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UBC Math
Fri 27 Nov 2015, 3:00pm
Department Colloquium
MATX 1100
Pathway-centric modeling of microbial ecosystems (Graduate Research Award Colloquium)
MATX 1100
Fri 27 Nov 2015, 3:00pm-4:00pm


New molecular techniques such as DNA sequencing provide conceptual insights into microbial community metabolism and biogeochemical cycling in natural and engineered ecosystems. However, attempts to mechanistically integrate molecular data with biogeochemistry are faced with the inhibitory complexity of individual cells and a large number of unknown physiological parameters. Recent work suggests that biochemical pathways are, at ecosystem scales, strongly shaped by thermodynamic and stoichiometric constraints. Pathway-centric mathematical theories rooted in fluxes of matter and energy could thus provide holistic insight into microbial ecosystems and global biogeochemical fluxes.

Oxygen minimum zones (OMZ) are oxygen-depleted regions in the ocean that are dominated by microbial metabolism, thus constituting ideal systems for developing theories of microbial ecology. I will present our current efforts to model the biogeochemistry of an intensely studied OMZ off the coast of Vancouver Island using reaction-advection-diffusion models. In contrast to conventional approaches, we focus on individual enzymes catalyzing metabolic pathways and assume that energy fluxes translate directly to gene expression and biosynthesis. We use DNA, mRNA and protein sequence data, as well as geochemical depth profiles and process rate measurements to calibrate and validate our models.