Influence of DNA extraction methods on microbiome and resistome analysis in activated sludge

Abstract Amplicon sequencing, metagenomics, and quantitative polymerase chain reaction (qPCR) are commonly used techniques to analyse microorganisms and antibiotic resistance genes (ARGs) in activated sludge from wastewater treatment plants (WWTPs). However, the lack of workflow harmonisation poses challenges in comparing measurements across studies and research groups. To address this issue, we examined the impact of DNA extraction procedures on 16S rRNA gene amplicon sequencing, shotgun metagenomics, and qPCR analyses of activated sludge by combining two widely used DNA extraction kits (PowerSoil and FastDNA) and two commonly employed disruption instruments (bead-beater and vortex) through a 2×2 factorial experimental design involving four groups of three analysts performing DNA extractions in triplicates. Our findings revealed significant differences in DNA yield, purity, and reproducibility of amplicon sequencing profiles among the extraction kits. Operator variability also influenced the results. We compared microbiome profiles obtained by amplicon sequencing and metagenomics and observed that bead-beating introduced more variability among triplicates compared to vortexing. The combinations of extraction kits and disruption instruments impacted the relative abundances of specific phyla such as Actinobacteriota , Bacteroidota , and Nitrospirota . For resistome analysis, we employed metagenomics for high-resolution profiling and qPCR for high-sensitivity detection of ARGs. The compositions and diversities of resistome datasets were not significantly affected by the choice of extraction kits and disruption instruments. Although using the same method is ideal for accurate comparisons, our results suggest that acceptable reproducibility can still be achieved when using different methods. This finding encourages the implementation of ARG monitoring in wastewater treatment processes. However, it is important to consider biases introduced by DNA extraction workflows when designing analytical studies, interpreting their results, and comparing their findings. Striving for more harmonised molecular workflows is crucial in the field of wastewater microbiology and engineering. Abstract Figure Graphical abstract