Hotspot of dissimilatory nitrate reduction to ammonium (DNRA) process in freshwater sediments of riparian zones

Characterizing the impact of reservoir storage and discharge on nitrogen dynamics in an upstream wetland using a δ15N and δ18O dual-isotope approach

The identification of nitrate sources in reservoir water is important for watershed-scale surface pollution management. Significant fluctuations in river water levels arising from reservoir storage and discharge influence nitrate sources and transport processes. The Sanmenxia Reservoir, in the middle reaches of the Yellow River in China, undergoes significant water level changes (290-316 m), altering the composition of the nitrogen sources. This study employed a δ15N and δ18O dual-isotope method and MixSIAR modeling to quantify the contributions of nitrate sources. This reveals the impact of reservoir water impoundment and discharge on nitrogen dynamics in the upstream region of the wetland and the model sensitivity for each nitrate source. The results showed that the average concentrations of nitrate‑nitrogen (NO- 3-N) were elevated during the impoundment period compared to the discharge period. Nitrogen sources exhibited varying proportions in surface water, groundwater, and soil water during both the impoundment and discharge periods. The predominant sources include manure and sewage (MS), with a maximum proportion of 57.4 % in surface water. Soil nitrogen (SN) accounted for 25.8 % of groundwater nitrogen and 32.1 % of soil water nitrogen during the impoundment period, whereas, during the discharge period, soil nitrogen made up 41.4 % of surface water nitrogen, manure and sewage contributed 44.8 % of groundwater nitrogen, and manure and sewage dominated with 56.7 % of soil water nitrogen. Sensitivity analysis of the MixSIAR model revealed that the isotopic composition of the manure and sewage primary source most significantly influenced the apportionment results of the riverine nitrate source. Reservoir discharge facilitates the dissimilatory nitrate reduction to ammonium (DNRA). The migration of NO- 3 from surface water to soil water and groundwater occurred from the impoundment period to the discharge period.

Toward nitrogen recovery: Co-cultivation of microalgae and bacteria enhances the production of high-value nitrogen-rich cyanophycin

The algal-bacterial wastewater treatment process has been proven to be highly efficient in removing nutrients and recovering nitrogen (N). However, the recovery of the valuable N-rich biopolymer, cyanophycin, remains limited. This research explored the synthesis mechanism and recovery potential of cyanophycin within two algal-bacterial symbiotic reactors. The findings reveal that the synergy between algae and bacteria enhances the removal of N and phosphorus. The crude contents of cyanophycin in the algal-bacterial consortia reached 115 and 124 mg/g of mixed liquor suspended solids (MLSS), respectively, showing an increase of 11.7 %-20.4 % (p < 0.001) compared with conventional activated sludge. Among the 170 metagenome-assembled genomes (MAGs) analyzed, 50 were capable of synthesizing cyanophycin, indicating that cyanophycin producers are common in algal-bacterial systems. The compositions of cyanophycin producers in the two algal-bacterial reactors were affected by different lighting initiation time. The study identified two intracellular synthesis pathways for cyanophycin. Approximately 36 MAGs can synthesize cyanophycin de novo using ammonium and glucose, while the remaining 14 MAGs require exogenous arginine for production. Notably, several MAGs with high abundance are capable of assimilating both nitrate and ammonium into cyanophycin, demonstrating a robust N utilization capability. This research also marks the first identification of potential horizontal gene transfer of the cyanophycin synthase encoding gene (cphA) within the wastewater microbial community. This suggests that the spread of cphA could expand the population of cyanophycin producers. The study offers new insights into recycling the high-value N-rich biopolymer cyanophycin, contributing to the advancement of wastewater resource utilization.

Community coalescence under variable hydrochemical conditions of the Chesapeake Bay shaped bacterial diversity and functional traits

Community coalescence related to bacterial mixing events regulates community characteristics and affects the health of estuary ecosystems. At present, bacterial coalescence and its driving factors are still unclear. The present study used a dataset from the Chesapeake Bay (2017) to address how bacterial community coalescence in response to variable hydrochemistry in estuarine ecosystems. We determined that variable hydrochemistry promoted the deterioration of water quality. Temperature, orthophosphate, dissolved oxygen, chlorophyll a, Secchi disk depth, and dissolved organic phosphorus were the key environmental factors driving community coalescence. Bacteria with high tolerance to environmental change were the primary taxa accumulated in community coalescence, and the significance of deterministic processes to communities was revealed. Community coalescence was significantly correlated with the pathways of metabolism and organismal systems, and promoted the co-occurrence of antibiotic resistance and virulence factor genes. Briefly, community coalescence under variable hydrochemical conditions shaped bacterial diversity and functional traits, to optimise strategies for energy acquisition and lay the foundation for alleviating environmental pressures. However, potential pathogenic bacteria in community coalescence may be harmful to human health and environmental safety. The present study provides a scientific reference for ecological management of estuaries.

Response of microbial communities to exogenous nitrate nitrogen input in black and odorous sediment

Since nitrate nitrogen (NO3--N) input has proved an effective approach for the treatment of black and odorous river waterbody, it was controversial whether the total nitrogen concentration standard should be raised when the effluent from the sewage treatment plant is discharged into the polluted river. To reveal the effect of exogenous nitrate (NO3--N) on black odorous waterbody, sediments with different features from contaminated rivers were collected, and the changes of physical and chemical characteristics and microbial community structure in sediments before and after the addition of exogenous NO3--N were investigated. The results showed that after the input of NO3--N, reducing substances such as acid volatile sulfide (AVS) in the sediment decreased by 80 % on average, ferrous (Fe2+) decreased by 50 %, yet the changing trend of ammonia nitrogen (NH4+-N) in some sediment samples increased while others decreased. High-throughput sequencing results showed that the abundance of Thiobacillus at most sites increased significantly, becoming the dominant genus in the sediment, and the abundance of functional genes in the metabolome increased, such as soxA, soxX, soxY, soxZ. Network analysis showed that sediment microorganisms evolved from a single sulfur oxidation ecological function to diverse ecological functions, such as nitrogen cycle nirB, nirD, nirK, nosZ, and aerobic decomposition. In summary, inputting an appropriate amount of exogenous NO3--N is beneficial for restoring and maintaining the oxidation states of river sediment ecosystems.

The function and keystone microbiota in typical habitats under the influence of anthropogenic activities in Baiyangdian Lake

Microbe is an essential driver in regulating the biochemical cycles of carbon, nitrogen, and sulfur. In freshwater lake, microbial communities and functions are influenced by multiple factors, especially anthropogenic activities. Baiyangdian Lake consisted of various habitats, and was frequently interfered with human activities. In this study, 16 S rRNA sequencing and metagenomic sequencing were performed to characterize the microbial communities, determine keystone taxa and reveal dominated metabolic functions in typical habitats in Baiyangdian Lake. The results showed that the diversity of microbial community was significantly higher in sediment compared with corresponding water sample. Microbial community showed strong spatial heterogeneity in sediment, and temporal heterogeneity in water. As for different habitats, significantly higher alpha diversity was observed in ecotone, where the interference of human activities was relatively weak. The shared OTUs were distinguished from the keystone taxa, which indicated the uniqueness of microbiota in different ecological habitat. Moreover, the interactions of microbial in ecological restoration area (abandoned fish pond) were relatively simple, suggesting that this ecosystem was relatively fragile compared with others. Based on the metagenomic sequencing, we recognized that the canal, open water, and abandoned fish pond were beneficial for methanogenic and the ecotone might be a hot zone for the oxidation of methane. Notably, most of the microbes that participated in these predominant metabolisms were unclassified, which indicated the hug potential for exploring functional microorganisms in Baiyangdian Lake. This study provided a comprehensive understanding of the ecology characteristics of microbiota in habitats undergoing various human interference in Baiyangdian Lake.

Insights into biogeochemistry and hot spots distribution characteristics of redox-sensitive elements in the hyporheic zone: Transformation mechanisms and contributing factors

Biogeochemical hot spots play a crucial role in the cycling and transport of redox-sensitive elements (RSEs) in the hyporheic zone (HZ). However, the transformation mechanisms of RSEs and patterns of RSEs hot spots in the HZ remain poorly understood. In this study, hydrochemistry and multi-isotope (N/C/S/O) datasets were collected to investigate the transformation mechanisms of RSEs, and explore the distribution characteristics of RSEs transformation hot spots. The results showed that spatial variability in key drivers was evident, while temporal change in RSEs concentration was not significant, except for dissolved organic carbon. Bacterial sulfate reduction (BSR) was the primary biogeochemical process for sulfate and occurred throughout the area. Ammonium enrichment was mainly caused by the mineralization of nitrogenous organic matter and anthropogenic inputs, with adsorption serving as the primary attenuation mechanism. Carbon dynamics were influenced by various biogeochemical processes, with dissolved organic carbon mainly derived from C3 plants and dissolved inorganic carbon from weathering of carbonate rocks and decomposition of organic matter. The peak contribution of dissolved organic carbon decomposition to the DIC pool was 46.44 %. The concentration thresholds for the ammonium enrichment and BSR hot spots were identified as 1.5 mg/L and 8.84 mg/L, respectively. The distribution pattern of RSEs hot spots was closely related to the hydrogeological conditions. Our findings reveal the complex evolution mechanisms and hot spots distribution characteristics of RSEs in the HZ, providing a basis for the safe utilization and protection of groundwater resources.

Review of the mechanisms involved in dissimilatory nitrate reduction to ammonium and the efficacies of these mechanisms in the environment

Dissimilatory nitrate reduction to ammonium (DNRA) is currently of great interest because it is an important method for recovering nitrogen from wastewater and offers many advantages, over other methods. A full understanding of DNRA requires the mechanisms, pathways, and functional microorganisms involved to be identified. The roles these pathways play and the effectiveness of DNRA in the environment are not well understood. The objectives of this review are to describe our current understanding of the molecular mechanisms and pathways involved in DNRA from the substrate transfer perspective and to summarize the effects of DNRA in the environment. First, the mechanisms and pathways involved in DNRA are described in detail. Second, our understanding of DNRA by actinomycetes is reviewed and gaps in our understanding are identified. Finally, the effects of DNRA in the environment are assessed. This review will help in the development of future research into DNRA to promote the use of DNRA to treat wastewater and recover nitrogen.

