I work to better understand the interactions between microorganisms, their biogeochemical environment, and the Earth’s climate. A relatively small number of metabolic pathways drive the global cycles of climatically important elements, and bacteria and archaea mediate the majority of this cycling. My work hypothesizes that the activity of microbes within an ecosystem is sufficiently predictable to provide insight into the formation of large-scale biogeochemical features, such as anoxic oxygen minimum zones and patterns of nitrification. The predictability results from an assumption that much of the large-scale function of the microbial community can be understood by reducing that activity to its underlying chemistry and to the physiology of a microbial cell. Interactions of diverse microbial populations with each other and the environment results in the geochemical distributions that we observe. I work to develop simple models with mechanistic description of microbial growth and respiration to examine these distributions, their connections to rates of microbial activity and the biogeography of the microbial communities, and their sensitivity to changes in climate.

What is it that we want to know about global biogeochemistry and microbial metabolisms, and why? Here are the motivations behind a few projects that I’m working on, followed by some specific research questions for each:

Deoxygenation and the transition to anaerobic metabolisms

What will be the effects of the projected deoxygenation of the oceans due to global warming?  Deoxygenation is expected as a consequence of the decrease in solubility of oxygen in warming waters, and should lead to significant decreases in ocean oxygen content over the next century. This effect takes place at the air-sea interface, where waters warm, and so will take hundreds or thousands of years to affect the oxygen in the least ventilated areas of the ocean. However, depending on the location, the oxygen minimum of the water columns in some locations may be affected by deoxygenation over the decadal timescales that govern the thermocline. In much of the tropical Pacific ocean, for example, oxygen reaches relatively low concentrations that are relevant for the viability of larger animal growth and respiration. Thus, deoxygenation could contract the habitat for fish and other marine animals. Given human dependency on fisheries, deoxygenation could potentially affect human society in decadal or centurial timescales, and so, understanding the biogeochemical and physical interactions that control oxygen distributions is important for anticipating such changes.

Another effect of deoxygenation is the potential change in the rates of anaerobic activity in marine anoxic zones. Oxygen has been depleted to nanomolar concentrations or lower by aerobic respiration in these zones, and an open question is whether or not further loss of oxygen will lead their expansion. Anaerobic processes result in denitrification — the loss of fixed nitrogen to nitrogen gas and/or the potent greenhouse gas nitrous oxide. The transition from aerobic to anaerobic microbial respiration thus controls rates of denitrification, but this transition has not been quantitatively understood.

Specific research questions:

Why is oxygen depleted to nanomolar concentrations in marine anoxic zones?

What governs the transition from aerobic to anaerobic metabolisms in marine anoxic zones? What enables their coexistence?

Nitrification and its relationship to the biological pump

A second area of emphasis is relevant for understanding the structure of marine ecosystem production and the biological pump. The biological pump refers to the increase in dissolved inorganic nutrients with depth, and is a consequence of the remineralization of exported organic matter at depth. This sequestration of nutrients at depth leads to an enhanced storage of carbon in the ocean. An active area of research is to develop a more mechanistic understanding and quantification of the export production that enables this sequestration.

The inverse of this export production is the `new production’ that occurs due to the upwelling of nutrients from depth. The amount of organic matter exported to depth must be balanced by this new production over large time and space scales. Nitrification — the microbially-mediated oxidation of ammonium to nitrate — is relevant for estimating amounts of new production. Whether nitrification occurs in the euphotic zone and/or mixed layer or in the deep mesopelagic has impacts on the locations of exported organic matter, and thus the degree to which exported carbon is sequestered in the deep ocean. How much nitrification occurs in the euphotic zone versus at depth, and why?

Nitrification typically peaks at depth, just below the euphotic zone. Because nitrite is an intermediate product in the two-step nitrification process, understanding what forms the primary nitrite maximum (PNM) — the accumulation of nitrite at the base of the euphotic zone in stratified water columns — serves as a focusing feature for understanding nitrification more generally. Though ubiquitous in the ocean, the formation of the PNM is still not well understood.

Specific research questions:

What forms the primary nitrite maximum?

How does microbial ecology control the distributions of nitrite in the oxygenated ocean?