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Nitrification, the stepwise oxidation of ammonia to nitrate via nitrite, is a key process in the marine nitrogen cycle. Reported nitrite oxidation rates frequently exceed ammonia oxidation rates below the euphotic zone, raising the fundamental question of whether the two steps are balanced and if alternative sources contribute to nitrite production in the dark ocean. Here we present vertically resolved profiles of ammonia, urea, and nitrite oxidation rates and their kinetic traits in the oligotrophic Subtropical North Pacific. Our results show active urea‐derived nitrogen oxidation (urea‐N oxidation) in the presence of experimental ammonium amendment, suggesting direct urea utilization. The depth‐integrated rates of urea‐N oxidation and ammonia oxidation are comparable, demonstrating that urea‐N oxidation is a significant source of nitrite. The additional nitrite from urea‐N oxidation helps to balance the two steps of nitrification in our study region. Nitrifiers exhibit high affinity for their substrates, and the apparent half‐saturation constants for ammonia and nitrite oxidation decrease with depth. The apparent half‐saturation constant for urea‐N oxidation is higher than that for ammonia oxidation and shows no clear vertical trend. Such kinetic traits may account for the relatively higher urea concentration than ammonium concentration in the ocean's interior. Moreover, a compilation of our results and reported data shows a trend of increased urea‐N oxidation relative to ammonia oxidation from the eutrophic coastal zone to the oligotrophic open ocean. This trend reveals a substrate‐dependent biogeographic distribution of urea‐N oxidation across marine environments and provides new information on the balance and flux of the marine nitrification process. Key Points: Active urea‐derived nitrogen oxidation in the presence of added ammonium suggests direct urea utilization by marine ammonia oxidizersSubstrate affinity regulates the vertical distribution of ammonia, urea, and nitrite in the ocean's interiorNitrite production from urea is comparable to that from ammonia oxidation in the energy‐starved mesopelagic ocean [ABSTRACT FROM AUTHOR]

[Display omitted] Fine-tuning the surface structure of transition metal oxides at the atomic level is a promising way to improve the catalytic properties of materials. However, the influence of crystal surface structure on electrode reaction kinetics is still limited. In this study, we propose an in-situ synthesis strategy to obtain two-dimensional carbon/cerium oxide core–shell nanosheets by thermal decomposition of Ce-MOF nanosheets grown on the surface of carbon nanostructures, and fine-tuning the surface structure by introducing oxygen vacancies through defect engineering during the oxide nucleation process is conducted to obtain controllable exposed {1 1 1} and {1 1 0} surface CeO 2 @C composites. Both experiments and theoretical calculations show that the {1 1 0} -dominated nanocomplex (CeO 2 @C-350S) has better kinetic behavior and catalytic activity due to its abundant surface defects, which is manifested in higher active surface area, richer carrier concentration, and better promotion of diffusion and adsorption. In addition, CeO 2 @C-350S electrode has an extremely wide linear range and good stability in the electrochemical detection of nitrite. After 1000 times of the accelerated cycle experiments, CeO 2 @C-350S electrode still maintains 79.3 % of its initial current response, and recovers to 87.3 % after 10 min of stopping the test. The electrode stability is excellent, which is attributed to the clever carbon shell structure of the material. This synthesis strategy can be extended to other carbon-based oxide composite catalysts to improve the electrocatalytic performance and overall stability by adjusting the surface structure. [ABSTRACT FROM AUTHOR]

