The use of organic amendments in agriculture is a common practice due to their potential to increase crop productivity and enhance soil health. Indeed, organic amendments of different origin and composition (e.g., animal slurry, manure, compost, sewage sludge, etc.) can supply valuable nutrients to the soil, as well as increase its organic matter content, with concomitant benefits for soil health. However, the application of organic amendments to agricultural soil entails a variety of risks for environmental and human health. Organic amendments often contain a range of pollutants, including heavy metals, persistent organic pollutants, potential human pathogens, and emerging pollutants. Regarding emerging pollutants, the presence of antibiotic residues, antibiotic-resistant bacteria, and antibiotic-resistance genes in agricultural amendments is currently a matter of much concern, due to the concomitant risks for human health. Similarly, currently, the introduction of microplastics to agricultural soil, via the application of organic amendments (mainly, sewage sludge), is a topic of much relevance, owing to its magnitude and potential adverse effects for environmental health. There is, currently, much interest in the development of efficient strategies to mitigate the risks associated to the application of organic amendments to agricultural soil, while benefiting from their numerous advantages.

The application of organic amendments to agricultural soil provides organic matter and valuable nutrients, improves soil structure, increases its water holding capacity and stimulates soil microbial communities. However, when using organic amendments of animal and/or anthropogenic origin, the risk of contamination with organic and/or inorganic compounds, as well as the risk of dissemination of potential human pathogens and antibiotic resistance genes, must be taken into account. Here, we characterized seven amendments used in organic farming, in order to evaluate the agro-environmental consequences of their utilization. Amendments (vermicompost, bokashi, municipal solid waste, compost in pellet form, composted cow manure from intensive farms, composted cow manure from organic farms, composted sheep manure from organic farms) were sampled for the determination of (i) the presence of chemical (metals, aromatics, halogenated hydrocarbons, pesticides, phthalates and total petroleum hydrocarbons) and biological (Escherichia coli, Salmonella, relative abundance of the integrase intl1 gene) contaminants; and (ii) their quality, in terms of physicochemical (moisture, organic matter, nutrients, C/N ratio) and microbial (potentially mineralizable nitrogen, microbial biomass carbon, bacterial and fungal abundance by real-time PCR, community-level physiological profiles through Biolog EcoPlates™) properties. Regarding metal concentrations, the only amendments that met the Spanish legal requirements for “Class A” fertilizers were composted intensive and organic cow manure. Zinc was the most limiting metal for the use of these amendments. None of the amendments showed high concentrations of organic contaminants. Bokashi was the only amendment in which Salmonella was detected. Besides, bokashi showed a high abundance of the integrase intl1 gene associated with class 1 integrons. Composted organic sheep manure showed the highest content of organic matter, total nitrogen and extractable humic acids. Composted intensive cow manure showed highest values of microbial activity (potentially mineralizable N) and biomass (microbial biomass C, total bacteria). Owing to its low content of potentially health-threatening contaminants and its highest quality, as reflected by the Amendment Quality Index, composted intensive cow manure was concluded to be the most suitable amendment for agricultural use.

There is a growing concern about the risk of antibiotic resistance emergence and dissemination in the environment. Here, we evaluated the spatio-seasonal patterns of the impact of wastewater treatment plant (WWTP) effluents on antibiotic resistance in river sediments. To this purpose, sediment samples were collected in three river basins affected by WWTP effluents in wet (high-water period) and dry (low-water period) hydrological conditions at three locations: (i) upstream the WWTPs; (ii) WWTP effluent discharge points (effluent outfall); and (iii) downstream the WWTPs (500 m downriver from the effluent outfall). The absolute and relative abundances of 9 antibiotic resistance genes (ARGs), 3 mobile genetic element (MGE) genes, and 4 metal resistance genes (MRGs) were quantified in sediment samples, as well as a variety of physicochemical parameters, metal contents, and antibiotic concentrations in both sediment and water samples. In sediments, significantly higher relative abundances of most genes were observed in downstream vs. upstream sampling points. Seasonal changes (higher values in low-water vs. high-water period) were observed for both ARG absolute and relative abundances in sediment samples. Chemical data revealed the contribution of effluents from WWTPs as a source of antibiotic and metal contamination in river ecosystems. The observed positive correlations between ARG and MGE genes relative abundances point out to the role of horizontal gene transfer in antibiotic resistance dissemination. Monitoring plans that take into consideration spatio-temporal patterns must be implemented to properly assess the environmental fate of WWTP-related emerging contaminants in river ecosystems.