Inorganic Nitrogen Species Research Articles

Environmental signatures and fish proteomics: a multidisciplinary study to identify the major stressors in estuaries located in French agricultural watersheds

Watersheds and estuaries are impacted by multiple anthropogenic stressors that affect their biodiversity and functioning. Assessing their ecological quality has consequently remained challenging for scientists and stakeholders. In this paper, we propose a multidisciplinary approach to identify the stressors in seven small French estuaries located in agricultural watersheds. We collected data from landscape (geography, hydrobiology) to estuary (pollutant chemistry) and fish individual scales (environmental signatures, proteomics). This integrative approach focused on the whole hydrosystems, from river basins to estuaries. To characterize each watershed, we attempted to determine the land use considering geographic indicators (agricultural and urbanised surfaces) and landscape patterns (hedges density and riparian vegetation). Juveniles of European flounder (Platichthys flesus) were captured in September, after an average residence of five summer months in the estuary. Analyses of water, sediments and biota allowed to determine the concentrations of dissolved inorganic nitrogen species, pesticides and trace elements in the systems. Environmental signatures were also measured in flounder tissues. These environmental parameters were used to establish a typology of the watersheds. Furthermore, data from proteomics on fish liver were combined with environmental signatures to determine the responses of fish to stressors in their environments. Differential protein abundances highlighted a dysregulation related to the detoxification of xenobiotics (mainly pesticides) in agricultural watersheds, characterized by intensive cereal and vegetable crops and high livestock. Omics also revealed a dysregulation of proteins associated with the response to hypoxia and heat stress in some estuaries. Furthermore, we highlighted a dysregulation of proteins involved in urea cycle, immunity and metabolism of fatty acids in several systems. Finally, the combination of environmental and molecular signatures appears to be a relevant method to identify the major stressors operating within hydrosystems.

Electrochemical treatment of simulated wastewater containing nitroaromatic compound with cobalt–titanium electrode

The Co3O4–Ti electrodes were successfully prepared via calcination method to degrade nitrogen-containing (TNP) simulate wastewater in this reaserch. SEM and EDS were employed to analyze the morphology and element composition on Co3O4–Ti electrode, revealing the successful load of cobalt element. Then the electrochemical performance was evaluated by CV and indicated a better redox performance of electrode. Furthermore, five factors as processing time (A), electrolyte concentration (B), pH (C), initial concentration of TNP (D), and current density (E) were systematic studied in electrical treatment process. The removal rate of TN could be 77%. After the optimization work by RSM, the removal rate of TN raised up to 81% with the condition as: A of 180 min, B of 0.05 M, C of 3, D of 400 mg L−1, and E of 20 mA cm−2. The sequence of significants is: C > D > A > E > B. Mechanism analysis revealed that the entire process could be divided into two stages. In the first stage, organic nitrogen compounds were converted into inorganic nitrogen species, such as NO3–N. The oxidation and reduction would react owing to the generating of ·OH at second stage in order to turn the NO3–N into NO2–N, NH4–N or N2. The activation of ·OH on the surface of Co3O4–Ti electrode possesses the exothermic nature with transition theory. The energy calculation of 1.168 eV indicated these reactions could occur spontaneously.

Shifts in the nitrogen cycle under different fertilizer management practices

Human population is dependent on agricultural production, but these activities pose multiple threats to soil health and indirectly to ecological sustainability. Synthesis of fertilizers proved to be a miraculous solution to enhance soil productivity, but this advancement came with many unseen risks. Long-term research stations that have decades long experiments with fertilizers additions are paramount in better understanding long-term impact of fertilizer use. Our study focused on ammonium and nitrate levels found in soils in an experiment of inorganic nitrogen addition than began in 1975. We further directed our attention to soil mineralization potential, nitrate reductase activities and densities of two major microbial functional groups: ammonifiers and denitrifiers. Our data suggests that ammonium has a stronger tendency of soil buildup than nitrate and that increased levels of inorganic nitrogen species also impacted molecular compartments and processes such as mineralization potential, soil microbiota and enzymatic activities. Another result indicates that analysed soils reached a storage limit for phosphorus which threatens to overburden other ecosystems.

