Microbial Nitrification Research Articles

Identification of groundwater nitrate sources and its human health risks in a typical agriculture-dominated watershed, North China.

Identifying nitrate sources and migratory pathways is crucial for controlling groundwater nitrate pollution in agricultural watersheds. This study collected 35 shallow groundwater samples in the Nansi Lake Basin (NLB) to identify groundwater nitrate sources and potential health risks. Results showed that NO3- concentration in 62.9% of groundwater samples exceeded the drinking water standard (50 mg/L). Hierarchical cluster analysis (HCA) was used to classify the sampling points into three groups based on hydrochemical and isotopic data. Groups A and C were situated in the eastern recharge and discharge regions of Nansi Lake, while Group B was located in the Yellow River floodplain west of the lake. Hydrochemical data and nitrate stable isotopes (δ15N-NO3- and δ18O-NO3-) indicated that elevated NO3- primarily originated from soil organic nitrogen (SON) in Group A, while manure and sewage (M&S) were the primary sources in Groups B and C samples. Microbial nitrification was identified as the primary nitrogen transformation process across all groups. The source apportionment results indicated that SON contributed approximately 40.1% in Group A, while M&S contributed about 53.9% and 81.2% in Groups B and C, respectively. The Human Health Risk Assessment (HHRA) model indicated significant non-carcinogenic risks for residents east of Nansi Lake, primarily through the oral pathway, with NO3- concentration identified as the most influential factor by sensitivity analysis. These findings provide new perspectives on identifying and handling groundwater nitrogen pollution in agriculture-dominated NLB and similar basins that require enhanced nitrogen contamination management.

A hybrid oxidation approach for converting high-strength urine ammonia into ammonium nitrate

Nutrient resources contained in human urine have great potential to alleviate global agricultural fertilizer demand. Microbial nitrification is a recognized strategy for stabilizing urine ammonia into ammonium nitrate, a common fertilizer worldwide, but faces a core bottleneck of process instability due to microbial inhibition. This study reports a new approach by developing a hybrid oxidation process involving three stages—microbial ammonia oxidation, chemical nitrite oxidation and microbial nitrite oxidation. Candidatus Nitrosoglobus, a γ-proteobacterial ammonia oxidizer highly tolerant to free nitrous acid, was introduced in the first stage to oxidize half of the total ammonia in the influent (8 g NH4+-N/L) to nitrite. The nitrite was then chemically oxidized by using hydrogen peroxide via a rapid chemical reaction to form nitrate. The third stage, microbial nitrite oxidation, was employed to ensure the complete removal of residual nitrite following chemical oxidation. The overall concept demonstrated in this work showcased the robust performance of the hybrid system. Moreover, the system also had a dual advantage in achieving antimicrobial ability in the first and second stages, making treated urine a safe fertilizer.

Copper and cadmium co-contamination increases the risk of nitrogen loss in red paddy soils

The microbiome plays a crucial role in soil nitrogen (N) cycling and in regulating its bioavailability. However, the functional and genomic information of microorganisms encoding N cycling in response to copper (Cu) and cadmium (Cd) contamination is largely unknown. Here, metagenomics and genome binning were used to examine microbial N cycling in Cu and Cd co-contaminated red paddy soils collected from a polluted watershed in southern China. The results showed that soil Cu and Cd concentrations induced more drastic changes in microbial N functional and taxonomic traits than soil general properties. Soil Cu and Cd co-contamination stimulated microbial nitrification, denitrification, and dissimilatory nitrate reduction processes mainly by increasing the abundance of Nitrospira (phylum Nitrospirota), while inhibiting N fixation by decreasing the abundance of Desulfobacca. These contrasting changes in microbial N cycling processes suggested a potential risk of N loss in paddy soils. A high-quality genome was identified as belonging to Nitrospirota with the highest abundance in heavily contaminated soils. This novel Nitrospirota strain possessed metabolic capacities for N transformation and metal resistance. These findings elucidate the genetic mechanisms underlying soil N bioavailability under long-term Cu and Cd contamination, which is essential for maintaining agricultural productivity and controlling heavy metal pollution.

