Anammox bacteria drive fixed nitrogen loss in hadal trench sediments.

Benthic N2 production by microbial denitrification and anammox is the largest sink for fixed nitrogen in the oceans. Most N2 production occurs on the continental shelves, where a high flux of reactive organic matter fuels the depletion of nitrate close to the sediment surface. By contrast, N2 production rates in abyssal sediments are low due to low inputs of reactive organics, and nitrogen transformations are dominated by aerobic nitrification and the release of nitrate to the bottom water. Here, we demonstrate that this trend is reversed in the deepest parts of the oceans, the hadal trenches, where focusing of reactive organic matter enhances benthic microbial activity. Thus, at ∼8-km depth in the Atacama Trench, underlying productive surface waters, nitrate is depleted within a few centimeters of the sediment surface, N2 production rates reach those reported from some continental margin sites, and fixed nitrogen loss is mainly conveyed by anammox bacteria. These bacteria are closely related to those known from shallow oxygen minimum zone waters, and comparison of activities measured in the laboratory and in situ suggest they are piezotolerant. Even the Kermadec Trench, underlying oligotrophic surface waters, exhibits substantial fixed N removal. Our results underline the role of hadal sediments as hot spots of deep-sea biological activity, revealing a fully functional benthic nitrogen cycle at high hydrostatic pressure and pointing to hadal sediments as a previously unexplored niche for anaerobic microbial ecology and diagenesis.

Uniform selective pressures within redox zones drive gradual changes in microbial community composition in hadal sediments.

Microbial communities in marine sediments are highly diverse, yet the processes that give rise to this complexity are unclear. It has been proposed that benthic microbial communities must be continuously re-seeded from the water column because dispersal within the sediment is severely limited. Previous studies consistently report that the composition of the microbial community gradually changes with sediment depth. However, the relative contributions of the processes that underlie these compositional gradients have not been determined, and it is unknown whether microbial dispersal is indeed too slow to outpace burial. Here, we applied ecological statistical frameworks to 16S rRNA gene amplicon-based community composition data from Atacama Trench sediments to investigate the links between biogeochemistry, burial, and microbial community assembly processes. We confirm that dispersal limitation affects microbial communities and find that gradual changes in community composition are driven by selective pressures that change abruptly across the discrete boundaries between redox zones rather than along continuous biogeochemical gradients, while selective pressures are uniform within each zone. The gradual changes in community composition over centimetres of depth within a zone hence reflects a decades-long response to the abruptly changing selective pressures.

Anaerobic methane oxidation in a coastal oxygen minimum zone: spatial and temporal dynamics.

Coastal waters are a major source of marine methane to the atmosphere. Particularly high concentrations of this potent greenhouse gas are found in anoxic waters, but it remains unclear if and to what extent anaerobic methanotrophs mitigate the methane flux. Here we investigate the long-term dynamics in methanotrophic activity and the methanotroph community in the coastal oxygen minimum zone (OMZ) of Golfo Dulce, Costa Rica, combining biogeochemical analyses, experimental incubations and 16S rRNA gene sequencing over 3 consecutive years. Our results demonstrate a stable redox zonation across the years with high concentrations of methane (up to 1.7 µmol L-1 ) in anoxic bottom waters. However, we also measured high activities of anaerobic methane oxidation in the OMZ core (rate constant, k, averaging 30 yr-1 in 2018 and 8 yr-1 in 2019-2020). The OPU3 and Deep Sea-1 clades of the Methylococcales were implicated as conveyors of the activity, peaking in relative abundance 5-25 m below the oxic-anoxic interface and in the deep anoxic water respectively. Although their genetic capacity for anaerobic methane oxidation remains unexplored, their sustained high relative abundance indicates an adaptation of these clades to the anoxic, methane-rich OMZ environment, allowing them to play major roles in mitigating methane fluxes.

Aerobic and anaerobic methane oxidation in a seasonally anoxic basin.

