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Variations of N transformation processes, N2O release rates, and N2O emission pathways were investigated at different levels of salinity (stage 1, low salinity inhibition stage; stage 2, medium salinity promotion stage; and stage 3, high salinity promotion stage) using 15 N-18O dual-isotope labeling technique. Potential nitrification rates were reduced by saltwater incursion in stage 1, increased markedly in stage 3, and significantly inhibited potential denitrification rate under higher salinity. N2O emission significantly increased along salinity gradient in stage 3 due to the changes of potential nitrification rates. Saltwater incursion significantly increased the contribution of heterotrophic denitrification to N2O emission in stage 1. In stages 2 and 3, contributions of nitrifier denitrification and nitrification-coupled denitrification to N2O emission increased gradually, and nitrifier denitrification became the dominant pathway of N2O emission under high salinity. Changes of N transformations, N2O emission rates, and their pathways were regulated both by composition of microbial community and physicochemical properties of the sediment. Due to increased ammonification rate, organic N decomposition accelerated by saltwater can reduce the wetland N sink and may turn coastal wetland to significant reactive N source. [ABSTRACT FROM AUTHOR]

Marine aquaculture in semi-enclosed bays can significantly influence nutrient cycling in coastal ecosystems. However, the impact of marine aquaculture on the dynamics of dissimilatory nitrate reduction processes (DNRPs) and the fate of reactive nitrogen remain poorly understood. In this study, the rates of DNRPs and the abundances of related functional genes were investigated in aquaculture and non-aquaculture areas. The results showed that marine aquaculture significantly increased the denitrification (DNF) and dissimilatory nitrate reduction to ammonium (DNRA) rates and decreased the rate of anaerobic ammonium oxidation (ANA), as compared with non-aquaculture sites. DNF was the dominant pathway contributing to the total nitrate reduction, and its contribution to the total nitrate reduction significantly increased from 66.72% at non-aquaculture sites to 78.50% at aquaculture sites. Marine aquaculture can significantly affect the physicochemical characteristics of sediment and the abundances of related functional genes, leading to variations in the nitrate reduction rates. Although nitrate removal rates increased in the marine aquaculture area, ammonification rates and the nitrogen retention index in the aquaculture areas were 2.19 and 1.24 times, respectively, higher than those at non-aquaculture sites. Net reactive nitrogen retention exceeded nitrogen removal in the aquaculture area, and the retained reactive nitrogen could diffuse with the tidal current to the entire bay, thereby aggravating N pollution in the entire study area. These results show that marine aquaculture is the dominant source of nitrogen pollution in semi-enclosed bays. This study can provide insights into nitrogen pollution control in semi-enclosed bays with well-developed marine aquaculture. [Display omitted] [ABSTRACT FROM AUTHOR]

• The response of denitrification to MPs is spatially heterogeneous in coastal areas. • The response of N 2 O emission to MPs is not affected by coastal heterogeneity. • Denitrification response patterns to MPs are controlled by sulfide and NO 3 −. • MPs cause distinct SRB-DNB interactions under distinct sulfide and NO 3 − scenarios. • Altered microbial interactions by MPs have vital effects on biogeochemical cycles. Global estuarine and coastal zones are facing severe microplastics (MPs) pollution. Sulfate reducers (SRB) and denitrifiers (DNB) are two key functional microorganisms in these zones, exhibiting intricate interactions. However, whether and how MPs modulate the interactions between SRB and DNB, with implications for denitrification and associated N 2 O emissions, remains poorly understood. Here, we simultaneously investigated the spatial response patterns of SRB-DNB interactions and denitrification and associated N 2 O emissions to different MPs exposure along an estuarine gradient in the Yangtze Estuary. Spatial responses of denitrification to polyvinyl chloride (PVC) and polyadipate/butylene terephthalate (PBAT) MPs exposure were heterogeneous, while those of N 2 O emissions were not. Gradient-boosted regression tree and multiple regression model analyses showed that sulfide, followed by nitrate (NO 3 −), controlled the response patterns of denitrification to MPs exposure. Further mechanistic investigation revealed that exposure to MPs resulted in a competitive and toxic (sulfide accumulation) inhibition of SRB on DNB, ultimately inhibiting denitrification at upstream zones with high sulfide but low NO 3 − levels. Conversely, MPs exposure induced a competitive inhibition of DNB on SRB, generally promoting denitrification at downstream zones with low sulfide but high NO 3 − levels. These findings advance the current understanding of the impacts of MPs on nitrogen cycle in estuarine and coastal zones, and provide a novel insight for future studies exploring the response of biogeochemical cycles to MPs in various ecosystems. [Display omitted] [ABSTRACT FROM AUTHOR]

[Display omitted] • Bacterial and fungal succession along a reclamation chronosequence were explored. • Coastal reclamation to paddy soils caused biotic homogenization of microbiomes. • Fungal community was more affected by homogeneous selection than that of bacteria. • Coastal reclamation simplified and destabilized bacterial and fungal networks. • Fungal network complexity and α-diversity regulated coastal multifunctionality. Coastal soil microbiomes play a key role in coastal ecosystem functioning and are intensely threatened by land reclamation. However, the impacts of coastal reclamation on soil microbial communities, particularly on their assembly processes, co-occurrence patterns, and the multiple soil functions they support, remain poorly understood. This impedes our capability to comprehensively evaluate the impacts of coastal reclamation on soil microbiomes and to restore coastal ecosystem functions degraded by reclamation. Here, we investigated the temporal dynamics of bacterial and fungal communities, community assembly processes, co-occurrence patterns, and ecosystem multifunctionality along a 53-year chronosequence of paddy soil following reclamation from tidal flats. Reclamation of tidal flats to paddy soils resulted in decreased β-diversity, increased homogeneous selection, and decreased network complexity and robustness of both bacterial and fungal communities, but caused contrasting α-diversity response patterns of them. Reclamation of tidal flats to paddy soils also decreased the multifunctionality of coastal ecosystems, which was largely associated with the fungal network complexity and α-diversity. Collectively, this work demonstrates that coastal reclamation strongly reshaped the soil microbiomes at the level of assembly mechanisms, interaction patterns, and functionality level, and highlights that soil fungal community complexity should be considered as a key factor in restoring coastal ecosystem functions deteriorated by land reclamation. [ABSTRACT FROM AUTHOR]

Denitrification is a dominant reactive nitrogen removal pathway in most estuarine and coastal ecosystems, and plays a significant role in regulating N 2 O release. Although multiple antibiotics residues are widely detected in aquatic environment, combined effects of antibiotics on denitrification remain indistinct. In this work, 5 classes of antibiotics (sulfonamides, chloramphenicols, tetracyclines, macrolides, and fluoroquinolones) were selected to conduct orthogonal experiments in order to explore their combined effects on denitrification. 15 N-based denitrification and N 2 O release rates were determined in the orthogonal experiments, while denitrifying functional genes were examined to illustrate the microbial mechanism of the combined antibiotics effect. Denitrification rates were inhibited by antibiotics treatments, and synergistic inhibition effect was observed for multiple antibiotics exposure. Different classes of antibiotics had different influence on N 2 O release rates, but multiple antibiotics exposure mostly led to stimulatory effect. Abundances of denitrifying functional genes were inhibited by multiple antibiotics exposure due to the antimicrobial properties, and different inhibition on denitrifiers may be the major mechanism for the variations of N 2 O release rates. Combined effects of antibiotics on denitrification may lead to nitrate retention and N 2 O release in estuarine and coastal ecosystems, and consequently cause cascading environmental problems, such as greenhouse effects and hyper-eutrophication. [ABSTRACT FROM AUTHOR]

• Dissimilatory nitrate reduction rates increased along reclamation chronosequences. • The rates varied due to the altered soil physicochemical characteristics. • Denitrification was the dominant pathway contributing to total nitrate reduction. • N 2 O emission was stimulated significantly along reclamation chronosequences. • More reactive nitrogen was exported in converted paddy soil than in coastal wetland. Conversion of coastal wetland to paddy soil can significantly affect soil biogeochemistry cycling. However, the impacts of coastal wetland reclamation on dissimilatory nitrate reduction processes and nitrogen fate remain poorly understood. In this study, the effects of coastal wetland reclamation on the rates and related functional gene abundances of dissimilatory nitrate reduction processes, N 2 O emission, and the fate of reactive nitrogen were investigated in Chongming Island, China. Conversion of coastal wetland to paddy soil can significantly increase dissimilatory nitrate reduction rates. Denitrification was the dominant pathway contributing to the total nitrate reduction, while anammox and DNRA played an important role. Conversion of coastal wetland to paddy soil can significantly affect soil physicochemical characteristics and abundances of related functional genes, leading to the variations of nitrate reduction rates. Although the nitrate removal rates increased along the reclamation chronosequences, due to the intensive N fertilizer application and increased nitrification and ammonification rates, more reactive N can be exported in paddy soil than in wetland, and N 2 O emission was stimulated significantly along reclamation chronosequences. This study can provide valuable insights into the mechanisms of reclamation influences on soil N recycling. [ABSTRACT FROM AUTHOR]

