Study could spawn better ways to combat crop-killing fungus

Rutgers-led genome research finds fungus that causes disease in rice became harmful 21 million years ago

Rutgers University

IMAGE: Ning Zhang, associate professor in the Department of Plant Biology and the Department of Biochemistry and Microbiology at Rutgers University-New Brunswick, holds a Petri dish with switchgrass seedlings inoculated with… view more 

Credit: Nick Romanenko/Rutgers University

About 21 million years ago, a fungus that causes a devastating disease in rice first became harmful to the food that nourishes roughly half the world’s population, according to an international study led by Rutgers University-New Brunswick scientists.

The findings may help lead to different ways to fight or prevent crop and plant diseases, such as new fungicides and more effective quarantines.

Rice blast, the staple’s most damaging fungal disease, destroys enough rice to feed 60 million people annually. Related fungal pathogens (disease-causing microorganisms) also infect turfgrasses, causing summer patch and gray leaf spot that damage lawns and golf courses in New Jersey and elsewhere every summer. And now a new fungal disease found in wheat in Brazil has spread to other South American countries.

Results from the study published online in Scientific Reports may lead to better plant protection and enhanced national quarantine policies, said Ning Zhang, study lead author and associate professor in the Department of Plant Biology and the Department of Biochemistry and Microbiology in the School of Environmental and Biological Sciences.

“The rice blast fungus has gotten a lot of attention in the past several decades but related species of fungi draw little attention, largely because they’re not as severe or not harmful,” Zhang said. “But they’re all genetically related and the relatives of severe pathogens have been little-studied. You have to know your relatives to have a holistic understanding of how the rice blast pathogen became strong and others did not.”

The study is the outcome of a 2016 international symposium at Rutgers-New Brunswick hosted by Zhang and Debashish Bhattacharya, study senior author and distinguished professor in the Department of Biochemistry and Microbiology. The National Science Foundation, Rutgers Center for Turfgrass Science, and School of Environmental and Biological Sciences funded the symposium by researchers from the U.S., France and South Korea.

The scientists studied Magnaporthales, an order of about 200 species of fungi, and some of the new members were discovered in the New Jersey Pine Barrens. About half of them are important plant pathogens like the rice blast fungus – ranked the top fungal pathogen out of hundreds of thousands. After the first sign of infection, a rice field may be destroyed within days, Zhang said.

To get a holistic understanding of how the rice blast fungus evolved, scientists genetically sequenced 21 related species that are less harmful or nonpathogenic. They found that proteins (called secretomes) that fungi secrete are especially abundant in important pathogens like the rice blast fungus.

Based on previous research, the proteins perhaps became more abundant over time, allowing the fungi to infect crops, Zhang said. The researchers identified a list of genes that are abundant in pathogens but less so in nonpathogens, so the abundant genes might promote pathogens that can infect crops. The results will allow scientists to look into the mechanism behind the infection process.

“With climate change, I think the rice blast problem can only get worse because this is a summer disease in warm climates where rice is grown,” Zhang said, adding that wheat, turfgrass and other important plants may also be affected.


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UK: Pollinator health


Buzzing activity around pollinator health

By Anu Veijalainen, CABI. Reblogged from CABI Hand-picked blog.

Yesterday I cherished the start of spring in England by attending an event devoted to pollinators and pollination at the University of Reading. Most presentations at this meeting organised by the Royal Entomological Society were understandably about bees, but we also heard a few talks highlighting the importance of other pollinator groups.

For about five years now the media has been broadcasting alarming news about declining bee populations especially in Europe and North America. While the amounting evidence points to neonicotinoid insecticides being a major cause for the decline, I learnt yesterday that the situation is actually rather complex, other stressors are also involved, and scientists are still eagerly trying to form a complete understanding of the issue.

European Honey Bee Touching Down
Photo by Autan, under Creative Commons BY-NC-ND 2.0 license

Multiple stressors threaten bee populations

The mysterious decline of bee populations has granted these insects a lot of press exposure in recent years – and rightly so; after all, pollinators provide a crucial ecosystem service. However, in the midst of following this growing information load, I realised that it was hard to keep up with the prevailing scientific consensus on the matter, especially on neonicotinoids. Therefore, I was glad to see that a review article summarising the current scientific evidence concerning the effects of neonicotinoid insecticides on insect pollinators intended to assist political decision-making was published at the end of last year. Another interesting review focusing on neonicotinoids and the prevalence of parasites and disease in bees came out earlier this month. Both reviews list a substantial number of recent studies indicating a connection between bee deaths and neonicotinoids.

