Abstract
Microalgae represent large and diverse group of unicellular photosynthetic microorganisms that, being most abundant and efficient unicellular producer of a rich and complex biomass in all aquatic systems.Microalgae have gained global importance in recent years as potential source of renewable energy as well as bioindicators to manage an aquatic ecosystem.The accurate identification of diversity is a key challenge in microalgal ecology research.Moreover, the increased knowledge of the scope, structure, and dynamics of microalgal biodiversity is urgently needed.A rapid and reliable identification of Microalgae in general, and at lower taxonomic levels in particular, cannot be accomplished by morphological methods alone.Amplicon-based metagenome analysis using multiple primers approach can provide novel insight into the biological and ecological inferences, and address many general questions with a special focus on phylogenetics and taxonomy, to cast the widest possible taxonomic net for microalgae and yet reduce sequencing of non-microalgal eukaryotes.In this review, we highlight main advances taken place in the field of metagenomics over the last two decades, present statistics of the main metagenomic techniques and databases, and discuss opportunities, challenges and perspectives in metagenomics with special reference to analyzing microalgal diversity in different ecosystems.