Denitrification is a dominant reactive nitrogen removal pathway in most estuarine and coastal ecosystems, and plays a significant role in regulating N2O release. Although multiple antibiotics residues are widely detected in aquatic environment, combined effects of antibiotics on denitrification remain indistinct. In this work, 5 classes of antibiotics (sulfonamides, chloramphenicols, tetracyclines, macrolides, and fluoroquinolones) were selected to conduct orthogonal experiments in order to explore their combined effects on denitrification. 15N-based denitrification and N2O release rates were determined in the orthogonal experiments, while denitrifying functional genes were examined to illustrate the microbial mechanism of the combined antibiotics effect. Denitrification rates were inhibited by antibiotics treatments, and synergistic inhibition effect was observed for multiple antibiotics exposure. Different classes of antibiotics had different influence on N2O release rates, but multiple antibiotics exposure mostly led to stimulatory effect. Abundances of denitrifying functional genes were inhibited by multiple antibiotics exposure due to the antimicrobial properties, and different inhibition on denitrifiers may be the major mechanism for the variations of N2O release rates. Combined effects of antibiotics on denitrification may lead to nitrate retention and N2O release in estuarine and coastal ecosystems, and consequently cause cascading environmental problems, such as greenhouse effects and hyper-eutrophication. [ABSTRACT FROM AUTHOR]

Dark carbon fixation (DCF), through which chemoautotrophs convert inorganic carbon to organic carbon, is recognized as a vital process of global carbon biogeochemical cycle. However, little is known about the response of DCF processes in estuarine and coastal waters to global warming. Using radiocarbon labelling method, the effects of temperature on the activity of chemoautotrophs were investigated in benthic water of the Yangtze estuarine and coastal areas. A dome‐shaped thermal response pattern was observed for DCF rates (i.e., reduced rates at lower or higher temperatures), with the optimum temperature (Topt) varying from about 21.9 to 32.0°C. Offshore sites showed lower Topt values and were more vulnerable to global warming compared with nearshore sites. Based on temperature seasonality of the study area, it was estimated that warming would accelerate DCF rate in winter and spring but inhibit DCF activity in summer and fall. However, at an annual scale, warming showed an overall promoting effect on DCF rates. Metagenomic analysis revealed that the dominant chemoautotrophic carbon fixation pathways in the nearshore area were Calvin‐Benson‐Bassham (CBB) cycle, while the offshore sites were co‐dominated by CBB and 3‐hydroxypropionate/4‐hydroxybutyrate cycles, which may explain the differential temperature response of DCF along the estuarine and coastal gradients. Our findings highlight the importance of incorporating DCF thermal response into biogeochemical models to accurately estimate the carbon sink potential of estuarine and coastal ecosystems in the context of global warming. [ABSTRACT FROM AUTHOR]

Bacteria play an important role in regulating carbon (C), nitrogen (N), and sulfur (S) in estuarine intertidal wetlands. To gain insights into the ecological and metabolic modes possessed by bacteria in estuarine intertidal wetlands, a total of 78 surface soil samples were collected from China's coastal intertidal wetlands to examine the spatial and seasonal variations of bacterial taxonomic composition, assembly processes, and ecological system functions through shotgun metagenomic and 16S rRNA gene sequencing. Obvious spatiotemporal dynamic patterns in the bacterial community structure were identified, with more pronounced seasonal rather than spatial variations. Dispersion limitation was observed to act as a critical factor affecting community assembly, explaining approximately half of the total variation in the bacterial community. Functional bacterial community structure exhibited a more significant latitudinal change than seasonal variability, highlighting that functional stability of the bacterial communities differed with their taxonomic variability. Identification of biogeochemically related links between C, N, and S cycles in the soils showed the adaptive routed metabolism of the bacterial communities and the strong interactions between coupled metabolic pathways. Our study broadens the insights into the taxonomic and functional profiles of bacteria in China's estuarine intertidal soils and helps us understand the effects exerted by environmental factors on the ecological health and microbial diversity of estuarine intertidal flats. [ABSTRACT FROM AUTHOR]

Aquatic environments are hot spots of nitrogen (N) cycling and nitrous oxide (N2O) emission. Understanding key N biogeochemical processes and N2O dynamics is critical for uncovering the responses of aquatic environments to human activities. In this study, we summarized the development of techniques and approaches for determination of N cycling processes and N2O sources in aquatic environments of China. We also reviewed the main N transformation processes and associated biogeochemical controls in aquatic environments of China (e.g., constructed wetlands, paddy fields, lakes, rivers, aquaculture ponds, and estuaries and coasts). In addition, we further synthesized N2O dynamics in these aquatic environments. The results suggested that N cycling processes have been greatly concerned in various aquatic environments of China, whereas more comprehensive analyses of N cycling processes are still sparse for projecting N fates and dynamics in response to changing environments, largely limiting the implementation of N management strategy of China. Aquatic environments of China may be the important sources of atmospheric N2O, but the production and consumption processes of N2O need to be further studied for effective greenhouse gas mitigation. We also argued that it is urgently necessary to incorporate microbial traits into biogeochemical ecosystem modeling to improve the estimation reliability of N cycling and N2O dynamics. This review highlights the importance of N cycling and N2O dynamics, as well as associated environmental implications, and presents the directions of future research on N cycling in aquatic environments of China. [ABSTRACT FROM AUTHOR]

• N input influenced the response of nitrifying microbes to coastal acidification. • Elevated N input alleviated the inhibitory effect of acidification on nitrification. • Increase of N input intensified the production of N 2 O under coastal acidification. • Metatranscriptome data further provided microbial evidence at transcriptional level. Acidification of coastal waters, synergistically driven by increasing atmospheric carbon dioxide (CO 2) and intensive land-derived nutrient inputs, exerts significant stresses on the biogeochemical cycles of coastal ecosystem. However, the combined effects of anthropogenic nitrogen (N) inputs and aquatic acidification on nitrification, a critical process of N cycling, remains unclear in estuarine and coastal ecosystems. Here, we showed that increased loading of ammonium (NH 4 +) in estuarine and coastal waters alleviated the inhibitory effect of acidification on nitrification rates but intensified the production of the potent greenhouse gas nitrous oxide (N 2 O), thus accelerating global climate change. Metatranscriptomes and natural N 2 O isotopic signatures further suggested that the enhanced emission of N 2 O may mainly source from hydroxylamine (NH 2 OH) oxidation rather than from nitrite (NO 2 −) reduction pathway of nitrifying microbes. This study elucidates how anthropogenic N inputs regulate the effects of coastal acidification on nitrification and associated N 2 O emissions, thereby enhancing our ability to predict the feedbacks of estuarine and coastal ecosystems to climate change and human perturbations. [Display omitted] [ABSTRACT FROM AUTHOR]

Coastal wetlands are significant sources of nitrous oxide (N 2 O), a potent greenhouse gas and ozone depleting agent. Land reclamation is known to change N 2 O emissions from coastal wetlands, but the long-term impacts on N 2 O sources and emissions are not well-understood. Here, we performed respiration inhibition and molecular techniques to dissect the long-term effects of coastal reclamation on bacterial, fungal and overall N 2 O emissions across a 53-year chronosequence of paddy soils reclaimed from coastal wetlands. Our findings showed that reclamation of coastal wetlands to paddy soils generally promoted N 2 O emissions in the chronosequences, despite a significant reduction in uncultivated paddy soils. The observed increase in N 2 O emissions was primarily attributed to an imbalance between N 2 O production and consumption driven by bacterial denitrifiers. Additionally, reclamation of coastal wetlands to paddy soils shifted N 2 O emissions from fungal to bacterial predominance in the chronosequences, with denitrification mediated by bacterial denitrifiers dominating bacterial N 2 O emissions. By integrating the analysis of N 2 O emission rates with soil physicochemical and microbiological properties, we demonstrated that the reduced salinity following coastal reclamation diminished the relative abundance of key fungal denitrifiers (e.g., Paraconiothyrium, Penicillium and Trichoderma), thus lowering the fungal contribution to N 2 O emissions. This study provides novel insights into the long-term influences of coastal reclamation on the sources and emissions of N 2 O, and enhance our knowledge of the underlying mechanisms driving these impacts, thereby contributing to improving future models of N 2 O emissions from coastal ecosystems under global change. [Display omitted] • Long-term impacts of coastal reclamation on N 2 O source and emission were explored. • Influences of coastal reclamation on N 2 O emission depend on reclamation types. • Coastal reclamation shifted N 2 O emission from fungal to bacterial dominance. • Bacterial denitrifiers mediated denitrification dominated bacterial N 2 O emission. • Reduction in the abundance of key fungal denitrifiers led to shift in N 2 O source. [ABSTRACT FROM AUTHOR]

