Tools for Metagenomic Analysis at Wastewater Treatment Plants:
Application to a Foaming Episode

Abstract

Metagenomic analysis is a powerful approach for wholesale characterizations of microbial populations like those that operate within municipal wastewater treatment plants. It is well known that many problems are associated with the overgrowth or undergrowth of specific bacterial genera. We describe a database of the combined metagenomes of activated sludge aeration basins from around the globe and use it as a reference to study the population of a foamy activated sludge aeration basin. We show that foam production is associated with blooms of mycolic acid producing genera, especially Mycobacterium. We confirm this bloom using the acid-fast stain, and we show that genes involved with mycolic acid production are enriched in the foam-producing sample. In addition, we show that this sample has unusual nitrifying populations. We suggest that low-cost DNA sequencing and publicly available tools for shotgun metagenomic analyses, including those described here, might broadly facilitate wastewater treatment plant operation.

Consistent and correctable bias in metagenomic sequencing experiments

“…Applications of MGS, often under the alternative terms eDNA sequencing or metabarcoding, increasingly extend beyond microbes to the measurement and monitoring of plants, insects, and vertebrates (Bell et al, 2019; Krehenwinkel et al, 2017; Thomas et al, 2016). MGS methods are now being adopted in fields ranging from food safety (Cocolin et al, 2018) to wastewater remediation (Rosso et al, 2018) to forensics (Metcalf et al, 2017) along with biology and medicine. Unfortunately, however, the community compositions measured by MGS are wrong.…”

Characterization of persistent organic pollutants and culturable and non-culturable bacterial communities in pulp and paper sludge after secondary treatment

“…These refractory chloro-organic pollutants found in discharged of pulp-paper mills are recalcitrant, persist in the environment for a long time and have the capacity to travel far across the ecosystem, eventually accumulating in organisms' fatty tissues. Moreover, several anaerobic microbes have capacity to methylate the chlorinated pollutants which further increase the toxicity and lipophilicity of the pollutants (Rosso et al, 2018). As a result of the insufficient secondary treatment, effluent from pulp and paper mills could contain significant concentrations of persistent pollutants that impaction microbial activities in the environment (Sharma et al, 2021a;Tripathi et al, 2021b).…”

The source and fate of Mycobacterium tuberculosis complex in wastewater and possible routes of transmission

“…Some of these reports do not provide species identification, with identification down to only the genus [114][115][116][117][118][119]. However, others have identified known human pathogens, such as M. tuberculosis [120] and animal pathogens, M. avium and M. bovis [121]. Additionally, other lesser-known species have been identified through this sequencing approach [122,123].…”