The study, published this week in Applied and Environmental Microbiology, an open-access journal of the American Society for Microbiology, was led by microbiologist Eric Déziel of the Institut national de la recherche scientifique (INRS) in Quebec, Canada. Déziel describes C. michiganensis as a genuinely problematic pathogen, particularly in greenhouse settings where dense planting, shared equipment, and constant human handling create ideal conditions for transmission. Once the bacterium gains a foothold in a facility, it typically establishes itself in one section before workers inadvertently carry it from plant to plant as they prune, tie, and harvest. The result is a creeping wave of infection that is notoriously difficult to contain with conventional tools.

What makes the new research distinctive is its dual focus. Most studies of biological control agents, Déziel notes, tend to concentrate on a single objective: either suppressing a pathogen or stimulating plant growth. The Canadian team set out to find microbes capable of doing both at once. Their screening strategy was deliberately broad and systematic, drawing on a resource the laboratory had been building for roughly two decades. For about twenty years, researchers in Déziel’s group have pursued biological solutions to agricultural problems, accumulating a large collection of bacterial strains isolated from a wide variety of food plants and environments.

The opportunity to apply that collection to tomato canker arose a few years ago, during the COVID-19 pandemic, when tomato growers brought the problem of bacterial canker in greenhouses to the lab’s attention. Déziel admits he had never heard of the disease at the time, but the growers’ concerns were enough to launch an intensive search for answers. The team began at home, so to speak, testing some 500 strains from their own collection for the ability to antagonize C. michiganensis in laboratory assays. These strains had been isolated from strawberries, lettuce, apples, and other foods, and had been recovered from leaves, roots, and other plant parts. Crucially, none of them had previously been isolated from bacteria-infected plants or fruits, meaning the researchers were working with microbes drawn from healthy contexts rather than from diseased tissue.

The initial screen was designed to cast a wide net. In antagonism assays, candidate bacteria are grown alongside the pathogen, allowing researchers to observe whether the candidate produces compounds, competes for resources, or otherwise interferes with the pathogen’s growth. From the 500 strains tested, a few dozen showed promising activity against C. michiganensis. That shortlist then faced a second, more demanding filter: the strains had to do more than fight the pathogen. They also needed to promote plant growth, a property that matters enormously for any biocontrol agent intended for real-world agriculture, since growers are far more likely to adopt a treatment that delivers a visible agronomic benefit in addition to disease protection.

The evaluation proceeded in stages, moving from simple bacterial cultures to living plants. This progression is essential in biocontrol research because activity observed on a laboratory plate does not always translate to the complex environment of a plant’s surfaces and internal tissues. When the team tested their shortlisted strains on tomato plants infected with bacterial canker, the experiments ultimately yielded three bacterial strains that demonstrated a clear dual benefit. One of these, Pantoea agglomerans SO16PY, originally isolated from the leaf of a healthy tomato plant, proved especially interesting: it delayed the onset of canker symptoms in infected plants by up to a week and reduced the overall severity of the disease. The other two strains, both members of the species Pseudomonas marginalis, similarly restricted both the development and the severity of the disease in infected plants.

The significance of a week’s delay should not be underestimated in commercial greenhouse production. Bacterial canker moves quickly through a crop, and every day of slowed progression gives growers additional time to detect the outbreak, remove affected plants, and adjust handling practices to limit the spread that occurs through workers’ hands and tools. Reduced disease severity, meanwhile, translates directly into preserved yield and plant vigor. Combined with the growth-promoting effects observed in the same strains, these microbes appear to function as what researchers sometimes describe as plant probiotics: living allies that shift the balance of the plant’s microbial environment away from pathogens and toward health.