Estuarine antibiotic residues are profoundly impacting microbial nitrogen (N) cycling and associated N 2 O production, but the response of N 2 O production pathways to antibiotics remains poorly understood. Here, 15N–18O labeling technique combined with molecular methods were used to investigate the impacts of sulfamethoxazole on the contribution of ammonia oxidation (nitrifier nitrification, nitrifier denitrification, and nitrification-coupled denitrification) and heterotrophic denitrification (HD) to N 2 O production in estuarine sediments. Results showed that environmental concentration of sulfamethoxazole (4 ng/g) promoted the total N 2 O production by 17.1% through nitrifier denitrification. Environmentally relevant (40–4000 ng/g) and irrelevant (40,000 ng/g) concentration of sulfamethoxazole drove nitrification denitrification to gradually lose the dominant role in total N 2 O production and ammonia oxidation-derived N 2 O, replaced by HD and nitrifier nitrification, while total N 2 O production were inhibited. Furthermore, when HD dominated the total N 2 O production, the HD-derived N 2 O increased by 63.6% with sulfamethoxazole concentration reaching 40,000 ng/g. The mechanistic investigation further showed that nitrifying bacteria were more susceptible to sulfamethoxazole than nitrifying archaea and denitrifiers. The increased expression of nirS gene carried by non-dominant denitrifiers improved the ratio of nirS : nosZ and hence increased HD-derived N 2 O under high sulfamethoxazole stresses. Overall, our results provide a comprehensive view into how antibiotics regulate N 2 O production and its pathways in estuarine sediments. [Display omitted] • Environmental dose of SMX enhanced the N 2 O production via ND. • Environmentally relevant and irrelevant dose of SMX altered N 2 O production avenues. • SMX altered the keystone species involved in N 2 O production from HD. • SMX increased N 2 O production from HD when HD dominated the total N 2 O production. • Nitrifying bacteria were more vulnerable to SMX than archaea and denitrifiers. [ABSTRACT FROM AUTHOR]

The spatiotemporal distributions of antibiotics in different media have been widely reported; however, their occurrence in the environmental dimension of the Chinese urban agglomerations has received less attention, especially in bioaccumulation and health risks of antibiotics through the "One Health" lens. The review presents the current knowledge on the environmental occurrence, bioaccumulation, as well as health exposure risks in urban agglomerations through the "One Health" lens, and identifies current information gaps. The reviewed studies suggested antibiotic concentrations in water and soil were more sensitive to social indicators of urban agglomerations than those in sediment. The ecological risk and resistance risk of antibiotics in water were much higher than those of sediments, and the high-risk phenomenon occurred at a higher frequency in urban agglomerations. Erythromycin-H 2 O (ETM-H 2 O), amoxicillin (AMOX) and norfloxacin (NFC) were priority-controlled antibiotics in urban waters. Tetracyclines (TCs) posed medium to high risks to soil organisms in the soil of urban agglomerations. Health risk evaluation based on dietary intake showed that children had the highest dietary intake of antibiotics in urban agglomerations. The health risk of antibiotics was higher in children than in other age groups. Our results also demonstrated that dietary structure might impact health risks associated with target antibiotics in urban agglomerations to some extent. [Display omitted] • The pollution patterns of antibiotics in China urban agglomerations were revealed. • Antibiotics in urban waters were most sensitive to social indicators. • Erythromycin-H 2 O and amoxicillin should be priority-controlled in urban waters. • Dietary structure could impact human health risks associated with antibiotics. [ABSTRACT FROM AUTHOR]

Aims: N-acyl-L-homoserine lactones (AHLs) based quorum sensing (QS) phenomenon is recognized as an effective agent for regulating bacterial growth and metabolism. However, diversity and biological role of AHLs in natural environments remain largely unknown. This study focuses on compositions of AHLs and their potential role in nitrogen transformation in intertidal marshes. Methods: We investigated the levels of AHLs in rhizosphere (Phragmites australis, Spartina alterniflora and Scirpus mariqueter) and non-rhizosphere soils from Chongming eastern intertidal wetland of the Yangtze Estuary using gas chromatography-mass spectrometry (GC/MS). Molecular techniques were employed to investigate the compositions and structure of bacterial community. Soil-slurry experiments in combination with nitrogen isotope tracing technique were conducted to examine the effects of AHLs on nitrogen transformation processes. Results: AHLs were higher in rhizosphere than non-rhizosphere soils, and correlated significantly with soil organic carbon and pH. C6-, C8-, C10- and C12-HSLs were identified as the probably universal QS signal molecules in intertidal marsh soils. The bacterial biodiversity might be regulated by AHLs, and 12 of the 50 most abundant microorganisms in intertidal marsh soils were related significantly with AHL concentrations. Furthermore, C6-, C8- and C12-HSLs might play an important role in mediating nitrogen transformation processes including nitrification, denitrification and anaerobic ammonium oxidation (anammox). Conclusions: AHLs are favored to accumulate in rhizospheric environments and thus further mediate the bacterial diversity and soil nitrogen cycling. This study highlights the associations of QS signal molecules with the dynamics and activity of nitrogen cycling bacteria in intertidal marshes. [ABSTRACT FROM AUTHOR]

Estuarine and intertidal wetlands are important sites for nitrogen transformation and elimination. However, the factors controlling nitrogen removal processes remain largely uncertain in the highly dynamic environments. In this study, continuous-flow experiment combined with 15N isotope pairing technique was used to investigate in situ rates of denitrification and anaerobic ammonium oxidation (anammox) and their coupling with nitrification in intertidal wetlands of the Yangtze Estuary. The measured rates varied from below the detection limit to 152.39 µmol N/(m2·hr) for denitrification and from below the detection limit to 43.06 µmol N/(m2·hr) for anammox. The coupling links of nitrogen removal processes with nitrification were mainly dependent on nitrate, organic carbon, sulfide, dissolved oxygen and ferric iron in the estuarine and intertidal wetlands. Additionally, it was estimated that the actual nitrogen removal processes annually removed approximately 5% of the terrigenous inorganic nitrogen discharged into the Yangtze Estuary. This study gives new insights into nitrogen transformation and fate in the estuarine and intertidal wetlands. Image, graphical abstract [ABSTRACT FROM AUTHOR]

Objective: Mononuclear cell infiltration and type I interferon (IFN) system activation play an important role in primary Sjögren's syndrome (SS). We undertook this study to investigate the mechanism of poly(ADP‐ribose) polymerase family member 9 (PARP‐9) on mononuclear cell infiltration triggered by type I IFN. Methods: A proteomic study was conducted in peripheral blood mononuclear cells from patients with primary SS (n = 30) and healthy controls (n = 30) to determine differentially expressed proteins (DEPs) (P < 0.05; fold change >1.20). Labial salivary glands (LSGs) were isolated for hematoxylin and eosin staining and immunohistochemical analysis. CD19+ B cells were purified by magnetic cell sorting for immunofluorescence staining, lentivirus–PARP‐9 transfection, and IFNα treatment experiments. PARP‐9 small interfering RNA (siRNA) and DTX3L siRNA were delivered into female NOD/LtJ female mice to determine their effect. Results: The overexpression of PARP‐9 and CXCL10 as well as their colocalization was confirmed in primary SS. PARP‐9 levels in LSGs rose with increased Chisholm scores in patients with primary SS. PARP‐9 and DTX3L were present in the infiltrating mononuclear cells from salivary glands in female NOD/LtJ mouse models. Additionally, Ingenuity Pathway Analysis networks of DEPs demonstrated that PARP‐9, STAT1, and IFN‐induced protein with tetratricopeptide repeats 1 (IFIT‐1) participated in the IFN‐related pathway. Furthermore, PARP‐9 could up‐regulate the expression of IFIT1 and CXCL10 in B cells. Moreover, PARP‐9 and CXCL10 could be induced by IFNα in B cells. Conclusion: This study is the first to implicate PARP‐9 as a regulator of infiltration of mononuclear cells in primary SS progression and to reveal that PARP‐9 increases CXCL10 expression through up‐regulating IFIT‐1, which is mediated by the phosphorylation of STAT1. PARP‐9 might therefore be a novel therapeutic target for primary SS. [ABSTRACT FROM AUTHOR]

