Nitrous oxide as a function of oxygen and archaeal gene abundance in the North Pacific

Contribution of Microorganisms with the Clade II Nitrous Oxide Reductase to Suppression of Surface Emissions of Nitrous Oxide

The sources and sinks of nitrous oxide, as control emissions to the atmosphere, are generally poorly constrained for most environmental systems. Initial depth-resolved analysis of nitrous oxide flux from observation wells and the proximal surface within a nitrate contaminated aquifer system revealed high subsurface production but little escape from the surface. To better understand the environmental controls of production and emission at this site, we used a combination of isotopic, geochemical, and molecular analyses to show that chemodenitrification and bacterial denitrification are major sources of nitrous oxide in this subsurface, where low DO, low pH, and high nitrate are correlated with significant nitrous oxide production. Depth-resolved metagenomes showed that consumption of nitrous oxide near the surface was correlated with an enrichment of Clade II nitrous oxide reducers, consistent with a growing appreciation of their importance in controlling release of nitrous oxide to the atmosphere. Our work also provides evidence for the reduction of nitrous oxide at a pH of 4, well below the generally accepted limit of pH 5.

Variations in dissolved oxygen and aquatic biological responses in China's coastal seas

Coastal areas can represent an ecological transition zone with the function of biodiversity conservation, and good water quality is fundamental to maintaining this function. In this study, we analyzed data from 2011 to 2020 to reveal the variation in dissolved oxygen (DO) and the aquatic biological response in China's coastal seas. Results showed that DO in coastal waters exhibited an upward trend from 2011 to 2020 because of reduction in terrestrial anthropogenic pollutant (TAP) input. In comparison with DO in other seas, the DO content in the East China Sea was lower owing to higher TAP input, i.e., the proportion of DO of <5 mg L^-1 accounted for approximately 60% of the total. Species numbers, density, and the species diversity index of phytoplankton, zooplankton, and macrobenthos were different in the different sea areas because phytoplankton, zooplankton, and macrobenthos have different responses to changes in DO. In comparison with the species numbers of zooplankton and macrobenthos, the species numbers of phytoplankton were more significantly related to DO, and showed a negative linear relationship with a better DO environment (DO ≥ 5 mg L^-1; r² = 0.39, p < 0.01) and positive correlation with a poor DO environment (DO < 3 mg L^-1; r² = 0.52, p < 0.01). A better DO environment is conducive to increased density of macrobenthos. Studies have shown that a good DO environment contributes to coastal ecosystem health, and continuous control of TAP input is an effective means of ensuring DO recovery.

Emissions of Nitric Oxide from Photochemical and Microbial Processes in Coastal Waters of the Yellow and East China Seas

Nitric oxide (NO) is an atmospheric pollutant and climate forcer as well as a key intermediary in the marine nitrogen cycle, but the ocean's NO contribution and production mechanisms remain unclear. Here, high-resolution NO observations were conducted simultaneously in the surface ocean and the lower atmosphere of the Yellow Sea and the East China Sea; moreover, NO production from photolysis and microbial processes was analyzed. The NO sea-air exchange showed uneven distributions (RSD = 349.1%) with an average flux of 5.3 ± 18.5 × 10^-17 mol cm^-2 s^-1. In coastal waters where nitrite photolysis was the predominant source (89.0%), NO concentrations were remarkably higher (84.7%) than the overall average of the study area. The NO from archaeal nitrification accounted for 52.8% of all microbial production (11.0%). We also examined the relationship between gaseous NO and ozone which helped identify sources of atmospheric NO. The sea-to-air flux of NO in coastal waters was narrowed by contaminated air with elevated NO concentrations. These findings indicate that the emissions of NO from coastal waters, mainly controlled by reactive nitrogen inputs, will increase with the reduced terrestrial NO discharge.

Structure and function of the soil microbiome underlying N2O emissions from global wetlands

Wetland soils are the greatest source of nitrous oxide (N₂O), a critical greenhouse gas and ozone depleter released by microbes. Yet, microbial players and processes underlying the N₂O emissions from wetland soils are poorly understood. Using in situ N₂O measurements and by determining the structure and potential functional of microbial communities in 645 wetland soil samples globally, we examined the potential role of archaea, bacteria, and fungi in nitrogen (N) cycling and N₂O emissions. We show that N₂O emissions are higher in drained and warm wetland soils, and are correlated with functional diversity of microbes. We further provide evidence that despite their much lower abundance compared to bacteria, nitrifying archaeal abundance is a key factor explaining N₂O emissions from wetland soils globally. Our data suggest that ongoing global warming and intensifying environmental change may boost archaeal nitrifiers, collectively transforming wetland soils to a greater source of N₂O.

