Archive for the ‘Bacteria’ Category

SEPTEMBER 14, 2022

Can wild potato relatives help tame zebra chip disease?

by Paul Schattenberg, Texas A&M University

Can wild potato relatives help tame zebra chip disease?
Kranthi Mandadi, Ph.D, a Texas A&M AgriLife Research scientist at the Texas A&M AgriLife Research and Extension Center in Weslaco, was the primary investigator for the new zebra chip-related study. Credit: Texas A&M AgriLife photo

A new study led by Texas A&M AgriLife researchers has revealed some resistance to zebra chip disease among certain wild species of potato.

The study of 52 wild potato species—of which one accession was resistant and three were tolerant to the disease—took place as part of an effort to identify novel genetic resistance to the disease, which affects potato production worldwide.

The study, “Identification and Characterization of Potato Zebra Chip Resistance Among Wild Solanum Species,” appeared recently in the journal Frontiers in Microbiology.

The primary investigator for the study was Kranthi Mandadi, Ph.D., a Texas A&M AgriLife Research scientist at the Texas A&M AgriLife Research and Extension Center at Weslaco and associate professor in Texas A&M’s Department of Plant Pathology and Microbiology.

Study co-investigators include Isabel Vales, Ph.D., AgriLife Research associate professor and potato breeder, Bryan-College Station, and Carlos Avila, Ph.D., AgriLife Research associate professor and vegetable breeder, Weslaco, both in the Department of Horticultural Sciences; and Freddy Ibanez, Ph.D., an AgriLife Research scientist at the center and assistant professor in the Texas A&M Department of Entomology.

Others involved in the study were Texas A&M AgriLife Research scientists Victoria Mora, M.S., Manikandan Ramasamy, Ph.D., Mona Damaj, Ph.D., and Sonia Irigoyen, Ph.D., at the Weslaco center, as well as Veronica Ancona, Ph.D., a plant pathologist and associate professor at Texas A&M University-Kingsville.

“This type of outcome was precisely what AgriLife Research envisioned when we decided to fund Insect Vector Diseases Seed Grants,” said Henry Fadamiro, Ph.D., chief scientific officer and associate director, AgriLife Research, and associate dean, Texas A&M College of Agriculture and Life Sciences. “We would like to thank the Texas Legislature for funding AgriLife Research’s IVD Exceptional Item Request that has made these seed grants possible. Their continued support is invaluable.”

What is zebra chip disease?

Zebra chip is a complex disease due to its association with the unculturable bacteria Candidatus Liberibacter solanacearum and transmission by an insect vector, the potato psyllid. First reported in Saltillo, Mexico, and subsequently in South Texas, the disease was detected in many other states and commercial potato-growing regions of the world. Left unchecked, it can result in potato yield losses of up to 94%.

Can wild potato relatives help tame zebra chip disease?
Potato tubers affected by zebra chip disease are of poor quality, have a bitter taste and display dark brown zebra-like patterns when fried. Credit: Texas A&M AgriLife photo

Above-ground symptoms of zebra chip-affected plants include purplish discoloration of young leaves, upward rolling of top leaves, the presence of aerial tubers, wilting, stunted growth and plant death.

“Zebra chip-affected tubers are of poor quality, exhibiting vascular ring browning and brown flecks,” Mandadi said. “These chips also have a bitter taste and dark brown striped, zebra-like patterns when fried.”

He said the disease ultimately lowers yield and tuber quality becomes unmarketable.

“If left uncontrolled, the disease can become a significant detriment to potato production.”

Why the study?

The potato is cultivated in over 160 countries and is considered the fourth most important staple food crop after wheat, corn and rice. It is a rich source of carbohydrates and provides other essential nutrients, such as dietary fiber, vitamins, minerals, protein and antioxidants.

“The potato is an important food crop worldwide,” Mandadi said. “As the demand for fresh and processed potato products increases globally, there is a need to manage and control emerging diseases such as zebra chip.”

In Texas, potatoes are grown in all regions that have a significant amount of commercial vegetable production. Commercial acreage for potato production is found in the South Plains, Panhandle and Rolling Plains, as well as the Winter Garden and Rio Grande Valley areas.

“In Texas, we have been dealing with the zebra chip issues for more than 20 years,” Vales said. “Over that time, the disease has become pervasive and has expanded not only in this state but also in other potato-producing states.”

Can wild potato relatives help tame zebra chip disease?
The Texas A&M AgriLife-led study involved the assessment of plant material from 52 wild potato accessions. Credit: Texas A&M AgriLife photo by Kranthi Mandadi

The bacterium and the insect vector associated with zebra chip disease can also affect other vegetable crops and produce, including tomatoes, peppers and carrots.

Vales said current zebra chip management strategies revolve primarily around controlling the psyllid vector with insecticides or by altering cultural practices, such as timing planting dates to delay exposure to the psyllid population.

“But both of these have only marginal benefits, and while using chemical measures has helped control the psyllid population, this approach is associated with high costs and the potential for increased insecticide resistance,” she said. “That’s why identifying and breeding novel genetic resistance and tolerance to the zebra chip is another important avenue to achieve integrated pest management.”

Vales said previous studies have reported variations in the psyllid’s preference for wild potato species and their breeding clones.

The study results

“For the past four years, our team has been studying approaches to control zebra chip disease thanks to seed funding from projects associated with the Insect Vector Diseases Grant Program,” Mandadi said.

The plant material of 52 wild potato accessions belonging to a Solanum sect. Petota diversity panel, grown from true potato seeds obtained from the U.S. National Plant Germplasm System in Wisconsin, was used in the study.

“New sources of zebra chip resistance were identified among a wild collection of tuber-bearing Solanum species present in the Petota panel,” Mandadi said. “This panel of wild potato is a taxonomically well-characterized and diverse collection from which one can mine for valuable potato traits.”

Several of the 52 accessions were susceptible and moderately susceptible, showing some upward leaf rolling, chlorosis and plant stunting, Mandadi said.

Can wild potato relatives help tame zebra chip disease?
According to the study, the S. berthautii wild potato accession, shown here, demonstrated zebra chip psyllid resistance. Credit: Texas A&M AgriLife photo by Kranthi Mandadi

“But following the screening, phenotypic evaluations and quantification of the bacteria in the accessions infected with bacteria-carrying psyllids, we identified one zebra chip resistant accession, Solanum berthaultii, along with three other accessions that were moderately tolerant to zebra chip.”

The three accessions identified in the study as moderately tolerant to zebra chip were S. kurtzianum, S. okadae and S. raphanifolium.

Mandadi’s team also found S. berthaultii has dense glandular leaf trichomes, and this foliar structural modification could be one factor responsible for much of the observed zebra chip resistance.

“The foliar portion produces a sticky substance that seems to trap the psyllid to the plant when it comes in contact with it,” Mandadi explained. “As a result, many psyllids die before reproducing, thus reducing transmission of the bacterium into plants.”