Biodegradability and bioavailability of dissolved substances in aquaculture effluent: Performance of indigenous bacteria, cyanobacteria, and green microalgae

Aquaculture is a controlled aquatic farming sector and one of the most important human food sources. Fish farming is one of the predominant, fast-growing sectors that supply seafood products worldwide. Along with its benefits, aquaculture practices can discharge large quantities of nutrients into the environment through non-treated or poorly treated wastewater. This study aims to understand the nutrient composition of fish wastewater and the use of indigenous bacteria, cyanobacteria, and microalgae as an alternative biological treatment method. Wastewater samples from a local fish farming facility were collected and treated using six different species of cyanobacteria and microalgae include Chroococcus minutus, Porphyridium cruentum, Chlorella vulgaris, Microcystis aeruginosa, Chlamydomonas reinhardtii, and Fischerella muscicola. All the samples were incubated for 21 days, and the following parameters were measured weekly: Chemical oxygen demand (COD), phosphate, total dissolved nitrogen, and dissolved inorganic nitrogen. In addition, dissolved organic nitrogen (DON), bioavailable DON (ABDON), and biodegradable DON (BDON) were calculated from the mass-balance equations. Colorimetric and digestive methods were used for the parameter measurements. The results showed that C. reinhardtii reduced the soluble COD concentration by 74.6 %, DON by 94.3 %, and phosphorous by more than 99 %. Moreover, M. aeruginosa, and C. minutus significantly reduced inorganic nitrogen species (>99 %). This alternative fish wastewater treatment method was explored to gain insight into fish wastewater nutrient composition and to create a sustainable alternative to conventional fish wastewater treatment methods.

Enhancing characterization of organic nitrogen components in aerosols and droplets using high-resolution aerosol mass spectrometry

Abstract. This study aims to enhance the understanding and application of the Aerodyne high-resolution aerosol mass spectrometer (HR-AMS) for the comprehensive characterization of organic nitrogen (ON) compounds in aerosol particles and atmospheric droplets. To achieve this goal, we analyzed 75 N-containing organic compounds, representing a diverse range of ambient non-organonitrate ON (NOON) types, including amines, amides, amino acids, N heterocycles, protein, and humic acids. Our results show that NOON compounds can produce significant levels of NHx+ and NOx+ ion fragments, which are typically recognized as ions representative of inorganic nitrogen species. We also identified the presence of CH2N+ at m/z = 28.0187, an ion fragment rarely quantified in ambient datasets due to substantial interference from N2+. As a result, the utilization of an updated calibration factor of 0.79 is necessary for accurate NOON quantification via the HR-AMS. We also assessed the relative ionization efficiencies (RIEs) for various NOON species and found that the average RIE for NOON compounds (1.52 ± 0.58) aligns with the commonly used default value of 1.40 for organic aerosol. Moreover, through a careful examination of the HR-AMS mass spectral features of various NOON types, we propose fingerprint ion series that can aid the NOON speciation analysis. For instance, the presence of CnH2n+2N+ ions is closely linked with amines, with CH4N+ indicating primary amines, C2H6N+ suggesting secondary amines, and C3H8N+ representing tertiary amines. CnH2nNO+ ions (especially for n values of 1–4) are very likely derived from amides. The co-existence of three ions, C2H4NO2+, C2H3NO+, and CH4NO+, serves as an indicator for the presence of amino acids. Additionally, the presence of CxHyN2+ ions indicates the occurrence of 2N-heterocyclic compounds. Notably, an elevated abundance of NH4+ is a distinct signature for amines and amino acids, as inorganic ammonium salts produce only negligible amounts of NH4+ in the HR-AMS. Finally, we quantified the NOON contents in submicron particles (PM1) and fog water in Fresno, California, and PM1 in New York City (NYC). Our results revealed the substantial presence of amino compounds in both Fresno and NYC aerosols, whereas concurrently collected fog water in Fresno contained a broader range of NOON species, including N-containing aromatic heterocycle (e.g., imidazoles) and amides. These findings highlight the significant potential of employing the widespread HR-AMS measurements of ambient aerosols and droplets to enhance our understanding of the sources, transformation processes, and environmental impacts associated with NOON compounds in the atmosphere.

