Nitrous oxide emissions from subtropical estuaries: Insights for environmental controls and implications

Comparative analysis of niche adaptation strategies of AOA, AOB, and comammox along a gate-controlled river-estuary continuum

Ammonia oxidizers are key players in the biogeochemical nitrogen cycle. However, in critical ecological zones such as estuaries, especially those affected by widespread anthropogenic dam control, our understanding of their occurrence, ecological performance, and survival strategies remains elusive. Here, we sampled sediments along the Haihe River-Estuary continuum in China, controlled by the Haihe Tidal Gate, and employed a combination of biochemical and metagenomic approaches to investigate the abundance, activity, and composition of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and complete ammonia oxidizers (comammox). We also conducted an extensive comparison of the salinity adaptation mechanisms of different ammonia oxidizers. We found that AOB (57.55 ± 11.46 %) dominated the nitrification process upstream of the tidal gate, while comammox (68.22 ± 14.42 %) played the major role downstream. Redundancy analysis results showed that total nitrogen, ammonium, and salinity were the primary factors influencing the abundance, activity, and contribution of ammonia oxidizers. The abundance and activity of AOB were significantly positively correlated with ammonium. KEGG annotation results showed that AOA Nitrososphaera, AOB Nitrosomonas, and comammox Nitrospira had 7, 31, and 22 genes associated to salinity adaptation, respectively, and were capable of employing both the "salt-in" and "salt-out" strategies. Metagenome assembly results indicated that comammox outperformed AOA primarily in compatible solute accumulation; AOA can synthesize glutamate, whereas comammox Nitrospira can additionally synthesize glycine betaine, choline, and trehalose. The tidal gate caused sharp shifts in ammonium (from 4.10 ± 3.28 mg·kg-1 to 0.45 ± 0.10 mg·kg-1) and salinity (from 1.64 ± 0.48 ppt to 3.26 ± 0.89 ppt), playing a dominant role in driving niche differentiation of ammonia oxidizers along the Haihe River-Estuary continuum. These findings provide profound insights into the nitrogen cycle in freshwater-saltwater transition zones, especially in today's world where estuaries are widely controlled by tidal gates.

Assessment of carbon flux gradients and dominant processes in a subtropical highly urbanized coastal ecosystem

Highly urbanized coastal ecosystems are vital in the global carbon budget. However, there are limited researches on carbon flux gradients in these nearshore areas, considering both natural and anthropogenic influences. Through on-site measurements and field samplings during wet-to-dry season in 2023, this study investigated spatial variations and factors affecting carbon fluxes, focusing on the impacts of salinity and eutrophic status in five geographically connected coastal waters of the Guangdong-Hong Kong-Macau Greater Bay Area (GBA). By estimating carbon exchange at land-sea-air interface, dominant processes in carbon dynamics were identified as well. Results showed that partial pressure of CO2 (pCO2) varied from 391 to 2290 μatm, and sea-air CO2 exchange fluxes (FCO2) ranged from -3.07 to 70.07 mmol m-2 d-1, indicating significant geographical distinctions among five coastal waters of the GBA. The total carbon transport from rivers to these nearshore waters was approximated at 6.44 Tg C yr-1, with the Pearl River (PR) contributing 99.7%, primarily in dissolved forms. Atmospheric CO2 release was calculated at 0.29 Tg C yr-1 for studied five coastal waters, primarily as carbon sources, except for Dapeng Bay (DPB) as a sink. CO2 emissions inversely correlated with salinity, yet positively with eutrophication status, particularly in river-dominated estuaries. Moreover, CO2 flux decreased 23 times as eco-status shift from eutrophic to non-eutrophic. River plumes, terrestrial pollutant inputs, and economic structure were underlying drivers, influencing carbon species concentrations and fluxes. Elevated CO2 concentrations in eutrophic coastal waters were mainly attributed to terrestrial carbon and nutrients inputs, supporting active biological respiration and microbial decomposition. Conversely, carbon dynamics potentially depend on the balance of respiration and photosynthesis in non-eutrophic coastal waters. This study offers high geographic precision and specificity of carbon species, and provides land-sea integration insight to understand carbon dynamic mechanisms, promoting advancements in water quality management and climate mitigation.