Association between oral microbial nitrate metabolism and poor prognosis in acute ischemic stroke patients with a history of hypertension

ABSTRACT Background Oral microbes mediate the production of nitric oxide (NO) through the denitrification pathway. This study aimed to investigate the association between oral microbial nitrate metabolism and prognosis in acute ischemic stroke (AIS) patients. Methods This prospective, observational, single-center cohort study included 124 AIS patients admitted within 24 hours of symptom onset, with 24-hour ambulatory blood pressure data. Oral swabs were collected within 24 hours. Hypertensive AIS patients were stratified by the coefficient of variation (CV) of 24-hour systolic blood pressure. Microbial composition was analyzed using LEfSe and PICRUSt2 for bacterial and functional pathway identification. Results Significant differences in oral microbiota composition were observed between hypertensive AIS patients with varying CVs. Lower CV groups showed enrichment of nitrate-reducing bacteria and “Denitrification, nitrate => nitrogen” pathways. The TAX score of oral nitrate-reducing bacteria, derived from LASSO modeling, independently correlated with 90-day modified Rankin Scale scores, serving as an independent risk factor for poor prognosis. Mediation analyses suggested indirect that the TAX score not only directly influences outcomes but also indirectly affects them by modulating 24-hour systolic blood pressure CV. Conclusions AIS patients with comorbid hypertension and higher systolic blood pressure CV exhibited reduced oral nitrate-reducing bacteria, potentially worsening outcomes.

Microbial nitrate reduction electro-assisted by exo-electrogenic reduction of dioxygen with a Pseudomonas dominated cathodic biofilm

A nitrate reducing microbial biocathode was developed through constant polarization at -0.5 V vs SCE using two types of inoculums: a pure culture of Thiobacillus denitrificans and water collected from the artificial wetland of Rampillon (France). The results show a clear increase of the nitrate removal efficiency for the Pilots with the natural water although no catalytic nitrate reduction can be evidenced by cyclic voltammetry. Further studies show a catalytic oxygen reduction through exo-electrogenic metabolism and a correlation between the cathode polarization at -0.5 V vs SCE and the nitrate remediation. 16S rRNA gene amplicon sequencing of the biofilm bacterial DNA shows a very large predominance of Pseudomonas, a genus that includes many species able to reduce nitrate and/or reduce dioxygen (O2) using electrons from a cathode. The increased nitrate reduction performance is hypothesized to arise from an indirect bioelectro-assistance that allows the emergence of local anoxic conditions caused by microbial endo-electrogenic pathway for oxygen reduction.

Genetic variation in Zea mays influences microbial nitrification and denitrification in conventional agroecosystems

Abstract Background and Aims Nitrogenous fertilizers provide a short-lived benefit to crops in agroecosystems, but stimulate nitrification and denitrification, processes that result in nitrate pollution, N2O production, and reduced soil fertility. Recent advances in plant microbiome science suggest that genetic variation in plants can modulate the composition and activity of rhizosphere N-cycling microorganisms. Here we attempted to determine whether genetic variation exists in Zea mays for the ability to influence the rhizosphere nitrifier and denitrifier microbiome under “real-world” conventional agricultural conditions. Methods To capture an extensive amount of genetic diversity within maize we grew and sampled the rhizosphere microbiome of a diversity panel of germplasm that included ex-PVP inbreds (Z. mays ssp. mays), ex-PVP hybrids (Z. mays ssp. mays), and teosinte (Z. mays ssp. mexicana and Z. mays ssp. parviglumis). From these samples, we characterized the microbiome, a suite of microbial genes involved in nitrification and denitrification and carried out N-cycling potential assays. Results Here we are showing that populations/genotypes of a single species can vary in their ecological interaction with denitrifers and nitrifers. Some hybrid and teosinte genotypes supported microbial communities with lower potential nitrification and potential denitrification activity in the rhizosphere, while inbred genotypes stimulated/did not inhibit these N-cycling activities. These potential differences translated to functional differences in N2O fluxes, with teosinte plots producing less GHG than maize plots. Conclusion Taken together, these results suggest that Zea genetic variation can lead to changes in N-cycling processes that result in N leaching and N2O production, and thereby are selectable targets for crop improvement. Understanding the underlying genetic variation contributing to belowground microbiome N-cycling into our conventional agricultural system could be useful for sustainability.

