Soil oomycetes contain some of the most devastating plant pathogens, and are widespread within the soil microbiome, yet how individual plant species structure oomycete communities in natural soils, and whether any such structuring is consistent across space, remains poorly resolved. Because host-specific pathogen accumulation is a central prediction of plant-soil feedback theory but is rarely tested outside greenhouse conditions, we focused on whether the host-specific fraction of these communities is preferentially pathogenic. Using oomycete-specific ITS amplicons, we sequenced rhizosphere-associated and paired bulk soils from four grassland species across 25 sites on the Canadian Prairies spanning more than 200,000 km², totalling 1800 samples. Each host supported a distinctive core of taxa, with two species more likely to host pathogenic taxa unique to their rhizosphere. This enrichment was decoupled from richness of oomycete taxa in the rhizosphere, indicating selective accumulation rather than a by-product of resource-rich environments. Community composition also differed among hosts after accounting for site level edaphic variation. Host plant identity therefore leaves a detectable, spatially repeatable imprint on soil oomycete communities, one expressed most strongly through the selective accumulation of pathogenic taxa.
Exudative epidermitis (EE) in piglets, caused by the bacterium Staphylococcus hyicus, remains a major concern for the swine industry, particularly due to antimicrobial resistance. Bacteriophages represent a promising alternative treatment. This study aimed to isolate and characterize phages infecting S. hyicus from EE-affected swine farm environments in Quebec. Four novel phages (BQE1, BQE4, BQE7, BQL4) were isolated from water and manure samples. All produced clear plaques (<1 mm) and reached titers of 108-1010 PFU/mL. Electron microscopy revealed myovirus morphology. Their genomes (115.4-134.5 kb) are closely related to the already described Twort phage but distinct from other S. hyicus phages. No virulence or antimicrobial resistance genes were detected in their genome. Host range analysis across 58 staphylococcal strains showed broad activity against S. hyicus (77%-80% susceptibility), whereas the Twort phage was largely ineffective (4%). Adsorption and growth assays indicated efficient infection, with latent periods of ∼50 min and burst sizes of 10-13 PFU/cell. Phages remained stable at 4 °C and room temperature but were less stable at 31 °C. Overall, these Twort-like phages display strong lytic activity and favorable genomic and biological characteristics, supporting their potential as targeted alternatives to antibiotics for controlling EE in swine production.
Blue light is a critical environmental signal that triggers fruiting body initiation in mushroom-forming fungi. Pleurotus ostreatus is a widely cultivated model mushroom, yet the molecular mechanisms linking light perception to primordia formation remain poorly understood. Here, we functionally characterized the blue light receptor gene PoWC-1, a homolog of Neurospora crassa white collar 1, during early morphogenesis. Antisense-mediated silencing of PoWC-1 caused a marked delay in primordia formation under light/dark cycles and complete arrest at the undifferentiated mycelial stage under continuous darkness, underscoring its role in developmental progression. Even in darkness, PoWC-1 silencing downregulated key developmental transcription factors, including hom1, hom2, Pofst3, and fst4, suggesting that PoWC-1 may contribute to developmental competence independently of light. Comparative transcriptomics further revealed that PoWC-1 influences a range of metabolic pathways-such as glycolysis/gluconeogenesis, the pentose phosphate pathway, and amino sugar metabolism-that may support the energetic and biosynthetic demands of fruiting initiation. In addition, PoWC-1 appears to affect upstream signaling components, including the MAPK pathway and the two-component system, along with a suite of downstream transcription factors. These findings suggest that PoWC-1 functions as a key regulator integrating blue light signals into a multi-layered network involved in metabolic reprogramming, signal transduction, and transcriptional regulation during primordia formation in P. ostreatus. Collectively, this study provides a molecular framework for understanding photomorphogenesis in edible mushrooms.
