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Remote-sensing models to combat Banana bunchy top virus in Africa
The IITA–CGIAR team has published a method using drones and satellite imager-based remote sensing approaches for mapping banana farms to guide surveillance for the detection and mapping of the banana bunchy top virus spread and support data-informed decision-making on virus containment strategies in sub-Saharan Africa.
The study, Banana Mapping in Heterogenous Smallholder Farming Systems Using High-Resolution Remote Sensing Imagery and Machine Learning Models with Implications for Banana Bunchy Top Disease Surveillance, was published in the peer-reviewed, open access Remote Sensing journal.
BBTV has emerged as a major threat to banana production in sub-Saharan Africa. The virus infection results in severe dwarfing (bunching) of the shoots and cessation of fruit production, denting the food and income security of smallholder farmers.
Volatile organic compounds (VOCs) produced by soil bacteria have been shown to exert plant pathogen biocontrol potential owing to their strong antimicrobial activity. While the impact of VOCs on soil microbial ecology is well established, their effect on plant pathogen evolution is yet poorly understood. Here we experimentally investigated how plant-pathogenic Ralstonia solanacearum bacterium adapts to VOC-mixture produced by a biocontrol Bacillus amyloliquefaciens T-5 bacterium and how these adaptations might affect its virulence. We found that VOC selection led to a clear increase in VOC-tolerance, which was accompanied with cross-tolerance to several antibiotics commonly produced by soil bacteria. The increasing VOC-tolerance led to trade-offs with R. solanacearum virulence, resulting in almost complete loss of pathogenicity in planta. At the genetic level, these phenotypic changes were associated with parallel mutations in genes encoding lipopolysaccharide O-antigen (wecA) and type-4 pilus biosynthesis (pilM), which both have been linked with outer membrane permeability to antimicrobials and plant pathogen virulence. Reverse genetic engineering revealed that both mutations were important, with pilM having a relatively larger negative effect on the virulence, while wecA having a relatively larger effect on increased antimicrobial tolerance. Together, our results suggest that microbial VOCs are important drivers of bacterial evolution and could potentially be used in biocontrol to select for less virulent pathogens via evolutionary trade-offs.
Review highlights a century of science in tackling emerging fungal diseases in response to climate change
by CABI
Dr David Smith examines CABI’s living culture collection of over 30,000 strains of fungi and bacteria including 5,000 plant pathogens and other microorganisms. Credit: CABI
A new CABI-led review published in the journal Microbiology Australia highlights how CABI has spent over 100 years identifying and combatting emerging fungal diseases of plants in response to the impacts of climate change.
Dr. David Smith, Emeritus Fellow and former Director, Biological Resources at CABI, led a team of scientists who focused on how climate change is influencing disease occurrence and how CABI’s work and resources can help in the battle to help reduce them.
Ultimately, the researchers highlight how CABI and its 49 Member Countries are working collaboratively with a global network of partners to manage emerging and spreading diseases which can affect livelihoods and impact upon food security.
This includes diseases such as Maize Lethal Necrosis Disease (MLND) which has been negatively affecting maize crops and their seeds in eastern and central Africa. Part of CABI’s work to help mitigate this included a project that sought to enhance the knowledge base on MLND viruses and the epidemiology of the disease in the affected countries.
A key component of CABI’s work in the field is its living culture collection. This was born from the establishment of the Imperial Bureau of Mycology in 1920 and laid the foundation of CABI’s expertise in mycology which continues to this day.
Currently there are over 30,000 strains of fungi and bacteria—including 5,000 plant pathogens and other microorganisms—in the collection of which 90% are unique to CABI. It represents one of the world’s largest genetic resource collections and holds the UK’s National Collection of Fungus Cultures.
Another aspect of CABI’s work is its Diagnostic and Advisory Service (DAS) which provides diagnostic advice on pests and diseases on crops from around the world. An example of this was the confirmation of the invasive apple snail (Pomacea canaliculate)—which threatens Kenya’s rice crops—using DNA analysis.
In addition to sequencing, techniques such as MALDI-TOF (matrix-assisted laser desorption ionization—time of flight analysis) are used are used to identify and characterize disease causing microorganisms.
