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Research on the impact of seawater intrusion on nitrogen (N) cycling in coastal estuarine ecosystems is crucial; however, there is still a lack of relevant research conducted under in-situ field conditions. The effects of elevated salinity on N cycling processes and microbiomes were examined in situ seawater intrusion experiments conducted from 2019 to 2021 in the Nakdong River Estuary (South Korea), where an estuarine dam regulates tidal hydrodynamics. After the opening of the Nakdong Estuary Dam (seawater intrusion event), the density difference between seawater and freshwater resulted in varying degrees of seawater trapping at topographically deep stations. Bottom-water oxygen conditions had been altered in normoxia, hypoxia, and weak hypoxia due to the different degrees of seawater trapping in 2019, 2020, and 2021, respectively. Denitrification mostly dominated the nitrate (NO3-) reduction process, except in 2020 after seawater intrusion. However, denitrification rates decreased because of reduced coupled nitrification after seawater intrusion due to the dissolved oxygen limitation in 2020. Dissimilatory nitrate reduction to ammonium (DNRA) rates immediately increased after seawater intrusion in 2020, replacing denitrification as the dominant pathway in the NO3- reduction process. The enhanced DNRA rate was mainly due to the abundant organic matter associated with seawater invasion and more reducing environment (maybe sulfide enhancement effects) under high seawater-trapping conditions. Denitrification increased in 2021 after seawater intrusion during weak hypoxia; however, DNRA did not change. Small seawater intrusion in 2019 caused no seawater trapping and overall normoxic condition, though a slight shift from denitrification to DNRA was observed. Metagenomic analysis revealed a decrease in overall denitrification-associated genes in response to seawater intrusion in 2019 and 2020, while DNRA-associated gene abundance increased. In 2021 after seawater intrusion, microbial gene abundance associated with denitrification increased, while that of DNRA did not change significantly. These changes in gene abundance align mostly with alterations in nitrogen transformation rates. In summary, ecological change effects in N cycling after the dam opening (N retention or release, that is, eutrophication deterioration or mitigation) depend on the degree of seawater intrusion and the underlying freshwater conditions, which constitute the extent of seawater-trapping.

Mangrove wetlands are hotspots of the global nitrogen (N) cycle and important sinks of microplastics (MPs) due to their ecotone location between terrestrial and marine ecosystems. However, the effects of MPs on N cycle processes in mangrove ecosystems are still poorly understood. Thus, the present study assessed the impacts by adding MPs to mangrove sediments in a microcosm incubation experiment. The results showed that MPs increased dissolved organic carbon and nitrate but reduced ammonium contents in the sediments. MPs increased C:N stoichiometric and N:C-acquiring enzymatic ratios, indicating an intensified N limitation in mangrove sediments following exposure of MPs. MPs decreased microbial community diversity and shifted sediment microbial communities from r- to K-strategists, consistent with the intensified N limitation. In response, dissimilatory nitrate reduction to ammonium (DNRA) rates increased while nitrous oxide (N2O) production reduced suggesting more efficient N utilization in MPs treatments. The MPs with heteroatoms such as PLA- and PVC-MPs, increased DNRA rates by 67.5–78.7%, exhibiting a stronger impact than PE-MPs. The variation partitioning analysis revealed that the variances of DNRA rates and N2O production could be attributed to synergistic effects of physicochemical properties, nutrient limitation, and microbial community in mangrove sediments. Overall, this study provides pertinent insights into the impacts of MPs as a new carbon source on nutrient limitation and N turnover in mangrove ecosystems.

A comprehensive understanding of the mobility of both nitrogen (N) and phosphorus (P) and the inter-relationships between P, N, and iron (Fe) in sediments is important for controlling the "internal loadings" of nutrients in lakes. In this research, diffusive gradients in thin film (DGT) assemblies with binding layers (ZrO-AT, chelex, and ZrO) were designed for PO4-P, Fe, ammonium (NH4-N), and nitrate (NO3-N) at sediment/water interface (SWI) in Western Lake Taihu (China). The biogeochemical processes of N and P related to the physicochemical properties, the dynamic P transfer, the distribution characteristics of P microniches, and the estimation of the release risks in sediments in Western Lake Taihu were simultaneously revealed by the passive sampling technique-DGT with the high spatial resolutions (millimeter and sub-millimeter). Based on DGT concentration (CDGT) related to physicochemical properties in sediments, (1) P biogeochemical reactions included P release from Fe-bound P during Fe reduction, algae biomass decomposition, and phosphatase enzyme activity increased by NH4-N; (2) denitrification and dissimilatory nitrate reduction to ammonium (DNRA) led to exchangeable ammonium (NH4ex) enrichment and NH4-N release; anammox depleted NH4-N transfer; organic matter (OM) mineralization favored NH4-N release; and (3) aerobic nitrification led to NO3-N remobilization; denitrification and DNRA reduced NO3-N release. Redox status, OM, Fe, aluminum, or calcium influenced mobilization of nutrients. The numerical model of DGT-induced fluxes in sediments was used for dynamic P transfers with resupply types ("slow" ~ "fast") controlled by labile P pool, resupply constant, response time, and Dspt rate. The formation of P microniches in two dimensions was revealed. Sediment P release risk index (0.49 ~ 36.85 [lg (nmol cm−3 d−1)]) with "light" ~ "high" risks and diffusive fluxes across SWI (µg m−2 d−1) of 15.0 ~ 639 (PO4-P), − 1403 ~ 5010 (NH4-N), and − 1395 ~ 149 (NO3-N) were derived and lake management strategies were provided. The DGT technique provides the characterization of the mobilization of nutrients and evidence for biogeochemical processes at the fine spatial scales for control of internal loadings in sediments. [ABSTRACT FROM AUTHOR]

Invasive plants can increase soil nitrogen (N) pools and accelerate soil N cycling rates, but their effect on gross N cycling and nitrous oxide (N2 O) emissions has rarely been studied. We hypothesized that perennial pepperweed (Lepidium latifolium) invasion would increase rates of N cycling and gaseous N loss, thereby depleting ecosystem N and causing a negative feedback on invasion. We measured a suite of gross N cycling rates and net N2 O fluxes in invaded and uninvaded areas of an annual grassland in the Sacramento-San Joaquin River Delta region of northern California. During the growing season, pepperweed-invaded soils had lower microbial biomass N, gross N mineralization, dissimilatory nitrate reduction to ammonium (DNRA), and denitrification-derived net N2 O fluxes (P

Dissimilatory nitrate reduction to ammonium (DNRA) has an important role in soil nitrogen retention and is considered to be constrained to anaerobic conditions. However, a recent study found that Pseudomonas putida Y-9 is capable of DNRA under aerobic conditions. In this study, four species of Pseudomonas spp. were found to produce ammonium during the nitrite reduction process under aerobic conditions, similar to the Y-9 strain. The detectable ammonium in the culture supernatant during the nitrite reduction process for each of the four strains originated intracellularly. A subsequent 15N isotope experiment showed that these four strains were able to transform 15NO2− to 15NH4+ in 3 h under aerobic conditions. The NirBD sequence in each of the four strains showed high similarity with that in the Y-9 strain (approximately 94.61%). Moreover, the nirBD sequences in the four strains and the Y-9 strain were all similar to those of other Pseudomonas spp., while they were relatively distant in terms of their phylogenetic relationship from those of other genera. Overall, these results suggest that these four strains of Pseudomonas spp. are capable of DNRA under aerobic conditions, which might be attributed to the existence of nirBD.

