As a microbial ecologist interested in aquatic biofilms associated with eukaryotic organisms, I was fascinated to read this article. You have provided me with a number of considerations for understanding the complex interactions and abiotic variables that structure these micro-environments.
I have several questions regarding some of the methods used in this study and I would also like to offer some thoughts that you may find interesting or relevant to explore using the existing model that you have built.
For computing bacterial biomass dynamics, you mention a ‘shoving’ condition. Could you expound upon the need for this condition within the model? Is this condition used to control bacterial density within each grid to account for limited physical space for cells within the biofilm?
I understand that your model uses a fixed incubation time of 28.8 minutes. If this incubation time were to decrease throughout the incubation (say if the phages were to increase the growth rate of their hosts by hijacking the host’s cellular machinery), how might that change the stability of the system?
Would we expect to see differences in host-phage dynamics if there was a concentration gradient in the nutrient (i.e. diffusing from the substratum), causing different bacterial growth rates as a function of depth or position of a cell within the biofilm?
Based on your results that coexistence of phages and bacteria becomes increasingly more likely as phage diffusivity increases, should we expect host-phage coevolution to occur at a faster rate than in the water column? Can biofilms be sources for ‘super’ phages?
Really great work- I am excited to read more!