Other recent new country reports of pests and diseases confirmed by the DAS laboratory include Moniliophthora roreri causing frosty pod rot on cocoa in Jamaica and the fall armyworm (Spodoptera frugiperda) which affects more than 100 plant species and is found in Africa and Asia.
Dr. Smith said, “An understanding of microbes and microbial communities is essential for improving crop yields and facilitating interventions, such as biocontrol of pests, diseases, and invasive species.
“In parallel to the scientific work, CABI information resources are supporting the science and fieldwork to increase the reach, application, and understanding of the science worldwide.”
“In carrying out its work, CABI has seen an impact on emerging disease due to climate change and has implemented programs to help farmers adapt to its impact.”
These programs include the global PlantwisePlus program which works closely with national agricultural advisory services to establish a global network of plant clinics, run by trained ‘plant doctors’.
Rural plant clinics, staffed by agricultural advisors trained through PlantwisePlus, receive diseased samples and provide a timely diagnosis and appropriate remedial advice.
The program has been introduced to 34 countries in Africa, Asia and the Americas, presented over 5,000 plant clinics, trained over 13, 200 plant doctors and reached over 54 million smallholder farmers.
Recommendations to farmers have resulted in halving the use of restricted chemicals, increasing yields by more than 20% and over 1.5 million farmers have improved food security.
Another program is the Pest Risk Information Service (PRISE) which, in sub-Saharan Africa, used earth observation environmental data and models on pest life cycles to create early-warning alerts and advice to farmers on the timely application of pest control products.
It has delivered pest alerts in Kenya, Ghana, Zambia and Malawi to over 1.8 million farmers since it began in 2017. SMS information was sent to 6,000 farmers in Kenya, for example, on the fall armyworm which resulted in 60% of the farmers reporting a change in their farming practices as a result.
Dr. Smith added, “It is clear that climate change exacerbates problems and broadens the scope and range of plant pests and invasive species by enabling organisms to grow in environments from which they have normally been excluded.”
“Predictive models and early warning systems are needed if we are to combat such problems, for which CABI’s information resources and dissemination systems can play a critical role.”
A CABI-led review in the Journal of Economic Entomology has already highlighted several management options for the fall armyworm after recent climatic models reveal that the pest is likely to itself in the southern parts of Europe including southern Spain, Italy, Portugal or Greece.
More information: David Smith et al, CABI’s 100 years in identifying and combating emerging fungal diseases in response to climate change, Microbiology Australia (2022). DOI: 10.1071/MA22054
Dirk Babendreier et al, Potential Management Options for the Invasive Moth Spodoptera frugiperda in Europe, Journal of Economic Entomology (2022). DOI: 10.1093/jee/toac089
When eucalypt-destroying myrtle rust was detected on a cut flower farm and in two nurseries north of Sydney 12 years ago, a major containment operation was launched.
Millions of dollars were spent but to no avail. Within months, the invasive fungus, identified by its bright yellow spots, had swept up the coast and been discovered as far north as Cairns.
It has since spread across the Australian landscape and now flourishes in bushland reserves, backyards, commercial operations, nature strips and park lands alike.
With the exception of South Australia, it’s infiltrated every state including Tasmania, as well as the Tiwi Islands in the Northern Territory.
Authorities agree myrtle rust is now endemic and cannot be eradicated.
In South America, from where it originated, it’s relatively harmless. Not so locally, given that almost 80 per cent of Australian native trees belong to Austropuccinia psidii’s primary victim, the myrtaceae family.
Among 2000 Australian plants in total, the bottle brush, lemon myrtle, tea tree, lilly pilly, blackbutt and broad-leaved paperbark tree melaleuca quinquenervia are among its most vulnerable members.
According to the Invasive Species Council, myrtle rust could eventually universally “alter the composition and function of forest, woodland, heath and wetland ecosystems”.
It says the incursion “is about as bad as it can get for biosecurity in Australia”.
Federal Environment Minister Tanya Plibersek agrees a co-ordinated response is needed.
