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Non-fermentative nitrite reduction to ammonium, resulting in the release of ammonium in the environment, can be performed by a variety of enzymes found among bacteria and archaea. NrfA-dependent ammonifiers are phylogenetically diverse and are present in terrestrial and aquatic environments, and for the latter especially in sediments. NrfA-dependent ammonifiers often carry genes involved in denitrification and redox reactions with sulfur or iron compounds, suggesting that they play a role in multiple biogeochemical cycles. In most aquatic and terrestrial environments, denitrifiers dominate over nitrate ammonifiers, and denitrification is the dominating process of nitrate reduction. However, nitrate ammonification rates can be significant under certain redox conditions. Nitrate ammonifiers are a taxonomically diverse group of microorganisms that reduce nitrate to ammonium, which is released, and thereby contribute to the retention of nitrogen in ecosystems. Despite their importance for understanding the fate of nitrate, they remain a largely overlooked group in the nitrogen cycle. Here, we present the latest advances on free-living microorganisms using NrfA to reduce nitrite during ammonification. We describe their diversity and ecology in terrestrial and aquatic environments, as well as the environmental factors influencing the competition for nitrate with denitrifiers that reduce nitrate to gaseous nitrogen species, including the greenhouse gas nitrous oxide (N 2 O). We further review the capacity of ammonifiers for other redox reactions, showing that they likely play multiple roles in the cycling of elements. [ABSTRACT FROM AUTHOR]

Sponges are an important component of deep-water ecosystems enhancing eukaryotic biodiversity by hosting diverse endo- and epibiota and providing three dimensional habitats for benthic invertebrates and fishes. As holobionts they are important hosts of microorganisms which are involved in carbon and nitrogen cycling. While increasing exploration of deep-water habitats results in new sponge species being discovered, little is known about their physiology and role in nutrient fluxes. Around New Zealand (Southwest Pacific), the sponge biodiversity is particularly high, and we selected six deep-sea sponge genera (Saccocalyx , Suberites , Tedania , Halichondria / Dendoricella , Lissodendoryx) and a member of the Sceptrulophora order for in-situ and ex-situ experiments. We investigated the biochemical composition of the sponges, measured oxygen consumption and inorganic nutrient fluxes, as well as bacterial and phospholipid-derived fatty acid (PLFA) compositions. Our aim was to assess differences in fluxes and fatty acid composition among sponges and linking their bacterial communities to nitrogen cycling processes. All sponges excreted nitrite and ammonia. Nitrate and phosphate excretion were independent of phylum affiliation (Demospongiae, Hexactinellida). Nitrate was excreted by Halichondria / Dendoricella and Lissodendoryx , whereas Suberites , Tedania , and Sceptrulophora consumed it. Phosphate was excreted by Sceptrulophora and Halichondria / Dendoricella and consumed by all other sponges. Oxygen consumption rates ranged from 0.17 to 3.56 ± 0.60 mmol O 2 g C-1 d−1. The PLFA composition was very sponge-genera dependent and consisted mostly of long-chain fatty acids. Most PLFAs were sponge-specific, followed by bacteria-specific PLFAs, and others. All sponges, except for Suberites , were low-microbial abundance (LMA) sponges whose bacterial community composition was dominated by Proteobacteria, Bacteroidota, Planctomycetota, and Nitrospinota. Suberites consisted of high-microbial abundance (HMA) sponges with Proteobacteria, Chloroflexota, Acidobacteriota, and Actinobacteriota as dominant bacteria. Based on the inorganic nitrogen flux measurements, we identified three types of nitrogen cycling in the sponges: In type 1, sponges (Dendoricella spp. indet., Lissodendoryx) respired aerobically and ammonificated organic matter (OM) to ammonium, fixed N 2 to ammonium, and nitrified aerobically heterotrophically produced ammonium to nitrate and nitrite. In type 2, sponges (Halichondria sp., Sceptrulophora, Suberites , Tedania) respired OM aerobically and ammonificated it to ammonium. They also reduced nitrate anaerobically to ammonium via dissimilatory nitrate reduction to ammonium. In type 3, ammonium was microbially nitrified to nitrite and afterwards to nitrate presumably by ammonium-oxidizing Bacteria and/or Archaea. • Sponges had δ 13 org. C/δ15N values from −20.1‰/18.5‰ to −14.1‰/23.5‰. • Oxygen consumption ranged from 0.17 mmol O 2 g C d−1 to 3.56 ± 0.60 mmol O 2 g C d−1. • Nitrogen cycling included aerobic ammonification, nitrification, and anaerobic DNRA. • Low microbial abundance sponges hosted dominantly Proteobacteria. • Most PLFAs in sponge-tissue were sponge-specific PLFAs. [ABSTRACT FROM AUTHOR]

[Display omitted] • Reaction mechanism of DNRA pathway within vary electron donors were summarized. • Nitrate selectively transformation between denitrification and DNRA was discussed. • Characteristic of key DNRA bacteria in various environments were comprehensively summarized. • MET-assisted DNRA presents a sustainable approach for recycling nitrate-containing wastewater. • Opportunities and challenges were proposed for advancing MET-assisted DNRA development. The rapid increase in population, urbanization, and industrialization have led to the discharge of wastewater with high-concentration of nitrate contaminant. Here we emphasize the intervention point of nitrate fate, dissimilatory nitrate reduction to ammonium (DNRA), and propose a potential strategy to achieve nitrogen recovery. The resource recovery process of applying microbial electrochemical technologies (METs) to traditional energy-intensive wastewater treatment to recover valuable nitrogen products was investigated. This review systematically elucidates the DNRA pathway, focusing on recent trends of METs-assisted DNRA-driven nitrogen recycling and the use of different electron donors in current research. Different types of DNRA functional microorganisms were critically summarized and compared, laying the foundations for applying DNRA keystone species. In addition, the competition and switching mechanism between denitrification process and DNRA process are analyzed in detail, which provides support for DNRA-driven nitrogen recovery by microbial electrochemical technology. Finally, the present challenges and prospects in METs-assisted DNRA for nitrogen recovery are discussed, including enhancement strategies, possible integration with other processes, and the potential application of multi-component substrates. [ABSTRACT FROM AUTHOR]

• DNRA dominated dissimilatory nitrate reduction under flash drought. • Flash drought favored greater N 2 O emissions and ammonia retention. • DNRA bacteria and denitrifiers cooperatively produce N 2 O under flash drought. • Flash drought aggravated a positive climate feedback in freshwater lakes. Flash drought (FD) events induced by climate change may disrupt the normal hydrological regimes of floodplain lakes and affect the plant-microbe mediated dissimilatory nitrate reduction (DNR), i.e., denitrification, anammox and dissimilatory nitrate reduction to ammonium (DNRA), thus having important consequences for nitrous oxide (N 2 O) emissions and nitrogen (N) retention. However, the responses of the DNR pathways in the floodplain lake to the record-breaking FD in 2022 in Yangtze River of China, as well as the underlying microbial mechanisms and feedbacks to climate change remain poorly understood. Here, we collected exposed sediments and Carex cinerascens– associated soils in the littoral wetlands of Poyang Lake during 2022 FD and the dry seasons prior to and after this event. The potential DNR rates and the synergistic metabolism of microbial guilds involved in DNR were investigated using 15N isotope pairing technique, high-throughput and metagenomic sequencing. We found that the in situ N 2 O fluxes in the littoral wetlands were highest during the flash drought, especially in the exposed sediments. The potential DNRA rates were highest under flash drought conditions, and DNRA dominated the DNR for both exposed sediments (80.4 %) and Carex cinerascens -associated soils (57.5 %). Nutrients (i.e., N and P) and DNRA bacterial communities played a key role in producing the extremely high N 2 O fluxes from exposed sediments, which could be explained by the synergistic metabolism of DNRA bacteria and denitrifiers through the exchange of the key intermediates in DNR. Therefore, the climate change–induced flash drought promoted greater nitrous oxide emissions and N retention in the littoral wetlands of Poyang Lake, producing a greater flux of greenhouse gas emissions and elevating the risk of lake eutrophication. Hence, flash droughts reinforce a positive feedback between climate change and nitrous oxide emission from these aquatic ecosystems. [Display omitted] [ABSTRACT FROM AUTHOR]

