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Marine phytoplankton forms the base of oceanic food webs and is integral to biogeochemical cycles that maintain Earth’s habitability. Marine diatoms are a diverse lineage of single-celled microalgae responsible for 20% of planetary primary production. Genome sequencing and genetic engineering techniques have established diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana as marine microbiology “yeasts” making them invaluable to modern research on cellular mechanisms of elemental cycling in marine environments. We here describe advances on fundamental aspects of diatom cell biology related to iron, carbon, and silicon metabolism. We first present the foundational work to use engineered soybean ascorbate peroxidase APEX2 for subcellular proteomic profiling in diatoms. APEX2 permits spatially resolved proteomic mapping by oxidizing biotin-phenol to phenoxyl radicals which can covalently react with nearby proteins. Tagged proteins can be isolated and analyzed using mass spectrometry. Using APEX2-mediated proteomics, we cataloged vicinal proteins of Phaeodactylum tricornutum phytotransferrin, an environmentally ubiquitous endocytosed iron receptor. Proteins encoded by iron-sensitive genes expressed from a chromosomal gene cluster were identified and two of them colocalized with phytotransferrin adjacent to the chloroplast. This, along with their phylogenetic, domain, and biochemical analyses, suggests they are involved in intracellular iron processing. Next, using fluorescence microscopy and circular dichroism we confirmed that PtEPYC1, an iron- and CO2-sensitive gene in P. tricornutum, encodes a chloroplast-localized disordered protein. Expression of its APEX2 fusion revealed a proteolytic pattern consistent with spacing of the identified protease cleavage sites. We hypothesize PtEPYC1 is involved in pyrenoid—RuBisCO-containing subchloroplastic organelle crucial for CO2 fixation—organization in P. tricornutum and provide insights that suggest this role is coupled to cell cycle control mechanisms. Finally, we used bacterial conjugation to localize a biosilica-associated protein in Thalassiosira pseudonana and provide evidence for its expression as an APEX2 fusion. Biomineral morphogenesis proceeds inside a silica deposition vesicle (SDV), a hallmark, yet elusive, diatom compartment. T. pseudonana is a prime model system to study biosilicification which makes this result a valuable advance for the diatom community. In summary, proximity proteomics holds enormous potential to glean new insights into subcellular proteomic composition in these evolutionarily, ecologically, and biotechnologically relevant microalgae.

Nitrous oxide (N2O) is a potent greenhouse gas and ozone-depleting substance produced by many different pathways in the nitrogen cycle, including nitrification, denitrification, and chemodenitrification. Abiotic sources of N2O such as the chemical reaction between nitrite (NO2-) and ferrous ion (Fe[II]) are generally neglected in studies of N turnover in soils. Abiotic controls containing nitrate (NO3-) and ferric iron (Fe[III]) fail to capture potential reactions between intermediates of N cycle pathways (e.g., NO2- as an intermediate in NO3 - reduction to ammonium [NH4+] or nitrogen gas) or replenishment of reactants by iron cycling. Recent studies suggest that Fe(II) plays an important role in N turnover through combined biotic and abiotic reactions. Anaeromyxobacter dehalogenans strain 2CP-C is a common soil bacterium with a versatile metabolism, including microaerobic and anaerobic respiration. A. dehalogenans reduces Fe(III) to Fe(II) and reduces NO3- to NH4+ via respiratory ammonification. The present work investigates the mechanisms by which A. dehalogenans utilizes O2 and the synergistic effects of Fe(III) and NO3- reduction. Evidence for respiration of 21% O2 via a low-affinity cytochrome c oxidase is presented, further expanding the respiratory versatility of A. dehalogenans. A previously unrecognized ecophysiological role is revealed in which A. dehalogenans reduces NO3- to approximately 50% N2 and 50% NH4+ via coupled biotic-abiotic reactions, revealing a mechanism for denitrification in the absence of nitric oxide (NO)-forming NO2- reductases. Further analysis of publicly available sequenced genomes reveal other microorganisms with the potential to couple biotic-abiotic reactions for reduction of NO3- to N2 in the absence of NO-forming NO2- reductases. Finally, the effects of sulfide and molybdenum are tested, demonstrating that A. dehalogenans reduces NO3- to NH4+ and NO2- to N2O in the presence of Fe(II) and sulfide, due to the inhibition of NO3- and N2O reductases by sulfide sequestration of trace metals. Collectively, this work demonstrates an underestimated mechanism for denitrification and expands our knowledge of the role of A. dehalogenans in O2 respiration and Fe and N cycling. Future efforts assessing the fate of N in agricultural soils should take into account the iron, molybdenum, and sulfide content of soils in addition to molecular information.