Unveiling riverine N2O dynamics along urbanization gradients by integrating hydrological, biogeochemical and microbial processes

Human-disturbed rivers are globally significant sources of atmospheric nitrous oxide (N2O). Yet, the underlying mechanisms of urbanization impact on riverine N2O dynamics are not well understood. This study unveiled the effects of urbanization on N2O dynamics by integrating hydrological, biogeochemical and microbial processes in a river with various urbanization intensities. Riverine NO3- concentration enhanced with increasing urban land percentage, primarily because of the increased proportional contribution of sewage & manure source. The 15N site preference and relevant isotopic evidences revealed that the proportion of denitrification derived N2O increased from 60 % to 76 %, with the urban land percentage increasing from 〈 5 % to 〉 22 %, which was caused by decreases in flow velocity and dissolved oxygen saturation, increases in NO3- concentration and N2O-denitrifying genes. The non-negligible contribution of nitrification to N2O production (∼ 40 %) in lower-urbanized river stretches may be attributed to aerobic conditions and lower impermeable riparian zone facilitating the occurrence of in-river nitrification and the access of in-soil nitrification to river. Urbanization-mediated decreases in flow velocity and dissolved oxygen and increases in nitrogen availability and denitrification process resulted in an increase in N2O concentration and flux, with N2O concentration approximately four times higher in higher-urbanized river reaches (50.7 ± 26.3 nmol/L) than in lower-urbanized river reaches (14.4 ± 2.5 nmol/L). In addition, increased proportional contribution of sewage & manure source also provides the possibility for exogenous N2O inputs with urban expansion. These findings contribute to deepening our understanding of how urbanization drives N2O dynamics in river systems.

Seasonal isotopic and isotopomeric signatures of nitrous oxide produced microbially in a eutrophic estuary

Anthropogenic input of excess nutrients stimulates massive nitrous oxide (N2O) production in estuaries with distinct seasonal variations. Here, nitrogen isotopic and isotopomeric signatures were utilized to investigate the seasonal dynamics of N2O production and nitrification at the middle reach of the eutrophic Pearl River Estuary in the south of China. Elevated N2O production primarily via ammonia oxidation (> 1 nM-N d-1) occurred from April to November, along with increased temperature and decreased dissolved oxygen concentration. This consistently oxygenated water column showed active denitrification, contributing 20-40 % to N2O production. The water column microbial N2O production generally constituted a minor fraction (10-15 %) of the estuarine water-air interface efflux, suggesting that upstream transport and tidal dilution regulated the dissolved N2O inventory in the middle reach of the estuary. Nitrification (up to 3000 nM-N d-1) played a critical role in bioavailable nitrogen conversion and N2O production, albeit with N2O yields below 0.05 %.

Elucidating the links between N2O dynamics and changes in microbial communities following saltwater intrusions

Saltwater intrusion in estuarine ecosystems alters microbial communities as well as biogeochemical cycling processes and has become a worldwide problem. However, the impact of salinity intrusion on the dynamics of nitrous oxide (N2O) and associated microbial community are understudied. Here, we conducted field microcosms in a tidal estuary during different months (December, April and August) using dialysis bags, and microbes inside the bags encountered a change in salinity in natural setting. We then compared N2O dynamics in the microcosms with that in natural water. Regardless of incubation environment, saltwater intrusion altered the dissolved N2O depending on the initial saturation rates of N2O. While the impact of saltwater intrusion on N2O dynamics was consistent across months, the dissolved N2O was higher in summer than in winter. The N-related microbial communities following saltwater intrusion were dominated by denitrifers, with fewer nitrifiers and bacterial taxa involved in dissimilatory nitrate reduction to ammonium. While denitrification was a significant driver of N2O dynamics in the studied estuary, nitrifier-involved denitrification contributed to the additional production of N2O, evidenced by the strong associations with amoA genes and the abundance of Nitrospira. Higher N2O concentrations in the field microcosms than in natural water limited N2O consumption in the former, given the lack of an association with nosZ gene abundance. The differences in the N2O dynamics observed between the microcosms and natural water could be that the latter comprised not only indigenous microbes but also those accompanied with saltwater intrusion, and that immigrants might be functionally rich individuals and able to perform N transformation in multiple pathways. Our work provides the first quantitative assessment of in situ N2O concentrations in an estuary subjected to a saltwater intrusion. The results highlight the importance of ecosystem size and microbial connectivity in the source-sink dynamics of N2O in changing environments.

The concentration of CH4, N2O and CO2 in the Pearl River estuary increased significantly due to the sediment particle resuspension and the interaction of hypoxia