Shallow coastal waters are dynamic environments that dominate global marine methane emissions. Particularly high methane concentrations are found in seasonally anoxic waters, which are spreading in eutrophic coastal systems, potentially leading to increased methane emissions to the atmosphere. Here we explore how the seasonal development of anoxia influenced methane concentrations, rates of methane oxidation, and the community composition of methanotrophs in the shallow eutrophic water column of Mariager Fjord, Denmark. Our results show the development of steep concentration gradients toward the oxic-anoxic interface as methane accumulated to 1.4 µM in anoxic bottom waters. Yet, the fjord possessed an efficient microbial methane filter near the oxic-anoxic interface that responded to the increasing methane flux. In experimental incubations, methane oxidation near the oxic-anoxic interface proceeded both aerobically and anaerobically with nearly equal efficiency reaching turnover rates as high as 0.6 and 0.8 d-1, respectively, and was seemingly mediated by members of the Methylococcales belonging to the Deep Sea-1 clade. Throughout the period, both aerobic and anaerobic methane oxidation rates were high enough to consume the estimated methane flux. Thus, our results indicate that seasonal anoxia did not increase methane emissions.

SAR11 bacteria linked to ocean anoxia and nitrogen loss.

Bacteria of the SAR11 clade constitute up to one half of all microbial cells in the oxygen-rich surface ocean. SAR11 bacteria are also abundant in oxygen minimum zones (OMZs), where oxygen falls below detection and anaerobic microbes have vital roles in converting bioavailable nitrogen to N2 gas. Anaerobic metabolism has not yet been observed in SAR11, and it remains unknown how these bacteria contribute to OMZ biogeochemical cycling. Here, genomic analysis of single cells from the world's largest OMZ revealed previously uncharacterized SAR11 lineages with adaptations for life without oxygen, including genes for respiratory nitrate reductases (Nar). SAR11 nar genes were experimentally verified to encode proteins catalysing the nitrite-producing first step of denitrification and constituted ~40% of OMZ nar transcripts, with transcription peaking in the anoxic zone of maximum nitrate reduction activity. These results link SAR11 to pathways of ocean nitrogen loss, redefining the ecological niche of Earth's most abundant organismal group.

Spatial variability of prokaryotic and viral abundances in the Kermadec and Atacama Trench regions.

Hadal trenches represent the deepest part of the ocean and are dynamic depocenters with intensified prokaryotic activity. Here, we explored the distribution and drivers of prokaryotic and viral abundance from the ocean surface and 40 cm into sediments in two hadal trench regions with contrasting surface productivity. In the water column, prokaryotic and viral abundance decreased with water depth before reaching a rather stable level at ~ 4000 m depth at both trench systems, while virus to prokaryote ratios were increasing with depth, presumably reflecting the declining availability of organic material. Prokaryotic and viral abundances in sediments were lower at the adjacent abyssal sites than at the hadal sites and declined exponentially with sediment depth, closely tracking the attenuation of total organic carbon (TOC) content. In contrast, hadal sediment exhibited erratic depth profiles of prokaryotes and viruses with many subsurface peaks. The prokaryotic abundance correlated well to extensive fluctuations in TOC content at centimeter scale, which were likely caused by recurring mass wasting events. Yet while prokaryotic and viral abundances cross correlated well in the abyssal sediments, there was no clear correlation in the hadal sites. The results suggested that dynamic depositional conditions and higher substrate availability result in a high spatial heterogeneity in viral and prokaryotic abundances in hadal sediments in comparison to more stable abyssal settings. We argue that these conditions enhance the relatively importance of viruses for prokaryotic mortality and carbon recycling in hadal settings.

Ammonium and nitrite oxidation at nanomolar oxygen concentrations in oxygen minimum zone waters.