He noted the S. berthautii wild potato accession originated in Bolivia, which is adjacent to Peru, historically identified as the ancestral “birthplace” of the cultivated potato.

He said S. berthaultii is a promising source for zebra chip psyllid resistance that can be further studied to understand insect resistance mechanisms and incorporated into the potato production system.

“It could possibly be used in breeding new potato cultivars or even as a ‘trap crop’ that can be planted next to more traditional potato cultivars as a way to help eliminate psyllids,” Mandadi said.

He also noted that similar approaches in identifying novel genetic resistance and tolerance in wild plant species could help control other devastating crop diseases, such as potato late blight, citrus greening, Pierce’s disease of grapes and banana wilt.

Explore further

New variety of zebra chip disease threatens potato production in southwestern Oregon

More information: Victoria Mora et al, Identification and Characterization of Potato Zebra Chip Resistance Among Wild Solanum Species, Frontiers in Microbiology (2022). DOI: 10.3389/fmicb.2022.857493

Provided by Texas A&M University 

Read Full Post »

Penang paddy farmers suffer losses due to bacterial blight


  • Wednesday, 10 Aug 202212:22 PM MYT

Azahri Hariff holding up stalks of affected rice plants. BPB has left much of his crop half-filled or empty of grain.

BALIK PULAU: More than 50 rice farmers in the Sungai Burung area here have to bear losses after more than 121ha of rice fields produced half-filled or empty grain, following an attack of ‘hawar bulir bakteria’ (bacterial panicle blight or BPB).

This grim situation has affected the paddy farmers’ income and is even more distressing when it happens when they need money for daily expenses during the post-pandemic recovery phase.

One of them, Azahri Hariff, 44, who cultivates 14ha of rice fields in Sungai Burung said that every season he would spend RM60 thousand on his land to cultivate paddy.

However, when he checked his paddy fields recently, he found that most of the plants were attacked by BPB disease which would affect the production of rice.

“Every rice harvest season, I can produce between 80 and 90 tonnes of rice but this season the production is affected due to the disease.

“I believe that the BPB disease that is attacking the rice fields in the Sungai Burung area is caused by the unpredictable weather changes that are currently affecting the country,” he told Bernama recently.

He added that he was concerned to see the condition of the paddy fields in the area that were attacked by BPB disease and farmers such as himself would suffer losses.


Top five courses at University of Nottingham Malaysia

Azahri hoped that the Ministry of Agriculture and Food Industries could help paddy farmers whose income was affected by the disease.

Another rice farmer in Sungai Burung, Talib Hamid, 70, claimed that this season he only managed to harvest five tonnes of rice from his 2.02 hectare of land, compared with the usual 15 to 16 tonnes.

Talib said that this was the first time his paddy was attacked by the disease which affected his rice yields. – Bernama

Subscribe now to our Premium Plan for an ad-free and unlimited reading experience!

TAGS / KEYWORDS:Paddy Field , Rice , Sungai Burung , Disease ,  Hawar Bulir Bakteria ,  Bacterial Panicle Blight ,

Read Full Post »

Cousin of crop-killing bacteria mutating rapidly

Citrus-destroying bacterial relative may also be infectious


August 12, 2022



A bacterial species closely related to deadly citrus greening disease is rapidly evolving its ability to infect insect hosts, and possibly plants as well.

Asian citrus psyllid
Asian citrus psyllids, which transmit Liberibacter bacteria to citrus trees. The new Liberibacter species was found in a related type of psyllid. (California Department of Food and Agriculture)

The newly identified species belongs to Liberibacter, a family of bacteria known to infect several economically important crops. There are nine known Liberibacter species, including one that infects potatoes and three that are associated with citrus greening. 

Citrus greening, also known as Huanglongbing, is the number one killer of citrus trees worldwide. Though many are working on solutions, there is presently no effective prevention or treatment option on the market. 

Given its relatives’ destructive qualities, UC Riverside scientists set out to understand the ways the new species, L. capsica, genetically resembles other types of Liberibacter. 

“As with new strains of COVID-19, bacteria become variants of concern if their mutations can impact pathogenic or transmissible properties,” said Allison Hansen, UCR entomologist and study lead. 

Peppers like the ones in Brazil on which a pair of psyllids were found harboring L. capsica.

Many Liberibacters share genes that enable their ability to live inside a host. 

“These bacteria acquire DNA from their hosts, so without a host, they’re gone, they will die,” Hansen said. 

For this study, the research team identified 21 genes in L. capsica that are rapidly evolving amino acid mutations associated with infectious qualities. This evolution is documented in a new Microbiology Spectrum journal paper

One subset of mutations the team found repeatedly are on genes affecting pilus, tiny bacterial “hairs” that allow the bacteria to move into host insects and uptake DNA. Insects then transmit the bacteria to plants.

L. capsica was found by chance in a pair of flying insects on a pepper plant in Brazil. These insects, psyllids, are known pepper pests. However, it’s not yet known whether L. capsica infect peppers or other crops.

Gathering direct evidence about whether the bacteria infect pepper tissues may prove difficult, as Hansen’s team only had a single sample, and L. capsica cannot be grown in a laboratory.

The psyllids were collected in Brazil by Diana Percy, an entomologist at the University of British Columbia and Hansen’s frequent collaborator. Percy travels the world searching for psyllids but did not know these would harbor novel bacteria. That discovery was made in Hansen’s laboratory after Percy shared the psyllids she obtained abroad.

potato psyllid
The potato psyllid infects a potato plant with L. solanacearum, the bacteria causing zebra chip disease. (Whitney Cranshaw/Colorado State University)

“We’re informing scientists in Brazil and other places to screen plants for it,” Hansen said. “It should be on everyone’s radar for outbreak potential given the propensity of Liberibacter for being serious plant pathogens on domesticated crops.”

Integral to this study was the work of Ariana Sanchez, a UCR undergraduate microbiology major interested in bacterial pathogens transmitted by insects. Sanchez is the entomology department’s first Inclusivity Scholar. 

The department created the Advancing Inclusivity in Entomology scholarship in response to the Black Lives Matter movement and death of George Floyd in 2020. Faculty recognized the need to support students from marginalized groups who have a passion for studying insects but face systemic barriers excluding them from research opportunities. 

By helping identify the ways in which L. capsica is evolving, Sanchez has made an important contribution to Liberibacter knowledge. 

“Being able to understand pathogens like these, and how they interact with the insects that carry them, is so critical for the security of our food supply,” Hansen said. 

Cover image: Fruit infected with citrus greening. (emarys/iStock/Getty)



Read Full Post »

Soil Health and Pest Management: Challenges in the European Union



Jackie Pucci of AgriBusiness Global sat down with Dr. Arben Myrta, Corporate Development Manager with Certis Belchim B.V., based in Italy, to discuss developments in soil health and pest management solutions at the company and wider trends he is witnessing in the space.

