We performed incubation experiments with 15 N-labeled nitrogen compounds to investigate the vertical distribution of pathways of N 2 production through the suboxic zone of the central Black Sea and the impact of oxygen and sulfide on the anammox process. Anammox rates increased with depth through the upper suboxic zone and reached a maximum of ,11 nmol N 2 L 21 d 21 at the sharp interface between nitrate and ammonium, below which rates decreased toward the depth of sulfide accumulation. Heterotrophic denitrification was not detected, and therefore anammox was the prevailing sink for fixed nitrogen in the central Black Sea. In incubations with low oxygen concentrations, anammox activity was only partially inhibited, with a decrease in anammox rates to ,70% and 50% of the anoxic level at ,3.5 and ,8 mmol L 21 O 2 , respectively, and complete inhibition at ,13.5 mmol L 21 O 2 . Thus, the anammox process is not constrained to anoxic marine waters. This increases the volume of the major open-ocean oxygen-deficient zones, where anammox is potentially active, which has important implications for the contribution of anammox to the marine nitrogen cycle. We observed an inhibitory effect of micromolar sulfide concentrations on anammox activity, indicating that the vertical and likely horizontal distribution of active anammox bacteria is constrained to nonsulfidic water layers, which may explain the absence of the process in sulfidic basins with no suboxic zone.The discovery of anaerobic ammonium oxidation (anammox) in wastewater treatment systems and natural aquatic environments resolved the mystery of ammonium deficiency in anoxic waters and challenged the preeminence of microbial denitrification as the only significant pathway for the removal of fixed nitrogen in the oceans (Devol 2003;Dalsgaard et al. 2005;Kuypers et al. 2006). Anaerobic ammonium oxidation with nitrite as an electron acceptor is mediated by a monophyletic group of bacteria that branches deeply in the phylum Planctomycetes (Strous et al. 1999;Schmid et al. 2003). The one-to-one coupling of nitrogen from ammonium and nitrite into gaseous N 2 , NH Graaf et al. 1995), distinguishes the anammox process from denitrification, where two molecules of nitrate are combined to N 2 in a stepwise pathway (2NOAlthough a number of studies demonstrate the importance of anammox bacteria in the biological nitrogen cycle (Dalsgaard et al. 2005;Kuypers et al. 2006;, little is known about the main factors that control the distribution and magnitude of the process. Expectedly, oxygen is such an important regulator. Experimental work with enrichments of anammox bacteria from laboratory wastewater bioreactors has shown that anammox activity is reversibly inhibited by oxygen levels as low as 1 mmol L 21 (Strous et al. 1997), indicating that the process is active only under strictly anoxic conditions. Still, in the Benguela upwelling system off Namibia, the observed dominance of anammox was suggested to result from anammox being less sensitive than denitrification tow...

Summary Emission of the greenhouse gas nitrous oxide (N2O) from freshwater and terrestrial invertebrates has exclusively been ascribed to N2O production by ingested denitrifying bacteria in the anoxic gut of the animals. Our study of marine molluscs now shows that also microbial biofilms on shell surfaces are important sites of N2O production. The shell biofilms of Mytilus edulis, Littorina littorea and Hinia reticulata contributed 18–94% to the total animal‐associated N2O emission. Nitrification and denitrification were equally important sources of N2O in shell biofilms as revealed by 15N‐stable isotope experiments with dissected shells. Microsensor measurements confirmed that both nitrification and denitrification can occur in shell biofilms due to a heterogeneous oxygen distribution. Accordingly, ammonium, nitrite and nitrate were important drivers of N2O production in the shell biofilm of the three mollusc species. Ammonium excretion by the animals was found to be sufficient to sustain N2O production in the shell biofilm. Apparently, the animals provide a nutrient‐enriched microenvironment that stimulates growth and N2O production of the shell biofilm. This animal‐induced stimulation was demonstrated in a long‐term microcosm experiment with the snail H. reticulata, where shell biofilms exhibited the highest N2O emission rates when the animal was still living inside the shell.