Microfluidic paper-based analytical device for the speciation of inorganic nitrogen species

A microfluidic paper-based analytical device (μPAD) utilizing gas-diffusion separation and solid-phase reduction was developed for the first time for the determination of both ammonium and nitrate, which are the dominant inorganic nitrogen species in environmental waters. The device consists of 3 filter paper layers accommodating the sample, reagent and detection zones. The reagent zone is separated from the detection zone by a semipermeable hydrophobic membrane and acts as a solid-phase reactor where nitrate is reduced to ammonia by Devarda's alloy microparticles, integrated into a μPAD for the first time. The detection zone incorporates the acid-base indicators bromothymol blue (BTB) or nitrazine yellow (NY) and changes colour in two steps. Initially the colour change is caused by ammonia generated by the reaction of ammonium and sodium hydroxide in the sample zone. This colour change is followed by a subsequent colour change as a result of the ammonia produced by the reduction of nitrate by the Devarda's alloy microparticles. The corresponding reflectance value changes are used for the quantification of the two inorganic nitrogen species in the ranges 6.5–100.0 or 2.1–15.0 mg N L−1 for ammonium and 18.2–100.0 or 4.2–15.0 mg N L−1 for nitrate when BTB or NY are used, respectively. Under optimal conditions the limits of quantification of ammonium and nitrate in the case of BTB were determined as 6.5 and 18.2 mg N L−1, respectively, while the corresponding values in the case of NY were found to be 2.1 and 4.2 mg N L−1. The newly developed μPAD was stable for 62 days when stored in a freezer and 1 day at ambient temperature. It was validated with a certified reference material and successfully applied to the determination of ammonium and nitrate in spiked environmental water samples and soil extracts.

Advances in Understanding the Marine Nitrogen Cycle in the GEOTRACES Era

Because nitrogen availability limits primary production over much of the global ocean, understanding the controls on the marine nitrogen inventory and supply to the surface ocean is essential for understanding biological productivity and exchange of greenhouse gases with the atmosphere. Quantifying the ocean’s inputs, outputs, and internal cycling of nitrogen requires a variety of tools and approaches, including measurements of the nitrogen isotope ratio in organic and inorganic nitrogen species. The marine nitrogen cycle, which shapes nitrogen availability and speciation in the ocean, is linked to the elemental cycles of carbon, phosphorus, and trace elements. For example, the majority of nitrogen cycle oxidation and reduction reactions are mediated by enzymes that require trace metals for catalysis. Recent observations made through global-scale programs such as GEOTRACES have greatly expanded our knowledge of the marine nitrogen cycle. Though much work remains to be done, here we outline key advances in understanding the marine nitrogen cycle that have been achieved through these analyses, such as the distributions and rates of dinitrogen fixation, terrestrial nitrogen inputs, and nitrogen loss processes.

Factors regulating interaction among inorganic nitrogen and phosphorus species, plant uptake, and relevant cycling genes in a weakly alkaline soil treated with biochar and inorganic fertilizer

