iDynoMiCS projects and publications

Metabolic Switching

This example is about metabolic switching between aerobic and anaerobic respiration (denitrification) depending on oxygen availability. Some species can switch denitrification on faster but incur a higher cost of switching. Colours for fastest switcher (1 hour lag) are black=on, white=off; intermediate (3 hour lag) red=on, green=off; slowest switcher (3 hour lag) yellow=on, blue=off; EPS particles in pink.

A study on how environmentally fluctuating oxygen availability affects the diversity and composition of a community of denitrifying bacteria that have different lag times for inducing the denitrification pathway under anoxic (or low oxygen conditions). We tested the hypothesis that the existence of these diverse strategies of denitrification can be explained solely by assuming that faster response incurs higher costs. We found that if the ability to switch metabolic pathways quickly incurs no costs, the fastest responder is always the best. However, if there is a trade-off where faster switching incurs higher costs, there is a strategy with optimal response time for any frequency of environmental fluctuations, suggesting that different types of denitrifying strategies win in different environments. In a single environment, biodiversity of denitrifiers is higher in biofilms than chemostats, higher with than without costs, and higher at intermediate frequency of change.

This project was published as a case study in the first iDynoMiCS paper.

Plasmid Invasion of Biofilms

Modelling the plasmid-host-environment interactions in spatially complex systems (e.g. biofilms) is a major challenge. If successful, it will allow us to obtain a qualitative (and/or quantitative) understanding about the most important factors governing plasmid transfer dynamics. The individual-based model iDynoMiCS offers the perfect framework to explicitly model the impact of spatial structure on the individual’s characteristics which in turn may change due to the transfer of the genes, e.g. giving extra metabolic functions as in the TOL plasmid.

This study has been published in our first HGT paper

Is broader host range better for plasmid spread?

We are interested in the evolution of a plasmid's host-range and its ecological significance and also the impact of fluctuating environmental conditions on plasmid transfer and maintenance. Above is an example of the conjugative transfer of two compatible plasmids with different host-ranges in a two species biofilm community.

This is on ongoing project and more information is available on the Kreft Group website.