[Display omitted] • Anammox sludge drives iron reduction using extracellular polymeric substances. • Fe(II) promotes partial DNRA pathway of anammox with nitrite as end products. • Accumulated nitrite is further eliminated with ammonium via anammox pathway. • Nitrogen removal efficiency of the iron-assisted anammox process reaches 95%. Anammox is recognized as a prospective alternative for future biological nitrogen removal technologies. However, the nitrate by-products produced by anammox bacteria limit its overall nitrogen removal efficiency below 88 %. This study introduced Fe(III) into the anammox bioreactor to enhance the nitrogen removal efficiency to approximately 95 %, surpassing the biochemical limit of 88 % imposed by anammox stoichiometry. Anammox sludge was demonstrated to utilize extracellular polymeric substances to reduce Fe(III) into Fe(II), and this process promoted the dominance of Ca. Brocadia. The iron addition improved the abundance of narGHI genes and facilitated the partial dissimilatory nitrate reduction to ammonium, with nitrite as the end product. The accumulated nitrite was then eliminated through the anammox pathway, along with the excess ammonium (30 mg/L) in the influent. Overall, this study deepens our understanding of the enhanced nitrogen removal triggered by Fe(III) in anammox sludge and offers an effective approach to boost anammox process. [ABSTRACT FROM AUTHOR]

[Display omitted] • nZVI-BC adoption improved N removal during DO shock, recovery, and stable periods. • nZVI-BC was conducive to enrich AnAOB and anammox-related functional genes. • nZVI-BC adoption heightened the robustness and interaction of microbial community. • EPS-mediated EET process was improved due to the superior electroactivity of nZVI-BC. • Candidatus Brocadia driven-DNRA enhanced by nZVI-BC also promoted the N removal. Anaerobic ammonium oxidation (Anammox) is recognized as a promising option to energy-neutral wastewater treatment, yet difficulties encountered in practice due to its poor stability. This work investigated the effects of biochar-supported nano zero-valent iron (nZVI-BC) on nitrogen removal performance of anammox process. Three membrane bioreactors (MBRs) suitable for slowly growing anammox bacteria was operated for 100 days, undergoing startup, dissolved oxygen (DO) inhibition, performance recovery and stabilization periods. The results showed that nZVI-BC adoption could improve the nitrogen removal efficiency (NRE) by 5.5–27.3 % and 3.1–20.7 % and nitrogen removal rate (NRR) by 5.4–28.6 % and 3.2–22.9 %, compared with control group and biochar adoption, respectively. Throughout the experimental periods, nZVI-BC was conducive to enrich anammox bacteria and increased the functional gene copies associated with anammox metabolism. Meanwhile, co-occurrence network analysis promulgated that nZVI-BC boosted the robustness and interaction of microbial community. Furthermore, the electrochemical analysis of the extracellular polymeric substance (EPS) revealed that nZVI-BC adoption augmented the extracellular electron transport (EET) process of anammox biomass. Metagenomic sequencing revealed that nZVI-BC reinforced the complete dissimilatory nitrate reduction to ammonium (DNRA) pathway in Candidatus Brocadia , the dominant anammox bacteria, potentially reducing nitrate production and enhancing nitrogen removal. The study manifested the possibility of nZVI-BC to improve the anammox robustness and nitrogen removal performance, and provided operational guidance for its engineering application. [ABSTRACT FROM AUTHOR]

Bacteria belonging to the order Fimbriimonadales are frequently detected in anammox reactors. However, the principal functions of these bacteria and their potential contribution to nitrogen removal remain unclear. In this study, we aimed to systematically validate the roles of Fimbriimonadales in an anammox reactor fed with synthetic wastewater. High-throughput 16S rRNA gene sequencing analysis revealed that heterotrophic denitrifying bacteria (HDB) were the most abundant bacterial group at the initial stage of reactor operation and the abundance of Fimbriimonadales members gradually increased to reach 38.8 % (day 196). At the end of reactor operation, Fimbriimonadales decreased to 0.9 % with an increase in anammox bacteria. Correlation analysis demonstrated nitrate competition between Fimbriimonadales and HDB during reactor operation. Based on the phylogenetic analysis, the Fimbriimonadales sequences acquired from the reactor were clustered into three distinct groups, which included the sequences obtained from other anammox reactors. Metagenome-assembled genome analysis of Fimbriimonadales allowed the identification of the genes narGHI and nrfAH, responsible for dissimilatory nitrate reduction to ammonium (DNRA), and nrt and nasA, responsible for nitrate and nitrite transport. In a simulation based on mass balance equations and quantified bacterial groups, the total nitrogen concentrations in the effluent were best predicted when Fimbriimonadales was assumed to perform DNRA (R 2 = 0.70 and RMSE = 18.9). Moreover, mass balance analysis demonstrated the potential contribution of DNRA in enriching anammox bacteria and promoting nitrogen removal. These results prove that Fimbriimonadales compete with HDB for nitrate utilization through DNRA in the anammox reactor under non-exogenous carbon supply conditions. Overall, our findings suggest that the DNRA pathway in Fimbriimonadales could enhance anammox enrichment and nitrogen removal by providing substrates (nitrite and/or ammonium) for anammox bacteria., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

[Display omitted] • Redox CDs were prepared using sludge via the pyrolysis-Fenton reaction. • A strain MR-1/CDs-500 hybrid was constructed for the photosynthesis of NH 3. • CDs-500 provided a short-range photoelectron transfer pathway for NH 3 production. • CDs-500 addition resulted in 5.9-fold increase in NH 3 production efficiency. Combining the light-harvesting capabilities of photosensitizers with microbial catalysis shows great potential in solar-driven biomanufacturing. However, little information is available about the effects of photosensitizers on the photoelectron transport during the dissimilatory nitrate reduction to ammonium (DNRA) process. Herein, redox carbon dots (CDs-500) were prepared from sludge via the pyrolysis-Fenton reaction and then used to construct a photosynthetic system with Shewanella oneidensis MR-1. The MR-1/CDs-500 photosynthetic system showed a 5.9-fold increase in ammonia production (4.9 mmol(NH 3)·g−1(protein)·h−1) with a high selectivity of 94.0 %. The photoelectrons were found to be stored in CDs-500 and transferred into the cells. During the inward electron transport, the intracellular CDs-500 could be used as the direct photoelectron transfer stations between outer membrane cytochrome c and DNRA-related enzymes without the involvement of CymA and MtrA. This work provides a new method for converting waste into functional catalysts and increases solar-driven NH 3 production to a greater extent. [ABSTRACT FROM AUTHOR]

Microbial electrosynthesis is a promising solution for removing nitrate from water with a low concentration of electron donors. Three single-chamber microbial electrosynthesis reactors were constructed and operated for almost 2 years. The single-chamber reactor design saves on construction costs, and the pH of the solute is more stable than that in the case of a two-chamber reactor. Nitrate reduction started at the working electrode potential of −756 mV versus standard hydrogen electrode (SHE), and subsequently, the working electrode potential could be increased without hindering the process. The optimal potential was −656 mV versus SHE, where the highest Faradaic efficiency of 71% and the nitrate removal rate of 3.8 ± 1.2 mgN-NO3/(L×day) were registered. The abundances of nitrite reductase and nitrous oxide reductase genes were significantly higher on the working electrode compared to the counter electrode, indicating that the process was driven by denitrification. Therefore, a microbial electrosynthesis reactor was successfully applied to remove nitrate and can be utilized for purifying water when adding organic compounds as electron donors is not feasible, that is, groundwater. In addition, at the lower working electrode potentials, the dissimilatory nitrate reduction to ammonium was observed.

• Overlooked SDP enables nitrate to bypass denitrification to produce 61.1 % ammonium. • A previously concealed nitrogen fate with novel implication for ammonium recovery. • Addition of organic matter inhibits DNRA and weakens the robust network. • Genome-level interspecific relationship of SDP-coupled DNRA was discussed. Sulfur-based denitrification is a promising technology in treatments of nitrate-contaminated wastewaters. However, due to weak bioavailability and electron-donating capability of elemental sulfur, its sulfur-to-nitrate ratio has long been low, limiting the support for dissimilatory nitrate reduction to ammonium (DNRA) process. Using a long-term sulfur-packed reactor, we demonstrate here for the first time that DNRA in sulfur-based system is not negligible, but rather contributes a remarkable 40.5 %–61.1 % of the total nitrate biotransformation for ammonium production. Through combination of kinetic experiments, electron flow analysis, 16S rRNA amplicon, and microbial network succession, we unveil a cryptic in-situ sulfur disproportionation (SDP) process which significantly facilitates DNRA via enhancing mass transfer and multiplying 86.7–210.9 % of bioavailable electrons. Metagenome assembly and single-copy gene phylogenetic analysis elucidate the abundant genomes, including uc_VadinHA17, PHOS-HE36, JALNZU01, Thiobacillus , and Rubrivivax , harboring complete genes for ammonification. Notably, a unique group of self-SDP-coupled DNRA microorganism was identified. This study unravels a previously concealed fate of DNRA, which highlights the tremendous potential for ammonium recovery and greenhouse gas mitigation. Discovery of a new coupling between nitrogen and sulfur cycles underscores great revision needs of sulfur-driven denitrification technology. [Display omitted] [ABSTRACT FROM AUTHOR]

