Canadian journal of microbiology最新文献

Colletotrichum gloeosporioides is a destructive pathogen that causes significant economic and ecological losses in agricultural and forestry production. In search of effective biocontrol agents, this study isolated an endophytic fungus, Coniochaeta velutina, from healthy Camellia oleifera leaves and investigated its in vitro inhibitory mechanism on Colletotrichum gloeosporioides using transcriptomics and metabolomics analyses. These findings were used to evaluate the differences in gene expression and metabolite content between the treatment (Coniochaeta velutina-treated Colletotrichum gloeosporioides) and control (untreated Colletotrichum gloeosporioides) groups. The transcriptomic analysis detected a total of 15 310 expressed genes, with 3938 showing significant differential expression (p < 0.05) (2093 upregulated and 1845 downregulated genes). These genes were enriched primarily in the following pathways: mitogen-activated protein kinase (MAPK) signalling, antibiotic biosynthesis, amino acid metabolism, carbon metabolism, and peroxidase pathways. Metabolomic analysis revealed 452 metabolites in both groups, with 138 showing significant differences. These genes were enriched mainly in secondary metabolite biosynthesis, amino acid biosynthesis, and α-linolenic acid metabolism. Transcriptome and metabolome association analyses, along with qRT-PCR results, revealed that the levels of intracellular pectolinarigenin metabolites significantly increased in the treatment group, leading to disrupted MAPK signalling and reduced amino acid biosynthesis, which are essential for maintaining normal cell growth. Notably, the decrease in terpenoid compounds was the primary reason that Colletotrichum gloeosporioides was inhibited by the biocontrol fungus Coniochaeta velutina. Therefore, these findings provide valuable insights into the biocontrol mechanisms of Coniochaeta velutina against Colletotrichum gloeosporioides and offer a promising foundation for the development of new anthracnose prevention and control strategies.

In northern ecosystems such as the subarctic tundra, mining activities increase stress to a point where actions are needed to promote site reclamation. Ecological restoration of these mining-impacted sites with beneficial microorganisms, such as mycorrhizal fungi, is considered necessary and useful for the growth and survival of their host plants, but also for their tolerance to poor and contaminated environments, such as mine tailings. Here, we are interested in root symbionts associated with plants from the Schefferville mining site in northern Quebec. Very few studies of root fungal communities have been conducted in such a northern environment. The spatial and host plant variation of root fungal isolates was investigated. A total of 456 culturable fungi were isolated, of which 376 were successfully identified and assigned to 106 taxa based on rDNA internal transcribed spacer analysis using ITSF-1 and ITS-4 primers. The most commonly isolated fungi belonged to three genetically related groups: the Rhizoscyphus ericae aggregate, the dark septate endophytes, and Umbelopsis rammaniana and Mortierella sp., which are known to be genetically very close and often misclassified as one another. These groups were present on both disturbed and natural sites, but it appears that plants from disturbed sites had a greater affinity for dark septate endophytes. This study is the first step in the development of a restoration plan for the Schefferville mining site, and the baseline data obtained open new avenues for future studies, including the use of indigenous mycorrhizal-based biofertilizers to implement ecological revegetation strategies.

Declining costs of sequencing technology have catalyzed the widespread use of high-dimensional complex omics datasets in microbiology. While rich in information, these datasets present major analytical challenges, including sparsity, heterogeneity, and the need for robust statistical validation. Concerns about the reproducibility of findings across microbiological studies underscore the importance of standardized, transparent analytical approaches. Despite the availability of diverse statistical frameworks and machine learning methods, designing an appropriate statistical workflow (from method selection to model evaluation) remains challenging, particularly for researchers with limited advanced statistical training. Missteps in this process can lead to misinterpretation, irreproducibility, and flawed conclusions. This paper provides a structured, step-by-step framework to guide and validate the methodology of choosing the right statistical methods for both explanatory and predictive modeling in microbiology and translational research. We outline essential decision points spanning data preprocessing, feature selection, model assumptions, and model evaluation, and highlight common trade-offs and practical considerations. To demonstrate the guide's utility, we analyze a real-world COVID-19 dataset to identify cytokine biomarkers associated with disease severity. By aligning analytical strategies with microbiology inquiry, this guide aims to enhance reproducibility, empower data-informed decisions, and promote more rigorous, interpretable research in microbiology and public health.

Lake Guamuez is the second largest lake in Colombia and economically supports hundreds of families in the area. The main activities carried out in the region have focused on tourism, agriculture, livestock, and rainbow trout production; however, these activities have been associated with contamination of the lake. This research aimed to evaluate the water quality of Lake Guamuez using somatic coliphages (SCs) as bioindicators. For this purpose, periodic sampling was carried out for 6 months at nine strategic points of the lake. For the detection of SCs, the method described in 9211 D of the Standard Methods for the Examination of Water and Wastewater was used. The genomic variability and presence of virulence genes in the isolated SCs were determined. Water contamination in the lake is evident, and the SCs titer is greater in areas with a high flow of anthropogenic activities. An important degree of genetic diversity and a high prevalence of virulence genes could be observed among the SCs analyzed. The results when compared with guidelines and water quality standards from various countries showed concentrations of SCs higher than those allowed. The high prevalence of gastrointestinal diseases in the region suggests a link to water contamination.

