Archive for the ‘Fungi’ Category

The Conversation


  1. Diane Saunders

    Research Fellow in Computational Biology at The Genome Analysis Centre and at John Innes Centre

wheat fungus

Yellow Rust spores can be seen bursting out of a wheat leaf from the inside, tearing their way through the epidermis. Kim Findlay/John Innes Centre, CC BY-NC-SA

One of the major diseases of wheat is caused by the yellow rust fungus, Puccinia striiformis, which threatens all major wheat-producing areas of the world. Ominously, we have discovered that the UK population of this pathogen is shifting dramatically, with the emergence of new strains which can overcome some of our most important wheat varieties.

We have developed a genetic technique that helps us characterise the pathogen, allowing farmers to make informed decisions about which wheat varieties to plant.

Wheat is a critical staple crop, providing 20% of the calories and 25% of the protein consumed globally by humankind. Despite modern agricultural practices, diseases of major food crops can cause pre-harvest yield losses of up to 15%.

In 2013, I joined forces with colleagues at the John Innes Centre and The Sainsbury Laboratory in Norwich with the National Institute of Agricultural Botany in Cambridge to develop a new genomics-driven surveillance method to track the devastating yellow rust fungus and investigate the genetic basis of the new pathogen population.

Our new “field pathogenomics” method is a fast way to analyse fungal diseases from field samples and pinpoint the exact genotype. Current techniques rely on time-consuming phenotypic characterisation – checking the response of different plant varieties to infection by the pathogen – or costly in-lab processes. These methods can only sample a relatively small proportion of the fungal population.

With help from contributors to the UK Cereal Pathogen Virulence Survey, we collected wheat samples infected with the wheat yellow rust pathogen from 17 different counties across the UK. We then used our newly developed “field pathogenomics” method to characterise the genotypes of the samples. As each field sample consists of both the pathogen and its host plant, we were able to analyse both the pathogen and the susceptible host. In the future, this will provide a rapid means for confirming the presence of disease on wheat varieties that may have previously been resistant to disease.

wheat rust 2
Under siege: wheat is a major global crop, but threatened by fungal pathogens. Takkk, CC BY-SA

Invasive pathogens

We found that the wheat yellow rust pathogen population has undergone a major shift in recent years. Interestingly, the yellow rust population detected in the UK in 2013 was completely different at the genetic level to previous UK populations. This difference seems to represent a number of recent exotic introductions into the UK and could have serious implications for wheat production in the UK.

A subset of the new pathogen population was able to infect the same wheat varieties as a subset of the older UK pathogen population. Because the same varieties are infected, this new pathogen population would have been missed if analysis were based on traditional phenotypic characterisation alone. Spotting this new pathogen population is important, because even if it infects the same wheat varieties it could still have serious implications for disease incidence. The new pathogen population may have other important traits or infect other wheat varieties not included in our test set.

As we move forward, “field pathogenomics” could be applied to the surveillance of many pathogens besides wheat yellow rust pathogens, and could contribute to addressing human, animal and plant health issues. Such detailed knowledge of shifts in pathogen populations is important for both understanding and managing emerging diseases. For wheat yellow rust, our new technology could provide farmers with early indications of changes in the pathogen population, and have a positive impact on decisions regarding which varieties to plant in the field.



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ACIARhexagonsmallACIAR Blog
Every few years, it seems, a scare goes around threatening the end of the global commercial banana industry—and usually the focus of the scare-stories is Panama disease, caused by the fungus ‘Foc’ (short for Fusarium oxysporum f. sp. cubense).
The variety that made banana the ‘world’s favourite fruit’ was Gros Michel, but it was knocked out as a commercial crop in the 1950s and 1960s by Panama disease, specifically a form that we now call ‘Foc Race 1’. The banana that took its place was Cavendish, a variety found to be resistant to that form of Panama disease and subsequently distributed around the world. It currently dominates the global trade in bananas. But now the Cavendish banana has met its nemesis in the form of Tropical Race 4 of Panama disease—Foc-TR4. The new form of the disease has just about wiped out commercial Cavendish production in Malaysia and Indonesia (despite the best efforts of ACIAR’s previous Panama disease project in Indonesia), and this year there have been outbreaks, for the first time, in Africa and the Middle East.

banana panama disease
A banana plantation devastated by Panama disease (Tropical Race 4). Photo: Richard Markham/ACIAR

The front line in ACIAR’s battle with Foc-TR4 has now shifted to the southern Philippines, where ACIAR has recently launched a new project. There, some of the key players who were involved in the Indonesian project—Bioversity International and Queensland’s Department of Agriculture, Fisheries and Forestry—have taken on board the lessons learned and are now trying to apply them to managing the disease, in collaboration with Filipino research organisations and commercial industry partners.