Rice is one of the most important food crops for billions of people but the plants are susceptible to a wide variety of diseases that are not always easy to identify in the field. New work in the International Journal of Engineering Systems Modelling and Simulation has investigated whether an application based on a convolution neural network algorithm could be used to quickly and effectively determine what is afflicting a crop, especially in the early stages when signs and symptoms may well be ambiguous.
Manoj Agrawal and Shweta Agrawal of Sage University in Indore, Madhya Pradesh, suggest that an automated method for rice disease identification is much needed. They have now trained various machine learning tools with more than 4,000 images of healthy and diseased rice and tested them against disease data from different sources. They demonstrated that the ResNet50 architecture offers the greatest accuracy at 97.5%.
The system can determine from a photograph of a sample of the crop whether or not it is diseased and if so, can then identify which of the following common diseases that affect rice the plant has: Leaf Blast, Brown Spot, Sheath Blight, Leaf Scald, Bacterial Leaf Blight, Rice Blast, Neck Blast, False Smut, Tungro, Stem Borer, Hispa, and Sheath Rot.
Overall, the team’s approach is 98.2% accurate on independent test images. Such accuracy is sufficient to guide farmers to make an appropriate response to a given infection in their crop and thus save both their crop and their resources rather than wasting produce or money on ineffective treatments.
The team emphasizes that the system works well irrespective of the lighting conditions when the photograph is taken or the background in the photograph. They add that accuracy might still be improved by adding more images to the training dataset to help the application make predictions from photos taken in disparate conditions.
More information: Shweta Agrawal et al, Rice plant diseases detection using convolutional neural networks, International Journal of Engineering Systems Modelling and Simulation (2022). DOI: 10.1504/IJESMS.2022.10044308
EPPO Reporting Service no. 11 – 2022Num. article: 2022/244
First record of sweet potato chlorotic stunt virus in the Netherlands
The NPPO of the Netherlands recently informed the EPPO Secretariat of the first finding ofsweet potato chlorotic stunt virus (Crinivirus, SPCSV – EU Annexes) in sweet potato (Ipomoea batatas) plants on its territory. SPCSV was found in September 2022 in two open fields in Noord-Brabant province (11.83 and 4.72 ha) and one in Limburg province (0.5 ha). The official survey was part of the Euphresco project ‘Phytosanitary risks of newly introduced crops’ (PRONC). Tracing back investigations to the origin of the finding showed that the sweet potato slips used for planting originated from a company in another EU Member State. Sweet potato is a new crop in the Netherlands. During the survey, plants with and without virus symptoms were sampled and tested. SPCSV was identified in several plants with virus-like symptoms (e.g. vein banding, discoloration, rings, dots). Additionally, in several of these symptomatic plants a second, non-EU listed, virus was identified: sweet potato virus G (Potyvirus, SPVG00). The mixed infection may have increased the severity of the observed symptoms.
Official phytosanitary measures have been taken. The companies have to report to the NPPO when all tubers of the Ipomoea batatas plants have been harvested and the total quantity thereof. All infected lots should be stored in a traceable manner, separately from other harvested lots. Only sales for consumption/industry are allowed, otherwise the lots have to be destroyed. The companies should report when the infected lots are sold or destroyed. The lots must be sold/destroyed before 31 March 2023.
The pest status of sweet potato chlorotic stuntvirus in the Netherlands is officially declared as: Transient, actionable, under eradication.
Up to 60 percent of the dried vine fruit in the Sunraysia region (southwestern New South Wales/northwestern Victoria) could be lost to the worst downy mildew outbreak in decades, triggered by recent rain. About 9000 tonnes of crops could be lost to the infection. The region produces 98 percent of the country’s dried vine fruit exports.