Climate change is increasing the frequency and intensity of large precipitation events that flood soils and establish anoxic conditions that promote microbial denitrification, a predominant source of atmospheric nitrous oxide (N 2 O, a strong greenhouse gas). Denitrification may be favored within topographic depressions in otherwise flat fields that are prone to ponding, establishing "hotspots" of N 2 O emissions. The location of N 2 O hotspots may also depend on the distribution of soil microbial communities that are responsible for the production and consumption of N 2 O in soils. Yet, relating soil microbial community composition to N 2 O emissions remains challenging. To assess how spatial variation in soil microbial communities affects N 2 O emissions, we measured the community composition of active microorganisms using amplicon-based sequencing of cDNA generated from mRNA transcripts associated with N-cycling processes in response to experimentally flooding and draining soils in the lab. We also used stable isotope tracers to relate microbial communities to process rates. Consistent with the hypothesis that denitrifying microbial communities are not functionally redundant, we found that the diversity of microbial taxa expressing nitrite reduction genes (nirK) and N 2 O reduction genes (Clade I nosZ) were correlated with denitrifier-derived N 2 O emissions. Depressional soils had more diverse active N 2 O consuming communities (assessed using Clade I nosZ) under flooded conditions, limiting net N 2 O emissions compared to upslope soils. Our results show that depressional soils maintain distinct microbial communities that likely promote higher rates of N 2 O reduction compared to upslope soils. Soil microtopography can, therefore, select for distinct microbial communities that emit different amount of N 2 O in response to large precipitation events. • Active denitrifying microbial communities were not functionally redundant. • Transcript diversity of denitrification genes was associated with N 2 O emissions. • Soils with more diverse nitrite reductase transcripts emitted more N 2 O. • Depressional soils had diverse N 2 O-reducing transcripts and emitted less N 2 O. • Microtopographic variation in denitrifier communities affects soil N 2 O emissions. [ABSTRACT FROM AUTHOR]

Nitrate (NO 3 −) contamination has become a significant global environmental issue. Traditional nitrate reduction processes typically require external pH control to maintain neutral conditions and prevent nitrite accumulation. In this study, a hydrogen-based membrane biofilm reactor (H 2 -MBfR) was constructed without external pH regulation. The reactor relied on the alkalinity generated by the nitrate reduction process itself, maintaining a highly alkaline environment with stable denitrification and up to 60% ammonium conversion at pH levels reaching 11.70. The DNRA process was found to be independent of substrate type, inversely proportional to electron supply, and exhibited the highest reaction rate at pH 11, as confirmed by both ex-situ and in-situ batch experiments. Microbial community analysis indicated that Meiothermus was the predominant genus within the biofilm. This research reveals a novel nitrogen transformation phenomenon, demonstrating the coexistence of DNRA and denitrification processes under high alkalinity conditions in the H 2 -MBfR system. These findings offer new insights into nitrate reduction processes and suggest potential advancements in wastewater treatment and resource recovery. [Display omitted] • The H 2 -MBfR maintained a pH of 11.70 through nitrate reduction-derived alkalinity. • DNRA and denitrification coexisted in the MBfR under high alkalinity. • DNRA was unaffected by nitrogen form and inversely related to electron supply. • Meiothermus was the dominant genus in the H 2 -fed biofilm. [ABSTRACT FROM AUTHOR]

Denitrification, anammox, and DNRA are three important nitrogen (N) reduction pathways in estuarine sediments. Although salinity is an important variables controlling microbial growth and activities, knowledge about the effects of changing salinity on those three processes in estuarine and coastal wetland sediments are not well understood. Herein, we performed a 60-d microcosms experiment with different salinities (0, 5, 15, 25 and 35 ‰) to explore the vital role of salinity in controlling N-loss and N retention in estuarine wetland sediments. The results showed that sediment organic matter, sulfide, and nitrate (NO 3 −) were profoundly decreased with increasing salinity, while sediment ammonium (NH 4 +) and ferrous (Fe2+) varied in reverse patterns. Meanwhile, N-loss and N retention rates and associated gene abundances were differentially inhibited with increasing salinity, while the contributions of denitrification, anammox, and DNRA to total nitrate reduction were apparently unaffected. Moreover, denitrification rate was the most sensitive to salinity, and then followed by DNRA, while anammox was the weakest among these three processes. In other words, anammox bacteria showed a wide range of salinity tolerance, while both denitrification and DNRA reflected a relatively limited dynamic range of it. Our findings could provide insights into temporal interactive effects of salinity on sediment physico-chemical properties, N reduction rates and associated gene abundances. Our findings can improve understanding of the effects of saltwater incursion on the N fate and N balance in estuarine and coastal sediments. • Salinity plays a key role in regulating the nitrate reduction processes. • N-loss rates and N retention were both inhibited with increasing salinity. • Denitrification bacteria activity was the most sensitive to salinity. • Anammox bacteria activity showed a wide range of salinity tolerance. [ABSTRACT FROM AUTHOR]

• Denitrification is predominant in surface coastal mangrove sediments, while DNRA becomes more advantageous at deeper depths. • Functional gene quantification and microbial profiles validate activity trends by depth. • C/N, salinity, and carbon quality regulate denitrification-DNRA competition across depths. Mangrove aquatic ecosystems receive substantial nitrogen (N) inputs from both land and sea, playing critical roles in modulating coastal N fluxes. The microbially-mediated competition between denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in mangrove sediments significantly impacts the N fate and transformation processes. Despite their recognized role in N loss or retention in surface sediments, how these two processes vary with sediment depths and their influential factors remain elusive. Here, we employed a comprehensive approach combining 15N isotope tracer, quantitative PCR (qPCR) and metagenomics to verify the vertical dynamics of denitrification and DNRA across five 100-cm mangrove sediment cores. Our results revealed a clear vertical partitioning, with denitrification dominated in 0-30 cm sediments, while DNRA played a greater role with increasing depths. Quantification of denitrification and DNRA functional genes further explained this phenomenon. Taxonomic analysis identified Pseudomonadota as the primary denitrification group, while Planctomycetota and Pseudomonadota exhibited high proportion in DNRA group. Furthermore, genome-resolved metagenomics revealed multiple salt-tolerance strategies and aromatic compound utilization potential in denitrification assemblages. This allowed denitrification to dominate in oxygen-fluctuating and higher-salinity surface sediments. However, the elevated C/N in anaerobic deep sediments favored DNRA, tending to generate biologically available NH 4 +. Together, our results uncover the depth-related variations in the microbially-mediated competition between denitrification and DNRA, regulating N dynamics in mangrove ecosystems. [Display omitted] [ABSTRACT FROM AUTHOR]

Nitrogen removal is essential for restoring eutrophic lakes. Microorganisms and aquatic plants in lakes are both crucial for removing excess nitrogen. However, microplastic (MP) pollution and the invasion of exotic aquatic plants have become increasingly serious in lake ecosystems due to human activity and plant-dominant traits. This field mesocosm study explored how the diversity of invasive submerged macrophytes affects denitrification (DNF), anammox (ANA), and dissimilatory nitrate reduction to ammonium (DNRA) in lake sediments with varying MPs. Results showed that invasive macrophytes suppressed DNF rates, but DNRA and ANA were less sensitive than DNF to the diversity of invasive species. Sediment MPs increased the biomass of invasive species more than native species, but did not affect microbial processes. The effects of MPs on nitrate dissimilatory reduction were process-specific. MPs increased DNF rates and the competitive advantage of DNF over DNRA by changing the sediment environment. The decoupling of DNF and ANA was also observed, with increased DNF rates and decreased ANA rates. The study findings suggested new insights into how the invasion of exotic submerged macrophytes affects the sediment nitrogen cycle complex environments. [Display omitted] • Growth of invasive species was more sensitive than native species to MPs. • DNF rates increased with the increasing MPs, while ANA rates were inhibited. • Invasive species diversity significantly altered DNRA. • DNF was mainly governed by abiotic factors, e.g. pH, NH 4 +. • Both DNRA and ANA were predominantly influenced by gene abundance. [ABSTRACT FROM AUTHOR]

