Biogeochemistry of Nitrogen Cycling in Low O2 Waters from Oxygen Minimum Zones, Soda Lakes, to Cultures

Abstract

Nitrogen (N) is an essential component of proteins and nucleic acids and therefore, an essential element for life. N can take many forms in the environment, all with different biological availabilities. Microorganisms play an outsize role in determining the partitioning of N between these forms. Here we present four studies that investigated the genetic capabilities, biochemical intricacies, and environmental significance of N cycling microbes, with a focus on low O2 environments and anaerobic ammonium oxidizing (anammox) bacteria, a clade responsible for substantial fixed nitrogen loss in oxygen minimum zones (OMZs), large naturally occurring anoxic marine regions. In chapter 2, we report genetic and biochemical evidence that three anammox bacteria encode an encapsulin system, a novel type of protein based cellular compartment. Searches through metagenomic databases returned 25 additional new encapsulins. Chapter 3 reports experiments that tested two hypotheses for how the most common type of anammox encapsulin functions: (1) that anammox encapsulins protect against reactive compounds and (2) that anammox encapsulins reduce NO2- to NO for the central anammox metabolism. In experiments using aerobic and anaerobic E. coli cultures engineered to express a model anammox encapsulin, no evidence for either hypothesis was observed. As a result, the biochemical function and role of encapsulins in anammox bacteria remains unexplained. Chapter 4 examines the N cycle in the soda lake Mono Lake by delving into a metagenomic data series across major chemical changes in oxygen, salinity, and winter mixing. Members of the Nitriliruptorales order were observed to be abundant at all times, depths, and oxygen concentrations, a phenomenon possibly due to an ability to metabolize a great variety of carbohydrates. Chapter 5 presents a comprehensive suite of stable isotope incubations designed to estimate the rates of microbial N transformations in OMZs. The results provide support for several new views of the marine N cycle: (1) that a rapid cycle of NO3- reduction and NO2- oxidation is of greater magnitude than N loss rates in OMZs, (2) that this rapid cycle maintains the deep secondary nitrite maximum observed in all OMZs, and (3) that anaerobic NO2- oxidation occurs in OMZ regions.