Canadian journal of microbiology最新文献

This study employed Illumina HiSeq high-throughput sequencing technology to analyze the V4-V5 regions of myxobacterial 16S rRNA in rhizosphere and nonrhizosphere soils of Haloxylon ammodendron in the saline-alkaline wetland of Ebinur Lake, with the aim of investigating the community structure and diversity of myxobacteria. Results indicated that myxobacterial communities in rhizosphere soils exhibited greater diversity and richness compared to nonrhizosphere soils. Soil physicochemical properties, particularly moisture content, were identified as key environmental factors influencing myxobacterial diversity. The halotolerant genus Haliangium was found to be predominant under saline-alkaline conditions. Additionally, myxobacteria demonstrated distinct ecological specificity and environmental adaptability between rhizosphere and nonrhizosphere soils. For example, the genus Enhygromyxa exhibited a negative correlation with soil moisture content in rhizosphere soils but a positive correlation with soil electrical conductivity in nonrhizosphere soils. Co-occurrence network analysis revealed complex interaction patterns among myxobacterial genera and other bacterial genera, with closer interactions observed in rhizosphere soils. This study highlights the importance of environmental factors in regulating microbial community structure and function in saline-alkaline wetlands, providing new insights into the ecological roles and interaction mechanisms of myxobacteria within the ecosystem.

RNA-Seq analysis of Mesorhizobium japonicum infected by phage Cp1R7A-A1 (full name vB_MloS_Cp1R7A-A1) revealed the transcription of all 237 putative phage genes, including 27 tRNA and 210 protein-encoding genes. All predicted protein-encoding genes of Cp1R7A_A1 showed expression. The phage tRNA genes also showed a notable expression, indicating a possible tRNA-dependant phage survival strategy. Host genes related to nutrient uptake and energy metabolism were significantly upregulated within 1-2 h post infection, likely reflecting the phage's metabolic demands. Notably, peptidoglycan-cleaving enzymes showed elevated expression after 3 h, suggesting host stress responses. These findings show the transcriptional interplay between phage Cp1R7A-A1 and M. japonicum, providing a foundation for future functional studies.

Surveillance methods for antimicrobial resistance genes (ARGs) are needed to assess potential risk of antimicrobial resistance, especially in complex environmental samples with limited data on ARG distribution. This study employed target-enrichment metagenomics (bait-capture) and a Resistomap qPCR assay to assess the resistome in marine and freshwater sediments associated with active Canadian finfish aquaculture operations. Differences in resistome profiles were considered with distance to the net-pens, concentrations of three aquaculture-associated chemical residues, and microbial communities as detected with 16S rRNA gene amplicon sequencing. With bait-capture, a total of 194 ARGs and 41 replicon types were detected across the sediment samples. Differences due to aquaculture proximity were noted in the composition of the resistome, which was dominated by tetracycline resistance genes. With qPCR, 37 out of 51 ARGs targets were detected, and proximity to net-pens or region did not show changes in resistome composition. Co-occurrence networks revealed significant correlations among genera and the resistome detected with bait-capture, highlighting a potential influence of aquaculture on ARGs in the environment. This study demonstrates the utility of bait-capture and qPCR assays in detection of ARGs in both freshwater and marine sediments from aquaculture sites that will assist further ARG surveillance.

Microscopy has always been an important tool in the investigation of the structure and growth of bacteria that possess a developmental life cycle. Prokaryotic predators are no exception. Phase contrast light microscopy and transmission electron microscopy were utilized in the 1960s to describe Bdellovibrio bacteriovorus, the first Bdellovibrio and like organism (BALO). New prokaryotic predators continue to be isolated to the present day. At the same time, new techniques in microscopy have been developed that allow researchers to ask ever more fundamental questions about the periplasmic and epibiotic life cycles of BALOs. This review outlines current methodologies available in light, electron and fluorescence microscopy and provides examples of their use in the study of BALOs. It is our fitting tribute to R.G.E. Murray.

Biotechnology offers unique opportunities for mitigating and upcycling plastic waste with low-intensity bioprocesses. Synthetic biology can further enhance bioprocesses for sustainably dealing with plastic waste and supporting a circular plastics economy. We provide an overview of current strategies for leveraging synthetic biology and microbial community engineering to degrade and upcycle plastic waste, with application to both industrial and environmental settings. We further discuss complementary strategies for pre-treating plastic materials and altering recalcitrant vinyl polymers to enhance bioprocessing efficiency. Additionally, we provide commentary on future research directions that would propel biotechnological solutions toward application in a circular plastics economy.

