New technology to tackle biosecurity challenges down the track is one of the five megatrends identified in today’s CSIRO report Australia’s Biosecurity Future: preparing for future biological challenges.
As manpower in the agriculture and biosecurity sectors declines, we must look to technological innovation to protect crops. Monitoring and surveillance, genetics, communication and data analysis have been identified in today’s report as future work priorities, along with developing smaller, smarter, user-friendly devices.
But this is easier said than done. There are a number of potential barriers that need to be addressed to make sure that appropriate technologies are used to maximum effect. It might sound obvious, but making sure farmers can – and want to – use new technology is a crucial step.
With an ageing population and fewer young people entering agriculture, we are seeing the loss of the wealth of knowledge and experience held by long-time farmers.
Many farmers have a deep understanding of the day-to-day activities that can protect properties and reduce the spread of pests and diseases across the country, and this on-farm biosecurity knowledge may be lost.
We are also seeing a decline in specialists in areas crucial to biosecurity management such as taxonomy, plant pathology and entomology. This is prevalent throughout the biosecurity landscape, reducing our overall pest and disease response capability.
With fewer people training in taxonomy, we’ve estimated that 50% of Australia’s diagnostics capability will be lost by 2028.
Without adequate surveillance in place, pests can cripple emerging industries. In recent seasons, we have seen two new diseases devastate local farmers in the Northern Territory:
- the recent invasion of banana freckle, which authorities are working to eradicate
- the cucumber green mottle mosaic virus (CGMMV) infected melon crops near Katherine this year. Lack of CGMMV knowledge meant a delay identifying the disease and starting treatment.
Surveillance is critical to the delivery of effective biosecurity, both for early detection of a disease and for effective response. Yet delivery of effective surveillance faces a growing challenge which becomes greater in the more remote parts of Australia.
Constraints on surveillance include declining investment among jurisdictions, declining expertise or limited availability of personnel, expense and occupational health and safety requirements.
In response to these challenges there is a strong drive to draw on technological innovation to deliver biosecurity previously provided by people.
Research is already underway with new applications of technology for surveillance and detection, sensitive diagnostics, as well as preventative pre-border technologies.
Access to low-cost sensors and development of automated systems are opening up opportunities for rapid identification and response to pests and diseases. Sensors smaller than a pea can, for example, help monitor the health of oysters in real time.
Pestpoint, a mobile device application being developed by staff of the Plant Biosecurity Cooperative Research Centre (PBCRC) provides access to an online community of people working in the agricultural sector who need to identify plant pests in order to make decisions about how to manage those pests.
By using genetic techniques, scientists with the PBCRC are developing rapid tests using molecular sequences for identifying pests and diseases. The next phase is to transfer these tools to biosecurity practitioners, including diagnosticians and port inspectors.
Sounds great … but there are barriers
The adoption of a new technology hinges on how easily it can be incorporated into the existing biosecurity system, which means that the technology needs to be integrated into a human system:
- the connection to institutional arrangements governing biosecurity regulation, response and compliance
- the social acceptability of deploying smart technologies and information systems.
The Queensland Biosecurity Strategy: 2009–14 highlighted that biosecurity risks are inherently social, and that a better understanding of human behaviours, values and attitudes has the ability to improve engagement.
Similarly, the 2007 New Zealand Biosecurity Science Strategy indicated that the application of social research could increase biosecurity compliance and reporting, and support post-border invasion response programs.
Farmers and indigenous communities in remote and regional Australia are currently working together on a project to understand how each group decides to manage plant pests and diseases, and to increase their capacity to engage in biosecurity surveillance activities.
In the face of declining resources and investment, science and technology offer opportunities to create greater efficiencies in biosecurity while at the same time driving competitive advantage in primary industries.
Paul De Barro receives funding from the Bill and Melinda Gates Foundation and the Cotton Research and Development Corporation.
Grant Smith is a co-PI on the PBCRC bacterial diagnostics project described in this article. He is a member of various organisations including Australasian Plant Pathology Society (APPS), the Royal Society of New Zealand (MRSNZ) and the Project Management Institute (PMI).
By Gary Fitt, CSIRO
A nationwide outbreak of foot and mouth disease; an invasion of a devastating wheat disease; our honeybees completely wiped out. These are just three possible disastrous scenarios facing Australia; they’re considered in the Australia’s Biosecurity Future report published today by CSIRO and its partners.
Intensifying and expanding agriculture, biodiversity loss, and more people and goods moving around the world are the “megatrends” driving what we have called “megashocks” — new outbreaks of diseases and pests.
These three events alone could not only cost Australia’s economy billions of dollars, but would also devastate our agricultural industries and environment and severely alter our way of life.
How well prepared is Australia, and how would our biosecurity system cope with such a situation?
