Mechanisms of nitrous oxide production in the subtropical North Pacific based on determinations of the isotopic abundances of nitrous oxide and di-oxygen

Water residence time controls seasonal nitrous oxide budget in a semi-enclosed bay: Insights from an improvement estimation method

This study developed an estimation method for the N2O budget using 15N stable isotope labeling techniques, a dual-layer model and a box model, which was used to elucidate the underlying dynamics of N2O accumulation in Zhanjiang Bay. The results showed that although the net input of N2O during the rainy season was 2.36 times higher than that during the dry season, the overall N2O concentration was only 66.6 % of that during the dry season due to the extended water residence time in the dry season. Our findings highlighted that water residence time was the key factor for the N2O emission, and a longer water residence time was unfavorable for the efflux of N2O through hydrodynamic processes and was more conducive to the production and accumulation of N2O within the bay. This research enhanced our comprehension of N2O dynamics and provided crucial insights for refining nitrogen management strategies and mitigation efforts.

The impact of algal blooms on promoting in-situ N2O emissions: A case in Zhanjiang bay, China

Under the influence of many factors, such as climate change, anthropogenic eutrophication, and the development of aquaculture, the area and frequency of algal blooms have showed an increasing trend worldwide, which has become a challenging issue at present. However, the coupled relationship between nitrous oxide (N2O) and algal blooms and the underlying mechanisms remain unclear. To address this issue, 15N isotope cultures and quantitative polymerase chain reaction (qPCR) experiments were conducted in Zhanjiang Bay during algal and non-algal bloom periods. The results showed that denitrification and nitrification-denitrification were the two processes responsible for the in-situ production of N2O during algal and non-algal bloom periods. Stable isotope rate cultivation experiments indicated that denitrification and nitrification-denitrification were promoted in the water during the algal bloom period. The in-situ production of N2O during the algal bloom period was three-fold that during the non-algal bloom period. This may be because fresh particulate organic matter (POM) from the organisms responsible for the algal bloom provides the necessary anaerobic and hypoxic environment for denitrification and nitrification-denitrification in the degradation environment. Additionally, a positive linear correlation between N2O concentrations and ammonia-oxidizing bacteria (AOB) and denitrifying bacteria (nirK and nirS) also supported the significant denitrification and nitrification-denitrification occurring in the water during the algal bloom period. However, the algal bloom changed the main process for the in-situ production of N2O, wherein it shifted from denitrification during the non-algal bloom period to nitrification-denitrification during the algal bloom period. The results of our study will improve our understanding of the processes responsible for the in-situ production of N2O during the algal bloom period, and can help formulate effective policies to mitigate N2O emissions in the bay.

Distinct Distribution of Archaea From Soil to Freshwater to Estuary: Implications of Archaeal Composition and Function in Different Environments

In addition to inhabiting extreme territories, Archaea are widely distributed in common environments spanning from terrestrial to aquatic environments. This study investigated and compared archaeal community structures from three different habitats (representing distinct environments): agriculture soils (from farming system trials FST, PA, United States), freshwater biofilms (from White Clay Creek, PA, United States), and estuary water (Chesapeake Bay, United States). High-throughput sequencing of 16S rRNA genes indicated that Thaumarchaeota, Euryarchaeota, Nanoarchaeota, Crenarchaeota, and Diapherotrites were the commonly found dominant phyla across these three environments. Similar to Bacteria, distinct community structure and distribution patterns for Archaea were observed in soils vs. freshwater vs. estuary. However, the abundance, richness, evenness, and diversity of archaeal communities were significantly greater in soils than it was in freshwater and estuarine environments. Indicator species (or amplicon sequence variants, ASVs) were identified from different nitrogen and carbon cycling archaeal groups in soils (Nitrososphaerales, Nitrosotaleales, Nitrosopumilales, Methanomassiliicoccales, Lainarchaeales), freshwater biofilms (Methanobacteria, Nitrososphaerales) and Chesapeake Bay (Marine Group II, Nitrosopumilales), suggesting the habitat-specificity of their biogeochemical contributions to different environments. Distinct functional aspects of Archaea were also confirmed by functional predictions (PICRUSt2 analysis). Further, co-occurrence network analysis indicated that only soil Archaea formed stable modules. Keystone species (ASVs) were identified mainly from Methanomassiliicoccales, Nitrososphaerales, Nitrosopumilales. Overall, these results indicate a strong habitat-dependent distribution of Archaea and their functional partitions within the local environments.