Dr Arben Myrta, Certis Belchim B.V.
Quality produce with good soil pest management
Damage by Fusarium wilt in melon
Destroyed tomato plants from the attack of Meloidogyne spp.
Damaged roots of tomato by the nematode Meloidogyne spp.
Nematode damage in carrots from Meloidogyne spp.

Can you talk about some of the key developments in ‘soil health management’ in agriculture and what is driving adoption in Europe?

Soil health in its broad scientific definition considers its capacity, thanks to biotic and abiotic components, to function as a vital living ecosystem to sustain plants and animals. A soil may be healthy in terms of the functioning of its eco-system but not necessarily for crop production. In agriculture, good soil pest management remains a cornerstone for the quantity and quality of production at farm level. When farmers cultivate the same plants for a long time in the same soil without crop rotations or other agronomic measures, the soil starts to evidence nutritional and phytopathological problems for the plants. This is more evident in horticulture, and particularly, in protected crops in Europe, where this problem is of major importance.

In the past, in Europe, soil pest management in horticulture was mostly covered by chemical fumigation, lead first by methyl bromide (MB). MB was later globally banned for depleting the ozone layer, while other fumigants, which were intended to replace it, were not approved during the regulatory renewal process, thus creating a gap between the farmers’ needs and the possibilities to have adequate solutions for their cropping.  Meanwhile, in the last decades there has also been huge progress in research and technology, developing more effective biorational soil products (beneficial microorganisms, such as fungi, bacteria, etc.., plant extracts, etc..) and increased public awareness around human health and the environment, followed by more restrictive legislation on the use of chemicals in agriculture.

Driven by the legislation and the general attention of society on the use of plant protection products in agriculture, the industry has been proactive in looking for new solutions with safer tox and eco-tox profile, focusing on biorational products, whose number, as new plant protection products for the control of soil-borne pests and diseases, is continuously increasing in the EU.

How important do you see soil health and soil pest management in the complete picture of agricultural productivity, and how has that view changed?

Soil health and good soil pest management practices in crop production have always been considered important. In Europe, the level of attention and knowledge on this topic has been higher among professionals and farmers working in horticulture, the ornamentals industry, nurseries and particularly protected crops, basically everywhere where long crop rotations are not easily practiced, and pest-infested soils become a big problem for the farmers.

The rapid banning or limitation of several traditional synthetic products used to control soil pests raised the question for field advisors and farmers of how to deal with soil problems in the new situation. In recent years European farmers have been facing particular difficulties in controlling plant-parasitic nematodes.

Biorational products available today in EU countries represent a very good tool for the management of several soil pests in many crops and targets, but are still not sufficiently effective to guarantee full satisfaction to the growers in important crops like protected fruiting vegetables, strawberry, carrots, potato, ornamentals, etc., which explains why ‘emergency uses’ are still granted at EU country level following the request of grower associations to cover the needs of their farmers. The continuous increase in the numbers of new biorational products in the future, and particularly the innovative formulations that will follow, will be of paramount importance for their role in soil pest management.

A second, but important obstacle, is the generally limited knowledge on soil components (including its fertility and capacity to suppress pests by beneficial microorganisms) and the correct use of the biorational products, which cannot be expected to be effective quickly or be used as solo products, as the ‘old’ chemicals were. They should be seen more in programs with other soil management solutions, as recommended by the integrated production guidelines. Here, a further important obstacle is the lack of an effective public extension service to advise farmers, which is limited or totally lacking in many European Countries.

Everybody in the EU is now convinced that soil management in the future will rely on biorational and integrated solutions, but the question is how to reach this objective gradually, being pragmatic and reliable, balancing the environmental, economic and agricultural perspective. Legislation always steers the direction of progress but should be carefully considering the real product capabilities to make it happen in a short time and not focusing on ‘emergency situations’ as has now been the case for more than a decade.

What are some of the perceptions, either correct or incorrect, and other challenges you are dealing with in the region with respect to products for soil health?

This market has seen a rapid change from chemistry to biorational solutions, but in the meantime is facing a lot of challenges in order to meet the expectations of the farmers for quantity and quality of produce. This topic is widely discussed in dedicated scientific forums like that of the International Society of Horticultural Sciences, of which the last International Symposium on Soil and Substrate Disinfestation was held in 2018 in Crete, Greece. A dedicated round table was organized with soil experts to discuss the important challenges faced by the European growers due to the lack of plant protection solutions for an effective control of several soil pests, most of all nematodes. I participated in that round table discussion, whose main conclusions were the following concerns, considered as target actions for the scientific community:

  • the farmer needs various tools for soil disinfestation (SD) in the light of the limited current arsenal of SD tools;
  • the lengthy and unpredictable European registration process (sometimes more than 10 years from dossier submission to the first national approval) of new plant protection products (including biorational) and the cautious approach of EU regulation, as well as restrictions imposed, has led to a reduction of active ingredients available in the past years;
  • a more effective and faster evaluation system is needed, especially for naturally occurring and low risk products (biological, plant extracts, etc.). That is, all products which are essential for Integrated Pest Management (IPM) programs;
  • following the implementation of Regulation EC 1107/2009, the only tool available to fill the gaps in local production systems is Art. 53 of the above-mentioned Regulation, which provides “derogations” for exceptional authorizations of plant protection products. Such authorizations increased exponentially in the last years, indicating that existing solutions in the European market are not considered sufficient;
  • the above-mentioned EU Regulation has a high socio-economic impact on various production systems in Europe and a Spanish case shows clearly the importance of maintaining a sustainable agricultural activity in local communities that, in the case of protected crops area, includes 13% of the active population employed in agriculture;
  • several European agricultural sectors are affected as the EU authority is allowing increased importation from extra-EU countries, considered unfair competition due to their more flexible registration system for plant protection products than that of the EU;
  • reduced capacity of soil pest research, where experts are retired and not being replaced, alongside weak, or in many areas non-existent, extension services together are causing the loss of soil knowledge and good advice for our farmers. Today, soil diagnosis is frequently completely lacking or insufficient before any soil pest and crop management decisions are taken.

The clear message from the scientific experts at that meeting was that these issues must be correctly addressed at all levels of stakeholders, in such a way that all available tools, including sustainable use of soil disinfestation, may be used in a combined IPM system to allow sustainable production in Europe.

What are some of the most exciting developments at Certis Belchim in soil health and pest management?

Since the establishment of Certis Europe in 2001, we have focused on soil pest and disease management. In 2003, Certis built the first CleanStart program providing integrated solutions for sustainable soil management, combining cultural, biological and chemical approaches. After more than a decade, in the mid-2010s, the CleanStart integrated approach started combining biological and chemical inputs with agronomic services (training to farmers and field advisors, soil pest diagnosis support for partner farms and stewardship product advice for applicators and/or farmers) to provide sustainable soil management for the future, aligned with the principles of the Sustainable Use of pesticides as per the EU Directive. All these activities were carried out successfully thanks to a wide international network created with many research institutes across Europe on soil pest management topics. This approach facilitated our participation in soil research projects funded also by the EU. Thanks to this experience we have been able to prepare and share many publications and communications, in particular the coordination for several years of an International Newsletter on Soil Pest Management (CleanStart).

