Abstract Coral reef health depends on an intricate relationship among the coral animal, photosynthetic algae, and a complex microbial community. The holobiont can impact the nutrient balance of their hosts amid an otherwise oligotrophic environment, including by cycling physiologically important nitrogen compounds. Here we use 15N-tracer experiments to produce the first simultaneous measurements of ammonium oxidation, nitrate reduction, and nitrous oxide (N2O) production among five iconic species of reef-building corals (Acropora palmata, Diploria labyrinthiformis, Orbicella faveolata, Porites astreoides, and Porites porites) in the highly protected Jardines de la Reina reefs of Cuba. Nitrate reduction is present in most species, but ammonium oxidation is low potentially due to photoinhibition and assimilatory competition. Coral-associated rates of N2O production indicate a widespread potential for denitrification, especially among D. labyrinthiformis, at rates of ~1 nmol cm−2 d−1. In contrast, A. palmata displays minimal active nitrogen metabolism. Enhanced rates of nitrate reduction and N2O production are observed coincident with dark net respiration periods. Genomes of bacterial cultures isolated from multiple coral species confirm that microorganisms with the ability to respire nitrate anaerobically to either dinitrogen gas or ammonium exist within the holobiont. This confirmation of anaerobic nitrogen metabolisms by coral-associated microorganisms sheds new light on coral and reef productivity.
Abstract. Oxygen minimum zones (OMZs), due to their large volumes of perennially deoxygenated waters, are critical regions for understanding how the interplay between anaerobic and aerobic nitrogen (N) cycling microbial pathways affects the marine N budget. Here we present a suite of measurements of the most significant OMZ N cycling rates, which all involve nitrite (NO2–) as a product, reactant, or intermediate, in the Eastern Tropical North Pacific (ETNP) OMZ. These measurements and comparisons to data from previously published OMZ cruises present additional evidence that NO3– reduction is the predominant OMZ N flux, followed by NO2– oxidation back to NO3–. The combined rates of both of these N recycling processes were observed to be much greater (up to nearly 200x) than the combined rates of the N loss processes of anammox and denitrification, especially in waters near the anoxic / oxic interface. We also show that NO2– oxidation can occur in functionally anoxic incubations, measurements that further strengthen the case for truly anaerobic NO2– oxidation. We also evaluate the possibility that NO2– dismutation provides the oxidative power for anaerobic NO2– oxidation. Although almost all treatments returned little evidence for dismutation (as based on product inhibition, substrate stimulation, and stoichiometric hypotheses), results from one treatment under conditions closest to in situ NO2– values may support the occurrence of NO2– dismutation. The partitioning of N loss between anammox and denitrification differed widely from stoichiometric predictions of at most 29 % anammox; in fact, N loss rates at many depths consisted entirely of anammox. Through investigating the magnitudes of NO3– reduction and NO2– oxidation, testing for anaerobic NO2– oxidation, examining the possibility of NO2– dismutation, and further documenting the balance of N loss processes, these new data shed light on many open questions in OMZ N cycling research.
Microorganisms in marine oxygen minimum zones (OMZs) drive globally impactful biogeochemical processes. One such process is the multi-step denitrification, the dominant pathway for bioavailable nitrogen (N) loss and nitrous oxide (N2O) production. Denitrification-derived N loss is typically measured and modeled as a single step, but observations reveal that most denitrifiers in OMZs contain only subsets (modules) of the complete pathway. Here, we identify the ecological mechanisms sustaining diverse denitrifiers, explain the observed prevalence of certain modules, and examine the implications for N loss. We describe microbial functional types carrying out diverse denitrification modules by their underlying redox chemistry, constraining their traits with thermodynamics and pathway length penalties, in an idealized OMZ ecosystem model. Biomass yields of single-step modules increase along the denitrification pathway when growth is limited by organic matter (OM), explaining the viability of populations respiring nitrite and N2O in a nitrate-filled ocean. Results predict denitrifier community succession along environmental gradients: shorter versus longer modules are favored when OM versus N limits growth, respectively, suggesting a niche for the NO3- -> NO2- module in free-living communities and for the complete pathway in organic particles, consistent with observations. The model captures and mechanistically explains the observed dominance and higher oxygen tolerance of the NO3- -> NO2- module. Results also capture observations that nitrate is the dominant source of N2O. These results advance the mechanistic understanding of the relationship between microbial ecology and N loss, which is essential for accurately predicting the ocean's future.
Abstract Anammox bacteria inhabiting oxygen deficient zones (ODZs) are a major functional group mediating fixed nitrogen loss and thus exerting a critical control on the nitrogen budget in the global ocean. However, the diversity, origin, and broad metabolisms of ODZ anammox bacteria remain unknown. Here we report two novel metagenome-assembled genomes of Scalindua , which represent most, if not all, of the anammox bacteria in the global ODZs. Beyond the core anammox metabolism, both organisms contain cyanase and the more dominant one encodes a urease, indicating ODZ anammox bacteria can utilize cyanate and urea in addition to ammonium. The first ODZ Scalindua likely derived from the benthos ∼200 million years ago. Compared to benthic strains of the same clade, ODZ Scalindua uniquely encode genes for urea utilization but lost genes related to growth arrest, flagellum synthesis, and chemotaxis, presumably for adaptation to the anoxic water column.
