Source: SpudSmart
You need to know your enemy if you want to fight it, says Martin Filion, an associate professor at the Université de Moncton in New Brunswick.
“Genetic diversity of a pathogen means differences in functions the pathogen might have,” he says. “For instance, different species or strains might have different responses to chemicals or agricultural practices you are using to manage the disease.”
Information about which common scab species and strains are present and their particular characteristics is very important to developing more effective control methods for the specific pathogens in growers’ fields.
Streptomyces scabies is the main species causing common scab worldwide, but other Streptomyces species can also cause the disease. “A dozen or so pathogenic Streptomyces species have been reported in the literature, and periodically new ones are discovered. Research also shows there can be regional variations in the species that are present, and there can be multiple pathogenic species within a particular region and even within a single field,” says Dawn Bignell, an associate professor at Memorial University of Newfoundland.
“We really need to understand what common scab species and strains are present within a particular region. You can have significant variations in aggressiveness between different species and different strains, meaning some cause more severe disease symptoms than others. Also, some research published in 2009 shows different potato cultivars can respond differently to individual pathogenic species or strains, and this in turn may contribute to regional differences in the disease’s severity.”
Filion and Bignell are in the vanguard of researchers who are starting to fill the information gaps around common scab species and strains in the different regions of Atlantic Canada.
Impacts in Atlantic Canada
Common scab is a widespread, economically important disease in Atlantic Canada. “The disease is always present in almost every field,” says Filion, who has been researching common scab for about 14 years. “Some producers will have more losses than others, but producers will face diseased tubers year after year.”
Tubers with common scab lesions are safe to consume. The disease is mainly a quality issue, although Bignell says some studies suggest it can sometimes also cause lower yields or decreased tuber size.
“The major impact of common scab is it reduces the market value of the potato crop. Common scab lesions can be superficial, raised, warty-like, or deep pitted. Potatoes simply aren’t worth as much if they are covered with these lesions when compared with blemish-free potatoes,” she says. “Fresh market potatoes, seed potatoes and processing potatoes are all affected.”
Filion says a large portion of potatoes are produced for the processing market, and potato processors “will usually not buy tubers that have more than seven to 10 per cent lesion coverage on the tuber’s surface because the lesions can make processing difficult. Some of the lesions are quite deep and will interfere with peeling of the tubers. Some producers if they have, let’s say, lesions in the 15 to 20 per cent range, will lose a significant part of their production to this disease.”
Common scab may be increasing in Atlantic Canada. “I’m in close contact with companies involved in potato production, such as Cavendish Agri Services, the Little Potato Company and a few others, and each company tells me they have been seeing an increase in common scab problems for the last couple of years. I am also in contact with potato producers directly, and most producers in the Maritimes are seeing a small increase in the number of tubers with common scab,” says Filion.
Surprising Species Diversity in Newfoundland
No research had been done on the species causing common scab in Newfoundland until Bignell started her study in 2011. She was interested in this issue because the disease is very common in the province and, as an island, Newfoundland is somewhat biologically isolated, which could be an important factor in the pathogen’s genetic diversity.
In her study, Bignell and her research group collected tubers with common scab at three locations in 2011 and 2012, and they isolated Streptomyces bacteria from the lesions. “Both pathogenic and non-pathogenic Streptomyces species can be present within potato lesions, so we screened our isolates to find the pathogenic ones,” says Bignell. “We did a very simple radish seedling bioassay where we treated seedlings with the different isolates, and identified the ones that caused stunting and necrosis of the seedlings.” Radish bioassays are faster and easier than potato bioassays for detecting pathogenic isolates.
Dawn Bignell holds a culture plate with isolates of a common scab pathogen and a potato tissue bioassay for testing the pathogenicity of isolates. Photo courtesy of Dawn Bignell/Memorial University.
Out of 52 Streptomyces isolates, they found 17 pathogenic ones. Next, the research group did some genetic and phenotypic characterization of the pathogenic isolates. For example, they looked for known virulence genes and for the production of a pathogenicity factor called thaxtomin, a plant toxin that contributes to common scab development. For species identification, they compared key gene sequences to see how closely related the isolates are to each other and to known Streptomyces species.
“There were three key findings from our study,” says Bignell. “The first was scab lesions on potatoes harvested in Newfoundland are associated with several different pathogenic species.”
Eight of the 17 isolates were Streptomyces europaeiscabiei, a known common scab pathogen. “This species is commonly found in Europe, and it has been found in different regions in North America, including Canada.”
The second key finding was the other nine isolates appear to be previously unknown common scab pathogens. Bignell was surprised to find so many novel isolates, especially given the small sample size.
None of the novel pathogenic strains produce thaxtomin. “We currently don’t know what pathogenicity factors they produce, but it is something different than thaxtomin,” she says.
“This was particularly exciting because it has long been thought that thaxtomin is the primary pathogenicity factor produced by all common scab pathogens. Some studies have even suggested if we target thaxtomin production, we can control common scab disease. But our study and some other studies are showing some common scab pathogens don’t produce thaxtomin, but they produce other virulence factors that are likely contributing to common scab.”
