Nitrous oxide in the oxygen minimum of the eastern tropical North Pacific: evidence for its consumption during denitrification and possible mechanisms for its production

Chlamydomonas reinhardtii, an Algal Model in the Nitrogen Cycle

Nitrogen (N) is an essential constituent of all living organisms and the main limiting macronutrient. Even when dinitrogen gas is the most abundant form of N, it can only be used by fixing bacteria but is inaccessible to most organisms, algae among them. Algae preferentially use ammonium (NH₄⁺) and nitrate (NO₃⁻) for growth, and the reactions for their conversion into amino acids (N assimilation) constitute an important part of the nitrogen cycle by primary producers. Recently, it was claimed that algae are also involved in denitrification, because of the production of nitric oxide (NO), a signal molecule, which is also a substrate of NO reductases to produce nitrous oxide (N₂O), a potent greenhouse gas. This review is focused on the microalga Chlamydomonas reinhardtii as an algal model and its participation in different reactions of the N cycle. Emphasis will be paid to new actors, such as putative genes involved in NO and N₂O production and their occurrence in other algae genomes. Furthermore, algae/bacteria mutualism will be considered in terms of expanding the N cycle to ammonification and N fixation, which are based on the exchange of carbon and nitrogen between the two organisms.

Algal photosynthesis converts nitric oxide into nitrous oxide

Nitrous oxide (N₂O), the third most important greenhouse gas in the atmosphere, is produced in great quantities by microalgae, but molecular mechanisms remain elusive. Here we show that the green microalga Chlamydomonas reinhardtii produces N₂O in the light by a reduction of NO driven by photosynthesis and catalyzed by flavodiiron proteins, the dark N₂O production being catalyzed by a cytochrome p450. Both mechanisms of N₂O production are present in chlorophytes, but absent from diatoms. Our study provides an unprecedented mechanistic understanding of N₂O production by microalgae, allowing a better assessment of N₂O-producing hot spots in aquatic environments.

Nitrous oxide (N₂O), a potent greenhouse gas in the atmosphere, is produced mostly from aquatic ecosystems, to which algae substantially contribute. However, mechanisms of N₂O production by photosynthetic organisms are poorly described. Here we show that the green microalga Chlamydomonas reinhardtii reduces NO into N₂O using the photosynthetic electron transport. Through the study of C. reinhardtii mutants deficient in flavodiiron proteins (FLVs) or in a cytochrome p450 (CYP55), we show that FLVs contribute to NO reduction in the light, while CYP55 operates in the dark. Both pathways are active when NO is produced in vivo during the reduction of nitrites and participate in NO homeostasis. Furthermore, NO reduction by both pathways is restricted to chlorophytes, organisms particularly abundant in ocean N₂O-producing hot spots. Our results provide a mechanistic understanding of N₂O production in eukaryotic phototrophs and represent an important step toward a comprehensive assessment of greenhouse gas emission by aquatic ecosystems.

Niche Partitioning of the N Cycling Microbial Community of an Offshore Oxygen Deficient Zone

Microbial communities in marine oxygen deficient zones (ODZs) are responsible for up to half of marine N loss through conversion of nutrients to N2O and N2. This N loss is accomplished by a consortium of diverse microbes, many of which remain uncultured. Here, we characterize genes for all steps in the anoxic N cycle in metagenomes from the water column and >30 μm particles from the Eastern Tropical North Pacific (ETNP) ODZ. We use an approach that allows for both phylogenetic identification and semi-quantitative assessment of gene abundances from individual organisms, and place these results in context of chemical measurements and rate data from the same location. Denitrification genes were enriched in >30 μm particles, even in the oxycline, while anammox bacteria were not abundant on particles. Many steps in denitrification were encoded by multiple phylotypes with different distributions. Notably three N2O reductases (nosZ), each with no cultured relative, inhabited distinct niches; one was free-living, one dominant on particles and one had a C terminal extension found in autotrophic S-oxidizing bacteria. At some depths >30% of the community possessed nitrite reductase nirK. A nirK OTU linked to SAR11 explained much of this abundance. The only bacterial gene found for NO reduction to N2O in the ODZ was a form of qnorB related to the previously postulated "nitric oxide dismutase," hypothesized to produce N2 directly while oxidizing methane. However, similar qnorB-like genes are also found in the published genomes of many bacteria that do not oxidize methane, and here the qnorB-like genes did not correlate with the presence of methane oxidation genes. Correlations with N2O concentrations indicate that these qnorB-like genes likely facilitate NO reduction to N2O in the ODZ. In the oxycline, qnorB-like genes were not detected in the water column, and estimated N2O production rates from ammonia oxidation were insufficient to support the observed oxycline N2O maximum. However, both qnorB-like and nosZ genes were present within particles in the oxycline, suggesting a particulate source of N2O and N2. Together, our analyses provide a holistic view of the diverse players in the low oxygen nitrogen cycle.