For example, governments and farmers near Katherine in the Northern Territory are mounting an emergency response to deal with an outbreak of a new disease — Cucumber Green Mottle Mosaic Virus — and while this virus is not likely to create headlines, it is devastating crops, severely affecting the NT farming community financially and threatening industries elsewhere in Australia.
An ever-hungrier world
As part of the drive to help feed the world, Australia will have to increase agricultural production — both through intensification and expansion. Both of these processes could expose new biosecurity challenges.
The United Nations Food and Agriculture Organization (FAO) has forecast that food production will need to increase by 60% (compared to 2005/2007 levels) to meet demand in 2050.
This 2050 scenario could see the value of Australian food exports increasing by 140% compared to 2007 levels.
However, Australia’s agriculture sector is already constrained by limited soil and water resources and future intensification will bring its own challenges through herbicide resistance and more intensive animal production systems. These factors could all increase the impacts of a biosecurity incident, and reduce the industry’s ability to sustainably meet demand.
In 1973 Australia’s wheat production industry was devastated by an outbreak of wheat stem rust, causing an estimated A$200-300 million in damages. While wheat stem rust has been under control since that time, there are new threats on the horizon.
Currently sweeping the world is the even more virulent Ug99, and without stepping up our biosecurity, it is likely to reach Australia. Luckily in this case we have time to prepare by developing varieties resistant to Ug99, but we may not always have such forewarning.
Expanding into new areas
Intensifying food production alone may not be sufficient to meet global demand. We may also have to expand into new or previously marginal areas. This could expose agriculture to new biosecurity threats, some that we may not fully understand, through new pathways or new hosts for pests and diseases.
For example, there is considerable government and industry interest in increased agricultural development in Northern Australia. Various reports, including the recent Green Paper on Developing Northern Australia suggest that northern agricultural production could increase substantially through targeted use of soil and water resources.
But this could expose Australia to new biosecurity threats. There are already a number of established pests and diseases in NT. And, importantly, these small areas of northern irrigated agriculture could act as a target for exotic pests and as a bridge for exotic pests to enter, establish and spread southwards.
This could have more severe consequences for established agricultural systems in southern Australia. In 1998 sugarcane smut appeared in the Ord, Western Australia. It then spread to Queensland in 2006, ultimately costing a 10-30% reduction in gross margins thanks to loss of yield, and the cost of planting resistant sugarcane varieties.
So biosecurity needs to be explicitly considered in any plan to expand agriculture in northern Australia – we need to anticipate future threats and mitigate them where possible.
Invasive species are one of the most significant known threats to biodiversity and ecosystem services around the world. In Australia invasive vertebrates such as rabbits, feral cats, pigs and camels impose severe impacts on Australian habitats and wildlife.
But biodiversity is also important in underpinning the ecosystem services for agriculture and the economy. Healthy soil function, pollination, and natural pest control are all driven by biodiversity within agricultural landscapes. Over the past century, crops have lost 75% of their genetic diversity, making them potentially more susceptible to new pathogens or pests.
We rely on some species for the services they provide, such as the European honeybees which pollinate our largely non-indigenous crops. Australia is fortunate to be the only continent not yet affected by the devastating bee pest, varroa mite. There is very real potential for it to arrive and spread in Australia.
Elsewhere in the world, varroa mite is driving a complex of factors leading to a global decline of honeybees, and native pollinators are also threatened through pesticide use and habitat loss.
Losing these pollination services, would severely impact the 30% of food crops which are dependent on honeybees, particularly many fruits and vegetables. The impact on our economy would be in the order of A$4-6 billion each year.
On the move
The increased movement of people, goods and vessels around the globe increases the chance of biosecurity threats hitting our shores. That’s why our biosecurity border protection is so important.
Inadvertent spread of exotic organisms in shipping containers such as European house borer in Western Australia, on contaminated equipment or carried by people such as the introduction of fire ants, as well as the spectra of deliberate introductions which haven’t yet happened in Australia show the scale and breadth of the issues we have to deal with.
An outbreak of an exotic pest or disease, such as foot and mouth disease (FMD) in Australia, which affects cloven hoofed animals such as cattle, pigs and sheep, could close down export markets overnight or make other countries more competitive.
An FMD outbreak in Australia could lead to industry-wide revenue losses for livestock producers of around A$6 billion for a small outbreak and A$50 billion for a large multi-state outbreak over a 10-year period. Additional costs related to disease control, such as labour, decontamination, slaughter, disposal and facilities, would be expected to range from A$60 million to A$373 million.
Pre-empting the threat
As an island nation, Australia has been able to maintain an enviable biosecurity status, keeping out many of the world’s worst pests and diseases. This means we have market access for a vast array of export produce, a status which will be increasingly valuable in a growing and highly competitive global market for food.