Some of the novel isolates appear to be related to each other, while others are distinctly different. Most of these isolates still need to be tested on potatoes. “The radish assay shows the isolates are pathogenic to plants, and the fact that we isolated them from potato lesions strongly suggests they are common scab pathogens, but we need to verify that,” says Bignell.
The third key finding was one of the novel isolates is very aggressive. “In all of our plant bioassays, this isolate was much more pathogenic than our control common scab strains.”
Another surprise was no Streptomyces scabies isolates were found. “Streptomyces scabies has a worldwide distribution, and it’s quite common in Canada, particularly in Eastern Canada. So we highly expected to find S. scabies among our isolates,” says Bignell. “One reason why we didn’t find it was likely due to our small sample size. I suspect if we were to do a much larger survey, we would find it.”
They didn’t find any geographical patterns in the distribution of the different common scab species. At some locations, they found more than one species.
Bignell’s study was funded by an Agriculture Research Initiative grant from the Newfoundland and Labrador provincial government. She has additionally received funding for infrastructure, equipment and basic operation of her lab from the Natural Sciences and Engineering Research Council of Canada(NSERC), the Canada Foundation for Innovation, and the Newfoundland and Labrador Research and Development Corporation.
Currently, her common scab research includes a detailed study of the very aggressive isolate discovered in her survey. “We sequenced the entire genome of that organism. Based on those results, we are able to confirm it is not one of the known common scab species. We have also confirmed it cannot produce thaxtomin because the genes needed to make that pathogenicity factor are not in the genome.”
Bignell and her group are in the process of figuring out what pathogenicity factor is being made by that organism. They know it is a plant toxin, but they still need to determine what the toxin is and what its role is in the disease.
In the future, Bignell hopes to do a broader survey of the common scab pathogens in Newfoundland. “This work could determine if Streptomyces europaeiscabiei is the predominant species on the island, what its distribution is across the island, and what other known and novel species are present.” Shewould also be happy to hear from potato growers and others in the potato industry who are interested in partnering with her on common scab initiatives.
Huge Strain Diversity
A few years ago, Filion was involved in the first study to investigate common scab species in New Brunswick, Nova Scotia and Prince Edward Island. In that research, which was published in 2008, Filion and his colleagues obtained 41 Streptomyces isolates from lesions on tubers. Most isolates were Streptomyces scabies, but two were Streptomyces acidiscabies, the first time this species was identified in the Maritimes.
Using genome fingerprinting, the researchers identified 10 distinct genetic groups among the strains, and they found the geographical distribution of the groups had a regional pattern.
About a year and a half ago, Filion started a three-year study to identify and characterize the Streptomyces strains on Prince Edward Island. “At present, P.E.I. is the most important potato-producing province. Also, as an island, P.E.I. is a more isolated region, so we’re interested in looking at the geographical distribution of the different strains,” he says.
“In the 2008 study, we found only Streptomyces scabies on P.E.I. However, keeping in mind we only had a few samples, we did find some genetic diversity within that species on P.E.I. In our current study, we want to get more information on this diversity. We now have access to many, many more samples, so hopefully we will be able to characterize the whole genetic diversity of Streptomyces scabies found on P.E.I.,” says Filion.
Through Cavendish Agri Services, a key partner in the study, Filion and his research group received about 1,000 tubers with common scab fromthe western, eastern and central regions of Prince Edward Island. They have isolated close to 800 different isolates of scab-causing agents. They have finished extracting the DNA from the isolates, and they have almost finished the molecular fingerprinting.
“We have found a huge diversity of common scab strains on P.E.I.,” says Filion. “And there are some geographic patterns — some strains are only found in certain places in P.E.I. We also sometimes find more than one strain in a particular field, so the diversity within a field is bigger than we originally expected. But what does that diversity mean? Is strain A important and strain B not important? Are both important? Are they both aggressive in the same way? These are the kinds of questions I’ll probably be more able to answer in a year from now.”
The group will soon be starting on sequencing the genomes of the most important strains they are discovering, and they’ll be identifying some key pathogenicity-related genes in those strains.
Filion and his team will also be developing DNA-based tools to specifically detect some of the main strains. These tools will allow diagnostic labs to rapidly identify and quantify the strains in tuber samples and soil samples submitted by producers. Knowing which strains are present, how virulent they are and how abundant they are, will help producers in managing the disease in their fields.These tools could be available within the next two to four years.
Funding for this common scab strain study is provided by Cavendish Agri Services, Genome Atlantic, Mitacs, New Brunswick Innovation Foundation, and NSERC.
Filion and his group have several other common scab studies on the go. For example, they are testing some cultivars in the lab to determine how they respond to different Streptomyces strains. In another project, they are working on biopesticides against common scab. “We are developing inoculants of beneficial bacteria that produce antimicrobial compounds, which can help fight against scab-causing Streptomyces.”
In addition, Filion will soon be working on a major common scab initiative that will investigate many aspects of the disease and its management. “We recently received more than $1 million from Agriculture and Agri-Food Canada for a five-year research project on common scab. This Canada-wide, collaborative initiative will involve researchers from AAFC and academia.”
Bignell’s and Filion’s studies on Streptomyces species and strains in Atlantic Canada are a valuable component in the effort to develop more effective, consistent control methods to combat common scab.