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Excess nitrogen in agricultural drainage poses a serious threat to the water quality safety of the Yellow River basin. Utilizing aquatic plants to modify the rhizosphere microbial community structure and facilitate nitrogen transformation is a crucial strategy for mitigating regional water eutrophication. We here compare key processes of nitrogen transformation occurring in the rhizosphere of sediments of a ditch artificially planted with a mix of species (Phragmites australis, Typha orientalis, Nymphaea tetragon) with the rhizosphere of a ditch occupied by naturally occurring aquatic vegetation, dominated either by P. australis or T. orientalis. Our results revealed a species effect, with an increased denitrification rate (DR) and dissimilatory nitrate reduction to ammonium rate (DNRAR) in the cultivated ditch for P. australis, compared to the naturally occurring T. orientalis vegetation. The nitrogen fixation rate (NFR) increased in the artificial setting with T. orientalis in comparison to natural P. australis vegetation. The richness of the bacterial community and the relative abundances of Bacteroidota, Firmicutes, and Geobacter were significantly greater in the rhizosphere of the artificially cultivated ditch due a greater availability in nitrogen and organic carbon. In the artificially cultivated ditch, the dominant functional genes affecting DRNARs in the rhizosphere sediments of P. australis were nrfC and nrfA, whereas DRs were driven mainly by norB and napA, which were influenced by the nitrogen and carbon levels. The dominant functional genes affecting NFRs in the rhizosphere sediments of T. orientalis were nifD, nifK, and nifH. Our results provide a scientific basis for the use of aquatic plants for mitigating excess nitrogen levels in agricultural drainage. [ABSTRACT FROM AUTHOR]

Abstract Background The phylum Bacteroidota represents a significant proportion of heterotrophic bacteria found in marine ecosystems. Members of the phylum Bacteroidota are actively involved in the degradation of biopolymers such as polysaccharides and proteins. Bacteroidota genomes exhibit a significant enrichment of various enzymes, including carbohydrate-active enzymes (CAZymes), carboxypeptidases, esterases, isomerases, peptidases, phosphatases, and sulfatases. The genus Marivirga, a member of the family Marivirgaceae within the phylum Bacteroidota, comprises six documented species. During a microbial diversity study, three novel Marivirga strains (BKB1-2 T, ABR2-2, and BDSF4-3 T) were isolated from the West Sea, Republic of Korea. Results To explore the taxonomic status and genomic characteristics of the novel isolates, we employed a polyphasic taxonomic approach, which included phylogenetic, chemotaxonomic and comprehensive genome analysis. The three isolates were Gram-stain-negative, aerobic, rod-shaped, moderately halophilic, and had a gliding motility. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among the two isolates, BKB1-2 T and BDSF4-3 T, and the six reference strains were 70.5–76.5% for ANI and 18.1–25.7% for dDDH. Interestingly, the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the strains harbor genes for a comprehensive pathway for dissimilatory nitrate reduction to ammonium (DNRA), as well as other nitrogen pathways for the reduction of nitrite, nitric oxide, and nitrous oxide. Additionally, the antiSMASH analysis indicated that the strains contained three to eight biosynthetic gene clusters (BGCs) associated with the synthesis of secondary metabolites. Furthermore, the strains carried a high number of CAZyme ranging from 53 to 152, which was also demonstrated by an in vitro analysis of degradation of the polysaccharide cellulose, chitin, laminarin, starch, and xylan. Additionally, all the strains carried genes for the metabolism of heavy metals, and exhibited tolerance to heavy metals, with minimum inhibitory concentrations (MICs) in millimoles (mM) in ranges of Co2+ (3–6), Cu2+ (0.2–0.4), Ni2+ (3–5), Zn2+ (2–4), Mn2+ (20–50), and Hg2+ (0.3). Conclusions Based on polyphasic taxonomic approach, the three isolated strains represent two novel species names Marivirga arenosa sp. nov. (BKB1-2 T = KCTC 82989 T = InaCC B1618T), and Marivirga salinae sp. nov. (BDSF4-3 T = KCTC 82973 T = InaCC B1619T).

With the increasing environmental impacts of human activities, the problem of polygenic multipollutants in groundwater has attracted the attention of researchers. Identifying the hydrobiogeochemical characteristics of the surface sewage that replenishes groundwater is crucial to addressing this problem. The input of polygenic multipollutants into groundwater leads to not only the mechanical superposition of pollutants but also the formation of secondary pollutant types. The evolution of polygenic multipollutants is influenced by aquifer characteristics, carbon sources, microbial abundance, etc. Therefore, this study took a sewage leakage point in Northwest China as the research object, carried out a controlled laboratory experiment on the impact of sewage discharge on groundwater, and, combined with long-term field monitoring results, determined the main hydrobiogeochemical processes of polygenic multipollutants and their secondary pollutants. The results showed that the redox environment and the gradient change in pH were identified as the most critical controlling factors. In oxidative groundwater during the early stage of vertical infiltration, sewage carries a substantial amount of NH4+, which is oxidized to form the secondary pollutant NO3−. As O2 is consumed, the reduction intensifies, and secondary pollutants NO3−, Mn (IV), and Fe(III) minerals are successively reduced. Compared with the natural conditions of rainwater vertical infiltration, the reaction rates and intensities of various reactions significantly increase during sewage vertical infiltration. However, there is a notable difference in the groundwater pH between sewage and rainwater vertical infiltration. In O2 and secondary pollutant NO3− reduction, a large amount of CO2 is rapidly generated. Excessive CO2 dissolves to produce a substantial amount of H+, promoting the acidic dissolution of Mn (II) minerals and generation of Mn2+. Sewage provides a higher carbon load, enhancing Mn (II) acidic dissolution and stimulating the activity of dissimilatory nitrate reduction to ammonium, which exhibits a higher contribution to NO3− reduction. This results in a portion of NO3− converted from NH4+ being reduced back to NH4+ and retained in the groundwater, reducing the denitrification's capacity to remove secondary NO3−. This has important implications for pollution management and groundwater remediation, particularly monitored natural attenuation. [ABSTRACT FROM AUTHOR]

An increase in water temperature is one of the main factors that can potentially modify biogeochemical dynamics in lowland rivers, such as the removal and recycling of nitrogen (N). This effect of climate change on N processing deserves attention, as it may have unexpected impacts on eutrophication in the coastal zones. Intact sediment cores were collected seasonally at the closing section of the Po River, the largest Italian river and one of the main N inputs to the Mediterranean Sea. Benthic oxygen fluxes, denitrification, and dissimilatory nitrate reduction to ammonium (DNRA) rates were measured using laboratory dark incubations. Different temperature treatments were set up for each season based on historical data and future predictions. Higher water temperatures enhanced sediment oxygen demand and the extent of hypoxic conditions in the benthic compartment, favoring anaerobic metabolism. Indeed, warming water temperature stimulated nitrate (NO3−) reduction processes, although NO3− and organic matter availability were found to be the main controlling factors shaping the rates between seasons. Denitrification was the main process responsible for NO3− removal, mainly supported by NO3− diffusion from the water column into the sediments, and much more important than N recycling via DNRA. The predicted increase in the water temperature of the Po River due to climate change may exert an unexpected negative feedback on eutrophication by strongly controlling denitrification and contributing to partial buffering of N export in the lagoons and coastal areas, especially in spring. [ABSTRACT FROM AUTHOR]