Mechanisms responsible for N2O emissions from intertidal soils of the Yangtze Estuary

Estuarine and coastal wetland ecosystems are important sources of atmospheric nitrous oxide (N₂O). However, the underlying driver of emitted N₂O from estuarine and coastal wetlands remains poorly understood. Here, natural-abundance isotope technique was applied to characterize the processes responsible for N₂O emission from the intertidal soils of the Yangtze Estuary. Measured N₂O emission rates ranged from 0.70 to 2.15 μmol m^-2 h^-1, with relatively high values at the upper estuarine sites. The δ¹⁵N, δ¹⁸O and SP (intramolecular ¹⁵N site preference) of emitted N₂O varied from -4.5 to 6.7‰, 42.4 to 53.2‰, and 6.7 to 15.4‰, respectively. Gross N₂O production and consumption rates were within the ranges of 3.16-14.34 μmol m^-2 h^-1 and 2.22-12.54 μmol m^-2 h^-1, respectively, showing a similar spatial pattern to N₂O emission. N₂O consumption proportion varied from 69.56 to 90.31%, which was generally lower at the upper estuarine sites. The gross production rates and consumption degree of N₂O simultaneously controlled the variations in N₂O emission. Bacterial denitrification was the dominant production pathway (78.22-97.36%), while hydroxylamine (NH₂OH) oxidation contributed 2.64-21.78% to N₂O production. Soil pH, Fe²⁺/Fe³⁺, sulfide and substrate availability were probably the main factors governing the N₂O emission dynamics. Overall, these results highlight the substantial role of NH₂OH oxidation and N₂O consumption in N₂O release in redox-dynamic soils of estuarine intertidal wetlands.

Nitrous oxide variability at sub-kilometre resolution in the Atlantic sector of the Southern Ocean

The Southern Ocean is an important region for global nitrous oxide (N₂O) cycling. The contribution of different source and sink mechanisms is, however, not very well constrained due to a scarcity of seawater data from the area. Here we present high-resolution surface N₂O measurements from the Atlantic sector of the Southern Ocean, taking advantage of a relatively new underway setup allowing for collection of data during transit across mesoscale features such as frontal systems and eddies. Covering a range of different environments and biogeochemical settings, N₂O saturations and sea-to-air fluxes were highly variable: Saturations ranged from 96.5% at the sea ice edge in the Weddell Sea to 126.1% across the Polar Frontal Zone during transit to South Georgia. Negative sea-to-air fluxes (N₂O uptake) of up to −1.3 µmol m⁻² d⁻¹ were observed in the Subantarctic Zone and highest positive fluxes (N₂O emission) of 14.5 µmol m⁻² d⁻¹ in Stromness Bay, coastal South Georgia. Although N₂O saturations were high in areas of high productivity, no correlation between saturations and chlorophyll a (as a proxy for productivity) was observed. Nevertheless, there is a clear effect of islands and shallow bathymetry on N₂O production as inferred from supersaturations.

Evidence for fungal and chemodenitrification based N2O flux from nitrogen impacted coastal sediments

Although increasing atmospheric nitrous oxide (N₂O) has been linked to nitrogen loading, predicting emissions remains difficult, in part due to challenges in disentangling diverse N₂O production pathways. As coastal ecosystems are especially impacted by elevated nitrogen, we investigated controls on N₂O production mechanisms in intertidal sediments using novel isotopic approaches and microsensors in flow-through incubations. Here we show that during incubations with elevated nitrate, increased N₂O fluxes are not mediated by direct bacterial activity, but instead are largely catalysed by fungal denitrification and/or abiotic reactions (e.g., chemodenitrification). Results of these incubations shed new light on nitrogen cycling complexity and possible factors underlying variability of N₂O fluxes, driven in part by fungal respiration and/or iron redox cycling. As both processes exhibit N₂O yields typically far greater than direct bacterial production, these results emphasize their possibly substantial, yet widely overlooked, role in N₂O fluxes, especially in redox-dynamic sediments of coastal ecosystems.

Isotopic signatures of N2O produced by ammonia-oxidizing archaea from soils

N2O gas is involved in global warming and ozone depletion. The major sources of N2O are soil microbial processes. Anthropogenic inputs into the nitrogen cycle have exacerbated these microbial processes, including nitrification. Ammonia-oxidizing archaea (AOA) are major members of the pool of soil ammonia-oxidizing microorganisms. This study investigated the isotopic signatures of N2O produced by soil AOA and associated N2O production processes. All five AOA strains (I.1a, I.1a-associated and I.1b clades of Thaumarchaeota) from soil produced N2O and their yields were comparable to those of ammonia-oxidizing bacteria (AOB). The levels of site preference (SP), δ(15)N(bulk) and δ(18)O -N2O of soil AOA strains were 13-30%, -13 to -35% and 22-36%, respectively, and strains MY1-3 and other soil AOA strains had distinct isotopic signatures. A (15)N-NH4(+)-labeling experiment indicated that N2O originated from two different production pathways (that is, ammonia oxidation and nitrifier denitrification), which suggests that the isotopic signatures of N2O from AOA may be attributable to the relative contributions of these two processes. The highest N2O production yield and lowest site preference of acidophilic strain CS may be related to enhanced nitrifier denitrification for detoxifying nitrite. Previously, it was not possible to detect N2O from soil AOA because of similarities between its isotopic signatures and those from AOB. Given the predominance of AOA over AOB in most soils, a significant proportion of the total N2O emissions from soil nitrification may be attributable to AOA.

