Phd in ENVIRONMENTAL AND EVOLUTIONARY BIOLOGY

Thesis title: Natural microbial communities and their resistance and resilience versus soil emerging contaminants

The attention to soil protection, due to its recognized overall degradation, has been raised only in the past few years. The EU proposal for a Directive on Soil Monitoring and Resilience (Soil Monitoring Law, 2024) aims at reducing the phenomenon of soil degradation and promote its good quality state necessary to achieve the soil health objective by 2050 and to comply with the international commitments relating to reset from zero land consumption and neutrality to soil and land degradation. Among the various causes of its degradation, there are decrease in organic matter, compaction and chemical contamination from legacy and emerging contaminants. However, a legal framework which reports a list of priority pollutants and their threshold limits for all soils have not been established so far. Agroecosystems are subjected to various anthropogenic impacts (e.g. use of machinery, pesticides, fertilizers) which affect its quality and the ecosystem services provided by soil biota and in particular by microbial communities. Heavy metals and antibiotics have been recognized as ubiquitous soil contaminants due to agricultural practices such as the use of agro-zootechnical waste (e.g. manure or biosolid as organic fertilizers) and reclaimed water which may contain antibiotic residues and some fungicides which contain copper. Both copper (Cu) and antibiotics (ABs) are known biocides and can also have toxic effects on natural soil microbial communities. The latter, due to their high adaptive capacity, can develop resistance to cope with presence of ABs and Cu and transmit them to other bacteria through intraspecific and interspecific mechanisms. The increase in antibiotic resistance bacteria (ARB) in natural environments is a high concern for human and ecosystem health in line with the One Health concept, which considers human health to be closely linked to that of environment and animals. The environmental antibiotic resistance spread is a complex phenomenon and can depend by various biotic and biotic factors, among them the co-presence of other contaminants and other stress factors, which can increase or decrease the resistance and resilience response of natural microorganisms. However, knowledge on this phenomenon among natural microorganisms is still limited. The overall purpose of this thesis was to improve knowledge on the effects of antibiotics, in different mixtures on soil natural microbial communities. The various experiments were performed using a degraded soil (from an organic farm, such as “L’Orto di Fabiana” Company involved in this PhD project). The soil was used for various microcosm experiments and it was differently spiked with some antibiotics (sulfamethoxazole, ciprofloxacin and chlortetracycline) and/or copper as contaminants, simulating the “worst scenarios” of multi-contamination due to various agricultural practices. In all experimental studies, the Lactuca sativa plant, an edible crop, was used to assess the effects of these contaminants in the plant-microbiome system. Moreover, three different organic soil amendments (cattle manure and its digestate and vegetal waste compost) were tested for both evaluating their use as appropriate organic fertilizers and the possibility of introducing antibiotic resistance genes in the soil.