The high availability of electron donors occurring in coastal upwelling ecosystems with marked oxyclines favours chemoautotrophy, in turn leading to high N₂O and CH₄ cycling associated with aerobic NH₄⁺ (AAO) and CH₄ oxidation (AMO). This is the case of the highly productive coastal upwelling area off central Chile (36° S), where we evaluated the importance of total chemolithoautotrophic vs. photoautotrophic production, the specific contributions of AAO and AMO to chemosynthesis and their role in gas cycling. Chemolithoautotrophy was studied at a time-series station during monthly (2007–2009) and seasonal cruises (January 2008, September 2008, January 2009) and was assessed in terms of the natural C isotopic ratio of particulate organic carbon (δ¹³POC), total and specific (associated with AAO and AMO) dark carbon assimilation (CA), and N₂O and CH₄ cycling experiments. At the oxycline, δ¹³POC averaged −22.2‰; this was significantly lighter compared to the surface (−19.7‰) and bottom layers (−20.7‰). Total integrated dark CA in the whole water column fluctuated between 19.4 and 2.924 mg C m⁻² d⁻¹, was higher during active upwelling, and contributed 0.7 to 49.7% of the total integrated autotrophic CA (photo plus chemoautotrophy), which ranged from 135 to 7.626 mg C m⁻² d⁻¹, and averaged 20.3% for the whole sampling period. Dark CA was reduced by 27 to 48% after adding a specific AAO inhibitor (ATU) and by 24 to 76% with GC7, a specific archaea inhibitor. This indicates that AAO and AMO microbes (most of them archaea) were performing dark CA through the oxidation of NH₄⁺ and CH₄. Net N₂O cycling rates varied between 8.88 and 43 nM d⁻¹, whereas net CH₄ cycling rates ranged from −0.41 to −26.8 nM d⁻¹. The addition of both ATU and GC7 reduced N₂O accumulation and increased CH₄ consumption, suggesting that AAO and AMO were responsible, in part, for the cycling of these gases. These findings show that chemically driven chemolithoautotrophy (with NH₄⁺ and CH₄ acting as electron donors) could be more important than previously thought in upwelling ecosystems, raising new questions concerning its relevance in the future ocean.

Environmental context. Nitrous oxide and methane are atmospheric trace gases and, because they are strong greenhouse gases, they contribute significantly to the ongoing global warming of the Earth’s atmosphere. Despite the well established fact that the world’s oceans release nitrous oxide and methane to the atmosphere, the oceanic emission estimates of both gases are only poorly quantified. The MEMENTO (MarinE MethanE and NiTrous Oxide) database initiative is proposed as an effective way by which existing nitrous oxide and methane measurements can be used to reduce the uncertainty of the oceanic emissions estimates by establishing a global database.

Despite the importance of nitrous oxide (N₂O) in the global radiative balance and atmospheric ozone chemistry, its sources and sinks within the Earth’s system are still poorly understood. In the ocean, N₂O is produced by microbiological processes such as nitrification and partial denitrification, which account for about a third of global emissions. Conversely, complete denitrification (the dissimilative reduction of N₂O to N₂) under suboxic/anoxic conditions is the only known pathway accountable for N₂O consumption in the ocean. In this work, it is demonstrated that the biological assimilation of N₂O could be a significant pathway capable of directly transforming this gas into particulate organic nitrogen (PON). N₂O is shown to be biologically fixed within the subtropical and tropical waters of the eastern South Pacific Ocean, under a wide range of oceanographic conditions and at rates ranging from 2 pmol N L⁻¹ d⁻ to 14.8 nmol N L⁻¹ d⁻¹ (mean ± SE of 0.522±1.06 nmol N L⁻¹ d⁻¹, n = 93). Additional assays revealed that cultured cyanobacterial strains of Trichodesmium (H-9 and IMS 101), and Crocosphaera (W-8501) have the capacity to directly fix N₂O under laboratory conditions; suggesting that marine photoautotrophic diazotrophs could be using N₂O as a substrate. This metabolic capacity however was absent in Synechococcus (RCC 1029). The findings presented here indicate that assimilative N₂O fixation takes place under extreme environmental conditions (i.e., light, nutrient, oxygen) where both autotrophic (including cyanobacteria) and heterotrophic microbes appear to be involved. This process could provide a globally significant sink for atmospheric N₂O which in turn affects the oceanic N₂O inventory and may also represent a yet unexplored global oceanic source of fixed N.

Mesoscale eddies are important, frequent, and persistent features of the circulation in the eastern South Pacific (ESP) Ocean, transporting physical, chemical and biological properties from the productive shelves to the open ocean. Some of these eddies exhibit subsurface hypoxic or suboxic conditions and may serve as important hotspots for nitrogen loss, but little is known about oxygen consumption rates and nitrogen transformation processes associated with these eddies. In the austral fall of 2011, during the Tara Oceans expedition, an intrathermocline, anticyclonic, mesoscale eddy with a suboxic (< 2 µmol kg⁻¹ of O₂), subsurface layer (200–400 m) was detected ∼ 900 km off the Chilean shore (30° S, 81° W). The core of the eddy's suboxic layer had a temperature-salinity signature characteristic of Equatorial Subsurface Water (ESSW) that at this latitude is normally restricted to an area near the coast. Measurements of nitrogen species within the eddy revealed undersaturation (below 44 %) of nitrous oxide (N₂O) and nitrite accumulation (> 0.5 µM), suggesting that active denitrification occurred in this water mass. Using satellite altimetry, we were able to track the eddy back to its region of formation on the coast of central Chile (36.1° S, 74.6° W). Field studies conducted in Chilean shelf waters close to the time of eddy formation provided estimates of initial O₂ and N₂O concentrations of the ESSW source water in the eddy. By the time of its offshore sighting, concentrations of both O₂ and N₂O in the subsurface oxygen minimum zone (OMZ) of the eddy were lower than concentrations in surrounding water and “source water” on the shelf, indicating that these chemical species were consumed as the eddy moved offshore. Estimates of apparent oxygen utilization rates at the OMZ of the eddy ranged from 0.29 to 44 nmol L⁻¹ d⁻¹ and the rate of N₂O consumption was 3.92 nmol L⁻¹ d⁻¹. These results show that mesoscale eddies affect open-ocean biogeochemistry in the ESP not only by transporting physical and chemical properties from the coast to the ocean interior but also during advection, local biological consumption of oxygen within an eddy further generates conditions favorable to denitrification and loss of fixed nitrogen from the system.