A major percentage of fixed nitrogen (N) loss in the oceans occurs within nitrite-rich oxygen minimum zones (OMZs) via denitrification and anammox. It remains unclear to what extent ammonium and nitrite oxidation co-occur, either supplying or competing for substrates involved in nitrogen loss in the OMZ core. Assessment of the oxygen (O2) sensitivity of these processes down to the O2 concentrations present in the OMZ core (<10 nmol⋅L(-1)) is therefore essential for understanding and modeling nitrogen loss in OMZs. We determined rates of ammonium and nitrite oxidation in the seasonal OMZ off Concepcion, Chile at manipulated O2 levels between 5 nmol⋅L(-1) and 20 µmol⋅L(-1) Rates of both processes were detectable in the low nanomolar range (5-33 nmol⋅L(-1) O2), but demonstrated a strong dependence on O2 concentrations with apparent half-saturation constants (Kms) of 333 ± 130 nmol⋅L(-1) O2 for ammonium oxidation and 778 ± 168 nmol⋅L(-1) O2 for nitrite oxidation assuming one-component Michaelis-Menten kinetics. Nitrite oxidation rates, however, were better described with a two-component Michaelis-Menten model, indicating a high-affinity component with a Km of just a few nanomolar. As the communities of ammonium and nitrite oxidizers were similar to other OMZs, these kinetics should apply across OMZ systems. The high O2 affinities imply that ammonium and nitrite oxidation can occur within the OMZ core whenever O2 is supplied, for example, by episodic intrusions. These processes therefore compete with anammox and denitrification for ammonium and nitrite, thereby exerting an important control over nitrogen loss.

Anammox and partial nitritation in the mainstream of a wastewater treatment plant in a temperate region (Denmark).

The Marselisborg WWTP (Aarhus, Denmark) fed the mainstream nitrification/denitrification tanks with excess sludge from a sidestream DEMON tank for more than three years to investigate if anammox can supplement conventional nitrification/denitrification in a mainstream of a temperate region. To evaluate this long-term attempt, anammox and also denitrification rates were measured in activated sludge from the main- and sidestream at 10, 20 and 30 °C using 15N-labelling (stable isotope) experiments. The results show that anammox contributes by approximately 1% of the total nitrogen removal in the mainstream tanks and that anammox conversion rates there are approximately 800-900 times lower than in the DEMON. A distinct temperature dependence of both anammox and denitrification rates was also confirmed, however, results from different temperatures did not significantly alter relative shares, e.g. anammox rates in activated sludge from the nitrification/denitrification tanks are also negligible at 30 °C. This indicates that the anammox bacteria abundance in the nitrification/denitrification tanks is too low to play an important role and that an adaptation to lower temperatures had not occurred. Additional in situ measurements in the nitrification/denitrification tanks further revealed that full nitrification dominates over partial nitritation. Dominant nitritation-anammox is therefore excluded per se and also nitrite shunt activities are not particularly supported.

Effect of settled diatom-aggregates on benthic nitrogen cycling.

The marine sediment hosts a mosaic of microhabitats. Recently it has been demonstrated that the settlement of phycodetrital aggregates can induce local changes in the benthic O2 distribution due to confined enrichment of organic material and alteration of the diffusional transport. Here, we show how this microscale O2 shift substantially affects benthic nitrogen cycling. In sediment incubations, the settlement of diatom-aggregates markedly enhanced benthic O2 and NO3- consumption and stimulated NO2- and NH4+ production. Oxygen microprofiles revealed the rapid development of anoxic niches within and underneath the aggregates. During 120 h following the settling of the aggregates, denitrification of NO3- from the overlying water increased from 13.5 µmol m-2 h-1 to 24.3 µmol m-2 h-1, as quantified by 15N enrichment experiment. Simultaneously, N2 production from coupled nitrification-denitrification decreased from 33.4 µmol m-2 h-1 to 25.9 µmol m-2 h-1, probably due to temporary inhibition of the benthic nitrifying community. The two effects were of similar magnitude and left the total N2 production almost unaltered. At the aggregate surface, nitrification was, conversely, very efficient in oxidizing NH4+ liberated by mineralization of the aggregates. The produced NO3- was preferentially released into the overlying water and only a minor fraction contributed to denitrification activity. Overall, our data indicate that the abrupt change in O2 microdistribution caused by aggregates stimulates denitrification of NO3- from the overlying water, and loosens the coupling between benthic nitrification and denitrification both in time and space. The study contributes to expanding the conceptual and quantitative understanding of how nitrogen cycling is regulated in dynamic benthic environments.