Nitrite-oxidizing bacteria (NOB) are undesirable in the anaerobic ammonium oxidation (anammox)-driven nitrogen removal technologies in the modern wastewater treatment plants (WWTPs). Diverse strategies have been developed to suppress NOB based on their physiological properties that we have understood. But our knowledge of the diversity and mechanisms employed by NOB for survival in the modern WWTPs remains limited. Here, Three NOB species (NOB01–03) were recovered from the metagenomic datasets of a full-scale WWTP treating duck breeding wastewater. Among them, NOB01 and NOB02 were classified as newly identified lineage VII, tentatively named Candidatus (Ca.) Nitrospira NOB01 and Ca. Nitrospira NOB02. Analyses of genomes and in situ transcriptomes revealed that these two novel NOB were active and showed a high metabolic versatility. The transcriptional activity of Ca. Nitrospira could be detected in all tanks with quite different dissolved oxygen (DO) (0.01–5.01 mg/L), illustrating Ca. Nitrospira can survive in fluctuating DO conditions. The much lower Ca. Nitrospira abundance on the anammox bacteria-enriched sponge carrier likely originated from the intensification substrate (NO2−) competition from anammox and denitrifying bacteria. In particular, a highlight is that Ca. Nitrospira encoded and treanscribed cyanate hydratase (CynS), amine oxidase, urease (UreC), and copper-containing nitrite reductase (NirK) related to ammonium and NO production, driving NOB to interact with the co-existed AOB and anammox bacteria. Ca. Nitrospira strains NOB01 and NOB02 showed quite different niche preference in the same aerobic tank, which dominanted the NOB communities in activated sludge and biofilm, respectively. In addition to the common rTCA cycle for CO2 fixation, a reductive glycine pathway (RGP) was encoded and transcribed by NOB02 likely for CO2 fixation purpose. Additionally, a 3b group hydrogenase and respiratory nitrate reductase were uniquely encoded and transcribed by NOB02, which likely confer a survival advantage to this strain in the fluctuant activated sludge niche. The discovery of this new genus significantly broadens our understanding of the ecophysiology of NOB. Furthermore, the impressive metabolic versatility of the novel NOB revealed in this study advances our understanding of the survival strategy of NOB and provides valuable insight for suppressing NOB in the anammox-based WWTP.

ABSTRACT The Mariana Trench (MT) is the deepest part of the ocean on Earth. Previous studies have described the microbial community structures and functional potential in the seawater and surface sediment of MT. Still, the metabolic features and adaptation strategies of the microorganisms involved in nitrogen cycling processes are poorly understood. In this study, comparative metagenomic approaches were used to study microbial nitrogen cycling in three MT habitats, including hadal seawater [9,600–10,500 m below sea level (mbsl)], surface sediments [0–46 cm below seafloor (cmbsf) at a water depth between 7,143 and 8,638 mbsl], and deep sediments (200–306 cmbsf at a water depth of 8,300 mbsl). We identified five new nitrite-oxidizing bacteria (NOB) lineages that had adapted to the oligotrophic MT slope sediment, via their CO2 fixation capability through the reductive tricarboxylic acid (rTCA) or Calvin-Benson-Bassham (CBB) cycle; an anammox bacterium might perform aerobic respiration and utilize sedimentary carbohydrates for energy generation because it contains genes encoding type A cytochrome c oxidase and complete glycolysis pathway. In seawater, abundant alkane-oxidizing Ketobacter species can fix inert N2 released from other denitrifying and/or anammox bacteria. This study further expands our understanding of microbial life in the largely unexplored deepest part of the ocean.IMPORTANCEThe metabolic features and adaptation strategies of the nitrogen cycling microorganisms in the deepest part of the ocean are largely unknown. This study revealed that anammox bacteria might perform aerobic respiration in response to nutrient limitation or O2 fluctuations in the Mariana Trench sediments. Meanwhile, an abundant alkane-oxidizing Ketobacter species could fix N2 in hadal seawater. This study provides new insights into the roles of hadal microorganisms in global nitrogen biogeochemical cycles. It substantially expands our understanding of the microbial life in the largely unexplored deepest part of the ocean.

The present work describes the electrocatalytic oxidation of nitrite in the presence of a composite of coordination polymer of cobalt‐4‐pyridylporphyrin and electrochemically reduced graphene oxide. The electrode was modified by drop‐casting a suspension of graphene oxide and polymeric cobalt‐4‐pyridylporphyrin followed by reduction through cyclic voltammetry in the potential range 0.0 V to −1.5 V. The electrocatalytic investigations were carried out by voltammetric (cyclic, linear sweep, differential pulse and hydrodynamic) and by amperometric methods. The LOD and the working range obtained through different techniques are compared. The rate constant for this heterogeneous electron transfer reaction is 2.45×10−2 cms−1. [ABSTRACT FROM AUTHOR]