New scientific case studies on bee health continue being published on a regular basis, and political and public discussion around bees and other pollinators remains active. This is demonstrated by searching for new records added to the CAB Abstracts database in the first four months of this year: using the searchstring ‘pollinator AND population AND decline‘ returns 25 results. Furthermore, last month the European Food Safety Authority (EFSA) launched a new website dedicated to bee health called #Efsa4Bees – Parasites, pathogens and pesticides: making sense of multiple stressors.

In conclusion, keeping up-to-date with the advancements in the field is challenging because there is a large amount of new information being produced and the studies have found somewhat conflicting results, i.e., indicating that bees are in decline due to a number of factors including pesticides, habitat loss and diseases. All these topics were also covered in the presentations given yesterday at the meeting ‘Progress in pollination and pollinator research’.

Potential for a brighter future 

Being concerned about the current state of bee and other pollinator populations, I felt a sense of relief entering the lecture hall yesterday and noticing that so many people – over 80 mainly UK-based scientists attending this one-day event – have dedicated their careers to understanding and conserving pollinators. A number of the studies presented at the event had investigated how diverse bee communities can be supported in different landscapes, reflecting the fact that pollinators are also threatened by agricultural intensification and other human-induced land use changes. My day, however, culminated towards the end of the last session when excellent talks were given on the effects of insecticides on bees.

In her expert presentation, Dr Linda Field of Rothamsted Research first explained why neonicotinoids had become such efficient and commonly used insecticides in agriculture. She then moved on to state that in her opinion, blaming neonicotinoids for bee population declines was fairly “easy” (compared to, e.g., diseases and adverse weather events) yet hard to prove, and closed the talk by expressing what she thought was needed of pest management in the future. She highlighted the encouraging progress made in two areas of research: first, understanding how insecticides interact with target proteins and the variation of these proteins in different insects, and second, how insecticides are detoxified by insects and the variation of these mechanisms in different insects.

According to Dr Field, future pest management strategies should apply, for example, biological and cultural control, pest-resistant crop plants, and pesticides that specifically affect target pests but are not harmful for beneficial organisms.

Further activities for the concerned and the curious

If you’re interested in finding out more about the role of neonicotinoids in bee deaths, the AgriSciences group of the Society of Chemical Industry (SCI) is organising a topical one-day event titled ‘Are neonicotinoids killing bees?’ in London this September. Registration is now open.

Finally, I’d like to share a list of links to relevant news articles and scientific papers I’ve encountered in the last a couple of months. They represent only a handful of the articles out there, but demonstrate the somewhat conflicting messages of studies and the active work scientists are conducting on pollinator health.


Godfray HCJ, Blacquière T, Field LM, Hails RS, Potts SG, Raine NE, Vanbergen AJ & McLean AR (2015) A restatement of recent advances in the natural science evidence base concerning neonicotinoid insecticides and insect pollinators. Proceedings of the Royal Society B 282: 20151821.

Sánchez-Bayoa F & Desneux N (2016) Neonicotinoids and the prevalence of parasites and disease in bees. Bee World 92: 34–40.

Alberta farmer

Key source of clubroot resistance goes AWOL

‘Grandparent’ can defeat new mutated clubroot strains but somehow it doesn’t get passed down

The ‘grandparent’ of clubroot resistance in most Canadian canola varieties is resistant to new virulent strains of clubroot — but its offspring aren’t.

“It’s possible that, in the course of breeding, some of the resistant genes were lost,” said provincial research scientist Rudolph Fredua-Agyeman.

European clubroot differential (ECD) 04 is a key source of clubroot resistance for canola-breeding programs around the world, including in Canada, Fredua-Agyeman said at Alberta Canola’s Science-O-Rama last month.

Because of its resistance to all the clubroot strains found in Canada so far, ECD 04 has been bred into most clubroot-resistant canola varieties, including Mendel — a European winter canola cultivar that has also been used as a source of resistance for Canadian varieties.

“When clubroot was found in Alberta, the natural source of resistance was ECD 04 and Mendel, which were resistant to most of the strains of clubroot that we had at the time,” said Fredua-Agyeman.

But in 2013, clubroot strains started to shift to overcome the resistance, and new, more virulent strains of the disease began to appear in Alberta canola fields. As of 2017, these new strains have been confirmed in at least 104 fields in Alberta — a conservative estimate, as researchers only test fields that have been brought to their attention. Most notable of these strains is 5x, which can cause disease severity of up to 90 per cent.

“We’ve found that these strains are causing much more severe disease on canola than the other strains,” said Fredua-Agyeman, adding at least nine other strains have also been identified.