Quantification of polycyclic aromatic hydrocarbons (PAHs) in contaminated soil and identification of potential PAH degraders are essential for comprehending their environmental fate and conducting bioremediation. However, the microbial population responsible for the breakdown of phenanthrene (PHE) in polluted soil environments is frequently disregarded. In this study, via DNA-stable-isotope probing (DNA-SIP), we found that soil microbiota likely plays a crucial part in the PHE degradation. The PHE removal rates were 98% and 99%, in 13C-PHE and 12C-PHE microcosmic incubations, respectively. 13CO 2 was produced along with the degradation of 13C-PHE. According to the analysis of 16S rRNA gene, there was a relatively higher presence of unidentified bacteria in the 'heavy' DNA fractions treated with 13C-PHE. Genus of Enterobacteriales , Acidobacteria , Alphaproteobacteria , Paenibacillaceae , Flavobacteriia , Chloroflexi , Cyanobacteria , Caldilineae , Latescibacteria , Armatimonadetes and Blastocatellia were succseesfully labeled during the degradation of 13C-PHE, indicating their capacity of utilizing PHE. Co-occurrence network of 13C-heavy fractions exhibited greater complexity compared with that of 12C-heavy fractions, revealling an enhancement of bacterial interspecies interactions. Collectivley, this study eluidated the soil microbes involed in the PHE degradation and offered fresh perspectives on the community pattern of potential PHE degrading bacteria. [Display omitted] • Degradation of phenylalanine (PHE) was facilitated by the activity of soil microorganisms. • Production of 13CO 2 occurred during the degradation of 13C-PHE. • Eleven bacterial genera were potentially involved in the PHE degradation. • Degradation activates enhanced the bacterial interspecies's interactions. [ABSTRACT FROM AUTHOR]

Aims: Exotic Spartina alterniflora invasion resulting from anthropogenic activities significantly affects microbial nitrogen (N) transformation and associated nitrous oxide (N2O) emission in coastal wetland soils. However, the responses of soil N2O emission dynamics to plant invasion remain unclear. This study assesses the effects of S. alterniflora invasion on soil N2O potential production and consumption processes. Methods: We used natural isotope tracing technique to investigate potential N2O production and consumption rates in S. alterniflora invaded and native saltmarsh zones (Phragmites australis, Scirpus mariqueter and bare mudflat) in the Yangtze Estuary. Results: Soil potential net N2O production rates in summer were lower in S. alterniflora stands than in S. mariqueter and bare mudflat stands, but no significant differences among these saltmarsh habitats occurred during winter. Potential gross N2O production and consumption rates were higher in S. alterniflora and P. australis stands compared to S. mariqueter and bare mudflat stands. The gross consumption proportion in S. alterniflora and P. australis stands was higher, which affected net N2O production. Hydroxylamine (NH2OH) oxidation and nitrifier denitrification contributed 4.52–12.62% and 13.87–21.58% of soil N2O source, respectively, but denitrification was the dominant pathway (69.83–80.09%). S. alterniflora invasion increased the contributions of NH2OH oxidation and nitrifier denitrification to N2O source slightly, but decreased the contribution of denitrification to N2O source. Soil potential N2O production and consumption processes were influenced by water-filled pore space, pH, sulfide, and carbon and N substrates. Conclusion: Exotic S. alterniflora invasion affected soil N2O dynamics by increasing substrates and altering microenvironments, thus mediating N2O emission from coastal saltmarsh soils. [ABSTRACT FROM AUTHOR]

Abstract Coupling of denitrification and anaerobic ammonium oxidation (anammox) with nitrification is an important mechanism for controlling nitrogen removal from aquatic ecosystems. In this work, we determined ambient rates of denitrification and anammox and their coupling links to nitrification in sediments of the Yangtze Estuary along a salinity gradient, using continuous-flow experiments combined with 15N isotope pairing technique. The rates of total denitrification and coupled nitrification-denitrification ranged from 0.44 to 7.03 μmol N m−2 h−1 and from below the detection limit to 4.26 μmol N m−2 h−1, respectively. The rates of total anammox and coupled nitrification-anammox varied from 0.09 to 1.21 μmol N m−2 h−1 and from below the detection limit to 0.73 μmol N m−2 h−1, respectively. It is shown that high availability of NO 3 − in bottom water as well as ferrous iron and organic carbon in sediments was beneficial to the uncoupled nitrogen removal processes, while low NO 3 − concentration in bottom water promoted the coupled nitrification-nitrogen removal processes. Along the salinity gradient, the coupled nitrification-nitrogen removal processes were the main nitrogen removal pathway in the Yangtze Estuary, and their contribution to total nitrogen removal was affected by NO 3 − concentrations, dissolved oxygen and salinity of sampling sites. Overall, this study improves the understanding of nitrate transformation processes in the estuarine and coastal environments. Highlights • Coupled nitrification-N removal processes were first examined in the Yangtze Estuary. • The coupling of N removal processes to nitrification depended tightly on NO 3 − content. • Coupled nitrification-N removal processes were the primary pathways removing N. [ABSTRACT FROM AUTHOR]

Complete ammonia oxidizers (comammox), as novel microbial communities, are predicted to play an important role in the nitrogen cycle. Here we reported the presence of complete nitrification in tidal sediments and examined the diversity and abundance of comammox in natural ecosystems. Metagenome and metatranscriptome of the enrichment culture from tidal sediments harbored the genes of comammox. Near-complete comammox AmoA/B/C- and Hao-like sequences showed close relationships to the known comammox (with sequence identity from 79 to 99%) rather than classical betaproteobacterial ammonia-oxidizing bacteria (β-AOB) (57 to 66%) and ammonia-oxidizing archaea (AOA) (24 to 38%). To analyze the diversity of comammox in natural environments, a new primer set targeting clade A comammox Nitrospira (COM-A) amoA genes was designed based on sequences obtained in this study and sequences from published database. In silico evaluation of the primers showed the high coverage of 89 and 100% in the COM-A amoA database. Application of the primers in six different ecosystems proved their strong availability. Community composition of COM-A suggested a relatively higher diversity than β-AOB in similar environments. Quantification results showed that COM-A amoA genes accounted for about 0.4-5.6% in total amoA genes. These results provide novel insight into our perception of the enigmatic comammox and have significant implications for profound understanding of complex nitrification process. [ABSTRACT FROM AUTHOR]

• Antibiotics inhibited potential sedimentary N removal and increased N 2 O yield. • Antibiotics had different effect on in situ sedimentary N removal along estuary. • Permeability of sediment determines the effect of antibiotics on N removal. • ARGs can't resist the inhibition of antibiotics on microbe related to N removal. Sedimentary denitrification takes place beneath the oxic layer at the sediment-water interface, where nitrate and antibiotics need to diffuse through the overlying water. However, the antibiotics' effect on sedimentary N removal and associated N 2 O production has not been adequately investigated under in situ conditions. Here, isotope pairing techniques, including slurry incubations (potential) and intact core incubations (in situ), combined with metagenomic analysis were applied to investigate the impacts of two protein-inhibiting antibiotics (oxytetracycline and thiamphenicol) on sediment nitrogen removal in a subtropical estuary. Slurry incubations showed that the two antibiotics significantly inhibited denitrification (67–98%) and anammox (49–99%), while intact core incubations presented no antibiotic effect at upstream but significant inhibition (23%-52%) at downstream. Meanwhile, N 2 O yields were stimulated up to 20 folds in slurry incubations yet showing insignificant response in intact cores. Such contrasting results between up- and down-stream and between slurry and intact core incubations strongly indicated that permeability, which determines diffusion of antibiotics to microbes, is the key to exert the effect of antibiotics on in situ sedimentary nitrogen removal processes regardless the existence of antibiotics resistance genes. This diffusive obstruction may mitigate the toxic effect of antibiotics on nitrogen removal related microbes in natural environments. [Display omitted] [ABSTRACT FROM AUTHOR]

