had an idea.

He knew about CSIRO’s work in titanium 3D, after reading about our work on producing an orthotic horseshoe in 2013. He got in touch with John Barnes, our titanium and 3D printing expert, asking whether his vision – a metallic implant which would support a human body’s weight – could become a reality.

3D printed heel implant

3D printed heel implant. Note the rough surface for flesh to adhere to

At the time, CSIRO was working with the Victorian-based biotech company Anatomics on metallic implant technology. John brought Anatomics into the discussion, to draw on their experience as a certified custom medical device manufacturer.

Our Manufacturing Flagship worked with Melbourne’s St Vincent’s Hospital and Victorian biotech company Anatomics on a world-first surgery, developing a heel bone implant printed in titanium on CSIRO’s state-of-the-art Arcam 3D printer.

Working from Anatomics’ schematics for the heel bone, teams at Anatomics and CSIRO developed the design requirements with Choong’s surgical team. These included smooth surfaces where the bone contacts other bone, holes for suture locations, and rough surfaces that would allow tissue to adhere to the implant. In the days before the surgery Anatomics and CSIRO produced three implant prototypes.

The entire process, from first phone call to surgery, took two weeks. Three months after the surgery, Mr Chandler has had his most recent check-up. He’s recovering well, and is able to place some weight on his implant.

3D heel 3As CSIRO’s Robert Wilson, part of the heel printing team, points out, ‘The customisation of 3D printing is good in emergency situations such as these’.

It’s also a local manufacturing process: Australian companies producing implants for our own doctors and patients. That means we don’t have to rely on imported parts, and the design can be truly personalised to the patient.

We’re working with a number of major companies and SMEs across Australia to build capacity in biotech and manufacturing.

The plan, says John Barnes, is that, ‘At some point in the future we expect that local for-profit businesses will have the capacity to work on projects like this, and until that momentum is built up in local industry, CSIRO is here to help local industries gain that momentum’.


World Food Day – let’s make it every day

Wheat rust on a wheat stem. Image: Evans Lagudah and Zakkie Pretorius.

Wheat rust on a wheat stem. Image: Evans Lagudah and Zakkie Pretorius.

It’s World Food Day, and this year’s focus is on the role smallholder farmers play in feeding the world.

Food production is at record levels, yet 842 million people are estimated to be suffering from chronic hunger and under-nourishment. Many of these are themselves small family farmers.

We’re trying to do our bit to help subsistence farmers grow more productive crops, combat plant diseases, farm seafood sustainably, develop climate change adaption strategies and grow coffee more sustainably.

One plant we’re working on is cow peas (one of the staple crops in parts of Africa). We recently got a Gates Foundation grant to further our research on improving their productivity.

On a broader scale, we’ve also cracked a problem with a globally-significant crop: wheat. With colleagues from the Sydney and Adelaide Universities, we’ve identified a gene that confers resistance to wheat rust – probably the biggest enemy of wheat crop yields worldwide.

Seafood is a major source of protein in both the developed and developing worlds, and we’ve found a way to farm the most delectable kind of all – prawns – more sustainably. Our Novacq™ fishless prawn food is now licenced for use in several South-East Asian countries. It makes use of the marine microbes at the base of the food chain to produce a prawn food that has the added benefit of increasing their growth rate by around 30 per cent.

Climate change is a pressing problem for us all, but some of the people most at risk are farming communities in countries in southern and south-eastern Asia. We’re collaborating with farmers in parts of Cambodia, Laos, Bangladesh and India to identify, select and test climate change adaptation options that are both viable and suitable for local communities. One of the things we’re aiming to do is develop and test new crop and water management practices for rice-based cropping systems that will outperform existing farming practices and can accommodate future climate variability and climate change.

There are about 400 000 PNG households involved in coffee production

There are about 400 000 PNG households involved in coffee production

After all that work, we might be tempted to celebrate with a good cup of coffee. Maybe a PNG blend. There are more than 400 000 households involved in coffee production in PNG, and it’s that country’s most important export cash crop.

With our Australian and international partners, we’re developing new ways for farmers and researchers to learn from each other and identify ways to improve the sustainability of PNG’s coffee industry. We hope to identify the points in the coffee-food farming system that can be targeted for the best possible result in retaining and reusing scarce nutrient resources.