To highlight how biochar affects the interaction between inorganic nitrogen species (ammonium nitrogen, nitrate nitrogen, and nitrite nitrogen: NH4+-N, NO3¯-N, and NO2¯-N) and phosphorus species (calcium phosphate, iron phosphate, and aluminum phosphate: CaP, FeP and AlP) in soil and plant uptake of these nutrients, walnut shell (WS)- and corn cob (CC)-derived biochars (0.5 %, 1 %, 2 %, and 4 %, w/w) were added to a weakly alkaline soil, and then Chinese cabbages were planted. The results showed that the changes in soil inorganic nitrogen were related to biochar feedstock, pyrolysis temperature, and application rate. For soil under the active nitrification condition (dominant NO3¯-N), a significant decrease in the NH4+-N/NO3¯-N ratio after biochar addition indicates enhanced nitrification (excluding WS-derived biochars at 2 % and 4 %), which can be explained by the most positive response of ammonia-oxidizing archaeal amoA to biochar addition. The CC-derived biochar more effectively enhanced soil nitrification than WS-derived biochar did. The addition of 4 % of biochars significantly increased soil inorganic phosphorus, and the addition of CC-derived biochars more effectively increased Ca2P than WS-derived biochars. Biochars significantly decreased plant uptake of phosphorus, while generally had little influence on plant uptake of nitrogen. Interestingly, NO2¯-N in soil significantly positively correlated with total phosphorus in both soil and plant, and significantly negatively correlated with phoC, indicating that a certain degree of NO2¯-N accumulation in soil slightly facilitated plant uptake of phosphorus but inhibited phoC-harboring bacteria. The NO3¯-N in soil significantly positively correlated with Ca2P and Ca8P, while the NH4+-N/NO3¯-N ratio significantly negatively correlated with Ca10P and FeP, indicating that the enhanced nitrification seemed to facilitate the change in phosphorus to readly available ones. This study will help determine how to scientifically and rationally use biochar to regulate inorganic nitrogen and phosphorus species in soil and plant uptake of these nutrients.

Ammonium changes the pathway of tetrabromobisphenol S degradation by sulfate radical oxidation

Sulfate radical (SO4•-)-based advanced oxidation processes (SR-AOPs) show great potential in the elimination of organic pollutants in wastewater treatment and groundwater remediation. Tetrabromobisphenol S (TBBPS) as an emerging contaminant can be effectively degraded in SR-AOPs. However, the present study found that SO4•- also reacted with ammonium (NH4+), a ubiquitous inorganic nitrogen species in aquatic environments, thus markedly affected the rates and pathways of TBBPS degradation in SR-AOPs. TBBPS underwent β-scission and debromination upon SO4•- attack, leading to various transformation products. The released bromide (Br-) underwent further oxidation by SO4•- to form free bromine which reacted with certain TBBPS intermediates, generating disinfection byproducts (DBPs). When NH4+ was present in such system, the abatement of TBBPS was apparently suppressed. Meanwhile, NH4+ was oxidized by SO4•- to nitrogen dioxide radical (NO2•) which coupled with certain radical intermediates of TBBPS oxidation, yielding nitrophenolic products including 2,6-dibromo-4-nitrophenol (DBNP) and mono-nitro substituted TBBPS. When 10 μM TBBPS was treated by heat activated peroxydisulfate with 1 mM NH4+, the molar yield of DBNP reached 22% in 2 h. More importantly, NH4+ scavenged the in situ formed free bromine to form monobromamine (NH2Br), decreasing regulated DBPs formation but leading to highly toxic dibromoacetonitrile (DBAN). This study broadens the understanding of interactions between the transformation of halogens and NH4+ during SO4•- oxidation. It also reveals the potential environmental risks when SR-AOPs are employed for the organohalogen pollutants degradation in realistic environments where NH4+ is present.

Interconversion and Removal of Inorganic Nitrogen Compounds via UV Irradiation

Dissolved inorganic nitrogen (DIN) species are key components of the nitrogen cycle and are the main nitrogen pollutants in groundwater. This study investigated the interconversion and removal of the principal DIN compounds (NO3−, NO2− and NH4+) via UV light irradiation using a medium-pressure mercury lamp. The experiments were carried out systematically at relatively low nitrogen concentrations (1.5 mM) at varying pHs in the presence and absence of oxygen to compare the reaction rates and suggest the reaction mechanisms. NO3− was fully converted into NO2− at a pH > 3 in both oxic and anoxic conditions, and the reaction was faster when the pH was increased following a first-order kinetic at pH 11 (k = 0.12 min−1, R2 = 0.9995). NO2− was partially converted into NO3− only at pH 3 and in the presence of oxygen and was stable at an alkaline pH. This interconversion of NO3− and NO2− did not yield nitrogen loss in the solution. The addition of formic acid as an electron donor led to the reduction of NO3− to NH4+. Conversely, NH4+ was converted into NO2−, NO3− and to an unidentified subproduct in the presence of O2 at pH 10. Finally, it was demonstrated that NO2− and NH4+ react via UV irradiation with stoichiometry 1:1 at pH 10 with the total loss of nitrogen in the solution. With these results, a strategy to remove DIN compounds via UV irradiation was proposed with the eventual use of solar light.

