Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology最新文献

Pollution by aromatic hydrocarbon compounds is closely associated with oil industry activities and poses significant environmental and human health risks. Biodegradation using hydrocarbon-degrading bacteria, particularly in combination with dispersants, offers a promising approach to mitigate such pollution. In this study, phenanthrene was used as a model compound to evaluate the effect of dispersant addition on the degradation capacity of Bacillus subtilis strain CYA27. Two dispersants were compared: a palm oil-based dispersant (Bio-OSD) and a petroleum-based dispersant (Non-Bio-OSD). The results showed that the presence of Bio-OSD and Non-Bio-OSD enhanced phenanthrene degradation, achieving up to 73.9% and 46.7% after 35 days, respectively. This improvement was attributed to increased substrate bioavailability, the potential use of dispersants as an auxiliary carbon source via a cometabolic mechanism, as supported by the detection of catechol dioxygenase activities (C12O and C23O) and selected metabolic intermediates, which provide preliminary evidence for possible enzymatic involvement in aromatic ring cleavage. Metabolic profiling using LC–MS/MS revealed that the degradation pathways utilised in the presence of dispersants included both the salicylic acid and phthalic acid pathways, which are further metabolised through the tricarboxylic acid (TCA) cycle. In contrast, phenanthrene biodegradation proceeded without a dispersant via the formation of 4-methoxy-1-naphthol, suggesting a methoxylation mechanism that potentially reduces toxicity but does not proceed to the TCA cycle. These findings revealed that dispersants not only enhance substrate bioavailability but also alter bacterial metabolic preferences, highlighting their dual role in oil spill bioremediation strategies. This work provides novel insight into phenanthrene catabolism and the mechanistic effects of dispersants on marine PAH biodegradation.

Continuous cropping obstacle from Chinese yam (Dioscorea spp.) is widespread in China, and it seriously reduced the yield and quality. Rhizosphere soil microbiome is rich and associated with continuous cropping obstacle. However, the effect of long-term consecutive monoculture (LTCM) of Chinese yam on rhizosphere soil fungal community is still limited. In this study, fields that were consecutively cropped with Chinese yam for 1, 10 and 20 years were subjected to rhizosphere soil fungal analysis. High-throughput sequencing was used to characterize rhizosphere soil fungal community structure and function, and to determine the effect of long-term consecutive monoculture (LTCM). Results indicated that LTCM induced soil acidification, increased concentration of soil available potassium (AK) and available phosphorus (AP), increased the richness but decreased the evenness of fungal community. However, the Shannon index in YF_10Y fungal community showed the lowest value. Increasing years of monoculture resulted in significant differentiation in community composition, marked by a reduction of biocontrol fungi and an increase of pathogens. Additionally, consecutive monoculture decreased the rate of carbohydrate and amino acid degradation. The comprehensive analysis conducted in this study provides insight into rhizosphere fungal structure and function in response to LTCM of Chinese yam. Information obtained in this study could be used for the development of new microbial fertilizers for Chinese yam, which would mitigate the problems associated with continuous monoculture.

Edible mushrooms face persistent challenges in yield optimization, bioactive compound production, and climate resilience that conventional breeding methods struggle to address. Traditional approaches such as cross-breeding, protoplast fusion, and mutagenesis are limited by genetic noise, laborious screening, and unstable trait inheritance. This review proposes a transformative paradigm built upon converging advances in molecular biology and data science: the bio-digital feedback loop (BDFL) framework, integrating multi-omics, CRISPR-engineered chassis strains, and predictive phenomics for precision mushroom breeding. Our framework employs multi-omics to decipher gene networks governing critical traits, such as substrate degradation enzymes, developmental synchrony regulators, and secondary metabolite pathways. CRISPR-Cas9 and synthetic biology tools then deploy these insights to verify and design modular gene circuits in pre-engineered "plug-and-play" chassis strains, enabling conflict-free stacking of desirable traits. Artificial intelligence serves as the linchpin, not only automating high-throughput phenotyping through advanced imaging but also accelerating the entire breeding cycle by predicting trait heritability from omics data and optimizing the design of CRISPR guide RNAs and genetic constructs for efficient editing. The BDFL we describe iteratively refines strains by feeding phenomics data back into AI algorithms, enabling rapid trait optimization cycles. This transcends the trial-and-error limitations of classical methods, accelerating development of climate-smart mushrooms for circular bioeconomies including strains engineered to thrive on agricultural waste, overproduce immunomodulatory compounds, or resist emerging pathogens. The integration of predictive genomics, AI-driven phenomics, and CRISPR-edited chassis strains heralds a new era of precision mycology, where mushrooms are computationally designed as sustainable solutions for global food security, pharmaceutical innovation, and ecological resilience, ultimately transforming fungi into programmable biological factories tailored to address pressing agricultural and ecological challenges.

The emergence of multidrug-resistant pathogens has increased the urgency for alternative treatment options for infections like cystitis. This study focused on the green synthesis of silver nanoparticles and cysteine-conjugated silver nanoparticles utilizing Melaleuca lanceolata leaf extract, optimized via artificial neural networks for controlled nanoparticle size. The ANN model provided precise prediction and control of nanoparticle size, reducing experimental variability. The characterization was performed using UV–Vis spectroscopy, which showed peaks at 445 nm for AgNPs and 405 nm for Cys-AgNPs. Additionally, FTIR, SEM, and EDX analysis confirmed the successful synthesis of AgNPs and their conjugation with cysteine. Biological analyses revealed that Cys-AgNPs had increased antioxidant and anti-inflammatory effects over AgNPs and controls. Notably, they demonstrated better antibacterial activity against Staphylococcus nepalensis, a new uropathogen causing cystitis, with a 17 mm inhibitory zone and a lowest inhibitory concentration of 25 µg/ml. Direct cytotoxicity assays and in vivo studies in animal models were not carried out, but the observed reduction in hemolysis in vitro demonstrates that it may be biocompatible. These results demonstrate the novelty of using ANN-based optimization and green nanotechnology to produce stable, functionalized nanoparticles of therapeutic interest. It is recommended that cytotoxicity analyses, in vivo confirmation, and wider MDR pathogen testing should be performed in the future to ensure clinical relevance.

