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This research was funded by Ministerio de Ciencia e Innovacion, Spain, Grant number PID2019-105691RB-I00 and Generalitat Valenciana (Comunitat Valenciana, Spain), Grant number CIAICO/2021/149. Funding for open access charge: Universitat Politecnica de Valencia.

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Characterization of microbial communities and antibiotic resistance in the water-soil-vegetable interface of a small-scale organic field

Publicat a:Alzheimers Res Ther. 345 114147- - 2025-04-01 345(), DOI: 10.1016/j.scienta.2025.114147

Autors: Soler, Lara; Moreno-Mesonero, Laura; Jimenez-Belenguer, Ana; Castillo, Maria Angeles; Zornoza, Andres; Garcia-Ferrus, Miguel; Garcia-Hernandez, Jorge; Moreno, Yolanda

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The consumption of organic fresh vegetables and fruits is on the rise globally, offering a more sustainable option compared to conventional products. However, their raw or minimally processed nature raises concerns about microbiological safety. This study investigates the microbiota diversity, free-living amoebae (FLA) microbiome, and antibiotic-resistant genes (ARG) and bacteria in irrigation water, soil, and vegetables from a small-scale organic field in Spain, to understand how the microbiomes of irrigation water and soil influence the microbial composition of fresh produce. Samples from irrigation water, soil, and fresh produce were analyzed using next-generation sequencing (NGS) to characterize bacterial, eukaryotic, and FLA microbiomes. The presence of betalactamase antibiotic-resistant Gram-negative bacteria and ARGs was also examined. Soil samples had the highest microbial richness, followed by water and fresh produce. Predominant bacterial phyla included Proteobacteria, Firmicutes, Actinobacteria, Bacteroidota, and Acidobacteriota, with Proteobacteria being the most prevalent. Beta diversity analysis revealed significant differences between soil and water, and soil and fresh produce, with clustering between water and fresh produce indicating potential microbiological transfer. Distinct eukaryotic microbial communities were identified in each sample type, reflecting their unique ecological roles. The common genera between bacterial and FLA-associated microbiomes suggested selective endocytosis by FLA. Beta-lactam and carbapenem-resistant bacteria, mainly Enterobacteriaceae and Acinetobacter spp., were prevalent in water and vegetables but scarce in soil. Resistance to third-generation cephalosporins was 65%, with 30% for carbapenems. Multi-drug resistance (MDR) was found in 31 isolates. Various resistance genes were detected, mostly in vegetables and water samples. This is the first study to jointly investigate the eukaryotic and bacterial micro-biomes of soil, irrigation water, and fresh produce, along with antibiotic-resistance determinants in an organic field ecosystem. The findings highlight the need for stringent microbiological control in irrigation and a comprehensive approach to managing organic fresh produce contamination.

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