Antimicrobial resistance (AMR) is a global health challenge requiring cross-sector action, with research largely focused on chickens, leaving ducks underexplored. This study examines AMR dynamics in Ross 308 broilers and Cherry Valley ducks over 15 months and 15 stocking periods under consistent rearing conditions. A total of 96 pooled samples were collected: 50 from broiler farms (26 biological, 24 environmental) and 46 from duck farms (24 biological, 22 environmental). Using next-generation shotgun sequencing, 3,665 distinct AMR types were identified: 1,918 in broilers and 1,747 in ducks. Host-specific AMRs comprised 25.3% in broilers and 18% in ducks, while 56.7% were shared. AMR diversity declined across production phases, with broilers losing 641 types and ducks losing 308, yet AMR frequencies increased significantly by the finisher phase (p < 0.0001). Based on in silico data, prophylactic antibiotic use significantly reduced the prevalence of multidrug-resistant bacteria in both poultry species (p < 0.05). Hospital-acquired infection-associated AMRs were higher in broilers than in ducks at the start of production but declined significantly by the end of the rearing period (p < 0.0001). Above-average resistance markers accounted for approximately 10% of all detected resistance determinants. Tetracycline and phenicol resistances emerged as the most prevalent. 13 high-resistance carrier (HRC) species were shared between both hosts. Broiler-specific HRCs exhibited significantly higher abundances (relative frequency: 0.08) than duck-specific HRCs (relative frequency: 0.003, p = 0.035). The grower phase emerged as a critical intervention point. In farm environments 15 broiler-specific and 9 duck-specific biomarker species were identified, each strongly correlated with poultry-core HRCs (correlation coefficient > 0.7). Broiler exhibited higher abundances of key resistance genes, with tetracycline resistance predominantly associated with Bacteroides coprosuis, Pasteurella multocida, and Acinetobacter baumannii. Despite its limitations, this research provides key insights into AMR trends in two major poultry types, guiding targeted interventions and sustainable management strategies.

Soil salinity is a major global challenge, reducing fertility and crop productivity. This study evaluated the effects of various soil management practices on the physical, chemical, and microbial properties of saline soils. Six treatments, combining loosening, ploughing, disking, and gypsum amendment, were applied to solonetzic meadow soil with high sodium levels. Soil penetration resistance was measured using a Penetronik penetrometer, while chemical analyses included pH, total salt content, calcium carbonate (CaCO₃), humus, and exchangeable cations (Na⁺, K⁺, Ca²⁺, Mg²⁺). Microbial composition was determined through DNA extraction and nanopore sequencing. The results showed that level A had the lowest penetration resistance (333 ± 200 N/m²), indicating better conditions for plant growth. Gypsum and loosening treatment significantly improved penetration resistance (141 N/m², p < 0.001), while gypsum amendment enhanced chemical properties (p < 0.05, p < 0.01, and p < 0.001). Gypsum application balanced soil parameters and influenced microbial communities. Reduced tillage favored functionally important microbial genera but did not support fungal diversity (p > 0.05). These findings highlight the effectiveness of gypsum amendment and tillage practices, like loosening and disking, in mitigating salinity stress and fostering beneficial microbial communities. Combining gypsum with these tillage methods proved most effective in enhancing soil health, offering insights for sustainable soil management in saline environments.

Bioaerosols have risen as pivotal constituents of airborne particles. Closely intertwined with the agricultural domain, these particles exert a significant influence on crops through the dissemination of various microorganisms that modulate crop growth dynamics, adaptive responses to environmental stimuli, and the nutritional profile of agricultural products. As the main vector, airborne particles are at the forefront in the transmission of plant pathogens. Therefore, this review explains the main factors influencing their composition in agricultural settings and their spreading. Furthermore, it elucidates the complex bioaerosol-based communication networks, including bacteria–bacteria, bacteria–plant, and plant–plant interactions, mediated by specialized volatile organic compounds (VOCs) released by plants and bacterial volatile compounds (BVCs) produced by bacteria. These compounds play a crucial role in synchronizing stress responses and facilitating adaptive processes. They serve as a pathway for influencing and regulating the behavior of both plants and microorganisms. Delving into their origin and dispersion, we assess the key methods for their collection and analysis while also comparing the strengths and weaknesses of various sampling techniques. The discussion also extends to delineating the roles of such particles in the formation of biodiversity. Central to this discourse is an in-depth exploration of their role in the agricultural context, particularly focusing on their potential utility in forecasting pathogen transmission and subsequent plant diseases. This review also highlights the importance of applying bioaerosol-based strategies in the promotion of sustainable agricultural practices, thus contributing to the advancement of ecological balance and food security, which remains a neglected area in scientific research.

