Frontiers in Microbiology最新文献

Utilizing beneficial plant growth-promoting rhizobacteria (PGPR) offers an effective approach for achieving sustainable crop production. However, research on the application and mechanisms of PGPR seed coating in potato (Solanum tuberosum L.) remains limited. Therefore, we conducted a two-year field experiment involving five seed-coating treatments: untreated (CK), chemical coating (CB), Bacillus velezensis coating (SM), and two composite formulations, CM1 (Bacillus subtilis + Paenibacillus mucilaginosus) and CM2 (Bacillus subtilis + Bacillus licheniformis). The results showed that PGPR markedly improved soil NO₃^--N and available P contents by stimulating carbon (C), nitrogen (N), and phosphorus (P) cycling enzymes. During potato flowering stages, soil NO₃^--N and available P increased by 16.29 and 17.29%, respectively. PGPR also increased plant height and stem diameter by 10.89 and 34.46% relative to CB, and elevated SPAD values and net photosynthetic rate (P_n ) at flowering by 20.22 and 32.22%, respectively. At maturity, potato aboveground, root, and tuber dry matter under PGPR increasing by 31.27, 44.21, and 41.88% compared with CB. Enhanced root biomass and nutrient acquisition promoted nutrient redistribution in potato, increasing N and P translocation to tubers by 17.13 and 50.48%, respectively. CM2 exhibited the highest tuber N and P accumulation, increasing by 66.74 and 55.25%, and achieved a 38.9% higher yield compared with the other treatments. Overall, PGPR enhanced soil nutrient availability, plant photosynthetic performance, nutrient acquisition, and nutrient translocation, thereby supporting greater biomass accumulation and promoting sustainable potato production. The PGPR seed coating represents an effective and scalable strategy for achieving resource-efficient and sustainable potato production.

Introduction: Shigella spp. are waterborne pathogens responsible for global diarrheal disease outbreaks via contaminated groundwater, drinking water, and recreational water systems. Their extremely low infectious dose necessitates the development of highly sensitive detection methods capable of distinguishing viable pathogens.

Methods: In this study, we developed and optimized a viability-discriminative droplet digital PCR (ddPCR) assay incorporating propidium monoazide (PMAxx) treatment and duplex amplification targeting both chromosomal and virulence plasmid genes. Key reaction parameters-including annealing temperature, primer and probe concentrations, and PMAxx treatment conditions-were systematically optimized. Singleplex and duplex assays were compared to verify amplification consistency. Additionally, three DNA concentration methods (direct centrifugation, PEG precipitation, and a commercial kit) were evaluated for their suitability in field applications using fecal-spiked water samples.

Results: The optimized PMAxx-ddPCR assay enabled simultaneous detection of viable S. flexneri and S. sonnei with excellent specificity. Duplex amplification showed amplification efficiencies comparable to those of singleplex assays across all targets. The method achieved a detection limit of ≤10 CFU/reaction in fecal-spiked water, and PMAxx treatment effectively suppressed signals from dead cells. Comparative evaluation of concentration methods identified effective protocols suitable for field deployment.

Conclusion: This PMAxx-ddPCR approach enables the simultaneous quantification of viable, virulent Shigella in water samples, offering a robust tool for advancing water safety monitoring and public health protection.

Introduction: Sugar beet is a crucial sugar crop, and its yield and quality are vulnerable to the adverse effects of continuous cropping. Plant growth-promoting rhizobacteria function as biological control agents and exhibit high potential for crop growth promotion.

Methods: In this study, soil subjected to continuous sugar beet cropping was selected as the experimental substrate to evaluate the effects of Sphingobium abikonense strain W2, Sphingomonas panni strain W9, Sphingomonas sp. strain W13, and their mixed bacterial suspension on sugar beet seedling growth and soil properties using pot experiments. High-throughput sequencing was used to characterize changes in the rhizosphere soil microbial community structure.

Results: The results indicated that Sphingomonads inoculation significantly improved the agronomic performance of sugar beet seedlings, as evidenced by increased plant height, stem diameter, aboveground and root fresh weight, and enhanced nitrogen and phosphorus uptake. In addition, inoculation increased soil pH, available potassium content, and sucrase activity. Microbial community analysis revealed that all inoculation treatments markedly altered the diversity and composition of the rhizosphere microbiome. Compared with the continuous cropping control, the inoculated soils exhibited a significantly higher abundance of Pseudomonadota, exceeding that observed under crop rotation. Moreover, beneficial genera (e.g., Pseudomonas, Cupriavidus, Massilia, and Novosphingobium) were enriched. Functional prediction demonstrated a significant enhancement of key metabolic processes, including ureolysis and xylanolysis.

Conclusion: Overall, Sphingomonad inoculation effectively regulated the structure and function of the rhizosphere microbial community, improved soil enzyme activity and nutrient availability, and promoted sugar beet seedling growth. This study provides a theoretical foundation and potential biocontrol strategy for mitigating continuous cropping obstacles in sugar beet cultivation.

