DNRA and Denitrification Coexist over a Broad Range of Acetate/N-NO3- Ratios, in a Chemostat Enrichment Culture

Relating the carbon sources to denitrifying community in full-scale wastewater treatment plants

Carbon source is a key factor determining the denitrifying effectiveness and efficiency in wastewater treatment plants (WWTPs). Whereas, the relationships between diverse and distinct denitrifying communities and their favorable carbon sources in full-scale WWTPs were not well-understood. This study performed a systematic analysis of the relationships between the denitrifying community and carbon sources by using 15 organic compounds from four categories and activated sludge from 8 full-scale WWTPs. Results showed that, diverse denitrifying bacteria were detected with distinct relative abundances in 8 WWTPs, such as Haliangium (1.98-4.08%), Dechloromonas (2.00-3.01%), Thauera (0.16-1.06%), Zoogloea (0.09-0.43%), and Rhodoferax (0.002-0.104%). Overall, acetate resulted in the highest denitrifying activities (1.21-4.62 mg/L/h/gMLSS), followed by other organic acids (propionate, butyrate and lactate, etc.). Detectable dissimilatory nitrate reduction to ammonium (DNRA) was observed for all 15 carbon sources. Methanol and glycerol resulted in the highest DRNA. Acetate, butyrate, and lactate resulted in the lowest DNRA. Redundancy analysis and 16S cDNA amplicon sequencing suggested that carbon sources within the same category tended to correlate to similar denitrifiers. Methanol and ethanol were primarily correlated to Haliangium. Glycerol and amino acids (glutamate and aspartate) were correlated to Inhella and Sphaerotilus. Acetate, propionate, and butyrate were positively correlated to a wide range of denitrifiers, explaining the high efficiency of these carbon sources. Additionally, even within the same genus, different amplicon sequence variants (ASVs) performed distinctly in terms of carbon source preference and denitrifying capabilities. These findings are expected to benefit carbon source formulation and selection in WWTPs.

The vertical partitioning between denitrification and dissimilatory nitrate reduction to ammonium of coastal mangrove sediment microbiomes

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 NH4+. Together, our results uncover the depth-related variations in the microbially-mediated competition between denitrification and DNRA, regulating N dynamics in mangrove ecosystems.

Simultaneous suppression of As mobilization and N2O emission from NH4+/As-rich paddy soils by combined nitrate and birnessite amendment

The environmental impacts of As mobilization and nitrous oxide (N2O) emission in flooded paddy soils are serious issues for food safety and agricultural greenhouse gas emissions. Several As immobilization strategies utilizing microbially-mediated nitrate reducing-As(III) oxidation (NRAO) and birnessite (δ-MnO2)-induced oxidation/adsorption have proven effective for mitigating As bioavailability in flooded paddy soils. However, several inefficiency and unsustainability issues still exist in these remediation approaches. In this study, the effects of a combined treatment of nitrate and birnessite were assessed for the simultaneous suppression of As(III) mobilization and N2O emission from flooded paddy soils. Microcosm incubations confirmed that the combined treatment achieved an effective suppression of As(III) mobilization and N2O emission, with virtually no As(T) released and at least a 87% decrease in N2O emission compared to nitrate treatment alone after incubating for 8 days. When nitrate and birnessite are co-amended to flooded paddy soils, the activities of denitrifying enzymes within the denitrification electron transport pathway were suppressed by MnO2. As a result, the majority of applied nitrate participated in nitrate-dependent microbial Mn(II) oxidation. The regenerated biogenetic MnO2 was available to facilitate subsequent cycles of As(III) immobilization and concomitant N2O emission suppression, sustainable remediation strategy. Moreover, the combined nitrate-birnessite amendment promoted the enrichment of Pseudomonas, Achromobacter and Cupriavidu, which are known to participate in the oxidation of As(III)/Mn(II). Our findings document strong efficacy for the combined nitrate/birnessite treatment as a remediation strategy to simultaneously mitigate As-pollution and N2O emission, thereby improving food safety and reducing greenhouse gas emissions from flooded paddy soils enriched with NH4+ and As.

Bioelectro-barriers prevent nitrate leaching into groundwater via nitrogen retention

Groundwater, the main freshwater resource for humans, has been widely contaminated with nitrate from fertilizers. Here, we report a new and chemical-free strategy to prevent nitrate leaching from soil based on the enrichment of electroactive bacteria, mainly of the genus Geobacter, with bioelectro-barriers, which leads to a nearly 100 % interception of nitrate and partly conserves reactive nitrogen in the form of weakly mobile ammonium by dissimilatory nitrate reduction to ammonium (DNRA). G. sulfurreducens was recognized to efficiently secrete nitrite reductase (NrfA) for rapid DNRA because it lacks nitrate reductase, which inhibits DNRA by competing with nitrite and producing toxic intracellular nitric oxide. With an increase in G. sulfurreducens abundance, near-zero nitrate leaching and 3-fold greater N retention was achieved. Periodic application of weak electricity to the bioelectro-barrier ensured the dominance of G. sulfurreducens in the microbial community and therefore its ability to consistently prevent nitrate leaching. The ability of G. sulfurreducens to intercept nitrate was further demonstrated in more diverse agricultural soils, providing a novel way to prevent nitrate leaching and conserve bioavailable nitrogen in the soil, which has broader implications for both sustainable agriculture and groundwater protection.

Field evaluation of carbon injection method for in-situ biological denitrification in groundwater using geochemical and metataxonomic analyses

This study focuses on the bioremediation of nitrate-contaminated groundwater, which has become a significant environmental problem due to the increasing usage of fertilizers and sewage disposal. The nitrate reduction efficiencies of biological denitrification by injection of carbon source in a pilot-scale treatment system setup were investigated at a groundwater contamination site. The field test was conducted using acetate as a carbon source for 22 days to assess the nitrate reduction efficiencies of in-situ treatment. Geochemical parameters and microbial community analysis using next-generation sequencing were performed before and after carbon source injection. After 12 h of reaction time, nitrate concentration decreased from 31.6 to 4.2 mg-N/L at PC-2, and then remained stable at 3.9 mg-N/L. The nitrate reduction rate when acetate was injected was 29.0 mg-N/L/day. Aquabacterium commune, pseudomonas brassicacearum, dechloromonas denitrificans, and Massilia FAOS were dominant species after acetate injection. Predictive metabolic pathway analysis indicated that nitrate reduction metabolisms during injection of acetate were denitrification and assimilatory nitrate reduction to ammonium. The evaluated hazard quotient of nitrate-contaminated groundwater significantly decreased after acetate injection (non-carcinogenic risk decreased from 1.176 to 0.134 for children). This research could provide fundamental information for decision-makers in nitrate-contaminated groundwater quality protection and management.

Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes

Nitrate ammonification is important for soil nitrogen retention. However, the ecology of ammonifiers and their prevalence compared with denitrifiers, being competitors for nitrate, are overlooked. Here, we screen 1 million genomes for nrfA and onr, encoding ammonifier nitrite reductases. About 40% of ammonifier assemblies carry at least one denitrification gene and show higher potential for nitrous oxide production than consumption. We then use a phylogeny-based approach to recruit gene fragments of nrfA, onr and denitrification nitrite reductase genes (nirK, nirS) in 1861 global terrestrial metagenomes. nrfA outnumbers the nearly negligible onr counts in all biomes, but denitrification genes dominate, except in tundra. Random forest modelling teases apart the influence of the soil C/N on nrfA-ammonifier vs denitrifier abundance, showing an effect of nitrate rather than carbon content. This study demonstrates the multiple roles nitrate ammonifiers play in nitrogen cycling and identifies factors ultimately controlling the fate of soil nitrate.

Integrative knowledge-based nitrogen management practices can provide positive effects on ecosystem nitrogen retention

Knowledge-based nitrogen (N) management provides better synchronization of crop N demand with N supply to enhance crop production while reducing N losses. Yet, how these N management practices contribute to reducing N losses globally is unclear. Here we compiled 5,448 paired observations from 336 publications representing 286 sites to assess the impacts of four common knowledge-based N management practices, including balanced fertilization, organic fertilization, co-application of synthetic and organic fertilizers, and nitrification inhibitors, on global ecosystem N cycling. We found that organic and balanced fertilization rather than N-only fertilization stimulated soil nitrate retention by enhancing microbial biomass, but also stimulated soil N leaching and emissions relative to no fertilizer addition. Nitrification inhibitors, however, stimulated soil ammonium retention and plant N uptake while reducing N leaching and emissions. Therefore, integrative application of knowledge-based N management practices is imperative to stimulate ecosystem N retention and minimize the risk of N loss globally.