Metabolic potential and in situ activity of marine Marinimicrobia bacteria in an anoxic water column.

Marinimicrobia bacteria are widespread in subeuphotic areas of the oceans and particularly abundant in oxygen minimum zones (OMZs). Information on Marinimicrobia metabolism is sparse, making the biogeochemical influence of this group challenging to predict. Here, metagenome-assembled genomes representing Marinimicrobia subgroups PN262000N21 and ARCTIC96B-7 were retrieved to near completion (97% and 94%) from OMZ metagenomes, with contamination (14.1%) observed only in ARCTIC96B-7. Genes for aerobic carbon monoxide (CO) oxidation, polysulfide metabolism and hydrogen utilization were identified only in PN262000N21, while genes for partial denitrification occurred in both genomes. Transcripts mapping to these genomes increased from <0.3% of total mRNA from the oxic zone to a max of 22% under anoxia. ARCTIC96B-7 transcript representation decreased an order of magnitude from non-sulfidic to sulfidic depths. In contrast, PN262000N21 representation was relatively constant throughout the OMZ, although transcripts encoding sulfur-utilizing proteins, including sulfur transferases, were enriched at sulfidic depths. PN262000N21 transcripts encoding a protein with fibronectin domains similar to those in cellulosome-producing bacteria were also abundant, suggesting a potential for high molecular weight carbon cycling. These data provide omic-level descriptions of metabolic potential and activity in OMZ-associated Marinimicrobia, suggesting differentiation between subgroups with roles in carbon and dissimilatory inorganic nitrogen and sulfur cycling.

Pathways and Controls of N2O Production in Nitritation-Anammox Biomass.

Nitrous oxide (N2O) is an unwanted byproduct during biological nitrogen removal processes in wastewater. To establish strategies for N2O mitigation, a better understanding of production mechanisms and their controls is required. A novel stable isotope labeling approach using 15N and 18O was applied to investigate pathways and controls of N2O production by biomass taken from a full-scale nitritation-anammox reactor. The experiments showed that heterotrophic denitrification was a negligible source of N2O under oxic conditions (≥0.2 mg O2 L-1). Both hydroxylamine oxidation and nitrifier denitrification contributed substantially to N2O accumulation across a wide range of conditions with varying concentrations of O2, NH4+, and NO2-. The O2 concentration exerted the strongest control on net N2O production with both production pathways stimulated by low O2, independent of NO2- concentrations. The stimulation of N2O production from hydroxylamine oxidation at low O2 was unexpected and suggests that more than one enzymatic pathway may be involved in this process. N2O production by hydroxylamine oxidation was further stimulated by NH4+, whereas nitrifier denitrification at low O2 levels was stimulated by NO2- at levels as low as 0.2 mM. Our study shows that 15N and 18O isotope labeling is a useful approach for direct quantification of N2O production pathways applicable to diverse environments.

Vertical partitioning of nitrogen-loss processes across the oxic-anoxic interface of an oceanic oxygen minimum zone.

We investigated anammox, denitrification and dissimilatory reduction of nitrite to ammonium (DNRA) activity in the Eastern Tropical South Pacific oxygen minimum zone (OMZ) off northern Chile, at high-depth resolution through the oxycline into the anoxic OMZ core. This was accompanied by high-resolution nutrient and oxygen profiles to link changes in nitrogen transformation rates to physicochemical characteristics of the water column. Denitrification was detected at most depths, but anammox was the most active N2 -producing process, while DNRA was not detectable. Anammox and denitrification were mainly active in the anoxic OMZ core while activity was low to not detectable in the oxycline, except in association with an intrusion of OMZ core water. This indicates that continuous exposure to even submicromolar oxygen levels inhibits the processes either directly or through nitrite limitation. Anammox activity did not peak at the oxic-anoxic boundary but 20-50 m below matching the salinity maximum of the Equatorial Subsurface Water. This suggests that water history plays a major role for anammox activity possibly due to slow growth of anammox bacteria. Denitrification peaked deeper than anammox, likely reflecting a shift in the balance between this process and nitrate reduction to nitrite, governed by the relative availability of nitrate and nitrite.