The World Health Organization includes Aspergillus fumigatus on the list of fungal pathogens of critical priority for the development of new therapeutic options, due to the emergence of antifungal-resistant strains and high mortality rates. This work evaluated the antifungal activity of vanillin, o-vanillin, ethyl vanillin and vanillin acetate against A. fumigatus. Broth microdilution assays were performed to determine the minimum inhibitory concentrations of the phenolic compounds. Moreover, the ability of vanillin and its derivatives to inhibit conidial adhesion and biofilm formation at subinhibitory concentrations was assessed. The possible mechanism of action of the compounds by molecular docking was determined. Finally, the therapeutic efficacy of the molecules was analyzed in an in vivo aspergillosis model. Vanillin and its derivatives exhibited antifungal effects against A. fumigatus at concentrations of 0.25 to 1 mM; notably, o-vanillin showed higher antifungal activity (0.25 mM). Furthermore, vanillin, o-vanillin and vanillin acetate reduced conidial adhesion, and biofilm formation at subinhibitory concentrations. These compounds decreased ergosterol concentration, and in silico analysis showed that phenolic compounds interact with ERG5, ERG6 and ERG11. Vanillin and o-vanillin demonstrated therapeutic efficacy against aspergillosis model. Overall, these results highlight the antifungal activity of vanillin and o-vanillin against A. fumigatus as a potential therapeutic alternative.
Bacillus cereus emetic poisoning is mediated by cereulide, a thermostable cyclic depsipeptide encoded by the cesA/cesB operon under PlcR-PapR control. Once formed, cereulide resists heat and standard food processing, making transcriptional intervention the only viable biocontrol strategy. Lacticaseibacillus casei NCIM 2125, Lactiplantibacillus plantarum NCIM 2083, and a three-strain consortia additionally containing Bifidobacterium bifidum NCIM 5697 were co-cultured with B. cereus NCIM 2217 in BHI broth (1:1 v/v; OD₆₀₀ = 0.1; 37 °C) over 24-72 h (n = 3). Viable counts were determined by standard plate count, cereulide by LC-MS following liquid-liquid extraction, and cesA/cesB transcripts by RT-qPCR (2⁻ΔΔCT, dual housekeeping-gene normalisation). L. casei inhibited growth at 24 h only (1.97 log CFU/mL; p = 0.021). The consortia achieved 18.0% area-under-curve reduction and 81.6% cereulide suppression at 48 h (p < 0.001; Cohen's d = 29.03). A protein-mRNA paradox emerged: L. plantarum suppressed cesA by 87.9% at 48 h yet cereulide rose 10.5% above control (p = 0.007), attributable to depsipeptide stability post-secretion. Consortium ces silencing at 24 h (cesA FC = 0.0031) preceded peak synthesis, yielding a 77.5 percentage-point synergy bonus. Effective cereulide biocontrol requires ces silencing before the synthesis window closes, a criterion met only by the consortia.
The objective of this study was to determine the presence of quaternary ammonium compound (QAC) resistance genes in Listeria spp. strains and to evaluate the effect of temperature and substrate on interspecies gene transfer. A total of 23 L. monocytogenes strains, four L. innocua and 37 Listeria spp. isolates (excluding L. grayi, L. ivanovii, L. seeligeri, and L. welshimeri) were recovered from surfaces in a frozen vegetable processing facility. The presence of the bcrABC gene was assessed by endpoint PCR. The bcrABC gene was detected in 73.91% (17/23) of L. monocytogenes isolates, in 50.00% (2/4) of L. innocua strains and was not detected in the other Listeria species (0/37). Two L. innocua strains carrying the bcrABC gene and two L. monocytogenes strains lacking it were selected for mixed culture experiments. Four co-cultures were prepared, inoculated into tryptic soy broth and spinach extract, and incubated at 4, 25, and 36 °C for 10 days. Horizontal transfer of the bcrABC gene was observed in 7.87% (17/216) of reactions in tryptic soy broth and spinach extract, with higher frequencies at 25 °C (10/216, 4.63%) and 36 °C (6/216, 2.78%) and lower frequencies at 4 °C (1/216, 0.46%). Recipient L. monocytogenes strains revealed increased resistance to QACs (500 μg/mL).