Trends of inorganic sulfur and nitrogen species at an urban site in western Canada (2004–2018)

A 15-year (2004–2018) record of measurement data of gaseous and particulate sulfur and nitrogen pollutants in air collected at an urban site in Burnaby in western Canada was analyzed for generating their decadal trends using three different methods, including linear regression, Mann-Kendall test and Theil-Sen trend estimator (MK-TS), and ensemble empirical mode decomposition (EEMD). Annual mean concentration of SO2 and SO42− decreased by about 59% and 42%, respectively, during the 15-year period. The slower decreases of SO42− than SO2 were mainly caused by the increased O3 concentration and temperature in spring and summer, which promoted conversion of SO2 to SO42− through gas-phase reaction, and by the increased aerosol pH value and availability of H2O2 in winter, which enhanced aqueous-phase SO42− formation. Accordingly, the sulfur oxidation ratio (SOR) increased by 23% or more in spring, summer, and winter during the 15-year period. Annual mean concentrations of NO2 and NO3− declined by 36% and 38%, respectively, during this period. On seasonal basis, NO3− decreased faster than NO2 in autumn and slower in winter. The non-linear responses of NO3− to NO2 concentration decreases were more evident in winter than the other seasons, partly due to the increased particulate NO3− fraction caused by decreased temperature, increased aerosol pH value, and enhanced NO3− formation caused by increased O3 concentrations. Annual mean concentration of NH3 showed small increases due to stable NH3 emission and reduced conversion of NH3 to NH4+. NH4+ concentration decreased by 51% during the 15-year period. These results suggest that reduced oxidants levels are likely responsible for weakened formation of secondary inorganic aerosols, besides emission reductions for SO2 and NO2.

Formation pathways and source apportionments of inorganic nitrogen-containing aerosols in urban environment: Insights from nitrogen and oxygen isotopic compositions in Guangzhou, China

Air quality issues caused by PM2.5-induced persistent extreme haze episodes have become increasingly serious in urban environments in recent years. Secondary water-soluble inorganic sulfate (SO42−), nitrate (NO3−) and ammonium (NH4+) ions are the major components of PM2.5. However, the contributions of inorganic nitrogen species, especially nitrate, to PM2.5 have greatly increased during haze episodes in many cities in China. Therefore, better understanding of their emission sources and formation pathways holds the key to controlling urban PM2.5 pollution more efficiently and effectively. In this study, water-soluble ionic characteristics and isotopic compositions and sources of NH4+ and NO3−, as well as NO3− formation pathways were determined in PM2.5 aerosol samples collected in Guangzhou, China, during 2015–2018. The PM2.5 concentrations varied from 30.5 to 189.8 μg⋅m−3 and their mean values were highest in spring (111.1 μg⋅m−3) and lowest in summer (63.5 μg⋅m−3). The δ15N–NH4+ and δ15N–NO3- values ranged from +4.5 to +20.2‰ and from +4.8 to +14.8‰, respectively, with their mean values being highest in winter (14.0‰ and 9.5‰, respectively) and lowest in summer (10.4‰ and 7.1‰, respectively). The seasonal δ15N variability was mainly attributed to isotopic equilibrium fractionation, and partly due to the changes in NH3 and NOx sources. The average δ18O–NO3- value of 63.0‰, ranging seasonally from +58.6‰ in summer to +68.0‰ in spring, suggests that NO2 +⋅OH pathway played a vital role (70.3–85.9%) in NO3− formation. The Bayesian isotope mixing model results revealed fossil fuel combustion sources as dominant sources of atmospheric NH3 and NOx. This study suggests that more effort should be devoted to reduce NH3 and NOx from combustion-related processes and highlights the importance of δ18O–NO3- analysis for exploring variations of nitrate formation pathways in urban atmospheres.