Metagenome-assembled genomes of deep-sea sediments: changes in microbial functional potential lag behind redox transitions.

Hadal sediments are hotspots of microbial activity in the deep sea and exhibit strong biogeochemical gradients. But although these gradients are widely assumed to exert selective forces on hadal microbial communities, the actual relationship between biogeochemistry, functional traits, and microbial community structure remains poorly understood. We tested whether the biogeochemical conditions in hadal sediments select for microbes based on their genomic capacity for respiration and carbohydrate utilization via a metagenomic analysis of over 153 samples from the Atacama Trench region (max. depth = 8085 m). The obtained 1357 non-redundant microbial genomes were affiliated with about one-third of all known microbial phyla, with more than half belonging to unknown genera. This indicated that the capability to withstand extreme hydrostatic pressure is a phylogenetically widespread trait and that hadal sediments are inhabited by diverse microbial lineages. Although community composition changed gradually over sediment depth, these changes were not driven by selection for respiratory or carbohydrate degradation capability in the oxic and nitrogenous zones, except in the case of anammox bacteria and nitrifying archaea. However, selection based on respiration and carbohydrate degradation capacity did structure the communities of the ferruginous zone, where aerobic and nitrogen respiring microbes declined exponentially (half-life = 125-419 years) and were replaced by subsurface communities. These results highlight a delayed response of microbial community composition to selective pressure imposed by redox zonation and indicated that gradual changes in microbial composition are shaped by the high-resilience and slow growth of microbes in the seafloor.

Competition for inorganic carbon between oxygenic and anoxygenic phototrophs in a hypersaline microbial mat, Guerrero Negro, Mexico.

While most oxygenic phototrophs harvest light only in the visible range (400-700 nm, VIS), anoxygenic phototrophs can harvest near infrared light (> 700 nm, NIR). To study interactions between the photosynthetic guilds we used microsensors to measure oxygen and gross oxygenic photosynthesis (gOP) in a hypersaline microbial mat under full (VIS + NIR) and VIS illumination. Under normal dissolved inorganic carbon (DIC) concentrations (2 mM), volumetric rates of gOP were reduced up to 65% and areal rates by 16-31% at full compared with VIS illumination. This effect was enhanced (reduction up to 100% in volumetric, 50% in areal rates of gOP) when DIC was lowered to 1 mM, but diminished at 10 mM DIC or lowered pH. In conclusion, under full-light illumination anoxygenic phototrophs are able to reduce the activity of oxygenic phototrophs by efficiently competing for inorganic carbon within the highly oxygenated layer. Anoxygenic photosynthesis, calculated from the difference in gOP under full and VIS illumination, represented between 10% and 40% of the C-fixation. The DIC depletion in the euphotic zone as well as the significant C-fixation by anoxygenic phototrophs in the oxic layer influences the carbon isotopic composition of the mat, which needs to be taken into account when interpreting isotopic biosignals in geological records.

Stark contrast in denitrification and anammox across the deep Norwegian trench in the Skagerrak.

Environmental anaerobic ammonium oxidation (anammox) was demonstrated for the first time in 2002, using (15)N labeling, in homogenized sediment from the Skagerrak, where it accounted for up to 67% of N2 production. We returned to some of these original sites in 2010 to make measurements of nitrogen and carbon cycling under conditions more representative of those in situ, quantifying anammox and denitrification, together with oxygen penetration and consumption, in intact sediment cores. Overall, oxygen consumption and N2 production decayed with water depth, as expected, but the drop in N2 production was relatively more pronounced. Whereas we confirmed the dominance of N2 production by anammox (72% and 77%) at the two deepest sites (∼700 m of water), anammox was conspicuously absent from two shallower sites (∼200 m and 400 m). At the shallower sites, we could measure no anammox activity with either intact or homogeneous sediment, and quantitative PCR (16S rRNA) gave a negligible abundance of anammox bacteria in the anoxic layers. Such an absence of anammox, especially at one locale where it was originally demonstrated, is hard to reconcile. Despite the dominance of anammox at the deepest sites, anammox activity could not make up for the drop in denitrification, and assuming Redfield ratios for the organic matter being mineralized, the estimated retention of fixed N actually increased to 90% to 97% of that mineralized, whereas it was 80% to 86% at the shallower sites.