Nitrate input inhibited the biodegradation of erythromycin through affecting bacterial network modules and keystone species in lake sediments

Antibiotic contamination and excessive nitrate loads are generally concurrent in aquatic ecosystems. However, little is known about the effects of nitrate input on the biodegradation of antibiotics. In this study, the effects of nitrate input on microbial degradation of erythromycin, a typical macrolide antibiotic widely detected in lake sediments, were investigated. The results showed that the nitrate input significantly inhibited the erythromycin removal and such an inhibitory effect was strengthened with the increased input dosages. Nitrate input significantly increased sediment nitrite concentration, indicating enhanced denitrification under high nitrate pressure. Bacterial network module and keystone species analysis showed that nitrate input enriched the keystone species involved in denitrification (e.g., Simplicispira and Denitratisoma). In contrast, some potential erythromycin-degrading bacteria (e.g., Desulfatiglandales, Pseudomonadales, Nitrospira) were inhibited by nitrate input. The variations in dominant bacterial groups implied competition between denitrification and erythromycin degradation in response to nitrate input. Based on the partial least squares path modeling analysis, keystone species (total effect: 0.419) and bacterial module (total effect: 0.403) showed strong association with erythromycin removal percentage. This indicated that the inhibitory effect of nitrate input on erythromycin degradation was mainly explained by bacterial network modules and keystone species. These findings will help us to assess the bioremediation potential of antibiotic-contaminated sediments suffering from excessive nitrogen discharge concurrently.

Denitrification dominates dissimilatory nitrate reduction across global natural ecosystems

Denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA) are three competing processes of microbial nitrate reduction that determine the degree of ecosystem nitrogen (N) loss versus recycling. However, the global patterns and drivers of relative contributions of these N cycling processes to soil or sediment nitrate reduction remain unknown, limiting our understanding of the global N balance and management. Here, we compiled a global dataset of 1570 observations from a wide range of terrestrial and aquatic ecosystems. We found that denitrification contributed up to 66.1% of total nitrate reduction globally, being significantly greater in estuarine and coastal ecosystems. Anammox and DNRA could account for 12.7% and 21.2% of total nitrate reduction, respectively. The contribution of denitrification to nitrate reduction increased with longitude, while the contribution of anammox and DNRA decreased. The local environmental factors controlling the relative contributions of the three N cycling processes to nitrate reduction included the concentrations of soil organic carbon, ammonium, nitrate, and ferrous iron. Our results underline the dominant role of denitrification over anammox and DNRA in ecosystem nitrate transformation, which is crucial to improving the current global soil N cycle model and achieving sustainable N management.

Non-rhizosphere reinforces the contributions of Feammox and anammox to nitrogen loss than rhizosphere in riparian zones

The emergence of anaerobic ammonium oxidation (anammox) coupled to iron reduction (named Feammox) refreshes the microbial pathways for nitrogen (N) loss. However, the ecological role of Feammox, compared with conventional denitrification and anammox, in microbial N attenuation in ecosystems remains unclear. Here, the specific contribution of Feammox to N loss and the underlying microbiome interactive characteristics in a riparian ecosystem were investigated through 15N isotope tracing and molecular analysis. Feammox was highlighted in the riparian interface soils and maximally contributed 14.2% of N loss. Denitrification remained the dominant contributor to N loss (68.0%-95.3%), followed by anammox (5.7%-19.1%) and Feammox (0-14.2%). The rates of Feammox and anammox significantly decreased in rhizosphere soils (0.15 ± 0.08 μg N g-1 d -1 for Feammox, 0.80 ± 0.39 μg N g-1 d -1 for anammox) compared with those in non-rhizosphere soils; however, the activities of denitrification remarkably increased in the rhizosphere (13.17 ± 3.71 μg N g-1 d -1). In rhizosphere soils, the competition between bioavailable organic matter (e.g., amino acids and carbohydrates) and ammonium for electron acceptor [i.e., Fe(III)] was the vital inducement for restricted Feammox, while the nitrite consumption boosted by heterotrophic denitrifiers was responsible for weakened anammox. The functional gene of autotrophic Acidimicrobiaceae bacterium A6, instead of heterotrophic Geobacteraceae spp., was significantly positively correlated with Feammox activity. Rare iron-reducing bacteria showed higher node degrees in the non-rhizosphere network than in the rhizosphere network. A syntrophic relationship was found between iron-reducing bacteria (e.g., Anaeromyxobacter, Geobacter) and iron-oxidizing bacteria (e.g., Sideroxydans) in the non-rhizosphere network and facilitated the Feammox pathway. This study provides an in-depth exploration of microbial driven N loss in a riparian ecosystem and introduces new insights into riparian management practices toward high-efficient N pollution alleviation.

Deterministic factors modulating assembly of groundwater microbial community in a nitrogen-contaminated and hydraulically-connected river-lake-floodplain ecosystem

The river-lake-floodplain system (RLFS) undergoes intensive surface-groundwater mass and energy exchanges. Some freshwater lakes are groundwater flow-through systems, serving as sinks for nitrogen (N) entering the lake. Despite the threat of cross-nitrogen contamination, the assembly of the microbial communities in the RLFS was poorly understood. Herein, the distribution, co-occurrence, and assembly pattern of microbial community were investigated in a nitrogen-contaminated and hydraulically-connected RLFS. The results showed that nitrate was widely distributed with greater accumulation on the south than on the north side, and ammonia was accumulated in the groundwater discharge area (estuary and lakeshore). The heterotrophic nitrifying bacteria and aerobic denitrifying bacteria were distributed across the entire area. In estuary and lakeshore with low levels of oxidation-reduction potential (ORP) and high levels of total organic carbon (TOC) and ammonia, dissimilatory nitrate reduction to ammonium (DNRA) bacteria were enriched. The bacterial community had close cooperative relationships, and keystone taxa harbored nitrate reduction potentials. Combined with multivariable statistics and self-organizing map (SOM) results, ammonia, TOC, and ORP acted as drivers in the spatial evolution of the bacterial community, coincidence with the predominant deterministic processes and unique niche breadth for microbial assembly. This study provides novel insight into the traits and assembly of bacterial communities and potential nitrogen cycling capacities in RLFS groundwater.

Seasonal variations of biofilm C, N and S cycling genes in a pilot-scale chlorinated drinking water distribution system

Biofilms in drinking water distribution systems (DWDS) host diverse microorganisms. However, the functional attributes of DWDS biofilms and their associations with seasonality remain unclear. This study aims to characterize variations in the microbial metabolic traits of DWDS biofilms collected during different seasons, using a pilot-scale DWDS in dark under plug-flow conditions during one-year operation period. Network analysis was used to predict the functional gene hosts. The overall functional attributes determined by shotgun metagenomics exhibited significant differences among seasons. Genes associated with aromatic metabolism, fatty acid biosynthesis and degradation, and capsular extracellular polymeric substance (EPS) were significantly upregulated in summer owing to the higher temperatures and chlorine in the influent of the DWDS. Moreover, the pathways associated with nitrogen, sulfur, glycolysis, and tricarboxylic acid (TCA) cycling, as well as carbon fixation were reconstructed and displayed according to the sampling season. Nitrogen reduction pathways [dissimilatory nitrate reduction to ammonium (DNRA) 73 %, assimilatory nitrate reduction to ammonium (ANRA) 21 %] were identified in DWDS biofilms, but nitrogen oxidation pathways were not. Sulfur cycling were involved in diverse pathways and genes. Glycolysis and TCA cycling offered electron donors and energy sources for nitrogen and sulfur reduction in biofilms. Carbon fixation was observed in DWDS biofilms, with the predominant pathway for fixing carbon dioxide being the reductive citrate cycle (38 %). Constructed functional gene networks composed of carbon, nitrogen, and sulfur cycling-related genes demonstrated synergistic effects (Positive proportion: 63.52-71.09 %). In addition, from spring to autumn, the network complexity decreased and network modularity increased. The assembly mechanism of carbon, nitrogen and sulfur cycling-related genes was driven by stochastic processes for all samples. These results highlight the diverse functional genes in DWDS biofilms, their synergetic interrelationships, and the seasonality effect on functional attributes.

Assessing the impacts of fine sediment removal on endogenous pollution release and microbial community structure in the shallow lakes

Resuspension is a crucial process for releasing endogenous pollution from shallow lakes into the overlying water. Fine particle sediment, which has a higher contamination risk and longer residence time, is the primary target for controlling endogenous pollution. To this end, a study coupling aqueous biogeochemistry, electrochemistry, and DNA sequencing was conducted to investigate the remediation effect and microbial mechanism of sediment elution in shallow eutrophic water. The results indicated that sediment elution can effectively remove some fine particles in situ. Furthermore, sediment elution can inhibit the release of ammonium nitrogen and total dissolved phosphorous into the overlying water from sediment resuspension in the early stage, resulting in reductions of 41.44 %-50.45 % and 67.81 %-72.41 %, respectively. Additionally, sediment elution greatly decreased the concentration of nitrogen and phosphorus pollutants in pore water. The microbial community structure was also substantially altered, with an increase in the relative abundance of aerobic and facultative aerobic microorganisms. Redundancy analysis, PICRUSt function prediction, and the correlation analysis revealed that loss on ignition was the primary factor responsible for driving changes in microbial community structure and function in sediment. Overall, the findings provide novel insights into treating endogenous pollution in shallow eutrophication water.