Anaerobic ammonium oxidation (anammox) plays a significant role in nitrogen removal in estuarine and coastal wetlands. However, the effects of changing salinity on anammox activity and anammox bacterial dynamics in these environments are not well understood. In this study, serial incubation experiments with a salinity gradient (0–40) were conducted to explore the responses of anammox bacterial activity, diversity and abundance to the changing salinity in the intertidal wetland of the Yangtze Estuary. Results show that activity and abundance of anammox bacteria firstly increased with the increase of salinity, but they were physiologically stressed by high-level salinity (>30) in a short-term incubation (<10 days). However, the treatment with salinity of 5 showed the maximal anammox activity and anammox bacterial abundance after a long-term incubation (60–120 days). In addition, Kuenenia ( Kuenenia stuttgartiensis ), Scalindua ( Scalindua wagner , marina , and brodae ), and three unknown anammox-like groups were observed, and anammox bacterial diversity increased along the salinity gradient. Anammox community structure varied slightly within the first 10-day incubation, but the dominant anammox bacterial group shifted from Kuenenia to Scalindua with increasing salinity after the long-term incubation. Overall, this study demonstrates the effects of salinity on anammox bacterial community and anammox activity, and suggests the importance of salinity in regulating the anammox process in estuarine and coastal wetlands with frequent salinity fluctuation. [ABSTRACT FROM AUTHOR]

• Feammox activities were widespread across the estuarine and coastal wetlands of China. • Feammox rates at the subtropical sites were generally higher than at the temperate sites. • Spatial variations of diversities and abundances of Fe reducing bacteria were similar to Feammox rates. • Sediment characteristics and geographical factors affected Feammox via altering relevant bacterial abundance. Anaerobic ammonium oxidation coupled with ferric iron reduction (Feammox) is a newly identified microbial nitrogen (N) removal process in natural ecosystems. However, little is known about the distributions of Feammox activity and their environmental drivers across estuarine and coastal wetlands at a continental scale. In this study, we determined the potential Feammox rates and related microbial diversities and abundances along the estuarine and coastal wetlands of China encompassing subtropical to temperate climate zones. Measured potential Feammox activity ranged from 0.05 to 0.23 mg N kg−1 d-1, and the process rates at the subtropical sites were generally higher than at the temperate sites. Partial least squares path model (PLS-PM) showed that the abundance of Fe reducing bacteria significantly and directly affected the potential Feammox rates, while sediment characteristics (mainly including sediment water content, Fe(III), TOC and NO 3 –) and geographical factors (longitude and latitude) had an indirect effect on the process rates. The N loss via the Feammox was approximately 1.72–7.89 kg N ha−1 year−1, accounting for 0.41–1.91 % of multi-annual average land-based inorganic N transported into the estuarine and coastal wetlands of China. Overall, this study reveals the distribution patterns and controlling factors of the Feammox process in estuarine and coastal wetlands of China, and provides a valuable database for N management in estuarine and coastal ecosystems. [ABSTRACT FROM AUTHOR]

The deposition of polycyclic aromatic hydrocarbon (PAHs) has far-reaching impacts on Earth's surface system and human health. However, a comprehensive understanding of PAHs' deposition in a high urbanized area is still lacking because of limited field measurements data and rough resolution of current models. In this research, a deposition map of PAHs with a resolution of 2 × 2 km in megacity Shanghai, China was established. Gridded annual total deposition of PAHs from July 2020 to June 2021 ranged from 385 to 10,631 ng/(m2·d), with a mean value of 2,611 ng/(m2·d). The highest PAHs deposition was found over the downtown Shanghai, which received 4.3 times the deposition flux of outlying areas. About 77 % of area in Shanghai was dominated by wet deposition which accounted for 62 % of total deposition in Shanghai. The total deposition showed a trend of summer>fall>spring>winter, which was similar to that of the amount of rain. Source apportionment and geographically weighted regression analysis showed that built-up land and human activities are key driving factors of PAHs' deposition in Shanghai. Our results suggest that intensive human activities could alter the PAHs deposition distribution in Shanghai, and improve the understanding of PAHs' environmental behavior in high urbanized area. [Display omitted] • One-year measurement of dry & wet deposition of PAHs in Shanghai was reported. • 2 km × 2 km deposition mapping of PAHs in megacity Shanghai was established by CMAQ. • LMW PAHs dominated wet deposition while MMW and HMW PAHs dominated dry deposition. • Built-up land and human activities are key factors driving PAH deposition. [ABSTRACT FROM AUTHOR]

• Effects of periodic drying-wetting on n-DAMO in intertidal wetlands were explored. • Tidal dynamics affect n-DAMO activity and its contribution to reducing CH 4 emission. • Reflooding of intertidal wetlands generally intensifies n-DAMO rates. • Higher biodiversity of n-DAMO microbes was observed under reflooded conditions. Nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) plays an important role in methane (CH 4) consumption in intertidal wetlands. However, little is known about the responses of n-DAMO in intertidal wetlands to periodic drying-wetting caused by tidal cycling. Here, comparative experiments (waterlogged, desiccated, reflooded) with the Yangtze estuarine intertidal sediments were performed to examine the effects of periodic tidal changes on n-DAMO microbial communities, abundances, and potential activities. Functional gene sequencing indicated the coexistence of n-DAMO bacteria and archaea in the tide-fluctuating environments and generally higher biodiversity under reflooded conditions than consecutive inundation or emersion. The n-DAMO microbial abundance and associated activity varied significantly during alternative exposure and inundation, with higher abundance and activity under the waterlogged than desiccated conditions. Reflooding of intertidal wetlands might intensify n-DAMO activities, indicating the resilience of n-DAMO microbial metabolisms to the wetting-drying events. Structural equation modeling and correlation analysis showed that n-DAMO activity was highly related to n-DAMO microbial abundance and substrate availability under inundation, whereas salt accumulation in sediment was the primary factor restraining n-DAMO activity under the desiccation. Overall, this study reveals tidal-induced shifts of n-DAMO activity and associated contribution to mitigating CH 4 , which may help accurately project CH 4 emission from intertidal wetlands under different tidal scenarios. [Display omitted] [ABSTRACT FROM AUTHOR]

• Gross N transformation rates at the freshwater and low-salinity sites were generally higher compared to high-salinity sites. • Distribution patterns of functional genes were similar to corresponding gross N transformation rates. • TOC, NO 2 – and Fe2+ were the key factors mediating N dynamics in intertidal sediments. Nitrogen (N) transformations in estuarine and coastal ecosystems play a crucial role in the global biogeochemical cycles. However, simultaneous estimation of gross N transformations and the underlying drivers across estuarine and intertidal wetlands remain poorly understood. Here, the spatial changes in gross N transformation rates and related functional gene abundances were explored in varying habitats of the intertidal zone in the Yangtze Estuary via an optimized 15N tracing model and quantitative PCR. The results indicate that the gross N transformation rates changed remarkably in estuarine and intertidal wetlands, with comparatively higher gross N transformation rates at the upper freshwater and low-salinity sites relative to high-salinity sites. Meanwhile, the functional gene abundances (amoB , UreC , hzo , nirS and nrfA) exhibited a similar spatial distribution pattern to corresponding N transformation processes. Sedimentary total organic carbon (TOC), nitrite (NO 2 –), ferrous iron (Fe(II)), and microbial functional gene abundances jointly mediated the gross N transformations. This study carried out the first simultaneous estimation of the gross N transformation pattern and driving factors in estuarine and intertidal ecosystems based on the optimized 15N tracing model, providing a better understanding of internal mechanisms on the N cycling and strategy for estuarine and coastal N management. [ABSTRACT FROM AUTHOR]

