Feedstock-dependent antibiotic resistance gene patterns and expression profiles in industrial scale biogas plants revealed by meta-omics technology

IF 11.4 1区环境科学与生态学 Q1 ENGINEERING, ENVIRONMENTAL Water Research Pub Date : 2024-10-18 DOI:10.1016/j.watres.2024.122650

Roland Wirth, Prateek Shetty, Zoltán Bagi, Kornél L. Kovács, Gergely Maróti

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Abstract

This study investigated antimicrobial resistance in the anaerobic digesters of two industrial-scale biogas plants processing agricultural biomass and municipal wastewater sludge. A combination of deep sequencing and genome-centric workflow was implemented for metagenomic and metatranscriptomics data analysis to comprehensively examine potential antimicrobial resistance in microbial communities. Anaerobic microbes were found to harbour numerous antibiotic resistance genes (ARGs), with 58.85% of the metagenome-assembled genomes (MAGs) harbouring antibiotic resistance. A moderately positive correlation was observed between the abundance and expression of ARGs. ARGs were located primarily on bacterial chromosomes. A higher expression of resistance genes was observed on plasmids than on chromosomes. Risk index assessment suggests that most ARGs identified posed a significant risk to human health. However, potentially pathogenic bacteria showed lower ARG expression than non-pathogenic ones, indicating that anaerobic treatment is effective against pathogenic microbes. Resistomes at the gene category level were associated with various antibiotic resistance categories, including multidrug resistance, beta-lactams, glycopeptides, peptides, and macrolide-lincosamide-streptogramin (MLS). Differential expression analysis revealed specific genes associated with potential pathogenicity, emphasizing the importance of active gene expression in assessing the risks associated with ARGs.

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元组学技术揭示工业规模沼气厂中原料依赖性抗生素耐药基因模式和表达谱

本研究调查了两个处理农业生物质和城市污水污泥的工业规模沼气厂厌氧消化池中的抗菌素耐药性。该研究结合深度测序和以基因组为中心的工作流程，对元基因组学和元转录组学数据进行分析，以全面研究微生物群落中潜在的抗菌药耐药性。研究发现厌氧微生物携带大量抗生素耐药性基因（ARGs），58.85%的元基因组组装基因组（MAGs）携带抗生素耐药性。ARGs的丰度和表达之间呈中度正相关。ARGs 主要位于细菌染色体上。与染色体相比，质粒上抗性基因的表达量更高。风险指数评估表明，大多数已发现的 ARGs 对人类健康构成重大风险。不过，潜在致病菌的 ARG 表达量低于非致病菌，这表明厌氧处理对致病微生物是有效的。在基因类别水平上，耐药性基因组与各种抗生素耐药性类别有关，包括多重耐药性、β-内酰胺类、糖肽类、肽类和大环内酯-林可酰胺-链霉亲和素（MLS）。差异表达分析揭示了与潜在致病性相关的特定基因，强调了活性基因表达在评估 ARGs 相关风险中的重要性。

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来源期刊

Water Research 环境科学-工程：环境

CiteScore

20.80

自引率

9.40%

发文量

1307

审稿时长

38 days

期刊介绍： Water Research, along with its open access companion journal Water Research X, serves as a platform for publishing original research papers covering various aspects of the science and technology related to the anthropogenic water cycle, water quality, and its management worldwide. The audience targeted by the journal comprises biologists, chemical engineers, chemists, civil engineers, environmental engineers, limnologists, and microbiologists. The scope of the journal include: •Treatment processes for water and wastewaters (municipal, agricultural, industrial, and on-site treatment), including resource recovery and residuals management; •Urban hydrology including sewer systems, stormwater management, and green infrastructure; •Drinking water treatment and distribution; •Potable and non-potable water reuse; •Sanitation, public health, and risk assessment; •Anaerobic digestion, solid and hazardous waste management, including source characterization and the effects and control of leachates and gaseous emissions; •Contaminants (chemical, microbial, anthropogenic particles such as nanoparticles or microplastics) and related water quality sensing, monitoring, fate, and assessment; •Anthropogenic impacts on inland, tidal, coastal and urban waters, focusing on surface and ground waters, and point and non-point sources of pollution; •Environmental restoration, linked to surface water, groundwater and groundwater remediation; •Analysis of the interfaces between sediments and water, and between water and atmosphere, focusing specifically on anthropogenic impacts; •Mathematical modelling, systems analysis, machine learning, and beneficial use of big data related to the anthropogenic water cycle; •Socio-economic, policy, and regulations studies.