Over the past 20–25 years, the poultry industry has evolved into a specific protein production system. However, the stress resulting from intensive rearing practices has led to numerous negative consequences, making the optimisation of livestock gut microbiome composition crucial for mitigating these effects. Advancements in modern molecular biology methods have brought attention to the impacts of nutrients on gut microbiota. In our study, we extensively investigated the changes induced by feed formulations rich in phytonutrients on the gastrointestinal microbiota of livestock using targeted 16S rRNA amplicon sequencing. Our objective is to examine how the developed feed prototype affects the composition of core microbiomes in raised poultry, community diversity, and the resilience of complex microbial networks. We seek correlations between biological livestock and environmental samples to identify which community constituents, in what proportions and occurrences, may play a role in the development of specific diseases. Based on our measurement results, it can be asserted that allithiamine positively modulated "beneficial" community constituents. Beyond the impact of allithiamine-enriched feed rich in phytonutrients, the composition of the microbial community in the poultry gastrointestinal tract is significantly influenced by the age of the birds. Furthermore, due to the presence of multi-drug-resistant pathogens in environmental samples from livestock facilities, appropriate transmission risk management measures are of paramount importance.

This study investigated phase-dependent changes in gut microbiome composition, predicted functional potential, and lipid metabolism in intensively reared broiler chickens and ducks across the starter, grower, and finisher phases (from day-old to 42 days of age), over six production cycles (four chicken and two duck cycles), using 16S rRNA sequencing and blood lipids profiling. A total of 70 pooled manure samples were collected (46 from chickens and 24 from ducks), along with 34 blood samples (22 from chickens and 12 from ducks), all obtained under standard production conditions. Microbial diversity remained stable across growth phases within each species, whereas clear interspecies differences were observed (p < 0.01). Microbiome maturation involved a shift from early facultative and environmentally associated taxa during the starter phase (day-old to 14 days of age), including Acinetobacter (p < 0.01) and Enterococcus (p < 0.001), toward a more stable, host-adapted community. At the level of predicted functional pathways, shifts between growth phases were more pronounced in ducks. Predicted gene-level profiles showed phase-specific differentiation in chickens, with starter-associated genes linked to core carbon and nitrogen metabolism and finisher-associated genes related to structural and transport functions, whereas ducks exhibited a more balanced reorganization involving carbohydrate, energy, and nitrogen metabolism. Host lipid profiles between adjacent growth phases showed dynamic shifts in ducks (p < 0.05). These species-specific lipid patterns were mirrored by microbiome–lipid associations, as demonstrated by correlation analyses between dominant bacterial genera and blood lipid parameters, revealing more coordinated relationships in chickens and more heterogeneous patterns in ducks. Overall, these findings demonstrate species-specific organization of gut microbiome changes and their integration with blood lipid profiles under intensive production conditions.

Background and aims: Tillage and fertilization are key soil management practices that influence soil microbial communities, nutrient cycling, and crop performance. However, how management − induced microbial changes relate to crop nutritional performance remains insufficiently understood. Therefore, this study aimed to evaluate the effects of ploughing and deep loosening, as well as contrasting fertilization regimes, on soil microbial community composition and diversity, and to relate these practices and microbial responses to grain nutritional traits, including protein content, antioxidant activity, and carotenoid concentration in maize and wheat. Methods: Field experiments were conducted within established long − term trial sites, using two tillage methods, ploughing and deep loosening combined with two fertilization regimes (moderate and extensive input) across fifteen nutrient treatments. Sixty − four soil and grain samples were analyzed. Microbial diversity and functions were analyzed by metagenomics, and grain traits by biochemical assays. Results: Tillage and fertilization significantly altered soil microbial communities and their network organization. Ploughing increased alpha diversity ( p < 0.05) but favored generalist, stress − tolerant taxa, whereas deep loosening supported more specialized assemblages. Balanced fertilization enhanced network density and modularity (density up to 0.46; modularity 0.108–0.121), while extensive fertilization disrupted network structure. These microbial shifts were mirrored in grain traits. Ploughing increased carotenoid concentrations ( p < 0.001), lipophilic antioxidants showed no treatment differences ( p > 0.05), and deep loosening was linked to greater accumulation of hydrophilic antioxidants ( p > 0.05). Conclusions: Soil management shapes crop nutrition: ploughing boosts carotenoids, deep loosening favors hydrophilic antioxidants, while excessive fertilization disrupts these benefits.