While the Indonesian project looked at specific antagonists to Foc, especially other fungi living in the soil that could compete with and control it, the Philippines project is focusing on encouraging farmers to grow groundcovers between the banana plants. Groundcovers can provide a favourable environment for a range of these antagonists to develop naturally. They also provide additional benefits, such as reducing soil erosion and surface water flow that can carry the fungus from plot to plot, as well as reducing the risk of farm workers carrying the disease in contaminated soil on their shoes.

In a recent visit to Davao, the hub of the Philippines’ banana industry, Queensland groundcover-advocate Tony Pattison engaged directly with some of the farmers to see what plant species might be acceptable within their production system. He also met with local researchers to see which species could be sourced locally and rapidly propagated. In addition the team discussed with the farmers how they liked the Foc-TR4-tolerant variants of Cavendish, selected in Taiwan and made available to other countries including the Philippines, through Bioversity International’s BAPNET.
The take-home message from our exploratory visit was that the banana industry is extremely competitive and, while producers are anxious to try our new combination of groundcovers and disease-tolerant varieties, the new technology will have to deliver high productivity quickly if it is going to save the local industry.

There are benefits to Australia too from this research. For example, Australian researchers and industry partners are evaluating and gaining experience in the use of groundcovers to manage Foc Race 1, which attacks Australia’s Lady Finger bananas. It will also serve as something of a ‘dress rehearsal’, in case Foc-TR4 should ever threaten the heart of Australia’s commercial banana industry—the Cavendish plantations in Queensland and northern New South Wales.

By Richard Markham, ACIAR Research Program Manager for Horticulture

More information:
ACIAR project HORT/2012/097—Integrated management of Fusarium wilt of bananas in the Philippines and Australia

ACIAR project HORT/2004/034—Diagnosis and management of wilt diseases of banana in Indonesia
ACIAR project HORT/2005/136—Mitigating the threat of banana Fusarium wilt: understanding the agroecological distribution of pathogenic forms and developing disease management strategies


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aps cover

Accepted for publication

Coconuts (Cocos nucifera) are an important tropical economic crop in Hainan and are used to enhance aesthetics of coastal areas. In April 2012, a new leaf blight disease of coconut was discovered in Wenchang, Hainan Province. The symptoms appeared on young and mature leaves of coconut. Initially, dark brown irregular spots surrounded by a yellow halo appeared on the leaf margins. As the disease progressed, the spots enlarged to thin and grayish-white lesions with brown margins. Black, minute, protuberant acervuli could be observed on both sides of the lesions. The lesions coalesced on each leaflet and spread to the entire leaf, leading to shriveling and defoliation. A survey of coconut gardens in Hainan indicated, led to a high incidence of recovery for the fungus Pestalotiopsis menezesiana, which can lead to premature defoliation, which would in turn, reduce vigor of support branches leading to early fruit drop. A total of 6 identical fungal isolates were obtained from coconut leaf lesions. The colony of the fungus on potato dextrose agar (PDA) medium was white, and cottony with smooth margin with a honey yellow colony reverse. The fungus produced acervuli on PDA medium, which were ink black, drop-shaped, and became dry after 40 days. Conidia were fusiform, slightly curved or straight, 5-celled, constricted at the septa, and 19-25.9×5.7-7.8 ųm (av. 23.4×6.7 ųm). The three median cells of conidia were pigmented, thick-walled, 14.8-19.5 ųm (av. 16.6 ųm) in length. The two upper cells were amber and the lowest cell was light-brown. The apical cell was hyaline with two or three cellar appendages arising at the apex. Appendages were hyaline, filiform, unbranched, nearly straight, and 13-23 ųm (av. 18.8 ųm) long. The basal cell had a single, hyaline, simple appendage, 4.1-6.9 ųm (av. 5.1 ųm) in length. The morphological characteristics of the fungus matched those of Pestalotiopsis menezesiana (1,2). For molecular identification, the ITS (internal transcribed spacer) region was amplified with primers ITS1 and ITS4, and the PCR product was sequenced (Genbank accession No.KJ605161). A BLASTn analysis demonstrated a 99% similarity with P. menezesiana (Genbank accession No. AY687302.1). 30 homologus strains in the Genbank were downloaded and a molecular phylogenetic tree was constructed. The result revealed that the closest relationship to the pathogen was with P. menezesiana. A pathogenicity test was established following Koch’s postulates. Ten 1.5-year-old coconut seedlings with four leaves per seedling were examined. Two leaves of every seedling were wounded-inoculated with a 2.7×105 spores﹒mL-1 suspension of conidia. Six leaves of three seedlings were wound-inoculated with sterile water as control. The seedlings were kept in greenhouse at 25°C for 10 days. Inoculated leaves showed typical symptoms matched those described above. The control leaves inoculated with sterile water did not show any symptoms. To our knowledge, P. palmarum was reported causing diseases of coconut palm in Tamil Nadu (3), but this was the first report of P. menezesiana on coconut in Hainan, China.