Life Detection and Microbial Biomarker Profiling with Signs of Life Detector-Life Detector Chip During a Mars Drilling Simulation Campaign in the Hyperarid Core of the Atacama Desert

The low organic matter content in the hyperarid core of the Atacama Desert, together with abrupt temperature shifts and high ultraviolet radiation at its surface, makes this region one of the best terrestrial analogs of Mars and one of the best scenarios for testing instrumentation devoted to in situ planetary exploration. We have operated remotely and autonomously the SOLID-LDChip (Signs of Life Detector-Life Detector Chip), an antibody microarray-based sensor instrument, as part of a rover payload during the 2019 NASA Atacama Rover Astrobiology Drilling Studies (ARADS) Mars drilling simulation campaign. A robotic arm collected drilled cuttings down to 80 cm depth and loaded SOLID to process and assay them with LDChip for searching for molecular biomarkers. A remote science team received and analyzed telemetry data and LDChip results. The data revealed the presence of microbial markers from Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Firmicutes, and Cyanobacteria to be relatively more abundant in the middle layer (40-50 cm). In addition, the detection of several proteins from nitrogen metabolism indicates a pivotal role in the system. These findings were corroborated and complemented on "returned samples" to the lab by a comprehensive analysis that included DNA sequencing, metaproteomics, and a metabolic reconstruction of the sampled area. Altogether, the results describe a relatively complex microbial community with members capable of nitrogen fixation and denitrification, sulfur oxidation and reduction, or triggering oxidative stress responses, among other traits. This remote operation demonstrated the high maturity of SOLID-LDChip as a powerful tool for remote in situ life detection for future missions in the Solar System.

Suggested role of NosZ in preventing N2O inhibition of dissimilatory nitrite reduction to ammonium

IMPORTANCE

Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) is a microbial energy-conserving process that reduces NO3 - and/or NO2 - to NH4 +. Interestingly, DNRA-catalyzing microorganisms possessing nrfA genes are occasionally found harboring nosZ genes encoding nitrous oxide reductases, i.e., the only group of enzymes capable of removing the potent greenhouse gas N2O. Here, through a series of physiological experiments examining DNRA metabolism in one of such microorganisms, Bacillus sp. DNRA2, we have discovered that N2O may delay the transition to DNRA upon an oxic-to-anoxic transition, unless timely removed by the nitrous oxide reductases. These observations suggest a novel explanation as to why some nrfA-possessing microorganisms have retained nosZ genes: to remove N2O that may otherwise interfere with the transition from O2 respiration to DNRA.

The Inhibiting Effects of High-Dose Biochar Application on Soil Microbial Metagenomics and Rice (Oryza sativa L.) Production

Biochar is usually considered as an organic improver which can improve soil and increase crop yields. However, the unrestricted application of biochar to normal-fertility farmland will cause chemical stress on crops and affect agricultural production. At present, the effects and mechanisms of high-dose applications of biochar on rice (Oryza sativa L.) production and soil biological characteristics have not been fully studied. In this greenhouse pot experiment, combined with soil microbial metagenomics, three treatments in triplicates were conducted to explore the responses of rice production, soil chemical properties, and soil biological properties to high-dose applications of biochar (5%, w/w) prepared using peanut waste (peanut hulls and straw). The results show that peanut hulls, with a loose texture and pore structure, are a raw material with stronger effects for preparing biochar than peanut straw in terms of its physical structure. In a rice monoculture system, high-dose applications of biochar (5%, w/w) can slightly increase the grains per spike, while significantly inhibiting the spike number per pot and the percentage of setting. High-dose applications of biochar also have significant negative effects on the diversity and stability of soil bacterial and archaeal communities. Moreover, the microbial metabolism and nutrient cycling processes are also significantly affected by changing the soil carbon/nitrogen ratio. This study discusses the response mechanisms of rice production and soil biology to high-dose biochar applications, and complements the understanding of irrational biochar application on agricultural production and land sustainability.

Trichlorobacter ammonificans, a dedicated acetate-dependent ammonifier with a novel module for dissimilatory nitrate reduction to ammonia

Dissimilatory nitrate reduction to ammonia (DNRA) is a common biochemical process in the nitrogen cycle in natural and man-made habitats, but its significance in wastewater treatment plants is not well understood. Several ammonifying Trichlorobacter strains (former Geobacter) were previously enriched from activated sludge in nitrate-limited chemostats with acetate as electron (e) donor, demonstrating their presence in these systems. Here, we isolated and characterized the new species Trichlorobacter ammonificans strain G1 using a combination of low redox potential and copper-depleted conditions. This allowed purification of this DNRA organism from competing denitrifiers. T. ammonificans is an extremely specialized ammonifier, actively growing only with acetate as e-donor and carbon source and nitrate as e-acceptor, but H2 can be used as an additional e-donor. The genome of G1 does not encode the classical ammonifying modules NrfAH/NrfABCD. Instead, we identified a locus encoding a periplasmic nitrate reductase immediately followed by an octaheme cytochrome c that is conserved in many Geobacteraceae species. We purified this octaheme cytochrome c protein (TaNiR), which is a highly active dissimilatory ammonifying nitrite reductase loosely associated with the cytoplasmic membrane. It presumably interacts with two ferredoxin subunits (NapGH) that donate electrons from the menaquinol pool to the periplasmic nitrate reductase (NapAB) and TaNiR. Thus, the Nap-TaNiR complex represents a novel type of highly functional DNRA module. Our results indicate that DNRA catalyzed by octaheme nitrite reductases is a metabolic feature of many Geobacteraceae, representing important community members in various anaerobic systems, such as rice paddy soil and wastewater treatment facilities.

Anthropogenic activities mediate stratification and stability of microbial communities in freshwater sediments

BACKGROUND

Freshwater sediment microbes are crucial decomposers that play a key role in regulating biogeochemical cycles and greenhouse gas emissions. They often exhibit a highly ordered structure along depth profiles. This stratification not only reflects redox effects but also provides valuable insights into historical transitions, as sediments serve as important archives for tracing environmental history. The Anthropocene, a candidate geological epoch, has recently garnered significant attention. However, the human impact on sediment zonation under the cover of natural redox niches remains poorly understood. Dam construction stands as one of the most far-reaching anthropogenic modifications of aquatic ecosystems. Here we attempted to identify the ecological imprint of damming on freshwater sediment microbiome.

RESULTS

We conducted a year-round survey on the sediment profiles of Lake Chaohu, a large shallow lake in China. Through depth-discrete shotgun metagenomics, metataxonomics, and geophysiochemical analyses, we unveiled a unique prokaryotic hierarchy shaped by the interplay of redox regime and historical damming (labeled by the 137Cs peak in AD 1963). Dam-induced initial differentiation was further amplified by nitrogen and methane metabolism, forming an abrupt transition governing nitrate-methane metabolic interaction and gaseous methane sequestration depth. Using a random forest algorithm, we identified damming-sensitive taxa that possess distinctive metabolic strategies, including energy-saving mechanisms, unique motility behavior, and deep-environment preferences. Moreover, null model analysis showed that damming altered microbial community assembly, from a selection-oriented deterministic process above to a more stochastic, dispersal-limited one below. Temporal investigation unveiled the rapid transition zone as an ecotone, characterized by high species richness, low community stability, and emergent stochasticity. Path analysis revealed the observed emergent stochasticity primarily came from the high metabolic flexibility, which potentially contributed to both ecological and statistical neutralities.

CONCLUSIONS

We delineate a picture in which dam-induced modifications in nutrient availability and sedimentation rates impact microbial metabolic activities and generate great changes in the community structure, assembly, and stability of the freshwater sediment microbiome. These findings reflect profound ecological and biogeochemical ramifications of human-Earth system interactions and help re-examine the mainstream views on the formation of sediment microbial stratification. Video Abstract.

Synergistic interactions between anammox and dissimilatory nitrate reducing bacteria sustains reactor performance across variable nitrogen loading ratios

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.

Effects of straw and plastic film mulching on microbial functional genes involved in soil nitrogen cycling

Introduction

Microorganisms regulate soil nitrogen (N) cycling in cropping systems. However, how soil microbial functional genes involved in soil N cycling respond to mulching practices is not well known.

Methods

We collected soil samples from a spring maize field mulched with crop straw (SM) and plastic film (FM) for 10-year and with no mulching (CK) in the Loess Plateau. Microbial functional genes involved in soil N cycling were quantified using metagenomic sequencing. We collected soil samples from a spring maize field mulched with crop straw (SM) and plastic film (FM) for 10-year and with no mulching (CK) in the Loess Plateau. Microbial functional genes involved in soil N cycling were quantified using metagenomic sequencing.