Background: The phylum Bacteroidota represents a significant proportion of heterotrophic bacteria found in marine ecosystems. Members of the phylum Bacteroidota are actively involved in the degradation of biopolymers such as polysaccharides and proteins. Bacteroidota genomes exhibit a significant enrichment of various enzymes, including carbohydrate-active enzymes (CAZymes), carboxypeptidases, esterases, isomerases, peptidases, phosphatases, and sulfatases. The genus Marivirga, a member of the family Marivirgaceae within the phylum Bacteroidota, comprises six documented species. During a microbial diversity study, three novel Marivirga strains (BKB1-2 T, ABR2-2, and BDSF4-3 T) were isolated from the West Sea, Republic of Korea. Results: To explore the taxonomic status and genomic characteristics of the novel isolates, we employed a polyphasic taxonomic approach, which included phylogenetic, chemotaxonomic and comprehensive genome analysis. The three isolates were Gram-stain-negative, aerobic, rod-shaped, moderately halophilic, and had a gliding motility. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among the two isolates, BKB1-2 T and BDSF4-3 T, and the six reference strains were 70.5–76.5% for ANI and 18.1–25.7% for dDDH. Interestingly, the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the strains harbor genes for a comprehensive pathway for dissimilatory nitrate reduction to ammonium (DNRA), as well as other nitrogen pathways for the reduction of nitrite, nitric oxide, and nitrous oxide. Additionally, the antiSMASH analysis indicated that the strains contained three to eight biosynthetic gene clusters (BGCs) associated with the synthesis of secondary metabolites. Furthermore, the strains carried a high number of CAZyme ranging from 53 to 152, which was also demonstrated by an in vitro analysis of degradation of the polysaccharide cellulose, chitin, laminarin, starch, and xylan. Additionally, all the strains carried genes for the metabolism of heavy metals, and exhibited tolerance to heavy metals, with minimum inhibitory concentrations (MICs) in millimoles (mM) in ranges of Co2+ (3–6), Cu2+ (0.2–0.4), Ni2+ (3–5), Zn2+ (2–4), Mn2+ (20–50), and Hg2+ (0.3). Conclusions: Based on polyphasic taxonomic approach, the three isolated strains represent two novel species names Marivirga arenosa sp. nov. (BKB1-2 T = KCTC 82989 T = InaCC B1618T), and Marivirga salinae sp. nov. (BDSF4-3 T = KCTC 82973 T = InaCC B1619T). [ABSTRACT FROM AUTHOR]

Dissimilatory nitrate reduction to ammonium (DNRA) is an important nitrate reduction pathway in freshwater sediments. Many studies have focused on the DNRA process in various natural habitats. However, the joint operation of cascade reservoirs will affect the physical and chemical properties of sediments, which may change the DNRA process and bacterial community pattern in the surface sediments of cascade reservoirs. Our study was the first to investigate the spatiotemporal distribution patterns of potential DNRA rate, nrfA gene abundances, and DNRA bacterial community diversity in surface sediments of the Lancang River cascade reservoirs. The results of slurry incubation experiments combined with the 15N isotope tracer experiment ascertained that the potential rates of DNRA were 0.01-0.15 nmol-N cm-3 h-1, and qPCR results indicated that the abundance range of nrfA was 1.08 × 105-2.51 × 106 copies g-1 dry weight. High throughput sequencing of the nrfA gene revealed that the relative abundance of Anaeromyxobacter (4.52% on average), Polyangium (4.09%), Archangium (1.86%), Geobacter (1.34%), and Lacunisphaera (1.32%) were high. Pearson and RDA correlation analysis exhibited that nrfA gene abundance was positively correlated with altitude, pH, OC, and sand concentration. Anaeromyxobacter was positively correlated with reservoir age and DNRA potential rate. The deterministic environmental selection process plays a crucial role in the formation of the DNRA bacterial community. Network analysis displayed that the dominant DNRA genus was the key population of the DNRA microbial community in the sediments of Lancang River cascade reservoirs. This study reveals that the variation of DNRA bacterial activity and community structure is largely driven by the construction of cascade reservoirs, and provides a new idea for further understanding the characteristics of the DNRA community in the cascade reservoir ecosystem. [ABSTRACT FROM AUTHOR]

Deep‐marine brine seeps in the modern ocean are considered analogs for settings that favored the formation of sedimentary‐exhalative zinc and lead deposits in deep time. Microbial activity plays an important role in the accumulation of ore minerals, meaning that the extent of mineralization is at least indirectly dependent on nutrient fluxes. Here, we investigated the biogeochemical nitrogen cycle in shallow (15–50 cm) sediment cores from the Orca Basin brine pool and surrounding sites, as well as from an active brine seep area near Dead Crab Lake in the Gulf of Mexico, with the aim of constraining the effect of brine seepage on this bio‐essential element. We find high porewater ammonium concentrations in the millimolar range, paired with elevated ratios of organic carbon to nitrogen in sediments, which confirm previous hypotheses that the brine recycles ammonium from sedimentary strata back into the water column. Within Orca Basin, we note tentative evidence of microbial ammonium utilization. At the active seep, ammonium is mixed into the overlying water column and likely undergoes oxidation. Isotopic data from sediments and dissolved ammonium, paired with previously published genomic data, suggest the presence of dissimilatory nitrate reduction to ammonium at the brine‐seawater interface. We conclude that brine seeps can stimulate biological nitrogen metabolisms in multiple ways. Our results may help calibrate studies of biogeochemical cycles around brine seeps that are archived in the rock record. Plain Language Summary: Brine seeps in the deep ocean are sites where fluids with exceptionally high salinity, up to 10 times that of seawater, seep up through marine sediments and are dispersed into the water column. Such saline fluids can carry high concentrations of metals such as iron, zinc, lead and copper, and therefore brine seeps have been proposed as mechanisms for the formation of ore deposits in the past. An important aspect in this theory is that high microbial activity of primary and secondary producers near the brine seeps creates locally anoxic conditions under which metals are trapped in sulfide minerals. Such biological activity would require input of nutrients, including nitrogen. To shed more light on the biogeochemical nitrogen cycle in brine seeps, we investigated nitrogen isotopes and abundances in samples from the Gulf of Mexico. Here, ammonium concentrations in the millimolar range have previously been documented. Our results support the idea that nitrogen is leached by the brines from deeper sediments and released into the overlying water column. Furthermore, we find evidence for specific microbial metabolisms that are stimulated by mixing between anoxic brine fluids and oxygenated seawater, which may also have occurred in past ore‐forming environments. Key Points: Brine seeps in the Gulf of Mexico recycle bioavailable nitrogen from sediments back into the water columnNitrogen isotopes suggest that brine seepage stimulates biological activity, including dissimilatory nitrate reduction to ammoniumBiological productivity stimulated by brine seeps may have contributed to the formation of sedimentary ore deposits [ABSTRACT FROM AUTHOR]

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]