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December 24th, 2014

The United Nations’ Food and Agriculture Organization (FAO) and its partners say that a global effort is needed to prevent the rapid spread of the deadly Fusarium wilt disease in bananas.

bananas 3

Photo: http://www.shutterstock.com

The disease is caused by the pathogen Fusarium oxysporum, and is said to pose a severe threat to economic welfare and food security in developing countries.

Plant scientists have been warning for several years that the world’s most popular banana variety, the Cavendish, has fallen victim to a new strain of the fungus causing wilting and the widespread death of plants.

Now the FAO and a group of international experts have agreed on the framework for a global program on Fusarium wilt that would work on three main fronts of action.

The three fronts are preventing future outbreaks, managing existing cases, and strengthening international collaboration and coordination among institutions, researchers, governments and producers.

Key aspects of the program would include supporting ongoing research, educating producers and assisting governments in developing country-specific policies and regulation for prevention of the disease.

The FAO estimates funds of around US$47 million are needed for the program, and part of that would be used to provide swift on-the-ground assistance to countries facing new outbreaks.

Tropical Race 4 (TR4) of the Fusarium wilt fungus is considered a top threat to global banana production worth US$36 billion, which provides a source of income or food to some 400 million people.

“Fusarium wilt disease has been a major challenge in the history of banana production,” FAO head of plant protection Clayton Campanhola said at a meeting of experts at FAO headquarters last week.

“After the devastation TR4 recently caused to bananas in parts of Asia, we have to fear its spread in Africa and the Middle East and also to Latin America, and consider it as a threat to production globally.”

Spread and Containment

The FAO’s plan for a new intervention and prevention program comes on the coattails of a recent case in Mozambique, prompting an FAO emergency project in December to contain the fungus in the African country.

Earlier outbreaks of the TR4 strain of the Fusarium wilt disease, colloquially known as Panama Disease, brought Indonesia’s banana exports of more than 100,000 metric tons (MT) annually to a grinding halt, causing annual losses of some US$134 million in revenue in Sumatra alone.

Currently the disease is severely affecting more than 6,000 hectares in Philippines and 40,000 hectares in China.

Fusarium wilt spreads rapidly through soil, water and contact with contaminated farm equipment and vehicles, making swift responses essential to preventing incursions and outbreaks.

Once soil is contaminated with the fungus, an affected field becomes unfit for producing bananas susceptible to the disease for up to three decades.

The case for genetic diversity

Experts warn that the panacea to Fusarium wilt does not lie only in finding a new immune variety, but to making the banana production systems as a whole more genetically diverse and resilient.

Better use of available local varieties is key to building resilience to disease, preventing food insecurity and major economic losses, according to plant disease expert Fazil Dusunceli.

“We are seeing that production systems with more diverse varieties and crops are more resilient to the disease,” he said.

While many wild varieties of bananas and plantains are not edible, they hold a wealth of untapped genetic material that – with increased investment in research – could be used to make the banana production and industry more resilient to disease.

But experts also stress that the most effective way of combatting the disease is vigilance to employ preventive measures to stop entrance of the fungus into a country or region, and rapid containment if it does.

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High country news

NYT2008111213243014CTo save whitebark pines, apply slippery jack.

Ben Goldfarb Dec. 22, 2014

When most Westerners venture into the woods in search of fungus, they’re looking for dinner. When Cathy Cripps goes mushroom hunting, she’s trying to save a tree.

The tree in question is the whitebark pine, an iconic species that’s been devastated throughout the Northern Rockies by mountain pine beetles and a fungal disease called blister rust. We’re accustomed to thinking of fungi as a danger to biodiversity: In addition to pines, witness bats and frogs, imperiled by white-nose syndrome and chytrid, respectively. But Cripps, a mycologist at Montana State University, is captivated by the opposite story — a certain fungus may yet be what whitebark pine needs to survive.

That notion emerged from years of fieldwork in whitebark pine forests throughout the Greater Yellowstone Ecosystem. There, Cripps noticed that the soil was rife with a particular fungal species: Suillus sibericus, aka Siberian slippery jack. Suillus sibericus is a mycorrhizal fungus, meaning that it forms close symbiotic relationships with the roots of plants. The fungus draws sugar from roots, and in turn pipes nutrients back to its host tree through an underground network of fine filaments. “Each root tip gets surrounded by the fungus, just like a little sock,” Cripps says.

siberian slippery jackCripps wondered if mycorrhizal fungi could change the survival odds for whitebark pine seedlings grown in nurseries and planted for restoration. Cultivating whitebarks is an arduous process — among other complications, the seeds have to be exposed to elaborate temperature cycles in order to germinate — and not always successful. One graduate student who surveyed more than 100,000 whitebark seedlings planted in the region found that just 42 percent lived.