Dried Fruits Australia said the vines look quite good, but there are no bunches of grapes, they have dried up and fallen off. Some growers may not even harvest their grapes this 2022 season. Wine grapes have also been devastated by downy mildew. One grower said he has lost 70 percent of his wine crop
[Byline: Peter Sanders, Kellie Hollingworth]
— Communicated by: ProMED
[Downy mildew on grapevine is caused by the fungus-like organism (oomycete) _Plasmopara viticola_. It causes lesions on leaves which later become covered with white downy growth and turn necrotic. It can also affect flowers and fruits. Disease development is favoured by temperatures of 15 to 20 deg C (59 to 68 deg F) and moist conditions. In years with warm, extended wet periods during bloom, fruit clusters may be partially or totally destroyed. The disease can cause severe crop losses and occurs irregularly in most grape growing regions worldwide.
Spores are spread within a crop mainly by splashing rain, wind, or mechanical means. The pathogen survives between crops on infected plant debris as oospores, which are formed inside the host tissues. It is an obligate parasite and cannot be cultured in vitro. Disease management relies mainly on preventative fungicide applications according to forecasting services. Systemic fungicides are also available. All commercial grape cultivars are susceptible.
Downy mildews include many species of oomycetes in several genera which cause similar symptoms in a range of hosts, including many crops. Individual species usually have a narrow host range affecting only one or a few different hosts.
Abstract The role of rhizosphere microbiota in the resistance of tomato plant against soil-borne Fusarium wilt disease (FWD) remains unclear. Here, we showed that the FWD incidence was significantly negatively correlated with the diversity of both rhizosphere bacterial and fungal communities. Using the microbiological culturomic approach, we selected 205 unique strains to construct different synthetic communities (SynComs), which were inoculated into germ-free tomato seedlings, and their roles in suppressing FWD were monitored using omics approach. Cross-kingdom (fungi and bacteria) SynComs were most effective in suppressing FWD than those of Fungal or Bacterial SynComs alone. This effect was underpinned by a combination of molecular mechanisms related to plant immunity and microbial interactions contributed by the bacterial and fungal communities. This study provides new insight into the dynamics of microbiota in pathogen suppression and host immunity interactions. Also, the formulation and manipulation of SynComs for functional complementation constitute a beneficial strategy in controlling soil-borne disease.
Fruiting bodies of shaggy scalycap (Pholiota sp.) on a log just off the Appalachian Trail in Hanover, New Hampshire. Credit: Bala Chaudhary
New scientific review analyzes what we know about how fungi disperse.
When you say “fungi,” most people think of mushrooms, the fleshy fruiting bodies above the ground or food source, but most fungi do not actually produce mushrooms. Furthermore, of the estimated 3 to 13 million fungal species on Earth, many are microscopic in size, and therefore invisible to the naked eye.
Fungi live in a wide range of environments including in soils, inside the tissues of leaves in rainforests, and in deep oceans. Understanding how fungi move across a range of spatial scales is importantto understanding ecosystems and has significant implications for agriculture and human health, according to a new review published in the journal Annual Review of Ecology, Evolution, and Systematics.
Fungi are frequently associated with death and decay, such as mold that grows on old food, or mushrooms that decompose leaves on the forest floor. “We typically think of fungi as decomposers, but they are cryptic and do many different things,” says lead author Bala Chaudhary, an associate professor of environmental studies at Dartmouth. “Fungi can also function as nutrient cyclers, pathogens, and mutualists that live in a beneficial association with plants and other organisms.”
Fungi can also be human pathogens. For example, Coccidiodes is another soil-borne fungus that releases spores into the air as a result of land disturbance and soil degradation. When the spores of this fungus are inhaled, Coccidiodes can cause a serious respiratory disease called Valley fever, also known as coccidioidomycosis. Soil ecology, climate justice, and environmental health are three fields that interconnect and might benefit from a better knowledge of fungal dispersal.
“Experts working in agriculture, public health, and many other fields are interested in understanding fungal dispersal, as this information can be used to predict things like future crop pandemics and outbreaks of human disease,” says Chaudhary, who is an ecologist. “Furthermore, studying how fungi disperse is central to understanding fungal biodiversity and where species are distributed on Earth.”
Chaudhary’s co-authored analysis on how fungi disperse is the result of a collaboration with senior author Matthias Rillig, a professor of plant ecology at the Institute of Biology at Freie Universität Berlin, and members of his lab, during her sabbatical in 2019-20.