Plants absorb more CO2 than we thought, but …

Plants doing the photosynthesis thing

A new study shows plants may absorb more carbon than we thought. Jason Samfield/Flickr, CC BY-NC-SA

By Pep Canadell, CSIRO

Through burning fossil fuels, humans are rapidly driving up levels of carbon dioxide in the atmosphere, which in turn is raising global temperatures.

But not all the CO2 released from burning coal, oil and gas stays in the air. Currently, about 25% of the carbon emissions produced by human activity are absorbed by plants, and another similar amount ends up in the ocean.

To know how much more fossils fuels we can burn while avoiding dangerous levels of climate change, we need to know how these “carbon sinks” might change in the future. A new study led by Dr. Sun and colleagues published today in PNAS shows the land could take up slightly more carbon than we thought.

But it doesn’t change in any significant way how quickly we must decrease carbon emissions to avoid dangerous climate change.

Models overestimate CO2

The new study estimates that over the past 110 years some climate models over-predicted the amount of CO2 that remains in the atmosphere, by about 16%.

Models are not designed to tell us what the atmosphere is doing: that’s what observations are for, and they tell us that CO2 concentrations in the atmosphere are currently over 396 parts per million, or about 118 parts per million over pre-industrial times. These atmospheric observations are in fact the most accurate measurements of the carbon cycle.

But models, which are used to understand the causes of change and explore the future, often don’t match perfectly the observations. In this new study, the authors may have come up with a reason that explains why some models overestimate CO2 in the atmosphere.

Looking to the leaves

Plants absorb carbon dioxide from the air, combine it with water and light, and make carbohydrates — the process known as photosynthesis.

It is well established that as CO2 in the atmosphere increases, the rate of photosynthesis increases. This is known as the CO2 fertilisation effect.

But the new study shows that models may not have quite right the way they simulate photosynthesis. The reasons comes down to how CO2 moves around inside a plant’s leaf.

Models use the CO2 concentration inside a plant’s leaf cells, in the so called sub-stomatal cavity, to drive the sensitivity of photosynthesis to increasing amounts of CO2. But this isn’t quite correct.

The new study shows that CO2 concentrations are actually lower inside a plant’s chloroplasts — the tiny chambers of a plant cell where photosynthesis actually happens. This is because the CO2 has to go through an extra series of membranes to get into the chloroplasts.

This means that photosynthesis takes place at lower CO2 than models assume. But counterintuitively, because photosynthesis is more responsive to increasing levels of CO2 at lower concentrations, plants are removing more CO2 in response to increasing emissions than models show.

Photosynthesis increases as CO2 concentrations increase but only up until a point. At some point more CO2 has no effect on photosynthesis, which stays the same. It becomes saturated.

But if concentrations inside a leaf are lower, this saturation point is delayed, and growth in photosynthesis is higher, which means more CO2 is absorbed by the plant.

The new study shows that when accounting for the issue of CO2 diffusivity in the leaf, the 16% difference between modelled CO2 in the atmosphere and the real observations disappear.

It is a great, neat piece of science, which connects the intricacies of leaf level structure to the functioning of the Earth system. We will need to reexamen they way we model photosynthesis in climate models and whether a better way exists in light of the new findings.

Does this change how much CO2 the land absorbs?

This study suggests that some climate models models under-simulate how much carbon is stored by plants, and in consequence over-simulate how much carbon goes into the atmosphere. The land sink might be a little bigger — although we don’t know yet how much bigger.

If the land sink does a better job, it means that for a given climate stabilisation, we would have to do a little bit less carbon mitigation.

But photosynthesis is a long, long way before a true carbon sink is created, one that actually stores carbon for a long time.

About 50% of all CO2 taken in by photosynthesis goes back to the atmosphere soon after through plant respiration.

Of what remains, more than 90% also returns back to the atmosphere through microbial decomposition in the soils and disturbances such as fire over the following months to years — what stays, is the land sink.

Good news, but not time for complacency

The study is a rare and welcome piece of possible good news, but it needs to be placed in context.