Results

Compared to that in CK, the total abundance of genes involved in soil N cycling increased in SM but had no significant changes in FM. Specifically, SM increased the abundances of functional genes that involved in dissimilatory nitrate reduction to ammonium (nirB, napA, and nrfA), while FM decreased the abundances of functional genes that involved in ammonification (ureC and ureA) in comparison with CK. Other genes involved in assimilatory nitrate reduction, denitrification, and ammonia assimilation, however, were not significantly changed with mulching practices. The nirB and napA were derived from Proteobacteria (mainly Sorangium), and the ureC was derived from Actinobacteria (mainly Streptomyces). Mental test showed that the abundance of functional genes that involved in dissimilatory nitrate reduction was positively correlated with the contents of soil microbial biomass N, potential N mineralization, particulate organic N, and C fractions, while ammonification related gene abundance was positively correlated with soil pH, microbial biomass C and N, and mineral N contents.

Discussion

Overall, this study showed that SM could improve soil N availability and promote the soil N cycling by increasing the abundance of functional genes that involved in DNRA, while FM reduced the abundance of functional genes that involved in ammonification and inhibited soil N cycling.

NosZ-II-type N2O-reducing bacteria play dominant roles in determining the release potential of N2O from sediments in the Pearl River Estuary, China

The microbial reduction of N₂O serves as a "gatekeeper" for N₂O emissions, determining the flux of N₂O release into the atmosphere. Estuaries are active regions for N₂O emissions, but the microbial functions of N₂O-reducing bacteria in estuarine ecosystems are not well understood. In this study, the ¹⁵N isotope tracer method, qPCR, and high-throughput sequencing were used to analyze N₂O production, reduction, and emission processes in surface sediments of the Pearl River Estuary. The ¹⁵N isotope tracer experiment showed that the N₂O production rates declined and the N₂O reduction potential (R_r, the ratio of N₂O reduction rates to N₂O production rates) increased from upstream to downstream of the Pearl River Estuary, leading to a corresponding decrease of the N₂O emission rates from upstream to downstream. The gene abundance ratio of nosZ/nir gradually increased from upstream to downstream and was negatively correlated with the water N₂O saturation. The gene abundance of nosZ II was significantly higher than that of nosZ I in the estuary, and the nosZ II/nosZ I abundance ratio was positively correlated with N₂O reduction potential. Furthermore, the community composition of NosZ-I- and NosZ-II-type N₂O-reducing bacteria shifted from upstream to downstream. NosZ-II-type N₂O-reducing bacteria, especially Myxococcales, Thiotrichales, and Gemmatimonadetes species, contributed to the high N₂O reduction potential in the downstream. Our results suggest that NosZ-II-type N₂O-reducing bacteria play a dominant role in determining the release potential of N₂O from sediments in the Pearl River Estuary. This study provides a new insight into the function of microbial N₂O reduction in estuarine ecosystems.

Global soil nitrogen cycle pattern and nitrogen enrichment effects: Tropical versus subtropical forests

Tropical and subtropical forest biomes are a main hotspot for the global nitrogen (N) cycle. Yet, our understanding of global soil N cycle patterns and drivers and their response to N deposition in these biomes remains elusive. By a meta-analysis of 2426-single and 161-paired observations from 89 published ¹⁵  N pool dilution and tracing studies, we found that gross N mineralization (GNM), immobilization of ammonium ( I NH 4 ) and nitrate ( I NO 3 ), and dissimilatory nitrate reduction to ammonium (DNRA) were significantly higher in tropical forests than in subtropical forests. Soil N cycle was conservative in tropical forests with ratios of gross nitrification (GN) to I NH 4 (GN/ I NH 4 ) and of soil nitrate to ammonium (NO₃ ^- /NH₄ ⁺ ) less than one, but was leaky in subtropical forests with GN/ I NH 4 and NO₃ ^- /NH₄ ⁺ higher than one. Soil NH₄ ⁺ dynamics were mainly controlled by soil substrate (e.g., total N), but climatic factors (e.g., precipitation and/or temperature) were more important in controlling soil NO₃ ^- dynamics. Soil texture played a role, as GNM and I NH 4 were positively correlated with silt and clay contents, while I NO 3 and DNRA were positively correlated with sand and clay contents, respectively. The soil N cycle was more sensitive to N deposition in tropical forests than in subtropical forests. Nitrogen deposition leads to a leaky N cycle in tropical forests, as evidenced by the increase in GN/ I NH 4 , NO₃ ^- /NH₄ ⁺ , and nitrous oxide emissions and the decrease in I NO 3 and DNRA, mainly due to the decrease in soil microbial biomass and pH. Dominant tree species can also influence soil N cycle pattern, which has changed from conservative in deciduous forests to leaky in coniferous forests. We provide global evidence that tropical, but not subtropical, forests are characterized by soil N dynamics sustaining N availability and that N deposition inhibits soil N retention and stimulates N losses in these biomes.

Nitrate as an alternative electron acceptor destabilizes the mineral associated organic carbon in moisturized deep soil depths

Numerous studies have investigated the effects of nitrogen (N) addition on soil organic carbon (SOC) decomposition. However, most studies have focused on the shallow top soils <0.2 m (surface soil), with a few studies also examining the deeper soil depths of 0.5-1.0 m (subsoil). Studies investigating the effects of N addition on SOC decomposition in soil >1.0 m deep (deep soil) are rare. Here, we investigated the effects and the underlying mechanisms of nitrate addition on SOC stability in soil depths deeper than 1.0 m. The results showed that nitrate addition promoted deep soil respiration if the stoichiometric mole ratio of nitrate to O₂ exceeded the threshold of 6:1, at which nitrate can be used as an alternative acceptor to O₂ for microbial respiration. In addition, the mole ratio of the produced CO₂ to N₂O was 2.57:1, which is close to the theoretical ratio of 2:1 expected when nitrate is used as an electron acceptor for microbial respiration. These results demonstrated that nitrate, as an alternative acceptor to O₂, promoted microbial carbon decomposition in deep soil. Furthermore, our results showed that nitrate addition increased the abundance of SOC decomposers and the expressions of their functional genes, and concurrently decreased MAOC, and the ratio of MAOC/SOC decreased from 20% before incubation to 4% at the end of incubation. Thus, nitrate can destabilize the MAOC in deep soils by stimulating microbial utilization of MAOC. Our results imply a new mechanism on how above-ground anthropogenic N inputs affect MAOC stability in deep soil. Mitigation of nitrate leaching is expected to benefit the conservation of MAOC in deep soil depths.

Quantifying the effect of the nitrogen biogeochemical processes on the distribution of ammonium in the riverbank filtration system

Ammonium (NH₄⁺) enrichment of riverbank filtration (RBF) systems is gaining popularity. However, most previous research has concentrated on NO₃^- removal efficiencies, while the mechanisms of NH₄⁺ enrichment remain unknown. A nitrogen biogeochemical process model was developed for the quantitative analysis of NH₄⁺ enrichment in the Kaladian well field in northwest Songyuan City, NE China. Data from laboratory experiments and in-situ monitoring were used to determine initial values and calibrate the thermodynamic/kinetic parameters representing nitrogen (N) biogeochemical reactions. (1) The NO₃^- from river was subjected to denitrification (DNF) and dissimilatory nitrate reduction to ammonium (DNRA) within 10-14 m of the shore, whereas the NH₄⁺ in groundwater was caused by DNRA, organic nitrogen mineralization (MIN), and mixing with laterally recharged high NH₄⁺ groundwater. (2) DNF and DNRA were regulated by hydrodynamic processes, with the ranges of these processes being more significant in the wet season due to a higher hydraulic gradient. MIN occurred widely throughout the water flow path, with temperature primarily controlling the rates of the three reactions. (3) DNRA activity was relatively higher in the wet season when the water temperature was higher within 10-14 m of the shore. In the wet season, DNRA contributed 25%-30% to NO₃^- reduction, which was higher than in the dry season (5%-10%). DNRA contributed at least 40% and 15% to NH₄⁺ enrichment in the wet and dry seasons, respectively. (4). Organic N in media gradually released NH₄⁺ into groundwater via MIN and desorption across the entire flow path, with contributions to NH₄⁺ enrichment reaching 75% and 85%, respectively, in the wet and dry seasons.

Expanding agroforestry can increase nitrate retention and mitigate the global impact of a leaky nitrogen cycle in croplands

The internal soil nitrogen (N) cycle supplies N to plants and microorganisms but may induce N pollution in the environment. Understanding the variability of gross N cycling rates resulting from the global spatial heterogeneity of climatic and edaphic variables is essential for estimating the potential risk of N loss. Here we compiled 4,032 observations from 398 published 15N pool dilution and tracing studies to analyse the interactions between soil internal potential N cycling and environmental effects. We observed that the global potential N cycle changes from a conservative cycle in forests to a less conservative one in grasslands and a leaky one in croplands. Structural equation modelling revealed that soil properties (soil pH, total N and carbon-to-N ratio) were more important than the climate factors in shaping the internal potential N cycle, but different patterns in the potential N cycle of terrestrial ecosystems across climatic zones were also determined. The high spatial variations in the global soil potential N cycle suggest that shifting cropland systems towards agroforestry systems can be a solution to improve N conservation.