Microbial and Viral Genome and Proteome Nitrogen Demand Varies across Multiple Spatial Scales within a Marine Oxygen Minimum Zone.

Nutrient availability can significantly influence microbial genomic and proteomic streamlining, for example, by selecting for lower nitrogen to carbon ratios. Oligotrophic open ocean microbes have streamlined genomic nitrogen requirements relative to those of their counterparts in nutrient-rich coastal waters. However, steep gradients in nutrient availability occur at meter-level, and even micron-level, spatial scales. It is unclear whether such gradients also structure genomic and proteomic stoichiometry. Focusing on the eastern tropical North Pacific oxygen minimum zone (OMZ), we use comparative metagenomics to examine how nitrogen availability shapes microbial and viral genome properties along the vertical gradient across the OMZ and between two size fractions, distinguishing free-living microbes versus particle-associated microbes. We find a substantial increase in the nitrogen content of encoded proteins in particle-associated over free-living bacteria and archaea across nitrogen availability regimes over depth. Within each size fraction, we find that bacterial and viral genomic nitrogen tends to increase with increasing nitrate concentrations with depth. In contrast to cellular genes, the nitrogen content of virus proteins does not differ between size fractions. We identified arginine as a key amino acid in the modulation of the C:N ratios of core genes for bacteria, archaea, and viruses. Functional analysis reveals that particle-associated bacterial metagenomes are enriched for genes that are involved in arginine metabolism and organic nitrogen compound catabolism. Our results are consistent with nitrogen streamlining in both cellular and viral genomes on spatial scales of meters to microns. These effects are similar in magnitude to those previously reported across scales of thousands of kilometers. IMPORTANCE The genomes of marine microbes can be shaped by nutrient cycles, with ocean-scale gradients in nitrogen availability being known to influence microbial amino acid usage. It is unclear, however, how genomic properties are shaped by nutrient changes over much smaller spatial scales, for example, along the vertical transition into oxygen minimum zones (OMZs) or from the exterior to the interior of detrital particles. Here, we measure protein nitrogen usage by marine bacteria, archaea, and viruses by using metagenomes from the nitracline of the eastern tropical North Pacific OMZ, including both particle-associated and nonassociated biomass. Our results show higher genomic and proteomic nitrogen content in particle-associated microbes and at depths with higher nitrogen availability for cellular and viral genomes. This discovery suggests that stoichiometry influences microbial and viral evolution across multiple scales, including the micrometer to millimeter scale associated with particle-associated versus free-living lifestyles.

Differential contribution of nitrifying prokaryotes to groundwater nitrification.

The ecophysiology of complete ammonia-oxidizing bacteria (CMX) of the genus Nitrospira and their widespread occurrence in groundwater suggests that CMX bacteria have a competitive advantage over ammonia-oxidizing bacteria (AOB) and archaea (AOA) in these environments. However, the specific contribution of their activity to nitrification processes has remained unclear. We aimed to disentangle the contribution of CMX, AOA and AOB to nitrification and to identify the environmental drivers of their niche differentiation at different levels of ammonium and oxygen in oligotrophic carbonate rock aquifers. CMX ammonia monooxygenase sub-unit A (amoA) genes accounted on average for 16 to 75% of the total groundwater amoA genes detected. Nitrification rates were positively correlated to CMX clade A associated phylotypes and AOB affiliated with Nitrosomonas ureae. Short-term incubations amended with the nitrification inhibitors allylthiourea and chlorate suggested that AOB contributed a large fraction to overall ammonia oxidation, while metaproteomics analysis confirmed an active role of CMX in both ammonia and nitrite oxidation. Ecophysiological niche differentiation of CMX clades A and B, AOB and AOA was linked to their requirements for ammonium, oxygen tolerance, and metabolic versatility. Our results demonstrate that despite numerical predominance of CMX, the first step of nitrification in oligotrophic groundwater appears to be primarily governed by AOB. Higher growth yields at lower ammonia turnover rates and energy derived from nitrite oxidation most likely enable CMX to maintain consistently high populations.

