Synteny Patterns of Class 1 Integrons Reflect Microbial Adaptation and Soil Health in Agroecosystems

Andrea Visca (), Manuela Costanzo, Luciana Di Gregorio, Lorenzo Nolfi, Roberta Bernini and Annamaria Bevivino
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Andrea Visca: Department for Sustainability, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, Via Anguillarese 301, 00123 Rome, Italy
Manuela Costanzo: Department for Sustainability, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, Via Anguillarese 301, 00123 Rome, Italy
Luciana Di Gregorio: Department for Sustainability, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, Via Anguillarese 301, 00123 Rome, Italy
Lorenzo Nolfi: Department for Sustainability, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, Via Anguillarese 301, 00123 Rome, Italy
Roberta Bernini: Department of Agriculture and Forest Sciences, University of Tuscia, 01100 Viterbo, Italy
Annamaria Bevivino: Department for Sustainability, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Casaccia Research Center, Via Anguillarese 301, 00123 Rome, Italy

Agriculture, 2025, vol. 15, issue 17, 1-14

Abstract: Mobile genetic elements such as integrons are key drivers of microbial evolution, enabling rapid adaptation to environmental pressures through the acquisition and rearrangement of gene cassettes. In this study, we explored the structural diversity and synteny of class 1 integrons ( intI1 ) across a set of agroecosystem-related environments, including digestate, compost, and rhizosphere soils from wheat crops ( Triticum durum and T. aestivum ). Our results reveal distinct gene cassette architectures shaped by the origin of the samples: digestate harbored the most diverse and complex arrays, while compost displayed streamlined structures. Rhizosphere soils exhibited intermediate configurations, reflecting a dynamic balance between environmental exposure and host influence. Genes associated with resistance to antibiotics and heavy metals, such as qacEΔ1 and ebrA , were differentially distributed, suggesting site-specific selective pressures. The observed patterns of cassette organization and diversity underscore the role of integron synteny as a molecular fingerprint of microbial adaptation. These findings position class 1 integrons as promising bioindicators of soil health and functional resilience, supporting a One Health approach to sustainable agriculture and microbial risk monitoring.

Keywords: intI1; resistome; mobilome; antimicrobial resistance; gene cassette (search for similar items in EconPapers)
JEL-codes: Q1 Q10 Q11 Q12 Q13 Q14 Q15 Q16 Q17 Q18 (search for similar items in EconPapers)
Date: 2025
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