Electrochemical treatment of aquaculture wastewater effluent and optimization of the parameters using response surface methodology

The electrocoagulation (EC) and electrooxidation (EO) processes are employed widely as treatment processes for industrial, agricultural, and domestic wastewater. In the present study, EC, EO, and a combination of EC + EO were evaluated as methods of removing pollutants from shrimp aquaculture wastewater. Process parameters for electrochemical processes, including current density, pH, and operation time were studied, and response surface methodology was employed to determine the optimum condition for the treatment. The effectiveness of the combined EC + EO process was assessed by measuring the reduction of targeted pollutants, including dissolved inorganic nitrogen species, total dissolved nitrogen (TDN), phosphate, and soluble chemical oxygen demand (sCOD). Using EC + EO process, more than 87% reduction was achieved for inorganic nitrogen, TDN, and phosphate, while 76.2% reduction was achieved for sCOD. These results demonstrated that the combined EC + EO process provided better treatment performance in removing the pollutants from shrimp wastewater. The kinetic results suggested that the effects of pH, current density, and operation time were significant on the degradation process when using iron and aluminum electrodes. Comparatively, iron electrodes were effective at reducing the half-life (t1/2) of each of the pollutants in the samples. The application of the optimized process parameters on shrimp wastewater could be used for large-scale treatment in aquaculture.

Aerobic bacteria produce nitric oxide via denitrification and promote algal population collapse

Microbial interactions govern marine biogeochemistry. These interactions are generally considered to rely on exchange of organic molecules. Here we report on a novel inorganic route of microbial communication, showing that algal-bacterial interactions between Phaeobacter inhibens bacteria and Gephyrocapsa huxleyi algae are mediated through inorganic nitrogen exchange. Under oxygen-rich conditions, aerobic bacteria reduce algal-secreted nitrite to nitric oxide (NO) through denitrification, a well-studied anaerobic respiratory mechanism. The bacterial NO is involved in triggering a cascade in algae akin to programmed cell death. During death, algae further generate NO, thereby propagating the signal in the algal population. Eventually, the algal population collapses, similar to the sudden demise of oceanic algal blooms. Our study suggests that the exchange of inorganic nitrogen species in oxygenated environments is a potentially significant route of microbial communication within and across kingdoms.

Pilot-scale demonstration of dissolved organic nitrogen removal from an advanced water reclamation facility using enhanced coagulation

Most wastewater treatment facilities that satisfy stricter discharge restrictions for nutrients, remove dissolved inorganic nitrogen (DIN) species efficiently, leaving dissolved organic nitrogen (DON) to be present at a higher proportion (up to 85 %) of total nitrogen (TN) in the effluent. Discharged DON promotes algae growth in receiving water bodies and is a growing concern in effluent potable reuse applications considering its potential to form hazardous nitrogenous disinfection byproducts (N-DBPs). Enhanced coagulation is an established process in the advanced water treatment train for most potable reuse applications. However, so far, no information has been collected at the pilot scale to address DON removal efficiency and process implications by enhanced coagulation under real conditions. This study performed a comprehensive evaluation of DON removal from the effluent of the Truckee Meadows Water Reclamation Facility (TMWRF) by enhanced coagulation over the course of 11 months at the pilot scale. Three different coagulants (aluminum sulfate (alum), poly‑aluminum chloride (PACl), ferric chloride (FC)) and a cationic polymer coagulant aid (Clarifloc) were used. Optimum doses for each coagulant and polymer and ideal pH were determined by jar tests and applied at the pilot. Alum (24 mg/L) resulted in highly variable DON removal (6 % – 40 %, 21 % on average), which was enhanced by the addition of polymer, leading to 32 % DON removal on average. PACl (40 mg/L) and FC (100 mg/L) resulted in more consistent DON removal (on average 45 % and 57 %, respectively); however, polymer addition exerted minimal enhancement for these coagulants. Overall, enhanced coagulation effectively reduced DON in the tertiary effluent at the pilot scale. The treatment showed auxiliary benefits, including dissolved organic carbon (DOC) and orthophosphate removal.