Effects of carbon load on nitrate reduction during riverbank filtration: Field monitoring and batch experiment

Riverbank filtration (RBF) is a well-established technique worldwide, and is critical for the maintenance of groundwater quality and production of clean drinking water. Evaluation of the decay of exogenous nitrate (NO₃^-) in river water and the enrichment of ammonium (NH₄⁺) in groundwater during RBF is important; these two processes are mainly influenced by denitrification (DNF) and dissimilatory nitrate reduction to ammonium (DNRA) controlled by the groundwater carbon load. In this study, the effects of carbon load (organic carbon [OC]: NO₃^-) on the competing nitrate reduction (DNRA and DNF) were assessed during RBF using field monitoring and a laboratory batch experiment. Results show the groundwater OC: NO₃^- ratio did not directly affect the reaction rate of DNRA and DNF, however, it could control the competitive partitioning between the two. In the near-shore zone, the groundwater OC: NO₃^- ratio shows significant seasonal variations along the filtration path owing to the changing conditions of redox, OC-rich, and NO₃^--limited. A greater proportion of NO₃^- would be available for DNRA in the wet season with higher OC: NO₃^- ratio (> 10), resulting in a significantly NH₄⁺-N enrichment rate (from 1.43 × 10^-3 to 9.54 × 10^-4 mmol L^-1 d^-1) in the near-shore zone where the zone of Mn (IV) oxide reduction. However, the activity of DNRA was suppressed with lower OC: NO₃^- ratio (< 10) in the dry season, resulting in a stable NH₄⁺-N enrichment rate (from 3.12 × 10^-4 to 1.30 × 10^-4 mmol L^-1 d^-1). Benefiting from seasonal variation of OC-rich and NO₃^--limited conditions, DNRA bacteria outcompeted denitrifiers, which eventually led to seasonal differences in NO₃^- reduction in the near-shore zone. Overall, under the effect of DNRA induced by continuous high carbon load in RBF systems, nitrogen input is not permanently removed but rather retained in groundwater during RBF.

Identification of nosZ-expressing microorganisms consuming trace N2O in microaerobic chemostat consortia dominated by an uncultured Burkholderiales

Microorganisms possessing N₂O reductases (NosZ) are the only known environmental sink of N₂O. While oxygen inhibition of NosZ activity is widely known, environments where N₂O reduction occurs are often not devoid of O₂. However, little is known regarding N₂O reduction in microoxic systems. Here, 1.6-L chemostat cultures inoculated with activated sludge samples were sustained for ca. 100 days with low concentration (<2 ppmv) and feed rate (<1.44 µmoles h⁻¹) of N₂O, and the resulting microbial consortia were analyzed via quantitative PCR (qPCR) and metagenomic/metatranscriptomic analyses. Unintended but quantified intrusion of O₂ sustained dissolved oxygen concentration above 4 µM; however, complete N₂O reduction of influent N₂O persisted throughout incubation. Metagenomic investigations indicated that the microbiomes were dominated by an uncultured taxon affiliated to Burkholderiales, and, along with the qPCR results, suggested coexistence of clade I and II N₂O reducers. Contrastingly, metatranscriptomic nosZ pools were dominated by the Dechloromonas-like nosZ subclade, suggesting the importance of the microorganisms possessing this nosZ subclade in reduction of trace N₂O. Further, co-expression of nosZ and ccoNO/cydAB genes found in the metagenome-assembled genomes representing these putative N₂O-reducers implies a survival strategy to maximize utilization of scarcely available electron acceptors in microoxic environmental niches.

Interacting Bioenergetic and Stoichiometric Controls on Microbial Growth

Microorganisms function as open systems that exchange matter and energy with their surrounding environment. Even though mass (carbon and nutrients) and energy exchanges are tightly linked, there is a lack of integrated approaches that combine these fluxes and explore how they jointly impact microbial growth. Such links are essential to predicting how the growth rate of microorganisms varies, especially when the stoichiometry of carbon- (C) and nitrogen (N)-uptake is not balanced. Here, we present a theoretical framework to quantify the microbial growth rate for conditions of C-, N-, and energy-(co-) limitations. We use this framework to show how the C:N ratio and the degree of reduction of the organic matter (OM), which is also the electron donor, availability of electron acceptors (EAs), and the different sources of N together control the microbial growth rate under C, nutrient, and energy-limited conditions. We show that the growth rate peaks at intermediate values of the degree of reduction of OM under oxic and C-limited conditions, but not under N-limited conditions. Under oxic conditions and with N-poor OM, the growth rate is higher when the inorganic N (N_Inorg)-source is ammonium compared to nitrate due to the additional energetic cost involved in nitrate reduction. Under anoxic conditions, when nitrate is both EA and N_Inorg-source, the growth rates of denitrifiers and microbes performing the dissimilatory nitrate reduction to ammonia (DNRA) are determined by both OM degree of reduction and nitrate-availability. Consistent with the data, DNRA is predicted to foster growth under extreme nitrate-limitation and with a reduced OM, whereas denitrifiers are favored as nitrate becomes more available and in the presence of oxidized OM. Furthermore, the growth rate is reduced when catabolism is coupled to low energy yielding EAs (e.g., sulfate) because of the low carbon use efficiency (CUE). However, the low CUE also decreases the nutrient demand for growth, thereby reducing N-limitation. We conclude that bioenergetics provides a useful conceptual framework for explaining growth rates under different metabolisms and multiple resource-limitations.

Metagenomic Insights Into Competition Between Denitrification and Dissimilatory Nitrate Reduction to Ammonia Within One-Stage and Two-Stage Partial-Nitritation Anammox Bioreactor Configurations

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.

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

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

Global Patterns and Drivers of Soil Dissimilatory Nitrate Reduction to Ammonium

Dissimilatory nitrate reduction to ammonium (DNRA), the nearly forgotten process in the terrestrial nitrogen (N) cycle, can conserve N by converting the mobile nitrate into non-mobile ammonium avoiding nitrate losses via denitrification, leaching, and runoff. However, global patterns and controlling factors of soil DNRA are still only rudimentarily known. By a meta-analysis of 231 observations from 85 published studies across terrestrial ecosystems, we find a global mean DNRA rate of 0.31 ± 0.05 mg N kg^-1 day^-1, being significantly greater in paddy soils (1.30 ± 0.59) than in forests (0.24 ± 0.03), grasslands (0.52 ± 0.15), and unfertilized croplands (0.18 ± 0.04). Soil DNRA was significantly enhanced at higher altitude and lower latitude. Soil DNRA was positively correlated with precipitation, temperature, pH, soil total carbon, and soil total N. Precipitation was the main stimulator for soil DNRA. Total carbon and pH were also important factors, but their effects were ecosystem-specific as total carbon stimulates DNRA in forest soils, whereas pH stimulates DNRA in unfertilized croplands and paddy soils. Higher temperatures inhibit soil DNRA via decreasing total carbon. Moreover, nitrous oxide (N₂O) emissions were negatively related to soil DNRA. Thus, future changes in climate and land-use may interact with management practices that alter soil substrate availability and/or soil pH to enhance soil DNRA with positive effects on N conservation and lower N₂O emissions.

Low temperature Moving Bed Bioreactor denitrification as mitigation measure to reduce agricultural nitrate losses

The negative impact of agriculture on the quality of local water streams is widely recognized. Fertilizer residues not taken up by the crops leach into the drainage water and enter the surface water, resulting in eutrophication. Despite various initiatives to prevent this leaching by optimizing fertilizer schemes, the desired effect was not achieved, and the focus has shifted to denitrifying end-of-pipe techniques. Because the available area for installing such treatment systems is often limited, the development of intensified systems is a trend that has emerged recently. In this scope, the main goal of this study was therefore to investigate the suitability of a denitrifying Moving Bed Bioreactor (MBBR) as a low footprint technology, which can compete with conventional technologies. Two parallel lab-scale pilot MBBRs, one at low temperature and one at ambient temperature, were operated for 850 days to investigate the effectiveness and robustness under changing process parameters (hydraulic retention time (HRT), temperature, shutdown). Eventually, the system was scaled up to a full-scale installation and monitored during a full drainage season in the field. The pilot-scale MBBRs achieved removal efficiencies above 90% under optimal conditions (high C/N ratio and minimal HRT of 8 h), even while operating at low temperatures. The robustness of the system was also demonstrated by the immediate start-up after a shutdown period of 220 days. Overall, the full-scale MBBR treated 2910.1 m³ drainage water and removed approximately 59 kg NO₃-N. Unfortunately, the average removal efficiency, i.e., 70%, was lower than the lab-scale system, but by intensifying the mixing in the MBBR, improved results were obtained. Nitrite accumulation was furthermore also prevented.