To synthesize existing information on fungal dispersal and highlight emerging research in this area, the team used a research-weaving approach that combines reviewing journal articles with analyzing trends in publishing, also known as “bibliometrics.” The team examined over 4,500 documents from nearly 1,200 sources from 1951 to 2021. Most of the articles pertained to fungal dispersal research in the United States, the United Kingdom, and China.
The researchers found that scientific literature on fungal dispersal has focused on three topical areas: fungal disease, including climate change, which was the most prominent theme represented; fungal diversity, communities, and mycorrhizal fungi, including soils and forests; and the evolution of fungi, including molecular methods.
As part of their analysis, the researchers pose theoretical relationships between the relative importance of vectors of dispersal and spatial scale and vectors of dispersal. They identified four scales of fungal movement from microscopic to landscape scales.
Tiny root-like structures of fungi at the mycelial level move through the soil on the smallest scale. Invertebrate animals, including micro/macroarthropods such as ants, and earthworms can transport fungi through their castings and nests, and small mammals and birds who may transport fungi via their feet, feathers, and digestive tracks serve as vectors for moving fungi at larger scales. Abiotic vectors, such as water and wind, are responsible for fungal movement at the largest scale across the landscape and continents. Rivers transport sediment containing fungi propagules across continents, ocean currents and tides, and precipitation, as well as humans, all play a role in the global transit of fungi.
“With climate change, environments are getting dryer in some regions and wetter in others, factors that can change where fungi reside,” says Chaudhary. “Soil disturbance from agriculture, land development, and other human activities can also release soil fungi into the air.”
“Climate change, coupled with anthropogenic land use, can really impact the way that fungi move. The relative importance of movement vectors changes across spatial scale, but there’s very little data to support these relationships,” she says.
“More data is needed to understand the biodiversity of fungi and the many factors affecting their movement in our ecosystems.”
Reference: “Fungal Dispersal Across Spatial Scales” by V. Bala Chaudhary, Carlos A. Aguilar-Trigueros, India Mansour and Matthias C. Rillig, 25 July 2022, Annual Review of Ecology Evolution and Systematics. DOI: 10.1146/annurev-ecolsys-012622-021604
Carlos Aguilar-Trigueros and India Mansour at the Institute of Biology at Freie Universität Berlin also contributed to the study.
Editor’s note: This is the first in a two-part series about plant diseases on Guam and Micronesia.What happened to the huge, lush, towering, 100-year-plus gagu, or ironwood trees, that commonly dotted the island’s landscape at the University of Guam, Tiyan, Windward Hills Country Club golf course and elsewhere?
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Andersen Air Force Base’s Palm Tree Golf Course won an environmental innovation award for its handling of the coconut rhinoceros beetle.
Known by its scientific name Casuarina equisetifolia, ironwood trees are tightly integrated into Guam’s environment and local culture.
It is a hardy, pioneer, salt-resistant tree that occurs on the island’s main soil types: limestone, volcanic, and coral sand. It is propagated for windbreaks, erosion control, and urban landscapes.
Because C. equisetifolia is the dominant tree species on many of the sandy beaches of the Mariana Islands, it has become an important perching tree for the white-collared kingfisher (Halcyon chloris), the Mariana fruit-dove (Ptilinopus roseicapilla), and the white fairy tern (Gygis alba), which commonly lays eggs in the trees.
It has been continually propagated since the 1600s. Due to its buoyant cones, it likely floated to Guam’s sandy beaches thousands of years ago on currents from the central Indo-Pacific coastline.From these cones, seeds were shed and grew into trees. Over time, ironwood became one of Guam’s prominent members of the halophytic (sea-salt adapted) vegetation type.Based on what we now know, Guam’s healthiest trees tend to occur in natural areas, near the coastline and in areas not prone to drought.Cocos Island and Ritidian are just a few of the places where healthy coastal stands of ironwood can still be found.
Huge, healthy ironwood trees still dominate the shoreline of Ritidian Point in northern Guam.
