Work

Microbiological Risks in Organic Farming: Implications for Food Safety, Farmers’ Health and Agroecosystem Functioning

Year: 2026

Type: article

Abstract: Environmental microbiology provides essential tools for understanding and managing biological risks in sustainable agricultural systems. Organic farming, which prioritises closed nutrient cycles, soil biological activity and reduced reliance on synthetic inputs, exemplifies the principles of sustainable agriculture. Yet the same practices that support agroecosystem functioning—application of animal manure, outdoor livestock access and limited use of chemical disinfectants—can increase the environmental occurrence of pathogenic microorganisms, antimicrobial-resistance determinants and other biological contaminants. This review examines how concepts and methods of environmental microbiology can be adapted to strengthen pollution control, food safety and agroecosystem resilience in organic production. Major biological hazards are evaluated, including enteric bacteria (Campylobacter spp., Shiga toxin-producing Escherichia coli, Salmonella spp., Listeria monocytogenes), antimicrobial-resistant bacteria and resistance genes, foodborne viruses, intestinal parasites and mycotoxins (as secondary metabolites of filamentous fungi). Quantitative microbial risk assessment (QMRA) is presented as a framework that links environmental occurrence data to public-health outcomes and identifies critical control points along the farm-to-fork continuum. Transmission pathways through organic fertilisers, soil, irrigation water and agricultural bioaerosols are analysed together with microbial survival strategies (biofilm formation, the viable-but-non-culturable state and internalisation into plant tissues). Available evidence indicates that microbiological risks appear to be driven more by management practices than by the organic or conventional production label itself; however, this conclusion must be interpreted with caution because comparative studies are frequently confounded by geographical area, livestock and housing type, farm size, climatic conditions, antimicrobial-use patterns, manure-treatment regimes and methodological differences. Validated composting, appropriate pre-harvest intervals, protection of water sources, biosecurity measures and continuous environmental monitoring effectively reduce pathogen dissemination while preserving the ecological benefits of organic farming. Lower antimicrobial resistance in organic livestock further contributes to pollution control within a One Health perspective. Occupational exposure to bioaerosols remains a relevant concern for farmers’ health, yet differences between organic and conventional systems are driven more by activity type and housing conditions than by certification status. By integrating environmental microbiology, quantitative risk assessment and practical management strategies, this review provides a distinctive One Health framework for adapting microbial knowledge to organic systems in a way that simultaneously advances pollution control, food safety and agroecosystem functioning. Importantly, elevated occurrence of a hazard does not automatically equate to elevated health risk; the latter requires quantitative exposure assessment within a QMRA framework.

Source: Sustainability

DOI: 10.3390/su181910085

Authors: Anna Ligocka, Julia Czuba

Institutions: Bydgoszcz University of Science and Technology, Nicolaus Copernicus University

Language: English

Topic: Listeria monocytogenes in Food Safety

Subfield: Biotechnology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Zero hunger

Open Access status: gold

Estimated APC paid: $2,896