Cyanobacteria are ancient photoautotrophic bacteria, and their occurrence is ubiquitous throughout aquatic bodies, although they can also be found in terrestrial ecosystems or in symbiosis with other organisms, or even in extreme environments such as in hypersaline lakes, hot springs, polar regions, and deserts ^[1][2][3][4][1,2,3,4]. However, in freshwaters, the study of the cyanobacterial community has been the focus of particular interest due to the occurrence of Harmful Cyanobacterial Blooms (HCBs), resulting from the massive growth of cyanobacteria that are potentially toxic, with impacts on both aquatic and terrestrial organisms, leading to serious health impacts or even death ^{[5][6][7][8][9][10][11][12][13][14][15][16]}[5,6,7,8,9,10,11,12,13,14,15,16]. Moreover, under a climate change scenario, the concern with HCBs is growing due to their spread and increased persistence worldwide ^{[17][18][19][20][21][22]}[17,18,19,20,21,22], with major changes on the ecosystems ^{[8][13][23][24]}[8,13,23,24] but also posing risks to human health ^[5][25][26][5,25,26] and leading to socio-economic impacts in local communities ^{[18][27][28][29][30][31][32]}[18,27,28,29,30,31,32].

In fact, many bloom-forming cyanobacteria have been reported as toxic, with the production of a wide range of toxins generally classified into hepatotoxins, neurotoxins, cytotoxins and dermatotoxins/irritant toxins ^[26][33][34][26,33,34]. Nevertheless, the list of new cyanotoxins is still increasing ^{[11][14][35][36]}[11,14,35,36]. The most reported cyanotoxins include: microcystins and nodularin (hepatotoxins); saxitoxins, anatoxins and β-methylamino-l-alanine (neurotoxins); cylindrospermopsin (cytotoxin); lyngbyatoxins and aplysiatoxins (dermatotoxins); and lipopolysaccharides (irritant toxins) ^{[14][15][22][37][38][39][40]}[14,15,22,37,38,39,40]. For a long time, most attention has been given to microcystins, mainly due to its global spread occurrence and impacts on human health, either by acute or chronic exposure ^{[5][39][41][42][43][44]}[5,39,41,42,43,44]. However, neurotoxic saxitoxins and anatoxin-a also pose significant health risks due to their rapid and acute poisonings ^[39][45][46][39,45,46] as well as the potential for chronic effects by extended exposure to low doses [47]. Cylindrospermopsin is another very frequent cyanotoxin ^[48][49][48,49], responsible for cytotoxic [26] and neurotoxic effects ^[50][51][50,51]. In fact, the proposed guideline value for long-term exposure to cylindrospermopsin in drinking water is 0.7 μg/L, which is even lower than the same guideline for microcystins (1.0 μg/L) [52]. Additionally, both hepatotoxins and neurotoxins can persist in water for long periods of time (from days up to several weeks) until its degradation ^[26][53][26,53], which increases the concern for extended exposure. The bioaccumulation of these toxins has also been addressed for aquatic organisms such as molluscs and fish ^{[49][54][55][56][57]}[49,54,55,56,57] but also for crops irrigated with contaminated water ^{[12][35][58][59][60]}[12,35,58,59,60], highlighting the risk range and potentially wider effects of cyanotoxins’ occurrence. The most common exposure routes to cyanotoxins include the consumption/drinking of contaminated water, but recreational exposure can also occur through the accidental water swallowing, skin contact or even inhalation of scum aerosols ^{[33][45][61][62]}[33,45,61,62].

Most historical records and ecological studies concerning cyanobacterial blooms have been based on the identification of bloom-forming cyanobacteria using classical taxonomy mainly sustained by phenotypic features, which can be tricky due to several reasons, namely the diversity of strains/ecotypes ^[63][94]. Moreover, with the rise of DNA-based molecular approaches (using mostly 16S rRNA gene sequences), the polyphyletic nature of some genera has become controversial ^{[64][65][66][67]}[65,95,96,97] and several taxonomical revisions have been made for several species and even genera ^{[63][68][69][70][71][72][73]}[94,98,99,100,101,102,103], using polyphasic approaches to integrate morphological, biochemical and molecular information ^[69][71][73][99,101,103]. This re-classification into new genera and species also amplified the confusion regarding the taxonomy of blooming cyanobacteria and their correct identification, particularly for Nostocaceae genera such as Anabaena and Aphanizomenon, which were divided into new genera including Dolichospermum, Chrysosporum, Cuspidothrix or Sphaerospermopsis ^{[67][73][74][75]}[97,103,104,105]. For instance, Sphaerospermopsis aphanizomenoides was formerly known as Aphanizomenon aphanizomenoides (Forti) Horecká and Komárek and Anabaena aphanizomenoides Forti ^{[68][69][73][76]}[98,99,103,106]. Other examples can be Raphidiopsis raciborskii and Cuspidothrix issatschenkoi, which were formerly known as Cylindrospermopsis raciborskii (Woloszynska) Seenayya and Subba Raju and Aphanizomenon issatschenkoi (Usačev) Proshkina–Lavrenko, respectively ^[77][78][107,108]. Therefore, many concerns have been raised related to the probability of misidentifications only relying on morphological characters under a light microscope, particularly when heterocysts and akinetes are not visible for nostocacean cyanobacteria ^{[79][80][81][82][83][84]}[88,109,110,111,112,113]. In fact, although necessary, the controversy over the past decades on cyanobacterial taxonomy regarding Nostocales order, in particular, has also increased the confusion for a proper identification ^{[64][65][66][67][69][71][73][85][86]}[65,95,96,97,99,101,103,114,115]. This can have major implications for the previous knowledge regarding the distribution and dynamics of species-specific blooms and their ecology and toxicity ^[87][63]. Therefore, polyphasic approaches are crucial for the identification and characterization of isolated cyanobacterial strains ^[71][88][101,116], allowing ulterior DNA sequence match and identification through phylogenetic affiliation, along with ecological and toxicological features ^[84][89][90][113,117,118]. This is the basis for a deeper exploration of global distribution patterns of cyanobacterial species by comparing strains from diverse geographical origins or from time-dispersed blooms ^[75][91][105,119].