Plant-Pathogenic Ralstonia Phylotypes Evolved Divergent Respiratory Strategies and Behaviors To Thrive in Xylem.

Bacterial pathogens in the Ralstonia solanacearum species complex (RSSC) infect the water-transporting xylem vessels of plants, causing bacterial wilt disease. Strains in RSSC phylotypes I and III can reduce nitrate to dinitrogen via complete denitrification. The four-step denitrification pathway enables bacteria to use inorganic nitrogen species as terminal electron acceptors, supporting their growth in oxygen-limited environments such as biofilms or plant xylem. Reduction of nitrate, nitrite, and nitric oxide all contribute to the virulence of a model phylotype I strain. However, little is known about the physiological role of the last denitrification step, the reduction of nitrous oxide to dinitrogen by NosZ. We found that phylotypes I and III need NosZ for full virulence. However, strains in phylotypes II and IV are highly virulent despite lacking NosZ. The ability to respire by reducing nitrate to nitrous oxide does not greatly enhance the growth of phylotype II and IV strains. These partial denitrifying strains reach high cell densities during plant infection and cause typical wilt disease. However, unlike phylotype I and III strains, partial denitrifiers cannot grow well under anaerobic conditions or form thick biofilms in culture or in tomato xylem vessels. Furthermore, aerotaxis assays show that strains from different phylotypes have different oxygen and nitrate preferences. Together, these results indicate that the RSSC contains two subgroups that occupy the same habitat but have evolved divergent energy metabolism strategies to exploit distinct metabolic niches in the xylem. IMPORTANCE Plant-pathogenic Ralstonia spp. are a heterogeneous globally distributed group of bacteria that colonize plant xylem vessels. Ralstonia cells multiply rapidly in plants and obstruct water transport, causing fatal wilting and serious economic losses of many key food security crops. The virulence of these pathogens depends on their ability to grow to high cell densities in the low-oxygen xylem environment. Plant-pathogenic Ralstonia can use denitrifying respiration to generate ATP. The last denitrification step, nitrous oxide reduction by NosZ, contributes to energy production and virulence for only one of the three phytopathogenic Ralstonia species. These complete denitrifiers form thicker biofilms in culture and in tomato xylem, suggesting they are better adapted to hypoxic niches. Strains with partial denitrification physiology form less biofilm and are more often planktonic. They are nonetheless highly virulent. Thus, these closely related bacteria have adapted their core metabolic functions to exploit distinct microniches in the same habitat.

Peering down the sink: A review of isoprene metabolism by bacteria.

Isoprene (2-methyl-1,3-butadiene) is emitted to the atmosphere each year in sufficient quantities to rival methane (>500 Tg C yr-1 ), primarily due to emission by trees and other plants. Chemical reactions of isoprene with other atmospheric compounds, such as hydroxyl radicals and inorganic nitrogen species (NOx ), have implications for global warming and local air quality, respectively. For many years, it has been estimated that soil-dwelling bacteria consume a significant amount of isoprene (~20 Tg C yr-1 ), but the mechanisms underlying the biological sink for isoprene have been poorly understood. Studies have indicated or confirmed the ability of diverse bacterial genera to degrade isoprene, whether by the canonical iso-type isoprene degradation pathway or through other less well-characterized mechanisms. Here, we review current knowledge of isoprene metabolism and highlight key areas for further research. In particular, examples of isoprene-degraders that do not utilize the isoprene monooxygenase have been identified in recent years. This has fascinating implications both for the mechanism of isoprene uptake by bacteria, and also for the ecology of isoprene-degraders in the environments.