Coupled processes involving ammonium inputs, microbial nitrification, and calcite dissolution control riverine nitrate pollution in the piedmont zone (Qingshui River, China)

Rivers in agricultural countries widely suffer from diffuse nitrate (NO3−) pollution. Although pollution sources and fates of riverine NO3− have been reported worldwide, the driving mechanisms of riverine NO3− pollution associated with mineral dissolution in piedmont zones remain unclear. This study combined hydrogeochemical compositions, stable isotopes (δ18O–NO3−, δ15N–NO3−, δ18O–H2O, and δ2H–H2O), and molecular bioinformation to determine the pollution sources, biogeochemical evolution, and natural attenuation of riverine NO3− in a typical piedmont zone (Qingshui River). High NO3− concentration (37.5 ± 9.44 mg/L) was mainly observed in the agricultural reaches of the river, with ~15.38 % of the samples exceeding the acceptable limit for drinking purpose (44 mg/L as NO3−) set by the World Health Organization. Ammonium inputs, microbial nitrification, and HNO3-induced calcite dissolution were the dominant driving factors that control riverine NO3− contamination in the piedmont zone. Approximately 99.4 % of riverine NO3− contents were derived from NH4+-containing pollutants, consisted of manure & domestic sewage (74.0 % ± 13.0 %), NH4+-synthetic fertilizer (16.1 % ± 8.99 %), and soil organic nitrogen (9.35 % ± 4.49 %). These NH4+-containing pollutants were converted to HNO3 (37.2 ± 9.38 mg/L) by nitrifying bacteria, and then the produced HNO3 preferentially participated in the carbonate (mainly calcite) dissolution, which accounted for 40.0 % ± 12.1 % of the total riverine Ca2+ + Mg2+, also resulting in the rapid release of NO3− into the river water. Thus, microbial nitrification could be a new and non-negligible contributor of riverine NO3− pollution, whereas the involvement of HNO3 in calcite dissolution acted as an accelerator of riverine NO3− pollution. However, denitrification had lesser contribution to natural attenuation for high NO3− pollution. The obtained results indicated that the mitigation of riverine NO3− pollution should focus on the management of ammonium discharges, and the HNO3-induced carbonate dissolution needs to be considered in comprehensively understanding riverine NO3− pollution in piedmont zones.

Microbial mechanisms of C/N/S geochemical cycling during low-water-level sediment remediation in urban rivers

Low-water-level regulation has been effectively implemented in the restoration of urban river sediments in Guangzhou City, China. Further investigation is needed to understand the microbial mechanisms involved in pollutant degradation in low-water-level environments. This study examined sediment samples from nine rivers, including low-water-level rivers (LW), tidal waterways (TW), and enclosed rivers (ER). Metagenomic high-throughput sequencing and the Diting pipeline were utilized to investigate the microbial mechanisms involved in sediment C/N/S geochemical cycling during low-water-level regulation. The results reveal that the degree of pollution in LW sediment is lower compared to TW and ER sediment. LW sediment exhibits a higher capacity for pollutant degradation and elimination of black, odorous substances due to its stronger microbial methane oxidation, nitrification, denitrification, anammox, and oxidation of sulfide, sulfite, and thiosulfate. Conversely, TW and ER sediment showcase greater microbial methanogenesis, anaerobic fermentation, and sulfide generation abilities, leading to the persistence of black, odorous substances. Factors such as grit and silt content, nitrate, and ammonia concentrations impacted microbial metabolic pathways. Low-water-level regulation improved the micro-environment for functional microbes, facilitating pollutant removal and preventing black odorous substance accumulation. These findings provide insights into the microbial mechanisms underlying low-water-level regulation technology for sediment restoration in urban rivers.

