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.

Porcini

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.


Less is more with the Water Use Efficiency Initiative

Wheat harvest in SA

A fine wheat crop. Image by John Coppi

Australia is not what you’d call over-burdened with water, and yet we grow vast amounts of wheat and other grains. To continue to do so, we need to use the water we have as efficiently as possible. To do more with less.

Together with the Grains Research and Development Corporation, we started a multi-pronged project to increase the water use efficiency of grain production in Australia. And it worked so well that two of our scientists, James Hunt and John Kirkegaard, have just shared a Eureka Prize for it.

Their research has shown that it’s possible to increase the long term average winter crop yield, without increasing input costs. This would lift the average Australian wheat yield by around 25 per cent across all regions. They have also shown an increase in the long term average yields of winter grain crops, including barley and canola.

To make sure they covered all types of climate and soil conditions, they worked with 16 regional grower groups and research institutions across Australia, from the WA Sandplain to Tasmania.

They studied the many factors that influence water use efficiency and looked into the kinds of management practices that lead to more efficient use of water.

Instead of looking at a single crop or a single paddock, the research focussed on the capacity of the whole farm, and then assessed the farm’s potential for production and profitability, as well as the risks that might be associated with a change in the water use regime.

Some of the results returned big numbers. Improved summer fallow management, including weed management and stubble retention can lead to a 60 per cent increase in grain yield. The use of a legume crop after two consecutive grain crops can lead to increases in a range between 16 and 83 per cent.

The results also revealed that matching nitrogen supply to the soil type produce yield increases of up to 91 per cent.

In a world that needs to be fed, these are important findings. If we can do more to work to our conditions, it’s an all-round win.

So big congratulations to James and John, for making less more.


Can we feed the world and save our species?

Australia’s Biodiversity series – Part 7: Farming, pastoralism and forestry

Australian agriculture provides food and fibre for millions of people in Australia and around the world, but it can come at a cost to our environment and biodiversity.

There is a range of intensities of primary production in Australia today. Hunting and gathering and use of fire to manipulate the abundance of native species is at the lowest end of the spectrum, then livestock grazing of native pastures, right through to complete replacement of native species for intensive cropping and forestry plantation (the latter requiring inputs in the way of fertilisers, machinery, chemicals etc.). The more intensive the production method, the more food and fibre can be produced per unit area, but with greater impact on biodiversity. Less intensive production methods provide opportunities for native species to coexist with production.

Better management of our agricultural landscapes can enhance biodiversity, and in turn, enhanced biodiversity can benefit agriculture through services like pollination and recycling nutrients in soils.

In the seventh video of our Australia’s Biodiversity series, Dr Sue McIntyre talks about the different intensities of agriculture in operation across Australia and what research is telling us about better managing practices to continue supporting biodiversity in those landscapes:

To find out more about managing agricultural landscapes for biodiversity, you might like to read the corresponding chapter of CSIRO’s Biodiversity Book.

Last week’s video looked at Indigenous perspectives on Australia’s biodiversity and its management. You can review it and the other videos in the series on our YouTube channel.


Spring forth and eat dung

A male Onthophagus vacca dung beetle

Onthophagus vacca – getting into it in WA

There are about 28.5 million head of cattle in Australia. Each one produces between ten and 12 cowpats a day, at an average 2.5kg each. Over a 14-day period, that’s about 14 million tonnes of dung. And every one of those cowflops can generate about 3000 flies in that time. But you may have noticed that Australia hasn’t been buried in manure or completely blanketed in flies. That’s because, for more than 40 years, we’ve been working to make sure cow dung doesn’t hang around, polluting pastures and waterways and providing the ideal breeding ground for flies.

This is a special week for us. One of our two new species of European dung beetle is ready for field release. The other is planned for release in 2015.

Our scientist, Dr Jane Wright, personally carried her shy but important companions, Onthophagus vacca, (a native of France and Spain) from Canberra to Western Australia. The spring-active dung beetles will be burrowing into new homes at field sites around Kojonup in Western Australia. These sites were chosen because they are home to numerous large herds of cattle, which means a lot of cow dung is available.

Here they are, making themselves at home.

Up until now, there has been a gap between one species of beetle settling down for a well-earned break and the next gearing up for action. These new beetles have been carefully selected to fill the seasonal break in activity in early spring across southern and western Australia. By introducing the spring-active beetle, the long term goal is to ensure dung is buried in early spring, getting the nutrients into the ground and accessible to the plant roots. The result is increased pasture productivity and reduced runoff of nutrients into waterways.  Another benefit is that the beetles will compete with bush flies for the dung, thus slowing the buildup of fly numbers over spring, enabling the existing beetles to have a greater impact on fly populations over summer.

With financial support from Meat and Livestock Australia and WA Agriculture and Food, we imported two new species of dung beetle in 2012. These were placed in quarantine and set up to breed. Then their eggs were surface-sterilised following AQIS protocols. Following that the eggs were taken into the laboratory outside quarantine and transferred to artificial brood balls. These beetles were the start of a laboratory colony that has allowed us to produce sufficient beetles for field releases, like this one.

If you’d like to learn more about these little scuttling wonders, there’s a more in-depth article over at The Conversation.


Cattle industry swings behind safety gate

Cattle yards play a huge part in our local farming industry. In fact, with over 28 million head of cattle grazing on our big brown land, there are more cows in Australia than people.

Not only are our cows big in numbers, they are also big in size. Weighing in at up to 450kg, the risk of our bovine friends causing serious injury, and even death, is very real – to the point where cattle handling is one of the most hazardous jobs in the livestock industry.