Members of the epsilonproteobacterial genus Arcobacter have been identified to be potentially important sulfide oxidizers in marine coastal, seep, and stratified basin environments. In the highly productive upwelling waters off the coast of Peru, Arcobacter cells comprised 3 to 25% of the total microbial community at a near-shore station where sulfide concentrations exceeded 20 μM in bottom waters. From the chemocline where the Arcobacter population exceeded 106 cells ml−1 and where high rates of denitrification (up to 6.5 ± 0.4 μM N day−1) and dark carbon fixation (2.8 ± 0.2 μM C day−1) were measured, we isolated a previously uncultivated Arcobacter species, Arcobacter peruensis sp. nov. (BCCM LMG-31510). Genomic analysis showed that A. peruensis possesses genes encoding sulfide oxidation and denitrification pathways but lacks the ability to fix CO2 via autotrophic carbon fixation pathways. Genes encoding transporters for organic carbon compounds, however, were present in the A. peruensis genome. Physiological experiments demonstrated that A. peruensis grew best on a mix of sulfide, nitrate, and acetate. Isotope labeling experiments further verified that A. peruensis completely reduced nitrate to N2 and assimilated acetate but did not fix CO2, thus coupling heterotrophic growth to sulfide oxidation and denitrification. Single-cell nanoscale secondary ion mass spectrometry analysis of samples taken from shipboard isotope labeling experiments also confirmed that the Arcobacter population in situ did not substantially fix CO2. The efficient growth yield associated with the chemolithoheterotrophic metabolism of A. peruensis may allow this Arcobacter species to rapidly bloom in eutrophic and sulfide-rich waters off the coast of Peru. IMPORTANCE Our multidisciplinary approach provides new insights into the ecophysiology of a newly isolated environmental Arcobacter species, as well as the physiological flexibility within the Arcobacter genus and sulfide-oxidizing, denitrifying microbial communities within oceanic oxygen minimum zones (OMZs). The chemolithoheterotrophic species Arcobacter peruensis may play a substantial role in the diverse consortium of bacteria that is capable of coupling denitrification and fixed nitrogen loss to sulfide oxidation in eutrophic, sulfidic coastal waters. With increasing anthropogenic pressures on coastal regions, e.g., eutrophication and deoxygenation (D. Breitburg, L. A. Levin, A. Oschlies, M. Grégoire, et al., Science 359:eaam7240, 2018, https://doi.org/10.1126/science.aam7240), niches where sulfide-oxidizing, denitrifying heterotrophs such as A. peruensis thrive are likely to expand.

The Arabian Sea harbours one of the three major oxygen minimum zones (OMZs) in the world's oceans, and it alone is estimated to account for ~10–20 % of global oceanic nitrogen (N) loss. While actual rate measurements have been few, the consistently high accumulation of nitrite (NO₂^&minus;) coinciding with suboxic conditions in the central-northeastern part of the Arabian Sea has led to the general belief that this is the region where active N-loss takes place. Most subsequent field studies on N-loss have thus been drawn almost exclusively to the central-NE. However, a recent study measured only low to undetectable N-loss activities in this region, compared to orders of magnitude higher rates measured towards the Omani Shelf where little NO₂^&minus; accumulated (Jensen et al., 2011). In this paper, we further explore this discrepancy by comparing the NO₂^&minus;-producing and consuming processes, and examining the relationship between the overall NO₂^&minus; balance and active N-loss in the Arabian Sea. Based on a combination of ¹⁵N-incubation experiments, functional gene expression analyses, nutrient profiling and flux modeling, our results showed that NO₂^&minus; accumulated in the central-NE Arabian Sea due to a net production via primarily active nitrate (NO₃^&minus;) reduction and to a certain extent ammonia oxidation. Meanwhile, NO₂^&minus; consumption via anammox, denitrification and dissimilatory nitrate/nitrite reduction to ammonium (NH₄⁺) were hardly detectable in this region, though some loss to NO₂^&minus; oxidation was predicted from modeled NO₃^&minus; changes. No significant correlation was found between NO₂^&minus; and N-loss rates (<i>p</i>>0.05). This discrepancy between NO₂^&minus; accumulation and lack of active N-loss in the central-NE Arabian Sea is best explained by the deficiency of labile organic matter that is directly needed for further NO₂^&minus; reduction to N₂O, N₂ and NH₄⁺, and indirectly for the remineralized NH₄⁺ required by anammox. Altogether, our data do not support the long-held view that NO₂^&minus; accumulation is a direct activity indicator of N-loss in the Arabian Sea or other OMZs. Instead, NO₂<sup>&...