Unveiling unique microbial nitrogen cycling and nitrification driver in coastal Antarctica

Largely removed from anthropogenic delivery of nitrogen (N), Antarctica has notably low levels of nitrogen. Though our understanding of biological sources of ammonia have been elucidated, the microbial drivers of nitrate (NO3−) cycling in coastal Antarctica remains poorly understood. Here, we explore microbial N cycling in coastal Antarctica, unraveling the biological origin of NO3− via oxygen isotopes in soil and lake sediment, and through the reconstruction of 1968 metagenome-assembled genomes from 29 microbial phyla. Our analysis reveals the metabolic potential for microbial N2 fixation, nitrification, and denitrification, but not for anaerobic ammonium oxidation, signifying a unique microbial N-cycling dynamic. We identify the predominance of complete ammonia oxidizing (comammox) Nitrospira, capable of performing the entire nitrification process. Their adaptive strategies to the Antarctic environment likely include synthesis of trehalose for cold stress, high substrate affinity for resource utilization, and alternate metabolic pathways for nutrient-scarce conditions. We confirm the significant role of comammox Nitrospira in the autotrophic, nitrification process via 13C-DNA-based stable isotope probing. This research highlights the crucial contribution of nitrification to the N budget in coastal Antarctica, identifying comammox Nitrospira clade B as a nitrification driver.

Groundwater hydrochemical signatures, nitrate sources, and potential health risks in a typical karst catchment of North China using hydrochemistry and multiple stable isotopes.

Nitrate pollution in aquatic ecosystems has received growing concern, particularly in fragile karst basins. In this study, hydrochemical compositions, multiple stable isotopes (δ2H-H2O, δ18Ο-Η2Ο, δ15Ν-ΝΟ3-, and δ18Ο-ΝΟ3-), and Bayesian stable isotope mixing model (MixSIAR) were applied to elucidate nitrate pollution sources in groundwater of the Yangzhuang Basin. The Durov diagram identified the dominant groundwater chemical face as Ca-HCO3 type. The NO3- concentration ranged from 10.89 to 90.45mg/L (average 47.34mg/L), showing an increasing trend from the upstream forest and grassland to the downstream agricultural dominant area. It is worth noting that 47.2% of groundwater samples exceeded the NO3- threshold value of 50mg/L for drinking water recommended by the World Health Organization. The relationship between NO3-/Cl- and Cl- ratios suggested that most groundwater samples were located in nitrate mixed endmember from agricultural input, soil organic nitrogen, and manure & sewage. The Self-Organizing Map (SOM) and Pearson correlations analysis further indicated that the application of calcium fertilizer, sodium fertilizer, and livestock and poultry excrement in farmland elevated NO3- level in groundwater. The output results of the MixSIAR model showed that the primary sources of NO3- in groundwater were soil organic nitrogen (55.3%), followed by chemical fertilizers (28.5%), sewage & manure (12.7%), and atmospheric deposition (3.4%). Microbial nitrification was a dominant nitrogen conversion pathway elevating NO3- levels in groundwater, while the denitrification can be neglectable across the study area. The human health risk assessment (HHRA) model identified that about 88.9%, 77.8%, 72.2%, and 50.0% of groundwater samples posing nitrate's non-carcinogenic health hazards (HQ > 1) through oral intake for infants, children, females, and males, respectively. The findings of this study can offer useful biogeochemical information on nitrogen pollution in karst groundwater to support sustainable groundwater management in similar human-affected karst regions.

High hydrostatic pressure stimulates microbial nitrate reduction in hadal trench sediments under oxic conditions