Role of organic/sulfide ratios on competition of DNRA and denitrification in a co-driven sequencing biofilm batch reactor

Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are two competing pathways in nitrate-reducing process. In this study, a series of C/S ratios from 8:1 to 2:4 were investigated in a sequencing biofilm batch reactor (SBBR) to determine the role of reducers (sulfide and acetate) on their competition. The results showed that the proportion of DNRA increased in high electron system, either in organic-rich system or in sulfide-rich system. The highest DNRA ratio increased to 16.4% at the C/S ratio of 2:3. Excess electron donors, particularly sulfide, were favorable for DNRA in a limited nitrate environment. Moreover, a higher reductive environment could facilitate DNRA, especially, when ORP was lower than - 400 mV in this system. 16S rRNA gene sequencing analysis demonstrated that Geobacter might be the important participant involved in DNRA process in organic-rich system, while Desulfomicrobium might be the dominant DNRA bacteria in sulfide-rich system. DNRA cultivation could enrich nitrogen conversion pathways in conventional denitrification systems and deepen the insight into nitrogen removal at low C/N.

Biological Nitrogen Removal Database: A Manually Curated Data Resource

Biological nitrogen removal (BNR) technologies are the most effective approaches for the remediation of environmental nitrogen pollutants from wastewater treatment plants (WWTPs). Presently, research is going on to elucidate the structure and function of BNR microbial communities and optimizing BNR treatment systems to enhance nitrogen removal efficiency. The literature on BNR microbial communities and experimental datasets is not unified across various repositories, while a uniform resource for the collection, annotation, and structuring of these BNR datasets is still unavailable. Herein, we present the Biological Nitrogen Removal Database (BNRdb), an integrated resource containing various manually curated BNR-related data. At present, BNRdb contains 23,308 microbial strains, 46 gene families, 24 enzymes, 18 reactions, 301 BNR treatment datasets, 860 BNR-associated next-generation sequencing datasets, and 6 common BNR bioreactor systems. BNRdb provides a user-friendly interface enabling interactive data browsing. To our knowledge, BNRdb is the first BNR data resource that systematically integrates BNR data from archaeal, bacterial, and fungal communities. We believe that BNRdb will contribute to a better understanding of BNR process and nitrogen bioremediation research.

Application of pyritic sludge with an anaerobic granule consortium for nitrate removal in low carbon systems

Granules recovered from a highly reduced anaerobic digester were capable of active nitrogen removal in the absence of exogenous electron donors, averaging 0.25 mg mgNO3--N /gVSS/d over 546 days of operation. Electron mass balance indicated that about half the influent nitrate was converted to ammonia via DNRA and another half denitrified. This capacity was associated with an onion-like structure of multiple layers enriched in reduced iron and sulfur, and a complex microbial community shown by metagenomic sequencing to consist of multiple physiological groups and associated activities, including methanogenesis, denitrification, dissimilatory nitrate reduction to ammonia (DNRA), iron oxidation and reduction, and sulfur reduction and oxidation. Nitrate reduction was supported by both entrained organic material and reduced iron and sulfur species, corresponding to 2.13 mg COD/gVSS/d. Batch incubations showed that approximately 15% of denitrified nitrate was coupled to the oxidation of sulfur derived from both sulfate respiration and granular material enriched in iron-sulfide. Inhibition of sulfate reduction resulted in redirection of electron flow to methanogenesis and, in combination with other batch tests, showed that these granules supported a complex microbial community in which cryptic redox cycles linked carbon, sulfur, and iron oxidation with nitrate, sulfate, iron, and carbon dioxide reduction. This system shows promise for treatment of nitrate contaminated ground water without addition of an external organic carbon source as well as wastewater treatment in combination with (granular) sludge elimination leading in a net reduction of solid treatment costs.

Unique high Arctic methane metabolizing community revealed through in situ 13CH4-DNA-SIP enrichment in concert with genome binning

Greenhouse gas (GHG) emissions from Arctic permafrost soils create a positive feedback loop of climate warming and further GHG emissions. Active methane uptake in these soils can reduce the impact of GHG on future Arctic warming potential. Aerobic methane oxidizers are thought to be responsible for this apparent methane sink, though Arctic representatives of these organisms have resisted culturing efforts. Here, we first used in situ gas flux measurements and qPCR to identify relative methane sink hotspots at a high Arctic cytosol site, we then labeled the active microbiome in situ using DNA Stable Isotope Probing (SIP) with heavy 13CH4 (at 100 ppm and 1000 ppm). This was followed by amplicon and metagenome sequencing to identify active organisms involved in CH4 metabolism in these high Arctic cryosols. Sequencing of 13C-labeled pmoA genes demonstrated that type II methanotrophs (Methylocapsa) were overall the dominant active methane oxidizers in these mineral cryosols, while type I methanotrophs (Methylomarinovum) were only detected in the 100 ppm SIP treatment. From the SIP-13C-labeled DNA, we retrieved nine high to intermediate quality metagenome-assembled genomes (MAGs) belonging to the Proteobacteria, Gemmatimonadetes, and Chloroflexi, with three of these MAGs containing genes associated with methanotrophy. A novel Chloroflexi MAG contained a mmoX gene along with other methane oxidation pathway genes, identifying it as a potential uncultured methane oxidizer. This MAG also contained genes for copper import, synthesis of biopolymers, mercury detoxification, and ammonia uptake, indicating that this bacterium is strongly adapted to conditions in active layer permafrost and providing new insights into methane biogeochemical cycling. In addition, Betaproteobacterial MAGs were also identified as potential cross-feeders with methanotrophs in these Arctic cryosols. Overall, in situ SIP labeling combined with metagenomics and genome binning demonstrated to be a useful tool for discovering and characterizing novel organisms related to specific microbial functions or biogeochemical cycles of interest. Our findings reveal a unique and active Arctic cryosol microbial community potentially involved in CH4 cycling.

Certain Environmental Conditions Maximize Ammonium Accumulation and Minimize Nitrogen Loss During Nitrate Reduction Process by Pseudomonas putida Y-9

Realizing the smallest nitrogen loss is a challenge in the nitrate reduction process. Dissimilatory nitrate reduction to ammonium (DNRA) and nitrate assimilation play crucial roles in nitrogen retention. In this study, the effects of the carbon source, C/N ratio, pH, and dissolved oxygen on the multiple nitrate reduction pathways conducted by Pseudomonas putida Y-9 are explored. Strain Y-9 efficiently removed nitrate (up to 89.79%) with glucose as the sole carbon source, and the nitrogen loss in this system was 15.43%. The total nitrogen decrease and ammonium accumulation at a C/N ratio of 9 were lower than that at 12 and higher than that at 15, respectively (P < 0.05). Besides, neutral and alkaline conditions (pH 7–9) favored nitrate reduction. Largest nitrate removal (81.78%) and minimum nitrogen loss (10.63%) were observed at pH 7. The nitrate removal and ammonium production efficiencies of strain Y-9 increased due to an increased shaking speed. The expression patterns of nirBD (the gene that controls nitrate assimilation and DNRA) in strain Y-9 were similar to ammonium patterns of the tested incubation conditions. In summary, the following conditions facilitated nitrate assimilation and DNRA by strain Y-9, while reducing the denitrification: glucose as the carbon source, a C/N ratio of 9, a pH of 7, and a shaking speed of 150 rpm. Under these conditions, nitrate removal was substantial, and nitrogen loss from the system was minimal.

Effects of drift algae accumulation and nitrate loading on nitrogen cycling in a eutrophic coastal sediment

The permeable (sandy) sediments that dominate the world's coastlines and continental shelves are highly exposed to nitrogen pollution, predominantly due to increased urbanisation and inefficient agricultural practices. This leads to eutrophication, accumulation of drift algae and changes in the reactions of nitrogen, including the potential to produce the greenhouse gas nitrous oxide (N₂O). Nitrogen pollution in coastal systems has been identified as a global environmental issue, but it remains unclear how this nitrogen is stored and processed by permeable sediments. We investigated the interaction of drift algae biomass and nitrate (NO₃^-) exposure on nitrogen cycling in permeable sediments that were impacted by high nitrogen loading. We treated permeable sediments with increasing quantities of added macroalgal material and NO₃^- and measured denitrification, dissimilatory NO₃^- reduction to ammonium (DNRA), anammox, and nitrous oxide (N₂O) production, alongside abundance of marker genes for nitrogen cycling and microbial community composition by metagenomics. We found that the presence of macroalgae dramatically increased DNRA and N₂O production in sediments without NO₃^- treatment, concomitant with increased abundance of nitrate-ammonifying bacteria (e.g. Shewanella and Arcobacter). Following NO₃^- treatment, DNRA and N₂O production dropped substantially while denitrification increased. This is explained by a shift in the relative abundance of nitrogen-cycling microorganisms under different NO₃^- exposure scenarios. Decreases in both DNRA and N₂O production coincided with increases in the marker genes for each step of the denitrification pathway (narG, nirS, norB, nosZ) and a decrease in the DNRA marker gene nrfA. These shifts were accompanied by an increased abundance of facultative denitrifying lineages (e.g. Pseudomonas and Marinobacter) with NO₃^- treatment. These findings identify new feedbacks between eutrophication and greenhouse gas emissions, and in turn have potential to inform biogeochemical models and mitigation strategies for marine eutrophication.