Anaerobic ammonium oxidizing (anammox) bacteria are utilized for high efficiency nitrogen removal from nitrogen-laden sidestreams in wastewater treatment plants. The anammox bacteria form a variety of competitive and mutualistic interactions with heterotrophic bacteria that often employ denitrification or dissimilatory nitrate reduction to ammonium (DNRA) for energy generation. These interactions can be heavily influenced by the influent ratio of ammonium to nitrite, NH4+:NO2-, where deviations from the widely acknowledged stoichiometric ratio (1:1.32) have been demonstrated to have deleterious effects on anammox efficiency. Thus, it is important to understand how variable NH4+:NO2- ratios impact the microbial ecology of anammox reactors. We observed the response of the microbial community in a lab scale anammox membrane bioreactor (MBR) to changes in the influent NH4+:NO2- ratio using both 16S rRNA gene and shotgun metagenomic sequencing. Ammonium removal efficiency decreased from 99.77 ± 0.04% when the ratio was 1:1.32 (prior to day 89) to 90.85 ± 0.29% when the ratio was decreased to 1:1.1 (day 89-202) and 90.14 ± 0.09% when the ratio was changed to 1:1.13 (day 169-200). Over this same timespan, the overall nitrogen removal efficiency (NRE) remained relatively unchanged (85.26 ± 0.01% from day 0-89, compared to 85.49 ± 0.01% from day 89-169, and 83.04 ± 0.01% from day 169-200). When the ratio was slightly increased to 1:1.17-1:1.2 (day 202-253), the ammonium removal efficiency increased to 97.28 ± 0.45% and the NRE increased to 88.21 ± 0.01%. Analysis of 16 S rRNA gene sequences demonstrated increased relative abundance of taxa belonging to Bacteroidetes, Chloroflexi, and Ignavibacteriae over the course of the experiment. The relative abundance of Planctomycetes, the phylum to which anammox bacteria belong, decreased from 77.19% at the beginning of the experiment to 12.24% by the end of the experiment. Analysis of metagenome assembled genomes (MAGs) indicated increased abundance of bacteria with nrfAH genes used for DNRA after the introduction of lower influent NH4+:NO2- ratios. The high relative abundance of DNRA bacteria coinciding with sustained bioreactor performance indicates a mutualistic relationship between the anammox and DNRA bacteria. Understanding these interactions could support more robust bioreactor operation at variable nitrogen loading ratios.

The effects of different soil properties on hydrology and nitrogen removal were studied in a simulated bioretention system. Soil capacity of permeability and water retention, changes in the soil environment, leachate concentrations at the surface and bottom layers, quantification of N removal from soil, microorganism and plant by 15N isotope tracer technique, and functional genes abundance at different depths were evaluated. The results showed that shallow root plants, soil compaction, and low organic matter content were not conducive to the infiltration of bioretention systems. In the 72 h experiment, compaction (especially surface compaction) and planting of herbaceous plants (Ophiopogon japonicus) were not beneficial to the removal of TN, TP, and COD. Adding an appropriate amount of organic matter also affects nitrogen and phosphorus removal. In the process of denitrification, the order of the ability to remove nitrogen is soil adsorption > microbial assimilation > plant uptake. The contribution of soil denitrification is affected by soil compaction, compaction location, plant species and organic matter content. The abundance of 16S rRNA, nitrifying, denitrifying and nrfA genes decreased with soil depth. More copies of genes in topsoil were thought to be due to sufficient nutrients, aerobic condition, anaerobic microsites and submerged state. Soil compaction, organic matter content and plant species affected nitrification, denitrification and DNRA gene characteristics. [ABSTRACT FROM AUTHOR]

Estuaries can remove and/or retain land-derived nitrogen (N) and act as filters buffering N loads to the open sea. The N coastal filter can be seasonally variable depending on water temperature and transported loads, two factors acting in synergy and strongly influenced by climate change. The capacity of sediments to mitigate riverine N loads was investigated at four sites in the Vistula River plume area (Gulf of Gdańsk, Southern Baltic Sea). Samplings were carried out in two contrasting seasons: spring and summer, characterized by different water temperatures and nitrate (NO3) levels. Inorganic N fluxes, and rates of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) were measured in intact sediment cores by means of dark incubations and 15N-nitrate concentration-series experiments. Sampling sites were selected along a gradient of depth (5 to 24 m), that was also a gradient of sediment organic matter content. In both seasons, denitrification rates increased along with depth and from spring (6.5 ± 7.0 µmolm-) levels. Inorganic N fluxes, and rates of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) were measured in intact sediment cores by means of dark incubations and 15N-nitrate concentration-series experiments. Sampling sites were selected along a gradient of depth (5 to 24 m), that was also a gradient of sediment organic matter content. In both seasons, denitrification rates increased along with depth and from spring (6.5 ± 7.0 µmolm-2 h-1) to summer (20.4 ± 15.4 µmolm-2 h-1), despite lower NO3 - across all sites and seasons, contributing to over 80% of the total denitrification. Notably, no anammox was detected at the sampling sites. DNRA exhibited low to undetectable rates in spring, especially at the shallowest sites. However, during summer, N recycling via DNRA increased and ranged from 0.7 to 14.9 µmol m3 -. The denitrification efficiency (DE), calculated as the ratio between molecular nitrogen (N2) flux and dissolved inorganic N effluxes from sediments, ranged from 0 to 37% in spring, whereas in summer DE did not exceed 16%. Despite the dominance of denitrification over DNRA, the analyzed sediments acted as weak N buffers under in situ dark conditions. However, concentrationseries experiments suggested high potential denitrification capacity, exceeding 400 µmol m3 - across all sites and seasons, contributing to over 80% of the total denitrification. Notably, no anammox was detected at the sampling sites. DNRA exhibited low to undetectable rates in spring, especially at the shallowest sites. However, during summer, N recycling via DNRA increased and ranged from 0.7 to 14.9 µmol m-2 h-1. The denitrification efficiency (DE), calculated as the ratio between molecular nitrogen (N2) flux and dissolved inorganic N effluxes from sediments, ranged from 0 to 37% in spring, whereas in summer DE did not exceed 16%. Despite the dominance of denitrification over DNRA, the analyzed sediments acted as weak N buffers under in situ dark conditions. However, concentrationseries experiments suggested high potential denitrification capacity, exceeding 400 µmol m-2 h-1, in response to short-term, large riverine inputs of NO³ -. [ABSTRACT FROM AUTHOR]

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

Excess nitrogen in agricultural drainage poses a serious threat to the water quality safety of the Yellow River basin. Utilizing aquatic plants to modify the rhizosphere microbial community structure and facilitate nitrogen transformation is a crucial strategy for mitigating regional water eutrophication. We here compare key processes of nitrogen transformation occurring in the rhizosphere of sediments of a ditch artificially planted with a mix of species (Phragmites australis, Typha orientalis, Nymphaea tetragon) with the rhizosphere of a ditch occupied by naturally occurring aquatic vegetation, dominated either by P. australis or T. orientalis. Our results revealed a species effect, with an increased denitrification rate (DR) and dissimilatory nitrate reduction to ammonium rate (DNRAR) in the cultivated ditch for P. australis, compared to the naturally occurring T. orientalis vegetation. The nitrogen fixation rate (NFR) increased in the artificial setting with T. orientalis in comparison to natural P. australis vegetation. The richness of the bacterial community and the relative abundances of Bacteroidota, Firmicutes, and Geobacter were significantly greater in the rhizosphere of the artificially cultivated ditch due a greater availability in nitrogen and organic carbon. In the artificially cultivated ditch, the dominant functional genes affecting DRNARs in the rhizosphere sediments of P. australis were nrfC and nrfA, whereas DRs were driven mainly by norB and napA, which were influenced by the nitrogen and carbon levels. The dominant functional genes affecting NFRs in the rhizosphere sediments of T. orientalis were nifD, nifK, and nifH. Our results provide a scientific basis for the use of aquatic plants for mitigating excess nitrogen levels in agricultural drainage.

