Search Results (958)

The increasing consumption of fresh organic produce has given rise to concerns regarding the microbiological safety of minimally processed foods. Organic cultivation may be associated with increased exposure to environmental microorganisms due to soil-based inputs and reduced chemical interventions, including both beneficial taxa and potential foodborne pathogens. Fresh produce is known to harbour complex microbial ecosystems, which are shaped by farming practices, plant physiology, handling, packaging and storage, particularly in raw-consumed products such as leafy greens and strawberries. In this study, bacterial (16S rRNA) and eukaryotic (18S rRNA) communities were characterized by amplicon sequencing. In parallel, an amoeba-associated bacterial microbiome was analyzed and DVC-FISH was used to assess the viability and metabolic activity of pathogenic bacteria internalized within free-living amoebae (FLA). No significant differences in alpha or beta diversity were observed between organic and conventional products, suggesting microbiome convergence at the retail stage driven by post-harvest handling and processing. Potentially pathogenic genera, including Pseudomonas, Stenotrophomonas, and Acinetobacter (bacterial), as well as Tilletiopsis, Candida, and Naegleria (eukaryotic), were identified in both organic and non-organic microbiomes. The viability of FLA-internalized Pseudomonas spp. was confirmed by DVC-FISH, demonstrating that FLA act as reservoirs, enhancing pathogen persistence in fresh produce. This integrated assessment of organic and conventional fruits and vegetables at the retail stage highlights the importance of post-harvest handling and retail conditions in shaping microbiological safety. The integration of microbiome profiling with targeted viability analyses demonstrates that downstream stages are critical control points for food safety and consumer exposure, beyond the influence of the production system alone. Full article

Picea koraiensis Nakai is a precious tree species in Northeast China with excellent traits, but research on thinning effects on its growth remains limited, especially regarding soil-thinning–growth interactions. This study focused on a 50-year-old Picea koraiensis plantation in the Mengjiagang Forest Farm, Jiamusi. Four thinning intensities were set: CK (no thinning), T1 (10%–20%), T2 (20%–30%), and T3 (40%–50%). Short-term (1–3 years) stand growth, soil properties, microbial biomass, and extracellular enzyme activities were measured, with stand volume and large-diameter timber yield estimated via self-established equations. Results showed that T3 significantly promoted average DBH (1.98 × CK) and tree height growth (1.60 × CK). T2 achieved the highest increases in stand volume (38.07 m³/ha) and large-diameter timber yield (56.02 m³/ha), exceeding other treatments by 1.20–7.12 m³/ha and 5.60–11.64 m³/ha, respectively. Stand growth indices were positively correlated with thinning intensity, soil microbial biomass carbon, and soil C/P ratio; DBH and height also correlated with soil catalase activity. Thinning intensity has a direct effect on stand growth. Meanwhile, observational data show that it is significantly correlated with changes in soil organic carbon fractions and soil extracellular enzyme activity, and these correlations may constitute potential pathways that indirectly affect stand growth. Moderate-intensity thinning (20%–30%) is recommended for scientific tending and large-diameter timber cultivation of middle-aged Picea koraiensis plantations in this region. Full article

Rising global temperatures and recurrent heat waves increasingly threaten vegetable production, as vegetable crops are more thermosensitive than most field crops. Vegetable crops frequently experience severe reductions in pollen viability, fruit set, marketable yield, and quality under heat waves. Numerous reviews have substantially advanced our understanding of heat stress perception, signal transduction networks, transcriptional regulation, and thermotolerance mechanisms, primarily in model species and major field crops. However, comprehensive review articles of field-applied mitigation strategies specifically tailored to vegetable production remain limited. This review provides a critical analysis of the use of genetic resources (cultivars and grafting), field management approaches (optimized planting dates, crop rotation, canopy management, and intercropping), irrigation, nutrient optimization, biostimulants, microbial inoculants, and physical microclimate modification strategies. The research consolidates current applied and mechanistic evidence on heat-stress mitigation in vegetable crops and identifies targeted, actionable priorities for field adoption. Emphasis is placed on the integration of complementary mitigation strategies at the field scale where combined approaches may generate synergistic effects. Key research gaps include limited studies on combined heat–drought/salinity stress, lack of standardized field protocols for biostimulants, and insufficient farm-scale economic evaluations of mitigation strategies. Advancing interdisciplinary, field-validated, and climate-smart management frameworks will be essential to ensure sustainable vegetable productivity and quality stability in accelerating global warming. Full article

