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REVIEW PAPER
Managing soil contamination risks: Microbiome and agricultural practices: a review
1
Council for Agricultural Research and Economics (CREA) – Center for Agriculture and Environment, Rome, Italy
2
Council for Agricultural Research and Economics (CREA) – Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
3
Ente Regionale per i Servizi all’Agricoltura e alle Foreste (ERSAF) - Department of Agriculture, Milan, Italy
4
Council for Agricultural Research And Economics (CREA) – Center for Viticulture and Enology, Asti, Italy
5
Department of Plant Protection, The National Institute of Horticultural Research, Konstytucji 3 Maja 1-3, 96-100 Skierniewice, Poland
Final revision date: 2026-07-26
Acceptance date: 2026-07-29
Publication date: 2026-09-17
Corresponding author
Loredana Canfora
Center for Agriculture and Environment, Rome, Italy, Council for agricultural research and economics (CREA), Italy
Center for Agriculture and Environment, Rome, Italy, Council for agricultural research and economics (CREA), Italy
Eligio Malusà
Council for Agricultural Research And Economics (CREA) – Center for Viticulture and Enology, Asti, Italy
Council for Agricultural Research And Economics (CREA) – Center for Viticulture and Enology, Asti, Italy
Int. Agrophys. 2026, 40(4): 449-467
HIGHLIGHTS
- Better risk tools are needed for antibiotics and microplastics in soils
- Microbial treatments can lower contaminants in soils and organic fertilisers
- Microbiome indicators support EU soil health and sustainable farming
KEYWORDS
TOPICS
ABSTRACT
Microbial diversity and function are central components of soil quality and overall soil health. When ecological conditions shift-whether because of farming practices or contamination-soil microbial communities can undergo structural and functional changes that ultimately alter soil fertility and ecosystem performance. To effectively assess how anthropogenic agricultural stressors affect soil functions, we need tools that provide valuable information to various soil stakeholders (farmers, industry, authorities, and citizens) to address these stressors through environmental risk assessment. Some measures should also be implemented to reduce the risk of ongoing contamination from common agricultural practices, such as the distribution of fertiliser products, particularly those of livestock origin. This review presents potential methods for assessing soil contamination using soil microbiome analysis, highlighting their challenges. Moreover, methods to reduce the load of emerging soil contaminants (antibiotics, microplastics) and organic fertilising products based on microbial processes are also described.
CONFLICT OF INTEREST
The authors declare that they have no conflict of interest.
AUTHORS' CONTRIBUTIONS
L.C., E.M.: conceived the study; All authors wrote the papers; All authors reviewed the papers. All authors have read and agreed to the published version of the manuscript.
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