Modelling the assembly and structure of microbial communities with applications to waste treatment strategies

The central premise of this thesis is that combining models in theoretical ecology with our newfound ability to observe and measure microbial systems will allow for a suite of laws to be developed which can describe and predict the assembly and structure of microbial communities. This would allow environmental engineers to modify and improve the design and efficiency of wastewater treatment systems. It is demonstrated here that there is significant evidence that microbial community assembly is at least partly a random process. A simple Neutral Community Model (NCM) is shown to replicate much of the variability observed in real systems as diverse as the waste water treatment plants, estuaries and the human lung. This is in contrast to the prevailing view in microbial ecology that community composition is shaped by deterministic processes. Molecular methods in microbial ecology yield very small, sometimes biased, samples from what are ostensibly very large communities. It is demonstrated, using published literature on taxa-area relationships for microorganisms that sampling effects have the capacity to significantly distort the true, underlying ecological patterns. In doing so, a potential reconciliation is offered between some seemingly contradictory published reports on the nature of taxa-area relationships for microorganisms. The effects of sampling are built directly into the NCM, which allows the model to be tested using the data which are typically collected by microbial ecologists. The model is calibrated using the taxa-abundance distribution observed in a small waterborne bacterial community housed in a bark lined tree hole in a beech tree. Using these parameters, unchanged, it is shown that the model can predict the taxa-abundance distributions and taxa-volume relationship observed in 26 other beech tree communities whose sizes span three orders of magnitude. This represents the strongest test, so far, for any biological community, microbial or otherwise, that NCMs provide a useful tool in predicting community composition