Last year we were also granted a SMART Expertise funding from the Welsh Government, which is co-founded by Certis, in a research project lead by Swansea University, with Certis Belchim B.V. the industry partner, alongside major Welsh growers, Maelor Forest Nurseries Ltd and Puffin Produce Ltd. This project, now ongoing, looks to develop new and innovative products to control soil pests, primarily nematodes.

Thanks to this team involvement on soil topics, our present soil portfolio includes several biorational solutions such as Trichoderma spp. (TriSoil), Bacillus spp. (Valcure), garlic extract (NemGuard), etc. and this is continuously increasing through our research and development pipeline. With the soil biorational products we have developed a good knowledge not only on the products, but also in their interaction with biotic and abiotic soil components and with other similar products.

Our new company, Certis Belchim, in the future will continue to be particularly interested in this market segment and will be focusing mostly on biorational products. Our plans mainly encompass: (i) label extension to more crops and targets for the existing products; (ii) development and registration of new active ingredients for the control of soil borne pathogens, insects and nematodes; (iii) development of innovative formulations for soil use with focus on slow-release; (iv) field validation of effective programs with bio-solutions and other control methods.

In all these research and development activities, supported by the long experience we have in such topics, we are looking to generate our own IP solutions for soil pest management.

How have you seen this space evolve over the past of years, and what are you expecting the next years will bring?

From a technical perspective, we expect the nematode problems to increase globally in the future. This is due in part to the gradual global increase in average temperature, now recorded over recent decades, which will allow the most damaging nematodes, Meloidogyne spp., to establish at higher elevation and higher latitudes while in areas already infested, they will develop for a longer damaging period of time, thus leading to larger nematode soil population densities by the end of the crop cycle and, in turn, to greater damage to the succeeding crops.

From a regulatory perspective in Europe, if the approval process for new effective nematicides is not shortened and remains as restrictive as today, less effective solutions will be available, and there will be more reductions in rates and crops on which their use is permitted (e.g. not every year). This again will certainly lead to an increase in the severity of the nematodes that in many areas could be overlooked.

From a quarantine perspective, the globalization of trade has facilitated the introduction into Europe of new damaging nematodes and diseases and pests in general, events which are expected to increase in the future. The most critical situation can occur in protected and nursery crops, and for the production of healthy propagating material of annual crops, such as potato seed, bulbs and seeds of bulbous plant crops, including flowers, strawberry runners, woody nursery plants, of both crop and ornamental plants, and in all crops for which quarantine issues must be considered, especially when seeds, bulbs and any kind of plant propagating material are to be exported out of the EU.

The expectation is also that positive results will come from public research (more focus on resources is needed) and private industry where work is ongoing to bring to the market new biorational solutions and innovative methods with higher efficacy in controlling soil pests and to fulfill the increasing needs of this market. However, this will only be realized if regulatory hurdles are reduced in the EU, for example for low risk biorational solutions.

How are external factors (e.g., soaring input costs) impacting the adoption of these products?

Today agriculture and plant protection products, like the whole economy, are affected by higher prices due to the increased cost of energy and raw materials globally. Considering that the costs in agricultural production are already high and sometimes, those of soil pest control are not applicable for several crops, any further increase in production costs may lead to the abandonment of effective solutions, resulting in additional increase in the complexities of soil problems on our farms. This trend, if allowed to persist, will severely affect our agricultural sector.

This said, there will also be a potential increase in the new solutions entering the market in the coming years, which will face higher costs during development and the registration process as well.

From a technical perspective, the only way to reduce such risks is to support farmers with the right knowledge on how to use new soil products correctly (dose rate, timing and method of application, etc..) and increase cost effectiveness.

Can you share highlights of research and case studies that your company has conducted with respect to soil health?

Our company has been involved in many research and market studies dedicated to the soil pest management sector. The last important one was ‘Sustainability of European vegetable and strawberry production in relation to fumigation practices,’ prepared by a European team of independent soil experts. The aim of the study was to understand technically the role and economic impact of chemical soil fumigation in key European areas of vegetable and strawberry production. Three cases of representative crops were investigated: strawberries, solanaceous/cucurbitaceous crops cultivated under protected conditions and carrots as a relevant open field crop.

The study concluded that vegetable production is a key agricultural sector in Europe: including high-value crops like solanaceous and cucurbitaceous crops produced under protected conditions (tomatoes, peppers, aubergines, courgettes, cucumbers and melons), carrots and strawberries, the production value at farmer level is €12.5 billion; the cultivated area involved is roughly 330,000 ha. The importance of these crops is even greater when the entire food value chain, in economic and social terms, is also considered.

High standards in terms of food quality/safety and certificated production, along with affordable consumer prices and consistent availability across the seasons are demanded of European vegetable production and, as a consequence, are the drivers for the growers who have to protect such crops effectively and economically. The growers face very significant issues deriving from soil-borne pests, which are the key limiting factor to achieving quality and economically sustainable yields. As strongly indicated by farmers and crop experts, among the soil-borne pests, nematodes present the most impactful and frequent challenges.

According to the survey carried out in key EU countries (Spain, Italy, France, Belgium,…), the most common soil management practices for vegetable crops and strawberries are: chemical fumigation, crop rotation, resistant cultivars and rootstocks, followed by soil-less systems, non-fumigant treatments, soil solarization, biological products, organic soil amendments, catch and cover crops.

This shows clearly that soil pest management today and in the near future will rely on IPM systems combining and rotating different management practices, with a different degree of implementation depending on the cropping system.

Read Full Post »

APRIL 18, 2022

Scientists record first case of harmful bacteria in ubiquitous weed found throughout US

by University of Florida

Scientists record first case of harmful bacteria in ubiquitous weed found throughout U.S.
Credit: University of Florida

Scientists at the University of Florida Institute of Food and Agricultural Sciences (UF/IFAS) have recorded the first North American case of a harmful phytoplasma disease known for its threat to fruit, vegetable and ornamental crops in South America and the Middle East.


To make matters worse, scientists confirmed the host for the disease to be one of the most noxious and rapidly spreading weeds commonly found in a wide range of environments throughout the United States and into Canada.

Findings of the “First report of ‘Cadidatus Phytoplasma brasiliense‘ in North America and in a new host, yellow nutsedge (Cyperus esculentus)” were just published in the journal Plant Health Progress.

“The host of the disease is known as one of the most widespread and problematic weeds found everywhere—called yellow nutsedge,” said Brian Bahder, assistant professor of entomology at UF/IFAS Fort Lauderdale Research and Education Center. “It is one of the most aggressive weeds that commonly grows in lawns, home landscapes, vegetable and flower gardens and agricultural systems.”

