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- Accessing Planktothrix species diversity and associated toxins using quantitative real-time PCR in natural watersPublication . Churro, Catarina; Vasconcelos, Vitor Manuel de OliveiraThe most common cyanotoxins in Portuguese freshwaters are microcystins and their occurrence has been mainly attributed to cyanobacteria from the Microcystis genus. However, most recently, it has been described the production of these toxins by species of the Planktothrix, suggesting that this genus is also a major producer of microcystin in Portuguese surface waters. Nevertheless, and conversely to the Microcystis species, the knowledge on the occurrence, distribution and toxigenesis of Planktothrix is still limited. Planktothrix species exhibits some particularities that difficult their sampling, identification, quantification and toxigenic characterization in natural samples - Chapter 2. Particularly, the morphology of Planktothrix colonies does not allow distinguishing easily the individual cells. This makes their identification and quantification by optical microscopy a very difficult task, although this is the method generally used in cyanobacteria monitoring. Moreover, the most common methods for the detection of microcystins (ELISA, HPLC) do not identify the producer strains. These strains can be identified by conventional PCR, but this method doesnt enable to quantify them. In resume, there is not yet available a method that allow simultaneously identify and quantify microcystin-producing strains. This work aimed to develop a method based on Real-Time PCR applied to the monitoring of toxic species of Planktothrix in surface freshwater reservoirs used as drinking water supply and for recreational activities. The experimental work was developed according to several phases that are listed and explained below. In a first approach, field surveys were conducted to access the occurrence and distribution of Planktothrix – Chapter 3. It was observed that Planktothrix has a wide distribution in Portuguese lakes and that Planktothrix agardhii is the most commonly found specie. Furthermore microcystin production was detected in isolates from this species. In a second stage, it was developed a method based on real-time PCR to detect and quantify Planktothrix agardhii - Chapter 4. The real-time PCR is a promising technique for cyanobacteria research and monitoring. The main advantage of real-time PCR over conventional PCR is the ability to quantify the target gene copy numbers on a sample. Thus, in addition to identifying Planktothrix strains, the real-time PCR also enables to quantify those strains, which constitutes an advantage over the procedures used in the routine monitoring of cyanobacteria. It should be noted that the determination of the cell FCUP Accessing Planktothrix species diversity and associated toxins using quantitative real-time PCR in natural waters vii density is critical in the risk assessment of toxic cyanobacteria, as the guideline values for cyanotoxins are based on cyanobacterial concentrations as well as on toxin cell quota. Another important aspect in cyanobacteria monitoring is the use of preserved samples. Preservation is used to maintain the morphologic features of cyanobacterial cells to further be used in their identification/quantification and also to avoid sample degradation during transport. In this work, the applicability of the real-time technique in the amplification of DNA from preserved samples was evaluated, by using the method previously developed for cell quantification – Chapter 5. The results indicate that real-time PCR is a robust technique applicable to those types of samples but that the most common preservation methods (Lugol’s solution, formaldehyde, glutaraldehyde) reduce the DNA quantity and quality. Since DNA degrades fast in those samples, the applicability of real-time PCR on preserved samples was tested using other preservation procedure – Chapter 6. The preservation in methanol 100% at -20ºC allowed maintaining the integrity of the samples both for morphologic and molecular analysis up to two years after preservation. The last chapter of this thesis reports the result of two years of monitoring of a reservoir having a persistent bloom of toxic P. agardhii (Appendix A) - Chapter 7. In this reservoir, high cell densities did not always correspond to high amounts of toxin and vice versa. Using the real-time PCR it was demonstrated that both toxic and non-toxic strains are present within the reservoirs and that they can flourish at different times. It was also detected a specie from another genus that also contributes to the production of microcystins. During the monitoring it was observed a chytrid parasite that infected the filaments of Planktothrix (Appendix A). The density of this parasite was also quantified by real-time PCR and the results showed that its development coincides with the increase of toxic Planktotrhix strains and of microcystin levels in the reservoir.