• Gross N transformation rates at the freshwater and low-salinity sites were generally higher compared to high-salinity sites. • Distribution patterns of functional genes were similar to corresponding gross N transformation rates. • TOC, NO 2 – and Fe2+ were the key factors mediating N dynamics in intertidal sediments. Nitrogen (N) transformations in estuarine and coastal ecosystems play a crucial role in the global biogeochemical cycles. However, simultaneous estimation of gross N transformations and the underlying drivers across estuarine and intertidal wetlands remain poorly understood. Here, the spatial changes in gross N transformation rates and related functional gene abundances were explored in varying habitats of the intertidal zone in the Yangtze Estuary via an optimized 15N tracing model and quantitative PCR. The results indicate that the gross N transformation rates changed remarkably in estuarine and intertidal wetlands, with comparatively higher gross N transformation rates at the upper freshwater and low-salinity sites relative to high-salinity sites. Meanwhile, the functional gene abundances (amoB , UreC , hzo , nirS and nrfA) exhibited a similar spatial distribution pattern to corresponding N transformation processes. Sedimentary total organic carbon (TOC), nitrite (NO 2 –), ferrous iron (Fe(II)), and microbial functional gene abundances jointly mediated the gross N transformations. This study carried out the first simultaneous estimation of the gross N transformation pattern and driving factors in estuarine and intertidal ecosystems based on the optimized 15N tracing model, providing a better understanding of internal mechanisms on the N cycling and strategy for estuarine and coastal N management. [ABSTRACT FROM AUTHOR]

For the past few decades, human activities have intensively increased the reactive nitrogen enrichment in China's coastal wetlands. Although denitrification is a critical pathway of nitrogen removal, the understanding of denitrifier community dynamics driving denitrification remains limited in the coastal wetlands. In this study, the diversity, abundance, and community composition of nirS-encoding denitrifiers were analyzed to reveal their variations in China's coastal wetlands. Diverse nirS sequences were obtained and more than 98 % of them shared considerable phylogenetic similarity with sequences obtained from aquatic systems (marine/estuarine/coastal sediments and hypoxia sea water). Clone library analysis revealed that the distribution and composition of nirS-harboring denitrifiers had a significant latitudinal differentiation, but without a seasonal shift. Canonical correspondence analysis showed that the community structure of nirS-encoding denitrifiers was significantly related to temperature and ammonium concentration. The nirS gene abundance ranged from 4.3 × 10 to 3.7 × 10 copies g dry sediment, with a significant spatial heterogeneity. Among all detected environmental factors, temperature was a key factor affecting not only the nirS gene abundance but also the community structure of nirS-type denitrifiers. Overall, this study significantly enhances our understanding of the structure and dynamics of denitrifying communities in the coastal wetlands of China. [ABSTRACT FROM AUTHOR]

Saltmarsh plants are important components of estuarine and coastal wetlands because they regulate ecosystem nitrogen (N) dynamics. However, complex interactions between the N uptake of saltmarsh plants and soil N transformation remain unclear. Here, we conducted a series of 15N tracing experiments with native Phragmites australis , invasive Spartina alterniflora , and bulk sediment without plants to explore the effect of plants on soil N cycling. The results showed that the NH 4 + and NO 3 − uptake rates by the saltmarsh plants were 4.62–5.38 mg N kg⁻1 d⁻1 and 1.29–2.90 mg N kg⁻1 d⁻1, respectively, and the invasive S. alterniflora had a higher N uptake than the native P. australis. The presence of saltmarsh plants promoted N mineralization and dissimilatory NO 3 − reduction to NH 4 +, increasing the available NH 4 + supply for the plants. Conversely, NH 4 + immobilization and autotrophic nitrification rates were drastically reduced in the presence of the saltmarsh plants, indicating that the plants were able to outcompete soil microorganisms in NH 4 + acquisition. Meanwhile, heterotrophic nitrification (organic N oxidation), which accounted for 66–82% of the total nitrification, was stimulated by the saltmarsh plants. Increased heterotrophic nitrification in the saltmarsh plants helped to provide NO 3 − substrates to meet the needs of the soil microorganisms and the plants. The regulatory effect of the invasive S. alterniflora on soil gross N transformation was more pronounced than that of the native P. australis due to the higher N requirements of the former. Microbial carbon sources and energy sources, relevant gene abundances and exoenzyme activities were the main factors by which the saltmarsh plants regulated gross N transformations. Overall, our results show that there are various interactions between soil microorganisms and saltmarsh plants and that S. alterniflora accelerates gross N transformations in the soil to meet its large demand for N. These findings provide valuable insights into the ecological management of invasive plants in estuarine and coastal ecosystems. • Interactions between saltmarsh plants' N uptake and soil N transformations were observed. • N mineralization was stimulated but NH 4 + immobilization was restricted by the presence of saltmarsh plants. • Plants increased heterotrophic nitrification to improve NO 3 − availability when autotrophic nitrification was limited. • The regulation effect of invasive S. alterniflora on gross N transformations was more pronounced than native P. australis. [ABSTRACT FROM AUTHOR]

Specific nitrification inhibitors (NIs) have been widely used to disentangle the contribution of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB) as well as nitrite oxidizers to the nitrification process in specific environments. However, if these previously reported NIs can also be used to evaluate the activity of the newly discovered complete ammonia oxidizers (comammox) Nitrospira , remains understudied. Here we evaluated various NIs for their impact and specificity regarding inhibition of comammox Nitrospira in batch cultures of pure and mixed strains of AOA, AOB and comammox. Using these cultures, we observed that chlorate could specifically inhibit the ammonia oxidation and nitrite oxidation activity of comammox Nitrospira , while it had no effect on the tested AOA and AOB strains. This inhibitory effect of chlorate on comammox Nitrospira was subsequently confirmed based on 13CO 2 -DNA-stable isotope probing (13C-DNA-SIP) analysis. Furthermore, by applying a set of specific NIs, the nitrification and nitrous oxide (N 2 O) production rates of comammox Nitrospira in coastal wetlands were estimated as 17.45 ng N g−1 h−1 (26.9% of the total rate) and 0.0083 μmol−1 L h−1 (28.5%). Altogether, we identified and applied an effective and specific inhibitor of comammox Nitrospira , which allowed quantifying comammox activity in wetlands of the Yangtze Estuary, shedding new light on the ecological roles of comammox bacteria in coastal wetland environments. [Display omitted] • Chlorate is an effective and specific inhibitor of comammox Nitrospira activity. • Comammox Nitrospira significantly contribute to nitrification and N 2 O production in coastal wetlands. • The active subcluster in coastal wetlands was identified as belonging to Clade A comammox Nitrospira. [ABSTRACT FROM AUTHOR]

Anaerobic ammonium oxidation (anammox) as an important nitrogen removal pathway has been investigated in intertidal marshes. However, the rhizosphere-driven anammox process in these ecosystems is largely overlooked so far. In this study, the community dynamics and activities of anammox bacteria in the rhizosphere and non-rhizosphere sediments of salt-marsh grass Spartina alterniflora (a widely distributed plant in estuaries and intertidal ecosystems) were investigated using clone library analysis, quantitative PCR assay, and isotope-tracing technique. Phylogenetic analysis showed that anammox bacterial diversity was higher in the non-rhizosphere sediments ( Scalindua and Kuenenia) compared with the rhizosphere zone (only Scalindua genus). Higher abundance of anammox bacteria was detected in the rhizosphere (6.46 × 10-1.56 × 10 copies g), which was about 1.5-fold higher in comparison with that in the non-rhizosphere zone (4.22 × 10-1.12 × 10 copies g). Nitrogen isotope-tracing experiments indicated that the anammox process in the rhizosphere contributed to 12-14 % N generation with rates of 0.43-1.58 nmol N g h, while anammox activity in the non-rhizosphere zone contributed to only 4-7 % N production with significantly lower activities (0.28-0.83 nmol N g h). Overall, we propose that the rhizosphere microenvironment in intertidal marshes might provide a favorable niche for anammox bacteria and thus plays an important role in nitrogen cycling. [ABSTRACT FROM AUTHOR]

Nitrogen mineralization is a key biogeochemical process transforming organic nitrogen to inorganic nitrogen in estuarine and coastal sediments. Although sedimentary nitrogen mineralization is an important internal driver for aquatic eutrophication, few studies have investigated sedimentary nitrogen mineralization in these environments. Sediment-slurry incubation experiments combined with 15N isotope dilution technique were conducted to quantify the potential rates of nitrogen mineralization in surface sediments of the Yangtze Estuary. The gross nitrogen mineralization (GNM) rates ranged from 0.02 to 5.13 mg N kg-1 d-1 in surface sediments of the study area. The GNM rates were generally higher in summer than in winter, and the relative high rates were detected mainly at sites near the north branch and frontal edge of this estuary. The spatial and temporal distributions of GNM rates were observed to depend largely on temperature, salinity, sedimentary organic carbon and nitrogen contents, and extracellular enzyme (urease and L-glutaminase) activities. The total mineralized nitrogen in the sediments of the Yangtze Estuary was estimated to be about 6.17 × 105 t N yr-1, and approximately 37% of it was retained in the estuary. Assuming the retained mineralized nitrogen is totally released from the sediments into the water column, which contributed 12–15% of total dissolved inorganic nitrogen (DIN) sources in this study area. This result indicated that the mineralization process is a significant internal nitrogen source for the overlying water of the Yangtze Estuary, and thus may contribute to the estuarine and coastal eutrophication. [ABSTRACT FROM AUTHOR]