The phytoplasma species called Candidatus Phytoplasma brasiliense is documented in regions of Brazil and Peru to harm hibiscus, papaya and cauliflower. Subsequently, research showed the same species infects peaches in the Middle East country of Azerbaijan.

Bahder and his team confirmed the phytoplasma and host in Fort Pierce. They found it while conducting research for a different disease—lethal bronzing—that attacks palm trees. Scientists were surveying and testing samples of grasses in hopes of finding a reservoir for lethal bronzing.

Research has shown that the adult planthopper insect that carries lethal bronzing feeds on the palm’s canopy, and the nymphs have been recorded among more than 40 species of grasses and sedges.

Because of the close association of nymphs with grasses and sedges, speculation has risen about the ability of these plants to serve as a reservoir for the lethal bronzing phytoplasma, Bahder said.

For the survey, scientists sampled three of the most abundant weeds known to serve as a host to the nymphs, yellow nutsedge being one of them.

While testing the samples, three of the outcomes resulted in a positive result.

“We thought we had found lethal bronzing in one of the grasses, so we proceeded to genetically sequence the sample,” said Bahder. “The results confirmed it was not lethal bronzing but that it was another phytoplasma.”

The DNA sequencing of that specimen confirmed their findings of a new phytoplasma in this weed, recorded for the first time in North America.

Implications of the disease and its spread through this weed cause scientists to consider it a threat to agriculture and ornamental industries. UF/IFAS scientists are seeking funding for the next steps of research.

“The next logical step is to find out which insect is spreading the disease. The good news is that we caught this early,” said Bahder. “We don’t know if this is an isolated incident or if the insect is spreading in the grass, and if it will feed on the papaya, hibiscus or cauliflower—which are economically important in Florida. The point is that we don’t know the extent of this disease in Florida or what threat it poses.”

Explore further

Palm tree disease in Florida transmitted by traveling bug from Jamaica

More information: Brandon Di Lella et al, First report of ‘Candidatus Phytoplasma brasiliense’ in North America and in a new host, yellow nutsedge (Cyperus esculentus), Plant Health Progress (2022). DOI: 10.1094/PHP-03-22-0027-BR

Provided by University of Florida 


Feedback to editors


Two teams use neutral atoms to create quantum circuits



Theoretical model offers a new perspective on black hole formation and evolution



Researchers take a step toward creating an axle-rotor nanomachine



Nanocapsule carrying a CRISPR-Cas9 editing tool used for noninvasive brain delivery and tumor cell targeting

APR 21, 2022


Trichaptum mushrooms found to have more than 17,000 gender alleles

APR 21, 2022


Federal research funding has positive ‘ripple effects’10 HOURS AGOBreakthrough in estimating fossil fuel carbon dioxide emissions10 HOURS AGOA roadmap for deepening understanding of a puzzling universal process11 HOURS AGOScientists turn a hydrogen molecule into a quantum sensor11 HOURS AGONew hardware integrates mechanical devices into quantum tech11 HOURS AGOLogging ‘amplified’ severity of Black Summer bushfires11 HOURS AGO

Relevant PhysicsForums posts

How can an event which has length and time have L = 0.


Collection of Lame Jokes


Today I learned


Tension between two rigid bodies


LHC starts up in 2022


Calculation of electric flux on trapezoidal surface


More from Physics Forums | Science Articles, Homework Help, Discussion


Read Full Post »

Getting to the Bottom of Common Scab in Canada


 Ashley Robinson


February 28, 2022

 Facebook Twitter Linkedin Email Print

The first national common scab research project has the Canadian potato industry seeing common scab in a whole new light.

Tubers across Canada have fallen victim to a bacterium lurking in the soil for years. When soils are dry, brown lesions appear on potatoes. And while these spuds can still be eaten safely, the lesions in some cases cut deep holes in them and cause problems for the industry.

While some research has been done in Canada on the potato disease common scab, there hasn’t been much done on a national level. It hasn’t just been one region of the Great White North affected by this disease, growers across the country have found themselves stuck with these ugly spuds.

For Tracy Shinners-Carnelley, vice president of research, quality and sustainability at Peak of the Market in Manitoba, and Newton Yorinori, director of plant breeding, seed development and research at Cavendish Farms in Prince Edward Island, they knew something needed to be done on a national level to address common scab.

At the time, the Canadian Potato Council (CPC) was looking for research projects to focus on. The group was applying for cluster projects funded by the Canadian Agricultural Partnership (CAP) with the Canadian Horticultural Council. Shinners-Carnelley and Yorinori thought a closer look at common scab was a good fit for the cluster projects.

“In Ontario, Prince Edward Island and New Brunswick, they had worked on scab a lot. But we hadn’t and my first thought was well, who do I know that’s been active in this research space? And that’s Claudia,” Shinners-Carnelley explains in a phone interview. “I was trying to find out what was already happening. And start to ask some questions about where we start potentially with some strategies around attempting to manage scab, which is always such a difficult one because there are no easy answers.”

Shinners-Carnelley and Yorinori approached Claudia Goyer, a research scientist at Agriculture and Agri-Food Canada (AAFC)’s Fredericton Research and Development Centre. They wanted to work with her to try and find a way to control the bacteria affecting potatoes.

What is Common Scab?

Common scab has been around for more than 100 years. It’s caused by a filamentous bacterium found in soil. When soil conditions are dry, it enters tubers through the lenticels making brownish lesions on spuds. As the potatoes grow the lesions become larger. As it’s a soil borne disease and a bacterium, Goyer says it’s harder to control as there are no chemicals available to control it.

“Once you have common scab in your fields, it’s really difficult to get rid of it. There’s different species that are causing common scab but the one that is found like pretty much everywhere in the world is Streptomyces scabies,” Goyer explains in a phone interview.

Claudia Goyer
Claudia Goyer holding potatoes with common scab symptoms. Photo: Julie Root

There are other species of common scab though that are found regionally, including Streptomyces acidiscabies and Streptomyces turgidiscabies. According to Goyer they all produce a group of plant toxins called thaxtomins — which is how common scab causes the brown lesions on potatoes.

Goyer notes the lesions aren’t dangerous to humans. Potatoes with common scab can still be consumed, however common scab makes them “ugly.” In the worse cases of common scab, the lesions can go deep making holes in the potatoes.

The industry rule is if more than five per cent of the surface of tubers are covered with common scab, they’re unable to be sold to the table market. Goyer says spuds with common scab are harder to peel, making them less desirable for the fry market also.

“It’s really an issue both for table and processing, then of course it’s even worse for seed production. They really don’t want common scab because nobody wants to spread that disease everywhere,” she adds.

Irrigation does help reduce common scab incidence though as it keeps soils from drying out, Goyer explains.