Long-term intensive farming has degraded the structural stability of black soil in Northeast China. This study evaluated the effects of fermentation-derived materials and fungal-derived chitin on water-stable aggregates and microbial functional potential in this soil. Four treatments were established: sterile water control (CK), uninoculated fermentation broth substrate (W), live Trichoderma asperellum fermentation broth (P), and cell-free fermentation filtrate (F). Aggregate stability was monitored during a 60-day incubation, and metagenomic sequencing was performed on the most responsive 0.5–0.25 mm dry-sieved fraction. An exogenous chitin addition experiment was also conducted to evaluate the potential contribution of fungal cell-wall-derived chitin to aggregate stabilisation. The W, P, and F treatments increased the proportion of water-stable aggregates >0.25 mm, mean weight diameter, and geometric mean diameter, while decreasing fractal dimension. Among the treatments, the uninoculated fermentation broth substrate showed the strongest effect, particularly in the 0.5–0.25 mm dry-sieved fraction. Metagenomic analysis showed that the uninoculated fermentation broth substrate altered microbial community composition, changed the relative abundances of taxa such as Sphingomonas sediminicola, Priestia megaterium, and Trichoderma asperellum, and increased the relative abundance of carbohydrate-active enzyme-related genes, including those encoding glycosyltransferases, carbohydrate esterases, and glycoside hydrolases. Chitin addition also improved aggregate stability and altered microbial community structure. These findings suggest that the uninoculated fermentation broth substrate and fungal-derived chitin improved black soil aggregate stability, potentially through shifts in microbial community composition and carbohydrate-related functional potential. This study provides a scientific basis for using fermentation-derived materials to improve the structure of degraded black soil. Full article

Salivary microbiota constitutes complex microbial assemblages and acts as a source of reliable non-invasive biomarkers for evaluating growth, metabolism, and health status of farm animals. This review explores the research value of saliva and its resident microbes in livestock health monitoring. We summarize saliva composition, physiological functions, and sampling protocols for pigs, cattle, sheep, and goats. Core microbial taxa of monogastric and ruminant species are outlined, together with their roles in digestion, rumen fermentation, growth, and stress responses. We also present classic salivary diagnostic indicators and the impacts of oral bacteria on common livestock diseases. Current research is limited by undefined causal relationships, low diagnostic specificity, and heterogeneous technical standards, and thus fails to support accurate diagnosis at the individual animal level. Future studies should elucidate microbial interaction mechanisms, standardize experimental protocols, and establish multi-index evaluation models. This review advances theoretical research and promotes the practical application of salivary microbiota in precision livestock farming. Full article

Silver pomfret (Pampus argenteus), a highly valued marine fish, faces challenges in aquaculture due to its sensitivity to environmental conditions. Recirculating aquaculture system (RAS) is likely to become a primary indoor cultivation method for silver pomfret in the future, so studying hydrodynamic characteristics at varying flow rates in silver pomfret RAS is crucial and has far-reaching implications for both aquaculture practices and economic returns. This study investigated the effects of water flow rates (low: 400 L/h, moderate: 600 L/h, high: 800 L/h) on the growth performance, nutritional metabolism, and gut microbiota of silver pomfret over an 8-week period. Transcriptome and 16S rRNA sequencing revealed that the moderate-flow-rate group exhibited superior growth performance, with enhanced expression of genes related to protein synthesis (HYOU1, PDIA6, ITGA11) and redox regulation (GLUL, DUSP1, GST). Additionally, the moderate flow rate promoted gut microbial diversity and stability, with higher abundances of fermentation- and chemoheterotrophy-related functions, suggesting improved nutrient metabolism. In contrast, high flow rates induced anaerobic metabolism, leading to lactate accumulation and reduced growth. These findings demonstrate that a moderate flow rate of 600 L/h optimizes silver pomfret aquaculture by enhancing growth, metabolic efficiency, and microbial health, providing a foundation for sustainable large-scale farming practices. Full article

