Antibiotic resistance genes in composted manures and compost-amended tropical soils

• Ano de defesa: 2024
• Autor(a) principal: Osti, Julio Flavio
• Tipo de documento: Tese
• Tipo de acesso: Acesso aberto
• Idioma: eng
• Instituição de defesa: Biblioteca Digitais de Teses e Dissertações da USP
• Palavras-chave em Português: Antibiotic resistance genes; Compostagem; Composting; Estercos; Genes de resistência a antibióticos; Heavy metals; Manure; Metagenoma; Metagenome; Metais pesados
• Link de acesso: https://www.teses.usp.br/teses/disponiveis/11/11138/tde-04022025-103905/

The high production of animal protein results in a large production of manure, which has the soil as its final destination. The use of antibiotics in livestock stimulates the proliferation of antibiotic resistance genes (ARGs). This is problematic given the rise in antimicrobial resistance in human and animal pathogens. Composting is an established and viable method for the stabilization and satinization of manure. Therefore, it is important to evaluate the effect of composting on the set of ARGs in manure, the resistome. Furthermore, it is important to compare the effect of the application of the composts in soils, in order to assess their effectiveness on the reduction of the risk of ARGs proliferation in this environment. Chapter 1 examined the effect of composting on the reduction of the diversity and abundance of ARGs in the poultry manures, poultry litter and layer manure. Therefore, the objective of this step was to investigate whether two different composting strategies are effective on the reduction of ARGs in poultry litter. Additionally, it was evaluated which type of poultry manure is more effective in the attenuation of ARGs through composting. The two composting strategies evaluated in poultry litter proved to be effective in the reduction of the diversity of ARGs, although without effect on abundance. Composting proved to be even more effective in the attenuation of ARGs in layer manure, reducing the abundance and diversity of these genes. In chapter 2, the effect of the poultry manures, chicken litter and layer manure and their composts was evaluated on the ARGs of soils cultivated with the fresh vegetable salad rocket, Eruca sativa. It was observed that both types of composts do not increase the total abundance of ARGs, although both increase the richness and Shannon diversity in soils, to the same extent as fresh manures. Furthermore, it was observed that all organic fertilizers applied increased some specific ARGs classes. Finally, the application of manure and compost caused an increase in the abundance of plasmids, indicating a possible increase in horizontal transmission of ARGs. Thus, both fresh poultry manure and its composts can increase the dissemination of ARGs in soils. Chapter 3 explored the effect of successive applications of poultry or swine manure composts on ARGs in commercial field agricultural soils. Additionally, the interaction of physicochemical properties and heavy metals in the modulation of the resistome in these soils was evaluated. Soils with heavy metals in high concentrations are the dominant factor in the modulation of the resistome, attenuating the effect of compost application. The main factors modulating ARGs in soils with normal levels of heavy metals are available P and pH, which present elevated levels due to the successive application of composts. The heavy metal resistance genes for Cu and Zn are the most related to different classes of ARGs. The genus Bradyrhizobium stands out as a host for a large number of ARGs. This thesis highlights that composting reduces the diversity of ARGs in the manures. However, the application of composts to the soil increases the diversity of ARGs, whether with the successive application of composts in field soils or a single application in soils in a pot experiment. Physicochemical factors involved in fertility and heavy metals play an important role on the modulation of ARGs in soils.