Nitrogen fixation and transcriptome of a new diazotrophic Geomonas from paddy soils

Nitrogen gas (N2) fixation driven by diazotrophs is a crucial process for supplying nitrogen to paddy soil ecosystems. The genus Geomonas has been considered to be an important potential diazotroph in paddy soils, but direct experimental evidence of the nitrogen-fixing ability of Geomonas in pure culture is still lacking. Hence, we aimed to demonstrate this nitrogen-fixing capability and shed light on how this process was regulated in response to ammonium (NH4 +) in Geomonas. In this study, we determined that a key nitrogenase gene (nifH) was present in 50 isolates from paddy soils. Members of Geomonas contained the minimum nitrogen fixation gene cluster (nifBHDKEN) based on genomic analysis, implying Geomonas species had the potential to fix nitrogen. Acetylene reduction assay (ARA), 15N2 isotope labeling, and total nitrogen accumulation assays validated that Geomonas was, indeed, able to fix nitrogen in pure culture. Under nitrogen-fixing conditions, the cell morphology of Geomonas changed from short rod-shaped (with NH4 +) to long rod-shaped and flagella became longer and thicker. The expression of genes correlated to nitrogen fixation in the Geomonas transcriptome was quantified in response to NH4 +. Expression of genes associated with nitrogenase, flavin-based electron bifurcation complexes (such as the FixAB system), NH4 + uptake, and transformation (e.g., glutamine and glutamate synthetases) were significantly upregulated under nitrogen-fixing conditions, suggesting these mechanisms might be involved in N2 fixation in Geomonas. These results were verified by RT-qPCR. Taken together, our results demonstrate that Geomonas species possess the ability to fix N2 and expand our understanding on the ecological significance and potential applications of Geomonas in paddy soil ecosystems. IMPORTANCE The ability of Geomonas species to fix nitrogen gas (N2) is an important metabolic feature for its application as a plant growth-promoting rhizobacterium. This research is of great importance as it provides the first comprehensive direct experimental evidence of nitrogen fixation by the genus Geomonas in pure culture. We isolated a number of Geomonas strains from paddy soils and determined that nifH was present in these strains. This study demonstrated that these Geomonas species harbored genes encoding nitrogenase, as do Geobacter and Anaeromyxobacter in the same class of Deltaproteobacteria. We demonstrated N2-dependent growth of Geomonas and determined regulation of gene expression associated with nitrogen fixation. The research establishes and advances our understanding of nitrogen fixation in Geomonas.

Relationships between environmental factors and N-cycling microbes reveal the indirect effect of further eutrophication on denitrification and DNRA in shallow lakes

Traditional views indicate that eutrophication and subsequent algal blooms favor denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in lake ecosystems. However, lakes tend to show an increasing propensity for inorganic nitrogen (N) limitation as they become more eutrophic. Thus, the influence of further eutrophication on denitrification and DNRA in eutrophic lakes are unclear due to the uncertainty of N availability. To fill this gap, we investigated the genes abundance (AOA, AOB, nirS, nirK and nrfA) and the composition of N-cycling microbes through quantitative PCR and 16S rRNA sequencing analysis, respectively, in 15 shallow eutrophic lakes of the Yangtze-Huaihe River basin, China. The results indicated that denitrification and DNRA rates could be modulated mainly by their functional gene abundances (nirS, nirK and nrfA), followed by the environmental factors (sediment total organic carbon and nitrogen). Denitrification rates significantly increased from slightly to highly eutrophic lakes, but DNRA rates were not. An explanation is that nitrification provided ample nitrate for denitrification, and this cooperative interaction was indicated by the positive correlation of their gene abundances. In addition, Pseudomonas and Anaeromyxobacter was the dominant genus mediated denitrification and DNRA, showing the potential to perform facultative anaerobic and strict anaerobic nitrate reduction, respectively. High level of dissolved oxygen might favor the facultatively aerobic denitrifiers over the obligately anaerobic fermentative DNRA bacteria in these shallow lakes. Chlorophyll a had a weak but positive effect on the gene abundances for nitrification (AOA and AOB). Further eutrophication had an indirect effect on denitrification and DNRA rates through modulating the genes abundances of N-cycling microbes.

Impact of seasonal change on dissimilatory nitrate reduction to ammonium (DNRA) triggering the retention of nitrogen in lake

Nitrogen (N) reduction processes including denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are critical for the eutrophication in the lake water. However, the understanding about the dominant pathways of N cycling keep limited due to the high complexity of N cycle processes in lacustrine environment. The N fractions in sediments collected from Shijiuhu Lake were measured using high-resolution (HR)-Peeper technique and chemical extraction method in varied seasons. The abundance and microbial community compositions of functional genes involved in various N-cycling processes were also obtained using high-throughput sequencing. The results showed that NH4+ concentrations in the pore water remarkably increased from the upper layer toward the deeper layer and from winter to spring. This trend suggested that higher temperature facilitated the accumulation of NH4+ in the water. Decreased NO3- concentrations were also detected at deeper sediment layers and higher temperature, indicating the intensification of N reduction on anaerobic conditions. The NH4+-N concentrations reduced in spring along with the slight change of NO3--N in solid sediment, indicating the desorption and release of mobile NH4+ from solid phase to the solution. Remarkably decreased absolute abundances of functional genes were found in spring with DNRA bacteria nrfA gene as dominant genus and Anaeromyxobacter as the most dominant bacterium (21.67 ± 1.03%). Higher absolute abundance (146.2-788.1 × 105 Copies/g) of nrfA gene relative to other genes was mainly responsible for the increase of bio-available NH4+ in the sediments. Generally, microbial DNRA pathway predominated the N reduction and retention processes in the lake sediment at higher temperature and water depth even experiencing the suppression of DNRA bacteria abundance. These results suggested the existence of ecological risk via N retention by the action of the DNRA bacteria in the sediment on the condition of higher temperature, further provided valuable information for N management of eutrophic lakes.

Nitrogen removal in freshwater sediments of riparian zone: N-loss pathways and environmental controls

The riparian zone is an important location of nitrogen removal in the terrestrial and aquatic ecosystems. Many studies have focused on the nitrogen removal efficiency and one or two nitrogen removal processes in the riparian zone, and less attention has been paid to the interaction of different nitrogen transformation processes and the impact of in situ environmental conditions. The molecular biotechnology, microcosm culture experiments and 15N stable isotope tracing techniques were used in this research at the riparian zone in Weinan section of the Wei River, to reveal the nitrogen removal mechanism of riparian zone with multi-layer lithologic structure. The results showed that the nitrogen removal rate in the riparian zone was 4.14-35.19 μmol·N·kg-1·h-1. Denitrification, dissimilatory reduction to ammonium (DNRA) and anaerobic ammonium oxidation (anammox) jointly achieved the natural attenuation process of nitrogen in the riparian zone, and denitrification was the dominant process (accounting for 59.6%). High dissolved organic nitrogen and nitrate ratio (DOC:NO3-) would promote denitrification, but when the NO3- content was less than 0.06 mg/kg, DNRA would occur in preference to denitrification. Furthermore, the abundances of functional genes (norB, nirS, nrfA) and anammox bacterial 16S rRNA gene showed similar distribution patterns with the corresponding nitrogen transformation rates. Sedimentary NOX-, Fe(II), dissolved organic carbon (DOC) and the nitrogen transformation functional microbial abundance were the main factors affecting nitrogen removal in the riparian zone. Fe (II) promoted NO3- attenuation through nitrate dependent ferrous oxidation process under microbial mediation, and DOC promotes NO3- attenuation through enhancing DNRA effect. The results of this study can be used for the management of the riparian zone and the prevention and control of global nitrogen pollution.

Nitrate Bioreduction under Cr(VI) Stress: Crossroads of Denitrification and Dissimilatory Nitrate Reduction to Ammonium

This study explored the response of NO₃^--N bioreduction to Cr(VI) stress, including reduction efficiency and the pathways involved (denitrification and dissimilatory nitrate reduction to ammonium (DNRA)). Different response patterns of NO₃^--N conversion were proposed under Cr(VI) suppress (0, 0.5, 5, 15, 30, 50, and 80 mg/L) by evaluating Cr(VI) dose dependence, toxicity accumulation, bioelectron behavior, and microbial community structure. Cr(VI) concentrations of >30 mg/L rapidly inhibited NO₃^--N removal and immediately induced DNRA. However, denitrification completely dominated the NO₃^--N reduction pathway at Cr(VI) concentrations of <15 mg/L. Therefore, 30 and 80 mg/L Cr(VI) (R₄ and R₆) were selected to explore the selection of the different NO₃^--N removal pathways. The pathway of NO₃^--N reduction at 30 mg/L Cr(VI) exhibited continuous adaptation, wherein the coexistence of denitrification (51.7%) and DNRA (13.6%) was achieved by regulating the distribution of denitrifiers (37.6%) and DNRA bacteria (32.8%). Comparatively, DNRA gradually replaced denitrification at 80 mg/L Cr(VI). The intracellular Cr(III) accumulation in R₆ was 6.60-fold greater than in R₄, causing more severe oxidant injury and cell death. The activated NO₃^--N reduction pathway depended on the value of nitrite reductase activity/nitrate reductase activity, with 0.84-1.08 associated with DNRA activation and 1.48-1.57 with DNRA predominance. Although Cr(VI) increased microbial community richness and improved community structure stability, the inhibition or death of nitrogen-reducing microorganisms caused by Cr(VI) decreased NO₃^--N reduction efficiency.

Responses of bacterial community and N-cycling functions stability to different wetting-drying alternation frequencies in a riparian zone

Wetting-drying alternation (WD) of the soil is one of the key characteristics of riparian zones shaped by dam construction, profoundly impacting the soil microenvironment that determines the bacterial community. Knowledge concerning the stability of bacterial community and N-cycling functions in response to different frequencies of WD remains unclear. In this study, samples were taken from a riparian zone in the Three Gorges Reservoir (TGR) and an incubation experiment was conducted including four treatments: constant flooding (W), varied wetting-drying alternation frequencies (WD1 and WD2), and constant drying (D) (simulating water level of 145 m, 155 m, 165 m, and 175 m in the riparian zone respectively). The results revealed that there was no significant difference in the diversity among the four treatments. Following the WD1 and WD2 treatments, the relative abundances of Proteobacteria increased, while those of Chloroflexi and Acidobacteriota decreased compared to the W treatment. However, the stability of bacterial community was not affected by WD. Relative to the W treatment, the stability of N-cycling functions estimated by resistance, which refers to the ability of functional genes to adapt to changes in the environment, decreased following the WD1 treatment, but showed no significant change following the WD2 treatment. Random forest analysis showed that the resistances of the nirS and hzo genes were core contributors to the stability of N-cycling functions. This study provides a new perspective for investigating the impacts of wetting-drying alternation on soil microbes.

Mill dams impact microbiome structure and depth distribution in riparian sediments

Introduction

Damming has substantially fragmented and altered riverine ecosystems worldwide. Dams slow down streamflows, raise stream and groundwater levels, create anoxic or hypoxic hyporheic and riparian environments and result in deposition of fine sediments above dams. These sediments represent a good opportunity to study human legacies altering soil environments, for which we lack knowledge on microbial structure, depth distribution, and ecological function.