Searching for a Canadian Solution to Common Scab

In 2018, Goyer started on her common scab project. Working with collaborators in Manitoba, Ontario, P.E.I. and New Brunswick, they collected samples of potatoes with common scab symptoms for testing. Pathogens of common scab present in Canada were then isolated from infected tubers and characterized using molecular testing. So far Goyer says they have a collection of 300 isolates with at least 20 genetic groups.

“This shows that there’s a lot of diversity in the pathogens, which then might explain why we’re having so much trouble finding solutions to control the disease, right? Like it’s so widely different in how they behave, it becomes more difficult to find a control method that works everywhere,” she explains.

Goyer says the most common species found in Canada is Streptomyces scabies. Another species, Streptomyces acidiscabies, was also found to be present, but it’s more common in acidic soils and was first discovered in Maine.


After determining the genetic groups, Goyer and her team started to develop tools to look closer at how they are distributed across Canada. The group is also looking at ways to control common scab in fields.

Goyer says they’ve looked at how growing certain crops before potatoes can help hold soil moisture in to reduce common scab incidence. However, they’ve had trouble establishing the nurse crops. They have also tried beef manure compost, liquid mustard and peroxide based products.

“We also tried different fertilizer products like ammonium sulfate, which is supposed to make the soil more acidic. The common scab pathogen doesn’t grow well when it’s more acidic, so we thought perhaps this would help. And none of these really work,” she adds.

There have been two options which have shown promise though. They tried the biopesticide Serenade Soil in Fredericton and saw good results for several years. In Manitoba, it reduced common scab severity by 40 per cent compared to an untreated control. The best results were seen with an auxin product, 2,4-D, which is basically an herbicide Goyer says. Used in miniscule amounts applied as a fine mist in Manitoba, it reduced common scab severity and produced 69 per cent marketable tubers compared to less than five per cent in the untreated control.

“We’re now evaluating if we need to tweak how much 2,4-D to put in or maybe we need to apply it at a different time depending on the cultivars,” Goyer explains.

The project will complete its final year of trials in 2022 with full results released in 2023.

Common Scab Project Breakdown

  • Research team
    • Claudia Goyer with AAFC in Fredericton, N.B.
    • Martin Filion with Université de Moncton in New Brunswick
    • Tracy Shinners-Carnelley with Peak of the Market in Manitoba
    • Newton Yorinori with Cavendish Farms in P.E.I.
    • Rick Peters with AAFC in Charlottetown, P.E.I.
  • Provinces where trials are being done:
    • Manitoba
    • New Brunswick
    • Prince Edward Island

Header Photo — Potatoes with common scab symptoms on them. Photo: Claudia Goyer

Related Articles

Common Scab, a Problem without a Solution?

Combatting Common Scab

Cultivar and Common Scab

Read Full Post »

Copied from PestNet

Thursday, 17 February 2022 06:49:28

Grahame Jackson posted a new submission ‘ PANTOEA LEAF BLIGHT, RICE – CHINA: FIRST REPORT’




Source: Plant Disease [summ. Mod.DHA, edited]

Citation: Yu L, Yang C, Ji Z, et al. First Report of New Bacterial Leaf Blight of Rice Caused by _Pantoea ananatis_ in Southeast China. Plant Disease. 2022; 106 (1); doi: 10.1094/PDIS-05-21-0988-PDN.
In autumn 2020, leaf blight was observed on a number of varieties of rice (_Oryza sativa_) in Zhejiang and Jiangxi provinces. The disease incidence was 45-60%. The symptoms were assumed to be caused by _Xanthomonas oryzae_ pv. _oryzae_ (Xoo), the pathogen of rice bacterial blight.

Sixty-three isolates were obtained from collected diseased leaves. 16S rRNA sequence analysis from 6 isolates revealed that the amplified fragments shared 98% similarity with the _Pantoea ananatis_ type strain in GenBank. Analysis of further sequences and phylogenetic analyses was carried out. Based on the obtained morphological, physiological, biochemical, and molecular data, the isolates were confirmed as _P. ananatis_. Pathogenicity tests resulted in symptoms similar to those in the field.

_P. ananatis_ has previously been reported to cause grain discolouration of rice in the country, but this is the 1st report of _P. ananatis_ as the causative agent of rice leaf blight. This raises the alarm that the emerging rice bacterial leaf blight might be caused by _P. ananatis_, instead of Xoo as traditionally assumed. Further, the differences of occurrence, spread, and control between these 2 diseases will need to be determined.

Communicated by:

[_Pantoea ananatis_ symptoms in rice may include lesions on stems, stem necrosis, and leaf blight. The pathogen has also been reported to cause sheath and grain rot, as well as kernel discolouration. _P. stewartii_, previously known to occur on rice seeds, has also recently been associated with a leaf blight of the crop in Africa (ProMED post 20170504.5012251). Both species are considered emerging rice pathogens. The effects of different bacterial strains on hosts can vary dramatically. The bacteria are generally transmitted by insect vectors, plant material, and infected seed, making them a quarantine risk.

Species in the genus can cause diseases on a number of crops, such as Stewart’s bacterial wilt on maize and fruit bronzing of jack fruit (_P. stewartii_); leaf blights of cereals, including rice (_P. agglomerans_); pink disease of pineapple (_P. citrea_); brown stalk rot of maize (_P. ananatis_ and a novel _Pantoea_ species); and centre rot of onion (_P. ananatis_). A bacterial blight of _Eucalyptus_ and a leaf blotch disease of sudangrass have also been associated with _Pantoea_ species.

_Xanthomonas oryzae_ pv. _oryzae_ (Xoo) causes bacterial leaf blight (BLB) of rice. In Asia, millions of hectares of rice paddies are severely affected every year, with reported yield losses of up to 60% (e.g., see ProMED post 20211216.8700304). Xo pv. _oryzicola_ (Xoc) is the causal agent of bacterial leaf streak (BLS; e.g., see ProMED post 20210713.8514345), which is currently considered one of the most important emerging diseases of rice in the region. Xoc is thought to have originated in Asia but is now also spreading in Africa (e.g., recent 1st report from Senegal, see link below).

China provinces:

_P. ananatis_ symptoms on rice:

_P. ananatis_ on rice:
https://doi.org/10.1094/PDIS-94-4-0482B and
Information & review on _P. ananatis_:
https://doi.org/10.1111/j.1364-3703.2009.00542.x and
_P. ananatis_ taxonomy and strains:
https://www.uniprot.org/taxonomy/553 and
Description of genus _Pantoea_:
Information on _Pantoea_ species and subspecies:
http://www.bacterio.net/pantoea.html and
First report of Xoc in Senegal 2022:
Genus _Xanthomonas_ taxonomy, species & strains via:
– Mod.DHA]

Read Full Post »

Transforming tomatoes with molecular biotechnology

James Duduit, a Horticultural Science doctoral student, utilizes molecular biotechnology to transform tomatoes and improve the crop’s resistance to bacterial wilt and other common pathogens. Molecular biotechnology has many crop applications and is seen as a critical area of research because it increases the speed at which new varieties are developed.