• Fe(III) induced ammonium formation via DNRA during nitrate dependent AOM. • N 2 O was produced during simultaneous Fe(III) and nitrate dependent AOM. • The Nrf bypass and reverse HURM-Cyt P460 pathways contributed to N 2 O production. • ' Ca. M. nitroreducens' producing N 2 O may offset its greenhouse gas reduction potential. ' Candidatus Methanoperedens nitroreducens' is an archaeal methanotroph with global importance that links carbon and nitrogen cycles and great potential for sustainable operation of wastewater treatment. It has been reported to mediate the anaerobic oxidation of methane through a reverse methanogenesis pathway while reducing nitrate to nitrite. Here, we demonstrate that ' Ca. M. nitroreducens' reduces ferric iron forming ammonium (23.1 %) and nitrous oxide (N 2 O, 46.5 %) from nitrate. These results are supported with the upregulation of genes coding for proteins responsible for dissimilatory nitrate reduction to ammonium (nrfA), N 2 O formation (norV, cyt P460), and multiple multiheme c-type cytochromes for ferric iron reduction. Concomitantly, an increase in the N 2 O-reducing SJA-28 lineage and a decrease in the nitrite-reducing ' Candidatus Methylomirabilis oxyfera' are consistent with the changes in ' Ca. M. nitroreducens' end products. These findings demonstrate the highly flexible physiology of ' Ca. M. nitroreducens' in anaerobic ecosystems with diverse electron acceptor conditions, and further reveals its roles in linking methane oxidation to global biogeochemical cycles. ' Ca. M. nitroreducens' could significantly affect the bioavailability of nitrogen sources as well as the emission of greenhouse gas in natural ecosystems and wastewater treatment plants. [Display omitted] [ABSTRACT FROM AUTHOR]

• Fe(Ⅲ)/ Fe(Ⅱ) cycle enables nitrate bio-reduction to ammonium at low C/N ratios. • Insoluble iron serves as the electron carrier. • Fe(Ⅲ)/ Fe(Ⅱ) cycle stimulated the upregulation of nrfA and downregulation of nirK. • Geobacter reserved by the Fe cycle exerted a vital role in ammonium production. The recovery of reactive nitrogen from industrial wastewater by biological ammoniation is a promising strategy of sustainable wastewater treatment. However, the low C/N ratio of pickling wastewater restricts nitrate towards ammonium, resulting in nitrogen loss. Here, we have proven the feasibility of nitrate ammoniation utilizing the Fe(Ⅲ)/Fe(Ⅱ) cycle at low C/N ratios, where partial organic electrons were employed to reduce Fe(Ⅲ) and the regenerated Fe(Ⅱ) facilitated ammoniation. It achieved the nitrate reduction efficiency of 96 ± 2 % and ammoniation efficiency of 49 ± 2 % for 3 cycles. Iron cycle enhanced the DNRA, demonstrated by the upregulation of nrfA and the downregulation of nirK. Electroactive Geobacter spp. with DNRA capability was sustained at high abundance (∼23 %) by the electron exchange process with extracellular iron. These findings provided a novel approach to recover active N using the iron cycle from wastewater, which has broader implications for sustainable circular economy and the ecology of carbon, iron and nitrogen cycle. [Display omitted] [ABSTRACT FROM AUTHOR]

Background: Assessments of the soil microbiome provide valuable insight to ecosystem function due to the integral role microorganisms play in biogeochemical cycling of carbon and nutrients. For example, treatment effects on nitrogen cycling functional groups are often presented alongside one another to demonstrate how agricultural management practices affect various nitrogen cycling processes. However, the functional groups commonly evaluated in nitrogen cycling microbiome studies range from phylogenetically narrow (e.g., N-fixation, nitrification) to broad [e.g., denitrification, dissimilatory nitrate reduction to ammonium (DNRA)]. The bioinformatics methods used in such studies were developed for 16S rRNA gene sequence data, and how these tools perform across functional genes of different phylogenetic diversity has not been established. For example, an OTU clustering method that can accurately characterize sequences harboring comparatively little diversity may not accurately resolve the diversity within a gene comprised of a large number of clades. This study uses two nitrogen cycling genes, nifH, a gene which segregates into only three distinct clades, and nrfA, a gene which is comprised of at least eighteen clades, to investigate differences which may arise when using heuristic OTU clustering (abundance-based greedy clustering, AGC) vs. true hierarchical OTU clustering (Matthews Correlation Coefficient optimizing algorithm, Opti-MCC). Detection of treatment differences for each gene were evaluated to demonstrate how conclusions drawn from a given dataset may differ depending on clustering method used. Results: The heuristic and hierarchical methods performed comparably for the more conserved gene, nifH. The hierarchical method outperformed the heuristic method for the more diverse gene, nrfA; this included both the ability to detect treatment differences using PERMANOVA, as well as higher resolution in taxonomic classification. The difference in performance between the two methods may be traced to the AGC method’s preferential assignment of sequences to the most abundant OTUs: when analysis was limited to only the largest 100 OTUs, results from the AGC-assembled OTU table more closely resembled those of the Opti-MCC OTU table. Additionally, both AGC and Opti-MCC OTU tables detected comparable treatment differences using the rank-based ANOSIM test. This demonstrates that treatment differences were preserved using both clustering methods but were structured differently within the OTU tables produced using each method. Conclusion: For questions which can be answered using tests agnostic to clustering method (e.g., ANOSIM), or for genes of relatively low phylogenetic diversity (e.g., nifH), most upstream processing methods should lead to similar conclusions from downstream analyses. For studies involving more diverse genes, however, care should be exercised to choose methods that ensure accurate clustering for all genes. This will mitigate the risk of introducing Type II errors by allowing for detection of comparable treatment differences for all genes assessed, rather than disproportionately detecting treatment differences in only low-diversity genes. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Ecology & Rural Environment is the property of Journal of Ecology & Rural Environment Editorial Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

BackgroundAssessments of the soil microbiome provide valuable insight to ecosystem function due to the integral role microorganisms play in biogeochemical cycling of carbon and nutrients. For example, treatment effects on nitrogen cycling functional groups are often presented alongside one another to demonstrate how agricultural management practices affect various nitrogen cycling processes. However, the functional groups commonly evaluated in nitrogen cycling microbiome studies range from phylogenetically narrow (e.g., N-fixation, nitrification) to broad [e.g., denitrification, dissimilatory nitrate reduction to ammonium (DNRA)]. The bioinformatics methods used in such studies were developed for 16S rRNA gene sequence data, and how these tools perform across functional genes of different phylogenetic diversity has not been established. For example, an OTU clustering method that can accurately characterize sequences harboring comparatively little diversity may not accurately resolve the diversity within a gene comprised of a large number of clades. This study uses two nitrogen cycling genes, nifH, a gene which segregates into only three distinct clades, and nrfA, a gene which is comprised of at least eighteen clades, to investigate differences which may arise when using heuristic OTU clustering (abundance-based greedy clustering, AGC) vs. true hierarchical OTU clustering (Matthews Correlation Coefficient optimizing algorithm, Opti-MCC). Detection of treatment differences for each gene were evaluated to demonstrate how conclusions drawn from a given dataset may differ depending on clustering method used.ResultsThe heuristic and hierarchical methods performed comparably for the more conserved gene, nifH. The hierarchical method outperformed the heuristic method for the more diverse gene, nrfA; this included both the ability to detect treatment differences using PERMANOVA, as well as higher resolution in taxonomic classification. The difference in performance between the two methods may be traced to the AGC method’s preferential assignment of sequences to the most abundant OTUs: when analysis was limited to only the largest 100 OTUs, results from the AGC-assembled OTU table more closely resembled those of the Opti-MCC OTU table. Additionally, both AGC and Opti-MCC OTU tables detected comparable treatment differences using the rank-based ANOSIM test. This demonstrates that treatment differences were preserved using both clustering methods but were structured differently within the OTU tables produced using each method.ConclusionFor questions which can be answered using tests agnostic to clustering method (e.g., ANOSIM), or for genes of relatively low phylogenetic diversity (e.g., nifH), most upstream processing methods should lead to similar conclusions from downstream analyses. For studies involving more diverse genes, however, care should be exercised to choose methods that ensure accurate clustering for all genes. This will mitigate the risk of introducing Type II errors by allowing for detection of comparable treatment differences for all genes assessed, rather than disproportionately detecting treatment differences in only low-diversity genes.