• We summarized adaptive versatility of anammox bacteria associated with organics. • We re-evaluated the Krebs cycle in anammox bacteria for mixotrophic metabolism. • Brocadia exhibit remarkable organotrophic lifestyle in eutrophic surroundings. • Nitrate reduction to ammonium in anammox bacteria is associated with organotrophy. Anaerobic ammonium oxidizing (anammox) bacteria, which were first discovered nearly three decades ago, are crucial for treating ammonium-containing wastewater. Studies have reported on the biochemical nitrogen conversion process and the physiological, phylogenic, and ecological features of anammox bacteria. For a long time, anammox bacteria were assumed to have a lithoautotrophic lifestyle. However, recent studies have suggested the functional versatility of anammox bacteria. Genome-based analysis and experiments with enrichment cultures have demonstrated the association of the metabolic activities of anammox bacteria with different stress conditions, revealing the importance of utilizing specific organic substances, including organoautotrophy, for growth and adaptation to stress conditions. Our understanding regarding the utilization and metabolism of organic substances and their associations with anammox reactions in anammox bacteria is growing but still incomplete. In this review, we summarize the effect of the utilization of organic substances by anammox bacteria under environmental stress conditions, emphasizing their potential organoautotrophic activity and metabolic flexibility. Although most anammox bacteria may utilize specific organic substances, Ca. Brocadia exhibited the highest level of mixoautotrophic activity. The environmental factors that substantially affect the organoautotrophic activities of anammox bacteria were also examined. This review provides a new perspective on the organoautotrophic capacity of anammox bacteria. [Display omitted] [ABSTRACT FROM AUTHOR]

[Display omitted] • Competitive DNRA vs. DEN partitioning and simultaneous fermentation were determined. • Moderate COD/N ratio and readily available COD favored DNRA. • A kinetic model to include DNRA and DEN for nitrogen conversion was developed. • Limited COD, high NO 3 − input, and low sludge concentration triggered N 2 O emissions. • VFA composition shifted from mixed type to acetic acid in the presence of nitrate. The complex interaction between nitrate (NO 3 −) reduction and fermentation is poorly understood when high levels of NO 3 − are introduced into anaerobic systems. This study investigated the competitive distribution between conventional denitrification (DEN) and dissimilatory nitrate reduction to ammonium (DNRA) during simultaneous denitrification and fermentation in arrested methanogenesis. Up to 62% of initial NO 3 − (200 mg-N/L) was retained as ammonium through DNRA at a chemical oxygen demand (COD)/N ratio of 25. Significant N 2 O emission occurred (1.7 – 8.0% of the initial NO 3 −) with limited carbon supply (≤1600 mg COD/L) and sludge concentration (≤3000 mg COD/L). VFA composition shifted predominantly towards acetic acid (>50%) in the presence of nitrate. A novel kinetic model was developed to predict DNRA vs. DEN partitioning and NO 2 − accumulation. Overall, NO 3 − input, organic loading, and carbon source characteristics independently and collectively controlled competitive DNRA vs. DEN partitioning. [ABSTRACT FROM AUTHOR]

• Denitrification and DNRA contributed more to N transformation than anammox. • Salinity increase shifted nitrate reduction regime from denitrification toward DNRA. • Both C/N ratio and sulfide content are the important factors partitioning the shift. Salinization in estuarine wetlands significantly alters the balance between their nitrogen (N) removal and retention abilities but these processes have not yet been characterized effectively. In the present study, the potential rates of sediment denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA) were mapped using N isotope tracing methods along salinity gradients across the Yellow River Delta wetland (YRDW) in China. The contribution of anammox to total dissimilatory N transformations in YRDW was merely 6.8%, whereas denitrification and DNRA contributed 52.3% and 40.9%, respectively. The potential rate of denitrification (5.82 μmol/kg/h) decreased significantly along salinity gradients and markedly exceeded DNRA potential rate (2.7 μmol/kg/h) in fresh wetlands, but was lower than that of DNRA in oligohaline wetlands (3.06 and 3.18 μmol/kg/h, respectively). Moreover, a significantly positive relationship between salinity and DNRA/denitrification was obeserved, indicating that increased salinity may favor DNRA over denitrification. Furthermore, total sulfur (TS) content and ratio of total organic carbon to total nitrogen (C/N) increased with the salinity gradient and showed evident positive relationships with the DNRA/denitrification ratio. In this study, we proved that increased salinization resulted in the dominance of DNRA over denitrification, possible through the addition of S and alteration of the C/N in estuarine wetlands, leading to increased N retention in estuarine wetlands during salinization, which would enhance the eutrophication potential within wetlands and in downstream ecosystems. [Display omitted] [ABSTRACT FROM AUTHOR]

• Saltmarsh groundwater releases large amounts of NH 4 -N to coastal waters. • Saltmarshes as a filter can remove anthropogenic NO 3 -N. • Multiple isotopes help identify the sources and pathways of saltmarsh nutrients. • Global studies show NH 4 -N dominates coastal wetlands' groundwater DIN flux. • Large groundwater NH 4 -N flux may contribute to local algal blooms. Saltmarshes are commonly regarded as coastal filters for removing terrestrial nutrients. However, the behavior of different nutrient species in saltmarshes, in terms of removal or production, can vary greatly and is still poorly understood. In this study, we quantified groundwater-derived nutrient fluxes and examined their sources and pathways in a saltmarsh using multiple isotopes (222Rn, δ15N-NO 3 −, δ18O-NO 3 − and δ15N-NH 4 +). Our findings reveal that tidal-driven groundwater flow significantly facilitates the removal of nitrate and phosphorus from saltmarshes. However, it also leads to the release of substantial amounts of ammonium and dissolved silicate into coastal waters. This suggests that saltmarshes function more specifically as nitrate filters rather than general nutrient filters when it comes to removing anthropogenic solutes. As phytoplankton preferentially use ammonium, groundwater-derived large ammonium flux with high N/P ratio (∼158) in saltmarshes would significantly affect the nutrient structure and phytoplankton biomass of coastal seawater dominated by nitrate, suggesting that groundwater-derived ammonium export is probably a key driving force in controlling local algal blooms. [ABSTRACT FROM AUTHOR]

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. [Display omitted] • The pathways of dissimilatory nitrate reduction to ammonium (DNRA) were clarified. • DNRA can recover nitrogen from wastewater plants and retain nitrogen in the soil. • Actinomycetes have great potential for performing DNRA. • The enzymes of Nap/NrfA and Nar/Nir are responsible for DNRA process. [ABSTRACT FROM AUTHOR]

We present new data on the rates of sedimentary denitrification and its component processes (canonical denitrification, anammox and dissimilatory nitrate reduction to ammonium) for intertidal and subtidal sites in the North Sea using nitrogen isotope addition methods. We find overall average denitrification rates of 6.3 (range 0.4–10.6) µmol m−2 h−1, similar to those previously reported for this region and other temperate shelf environments. We find canonical denitrification to be the dominant (>90%) process of the three. At the subtidal sites, most of the denitrification is supported by nitrate generated within the sediments, while at the intertidal site the main source is from the water column. We go on to consider the impact of these rates on nitrogen cycling within the North Sea region and compare the sediment core incubation rate results to estimates derived from modelling approaches. Model rates are somewhat higher than those directly measured and we consider possible reasons for this. • New measurements of denitrification, anammox and DNRA rates in North Sea sediments. • Denitrification is the dominant process and rates measured compare well to other direct measurements. • Model estimates suggest rather higher rates of nitrogen loss compared to direct measurements and some reasons for this difference are considered. [ABSTRACT FROM AUTHOR]