That’s why this National Farm Safety Week, we’re revisiting a cattle gate which was purpose built to keep our farmers safe.

Designed by NSW farmer Edward Evans, SaferGate swings away from the operator when an animal charges it. This time two years ago we put the gate through rigorous testing. How did we do this? We thought we’d use our very own ‘crash test cow’. See how it went down:

Since our bovine testing rook place in 2012, SaferGate has hit the market and been installed in over 100 cattle fences around the country.

Australian Agricultural Co’s chief operating officer Troy Setter, said his company had installed some SaferGate units last year, which had already prevented potential injury to one of his livestock staff when a beast struck the gate she was attempting to close.

“If it was a normal gate, she would have been hit and possibly seriously injured, however the SaferGate simply folded away,” Mr Setter said. “Stopping just one injury makes the investment worthwhile,” he said.

Read more about the development of SaferGate or get involved in National Farm Safety Week.


Keeping your wine delish

 

As the weather turns dark and dreary, many of us are choosing to stay indoors and seek comfort in a nice bottle of red. After all, when it’s drizzling outside it’s hard to beat a rich pinot by the fireplace.

In Australia, we’re lucky to enjoy some of the best wine in the world. In fact, Australia’s wine and grape industry has been one of the nation’s great agricultural success stories. Last year we produced over a billion litres of wine. Shiraz was our number one drop of choice, followed by a Cabernet Sauvignon.

It’s clear, when it comes to wine, we’ve struck it rich. But many wine enthusiasts don’t realise one of the reasons for this is the science behind our grapevines.

We’ve been looking at how different rootstocks – the underground part of the vine – reduce the impact of salty soils on the appearance and taste of wine. While the prospect of ‘salty wine’ might sound like a first world problem, it’s actually becoming a widespread concern in viticulture as climate change brings longer, hotter and drier summers.

Our scientists recently carried out trials in South Australia that examined the salt tolerance of eight commercially available rootstocks.

“We had a particular interest in how much salt might have accumulated in the juice and carried through to the wine, and just what that accumulated salt did in terms of how the wine looks and tastes,” said principal investigator Dr Rob Walker.

Dr Rob Walker

Dr Rob Walker (photo credit: Carl Davies)

This led to the creation of a rootstock Salt Tolerance Index based on characteristics such as yield, leaf area, sodium concentrations and wine colour density. Salt tolerant rootstocks appear to work by limiting chloride accumulation in leaves and fruit through lower root to shoot transport.

As well as providing an insight into saltiness, the study also provided valuable data about other wine attributes related to the rootstocks, such as differences in flavour intensity and colour.

It is hoped that the research, funded by the Australian Grape and Wine Authority, and the wine sensory evaluation carried out in collaboration with the Australian Wine Research Institute, will lead to the development of new rootstock types designed specifically for Australian conditions.

Read more about how we’re keeping your wine tasty (and not too salty) on our website.


It’s like Tinder… for cows

Cow's nuzzling

Cow wants a wife. Image: Flickr / orangebrompton

By Ali Green

Have you herd? We’ve worked out a way to tell when Daisy’s in the moood.

Our scientists have been working with UTAS as part of the Sense-T program, to develop a smart collar that monitors the behaviour of dairy cows.

What is so extraordinary about the secret lives of cows, you ask? Well, quite a lot it turns out. Understanding a dairy cow’s eating habits, knowing with certainty when they’re in heat, and how they’re feeling generally, impacts a farmer’s management practices and can be the difference between a farm’s profit or loss.

A cow only produces milk after she has had her first calf, and she needs to be pregnant at least once a year in order to keep producing milk. Timely detection of oestrus events (when a cow is in heat) is crucial to ensuring successful artificial insemination and a continuing milk supply. It is recommended that artificial insemination takes place within 4-12 hours of an oestrus event, but the majority of oestrus events occur during the night when farmers are asleep and can be missed the following morning.

Cow with collar

Data collected by Daisy’s collar can tell when she’s in the mood for love.

Our hi-tech collar has been designed to monitor and predict cattle behaviour using highly accurate machine learning algorithms. Data collected from accelerometers (measures accelerations in 3 dimensions) and magnetometers (measures orientation – head down, up or tilted etc) identifies behaviours and divides them into ten classifications including grazing, ruminating, resting, searching, walking and standing. It is believed these behavioural classifications (accurate to 95%) will also be able to detect oestrus events, so if a cow is feeling frisky a farmer could be alerted via SMS that it’s time for insemination.

There are a number of heat-detecting cow collars currently on the market, but our collar’s unique behaviour classification capability means it can be used to target a wide range of applications.  One example is identifying individual cow feeding patterns in order to optimise grain distribution, saving farmers on grain costs. Supplementary grain currently makes up about 30% of a dairy farm’s expenditure.

Sick cows also impact a farm’s profit. Trials will begin shortly to recognise precursor behaviour patterns for illnesses like mastitis and lameness so they can be caught early.

The Sense-T program is all about combining collected data and using it for purposes it wasn’t originally intended. The cow collar behavioural data, combined with soil moisture data for example can be used to estimate water quality in local rivers. If you know where the cows have been and you know the soil is wet and there’s been a rainfall event, then you might say there’s a pretty good chance that the nearby river is carrying a high faecal load and that could directly impact on oyster farmers downstream…

Sense-T is a partnership between the University of Tasmania, CSIRO, the Tasmanian Government and IBM.


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