Fixed nitrogen limits primary productivity in most areas of the surface ocean. Nitrite oxidation is the main source of nitrate, the most abundant form of inorganic fixed nitrogen. Even though known as an aerobic process, nitrite oxidation is not always stimulated by increased oxygen concentration, and nitrite oxidation occurs in layers of oxygen minimum zones (OMZs) where oxygen is not detectable. Nitrite‐oxidizing bacteria, known since their original isolation as aerobes, were also detected in these layers. Whether and how nitrite oxidation is occurring in the anoxic seawater is debated. Here, we reassess recent advances in marine nitrite oxidation in OMZ regions using previous work and new data sets we collected in two Pacific OMZs. We analyze the complex relationship between nitrite oxidation and oxygen. We discuss potential mechanisms explaining nitrite oxidation in different layers of OMZs based on recent findings and propose future directions to resolve the controversial question of apparently anaerobic nitrite oxidation in anoxic layers. Plain Language Summary: No organism can survive without nitrogen. The scarcity of fixed nitrogen in large surface areas of the ocean limits the capacity of phytoplankton to fix carbon dioxide. Oxygen minimum zones (OMZs) are critical oceanic regions for marine nitrogen inventory because the full spectrum of oxygen conditions in OMZs allows the retention and the loss of fixed nitrogen. The anoxic layer in OMZs was thought to host only anaerobic nitrogen loss processes. However, nitrite oxidation, conventionally known as an aerobic process that retains fixed nitrogen, was also detected in the anoxic zone. We revisit the complex relationship between nitrite oxidation and oxygen, and present mechanisms explaining nitrite oxidation in different layers of the ocean. We also chart a way forward for deciphering the mystery of anaerobic nitrite oxidation. Key Points: The detection of nitrite oxidation in anoxic seawater suggests the necessity to reevaluate our understanding of the nitrogen budgetDifferent mechanisms explaining nitrite oxidation in different oceanic layers are discussedThe complex relationship between nitrite oxidation and O2 indicates the importance of rigorous O2 control during experimental manipulations [ABSTRACT FROM AUTHOR]

The genus Nitrospira represents the dominant nitrite-oxidizing clade in most wastewater treatment plants (WWTPs) globally, and several Nitrospira strains have been isolated from activated sludge. Using a pre-enrichment strategy with alternating nitrifying and denitrifying conditions, followed by incubation at elevated temperatures, we isolated a novel Nitrospira species, named Nitrospira tepida. This moderately thermophilic species with optimal growth between 37 and 45°C is only distantly related to other Nitrospira and forms a novel lineage VII within the genus, together with few environmental 16S rRNA gene sequences predominantly detected in thermal wastewater or oxygen-limited systems. Genomic and physiological analyses revealed remarkable differences between N. tepida and two other isolates previously obtained from the same WWTP, suggesting niche differentiation between these nitrite oxidizers. N. tepida grows in aggregates, and tolerates nitrite and nitrate concentrations of up to 20 mM and 40 mM, respectively. The Km value for nitrite of N. tepida is 77 ± 26 µM. In summary, this novel Nitrospira lineage seems to be well-adapted for wastewater treatment processes at elevated temperatures and limited aeration, conditions that potentially reduce operational costs of such systems. [ABSTRACT FROM AUTHOR]

The recent discovery of comammox Nitrospira, a complete ammonia oxidizer, capable of completing the nitrification on their own has presented tremendous challenges to our understanding of the nitrification process. There are two divergent clades of comammox Nitrospira, Clade A and B. However, their population abundance, community structure and role in ammonia and nitrite oxidation are poorly understood. We conducted a 94- day microcosm study using a grazed dairy pasture soil amended with urea fertilizers, synthetic cow urine, and the nitrification inhibitor, dicyandiamide (DCD), to investigate the growth and community structure of comammox Nitrospira spp. We discovered that comammox Nitrospira Clade B was two orders of magnitude more abundant than Clade A in this fertile dairy pasture soil and the most abundant subcluster was a distinctive phylogenetic uncultured subcluster Clade B2. We found that comammox Nitrospira Clade B might not play a major role in nitrite oxidation compared to the role of canonical Nitrospira nitrite-oxidizers, however, comammox Nitrospira Clade B is active in nitrification and the growth of comammox Nitrospira Clade B was inhibited by a high ammonium concentration (700 kg synthetic urine-N ha–1) and the nitrification inhibitor DCD. We concluded that comammox Nitrospira Clade B: (1) was the most abundant comammox in the dairy pasture soil; (2) had a low tolerance to ammonium and can be inhibited by DCD; and (3) was not the dominant nitrite-oxidizer in the soil. This is the first study discovering a new subcluster of comammox Nitrospira Clade B2 from an agricultural soil. [ABSTRACT FROM AUTHOR]