Effects of root exudates on rhizosphere bacteria and nutrient removal in pond-ditch circulation systems (PDCSs) for rural wastewater treatment

Pond-ditch circulation system (PDCS) is a promising remediation strategy for rural wastewater treatment. Aquatic plants play nonnegligible roles in the nutrient removal of the PDCS. However, mechanisms of root exudates regulating nutrient removal in PDCSs remained unclear. In our study, the PDCS achieved higher total nitrogen (TN) and phosphorus (TP) removal rates (72.7-97.4%) compared to the static system. Protein contents in root exudates of the PDCS ranged from 0.041 to 1.332 mg L^-1, showing negative associations with Simpson index. Lactic acid and tartaric acid in the PDCS varied from 0.045 to 0.380 mg L^-1 and 0.024 to 5.446 mg L^-1, which were tightly linked with TN, TP, and TP removal rates and most sediment properties, especially sediment total nitrogen (STN) and total organic carbon (TOC), and sediment inorganic phosphorus (SIP). Moreover, the top 3 relative dominant genus were Bacillus (0.11%-17.90%), Geobacter (0.35%-12.04%), and Clostridium sensu stricto 1 (0.14%-12.05%), which might be the predominant groups in nutrient removal of PDCSs. RDA results indicated that lactic acid, protein, and amino acids were positively correlated with Geobacter; while Bacillus was significantly affected by water content. Path analysis further demonstrated that the indirect effect of secretion from plant roots on nutrient removal rates was mainly through modulating bacteria diversity and relative abundance. Taken together, root exudates, especially protein, amino acids, and lactic acid, altered rhizosphere microbial relative abundance and diversity, where the impacts were bacterial species-dependent.

Impact of compost reactive layer on hydraulic transport and C & N cycles: Biogeochemical modeling of infiltration column experiments

Managed Aquifer Recharge (MAR) is a key strategy to increase freshwater resources in many regions facing water scarcity. MAR issues are related to both quantity and quality of the infiltrating water. In most countries, very high quality of the infiltrating water is required, to limit the impact on the aquifer geochemistry. In this paper, the possibility of injecting water of lower quality in the aquifer and letting the biogeochemical reactions take place in order to enhance its quality is explored. Here, we present the fate of nutrients (C, N) in the biogeochemical system of a reactive barrier formed by mixture of different proportions of sand and compost, supplied with treated wastewater to mimic MAR. An integrated conceptual model involving the nutrient cycles and biomass dynamics (auto- and heterotrophic) was developed, and then tested with a number of solute transport experiments in columns with different compost fraction in the column filling. The model incorporated both saturation and inhibition processes (regarding the nutrients and their byproducts) to provide a comprehensive picture of the nutrient dynamics within the column. The model developed (three if considering the 3 column setups) allowed to discriminate the processes that govern the fate of nutrients in relation with the compost enhancing long-term nutrient degradation, yet hindering hydraulic parameters that affect infiltration rates.

Soil redox dynamics under dynamic hydrologic regimes - A review

Electron transfer (redox) reactions, mediated by soil microbiota, modulate elemental cycling and, in part, establish the redox poise of soil systems. Understanding soil redox processes significantly improves our ability to characterize coupled biogeochemical cycling in soils and aids in soil health management. Redox-sensitive species exhibit different reactivity, mobility, and toxicity subjected to their redox state. Thus, it is crucial to quantify the redox potential (E_h) in soils and to characterize the dominant redox couples therein. Several, often coupled, external drivers, can influence E_h. Among these factors, soil hydrology dominates. It controls soil physical properties that in turn further regulates E_h. Soil spatial heterogeneity and temporally dynamic hydrologic regimes yield complex distributions of E_h. Soil redox processes have been studied under various environmental conditions, including relatively static and dynamic hydrologic regimes. Our focus here is on dynamic, variably water-saturated environments. Herein, we review previous studies on soil redox dynamics, with a specific focus on dynamic hydrologic regimes, provide recommendations on knowledge gaps, and targeted future research needs and directions. We review (1) the role of soil redox conditions on the soil chemical-species cycling of organic carbon, nitrogen, phosphorus, redox-active metals, and organic contaminants; (2) interactions between microbial activity and redox state in the near-surface and deep subsurface soil, and biomolecular methods to reveal the role of microbes in the redox processes; (3) the effects of dynamic hydrologic regimes on chemical-species cycling and microbial dynamics; (4) the experimental setups for mimicking different hydrologic regimes at both laboratory and field scales. Finally, we identify the current knowledge gaps related to the study of soil redox dynamics under different hydrologic regimes: (1) fluctuating conditions in the deep subsurface; (2) the use of biomolecular tools to understand soil biogeochemical processes beyond nitrogen; (3) limited current field measurements and potential alternative experimental setups.

Experimental infrastructure requirements for quantitative research on microbial communities

Natural microbial communities are composed of a large diversity of interacting microorganisms, each with a specific role in the functional properties of the ecosystem. The objectives in microbial ecology research are related to identifying, understanding and exploring the role of these different microorganisms. Because of the rapidly increasing power of DNA sequencing and the rapid increase of genomic data, main attention of microbial ecology research shifted from cultivation-oriented studies towards metagenomic studies. Despite these efforts, the direct link between the molecular properties and the measurable changes in the functional performance of the ecosystem is often poorly documented. A quantitative understanding of functional properties in relation to the molecular changes requires effective integration, standardization, and parallelization of experiments. High-resolution functional characterization is a prerequisite for interpretation of changes in metagenomic properties, and will improve our understanding of microbial communities and facilitate their exploration for health and circular economy related objectives.

Elucidating the Competition between Heterotrophic Denitrification and DNRA Using the Resource-Ratio Theory

Heterotrophic denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are two microbial processes competing for two shared resources, namely, nitrate and organic carbon (COD). Their competition has great implications for nitrogen loss, conservation, and greenhouse gas emissions. Nevertheless, a comprehensive and mechanistic understanding of the governing factors for this competition is still lacking. We applied the resource-ratio theory to study this competition and validated the theory with experimental data from continuous cultures reported in the literature. Based on this theory, we revealed that influent COD/N ratio alone was not sufficient to predict the competition outcome as the boundary values for different competition outcomes changed substantially with influent resource concentrations. The stoichiometry of the two processes was determinative for the boundaries, whereas the affinity for the shared resources (K_S), maximum specific growth rate (μ_max) of the two species, and the dilution rate had significant impacts as well but mainly at low influent resource concentrations (e.g., <100 μM nitrate). The presented approach allows for a more comprehensive understanding of the parameters controlling microbial competition. The computational comparison between continuous and batch cultures could explain seemingly conflicting experimental results as to the impact of the COD/N ratio. The results also include testable hypotheses and tools for understanding and managing the fate of nitrate in ecosystems, which could also be applied more widely to other species competing for two shared resources.

Quantification of nosZ genes and transcripts in activated sludge microbiomes with novel group-specific qPCR methods validated with metagenomic analyses

Substantial N₂O emission results from activated sludge nitrogen removal processes. N₂O-reducing organisms possessing NosZ-type N₂O reductases have been recognized to play crucial roles in suppressing emission of N₂O produced in anoxic activated sludge via denitrification; however, which of the diverse nosZ-possessing organisms function as the major N₂O sink in situ remains largely unknown. Here, nosZ genes and transcripts in wastewater microbiomes were analyzed with the group-specific qPCR assays designed de novo combining culture-based and computational approaches. A sewage sample was enriched in a batch reactor fed continuous stream of N₂ containing 20-10,000 ppmv N₂O with excess amount (10 mM) of acetate as the source of carbon and electrons, where 14 genera of potential N₂O-reducers were identified. All available amino acid sequences of NosZ affiliated to these taxa were grouped into five subgroups (two clade I and three clade II groups), and primers/probe sets exclusively and comprehensively targeting the subgroups were designed and validated with in silico PCR. Four distinct activated sludge samples from three different wastewater treatment plants in Korea were analyzed with the qPCR assays and the results were validated with the shotgun metagenome analysis results. With these group-specific qPCR assays, the nosZ genes and transcripts of six additional activated sludge samples were analyzed and the results of the analyses clearly indicated the dominance of two clade II nosZ subgroups (Flavobacterium-like and Dechloromonas-like) among both nosZ gene and transcript pools.

