Linking microbes and climate : insights into the marine oxygen and nitrogen cycles with microbial metabolic functional types

Abstract

This thesis posits that understanding the controls on microbially-mediated marine biogeochemical cycling requires a mechanistic description of microbial activity in biogeochemical models. In the work here, the diverse microbial community is resolved using metabolic functional types, which represent metabolisms as a function of their underlying redox chemistry and physiology. In Chapter 2, I use a simple model to predict the limiting oxygen concentration of aerobic microbial growth in an ecosystem. This limiting concentration is in the nanomolar range for much of the parameter space that describes microbial activity in marine environments, and so anticipates the recent measurements of oxygen to nanomolar concentrations or lower in anoxic zones. Anaerobic metabolisms should become favorable at this limiting concentration. The model provides a parameterization for dynamic oxygen depletion and limitation, without a prescribed critical oxygen concentration. In Chapter 3, I extend the above analysis to determine the full set of conditions required for favorable anaerobic metabolism. Resource ratio theory is used to explain the competitive exclusion of anaerobic metabolisms in oxygenated environments as well as the stable coexistence of aerobic and anaerobic metabolisms when oxygen is limiting. The onset of this coexistence is a function of the relative availability of oxygen and a mutually required substrate. Results hypothesize the likelihood of coexisting aerobic and anaerobic metabolisms at limiting oxygen concentrations, which is consistent with observations. These dynamics are demonstrated in an idealized oxygen minimum zone model. In Chapter 4, I use a mechanistic description of nitrification to explain the location and intensity of the primary nitrite maximum. First, competition with phytoplankton excludes nitrification from the sunlit layer of the ocean, resulting in peak nitrification at depth, as widely observed. Second, differences in the metabolisms of the microbial clades responsible for the two steps of nitrification explain why nitrite accumulates consistently as an intermediate. The model provides a dynamic resolution of nitrification in the ocean. It predicts that nitrification is favorable in sunlit waters where phytoplankton growth is limited by light or by a substrate other than reduced inorganic nitrogen.