Catechol is one of the central intermediates in the aerobic biodegradation of numerous benzene-based aromatic contaminants derived from coal and petroleum sources as a result of unsustainable production processes. In O 2 -limiting environments, such as aquifers and sediments, accumulation of dead-end and inhibitory catechol can lead to a complete shutdown of further biodegradation. Thus, O 2 -independent catechol biotransformation plays an essential role in biodegrading aromatic contaminants in anoxic zones. In this study, we investigated redox processes and microbial community change during anaerobic catechol biodegradation coupled to nitrate and sulfate reductions by a sediment consortium. Denitrifiers and sulfate-reducing bacteria initially oxidized soluble non-catechol organics present in the sediments as electron donors to drive denitrification and sulfate reduction, respectively. Once the non-catechol organics were depleted, catechol was activated by denitrifiers capable of benzoyl-CoA metabolism. Subsequent ring cleavage and mineralization produced electrons and energy that could be coupled by denitrifiers and sulfate reducers to nitrate and sulfate reduction to N 2 and sulfide, respectively. When nitrate and sulfate coexisted, accumulation of sulfide stimulated sulfide oxidizers to growth via sulfide oxidation coupled to nitrate reduction to ammonium and nitrite. The resulting buildup of nitrite triggered abiotic conversion of catechol to a significantly less bioavailable form, probably 1,2-benzoquinone, that eventually blocked the biological process of catechol mineralization. This study documents the interactions of the several anaerobic microbial groups during catechol biodegradation with multiple endogenous electron acceptors and provides baseline for sustainable in-situ bioremediation of aromatic-contaminated environments. Image 1 • Anaerobic catechol scavenge is crucial for complete aromatic degradation in O 2 -limiting zones. • Catechol activation was initiated after the majority of non-catechol organics were depleted. • Catechol was activated by denitrifiers capable of benzoyl-CoA metabolism. • Catechol and other sCOD breakdown produced electrons for denitrification and SO 4 2− reduction. • NO 3 − accumulation during SOB-enabled DNRA abiotically blocked catechol biodegradation. [ABSTRACT FROM AUTHOR]

Abstract Denitrification (DNF) and dissimilatory nitrate reduction to ammonium (DNRA) are two competing nitrate reduction pathways that remove or recycle nitrogen, respectively. However, factors controlling the partitioning between these two pathways are manifold and our understanding of these factors is critical for the management of N loads in constructed wetlands. An important factor that controls DNRA in an aquatic ecosystem is the electron donor, commonly organic carbon (OC) or alternatively ferrous iron and sulfide. In this study, we investigated the role of natural organic carbon (NOC) and acetate at different OC/NO 3 − ratios and ferrous iron on the partitioning between DNF and DNRA using the 15N-tracer method in slurries from four constructed stormwater urban wetlands in Melbourne, Australia. The carbon and nitrate experiments revealed that DNF dominated at all OC/NO 3 − ratios. The higher DNF and DNRA rates observed after the addition of NOC indicates that nitrate reduction was enhanced more by NOC than acetate. Moreover, addition of NOC in slurries stimulated DNRA more than DNF. Interestingly, slurries amended with Fe2+ showed that Fe2+ had significant control on the balance between DNF and DNRA. From two out of four wetlands, a significant increase in DNRA rates (p <.05) at the cost of DNF in the presence of available Fe2+ suggests DNRA is coupled to Fe2+ oxidation. Rates of DNRA increased 1.5–3.5 times in the Fe2+ treatment compared to the control. Overall, our study provides direct evidence that DNRA is linked to Fe2+ oxidation in some wetland sediments and highlights the role of Fe2+ in controlling the partitioning between removal (DNF) and recycling (DNRA) of bioavailable N in stormwater urban constructed wetlands. In our study we also measured anammox and found that it was always <0.05% of total nitrate reduction in these sediments. Graphical abstract Unlabelled Image Highlights • Natural organic carbon (NOC) and ferrous iron showed significant effect on the partitioning between DNF and DNRA. • Nitrate reduction was stimulated more by the addition of NOC than acetate. • NOC enhanced DNRA more than denitrification. • Fe2+ had a significant control on the balance between denitrification and DNRA. • There was a link between DNRA and Fe2+ oxidation in Fe2+ amended slurries. [ABSTRACT FROM AUTHOR]

Abstract Dissimilatory nitrate reduction to ammonium (DNRA) is now known to be a more prevalent process in terrestrial ecosystems than previously thought. The key enzyme, a pentaheme cytochrome c nitrite reductase NrfA associated with respiratory nitrite ammonification, is encoded by the nrfA gene in a broad phylogeny of bacteria. The lack of reliable and comprehensive molecular tools to detect diverse nrfA from environmental samples has hampered efforts to meaningfully characterize the genetic potential for DNRA in environmental systems. In this study, modifications were made to optimize the amplification efficiency of previously-designed PCR primers, targeting the diagnostic region of NrfA between the conserved third- and fourth heme binding domains, and to increase coverage to include detection of environmentally relevant Geobacteraceae-like nrfA. Using an alignment of the primers to >270 bacterial nrfA genes affiliated with 18 distinct clades, modifications to the primer sequences improved coverage, minimized amplification artifacts, and yielded the predicted product sizes from reference-, soil-, and groundwater DNA. Illumina sequencing of amplicons showed the successful recovery of nrfA gene fragments from environmental DNA based on alignments of the translated sequences. The new primers developed in this study are more efficient in PCR reactions, although gene targets with high GC content affect efficiency. Furthermore, the primers have a broader spectrum of detection and were validated rigorously for use in detecting nrfA from natural environments. These are suitable for conventional PCR, qPCR, and use in PCR access array technologies that allow multiplex gene amplification for downstream high throughput sequencing platforms. Highlights • New primer sets expand coverage of diverse bacterial nrfA genes involved in the nitrite ammonification step for DNRA. • The coverage of the developed primers now extends to the NrfA clade containing Geobacteraceae. • Primer sets allow efficient PCR amplification of nrfA genes from a wide variety of natural environments. • Primers are suitable for multiple applications including conventional PCR, qPCR, multiplex arrays, and high-throughput sequencing. [ABSTRACT FROM AUTHOR]

Abstract Dissimilatory nitrate reduction to ammonium (DNRA) and diazotrophic N 2 fixation contribute to nitrogen (N) supply in rice paddies, whereas denitrification contributes to N loss. Continuous N fertilization in rice paddies is known to increase denitrification and reduce N 2 fixation, however little is known about its effect on DNRA and the NO 3 − partitioning between DNRA and denitrification. Here, we investigated the rates of DNRA, denitrification and N 2 fixation, and their relevant microbial gene abundances, in long-term high and low N fertilized rice paddies using a 15NO 3 − tracer, an acetylene reduction assay and quantitative PCR analysis, in laboratory incubation studies. We observed that DNRA exceeded denitrification by a factor of eight in low N fertilized rice paddies, while DNRA was almost half of the denitrification rate in high N fertilized rice paddies. The nrfA gene abundance, related to DNRA, was significantly higher in the low N fertilized rice paddies and was positively correlated with DNRA rates. However, no clear difference in denitrifying gene (narG, nirK and nosZ) abundances was observed between the N fertilization regimes. The proportion of total NO 3 − reduced by DNRA had a significantly positive correlation with the soil organic carbon-to-NO 3 - ratio and negative correlation with the soil NO 3 − concentration. N 2 fixation added ten times more N in the low N input than in the high N input paddies. Our findings highlight the self-regulated microbial N cycling in low N input paddy systems which maintain long-term paddy soil N nutrition. Highlights • N 2 fixation added ten times more N to low N input than to high N input rice paddies. • DNRA retained the majority of nitrate in long-term low N input rice paddies. • Denitrification dominated nitrate reduction in long-term high N input rice paddies. • High SOC:NO 3 − ratio favours NO 3 − partitioning to DNRA in NO 3 − limited paddy soils. [ABSTRACT FROM AUTHOR]