DNRA: A short-circuit in biological N-cycling to conserve nitrogen in terrestrial ecosystems

This paper reviews dissimilatory nitrate reduction to ammonium (DNRA) in soils - a newly appreciated pathway of nitrogen (N) cycling in the terrestrial ecosystems. The reduction of NO₃^- occurs in two steps; in the first step, NO₃^- is reduced to NO₂^-; and in the second, unlike denitrification, NO₂^- is reduced to NH₄⁺ without intermediates. There are two sets of NO₃^-/NO₂^- reductase enzymes, i.e., Nap/Nrf and Nar/Nir; the former occurs on the periplasmic-membrane and energy conservation is respiratory via electron-transport-chain, whereas the latter is cytoplasmic and energy conservation is both respiratory and fermentative (Nir, substrate-phosphorylation). Since, Nir catalyzes both assimilatory- and dissimilatory-nitrate reduction, the nrfA gene, which transcribes the NrfA protein, is treated as a molecular-marker of DNRA; and a high nrfA/nosZ (N₂O-reductase) ratio favours DNRA. Recently, several crystal structures of NrfA have been presumed to producee N₂O as a byproduct of DNRA via the NO (nitric-oxide) pathway. Meta-analyses of about 200 publications have revealed that DNRA is regulated by oxidation state of soils and sediments, carbon (C)/N and NO₂^-/NO₃^- ratio, and concentrations of ferrous iron (Fe²⁺) and sulfide (S^2-). Under low-redox conditions, a high C/NO₃^- ratio selects for DNRA while a low ratio selects for denitrification. When the proportion of both C and NO₃^- are equal, the NO₂^-/NO₃^- ratio modulates partitioning of NO₃^-, and a high NO₂^-/NO₃^- ratio favours DNRA. A high S^2-/NO₃^- ratio also promotes DNRA in coastal-ecosystems and saline sediments. Soil pH, temperature, and fine soil particles are other factors known to influence DNRA. Since, DNRA reduces NO₃^- to NH₄⁺, it is essential for protecting NO₃^- from leaching and gaseous (N₂O) losses and enriches soils with readily available NH₄⁺-N to primary producers and heterotrophic microorganisms. Therefore, DNRA may be treated as a tool to reduce ground-water NO₃^- pollution, enhance soil health and improve environmental quality.

Involvement of NO3 - in Ecophysiological Regulation of Dissimilatory Nitrate/Nitrite Reduction to Ammonium (DNRA) Is Implied by Physiological Characterization of Soil DNRA Bacteria Isolated via a Colorimetric Screening Method

Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) has recently regained attention as a nitrogen retention pathway that may potentially be harnessed to alleviate nitrogen loss resulting from denitrification. Until recently, the ecophysiology of DNRA bacteria inhabiting agricultural soils has remained largely unexplored, due to the difficulty in targeted enrichment and isolation of DNRA microorganisms. In this study, >100 DNRA bacteria were isolated from NO₃ ^--reducing anoxic enrichment cultures established with rice paddy soils using a newly developed colorimetric screening method. Six of these isolates, each assigned to a different genus, were characterized to improve the understanding of DNRA physiology. All the isolates carried nrfA and/or nirB, and the Bacillus sp. strain possessed a clade II nosZ gene conferring the capacity for N₂O reduction. A common prominent physiological feature observed in the isolates was NO₂ ^- accumulation before NH₄ ⁺ production, which was further examined with Citrobacter sp. strain DNRA3 (possessing nrfA and nirB) and Enterobacter sp. strain DNRA5 (possessing only nirB). Both isolates showed inhibition of NO₂ ^--to-NH₄ ⁺ reduction at submillimolar NO₃ ^- concentrations and downregulation of nrfA or nirB transcription when NO₃ ^- was being reduced to NO₂ ^- In batch and chemostat experiments, both isolates produced NH₄ ⁺ from NO₃ ^- reduction when incubated with excess organic electron donors, while incubation with excess NO₃ ^- resulted in NO₂ ^- buildup but no substantial NH₄ ⁺ production, presumably due to inhibitory NO₃ ^- concentrations. This previously overlooked link between NO₃ ^- repression of NO₂ ^--to-NH₄ ⁺ reduction and the C-to-N ratio regulation of DNRA activity may be a key mechanism underpinning denitrification-versus-DNRA competition in soil.IMPORTANCE Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) is an anaerobic microbial pathway that competes with denitrification for common substrates NO₃ ^- and NO₂ ^- Unlike denitrification, which leads to nitrogen loss and N₂O emission, DNRA reduces NO₃ ^- and NO₂ ^- to NH₄ ⁺, a reactive nitrogen compound with a higher tendency to be retained in the soil matrix. Therefore, stimulation of DNRA has often been proposed as a strategy to improve fertilizer efficiency and reduce greenhouse gas emissions. Such attempts have been hampered by lack of insights into soil DNRA bacterial ecophysiology. Here, we have developed a new screening method for isolating DNRA-catalyzing organisms from agricultural soils without apparent DNRA activity. Physiological characteristics of six DNRA isolates were closely examined, disclosing a previously overlooked link between NO₃ ^- repression of NO₂ ^--to-NH₄ ⁺ reduction and the C-to-N ratio regulation of DNRA activity, which may be a key to understanding why DNRA activity is rarely observed at substantial levels in nitrogen-rich agricultural soils.

Electron Flow Shifts from Anode Respiration to Nitrate Reduction During Electroactive Biofilm Thickening

As electrons generated through substrate oxidation compete with electrodes, dissimilatory nitrate reduction to ammonium (DNRA), denitrification in bioelectrochemical systems in the presence of nitrate, and nitrate reduction through an electroactive biofilm (EAB) are unpredictable. We find that pathways of nitrate reduction are related to EAB thickness and that 76 ± 2 μm is the critical thickness of a biofilm at which both the inner and outer layers simultaneously include DNRA, leading to a maximum level of DNRA efficiency of 42%. Fractions of electrons flowing during nitrate reduction are relatively stable, but their distributions between DNRA and denitrification vary with biofilm thickness. Electrons prefer denitrification in an EAB that is 66 ± 2 μm, while DNRA reversely surpasses denitrification when the thickness increases in the range of 76 ± 2 to 210 ± 2 μm. Biofilm thickening enhances the DNRA of all biofilms close to solution, where nirK remains constant and nrfA is significantly upregulated. However, nrfA is downregulated in layers close to the electrode when the biofilm is thicker than 76 ± 2 μm. These findings reveal the spatially heterogeneous reduction of nitrate in thick EABs, highlighting the importance of biofilm thickness to the regulation of end products of nitrate reduction.

Controls of H2S, Fe2 +, and Mn2 + on Microbial NO3 --Reducing Processes in Sediments of an Eutrophic Lake

Understanding the biogeochemical controls on the partitioning between nitrogen (N) removal through denitrification and anaerobic ammonium oxidation (anammox), and N recycling via dissimilatory nitrate (NO3 -) reduction to ammonium (DNRA) is crucial for constraining lacustrine N budgets. Besides organic carbon, inorganic compounds may serve as electron donors for NO3 - reduction, yet the significance of lithotrophic NO3 - reduction in the environment is still poorly understood. Conducting incubation experiments with additions of 15N-labeled compounds and reduced inorganic substrates (H2S, Fe2+, Mn2+), we assessed the role of alternative electron donors in regulating the partitioning between the different NO3 --reducing processes in ferruginous surface sediments of Lake Lugano, Switzerland. In sediment slurry incubations without added inorganic substrates, denitrification and DNRA were the dominant NO3 --reducing pathways, with DNRA contributing between 31 and 46% to the total NO3 - reduction. The contribution of anammox was less than 1%. Denitrification rates were stimulated by low to moderate additions of ferrous iron (Fe2+ ≤ 258 μM) but almost completely suppressed at higher levels (≥1300 μM). Conversely, DNRA was stimulated only at higher Fe2+ concentrations. Dissolved sulfide (H2S, i.e., sum of H2S, HS- and S2-) concentrations up to ∼80 μM, strongly stimulated denitrification, but did not affect DNRA significantly. At higher H2S levels (≥125 μM), both processes were inhibited. We were unable to find clear evidence for Mn2+-supported lithotrophic NO3 - reduction. However, at high concentrations (∼500 μM), Mn2+ additions inhibited NO3 - reduction, while it did not affect the balance between the two NO3 - reduction pathways. Our results provide experimental evidence for chemolithotrophic denitrification or DNRA with Fe2+ and H2S in the Lake Lugano sediments, and demonstrate that all tested potential electron donors, despite the beneficial effect at low concentrations of some of them, can inhibit NO3 - reduction at high concentration levels. Our findings thus imply that the concentration of inorganic electron donors in lake sediments can act as an important regulator of both benthic denitrification and DNRA rates, and suggest that they can exert an important control on the relative partitioning between microbial N removal and N retention in lakes.