Novel Viral Communities Potentially Assisting in Carbon, Nitrogen, and Sulfur Metabolism in the Upper Slope Sediments of Mariana Trench

Viruses are ubiquitous in the oceans. Even in the deep sediments of the Mariana Trench, viruses have high productivity. However, little is known about their species composition and survival strategies in that environment. Here, we uncovered novel viral communities (3,206 viral scaffolds) in the upper slope sediments of the Mariana Trench via metagenomic analysis of 15 sediment samples. Most (99%) of the viral scaffolds lack known viral homologs, and ca. 59% of the high-quality viral genomes (total of 111 with completeness of >90%) represent novel genera, including some Phycodnaviridae and jumbo phages. These viruses contain various auxiliary metabolic genes (AMGs) potentially involved in organic carbon degradation, inorganic carbon fixation, denitrification, and assimilatory sulfate reduction, etc. This study provides novel insight into the almost unknown benthic viral communities in the Mariana Trench. IMPORTANCE The Mariana Trench harbors a substantial number of infective viral particles. However, very little is known about the identity, survival strategy, and potential functions of viruses in the trench sediments. Here, through metagenomic analysis, unusual benthic viral communities with high diversity and novelty were discovered. Among them, 59% of the viruses with a genome completeness of >90% represent novel genera. Various auxiliary metabolic genes carried by these viruses reflect the potential adaptive characteristics of viruses in this extreme environment and the biogeochemical cycles that they may participate in. This study gives us a deeper understanding of the peculiarities of viral communities in deep-sea/hadal sediments.

Production and Excretion of Polyamines To Tolerate High Ammonia, a Case Study on Soil Ammonia-Oxidizing Archaeon "Candidatus Nitrosocosmicus agrestis"

Ammonia tolerance is a universal characteristic among the ammonia-oxidizing bacteria (AOB); in contrast, the known species of ammonia-oxidizing archaea (AOA) have been regarded as ammonia sensitive, until the identification of the genus “Candidatus Nitrosocosmicus.” However, the mechanism of its ammonia tolerance has not been reported. In this study, the AOA species “Candidatus Nitrosocosmicus agrestis,” obtained from agricultural soil, was determined to be able to tolerate high concentrations of NH₃ (>1,500 μM). In the genome of this strain, which was recovered from metagenomic data, a full set of genes for the pathways of polysaccharide metabolism, urea hydrolysis, arginine synthesis, and polyamine synthesis was identified. Among them, the genes encoding cytoplasmic carbonic anhydrase (CA) and a potential polyamine transporter (drug/metabolite exporter [DME]) were found to be unique to the genus “Ca. Nitrosocosmicus.” When “Ca. Nitrosocosmicus agrestis” was grown with high levels of ammonia, the genes that participate in CO₂/HCO₃⁻ conversion, glutamate/glutamine syntheses, arginine synthesis, polyamine synthesis, and polyamine excretion were significantly upregulated, and the polyamines, including putrescine and spermidine, had significant levels of production. Based on genome analysis, gene expression quantification, and polyamine determination, we propose that the production and excretion of polyamines is probably one of the reasons for the ammonia tolerance of “Ca. Nitrosocosmicus agrestis,” and even of the genus “Ca. Nitrosocosmicus.”

IMPORTANCE Ammonia tolerance of AOA is usually much lower than that of the AOB, which makes the AOB rather than AOA a predominant ammonia oxidizer in agricultural soils, contributing to global N₂O emission. Recently, some AOA species from the genus “Ca. Nitrosocosmicus” were also found to have high ammonia tolerance. However, the reported mechanism for the ammonia tolerance is very rare and indeterminate for AOB and for AOA species. In this study, an ammonia-tolerant AOA strain of the species “Ca. Nitrosocosmicus agrestis” was identified and its potential mechanisms for ammonia tolerance were explored. This study will be of benefit for determining more of the ecological role of AOA in agricultural soils or other environments.

Density currents reduce nitrous oxide emissions in a tributary bay of Three Gorges Reservoir

Reservoirs are a significant source of the potent greenhouse gas nitrous oxide (N₂O), but there are few data on N₂O in the world's largest reservoirs and limited understanding of the factors controlling their emission rates. Here we analyzed high-resolution measurements of dissolved N₂O concentrations and fluxes in a typical tributary bay of Three Gorges Reservoir. The surface water was oversaturated in N₂O during both low and high water level (8.6 -16.4 nmol/L, 107% - 180% saturation) and N₂O fluxes varied nearly tenfold (0.2 and 1.6 μmol/(m² h)). Dissolved N₂O concentrations were characterized by pronounced vertical gradients, which were controlled by bidirectional density currents. The river water with high concentrations entered the bay as an underflow along the riverbed, the upper part of the water column was formed by intrusive backwater of Three Gorges Reservoir having significantly lower N₂O concentrations. In consequence, the N₂O emission potential of the impoundment was reduced compared to pre-impoundment conditions. These results reveal the importance of hydraulic conditions on N₂O emission from large reservoirs and suggest that flow regulation can be a potential tool for mitigating greenhouse gas emissions from manmade impoundments.

