Development of a new primer tool for quantification and identification of geosmin-producing cyanobacteria in drinking water reservoirs

Abstract

Elevated geosmin concentrations in drinking water reservoirs can lead to customer complaints and increased treatment costs for utilities. Use of molecular approaches, like qPCR and targeted amplicon sequencing, can help with prediction and preventive measures, but many of the primers targeting the geosmin synthase gene suffer from limited coverage of taxa or poor specificity. Here, a set of primers (CGeo1F/R) were developed that had high specificity for geosmin synthase in cyanobacteria without the use of probes. When tested on samples from three drinking water reservoirs with elevated geosmin levels, these primers amplified the geosmin synthase gene in seven cyanobacterial genera, including Dolichospermum, Aphanizomenon, Cylindrospermum, Planktothrix, Nostoc, Coelosphaerium, and Tychonema. These primers exhibited acceptable amplification efficiency (∼ 90 %) and a linear amplification range of 6 × 10¹–6 × 10⁵ copies per ml in lake water. Within the limited set of samples used to evaluate these primers, a good correlation was observed (r = 0.8) between abundance of geosmin synthase and geosmin concentration. When compared to some existing, well-utilized primers in the literature, these new primers had better specificity and amplification properties, and thus may prove valuable to other researchers.