Diversity and Virulence of Streptomyces spp. Causing Potato Common Scab in Prince Edward Island, Canada

Exploring the antagonistic mechanism of Bacillus atrophaeus CY1 for the biological control of potato common scab

Streptomyces scabies is a pathogenic actinomycete that infects potato crops and commonly causes scab-like lesions on potato tubers. Screening of strains antagonistic towards S. scabies in the natural environment was performed in this study. This study focused on the extraction of antibacterial substances and changes in potato defense enzymes and the rhizosphere microbiota. Together, these factors constitute biological control mechanisms. Pot experiments showed that Bacillus atrophaeus CY1 reduced the infection of scabs caused by S. scabies from 92 % to 60 % and the disease index from 62 % to 25 %. Scanning electron microscopy analysis revealed that B. atrophaeus CY1 repressed the growth of S. scabies by disrupting the mycelium and affecting potato defense enzymes. Compared with the infected group, catalase, peroxidase, and polyphenol oxidase activities in potato tubers of the co-culture group increased by 21.98 %, 71.49 %, and 116.15 %, respectively, and SOD activity decreased by 4.9 %. Moreover, at different developmental stages, the microbiota counts in the CY1 cocultured groups were significantly higher, and the actinomycete count was considerably lower. At the budding stage, urease activity was 13.39 mg g-1 in the co-culture group, representing an increase of 37.37 % and 20.62 %, respectively, compared to the control group. Cellulase activity in the SC group was 0.675 mg-1, which represented increases of 39.18 % and 43.92 %, respectively. These results demonstrate that B. atrophaeus CY1 is a potential candidate for the biological control of S. scabies.

Virulence Determinants Are Unevenly Distributed Within Streptomyces Species and Strains Causing Potato Common Scab in the Province of Quebec, Canada

Potato common scab is an important bacterial disease afflicting potatoes around the world. Better knowledge of the local Streptomyces spp. populations causing this disease is key to developing durable control strategies. In this study, we isolated 230 Streptomyces strains from scab-infected potato tubers harvested from commercial potato fields located across the province of Quebec, Canada. The genetic diversity of this collection was first studied using repetitive element-based PCR fingerprinting, and the genomes of 36 representative strains were sequenced using PacBio's sequencing technology. This enabled us to identify the strains to the species level, to study the distribution of previously characterized virulence-associated genes and clusters, and to explore the repertoires of putative plant cell wall-degrading enzymes. In parallel, the virulence of the 36 strains was evaluated using a potato tuber slice assay. The diversity was higher than previously reported, as 11 phytopathogenic species were found across the province. Among them, S. scabiei and S. acidiscabies were the most abundant as well as the most virulent. Strains belonging to these two species harbored numerous virulence determinants, including the thaxtomin biosynthetic gene cluster. By contrast, most weakly virulent strains lacked this cluster but harbored at least one known virulence determinant. The results obtained suggest that a higher number of virulence-associated genes and clusters in the genome of phytopathogenic Streptomyces spp. are associated with greater virulence. This study contributes to increasing the publicly available genomic resources of scab-causing Streptomyces spp. and expands our knowledge on the diversity and virulence of this important bacterial pathogen.

Proteomics fingerprinting reveals importance of iron and oxidative stress in Streptomyces scabies-Solanum tuberosum interactions

Introduction

The Gram-positive actinobacterium Streptomyces scabies is the major causal agent of potato common scab. The main pathogenicity factor is thaxtomin A, a phytotoxin that causes atypical cell death, although other secondary metabolites have been described to play a role in S. scabies virulence. Despite this, many aspects of the interaction between S. scabies and its primary host Solanum tuberosum L. remain to be elucidated.

Methods

Intracellular proteins of S. scabies EF-35 grown in the presence of in vitro produced tubers (microtubers) of the Russet Burbank and Yukon Gold potato cultivars were extracted and analysed by electrospray mass spectrometry (ES MS/MS). Based on the results of proteomic analysis, iron quantification by ICP-MS and nitrite quantification using Griess reagent in growth media as well as RT-qPCR analysis of the siderophore pyochelin gene expression were performed in the presence and absence of microtubers. Hydrogen peroxide accumulation was also determined in the nutrient medium used for co-cultivation of bacteria and potato microtubers.

