Evaluation of the long-term effects of anaerobic digestion on bovine manure resistomes and mobilomes and the molecular and microbial mechanisms involved
Notice bibliographique
Résumé
Anaerobic digestion (AD) has shown the potential to reduce the abundance of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in animal manures. It stands as a promising option to reduce the risk of the spread of antimicrobial resistance (AMR) due to livestock production and manure applications. However, the underlying mechanisms driving these changes still need to be fully understood. This multidisciplinary study aimed to utilize metagenomics to investigate the molecular and microbial mechanisms associated with the evolution of ARGs and MGEs during the anaerobic digestion (AD) of bovine dairy manure. The research focused on three main aspects: 1) examining the long-term effects of mesophilic (MAD) and thermophilic (TAD) anaerobic digestion on the entire set of ARGs (resistome) and MGEs (mobilome) in manure; 2) comparing the impact of alternative manure treatments, such as storage and solid-liquid separation, on resistomes and mobilomes; 3) identifying microbial groups potentially associated with ARGs and MGEs and microbial shifts potentially driving changes in resistomes and mobilomes. A meta-analysis conducted early in this research informed the primary focus of this research. Two anaerobic digesters operating at mesophilic (36 °C) and the other at thermophilic (55 °C) temperatures were set up, operated, monitored, and studied for 4 and 2 years, respectively. Metagenomics analyses were used to evaluate resistomes, mobilomes, and microbiomes in the mesophilic and thermophilic digesters operating under steady state and in the bovine manure used as substrate. The results indicated that MAD and TAD lowered ARG levels in fresh cattle manure by over 50% and MGEs by over 65%. Surprisingly, TAD did not outperform MAD at reducing ARGs and MGEs. Co-occurrence analysis indicated a strong association between microbial groups from the phyla Bacillota (e.g., Jeotgalicoccus, Streptococcus, Enterococcus), Actinomycetota (e.g., Brevibacterium, Rhodococcus), and Pseudomonadota (e.g., Acinetobacter, Comamonas) with these AMR elements. The decline in the abundance of aerobic and facultative anaerobes likely linked to hydrolytic functions was suggested as one of the main drivers of the changes in resistomes and mobilomes. The proximity of toxin-antitoxin systems and transposon structures to specific ARGs (e.g., Erm, tet, Ant(6)-la) was discovered, which could explain the persistence of such ARGs in digestates. The study of the effects of other manure treatments, such as aerobic storage in an open tank and solid-liquid separation, revealed that they are less efficient in reducing ARGs and MGEs from manures than AD. In this study, the high levels of ARGs and genes conferring resistance to heavy metals in a farm operating in an antibiotic-free environment suggested that other antimicrobials, such as foot bathing solutions, may be causing the indirect selection of ARGs. Overall, this research made several contributions to understanding AMR in the context of anaerobic digestion of animal manure that could be extrapolated to other manure treatments. These contributions not only bridge existing gaps in the literature but also pave the way for future research, providing valuable insights that can be used to inform the development of more effective strategies to mitigate the dissemination of AMR associated with manure management, application, and disposal.
Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.
Comment cette classification a été obtenuedéplier
Prédiction machine sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Le volet Gemma est une étiquette directe du modèle pour chaque travail de la base, lue sur la notice réduite au titre. Le volet Codex est un classifieur appris des 10 348 étiquettes directes de Codex et calibré sur les taux pondérés de l'échantillon; les champs sans appui suffisant ne portent aucun appel Codex. Le mode candidate est l'union des deux volets; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont pas des étiquettes humaines.
Scores du classifieur distillé par catégorie (deux têtes)
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,001 | 0,001 |
| Méta-épidémiologie (sens strict) | 0,001 | 0,000 |
| Méta-épidémiologie (sens large) | 0,001 | 0,001 |
| Bibliométrie | 0,001 | 0,001 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,001 | 0,001 |
| Science ouverte | 0,000 | 0,001 |
| Intégrité de la recherche | 0,001 | 0,001 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,000 | 0,000 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule source (Gemma direct ou Codex distillé), pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».