To enhance rice yields, synthetic nitrogen (N) fertilizers are often applied in rice paddy fields. Under waterlogged conditions, denitrification, anaerobic ammonium oxidation (anammox) and dissimilatory nitrate reduction to ammonium (DNRA) are the main N transformation processes. However, the effects of longterm fertilization on the dissimilatory nitrate reduction processes remain largely unclear. Here, we investigated rates of denitrification, anammox and DNRA and the abundance of bacterial and nitrate reduction-related genes (16S rRNA, narG, nirK, nirS, nosZ and hzsB) in rice paddy fields under different fertilization regimes [i.e., non-fertilization (CK), NPK fertilization (NPK) and NPK fertilization plus straw returning (NPKS)]. The rates of denitrification, anammox and DNRA in the CK treatment were 46.18, 0.35 and 1.29 nmoL N g-1 h-1, respectively, which were significantly (p < .05) increased by 7.32%-27.78%, 2.45-4.12 folds and 1.01-13.23 folds by NPK and NPKS treatments. This was largely consistent with the increased bacterial and nitrate reduction-related gene abundances in the NPK and NPKS treatments. In addition, NPKS also significantly increased the relative contribution of DNRA to the total nitrate reduction relative to NPK and CK treatments, indicating that NPKS was more beneficial to N retention in the paddy field. Changes in rates of dissimilatory nitrate reduction processes in response to NPK and NPKS treatments were correlated to variations of soil total N, ammonium contents, pH, soil organic carbon (SOC) contents and nitrate reduction-related genes, among which SOC contents had the highest explanation. Specifically, fulvic-like compounds, alkyl C and methoxyl and nitrogen-alkyl C were the key components determining denitrification, anammox and DNRA rates, respectively. Overall, our study suggests that long-term NPK and NPKS fertilization stimulate rates of dissimilatory nitrate reduction processes mainly by altering soil C components and NPKS is more effective in maintaining soil fertility in the paddy field. [ABSTRACT FROM AUTHOR]

ABSTRACTThe biological route of nitrate reduction has important implications for the bioavailability of nitrogen within ecosystems. Nitrate reduction via nitrite, either to ammonium (ammonification) or to nitrous oxide or dinitrogen (denitrification), determines whether nitrogen is retained within the system or lost as a gas. The acidophilic sulfate-reducing bacterium (aSRB) Acididesulfobacillus acetoxydans can perform dissimilatory nitrate reduction to ammonium (DNRA). While encoding a Nar-type nitrate reductase, A. acetoxydans lacks recognized nitrite reductase genes. In this study, A. acetoxydans was cultivated under conditions conducive to DNRA. During cultivations, we monitored the production of potential nitrogen intermediates (nitrate, nitrite, nitric oxide, hydroxylamine, and ammonium). Resting cell experiments were performed with nitrate, nitrite, and hydroxylamine to confirm their reduction to ammonium, and formed intermediates were tracked. To identify the enzymes involved in DNRA, comparative transcriptomics and proteomics were performed with A. acetoxydans growing under nitrate- and sulfate-reducing conditions. Nitrite is likely reduced to ammonia by the previously undescribed nitrite reductase activity of the NADH-linked sulfite reductase AsrABC, or by a putatively ferredoxin-dependent homolog of the nitrite reductase NirA (DEACI_1836), or both. We identified enzymes and intermediates not previously associated with DNRA and nitrosative stress in aSRB. This increases our knowledge about the metabolism of this type of bacteria and helps the interpretation of (meta)genome data from various ecosystems on their DNRA potential and the nitrogen cycle.IMPORTANCENitrogen is crucial to any ecosystem, and its bioavailability depends on microbial nitrogen-transforming reactions. Over the recent years, various new nitrogen-transforming reactions and pathways have been identified, expanding our view on the nitrogen cycle and metabolic versatility. In this study, we elucidate a novel mechanism employed by Acididesulfobacillus acetoxydans, an acidophilic sulfate-reducing bacterium, to reduce nitrate to ammonium. This finding underscores the diverse physiological nature of dissimilatory reduction to ammonium (DNRA). A. acetoxydans was isolated from acid mine drainage, an extremely acidic environment where nitrogen metabolism is poorly studied. Our findings will contribute to understanding DNRA potential and variations in extremely acidic environments.

Estuaries can remove and/or retain land-derived nitrogen (N) and act as filters buffering N loads to the open sea. The N coastal filter can be seasonally variable depending on water temperature and transported loads, two factors acting in synergy and strongly influenced by climate change. The capacity of sediments to mitigate riverine N loads was investigated at four sites in the Vistula River plume area (Gulf of Gdańsk, Southern Baltic Sea). Samplings were carried out in two contrasting seasons: spring and summer, characterized by different water temperatures and nitrate (NO3-) levels. Inorganic N fluxes, and rates of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) were measured in intact sediment cores by means of dark incubations and 15N-nitrate concentration-series experiments. Sampling sites were selected along a gradient of depth (5 to 24 m), that was also a gradient of sediment organic matter content. In both seasons, denitrification rates increased along with depth and from spring (6.5 ± 7.0 µmol m-2 h-1) to summer (20.4 ± 15.4 µmol m-2 h-1), despite lower NO3- concentrations in summer. In spring, at higher NO3- loading, denitrification was likely limited by low water temperature, and elevated sediment oxygen penetration. Coupled denitrification-nitrification prevailed over denitrification of water column NO3- across all sites and seasons, contributing to over 80% of the total denitrification. Notably, no anammox was detected at the sampling sites. DNRA exhibited low to undetectable rates in spring, especially at the shallowest sites. However, during summer, N recycling via DNRA increased and ranged from 0.7 to 14.9 µmol m-2 h-1. The denitrification efficiency (DE), calculated as the ratio between molecular nitrogen (N2) flux and dissolved inorganic N effluxes from sediments, ranged from 0 to 37% in spring, whereas in summer DE did not exceed 16%. Despite the dominance of denitrification over DNRA, the analyzed sediments acted as weak N buffers under in situ dark conditions. However, concentration-series experiments suggested high potential denitrification capacity, exceeding 400 µmol m-2 h-1, in response to short-term, large riverine inputs of NO3-.