Soil salinization commonly prevails in global arid and semi-arid areas, shrinking farmland and endangering ecological, agricultural and social sustainability. Therefore, it is essential to develop effective strategies for salinized soil remediation. In this study, soil samples were collected from Nanliang Farm in Yinchuan, China. Compound microbial strains (CMS) and humic acid (HA) were selected as soil amendments. A total of eight treatments with different application rates of CMS and HA were set up in pot cultivation experiments, where oil sunflower was planted. The results showed that both amendments effectively elevated soil water content and chlorophyll content, as well as multiple physiological indices of sunflower. Meanwhile, they decreased soil total salinity, proline content and malondialdehyde (MDA) content. For single humic acid treatments, Treatment F1 achieved the optimal amelioration effect: it reduced soil total salinity by an average of 24.34%, and increased sunflower plant height, leaf area and aboveground fresh weight by 5.84%, 95.01% and 77.40%, respectively. Among the single CMS treatments, Treatment S3 performed best, with an average reduction of 31.04% in soil total salinity, and increases of 5.66%, 2.85% and 8.16% in plant height, leaf area and aboveground fresh weight correspondingly. Notably, among all eight groups, the control group CK1 exhibited the most prominent improvement effect, which was significantly superior to F1 and S3. This finding suggests that long-term application (one year or more) of CMS can produce an especially strong ameliorative effect on salinized soil. Full article

Lameness in cattle is generally described as a condition characterized by an abnormal walking or posture which is often managed with copper sulfate (CuSO₄) hoofbaths, e.g., in case of digital dermatitis (DD). This review evaluates in vivo trials from the last 15 years (January 2010–March 2026) and the efficacy of CuSO₄ hoofbaths, their environmental impact, and the availability and performance of alternative products and agents (e.g., nanomaterials), with the aim of identifying sustainable management strategies for dairy farms and One Health goals. The selection criteria focused on peer-reviewed references and technical reports published in English. Hoofbath wastes can introduce high copper (Cu) loads into manure (500–2000 mg/L), leading to soil accumulation, impaired non-pathogenic microbial populations, and potential co-selection for pathogen resistance. Therefore, CuSO₄ can be effective but poses environmental risks due to Cu accumulation in soil and water, with mean concentrations reaching 5.7 ± 6.6 ppm Cu in areas where hoofbath effluent is discharged. Cu-free alternatives (e.g., quaternary ammonium compounds, organic acids) show comparable efficacy in some studies, but independent data on their environmental degradation and ecotoxicity are lacking. Although CuSO₄ hoofbaths pose environmental risks, they remain the most effective solution in improving hoof health. Controlled in vivo trials revealed that weekly 5% CuSO₄ hoofbaths can reduce the occurrence of lameness caused by hoof problems including DD by over 50%. Full article

Dairy production in Indonesia relies on two contrasting calf-rearing systems: concentrate-driven commercial dairy systems (CDS) and smallholder farms (SH). As these systems differ in feeding practices, they may influence gut development in calves. This study examined how farm management affects the fecal microbiota and metabolites in healthy and diarrhea post-weaning calves. Fecal samples were collected from 11 and 14 calves from CDS and SH facilities, respectively. Gut bacterial communities were analyzed using 16S rRNA gene amplicon sequencing, and metabolites were characterized using untargeted gas chromatography–mass spectrometry (GC-MS). Microbial diversity, metabolite profiles, and correlation networks were compared between the farm types and diarrhea status. Our results showed that farm management strongly shaped microbial community structure and metabolic outputs, but did not alter microbial richness. Although diarrhea is typically associated with reduced microbial richness, it did not affect the microbial community structure, suggesting that it primarily impacted microbial function, particularly the metabolic environment. Correlation network analysis revealed stronger linkages between microbes and metabolites in SH calves, especially under healthy conditions. Overall, these findings indicate that dietary structure is a key determinant of fermentation stability, with CDS calves showing greater metabolic instability. In contrast, SH calves maintain a more resilient, fiber-driven functional state. Full article

Global salinization affects approximately one billion hectares of land in more than 100 countries, posing a severe threat to food security and ecosystem sustainability. Microbial remediation using plant growth-promoting microorganisms offers an eco-friendly alternative to physicochemical methods. However, bridging the gap between laboratory cultivation of single strains and field-scale application of synthetic microbial communities (SynComs) remains difficult, owing to inconsistent efficacy and a lack of unified design frameworks. This review examines the evolution from single strains to rationally designed SynComs for saline soil remediation. A ‘structure–function–mechanism’ framework is proposed, integrating five core microbial modules, namely ion regulation and osmotic stabilization, ethylene and phytohormone modulation, antioxidant activation, nutrient cycle activation, and systemic resistance induction. The review elucidates key determinants of synthetic community success, including functional complementarity, strain compatibility, and host–environment matching, while revealing a marked quantitative gap between controlled experiments and field performance. Key bottlenecks are identified, including the lack of high-throughput compatibility screening, poorly quantified long-term ecological risks, and the absence of standardized application guidelines across agro-ecological zones. Finally, emerging avenues are discussed, such as microbial–microalgal symbiosis and AI-assisted design, outlining a roadmap for next-generation smart microbial products integrated into climate-resilient farming systems. Full article