To ensure we maintain this status, the management of Australia’s biosecurity will require a step change towards smarter and more efficient strategies that are ideally ahead of the pace of change around the world. Smarter technologies, strengthened integration across governments and industry and great commitment will be needed. If we do this, we are surely better able to protect our farmers, communities and environment from the impacts of exotic pests and diseases.
Clearly, we can’t afford to become complacent with our nation’s biosecurity measures. As is true of any threat, it is much better to pre-empt and avoid than have to deal with the costly consequences.
The CSIRO Biosecurity Flagship receives funding from government and industry R&D bodies and works in collaboration with many research and industry partners..
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.
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.
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.
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.
Pep Canadell receives funding from the Australian Climate Change Science Program.
By Emily Lehmann
There’s been a buzz around town about our bee research this year, and for good reason.
In a world first, we’ve been microchipping thousands of bees with tiny sensors in Australia and South America to monitor their activity and the way they interact with the environment.
We’ve called this ‘swarm sensing’ and it could help gather the information we need to find a solution to the mysterious and devastating decline of bees around the world.
Swarm sensing hit the polls earlier this week, as one of five finalists in The Australian Innovation Challenge’s category for Environment, Agriculture and Food. And, it’s up to the people – that means you – to decide which one of these innovations deserves to win $5000.
Now, if cute honey bees wearing mini, colour-coordinated ‘backpacks’, isn’t enough to sway your vote, then we’ve gathered a few hot facts about why this work is so critical to get you over the line:
- Around one third of the food we eat relies on bees for pollination.
- By aiding agriculture, honey bees earn an estimated $4-6 billion for Australia every year.
- Wild honey bee populations are dropping drastically or vanishing all together around the world. There are two major problems causing their decline: the varroa mite and the little understood Colony Collapse Disorder
- While there is a real risk, bees in Australia have not been affected by the Varroa mite or Colony Collapse Disorder.
- Parasites, pollution and pesticides are potential factors in the decline of honey bee populations.
To vote CSIRO, visit The Australian Innovation Challenge article and select ‘swarm sensing’ in the poll at the bottom of the page. Go on, #voteCSIRO and do it for the bees!
It’s a hard life being a small farmer in sub-Saharan Africa. About 200 million people in the region are poor and undernourished. Most of them are smallholder farmers in rural areas, who rely on agriculture as their main source of food and income.
Part of the reason for their level of hardship is that the major staple crops, sorghum and cowpeas (which provide not just food but fuel and fodder for livestock) have low yields. Poor soil, low-quality seed, drought and disease all play their part.
Obviously, if these farmers could get greater productivity from their crops, they could have a secure supply of food, and possibly even be able to sell the excess and bring in some extra money. But conventional genetic improvement to increase yield is a slow process, and these farmers are hungry now.
So: how to make improved yields happen?
The Bill and Melinda Gates Foundation has just awarded us a $14.5 million grant to work on it. The five year project, in partnership with other world leading research teams from Switzerland, USA, Germany and Mexico, will develop tools to generate self-reproducing hybrid cowpea and sorghum crops.
What we’re planning to do is to develop high-yielding sorghum and cowpea crops that have seeds the farmers can save and grow, and which don’t decrease in quality or yield. And that’s going to mean making a very fundamental change to the way they’re bred – changing from sexual reproduction to asexual.
Hybrid crops can produce yield increases of 30 per cent or more, because of what’s known as hybrid vigour – basically that some crosses between two strains of crop will combine the favourable traits of both parents and be more successful than either.
Hybrid vigour is the same mechanism which produces the loveable labradoodle. A labradoodle puppy inherits the favourable traits from its purebred Labrador and poodle parents. However, two labradoodles won’t produce labradoodle puppies (they’ll be more Labrador-ish, or more poodle-ish). In just the same way, the seed from hybrid crops will not express the favourable traits. The puppy’s increased adorableness is of course a matter of personal opinion but it is a furry demonstration of hybrid vigour.
Unfortunately, current technologies to produce hybrid seed (and labradoodles) are expensive, and farmers need to buy new seed every year as the favourable traits only last one generation.
If we can develop self-reproducing hybrid cowpea and sorghum crops the farmers would then be able to self-harvest high-quality seed, giving them a more secure food supply and possibly even increased income from selling excess seed.
It’s a big challenge. As project leader Dr Anna Koltunow explains ‘It’s not going to be easy, otherwise it would have been done already. The idea of changing the plants’ reproductive process to an asexual one is a complex undertaking’.
The first stage of the project will involve developing the techniques that will allow cowpea and sorghum plants to reproduce asexually. This is lab-based work. If this stage is successful, African breeders and institutes will join the project for the subsequent phases.
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.
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.
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 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.