The effects of seasonal hypoxia on sediment-water interface nitrogen (N) transformations in Jinhae Bay were examined from 2015 to 2019. The rates of benthic denitrification, anaerobic ammonium oxidation (anammox), dissimilatory nitrate reduction to ammonium (DNRA), nutrient exchange, and sediment oxygen consumption were measured seasonally. The oxygen (O2) and hydrogen sulfide (H2S) depth profiles were measured using microelectrodes. Neither penetration nor consumption of oxygen decreased during hypoxia. Denitrification, anammox, and DNRA ranged from 0 to 0.73, 0.13, and 1.09 mmol N m-2 day-1, respectively. Denitrification, the dominant N removal pathway, increased by 75% while anammox ceased, which led to an overall increase of 55% in the total N2 gas production during hypoxia relative to that during normoxia. Enhanced denitrification is the result of increased coupled nitrification–denitrification due to the intermittent supply of oxygen during bottom water hypoxia (“weak hypoxia”). In the hypoxic period, DNRA decreased by 62%, and the relative contribution of DNRA to the total nitrogen reduction process decreased from 81 to 58%, but it still outperformed denitrification as the main nitrate reduction pathway. Sediments were strong sources of ammonium for the water column, both under normoxia and hypoxia, whereas they were a sink of nitrate from the water column during hypoxia. Bioturbation may be important for maintaining oxygen penetration and consumption in sediments. The dominance of DNRA was mainly due to the relatively high content of sulfide and organic-rich sediments. The repressed macrofaunal activity and increased coupling of nitrification and denitrification during hypoxia may have contributed to enhanced denitrification. Taken together, the overall dominance of DNRA might contribute to the development and maintenance of eutrophication and seasonal hypoxia in this system. However, in contrast to the previous results, denitrification was enhanced during “weak hypoxia,” which might be helpful in alleviating eutrophication.

Copyright of Journal of Henan University of Science & Technology, Natural Science is the property of Editorial Office of Journal of Henan University of Science & Technology and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Human activities have led to 1–2% of coastal wetlands lost per year globally, with subsequent losses in ecosystem services such as nutrient filtering and carbon sequestration. Wetland construction is used to mitigate losses of marsh cover and services resulting from human impacts in coastal areas. Though marsh structure can recover relatively quickly (i.e., <10 years) after construction, there are often long‐term lags in the recovery of ecosystem functions in constructed marshes. We conducted a year‐long study comparing seasonal plant productivity, ecosystem respiration (ERCO2), denitrification, and dissimilatory nitrate reduction to ammonium (DNRA) between two 33‐year‐old constructed marshes (CON‐1, CON‐2) and a nearby natural reference marsh (NAT). We found that CON‐1 and CON‐2 were structurally similar to NAT (i.e., plant aboveground and belowground biomass did not differ). Likewise, gross ecosystem productivity (GEP), ERCO2, and net ecosystem exchange (NEE) were similar across all marshes. Further, DNRA and denitrification were similar across marshes, with the exception of greater denitrification rates at CON‐2 than at the other two sites. While pore‐water ammonium concentrations were similar across all marshes, organic matter (OM) content, pore‐water phosphate, nitrate + nitrite, and hydrogen sulfide concentrations were greater in NAT than CON‐1 and CON‐2. Collectively, this work suggests that current marsh construction practices could be a suitable tool for recovering plant structure and some ecosystem functions. However, the lag in recovery of pore‐water nutrient stocks and OM content also suggests that some biogeochemical functions may take longer than a few decades to fully recover in constructed marshes. [ABSTRACT FROM AUTHOR]

Salt marshes currently play an important role as filters for upslope nitrogen (N) inputs. This could change in the future with sea level rise, warming and eutrophication, which are expected to favor monocultures over diverse plant communities. We explored patterns in gross N cycling, dissimilatory nitrate (NO3-) reduction to ammonium (NH4+) (DNRA), and denitrification in a salt marsh soil under two typical redox conditions (aerobic and anaerobic), and in soils under plant communities manipulated to simulate potential future composition (forb and graminoid monocultures). Natural salt marsh soils exhibited high potential gross N mineralization rates. Averaging 50.4 6 5.7 lg N g-1 d-1 under aerobic conditions; rates declined to 23.6 6 3.4 lg N g-1 d-1 under an N2 headspace. Microbial NH4+ uptake and gross nitrification together accounted for only 14 % of gross N mineralization. Nitrogen retention via DNRA and microbial uptake greatly exceeded N losses via denitrification. Gross nitrification rates were greater in the forb and graminoid monocultures than in the control. This effect may be mediated by the lower plant biomass in the monocultures than in the control, which may have reduced competition between plants and nitrifiers for NH4+. Soil NO3- concentrations and net nitrous oxide (N2O) fluxes were greatest for the forb monoculture, likely due to higher soil oxygen (O2) concentrations in these plots. Our results suggest that salt marsh soils with a diverse plant community have high potential rates of N mineralization and microbial N retention, and the establishment of forb monocultures could lead to greater ecosystem N losses.

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

[Display omitted] • MPs altered nitrogen (N) turnover in mangrove sediments. • Stochiometric and enzymatic ratios showed MPs intensified N limitation. • MPs shifted the microbial communities from r - to K -strategists. • MPs promoted DNRA rates but inhibited N 2 O production for efficient N utilization. Mangrove wetlands are hotspots of the global nitrogen (N) cycle and important sinks of microplastics (MPs) due to their ecotone location between terrestrial and marine ecosystems. However, the effects of MPs on N cycle processes in mangrove ecosystems are still poorly understood. Thus, the present study assessed the impacts by adding MPs to mangrove sediments in a microcosm incubation experiment. The results showed that MPs increased dissolved organic carbon and nitrate but reduced ammonium contents in the sediments. MPs increased C:N stoichiometric and N:C-acquiring enzymatic ratios, indicating an intensified N limitation in mangrove sediments following exposure of MPs. MPs decreased microbial community diversity and shifted sediment microbial communities from r - to K -strategists, consistent with the intensified N limitation. In response, dissimilatory nitrate reduction to ammonium (DNRA) rates increased while nitrous oxide (N 2 O) production reduced suggesting more efficient N utilization in MPs treatments. The MPs with heteroatoms such as PLA- and PVC-MPs, increased DNRA rates by 67.5–78.7%, exhibiting a stronger impact than PE-MPs. The variation partitioning analysis revealed that the variances of DNRA rates and N 2 O production could be attributed to synergistic effects of physicochemical properties, nutrient limitation, and microbial community in mangrove sediments. Overall, this study provides pertinent insights into the impacts of MPs as a new carbon source on nutrient limitation and N turnover in mangrove ecosystems. [ABSTRACT FROM AUTHOR]

[Display omitted] • NO 3 –-N transformation was affected by simultaneous intervention of pyrite and C/N. • Pyrite exerted different effects on NO 3 –-N removal pathways at different C/N ratio. • Pyrite facilitated TOC and NO 3 –-N removal of CWs. • Incorporating the pyrite significantly reduced the GHGs emissions from CWs. • Key functional genes of denitrification and DNRA were enriched in PY-VFCW. Pyrite-based constructed wetlands (CWs) stimulated nitrate removal performance at low carbon to nitrogen (C/N) ratio has been gaining widely attention. However, the combined effects of pyrite and C/N on the nitrate removal mechanisms and greenhouse gases (GHGs) reduction were ignored. This study found that pyrite-based CWs significantly enhanced nitrate removal in C/N of 0, 1.5 and 3 by effectively driving autotrophic denitrification with high abundance of autotrophs denitrifiers (Rhodanobacter) and nitrate reductase (EC 1.7.7.2), while the enhancement was weakened in C/N of 6 by combined effect of mixotrophic denitrification and dissimilatory nitrate reduction to ammonium (DNRA) with high abundance of organic carbon-degrading bacteria (Stenotrophobacter) and DNRA-related nitrite reductase genes (nrf). Moreover, pyrite addition significantly reduced GHGs emissions from CWs in all stages with the occurrence of iron-coupled autotrophic denitrification. The study shed light on the potential mechanism for pyrite-based CWs for treating low C/N ratio wastewater. [ABSTRACT FROM AUTHOR]