Hadal trenches are extreme environments situated over 6000 m below sea surface, where enormous hydrostatic pressure affects the biochemical cycling of elements. Recent studies have indicated that hadal trenches may represent a previously overlooked source of fixed nitrogen loss; however, the mechanisms and role of hydrostatic pressure in this process are still being debated. To this end, we investigate the effects of hydrostatic pressure (0.1 to 115 MPa) on the chemical profile, microbial community structure and functions of surface sediments from the Mariana Trench using a Deep Ocean Experimental Simulator supplied with nitrate and oxygen. We observe enhanced denitrification activity at high hydrostatic pressure under oxic conditions, while the anaerobic ammonium oxidation – a previously recognized dominant nitrogen loss pathway – is not detected. Additionally, we further confirm the simultaneous occurrence of nitrate reduction and aerobic respiration using a metatranscriptomic dataset from in situ RNA-fixed sediments in the Mariana Trench. Taken together, our findings demonstrate that hydrostatic pressure can influence microbial contributions to nitrogen cycling and that the hadal trenches are a potential nitrogen loss hotspot. Knowledge of the influence of hydrostatic pressure on anaerobic processes in oxygenated surface sediments can greatly broaden our understanding of element cycling in hadal trenches.

Spatial and seasonal pattern of microbial nitrate reduction in coastal sediments in the Vistula River plume area, Gulf of Gdańsk

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-.

Denitrification dominates dissimilatory nitrate reduction across global natural ecosystems.

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

Nitrate dynamics in the streamwater-groundwater interaction system: Sources, fate, and controls

Nitrate (NO3−) pollution has attracted widespread attention as a threat to human health and aquatic ecosystems; however, elucidating the controlling factors behind nitrate dynamics under the context of changeable hydrological processes, particularly the interactions between streamwater and groundwater (SW-GW), presents significant challenges. A multi-tracer approach, integrating physicochemical and isotopic tracers (Cl−, δ2H-H2O, δ18O-H2O, δ15N-NO3− and δ18O-NO3−), was employed to identify the response of nitrate dynamics to SW-GW interaction in the Fen River Basin. The streamwater and groundwater NO3− concentrations varied greatly with space and time. Sewage and manure (28 %–73 %), fertilizer (14 %–36 %) and soil organic nitrogen (12 %–28 %) were the main NO3− sources in water bodies. Despite the control of land use type on streamwater nitrate dynamics in losing sections, SW-GW interactions drove NO3− dynamics in both streamwater and groundwater under most circumstances. In gaining streams, streamwater nitrate dynamics were influenced either by groundwater dilution or microbial nitrification, depending on whether groundwater discharge ratios exceeded or fell below 25 %, respectively. In losing streams, groundwater nitrate content increased with streamwater infiltration time, but the influence was mainly limited within 3 km from the river channel. This study provides a scientific basis for the effective management of water nitrate pollution at the watershed scale.

Soil properties and fungal community jointly explain N2O emissions following N and P enrichment in an alpine meadow

Nutrient enrichment, such as nitrogen (N) and phosphorus (P), typically affects nitrous oxide (N2O) emissions in terrestrial ecosystems, predominantly via microbial nitrification and denitrification processes in the soil. However, the specific impact of soil property and microbial community alterations under N and P enrichment on grassland N2O emissions remains unclear. To address this, a field experiment was conducted in an alpine meadow of the northeastern Qinghai-Tibetan Plateau. This study aimed to unravel the mechanisms underlying N and P enrichment effects on N2O emissions by monitoring N2O fluxes, along with analyzing associated microbial communities and soil physicochemical properties. We observed that N enrichment individually or in combination with P enrichment, escalated N2O emissions. P enrichment dampened the stimulatory effect of N enrichment on N2O emissions, indicative of an antagonistic effect. Structural equation modeling (SEM) revealed that N enrichment enhanced N2O emissions through alterations in fungal community composition and key soil physicochemical properties such as pH, ammonium nitrogen (NH4+-N), available phosphorus (AP), microbial biomass carbon (MBC), and microbial biomass nitrogen (MBN)). Notably, our findings demonstrated that N2O emissions were significantly more influenced by fungal activities, particularly genera like Fusarium, rather than bacterial processes in response to N enrichment. Overall, the study highlights that N enrichment intensifies the role of fungal attributes and soil properties in driving N2O emissions. In contrast, P enrichment exhibited a non-significant effect on N2O emissions, which highlights the critical role of the fungal community in N2O emissions responses to nutrient enrichments in alpine grassland ecosystems.