Methods

Here, we compared high throughput sequencing of bacterial/ archaeal and fungal community structure (diversity and composition) and functional genes (i.e., nitrification and denitrification) at different depths (ranging from 0 to 4 m) in riparian sediments above breached and existing milldams in the Mid-Atlantic United States.

Results

We found significant location- and depth-dependent changes in microbial community structure. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Chloroflexi, Acidobacteria, Planctomycetes, Thaumarchaeota, and Verrucomicrobia were the major prokaryotic components while Ascomycota, Basidiomycota, Chytridiomycota, Mortierellomycota, Mucoromycota, and Rozellomycota dominated fungal sequences retrieved from sediment samples. Ammonia oxidizing genes (amoA for AOA) were higher at the sediment surface but decreased sharply with depth. Besides top layers, denitrifying genes (nosZ) were also present at depth, indicating a higher denitrification potential in the deeper layers. However, these results contrasted with in situ denitrification enzyme assay (DEA) measurements, suggesting the presence of dormant microbes and/or other nitrogen processes in deep sediments that compete with denitrification. In addition to enhanced depth stratification, our results also highlighted that dam removal increased species richness, microbial diversity, and nitrification.

Discussion

Lateral and vertical spatial distributions of soil microbiomes (both prokaryotes and fungi) suggest that not only sediment stratification but also concurrent watershed conditions are important in explaining the depth profiles of microbial communities and functional genes in dammed rivers. The results also provide valuable information and guidance to stakeholders and restoration projects.

Effects of dam building on the occurrence and activity of comammox bacteria in river sediments and their contribution to nitrification

The recent discovery of complete ammonia oxidizers (comammox) has fundamentally changed our understanding of nitrification. However, studies on the occurrence and activity of comammox bacteria and their contribution to nitrification remain unclear. Here, we investigated the abundance, activity, and diversity of comammox bacteria and their contribution to nitrification in sediments from dammed rivers in winter and summer. Our results indicated that comammox clade A was ubiquitous in all sediment samples and the community structure in comammox varied between the upper and lower reaches, but not on the time scale (winter and summer). Comammox activity in the dammed river sediments in summer was prominently higher than in winter (summer: 1.08 ± 0.52; winter: 0.197 ± 0.148 mg N kg-1 day-1). Furthermore, the activity of comammox bacteria in summer appeared higher in the vicinity of the dammed river and in the Sanjiang estuary, which is located downstream of the dammed river. The activity of ammonia-oxidizing bacteria (AOB) (0.77 ± 0.478 mg N kg-1 day-1) was higher compared to comammox (0.639 ± 0.588 mg N kg-1 day-1) and ammonia-oxidizing archaea (AOA) (0.026 ± 0.022 mg N kg-1 day-1) in both winter and summer. In terms of contribution to the nitrification process, AOB (winter: 67.13 ± 12.21 %; summer: 50.57 ± 16.14 %) outperformed comammox (winter: 28.59 ± 12.51 %; summer: 48.38 ± 16.62 %) and AOA (winter: <7.39 %; summer: <2.09 %). These findings indicated that the nitrification process in dammed river sediments was mainly dominated by AOB. Additionally, comammox activity was significantly affected by temperature and NH4+, suggesting that these variables were key determinants of the niche partitioning of comammox. Collectively, our findings provide novel perspectives into the widespread distribution and contribution of comammox to nitrification in dammed river ecosystems, thus broadening our understanding of the nitrification processes.

Contribution of Ammonium-Induced Nitrifier Denitrification to N2O in Paddy Fields

Paddy fields are one of the most important sources of nitrous oxide (N₂O), but biogeochemical N₂O production mechanisms in the soil profile remain unclear. Our study used incubation, dual-isotope (¹⁵N-¹⁸O) labeling methods, and molecular techniques to elucidate N₂O production characteristics and mechanisms in the soil profile (0-60 cm) during summer fallow, rice cropping, and winter fallow periods. The results pointed out that biotic processes dominated N₂O production (72.2-100%) and N₂O from the tillage layer accounted for 91.0-98.5% of total N₂O in the soil profile. Heterotrophic denitrification (HD) was the main process generating N₂O, contributing between 53.4 and 96.6%, the remainder being due to ammonia oxidation pathways, which was further confirmed by metagenomics and quantitative polymerase chain reaction (qPCR) assays. Nitrifier denitrification (ND) was an important N₂O production source, contributing 0-46.6% of total N₂O production, which showed similar trends with N₂O emissions. Among physicochemical and biological factors, ammonium content and the ratio of total organic matter to nitrate were the main driving factors affecting the contribution ratios of the ammonia oxidation pathways and HD pathway, respectively. Moisture content and pH affect norC-carrying Spirochetes and thus the N₂O production rate. These findings confirm the importance of ND to N₂O production and help to elucidate the impact of anthropogenic activities, including tillage, fertilization, and irrigation, on N₂O production.

Spatial and Seasonal Patterns of Sediment Bacterial Communities in Large River Cascade Reservoirs: Drivers, Assembly Processes, and Co-occurrence Relationship

Sediment bacteria play an irreplaceable role in promoting the function and biogeochemical cycle of the freshwater ecosystem; however, little is known about their biogeographical patterns and community assembly mechanisms in large river suffering from cascade development. Here, we investigated the spatiotemporal distribution patterns of bacterial communities employing next-generation sequencing analysis and multivariate statistical analyses from the Lancang River cascade reservoirs during summer and winter. We found that sediment bacterial composition has a significant seasonal turnover due to the modification of cascade reservoirs operation mode, and the spatial consistency of biogeographical models (including distance-decay relationship and covariation of community composition with geographical distance) also has subtle changes. The linear regression between the dissimilarity of bacterial communities in sediments, geographical and environmental distance showed that the synergistic effects of geographical and environmental factors explained the influence on bacterial communities. Furthermore, the environmental difference explained little variations (19.40%) in community structure, implying the homogeneity of environmental conditions across the cascade reservoirs of Lancang River. From the quantification of the ecological process, the homogeneous selection was recognized as the dominating factor of bacterial community assembly. The co-occurrence topological network analyses showed that the key genera were more important than the most connected genera. In general, the assembly of bacterial communities in sediment of cascade reservoirs was mediated by both deterministic and stochastic processes and is always dominated by homogeneous selection with the seasonal switching, but the effects of dispersal limitation and ecological drift cannot be ignored.

Subsurface biogeochemical cycling of nitrogen in the actively serpentinizing Samail Ophiolite, Oman

Nitrogen (N) is an essential element for life. N compounds such as ammonium ( NH 4 + ) may act as electron donors, while nitrate ( NO 3 - ) and nitrite ( NO 2 - ) may serve as electron acceptors to support energy metabolism. However, little is known regarding the availability and forms of N in subsurface ecosystems, particularly in serpentinite-hosted settings where hydrogen (H₂) generated through water-rock reactions promotes habitable conditions for microbial life. Here, we analyzed N and oxygen (O) isotope composition to investigate the source, abundance, and cycling of N species within the Samail Ophiolite of Oman. The dominant dissolved N species was dependent on the fluid type, with Mg²⁺- HCO 3 - type fluids comprised mostly of NO 3 - , and Ca²⁺-OH^- fluids comprised primarily of ammonia (NH₃). We infer that fixed N is introduced to the serpentinite aquifer as NO 3 - . High concentrations of NO 3 - (>100 μM) with a relict meteoric oxygen isotopic composition (δ¹⁸O ~ 22‰, Δ¹⁷O ~ 6‰) were observed in shallow aquifer fluids, indicative of NO 3 - sourced from atmospheric deposition (rainwater NO 3 - : δ¹⁸O of 53.7‰, Δ¹⁷O of 16.8‰) mixed with NO 3 - produced in situ through nitrification (estimated endmember δ¹⁸O and Δ¹⁷O of ~0‰). Conversely, highly reacted hyperalkaline fluids had high concentrations of NH₃ (>100 μM) with little NO 3 - detectable. We interpret that NH₃ in hyperalkaline fluids is a product of NO 3 - reduction. The proportionality of the O and N isotope fractionation (¹⁸ε / ¹⁵ε) measured in Samail Ophiolite NO 3 - was close to unity (¹⁸ε / ¹⁵ε ~ 1), which is consistent with dissimilatory NO 3 - reduction with a membrane-bound reductase (NarG); however, abiotic reduction processes may also be occurring. The presence of genes commonly involved in N reduction processes (narG, napA, nrfA) in the metagenomes of biomass sourced from aquifer fluids supports potential biological involvement in the consumption of NO 3 - . Production of NH 4 + as the end-product of NO 3 - reduction via dissimilatory nitrate reduction to ammonium (DNRA) could retain N in the subsurface and fuel nitrification in the oxygenated near surface. Elevated bioavailable N in all sampled fluids indicates that N is not likely limiting as a nutrient in serpentinites of the Samail Ophiolite.

Climate-induced salinization may lead to increased lake nitrogen retention

Salinization caused by climate change and nitrogen (N) pollution are both important environmental threats for inland lakes. However, evaluating their interactive effects continues to be challenging. Here, field observation and microcosmic experiments were conducted in six lakes of East Asia with the different salinity and climate characteristics, to explore the response of the key N cycle processes related to N fate to the climate-induced change in salinity. The results indicated that increased salinity inhibited denitrification, which was the outcome of two cumulative effects: the long-term microbial adaptation effect and the direct salinity stress. Whereas increased salinity had unsignificant or positive effects on dissimilatory nitrate reduction to ammonium. It had caused that N retention capacity is relatively stronger in saline than freshwater lakes. Inland lakes are long-term basin-wide integrators of climatic conditions that drying (salinization) and wetting (desalination) with climate change. In semi-arid regions of East Asia, lake shrinkage, salinization and increasing temperature driven by climate warming and drying may exert a negative impact on N pollution through concentrating, decreasing denitrification and increasing ammonium release from sediment. The threat of climate change on these lakes is not just the quantity of water, but its quality.

