Agricultural soils as potential habitat for human pathogens

Soil is the surface layer of the earth's crust. This thin layer of earth that we tread on without thinking about it is essential to the proper functioning of our planet. Soils provide major ecosystem services, notably for plant growth and agricultural production in general. Each soil is unique, so great is the diversity of its physico-chemical and biotic characteristics. The soil's biotic environment is particularly rich and complex. Its microscopic fraction contains microscopic animals (the microfauna), bacteria, archaea, protozoa, fungi and viruses (the microbiota). Among the extraordinary diversity of micro-organisms found in soils, some can be pathogenic to humans. Their presence, whether transitory or over very long periods, can be a source of direct or indirect contamination. This article deals with human pathogenic micro-organisms in soils. From the microbiologist's point of view, soil is considered as one of the many habitats where, under certain conditions, pathogenic micro-organisms can reside. This article will focus on agricultural soils defined in terms of their nature or productive qualities. Similarly, a detailed description of virulence mechanisms and associated pathologies is outside the scope of this article. The term "pathogen" will be understood as a human pathogen. Finally, this article will be limited to the geographical area of Europe. Following a description of the various types and species of pathogens likely to be present in soils, the links between their persistence and edaphic characteristics will be discussed. The fate of pathogens also depends on the farming practices applied to the plot, as well as climatic conditions and the time of year. Last but not least, soil is a key pathway for the transmission of pathogens in agro-environments. The presence of these undesirable micro-organisms in the soil can potentially lead to their transfer to plants and animals. Contamination of agricultural raw materials during production is therefore a potential route of entry into the food chain.

At the crossroads of environmental microbiology and epidemiology, a better understanding of the ecology of pathogens in agro-environments is necessary for a global approach to health risk management.