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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]

Abstract Sediment nitrogen fixation and associated functional gene in the East China Sea were investigated using nitrogen-isotope tracing and molecular techniques. Potential rates of nitrogen fixation were detected, with values of 0.06–5.51 nmol N g−1 h−1. Abundance of functional gene (nifH) ranged from 0.36 × 106 to 5.39 × 107 copies g−1. Nitrogen fixation rates were not related to the abundance of nifH gene but to temperature, salinity, sulfide, iron and C/N, indicating that the sediment properties rather than microbial abundance dominated the nitrogen fixation. It is also estimated that sediment nitrogen fixation annually contributed about 3.43 × 105 to 3.10 × 107 tons nitrogen to the East China Sea, which accounted for 8.2–22.6% of the total inorganic nitrogen input. Overall, this study highlights the importance of benthic nitrogen fixation in controlling nitrogen budget in the East China Sea and improves our knowledge on nitrogen cycling in the coastal marine environments. Highlights • Occurrence of benthic nitrogen fixation is detected in the East China Sea sediments. • Benthic nitrogen fixation is associated closely with sediment properties. • Benthic nitrogen fixation plays an important role in controlling nitrogen budget. [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]

Nitrate overload is an important driver of water pollution in most estuarine and coastal ecosystems, and thus nitrate reduction processes have attracted considerable attention. Antibiotics contamination is also an emerging environmental problem in estuarine and coastal regions as a result of growing production and usage of antibiotics. However, the effects of antibiotics on nitrate reduction remain unclear in these aquatic ecosystems. In this study, continuous-flow experiments were conducted to examine the effects of thiamphenicol (TAP, a common chloramphenicol antibiotic) on nitrate reduction and greenhouse gas N 2 O release. Functional genes involved in nitrogen transformation were also quantified to explore the microbial mechanisms of the TAP influence. Production of N 2 were observed to be inhibited by TAP treatment, which implied the inhibition effect of TAP on nitrate reduction processes. As intermediate products of nitrogen transformation processes, nitrite and N 2 O were observed to accumulate during the incubation. Different TAP inhibition effects on related functional genes may be the microbial mechanism for the changes of nutrient fluxes, N 2 fluxes and N 2 O release rates. These results indicate that the antibiotics residues in estuarine and coastal ecosystems may contribute to nitrate retention and N 2 O release, which could be a major factor responsible for eutrophication and greenhouse effects. [ABSTRACT FROM AUTHOR]

Estuarine environments faced with contaminations from coastal zones and the inland are vital sinks of antibiotic resistance genes (ARGs). However, little is known about the temporal-spatial pattern of ARGs and its predominant constraints in estuarine environments. Here, we leveraged metagenomics to investigate ARG profiles from 16 China's estuaries across 6 climate zones in dry and wet seasons, and disentangled their relationships with environmental constraints. Our results revealed that ARG abundance, richness, and diversity in dry season were higher than those in wet season, and ARG abundance exhibited an increasing trend with latitude. The prevalence of ARGs was significantly driven by human activities, mobile gene elements, microbial communities, antibiotic residuals, physicochemical properties, and climatic variables. Among which, climatic variables and human activities ranked the most important factors, contributing 44% and 36% of the total variance of observed ARGs, respectively. The most important climatic variable shaping ARGs is temperature, where increasing temperature is associated with decreased ARGs. Our results highlight that the prevalence of ARGs in estuarine environments would be co-driven by anthropogenic activities and climate, and suggest the dynamics of ARGs under future changing climate and socioeconomic development. [Display omitted] • Metagenomics is used to explore ARG profiles in China's estuaries. • The abundance, richness, and diversity in dry season exceeds those in wet season. • The leading driver of ARGs on large scale is climate and human activities. • ARG abundance exhibits a significant upward with latitude. • Climate warming would result in decreased ARGs. [ABSTRACT FROM AUTHOR]