Insights into microbial interactive mechanism regulating dissimilatory nitrate reduction processes in riparian freshwater aquaculture sediments

Aquaculture can substantially alter the accumulation and cycling of nutrients in sediments. However, the microbial mechanisms mediating sediment dissimilatory nitrate (NO₃^-) reduction in freshwater aquaculture ponds are still unclear, which rule the removal and retention of N element. In the present study, three microbial NO₃^- reduction processes in riparian aquaculture pond sediments (i.e., crab, shrimp and fish ponds) and natural freshwater sediments (i.e., lakes and rivers) were investigated via isotopic tracing and molecular analyses. The potential rates of denitrification, anaerobic ammonium oxidation (anammox) and dissimilatory nitrate reduction to ammonium (DNRA) significantly increased in the aquaculture ponds compared with the natural freshwaters. Denitrification contributed 90.40-94.22% to the total NO₃^- reduction (product as N₂), followed by 2.49-5.82% of anammox (product as N₂) and 2.09-5.18% of DRNA (product as NH₄⁺). The availability of C and N substrates, rather than functional gene abundance, regulated the activities of NO₃^- reductions and microbiome composition. Microbial mechanism based on network analysis indicated that heterotrophic denitrifiers and DNRA bacteria (e.g., Bacillus, Micromonospora, Mycobacterium and Brachybacterium) determined the community structure and function for N conversions in aquaculture ponds, whereas the such microbial network in natural freshwater sediments was manipulated by autotrophic denitrifiers (e.g., Desulfuromonas, Polaromonas, Solitalea). Collectively, this study provides an in-depth exploration of microbial nitrogen removal in freshwater aquaculture areas and supports management strategies for N pollution caused by reclamation for aquaculture in riparian zones.

Depth induced assembly discrepancy of multitrophic microbial communities affect microbial nitrogen transformation processes in river cross-sections

Understanding how the structures and functions of bacterial and microeukaryotic communities vary within cross-sections will improve managements aimed at restoring river ecological functions. However, no comprehensive investigation has examined how microbial community characteristics vary within cross-sections, which makes the accurate calculation and prediction of microbial metabolic processing of substances in rivers difficult. Here, the distributions, co-occurrence networks, and assemblies of bacterial and microeukaryotic communities and their feedback to nitrogen transformation in cross-sections of the Yangtze River were studied by coupling ecological theory, biogeochemistry, and DNA meta-barcoding methods. The study found that depth in cross-sections was the primary driving factor regulating the composition of sediment bacterial and microeukaryotic communities. Co-occurrence network analysis indicated that the effect of bacteria on the co-occurrence network decreased and the network become more simplified and instability with depth in river cross-sections. Quantified using the β-nearest taxon index, the H2 layer sediment (depth 10-20 m) displayed the largest variation in selection processes for microbial assemblies, while homogeneous selection and homogenizing dispersal contributed most to the bacterial and microeukaryotic assemblies in the H3 layer (depth >20 m). Cross-sectional depth and denitrification genes had a significant quadratic correlation, with the highest microbial nitrogen-removal potential occurring in the H2 layer sediment. Structural equation models showed that the sediment nitrogen distributions were regulated by distinct environmental pathways at different depths, and that the H2 layer sediment was primary driven by bacterial community. In this layer, river cross-sectional depth influenced nitrogen transformation by regulating the distribution of sediment particle sizes, which then influenced the assembly of the multitrophic microbial communities. This study will improve river management by clarifying the importance of cross-sectional depth to the ecological function of rivers.

Evidence for Assimilatory Nitrate Reduction as a Previously Overlooked Pathway of Reactive Nitrogen Transformation in Estuarine Suspended Particulate Matter

Suspended particulate matter (SPM) contributes to the loss of reactive nitrogen (Nr) in estuarine ecosystems. Although denitrification and anaerobic ammonium oxidation in SPM compensate for the current imbalance of global nitrogen (N) inputs and sinks, it is largely unclear whether other pathways for Nr transformation exist in SPM. Here, we combined stable isotope measurements with metagenomics and metatranscriptomics to verify the occurrence of dissimilatory nitrate reduction to ammonium (DNRA) in the SPM of the Pearl River Estuary (PRE). Surprisingly, the conventional functional genes of DNRA (nirBD) were abundant and highly expressed in SPM, which was inconsistent with a low potential rate. Through taxonomic and comparative genomic analyses, we demonstrated that nitrite reductase (NirBD) in conjunction with assimilatory nitrate reductase (NasA) performed assimilatory nitrate reduction (ANR) in SPM, and diverse alpha- and gamma-proteobacterial lineages were identified as key active heterotrophic ANR bacteria. Moreover, ANR was predicted to have a relative higher occurrence than denitrification and DNRA in a survey of Nr transformation pathways in SPM across the PRE spanning 65 km. Collectively, this study characterizes a previously overlooked pathway of Nr transformation mediated by heterotrophic ANR bacteria in SPM and has important implications for our understanding of N cycling in estuaries.

Ammonia level influences the assembly of dissimilatory nitrate reduction to ammonia bacterial community in soils under different heavy metal remediation treatments

Heavy metal remediation treatments might influence functional microbial community assembly. Dissimilatory nitrate reduction to ammonia (DNRA) contributes to the nitrogen retention processes in soil ecosystems. We assumed that remediation might reduce heavy metal toxicity and increase some available nutrients for the DNRA microbes, thus balancing the deterministic and stochastic process for DNRA community assembly. Here, we investigated the process of DNRA bacterial community assembly under different heavy metal remediation treatments (including control, biochar, limestone, rice straw, rice straw + limestone, and biochar + limestone) in an Alfisol soil. The abundance of DNRA bacteria diverged across treatments. The α-diversity of the DNRA bacterial community was correlated with pH, available phosphorus (AP), ammonium (NH₄⁺), and extractable Fe (EFe). Metal Cd and Fe significantly affected the abundance of the nrfA gene. The β-diversity was associated with pH, NH₄⁺, and EFe. Deterministic processes dominantly drove the assembly processes of the DNRA bacterial community. NH₄⁺ level played an essential role in the assembly processes than the other soil physicochemical properties and metal availability. High, moderate, and low levels of NH₄⁺ could advocate stochastic process plus selection, heterogeneous selection to stochastic process, and heterogeneous selection, respectively. Network analysis highlighted a predominant role of NH₄⁺ in regulating DNRA bacterial community assembly. However, the relative abundance of modules and some keystone species also were influenced by pH and EFe, respectively. Therefore, the DNRA bacterial community assembly under different heavy metal remediation treatments in this study was dominantly driven by nitrogen availability. pH, phosphorus, and metal availability were auxiliary regulators on DNRA bacterial community.

Dissimilatory nitrate reduction to ammonium (DNRA) potentially facilitates the accumulation of phosphorus in lake water from sediment

Nitrogen (N) and phosphorus (P) are crucial nutrients for eutrophication in the lacustrine ecosystem and attract the attention worldwide. However, the interaction between them need further clarification. This study aimed to assess the influence of dissimilatory nitrate reduction to ammonia (DNRA) on the cycle of P in lacustrine sediment. Different fractions of N and P in the pore water were measured using high-resolution in-situ measurement techniques, HR-Peeper and DGT, coupling with sequential extraction for solid sediment from a shallow freshwater lake. The results showed that elevated nitrate (NO₃^-) reduction via DNRA rather than denitrification was verified at deeper sediment layer, suggesting the generation of inorganic ammonia (NH₄⁺) as electron donor under anaerobic episodes. High abundance of DNRA bacteria (nrfA gene) obtained using high-throughput sequencing analysis were detected at upper layer and responsible for the accumulation of NH₄⁺ in the sediment coupling with chemolithoautotrophic metabolism. Additionally, significant desorption of ionic ferrous iron (Fe²⁺) and dissolved reactive phosphate (DRP) from solid phase and the enrichment in the solution was simultaneously detected. Higher concentration of solid Fe bound P (Fe-P) at deeper layer indicated the potential re-oxidation of Fe²⁺ as electron donor during DNRA process and sorption of DRP toward the Fe-containing minerals. However, obvious evidence of desorption proved by DGT indicated that higher NH₄⁺ concentrations favored the reduction of Fe(III) oxy(hydr)oxides and the desorption of DRP into the pore water and diffusion toward the overlying water. Finally, noteworthy S^2- release from solid sediment was speculated to stimulate the DNRA and facilitated the accumulation of NH₄⁺ in the solution, which further induced the enrichment of DRP in water from the solid phase. Overall, DNRA potentially facilitates the accumulation of P in lake water, and the synchronous control of N and P is important for the eutrophication management and restoration of lake eutrophication.

Periphytic biofilms-mediated microbial interactions and their impact on the nitrogen cycle in rice paddies

Rice paddies are unique waterlogged wetlands artificially constructed for agricultural production. Periphytic biofilms (PBs) at the soil-water interface play an important role in rice paddies characterized by high nutrient input but low utilization efficiency. PBs are composed of microbial aggregates, including a wide variety of microorganisms (algae, bacteria, fungi, protozoa, and metazoa), extracellular polymeric substances and minerals (iron, aluminum, and calcium), which form an integrated food web and energy flux within a relatively stable micro-ecosystem. PBs are crucial to regulate and streamline the nitrogen cycle by neutralizing nitrogen losses and improving rice production since PBs can serve as both a sink by capturing surplus nitrogen and a source by slowly re-releasing this nitrogen for reutilization. Here the ecological advantages of PBs in regulating the nitrogen cycle in rice paddies are illustrated. We summarize the key functional importance of PBs, including the intricate and delicate community structure, microbial interactions among individual phylotypes, a wide diversity of self-produced organics, the active adaptation of PBs to constantly changing environments, and the intricate mechanisms by which PBs regulate the nitrogen cycle. We also identify the future challenges of microbial interspecific cooperation in PBs and their quantitative contributions to agricultural sustainability, optimizing nitrogen utilization and crop yields in rice paddies.