That low success rate is partly due to the fact that whitebark seedlings are often outcompeted by rival trees, like spruce and fir. Slippery jack offered a solution: While many other mycorrhizal fungi are “promiscuous” — they partner with more than one tree species — S. sibericus almost exclusively cohabitates with whitebark and its relatives. “We figured sibericus would give whitebark pine an advantage, without helping the tree species that are competitive with it,” Cripps says.

That’s when the hunt began. Cripps and a graduate student named Erin Lonergan foraged for slippery jack’s lemon curd-colored mushrooms in the mountains around Yellowstone and Canada’s Waterton Lakes National Park; back at MSU, they used a coffee grinder to mill the underside of the mushrooms, where spores reside, into a powder. Finally, Cripps diluted the powder with water and employed an inoculation gun — the kind you’d use to vaccinate cattle — to implant her spore concoction into the soil around whitebark seedlings growing in the Glacier National Park nursery.

In September 2010, volunteers planted about a thousand seedlings from the Glacier nursery at test sites across the border in Waterton. This summer, Cripps and Lonergan reported that, after three years, the fungal inoculation had enhanced survival by 11 percent. “Given how difficult it is to grow seedlings, even a small increase in survival is very important,” Cripps says.

Parks Canada agrees with her: They’ll be using slippery jack on future whitebark plantings in Waterton, Banff and Jasper National Parks. (Nurseries in the U.S. haven’t yet committed to the technique, but they’re interested.) Cripps still isn’t positive how slippery jack benefits pines, though she suspects it aids the tree by helping it take up nitrogen. Just as scientists are still coming to understand how certain trees die, they have a ways to go in figuring out why others live.

But for all the concern about whitebark survival, Cripps is equally worried about the other side of the symbiotic coin. “If you have a whitebark pine ghost forest where all the trees are just skeletons,” she wonders, “how long can these specific fungi persist in the soil?”

Ben Goldfarb is a Seattle-based correspondent for High Country News.

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Released: 16-Dec-2014 11:00 AM EST
Source Newsroom: Institute of Food Technologists (IFT)


Newswise — CHICAGO –Argentina is the second highest corn producing country in the world. But because of the slow drying process in corn kernels and wet weather conditions in Argentina, corn grown there can easily become infected with fungi. A new study in the Journal of Food Science published by the Institute of Food Technologists (IFT) found that the essential oils from oregano can have an antifungal effect on corn.
Generally, fungicide is controlled with the use of synthetic chemicals. However, it may require greater synthetic chemical usage as resistant strains of pathogens increase. Essential oils are an alternative strategy to controlling the growth of fungus without a negative impact. Since only small amounts of oils are needed, they have a low toxicity to animals and they do not remain in water or soil for a long time (Isman, 2000).
Oregano proved to be the best antifungal agent because of the presence of thymol, but oils of peppermints and suico grown in Argentina may also be used as a natural alternative to control the presence of postharvest fungi in corn.

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Kansas State University
Released: 13-Nov-2014 10:00 AM EST
Source Newsroom: Kansas State University

Newswise — MANHATTAN, Kansas — Several states, including Kansas, are trying to protect their borders from a little beetle that could cost the black walnut industry millions of dollars. Kansas Forest Service specialists at Kansas State University say you could be spreading the disease without knowing it.
Thousand cankers disease has been confirmed in Colorado, New Mexico, Arizona, Vermont, Nevada, California, Idaho, Washington, Pennsylvania, Tennessee, North Carolina and Virginia. Several quarantines have been established in an attempt to prevent the disease from spreading. States in quarantine include Kansas, Oklahoma, Nebraska, Missouri, Arkansas, Illinois, Indiana, Ohio, Michigan, Wyoming and Montana.
“It’s an interesting disease that requires two parts,” said Ryan Armbrust, a forest health specialist with the Kansas Forest Service. “There’s a small walnut twig beetle that will feed on the twigs of black walnut trees. In doing this, it will spread a fungus that causes cankers and causes the tree’s vascular system to clog up and die.”
The beetle is tiny —about the size of the letter “i” in the word Liberty on a dime. The flight season for the beetle is typically in the warmer months, but it can survive in the tree throughout the year. Since there are currently no viable treatment options, Armbrust says the best defense is to avoid moving black walnut tree firewood or lumber out of an area, especially if it still contains the bark.
“While it may seem safer to move black walnut material in the wintertime, when the beetle isn’t flying around, that beetle could still be contained within that bark. When it warms up in the spring, it could come out,” Armbrust said. “There really is no safe time of year to move black walnut lumber, especially from an area that has been infested.”
Kansas is home to about 25 million black walnut trees, which are an important part of the economy. The Kansas Forest Service estimates the state would lose at least $160 million in revenue from the lumber and nut production if these trees were destroyed by thousand cankers disease.


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