“The challenge posed to the canola industry by these new strains is real and very aggressive.”

The good news is that ECD 04 still shows complete resistance to these new strains, including 5x. Unfortunately, Mendel — and the commercial varieties that were spawned from it — are not.

“We went from ECD 04 — complete resistance — to Mendel, where we’re getting resistance to only 50 per cent of the new strains, and then to the commercial varieties, none of which are resistant to these new strains,” he said. “Not all the resistant genes were passed on from ECD 04 to Mendel, and from Mendel to the commercial varieties.

“The loss of this gene has contributed significantly to the breakdown of resistance.”

Integrated approach needed

Until new resistant varieties can be developed and new resistant sources found, canola growers will need to take a more “integrated” approach to clubroot management.

“Our resistance is very good, but it’s not a magic bullet,” said Stephen Strelkov, a plant pathologist and professor at the University of Alberta.

“Resistance is vulnerable, and we need proper resistance stewardship.”

When clubroot was first discovered in Alberta in 2003, producers were interested in finding a variety of tools to manage the disease. But when the first clubroot-resistant canola variety came online in 2009, farmers began to rely heavily on resistance instead of integrated disease management (which includes equipment sanitation and extended rotations).

“Clubroot resistance was such a strong tool that the extension messaging probably fell on deaf ears a little bit, and farmers grew resistant varieties in very short rotations,” said Strelkov, who also spoke at Science-O-Rama.

“People thought, ‘We have resistant varieties that do so well now — why should we worry about it?’”

But that reliance on resistant varieties has caused resistance to break down in record time. It only takes about two crops of a resistant variety for the pathogen to start to shift to overcome the resistance, and if those two crops are seeded back to back, it takes less than three years for the resistance to break down — not nearly enough time to find new sources of resistance or breed new resistant varieties.

“Resistance is the most widely used management strategy — nothing really compares to genetic resistance,” said Strelkov. “But these new strains highlight that our crop is still at risk from clubroot.”

Researchers are exploring other tools for clubroot management — including soil fumigants, liming, and bait crops — but until producers have more tools to add to their tool box, they need to take care of the ones they already have. That means using resistant varieties, rotating sources of resistance, sanitizing equipment, and (yes) extending rotations to four years.

If they don’t, they risk finding themselves in the same boat if and when new sources of resistance are found.

“It’s not a stable situation. The pathogen is changing and evolving,” said Strelkov.

“We’ll need a more integrated way of thinking to sustainably manage clubroot. Resistance will need to be used in conjunction with other tools.”

About the author


Jennifer Blair is a Red Deer-based reporter with a post-secondary education in professional writing and nearly 10 years of experience in corporate communications, policy development, and journalism. She’s spent half of her career telling stories about an industry she loves for an audience she admires–the farmers who work every day to build a better agriculture industry in Alberta.


SE farm press


Aphid-transmitted virus found in lower Southeast cotton

Cotton blue disease is a big problem in Brazil, and it seems to have come to the U.S. by a hurricane, like soybean rust did with Hurricane Katrina.

Patrick R. Shepard | May 03, 2018

A virus that is previously known to be vectored by aphids into cotton has been recently identified as the primary suspect virus from limited samples of cotton in Alabama. Similar symptomology has been reported in the coastal counties of Alabama, Georgia and the Florida Panhandle.

“The cotton blue disease (CBD) symptomology was observed at the end of 2016 by one of my former graduate students, Drew Schrimsher, in his grower cotton variety trials,” says Auburn University plant pathologist Dr. Kathy Lawrence.

“He observed it again at the end of 2017 and it was much worse; symptomology was observed in areas beyond the area where it was first observed. CBD is a big problem in Brazil, and we hypothesize it may have come to the U.S. by a hurricane, like soybean rust did with Hurricane Katrina.”

Symptoms include mosaic cupping and thickening of the dark blue/green leaves, yellowed leaf veins, and dwarfing of the plant. Other symptoms include no boll set on new growth, swollen and brittle stems, and decreased yields; fields with symptoms in early bloom had fewer bolls per plant.

“Once the virus starts showing its symptoms, the plant stops producing any more cotton,” Lawrence adds. “There’s not a top crop, which many growers depend on for income.

 “We seldom spray for aphids in cotton, and we don’t recommend spraying for them to prevent this suspect disease, which would take out beneficials and flare other insect pest problems. We do encourage growers and consultants to watch for the CBD virus symptomology, and if they find it, to call their state plant pathologist to help us keep up with it.