• Bacterial genes involved in carbon and nitrogen cycling in a tropical peatland were identified. • All isolates likely performed methanotrophy. • Nitrogen is likely retained in tropical peatlands through dissimilatory nitrate reduction to ammonium. Tropical peat swamp forests are waterlogged, acidic, anoxic and oligotrophic ecosystems. They are important terrestrial carbon pools that help mitigating global warming through carbon sequestration in peat. This study aimed at investigating putative roles of bacteria in the carbon and nitrogen cycles in North Selangor peat swamp forest, Malaysia. Whole-genome sequencing was performed on four bacterial isolates using Illumina NextSeq 500 to decipher their genetic information while Gen III Microplate (Biolog) was applied to verify carbon source utilization. The isolates were identified as Dyella sp. strain C9, Dyella sp. strain C11, Klebsiella sp. strain C31 and Paraburkholderia sp. strain C35. Both Dyella spp. and Paraburkholderia sp. strain C35 were likely novel species while Klebsiella sp. strain C31 was a different strain of the type species, Klebsiella pneumoniae. Both genomic and bioassay results suggested the involvement of the isolates in the degradation of lignocellulose, carbohydrates, sugar alcohols, organic acids and aromatic compounds. The isolates could potentially perform methanotrophy, which helps to mitigate methane emissions from tropical peatlands. In addition, the isolates also contained genes encoding enzymes for nitrite, nitrate and nitric oxide reduction, as well as dissimilatory nitrate reduction to ammonium, which retains the nitrogen in the ecosystems. The results generated insights into potential functions of bacteria in the energy production and nutrient cycling of tropical peatlands, which are essential for the sustainability of high biomass and biodiversity in these ecosystems. [ABSTRACT FROM AUTHOR]

Un-fertilized rice paddies have shown maintained soil nitrogen (N) status, stable N supply to the rice plant and sustained rice yields at moderate levels for hundreds of years. Microbial N2 fixation is known to contribute N to un-fertilized paddies, but it cannot fully explain the maintained N nutrition, where favourable conditions exist for N loss by denitrification. We used 15N tracer, 15N2 uptake, acetylene reduction assay and qPCR to simultaneously investigate N2 fixation, dissimilatory nitrate reduction to ammonium (DNRA), denitrification and related microbial gene abundances in long-term low (or no) and high N input rice paddies of Myanmar. We also determined how varying soil organic carbon-to-nitrate (SOC/NO3−) ratios affect nitrate partitioning between DNRA and denitrification by manipulating these ratios through labile organic carbon addition. We observed more than 2.5 times higher N2 fixation (1.49–2.08 μg N g−1 soil day−1) and significantly higher N2 fixing gene (nifH) abundance in low compared with high N input paddies. Up to 60% of the soil nitrate (1.51–2.67 μg NO3−-N g−1 soil day−1) was ammonified through DNRA, and only 15% was lost as N2 through denitrification in low N input paddies, whereas denitrification exceeded DNRA in high N input paddies. The microbial gene related to DNRA activity (nrfA) was also higher in low input than in high input rice paddies. We found that nitrate retention can be improved in high N input rice paddies by maintaining a higher soil organic carbon-to-nitrate ratio. Our findings highlight the unique microbial N-cycling strategies in resource-limited paddies which support maintained N nutrition of the paddy system. [ABSTRACT FROM AUTHOR]

Aims: This study was done to obtain denitrifiers that could be used for bioaugmentation in woodchip bioreactors to remove nitrate from agricultural subsurface drainage water. Methods and Results: We isolated denitrifiers from four different bioreactors in Minnesota, and characterized the strains by measuring their denitrification rates and analysing their whole genomes. A total of 206 bacteria were isolated from woodchips and thick biofilms (bioslimes) that formed in the bioreactors, 76 of which were able to reduce nitrate at 15°C. Among those, nine potential denitrifying strains were identified, all of which were isolated from the woodchip samples. Although many nitrate‐reducing strains were isolated from the bioslime samples, none were categorized as denitrifiers but instead as carrying out dissimilatory nitrate reduction to ammonium. Conclusions: Among the denitrifiers confirmed by 15N stable isotope analysis and genome analysis, Cellulomonas cellasea strain WB94 and Microvirgula aerodenitrificans strain BE2.4 appear to be promising for bioreactor bioaugmentation due to their potential for both aerobic and anaerobic denitrification, and the ability of strain WB94 to degrade cellulose. Significance and Impact of the Study: Denitrifiers isolated in this study could be useful for bioaugmentation application to enhance nitrate removal in woodchip bioreactors. [ABSTRACT FROM AUTHOR]

The bacterial species "Candidatus Alkanivorans nitratireducens" was recently demonstrated to mediate nitrate-dependent anaerobic oxidation of short-chain gaseous alkanes (SCGAs). In previous bioreactor enrichment studies, the species appeared to reduce nitrate in two phases, switching from denitrification to dissimilatory nitrate reduction to ammonium (DNRA) in response to nitrite accumulation. The regulation of this switch or the nature of potential syntrophic partnerships with other microorganisms remains unclear. Here, we describe anaerobic multispecies cultures of bacteria that couple the oxidation of propane and butane to nitrate reduction and the oxidation of ammonium (anammox). Batch tests with 15N-isotope labelling and multi-omic analyses collectively supported a syntrophic partnership between "Ca. A. nitratireducens" and anammox bacteria, with the former species mediating nitrate-driven oxidation of SCGAs, supplying the latter with nitrite for the oxidation of ammonium. The elimination of nitrite accumulation by the anammox substantially increased SCGA and nitrate consumption rates, whereas it suppressed DNRA. Removing ammonium supply led to its eventual production, the accumulation of nitrite, and the upregulation of DNRA gene expression for the abundant "Ca. A. nitratireducens". Increasing the supply of SCGA had a similar effect in promoting DNRA. Our results suggest that "Ca. A. nitratireducens" switches to DNRA to alleviate oxidative stress caused by nitrite accumulation, giving further insight into adaptability and ecology of this microorganism. Our findings also have important implications for the understanding of the fate of nitrogen and SCGAs in anaerobic environments., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

Abstract The production and consumption pathways of nitrate (NO 3 −-N) are key factors for NO 3 −-N retention capacity (NR) in soils, especially in subtropical regions with high precipitation. This study was designed to examine the effect of land-use type on NO 3 −-N production and consumption pathways, in acidic soils in a subtropical region. Soils were collected from 5 differing land-use types: shrubland (SB), a eucalyptus plantation (ET), a sweet potato farm (SP), a citrus orchard (CO) and a mixed-vegetable farm (VE), in southeast China. In our study, SB was considered a natural system, ET was considered an artificial plantation system, and SP, CO and VE were considered agricultural systems. An incubation experiment was conducted with two 15N tracing treatments, and a numerical modeling method was applied to the experimental data to quantify gross N transformation rates. The results showed that 76% and 69% of NO 3 −-N was produced by heterotrophic nitrification (O Nrec) in SB and ET respectively. Whereas, O Nrec was negligible in SP, CO and VE, with >99% of NO 3 −-N produced by autotrophic nitrification. Dissimilatory NO 3 −-N reduction to NH 4 +-N (DNRA) had an important role in soil NO 3 −-N consumption in SB and ET, with >90% of NO 3 −-N produced in SB being simultaneously consumed via DNRA. However, DNRA was unimportant in SP, CO and VE. Nitrate immobilization and denitrification (I NO3) was negligible for all land-use types. Soil NR under different land-use types was in the order SB > ET > SP ≈ CO ≈ VE. Although N fertilizer was applied at low rates, for only the following two years after planting eucalyptus saplings, the NR in ET was significantly lower than in SB (natural system). Nitrate retention capacity was negatively correlated with soil organic carbon (SOC) and total nitrogen (TN) concentrations, and positively correlated soil C:N and C: NO 3 −-N ratios. The lower NR in SP, CO and VE may therefore be due to higher SOC and TN concentrations and lower C:N and C:NO 3 −-N ratios in those soils relative to SB and ET soils. Our observations imply that O Nrec and DNRA play an important role in soil NO 3 −-N production and consumption in SB and ET land-uses, but not in agricultural land-use (SP, CO and VE), within the subtropical region of China studied. These findings could contribute to a theoretical and practical framework for managing NO 3 −-N in subtropical acidic soils. Graphical abstract Relative contributions (%) of autotrophic nitrification and heterotrophic nitrification to soil NO 3 −-N production under different land-use types. Unlabelled Image Highlights • Heterotrophic nitrification and DNRA played important roles in SB and ET soil. • NO 3 −-N in SP, CO and VE soils were mainly produced by autotrophic nitrification. • NO 3 − retention capacity was higher in SB and ET soil than in SP, CO and VE soil. [ABSTRACT FROM AUTHOR]