Microbial N2O consumption in and above marine N2O production hotspots

The ocean is a net source of N₂O, a potent greenhouse gas and ozone-depleting agent. However, the removal of N₂O via microbial N₂O consumption is poorly constrained and rate measurements have been restricted to anoxic waters. Here we expand N₂O consumption measurements from anoxic zones to the sharp oxygen gradient above them, and experimentally determine kinetic parameters in both oxic and anoxic seawater for the first time. We find that the substrate affinity, O₂ tolerance, and community composition of N₂O-consuming microbes in oxic waters differ from those in the underlying anoxic layers. Kinetic parameters determined here are used to model in situ N₂O production and consumption rates. Estimated in situ rates differ from measured rates, confirming the necessity to consider kinetics when predicting N₂O cycling. Microbes from the oxic layer consume N₂O under anoxic conditions at a much faster rate than microbes from anoxic zones. These experimental results are in keeping with model results which indicate that N₂O consumption likely takes place above the oxygen deficient zone (ODZ). Thus, the dynamic layer with steep O₂ and N₂O gradients right above the ODZ is a previously ignored potential gatekeeper of N₂O and should be accounted for in the marine N₂O budget.

A Critical Review on Nitrous Oxide Production by Ammonia-Oxidizing Archaea

The continuous increase of nitrous oxide (N₂O) in the atmosphere has become a global concern because of its property as a potent greenhouse gas. Given the important role of ammonia-oxidizing archaea (AOA) in ammonia oxidation and their involvement in N₂O production, a clear understanding of the knowledge on archaeal N₂O production is necessary for global N₂O mitigation. Compared to bacterial N₂O production by ammonia-oxidizing bacteria (AOB), AOA-driven N₂O production pathways are less-well elucidated. In this Critical Review, we synthesized the currently proposed AOA-driven N₂O production pathways in combination with enzymology distinction, analyzed the role of AOA species involved in N₂O production pathways, discussed the relative contribution of AOA to N₂O production in both natural and anthropogenic environments, summarized the factors affecting archaeal N₂O yield, and compared the distinctions among approaches used to differentiate ammonia oxidizer-associated N₂O production. We, then, put forward perspectives for archaeal N₂O production and future challenges to further improve our understanding of the production pathways, putative enzymes involved and potential approaches for identification in order to potentially achieve effective N₂O mitigations.

Nitrous oxide production by ammonia oxidizers: Physiological diversity, niche differentiation and potential mitigation strategies

Oxidation of ammonia to nitrite by bacteria and archaea is responsible for global emissions of nitrous oxide directly and indirectly through provision of nitrite and, after further oxidation, nitrate to denitrifiers. Their contributions to increasing N₂ O emissions are greatest in terrestrial environments, due to the dramatic and continuing increases in use of ammonia-based fertilizers, which have been driven by requirement for increased food production, but which also provide a source of energy for ammonia oxidizers (AO), leading to an imbalance in the terrestrial nitrogen cycle. Direct N₂ O production by AO results from several metabolic processes, sometimes combined with abiotic reactions. Physiological characteristics, including mechanisms for N₂ O production, vary within and between ammonia-oxidizing archaea (AOA) and bacteria (AOB) and comammox bacteria and N₂ O yield of AOB is higher than in the other two groups. There is also strong evidence for niche differentiation between AOA and AOB with respect to environmental conditions in natural and engineered environments. In particular, AOA are favored by low soil pH and AOA and AOB are, respectively, favored by low rates of ammonium supply, equivalent to application of slow-release fertilizer, or high rates of supply, equivalent to addition of high concentrations of inorganic ammonium or urea. These differences between AOA and AOB provide the potential for better fertilization strategies that could both increase fertilizer use efficiency and reduce N₂ O emissions from agricultural soils. This article reviews research on the biochemistry, physiology and ecology of AO and discusses the consequences for AO communities subjected to different agricultural practices and the ways in which this knowledge, coupled with improved methods for characterizing communities, might lead to improved fertilizer use efficiency and mitigation of N₂ O emissions.