“We also recommend keeping cotton fields and surrounding areas weed-free, especially of legume and malvaceae weeds including pigweed and sida as the literature shows they harbor the virus. If the virus is in the weeds, aphids can pick it up and transmit it to cotton. So management might come down to taking out weed host plants.”

Schrimsher, who is now an agronomist with AGRI AFC, observed mild leaf crumpling symptoms in his cotton variety trials that he was conducting in growers’ fields in south Alabama and the Florida Panhandle in late summer to early fall 2016. He observed extensive severe leaf crumpling in 2017.

Lawrence says, “The virus was much worse by that time; CBD had progressed beyond the area where it was found in 2016. However, infected areas were patchy like aphid infestations are patchy along the outer edges of a field, and close to areas with other plants and trees. It didn’t take over the whole field.

“Schrimsher told me about the symptoms in August 2017. We took samples, and found it’s a virus. We normally don’t have viruses in Alabama, so to get an identification, leaves, petioles and stems were collected from the newest terminal of plants expressing leaf crumpling symptoms and sent to University of Arizona plant pathologist Dr. Judy Brown, who researches the viruses in her state. She tested the samples and ruled out leaf crumple or leaf curl virus; instead, she found a virus associated with aphids that matches the one in Brazil.”

It appears from Schrimsher’s variety trials that the U.S. cotton varieties that were in the trials and are grown in the Southeast region all demonstrated the symptomology. “He saw the virus’ symptoms across all company varieties in his tests,” Lawrence says. “CBD is a big problem in Brazil, but they do have cotton varieties that are tolerant to the disease. The U.S. seed companies have gene markers in their breeding program. It’ll take time to develop resistant varieties for the U.S., but it’s not like starting from scratch.

“We will observe CBD closely this year. We’ve seen it for two years and hope it’s not here to stay. We hope that it will have a limited economic impact like soybean rust did.”

Official confirmation of the suspect virus will require additional sampling and verification by APHIS.


fresh plaza logo

Researchers discover wild tomato resistant to a wide range of pests and insects

Scientists at the University of Wageningen (The Netherlands) have discovered a species of wild tomato from the Galapagos Islands that is resistant to a wide range of insect pests. The wild tomato is genetically closely related to the cultivated tomato, which makes it easy to cross-breed it at the agricultural level and make it resistant to different insects.
Cultivated tomatoes are more vulnerable to pests and diseases, since they have lost their natural resistance in the reproduction process. Researchers are working to reverse this by reintroducing the resistance of the wild varieties through breeding, but they still haven’t been able to successfully cross breed the wild tomatoes with the cultivated tomatoes to obtain the necessary traits. The wild tomato of the Galapagos Islands, however, is genetically very similar to the cultivated tomato, and its resistance is encoded within a single chromosome, which should make crossing between the existing plants much easier.
Ben Vosman, a scientist at Wageningen University, said “we work with samples of the wild tomato species Solanum galapagense from a gene bank. The first discovery was that this tomato species is resistant to whiteflies. Then, we discovered it was actually resistant to many other insects as well, including the green peach aphid and the caterpillars of the soldier beetworm. It was a very pleasant surprise.” They have been working on this research since 2010,
“If we can make the cultivated tomatoes resistant to whiteflies, this will directly benefit the environment,” Vosman said. While this problem is still relatively manageable in greenhouses, through integrated control, for example, there are also pests there. In the field crops, the problems with insects are much greater. “We hope that most of the advantages are in the field crops and in the tropics,” he added.
Source: Wageningen University & Research


Publication date: 5/3/2018


How one parasitic wasp becomes the victim—of another parasitic wasp

Karma is a real pest for parasitoids, tiny parasitic wasps that lay their eggs on caterpillars. That’s because the way they protect their hungry young from the caterpillar’s immune system sends out a chemical calling card that lures other parasites, which feast on the offspring, according to a new study.

For the parasitoid’s brood, a caterpillar is a walking nursery and buffet. But that brood is on the menu for wasps called hyperparasitoids, which lay their eggs on the parasitoid offspring. Researchers previously found that hyperparasitoids sniff out their victims using the distinctive aroma a plant emits when being munched by a parasitized caterpillar.

What’s ultimately responsible for the release of this odor, scientists report today in the Proceedings of the National Academy of Sciences, is a virus that parasitoids squirt into a caterpillar to suppress its immune system and shield their offspring. When the researchers injected caterpillars with the virus and let the insects gnaw on wild cabbage plants, they found that the scent of the plants was particularly attractive to the hyperparasitoid Lysibia nana (above, laying its eggs on the parasitoid’s cocoons). The study suggests the virus changes the chemical composition of the caterpillars’ saliva, which in turn causes the plant to release molecules that are wasp-nip for hyperparasitoids.