Co-occurrence of autotrophic and heterotrophic denitrification in electrolysis assisted constructed wetland packing with coconut fiber as solid carbon source

Aiming at the problems of lack of carbon sources for nitrogen removal and low phosphorus removal efficiency of constructed wetlands (CWs) in treating wastewater treatment plant (WWTP) effluent, an electrolysis assisted constructed wetland (E-CW) with coconut fiber as substrate and solid carbon sources was constructed. The synthetic secondary effluent was used as the influent of the E-CW with a wastewater treatment capacity of 140 L d^-1. The total nitrogen (TN) and the total phosphorus (TP) removal efficiency of the E-CW with coconut fiber treating WWTP effluent were 69.4% and 93.3%, respectively, which were 54.3% and 88.2% higher than those of CW with coconut fiber and no electrolysis. The removal efficiency of TN was 39.9% higher than that of E-CW with gravel. The current intensity had significant effect on nitrogen removal efficiency and the release of carbon sources from coconut fiber. When current intensity increased from 0.25 A to 1.00 A, the TN removal efficiency and nitrate removal rate increased by 21.1% and 0.21 mg L^-1 h^-1, respectively, and the volatile fatty acids (VFAs) released from coconut fiber increased by 57.7 mg L^-1. The 16S rRNA high-throughput sequencing results indicated that the main functional nitrogen-removing microbes were Hydrogenophaga, Thauera, Rhodanobacteraceae_norank, Xanthobacteraceae_norank, etc. Multiple paths including autotrophic denitrification with hydrogen and Fe²⁺ as electron donors and heterotrophic denitrification were achieved in the system. Meanwhile, the main functional lignocellulose degradation microbes were enriched in the system, including Cytophaga_xylanolytica_group, and Caldilineaceae. Because electrolysis created a favorable environment for them to release carbon sources from coconut fiber. This study provided a new perspective for advanced nutrients removal of WWTP effluent in CWs.

Co-Occurrence Relationship and Stochastic Processes Affect Sedimentary Archaeal and Bacterial Community Assembly in Estuarine-Coastal Margins

Sedimentary microorganisms play crucial roles in maintaining the functional stability of aquatic ecosystems. However, their taxonomic composition and assembly processes are not well known in estuarine−coastal margins because of their complex environment. We investigated microbial communities, co-occurrence relationships, and underlying mechanisms in 33 surface sediment samples collected in the Jiulong River Estuary and the Taiwan Strait to reveal their composition dynamics. The abundance, diversity, and composition of microorganisms demonstrated obvious spatial variables. Methanobacterium and Methanosarcina, as well as Candidatus_Nitrosopumilus and Nitrososphaeraceae were the main methanogenic and ammonia-oxidizing archaea, with an average abundance of more than 5.91% and 4.27%, respectively. Along with a salinity gradient increase, the relative abundance of methanogenic archaea (from 42.9% to 16.6%) contrasted with the trend of ammonia-oxidizing archaea (from 6.04% to 18.7%). The number of methanogenic archaea gradually decreased with increasing geographic distance (p < 0.05), whereas ammonia-oxidizing archaea showed no significant change (p > 0.05). In co-occurrence patterns, closer inter-taxa connections were observed among archaea−archaea and bacteria−bacteria than in archaea−bacteria, which indicated that coexistence within the same kingdom was greater than interaction between different kingdoms in shaping the community structure along the salinity gradient. Furthermore, null model analyses of the microbial community showed that undominated was the most prominent process, explaining over 44.9% of community variation, followed by heterogeneous selection and dispersal limitation, which contributed to 27.7% and 16.3%, respectively. We demonstrated that stochasticity, rather than determinism, regulates community assembly. These results further highlight that intra-kingdom co-occurrence and stochastic processes shape the structure and assembly of microbial communities in estuarine−coastal margins.

Streambed microbial communities in the transition zone between groundwater and a first-order stream as impacted by bidirectional water exchange

The input of nitrate and other agricultural pollutants in higher-order streams largely derives from first-order streams. The streambed as the transition zone between groundwater and stream water has a decisive impact on the attenuation of such pollutants. This reactivity is not yet well understood for lower-order agricultural streams, which are often anthropogenically altered and lack the streambed complexity allowing for extensive hyporheic exchange. Reactive hot spots in such streambeds have been hypothesized as a function of hydrology, which controls the local gaining (groundwater exfiltration) or losing (infiltration) of stream water. However, streambed microbial communities and activities associated with such reactive zones remain mostly uncharted. In this study, sediments of a first-order agriculturally impacted stream in southern Germany were investigated. Along with a hydraulic dissection of distinct gaining and losing reaches of the stream, community composition and the abundance of bacterial communities in the streambed were investigated using PacBio long-read sequencing of bacterial 16S rRNA gene amplicons, and qPCR of bacterial 16S rRNA and denitrification genes (nirK and nirS). We show that bidirectional water exchange between groundwater and the stream represents an important control for sediment microbiota, especially for nitrate-reducing populations. Typical heterotrophic denitrifiers were most abundant in a midstream net losing section, while up- and downstream net gaining sections were associated with an enrichment of sulfur-oxidizing potential nitrate reducers affiliated with Sulfuricurvum and Thiobacillus spp. Dispersal-based community assembly was found to dominate such spots of groundwater exfiltration. Our results indicate a coupling of N- and S-cycling processes in the streambed of an agricultural first-order stream, and a prominent control of microbiology by hydrology and hydrochemistry in situ. Such detailed local heterogeneities in exchange fluxes and streambed microbiomes have not been reported to date, but seem relevant for understanding the reactivity of lower-order streams.

Investigation of dissimilatory nitrate reduction to ammonium (DNRA) in urban river network along the Huangpu River, China: rates, abundances, and microbial communities

Dissimilatory nitrate reduction to ammonium (DNRA) is an essential intermediate step in the nitrogen cycle, and different sediment physicochemical properties can affect the DNRA process. But the detailed research on the environmental nitrogen cycling in urban river networks based on DNRA communities and the functional gene nrfA is lacking. In this study, the flow line of the Huangpu River in Shanghai was analyzed using isotope tracer, quantitative real-time PCR, and high-throughput sequencing techniques to evaluate the role of DNRA on the stability of the river network and marine. The significant positive correlation between the rate of DNRA and sediment organic carbon was identified. At the genus level, Anaeromyxobacter is the most dominant. Notably, both heterotrophic and autotrophic DNRA species were discovered. This study added diversity to the scope of urban freshwater river network ecosystem studies by investigating the distribution of DNRA bacteria along the Huangpu River. It provided new insights into the biological nitrogen cycle of typical urban inland rivers in eastern China.

Biofilm phenotypes and internal community succession determines distinct growth of anammox bacteria in functional anammox biofilms

In this study, time-series anammox functional biofilms were obtained in a lab-scale simultaneous partial nitritation/anammox process for treating high-strength ammonium. The variations in the biofilm phenotypes, community succession, and anammox bacteria abundance over time were evaluated using optical microscopy, 16S rRNA gene sequencing, and qPCR. The result revealed that biofilm has three distinct stages of the community development trajectory across a 182-day temporal scale. Anammox bacteria growth rates were 0.035 d^-1, 0.0015 d^-1, and 0.011 d^-1, respectively. The diversity and network analysis suggested that the positive priority effect of ammonia oxidizing bacteria was the primary factor for the rapid proliferation of anammox bacteria, and the species replacement triggering priority effect forfeiture and substituted functional recruitment were reasons for the slow proliferation and stable proliferation of anammox bacteria, respectively. Taken together, the higher microbial diversity and stable community composite were key prerequisites for the proliferation of the anammox bacteria.

High N2O reduction potential by denitrification in the nearshore site of a riparian zone

As a potent atmospheric greenhouse gas and a major source of ozone depletion, nitrous oxide (N₂O) emission has been given increasing attention in aquatic systems, particularly at the aquatic-terrestrial interfaces, such as riparian zones. However, the microbial mechanisms regulating N₂O emission in riparian zones remain unknown. Here, we measured the contributions of denitrification and ammonium oxidation to N₂O emission along with the abundance and community structure of nirK-, nirS-, nosZ I- and nosZ II-harbouring bacteria in both surface sediments (0-10 cm) and overlying water along a lake riparian zone (including nearshore sites and offshore sites). Overall, the nearshore sites of the riparian zones emitted less N₂O than the offshore sites. Nearshore N₂O emission was dominated by denitrification with a high N₂O reduction rate, whereas offshore N₂O emission was driven by ammonium oxidation. Furthermore, N₂O derived from ammonium oxidation was influenced by the NH₄⁺-N content, and denitrification N₂O was modulated by denitrifier communities. The N₂O-producing community was dominated by nirS-harbouring bacteria, while the N₂O-reducing community was dominated by nosZ I-harbouring bacteria. The relative abundance of Hydrogenophilales from nirS-denitrifiers and Chloroflexi unclassified from nosZ II-type communities influenced the N₂O produced by denitrification, according to high-throughput sequencing analysis. Additionally, we also found lower levels of N₂O production per unit volume in overlying water, which were 3-4 orders of magnitude less than in the surface sediment. Overall, we propose that using riparian zones can be an effective management tool for N₂O mitigation by enhancing the N₂O reduction process of denitrification and decreasing ammonium oxidation.

Effects of marine produced organic matter on the potential estuarine capacity of NOx- removal

Dissolved inorganic nitrogen (DIN) is very high in the Pearl River Estuary (PRE) and nitrate (NO_x^-) removal processes such as denitrification, anaerobic ammonium oxidation (anammox) and dissimilatory nitrate reduction to ammonium (DNRA) are important for determining export of DIN to coastal waters. However, fluxes of NO_x^- removal and influencing factors in the PRE are still unclear. We conducted 4 cruises at 11 sites in the PRE to investigate potential NO_x^- removal rates, their contributions, and corresponding gene abundances, and controlling factors in surface sediments (0-5 cm). The results showed that the potential rates of denitrification, anammox, and DNRA as well as their contributions varied spatially and seasonally. Denitrification (1.98 ± 1.7 μg N g^-1 d^-1) was the major NO_x^- removal processes (68.43 ± 14.61%) while DNRA (0.45 ± 0.28 μg N g^-1 d^-1) contributed 22.61 ± 14.89% in NO_x^- removal. The NO_x^- removal processes and corresponding gene abundances were correlated with the chlorophyll concentrations in both overlying water and sediment, indicating that marine-produced organic matter was the major driver for benthic NO_x^- removal processes. In addition, water column turbidity had important effects on primary production, which affects benthic N processes. Our study provides evidences for that the turbidity-regulated primary production in overlying water is the primary driver for benthic NO_x^- removal processes. The contribution of sediment NO_x^- removal fluxes to water column NO_x^- concentration was low in the upper estuary and increased in the lower estuary where marine produced chlorophyll a was higher. However, daily fluxes of NO_x^- removal were estimated to account for only 0.18-7.22% (mean 1.85 ± 1.62%) of NO_x^- in the whole overlying water column. This suggests that most riverine NO_x^- was exported out into the adjacent coastal waters.