Cyanobacterial blooms are frequently co-dominated by several species (some of which can be very similar under a microscope and difficult to distinguish and identify correctly ^[79][92][88,120]). Moreover, it is known that growth requirements can vary greatly between different cyanobacterial species ^{[19][22][52][93]}[19,22,52,121]. For instance, in spite of the relationship frequently reported between the occurrence of cyanobacterial blooms and eutrophication, blooms can occur under low levels of inorganic nitrogen and/or phosphorus, depending on the dominant species ^{[22][84][94][95]}[22,75,113,122]. Then again, climate change conditions produce variations in the physiological responses of cyanobacterial cells and lead to important changes in the composition of bloom-dominating strains and, consequently, impact the whole dynamics and toxicity potential of a cyanobacterial bloom ^[30][96][30,123]. Nitrogen-fixing cyanobacteria, in particular, can take special advantage of warmer and CO₂-rich conditions from climate change ^[96][97][123,124] and increase their geographic range of proliferation in the near future. In fact, as referred above, several Nostocales invasive diazotrophic and potentially toxic species (such as Raphidiopsis raciborskii, Cuspidothrix issatschenkoi and Sphaerospermopsis aphanizomenoides) have already been increasingly reported at higher latitudes ^{[98][99][100][101][102][103][104]}[81,85,86,89,125,126,127]. On the other hand, during a bloom, the co-occurrence of different strains from a same species is also common, which makes it impossible to differentiate them exclusively using morphological features ^[79][90][88,118]. The phenotypic plasticity of some species (namely the invasive R. raciborskii and S. aphanizomenoides) can also correspond to intraspecific genetic heterogeneity even among strains from the same geographical origin ^[90][105][118,128], suggesting a microevolution that can provide these species an increasing expansion potential. These species-specific strains may diverse significantly in their ecological requirements and/or toxic potential ^{[76][84][89][106][107][108]}[106,113,117,129,130,131], with implications not only for the bloom development and dynamics, but also for the toxicity outcomes and health risks, depending on the ratio of non-toxic vs. toxic strains. Therefore, the search for intraspecific information is becoming more and more important to understand local to global biogeographical, ecological and toxicity patterns. Here, DNA-based molecular methodologies play a crucial role not only by helping to overcome misidentifications based on morphological features but also by providing strain-specific data to track variations of cyanobacterial strains from geographically different regions ^{[75][109][110][111]}[82,105,132,133] or re-incidences of blooming strains over time in the same water body ^{[79][90][112][113]}[88,118,134,135].

As discussed above, the taxonomic confusion and controversy has also had an impact on the characterization of which cyanotoxins can be produced by each cyanobacterial species ^[64][65]. Additionally, each species can have toxic and non-toxic genotypes ^{[114][115][116][117]}[69,136,137,138], which brings even more entropy into toxicological studies. The synthesis of different cyanotoxins relies on the presence of specific gene clusters ^{[118][119][120]}[139,140,141], and some cyanobacteria can also have biosynthesis gene clusters for more than one cyanotoxin [11], meaning that cyanobacterial blooms can be also co-dominated by multiple-toxin-producing strains, as previously reported ^[121][122][142,143]. Additionally, the regulation of cyanotoxins production varies at the strain level and can be affected by environmental factors such as temperature, light, pH and concentration of nutrients such as iron and nitrogen ^[118][139] as well as the bacteria present in water ^[123][124][144,145]. For instance, increased water temperature can influence the toxic potential of a bloom by promoting a shift of dominance from non-toxic to toxic cyanobacterial strains; at the same time, it can also increase toxin expression in the toxic strains ^[115][125][136,146]. All these genetic and physiological variations at the species and strain levels have implications on the overall toxicity of a bloom and toxicity assessment for a particular species ^[126][147]. This highlights the need for more studies using polyphasic approaches at the strain level combining at least a molecular characterization along with geographical distribution, as the genotype differentiation in specific niches can be also attributed to a selection from environmental factors ^[114][69].