Agricultural soils are a major source of anthropogenic N 2 O, but their N 2 O emission estimates are highly uncertain, mainly due to the complexity of nitrogen (N) processes. Most soil N models include only primary N processes such as nitrification and denitrification, which limits their ability to realistically simulate N transformations in soils and accurately estimate N 2 O emissions from soils. This study introduces a Microbial-Explicit Model incorporating Comprehensive Nitrogen processes (MEMCN) to evaluate and quantify the influences of various N processes on the production of N 2 O as well as NO and N 2 , including nitrification, denitrification, anaerobic ammonium oxidation (ANAMMOX), dissimilatory nitrate reduction to ammonium (DNRA), mineralization, and microbial assimilation (i.e., growth) and death. The MEMCN was evaluated in laboratory experiments using agricultural soils with different levels of N additions under anaerobic and aerobic conditions, and reproduced well the dynamics of NH 4 +, NO 3 −, NO 2 −, NO, N 2 O, and N 2. After nitrification and denitrification, ANAMMOX and assimilation were found to be most important in controlling N transformations in agricultural soils. ANAMMOX directly increased N 2 emissions by 139% at the beginning of the simulations (i.e., 48 h) under anaerobic conditions, while microbial assimilation indirectly reduced NO, N 2 O, and N 2 emissions by 88%, 54%, and 58%, respectively, at the end of the simulations (i.e., 336 h) under aerobic conditions. Correspondingly, the biomass of ANAMMOX bacteria increased significantly at the beginning of the simulations under anaerobic conditions, while the biomass of nitrite oxidizing bacteria increased substantially under aerobic conditions. In contrast, DNRA, mineralization and microbial death had minor effect on soil N transformations, and the biomass of DNRA bacteria and heterotrophs did not change significantly during the simulations. Our study shows that it is necessary to include ANAMMOX and microbial assimilation in soil N models, while explicit simulation of microbial biomass dynamics may only be necessary if microbial biomass pools change significantly. • Develope a Microbial-Explicit Model incorporating Comprehensive N processes. • Quantify contributions of individual N processes to gaseous N production. • ANAMMOX increased N 2 produciton under aerobic and anaerobic condtions. • Assimilation reduced NO, N 2 O, and N 2 emissions under aerobic condtions. • Micoribal biomass should be explicitly expressed as they change substantially. [ABSTRACT FROM AUTHOR]

Microplastics (MPs) pollution in agriculture ecosystems profoundly affects biogeochemical cycles. However, the impacts of MPs, particularly biodegradable MPs, on dissimilatory nitrate reduction to ammonium (DNRA) process remain unclear. Herein, the alterations in denitrification and DNRA pathways and underlying mechanism by different MPs exposures (including conventional nonbiodegradable MPs (polyethylene (PE) and polypropylene (PP)) and biodegradable MPs (polylactic acid (PLA) and polybutylene adipate terephthalate (PBAT)) were explored via soil microcosm experiments accompanied with 15N isotope tracer technology and 16S rRNA high-throughput sequencing. Compared with control, PE and PP increased the rates of denitrification by 117–126% but significantly decreased DNRA rates by 39.3–63.4%, whereas DNRA activities in PLA and PBAT treatments were remarkably boosted by 163–242% and dominated soil nitrate bioreduction (6.67–8.69 μg N g−1 d −1). This differentiation was attributed to the nutrient imbalance induced by MPs and distinctly selective effects of MPs on functional microbes. Microbial interaction mechanism further suggested that limited bioavailable carbon intensified the competition between heterotrophic denitrifiers (e.g., Bacillus , Sphingomona s and Microvirga) and DNRA bacteria (e.g., Luteitalea and Streptomyces) for electron donor in nonbiodegradable MPs treatments, reducing the abundances of DNRA bacteria. However, the high bioavailable C/NO x – ratio resulting from biodegradable MPs degradation released such competition and more greatly promoted the activities of DNRA bacteria than denitrifiers, facilitating ammonium retention in soils. Collectively, this study highlights the promotion of biodegradable MPs on soil ammonium recycle via DNRA process in farmland ecosystems and can shed some light on current plastic mulch-film management toward a sustainable and cleaner agricultural industry. [Display omitted] • The impacts of MPs on soil denitrification and DNRA were investigated. • MPs altered the fates of N being removed from ecosystem versus that retained. • Nonbiodegradable MPs notably promoted denitrification but inhibited DNRA process. • Biodegradable MPs significantly enhanced NH 4 + retention via boosting DNRA pathway. • Biodegradable MPs alleviated the competition between denitrifers and DNRA bacteria. [ABSTRACT FROM AUTHOR]

With the increased soil contamination by crude oil, understanding the effects on the metabolic potential of petroleum hydrocarbons (PHs) as well as its coupling to nitrogen-cycling (N-cycling) is crucial for improving the efficiency of in-situ bioremediation. Chemical measurements combined with metagenomic sequencing were used to investigate soils with different oiling intensity in coastal area. We suggested that oil contamination exerted strong impacts on soil properties with increased ammonium but decreased nitrite and nitrate concentrations. Taxonomic analysis revealed that oil contamination molded a unique microbial community structure with a bias towards the PHs-degrading specific populations with halophilic and oligotrophic characteristics. Alcanivorax , Marinobacter and some other potential PHs degraders were also nitrate reducing bacteria, and thus involved in both PHs biodegradation and N-cycling pathways. Microbial community structure was mainly explained by soil C/N ratio based on redundancy analysis (RDA) results. Further, functional metagenomics demonstrated that the genetic potential of PHs oxidation as well as dissimilatory nitrate reduction to ammonium (DNRA) and N-fixation was activated by oil contamination. Overall, metagenomic results in conjunction with co-occurrence network demonstrated that PHs oxidation probably coupled to DNRA, N-fixation and N-immobilization in the contaminated soil. PHs biodegradation was coupled to DNRA by the electrons transfer to nitrate/nitrite. Ammonium accumulated through N-fixation and DNRA processes could be utilized by PHs-degrading heterotrophs through N-immobilization, which was another way that connected to PHs biodegradation. [Display omitted] • Alcanivorax and Marinobacter were involved in both PHs biodegradation and N-cycling. • PHs biodegradation coupled to DNRA, N-fixation and N immobilization. • PHs oxidation was coupled to DNRA by providing electrons to nitrate/nitrite. • Ammonium accumulated by DNRA and N-fixation was utilized by PHs degraders. [ABSTRACT FROM AUTHOR]

Abstract Levee construction results in the systematic replumbing of river systems and reduces the frequency of floodplain inundation, which impacts nutrient delivery and transformations in floodplains. Floodplain restoration via levee removal affects downstream water quality by restoring soil microbial metabolic pathways such as denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA). Although these metabolisms are important for the nitrogen cycle, few studies have quantified the contribution of all three pathways to nitrate retention or loss in restored floodplains. The objectives of this study were to quantify the relevance of denitrification, anammox and DNRA to nitrogen retention, characterize the hydrologic conditions most favorable to each pathway, and estimate the potential for floodplain restoration to improve nitrogen cycling in the Cosumnes River watershed. To address these goals, we simulated flood conditions in soil mesocosms collected from two floodplains where levees were breached in 1997 and 2014 along the Lower Cosumnes River in the San Joaquin Basin of California. River water enriched with K15NO 3 tracer was pumped into each mesocosm at a constant rate for a period of 3 months. Samples were collected from the surface water and soil pore water for measurements of NO 3 −, NO 2 −, and NH 4 + concentrations, and δ15N of dissolved gases (N 2 and N 2 O). To the best of our knowledge, this study reports the highest relative contribution to N 2 production due to anammox for freshwater systems (41 to 84%) to date. High anammox rates were associated with heterogeneous grain size distribution across depth and high nitrification rates. We quantify the capacity of restored floodplain soils with distinct textural and chemical characteristics to retain or release nitrogen during large and small floods in a particular water year. Graphical abstract Unlabelled Image Highlights • Anammox rates in inundated floodplain soils are high and unprecedented. • Large floods facilitate heterogeneous grain size distribution, which promotes anammox. • Denitrification and anammox are correlated with soil carbon and nitrification rates. • Timing and magnitude of annual nitrogen release or retention depends on flood type. [ABSTRACT FROM AUTHOR]

Abstract Stormwater control measures (SCMs) have the potential to mitigate negative effects of watershed development on hydrology and water quality. Stormwater regulations and scientific literature have assumed that SCMs are important sites for denitrification, the permanent removal of nitrogen, but this assumption has been informed mainly by short-term loading studies and measurements of potential rates of nitrogen cycling. Recent research concluded that SCM nitrogen removal can be dominated by plant and soil assimilation rather than by denitrification, and rates of nitrogen fixation can exceed rates of denitrification in SCM sediments, resulting in a net addition of nitrogen. Nitrogen cycling measurements from other human-impacted aquatic habitats have presented similar results, additionally suggesting that dissimilatory nitrate reduction to ammonium (DNRA) and algal uptake could be important processes for recycling nitrogen in SCMs. Future research should directly measure a suite of nitrogen cycling processes in SCMs and reveal controlling mechanisms of individual rate processes. There is ample opportunity for research on SCM nitrogen cycling, including investigations of seasonal variation, differences between climatic regions, and trade-offs between nitrogen removal and phosphorus removal. Understanding nitrogen dynamics within SCMs will inform more efficient SCM design and management that promotes denitrification to help mitigate negative effects of urban stormwater on downstream ecosystems. Graphical abstract Image 1 Highlights • SCMs are considered important sites for denitrification. • Studies reporting high denitrification rates in SCMs mostly used indirect assays. • Direct denitrification measurements suggest temporary removal pathways may dominate in SCMs. • Nitrogen cycling within SCMs should be measured using direct methods. • Quantifying seasonal and spatial variability of SCM nitrogen cycling is critical. [ABSTRACT FROM AUTHOR]