Courtesy of Elizabeth Hahn
Farmer seeks help
In 2002, local grower Bernard Watson contacted University of Guam professor Robert Schlub about a group of five ironwood trees in one of his windbreaks that exhibited symptoms of rapid yellowing and death. Death occurred within a few weeks of symptom onset.This was totally unexpected because the trees in question were only 10 years old.Cross-sections of these trees exhibited areas of wetwood that were dark, water-infused, and radiated from their centers. Droplets of bacterial ooze appeared inside and outside the wetwood stained areas.Also appearing on Watson’s farm in 2002 were trees with the same cross-sectional symptoms but this time it was accompanied by thinning foliage and a much slower lethal decline.
This latter condition was quickly discovered in other areas of Guam and was coined “ironwood tree decline” by Schlub and Zelalem Mersha, a former UOG post-doctoral fellow now working as a Virginia State University research and extension plant pathologist.Unraveling the cause or causes of IWTD would become a major focus of Schlub’s work at the University of Guam for the next two decades.In the course of the investigation, the Guam team would join forces with researchers from institutes in California, Georgia, Florida, Hawaii, Louisiana, South Africa, China and Australia.Many possible causes of IWTD have been eliminated by the team over the years.
Links to the disease
Age was ruled out as an IWTD contributor, when trees of varying ages began dying in areas where decline was most severe. The failure to find a correlation between the presence of beetles or nematodes (microscopic worms) ruled them out as causing IWTD.The normal appearance of tree buds and young foliage eliminated the likelihood of viruses being involved.Seeing no link between typhoon damage and decline in tree surveys in 2008 and 2009, Typhoons Paka in 1997 or Pongsona in 2002 were eliminated as causing Guam’s ‘sick’ trees.
Over time, five things were consistently linked to IWTD: The presence of termites on the side of trees. The occurrence of wood-rot fungi at the base of trees.The exposure of trees to harmful landscaping practices and the presence of bacterial ooze in tree cross-sections caused, namely the bacteria that causes wetwood and the bacteria that causes bacterial wilt.Bacterial wilt is caused by bacteria within the Ralstonia solanacearum species complex.
Trees decline in 13 years
We now know that Guam’s wilt pathogen strain is the same one that has been killing trees in China and India for decades.One of the team’s most recent projects included a resurvey of 200 trees that were part of a survey of 1,427 conducted in 2008-09. The project was funded by the McIntire-Stennis Cooperative Forestry Research Program (project GUA932, accession no. 1017908), under the U.S. Department of Agriculture’s National Institute of Food and Agriculture.The results suggest that the decline of Guam’s ironwood trees that began in 2002 is continuing to this day, and that trees with severe wilt symptoms or that are nearly dead have high bacterial wilt infection levels.From the data, it is reasonable to expect that half the trees that appear healthy today in areas of decline such as at the University of Guam campus or Fort Soledad will begin showing symptoms of decline over the next 13 years and that trees already suffering from IWTD will likely be dead or nearly dead within the same time period.
Foliage thinning is one of the ominous signs that this ironwood tree on the University of Guam campus is suffering from decline.
Courtesy of Elizabeth Hahn
How you can help
Several steps have been taken to reduce the impact of IWTD.Hundreds of trees from various countries have been planted to add new genes to Guam’s tree population through cross-pollination.Some of these trees have been used to establish new ironwood windbreaks and others have been used as replacement trees in windbreaks with high levels of decline.Professionals and the general public are now being advised to reduce lawnmower and weed-trimmer damage to roots and the base of trees as a means to reduce infection and spread of fungi and bacteria.
To reduce transmission of Ralstonia and wetwood bacterial ooze when pruning, individuals are instructed to disinfect all tools.
Huge, healthy ironwood trees still dominate the shoreline of Ritidian Point in northern Guam.
Courtesy of Elizabeth Hahn
The public is also being advised to remove severely declined trees as a means to protect nearby healthy trees.Planting healthy, young trees of different varieties or hosts is the quickest way to restore areas with high decline.
Robert L. Schlub is a plant pathology professor and extension specialist, and Elizabeth Hahn and Julia Delorm are extension associates with the Cooperative Extension Service at the University of Guam’s College of Natural and Applied Sciences.