Hydrocarbon contamination, particularly with polycyclic aromatic hydrocarbons (PAHs), poses a significant environmental challenge due to its persistence and carcinogenic effects on ecosystems and human health globally. This review explores how ML algorithms can enhance the efficiency of bio-augmentation and phytoremediation through predictive modeling, real-time optimization of microbial consortia, and plant species selection. Traditional bioremediation methods, such as bioaugmentation and phytoremediation, are characterized by slow degradation rates and sub-optimal performance in complex, multi-contaminant environmental milieus. The use of machine learning (ML) models with multi-omics data presents an advanced predictive approach to optimizing bioremediation processes by providing a systematic understanding of microbial and plant-mediated hydrocarbon degradation strategies and processes. ML models can predict which microbial strains or plant species will effectively degrade hydrocarbons under specific environmental conditions by utilizing supervised learning methods such as support vector machines and neural networks. Additionally, the combination of multi-omics data with ML facilitates the identification of critical genes, enzymes, and metabolic pathways involved in the degradation of hydrocarbons, and offers insights into the molecular mechanisms which drive the bioremediation process. The translation of laboratory-based ML models into large-scale, real-world bioremediation strategy is hindered by the complex, dynamic nature of our contaminated environments. This review paper showcases these hinderances and provides a direction for future research, including the development of field-deployable technologies, adaptive ML models, and real-time environmental monitoring strategies. The integration of ML with multi-omics holds substantial promise for enhanced efficiency, adaptability, and scalability of bioremediation strategies which ultimately mitigates carcinogenic risks often associated with hydrocarbon-polluted lithosphere.

Species in the genus Enterobacter are widely distributed and occupy diverse ecological niches. Although many species within this genus have been extensively isolated and characterized, their symbiotic associations with Tephritidae fruit flies remain understudied, particularly through comparative genomic analyses. To address this gap, we conducted a whole-genome comparative analysis of thirteen Enterobacter strains isolated from the most economically significant fruit fly species: Anastrepha fraterculus, Bactrocera dorsalis, Bactrocera zonata, Ceratitis capitata, and Zeugodacus cucurbitae. The results revealed that different fruit flies harbor distinct Enterobacter species, with Enterobacter hormaechei being the most prevalent across hosts. Notably, distinct E. hormaechei subspecies were associated with specific hosts, suggesting a potential host-driven adaptation and coevolution. Pangenome analysis highlighted a dynamic genetic structure among these strains, with significant differences in the core, shell, and species-specific gene composition. The high proportion of metabolism-related genes in the core genome suggests a conserved role in essential biological functions, whereas the enrichment of mobile genetic elements (prophages and transposons) and cell motility genes within the shell and species-specific genomes highlights the genomic plasticity and potential host-specific adaptations. Three distinct subtypes of T6SS (type VI secretion systems) gene clusters, T6SS_C1, T6SS_C2, and T6SS_C3, were detected across Enterobacter strains. T6SS_C1 and T6SS_C2 were identified in most Enterobacter strains, whereas T6SS_C3 cluster was restricted to a single isolate. Although these clusters contained thirteen core T6SS genes, they were characterized by different gene synteny and effector/immunity gene content, suggesting that different Enterobacter strains may utilize distinct mechanisms for interbacterial interactions, host manipulation, and environmental adaptation. Overall, our findings reveal the genetic basis of the symbiosis between Enterobacter species and fruit flies, shedding light on their evolutionary dynamics, diversity of T6SS, and functional traits. These results open new avenues for developing microbiome-based strategies for pest management, including the targeted manipulation of microbial communities to enhance sterile insect technique (SIT) outcomes.

New control strategies are necessary for the treatment of the bacterial diseases of hazelnut (Corylus avellana) incited by Pseudomonas avellanae and Xanthomonas arboricola pv. corylina, following the programmed phasing out of copper-based anti-cryptogamics. Based on recent evidence gathered on many crops, endophytic fungi are credited for playing a role as defensive mutualists of plants. Thus, an investigation was carried out in the hazelnut growing areas in Southern Italy in the aim to identify endophytic fungi possessing antimicrobial properties against these two pathogens. A panel of 50 endophytic isolates was selected, including species which are already known as being part of the hazelnut mycobiome, along with a few new records. These isolates were tested for antibiosis in an in vitro assay consisting in the inoculation of the two bacterial pathogens in their culture filtrates. Four isolates, belonging to Cladosporium perangustum, Talaromyces purpureogenus, Nemania diffusa and the Hypoxylon fuscum species complex, displayed consistent inhibitory effects, inducing about 90% growth suppression of both bacteria. Their capacity to effectively act as biocontrol agents will be further tested in planta.

Sources and sinks of methane within an advanced serpentinization-influenced system were investigated at the Coast Range Ophiolite Microbial Observatory (CROMO) in Lower Lake, California. Subsurface water-rock reactions at CROMO contribute to unique, high pH groundwaters and substantial methane emissions. We performed lipid analysis on biomass and measured radiocarbon and stable carbon isotopic composition of groundwater to trace the origins and fate of methane. Specific groups of microorganisms involved in methane cycling were identified through analysis of membrane lipid components. Aerobic methanotrophs dominated the samples, with evidence of heterotrophic bacteria but no detection of anaerobic methanotrophy or methanogens. Following these data, microbial activity may be a significant sink but not a major source of methane at this site.