Anaerobic ammonia oxidizing bacteria (Anammox) are implemented in high-efficiency wastewater treatment systems operated in two general configurations; one-stage systems combine aerobic ammonia oxidizing bacteria (AOB) and Anammox within a single aerated reactor, whereas two-stage configurations separate these processes into discrete tanks. Within both configurations heterotrophic populations that perform denitrification or dissimilatory nitrate reduction to ammonia (DNRA) compete for carbon and nitrate or nitrite and can impact reactor performance because DNRA retains nitrogen in the system. Therefore, it is important to understand how selective pressures imposed by one-stage and two-stage reactor configurations impact the microbial community structure and associated nitrogen transforming functions. We performed 16S rRNA gene and metagenomic sequencing on different biomass fractions (granules, flocs, and suspended biomass) sampled from two facilities treating sludge dewatering centrate: a one-stage treatment facility (Chambers Creek, Tacoma, WA) and a two-stage system (Rotterdam, Netherlands). Similar microbial populations were identified across the different samples, but relative abundances differed between reactor configurations and biomass sources. Analysis of metagenome assembled genomes (MAGs) indicated different lifestyles for abundant heterotrophic populations. Acidobacteria, Bacteroidetes, and Chloroflexi MAGs had varying capacity for DNRA and denitrification. Acidobacteria MAGs possessed high numbers of glycosyl hydrolases and glycosyl transferases indicating a role in biomass degradation. Ignavibacteria and Phycosphaerae MAGs contributed to the greater relative abundance of DNRA associated nrf genes in the two-stage granules and contained genomic features suggesting a preference for an anoxic or microoxic niche. In the one-stage granules a MAG assigned to Burkholderiales accounted for much of the abundant denitrification genes and had genomic features, including the potential for autotrophic denitrification using reduced sulfur, that indicate an ability to adapt its physiology to varying redox conditions. Overall, the competition for carbon substrates between denitrifying and DNRA performing heterotrophs may be impacted by configuration specific selective pressures. In one-stage systems oxygen availability in the bulk liquid and the oxygen gradient within granules would provide a greater niche space for heterotrophic populations capable of utilizing both oxygen and nitrate or nitrite as terminal electron acceptors, compared to two-stage systems where a homogeneous anoxic environment would favor heterotrophic populations primarily adapted to anaerobic metabolism.

ABSTRACTNitrogen (N) availability is one of the principal drivers of primary productivity across aquatic ecosystems. However, the microbial communities and emergent metabolisms that govern N cycling in tropical lakes are both distinct from and poorly understood relative to those found in temperate lakes. This latitudinal difference is largely due to the warm (>20°C) temperatures of tropical lake anoxic hypolimnions (deepest portion of a stratified water column), which result in unique anaerobic metabolisms operating without the temperature constraints found in lakes at temperate latitudes. As such, tropical hypolimnions provide a platform for exploring microbial membership and functional diversity. To better understand N metabolism in warm anoxic waters, we combined measurements of geochemistry and water column thermophysical structure with genome-resolved metatranscriptomic analyses of the water column microbiome in Lake Yojoa, Honduras. We sampled above and below the oxycline in June 2021, when the water column was stratified, and again at the same depths and locations in January 2022, when the water column was mixed. We identified 335 different lineages and significantly different microbiome membership between seasons and, when stratified, between depths. Notably, nrfA (indicative of dissimilatory nitrate reduction to ammonium) was upregulated relative to other N metabolism genes in the June hypolimnion. This work highlights the taxonomic and functional diversity of microbial communities in warm and anoxic inland waters, providing insight into the contemporary microbial ecology of tropical ecosystems as well as inland waters at higher latitudes as water columns continue to warm in the face of global change.IMPORTANCEIn aquatic ecosystems where primary productivity is limited by nitrogen (N), whether continuously, seasonally, or in concert with additional nutrient limitations, increased inorganic N availability can reshape ecosystem structure and function, potentially resulting in eutrophication and even harmful algal blooms. Whereas microbial metabolic processes such as mineralization and dissimilatory nitrate reduction to ammonium increase inorganic N availability, denitrification removes bioavailable N from the ecosystem. Therefore, understanding these key microbial mechanisms is critical to the sustainable management and environmental stewardship of inland freshwater resources. This study identifies and characterizes these crucial metabolisms in a warm, seasonally anoxic ecosystem. Results are contextualized by an ecological understanding of the study system derived from a multi-year continuous monitoring effort. This unique data set is the first of its kind in this largely understudied ecosystem (tropical lakes) and also provides insight into microbiome function and associated taxa in warm, anoxic freshwaters.

Groundwater level recovery has a significant effect on the sources and transformation of nitrogen in groundwater, but there are still few studies on the influences of the water table on the sources and transformation of nitrogen in groundwater using field data. In this study, the changes in groundwater level, geochemical composition, and isotopic signatures of NO3- and NH4+ during a period of groundwater level recovery at a pilot site were analyzed in detail. The water table underwent progressive recovery of almost 1.6 m in 16 months. At a depth of 5.5 m below the surface, both low NH4+ and high NO3- appeared in the groundwater, whereas below that depth, both high NH4+ and low NO3- simultaneously appeared in the groundwater. The main sources of NO3- were manure and septic waste, and NH4+ fertilizers. The main sources of NH4+ were mineral fertilizers. The main transformation process were nitrification and denitrification at a depth of 5.5 m below the surface; below that depth, the main transformation processes were denitrification and dissimilatory nitrate reduction to ammonium (DNRA). This study provides a theoretical understanding of the relationship between the changing water table and nitrogen in groundwater level recovery areas. [ABSTRACT FROM AUTHOR]

Recent studies in snowmelt-dominated catchments have documented changes in nitrogen (N) retention over time, such as declines in watershed exports of N, though there is a limited understanding of the controlling processes driving these trends. Working in the mountainous headwater East River Colorado watershed, we explored the effects of riparian hollows as N-cycling hotspots and as important small-scale controls on observed watershed trends. Using a modeling-based approach informed by remote sensing and in situ observations, we simulated the N-retention capacity of riparian hollows with seasonal and yearly hydrobiogeochemical perturbations imposed as drivers. We then implemented a scaling approach to quantify the relative contribution of riparian hollows to the total river corridor N budget. We found that riparian hollows primarily serve as N sinks, with N-transformation rates significantly limited by periods of enhanced groundwater upwelling and promoted at the onset of rainfall events. Given these observed hydrologic controls, we expect that the nitrate ((Formula presented.)) sink capacity of riparian hollows will increase in magnitude with future climatic perturbations, specifically the shift to more frequent rainfall events and fewer snowmelt events, as projected for many mountainous headwater catchments. Our current estimates suggest that while riparian hollows provision ~5–20% of (Formula presented.) to the river network, they functionally act as inhibitors to upland (Formula presented.) reaching the stream. Our work linking transient hydrological conditions to numerical biogeochemical simulations is an important step in assessing N-retaining features relative to the watershed N budget and better understanding the role of small-scale features within watersheds.

In the summer of 2022, the Po River Delta (Northern Italy), a eutrophication hotspot, was severely affected by high temperatures, exceptional lack of rainfall and saline water intrusion. The effect of saline intrusion on benthic nitrogen dynamics, and in particular the N removal capacity, was investigated during extreme drought conditions. Laboratory incubations of intact sediment cores were used to determine denitrification and DNRA rates at three sites along a salinity gradient in the Po di Goro, an arm of the Po River Delta. Denitrification was found to be the main process responsible for nitrate reduction in freshwater and slightly saline sites, whereas DNRA predominated in the most saline site, highlighting a switch in N cycling between removal and recycling. These results provide evidence that salinity is a key factor in regulating benthic N metabolism in transitional environments. In a climate change scenario, salinity intrusion, resulting from long periods of low river discharge, may become an unrecognized driver of coastal eutrophication by promoting the dissimilatory nitrate reduction to ammonium and N recycling of bioactive nitrogen within the ecosystem, rather than its permanent removal by denitrification. [ABSTRACT FROM AUTHOR]

