An improved method for PCR-based detection and routine monitoring of geosmin-producing cyanobacterial blooms

Production of taste and odour (T/O) compounds, principally geosmin, by complex cyanobacterial blooms is a major water quality issue globally. Control of these cyanobacteria imposes a significant cost on water producing and dependent industries, and requires routine monitoring and management. Classic monitoring methods, including microscopy and direct chemical analysis, lack sensitivity, are laborious, expensive or cannot reliably identify the source of geosmin production. Polymerase Chain Reaction (PCR) based tools targeting the geosmin synthase gene (geoA) provide a novel tool for routine monitoring. However, geoA is variable at the nucleotide level and potential geosmin producers represent a broad taxonomic distribution, such that multiple PCR primers with distinct amplification protocols are needed to target all potential sources of this important T/O compound. Development of novel primers is hindered by a lack of sequence data and limited field and laboratory data on geosmin producers prevents prioritizing taxa for PCR testing. Here we performed a genetic screen of 253 bloom samples from Victoria, Australia using each existing PCR protocol targeting geoA. We detected Dolichospermum ucrainicum as the major geosmin producer (87% of sequenced samples) along with 3 unknown geoA sequence types. Using these data, we designed a novel, short amplicon, PCR protocol utilising a single standardised primer pair, capable of amplifying all geoA positive samples in our study, as well as a Nostoc punctiforme positive control. This single protocol geoA PCR can further be tested on other geosmin producers and will simplify routine monitoring of T/O producing cyanobacteria.