The ocean’s biological pump is crucial for the carbon balance of the climate system, and the control of its three-dimensional “plumbing” on pump efficiency needed to be quantified. The nutrient cycles driving the biological pump are limited by dissolved iron (dFe). However, the iron cycle is poorly constrained, and the effects of iron source perturbations had never been quantified in a data-constrained model. In this thesis, we quantify the pathways and timescales of the biological pump, build an inverse model of the coupled phosphorus, silicon, and iron cycles, and explore the response of these cycles to changes in the aeolian iron supply. We use Green-function methods to show that the Southern Ocean (SO) is where (62±2)% of regenerated phosphate (PO4) reemerges after a mean sequestration time of 240±60yr. The pathways from productive regions to the SO contribute most to the biological pump, with a mean sequestration time of 130±70yr. Most PO4 is carried by abyssal paths with transit times exceeding 700yr, while ~1/3 of the regenerated PO4 from the equatorial Pacific that is destined for the SO is carried in Antarctic Intermediate Water. We use the model of the coupled nutrient cycles in inverse mode to objectively determine biogeochemical parameters by minimizing the mismatch with observed nutrient and phytoplankton concentrations. We generate a family of estimates, all consistent with the observations, for a wide range of iron source strengths, themselves not constrainable by current observations. The carbon and opal exports are well constrained in magnitude and pattern. We quantify the systematics of the carbon and opal exports supported by aeolian, hydrothermal, and sedimentary dFe and find that aeolian dFe is the most efficient for supporting production. The response to aeolian source perturbations is sensitive to the state of the iron cycle that is fitted to observations. A shutdown of the aeolian source does not completely untrap nutrients from the SO because sedimentary and hydrothermal dFe suffice to sustain production. A globally uniform 50-Gmol/yr aeolian iron addition fertilizes macronutrient-rich regions leading to increased deep regenerated and recycled dFe. This perturbation actually reduces iron fertilization supported by long-range transport because increased scavenging removes dFe before it can reach its destination. The response of the opal export is muted because the iron dependence of the Si:P uptake ratio counteracts fertilization.

Iron is a key micronutrient for marine biogeochemistry, limiting growth and nitrogen fixation in over a third of the ocean. However, the impacts of iron-binding ligands and iron source processes on dissolved iron distributions is not well known. The goal of this dissertation is to better understand the cycling of iron-binding ligands and the controls on their distributions and how that impacts dissolved iron. This dissertation also seeks to understand how individual iron sources influence iron distributions and biogeochemistry. To accomplish this, a new prognostic ligand tracer and iron-ligand speciation chemistry are incorporated into the Community Earth System Model (CESM). The CESM is now able to simulate realistic distributions of iron-binding ligands. The results show that with relatively few ligand sources and sinks the model was able to match observations of ligands, and that inclusion of a dynamic ligand tracer improves simulation of dissolved iron. To better understand the influence iron sources have on dissolved iron concentrations and biogeochemistry, sensitivity experiments for each source are conducted with the CESM. The results show that atmospheric dust and sedimentary iron inputs have the largest impact on dissolved iron concentrations and biogeochemistry. Hydrothermal vent inputs are important for deep ocean iron, and their inclusion in global biogeochemical ocean models would allow for more realistic iron simulation. This dissertation work also reevaluates the parameters governing the temperature influence on community phytoplankton growth rates. A dataset of in situ community phytoplankton growth rates was compiled and parameter values for the Q10 and Arrhenius models were optimized for use in global biogeochemical and ecosystem models. The results show and optimized Q10 value of 1.47 and an activation energy of 0.277 eV. Both the Q10 and Arrhenius models do equally well for estimating the temperature influence on community phytoplankton growth rates against the dataset. Evaluation of global biogeochemical and ecosystem models against our dataset will allow for further constraints on phytoplankton ecology and associated biogeochemitry.