Shotgun Metagenomic Profiles Have a High Capacity To Discriminate Samples of Activated Sludge According to Wastewater Type

Abstract

This study was conducted to investigate whether functions encoded in the metagenome could improve our ability to understand the link between microbial community structure and function in activated sludge. By analyzing data sets from six industrial and six municipal wastewater treatment plants covering different configurations, operational conditions and geographic regions, we found that wastewater influent composition was an overriding factor shaping the metagenomic composition of activated sludge. Community GC-content profiles were conserved within treatment plants on a time scale of years, and between treatment plants sharing similar influent wastewater. Interestingly, GC-content of represented phyla covary with the average GC-content of the corresponding WWTP metagenome. This suggests that the factors influencing nucleotide composition act similarly across taxa, and therefore that the variation in nucleotide content is driven by environmental differences between WWTPs. While taxonomic and functional richness were correlated, shotgun metagenomics complemented taxon-based analyses in the task of classifying microbial communities involved in wastewater treatment systems. The observed taxonomic dissimilarity between full-scale wastewater treatment plants receiving influent with varied composition, as well as the inferred taxonomic and functional assignment of recovered genomes from each metagenome, were consistent with underlying differences in the abundance of distinctive sets of functional categories. These conclusions were robust with respect to plant configuration, operational and environmental conditions and even to differences in laboratory protocols.