Microorganisms are ubiquitous and form complex, highly dynamic communities with interconnected metabolic dependencies whenever they inhabit the same environment. Well-known examples of microbial communities include the human gut microbiome, but equally important to life on earth are those in the aquatic environment. Composed of photosynthetic algae, protists and bacteria, the aquatic microcosm is responsible for >50% of global carbon fixation as well as the production of essential primary metabolites such as vitamin B12. In this talk, I will provide a comprehensive overview about our recent advancements at the intersection of microbiology, biotechnology, public health, and environmental science. On the example of vitamin B12, I will elucidate how multi-omics and functional genomics analyses enable us to comprehend, predict, and harness the intricacies of microbial interactions in the aquatic food web. In addition, I will showcase how we are utilising portable Nanopore sequencing to monitor microbial communities in the context of freshwater diagnostics as well as to study connections between environmental signalling and epigenetic changes. Finally, I will conclude with an overview of our ongoing research projects in the realm of Microbial Systems Biology, Real-Time Genomics and Long-read Bioinformatics, offering insights into the scientific trajectory for the upcoming years.