Anaerobic ammonium oxidizing (anammox) bacteria are utilized for high efficiency nitrogen removal from nitrogen-laden sidestreams in wastewater treatment plants. The anammox bacteria form a variety of competitive and mutualistic interactions with heterotrophic bacteria that often employ denitrification or dissimilatory nitrate reduction to ammonium (DNRA) for energy generation. These interactions can be heavily influenced by the influent ratio of ammonium to nitrite, NH4+:NO2−, where deviations from the widely acknowledged stoichiometric ratio (1:1.32) have been demonstrated to have deleterious effects on anammox efficiency. Thus, it is important to understand how variable NH4+:NO2− ratios impact the microbial ecology of anammox reactors. We observed the response of the microbial community in a lab scale anammox membrane bioreactor (MBR) to changes in the influent NH4+:NO2− ratio using both 16S rRNA gene and shotgun metagenomic sequencing. Ammonium removal efficiency decreased from 99.77 ± 0.04% when the ratio was 1:1.32 (prior to day 89) to 90.85 ± 0.29% when the ratio was decreased to 1:1.1 (day 89–202) and 90.14 ± 0.09% when the ratio was changed to 1:1.13 (day 169–200). Over this same timespan, the overall nitrogen removal efficiency (NRE) remained relatively unchanged (85.26 ± 0.01% from day 0–89, compared to 85.49 ± 0.01% from day 89–169, and 83.04 ± 0.01% from day 169–200). When the ratio was slightly increased to 1:1.17–1:1.2 (day 202–253), the ammonium removal efficiency increased to 97.28 ± 0.45% and the NRE increased to 88.21 ± 0.01%. Analysis of 16 S rRNA gene sequences demonstrated increased relative abundance of taxa belonging to Bacteroidetes, Chloroflexi, and Ignavibacteriae over the course of the experiment. The relative abundance of Planctomycetes, the phylum to which anammox bacteria belong, decreased from 77.19% at the beginning of the experiment to 12.24% by the end of the experiment. Analysis of metagenome assembled genomes (MAGs) indicated increased abundance of bacteria with nrfAH genes used for DNRA after the introduction of lower influent NH4+:NO2− ratios. The high relative abundance of DNRA bacteria coinciding with sustained bioreactor performance indicates a mutualistic relationship between the anammox and DNRA bacteria. Understanding these interactions could support more robust bioreactor operation at variable nitrogen loading ratios.

Anaerobic ammonium oxidation (anammox) has shown success in past years for the treatment of municipal and industrial wastewater containing inorganic nutrients (i.e., nitrogen). However, the increase in polycyclic aromatic hydrocarbon (PAH)-contaminated matrices calls for new strategies for efficient and environmentally sustainable remediation. Therefore, the present review examined the literature on the connection between the anammox process and PAHs using VOSviewer to shed light on the mechanisms involved during PAH biodegradation and the key factors affecting anammox bacteria. The scientific literature thoroughly discussed here shows that PAHs can be involved in nitrogen removal by acting as electron donors, and their presence does not adversely affect the anammox bacteria. Anammox activity can be improved by regulating the operating parameters (e.g., organic load, dissolved oxygen, carbon-to-nitrogen ratio) and external supplementation (i.e., calcium nitrate) that promote changes in the microbial community (e.g., Candidatus Jettenia), favoring PAH degradation. The onset of a synergistic dissimilatory nitrate reduction to ammonium and partial denitrification can be beneficial for PAH and nitrogen removal. [ABSTRACT FROM AUTHOR]

A vulnerability assessment of the aquifers in the agricultural area of Zacharo in SW, Peloponnese, Greece, was conducted using the DRASTIC index and the susceptibility index (SI). Sensitivity analysis was conducted and thematic maps for each parameter were generated to analyse the impact of individual parameter on the collective groundwater vulnerability. Results derived from the DRASTIC and SI maps revealed that the extremely highly vulnerable zones are concentrated at three coastal sites in the western part of the study area. Data from these maps also indicate low vulnerability areas throughout the eastern part of the region. The distribution of nitrate concentrations in groundwater is better correlated with the DRASTIC (79.2%) compared to SI (60.2%). Neither method takes into consideration the impact of dilution and nitrate to ammonium reduction, on the nitrate content of groundwater, thus overestimating the vulnerability index. Moreover, the SI method overestimates the impact of olive groves' land use type on the susceptibility index, thus resulting to a lower correlation with the observed nitrate concentrations. [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]

Intensive aquaculture in estuaries and coasts has resulted in several ecological and environmental problems. Among various nitrogen transformation pathway, dissimilatory nitrate (NO3-) reduction is considered to be highly important in regulating reactive nitrogen. However, there are relatively few studies on the processes and contribution of NOx- reduction in sediment during the shrimp pond culture period. Three sediment NO3- reduction processes, denitrification (DNF), anaerobic ammonium oxidation (ANA), and dissimilatory NO3- reduction to ammonium (DNRA), were surveyed in eight shrimp ponds across three subtropical estuaries using 15N isotope tracing experiments. The rates of DNF, ANA and DNRA ranged from 2.87–18.11, 0.10–1.92, and 0.21–1.25 nmol N g -1 h -1, respectively. DNF was responsible for 64.2–91.6% of the total NO3- reduction. Regarding environmental factors, C and N substrates, as well as salinity, significantly affected NO3- reduction. In general, the N losses were approximately 32.43–131.64 g N m-2 yr-1 for DNF and 2.38–15.85 g N m-2 yr-1 for ANA in this study, indicating that coastal reclamation is a nonnegligible way to remove nitrogen. Our results provide a scientific foundation for understanding the mechanism of nitrogen cycling in the artificial aquatic environment of shrimp ponds.

Peatlands are an important source of nitrous oxide (N2O) emissions, which is a potent greenhouse gas and is also involved in the depletion of stratospheric ozone. Due to the large number of N2O production and consumption processes, it is challenging to trace N2O emissions to an individual process. We investigated the effect of different water regimes (dry, intermediate and flooded) on N2O emissions via 15N tracing in a microcosm study with well-decomposed nitrogen-rich alluvial fen peat. The isotopic composition of the peat and emitted N2O gas was analysed in combination with qPCR analysis of abundances and diversity of N-cycle functional genes. Bacterial denitrification was the predominant source of N2O emission, followed by nitrification (ammonia oxidation). This was identified by a close relationship between 15N-N2O and 15N-NO3− under flooded (anoxic) and intermediate (sub-oxic) treatments and concomitant increases in nirK, nirS and nosZ after the flooding. The site preference and δ18O values fell within the previously observed range indicating multiple overlapping processes and bacterial denitrification as the dominant process. Although the combination of isotopic and microbial analyses indicates that bacterial denitrification is the primary process under intermediate and flooded treatments, the high abundance of amoA indicates that nitrification via comammox was present. High archaeal amoA and bacterial amoA gene copy numbers and second highest N2O emissions under the intermediate and flooded peats indicated that ammonia oxidation was, secondary to denitrification, also a source for N2O. The increase in emissions with nrfA gene copies also showed that dissimilatory nitrate reduction to ammonium (DNRA) potentially contributed to N2O emission under flooded treatment. [ABSTRACT FROM AUTHOR]

