Mechanic force (like shaking or running flow) influences bacterial biofilm formation and alter biofilm structure. Do you think the change of biofilm structure is a mere result of interactions with physical forces or might also involve the regulation of some biofilm genes in bacteria?
This is an interesting possibility. One mechanism that may underlay this is for example high pressure. It is describe, at least in E. coli, that high pressures can induce SOS system. There are many elements like insertion sequences and bacteriophages that are responsive to SOS activation and is known that many prophages can contribute to biofilm dynamic and diversification. Another effect of a running flow is that it can perturb the concentration of quorum sensing molecules by washing they away, which in turn have strong influence in biofilm morphology and dynamic. Biofilms to me is a very complex structure (embedded microbes in a matrix) with an extraordinary plasticity and are much more than gene expression, quorum sensing, mechanical forces or nutritional status. It is bacteria coordination system, communication and cooperation with a very strong bed hedging prone to enhance microbial survival. It is genetic diversity and physiological diversity acting together, sensing of the environment and elaboration of a responses that depends on the particular microenvironment of each component. We still do not know much about biofilms except some generic things and some particular characteristics of some models. Hacking its complexity is a very difficult task. I'm sorry for the long response. Most of it is just my point of view after reading many papers about it and make some modest experiments. I hope this helps.
I agree with the previous answers: a combination of both. Also, recent work by Siryapron et al. (2014) suggested that bacteria may be able to translate surface contact into physiological changes in gene expression (independent of flagellar function). Great paper, worth the read if you're interested in the topic, Daniel.
Siryaporn, A., Kuchma, S.L., O’Toole, G.A., and Gitai, Z. (2014). Surface attachment induces Pseudomonas aeruginosa virulence. Proc. Natl. Acad. Sci. USA 111, 16860–16865.
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