Results

Potato microtubers caused an increase in the content of bacterial proteins involved in stress and defense, secondary metabolism, and cell differentiation, as well as secreted proteins. Co-cultivation with potato microtubers induced the accumulation of S. scabies proteins implicated in siderophore pyochelin biosynthesis, nitrite production and oxidative stress perception and response. The increase in the abundance of proteins related to pyochelin biosynthesis was consistent with a significant decrease in the iron content in the culture medium, as well as with induction of expression of pyochelin biosynthesis genes. Elevated nitrite/sulfite reductase protein levels were associated with increased nitrite excretion by S. scabies cells in the presence of host microtubers. The increase in the levels of proteins associated with signaling and oxidative stress response could have been caused by the accumulation of ROS, in particular hydrogen peroxide, detected in the studied system.

Discussion

These findings show that interactions of S. scabies with living potato microtubers induce the production of secondary metabolites, defense responses, and protection from oxidative stress. This study suggests the importance of iron during host - S. scabies interactions, resulting in competition between pathogen and its host.

Seasonal Dynamics of Various Scab-Causing Streptomyces Genotypes Among Potato Fields on Prince Edward Island

Potato common scab is an important bacterial plant disease caused by numerous Streptomyces species and strains. A better understanding of the genetic diversity and population dynamics of these microorganisms in the field is crucial to develop effective control methods. Our research group previously studied the genetic diversity of scab-causing Streptomyces spp. in Prince Edward Island, one of Canada's most important potato-growing provinces. Fourteen distinct Streptomyces genotypes were identified and displayed contrasting aggressiveness toward potato tubers. To better understand the distribution and occurrence of these genotypes over time under field conditions, the population dynamics were studied in nine commercial potato fields throughout a growing season. A comparative genomic-driven approach was used to design genotype-specific primers and probes, allowing us to quantify, using quantitative polymerase chain reaction, the abundance of each of the 14 genotypes in field soil. Thirteen of the previously identified genotypes were detected in at least one soil sample, with various frequencies and population sizes across the different fields under study. Interestingly, weakly virulent genotypes dominated, independent of time or location. Among them, three genotypes accounted for more than 80% of the genotypes' combined population. Although the highly virulent genotypes were detected in lower relative abundance than the weakly virulent ones, an increase in the highly virulent genotypes' population size was observed over the growing season in most fields. The results will ultimately be useful for the development of targeted common scab control strategies.

Deciphering host-pathogen interaction during Streptomyces spp. infestation of potato

Potato crop, currently, is the staple food crop of about 1.3 billion global population. Potato is attaining even more admiration globally day by day owing to its public acceptability. However, potato sustainable production is distinctly challenged by multiple factors like diseases, pests and climate change etc. Among diseases, common scab is one of the prime threats to potato crop due to its soil-borne nature and versatility in phytotoxins' secretion. Common scab is caused multiple number of phytopathogenic streptomyces strains. Despite extensive research programs, researchers are still unable to identify a significant solution to this threat that is proliferating exceptional rate across the globe. To develop feasible remedies, adequate information regarding host-pathogen interaction should be available. This review possesses insights on existing pathogenic species, the evolution of novel pathogenic streptomyces spp. and phytotoxins produced by the pathogenic strains. Furthermore, which type of physiological, biochemical and genetic activities occur during pathogen's infestation of the host are also canvassed.

