Quantitative assessment of microbial dynamics in livestock manure and municipal wastewater treatment plants

Abstract We investigated microbial community dynamics and potential pathogen persistence across treatment stages in a livestock manure treatment plant (LMTP) and a municipal wastewater treatment plant (WWTP). To quantify taxon-specific absolute abundances, we used quantitative microbiome profiling (QMP) by combining 16 S rRNA gene amplicon sequencing with quantitative PCR (qPCR) and 16 S rRNA gene copy number (16 S GCN) correction. The LMTP influent was enriched with fermentative and methanogenic taxa such as Candidatus Cloacamonas and Methanobrevibacter and showed a consistent decline in the total microbial load through successive stages. In contrast, the WWTP influent was dominated by gut-associated bacteria, including Lactococcus and Segatella . During sludge treatment and anaerobic digestion, genera such as Xylanibacter and Methanothermobacter became enriched. Functional predictions indicated that anaerobic chemoheterotrophy generally predominated from influent to effluent in both facilities. Although total microbial abundance decreased substantially in the final effluents, potentially pathogenic genera such as Moraxella , Acinetobacter , and Mycobacterium remained detectable at low levels. Integrating absolute abundance data with microbial profiling revealed significant taxon shifts that were missed by relative abundance analysis. These findings provide a more robust basis for assessing microbial dynamics and pathogen persistence, and offer practical insights for risk-based management of wastewater treatment processes.