Elucidation of Taste- and Odor-Producing Bacteria and Toxigenic Cyanobacteria in a Midwestern Drinking Water Supply Reservoir by Shotgun Metagenomic Analysis

Abstract

While commonplace in clinical settings, DNA-based assays for identification or enumeration of drinking water pathogens and other biological contaminants remain widely unadopted by the monitoring community. In this study, shotgun metagenomics was used to identify taste-and-odor producers and toxin-producing cyanobacteria over a 2-year period in a drinking water reservoir. The sequencing data implicated several cyanobacteria, including Anabaena spp., Microcystis spp., and an unresolved member of the order Oscillatoriales as the likely principal producers of geosmin, microcystin, and 2-methylisoborneol (MIB), respectively. To further demonstrate this, quantitative PCR (qPCR) assays targeting geosmin-producing Anabaena and microcystinproducing Microcystis were utilized, and these data were fitted using generalized linear models and compared with routine monitoring data, including microscopic cell counts, sonde-based physicochemical analyses, and assays of all inorganic and organic nitrogen and phosphorus forms and fractions. The qPCR assays explained the greatest variation in observed geosmin (adjusted R 2 ‫؍‬ 0.71) and microcystin (adjusted R 2 ‫؍‬ 0.84) concentrations over the study period, highlighting their potential for routine monitoring applications. The origin of the monoterpene cyclase required for MIB biosynthesis was putatively linked to a periphytic cyanobacterial mat attached to the concrete drinking water inflow structure. We conclude that shotgun metagenomics can be used to identify microbial agents involved in water quality deterioration and to guide PCR assay selection or design for routine monitoring purposes. Finally, we offer estimates of microbial diversity and metagenomic coverage of our data sets for reference to others wishing to apply shotgun metagenomics to other lacustrine systems. IMPORTANCECyanobacterial toxins and microbial taste-and-odor compounds are a growing concern for drinking water utilities reliant upon surface water resources. Specific identification of the microorganism(s) responsible for water quality degradation is often complicated by the presence of co-occurring taxa capable of producing these undesirable metabolites. Here we present a framework for how shotgun metagenomics can be used to definitively identify problematic microorganisms and how these data can guide the development of rapid genetic assays for routine monitoring purposes. C yanobacterial harmful algal blooms (CyanoHABs) appear to be increasing globally in frequency, duration, and magnitude in response to human-accelerated eutrophication and climate change (1, 2). From a drinking water perspective, large accumulations of cyanobacteria pose a significant health concern due to their ability to produce a variety of bioactive metabolites, some of which are potent liver toxins or neurotoxins (3, 4). Additionally, cyanobacteria are widely considered the most common source of the taste-and-odor (T&O) compounds geosmin (4,8a-dimethyldecahydroaphthalen-4a-ol) and MIB (2-methylisoborneol), which impart unpalata...

Effects of Environmental Factors on Cyanobacterial Production of Odorous Compounds: Geosmin and 2-Methylisoborneol

“…Phylogenetic and evolutionary studies of the geosmin synthesis gene (geoA) recently reached to suggest that this gene has been spread by horizontal gene transfer and has a common origin with the 2-MIB gene [9]. qPCR for geoA showed a better correlation with geosmin concentration than Anabaena cell counting data [10]. Compared with such achievement in genetic studies, physiological research is still bewildering.…”

Isolation and Characterization of Cylindrospermopsis raciborskii Strains from Finished Drinking Water

“…The presence of cyanobacteria in treated water, even though they are not toxin producers, might compromise the water quality because cyanobacterial species can produce taste and odor compounds [38] and chlorinated byproduct precursors [39]. The improvement and suitability of the procedures at the WTP, along with a robust monitoring program, is thus essential in order to reduce the impacts and potential risks posed by cyanobacterial blooms in drinking water sources.…”

The molecular ecology of Microcystis sp. blooms in the San Francisco Estuary

“…A normalized subset of reads (∼ 34.6 million per sample) were mapped to the assembled contigs using BWA (Li and Durbin, ) and the coverage depth for each contig per sample was calculated as the average number of sequencing reads recruiting to each contig; this was done using samtools (Li et al ., ). Contigs were functionally and taxonomically characterized as previously described (Otten et al ., ). The annotated contigs and their relative read coverage depths were visualized in R using the mmgenome package (Albertsen et al ., ).…”