Transdisciplinary approaches for the study of cyanobacteria and cyanotoxins

•Transition from morphology-based taxonomy to genomic analysis enhances cyanobacteria classifications and toxins detection accuracy.•Advances in molecular biology enable precise monitoring of cyanotoxins by targeting toxin-producing genes through nucleic acid-based techniques.•Genetic identification can determine if cyanobacteria have potentially harmful effects on humans and/or nature.•Emerging bioinformatics tools enable the genomic mining of toxin-related genes, providing new insights into the evolution and regulation of cyanotoxins.•Current public genetic databases underrepresent cyanobacterial genomes, limiting our understanding of their diversity and toxin production potential. Cyanobacteria, ancient aerobic and photoautotrophic prokaryotes, thrive in diverse ecosystems due to their extensive morphological and physiological adaptations. They play crucial roles in aquatic ecosystems as primary producers and resource providers but also pose significant ecological and health risks through blooms that produce harmful toxins, called cyanotoxins. The taxonomic affiliation of cyanobacteria has evolved from morphology-based methods to genomic analysis, which offers detailed structural and physiological insights that are essential for accurate taxonomic affiliation and monitoring. However, challenges posed by uncultured species have been extrapolated to the detection and quantification of cyanotoxins. Current advances in molecular biology and informatics improve the precision of monitoring and allow the analysis of groups of genes related to toxin production, providing crucial information for environmental biosafety and public health. Unfortunately, public genomic databases heavily underrepresent cyanobacteria, which limits the understanding of their diversity and metabolic capabilities. Despite the increasing availability of cyanobacterial genome sequences, research is still largely focused on a few model strains, narrowing the scope of genetic and metabolic studies. The challenges posed by cyanobacterial blooms and cyanotoxins necessitate improved molecular, cultivation, and polyphasic techniques for comprehensive classification and quantification, highlighting the need for advanced genomic approaches to better understand and manage cyanobacteria and toxins. This review explores the application of transdisciplinary approaches for the study of cyanobacteria and cyanotoxins focused on diversity analysis, population quantification, and cyanotoxin monitoring, e