Coupling of nitrogen removal processes with nitrification (NR n) are vital synergistic nitrogen elimination mechanisms in aquatic environments. However, the effects of antibiotics on NR n are not well known. In the present work, 20-day continuous-flow experiments combined with 15N tracing techniques and quantitative PCR were performed to simulate the impact of sulfamethoxazole (SMX, a sulfonamide antibiotic) with near in situ concentration on NR n processes in sediments of Yangtze Estuary. Results showed that SMX with near in situ concentration significantly decreased NR n , NR w (uncoupling of nitrogen removal processes with nitrification) and actual nitrogen removal rates via inhibiting nitrogen transformation functional genes (AOB, narG , nirS , nosZ) and anammox 16S rRNA gene, while the coupling links between nitrification and nitrogen removal processes were not broken by the exposure. The proportion of NR n in total nitrogen removal processes decreased by approximately 10% with SMX addition, due to the different inhibition on AOB, denitrifying genes and anammox 16S rRNA gene. N 2 O production and nitrite accumulation remarkably increased with SMX addition under simultaneous nitrification and denitrification, and they strongly correlated with each other. The more severely inhibition on nirS gene (13.6–19.8%) than Nitrospira nxrB gene (0.3–8.2%) revealed that the increased nitrite accumulation with SMX addition mainly occurred in heterotrophic denitrification, suggesting that the increased N 2 O production was dominated by the heterotrophic nitrite reduction. Moreover, we estimated that the ratio of external inorganic N eliminated by actual nitrogen removal can upgrade to 6.4–7.4% under circumstances of no inhibition by SMX. This study revealed the effects of SMX with near in situ concentration on NR n processes and illustrated the microbial mechanism on functional genes level. Our results highlighted the inhibitory effects of SMX on NR n may contribute to reactive N retention and N 2 O production in estuarine and coastal ecosystems. Image 1 • SMX inhibits coupled, uncoupled and actual nitrogen removal rates. • SMX decreased the ratio of coupled nitrogen removal in total nitrogen removal. • Nitrification, denitrification and anammox functional genes were affected. • SMX increased N 2 O emission due to the increased heterotrophic nitrite reduction. SMX inhibited NR n rates and decreased NR n ratio in total nitrogen removal via suppressing AOB, denitrifying genes and anammox 16S rRNA gene. [ABSTRACT FROM AUTHOR]

Denitrification is an important pathway for reactive nitrogen removal from aquatic ecosystems. In this study, the biodiversity, abundance, and activity of cytochrome cd 1 -type nitrate reductase gene (nirS)-harboring denitrifiers in the sediments of the Indus River Estuary were examined by molecular and isotope-tracing techniques. Results showed that the nirS -harboring denitrifier communities showed significant geographical variations along the estuarine salinity gradient. Real-time quantitative PCR showed that the abundance of nirS -harboring denitrifiers ranged from 5.3 × 106 to 2.5 × 108 copies g−1, without significant spatiotemporal variation. The potential rates of denitrification varied from 0.01 to 6.27 μmol N kg−1 h−1 and correlated significantly to TOC and Fe(II) (P < 0.05). On the basis of 15N isotope-tracing experiments, the denitrification process contributed 18.4–99.4% to the total nitrogen loss in the sediments of the Indus River Estuary. This study provides novel insights into the microbial mechanism of nitrogen removal process in estuarine ecosystems. Unlabelled Image • nirS -type denitrifier community had significant spatial variation along the estuary. • Abundance of nirS -type denitrifier ranged from 5.3 × 106 to 2.5 × 108 copies g−1. • The potential rates of denitrification varied from 0.01 to 6.27 μmol N kg−1 h−1. • Denitrification contributed up to 99% to total N loss in the Indus River Estuary. [ABSTRACT FROM AUTHOR]

Denitrifying anaerobic methane oxidation (DAMO) and associated microbial diversity and abundance in the marsh sediments of Chongming eastern intertidal flat, the Yangtze Estuary, were investigated using carbon-isotope tracing and molecular techniques. Co-existence of nitrate-DAMO archaea and nitrite-DAMO bacteria was evidenced, with higher biodiversity of DAMO archaea than DAMO bacteria. Abundance of DAMO archaeal mcrA gene and DAMO bacterial pmoA gene ranged from 4.2 × 103 to 3.9 × 1010 copies g−1 and from 4.5 × 105 to 6.4 × 106 copies g−1, respectively. High DAMO potential was detected, ranging from 0.6 to 46.7 nmol 13CO 2 g−1 day−1 for nitrate-DAMO and from 1.3 to 39.9 nmol 13CO 2 g−1 day−1 for nitrite-DAMO. In addition to playing an important role as a CH 4 sink, DAMO bacteria also removed a substantial amount of reactive nitrogen (29.4 nmol N g−1 day−1) from the intertidal sediments. Overall, these results indicate the importance of DAMO bioprocess as methane and nitrate sinks in intertidal marshes. Image 1 • DAMO played an important role in CH 4 sink and N removal in intertidal marshes. • DAMO archaea and DAMO bacteria were both active in estuarine intertidal sediments. • Intertidal habitat differences affect the community and role of DAMO microbes. [ABSTRACT FROM AUTHOR]