Salt marshes currently play an important role as filters for upslope nitrogen (N) inputs. This could change in the future with sea level rise, warming and eutrophication, which are expected to favor monocultures over diverse plant communities. We explored patterns in gross N cycling, dissimilatory nitrate (NO3−) reduction to ammonium (NH4+) (DNRA), and denitrification in a salt marsh soil under two typical redox conditions (aerobic and anaerobic), and in soils under plant communities manipulated to simulate potential future composition (forb and graminoid monocultures). Natural salt marsh soils exhibited high potential gross N mineralization rates, averaging 50.4 ± 5.7 μg N g−1 d−1 under aerobic conditions; rates declined to 23.6 ± 3.4 μg N g−1 d−1 under an N2 headspace. Microbial NH4+ uptake and gross nitrification together accounted for only 14 % of gross N mineralization. Nitrogen retention via DNRA and microbial uptake greatly exceeded N losses via denitrification. Gross nitrification rates were greater in the forb and graminoid monocultures than in the control. This effect may be mediated by the lower plant biomass in the monocultures than in the control, which may have reduced competition between plants and nitrifiers for NH4+. Soil NO3− concentrations and net nitrous oxide (N2O) fluxes were greatest for the forb monoculture, likely due to higher soil oxygen (O2) concentrations in these plots. Our results suggest that salt marsh soils with a diverse plant community have high potential rates of N mineralization and microbial N retention, and the establishment of forb monocultures could lead to greater ecosystem N losses.

The dominance of different nitrate-reducing pathways determines nitrogen cycling patterns. Denitrification (DNF) has been widely studied, but assimilatory nitrate reduction (ANR) and dissimilatory nitrate reduction to ammonium (DNRA) have received much less attention. Their ecological patterns and responsible microbes are poorly understood. Here, we studied the structure and function succession of the three functional groups in the middle route of the South-to-North Water Diversion Project, which is a 1230 km canal spanning 8 degrees of latitude. The results reflected a nitrogen-removing pattern dominated by DNF in the summer and a nitrogen-retaining pattern dominated by ANR and DNRA in the winter. Stenotrophomonas , a typical denitrifier, was the keystone species in the summer and contributed to N 2 O production. Clostridium , a genus able to conduct ANR and DNRA, was the keystone species in the winter. Notably, a significant zonation pattern was discovered. According to the community structure, the system could be separated into two biogeographic zones, and the Yellow River (about latitude 35°N) is an important cut-off line. This bacterial biogeography followed different water characteristics and ecological processes. ANR was found to be an important process and seasonally transformed its habitat from the northern zone to the southern zone. DNRA bacteria were acclimated to the northern zone and favored at this region in both seasons. The generation of N 2 O, a strong greenhouse gas, also exhibited this zonation pattern. This is the first study to consider assimilatory and dissimilatory nitrate reducers together at a molecular level, and provides new insights into the underlying patterns of a nitrate-reducing bacterioplankton community. [ABSTRACT FROM AUTHOR]

Horizontal subsurface constructed wetlands (HSSF-CWs) planted with Phragmites australis were established to examine the effect of influent nitrogen loads on the removal efficiencies of nitrogen and chemical oxygen demand (COD) during different plant growth periods of plants. Under low influent nitrogen loads, most of the dissolved oxygen was consumed during the oxidation of organic matter in the wetland systems, and a dissimilatory nitrate reduction to ammonium (DNRA) may have occurred in HSSF-CWs when excessive amounts of organic matter were present, which limited the nitrification of ammonium nitrogen (NH 4 -N) and hindered the NH 4 -N removal. An increase in the influent nitrogen loads resulted in an enhancement of the removal efficiencies of NH 4 -N, nitrate nitrogen (NO 3 -N) and total nitrogen (TN) during the same growth period, except for NO 3 -N under the highest influent nitrogen loads, whereas fluctuations occurred for the COD removal efficiency. Compared with the rapid growth period, the removal efficiency of NH 4 -N, NO 3 -N and TN increased during the mature period; however, the COD removal efficiency decreased. The change of COD: N (COD:TN in wastewater) ratios with retention times indicated the sufficiency or deficiency of organic matter as an electron donor in the wetland systems. The changes in the pH value and oxidation-reduction potential (ORP) indirectly demonstrated that many factors affected the effluent pH value and ORP, such as retention time, influent loads, plants and wetland substrate, and microorganisms. In this study, the changes of ORP also illustrated that the dissolved oxygen concentrations decreased with increasing retention time in the HSSF-CWs; however, no significant increase in the ORP was observed during the two growth periods. [ABSTRACT FROM AUTHOR]

Dissimilatory nitrate reduction to ammonium (DNRA), denitrification, anaerobic ammonium oxidation (anammox) and biological N2 fixation (BNF) can influence the nitrogen (N) use efficiency of rice production. Whilst the effect of N application on BNF is known, little is known about its effect on NO3 - partitioning between DNRA, denitrification and anammox. Here, we investigated the effect of N application on DNRA, denitrification, anammox and BNF, and on the abundance of relevant genes in three paddy soils in Australia. Rice was grown in the glasshouse with (150 kg N ha-1 ) and without N-fertiliser for 75 days, and the rhizosphere and bulk soils were collected separately for laboratory incubation and quantitative PCR analysis. Nitrogen application reduced DNRA rates by >16% in all the soils regardless of the rhizospheric zone but it did not affect the nrfA gene abundance. Without N, the amount and proportion of NO3 - reduced by DNRA (0.42-0.52 µg g-1 soil day-1 , 45-55%) was similar or higher than that by denitrification. However, with N the amount of NO3 - reduced by DNRA (0.32-0.40 µg g-1 soil day-1 ) was 40-50% lower than the NO3 - reduced by denitrification. Denitrification loss increased by >20% with N addition, and was affected by the rhizospheric zones. Nitrogen loss was minimal through anammox, while BNF added 0.02-0.25 µg N g-1 soil day-1. We found that DNRA plays significant positive role in paddy soil N retention as it accounts for up to 55% of the total NO3 - reduction, but this is reduced by N application. [ABSTRACT FROM AUTHOR]

This study investigates the potential of an indigenous estuarine microbial consortium to degrade two polycyclic aromatic hydrocarbons (PAHs), naphthalene and fluoranthene, under nitrate-reducing conditions. Two physicochemically diverse sediment samples from the Lima Estuary (Portugal) were spiked individually with 25 mg L −1 of each PAH in laboratory designed microcosms. Sediments without PAHs and autoclaved sediments spiked with PAHs were run in parallel. Destructive sampling at the beginning and after 3, 6, 12, 30 and 63 weeks incubation was performed. Naphthalene and fluoranthene levels decreased over time with distinct degradation dynamics varying with sediment type. Next-generation sequencing (NGS) of 16 S rRNA gene amplicons revealed that the sediment type and incubation time were the main drivers influencing the microbial community structure rather than the impact of PAH amendments. Predicted microbial functional analyses revealed clear shifts and interrelationships between genes involved in anaerobic and aerobic degradation of PAHs and in the dissimilatory nitrate-reducing pathways (denitrification and dissimilatory nitrate reduction to ammonium - DNRA). These findings reinforced by clear biogeochemical denitrification signals (NO 3 − consumption, and NH 4 + increased during the incubation period), suggest that naphthalene and fluoranthene degradation may be coupled with denitrification and DNRA metabolism. The results of this study contribute to the understanding of the dissimilatory nitrate-reducing pathways and help uncover their involvement in degradation of PAHs, which will be crucial for directing remediation strategies of PAH-contaminated anoxic sediments. [ABSTRACT FROM AUTHOR]

• Both Thermomonospora and Modestobacter were the major DNRA bacteria. • The abundance of nrfA increased in the later phases of composting. • Denitrification and DNRA microbial interactive networks were identified. • NO 2 −-N was the main limiting factor for DNRA microbial community. This study investigated denitrification and dissimilatory nitrate reduction to ammonium (DNRA) competition for nitrite in composting of sugarcane pith and cow manure. Metagenomic analysis showed that Actinobacteria was the main DNRA microorganism. During heating phase and thermophilic phase, the abundances of denitrification functional genes (nirK and nirS decreased by 40.22% and 98.60%, respectively) and DNRA functional genes (nirB , nirD increased by 195.24% and 176.61%, and nrfA decreased by 45%, respectively) showed different trends. Interestingly, the abundance of nrfA increased by 250% during cooling and maturity phases. Mantel test revealed that competition between denitrification and DNRA microorganisms for NO 2 −-N limited the succession of their respective communities (P < 0.01). Network analysis showed that unclassified Solirubrobacterales , Altererythrobacter and Microbacterium were the key microorganisms in DNRA microbial communities. The results provided new insights into the key microorganisms and their driving factors affecting DNRA and nitrogen management in the composting ecosystems. [ABSTRACT FROM AUTHOR]