Aquaculture solid waste (ASW) from intensive farming poses significant environmental challenges, yet its potential as a composting feedstock remains insufficiently evaluated. This study systematically assessed the feasibility of aerobic composting for ASW valorization through integrated feedstock characterization, composting process monitoring, microbial community analysis, and pot experiment validation. ASW collected from intensive aquaculture facilities was characterized by high phosphorus (mean TP: 6.80 mg/g), potassium (TK generally >10 mg/g), and iron (mean Fe: 49,112 mg/kg) content but low organic matter (17.60%) and total nitrogen (0.72%). Composted with rice straw powder, meat and bone meal, and mineral amendments, ASW was successfully converted into mature compost, with the thermophilic phase (>50 °C) lasting only 4 days and the seed germination index exceeding the 80% safety threshold within 15 days. The composting process exhibited an organic matter degradation rate of approximately 20.82%, along with low electrical conductivity and stable pH in the final product. Microbial community analysis revealed that ASW addition significantly altered bacterial and fungal community structure, enriching functional taxa associated with organic matter decomposition and nutrient transformation. Pot experiments conducted under equal nutrient input conditions demonstrated that the ASW-derived compost supported satisfactory crop growth, with the fresh weight of Fast-growing Cabbage reaching 106.95 g per plant. The compost also improved soil properties, including reduced electrical conductivity (72.8% lower than urea), increased soil organic matter (17.8% increase over original soil), and enhanced available phosphorus (93.0% increase over original soil). These results indicate that aerobic composting is a technically viable pathway for converting ASW into a qualified organic fertilizer, providing a preliminary scientific basis for future waste management strategy for the sustainable development of the aquaculture industry. Full article

Background/Objectives: Probiotic feed additives are increasingly used in livestock production as antimicrobial-sparing tools, yet viable microbial products should not introduce clinically relevant antimicrobial resistance genes (ARGs) into the intestinal resistome. This study evaluated farm-animal probiotic products using an integrated phenotypic, metagenomic and mobilome-aware safety framework. Methods: Seven commercially available products intended for poultry, pigs, cattle or horses were assessed using product metadata, culture-based recovery, broth microdilution minimum inhibitory concentration (MIC) profiling and Illumina short-read sequencing as a screening-level resistome approach. Reads were quality controlled, assembled, screened using the Comprehensive Antibiotic Research Database (CARD)/Resistance Gene Identifier (RGI) workflow and interrogated for plasmid-, phage- and insertion sequence/mobile genetic element-associated genomic context. Results: MIC profiles were generated for viable bacterial isolates representing Enterococcus faecium, Pediococcus acidilactici, Pediococcus pentosaceus and Bacillus subtilis. One labelled Lactobacillus plantarum component was not recovered as viable culture, and one labelled P. acidilactici component was recorded as P. pentosaceus. Sequencing-based resistome screening identified 30 antimicrobial resistance (AMR)-associated CARD antibiotic-resistant organism (ARO) hits belonging to 13 determinants across six ARG-positive coded products, while one coded product had no retained CARD/RGI hit. Profiles were dominated by recurrent Enterococcus-associated background determinants, including aac(6′)-Ii, msrC and eatAv. Plasmid prediction was positive for five hits, whereas no iMGE- or phage-associated ARG context was detected. No vanA/vanB, mcr, optrA, poxtA, cfr, extended-spectrum β-lactamase (ESBL) or carbapenemase gene was detected. Conclusions: The investigated products did not show evidence of high-priority mobile ARG carriage. Nevertheless, AMR-associated determinants and occasional predicted mobile contexts support routine integrated MIC-sequencing-based resistome–mobilome assessment of veterinary probiotic products. Because short-read assemblies do not fully resolve plasmid architecture or transferability, mobile-context predictions should be considered screening-level indicators requiring confirmatory long-read or functional testing for higher-priority findings. Full article

