The expansion of animal husbandry for food production has necessitated effective management of livestock waste, including cattle manure and poultry litter. Using these byproducts as organic fertilizers in agriculture represents a sustainable approach to their disposal. While these residues offer known benefits for soil health and crop productivity, further studies are needed to explore the effect of different manure microbiota on soil composition. The objective of this study was to address this gap and contribute to the advancement of this area. A randomized block design experiment was set up in the field with three replications per treatment, including the application of cattle manure, poultry litter, and a control treatment without fertilizer. After a 60 day period, the chemical characteristics and bacterial population composition of the soil were analyzed using 16S rRNA gene sequencing. Organic carbon, phosphorus (P), aluminum (Al), and the pH level played pivotal roles in changing the structure of the soil’s bacterial community. Notably, the incorporation of poultry litter induced more pronounced changes in both the chemical properties and bacterial community composition compared with cattle manure. Bacterial groups were enriched in the soils treated with poultry litter, which may indicate enhanced soil fertility. This association may stem from both the chemical alterations resulting from poultry litter application and the direct transfer of microorganisms from this organic fertilizer to the soil.

Rivers provide essential water resources for humans. However, appear to be reservoirs of antimicrobial-resistant genes and dispersal routes of resistant pathogens because human activities promptly influence them. Sediments are the most propitious substrates for bacteria survival and can act as an antimicrobial reservoir. Three sediment samples were collected upstream of the water catchment point of the Guandu Water Treatment Plant (ETA Guandu) to evaluate microbial diversity and antimicrobial resistance genes to sulfonamide (sul1, sul2), tetracycline (tetA, tetB) and beta-lactam (blaCTX-M, blaoxa24 and blaoxa58) by PCR. The most abundant phylum in all samples was Proteobacteria, which was also the most dominant in sediments presenting a pattern already reported in the literature for diversity in tropical and temperate climate rivers. Sulfonamide resistance genes were detected in all samples. The blaCTX-M gene was detected only in one sample, and tetA, tetB, blaoxa24 and blaoxa58 genes were not found in any sample. The presence of antimicrobial resistance genes sul1, sul2, and blaCTX-M indicate that sediments can act as a reservoir of resistance. These findings will provide new data about the bacterial community and antimicrobial resistance genes in Brazilians river sediments.

Animal wastes have been commonly reused in agriculture due to improve organic matter and nutritional input. However, organic animal fertilizers can be sources of antimicrobials, bacteria resistant to antimicrobials, and antimicrobial resistance genes. In this perspective, this work aimed to investigate the presence of antimicrobial resistance genes in organic animal wastes, such as fresh bovine manure from organic and conventional production systems, fresh and tanned organic poultry litter, conventional poultry litter tanned and bone meal. Sulfonamide resistance genes were detected in all residues. On the other hand, colistin and carbapenem resistance genes were not detected in any samples. A tetracycline resistance gene was detected in poultry litter. Quinolone resistance genes were detected in all samples, except bone meal. Despite the advantage of applying animal wastes in agricultural production, the existence of resistance genes in all residues, regardless of whether they come from organic or conventional systems, fresh or tanned, represents a public health risk since we can increase antimicrobial resistance genes in the soil which can favor the transfer to pathogenic bacteria of humans and animals.

Antimicrobial resistance is a global public health concern that requires an integrated approach including human, animal and environmental health. Agricultural environments, such as soil, animal waste and irrigation water, play crucial roles in the dynamics of antimicrobial resistance, as they act as reservoirs and pathways for disseminating resistance determinants. However, these agricultural environments are still often underestimated or neglected in many studies. This study aimed to address antimicrobial resistance in agricultural environments in Brazil and summarize the current state of knowledge about this issue in the country. Google Scholar, Google, ISI Web of Knowledge and Web of Science databases were searched for Portuguese, English and Spanish articles addressing antimicrobial resistance in agricultural environments in Brazil published through 2023. Different terms were used, and the findings were categorized according to the research questions posed. A total of 36 articles were found, 20 of which focused on antimicrobial resistance in animal waste from livestock production, 13 addressed antimicrobial resistance in agricultural soils, two considered both environments, and only one considered antimicrobial resistance associated with irrigation water in different agricultural environments. In all studies, diverse classes of resistant bacteria and antimicrobial resistance genes and mobile genetic elements were detected. However, the number of articles addressing this topic in Brazilian agricultural environments - in animal waste, followed by soils and, to a lesser degree, irrigation water - is still quite limited, revealing significant gaps to be filled. Therefore, it is essential to conduct more studies on antimicrobial resistance in these environments to elucidate their roles as reservoirs and sources of antimicrobial resistance and assess the risks to public health.

This study evaluated the effectsof tillage systems on soil biological and physical attributes in a certified organic farming system in Brazil. The experiment was conducted using a randomized block design with four replications under two management systems: no-tillage and conventional tillage. Each plot received a cover crop consortium sown at 50% of the recommended seeding rate, consisting of millet (Pennisetum glaucum), sunn hemp (Crotalaria juncea), and jack bean (Canavalia ensiformis). Soil samples were collected after corn harvest, five years after the establishment of the tillage systems and cover crop consortia. No-tillage promoted greaterfungal richness than conventional tillage. Differential abundance analysis showed that conventional tillage significantly affected the relative abundance of bacterial and fungal phyla, particularly Chloroflexota and Ascomycota. Network analysis revealed distinct microbial co-occurrence patterns, with fungal networks showing higher connectivity under no-tillage, while bacterial networks exhibit contrasting structures under conventional tillage. No significant differences were observed in β-glucosidase or arylsulfatase activities between management systems. However, arylsulfatase accounted for most enzymatic activity in both no-tillage (72%) and conventional tillage (73%), highlighting the importance of sulfur cycling in this organic farming system. Principal component analysis associated no-tillage with Proteobacteria, soil bulk density, and mean weight diameter, whereas conventional tillage was associated with β-glucosidase, arylsulfatase, Actinobacteriota, Firmicutes, Acidobacteriota, and Ascomycota. The results demonstrate that tillage systems influence soil physical, microbiological, and enzymatic attributes under organic management, reducing soil disturbance combined with cover crops represents an effective strategy for maintaining soil biological and structural quality. Graphical Abstract Graphical Abstract