Isotopic signature of N(2)O produced by marine ammonia-oxidizing archaea

The ocean is an important global source of nitrous oxide (N(2)O), a greenhouse gas that contributes to stratospheric ozone destruction. Bacterial nitrification and denitrification are thought to be the primary sources of marine N(2)O, but the isotopic signatures of N(2)O produced by these processes are not consistent with the marine contribution to the global N(2)O budget. Based on enrichment cultures, we report that archaeal ammonia oxidation also produces N(2)O. Natural-abundance stable isotope measurements indicate that the produced N(2)O had bulk δ(15)N and δ(18)O values higher than observed for ammonia-oxidizing bacteria but similar to the δ(15)N and δ(18)O values attributed to the oceanic N(2)O source to the atmosphere. Our results suggest that ammonia-oxidizing archaea may be largely responsible for the oceanic N(2)O source.

Enrichment and characterization of ammonia-oxidizing archaea from the open ocean: phylogeny, physiology and stable isotope fractionation

Archaeal genes for ammonia oxidation are widespread in the marine environment, but direct physiological evidence for ammonia oxidation by marine archaea is limited. We report the enrichment and characterization of three strains of pelagic ammonia-oxidizing archaea (AOA) from the North Pacific Ocean that have been maintained in laboratory culture for over 3 years. Phylogenetic analyses indicate the three strains belong to a previously identified clade of water column-associated AOA and possess 16S ribosomal RNA genes and ammonia monooxygenase subunit a (amoA) genes highly similar (98-99% identity) to those recovered in DNA and complementary DNA clone libraries from the open ocean. The strains grow in natural seawater-based liquid medium while stoichiometrically converting ammonia (NH(3)) to nitrite (NO(2)(-)). Ammonia oxidation by the enrichments is only partially inhibited by allylthiourea at concentrations known to completely inhibit cultivated ammonia-oxidizing bacteria. The three strains were used to determine the nitrogen stable isotope effect ((15)ɛ(NH3)) during archaeal ammonia oxidation, an important parameter for interpreting stable isotope ratios in the environment. Archaeal (15)ɛ(NH3) ranged from 13‰ to 41‰, within the range of that previously reported for ammonia-oxidizing bacteria. Despite low amino acid identity between the archaeal and bacterial Amo proteins, their functional diversity as captured by (15)ɛ(NH3) is similar.

Phylogenetic analysis of nitric oxide reductase gene homologues from aerobic ammonia-oxidizing bacteria

Nitric oxide (NO) and nitrous oxide (N2O) are climatically important trace gases that are produced by both nitrifying and denitrifying bacteria. In the denitrification pathway, N2O is produced from nitric oxide (NO) by the enzyme nitric oxide reductase (NOR). The ammonia-oxidizing bacterium Nitrosomonas europaea also possesses a functional nitric oxide reductase, which was shown recently to serve a unique function. In this study, sequences homologous to the large subunit of nitric oxide reductase (norB) were obtained from eight additional strains of ammonia-oxidizing bacteria, including Nitrosomonas and Nitrosococcus species (i.e., both beta- and gamma-Proteobacterial ammonia oxidizers), showing widespread occurrence of a norB homologue in ammonia-oxidizing bacteria. However, despite efforts to detect norB homologues from Nitrosospira strains, sequences have not yet been obtained. Phylogenetic analysis placed nitrifier norB homologues in a subcluster, distinct from denitrifier sequences. The similarities and differences of these sequences highlight the need to understand the variety of metabolisms represented within a "functional group" defined by the presence of a single homologous gene. These results expand the database of norB homologue sequences in nitrifying bacteria.

Nitrogen isotopomer site preference of N2O produced by Nitrosomonas europaea and Methylococcus capsulatus Bath

The relative importance of individual microbial pathways in nitrous oxide (N(2)O) production is not well known. The intramolecular distribution of (15)N in N(2)O provides a basis for distinguishing biological pathways. Concentrated cell suspensions of Methylococcus capsulatus Bath and Nitrosomonas europaea were used to investigate the site preference of N(2)O by microbial processes during nitrification. The average site preference of N(2)O formed during hydroxylamine oxidation by M. capsulatus Bath (5.5 +/- 3.5 per thousand) and N. europaea (-2.3 +/- 1.9 per thousand) and nitrite reduction by N. europaea (-8.3 +/- 3.6 per thousand) differed significantly (ANOVA, f((2,35)) = 247.9, p = 0). These results demonstrate that the mechanisms for hydroxylamine oxidation are distinct in M. capsulatus Bath and N. europaea. The average delta(18)O-N(2)O values of N(2)O formed during hydroxylamine oxidation for M. capsulatus Bath (53.1 +/- 2.9 per thousand) and N. europaea (-23.4 +/- 7.2 per thousand) and nitrite reduction by N. europaea (4.6 +/- 1.4 per thousand) were significantly different (ANOVA, f((2,35)) = 279.98, p = 0). Although the nitrogen isotope value of the substrate, hydroxylamine, was similar in both cultures, the observed fractionation (delta(15)N) associated with N(2)O production via hydroxylamine oxidation by M. capsulatus Bath and N. europaea (-2.3 and 26.0 per thousand, respectively) provided evidence that differences in isotopic fractionation were associated with these two organisms. The site preferences in this study are the first measured values for isolated microbial processes. The differences in site preference are significant and indicate that isotopomers provide a basis for apportioning biological processes producing N(2)O.