Over the past several decades, human activities have caused substantial enrichment of reactive nitrogen in China’s coastal wetlands. Although anaerobic ammonium oxidation (anammox), the process of oxidizing ammonium into dinitrogen gas through the reduction of nitrite, is identified as an important process for removing reactive nitrogen, little is known about the dynamics of anammox and its contribution to nitrogen removal in nitrogen-enriched environments. Here, we examine potential rates of anammox and associate them with bacterial diversity and abundance across the coastal wetlands of China using molecular and isotope tracing techniques. High anammox bacterial diversity was detected in China’s coastal wetlands and included Candidatus Scalindua, Kuenenia, Brocadia, and Jettenia. Potential anammox rates were more closely associated with the abundance of anammox bacteria than to their diversity. Among all measured environmental variables, temperature was a key environmental factor, causing a latitudinal distribution of the anammox bacterial community composition, biodiversity and activity along the coastal wetlands of China. Based on nitrogen isotope tracing experiments, anammox was estimated to account for approximately 3.8–10.7% of the total reactive nitrogen removal in the study area. Combined with denitrification, anammox can remove 20.7% of the total external terrigenous inorganic nitrogen annually transported into China’s coastal wetland ecosystems. [ABSTRACT FROM AUTHOR]

• The presence of MPs significantly altered sedimentary nitrogen turnover. • Biodegradable MPs impacted bacterial community more profoundly. • Nitrogen cycling functional microbes had different responses to MPs. • Petroleum-based and biodegradable MPs promoted N 2 O production via varied avenues. • Biodegradable MPs have a greater potential to enhance global warming. Increasing microplastics (MPs) pollution in estuaries profoundly impacts microbial ecosystems and biogeochemical processes. Nitrous oxide (N 2 O), a powerful greenhouse gas, is an important intermediate product of microbial nitrogen cycling. However, how MPs regulate N 2 O production and its pathways remain poorly understood. Here, impacts of traditional petroleum-based and emerging biodegradable MPs on microbial N 2 O production and its pathways were studied through dual-isotope (15N–18O) labeling technique and molecular methods. Results indicated that both traditional petroleum-based and emerging biodegradable MPs promoted sedimentary N 2 O production, whereas pathways varied. Biodegradable polylactic acid (PLA) MPs displayed greater promotion of N 2 O production than petroleum-based MPs, polyvinyl chloride (PVC) and polyethylene (PE), of which PLA promoted through nitrifier nitrification (NN) and heterotrophic denitrification (HD), PE through nitrifier denitrification and HD, and PVC through NN. By combining the analysis of N 2 O production rates with sediment chemical and microbiological properties, we demonstrated that the enrichment of nitrifying and denitrifying bacteria, as well as related functional genes directly and/or indirectly increased N 2 O production primarily by interacting with carbon and nitrogen substrates. Different response of nitrogen cycling microbes to MPs led to the difference in N 2 O increase pathways, of which nitrifying bacteria significantly enriched in all MPs treatments due to the niches provided by MPs. However, part of denitrifying bacteria significantly enriched in treatments containing PLA and PE MPs, which may serve as organic carbon substrates. This work highlights that the presence of MPs can promote sedimentary N 2 O production, and the emerging biodegradable MPs represented by PLA may have a greater potential to enhance estuarine N 2 O emissions and accelerate global climate change. [Display omitted] [ABSTRACT FROM AUTHOR]

Coastal wetlands are hotspots for nitrogen (N) cycling and a significant natural source of the potent greenhouse gas nitrous oxide (N 2 O). Burrowing benthos are known to transform N in intertidal marsh soils, but their contribution to N 2 O emissions and the underlying molecular mechanisms remain unclear. Here, the effects of crab bioturbation on N 2 O emissions in coastal marshes, where Chiromantes dehaani and Helice tridens tientsinensis were the dominant crab species, were investigated in field and indoor experiments. The N 2 O emissions increased significantly in the presence of crabs, being positively correlated with the intensity of crab bioturbation but differing among crab species. Natural-abundance isotope analyses indicated that crab bioturbation greatly promoted the contribution of hydroxylamine oxidation to N 2 O production; nevertheless, bacterial denitrification (including heterotrophic denitrification and nitrifier denitrification) remained the dominant pathway. Molecular analyses suggested that the increased N 2 O emissions in crab-disturbed habitats might be driven by underlying changes to microbial communities, especially by the disproportionate stimulation of nitric oxide reductase-carrying microbes over nitrous oxide reductase-carrying microbes. This study highlights the importance of considering the burrowing activity, density, and species of benthos when evaluating the N cycle in coastal wetlands. [Display omitted] • Crab bioturbation greatly accelerates N 2 O emission in intertidal marsh soils. • Increase of N 2 O emission is closely related to reshaped microbial community by crab. • Different species of crabs exhibit different promoting effects on N 2 O emission. • Crab bioturbation affects N 2 O production pathways based on N 2 O isotopic signatures. • Activity and species of crabs should be considered when restoring coastal wetlands. [ABSTRACT FROM AUTHOR]

Denitrification plays a critical role in nitrogen removal in estuarine and coastal ecosystems. In this study, the community composition, diversity, abundance, and distribution of cytochrome cd1-type nitrite reductase gene ( nirS)-harboring denitrifiers in intertidal sediments of the Yangtze Estuary were analyzed using polymerase chain reaction (PCR)-based clone libraries and quantitative PCR techniques. Clone library analysis showed that the nirS-encoding bacterial biodiversity was significantly higher at the lower salinity sites than at the higher salinity sites. However, there was no significant seasonal difference in the nirS gene diversity between summer and winter. Phylogenetic analysis revealed that the nirS-harboring denitrifier communities at the study area had distinctive spatial heterogeneity along the estuary. At the lower salinity sites, the nirS-harboring bacterial community was co-dominated by clusters III and VII; while at the higher salinity sites, it was dominated by cluster I. Canonical correspondence analysis indicated that the community compositions of nirS-type denitrifiers were significantly correlated with salinity, ammonium, and nitrate. Quantitative PCR results showed that the nirS gene abundance was in the range of 1.01 × 10 to 9.00 × 10 copies per gram dry sediment, without significant seasonal variation. Among all the environmental factors, the nirS gene abundance was only significantly related to the change of salinity. These results can extend our current knowledge about the composition and dynamics of denitrification microbial community in the estuarine ecosystem. [ABSTRACT FROM AUTHOR]

• Dark carbon fixation (DCF) is an important organic C source in intertidal wetlands. • Reductive sulfur in intertidal sediments was a key factor controlling DCF. • cbbM -harboring bacteria were the dominant DCF microbes in intertidal sediments. • DCF may play an important role in linking C-N-S cycles in intertidal wetlands. Dark carbon fixation (DCF) contributes approximately 0.77 Pg C y−1 to oceanic primary production and the global carbon budget. It is estimated that nearly half of the DCF in marine sediments occurs in estuarine and coastal regions, but the environmental factors controlling DCF and the microorganisms responsible for its production remain under exploration. In this study, we investigated DCF rates and the active chemoautotrophic microorganisms in intertidal sediments of the Yangtze Estuary, using 14C-labeling and DNA-stable isotope probing (DNA-SIP) techniques. The measured DCF rates ranged from 0.27 to 3.37 mmol C m−2 day−1 in intertidal surface sediments. The rates of DCF were closely related to sediment sulfide content, demonstrating that the availability of reductive substrates may be the dominant factor controlling DCF in the intertidal sediments. A significant positive correlation was also observed between the DCF rates and abundance of the cbbM gene. DNA-stable isotope probing (DNA-SIP) results further confirmed that cbbM -harboring bacteria, rather than cbbL -harboring bacteria, played a dominant role in DCF in intertidal sediments. Phylogenetic analysis showed that the predominant cbbM -harboring bacteria were affiliated with Burkholderia, including Sulfuricella denitrificans, Sulfuriferula, Acidihalobacter, Thiobacillus , and Sulfurivermis fontis. Moreover, metagenome analyses indicated that most of the potential dark-carbon-fixing bacteria detected in intertidal sediments also harbor genes for sulfur oxidation, denitrification, or dissimilatory nitrate reduction to ammonium (DNRA), indicating that these chemoautotrophic microorganisms may play important roles in coupled carbon, nitrogen, and sulfur cycles. These results shed light on the ecological importance and the underlying mechanisms of the DCF process driven by chemoautotrophic microorganisms in intertidal wetlands. [Display omitted] [ABSTRACT FROM AUTHOR]