Nitrification rates and ammonia-oxidizer functional gene abundance were measured in the water column of Lake Lacawac, Pennsylvania, USA, a freshwater lake on a nature sanctuary that allowed an investigation with minimal human impacts. Nitrification is a 2-step process consisting of ammonia oxidation followed by nitrite oxidation. Recent studies have shown that these 2 nitrification steps may be uncoupled and respond in different ways to environmental conditions. Additionally, the relative contribution of ammonia-oxidizing archea (AOA) vs ammonia-oxidizing bacteria (AOB) to nitrification rates varies widely across aquatic systems. To determine how nitrification rates are related to environmental parameters and the ammonia-oxidizing community in a nearly pristine environment, rates and gene abundance were measured over multiple seasons where in-situ environmental conditions varied. Rates of ammonia and nitrite oxidation were measured separately and summed to calculate total nitrification rates ranging from 1 to 568 nM/d. Ammonia oxidation rates generally outpaced nitrite oxidation rates, and rates of both ammonia and nitrite oxidation were higher at depth (10 m) compared with near-surface and mid water column. Ammonia oxidation, nitrite oxidation, and total nitrification rates were all strongly, positively correlated with in-situ [NH4+] (Kendall's τ > 0.35, p < 0.02). AOB ammonia monooxygenase (amoA) gene copy numbers were generally greater than AOA amoA. However, AOB gene copy numbers were not correlated with any ammonia oxidation or total nitrification rates, whereas AOA abundance was positively correlated with both ammonia oxidation and total nitrification rates (Kendall's τ > 0.41, p < 0.01). A Bayesian generalized additive model, which accounted for sampling month, indicated that total nitrification rates were best explained by AOA and [NH4+]. Thus, substrate concentration and AOA likely play key roles in regulating rates of nitrification in this small, nearly pristine freshwater lake. These reported relationships between rates of ammonia and nitrite oxidation (and, thus, total nitrification), in-situ environmental parameters, and the ammonia-oxidizer community in a protected environment establish a reference for evaluating the impact of a changing environment on mesotrophic lake water quality. [ABSTRACT FROM AUTHOR]

Chemolitho-autotrophic microorganisms like the nitrite-oxidizing Nitrobacter winogradskyi create an environment for heterotrophic microorganisms that profit from the production of organic compounds. It was hypothesized that the assembly of a community of heterotrophic microorganisms around N. winogradskyi depends on the ecosystem from which the heterotrophs are picked. To test this hypothesis, pure cultures of N. winogradskyi were grown in continuously nitrite-fed bioreactors in a mineral medium free of added organic carbon that had been inoculated with diluted sewage sludge or with a suspension from a grassland soil. Samples for chemical and 16S rRNA gene amplicon analyses were taken after each volume change in the bioreactor. At the end of the enrichment runs, samples for shotgun metagenomics were also collected. Already after two volume changes, the transformations in community structure became less dynamic. The enrichment of heterotrophs from both sewage and soil was highly stochastic and yielded different dominant genera in most of the enrichment runs that were independent of the origin of the inoculum. Hence, the hypothesis had to be refuted. Notwithstanding the large variation in taxonomic community structure among the enrichments, the functional compositions of the communities were statistically not different between soil- and sludge-based enrichments. [ABSTRACT FROM AUTHOR]

N fertilization and straw incorporation often disturb the soil and may affect nitrite oxidation (NO); however, the underlying mechanism remains unclear. Here, we collected soil samples through a 4-year field experiment including no N fertilization, normal N application, excess N application (EN), and EN plus straw incorporation (ES) treatments. We measured the community composition, abundance, and activity of Nitrobacter-like and Nitrospira-like nitrite-oxidizing bacteria (NOB). N application and straw incorporation significantly enhanced potential NO activity (PNO). PNO was affected by the abundance of Nitrobacter but not Nitrospira and the community compositions of both NOB. With increasing N application rate, Nitrobacter abundance increased from 1.0 to 11.8 × 104 copies g−1 dry weight soil, whereas Nitrospira abundance increased initially then subsequently decreased, ranged from 2.1 to 5.2 × 106 copies g−1 dry weight soil. Moreover, N application and straw incorporation markedly affected the NOB community composition. Soil pH and organic C were the key factors shaping the NOB community composition. Overall, N fertilization combined with straw incorporation can affect NO by altering the Nitrobacter abundance and NOB community composition. These findings expand our understanding of mechanisms underlying the effects of straw incorporation on nitrification, particularly under N enrichment. [ABSTRACT FROM AUTHOR]