Abstract Stable isotopes (15,14N, 18,16O) of dissolved inorganic nitrogen (N) were measured in sediment porewaters and benthic flux chambers across the Peruvian oxygen minimum zone (OMZ) from 74 to 1000 m water depth. Sediments at all locations were net consumers of bottom water NO 3 −. In waters shallower than 400 m, this sink was largely attributed to dissimilatory nitrate reduction to ammonium (DNRA) by filamentous nitrate-storing bacteria (Marithioploca and Beggiatoa) and to denitrification by foraminifera. The apparent N isotope effect of benthic NO 3 − loss (15ε app) was 7.4 ± 0.7‰ at microbial mat sites and 2.5 ± 0.9‰ at the lower fringe of the OMZ (400 m) where foraminifera were abundant. The OMZ sediments were a source of 15N-enriched NO 2 − (28.9 to 65.5‰) and NH 4 + (19.4–20.5‰) to the bottom water. Model simulations generally support a previous hypothesis attributing the 15NH 4 + enrichment to a coupling between DNRA and anammox (termed DAX) using biologically-stored NO 3 − from Marithioploca and NH 4 + from the porewater. The model predicts that 40% of NO 3 − that is actively transported into the sediment by Marithioploca is reduced to N 2 by this pathway. DAX enhances N 2 fluxes by a factor of 2–3 and accounts for 70% of fixed N loss to N 2. Moreover, because most of the ambient porewater NH 4 + is generated by DNRA, up to two-thirds of biologically-transported NO 3 − could end up being lost to N 2. This challenges the premise that Marithioploca -dominated sediments tend to conserve fixed N. By limiting the flux of 15NH 4 + back to the ocean, DAX also tends to decrease benthic N fractionation. Tracking the fate of NH 4 + once it leaves the sediment is critical for understanding how the benthos contributes to N isotope signals in the water column. [ABSTRACT FROM AUTHOR]

Effects of antibiotics on the transformation of nitrate and the associated N 2 O release in paddy fields are obscure. Using soil slurry experiments combined with 15 N tracer techniques, the influence of tetracycline and sulfamethazine (applied alone and in combination) on the denitrification, anaerobic ammonium oxidation (anammox), dissimilatory nitrate reduction to ammonium (DNRA) and N 2 O release rates in the paddy soil were investigated, while genes related to nitrate reduction and antibiotic resistance were quantified to explore the microbial mechanisms behind the antibiotics’ effects. The potential rates of denitrification, anammox, and DNRA were significantly ( p  < 0.05) reduced, which were mainly attributed to the inhibitory effects of the antibiotics on nitrate-reducing microbes. However, the N 2 O release rates were significantly ( p  < 0.05) stimulated by the antibiotic treatments (0.6–6000 μg kg −1 soil dry weight), which were caused by the different inhibition effects of antibiotics on N 2 O production and N 2 O reduction as suggest by the changes in abundance of nirS (nitrite reduction step) and nosZ (N 2 O reduction to N 2 step) genes. Antibiotic resistance gene ( tetA , tetG , sulI, and sulIII ) abundances were significantly ( p  < 0.05) increased under high antibiotic exposure concentrations (>600 μg kg −1 soil dry weight). Our results suggest that the widespread occurrence of antibiotics in paddy soils may pose significant eco-environmental risks (nitrate accumulation and greenhouse effects) by altering nitrate transformation processes. [ABSTRACT FROM AUTHOR]

Soils under pasture are subjected to repeated wetting and drying cycles in response to rainfall, irrigation and evapotranspiration. The amplitude of these cycles is likely to increase under the predicted changes in rainfall variability, demanding a better quantitative understanding of the processes involved. The wetting of pasture soils triggers large pulses of N 2 O emissions, predominantly produced via denitrification. Under anaerobic conditions in the soil matrix, denitrification and dissimilatory nitrate reduction to ammonia (DNRA) are thought to compete for available NO 3 − . However, the relationship between gross NO 3 − production and consumption via denitrification (N 2 and N 2 O) and DNRA remains poorly understood. This study combines the direct quantification of N 2 and N 2 O with a numerical 15 N tracing model to establish the relationship between denitrification and DNRA in pasture soils after wetting. Soil microcosms were fertilised with NH 4 NO 3 (35 μg N g −1 soil) using a triple 15 N labelling approach, wetted to four different water-filled pore space (WFPS) levels and incubated over two days. The abrupt increase in soil moisture triggered a burst of N 2 and N 2 O emissions, with peak fluxes of N 2  > 13.1 μg N g −1 soil day −1  at high soil moisture levels. At 95% and 80% WFPS, denitrification was dominated by N 2 emissions, with the N 2 /(N 2 +N 2 O) ratio ranging from 0.5 to 0.9. At 60% and 40% WFPS, the N 2 /(N 2 +N 2 O) ratio ranged from 0.2 to 0.3, showing N 2 O as the main product of denitrification. The wetting of dry pasture soils resulted in increased DNRA rates across soils and WFPS. Both denitrification and DNRA increased exponentially with WFPS and responded to NO 3 − availability, demonstrating both processes as N-substrate driven. The labile C/NO 3 − ratio was not correlated to DNRA rates and as such did not explain NO 3 − partitioning between denitrification and DNRA, likely due to the high C availability in the pasture soils. Increasing labile C availability stimulated heterotrophic soil respiration, which had no effect on denitrification rates, but increased DNRA. Increased soil respiration is likely to have lowered the soil redox potential, promoting a shift of NO 3 − consumption from denitrification to DNRA, which implies the soil redox potential rather than the C/NO 3 − ratio as the key factor for NO 3 − partitioning between denitrification and DNRA in C rich pasture soils. Our findings suggest that the high labile C availability under perennial pastures, together with the increase of labile C upon rewetting, drives heterotrophic soil respiration, reduces the soil redox potential and ultimately shifts NO 3 − consumption from denitrification to DNRA. This shift limits denitrification losses and is therefore critical for limiting N loss and increasing N retention in subtropical pasture soils. [ABSTRACT FROM AUTHOR]

Abstract As more regions in the world look to replenish depleted aquifers, treated wastewater (TWW) is increasingly infiltrated in managed aquifer recharge (MAR) schemes. While MAR is a promising emerging technology, it also has the potential to generate pollutants along the infiltration flow path. In this study, we infiltrated treated wastewater through an organic-rich soil in column experiments operated with wetting and drying cycles. Ammonium, which was present only in trace concentrations in the TWW, increased in concentration with depth and exceeded the EU Water Framework Directive limit of 0.5 mg/L for up to a year, depending on the sampling depth. Pore water samples collected at the end of drying periods showed very high nitrate concentrations, indicating nitrification of some of the ammonium. Oxidation reduction potential often exceeded 200 mV during drying periods, showing conditions for nitrification, but dropped below −100 mV during wetting periods, creating several possible pathways for ammonium production. Potential sources of ammonium are (1) dissolved organic nitrogen in the TWW, (2) nitrate in the TWW, and (3) organic nitrogen in the soil. δ15N in ammonium in pore water samples (mean 4.7‰) was slightly higher than δ15N in the soil (2.4‰), indicating that the soil was likely the major source but also that nitrate (mean 17.2‰) may have been the source of some of the ammonium. Fractionation of 15N in nitrate as well as high concentrations of acetate (a labile organic carbon source) also indicate that dissimilatory nitrate reduction to ammonium may have formed some of the NH 4 +. Graphical abstract Image 1 Highlights • Infiltration of treated wastewater generated ammonium. • Conditions in the soil were strongly reducing and labile organic carbon was abundant. • Mass balance shows that soil nitrogen was a source of some of the ammonium. • Some ammonium may have been produced by dissimilatory nitrate reduction to ammonium. [ABSTRACT FROM AUTHOR]