Studying nitrous oxide (N 2 O) production and consumption processes along an intertidal elevation gradient can improve the understanding of N 2 O dynamics among coastal wetlands. A natural-abundance isotope technique was applied to characterize the processes responsible for N 2 O emission in high, middle and low intertidal zones in the Yangtze Estuary. The results showed that N 2 O emission rates in high tidal zones (0.84 ± 0.35 nmol g−1 h−1) were significantly higher than those in middle (0.21 ± 0.04 nmol g−1 h−1) and low tidal zones (0.26 ± 0.05 nmol g−1 h−1). Gross N 2 O production and consumption rates were greater in high and low tidal zones than in middle tidal zones, whereas N 2 O consumption proportions generally increased from high to low tidal zones. N 2 O consumption was quite pronounced, implying that N 2 O emission in estuarine wetlands accounts for only a small fraction of the total production. Higher degrees of N 2 O consumption were the pivotal driver of less N 2 O emission in low tidal zones. Bacterial denitrification (>84%) was the dominant pathway, although hydroxylamine (NH 2 OH) oxidation/fungal denitrification contributed substantially to N 2 O production in high tidal flats. The contribution to N 2 O production exhibited a decrease in NH 2 OH oxidation/fungal denitrification and an increase in bacterial denitrification with decreasing elevation. Changes in N 2 O dynamics along the elevation gradient were affected by carbon and nitrogen substrate availabilities as well as the redox environments. Overall, our findings highlight the importance of N 2 O consumption in controlling N 2 O emission in intertidal wetlands, especially with higher inundation frequencies and durations. • N2O production and consumption processes varied along the intertidal elevation. • N2O consumption played a critical role in controlling N2O emission. • NH2OH oxidation/fungal denitrification was also important in N2O source in high tidal flats. • N2O dynamics were affected by substrate availability and redox environment. [ABSTRACT FROM AUTHOR]

Ammonia oxidation plays a pivotal role in the cycling and removal of nitrogen in aquatic sediments. Certain bacterial groups and a novel group of archaea, which is affiliated with the novel phylum Thaumarchaeota, can perform this initial nitrification step. We examined the diversity and abundance of ammonia-oxidizing β-Proteobacteria (β-AOB) and ammonia-oxidizing archaea (AOA) in the sediments of Chongming eastern tidal flat using the ammonia monooxygenase-α subunit ( amoA) gene as functional markers. Clone library analysis showed that AOA had a higher diversity of amoA gene than β-AOB. The β-Proteobacterial amoA community composition correlated significantly with water soluble salts in the sediments, whereas the archaeal amoA community composition was correlated more with nitrate concentrations. Quantitative PCR (qPCR) results indicated that the abundance of β-AOB amoA gene (9.11 × 10-6.47 × 10 copies g sediment) was always greater than that of AOA amoA gene (7.98 × 10-3.51 × 10 copies g sediment) in all the samples analyzed in this study. The β-Proteobacterial amoA gene abundance was closely related to organic carbon, while no significant correlations were observed between archaeal amoA gene abundance and the environmental factors. Potential nitrification rates were significantly greater in summer than in winter and correlated strongly with the abundance of amoA genes. Additionally, a greater contribution of single amoA gene to potential nitrification occurred in summer (1.03-5.39 pmol N copy day) compared with winter (0.16-0.38 pmol N copy day), suggesting a higher activity of ammonia-oxidizing prokaryotes in warm seasons. [ABSTRACT FROM AUTHOR]

Human activity is suggested to increase polycyclic aromatic hydrocarbons (PAHs) pollution and also cause PAHs' sources complex in estuarine environments. However, the human impacts and source apportionment of PAHs in estuarine sediments at a continental scale remains poorly understood. In this study, we investigated geographical distribution of PAHs and used the compound-specific carbon isotope approach to characterize the sources of PAHs in the sediments of estuaries along the latitudinal gradient over China. We also used human population and economic size to characterize the human impacts on PAHs pollution in the estuaries. The concentrations of total PAHs (Σ 16 PAH) in wet and dry seasons ranged from 60.9 to 330.7 ng g−1 and from 103.9 to 620.6 ng g−1, respectively, across the estuaries. At the continental scale, the concentrations of PAHs were significantly higher in dry than in wet seasons. The proportions of low molecular weight (LMW, 2–3 ring PAHs), middle molecular weight (MMW, 4 ring PAH) and high molecular weight (HMW, 5–6 ring PAHs) of PAHs varied largely across the estuaries, with being in a range of 26.4–48.5%, 17.2–34.1%, 25.3–46.8% in wet season and in a range of 24.0–58.4%, 18.4–52.4%, 21.8–48.6% in dry season. The concentrations of PAHs were found to be significantly correlated with per capita GDP throughout the studied estuaries. The δ 13C of individual PAH ranged from −26 to −32‰ and from −24 to −29‰ in dry and wet seasons, respectively. The main sources of PAHs indicated by the δ 13C across the estuaries were coal-processing and biomass combustion. These results suggest that the increasing human activities intensity can increase the PAHs pollution in sediments of the estuaries. Unlabelled Image • The concentrations of PAHs in dry season are higher in wet season. • BC is an important factor controls pyrogenic PAHs. • δ 13C of individual PAHs is a powerful tool to identify certain sources. • Human activities are main factors of PAHs pollution in Chinese estuarine sediments. [ABSTRACT FROM AUTHOR]

• NO2−/NO3−-dependent anaerobic CH4 oxidation (n-DAMO) microbes are active in estuarine and intertidal wetlands • n-DAMO bacteria contribute more to CH4 oxidation than n-DAMO archaea • Abundance and role of n-DAMO microbes vary across estuarine habitats with different salinities • n-DAMO microbial dynamics are associated closely with sediment characteristics Nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) is a crucial link between carbon and nitrogen cycles in estuarine and coastal ecosystems. However, the factors that affect the heterogeneous variability in n-DAMO microbial abundance and activity across estuarine and intertidal wetlands remain unclear. This study examined the spatiotemporal variations in n-DAMO microbial abundance and associated activity in different estuarine and intertidal habitats via quantitative PCR and 13C stable isotope experiments. The results showed that Candidatus ' Methylomirabilis oxyfera ' (M. oxyfera)-like DAMO bacteria and Candidatus ' Methanoperedens nitroreducens ' (M. nitroreducens)-like DAMO archaea cooccurred in estuarine and intertidal wetlands, with a relatively higher abundance of the M. oxyfera -like bacterial pmoA gene (4.0 × 106-7.6 × 107 copies g−1 dry sediment) than the M. nitroreducens -like archaeal mcrA gene (4.5 × 105-9.4 × 107 copies g−1 dry sediment). The abundance of the M. oxyfera -like bacterial pmoA gene was closely associated with sediment pH and ammonium (P <0.05), while no significant relationship was detected between M. nitroreducens -like archaeal mcrA gene abundance and the measured environmental parameters (P >0.05). High n-DAMO microbial activity was observed, which varied between 0.2 and 84.3 nmol 13CO 2 g−1 dry sediment day−1 for nitrite-DAMO bacteria and between 0.4 and 32.6 nmol 13CO 2 g−1 dry sediment day−1 for nitrate-DAMO archaea. The total n-DAMO potential tended to be higher in the warm season and in the upstream freshwater and low-salinity estuarine habitats and was significantly related to sediment pH, total organic carbon, Fe(II), and Fe(III) contents (P <0.05). In addition to acting as an important methane (CH 4) sink, n-DAMO microbes had the potential to consume a substantial amount of reactive N in estuarine and intertidal environments, with estimated nitrogen elimination rates of 0.5-224.7 nmol N g−1 dry sediment day−1. Overall, our investigation reveals the distribution pattern and controlling factors of n-DAMO bioprocesses in estuarine and intertidal marshes and gains a better understanding of the coupling mechanisms between carbon and nitrogen cycles. Image, graphical abstract [ABSTRACT FROM AUTHOR]