The regulation effect of preventing soil nitrogen loss using microbial quorum sensing inhibitors

Preventing soil nitrogen (N) losses driven by microbial nitrification and denitrification contributes to improving global environmental concerns caused by NO3−-N leaching and N2O emission. Quorum sensing (QS) signals regulate nitrification and denitrification of N-cycling bacteria in pure culture and water treatment systems, and mediate the composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in activated sludge. However, whether disrupting QS could prevent soil N losses remains unclear. This study explored the feasibility of applying quorum sensing inhibitors (QSIs) as an innovative strategy to reduce N losses from agricultural soils. The two QSIs, penicillic acid and 4-iodo-N-[(3S)-tetrahydro-2-oxo-3-furanyl]-benzeneacetamide (4-iodo PHL), were more effective in reducing N losses than traditional inhibitors, including N-(n-butyl) thiophosphoric triamide and 3,4-dimethylpyrazole phosphate. After 36 days of aerobic incubation, penicillic acid and 4-iodo PHL inhibited nitrification by 39% and 68%, respectively. The inhibitory effects are attributed to the fact that 4-iodo PHL decreased the abundance of archaeal and bacterial amoA genes, as well as the relative abundance of Candidatus Nitrocosmicus (AOA), Candidatus Nitrososphaera (AOA), and Nitrospira (nitrite-oxidizing bacteria/comammox), while penicillic acid reduced archaeal amoA abundance and the relative abundance of Nitrosospira (AOB) and the microbes listed above. Penicillic acid also strongly inhibited denitrification (33%) and N2O emissions (61%) at the peak of N2O production (day 4 of anaerobic incubation) via decreasing nitrate reductase gene (narG) abundance and increasing N2O reductase gene (nosZ) abundance, respectively. Furthermore, the environmental risks of QSIs to microbial community structure and network stability, CO2 emissions, and soil animals were acceptable. Overall, QSIs have application potential in agriculture to reduce soil N losses and the associated effect on climate change. This study established a new method to mitigate N losses from the perspective of QS, and can serve as important basis of decreasing the environmental risks of agricultural non-point source pollution.

Fe(II) Oxidation Shaped Functional Genes and Bacteria Involved in Denitrification and Dissimilatory Nitrate Reduction to Ammonium from Different Paddy Soils.

Microbial nitrate reduction can drive Fe(II) oxidation in anoxic environments, affecting the nitrous oxide emission and ammonium availability. The nitrate-reducing Fe(II) oxidation usually causes severe cell encrustation via chemodenitrification and potentially inhibits bacterial activity due to the blocking effect of secondary minerals. However, it remains unclear how Fe(II) oxidation and subsequent cell encrustation affect the functional genes and bacteria for denitrification and dissimilatory nitrate reduction to ammonium (DNRA). Here, bacteria were enriched from different paddy soils with and without Fe(II) under nitrate-reducing conditions. Fe(II) addition decelerated nitrate reduction and increased NO2- accumulation, due to the rapid Fe(II) oxidation and cell encrustation in the periplasm and on the cell surface. The N2O accumulation was lower in the treatment with Fe(II) and nitrate than that in the treatment with nitrate only, although the proportions of N2O and NH4+ to the reduced NO3- were low (3.25% ∼ 6.51%) at the end of incubation regardless of Fe(II) addition. The dominant bacteria varied from soils under nitrate-reducing conditions, while Fe(II) addition shaped a similar microbial community, including Dechloromonas, Azospira, and Pseudomonas. Fe(II) addition increased the relative abundance of napAB, nirS, norBC, nosZ, and nirBD genes but decreased that of narG and nrfA, suggesting that Fe(II) oxidation favored denitrification in the periplasm and NO2--to-NH4+ reduction in the cytoplasm. Dechloromonas dominated the NO2--to-N2O reduction, while Thauera mediated the periplasmic nitrate reduction and cytoplasmic NO2--to-NH4+ during Fe(II) oxidation. However, Thauera showed much lower abundance than the dominant genera, resulting in slow nitrate reduction and limited NH4+ production. These findings provide new insights into the response of denitrification and DNRA bacteria to Fe(II) oxidation and cell encrustation in anoxic environments.

