Investigating microbial biofilm community mediated processes on surfaces: From single cell genomics to community meta-omics

The study of microbial biofilms on reactive surfaces integrates many disciplines including biogeochemistry, engineering, physics and microbiology and has benefited greatly from recent approaches based in genomics and bioinformatics. Experimental biofilm studies have been predominately conducted on model systems containing single species. Most processes in nature and many in human disease however are driven by reactions occurring within complex microbial biofilm communities in contrast to a few processes that are the result of a single species. Many hurdles still remain and overcoming these will rely on technological and experimental advances that disentangle the immense complexity of a multispecies biofilm. This dissertation deals with complex microbial biofilm communities involved in the degradation of minerals: hydroxyapatite-based biominerals in the oral cavity. This work is inherently and extensively interdisciplinary, involving microbiology, molecular biology, genomics and metagenomics, as well as microbial physiology and geology. This work has involved the development and use of methods for the study of the structure and function of biofilms on one hand, and for the genomic characterization of interacting community members with single cell genomics on the other. Both top-down and bottom up approaches are clearly needed to more fully understand the abiotic and biotic processes that contribute to the fundamental process of mineral dissolution. The goals of the work are focused on using this interdisciplinary approach to gain insight into how microbial biofilm communities interact with surfaces such as human biominerals (teeth enamel made of hydroxyapatite mineral). However, the approaches and techniques developed here involving sampling a complex biofilm for single cell genomic reconstruction are widely applicable to the study of biofilms involved with geobiological activities everywhere.