Antibiotic Resistance Genes and Correlations with Microbial Community and Metal Resistance Genes in Full-Scale Biogas Reactors As Revealed by Metagenomic Analysis

Abstract

Digested residues from biogas plants are often used as biofertilizers for agricultural crops cultivation. The antibiotic resistance genes (ARGs) in digested residues pose a high risk to public health due to their potential spread to the disease-causing microorganisms and thus reduce the susceptibility of disease-causing microorganisms to antibiotics in medical treatment. A high-throughput sequencing (HTS)-based metagenomic approach was used in the present study to investigate the variations of ARGs in full-scale biogas reactors and the correlations of ARGs with microbial communities and metal resistance genes (MRGs). The total abundance of ARGs in all the samples varied from 7 × 10 to 1.08 × 10 copy of ARG/copy of 16S-rRNA gene, and the samples obtained from thermophilic biogas reactors had a lower total abundance of ARGs, indicating the superiority of thermophilic anaerobic digestion for ARGs removal. ARGs in all the samples were composed of 175 ARG subtypes; however, only 7 ARG subtypes were shared by all the samples. Principal component analysis and canonical correspondence analysis clustered the samples into three groups (samples from manure-based mesophilic reactors, manure-based thermophilic reactors, and sludge-based mesophilic reactors), and substrate, temperature, and hydraulic retention time (HRT) as well as volatile fatty acids (VFAs) were identified as crucial environmental variables affecting the ARGs compositions. Procrustes analysis revealed microbial community composition was the determinant of ARGs composition in biogas reactors, and there was also a significant correlation between ARGs composition and MRGs composition. Network analysis further revealed the co-occurrence of ARGs with specific microorganisms and MRGs.

Is anaerobic digestion a reliable barrier for deactivation of pathogens in biosludge?

“…Correlation between bacterial community succession and pathogenic population in AD had been established (Luo et al, 2017). As both total organics and nitrogen in sewage sludge were reduced substantially during AD, this in turn led to the shift in the archaea and bacteria communities, including pathogens.…”

Resistome metagenomics from plate to farm: the resistome and microbial composition during food waste feeding and composting on a Vermont poultry farm

“…Prior work has demonstrated a relationship between antibiotic resistance genes and associated sample microbiome [50,51]. To investigate this potential relationship, Pearson correlations between richness, Shannon and Simpson diversities, and ARG counts and diversity were performed (Tables 4 and 5).…”

Antibiotic resistome and microbial community structure during anaerobic co-digestion of food waste, paper and cardboard

“…Microbial community composition has been suggested as one of the main drivers of ARGs in anaerobic digesters (35, 45). The microbial communities of the digester feed – a mix of food waste and lignocellulosic fibres – revealed aerobes and facultative aerobes that were distinct from the strictly anaerobic bacteria and archaea inside the digester.…”

“…Correlation and network analysis have been used in previous studies to link ARGs to their potential host organisms (35–37, 67). Here we used a combination of metagenomic assembly and binning methods to detect taxonomically annotated contigs and MAGs with ARGs.…”