Meromictic Lake Cadagno contains a persistent microbial bloom and resembles the conditions of the Proterozoic Ocean because of oxic-anoxic transition along with sulphide-rich water. Lake Cadagno is permanently stratified into mixolimnion (oxic), chemocline (oxic-anoxic), and monimolimnion (anoxic). The microbial community of Lake Cadagno has been extensively studied for at least 25 years; contrastingly, a collective picture of nutrient biogeochemical cycling modulation by microbial eukaryotes, bacteria, and viruses was still missing. The work extends the understanding of the Lake Cadagno microbial loop and provides the first insights into the genomics of microbial eukaryotes and viruses from this ancient ocean model. This thesis presents a novel genome of a photosynthetic microbial eukaryote (referred to as Chlorella cadagnis) from the chemocline of Lake Cadagno, and their genomic machinery shows protein-coding genes involved in carbon, sulphur, and nitrogen metabolism. These findings reveal how microbial eukaryotes might thrive in a harsh (low light, O₂) chemocline environment. Furthermore, the work also presents that phycocyanin and phycobilins signals used for the detection of cyanobacteria in Lake Cadagno likely originated from chloroplasts of microbial eukaryotes like Cryptomonas. This thesis also presents the first report on the viral ecology of Lake Cadagno and potentially reveals how viruses might modulate oxygenic and anoxygenic photosynthesis in the chemocline of the ancient oceans.