Reactions of main group compounds with azides forming organic nitrogen-containing species.

Since the seminal discovery of phenyl azide by Grieß in 1864, a variety of organic azides (R-N3) have been developed and extensively studied. The amenability of azides to a number of reactions has expanded their utility as building blocks not only in organic synthesis but also in bioorthogonal chemistry and materials science. Over the decades, it has been demonstrated that the reactions of main group compounds with azides lead to diverse N-containing main group molecules. In view of the pronounced progress in this area, this review summarizes the reactions of main group compounds with azides, emphatically introducing their reaction patterns and mechanisms. The reactions of forming inorganic nitrogen species are not included in this review.

Biosolids amendment effects on nitrogen cycling gene expression by the soil prokaryotic community as revealed by metatranscriptomic analysis

Context Large quantities of treated sewage sludge (biosolids) are produced and beneficially applied to agricultural fields to improve soil fertility in many countries. Biosolids have extremely high concentrations of ammonium and organic matter that can be beneficial but also detrimental to the environment by promoting microbially-mediated reactions that contribute to eutrophication and greenhouse gas emission. Aims The hypothesis of the study was that high concentrations of ammonium and labile organic matter in biosolids would significantly affect nitrogen transformations and nitrogen-cycling gene expression by different members of the prokaryotic community in a biosolids-amended agricultural soil. Methods An organically-managed agricultural soil was amended with biosolids and monitored for changes in carbon dioxide and inorganic nitrogen species for 3 weeks under laboratory conditions. Then, RNA was extracted and compared for nitrogen-cycling gene expression levels in biosolids-amended and unamended soil. Key results Biosolids amendment significantly increased ammonium concentration and decreased oxygen and nitrate concentrations in soil zones near biosolid particles, which coincided with significant changes in expression levels of genes for catabolic glutamate dehydrogenase, nitrification enzymes, denitrifying enzymes, and numerous other enzymes by different members of the prokaryotic community. Conclusions The application of biosolids to soil set in motion a dynamic organic nitrogen mineralisation–nitrification–denitrification cycle between the anaerobic biosolids zone and aerobic soil zone. Implications Biosolids-induced changes in nitrogen transformations by different members of the microbial community have implications on nitrogen availability/toxicity to nitrifying populations and plants, ammonium and nitrate in surface runoff, and nitrous oxide greenhouse gas emission from biosolids-amended soil.

Coincident Biogenic Nitrite and pH Maxima Arise in the Upper Anoxic Layer in the Eastern Tropical North Pacific

AbstractThe Eastern Tropical North Pacific (ETNP), like the other marine oxygen deficient zones (ODZs), is characterized by an anoxic water column, nitrite accumulation at the anoxic core, and fixed nitrogen loss via nitrite reduction to N2O and N2 gases. Here, we constrain the relative contribution of biogeochemical processes to observable features such as the secondary nitrite maximum (SNM) and local pH maximum by simultaneous measurement of inorganic nitrogen and carbon species. High‐resolution sampling within the top 1 km of the water column reveals consistent chemical features previously unobserved in the region, including a tertiary nitrite maximum. Dissolved inorganic carbon measurements show that pH increases with depth at the top of the ODZ, peaking at the potential density of the SNM at σθ = 26.15 ± 0.06 (1 s.d.). We developed a novel method to determine the relative contributions of anaerobic ammonium oxidation (anammox), denitrification, nitrite oxidation, dissimilatory nitrate reduction to nitrite, and calcium carbonate dissolution to the nitrite cycling in the anoxic ODZ core. The calculated relative contributions of each reaction are slightly sensitive to the assumed C:N:P ratio and the carbon oxidation state of the organic matter sinking through the ODZ. Furthermore, we identify the source of the pH increase at the top of ODZ as the net consumption of protons via nitrite reduction to N2 by the denitrification process. The increase in pH due to denitrification impacts the buffering effect of calcite and aragonite dissolving in the ETNP.