Cyanobacteria and cyanophage contributions to carbon and nitrogen cycling in an oligotrophic oxygen-deficient zone

Up to half of marine N losses occur in oxygen-deficient zones (ODZs). Organic matter flux from productive surface waters is considered a primary control on N₂ production. Here we investigate the offshore Eastern Tropical North Pacific (ETNP) where a secondary chlorophyll a maximum resides within the ODZ. Rates of primary production and carbon export from the mixed layer and productivity in the primary chlorophyll a maximum were consistent with oligotrophic waters. However, sediment trap carbon and nitrogen fluxes increased between 105 and 150 m, indicating organic matter production within the ODZ. Metagenomic and metaproteomic characterization indicated that the secondary chlorophyll a maximum was attributable to the cyanobacterium Prochlorococcus, and numerous photosynthesis and carbon fixation proteins were detected. The presence of chemoautotrophic ammonia-oxidizing archaea and the nitrite oxidizer Nitrospina and detection of nitrate oxidoreductase was consistent with cyanobacterial oxygen production within the ODZ. Cyanobacteria and cyanophage were also present on large (>30 μm) particles and in sediment trap material. Particle cyanophage-to-host ratio exceeded 50, suggesting that viruses help convert cyanobacteria into sinking organic matter. Nitrate reduction and anammox proteins were detected, congruent with previously reported N₂ production. We suggest that autochthonous organic matter production within the ODZ contributes to N₂ production in the offshore ETNP.

Solar UV radiation in a changing world: roles of cryosphere-land-water-atmosphere interfaces in global biogeochemical cycles

Global change influences biogeochemical cycles within and between environmental compartments (i.e., the cryosphere, terrestrial and aquatic ecosystems, and the atmosphere). A major effect of global change on carbon cycling is altered exposure of natural organic matter (NOM) to solar radiation, particularly solar UV radiation. In terrestrial and aquatic ecosystems, NOM is degraded by UV and visible radiation, resulting in the emission of carbon dioxide (CO2) and carbon monoxide, as well as a range of products that can be more easily degraded by microbes (photofacilitation). On land, droughts and land-use change can reduce plant cover causing an increase in exposure of plant litter to solar radiation. The altered transport of soil organic matter from terrestrial to aquatic ecosystems also can enhance exposure of NOM to solar radiation. An increase in emission of CO2 from terrestrial and aquatic ecosystems due to the effects of global warming, such as droughts and thawing of permafrost soils, fuels a positive feedback on global warming. This is also the case for greenhouse gases other than CO2, including methane and nitrous oxide, that are emitted from terrestrial and aquatic ecosystems. These trace gases also have indirect or direct impacts on stratospheric ozone concentrations. The interactive effects of UV radiation and climate change greatly alter the fate of synthetic and biological contaminants. Contaminants are degraded or inactivated by direct and indirect photochemical reactions. The balance between direct and indirect photodegradation or photoinactivation of contaminants is likely to change with future changes in stratospheric ozone, and with changes in runoff of coloured dissolved organic matter due to climate and land-use changes.

Planktonic Marine Archaea

Archaea are ubiquitous and abundant members of the marine plankton. Once thought of as rare organisms found in exotic extremes of temperature, pressure, or salinity, archaea are now known in nearly every marine environment. Though frequently referred to collectively, the planktonic archaea actually comprise four major phylogenetic groups, each with its own distinct physiology and ecology. Only one group-the marine Thaumarchaeota-has cultivated representatives, making marine archaea an attractive focus point for the latest developments in cultivation-independent molecular methods. Here, we review the ecology, physiology, and biogeochemical impact of the four archaeal groups using recent insights from cultures and large-scale environmental sequencing studies. We highlight key gaps in our knowledge about the ecological roles of marine archaea in carbon flow and food web interactions. We emphasize the incredible uncultivated diversity within each of the four groups, suggesting there is much more to be done.

A denitrifying community associated with a major, marine nitrogen fixer

The diazotrophic cyanobacterium, Trichodesmium, is an integral component of the marine nitrogen cycle and contributes significant amounts of new nitrogen to oligotrophic, tropical/subtropical ocean surface waters. Trichodesmium forms macroscopic, fusiform (tufts), spherical (puffs) and raft-like colonies that provide a pseudobenthic habitat for a host of other organisms including marine invertebrates, microeukaryotes and numerous other microbes. The diversity and activity of denitrifying bacteria found in association with the colonies was interrogated using a series of molecular-based methodologies targeting the gene encoding the terminal step in the denitrification pathway, nitrous oxide reductase (nosZ). Trichodesmium spp. sampled from geographically isolated ocean provinces (the Atlantic Ocean, the Red Sea and the Indian Ocean) were shown to harbor highly similar, taxonomically related communities of denitrifiers whose members are affiliated with the Roseobacter clade within the Rhodobacteraceae (Alphaproteobacteria). These organisms were actively expressing nosZ in samples taken from the mid-Atlantic Ocean and Red Sea implying that Trichodesmium colonies are potential sites of nitrous oxide consumption and perhaps earlier steps in the denitrification pathway also. It is proposed that coupled nitrification of newly fixed N is the most likely source of nitrogen oxides supporting nitrous oxide cycling within Trichodesmium colonies.