Plant growth-promoting rhizobacteria (PGPR) represent a sustainable alternative to reduce excessive agrochemical use and strengthen environmentally responsible agricultural practices. This study aimed to isolate, identify, and molecularly characterize endophytic bacteria associated with jalapeño pepper (Capsicum annuum L.) to evaluate their potential as PGPR and their antagonistic activity against phytopathogenic fungi. In vitro assays were conducted to determine functional traits related to plant growth promotion and biocontrol. Phylogenetic analysis identified the genera Stenotrophomonas, Pseudomonas, Paenibacillus, Klebsiella, Aeromonas, and Enterobacter. Among these isolates, Klebsiella sp. IR6 exhibited the most notable agronomic performance, increasing seedling leaf area (57%), fruit production (89%), and fruit size (15% in length and 31% in diameter) under field conditions. Additionally, IR6 was non-hemolytic, suggesting low risk to human health. This strain demonstrated antagonistic activity against Fusarium oxysporum (15-34%), siderophore production, and phosphate solubilization, confirming its potential as a biocontrol agent and PGPR. Transformation with plasmid pAD4325 carrying the GFP gene, followed by confocal microscopy, revealed its endophytic colonization within root tissues. Further evaluations using different jalapeño hybrids are necessary to validate the biotechnological potential of IR6 for sustainable agriculture.
Treatment wetlands are increasingly used to treat agricultural wastewater. While plants and substrates contribute to pesticide immobilization and removal, most metabolic degradation is mediated by microorganisms. However, pesticides may negatively affect the microbial communities responsible for their degradation. This study aimed to assess whether biochar, an organic amendment commonly used in treatment wetlands, could mitigate the effects of pesticides on microbial communities. Six treatment wetland mesocosms planted with Scirpus cyperinus were sampled before and after exposure to a pesticide mixture (atrazine, glyphosate, and chlorantraniliprole) applied at three concentration levels. Half of the mesocosms were amended with biochar. Biochar did not impact microbial alpha diversity but altered community composition, particularly by modifying the relative abundance of bacterial taxa involved in nitrogen cycling. Pesticide concentration influenced root-associated fungal communities only. Eight taxa with known pesticide-degrading potential increased in relative abundance following pesticide application. Overall, our results suggest that biochar and pesticide exposure can shape microbial community composition in treatment wetlands, but without clear mitigation of pesticide impacts under the conditions tested. These findings highlight the importance of considering microbial community structure when designing treatment wetlands and underscore the need for temporally resolved studies to better understand microbial responses to pesticide exposure.
Avian colibacillosis is an infectious disease that causes significant economic losses worldwide in the poultry industry. The bacterium avian pathogenic Escherichia coli (APEC) is the etiological agent of the disease and is primarily treated with antibiotics. Unfortunately, due to antibiotic resistance in APEC, therapeutic options for treating this disease are becoming increasingly limited. Bacteriophages-viruses that infect bacteria-represent promising therapeutic candidates; however, understanding how these viruses adapt is essential before considering them for commercial applications. This study investigated the adaptation of an APEC-infecting phage to a laboratory strain E. coli K-12 host. Successive passages of the phage on the K-12 strain resulted in clear adaptation to this new host, with only a slight fitness cost on APEC. The adapted phages also exhibited smaller capsids. Genomic comparison between the adapted phages and the wild-type phage revealed three mutations that may explain the adaptation to the K-12 strain: two point mutations located in a gene encoding a hypothetical protein and a 42-bp in-frame deletion in a homologue of the gene encoding the tail spike protein TSP4. This study, in addition to identifying molecular determinants involved in the adaptation of an APEC-infecting phage, further highlights the remarkable capacity of viruses to evolve.
Staphylococcus caprae is an emerging coagulase-negative staphylococcal pathogen. This study performed pan-genome analysis to comprehensively characterize the genomic landscape of S. caprae. Phylogenomic reconstruction confirmed that it forms a distinct monophyletic clade from closely related species (Staphylococcus epidermidis and Staphylococcus capitis). Pan-genome analysis revealed an open genome (γ = 0.149 according to Heap's law) comprising 3967 gene families, 53.5% of which constitute the core genome enriched in essential metabolic functions. Cloud gene families showed enrichment in defense mechanisms and traits associated with genomic plasticity. A total of 17 antimicrobial resistance (AMR) genes were identified, most of which were scattered sporadically across S. caprae genomes in the form of cloud genes, which indicates horizontal gene transfer. The coexistence of multiple resistance determinants (e.g., mecA, blaZ, erm(A)) could potentially lead to the development of high-risk multidrug-resistant phenotypes, which would severely limit the available therapeutic options. Virulence genotypic profiling revealed conserved pathogenic mechanisms, including the complete icaADBC operon (involved in biofilm formation), a type VII secretion system and iron acquisition systems (isd). These findings provide a pan-genome-level view of S. caprae and highlight its potential role as a reservoir of AMR genes and conserved virulence-related traits.