Hypoxia and sediment particle resuspension (SPR) alter the biogeochemical cycle of estuarine and coastal seas, which in turn affects the production and emission of methane (CH4), nitrous oxide (N2O) and carbon dioxide (CO2) greenhouse gases (GHGs) in estuaries. Despite the importance of CH4, N2O and CO2 in estuarine ecosystems, little is known about their magnitude and spatiotemporal variation under the combined influence of hypoxia and SPR. This study utilized continuous mooring observations to investigate the temporal and spatial variations of GHGs before and after hypoxia in the Pearl River Estuary (PRE). The results showed that the concentration of GHGs in the water column increased significantly following hypoxia as compared to its absence. The synergistic effect of SPR and hypoxia significantly enhances GHGs production and accumulation in bottom water. Anaerobic mineralization of organic matter (OM) in an environment with severely low dissolved oxygen (DO) is the primary determinant for increased CH4 concentration, while OM and CH4 oxidation are the main drivers for maintaining high CO2 concentration in subsurface water. Hypoxic development enhanced denitrification N2O production in the water column. The presence of SPR enhanced oxygen-consuming coupled hypoxia significantly stimulated the increase of CH4, N2O and CO2 concentrations in the water column. Hypoxic development results in an increased water-air GHGs flux, but this effect may be masked by runoff plumes with high GHGs concentrations in the regions near the river outlets. This study highlights that hypoxia leads to significant increases in anaerobic GHGs production and subsequent emissions from estuarine water columns.

Hypoxia and salinity constrain the sediment microbiota-mediated N removal potential in an estuary: A multi-trophic interrelationship perspective

Reactive nitrogen (N) enrichment is a common environmental problem in estuarine ecosystems, while the microbial-mediated N removal process is complicated for other multi-environmental factors. Therefore, A systematic investigation is necessary to understand the multi-trophic microbiota-mediated N removal characteristics under various environmental factors in estuaries. Here, we studied how multiple factors affect the multi-trophic microbiota-mediated N removal potential (denitrification and anammox) and N2O emission along a river-estuary-bay continuum in southeastern China using the environmental DNA (eDNA) approach. Results suggested that hypoxia and salinity were the dominant environmental factors affecting multi-trophic microbiota-mediated N removal in the estuary. The synergistic effect of hypoxia and salinity contributed to the loss of taxonomic (MultiTaxa) and phylogenetic (MultiPhyl) diversity across multi-trophic microbiota and enhanced the interdependence among multi-trophic microbiota in the estuary. The N removal potential calculated as the activities of key N removal enzymes was also significantly constrained in the estuary (0.011), compared with the river (0.257) and bay (0.461). Structural equation modeling illustrated that metazoans were central to all sediment N removal potential regulatory pathways. The top-down forces (predation by metazoans) restrained the growth of heterotrophic bacteria, which may affect microbial N removal processes in the sediment. Furthermore, we found that the hypoxia and salinity exacerbated the N2O emission in the estuary. This study clarifies that hypoxia and salinity constrain estuarine multi-trophic microbiota-mediated N removal potential and highlights the important role of multi-trophic interactions in estuarine N removal, providing a new perspective on mitigating estuarine N accumulation.

Role of hydrophytes in constructed wetlands for nitrogen removal and greenhouse gases reduction

With the prominence of global climate change and proposal of carbon reduction concept, how to maximize the comprehensive effect of nitrogen removal and greenhouse gases (GHGs) reduction in constructed wetlands (CWs) has become crucial. As indispensable biological component of CWs, hydrophytes have received extensive attention owing to their application potential. This review comprehensively evaluates the functions of hydrophytes in nitrogen removal and GHGs reduction in CWs in terms of plants themselves, plant-mediated microbes and plant residues (hydrophyte carbon sources and hydrophyte-derived biochars). On this basis, the strategies for constructing an ideal CW system are put forward from the perspective of full life-cycle utilization of hydrophytes. Finally, considering the variability of plant species composition in CWs, outlooks for future research are specifically proposed. This review provides guidance and novel perspectives for the full life-cycle utilization of hydrophytes in CWs, as well as for the construction of an ideal CW system.

Shifts in the high-resolution spatial distribution of dissolved N2O and the underlying microbial communities and processes in the Pearl River Estuary

Estuaries are significant sources of the ozone-depleting greenhouse gas N2O. However, owing to large spatial heterogeneity and discrete measurements, N2O emissions from estuaries are considerably uncertain. Microbial processes are disputed in terms of the dominant N2O production under severe human disturbance. Herein, combining real-time and high-resolution measurements with bioinformatics analysis, we accurately mapped the consecutive two-dimensional N2O distribution in the Pearl River Estuary (PRE), China, and revealed its underlying microbial mechanisms. Both the horizontal and vertical distributions of N2O concentrations varied greatly at fine scales. Supersaturated N2O concentrations (9.1 to 132.2 nmol/L) in the surface water decreased along the estuarine salinity gradient, with several emission hotspots scattering upstream. The vertical N2O distribution showed marked differences from complete mixing upstream to incomplete mixing downstream, with constant or changeable concentrations with increasing depth. Furthermore, spatially varied denitrifying and nitrifying microorganisms controlled the N2O production and distribution in the PRE, with denitrification playing the dominant role. The nirK-type and nirS-type denitrifying bacteria were the primary producers of N2O in the water and sediment columns, respectively. In addition, substrate concentration (NO3- and DOC) regulated N2O production by affecting key microbial processes, while physical influences (water-mass mixing and salt wedges) reshaped N2O distribution. With these information, a conceptual model of estuarine N2O production and distribution was constructed to generalize the possible biochemical processes under environmental constraints, which could provide insights into the N2O biogeochemical cycle and emission mitigation from a mechanistic perspective.