Hyperuricemia is a common metabolic disorder associated with gout, kidney injury, cardiovascular disease, and chronic low-grade inflammation. Increasing evidence indicates that abnormalities in intestinal uric acid handling and gut microbial metabolism contribute substantially to systemic urate imbalance, particularly when renal excretion is impaired. Among microbiota-derived metabolites, short-chain fatty acids (SCFAs) have emerged as key regulators linking gut microbial ecology with uric acid metabolism through coordinated effects on epithelial barrier integrity, inflammatory signaling, and urate transport. Growing interest in prebiotics and probiotics has further highlighted the therapeutic potential of targeting SCFAs production as a complementary strategy to traditional urate-lowering drugs. Given that hyperuricemia is the primary pathogenic precursor to gout, this review also examines the role of SCFAs in modulating gout-associated inflammation. This review integrates current findings on the microbiota-SCFA-urate axis and outlines how SCFA-centered gut modulation may provide a viable framework for managing hyperuricemia and gout.

Introduction: Antimicrobial resistance in the Enterobacteriaceae poses a global health concern by jeopardizing the effectiveness of antibiotics. The scarcity of new antibiotics has prompted increased interest in natural bioactive secondary metabolites derived from microbial sources and their co-action with existing antimicrobials.

Methods: In this study, we investigated the bioactivity of crude extracts from Pseudomonas aeruginosa MC9 (accession no. MK530186) and evaluated the in-vitro antimicrobial-augmenting efficacy of its quorum sensing (QS) effectors against multidrug-resistant strains of Salmonella Typhi (S. Typhi-29C), Salmonella Typhimurium (S. Typhimurium-W20), and Escherichia coli (E. coli SS1). Mass spectrometry was used to identify secondary metabolites, and combination assays followed by growth curve analysis were performed to assess interaction effects under sub-inhibitory conditions.

Results: The MC9 extract exhibited inhibition zones of 26±1.5, 24±1, and 19±1.5 mm, with minimum inhibitory concentrations of 16, 32, and 256 mg/mL against S. Typhimurium-W20, S. Typhi-29C, and E. coli-E92, respectively. Mass spectrometric analysis revealed the presence of 5-methyl-1(5H)-phenazinone (pyocyanin), rhamnolipids, 4-hydroxy-2heptylquinoline (PQS), and 2-heptyl-3-hydroxy-4(1H)-quinolone (HHQ). Notably, pyocyanin and rhamnolipids exhibited significant antimicrobial activities across a concentration range from 0.04 mg/mL to 50 mg/mL, whereas HHQ and PQS showed no anti-Enterobacteriaceae activity up to 5 mg/mL. Combination assays demonstrated that all four QS effectors potentiate the activity of conventional antibiotics. Pyocyanin showed the highest synergistic effect, with a 300% increase in the inhibition zone when combined with sulfamethoxazole/trimethoprim (23.75/1.25 µg/mL) against S. Typhimurium-W20. Rhamnolipids exhibited a 106% increase in synergy with ceftriaxone (30 μg/mL) against E. coli-SS1, whereas HHQ (10 μg/mL) showed a 257% increase with ampicillin (10 μg/mL) against E. coli-SS1. PQS displayed the highest synergistic effect of 109% with amoxicillin clavulanic acid (30 μg/mL) against E. coli-SS1. Moreover, growth curve analysis revealed a dose-dependent reduction in bacterial growth with sub-inhibitory concentrations of antimicrobials, particularly for the combinations exhibiting the highest synergy across the QS effectors.

Discussion: These findings demonstrate the potential of the QS effectors in reducing the required dosage of antibiotics against resistant Enterobacteriaceae strains and highlight the need to develop a comprehensive understanding of the underlying mechanisms for the co-action of antimicrobials and QS mediators.

The intracellular symbiont Wolbachia, which is widespread among insects, may induce cytoplasmic incompatibility (CI) between hosts with different infection statuses. Increasing evidence indicates that symbiotic bacteria can influence host reproduction, metabolism, and other biological processes by modulating non-coding small RNAs. However, it is still unclear how Wolbachia-induced CI affects the offspring reproduction. In this study, using Drosophila melanogaster as a model system, small RNA and transcriptome sequencing were conducted on the reproductive systems of the offspring resulting from crosses between Wolbachia-infected males and uninfected females. By comparing F1 males and females to their respective paternal or maternal lines, we identified distinct intergenerational discrepancies. The male offspring of the CI cross showed a significant upregulation of immune-related genes and a notable downregulation of reproductive-related genes. Moreover, the microRNA regulatory network in the testes of the offspring was significantly disrupted, with the target genes directly involved in embryonic development, energy metabolism, immune regulation, and reproductive behavior. Additionally, increased transposable element (TE) expression and piRNA dysregulation were observed in the testes of male offspring. Overall, this study offered new insights into the intergenerational regulatory effects of Wolbachia-induced CI and its potential mechanisms.