Distribution and genomic variation of ammonia-oxidizing archaea in abyssal and hadal surface sediments.

Ammonia-oxidizing archaea of the phylum Thaumarchaeota play a central role in the biogeochemical cycling of nitrogen in benthic sediments, at the interface between pelagic and subsurface ecosystems. However, our understanding of their niche separation and of the processes controlling their population structure in hadal and abyssal surface sediments is still limited. Here, we reconstructed 47 AOA metagenome-assembled genomes (MAGs) from surface sediments of the Atacama and Kermadec trench systems. They formed deep-sea-specific groups within the family Nitrosopumilaceae and were assigned to six amoA gene-based clades. MAGs from different clades had distinct distribution patterns along oxygen-ammonium counter gradients in surface sediments. At the species level, MAGs thus seemed to form different ecotypes and follow deterministic niche-based distributions. In contrast, intraspecific population structure, defined by patterns of Single Nucleotide Variants (SNV), seemed to reflect more complex contributions of both deterministic and stochastic processes. Firstly, the bathymetric range had a strong effect on population structure, with distinct populations in abyssal plains and hadal trenches. Then, hadal populations were clearly separated by trench system, suggesting a strong isolation-by-topography effect, whereas abyssal populations were rather controlled by sediment depth or geographic distances, depending on the clade considered. Interestingly, genetic variability between samples was lowest in sediment layers where the mean MAG coverage was highest, highlighting the importance of selective pressure linked with each AOA clade's ecological niche. Overall, our results show that deep-sea AOA genome distributions seem to follow both deterministic and stochastic processes, depending on the genomic variability scale considered.

Oxygen and nitrogen production by an ammonia-oxidizing archaeon.

Ammonia-oxidizing archaea (AOA) are one of the most abundant groups of microbes in the world's oceans and are key players in the nitrogen cycle. Their energy metabolism­the oxidation of ammonia to nitrite­requires oxygen. Nevertheless, AOA are abundant in environments where oxygen is undetectable. By carrying out incubations for which oxygen concentrations were resolved to the nanomolar range, we show that after oxygen depletion, Nitrosopumilus maritimus produces dinitrogen and oxygen, which is used for ammonia oxidation. The pathway is not completely resolved but likely has nitric oxide and nitrous oxide as key intermediates. N. maritimus joins a handful of organisms known to produce oxygen in the dark. On the basis of this ability, we reevaluate the role of N. maritimus in oxygen-depleted marine environments.

Microbial bioremediation of produced water under different redox conditions in marine sediments.

The discharge of produced water from offshore oil platforms is an emerging concern due to its potential adverse effects on marine ecosystems. In this study, we investigated the feasibility and capability of using marine sediments for the bioremediation of produced water. We utilized a combination of porewater and solid phase analysis in a series of sediment batch incubations amended with produced water and synthetic produced water to determine the biodegradation of hydrocarbons under different redox conditions. Significant removal of benzene, toluene, ethylbenzene and xylene (BTEX) compounds was observed under different redox conditions, with biodegradation efficiencies of 93-97% in oxic incubations and 45-93% in anoxic incubations with nitrate, iron oxide or sulfate as the electron acceptor. Higher biodegradation rates of BTEX were obtained by incubations dominated by nitrate reduction (104-149 nmolC/cm3/d) and oxygen respiration (52-57 nmolC/cm3/d), followed by sulfate reduction (14-76 nmolC/cm3/d) and iron reduction (29-39 nmolC/cm3/d). Chemical fingerprint analysis showed that hydrocarbons were biodegraded to smaller alcohols/acids under oxic conditions compared to anoxic conditions with nitrate, indicating that the presence of oxygen facilitated a more complete biodegradation process. Toxicity of treated produced water to the marine copepod Acartia tonsa was reduced by half after sediment incubations with oxygen and nitrate. Our study emphasizes the possibility to use marine sediment as a biofilter for treating produced water at sea without extending the oil and gas platform or implementing a large-scale construction.