Nitrite is a toxic intermediate compound in the nitrogen (N) cycle. Elevated concentrations of nitrite have been observed in the Seine River, raising questions about its sources and fate. Here, we assess the role of bottom sediments as potential sources or sinks of nitrite along the river continuum. Sediment cores were collected from two depocenters, one located upstream, the other downstream, from the largest wastewater treatment plant (WWTP) servicing the conurbation of Paris. Pore water profiles of oxygen, nitrate, nitrite and ammonium were measured. Ammonium, nitrate and nitrite fluxes across the sediment-water interface (SWI) were determined in separate core incubation experiments. The data were interpreted with a one-dimensional, multi-component reactive transport model, which accounts for the production and consumption of nitrite through nitrification, denitrification, anammox and dissimilatory nitrate reduction to ammonium (DNRA). In all core incubation experiments, nitrate uptake by the sediments was observed, indicative of high rates of denitrification. In contrast, for both sampling locations, the sediments in cores collected in August 2012 acted as sinks for nitrite, but those collected in October 2013 released nitrite to the overlying water. The model results suggest that the first step of nitrification generated most pore water nitrite at the two locations. While nitrification was also the main pathway consuming nitrite in the sediments upstream of the WWTP, anammox dominated nitrite removal at the downstream site. Sensitivity analyses indicated that the magnitude and direction of the benthic nitrite fluxes most strongly depend on bottom water oxygenation and the deposition flux of labile organic matter. [ABSTRACT FROM AUTHOR]

Sediment microbes have a great potential to transform reactive N to harmless N 2 , thus decreasing wastewater nitrogen load into aquatic ecosystems. Here, we examined if spatial allocation of the wastewater discharge by a specially constructed sediment diffuser pipe system enhanced the microbial nitrate reduction processes. Full-scale experiments were set on two Finnish lake sites, Keuruu and Petäjävesi, and effects on the nitrate removal processes were studied using the stable isotope pairing technique. All nitrate reduction rates followed nitrate concentrations, being highest at the wastewater-influenced sampling points. Complete denitrification with N 2 as an end-product was the main nitrate reduction process, indicating that the high nitrate and organic matter concentrations of wastewater did not promote nitrous oxide (N 2 O) production (truncated denitrification) or ammonification (dissimilatory nitrate reduction to ammonium; DNRA). Using 3D simulation, we demonstrated that the sediment diffusion method enhanced the contact time and amount of wastewater near the sediment surface especially in spring and in autumn, altering organic matter concentration and oxygen levels, and increasing the denitrification capacity of the sediment. We estimated that natural denitrification potentially removed 3–10% of discharged wastewater nitrate in the 33 ha study area of Keuruu, and the sediment diffusion method increased this areal denitrification capacity on average 45%. Overall, our results indicate that sediment diffusion method can supplement wastewater treatment plant (WWTP) nitrate removal without enhancing alternative harmful processes. [ABSTRACT FROM AUTHOR]

The eutrophication of estuaries results from increasing anthropogenic nutrient inputs to coastal waters. Ecosystem recovery from eutrophication is partly dependent on the ability of a system to assimilate or remove nutrients, and denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are important pathways for nitrogen (N) removal or retention. We measured rates of denitrification and DNRA over an annual cycle at two stations in Weeks Bay, AL, a shallow microtidal estuary receiving freshwater from two rivers with agricultural watersheds and high N inputs. We hypothesized that rates of DNRA would exceed denitrification in the sulfidogenic sediments in this estuary. Consistent with our hypothesis, we found that DNRA (44.4 ± 5.5 μmol N m −2 hr −1 ) exceeded in situ denitrification (0.9 ± 2.3 μmol N m −2 hr −1 ) and that even in the presence of abundant water column nitrate DNRA was favored over denitrification by a factor of two. DNRA is estimated to provide N to the water column at a rate equivalent to 15% of the N input that is retained within the estuary and is a significant component of the N budget in this highly impacted estuary. DNRA by retaining N in the system contributes to the N demand by primary producers and can impact this estuary through enhanced rates of primary production. Weeks Bay, like many coastal estuaries, experiences periods of hypoxia, blooms of harmful algae and fish kills. Future management efforts should focus on reducing nutrient input to this estuary without which the significant retention of N in this system through DRNA will contribute to the undesirable ecosystem attributes associated with eutrophication. [ABSTRACT FROM AUTHOR]

Understanding interrelations between an environment's hydrological past and its current biogeochemistry is necessary for the assessment of biogeochemical and microbial responses to changing hydrological conditions. The question how previous dry-wet events determine the contemporary microbial and biogeochemical state is addressed in this study. Therefore, sediments exposed to the atmosphere of areas with a different hydrological past within one kettle hole, i.e. (1) the predominantly inundated pond center, (2) the pond margin frequently desiccated for longer periods and (3) an intermediate zone, were incubated with the same rewetting treatment. Physicochemical and textural characteristics were related to structural microbial parameters regarding carbon and nitrogen turnover, i.e. abundance of bacteria and fungi, denitrifiers (targeted by the nirK und nirS functional genes) and nitrate ammonifiers (targeted by the nrfA functional gene). Our study reveals that, in combination with varying sediment texture, the hydrological history creates distinct microbial habitats with defined boundary conditions within the kettle hole, mainly driven by redox conditions, pH and organic matter (OM) composition. OM mineralization, as indicated by CO 2 -outgassing, was most efficient in exposed sediments with a less stable hydrological past. The potential for nitrogen retention via nitrate ammonification was highest in the hydrologically rather stable pond center, counteracting nitrogen loss due to denitrification. Therefore, the degree of hydrological stability is an important factor leaving a microbial and biogeochemical legacy, which determines carbon and nitrogen losses from small lentic freshwater systems in the long term run. [ABSTRACT FROM AUTHOR]

Poly (3-hydroxybutyrate-co-3-hydroxyvalerate)/poly (lactic acid) (PHBV/PLA), a biodegradable polymer blend, was used as both carbon source and biofilm carrier in a packed-bed bioreactor. The effect of influent pH on denitrification performance in PHBV/PLA supported denitrification system was further investigated. Results showed that the nitrate removal efficiency kept high level under an alkaline influent while largely decreased under an acidic influent. When the influent pH was 5.68, nitrate removal efficiency was about 34% of that on neutral or alkaline conditions. Meanwhile, dissimilatory nitrate reduction to ammonia process (DNRA) was enhanced on acidic condition. Furthermore, ΔpH (the difference between influent and effluent pH) and effluent TOC both increased on alkaline condition, and they sharply rose to 2.75 and 23.37 mg L −1 with an influent pH of 10.38. It was found that there were obvious positive correlations among influent pH, ΔpH and TOC. Moreover, based on the characteristics of microbial hydrolysis and denitrification processes, the effect mechanism of influent pH on nitrate removal was deeply explored. A better knowledge of the effect of influent pH on nitrate removal will be significant for the solid-phase denitrification in practice. [ABSTRACT FROM AUTHOR]

• Denitrification and DNRA rates were modulated mainly by their gene abundances, followed by the environmental factors. • Denitrification rates significantly increased as further eutrophication, but DNRA rates were not. • Pseudomonas and Anaeromyxobacter was the dominant genus mediated denitrification and DNRA, respectively. 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. [Display omitted] [ABSTRACT FROM AUTHOR]

As bivalve aquaculture expands globally, an understanding of how it alters nitrogen is important to minimize impacts. This study investigated nitrogen cycling associated with clam aquaculture in the Sacca di Goro, Italy ( Ruditapes philipinarum ) and the Eastern Shore, USA ( Mercenaria mercenaria ). Ammonium and dissolved oxygen fluxes were positively correlated with clam biomass; R. philippinarum consumed ~ 6 times more oxygen and excreted ~ 5 times more NH 4 + than M. mercenaria . There was no direct effect of clams on denitrification or dissimilatory nitrate reduction to ammonium (DNRA); rather, nitrate availability controlled the competition between these microbial pathways. Highest denitrification rates were measured at sites where both water column nitrate and nitrification were elevated due to high densities of a burrowing amphipod ( Corophium sp.). DNRA exceeded denitrification where water column nitrate was low and nitrification was suppressed in highly reduced sediment, potentially due to low hydrologic flow and high clam densities. [ABSTRACT FROM AUTHOR]