The imbalance between N2O production and reduction by multi-microbial communities determines sedimentary N2O emission potential in the Pearl River Estuary

Denitrification is the dominant process of nitrogen removal and nitrous oxide (N2O) emissions in estuarine ecosystems. However, little is known regarding the microbial mechanism of the production and reduction of N2O in estuaries. We investigated in situ dissolved N2O as well as potential N2O production rate (NPR), reduction rate (NRR), and emission rate (NER), and key functional genes related to N2O transformation of denitrification in the Pearl River Estuary. Higher N2O emission potential was found in the upstream and midstream regions with higher NPR and lower NRR values. In contrast, higher NRR values were detected in downstream. Notably, nirS and nirK type N2O producers dominated the upstream zone, whereas abundant N2O reducers, especially nosZ II type N2O reducers, were observed in downstream. Most importantly, the gene abundance ratio (Rnir/nosZ) was significantly correlated with the N2O emission potential (Re). Niche differentiation between N2O producers and N2O reducers from upstream to downstream affected N2O emission potential. This study highlights the N2O emission potential in estuarine sediments is determined by an imbalance between N2O production and the reduction of multi-bacterial communities.

Tracing Microbial Production and Consumption Sources of N2O in Rivers on the Qinghai-Tibet Plateau via Isotopocule and Functional Microbe Analyses

Nitrous oxide (N₂O), a potent greenhouse gas, is produced in rivers through a series of microbial metabolic pathways. However, the microbial source of N₂O production and the degree of N₂O reduction in river systems are not well understood and quantified. This work investigated isotopic compositions (δ¹⁵N-N₂O and δ¹⁸O-N₂O) and N₂O site preference as well as N₂O-related microbial features, thereby differentiating the importance of nitrification, denitrification, and N₂O reduction in controlling N₂O emissions from five rivers on the eastern Qinghai-Tibet Plateau (EQTP). The average N₂O concentration in overlying water (15.2 nmol L^-1) was close to that in porewater (17.5 nmol L^-1), suggesting that both overlying water and sediment are potentially important sources of N₂O. Canonical and nitrifier denitrification dominated riverine N₂O production, with contribution being approximately 90%. Nitrification is a non-negligible source of N₂O production, and N₂O concentration was positively correlated with nitrification genetic potential. The degree of N₂O reduction ranged from 78.1 to 94.1% (averaging 90%), significantly exceeding the reported values (averaging 70%) in other freshwaters, which was attributed to the higher ratios of organic carbon to nitrogen and lower ratio of (nirS + nirK)/nosZ in EQTP rivers. This study indicates that a combination of isotopic and isotopocule values with functional microbe analysis is useful for quantifying the microbial sources of N₂O in rivers, and the intense microbial reduction of N₂O significantly accounts for the low N₂O emissions observed in EQTP rivers, suggesting that both the production and consumption of N₂O in rivers should be considered in the future.

Increased Nitrogen Loading Facilitates Nitrous Oxide Production through Fungal and Chemodenitrification in Estuarine and Coastal Sediments

Estuarine and coastal environments are assumed to contribute to nitrous oxide (N₂O) emissions under increasing nitrogen loading. However, isotopic and molecular mechanisms underlying N₂O production pathways under elevated nitrogen concentration remain poorly understood. Here we used microbial inhibition, isotope mass balance, and molecular approaches to investigate N₂O production mechanisms in estuarine and coastal sediments through a series of anoxic incubations. Site preference of the N₂O molecule increased due to increasing nitrate concentration, suggesting the changes in N₂O production pathways. Enhanced N₂O production under high nitrate concentration was not mediated by bacterial denitrification, but instead was mainly regulated by fungal denitrification. Elevated nitrate concentration increased the contribution of fungal denitrification to N₂O production by 11-25%, whereas it decreased bacterial N₂O production by 16-33%. Chemodenitrification was also enhanced by high nitrate concentration, contributing to 13-28% of N₂O production. Elevated nitrate concentration significantly mediated nirK-type denitrifiers structure and abundance, which are the keystone taxa driving N₂O production. Collectively, these results suggest that increasing nitrate concentration can shift N₂O production pathways from bacterial to fungal and chemodenitrification, which are mainly responsible for the enhanced N₂O production and have widespread implications for N₂O projections under ongoing nitrogen pollution in estuarine and coastal ecosystems.