Microbial inoculants show potential for remediating nitrate-rich, salinized soils. However, native strains often exhibit suboptimal performance under high-salinity and high-nitrate conditions, limiting their practical application. To develop a nitrate-reducing strain suitable for saline soil remediation, we adaptively acclimated a nitrate-reducing Bacillus velezensis strain BV-1 under high-nitrate conditions to enhance its salt tolerance and nitrogen metabolic capacity. The acclimatized strain exhibited significantly upregulated nar genes (4.71- to 7.56-fold) and nirD expression (1.36-fold), indicating enhanced nitrate assimilation and dissimilatory nitrate reduction to ammonium activity. In pot experiments, inoculation with this strain resulted in 46.85% nitrate removal, improved nutrient utilization (with increases of 21.86% in ammonium-N and 29.64% in available phosphorus utilization), and a 20.82% increase in lettuce fresh weight. These findings demonstrate that microbial acclimatization is an effective strategy for developing robust bioinoculants, with broad implications for sustainable agriculture and microbial strain engineering in salinized environments.

The COVID-19 pandemic affected the global healthcare delivery system, raising concerns about its influence on antimicrobial resistance (AMR). This systematic review and meta-analysis assessed the impact of the COVID-19 pandemic on the prevalence of MDR bacteria in different healthcare environments. A systematic search was carried out in PubMed-MEDLINE, Embase, Web of Science, BIOSIS, Scopus, and Google Scholar for articles published from December 2019 to January 2024. After screening 77 full-text studies, 28 studies were included in the analysis. The inclusion criteria included original human studies presenting MDR bacteria incidence before and during/after COVID-19 with reference to Carbapenem-resistant Acinetobacter baumannii, Carbapenem-resistant Enterobacteriaceae, Vancomycin Resistant Enterococci, Carbapenem-Resistant Pseudomonas aeruginosa, Methicillin-resistant Staphylococcus aureus, and Extended-Spectrum Beta-Lactamase-producing Enterobacteriaceae. The overall odds ratio (OR = 0.91, 95% CI: 0.70–1.17) indicates no significant change in the prevalence of multidrug-resistant (MDR) bacterial infection between the pre-COVID-19 and the COVID-19 period. There was no significant change in the prevalence of MRSA, ESBL, and VRE pre- and post-COVID. However, there was a significant reduction in the prevalence of CR-Ab, CRE, and CRPA pre- and during/after-COVID-19. MDR prevalence was significantly increased in Asia (18%) while it decreased slightly in North America (10.3%), showing variations in antibiotic use. The findings show that COVID-19 has different effects on the prevalence of MDR bacteria across geographical regions and healthcare facilities.

The anti-inflammatory, antioxidant properties of many probiotic microbes and their ability to modulate the composition of intestinal flora suggest that they have the potential to prevent and/or treat nonalcoholic fatty liver disease (NAFLD). The present study provides evidence that Lactiplantibacillus plantarum HP-B1280 can significantly reduce fat accumulation and inflammatory cell infiltration within the hepatocytes of fatty liver mice and thus may have potential application value in the prophylaxis and treatment of NAFLD disease. HP-B1280 also exhibits an extremely high level of resistance to acids and bile salts. The fermentation broth of HP-B1280 cultures is effectively suppresses the growth of a variety of common human pathogens. A comprehensive analysis of the complete genome sequence of L. plantarum HP-B1280 was conducted. Results indicated that the genome of L. plantarum HP-B1280 was devoid of resistance genes, drug resistance genes, as well as virulence factors. The annotation of the genome provides a foundation for further studies on the mechanism underlying the prevention and treatment of NAFLD by L. plantarum HP-B1280. In summary, the findings of the present study provides valuable insights into the potential use of probiotics, such as L. plantarum HP-B1280 in the amelioration and prophylaxis of NAFLD.

Cordyceps militaris is a rare and highly valued medicinal fungus that has attracted considerable attention due to its production of diverse bioactive compounds, including nucleosides such as cordycepin, polysaccharides, lovastatin, carotenoids, etc., all of which exhibit significant nutritional and therapeutic potential. However, the large-scale utilization of C. militaris is constrained by several critical challenges. A major limitation is the progressive degeneration of strains over successive subcultures, which adversely affects fruiting body formation and metabolite biosynthesis. Moreover, genetic instability during long-term culture, contamination risks in large-scale production, and the lack of standardized cultivation and extraction protocols often result in variable product quality. The absence of efficient genetic transformation systems and the low success rate of genome editing approaches further complicate efforts in molecular strain improvement. This review provides a comprehensive overview of the principal bioactive compounds produced by C. militaris and critically evaluates the current challenges and limitations associated with both conventional and advanced strain improvement strategies. These include conventional approaches such as mutagenesis and protoplast fusion, as well as genome-editing technologies like CRISPR/Cas9, which are employed to enhance the biosynthesis of target metabolites. Moreover, the integration of metabolic engineering frameworks offers significant potential for rational strain design, optimization of bioprocesses, and the discovery of novel therapeutic agents.

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