Annals of Microbiology · Published 2025-09-26 · DOI 10.1186/s13213-025-01816-8
Abstract Background Microbiomes inhabiting different ecosystems are connected to each other. This is highly relevant in the One Health approach, which considers as a whole the wellbeing of humans, animals, plants, and the environments they share. Since environmental and human microbiomes can be connected through food production, agricultural ecosystems have a central role in the One Health framework. Nowadays agriculture needs to implement sustainable solutions to decrease the carbon and water footprints of crop production, and the impact of agricultural practices on the microbial ecology of agri-food systems should not be overlooked. Forward In this review, we focused on two primary ecological processes related to the establishment of bacterial players entering through agricultural practices in the agri-food environments: microbial invasion and antibiotic resistance spread through Horizontal Gene Transfer mechanisms. We centred on environmental niches associated to plants, which have been defined as the most relevant bridges connecting environmental and human microbiomes, emphasizing the role of widely applied agricultural practices. Conclusions Basing on the available scientific literature, we showed that treated wastewater reuse for irrigation, manure application, as well as the use of microbial based products represent the gateways for the entrance of microbial genera able to colonize habitats related to crop production (i.e., plant, soil and water) and to possibly establish in the animal and human microbiomes. Beyond that, we showed that these practices can vehiculate emerging contaminants and strongly impact the antibiotic cycle in the environment. All in all, we pointed out that the design of technological solutions for agricultural production should be driven by a holistic consideration of their benefits and risks.
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