The Arabian Sea harbours one of the three major oxygen minimum zones (OMZs) in the world's oceans, and it alone is estimated to account for ~10–20% of global oceanic nitrogen (N) loss. While actual rate measurements have been few, the consistently high accumulation of nitrite (NO₂^&minus;) coinciding with suboxic conditions in the central-northeastern part of the Arabian Sea has led to the general belief that this is the region where active N-loss takes place. Most subsequent field studies on N-loss have thus been drawn almost exclusively to the central-NE. However, a recent study measured only low to undetectable N-loss activities in this region, compared to orders of magnitude higher rates measured towards the Omani shelf where little NO₂^&minus; accumulated (Jensen et al., 2011). In this paper, we further explore this discrepancy by comparing the NO₂^&minus; producing and consuming processes, and examining the relationship between the overall NO₂^&minus; balance and active N-loss in the Arabian Sea. Based on a combination of ¹⁵N-incubation experiments, functional gene expression analyses, nutrient profiling and flux modeling, our results showed that NO₂^&minus; accumulated in the Central-NE Arabian Sea due to a net production via primarily active nitrate (NO₃^&minus;) reduction and to a certain extent ammonia oxidation. Meanwhile, NO₂^&minus; consumption via anammox, denitrification and dissimilatory nitrate/nitrite reduction to ammonium (NH₄⁺) were hardly detectable in this region, though some loss to NO₂^&minus; oxidation was predicted from modeled NO₃^&minus; changes. No significant correlation was found between NO₂^&minus; and N-loss rates (<i>p</i>>0.05). This discrepancy between NO₂^&minus; accumulation and lack of active N-loss in the Central-NE Arabian Sea is best explained by the deficiency of organic matter that is directly needed for further NO₂^&minus; reduction to N₂O, N₂ and NH₄⁺, and indirectly for the remineralized NH₄⁺ required by anammox. Altogether, our data do not support the long-held view that NO₂^&minus; accumulation is a direct activity indicator of N-loss in the Arabian Sea or other OMZs. Instead, NO<sub>...

Abstract. Recent modeling results suggest that oceanic oxygen levels will decrease significantly over the next decades to centuries in response to climate change and altered ocean circulation. Hence the future ocean may experience major shifts in nutrient cycling triggered by the expansion and intensification of tropical oxygen minimum zones (OMZs). There are numerous feedbacks between oxygen concentrations, nutrient cycling and biological productivity; however, existing knowledge is insufficient to understand physical, chemical and biological interactions in order to adequately assess past and potential future changes. We investigated the pelagic biogeochemistry of OMZs in the eastern tropical North Atlantic and eastern tropical South Pacific during a series of cruise expeditions and mesocosm studies. The following summarizes the current state of research on the influence of low environmental oxygen conditions on marine biota, viruses, organic matter formation and remineralization with a particular focus on the nitrogen cycle in OMZ regions. The impact of sulfidic events on water column biogeochemistry, originating from a specific microbial community capable of highly efficient carbon fixation, nitrogen turnover and N2O production is further discussed. Based on our findings, an important role of sinking particulate organic matter in controlling the nutrient stochiometry of the water column is suggested. These particles can enhance degradation processes in OMZ waters by acting as microniches, with sharp gradients enabling different processes to happen in close vicinity, thus altering the interpretation of oxic and anoxic environments.