Originally from Anderson, South Carolina, James Duduit studied Biology at Anderson University, where he graduated Magna Cum Laude, before attending NC State for his master of horticultural science degree. It was Wusheng Liu’s expertise in molecular biotechnology and translational genomics that convinced Duduit to stay and advance his doctoral degree.

James Duduit’s research efforts were recently awarded by U.S. Department of Education Graduate Assistance in Areas of National Need (GAANN) Program with a fellowship at NC State.

What brought you to NC State?
NC State seemed to have the broadest opportunities available for what I was interested in. The personnel with their diversity of expertise and experiences here has proven invaluable to my growth as an academic and scientist.

What are you doing now in research? What’s next?
My main focus right now is in trying to find a broadly applicable solution for the broad damage caused by bacterial wilt, especially in tomatoes. Using molecular biotechnology approaches, we hope that this economically devastating pathogen can be better mitigated. Another project that we are working on is related to a unique transformational technology for tomato and sweetpotato in order to increase the breeding speed with which new varieties can be developed. Our lab prioritizes biotechnological approaches to a broad diversity of horticulturally-relevant plants to overcome current challenges in pathogen/disease resistance, crop yield, transformation efficiency, and many other imposing but rewarding tasks.

How are you transforming challenges into opportunities?
Research is always a problem-solving process with unlimited challenges, but opportunities always naturally arise from these situations. I hope to critically think about each option and roadblock when performing experiments so that I can learn and make innovative and informative decisions throughout all of my actions. In addition, open communication with members of my lab and in the department allows a diversity of perspectives to be heard for more robust strategies to be employed.

What impact do you hope to have with your research?
My goal is to continue pushing the edge of our understanding in plant molecular biotechnology so that more enabling tools and choices can be developed for the betterment of growers and consumers. I hope that my work with tomato and sweetpotatoes can speed up cultivar development times to ultimately lead to cheaper and better products for consumers. And with my work in tomatoes, that the dangerous bacterial wilt disease can be better mitigated so that growers around the world can be benefited.

For more information:
North Carolina State University

Publication date: Wed 26 Jan 2022

Read Full Post »

Scientists identify genes key to microbial colonization of plant roots


Identification of an enzyme that microbes deploy in the presence of plants leads to discovery of candidate genes involved in root colonization.


Scientists Identify Genes Key to Microbial Colonization of Plant Roots

The Science

Some microbes can form thin films called biofilms. These biofilms give them an advantage over other microbes by protecting them from stresses such as a lack of nutrients or the presence of harmful substances in the environment. Researchers often focus on the biofilms that pathogens use to resist antibiotics. However, some biofilms can be helpful to plants and other host organisms. In previous work, researchers found that Pantoea sp. YR343, a bacterium that promotes plant growth, forms robust biofilms along the root surface of Populus, the genus which includes willow and cottonwood trees. Scientists know relatively little about the mechanisms behind the formation of biofilms on plant roots, particularly at the genetic level. However, research has found that enzymes called diguanylate cyclases are key to biofilm formation. This new research has identified a diguanylate cyclase, DGC2884, that is expressed specifically in the presence of plants when bacteria colonize roots and form biofilms.

The Impact

Diguanylate cyclases are found in many species of bacteria. These enzymes control multiple behaviors, including how bacteria form biofilms, cause disease, and move. This research shows that a particular diguanylate cyclase, DGC2884, operates specifically during biofilm formation and when bacteria are near a plant. This research also identified genes that could be involved in root colonization, suggesting that root colonization may be controlled at the genetic level. This will help microbiologists and other researchers better understand how bacteria colonize root surfaces and how gene expression may play a part. The results may also help scientists study similar behaviors in microbes important to medicine and agriculture.


This study used promoter-reporter constructs to identify a diguanylate cyclase, DGC2884, that is expressed in the presence of a plant. The researchers characterized this enzyme further and determined that when overexpressed, it affected exopolysaccharide production, biofilm formation, motility, and pellicle formation. They also demonstrated that the N-terminal transmembrane domain, as well as a functional GGDEF active site, are required for the activity of DGC2884. Based on phenotypes associated with overexpression of DGC2884 in Pantoea sp. YR343, the scientists performed transposon mutagenesis to identify genes that no longer exhibited the unique phenotypes observed when DGC2884 was overexpressed. They identified 58 different genes with this screen and selected a subset of transposon mutants for further characterization. Interestingly, mutations affecting Type VI secretion, as well as a nucleoside-diphosphate kinase and ABC transporter, exhibited increases in colonization, while mutations affecting exopolysaccharide production resulted in decreases in colonization when compared to the wild type control. Further, they found that some mutants exhibited differences primarily in the patterns of root colonization, more than the amount of colonization, suggesting that certain patterns of root colonization may be modulated on a genetic level.


This research was supported by the Department of Energy Office of Science, Biological and Environmental Research Genomic Science Program as part of the Plant Microbe Interfaces Scientific Focus Area.






Experimental study


Not applicable


Identification of a diguanylate cyclase expressed in the presence of plants and its application for discovering candidate gene products involved in plant colonization by Pantoea sp. YR343



Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases

Read Full Post »

DECEMBER 20, 2021

Microbe sneaks past tomato defense system, advances evolutionary battle

by Lauren Quinn, University of Illinois at Urbana-Champaign

Credit: CC0 Public Domain

When we think of evolution, many of us conjure the lineage from ape to man, a series of incremental changes spanning millions of years. But in some species, evolution happens so quickly we can watch it in real time.

That’s the case for Xanthomonas, the organism that causes bacterial leaf spot disease in tomato and pepper plants. Like many microbes with short generation times, it can evolve at lightning speed to acquire beneficial traits, such as the ability to elude its host’s defense system.

New research from the University of Illinois shows one Xanthomonas species, X. euvesicatoria (Xe), has evolved to avoid detection by the immune system of tomato plants.

“It’s part of the evolutionary warfare between plants and pathogens, where the plant has some defense trait and then some portion of the pathogen population evolves to escape it. The plant has to develop or acquire a new defense trait, but the process is much slower in plants compared to microbes. This study is a great example of that ongoing battle in progress. It tells us we can’t completely rely on this trait to combat bacterial spot disease caused by Xe,” says Sarah Hind, assistant professor in the Department of Crop Sciences at Illinois and co-author on a pair of recent studies published in Molecular Plant-Microbe Interactions and Physiological and Molecular Plant Pathology.

The tomato defense system keeps tabs on Xanthomonas and other bacteria with immune receptors that chemically detect flagella, the long whip-like tail structures that allow bacteria to move or “swim” through soil and plant tissues. Hind and her colleagues used laboratory and genomic modeling techniques to show one of tomato’s receptors, FLS3, no longer works to detect flagellin proteins in Xe.

