Simulated bacterial species succession
Year: 2024
Type: article
Abstract: • A simulator has been created that links metagenomic data on transporter proteins to the growth and succession of a set of bacterial taxa. • The model is based on a classical microbial food web, but with the addition of virtual transporter proteins to control the nutrient uptake of the bacteria. • The simulator generates a realistic annual pattern for the development of a microbial food web and a diverse bacterial community can be maintained in the simulator over several annual cycles. 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.
Source: Ecological Modelling
Language: English
Subfield: Ecology
Field: Environmental Science
Domain: Physical Sciences
Open Access status: hybrid
Estimated APC paid: $2,860
OpenAlex ID: W4403508151