The Mariana Trench (MT) is the deepest part of the ocean on Earth. Previous studies have described the microbial community structures and functional potential in the seawater and surface sediment of MT. Still, the metabolic features and adaptation strategies of the microorganisms involved in nitrogen cycling processes are poorly understood. In this study, comparative metagenomic approaches were used to study microbial nitrogen cycling in three MT habitats, including hadal seawater [9,600-10,500 m below sea level (mbsl)], surface sediments [0-46 cm below seafloor (cmbsf) at a water depth between 7,143 and 8,638 mbsl], and deep sediments (200-306 cmbsf at a water depth of 8,300 mbsl). We identified five new nitrite-oxidizing bacteria (NOB) lineages that had adapted to the oligotrophic MT slope sediment, via their CO 2 fixation capability through the reductive tricarboxylic acid (rTCA) or Calvin-Benson-Bassham (CBB) cycle; an anammox bacterium might perform aerobic respiration and utilize sedimentary carbohydrates for energy generation because it contains genes encoding type A cytochrome c oxidase and complete glycolysis pathway. In seawater, abundant alkane-oxidizing Ketobacter species can fix inert N 2 released from other denitrifying and/or anammox bacteria. This study further expands our understanding of microbial life in the largely unexplored deepest part of the ocean., Importance: The metabolic features and adaptation strategies of the nitrogen cycling microorganisms in the deepest part of the ocean are largely unknown. This study revealed that anammox bacteria might perform aerobic respiration in response to nutrient limitation or O 2 fluctuations in the Mariana Trench sediments. Meanwhile, an abundant alkane-oxidizing Ketobacter species could fix N 2 in hadal seawater. This study provides new insights into the roles of hadal microorganisms in global nitrogen biogeochemical cycles. It substantially expands our understanding of the microbial life in the largely unexplored deepest part of the ocean., Competing Interests: The authors declare no conflict of interest.

Nitrite-oxidizing bacteria (NOB) are undesirable in the anaerobic ammonium oxidation (anammox)-driven nitrogen removal technologies in the modern wastewater treatment plants (WWTPs). Diverse strategies have been developed to suppress NOB based on their physiological properties that we have understood. But our knowledge of the diversity and mechanisms employed by NOB for survival in the modern WWTPs remains limited. Here, Three NOB species (NOB01-03) were recovered from the metagenomic datasets of a full-scale WWTP treating duck breeding wastewater. Among them, NOB01 and NOB02 were classified as newly identified lineage VII, tentatively named Candidatus ( Ca. ) Nitrospira NOB01 and Ca. Nitrospira NOB02. Analyses of genomes and in situ transcriptomes revealed that these two novel NOB were active and showed a high metabolic versatility. The transcriptional activity of Ca. Nitrospira could be detected in all tanks with quite different dissolved oxygen (DO) (0.01-5.01 mg/L), illustrating Ca. Nitrospira can survive in fluctuating DO conditions. The much lower Ca. Nitrospira abundance on the anammox bacteria-enriched sponge carrier likely originated from the intensification substrate (NO 2 - ) competition from anammox and denitrifying bacteria. In particular, a highlight is that Ca. Nitrospira encoded and treanscribed cyanate hydratase (CynS), amine oxidase, urease (UreC), and copper-containing nitrite reductase (NirK) related to ammonium and NO production, driving NOB to interact with the co-existed AOB and anammox bacteria. Ca. Nitrospira strains NOB01 and NOB02 showed quite different niche preference in the same aerobic tank, which dominanted the NOB communities in activated sludge and biofilm, respectively. In addition to the common rTCA cycle for CO 2 fixation, a reductive glycine pathway (RGP) was encoded and transcribed by NOB02 likely for CO 2 fixation purpose. Additionally, a 3b group hydrogenase and respiratory nitrate reductase were uniquely encoded and transcribed by NOB02, which likely confer a survival advantage to this strain in the fluctuant activated sludge niche. The discovery of this new genus significantly broadens our understanding of the ecophysiology of NOB. Furthermore, the impressive metabolic versatility of the novel NOB revealed in this study advances our understanding of the survival strategy of NOB and provides valuable insight for suppressing NOB in the anammox-based WWTP., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors. Published by Elsevier Ltd.)