Their work shows Xe’s flagellin proteins have changed by just one amino acid, but it’s enough to escape detection by tomato’s FLS3 receptors.

Graduate student and study co-author Maria Malvino says, “It was surprising to see that only one amino acid change was making all the difference. It made us wonder how binding between flagellin and FLS3 could be so dramatically altered.”

The fact that Xe can sneak past tomato’s defenses means farmers can rely even less on inherent disease resistance. Instead, they’ll have to combat the disease in other ways, such as spraying copper-based pesticides.

In some locations, including the Midwest region and in Illinois specifically, Xe isn’t as much of a problem as two other Xanthomonas species, X. perforans and X. gardneri (Xp and Xg). Tomato can still hold its own against these species for the time being, but Hind is concerned Xe will share its evasion strategy.

“X. euvesicatoria [Xe] had been the predominant strain for a long time, but within the last decade or two, it’s become less prominent and has been overtaken by another species, Xp,” she says. “Xp and Xe are really genetically close, and it’s been shown that they can share their genetic material with each other. So it wouldn’t be out of the realm of possibility that that Xe’s evasion strategy could make its way into Xp and provide the same advantage against tomato.”

Hind says the tendency of these bacteria to defeat host defenses through rapid evolution makes breeding for disease resistance difficult in tomato.

“It’s like whack-a-mole for breeders. It takes a long time to release a resistant variety. Often, by the time they go to release a new one, the pathogen population shifts,” Hind says. “And when you add to that the difficulty of maintaining all the desirable traits of a tomato, it’s a tough situation. Again, that leaves us relying on fungicides and copper treatments to keep tomato production profitable here in Illinois.”

Explore furtherScientists find new system in tomato’s defense against bacterial speck disease

More information: Maria Laura Malvino et al, Influence of flagellin polymorphisms, gene regulation, and responsive memory on the motility of Xanthomonas species that cause bacterial spot disease of solanaceous plants, Molecular Plant-Microbe Interactions (2021). DOI: 10.1094/MPMI-08-21-0211-R

Julius Pasion et al, Utilizing Tajima’s D to identify potential microbe-associated molecular patterns in Xanthomonas euvesicatoria and X. perforans, Physiological and Molecular Plant Pathology (2021). DOI: 10.1016/j.pmpp.2021.101744Journal information:Molecular Plant-Microbe InteractionsProvided by University of Illinois at Urbana-Champaign

Read Full Post »


Smart soil bugs offer farmers an ecofriendly route to controlling diseases such as potato scab

on January 20, 2022

More in Europe, UK, Ireland:

An innovative method of controlling a range of damaging crop diseases using native, beneficial soil bacteria has emerged from a research-industry collaboration. The agri-tech innovation hopes to give farmers a way to reduce the cost and environmental damage caused by the chemical treatments currently in use to control crop diseases, such as common scab in potatoes.

The John Innes Centre team in the UK isolated and tested hundreds of strains of Pseudomonas bacteria from the soil of a commercial potato field, and then sequenced the genomes of 69 of these strains. By comparing the genomes of those strains shown to suppress pathogen activity with those that did not, the team were able to identify a key mechanism in some of the strains that protected the potato crop from harmful disease-causing bacteria.

Then using a combination of chemistry, genetics and plant infection experiments they showed that the production of small molecules called cyclic lipopeptides is important to the control of common potato scab.

These small molecules have an antibacterial effect on the pathogenic bacteria that cause common potato scab, and they help the protective Pseudomonas move around and colonise the plant roots. The experiments also showed that irrigation causes substantial changes to the genetically diverse Pseudomonas population in the soil.

First author of the study Dr Alba Pacheco-Moreno said, “By identifying and validating mechanisms of potato pathogen suppression we hope that our study will accelerate the development of biological control agents to reduce the application of chemical treatments which are ecologically damaging.

“The approach we describe should be applicable to a wide range of plant diseases because it is based on understanding the mechanisms of action that are important for biological control agents,” she added.

The study, which appears in eLife, proposes a method by which researchers can screen the microbiome of virtually any crop site, and take into account varying soil, agronomic and environmental conditions.

By exploiting advances in high-speed genetic sequencing, the method can screen the soil microbiome for therapeutic bacteria and work out which molecules are being producedto suppress pathogenic bacteria.

They can also show how these beneficial bugs are affected by agronomic factors such as soil type and irrigation.

The next step for the new approach is to put the beneficial bugs back into the same field in greater numbers or in cocktails of mixed strains as a soil microbiome boosting treatment.

Dr Jacob Malone, Group Leader at the John Innes centre and co-corresponding author of the study explains the benefits, “The massive advantage of this approach is that we are using bacterial strains that are taken from the environment and put back in the same specific biological context in larger numbers so there is no ecological damage.”

Potential methods to apply the microbiome boosters include applying the bacterial cocktails as seed coatings, as a spray or via drip irrigation.

Dr Andrew Truman, Group Leader at the John Innes Centre, and corresponding author of the study tells us about the long-term vision for this method, “In the future  it’s not the molecule produced by the bacteria that we would use, it would be the Pseudomonas strain itself. It offers a more sustainable route – we know these bacteria colonize the soil where potatoes grow, and they provide protection to the crop. Using a bacterium, you can easily grow and formulate it in an appropriate way and apply it to the field, and it is much greener than using a synthetic chemical.”

Plant diseases are an agricultural problem that leads to major losses of crops, such as potatoes. Important potato pathogens include Streptomyces scabies, a bacterial pathogen that causes potato scab, and Phytophthora infestans, an oomycete pathogen that causes potato late blight.

Pseudomonas bacteria are commonly associated with plants and have been widely studied as biological control agents, as they secrete natural products which promote plant growth and suppress pathogens. However, their use in the past has been hampered by inconsistency.

Previous studies on the suppression of potato scab have indicated a potential biocontrol role for Pseudomonas. However, progress was hampered by a lack of mechanistic knowledge. It was also widely known that irrigation can suppress Streptomyces scabies infection and now this study suggests that this is because of the effect that water has on microbial populations.

Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition, appears in eLife.

Source: John Innes Centre. Original news story here
Photo: John Innes Centre
Journal Reference:
Francesca L Stefanato, Alba Pacheco-Moreno, Jonathan J Ford, Christine Trippel, Simon Uszkoreit, Laura Ferrafiat, Lucia Grenga, Ruth Dickens, Nathan Kelly, Alexander DH Kingdon, Liana Ambrosetti, Sergey A Nepogodiev, Kim C Findlay, Jitender Cheema, Martin Trick, Govind Chandra, Graham Tomalin, Jacob G Malone, Andrew W Truman. Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibitioneLife, 2021; 10 DOI: 10.7554/eLife.71900

Share this news story with colleagues on social media or email:

Read Full Post »

Older Posts »