In this study we quantified nitrate (NO 3 − ) reduction (denitrification, anammox and DNRA) and N 2 O production in sediments and epibiont communities associated with Sydney Rock Oyster ( Saccostrea glomerata ) farming. In sediments beneath an active suspended oyster farm, DNRA accounted for 98% of NO 3 − reduction with rates of up to 169 ± 45 μmol N m −2 h −1 . Much of this DNRA was fuelled by NO 3 − derived from nitrification. Reference sediments had significantly lower DNRA rates of 83.8 ± 28.2 μmol N m −2 h −1 , however this constituted 96% of the sites total NO 3 − reduction. Fatty acid analysis showed that sediment organic matter was more labile in the oyster impacted sediments, facilitating subtle shifts in sediment oxygen demand which increased the Fe 2+ availability with respect to the reference sediments. The difference in DNRA rate between the sites was attributed to autotrophic oxidation of soluble Fe 2+ in sediments underlying the oyster cultures. DNRA was absent in the oyster shell epibiont communities and rates of anammox and denitrification were lower than in the sediments. Production of NH 4 + from the oysters and their associated epibionts was larger than DNRA and reached a rate of 206.2 μmol N m −2 h −1 . Nitrous oxide production rates were generally low compared to other aquaculture systems and the net flux of N 2 O for the combined oyster cultivation system (i.e. sediments plus epibionts) was negative, i.e. there was N 2 O consumption in the sediments beneath the oysters. Overall, subtropical suspended oyster farming systems favour inorganic N retention over N loss. [ABSTRACT FROM AUTHOR]

Microbial transformations of nitrogen (N) largely determine whether N is retained in ecosystems via net primary productivity or lost via gaseous emissions and leaching. The controls on soil N cycling are often studied at single locales, making it difficult to predict N cycling at regional to global scales. We hypothesized that contemporary soil properties exhibit consistent relationships with instantaneous gross N cycling rates across diverse biomes that create a continuum in these properties. We measured ex situ gross N cycling rates and soil properties at 33 study sites representing five biome classifications in California including deserts, grasslands, shrublands, forest, and wetlands. Desert soils had significantly lower total N, organic carbon (C), microbial biomass N, and soil moisture as well as higher pH than all other biomes, whereas forests and wetlands had significantly lower soil nitrate (NO 3 − ) concentrations (P < 0.001 for all). Gross mineralization rates were best predicted by the combination of soil moisture and soil C:N ratios (R 2 = 0.46), which exerted positive and negative controls, respectively. Grasslands exhibited marginally higher gross mineralization than all other biomes, whereas deserts had the lowest rates due to low soil moisture (P = 0.09). Gross nitrification rates were positively correlated to soil NO 3 − concentrations (R 2 = 0.34) and negatively correlated to soil C:N ratios (R 2 = 0.31). The negative relationship between gross nitrification and soil C:N ratios was driven by forest soils, which had significantly higher C:N ratios and lower gross nitrification than all other biomes (P < 0.05). Dissimilatory NO 3 − reduction to NH 4 + (DNRA) occurred in soils from all biomes. The strong positive correlation between DNRA rates and soil NO 3 − (R 2 = 0.41) suggests NO 3 − limitation of DNRA. Predictable patterns in gross N cycling across biomes in California suggest that contemporary soil properties are important drivers of instantaneous soil N cycling rates that integrate over differences in vegetation type, atmospheric N deposition rates, and local climate. [ABSTRACT FROM AUTHOR]

This study investigated the effects of plant presence, plant species and their species richness on plant biomass production, pH, dissolved oxygen (DO), oxidation-reduction potential (ORP), denitrification (DNF), dissimilatory NO reduction to ammonium (DNRA) and two associated bacterial community compositions in thirty vertical flow microcosm wetlands fed with the Hoagland solution, where three plant species richness levels (i.e. unvegetated, monocultured and 4-species polycultured treatment, respectively) were established using four macrophytes. Plant presence increased DO and ORP values, as well as the terminal restriction fragment (TRF) richness and Shannon-Weaver index of the DNRA community and also improved both potential DNF and DNRA rates. The microcosms monocultured with Cyperus alternifolius exhibited the greatest DO, ORP, smallest plant biomass parameters and DNF rates among all of the monocultured microcosms, whereas the microcosms monocultured with Canna glauca and Iris pseudacorus harbored the smallest pH, DO, ORP, the greatest plant biomass parameters and DNRA rates. Compared to both unvegetated and monocultured treatments, the 4-species polycultured treatment was effective in increasing both potential DNF and DNRA rates due to the greatest plant biomass parameters as confirmed by the correlation analysis, but was ineffective in terms of changing both DNF and DNRA community compositions. [ABSTRACT FROM AUTHOR]

[Display omitted] • The nitrogen removal was promoted by 20 μg/L FQs in an anammox system. • Simultaneous removal of FQs was achieved with an average efficiency of 36–51%. • Metagenomic analysis revealed three dominant MAGs belonging to AnAOB. • Enzymes were more active in nitrite reduction and hydrazine dehydrogenation. • Core metabolism and biosynthesis were up-regulated in anammox consortia. It has been widely reported that fluoroquinolones (FQs) can affect the anaerobic ammonium oxidization (anammox) microorganisms, which interferes with the performance of nitrogen removal from wastewater. However, the metabolic mechanism of anammox microorganisms responding to FQs has rarely been explored. In this study, it was found that 20 μg/L FQs promoted the nitrogen removal performance of anammox microorganisms in batch exposure assays, and 36–51% of FQs were removed simultaneously. Combined metabolomics and genome-resolved metagenomic analysis revealed up-regulated carbon fixation in anammox bacteria (AnAOB) , while purine and pyrimidine metabolism, protein generation and transmembrane transport were enhanced in AnAOB and symbiotic bacteria by 20 μg/L FQs. Consequently, hydrazine dehydrogenation, nitrite reduction, and ammonium assimilation were bolstered, improving the nitrogen removal efficiency of the anammox system. These results revealed the potential roles of specific microorganisms in response to emerging FQs and provided further information for practical application of anammox technology in wastewater treatment. [ABSTRACT FROM AUTHOR]

There is a lack of the understanding of the transfer of phosphate (PO 4 -P), ammonium (NH 4 -N) and nitrate (NO 3 -N) at the millimeter scale in sediments related to internal loadings in the semi-arid and cold Lake Hulun in China. In this paper, a passive sampling technique-diffusion gradients in thin films (DGT) has been used for the biogeochemical behaviors and dynamic transfer of PO 4 -P, NH 4 -N and NO 3 -N in sediments in this lake. The two-sided DGT probe (AMP-TH&ZrO-Chelex) and ZrO DGT piston are designed for sediment/water interface. Based on change characters of DGT concentration profiles (nutrients, Fe and Mn) related to redox status and chemical properties, N and P mobilizations are derived. The reductive dissolution of Mn(IV) or Fe(III) (oxyhydr)oxides accounts for subsequent P release is corresponded with the oxic or anoxic status in sediment layers; Fe(III)-reduction is the main reason for P remobilization. The breakdown of algae biomass deposited on the uppermost sediment and phosphatase enzymes activity enhanced by NH 4 -N also lead to P remobilization. In sub-anoxic or anoxic layer, denitrification and dissimilatory nitrate reduction to ammonium (DNRA) induce exchangeable ammonium (NH 4 ex) enrichment and NH 4 -N release, while, anammox depletes NH 4 -N mobility. Aerobic nitrification results in NO 3 -N remobilization. Organic matter favors NH 4 -N release. DGT induced fluxes in sediments (DIFS) model is used to derive the labile P pool (51.5–465.5 cm3 g−1), resupply constant (0.186–0.734), response time (54–11,070 s) and Dspt rate (32–382,517 nmol cm−3 d−1) for describing dynamic P transfers with two opposite types of "slow" and "fast" resupplies. The diffusive fluxes across sediment/water interface in ranges of 67.9–498.7 μg m−2 d−1 (PO 4 -P), −1416–106.8 (NH 4 -N) and –2147–301.1 μg m−2 d−1 (NO 3 -N) and DIFS parameters can be used for release risks in lake regions and the sediment remediation strategies are recommended. [Display omitted] • AMP-TH&ZrO-Chelex DGT probe and ZrO piston are used for nutrients in lake sediment. • P release is mainly due to Fe reduction and then Mn affected by redox status. • DNRA, anammox, nitrification and organic matter control NH 4 -N and NO 3 -N mobility. • Labile P pool, resupply constant and desorption rate are evaluated by DIFS model. • Lake management strategies are proposed based on diffusive flux and DIFS parameters. [ABSTRACT FROM AUTHOR]