By: Nala Rogers, Staff Writer

Inside Science

May 2, 2018

Sick Plants May Attract Distant Bacteria as Medicine

New study shows how sand sedges lure beneficial bacteria to their roots.


This experimental setup allows researchers to place bacteria at the ends of the glass tubes, then measure how much bacteria moves toward the plants.

Image credits: Kristin Schulz-Bohm

Rights information: This photo can be reproduced only with this Inside Science article.

Wednesday, May 2, 2018 – 12:15

Nala Rogers, Staff Writer

(Inside Science) — If there were a prize for long-distance, interspecies communication, few people would think to nominate a bacterium and a scraggly, grasslike plant. But according to a recent study, the roots of one such plant can call bacterial allies several inches away — a veritable marathon for tiny soil bacteria. Preliminary data suggest that the plants may even adjust their messages when they get sick, calling in different bacteria to act as medicine.

Scientists already knew that plants send signals above ground to communicate with animals. Flowers, for example, attract bees and other pollinators using color and scent. Some plants also use scent chemicals to call for help when they are attacked by plant-eating insects, luring in parasitic wasps that attack the insect herbivores.

But comparatively little is known about how plants communicate with microbes below ground. Plants rely on a complex microbiome to help them obtain nutrients from the soil, but most research on plants and soil microbes has focused on interactions that happen right at the edges of plant roots, said Paolina Garbeva, a microbial chemical ecologist at the Netherlands Institute of Ecology in Wageningen.

Garbeva and her colleagues suspected that plants use volatiles — substances that easily evaporate and can diffuse through air and water — to send long-distance “scent” messages belowground as well as above. In a study published this past January in The ISME Journal, they collected and analyzed the volatiles released by sand sedge roots, and then tested how bacteria responded to those volatiles.

To test the responses of bacteria, they filled glass cups with sterilized soil that contained no living bacteria, and used some of the cups to grow sand sedge plants. Each cup was connected to four horizontal glass tubes about 4 inches in length, which were also filled with sterile soil. The researchers placed a mixture of bacteria at the outer ends of the tubes, then measured how much of each strain of bacteria traveled through the tubes toward the cup.

Cups that contained plants attracted up to three times as many bacterial cells per strain as cups without plants, suggesting that bacteria were detecting the plants’ presence from 4 to 5 inches away, said Garbeva. The bacteria were presumably responding to volatiles released by the plants’ roots, since only volatile compounds could effectively diffuse so far through the soil, she said.
Next, the researchers infected some of the plants with a fungal disease. The infected plants released a different mix of volatiles from their roots, which in turn attracted a different suite of bacteria. When the researchers grew these bacteria in petri dishes with the infectious fungus, they found that the bacteria halted the fungus’s growth, raising the tantalizing possibility that the plant was recruiting specific bacteria as medicine.

The medicine-recruitment idea is still highly speculative, noted Garbeva. She and her colleagues are currently testing whether the bacteria attracted by sick plants can effectively combat the disease on the plants themselves. They have not yet compared the antifungal properties of the bacteria attracted by sick versus healthy plants, so it’s possible that healthy plants’ bacteria are just as good at stopping the fungus.

Moreover, these types of ecological processes are often context-dependent, said Sergio Rasmann, an ecologist at the University of Neuchatel in Switzerland, who was not involved in the study. If the researchers were to repeat their experiments while changing something like temperature or humidity, he said, they might get different results.

Nevertheless, the results are “very exciting,” said Rasmann. “The idea of plants recruiting microbes is not completely new. But the fact that they actively produce some chemicals in the soil to attract them — that’s very new,” he said.

Garbeva hopes that by examining the types of bacteria plants attract in nature, scientists may someday identify strains that could be added to crops as probiotics. Different strains may help with particular problems such as disease or drought, she said.

“Soil has the highest microbial diversity in the world,” said Garbeva. “We can find how plants can attract bacteria that are beneficial for them, and maybe we can use these bacteria in the future for plant protection.”

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Author Bio & Story Archive

Nala Rogers is a staff writer and editor at Inside Science, where she covers the Earth and Creature beats. She has a bachelor’s degree in biology from the University of Utah and a graduate certificate in science communication from U.C. Santa Cruz. Before joining Inside Science, she wrote for diverse outlets including Science, Nature, the San Jose Mercury News, and Scientific American. In her spare time she likes to explore wilderness.