NrfA is the molecular marker for dissimilatory nitrate reduction to ammonium (DNRA) activity, catalysing cytochrome c nitrite reductase enzyme. However, the limited study has been made so far to understand the structural homology modeling of NrfA protein in DNRA bacteria. Therefore, three model DNRA bacteria (Escherechia coli, Wolinella succinogenes and Shewanella oneidensis) were chosen in this study for in-silico protein modeling of NrfA which roughly consists of similar length of amino acids and molecular weight and they belong to two contrasting taxonomic families (γ-proteobacteria with nrfABCDEFG and ε-proteobacteria with nrfHAIJ operon). Multiple bioinformatic tools were used to examine the primary, secondary, and tertiary structure of NrfA protein using three distinct homology modeling pipelines viz., Phyre2, Swiss model and Modeller. The results indicated that NrfA protein in E. coli, W. succinogenes and S. oneidensis was mostly periplasmic and hydrophilic. Four conserved Cys-X1-X2-Cys-His motifs, one Cys-X1-X2-Cys-Lys haem-binding motif and Ca ligand were also identified in NrfA protein irrespective of three model bacteria. Moreover, 11 identical conserved amino acids sequence was observed for the first time between serine and proline in NrfA protein. Secondary structure of NrfA revealed that α-helices were observed in 77.9%, 73.4%, and 77.4% in E. coli, W. succinogenes and S. oneidensis, respectively. Ramachandran plot showed that number of residue in favored region in E. coli, W. succinogenes and S. oneidensis was 97.03%, 97.01% and 97.25%, respectively. Our findings also revealed that among three pipelines, Modeller was considered the best in-silico tool for prediction of NrfA protein. Overall, significant findings of this study may aid in the identification of future unexplored DNRA bacteria containing cytochrome c nitrite reductase. The NrfA system, which is linked to respiratory nitrite ammonification, provides an analogous target for monitoring less studied N-retention processes, particularly in agricultural ecosystems. Furthermore, one of the challenging research tasks for the future is to determine how the NrfA protein responds to redox status in the microbial cells. [ABSTRACT FROM AUTHOR]

To elucidate the effect of macroalgae blooms on dissimilatory nitrate reduction pathways (denitrification, anammox, and DNRA) in sediments of the hypereutrophic Yatsu tidal flat, eastern Japan, sediment denitrification, anammox, and DNRA rates were measured using a 15N tracer technique at two sites affected and unaffected by macroalgae (Ulva) blooms and in incubation experiments with and without Ulva. Anammox was insignificant at both sites and in both experiments. The denitrification rate was consistently higher than the DNRA rate, and its contributions to the total dissimilatory nitrate reduction were 82% and 85% at sites affected and unaffected by Ulva, respectively. In a sediment incubation experiment with Ulva, the contribution of DNRA had increased to approximately 30% on day 7, which is when the sulfide concentration was the highest. Sulfide produced by sulfate reduction during macroalgae blooms inhibited denitrification and did not change the DNRA, and consequently increased the DNRA contribution. On day 21, after reaching the peak sulfide concentration during the late macroalgae collapse, the DNRA contribution decreased to 15%. These results indicated that the DNRA contribution was greater during the macroalgae blooms than at the collapse, although denitrification dominated DNRA regardless of the macroalgal status. Therefore, vigorous macroalgae cover and sulfide production under the macroalgae cover had an important impact on the nitrogen dynamics. [ABSTRACT FROM AUTHOR]

Nitrate (NO 3 - -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) 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., 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.)

Dissimilatory nitrate reduction to ammonium (DNRA), driven by nitrate-ammonifying bacteria, is an increasingly appreciated nitrogen-cycling pathway in terrestrial ecosystems. This process reportedly generates nitrous oxide (N 2 O), a strong greenhouse gas with ozone-depleting effects. However, it remains poorly understood how N 2 O is produced by environmental nitrate-ammonifiers and how to identify DNRA-derived N 2 O. In this study, we characterize two novel enzymatic pathways responsible for N 2 O production in Geobacteraceae strains, which are predominant nitrate-ammonifying bacteria in paddy soils. The first pathway involves a membrane-bound nitrate reductase (Nar) and a hybrid cluster protein complex (Hcp-Hcr) that catalyzes the conversion of NO 2 - to NO and subsequently to N 2 O by Hcp-Hcr. These enzyme combinations are prevalent across the domain Bacteria. Moreover, we observe distinctive isotopocule signatures of DNRA-derived N 2 O by Hcp-Hcr. These enzyme combinations are prevalent across the domain Bacteria. Moreover, we observe distinctive isotopocule signatures of DNRA-derived N 2 O from other established N 2 O production pathways, especially through the highest 15 N-site preference (SP) values (43.0‰-49.9‰) reported so far, indicating a robust means for N 2 O production pathways in DNRA that can be isotopically distinguished from other pathways.IMPORTANCEStimulation of DNRA is a promising strategy to improve fertilizer efficiency and reduce N 2 O production pathways in DNRA that can be isotopically distinguished from other pathways.IMPORTANCEStimulation of DNRA is a promising strategy to improve fertilizer efficiency and reduce N 2 O emission in agriculture soils. This process converts water-leachable NO 3 - and NO 2 O emission resulting from denitrification. However, several studies have noted that DNRA can also be a source of N - into soil-adsorbable NH 4 O generation processes, leading to a limited understanding of DNRA as an N + , thereby alleviating nitrogen loss and N 2 O emission resulting from denitrification. However, several studies have noted that DNRA can also be a source of N 2 , the predominant DNRA bacteria in paddy soils, along with their distinctive isotopocule signatures. These findings offer novel insights into the role of the DNRA bacteria in N 2 O generation processes, leading to a limited understanding of DNRA as an N 2 O source. Our study reveals two widespread yet overlooked N 2 O production pathways in Geobacteraceae , the predominant DNRA bacteria in paddy soils, along with their distinctive isotopocule signatures. These findings offer novel insights into the role of the DNRA bacteria in N 2 O production and underscore the significance of N 2 O isotopocule signatures in microbial N 2 O source tracking.

The global nitrogen (N) cycle has been strongly altered by anthropogenic activities, including increased input of bioavailable N into aquatic ecosystems. Freshwater sediments are hotspots with regards to the turnover and elimination of fixed N, yet the environmental controls on the microbial pathways involved in benthic N removal are not fully understood. Here, we analyze the abundance and expression of microbial genes involved in N transformations using metagenomics and -transcriptomics across sediments of 12 Swiss lakes that differ in sedimentation rates and trophic regimes. Our results indicate that microbial N loss in these sediments is primarily driven by nitrification coupled to denitrification. N-transformation gene compositions indicated three groups of lakes: agriculture-influenced lakes characterized by rapid depletion of oxidants in the sediment porewater, pristine-alpine lakes with relatively deep sedimentary penetration of oxygen and nitrate, and large, deep lakes with intermediate porewater hydrochemical properties. Sedimentary organic matter (OM) characteristics showed the strongest correlations with the community structure of microbial N-cycling communities. Most transformation pathways were expressed, but expression deviated from gene abundance and did not correlate with benthic geochemistry. Cryptic N-cycling may maintain transcriptional activity even when substrate levels are below detection. Sediments of large, deep lakes generally showed lower in-situ N gene expression than agriculture-influenced lakes, and half of the pristine-alpine lakes. This implies that prolonged OM mineralization in the water column can lead to the suppression of benthic N gene expression., Competing Interests: The authors declare no competing interests., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