Abstract Sinking marine particles drive the biological pump that naturally sequesters carbon from the atmosphere. Despite their small size, the compartmentalized nature of particles promotes intense localized metabolic activity by their bacterial colonizers. Yet the mechanisms promoting the onset of denitrification, a metabolism that arises once oxygen is limiting, remain to be established. Here we show experimentally that slow sinking aggregates composed of marine diatoms—important primary producers for global carbon export—support active denitrification even among bulk oxygenated water typically thought to exclude anaerobic metabolisms. Denitrification occurs at anoxic microsites distributed throughout a particle and within microns of a particle’s boundary, and fluorescence-reporting bacteria show nitrite can be released into the water column due to segregated dissimilatory reduction of nitrate and nitrite. Examining intact and broken diatoms as organic sources, we show slowly leaking cells promote more bacterial growth, allow particles to have lower oxygen, and generally support greater denitrification.
Data directory includes prescribed emission in MITgcm for CFC-11 and CFC-12, and MITgcm output under different forcing runs. Code directory includes all the code used to generate plots in the paper entitled "On the Effects of the Ocean on Atmospheric CFC-11 Lifetimes And Emissions" (Wang et al. 2021, PNAS).
The Eastern Tropical South Pacific is one of the three major oxygen deficient zones (ODZs) in the global ocean, and is responsible for approximately one-third of marine water column nitrogen loss. It is the best studied of the ODZs, and like the others, features a broad nitrite maximum across the low oxygen layer. How the microbial processes that produce and consume nitrite in anoxic waters interact to sustain this feature is unknown. Here, we used 15N-tracer experiments to disentangle five of the biologically-mediated processes that control the nitrite pool, including a high-resolution profile of nitrogen loss rates. Nitrate reduction to nitrite likely depended on organic matter fluxes, but the organic matter did not drive detectable rates of denitrification to N2. However, multiple lines of evidence show that denitrification is important in shaping the biogeochemistry of this ODZ. Significant rates of anaerobic nitrite oxidation at the ODZ boundaries were also measured. Iodate was a potential oxidant that could support part of this nitrite consumption pathway. We additionally observed N2 production from labeled cyanate and postulate that anammox bacteria have the ability to harness cyanate as another form of reduced nitrogen rather than relying solely on ammonification of complex organic matter. The balance of the five anaerobic rates measured – anammox, denitrification, nitrate reduction, nitrite oxidation, and dissimilatory nitrite reduction to ammonium – are sufficient to reproduce broadly the observed nitrite and nitrate profiles in a simple one-dimensional model, but require an additional cryptic source of reduced nitrogen to the deeper ODZ to avoid ammonium overconsumption.
Abstract Nitrite is a ubiquitous compound found across aquatic systems and an intermediate in both the oxidative and reductive metabolisms transforming fixed nitrogen in the environment. Yet, the abiotic cycling of nitrite is often overlooked in favor of biologically mediated reactions. Here we quantify the apparent acid dissociation constant (p K a ) between nitrous acid and its conjugate base nitrite in both freshwater and seawater systems across a range of environmentally relevant temperatures (5–35°C) using potentiometric‐based titration. In freshwater, we measured a p K a,NBS of 3.14 at 25°C and a p K a, T of 2.87 for seawater at the same temperature. We quantify substantial effects of both salinity and temperature on the p K a , with colder and fresher water manifesting higher values and thus a greater proportion of protonated nitrite at any given pH. Because nitrous acid is unstable and decomposes to nitric oxide, the implications for the nitrous acid dissociation constant on ecosystem function are broad.
Connecting molecular information directly to microbial transformation rates remains a challenge, despite the availability of molecular methods to investigate microbial biogeochemistry. By combining information on gene abundance and expression for key genes with quantitative modeling of nitrogen fluxes, we can begin to understand the scales on which genetic signals vary and how they relate to key functions. We used quantitative PCR of DNA and cDNA, along with biogeochemical modeling to assess how the abundance and expression of microbes responsible for two steps in the nitrogen cycle changed over time in estuarine sediment mesocosms. Sediments and water were collected from coastal Massachusetts and maintained in replicated 20 L mesocosms for 45 days. Concentrations of all major inorganic nitrogen species were measured daily and used to derive rates of nitrification and denitrification from a Monte Carlo-based non-negative least-squares analysis of finite difference equations. The mesocosms followed a classic regeneration sequence in which ammonium released from the decomposition of organic matter was subsequently oxidized to nitrite and then further to nitrate, some portion of which was ultimately denitrified. Normalized abundances of ammonia oxidizing archaeal ammonia monoxoygenase (amoA) transcripts closely tracked rates of ammonia oxidation throughout the experiment. No such relationship, however, was evident between denitrification rates and the normalized abundance of nitrite reductase (nirS and nirK) transcripts. These findings underscore the complexity of directly linking the structure of the microbial community to rates of biogeochemical processes.