Geographical isolation and extreme climates have resulted in the long isolation of Antarctica and sub-Antarctic islands. The result is a unique assemblage of animals, many endemics to the region. Low pathogenicity avian influenza is present in Antarctica; however, we have a poor understanding of the epidemiology, ecology and evolution of these viruses in the region. Of concern is the arrival of high pathogenicity avian influenza (HPAI) H5N1 clade 2.3.4.4b in the austral summer of 2023/24, and subsequent range expansion in the 2024/25 austral summer. Herein we review data and information from the literature (including all pre-prints, reports, and press releases), providing a narrative of events in the sub-Antarctic and Antarctica. We also address the impacts of HPAI H5N1 on Antarctic wildlife, and the unique challenges of working in the region.
This study reports on a comprehensive genomic analysis of Vibrio cholerae strains isolated from shellfish grown in Atlantic Canada, specifically the non-choleragenic non-O1/non-O139 serogroups (NOVC), with the aim to provide a baseline in research of these bacteria and inform risk characterization to human exposure. Seafood homogenates were enriched using both standard saline and modified salt-free protocols, for recovery of V. cholerae. Isolates were identified by MALDI-TOF mass spectrometry (MS), and relatedness was assessed using composite correlation index (CCI) analysis and multilocus sequence typing (MLST). Genomic characterization through whole-genome sequencing revealed that Canadian NOVC isolates cluster with environmental strains previously reported from coastal New Hampshire, USA, while CCI and MLST analyses confirmed that the isolates are closely related to each other, with several representing novel sequence types. Bioinformatic screening identified gene clusters encoding secretion systems, adherence factors, and accessory toxins, although cholera toxin genes (ctx) and the toxin-coregulated pilus (tcp) were absent. Antimicrobial susceptibility testing indicated that all isolates were sensitive to the antibiotics tested and exhibited β-hemolysis. In light of the evidence of increase in sea surface water temperature, these findings provide the first comprehensive genomic and phenotypic baseline of NOVC strains from Canadian shellfish and underscore the importance of continued surveillance as a potential increase in NOVC prevalence and human exposure risk.
Infectious bursal disease virus (IBDV) is a major cause of immunosuppression in chickens that has been shown to affect influenza A virus (avian influenza virus (AIV)) pathogenicity and shedding patterns. In this study, we compared the shedding of a low passage duck origin AIV in two groups of specific- pathogen free chickens: one group that was IBDV-inoculated and one sham-inoculated group. At 3 weeks of age, the birds were divided and intranasally given one of three doses (102, 103, 105) of A/mallard/OH/421/1987 (H7N8) low pathogenicity AIV. Although the bursae of the IBDV-infected chicks had higher lesion scores, the damage was minimal. We observed that this low IBDV exposure increased resistance to AIV challenge. Uninoculated contacts co-housed with the treatment groups given 105 AIV became infected. Additionally, chicks shedding approximately 103-4 EID50/ml AIV (CT of 33 or less) transmitted virus to cage mates. These findings demonstrate that the impacts of immunosuppressive agents on AIV challenge may vary, based on a number of confounding factors.
RNA extraction demands careful sample handling and processing due to the lack of stability of RNA in the environment. However, these conditions are sometimes challenging to achieve when working with free-ranging animals. The main objective of this study was to evaluate the efficiency of three commercial RNA extraction kits for biological samples obtained from six wild bird species (black-headed gull, griffon vulture, house sparrow, mallard, song thrush, and common starling). We extracted 24 samples (faeces, oropharyngeal swabs, and cloacal swabs) using RNeasy PowerMicrobiome Kit, RNeasy PowerFecal Pro Kit, and RNeasy Mini Kit (Qiagen). The extraction performance was assessed based on total RNA yield, RNA integrity, and purity ratios (260/280 and 260/230). Moreover, an analysis to determine the inhibitory effect of the extracted samples and a multiple linear regression model were performed. RNA extraction performance varied considerably among species, sample types, and extraction kits. Overall, the RNeasy PowerFecal Pro Kit yielded higher RNA integrity and purity values and showed lower quantitative reverse transcription polymerase chain reaction inhibition than the other kits, particularly in faecal samples. Our findings highlight the importance of selecting extraction methods according to both species and sample type when working with wildlife samples.
