Bacteria and antimicrobial resistance profile during the composting process of wastes from animal production

Harnessing the potential of exogenous microbial agents: a comprehensive review on enhancing lignocellulose degradation in agricultural waste composting

Composting converts organic agricultural wastes into value-added products, yet the presence of significant non-biodegradable lignocelluloses hinders its efficiency. The introduction of various exogenous microbial agents has been shown to effectively addresses this challenge. In this context, basing on the microbial enzymatic mechanism for lignocellulose degradation, this paper synthesizes the latest research advancements and practical applications of exogenous microbial agents in agricultural waste composting. Given that the effectiveness of lignocellulose degradation is highly dependent on the waste's inherent characteristics, it is crucial to carefully consider the composition of fungi and bacteria, the dosage of microbial agents, and the composting process operation, tailored to the specific type of agricultural waste. Moreover, the combination of additives with exogenous microbial agents can further enhance the degradation of lignocelluloses and the humification of organic matters. Furthermore, insights into the future research and application trends of exogenous microbial agents in agricultural waste composting was prospected.

Chemical attributes, bacterial community, and antibiotic resistance genes are affected by intensive use of soil in agro-ecosystems of the Atlantic Forest, Southeastern Brazil

Soil is one of the largest reservoirs of microbial diversity in nature. Although soil management is vital for agricultural purposes, intensive practices can have a significant impact on fertility, microbial community, and resistome. Thus, the aim of this study was to evaluate the effects of an intensive soil management system on the chemical attributes, composition and structure of prevalent bacterial communities, and presence and abundance of antimicrobial resistance genes (ARGs). The chemical characterization, bacterial diversity and relative abundance of ARGs were evaluated in soils from areas of intensive vegetable cultivation and forests. Results indicate that levels of nutrients and heavy metals were higher in soil samples from cultivated areas. Similarly, greater enrichment and diversity of bacterial genera was detected in agricultural areas. Of the 18 target ARGs evaluated, seven were detected in studied soils. The oprD gene exhibited the highest abundance among the studied genes and was the only one that showed a significantly different prevalence between areas. The oprD gene was identified only from soil of the cultivated areas. The blaSFO, erm(36), oprD and van genes, in addition to the pH, showed greater correlation with in soil of cultivated areas, which in turn exhibited higher contents of nutrients. Thus, in addition to changes in chemical attributes and in the microbial community of the soil, intensive agricultural cultivation systems cause a modification of its resistome, reinforcing the importance of the study of antimicrobial resistance in a One Health approach.

Assessment of the combined inputs of antimicrobials from top soil improvers and irrigation waters on green leafy vegetable fields

Sustainable food systems involve the recycling of biowaste and water. This study characterizes thirty-one top soil improvers of anthropogenic, animal, and green waste origin, along with eleven irrigation waters from rivers, channels, and civil wastewater treatment plants (cWWTPs) for the presence of antimicrobials. Liquid chromatography coupled with hybrid High-Resolution Mass Spectrometry (LC-HRMS/MS) was employed to identify forty-eight drugs belonging to the classes of sulfonamides (11), tetracyclines (7), fluoroquinolones (10), macrolides (12), amphenicols (3), pleuromutilins (2), diaminopyrimidines (1), rifamycins (1) and licosamides (1). Sludge from cWWTPs, animal manure, slurry, and poultry litter exhibited the highest loads for sulfonamides, tetracyclines, fluoroquinolones and macrolides (80, 470, 885, and 4,487 ng g-1 wet weight, respectively) with nor- and ciprofloxacin serving as markers for anthropogenic sources. In compost and digestate, antimicrobials were found to be almost always below the limits of quantification. Reused water from cWWTPs for irrigation in open-field lettuce production were contaminated in the range of 12-221 ng L-1 with sulfonamides, tetracyclines, and fluoroquinolones, compared to very few detected in channels and surface waters. The Antimicrobials Hazard Index (HI), based on the Predicted No Effect Concentration for Antimicrobial Resistance (PNECAMR), was significantly >100 in contaminated topsoil improvers from urban and animal sources. Accounting for worst-case inputs from topsoil improvers and irrigation water, as well as dilution factors in amended soil, fluoroquinolones only exhibited an HI around 1 in open fields for lettuce production. The origin of topsoil improvers plays a pivotal role in ensuring safe and sustainable leafy vegetable production, thereby mitigating the risk of Antimicrobial Resistance (AMR) onset in food-borne diseases and the transfer of AMR elements to the human gut flora.