Herein, electrochemical oxidation of nitrite (NO2−) is demonstrated using metal‐free and electrochemically highly stable nanoporous carbon (NC) system. The surface features of nanoporous carbon were studied using both spectroscopic and microscopic techniques including scanning electron microscope (SEM), transmission electron microscope (TEM) and is having layered mesh‐like features with a particle size of ∼20 to ∼100 nm. The as‐synthesized electrocatalyst is found to be more active towards electrooxidation of nitrite (NO2−) at considerably low onset potential of 0.58 V vs SCE with a significantly high current density of 5.2 μA/cm2 determined from linear sweep voltammetry (LSV), and cyclic voltammetry (CV) studies. The concentration and scan rate dependent studies confirm the nitrite oxidation is diffusion‐controlled process. The interfacial electron transfer features and parameters involved are determined by electrochemical impedance spectroscopic (EIS) studies. Moreover, current stability at a nitrite oxidation (0.58 V vs SCE) potential is also tested by chronoamperometric (i‐t) measurements and it demonstrates nanoporous carbon is having long term electrochemical stability. These studies establish the metal‐free nanoporous carbon as an efficient electrocatalyst for nitrite oxidation and will be good futuristic electrode material for other energy and environmental based electrochemical monitoring studies. [ABSTRACT FROM AUTHOR]

Well‐known as a hazardous compound, nitrite constitute a real threat to the public health. So, there is a pressing need to detect and quantify them in different matrix. Even though conventional analytical methods can be used to address this issue, electrochemistry allows a fast, sensitive, and efficient analysis. Conducting polymers continue to raise great interest among scientific communities due to their properties. Moreover, their combination with carbon nanomaterials, or metallic nanoparticles improves their properties, and provides great results. In this paper, we will focus on some revealing works devoted to the electrochemical detection of nitrite using this kind of materials. [ABSTRACT FROM AUTHOR]

As the world's largest marginal sea, biogeochemical cycling of nitrite (NO2−) in the South China Sea (SCS) is still unclear. NO2− concentration generally shows a peak at or near the base of the sunlit euphotic zone, which is called primary NO2− maximum (PNM). The PNM appears widely in the SCS, but its formation mechanism has not yet been realized. In this study, the dual isotopes of NO2− are used for the first time to explore the NO2− cycle and PNM formation in the northern SCS (NSCS). We propose that the formation of the PNM in the NSCS is mainly driven by ammonia (NH3) oxidation. A steady‐state model is used to estimate the biogeochemical cycling rates of NO2− in the NSCS. Our results show that both the oxidation rate of NH3 and the assimilation rate of NO2− are significantly reduced from the shelf to the basin. Notably, the role of NO2− oxidation in the basin is not negligible, although the assimilation of NO2− mainly represents the fate of NO2− in the NSCS. The residence time of NO2− implies that the cycle of NO2− is dynamic and the PNM is an active signal in the NSCS. Our results further demonstrate the importance of NH3 oxidation in the formation of PNM in the marginal sea, which can be applied in global marginal seas to gain a deeper understanding of marine nitrogen (N) cycle. Plain Language Summary: Nitrite, a key intermediate in marine nitrogen cycle, is closely related to the production of nitrate and nitrous oxide and plays an important role in global nitrogen and carbon cycles. However, little is known about the nitrite cycle in the marine environment. In this study, we measured the δ15N and δ18O of nitrite in the northern South China Sea (NSCS) to describe the path of the nitrite cycle. Our results prove that the nitrite in primary nitrite maximum (PNM) is mainly derived from ammonia oxidation. We also estimated biogeochemical transformation rate of nitrite, which further revealed the residence time of nitrite in PNM. This knowledge of the nitrite cycle in the euphotic zone of NSCS will deepen our understanding of the nitrogen cycle in the upper ocean. Future research can be compared with the results of NSCS to better understand the nitrogen cycle in global marginal seas. Key Points: The dual isotopes of nitrite have been first reported in the northern South China SeaIsotopic evidence indicates ammonia oxidation as a main source of nitrite in the primary nitrite maximum (PNMs)The biogeochemical transformation rates of nitrite in the primary nitrite maximum are estimated [ABSTRACT FROM AUTHOR]