The land sink has very large uncertainties, they have been well quantified, and the reasons are multiple.

Some models suggest that the land will continue to absorb more carbon all throughout this century, some predict it will absorb more carbon up to a point, and some predict that the land will start releasing carbon — becoming a source, not a sink.

The reasons are multiple and include limited information on how the thawing of permafrost will effect large carbon reservoirs, how the lack of nutrients could limit the further expansion of the land sink, and how fire regimes might change under a warmer world.

These uncertainties put together are many times bigger than the possible effect of the leaf CO2 diffusion. The bottom line is that humans continue to be in full control of what’s happening to the climate system over the coming centuries, and what we do with greenhouse emissions will largely determine its trajectory.

The Conversation

Pep Canadell receives funding from the Australian Climate Change Science Program.

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


Sounding out the ghosts of the depths

Sonar image of shipwreck

MV Lake Illawarra lies on the floor of the Derwent River

Nearly 40 years ago, on 5 January 1975, the 135m bulk ore carrier MV Lake Illawarra was heading up the Derwent River in Hobart to offload its cargo of 10 000 tonnes of zinc ore concentrate. It was off course as it neared the Tasman Bridge linking Hobart’s eastern suburbs to the rest of the city.

MV Lake Illawarra wreckThere was a strong current running at the time, and the ship was travelling too slowly. It became unmanageable. Several unwise decisions by the captain added up to disaster: the ship drifted towards the eastern shore of the Derwent, striking two of the bridge pylons. Three spans of the bridge and a 127m section of roadway came crashing down into the river and onto the vessel’s deck.

Twelve people died as a result. Five were in cars that were on the bridge at the time and drove over the gap, falling 45m into the water below. The others were trapped crew members of the MV Lake Illawarra, which sank almost immediately after the impact in 34m of water. It was never salvaged, and remains there to this day.

The Geophysical Survey and Mapping (GSM) Team on our new research vessel, RV Investigator, works on mapping any part of the ocean floor to any depth. They recently took delivery of a new EM2040c, a High Resolution Multibeam Echosounder (shallow water sonar) that can map the sea floor to 500 metres. To calibrate it, they took out a support vessel and had a closer look at the wreck of MV Lake Illawarra.MV Lake Illawarra wreck

With this new sonar equipment, mapping the whole wreck took about an hour. It’s just an example of its capabilities. The EM2040c is mobile, can be lifted by a single person and can fit on almost any vessel. The beam can be up to four times the water depth and it’s able to send and receive signals at a rate of 50 times per second.

And there’s a lot to use it for. Only about 12 per cent of Australia’s ocean floor has been mapped: there’s a great deal to find out yet.


We still don’t know if domestic animals can spread Ebola

 

Man holding dog

It’s unclear whether Spanish dog Excalibur, pictured here with owner Javier Limon (husband of Ebola-infected nurse Teresa Ramos), was infected. EFE/PACMA

By Michelle Baker, CSIRO

Spanish authorities have euthanised the dog of Madrid nurse Teresa Romero Ramos, who contracted Ebola. The 12-year-old dog, Excalibur, was not showing symptoms and was not tested for Ebola. But he lived with Romero Ramos when she became ill and was destroyed as a precaution, despite widespread protests.

This has raised questions about the role domestic animals might play in the spread of Ebola. But before we get to dogs and cats, we need to start with bats – the natural host of Ebola and a number of other viruses including Hendra virus, rabies, SARS (sudden acute respiratory syndrome) and MERS (Middle East respiratory syndrom).

African fruit bats were established as the host of Zaire Ebola virus after antibodies were detected in a number of species. Though interestingly, bats are not affected by the virus.

Intermediate hosts in viral transmission

For many of the viruses carried by bats, there is no evidence of direct bat-to-human transmission. More often than not, an intermediate host – or spillover host – gets infected following contact with infected bat material.

Spillover hosts generally develop severe disease and are capable of shedding the virus in large quantities, which can pass to people who come in close contact with secretions from the infected animals.

Image by jomilo75/Flickr, CC BY-NC-ND

Ebola originated in African fruit bats.
jomilo75/Flickr, CC BY-NC-ND

Intermediate hosts can include horses in the case of Hendra virus, pigs for Nipah virus and palm civets in the case of SARS.