Low oxygen eddies in the eastern tropical North Atlantic: Implications for N2O cycling

Nitrous oxide (N₂O) is a climate relevant trace gas, and its production in the ocean generally increases under suboxic conditions. The Atlantic Ocean is well ventilated, and unlike the major oxygen minimum zones (OMZ) of the Pacific and Indian Oceans, dissolved oxygen and N₂O concentrations in the Atlantic OMZ are relatively high and low, respectively. This study, however, demonstrates that recently discovered low oxygen eddies in the eastern tropical North Atlantic (ETNA) can produce N₂O concentrations much higher (up to 115 nmol L⁻¹) than those previously reported for the Atlantic Ocean, and which are within the range of the highest concentrations found in the open-ocean OMZs of the Pacific and Indian Oceans. N₂O isotope and isotopomer signatures, as well as molecular genetic results, also point towards a major shift in the N₂O cycling pathway in the core of the low oxygen eddy discussed here, and we report the first evidence for potential N₂O cycling via the denitrification pathway in the open Atlantic Ocean. Finally, we consider the implications of low oxygen eddies for bulk, upper water column N₂O at the regional scale, and point out the possible need for a reevaluation of how we view N₂O cycling in the ETNA.

Influence of oxygen availability on the activities of ammonia-oxidizing archaea

Recent studies point to the importance of oxygen (O₂ ) in controlling the distribution and activity of marine ammonia-oxidizing archaea (AOA), one of the most abundant prokaryotes in the ocean. The AOA are associated with regions of low O₂ tension in oceanic oxygen minimum zones (OMZs), and O₂ availability is suggested to influence their production of the ozone-depleting greenhouse gas nitrous oxide (N₂ O). We show that marine AOA available in pure culture sustain high ammonia oxidation activity at low μM O₂ concentrations, characteristic of suboxic regions of OMZs (<10 µM O₂ ), and that atmospheric concentrations of O₂ may inhibit the growth of some environmental populations. We quantify the increasing N₂ O production by marine AOA with decreasing O₂ tensions, consistent with the plausibility of an AOA contribution to the accumulation of N₂ O at the oxic-anoxic redox boundaries of OMZs. Variable sensitivity to peroxide also suggests that endogenous or exogenous reactive oxygen species are of importance in determining the environmental distribution of some populations.