Herein, electrochemical oxidation of nitrite (NO2−) is demonstrated using metal‐free, electrochemically highly stable, and selective biomolecule i. e. tyramine functionalized graphene oxide (GT) electrocatalyst for nitrite oxidation in phosphate buffer at pH‐7. The successful functionalization of a biomolecule on graphene is carried out by a simple chemical method. The surface features of biomolecule functionalized graphene oxide were studied by using both spectroscopic and microscopic techniques including scanning electron microscope (SEM) which shows wrinkled and folded structures having a thickness of ∼20 nm corresponding to a few layer of graphene. Moreover, their structural analysis was carried out using X‐ray photoelectron spectroscopy nitrogen band at peak position of ∼400 eV reveals biomolecule functionalization, Fourier‐transform infrared spectroscopy (FTIR) reveals significant peak at 1580 cm−1 corresponding to amine functionalization, Raman Spectroscopy reveals enhanced ID/IG ratio as compared to GO. The electrochemical surface area (ECSA) found tobe 3.60 cm2. The as‐synthesized electrocatalyst is found to be more active towards electro‐oxidation of nitrite (NO2−) at a low onset potential of 0.6 V vs saturated calomel electrode (SCE) from linear sweep voltammetry (LSV), cyclic voltammetry (CV), and electrochemical impedance spectroscopy (EIS) measurements. Moreover, its current stability at a given potential is also tested by chronoamperometric (i‐t) measurements within a concentration range of 0 μM to 7 μM and is having long term good electrochemical stability at an onset potential of 0.6 V vs SCE. The onset potential of GT was 0.6 V vs SCE, the limit of detection (LOD) 0.933 μM and high current density 21 mA cm−2 as compared to GO 8.7 mA cm−2. Considering above perspectives, our findings emphasizes the importance of biomolecule functionalised GO is the best electrocatalyst for electro‐oxidation of nitrites, which is one of the important species for environmental remediation. [ABSTRACT FROM AUTHOR]

• A hybrid of worm-like Au NWs dispersed CNFs-Gr heterostructured network is designed. • Au WNWs/CNFs-Gr showed high sensitivity of 836 μA cm−2 mM−1 for nitrite oxidation. • The sensor showed a wide linear range of 1.98 µM – 3.77 mM and low LOD of 1.24 µM. • The sensor demonstrated accurate detection of nitrite in river water-based samples. The development of a rapid, selective, and sensitive sensor to precisely monitor nitrite oxidation is of growing importance, given the strong interest in the protection of drinking water quality, treatment of wastewater, food production, and control of remediation processes. In this research, we successfully fabricated a hybrid originated from worm-like gold nanowires (Au WNWs) assembled on a high-quality carbon nanofibers-graphene (CNFs–Gr) hybrid network through a facile synthesis method. The hybrid as a binder-free sensor exhibited excellent activity towards nitrite detection in phosphate buffer solution (pH of 7.4) with a wide linear detection range of (1.98 µM – 3.77 mM), excellent sensitivity of 836 μA cm−2 mM−1, low detection limit of 1.24 µM, and long-term durability. The results were attributed to a special synergistic effect originating from unique hybridization of Au WNWs with large-area CNFs–Gr network to produce more electroactive sites and excellent conductivity, favorably boosting catalytic performance of the sensor. The successful fabrication of Au WNWs/CNFs–Gr suggested an interesting candidate for practically determining low-level nitrite in analytical applications. [ABSTRACT FROM AUTHOR]