At the Kiruna iron ore mine in northern Sweden, mine drainage and process water contain elevated concentrations of nitrate (NO 3 − ) from the use of ammonium nitrate fuel oil explosives. In order to investigate the treatment capacity of a denitrifying woodchip bioreactor technique for the removal of NO 3 − through denitrification, a bioreactor was installed at the mine site in 2015 and operated for two consecutive years. Neutral-pH mine drainage and process water containing 22 mg NO 3 − -N and 1132 mg SO 4 2− (average) was passed through the bioreactor which was filled with a reactive mixture of pine woodchips and sewage sludge, at treatment temperatures ranging between 0.8 and 17 °C. At bioreactor temperatures above ∼5 °C, NO 3 − removal proceeded to below detection limits (0.06 mg N L −1 ) without substantial production of nitrite (NO 2 − ), ammonium (NH 4 + ), nitrous oxide (N 2 O), or methane (CH 4 ). The relative production of NH 4 + and N 2 O to the NO 3 − reduced increased as bioreactor temperatures decreased below ∼5 °C. Based on the resultant changes in alkalinity and pH from the production of bicarbonate (HCO 3 − ) and carbonic acid (H 2 CO 3 ), a stoichiometric mass balance model indicated that denitrification, nitrate reduction to ammonium (DNRA), sulfate reduction, and fermentation were the major biogeochemical processes controlling pH, alkalinity and nitrogen, sulfur and carbon concentrations in the system. It is suggested that fermentation changed from being mainly butyrate producing to acetate producing with time, triggering a decline in biogeochemical process diversity and leaving denitrification as the sole major electron accepting process. [ABSTRACT FROM AUTHOR]

Subterranean estuary seepage faces are recognized as important reactive interfaces that regulate solute transport to coastal ecosystems via Submarine Groundwater Discharge (SGD). Here we describe benthic processes and rates driving the biogeochemical regulation of SGD-borne inorganic N loading into the Ria Formosa lagoon (Iberian peninsula) through a sandy seepage face. Maximum potential NO 3 − reduction rates, obtained by kinetic modeling of advection-controlled flow-through reactor experiments, ranged from 2.33 ± 1.06 to 14.17 ± 0.22 nmol cm −3 “bulk” sediment (bs) h −1 . Maximum potential nitrification ranged from 0 to 7.5 ± 1.3 nmol cm −3 bs h −1 while potential ammonium assimilation was valued at 2.0 ± 0.3 nmol cm −3 bs h −1 . These NO 3 − reduction rates are in good agreement with previous estimates obtained by diagenetic modeling of in-situ porewater NO 3 − vertical profiles at the same location. Potential NO 3 − reduction rates were very sensitive to temperature (Q 10 = 3.5 ± 0.2). Porewater velocity seems to control net NO 3 − reduction rates, probably by determining solute distribution but also its supply to the microbial community by shaping the diffusive boundary layer around sediment particles. Nevertheless, NO 3 − reduction rates seem ultimately limited by organic matter availability at high velocities. Half-saturation constants of NO 3 − for NO 3 − reduction were low, suggesting that the NO 3 − reducing microbial community had high affinity for NO 3 − . In addition, our experiments provide evidence for the occurrence of alternative NO 3 − reduction pathways, including Dissimilatory Nitrate Reduction to Ammonium (DNRA) and apparent aerobic NO 3 − reduction within the shallow subsurface sediment layer (2–12 cm depth). [ABSTRACT FROM AUTHOR]

Understanding the magnitude of nitrogen (N) loss and recycling pathways is crucial for coastal N management efforts. However, quantification of denitrification and anammox by a widely-used method, the isotope pairing technique, is challenged when dissimilatory NO 3 − reduction to NH 4 + (DNRA) occurs. In this study, we describe a revised isotope pairing technique that accounts for the influence of DNRA on NO 3 − reduction (R-IPT-DNRA). The new calculation procedure improves on previous techniques by (1) accounting for N 2 O production, (2) distinguishing canonical anammox from coupled DNRA-anammox, and (3) including the production of 30 N 2 by anammox in the quantification of DNRA. This approach avoids the potential for substantial underestimates of anammox rates and overestimates of denitrification rates in systems where DNRA is a significant NO 3 − reduction pathway. We apply this technique to simultaneously quantify rates of anammox, denitrification, and DNRA in intact sediments adjacent to a seagrass bed in subtropical Australia. The effect of organic carbon lability on NO 3 − reduction was also addressed by adding detrital sources with differing C:N (phytoplankton- or seagrass-derived). DNRA was the predominant pathway, contributing 49–74% of total NO 3 − reduction (mean 0.42 µmol N m −2 h −1 ). In this high C:N system, DNRA outcompetes denitrification for NO 3 − , functioning to recycle rather than remove N. Anammox exceeded denitrification (mean 0.18 and 0.04 µmol N m −2 h −1 , respectively) and accounted for 64–86% of N loss, a rare high percentage in shallow coastal environments. Owing to low denitrification activity, N 2 O production was ∼100-fold lower than in other coastal sediments (mean 7.7 nmol N m −2 h −1 ). All NO 3 − reduction pathways were stimulated by seagrass detritus but not by phytoplankton detritus, suggesting this microbial community is adapted to process organic matter that is typically encountered. The R-IPT-DNRA is widely applicable in other environments where the characterization of co-existing NO 3 − reduction pathways is desirable. [ABSTRACT FROM AUTHOR]

Anammox bacteria can perform dissimilatory nitrate reduction to ammonium (DNRA) with nitrite as intermediate coupled to the oxidation of volatile fatty acids (VFA). Batch tests with enriched anammox and a co-culture of anammox and heterotrophic bacteria showed the capacity of Candidatus ‘Brocadia fulgida’ to perform the DNRA coupled to the anammox reaction (DNRA-anammox) at a high rate although the culture was not previously adapted to VFA. From thermodynamic calculations it could be stated that low COD/N influent ratios favour the DNRA-anammox transformation over heterotrophic conversions since more free energy is gained. A process scheme is proposed for an innovative nitrogen removal system in which the nitrate produced by nitrite oxidizing bacteria and/or anammox bacteria is converted during DNRA-anammox pathway, resulting in a sustainable nitrogen removal from municipal wastewater while circumventing the troublesome out-selection of nitrite oxidizing bacteria encountered in mainstream applications. [ABSTRACT FROM AUTHOR]

The fate of nitrogen in natural environments is controlled by anaerobic nitrate-reducing processes by which nitrogen is removed as N 2 or retained as NH 4 + . These processes can potentially be driven by oxidation of reduced inorganic compounds at oxic-anoxic interfaces. Several studies have investigated the use of Fe 2+ as an electron donor in nitrate reduction in bacterial cultures, however current information on this process in the environment is sparse. We aimed to determine whether nitrate-reducing processes in the freshwater Lake Almind (Silkeborg, Denmark) were linked to Fe 2+ oxidation. Anaerobic sediment slurries were supplemented with 15 N-substrates and electron donors (Fe 2+ and/or acetate) to characterize nitrate-reducing processes under environmentally relevant substrate concentrations and at higher concentrations traditionally used in microbial enrichment studies. Dissimilatory nitrate reduction to ammonium, DNRA, was stimulated by Fe 2+ addition in 7 of 10 slurry experiments and in some cases, denitrification was concomitantly reduced. The determined kinetic parameters (V max and K m ) for Fe 2+ -driven DNRA were 4.7 µmol N L −1 d −1 and 33.8 µmol Fe 2+ L −1 , respectively and reaction stoichiometry for Fe 2+ :NH 4 + (8.2:1) was consistent with that of predicted stoichiometry (8:1). Conversely, under enrichment conditions, denitrification was greatly increased while DNRA rates remained unchanged. Increased Fe 2+ concentrations may be exploited by DNRA organisms and have an inhibitory effect on denitrification, thus Fe 2+ may play a role in regulating N transformations in Lake Almind. Furthermore, we suggest enrichment conditions may promote the adaptation or change of microbial communities to optimally utilize the available high substrate concentrations; misrepresenting metabolisms occurring in situ . [ABSTRACT FROM AUTHOR]