Anaerobic ammonium oxidation (anammox) is recognized as an important bioprocess for nitrogen removal, yet little is known about the associated microbial communities in urban river networks which are intensively disturbed by human activity. In the present study, we investigated the community composition and abundance of anammox bacteria in the urban river network of Shanghai, and explored their potential correlations with nitrogen removal activities and the environmental parameters. High biodiversity of anammox bacteria was detected in the sediment of urban river networks, including Candidatus Brocadia, Scalindua, Jettenia, and Kuenenia. Anammox bacterial abundance ranged from 3.7 × 106 to 3.9 × 107 copies g−1 dry sediment based on 16S rRNA gene, which was strongly correlated to the metabolic activity of anammox bacteria (P < 0.01). A strong linkage between anammox bacteria and denitrifiers was detected (P < 0.05), implying a potential metabolic interdependence between these two nitrogen-removing microbes was existed in urban river networks. Sediment ammonium (NH 4 +) made a significant contribution to the anammox bacterial community-environment relationship, while anammox bacterial abundance related significantly with sediment total organic carbon (TOC) and silt contents (P < 0.05). However, no statistically significant correlation was observed between cell-specific anammox rate and the measured environmental factors (P > 0.05). In general, the community composition and abundance of anammox bacteria in different hierarchies of the river network was homogeneous, without significant spatial variations (P > 0.05). These results provided an opportunity to further understand the microbial mechanism of nitrogen removal bioprocesses in urban river networks. Image 1 • High biodiversity of anammox bacteria was detected in the Shanghai river network. • Anammox bacteria played an important role in N removal in urban river environment. • Anammox bacteria did not vary significantly among different urban river hierarchies. The main finding of the work: High biodiversity of anammox bacteria was detected in the Shanghai river network, which also played an important role in N removal in this unique ecosystem. [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]

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]

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]

• 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]

• 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]

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]

• 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]

• 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]

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]

• Nitric oxide reductase is largely responsible for the enzymatic production of N 2 O • The absence of NH 2 OH/NO transformation enzymes leads to the buildup of reactive N-compounds. • The comammox bacterium Nitrospira inopinata exhibits low yield NO y emission. Nitrous oxide (N 2 O) and NO y (nitrous acid (HONO) + nitric oxide (NO) + nitrogen dioxide (NO 2)) are released as byproducts or obligate intermediates during aerobic ammonia oxidation, and further influence global warming and atmospheric chemistry. The ammonia oxidation process is catalyzed by groups of globally distributed ammonia-oxidizing microorganisms, which are playing a major role in atmospheric N 2 O and NO y emissions. Yet, little is known about HONO and NO 2 production by the recently discovered, widely distributed complete ammonia oxidizers (comammox), able to individually perform the oxidation of ammonia to nitrate via nitrite. Here, we examined the N 2 O and NO y production patterns by comammox bacterium Nitrospira inopinata during aerobic ammonia oxidation, in comparison to its canonical ammonia-converting counterparts, representatives of the ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our findings, i) show low yield NO y production by the comammox bacterium compared to AOB; ii) highlight the role of the NO reductase in the biological formation of N 2 O based on results from NH 2 OH inhibition assays and its stimulation during archaeal and bacterial ammonia oxidations; iii) postulate that the lack of hydroxylamine (NH 2 OH) and NO transformation enzymatic activities may lead to a buildup of NH 2 OH/NO which can abiotically react to N 2 O ; iv) collectively confirm restrained N 2 O and NO y emission by comammox bacteria, an unneglectable consortium of microbes in global atmospheric emission of reactive nitrogen gases. Image, graphical abstract [ABSTRACT FROM AUTHOR]

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