Drought-induced tree mortality in Scots pine mesocosms promotes changes in soil microbial communities and trophic groups

Increased tree mortality related to water limitation is documented for various species at different sites globally. Nevertheless, our understanding of tree mortality effects on soil microbial communities remains scarce. Therefore, we conducted a mesocosm experiment with young Scots pine saplings and natural forest soil with differing drought legacies to follow changes in soil microbial communities during tree mortality. Scots pine saplings were completely deprived of water during the experiment until they died. Shifts in soil microbial communities during tree mortality were assessed by metabarcoding in parallel with measurements of tree vitality and physicochemical soil properties. Drought history influenced the rate at which trees died, although high individual differences were observed. Tree death was accompanied by reduced stomatal conductance, discoloring of needles, increased defoliation, and shrinkage of the stem diameter. Soil NO3− concentrations increased after tree death, potentially through diminished plant uptake and increased microbial nitrification. Microbial abundance and community composition were affected by tree death and drought legacy. Copiotrophic bacterial taxa decreased during tree mortality, while oligotrophic taxa increased, probably slowing down soil carbon turnover. Fungal saprotrophs decreased, while symbiotrophs, such as ectomycorrhizal (ECM) fungi, increased in abundance, potentially through facultative saprothrophy and as a survival strategy of the trees in the initial phase of dying. Overall, our results indicate that drought-induced tree mortality promotes changes in soil prokaryotic and fungal communities, potentially affecting soil processes in forest ecosystems.

Isotopic Evidence for Microbial Nitrogen Cycling in a Glacier Interior of High-Mountain Asia.

Glaciers are now acknowledged as an important biome globally, but biological processes in the interior of the glacier (englacial) are thought to be slow and to play only a minor role in biogeochemical cycles. In this study, we demonstrate extensive, microbially driven englacial nitrogen cycling in an Asian glacier using the stable isotopes (δ15N, δ18O, and Δ17O values) of nitrate. Apparent decreases in Δ17O values of nitrate in an 8 m shallow firn core from the accumulation area indicate that nitrifiers gradually replaced ∼80% of atmospheric nitrate with nitrate from microbial nitrification on a decadal scale. Nitrate concentrations did not increase with depth in this core, suggesting the presence of nitrate sinks by microbial assimilation and denitrification within the firn layers. The estimated englacial metabolic rate using isotopic mass balance was classified as growth metabolism, which is approximately 2 orders of magnitude more active than previously known cold-environment metabolisms. In a 56 m ice core from the interior of the ablation area, we found less nitrification but continued microbial nitrate consumption, implying that organic matter is microbially accumulated over centuries before appearing on the ablating surface. Such englacial microbial products may support supraglacial microbes, potentially promoting glacial darkening and melting. With predicted global warming and higher nitrogen loads, englacial nutrient cycling and its roles may become increasingly important in the future.

Drug discovery-based approach identifies new nitrification inhibitors

Nitrogen (N) fertilization is crucial to sustain global food security, but fertilizer N production is energy-demanding and subsequent environmental N losses contribute to biodiversity loss and climate change. N losses can be mitigated be interfering with microbial nitrification, and therefore the use of nitrification inhibitors in enhanced efficiency fertilizers (EEFs) is an important N management strategy to increase N use efficiency and reduce N pollution. However, currently applied nitrification inhibitors have limitations and do not target all nitrifying microorganisms. Here, to identify broad-spectrum nitrification inhibitors, we adopted a drug discovery-based approach and screened 45,400 small molecules on different groups of nitrifying microorganisms. Although a high number of potential nitrification inhibitors were identified, none of them targeted all nitrifier groups. Moreover, a high number of new nitrification inhibitors were shown to be highly effective in culture but did not reduce ammonia consumption in soil. One archaea-targeting inhibitor was not only effective in soil, but even reduced - when co-applied with a bacteria-targeting inhibitor - ammonium consumption and greenhouse gas emissions beyond what is achieved with currently applied nitrification inhibitors. This advocates for combining different types of nitrification inhibitors in EEFs to optimize N management practices and make agriculture more sustainable.