The meromictic Lake Cadagno (Swiss Alps) is an ideal study site for euxinic microbial communities due to the accessibility and the detailed scientific record spanning from biogeochemistry to biophysics and microbial ecology. The phototrophic sulfur oxidizing bacteria (PSOB) community of Lake Cadgno has been studied for years in situ and strains have been isolated and characterized, however information on genomic level was missing. For the first time, with this study we provide novel ecological insights on the biological functions encoded in two PSOB species preforming whole genome sequencing. We then elucidated in-depth the day/night differences in carbon and energy metabolic pathways of PSB ‘Thiodictyon syntrophicum' nov. sp. str. Cad16T in situ with a combination of quantitative proteomics and radiotracer uptake experiments. Finally we additionally demonstrated the use of genomic data as predictive biomarkers for rapid mass-spectrometry based typing of environmental isolates.