Antibiotic resistome and microbial community structure during anaerobic co-digestion of food waste, paper and cardboard
Antimicrobial resistance is a globally recognized public health risk. High incidence of antibiotic resistant bacteria and antibiotic resistance genes (ARGs) in solid organic waste necessitates the development of effective treatment strategies. The objective of this study was to assess ARG diversity and abundance as well as the relationship between resistome and microbial community structure during anaerobic co-digestion (AD) of food waste, paper and cardboard. A lab-scale solid-state AD system consisting of six sequentially fed leach beds (each with a solids retention time of 42 days) and an upflow anaerobic sludge blanket (UASB) reactor was operated under mesophilic conditions continuously for 88 weeks to successfully treat municipal organic waste and produce biogas. A total of ten samples from digester feed and digestion products were collected for microbial community analysis including SSU rRNA gene sequencing, total community metagenome sequencing and quantitative PCR. Taxonomic analyses revealed that AD changed the taxonomic profile of the microbial community: digester feed was dominated by bacterial and eukaryotic taxa while anaerobic digestate possessed a large proportion of archaea mainly belonging to the methanogenic genus Methanosaeta. ARGs were identified in all samples with significantly higher richness and relative abundance per 16S rRNA gene in digester feed compared to digestion products. Multidrug resistance was the most abundant ARG type. AD was not able to completely remove ARGs as shown by ARGs detected in digestion products. Using metagenomic assembly and binning we detected potential bacterial hosts of ARGs in digester feed, that included Erwinia, Bifidobacteriaceae, Lactococcus lactis and Lactobacillus. IMPORTANCESolid organic waste is a significant source of antibiotic resistance genes (ARGs) (1) and effective treatment strategies are urgently required to limit the spread of antimicrobial resistance. Here we studied the antibiotic resistome and microbial community structure within an anaerobic digester treating a mixture of food waste, paper and cardboard. We observed a significant shift in microbial community composition and a reduction in ARG diversity and abundance after 6 weeks of digestion. We identified the host organisms of some of the ARGs including potentially pathogenic as well as non-pathogenic bacteria, and we detected mobile genetic elements required for horizontal gene transfer. Our results indicate that the process of sequential solid-state anaerobic digestion of food waste, paper and cardboard tested herein provides a significant reduction in the relative abundance of ARGs per 16S rRNA gene.