This study aimed to address three major objectives. Firstly, it was aimed at characterizing two major sources of manure: cattle manure and poultry litter in terms of nutrient content, microbial composition, and selected antibiotic resistance genes abundance (Chapter 1). These manure sources were widely used as fertilizers in silvopastural systems in Arkansas, USA, to improve productivity. While cattle manure is land applied in fresh, poultry litter, which was composed of poultry manure and bedding, is aerated in-house windrows to increase the temperature and kill pathogens before land application. The results indicated poultry litter had lower microbial diversity and antimicrobial resistance genes (ARGs) abundance compared to cattle manure, possibly was due to the handling prior to its land application. Secondly, since poultry litter was safer to use than cattle manure, the next study was aimed at understanding the effect of poultry litter application on soil microbial diversity (Chapter 2). The result showed that poultry litter applied to soils under a silvopasture system did not affect soil microbiota despite it improved soil fertility. The study by these two objectives suggested poultry litter is environmentally safer and richer in nutrients supply than cattle manure in Arkansas region setting. However, in global setting, studies show that poultry litter is believed to contain greater ARGs abundance and other pollutants, possibly due to the absence of the kind of handling in Arkansas. Thus, the next step of the study was to conduct a thorough literature review, and unfortunately, the results showed that poultry litter contained greater pollutants (ARGs, antibiotics, etc.). Aerobic treatment is the most widely studied for its effect against such pollutants. However, it is inefficient, and sometimes it can be a hub for enrichment of ARGs. This was evidenced by the results of previous studies that found poor degradation of ARGs by aerobic digestion, where the abundance of ARGs in digestate (a byproduct of biogas production) is greater than in the feedstock (input for the biogas production). Consequently, the next chapter of the study was to look at a post-digestate treatment (Chapters 3 and 4). Composting was aimed to remove ARGs as well as mitigate release of trace elements from digestate. The results showed that composting reduced greater than 80% ARGs in digestate and immobilized trace elements up to 90%. In conclusion, with this study, it was revealed that cattle manure direct land application may pose greater environmental risk compared to poultry litter, and this can be mitigated by employing pre-treatments such as the bedding and aerating in-house windrows, the technique that is used for handling poultry litter in Arkansas region, the USA. However, this is not the case in Europe. For instance, in Italy, where part of this thesis was conducted, poultry litter comprises feedstock of biogas production, and it is used in fresh. It contained ARGs copies ranging from log(10) 6.46 to 11.46, which was the greatest in most of the other feedstocks. After 90 days of anaerobic digestion of mix of poultry litter, food processing byproduct and maize silage, log(10) 5.21 to 9.22 ARG copies were found, with the greatest copies of tet(M) in both scenarios. It implied anaerobic digestion effect against ARGs was not satisfactory. Thus, the next aim of the study was to further degrade ARGs in digestate before land application. Thus, composting and co-composting it with the other biogas feedstock elements was conducted, and up to 80% removal of ARGs was possible. In conclusion, the study suggests manure handling approaches may affect ARGs, and aerating could be a good practice to suppress the abundance. In the biogas production pathway, where fresh poultry litter may be used, the anerobic digestion may not be effective against ARGs removal, as it was reported in many other previous reports, and the subsequent post-digestate treatment, such as composting and drying, may be sought.
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