Aromatic compounds releases aroused by sediment resuspension alter nitrate transformation rates and pathways during aerobic-anoxic transition

Aromatic compounds (ACs) releases aroused by sediment resuspension would certainly change the concentrations of suspended sediment (SPS) and organic carbon, which may alter nitrate-N transformation during aerobic-anoxic transition. To prove this, three typical ACs (aniline, nitrobenzene, and methylbenzene) with different octanol-water partition coefficients (K_ow) were selected to investigate the effects of ACs releases aroused by sediment resuspension on nitrate-N transformation during aerobic-anoxic transition. ACs releases aroused by sediment resuspension accelerated nitrate-N transformation and enhanced the potential for dissimilatory nitrate reduction to ammonium (DNRA), compared to that without sediment resuspension. With sediment resuspension, methylbenzene releases affected nitrate-N transformation rates and pathways more significantly than aniline and nitrobenzene releases. Microbial analysis indicated that sediment resuspension created complicated microbial co-occurrence networks and changed the associations among bacteria; dominant bacteria abundance varied with different ACs releases. Further analysis revealed that ACs distributed in SPS, which increased with logK_ow, indirectly affected nitrate-N transformation rates and pathways via altering dominant bacteria abundance and electron transport system activity (ETSA). Especially, ETSA, which was positively associated with ACs distributed in SPS, affected nitrate-N transformation most directly. Overall, ACs release fate played important roles in nitrate-N transformation, causing ammonia-N retention and alterations in nitrogen cycle during aerobic-anoxic transition.

Denitrification and DNRA in Urban Accidental Wetlands in Phoenix, Arizona

Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) both require low oxygen and high organic carbon conditions common in wetland ecosystems. Denitrification permanently removes nitrogen from the ecosystem as a gas while DNRA recycles nitrogen within the ecosystem via production of ammonium. The relative prevalence of denitrification versus DNRA has implications for the fate of nitrate in ecosystems. Unplanned and unmanaged urban accidental wetlands in the Salt River channel near downtown Phoenix, Arizona, USA receive high nitrate relative to non-urban wetlands and have a high capacity for denitrification, but unknown capacity for DNRA. We conducted in-situ push-pull tests with isotopically labelled nitrate to measure denitrification and DNRA rates in three of the dominant vegetative patch types in these urban accidental wetlands. DNRA accounted for between 2 and 40% of nitrate reduction (DNRA plus denitrification) with the highest rates measured in patches of Ludwigia peploides compared to Typha spp. and non-vegetated patches. The wetland patches were similar with respect to dissolved organic carbon concentration but may have differed in carbon lability or strength of reducing conditions due to a combination of litter decomposition and oxygen supply via diffusion and aerenchyma. The ratio of DNRA to denitrification was negatively correlated with nitrate concentration, indicating that DNRA may become a more important pathway for nitrate attenuation at low nitrate concentration. Although DNRA was generally lower than denitrification, this pathway was an important component of nitrate attenuation within certain patches in these unmanaged urban accidental wetlands.

Response of microbial nitrogen transformation processes to antibiotic stress in a drinking water reservoir

Effects of antibiotics on microbial nitrogen transformation processes in natural aquatic ecosystems are largely unknown. In this study, we utilized the ¹⁵N stable isotope tracers and metagenomic sequencing to identify how antibiotics drive nitrogen transformation processes in Danjiangkou Reservoir, which is the largest artificial drinking water reservoir in China. We retrieved 51 nitrogen functional genes, and found that the highest abundances of nitrate reduction and denitrification-related genes occurred in dissimilatory nitrogen transformation pathways. ¹⁵N-labelling analysis substantiated that denitrification was the main pathway for nitrogen removal, accounting for 57.1% of nitrogen loss. Nitrogen functional genes and antibiotic resistance genes co-occurred in Danjiangkou Reservoir, and they were mainly carried by the denitrifying bacteria such as Rhodoferax, Polaromonas, Limnohabitans, Pararheinheimera, Desulfobulbus, and Pseudopelobacter. Genome annotation revealed that antibiotic deactivation, Resistance-Nodulation-Division and facilitator superfamily efflux pumps were responsible for the multiple-resistance to antibiotics in these bacteria. Moreover, antibiotics showed non-significant effects on nitrogen transformation processes. It is speculated that denitrifying bacteria harboring ARGs played crucial roles in protecting nitrogen transformation from low-level antibiotics stress in the reservoir. Our results highlight that denitrifying bacteria are important hosts of ARGs, which provides a novel perspective for evaluating the effects of antibiotics on nitrogen cycle in natural aquatic ecosystems.

Stimulation of N2 O emission via bacterial denitrification driven by acidification in estuarine sediments

Ocean acidification in nitrogen-enriched estuaries has raised global concerns. For decades, biotic and abiotic denitrification in estuarine sediments has been regarded as the major ways to remove reactive nitrogen, but they occur at the expense of releasing greenhouse gas nitrous oxide (N₂ O). However, how these pathways respond to acidification remains poorly understood. Here we performed a N₂ O isotopocules analysis coupled with respiration inhibition and molecular approaches to investigate the impacts of acidification on bacterial, fungal, and chemo-denitrification, as well as N₂ O emission, in estuarine sediments through a series of anoxic incubations. Results showed that acidification stimulated N₂ O release from sediments, which was mainly mediated by the activity of bacterial denitrifiers, whereas in neutral environments, N₂ O production was dominated by fungi. We also found that the contribution of chemo-denitrification to N₂ O production cannot be ignored, but was not significantly affected by acidification. The mechanistic investigation further demonstrated that acidification changed the keystone taxa of sedimentary denitrifiers from N₂ O-reducing to N₂ O-producing ones and reduced microbial electron-transfer efficiency during denitrification. These findings provide novel insights into how acidification stimulates N₂ O emission and modulates its pathways in estuarine sediments, and how it may contribute to the acceleration of global climate change in the Anthropocene.

Shift of DNRA bacterial community composition in sediment cores of the Pearl River Estuary and the impact of environmental factors

Dissimilatory nitrate reduction to ammonia (DNRA) process, competing with denitrification and anaerobic ammonia oxidation (anammox) for nitrate, is an important nitrogen retention pathway in the environment. Previous studies on DNRA bacterial diversity and composition focused on the surface sediments in estuaries, but studies on the deep sediments are limited, and the linkage between DNRA community structure and complex estuarine environment remains unclear. In this study, through high-throughput sequencing of nrfA gene followed by high-resolution sample inference, we examined spatially and temporally the composition and diversity of DNRA bacteria along a salinity gradient in five sediment cores of the Pearl River Estuary (PRE). We found a higher diversity and richness of DNRA bacteria in sediments with lower organic carbon, where sea water intersects fresh water. Moreover, the DNRA bacterial communities had the specific spatially distribution coupling with their metabolic difference along the salinity gradient of the Pearl River Estuary, but no obvious difference along the sediment depth. The distribution of DNRA bacteria in the PRE was largely driven by various environmental factors, including salinity, Oxidation-Reduction Potential (ORP), ammonium, nitrate and C_org/NO₃^-. Furthermore, dominant DNRA bacteria were found to be the key populations of DNRA communities in the PRE sediments by network analysis. Collectively, our results showed that niche difference of DNRA bacteria indeed occurs in the Pearl River Estuary.

Microbial river-to-sea continuum: gradients in benthic and planktonic diversity, osmoregulation and nutrient cycling

BACKGROUND

Coastal aquatic ecosystems include chemically distinct, but highly interconnected environments. Across a freshwater-to-marine transect, aquatic communities are exposed to large variations in salinity and nutrient availability as tidal cycles create periodic fluctuations in local conditions. These factors are predicted to strongly influence the resident microbial community structure and functioning, and alter the structure of aquatic food webs and biogeochemical cycles. Nevertheless, little is known about the spatial distribution of metabolic properties across salinity gradients, and no study has simultaneously surveyed the sediment and water environments. Here, we determined patterns and drivers of benthic and planktonic prokaryotic and microeukaryotic community assembly across a river and tidal lagoon system by collecting sediments and planktonic biomass at nine shallow subtidal sites in the summer. Genomic and transcriptomic analyses, alongside a suite of complementary geochemical data, were used to determine patterns in the distribution of taxa, mechanisms of salt tolerance, and nutrient cycling.

RESULTS

Taxonomic and metabolic profiles related to salt tolerance and nutrient cycling of the aquatic microbiome were found to decrease in similarity with increasing salinity, and distinct trends in diversity were observed between the water column and sediment. Non-saline and saline communities adopted divergent strategies for osmoregulation, with an increase in osmoregulation-related transcript expression as salinity increased in the water column due to lineage-specific adaptations to salt tolerance. Results indicated a transition from phosphate limitation in freshwater habitats to nutrient-rich conditions in the brackish zone, where distinct carbon, nitrogen and sulfur cycling processes dominated. Phosphorus acquisition-related activity was highest in the freshwater zone, along with dissimilatory nitrate reduction to ammonium in freshwater sediment. Activity associated with denitrification, sulfur metabolism and photosynthesis were instead highest in the brackish zone, where photosynthesis was dominated by distinct microeukaryotes in water (Cryptophyta) and sediment (diatoms). Despite microeukaryotes and archaea being rare relative to bacteria, results indicate that they contributed more to photosynthesis and ammonia oxidation, respectively.

CONCLUSIONS

Our study demonstrates clear freshwater-saline and sediment-water ecosystem boundaries in an interconnected coastal aquatic system and provides a framework for understanding the relative importance of salinity, planktonic-versus-benthic habitats and nutrient availability in shaping aquatic microbial metabolic processes, particularly in tidal lagoon systems. Video abstract.