Fusarium head blight is a limitation to grain production and can be caused by several different Fusarium species. We evaluated the ability of matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) to perform species identifications. The method generates a unique peptide mass fingerprint (PMF) for each sample that can be matched to a reference library. We first created a reference library of PMF profiles for Fusarium species from across Canada. Then, we tested the library to perform identifications using two validation panels. The first panel consisted of 820 fungal isolates from wheat (2021-2023 harvest years) and the second was 74 fungal isolates from oat and barley (2022 harvest year). The species identity of samples from the validation panels was confirmed with high-throughput quantitative PCR using species-specific DNA markers. The first validation panel was mostly F. graminearum and there was 95% overlap between the MALDI-TOF MS and DNA-based identifications. The second panel was mostly F. poae and the identifications from the two methods had 86% overlap. Our findings indicate that MALDI-TOF MS biotyping is sensitive enough to identify Fusarium strains to their species complexes and certain Fusarium strains to the species level.

Coffee plants and beans are prone to fungal contamination that pose health risks to consumers by producing mycotoxins like ochratoxin A (OTA). Thus, the present study aimed to analyze the mycobiota of Costa Rican coffee beans, focusing on potentially ochratoxigenic species and their in vitro susceptibility patterns to antifungal agents. Fungal isolates were obtained from cherry, green, and roasted coffee beans from Costa Rica; they were identified by morphology, MALDI-TOF technology, and sequencing. The isolation frequency (FR) was 33.10% for all the samples analyzed, 49.51% for the cherry fruits, 37.67% for the green coffee beans, and 17.33% for the roasted beans. The cherry beans were mainly contaminated with Geotrichum klebahni (46.34% FR and 90.91% relative density (RD)), while the green and roasted coffee beans were mainly infected with Aspergillus spp. (22.00% FR and 55.23% RD and 13.83% FR and 77.57% RD, respectively). A total of 46.67% of A. westerdijkiae and 20.00% of A. ochraceus produced fluorescence in YES broth related with ochratoxin production. The isolates of the Aspergillus section Circumdati were susceptible to the azole antifungals. Costa Rican coffee beans could be contaminated with mycotoxigenic fungi during storage.

Klebsiella pneumoniae is a ubiquitous opportunistic pathogen of the family Enterobacteriaceae. K. pneumoniae is a member of the ESKAPEE pathogens (Enterococcus faecium, Staphylococcus aureus, K. pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli), a group of bacteria that cause nosocomial infections and are able to resist killing by commonly relied upon antimicrobial agents. The acquisition of antimicrobial resistance (AMR) genes is increasing among community and clinical isolates of K. pneumoniae, making K. pneumoniae a rising threat to human health. In addition to the increase in AMR, K. pneumoniae is also thought to disseminate AMR genes to other bacterial species. In this review, the known mechanisms of K. pneumoniae AMR will be described and the current state of AMR K. pneumoniae within Canada will be discussed, including the impact of the coronavirus disease-2019 pandemic, current perspectives, and outlook for the future.

Plant growth promotion by Pseudomonas sp. 31-12 incorporated into a lettuce seed pelleting matrix was studied. We examined (1) the effect of five rhizosphere derived bacterial strains on green oak lettuce (Lactuca sativa L.) seed germination, root and shoot growth, as a strain selection step for seed coating and seed pelletizing studies, (2) population stability of Pseudomonas sp. 31-12 incorporated into a pelleting matrix on lettuce seed stored three months at 4 °C, and (3) lettuce growth promotion in the laboratory and greenhouse by Pseudomonas sp. 31-12 coated and pelletized seed. A spontaneous streptomycin mutant of Pseudomonas sp. 31-12 (str) was used to determine population size on seed and roots of 15- and 30-day-old lettuce. The population of Pseudomonas sp. 31-12str on coated and pelleted seed decreased from 10⁴ cfu/seed to 10³ cfu/seed after 3 months storage at 4 °C. However, the population exceeded 10⁴ cfu/g root dry mass and 10⁵/g root dry mass after 15 days and 30 days in the greenhouse. Leaf fresh mass was significantly increased (P ≤ 0.05) with Pseudomonas sp. 31-12 seed treatment as compared to noninoculated seed. In conclusion, pelletized lettuce seed with Pseudomonas sp. 31-12 promoted growth and yield in the greenhouse.