This PhD project employs an ecosystems biology approach to unravel important processes within natural plankton communities, including turnover dynamics, spatiotemporal functions, mutualistic and antagonistic interactions, and the relationship between biodiversity and functional diversity. High-throughput sequencing, specifically metatranscriptomics, is utilized to describe plankton communities, employing both long- and short-read sequencing and establishing a validated lab- and bioinformatics workflow. The resulting information enhances our understanding of ecosystem processes such as biogeochemical cycling, and its relevance in investigating the potential alterations under different global change scenarios. The interdisciplinary nature of this project integrates ecology, genomics, and bioinformatics, contributing valuable insights into plankton dynamics and functional roles, with implications for ecological decision-making and policy formulation.