For Ebola, it is believed that contact with wild animals including gorillas, chimpanzees and antelope have been the source of human infection.

Although the intermediate host is known for many bat-borne viruses, the role that other domestic animals play in the transmission cycle is largely unknown.

Are domestic animals a risk?

During previous Ebola outbreaks, scientists have found virus specific antibodies in dogs. But the canines showed no symptoms. It’s still unclear whether dog-to-human transmission is possible, as is the mechanism by which dogs and other domestic animals become infected.

A similar situation occurred in Australia in 2011 when Hendra virus specific antibodies were detected in a dog from a property where Hendra virus-infected horses were located. Again, we know little about the infection dynamics of this virus in dogs.

While cats are not resistant to Hendra virus disease, natural transmission from infected bats or horses to cats has not been demonstrated.

A complicating factor is that people who recover from infection with Hendra virus can experience a subsequent relapse in disease. Whether viruses such as Ebola or Hendra virus can also lie dormant in domestic animals and reactivate at a later time point remains to be investigated.

Opportunities for transmission

While research is underway, the mechanisms involved in the transmission of Ebola and other bat-borne viruses to intermediate hosts is currently poorly understood. It seems to occur as a result of contact with bat secretions or partially eaten fruit which the bats chew and drop to the ground.

But the transmission of viruses from bats to other species depends, to a large extent, on opportunity.

Palm civets can be intermediate hosts of SARS.  Kabacchi/Flickr, CC BY

Palm civets can be intermediate hosts of SARS.
Kabacchi/Flickr, CC BY

Bats and viruses have long coexisted but interactions between bats and other species including humans have occurred only relatively recently. Urbanisation and deforestation has resulted in increased encroachment of humans and domestic animals into bat habitats.

Similarly, live animal markets such as those in Southern China, where SARS was detected in palm civets, are associated with close contact between a variety of different species and provide an ideal melting pot for spillover to take place.

Social and cultural practices also play a role in viral transmission including the consumption of “bush meat” from wild animals including non-human primates and bats.

In each of these situations, humans have provided the opportunity for interspecies contacts which would not have otherwise occurred.

Bats have an important place in our ecosystem, and there is so much we can learn from them. To help manage and prevent future outbreaks, we need a more comprehensive, science-based understanding of risks associated with the increased interaction of people and animals with wildlife.

The Conversation

Michelle Baker receives funding from The Australian Research Council.

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


Under a blood red moon … or not

We asked, and you surely delivered. We put out a call for your photos of the lunar eclipse, and got so many that for a moment we were afraid we might break Facebook. Here are some of our favourites.

It was a little cloudy in Melbourne, but Rhonda Baum still managed to sneak a shot through the gloom.

Eclipse through clouds

Image by Rhonda Baum

Clear skies in Port Lincoln helped Peter Knife get this.

Lunar eclipse Port Lincoln

Image by Peter Knife

Meanwhile, in Albury, the eclipse really turned it on for Petra de Ruyter.

Eclipse from Albury

Image by Petra de Ruyter

And Tamworth lived up to its claim to be Big Sky Country.

Lunar eclipse from Tamworth

Image by Ekiama Apalisok-Brice

Some managed to catch the purple tones.

Purple moon

Image by Lisa Belgrave

Lunar eclipse purple

Image by Samantha Bright

Others managed to catch tones we found a little surprising. There’s always one, isn’t there, Peter Feeney?

Green moon

Image by Peter Feeney

We got images from Japan.

Lunar eclipse Japan

Image by Ivy B Ueama

And Indonesia.

Lunar eclipse Indonesia

Image by Muhammad Hasbi Alfarizi

We got spectacular montages.

Lunar eclipse montage

Image by Kelly Wilson

But for some of us, the weather didn’t co-operate at all. Kim Cook was able to remind those of us who missed out that clouds can be beautiful too.

Sunset clouds

Image by Kim Cook

But if we’re honest, we have to admit that Ali Ceyhan spoke for all of us who didn’t get to see it.

Lunar eclipse meme

Image by Ali Ceyhan

Next time, next time … And our sincere thanks to all of you for your photos.


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