Pseudomonas aeruginosa is a major opportunistic pathogen responsible for severe human infections and is increasingly associated with multidrug resistance and limited treatment options. In this study, we isolated and characterized bacteriophages targeting drug-resistant P. aeruginosa strains and evaluated their capacity to disrupt biofilms and modulate biofilm-associated gene expression. Phages recovered from sewage showed broad lytic activity against P. aeruginosa and were classified morphologically into the families Podoviridae and Myoviridae. Two phages, A2 and A4, exhibited the highest lytic activity against the resistant strains examined. Both phages significantly degraded preformed biofilms, with phage A4 showing comparatively stronger antibiofilm activity. In addition, phage exposure altered the expression of several biofilm-associated genes, including pelA, htpB, bifA, psl, fimW, and wspA. A notable finding was the reversal of bifA expression from downregulation at 12 h to upregulation at 24 h following treatment with phage A4. Collectively, these results demonstrate that phages A2 and A4 possess strong lytic and antibiofilm activities and are capable of modulating biofilm-associated transcriptional responses in drug-resistant P. aeruginosa. The findings support the potential application of bacteriophages as alternative therapeutic agents against drug-resistant biofilm-associated infections.
The biocontrol potential of Methylobacterium spp. against key phytopathogenic fungi was evaluated using in vitro antagonism assays and confined germination bioassays. Across 40 Methylobacterium isolates, inhibitory activity was highly variable and strain-dependent. Fusarium graminearum (UAMH 3329) was the most consistently suppressed pathogen; however, only M. thiocyanatum (NBRC 103124) and M. aminovorans (LMG 21752) produced significant inhibition (>30%, p < 0.05) across all three Fusarium species tested. Growth suppression was enhanced on nutrient-minimum agar amended with cell-free bacterial broth, supporting the involvement of diffusible inhibitory factors in fungal growth suppression. However, marked isolate- and substrate-dependent effects suggest that antagonism is contingent on specific bacterium-pathogen combinations. In germination assays, M. organophilum (LMG 6083) conferred protection to soybean (Glycine max) seeds challenged with F. graminearum, improving germination and seedling development in both artificial and soil substrates. Co-inoculated seeds exhibited lower disease severity scores (DSS), fewer necrotic lesions, and reduced fungal colonization during germination and emergence. Collectively, these findings identify candidate Methylobacterium strains with antagonistic activity against Fusarium spp. and provide a foundation for future characterization of their effectors relevant to integrated crop protection.
Influenza A (H5Nx) highly pathogenic avian influenza viruses of clade 2.3.4.4b were first detected in North America in late 2021, initiating a multi-year outbreak unprecedented in geographic extent, duration, and host range. Surveillance conducted across Canada, the United States, and Mexico has documented widespread detections in wild birds and poultry, and repeated spillover into wild and domestic mammals. Genomic analyses reveal successive lineage replacements and extensive reassortment between Eurasian and North American lineages, with over 100 distinct genotypes identified to date. Recent events, including detection of genotype B3.13 in United States dairy cattle and the emergence of genotype D1.1 across all four North American migratory bird flyways, highlight ongoing viral evolution and cross-species transmission risks. This synthesis provides a continental overview of the outbreak from 1 November 2021 to 31 March 2025, summarizing surveillance results and genomic trends to inform continued One Health preparedness and response efforts.
The IncI1 plasmid is an important driver of antimicrobial resistance (AMR) in Salmonella enterica collected from human and poultry sources in Canada. In the present study, isolates of S. enterica subsp. enterica serovars Heidelberg (n = 1791) and Kentucky (n = 266), collected over 15 years of surveillance of Canadian poultry production, were subjected to whole-genome sequencing, from which IncI1 plasmid sequences were identified and extracted for genomic and epidemiological analyses. Extracted IncI1 sequences (n = 1123) were used to construct a novel plasmid core-genome multilocus sequence typing (pcgMLST) scheme, which was applied to a subset of plasmids specifically from chicken production (n = 940). From the pcgMLST analysis, four IncI1 genomic groups were identified, corroborated by differences in AMR potential and allelic diversity within and between groups. These groups were used to inform a multilevel multinomial model, which revealed associations with sampling year, location, and production stage. Taken together, this work demonstrates that IncI1 plasmid population dynamics in S. Heidelberg and S. Kentucky circulating in Canadian poultry production are complex and influenced by multiple factors driving dissemination across Canada.