A livestock farm in southern Taiwan produces wastewater with high concentrations of nitrogen and organics, which inhibit anaerobic methanogens and limit the efficiency of its biogas system. To enhance energy recovery, this study developed a liter-scale microbial fuel cell (MFC) system aimed at harvesting electricity from livestock wastewater, serving as a supplementary energy recovery pathway alongside the biogas process. According to the five analyses, the chemical oxygen demand (COD) of raw wastewater ranged from 14 to 21 g L⁻¹, with acetate concentrations ranging between 40 and 112 mM. Propionate and butyrate were consistently below 32 mM and 18 mM, respectively. Ammonium ranged from 1.1 to 1.7 g-N L⁻¹, indicating the wastewater’s high organic load and elevated nitrogen content. Two liter-scale MFCs, ch5 and ch7, were operated for over 70 d. From days 7 to 28, both MFCs employed a fill-and-draw mode, achieving optimal COD removal exceeding 80%. After resolving leakage issues between days 30 and 40, the system was restarted on day 40, yielding 76% (ch5) and 82% (ch7) of COD removal. Continuous operation began on day 59, and both reactors maintained COD removal rates above 80% for most of the subsequent two-week period. The best power outputs for ch5 and ch7 reached 1.11 and 0.82 W m⁻³, respectively. Although both liter-scale reactors achieved COD removal and measurable power output, the most important finding was obtained from the inoculum comparison experiments. After 54 days of acclimating to raw wastewater solids, no significant current was observed. In contrast, digestate solids acclimated with carbon powder for 22 d produced a peak current of 42.5 A m⁻³ at 147 h, with COD removal rates of 67–73% and complete removal of organic acids. The key conclusion of this study is that anaerobic digestate exhibits electroactive microbial potential, whether operated in liter-scale reactors or acclimated with carbon powder. Further investigation into the microbial community structure is warranted to optimize system performance. Full article

Environmental biofilms are persistent structural components of livestock production systems and represent under-recognized drivers of pathogen persistence and antimicrobial resistance (AMR). This review examines the engineering, ecological, and operational factors that promote biofilm formation in dairy, poultry, and swine environments, with emphasis on drinking water distribution systems, feeding infrastructure, housing surfaces, and waste channels. Biofilms develop preferentially in low-shear zones, dead ends, and aging materials, where they enhance microbial tolerance to sanitation and facilitate horizontal gene transfer. Conventional monitoring approaches, largely based on planktonic sampling and single-time-point testing, underestimate attached biomass and fail to capture spatial heterogeneity. Although molecular and sensor-based technologies provide improved resolution, their farm-level implementation remains limited by cost, standardization challenges, and the absence of validated operational thresholds. Current EU surveillance frameworks focus primarily on antimicrobial use and resistance prevalence in animal isolates, while environmental compartments are rarely incorporated as monitored system elements. This review proposes a proportionate, risk-based approach that integrates existing farm data streams such as antimicrobial use metrics and biosecurity scoring systems with targeted environmental assessment of high-risk infrastructure. Mitigation strategies emphasize mechanical disruption, combined chemical sanitation, hydraulic optimization, material selection, and infrastructure lifecycle management. Embedding environmental biofilm control within existing engineering and stewardship frameworks supports more resilient, systems-based management of infectious and AMR risks in livestock production. Full article

In intensive animal production, the overuse of antibiotics has exacerbated bacterial antimicrobial resistance and environmental pollution. Together with gut microbiota dysbiosis and recurrent disease outbreaks, these challenges severely constrain the sector’s high-quality development. Quorum sensing (QS), a cell-density-dependent bacterial communication mechanism, can be modulated through agents that specifically inhibit or activate QS circuitry to regulate microbial community functions. Such QS modulators possess notable advantages, such as environmental benignity and high target specificity, and thus offer innovative strategies to decrease antibiotic reliance, enhance production efficiency, and reduce environmental emissions. This review examines QS modulators sourced from plants, microorganisms, animals, and synthetic processes, while highlighting key challenges such as environmental interference, resistance development, high costs, and the lack of standardized biosafety evaluations. Future research should focus on enhancing specificity, stability, affordability, and safety, with an emphasis on rational design, synergistic systems, improved manufacturing processes, and multi-target modulators. This review may provide a theoretical basis for translating QS-regulation technologies into farm-level applications, thereby advancing sustainable animal production and antibiotic-free husbandry. Full article