Denitrification and dissimilatory nitrate reduction to ammonium in freshwater lakes of the Eastern Plain, China: Influences of organic carbon and algal bloom

Denitrification (DNF) and dissimilatory nitrate reduction to ammonium (DNRA) are critical dissimilatory nitrate reduction pathways that determine nitrogen (N) removal and internal recycling in aquatic environments. However, the relative important of DNRA, and the influences of environmental factors on DNF and DNRA, have not been widely studied in freshwater lakes. In our study, we used N isotope-tracing to investigate the potential rates of DNF and DNRA in 27 lakes from the Eastern Plain Lake Zone (EPL), China. In the EPL lakes, DNF was the dominant nitrate reduction process, however DNRA was still important, accounting for around 4.3%-21.9% of total nitrate reduction. The sediment organic carbon was the primary factor controlling the rates of dissimilatory nitrate reduction, accounting for 28.3% and 37.9% of the variance in DNF and DNRA rates, respectively. High algal biomass accelerated DNF rates, while indirectly affected DNRA via changing the quality of organic carbon. The greater contributions of DNRA to dissimilatory nitrate reduction were found in lakes with higher sulfate concentrations. DNRA coupled to sulfur cycling may play an important role in lakes with high sulfate concentrations and high sediment organic carbon. This study highlights the important role played by DNRA in total nitrate reduction pathways of freshwater lakes. Mitigation strategies for N pollution and algal blooms should not only target decrease of nutrient input, strategies should also create a suitable environment for improving N removal and inhibit N recycling.

Bioelectrochemical Ammoniation Coupled with Microbial Electrolysis for Nitrogen Recovery from Nitrate in Wastewater

Nitrate-N in wastewaters is hard to be recovered because it is difficult to volatilize with an opposite charge to ammonium. Here, we have proved the feasibility of dissimilatory nitrate reduction to ammonia (DNRA) by the easy-acclimated mixed electroactive bacteria, achieving the highest DNRA efficiency of 44%. It was then coupled with microbial electrolysis to concentrate ammonium by a factor of 4 in the catholyte for recovery. The abundance of electroactive bacteria in the biofilm before nitrate addition, especially Geobacter spp., was found to determine the DNRA efficiency. As the main competitors of DNRA bacteria, the growth of denitrifiers was more sensitive to C/N ratios. The DNRA microbial community contrarily showed a stable and recoverable ammoniation performance over C/N ratios ranging from 0.5 to 8.0. A strong competition of the electrode and nitrate on electron donors was observed at the early stage (15 d) of electroactive biofilm formation, which can be weakened when the biofilm was mature on 40 d. Quantitative PCR showed a significant increase in nirS and nrfA transcripts in the ammoniation process. nirS was inhibited significantly after nitrate depletion while nrfA was still upregulated. These findings provided a novel way to recover nitrate-N using organic wastes as both electron donor and power, which has broader implications on the sustainable wastewater treatment and the ecology of nitrogen cycling.

The Water Hyacinth Microbiome: Link Between Carbon Turnover and Nutrient Cycling

Water hyacinth (WH), a large floating plant, plays an important role in the biogeochemistry and ecology of many freshwaters globally. Its biogeochemical impact on wetland functioning is strongly mediated by the microbiome associated with its roots. However, little is known about the structure and function of this WH rhizobiome and its relation to wetland ecosystem functioning. Here, we unveil the core and transient rhizobiomes of WH and their key biogeochemical functions in two of the world's largest wetlands: the Amazon and the Pantanal. WH hosts a highly diverse microbial community shaped by spatiotemporal changes. Proteobacteria lineages were most common, followed by Actinobacteria and Planctomycetes. Deltaproteobacteria and Sphingobacteriia predominated in the core microbiome, potentially associated with polysaccharide degradation and fermentation of plant-derived carbon. Conversely, a plethora of lineages were transient, including highly abundant Acinetobacter, Acidobacteria subgroup 6, and methanotrophs, thus assuring diverse taxonomic signatures in the two different wetlands. Our findings point out that methanogenesis is a key driver of, and proxy for, community structure, especially during seasonal plant decline. We provide ecologically relevant insights into the WH microbiome, which is a key element linking plant-associated carbon turnover with other biogeochemical fluxes in tropical wetlands.

Role of organic carbon, nitrate and ferrous iron on the partitioning between denitrification and DNRA in constructed stormwater urban wetlands

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/NO₃^- 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/NO₃^- 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.

Optimization of PCR primers to detect phylogenetically diverse nrfA genes associated with nitrite ammonification

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.

Electrodes Donate Electrons for Nitrate Reduction in a Soil Matrix via DNRA and Denitrification

Microbial strains and indigenous microbiota in soil slurries have been reported to use electrons from electrodes for nitrate (NO₃^-) reduction. However, few studies have confirmed this in a soil matrix hitherto. This study investigated if, and how, an electric potential affected NO₃^- reduction in a soil matrix. The results showed that, compared to a control treatment, applying an electric potential of -0.5 V versus the standard hydrogen electrode (SHE) significantly increased the relative abundance of NO₃^--reducing microbes (e.g., Alcaligenaceae and Pseudomonadaceae) and the abundances of the nrfA, nirK, nirS, and nosZ genes in soil matrices. Meanwhile, the electric potential treatment doubled the NO₃^- reduction rate and significantly increased the rates of production of ammonium (NH₄⁺), dinitrogen (N₂), and nitrous oxide (N₂O). The amount of NO₃^--N reduced under the electric potential treatment was comparable to the sum of the amounts of N observed in the increased N₂O, N₂, NH₄⁺, and nitrite (NO₂^-) pools. An open-air experiment showed that the electric potential treatment promoted soil NO₃^- reduction with a spatial scale of at least 38 cm. These results demonstrated that an electric potential treatment could enhance NO₃^- reduction via both denitrification and dissimilatory NO₃^- reduction to ammonium (DNRA) in the soil matrix. The mechanisms revealed in this study have implications for the future development of potential techniques for enhancing NO₃^- reduction in the vadose zone and consequently reducing the risk of NO₃^- leaching.

Nitrogen Addition Decreases Dissimilatory Nitrate Reduction to Ammonium in Rice Paddies

Dissimilatory nitrate reduction to ammonium (DNRA), denitrification, anaerobic ammonium oxidation (anammox), and biological N2 fixation (BNF) can influence the nitrogen (N) use efficiency of rice production. While the effect of N application on BNF is known, little is known about its effect on NO3- partitioning between DNRA, denitrification, and anammox. Here, we investigated the effect of N application on DNRA, denitrification, anammox, and BNF and on the abundance of relevant genes in three paddy soils in Australia. Rice was grown in a glasshouse with N fertilizer (150 kg N ha-1) and without N fertilizer for 75 days, and the rhizosphere and bulk soils were collected separately for laboratory incubation and quantitative PCR analysis. Nitrogen application reduced DNRA rates by >16% in all the soils regardless of the rhizospheric zone, but it did not affect the nrfA gene abundance. Without N, the amount and proportion of NO3- reduced by DNRA (0.42 to 0.52 μg g-1 soil day-1 and 45 to 55%, respectively) were similar to or higher than the amount and proportion reduced by denitrification. However, with N the amount of NO3- reduced by DNRA (0.32 to 0.40 μg g-1 soil day-1) was 40 to 50% lower than the amount of NO3- reduced by denitrification. Denitrification loss increased by >20% with N addition and was affected by the rhizospheric zones. Nitrogen loss was minimal through anammox, while BNF added 0.02 to 0.25 μg N g-1 soil day-1 We found that DNRA plays a significant positive role in paddy soil N retention, as it accounts for up to 55% of the total NO3- reduction, but this is reduced by N application.IMPORTANCE This study provides evidence that nitrogen addition reduces nitrogen retention through DNRA and increases nitrogen loss via denitrification in a paddy soil ecosystem. DNRA is one of the major NO3- reduction processes, and it can outcompete denitrification in NO3- consumption when rice paddies are low in nitrogen. A significant level of DNRA activity in paddy soils indicates that DNRA plays an important role in retaining nitrogen by reducing NO3- availability for denitrification and leaching. Our study shows that by reducing N addition to rice paddies, there is a positive effect from reduced nitrogen loss but, more importantly, from the conversion of NO3- to NH4+, which is the favored form of mineral nitrogen for plant uptake.