Microbial oceanography of anoxic oxygen minimum zones

Vast expanses of oxygen-deficient and nitrite-rich water define the major oxygen minimum zones (OMZs) of the global ocean. They support diverse microbial communities that influence the nitrogen economy of the oceans, contributing to major losses of fixed nitrogen as dinitrogen (N(2)) and nitrous oxide (N(2)O) gases. Anaerobic microbial processes, including the two pathways of N(2) production, denitrification and anaerobic ammonium oxidation, are oxygen-sensitive, with some occurring only under strictly anoxic conditions. The detection limit of the usual method (Winkler titrations) for measuring dissolved oxygen in seawater, however, is much too high to distinguish low oxygen conditions from true anoxia. However, new analytical technologies are revealing vanishingly low oxygen concentrations in nitrite-rich OMZs, indicating that these OMZs are essentially anoxic marine zones (AMZs). Autonomous monitoring platforms also reveal previously unrecognized episodic intrusions of oxygen into the AMZ core, which could periodically support aerobic metabolisms in a typically anoxic environment. Although nitrogen cycling is considered to dominate the microbial ecology and biogeochemistry of AMZs, recent environmental genomics and geochemical studies show the presence of other relevant processes, particularly those associated with the sulfur and carbon cycles. AMZs correspond to an intermediate state between two "end points" represented by fully oxic systems and fully sulfidic systems. Modern and ancient AMZs and sulfidic basins are chemically and functionally related. Global change is affecting the magnitude of biogeochemical fluxes and ocean chemical inventories, leading to shifts in AMZ chemistry and biology that are likely to continue well into the future.

Assessment of nitrogen and oxygen isotopic fractionation during nitrification and its expression in the marine environment

Nitrification is a microbially-catalyzed process whereby ammonia (NH(3)) is oxidized to nitrite (NO(2)(-)) and subsequently to nitrate (NO(3)(-)). It is also responsible for production of nitrous oxide (N(2)O), a climatically important greenhouse gas. Because the microbes responsible for nitrification are primarily autotrophic, nitrification provides a unique link between the carbon and nitrogen cycles. Nitrogen and oxygen stable isotope ratios have provided insights into where nitrification contributes to the availability of NO(2)(-) and NO(3)(-), and where it constitutes a significant source of N(2)O. This chapter describes methods for determining kinetic isotope effects involved with ammonia oxidation and nitrite oxidation, the two independent steps in the nitrification process, and their expression in the marine environment. It also outlines some remaining questions and issues related to isotopic fractionation during nitrification.

Nitrogen-15 and oxygen-18 characteristics of nitrous oxide: a global perspective

The global budget of N(2)O shows a significant imbalance between the known rate of destruction in the stratosphere and the estimated rates of natural and anthropogenic production in soils and the ocean. Measurements of the (15)N/(14)N and (18)O/(16)O ratios in two major tropospheric sources of N(2)O, tropical rain forest soils and fertilized soils, show that soil N(2)O from a tropical rain forest in Costa Rica and from sugar-cane fields in Maui is strongly depleted in both (15)N and (18)O relative to mean tropospheric N(2)O. A major source of heavy N(2)O, enriched in both (15)N and (18)O, must therefore be present to balance the light N(2)O from soils. One such source is the back-mixing flux of N(2)O from the stratosphere, which is enriched in (15)N and (18)O by photolysis and chemistry. However these return fluxes of (15)N and (18)O are so great that a large oceanic flux of N(2)O is required to balance the heavy isotope-enriched stratospheric flux. All these effects will be reflected in climatically related isotopic variations in trapped N(2)O in polar ice cores.

Global N2O cycles--terrestrial emissions, atmospheric accumulation and biospheric effects

Tropospheric nitrous oxide concentration has increased by 0.2-0.4% per year over the period 1975 to 1982, amounting to net addition to the atmosphere of 2.8-5.6 Tg N2O-N per year. This perturbation, if continued into the future, will affect stratospheric chemical cycles, and the thermal balance of the Earth. In turn it will have direct and indirect global effects on the biosphere. Though the budget and cycles of N2O on Earth are not yet fully resolved, accumulating information and recent modelling efforts enable a more complete evaluation and better definition of gaps in our knowledge.

Nitrous Oxide Production in Nearshore Marine Sediments

Coastal marine sediments are shown to be a net source of nitrous oxide. The rates of nitrous oxide flux from sediments in Narragansett Bay, Rhode Island, ranged from 20 to more than 900 nanomoles per square meter per hour. Sediments from a eutrophic area had higher rates of net nitrous oxide production than sediments from relatively unpolluted sites. The benthic, nitrous oxide source exceeds the nitrous oxide source to the bay from sewage treatment plant effluent.