The proposed Asgard superphylum of Archaea comprises the closest archaeal 19 relatives of eukaryotes, whose genomes hold clues pertaining to the nature host cell that 20 acquired the mitochondrion at the origin of eukaryotes 1-4 . Genomes of the Asgard candidate 21 Phylum 'Candidatus Lokiarchaeota' [Lokiarchaeon] suggest an acetogenic H2 -dependent 22 lifestyle 5 and mixotrophic capabilities 6 . However, data on the activity of Lokiarchaeon are 23 currently lacking, and the ecology of the host cell that acquired the mitochondrion is 24 debated 4,7 . Here, we show that in anoxic marine sediments underlying highly productive 25 waters on the Namibian continental shelf Lokiarchaeon gene expression increases with depth 26 below the seafloor, and was significantly different across a redox gradient spanning hypoxic 27 to sulfidic conditions. Notably, Lokiarchaeon increased expression of genes involved in 28 growth, carbohydrate metabolism, and the H2-dependent Wood-Ljungdahl (WLP) carbon 29 fixation pathway under the most reducing (sulfidic) conditions. Quantitative stable isotope 30 probing experiments revealed multiple populations of Lokiarchaeota utilizing both CO2 and 31 diatomaceous extracellular polymeric substances (dEPS) as carbon sources over a 10-day 32 incubation under anoxic conditions. This apparent anaerobic mixotrophic metabolism was 33 consistent with the expression of Lokiarchaeon genes involved in transport and fermentation 34 of sugars and amino acids. Remarkably, several Asgard populations were more enriched 35 with 13 C-dEPS compared to the community average, indicating a preference for dEPS as a 36 growth substrate. The qSIP and gene expression data indicate a metabolism of "Candidatus 37 Lokiarchaeota" similar to that of sugar fermenting homoacetogenic bacteria 8 , namely that 38 Lokiarchaeon can couple fermentative H2 production from organic substrates with electron 39 bifurcation and the autotrophic and H2-dependent WLP. Homoacetogenesis allows to access 40 a wide range of substrates and relatively high ATP gain during acetogenic sugar 41 fermentation 8 thereby providing an ecological advantage for Lokiarchaeon in anoxic, energy 42 limited settings. 43 The Benguela upwelling system is one of the most productive ecosystems of the world's 44 oceans and exhibits an oxygen minimum zone (OMZ) overlying the seafloor on the Namibian 45 continental shelf 9 . Below the Namibian seafloor relatively high amounts of sulfide (H2S) and H2 46 are produced by sulfate reduction and microbial fermentation, respectively 10 . During the Southern 47

The oscillating redox conditions that characterize coastal sandy sediments foster microbial communities capable of respiring oxygen and nitrate simultaneously, thereby increasing the potential for organic matter remineralization, nitrogen (N)-loss and emissions of the greenhouse gas nitrous oxide. It is unknown to what extent these conditions also lead to overlaps between dissimilatory nitrate and sulfate respiration. Here, we show that sulfate and nitrate respiration co-occur in the surface sediments of an intertidal sand flat. Furthermore, we found strong correlations between dissimilatory nitrite reduction to ammonium (DNRA) and sulfate reduction rates. Until now, the nitrogen and sulfur cycles were assumed to be mainly linked in marine sediments by the activity of nitrate-reducing sulfide oxidisers. However, transcriptomic analyses revealed that the functional marker gene for DNRA (nrfA) was more associated with microorganisms known to reduce sulfate rather than oxidise sulfide. Our results suggest that when nitrate is supplied to the sediment community upon tidal inundation, part of the sulfate reducing community may switch respiratory strategy to DNRA. Therefore increases in sulfate reduction rate in-situ may result in enhanced DNRA and reduced denitrification rates. Intriguingly, the shift from denitrification to DNRA did not influence the amount of N2O produced by the denitrifying community. Our results imply that microorganisms classically considered as sulfate reducers control the potential for DNRA within coastal sediments when redox conditions oscillate and therefore retain ammonium that would otherwise be removed by denitrification, exacerbating eutrophication.