Work Package 1

WP1 investigates manure management practices through a comprehensive literature review, alongside an assessment of manure-associated pollutants across selected case studies. The literature review establishes an inventory of the most current strategies by identifying and selecting relevant studies. To date, these efforts have resulted to a total of more than 10,000 relevant studies currently under full-text screening, which will form the foundation for this inventory.

The pollutant assessment spans 30 case-study farms across Belgium, the Netherlands, Germany, Ireland, Italy, Spain, and Poland. Sampling is designed to include manure intended for fertilization, along with corresponding soil samples collected immediately before fertilization, directly after manure application and three weeks post-application. At this time, analysis is still incomplete, but early results already point to widespread occurrence of antibiotic residues in manure. Residues have been detected in most the manure samples analyzed so far, often as mixtures of multiple compounds within a single sample. Among these, doxycycline, lincomycin and oxytetracycline appear most frequently, with particularly high concentrations observed in some cases, including lincomycin levels reaching 3,600 µg/kg in pig manure. As expected, concentrations measured in manure exceed those found in soil. However, the relationship between manure application and soil contamination is less straightforward. Initial comparisons between soils sampled before and immediately after fertilization show no significant increase in either the concentration or diversity of antibiotic residues. This suggests that residues are already present in many soils prior to manure application and may persist over time, independent of recent inputs. Across the soils analyzed, a diverse set of antibiotics has been detected, with oxytetracycline, flumequine and doxycycline among the most detected. In some instances, high post-fertilization concentrations are still recorded, such as chlortetracycline reaching 1,305 µg/kg, highlighting the variability between sites and compounds. So far, microbial indicators show a more dynamic response to fertilization. Manure itself frequently contains antibiotic-resistant bacteria, including ESBL-producing Escherichia coli and vancomycin-resistant Enterococci, and pathogens (Salmonella and Campylobacter). Following manure application, soil samples exhibit clear increases in total E. coli Enterococci populations. These increases appear to be temporary: within three weeks, levels of resistant E. coli and Enterococci decline back toward those observed before fertilization. In contrast, resistant bacteria and pathogens do not typically spread to the soil. Water bodies near farms do not show a clear response to manure fertilisation in terms of pathogens and antibiotic-resistant bacteria. However, they show a similar pattern of antibiotic resistance genes occurrence: genes that confer resistance to tetracycline (tetW, tetQ, tetO), beta-lactams (blaCMY) aminoglycosides (aac(3”)-Ib) and phenicols (fexA) were detected in most water samples, no matter the origin.

Further analyses are currently underway, including the quantification of a broad panel of antibiotic resistance genes, as well as the assessment of heavy metals and key physico-chemical properties. In parallel, air pollutant emissions, specifically ammonia, methane and nitrous oxide, are being incorporated as additional outputs, supported by case study–level questionnaires. Together with additional sampling data, these analyses are expected to provide a more comprehensive understanding of the environmental dynamics involved and will support other Nutritive tasks.