A platform using virtual transporter proteins to simulate nutrient uptake and bacterial multispecies dynamics has been created. The purpose of this simulator is to explore the extent to which different bacterial taxa can coexist based on a mechanistic understanding of their fitness. In the simulator, taxa with different combinations of fitness traits such as the abundance of specific transporter proteins, cell size, motility, metabolic strategies, and predation are allowed to freely compete for available resources. The bacterial taxa represented in the simulator feature bacterial stereotypes at the taxonomic level of order. Metagenomic data on the taxonomic distribution of molecular transporters, from a Baltic Sea time series, provide a framework for the uptake of nutrients by the bacteria. Physical space is not explicitly simulated, so the arena in the experiment is inherently homogeneous as this appears to be a good approximation to an aquatic microbial food web. However, the simulation scenario is based on physical constraints such as the diffusion encounter of nutrients and viruses as well as swimming predators. Examples of mechanisms that are parameterized include growth rate, virus infection, and predation. The overall structure is a classical pelagic microbial food web, where protozoa graze on bacteria and algae and are in turn grazed by microzooplankton. The annual growth pattern of primary producers, and thus the input of organic material over the course of a season, is driven by the flux of light at a given latitude. The results show that the model generates a realistic annual pattern for the development of an aquatic microbial food web and that a diverse bacterial community can be maintained in the simulator over several annual cycles. Notably, the simulator generated similar bacterial population dynamics compared to in situ data.