Community Composition of Nitrous Oxide Consuming Bacteria in the Oxygen Minimum Zone of the Eastern Tropical South Pacific

The ozone-depleting and greenhouse gas, nitrous oxide (N₂O), is mainly consumed by the microbially mediated anaerobic process, denitrification. N₂O consumption is the last step in canonical denitrification, and is also the least O₂ tolerant step. Community composition of total and active N₂O consuming bacteria was analyzed based on total (DNA) and transcriptionally active (RNA) nitrous oxide reductase (nosZ) genes using a functional gene microarray. The total and active nosZ communities were dominated by a limited number of nosZ archetypes, affiliated with bacteria from marine, soil and marsh environments. In addition to nosZ genes related to those of known marine denitrifiers, atypical nosZ genes, related to those of soil bacteria that do not possess a complete denitrification pathway, were also detected, especially in surface waters. The community composition of the total nosZ assemblage was significantly different from the active assemblage. The community composition of the total nosZ assemblage was significantly different between coastal and off-shore stations. The low oxygen assemblages from both stations were similar to each other, while the higher oxygen assemblages were more variable. Community composition of the active nosZ assemblage was also significantly different between stations, and varied with N₂O concentration but not O₂. Notably, nosZ assemblages were not only present but also active in oxygenated seawater: the abundance of total and active nosZ bacteria from oxygenated surface water (indicated by nosZ gene copy number) was similar to or even larger than in anoxic waters, implying the potential for N₂O consumption even in the oxygenated surface water.

Acidification Enhances Hybrid N2O Production Associated with Aquatic Ammonia-Oxidizing Microorganisms

Ammonia-oxidizing microorganisms are an important source of the greenhouse gas nitrous oxide (N₂O) in aquatic environments. Identifying the impact of pH on N₂O production by ammonia oxidizers is key to understanding how aquatic greenhouse gas fluxes will respond to naturally occurring pH changes, as well as acidification driven by anthropogenic CO₂. We assessed N₂O production rates and formation mechanisms by communities of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in a lake and a marine environment, using incubation-based nitrogen (N) stable isotope tracer methods with ¹⁵N-labeled ammonium (¹⁵NH4+) and nitrite (¹⁵NO2−), and also measurements of the natural abundance N and O isotopic composition of dissolved N₂O. N₂O production during incubations of water from the shallow hypolimnion of Lake Lugano (Switzerland) was significantly higher when the pH was reduced from 7.54 (untreated pH) to 7.20 (reduced pH), while ammonia oxidation rates were similar between treatments. In all incubations, added NH4+ was the source of most of the N incorporated into N₂O, suggesting that the main N₂O production pathway involved hydroxylamine (NH₂OH) and/or NO2− produced by ammonia oxidation during the incubation period. A small but significant amount of N derived from exogenous/added ¹⁵NO2− was also incorporated into N₂O, but only during the reduced-pH incubations. Mass spectra of this N₂O revealed that NH4+ and ¹⁵NO2− each contributed N equally to N₂O by a “hybrid-N₂O” mechanism consistent with a reaction between NH₂OH and NO2−, or compounds derived from these two molecules. Nitrifier denitrification was not an important source of N₂O. Isotopomeric N₂O analyses in Lake Lugano were consistent with incubation results, as ¹⁵N enrichment of the internal N vs. external N atoms produced site preferences (25.0–34.4‰) consistent with NH₂OH-dependent hybrid-N₂O production. Hybrid-N₂O formation was also observed during incubations of seawater from coastal Namibia with ¹⁵NH4+ and NO2−. However, the site preference of dissolved N₂O here was low (4.9‰), indicating that another mechanism, not captured during the incubations, was important. Multiplex sequencing of 16S rRNA revealed distinct ammonia oxidizer communities: AOB dominated numerically in Lake Lugano, and AOA dominated in the seawater. Potential for hybrid N₂O formation exists among both communities, and at least in AOB-dominated environments, acidification may accelerate this mechanism.