Large amounts of nitrogen fertilized to food production are lost via denitrification and leaching. Dissimilatory nitrate reduction to ammonium (DNRA) is a bioprocess competing with denitrification, and it conserves bioavailable nitrogen in soil ecosystems. The carbon to nitrogen (C/N) ratio has long been believed essential to balance the competition between DNRA and denitrification, but increasing evidence indicates that DNRA may occur unrelated to C/N ratio via a largely unknown mechanism. Taking Geobacter as representative bacteria, we found that the kinetic of nitrite bio-reduction to ammonium was the key to enhancing DNRA and demonstrated it in pure and mixed cultures and soil ecosystems. Compared to other two strains of DNRA bacteria, Geobacter sulfurreducens was confirmed for the first time to conduct a 3-fold more rapid DNRA (NO 2 −→NH 4 +) when it grew with the kinetically matched nitrite accumulator Delftia tsuruhatensis (NO 3 −→NO 2 −). They assisted and restricted each other to bring their population ratio close to the theoretical yield ratio of 2.7:1 while performing cross-feeding with nitrite and ammonium. This rapid DNRA was further demonstrated to conserve 2–8 times more reactive nitrogen in organic deficient soils, and up to 40% of 15NO 3 − was reduced to ammonium. Our results found a sustainable way of nitrogen retention in soils, and have broader implications for understanding nitrogen turnover in ecosystems. [Display omitted] • The kinetic of nitrite bio-reduction to ammonium was the key to enhancing DNRA. • Geobacter sulfurreducens was confirmed for the first time to conduct rapid DNRA. • Rapid DNRA conserved 2–8 times more reactive nitrogen in organic deficient soils. • G. sulfurreducens can perform cross-feeding with short denitrifier to reserve N. [ABSTRACT FROM AUTHOR]

Dissimilatory nitrate reduction to ammonium (DNRA) has an important role in soil nitrogen retention and is considered to be constrained to anaerobic conditions. However, a recent study found that Pseudomonas putida Y-9 is capable of DNRA under aerobic conditions. In this study, four species of Pseudomonas spp. were found to produce ammonium during the nitrite reduction process under aerobic conditions, similar to the Y-9 strain. The detectable ammonium in the culture supernatant during the nitrite reduction process for each of the four strains originated intracellularly. A subsequent 15 N isotope experiment showed that these four strains were able to transform 15 NO 2 - to 15 NH 4 + in 3 h under aerobic conditions. The NirBD sequence in each of the four strains showed high similarity with that in the Y-9 strain (approximately 94.61%). Moreover, the nirBD sequences in the four strains and the Y-9 strain were all similar to those of other Pseudomonas spp., while they were relatively distant in terms of their phylogenetic relationship from those of other genera. Overall, these results suggest that these four strains of Pseudomonas spp. are capable of DNRA under aerobic conditions, which might be attributed to the existence of nirBD ., Competing Interests: The authors declare no competing interests., (©2023PublishedbyElsevierLtd.)

[Display omitted] • High levels of NH 4 + occur in the coastal acidic groundwater of Beihai, South China. • Acid rain, FeS 2 oxidation, and NO 3 − reduction by Fe2+ jointly account for the low pHs. • DNRA with anthropogenic NO 3 − is largely responsible for groundwater NH 4 + enrichment. • Contribution of anthropogenic NH 4 + and algae decomposition to the loadings is minor. • DNRA is fueled by fermentation (of acetate and glucose) and (or) sulfide oxidation. High levels of ammonium (NH 4 +) in groundwater can threaten the health of surface ecosystems and the safety of water supplies. To ascertain the occurrence of NH 4 + in the coastal acidic groundwater of Beihai, Southern China, a combined hydrochemical and isotopic (δ15N in nitrate (NO 3 −) and NH 4 +; δ13C in dissolved inorganic carbon (DIC)) study was performed. In addition to a chloride concentration-based fresh water-seawater mixing model, δ15N NO3 vs δ15N NH4 , Δδ13C DIC,react (changes in δ13C DIC values caused by reaction), and ΔC SO4,react (changes in sulfate concentrations caused by reaction) were applied to interpret the genesis of NH 4 +. The results show groundwater NH 4 + loadings range from < 0.04 to 6.2 mg/L, with typically higher loadings along the coastline than in the plains. Elevated NH 4 + loadings (>0.2 mg/L) are commonly accompanied by enriched δ15N NO3 and depleted δ15N NH4 values in relation to the anthropogenic endmember, depleted or enriched Δδ13C DIC,react values, and ΔC SO4,react > 0.00 or < 0.00 mmol/L. Such isotopic fingerprints and hydrochemical features indicate dissimilatory nitrate reduction to ammonium (DNRA), glucose fermentation, methanogenesis (acetate fermentation), and sulfide oxidation or sulfate reduction. The findings suggest acidic rainwater, sulfide oxidation, and NO 3 − reduction by ferrous iron (Fe2+) could jointly account for the formation of acidic groundwater (pH as low as 4.0) that is of meteoric origin. Fermentative and sulfide-driven DNRA with anthropogenic NO 3 − is notably responsible for the enrichment of groundwater NH 4 + concentrations, with a minor contribution from anthropogenic NH 4 + infiltration and algae decomposition. As a result of silicate and carbonate weathering, seawater inputs, and fermentation, the addition of bicarbonate (HCO 3 −) results in circumneutral pH values. These results indicate DNRA plays a critical role in the enrichment of NH 4 + and, hence, improve understanding of its genesis in the groundwater of Beihai and other similar areas. [ABSTRACT FROM AUTHOR]

Nitrogen (N) removal in a tannery wastewater treatment plant was significantly enhanced by the bioaugmentation of the novel consortium BM-S-1. In order to identify dominant taxa responsible for N metabolisms in the different stages of the treatment process, Illumina MiSeq Sequencer was used to conduct metagenome sequencing of the microbial communities in the different stages of treatment system, including influent (I), buffering (B), primary aeration (PA), secondary aeration (SA) and sludge digestion (SD). Based on MG-RAST analysis, the dominant phyla were Proteobacteria, Bacteroidetes and Firmicutes in B, PA, SA and SD, whereas Firmicutes was the most dominant in I before augmentation. The augmentation increased the abundance of the denitrification genes found in the genera such asRalstonia(nirS, norBandnosZ),Pseudomonas(narG, nirSandnorB) andEscherichia(narG) in B and PA. In addition,Bacteroides, Geobacter, PorphyromonasandWolinellacarryingnrfAgene encoding dissimilatory nitrate reduction to ammonium were abundantly present in B and PA. This was corroborated with the higher total N removal in these two stages. Thus, metagenomic analysis was able to identify the dominant taxa responsible for dissimilatory N metabolisms in the tannery wastewater treatment system undergoing bioaugmentation. This metagenomic insight into the nitrogen metabolism will contribute to a successful monitoring and operation of the eco-friendly tannery wastewater treatment system. [ABSTRACT FROM AUTHOR]

In the context of studying the influence of N-fertilization on N and NO flux rates in relation to the soil bacterial community composition in fen peat grassland, a group of bacterial strains was isolated that performed dissimilatory nitrate reduction to ammonium and concomitantly produced NO. The amount of nitrous oxide produced was influenced by the C/N ratio of the medium. The potential to generate nitrous oxide was increased by higher availability of nitrate-N. Phylogenetic analysis based on the 16S rRNA and the rpoB gene sequences demonstrated that the investigated isolates belong to the genus Proteus, showing high similarity with the respective type strains of Proteus vulgaris and Proteus penneri. DNA-DNA hybridization studies revealed differences at the species level. These differences were substantiated by MALDI-TOF MS analysis and several distinct physiological characteristics. On the basis of these results, it was concluded that the soil isolates represent a novel species for which the name Proteus terrae sp. nov. (type strain N5/687 =DSM 29910 =LMG 28659) is proposed. [ABSTRACT FROM AUTHOR]