The practical context for this work is particularly important for organic growers. Déziel points out that bacterial canker can be a significant problem for organic farmers, who have fewer chemical options available to them. Although organic producers can purchase seeds that are certified or guaranteed to be free of the pathogen, the bacterium may still find its way into a greenhouse through contaminated equipment, infected transplants, or residual inoculum in the facility. Once inside, the disease follows its familiar pattern of localized establishment followed by mechanical spread through routine work. Today’s treatment solutions are limited, Déziel adds, and the few commercial options that do exist show poor efficacy, leaving growers with largely preventive measures and little recourse once infection takes hold.

That gap between need and available tools is precisely where the three beneficial strains could eventually make a difference. The researchers emphasize, however, that considerable development work remains before these microbes could be harnessed for commercial use. The central challenge is formulation and delivery: the bacteria must be stabilized in a product form that maintains their viability and effectiveness over time. As Déziel explains, the team needs to find a way to stabilize the bacteria so that their shelf life is long enough for the product to be actually usable in a greenhouse. A biocontrol agent that loses potency within days of manufacture is of little value to a grower who needs to apply it on a schedule determined by the crop and the disease, not by the laboratory.

If that stabilization challenge can be solved, the payoff could be substantial. The three strains identified in this study represent a sustainable, environmentally friendly approach to improving plant health in agriculture, one that works with the natural antagonisms among microbes rather than against them. For an industry grappling with a seedborne pathogen that spreads easily and resists conventional treatment, bacteria that can both hold the disease at bay and help the crop grow stronger offer a genuinely new kind of tool. The work also underscores the value of long-term microbial collections and of listening to growers: a problem brought to the lab’s attention during a pandemic has now produced candidate biocontrol agents isolated from healthy tomato leaves and other food plants, strains that had been sitting in a freezer for years waiting for the right question to be asked of them.

Subject of Research: Identification of beneficial bacterial strains that suppress tomato bacterial canker and promote tomato plant growth

Article Title: Beneficial bacteria support tomato growth & suppress disease

Article References: Beneficial bacteria support tomato growth & suppress disease. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: tomato, bacterial canker, Clavibacter michiganensis, biological control, Pantoea agglomerans, Pseudomonas marginalis, plant growth promotion, greenhouse agriculture, seedborne disease, microbiome, organic farming, Applied and Environmental Microbiology

Bacterial canker, caused by the pathogen Clavibacter michiganensis, is notoriously difficult to control, particularly in greenhouse production systems where conditions favor disease spread and where growers have limited options once an infection takes hold. The disease can cause significant production losses, affecting yield and fruit quality, and it has long been a source of frustration for commercial tomato growers. Because chemical treatments against the pathogen are limited in their effectiveness and increasingly constrained by regulatory and environmental pressures, the search for sustainable alternatives has become a priority for the agricultural sector. The INRS study was designed specifically to address this gap, drawing on a library of bacterial strains previously isolated from fields growing a variety of crops.

The screening process, led by Professor Éric Déziel of the INRS Armand-Frappier Santé Biotechnologie Research Centre, evaluated hundreds of candidate strains for their ability to combat the pathogen and support plant health. From this large-scale effort, the researchers identified three particularly promising bacterial strains. One of these delayed the appearance of disease symptoms by up to seven days in tomato plants exposed to Clavibacter michiganensis while also significantly reducing disease severity. In plant pathology, a delay of that magnitude can be commercially meaningful, giving crops a longer productive window and reducing the overall disease burden within a growing cycle. The two other strains also demonstrated the ability to protect plants while simultaneously promoting their growth.

Nasim Sedighian, an environmental microbiology researcher and first author of the study, who conducted the work during her postdoctoral fellowship at INRS, emphasized the significance of the dual function observed in the strains. “We identified bacteria capable of protecting plants against a major disease while also enhancing their growth. This dual function represents a highly promising opportunity for more sustainable agriculture,” she said. The combination of biocontrol and growth promotion in a single organism is what makes the finding especially attractive from a practical standpoint, since growers would not need to deploy separate products to achieve disease protection and improved plant vigor.