Leptographium wingfieldii is a fungal associate of Tomicus piniperda (the pine shoot beetle) and pathogen of pines and this species is an agent of blue stain in sapwood on infected trees. This fungus was first reported from Europe and has been recently introduced to Canadian forests. Ten new mitogenomes have been sequenced and characterized, including seven strains of L. wingfieldii, two strains of L. procerum and one strain of L. terebrantis. The data were combined with other members of the Ophiostomatales collected from NCBI to gain more insight into the genetic diversity, evolution, and systematics of these fungi. The size of the studied mitogenomes of Leptographium species ranged from 41 to 126 kb with the number of potential mobile introns embedded within these mitogenomes ranging from 13 to 45. These data show that introns generate genetic diversity and confirms the contribution of mobile introns in genome expansion in Ophiostomatales fungi. This study also uncovered complex intron arrangements (twintrons) suggesting the potential of mobile introns generating complex ribozymes that may have implications in gene regulation.

Petroleum-associated water harbors diverse microbial communities, including hydrocarbon-degrading bacteria, sulfate-reducing bacteria, and methanogenic archaea. The growth and metabolism of these organisms, as well as their community composition, can affect various aspects of oil field development and oil produced water treatment. In this study, Illumina-based 16S rRNA gene sequencing was used to analyze the microbial community structures of oilfield produced water processed at two treatment stations and subjected to different treatment protocols. Significant differences in microbial community α-diversity and richness resulted from the different treatment protocols. The treatment of oil produced water effectively reduced the oil content, accompanied by the a reduction in Desulfobacterota. Proteobacteria was the dominant phylum in oil produced water; its core presence, along with Patescibacteria and Desulfobacterota, was identified in a co-occurrence network analysis of the microbial community. Redundancy analysis showed significant positive correlations between microbial community diversity and the oil and suspended solids contents of the oil produced water, highlighting the role of treatment protocols in shaping both microbial composition and water characteristics. Thus, this study provides potential insights into the processes of souring in oil fields and contributes to the theoretical understanding of oil-produced water treatment, which may inform future optimization of treatment protocols.

Iron is an essential mineral for almost all pathogenic bacteria, including Salmonella enterica serovar Typhimurium and Enteritidis. We have investigated the effect of the deletion of iroN, fepA, and fhu genes on the transcriptomic profiles of S. Typhimurium and S. Enteritidis strains with double (ΔiroNΔfepA) and triple (ΔfhuΔiroNΔfepA) gene deletions and grown under iron-deficient conditions. Significant changes were observed in the expression of genes involved in virulence, stress-response, and energy metabolism in both Salmonella serovars. The pathways most affected were the tricarboxylic acid cycle, electron transport chain, and stress responses all of which were downregulated while cysteine biosynthesis was upregulated. In general, common and/or related genes were affected in the double and triple mutant strains which indicated that the additional deletion of the fhu gene affected a limited number of genes, although S. Typhimurium showed more differences than S. Enteritidis. Nevertheless, the main difference observed between the mutants of the two serovars grown under iron-depleted conditions is the enhanced upregulation of the flagellum genes in S. Enteritidis. This study reveals evidence of novel interactions between metabolic pathways and virulence under iron limitation, providing insights into adaptive strategies that may contribute to the enhanced virulence of these Salmonella serovars.

The genus Trichoderma comprises many common fungi species that are distributed across the ecosystems. Trichoderma species have been successfully used as biofungicides due to their ability to protect plants and produce secondary metabolites (SMs) such as peptaibols, butenolides, pyridines, koninginins, and polyketide compounds. These SMs possess antimicrobial properties that allow the microbe to suppress or eliminate other pathogens, enabling it to secure a competitive nutritional niche. These SMs function as key agents in biocontrol strategies, contributing to crop protection and plant growth promotion, and are increasingly utilized in the development of bio-fertilizers. Trichoderma functions through multiple mechanisms that support plant health by inducing systemic resistance and by activating plant defense pathways. This article aims to review the bioactivity of selected Trichoderma-derived SMs with an emphasis on their beneficial effects, growth promoting attributes, and their effects on fungal prey. Additionally, the article provides a comprehensive overview of SMs in promoting sustainable agriculture and biological control.

Clade 2.3.4.4b Eurasian-origin H5N1 entered North America in late 2021 and spread across the continent. While studies have characterized the antibody response mounted by dabbling ducks following exposure, little data are available for diving ducks. This study sought to identify influenza A virus (IAV) infection and antibodies in Lesser and Greater Scaup captured in Maryland, Illinois, and Rhode Island. In Maryland, IAV seroprevalence increased from the 2021/2022 to 2022/2023 sampling season, with IAV antibody prevalence increasing for juvenile (38%-80%) and adult (82%-90%) Lesser Scaup. While adult Lesser Scaup sampled in Illinois in 2021/2022 had IAV antibody prevalence comparable to those sampled in Maryland (76% and 82%, respectively), they had higher antibody prevalence to both H5 (48% and 18%) and N1 (68% and 35%), potentially due to being sampled in March versus December and January. Our data suggest that Lesser Scaup had limited antibodies to highly pathogenic H5 IAV prior to the introduction of clade 2.3.4.4b H5N1 to North America, but relevant antibodies were widely observed in the months and year following. Our more limited data suggest similar trends may have occurred in Greater Scaup as well.