Genome analysis of Pseudomonas sp. OF001 and Rubrivivax sp. A210 suggests multicopper oxidases catalyze manganese oxidation required for cylindrospermopsin transformation

BACKGROUND

Cylindrospermopsin is a highly persistent cyanobacterial secondary metabolite toxic to humans and other living organisms. Strain OF001 and A210 are manganese-oxidizing bacteria (MOB) able to transform cylindrospermopsin during the oxidation of Mn²⁺. So far, the enzymes involved in manganese oxidation in strain OF001 and A210 are unknown. Therefore, we analyze the genomes of two cylindrospermopsin-transforming MOB, Pseudomonas sp. OF001 and Rubrivivax sp. A210, to identify enzymes that could catalyze the oxidation of Mn²⁺. We also investigated specific metabolic features related to pollutant degradation and explored the metabolic potential of these two MOB with respect to the role they may play in biotechnological applications and/or in the environment.

RESULTS

Strain OF001 encodes two multicopper oxidases and one haem peroxidase potentially involved in Mn²⁺ oxidation, with a high similarity to manganese-oxidizing enzymes described for Pseudomonas putida GB-1 (80, 83 and 42% respectively). Strain A210 encodes one multicopper oxidase potentially involved in Mn²⁺ oxidation, with a high similarity (59%) to the manganese-oxidizing multicopper oxidase in Leptothrix discophora SS-1. Strain OF001 and A210 have genes that might confer them the ability to remove aromatic compounds via the catechol meta- and ortho-cleavage pathway, respectively. Based on the genomic content, both strains may grow over a wide range of O₂ concentrations, including microaerophilic conditions, fix nitrogen, and reduce nitrate and sulfate in an assimilatory fashion. Moreover, the strain A210 encodes genes which may convey the ability to reduce nitrate in a dissimilatory manner, and fix carbon via the Calvin cycle. Both MOB encode CRISPR-Cas systems, several predicted genomic islands, and phage proteins, which likely contribute to their genome plasticity.

CONCLUSIONS

The genomes of Pseudomonas sp. OF001 and Rubrivivax sp. A210 encode sequences with high similarity to already described MCOs which may catalyze manganese oxidation required for cylindrospermopsin transformation. Furthermore, the analysis of the general metabolism of two MOB strains may contribute to a better understanding of the niches of cylindrospermopsin-removing MOB in natural habitats and their implementation in biotechnological applications to treat water.

Unraveling bacterial community structure and function and their links with natural salinity gradient in the Yellow River Delta

Salinization can change the soil environment and affect microbial processes. In this study, soil samples were collected from Zone A (Phragmites australis wetlands), Zone B (P. australis and Suaeda salsa wetlands), and Zone C (Spartina alterniflora wetlands) in the Yellow River Delta. The microbial community and functional potential along the natural salinity gradient were investigated. Total nitrogen, ammonia nitrogen, and soil organic matter presented a downward trend, and salinity first increased and then decreased from Zone A to Zone C. Nitrospira and norank_f_Nitrosomonadaceae were widely distributed throughout the zones. Denitrifying bacteria Alcanivorax, Marinobacterter, and Marinobacterium were abundant in Zone B and preferred high salinity levels. However, denitrifying bacteria Azoarcus, Flavobacterium, and Pseudomonas were mainly distributed in low-salinity Zones A and C, suggesting their high sensitivity to salinity. Dissimilatory nitrate reduction to ammonia (DNRA) bacteria Aeromonas and Geobacter dominated Zone C, whereas Caldithrix performed DNRA in Zone B. Interestingly, DNRA with organic matter as the electron donor (C-DNRA) occurred in Zone A; DNRA coupled with sulfide oxidation (S-DNRA) was dominant in Zone B; and C-DNRA and DNRA with divalent iron as electron donor and S-DNRA occurred simultaneously in Zone C. Salinity was the key factor distinguishing low and high salinity zones, and total nitrogen and total phosphorus had important effects at the phylum and genus levels. The abundance of genes encoding cell growth and death was relatively stable, indicating that the microbial community had good environmental adaptability. The genes related to the biodegradation of xenobiotics and the metabolism of terpenoids and polyketides were abundant in Zone B, revealing high metabolic potential for exogenous refractory substances. The microorganisms under low-salinity Zones A and C were more sensitive to environmental changes than those under Zone B. These results suggest that salinity plays important roles in microbial processes and shapes specific functional zones in coastal wetlands.

Abundance and Functional Importance of Complete Ammonia Oxidizers and Other Nitrifiers in a Riparian Ecosystem

The discovery of complete ammonia oxidation (comammox) has altered our understanding of nitrification, which is the rate-limiting process in the global nitrogen cycle. However, understanding the ecological role of comammox or its contribution to nitrification in both natural and artificial ecosystems is still in its infancy. Here, we investigated the community distribution and function of comammox bacteria in riparian ecosystems and analyzed interactions between comammox and other nitrogen cycling microorganisms. The comammox bacterial abundance and rate were higher in summer than in winter and higher in nonrhizosphere soils than in the rhizosphere. Fringe soils in the riparian zone comprise a comammox hotspot, where the abundance (2.58 × 10⁸ copies g^-1) and rate (0.86 mg N kg^-1 d^-1) of comammox were not only higher than at other sampling sites but also higher than those of other ammonia oxidation processes. The comammox rate correlated significantly positively with relative abundance of the comammox species Candidatus Nitrospira nitrificans but not with that of the species Candidatus Nitrospira nitrosa. Analysis of comammox interaction with other ammonia-oxidizing processes revealed ammonia-oxidizing archaea to dominate interface soils, comammox to dominate in fringe soils, and anaerobic ammonium oxidation (anammox) to dominate in interface sediments of the riparian zone. These results indicate that comammox may constitute an important and currently underestimated process of microbial nitrification in riparian zone ecosystems.

Shift in nitrogen transformation in peatland soil by nitrogen inputs

Inputs of nitrogen (N) to peatlands in the form of fertilizers have rapidly increased due to the intensification of agricultural systems, impacting ecological processes, and the carbon storage function of peatland. However, detailed information on the impacts of long-term N inputs on the individual steps of N transformation processes in peatland soils still needs to be fully understood. We investigated N mineralization and nitrification rates as well as nitrite dependent anaerobic methane oxidation (n-damo), anaerobic ammonium oxidation (anammox), denitrification, and dissimilatory nitrate reduction to ammonium (DNRA) in a peatland affected by N inputs for >50 years, using isotope tracing technique and quantitative PCR. Based on the results, N inputs increased N mineralization and nitrification rates by 77 and 43%, respectively. Notably, the contributions of n-damo and anammox to N₂ production were enhanced by 242 and 170%, accounting for 30 and 12%, respectively. The contributions of denitrification and DNRA to N₂ production decreased by 27 and 52%, accounting for 48 and 10% of N₂ production, respectively. Nitrifier abundance increased significantly, with AOA being the dominant prokaryote (from 696 to 1090 copies g^-1), but AOB responded more strongly to N inputs (from 5 to 68 copies g^-1). The N inputs also promoted the growth of n-damo and anammox bacteria, whose abundances increased by 3.7% (from 565 to 586 copies g^-1) and 85.7% (from 305 to 567 copies g^-1), respectively, while denitrifier abundance was significantly reduced, with nirK and nirS abundances decreasing by 58% (from 738 to 308 copies g^-1) and 50% (from 218 to 109 copies g^-1), respectively. Soil pH was the key environmental factor influencing N transformations. We show that n-damo plays important roles in N cycling in peatland subjected to N inputs, providing a scientific basis for improved peatland management.

Response of ammonia oxidation activities to water-level fluctuations in riparian zones in a column experiment

Biogeochemical hotspots of nitrogen cycling such as ammonia oxidation commonly occur in riparian ecosystems. However, the responses of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to water-level fluctuations (WLF) in riparian zones remain unclear. In this study, two patterns of WLF (gradual waterlogging and drying) were investigated in a 9-month column experiment, and the abundances and activities of AOA and AOB were investigated. The recovery evaluation revealed AOB abundance had not returned to the initial level at the end of the experiment, while AOA abundance had recovered nearly completely. AOA outnumbered AOB at almost all depths, and AOA showed higher resistance and adaptation to WLF than AOB. However, higher microbial abundance was not always linked to the larger contribution to nitrification. Changes in environmental parameters such as moisture and dissolved oxygen caused by WLF instead of ammonia-oxidizing microorganism (AOM) abundance might play a key role in regulating the expression of amoA gene and thus the activity of ammonia oxidizers. In addition, the community structure of AOM evolved over the incubation period. The composition of AOA species in sediment changed in the same way as that in soil, and the Nitrosopumilus cluster showed strong resistance to WLF. Conversely, waterlogging changed the community structure of AOB in soil while drying had no significant effect on the AOB community structure in sediment. This study suggests that the ammonia oxidizers will respond to WLF and eventually affect N fate in riparian ecosystems considering the coupling with other N transformation processes.

The bacterial community structure and N-cycling gene abundance in response to dam construction in a riparian zone

Dam construction has significantly altered riparian hydrological regime and environmental conditions in the reservoir region, yet knowledge concerning how bacterial community and N-cycling genes respond to these changes remains limited. In this study, we investigated the bacterial community composition, network structure and N-cycling genes in the water level fluctuation zones (WLFZs) of the Three Gorges Reservoir (TGR). Here, samples collected from five different water levels were divided into three groups: waterward sediments, interface sediments, and landward soils. Our results show that higher contents of NO₂^--N, SOC, DOC, NH₄⁺-N, and TP were characterized in waterward and interface sediments whereas higherNO₃^--N content was observed in landward soils. The α-diversity of bacterial community decreased gradually from waterward sediments to landward soils. Compared with waterward sediments and landward soils, the interface sediments showed a unique bacterial community pattern with diverse primary producers as well as N-cycling microbes. The interface sediments also had a much more complex co-occurrence network and a higher possible community stability. Among all of N-cycling genes, higher abundances of nrfA and AOA amoA genes were observed in interface sediments. The dissimilarity in bacterial community composition and N-cycling gene abundance was mainly driven by water-level. Moreover, random forest model revealed that AOA amoA and nirS genes were the most sensitive indicators in response to water level fluctuations. Overall, this study suggests distinct abundance, diversity, and network structure of microbes in riparian sediments and soils across the gradient of water levels and enhances our understanding with respect to comprehensive effects of dam construction on nitrogen cycle.