Beyond the immediate agricultural implications, the study produced an intriguing taxonomic finding. Genomic analyses revealed that two of the strains studied may belong to a previously unrecognized lineage within the Pseudomonas marginalis group, a cluster of bacteria known for their close associations with plants. This observation opens new avenues of research into beneficial plant-associated microorganisms and suggests that the diversity of useful bacteria in agricultural soils and crop environments may be greater than currently appreciated. Understanding the evolutionary relationships and functional capabilities of these newly recognized lineages could help researchers identify additional strains with valuable biocontrol or growth-promoting properties in the future.

The research did not emerge in isolation. It was conducted in collaboration with Agro-100 Ltd., a long-standing partner of the Déziel laboratory, and was shaped by challenges identified directly by greenhouse tomato growers. This partnership-based approach reflects a growing trend in agricultural science, in which academic laboratories work closely with industry to ensure that laboratory discoveries can be translated into products and practices that meet the real-world needs of producers. For more than two decades, Professor Déziel’s laboratory has developed recognized expertise in beneficial microorganisms and their agricultural applications, building the strain collections and screening infrastructure that made the current study possible.

“This research highlights the importance of partnerships between academia and industry in addressing real-world challenges facing the agricultural sector. In the long term, these microorganisms could provide growers with new tools to protect their crops more sustainably,” said Déziel, who holds the Canada Research Chair in Fundamental and Applied Sociomicrobiology. His remarks underscore the practical orientation of the project, which from its inception aimed at developing biological solutions adapted to the realities of the greenhouse sector rather than pursuing purely fundamental questions about plant-microbe interactions.

The technical basis for how such beneficial bacteria operate is an active area of investigation in plant microbiology. Beneficial strains can protect plants through a variety of mechanisms, including competitive exclusion of pathogens, stimulation of the plant’s own immune responses, and the production of antimicrobial compounds that inhibit pathogen growth. Growth promotion, meanwhile, can result from improved nutrient acquisition, hormone modulation, or enhanced stress tolerance. While the published study documents the protective and growth-promoting effects of the three strains in tomato plants exposed to Clavibacter michiganensis, further work will be needed to characterize precisely which mechanisms underlie the observed benefits and how those mechanisms perform under the variable conditions of commercial production.

According to the research team, further testing under commercial growing conditions will be required to confirm the effectiveness of the bacterial strains and to determine how they can be used most effectively. Greenhouse environments differ from laboratory settings in temperature, humidity, light, and microbial community composition, and a strain that performs well in controlled experiments may behave differently at scale. Establishing application protocols, dosing strategies, and compatibility with existing growing practices will be essential steps on the path from discovery to deployment. The involvement of an industry partner such as Agro-100 positions the team to navigate this transition, and the study was supported financially by Agro-100, CRIBIQ, and the Natural Sciences and Engineering Research Council of Canada (NSERC).

The broader significance of the work lies in its contribution to the movement toward reduced chemical inputs in agriculture. As regulators and consumers push for lower pesticide residues and more environmentally friendly production methods, biological control agents derived from naturally occurring microorganisms have attracted growing interest. The INRS findings demonstrate that a systematic screen of existing strain collections, guided by clear industry needs, can surface organisms with the potential to address major crop diseases. If subsequent commercial-scale trials confirm the laboratory results, tomato growers could gain a new tool against bacterial canker that protects yields while supporting more sustainable farming systems, and the previously unrecognized Pseudomonas lineage identified along the way may yield further discoveries in the years ahead.

Subject of Research: Beneficial bacteria for tomato growth promotion and biocontrol of bacterial canker

Article Title: Beneficial bacteria protect tomatoes and promote plant growth

Article References: Beneficial bacteria protect tomatoes and promote plant growth. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: beneficial bacteria, tomato, bacterial canker, Clavibacter michiganensis, biocontrol, plant growth promotion, Pseudomonas marginalis, greenhouse production, sustainable agriculture, INRS, biological solutions, Applied and Environmental Microbiology