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Seasonal blooms of cyanobacteria (CB) are a typical feature of Lake Alto Flumendosa (Sardinia, Italy). The waters of this lake are used for drinking water supply, for agricultural and industrial uses, and fish farming activities. Since cyanotoxins are not monitored in edible organisms, diet could be a relevant route of human exposure. CB also represent a threat for the health of wild and domestic animals that use lake water for beverage. Therefore, to characterize the CB community and assess the risk for human and animal population, CB dynamic, mcyB+ fraction, and microcystins (MCs) concentration have been followed monthly for 18 months, in three stations. Results confirmed the presence of several toxigenic species. Planktothrix rubescens dominated between August 2011 and April 2012 (3.5×106 cells L-1), alternating with Woronichinia naegeliana (8×106 cells L-1) and Microcystis botrys (9×105 cells L-1). Dolichospermum planctonicum was always present at low densities (104 cells L-1). MCs were detected, at values well below the 1 µg L-1 threshold of WHO for drinking water. The molecular analysis of mcyB gene for P. rubescens indicated the presence of a persistent toxic population (average 0.45 mcyB/16S rDNA). Highly significant linear regressions were found between P. rubescens and the sum of the demethylated MC variants, and between M. botrys and the sum of MC-LR and MC-LA, also when co-occurring, suggesting that these two species were responsible for different MC patterns production. The regression lines indicated a quite stable MC cell quota. However, in some spotted samples very different values were obtained for both MC concentrations and cell quota (from 10-fold lower to 30-40-fold higher than the ‘average’) showing an unexpected significant variability in the rate of toxin production. The relatively low cell densities during the monitoring period is consistent with the low-to absent MC contamination level found in trout muscle; however, the analytical method was affected by low recovery, probably due to MC-protein binding. Our results show that, during the study period, no risk of exposure for the human and animal population occurred. However, the persistence of a complex CB community characterised by a significant toxic fraction suggests the need for periodic monitoring activity. Particularly, the hidden deep summer P. rubescens blooms, located where water is taken for drinking water supply, and M. botrys, able to produce the most toxic MC variants with high cell quota, should be kept under control. The documentation and interpretation of sudden changes in toxins concentrations deserve special attention. This is particularly relevant in proximity of fish farming plants and water catchment sites.