Common scab disease-induced changes in geocaulosphere microbiome assemblages and functional processes in landrace potato (Solanum tuberosum var. Rongpuria) of Assam, India

Common scab (CS) caused by pathogenic Streptomyces spp. plays a decisive role in the qualitative and quantitative production of potatoes worldwide. Although the CS pathogen is present in Assam's soil, disease signs and symptoms are less obvious in the landrace Rongpuria potatoes that indicate an interesting interaction between the plant and the geocaulosphere microbial population. Toward this, a comparative metagenomics study was performed to elucidate the geocaulosphere microbiome assemblages and functions of low CS-severe (LSG) and moderately severe (MSG) potato plants. Alpha diversity indices showed that CS occurrence modulated microbiome composition and decreased overall microbial abundances. Functional analysis involving cluster of orthologous groups (COG) too confirmed reduced microbial metabolism under disease incidence. The top-three most dominant genera were Pseudomonas (relative abundance: 2.79% in LSG; 12.31% in MSG), Streptomyces (2.55% in LSG; 5.28% in MSG), and Pantoea (2.30% in LSG; 3.51% in MSG). As shown by the high Pielou's J evenness index, the potato geocaulosphere core microbiome was adaptive and resilient to CS infection. The plant growth-promoting traits and potential antagonistic activity of major taxa (Pseudomonads, non-pathogenic Streptomyces spp., and others) against the CS pathogen, i.e., Streptomyces scabiei, point toward selective microbial recruitment and colonization strategy by the plants to its own advantage. KEGG Orthology analysis showed that the CS infection resulted in high abundances of ATP-binding cassette transporters and a two-component system, ubiquitous to the transportation and regulation of metabolites. As compared to the LSG metagenome, the MSG counterpart had a higher representation of important PGPTs related to 1-aminocyclopropane-1-carboxylate deaminase, IAA production, betaine utilization, and siderophore production.

Comparative Genomics of Potato Common Scab-Causing Streptomyces spp. Displaying Varying Virulence

Common scab of potato causes important economic losses worldwide following the development of necrotic lesions on tubers. In this study, the genomes of 14 prevalent scab-causing Streptomyces spp. isolated from Prince Edward Island, one of the most important Canadian potato production areas, were sequenced and annotated. Their phylogenomic affiliation was determined, their pan-genome was characterized, and pathogenic determinants involved in their virulence, ranging from weak to aggressive, were compared. 13 out of 14 strains clustered with Streptomyces scabiei, while the last strain clustered with Streptomyces acidiscabies. The toxicogenic and colonization genomic regions were compared, and while some atypical gene organizations were observed, no clear correlation with virulence was observed. The production of the phytotoxin thaxtomin A was also quantified and again, contrary to previous reports in the literature, no clear correlation was found between the amount of thaxtomin A secreted, and the virulence observed. Although no significant differences were observed when comparing the presence/absence of the main virulence factors among the strains of S. scabiei, a distinct profile was observed for S. acidiscabies. Several mutations predicted to affect the functionality of some virulence factors were identified, including one in the bldA gene that correlates with the absence of thaxtomin A production despite the presence of the corresponding biosynthetic gene cluster in S. scabiei LBUM 1485. These novel findings obtained using a large number of scab-causing Streptomyces strains are challenging some assumptions made so far on Streptomyces’ virulence and suggest that other factors, yet to be characterized, are also key contributors.

Irreplaceable Role of Amendment-Based Strategies to Enhance Soil Health and Disease Suppression in Potato Production

Soilborne diseases are a major constraining factor to soil health and plant health in potato production. In the toolbox of crop management, soil amendments have shown benefits to control these diseases and improve soil quality. Most amendments provide nutrients to plants and suppress multiple soilborne pathogens. Soil amendments are naturally derived materials and products and can be classified into fresh or living plants, organic or inorganic matters, and microbial supplements. Fresh plants have unique functions and continuously exude chemicals to interact with soil microbes. Organic and inorganic matter contain high levels of nutrients, including nitrogen and carbon that plants and soil microorganisms need. Soil microorganisms, whether being artificially added or indigenously existing, are a key factor in plant health. Microbial communities can be considered as a biological reactor in an ecosystem, which suppress soilborne pathogens in various mechanisms and turn soil organic matter into absorbable forms for plants, regardless of amendment types. Therefore, soil amendments serve as an energy input, nutrient source, and a driving force of microbial activities. Advanced technologies, such as microbiome analyses, make it possible to analyze soil microbial communities and soil health. As research advances on mechanisms and functions, amendment-based strategies will play an important role in enhancing soil health and disease suppression for better potato production.