Surface sediments of the coastal mud belt in the Benguela Upwelling System (BUS) off Namibia host extensive communities of chemotrophic large sulfur bacteria (LSB) of the family Beggiatoaceae such as Thiomargarita spp. and Candidatus Maribeggiatoa spp. In order to understand the role of these bacteria in N and P cycling, biogeochemical data from three sites in the mud belt were simulated with a biogeochemical model including LSB catabolic pathways. Organic carbon remineralization was dominated by the reduction of sulfate to hydrogen sulfide (5.0–7.7 mmol C m−2 d−1). At the two stations where LSB were observed, produced hydrogen sulfide was almost completely oxidized by LSB using nitrate as the electron acceptor. Modeled rates of nitrate reduction to N2 by LSB were over two times higher than nitrate reduction to ammonium. This points toward a potential negative feedback by LSB on primary production. Furthermore, loss of fixed N strongly enriched the benthic fluxes in P relative to N. Although the model included intracellular polyphosphate accumulation by LSB and subsequent breakdown to phosphate, a clear link between polyphosphate dynamics and hydroxyapatite precipitation and burial could not be clearly substantiated. This is partly due to simplifying assumptions in the model and analytical uncertainties in distinguishing between authigenic hydroxyapatite and allochthonous hydroxyapatite (e.g., fish bones), both of which are major components of particulate P in the BUS. Our modeling suggests a significant control of LSB on benthic N and P fluxes to the water column. Given the extensive coverage of LSB on the shelf (>30,000 km2), more accurate forecasts of nutrient cycling and primary production in the BUS necessitate a closer inspection of benthic P sources and sinks in the mud belt and a clearer understanding of the controls on the end product of nitrate reduction by LSB.

Coastal salt marshes provide valuable ecosystem services but are subjected to multiple concomitant stressors that may impact their ability to provide those services. Global climate change has led to the poleward expansion of mangroves into salt marshes on each continent where mangroves and marshes co-occur. In the northern Gulf of Mexico, warming winter temperatures have resulted in the expansion of Avicennia germinans (black mangrove) into forb-dominated salt marshes, resulting in a shift in ecosystem structure that can impact the ecosystem services marshes provide, including biogeochemical processes such as nitrogen removal. There have been limited studies addressing how mangrove expansion impacts nitrogen removal rates in salt marshes, but it is possible that mangroves enhance microbial nitrogen removal capacity through more efficient oxygen translocation to sediments. However, mangroves are more sensitive to oiling (such as occurred during the 2010 Deepwater Horizon spill) than marsh plants, such as Spartina alterniflora, which have a higher turnover. Thus, even if they enhance nitrogen removal, if they cannot withstand disturbances such as oiling, there still may be a loss of function associated with woody encroachment. We conducted a field study to assess the impact of woody encroachment in mediating biogeochemical recovery 7 to 8 years after the Deepwater Horizon oil spill. We collected sediments from S. alterniflora- and A. germinans-dominated plots in the Chandeleur Islands (LA, United States), a chain of barrier islands in the northern Gulf of Mexico subjected to a range of oiling following the spill. We compared nitrate reduction rates (denitrification and dissimilatory nitrate reduction to ammonium), microbial community composition, and denitrifier marker gene abundance at sites subjected to light and moderate oiling using a combination of isotope pairing on sediment slurries, 16S sequencing, and qPCR. We predicted that overall, denitrification rates and microbial functional capacity would be enhanced in mangrove-dominated sediments. We also predicted that these enhancements would be diminished at the more intensely oiled site due to the higher susceptibility of A. germinans to oiling. Denitrification potential rates were higher in mangrove sediments at the lightly oiled site, whereas dissimilatory nitrate reduction to ammonium potential rates were higher in marsh sediments. Indicator analysis of 16S rRNA data selected putative sulfur cycling taxa as indicators of marsh sediments, suggesting that changes in oxygen availability associated with encroachment may be driving the differences in process rates. There was no difference in process rates between plant types at the moderately oiled site, where heavily weathered oil residue was still present. Sediment nutrient stocks were lower in moderately oiled mangrove plots than in lightly oiled mangrove plots, suggesting that sediment fertility recovery following the spill may have been slower in the mangroves, contributing to a change in ecosystem function. This study shows that woody encroachment has the potential to impact both the biogeochemical services that marshes provide and their response to and recovery from disturbances.

Coastal marshes provide valuable ecosystem services including the removal of excess nitrogen (N) prior to reaching coastal waters. Crude oil contamination can disrupt N cycling processes, and while the impacts of crude oil on marsh structure and function are well studied, less is known about the effects of different oil components. The objective of this study was to determine how water accommodated fraction (WAF) of oil impacts marsh sediment N cycling capacity from three marshes with differing characteristics. One site was previously oiled following the Deepwater Horizon (DWH) oil spill while the other two sites had no known history of oil spills. We measured 16S rRNA gene composition from sediments collected from each marsh then conducted a laboratory incubation experiment on sediments treated with different concentrations (0%, 25%, 100%) of WAF. The DWH impacted site had a lower number of observed microbial taxa and lower Chao1 diversity, but a higher relative abundance of putative hydrocarbon degraders compared to the other sites. While there was no treatment effect of WAF on sediment denitrification, denitrification potential rates were 2.4 × higher in the DWH impacted sediment compared to the other sites. There were no differences in dissimilatory nitrate reduction to ammonium (DNRA) potential rates across sites, but 100% WAF treatments increased rates nearly twofold at one of the unoiled sites. These results suggest oil contamination alters the microbial community structure and impacts N cycling processes in salt marsh sediments. [ABSTRACT FROM AUTHOR]

Past research has demonstrated the effectiveness of teacher‐implemented, function‐based treatments for problem behavior, but no studies have evaluated the impact of distractions on teachers' procedural integrity. In this proof‐of‐concept study, the experimenters employed a laboratory analog to examine the impact of distractions on levels of integrity when 5 teachers implemented 3 different treatments. Although integrity was similar across treatments when the setting was free of distractions, integrity declined for all teachers in the presence of student‐driven distractions. In general, distractions had a greater impact on the integrity of differential negative reinforcement of alternative behavior (DNRA) compared to differential negative reinforcement of other behavior (DNRO) and noncontingent escape (NCE), particularly for the delivery of reinforcement. However, teachers tended to have lower levels of integrity when responding to problem behavior during DNRO. These findings support the potential viability of this approach for studying factors that impede procedural integrity in the classroom. [ABSTRACT FROM AUTHOR]

Nitrate (NO3−) dissimilatory reduction processes (denitrification, anammox and dissimilatory NO3− reduction to ammonium (DNRA)) in estuarine and coastal ecosystems play a crucial role in regulating reactive nitrogen loadings. However, nitrate reduction process rates and relative proportions along the estuarine salinity gradient remain poorly understood. Here, denitrification, anammox and DNRA were explored simultaneously along a salinity gradient in Yangtze Estuary based on nitrogen isotope-tracing experiments. Measured denitrification, anammox and DNRA process rates were in the range of 2.33–28.21 nmol g−1 h−1, 0.43–1.87 nmol g−1 h−1 and 0.28–0.74 nmol g−1 h−1, respectively, with a large spatio-temporal variation. The changes in these nitrate reduction process rates were mainly affected by the TOC, TN, NH4+ and NOx− concentrations, rather than salinity and related functional gene abundance. Denitrification dominated the total NO3− reduction process (67.52 to 93.85%), while anammox (3.67 to 25.01%) and DNRA (2.48 to 11.21%) also played a substantially important role in nitrate reduction. The proportions of denitrification to gross nitrate reduction in high-salinity areas were generally lower than those in freshwater, but the opposite was true for DNRA. Overall, our study reported the simultaneous observation of nitrate dissimilatory reduction processes along the salinity gradient of the estuary and highlighted that changes in sediment environmental variables affected by human activities can alter the distribution patterns of NO3− reduction processes. [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]