Purpose: Unraveling the drivers of the nitrogen cycling functional guilds variation in response to fertilizer management is a major goal in agroecosystem study. Nitrospira-like nitrite oxidizing bacteria can oxidize nitrite to nitrate, which play a critical role in the biogeochemical nitrogen cycle. However, how the Nitrospira community structure and co-occurrence patterns in a long-term inorganic and organic fertilization regimes within different soil aggregates have been largely unexplored. Materials and methods: The soil samples were collected from a long-term (39-year) inorganic and organic fertilized agricultural ecosystem, including no-fertilizer (CK); mineral-fertilizer (NPK); manure-fertilizer (M); nitrogen-fertilizer (N); and M + N (MN). Three sizes of soil aggregate were manually fractionated by soil wet sieving technique with a series of meshes: (i) 2000–250 μm (macroaggregates), (ii) 250–53 μm (microaggregates), and (iii) < 53 μm fractions (silt and clay). We performed qPCR and high-throughput-sequencing to assess the Nitrospira abundance and community structure, respectively. Results and discussion: Organic fertilization (M and MN) efficiently increased soil potential nitrite oxidation activity (PNO), which was higher in the < 53 μm than 250–53 μm and followed the 2000–250 μm fraction, than other treatments. All the fertilizer treatments resulted in a similar pattern, where the 250–53-μm fraction had significantly greater Nitrospira abundance than the 2000–250 μm and < 53 μm fractions. The alpha diversity of Nitrosipra did not change in response to the fertilization treatments and soil aggregate sizes. Nitrospira community shifted in fertilization types, while not in aggregate sizes. Nitrospira community composition and abundance significantly correlated with PNO. Network analysis suggested that organic fertilizations (M and MN) promote the complexity of Nitrospira networks and possess higher connectivity than inorganic fertilization networks. Conclusions: Our data suggested that fertilization strongly affected the Nitrospira community structure and co-occurrence patterns, which may implicate the importance of Nitrospira function in the nitrite oxidation process in soils with organic fertilization. [ABSTRACT FROM AUTHOR]

Marine oxygen deficient zones are dynamic areas of microbial nitrogen cycling. Nitrification, the microbial oxidation of ammonia to nitrate, plays multiple roles in the biogeochemistry of these regions, including production of the greenhouse gas nitrous oxide (N2O). We present here the results of two oceanographic cruises investigating nitrification, nitrifying microorganisms, and N2O production and distribution from the offshore waters of the Eastern Tropical South Pacific. On each cruise, high‐resolution measurements of ammonium ([NH4+]), nitrite ([NO2−]), and N2O were combined with 15N tracer‐based determination of ammonia oxidation, nitrite oxidation, nitrate reduction, and N2O production rates. Depth‐integrated inventories of NH4+ and NO2− were positively correlated with one another and with depth‐integrated primary production. Depth‐integrated ammonia oxidation rates were correlated with sinking particulate organic nitrogen flux but not with primary production; ammonia oxidation rates were undetectable in trap‐collected sinking particulate material. Nitrite oxidation rates exceeded ammonia oxidation rates at most mesopelagic depths. We found positive correlations between archaeal amoA genes and ammonia oxidation rates and between Nitrospina‐like 16S rRNA genes and nitrite oxidation rates. N2O concentrations in the upper oxycline reached values of >140 nM, even at the western extent of the cruise track, supporting air‐sea fluxes of up to 1.71 μmol m−2 day−1. Our results suggest that a source of NO2− other than ammonia oxidation may fuel high rates of nitrite oxidation in the offshore Eastern Tropical South Pacific and that air‐sea fluxes of N2O from this region may be higher than previously estimated. Key Points: Depth‐integrated ammonia oxidation rates are correlated with sinking particulate nitrogen flux, indicating substrate supply as a primary control of water column nitrificationNitrous oxide is produced from ammonium in the water column, with an instantaneous yield from nitrification lower than previous estimatesHigher than anticipated nitrous oxide concentrations were measured in offshore waters, which may arise from local production, leading to large air‐sea fluxes [ABSTRACT FROM AUTHOR]

Nitrification is a key process for N-removal in engineered and natural environments, but recent findings of novel nitrifying microorganisms with surprising features revealed that our knowledge of this functional guild is still incomplete. Especially nitrite oxidation – the second step of nitrification – is catalyzed by a phylogenetically diverse bacterial group, and only recently bacteria of the phylum Chloroflexi have been identified as thermophilic nitrite-oxidizing bacteria (NOB). Among these, Nitrolancea hollandica was isolated from a laboratory-scale nitrifying bioreactor operated at 35°C with a high load of ammonium bicarbonate. However, its distribution remains cryptic as very few closely related environmental 16S rRNA gene sequences have been retrieved so far. In this study, we demonstrate how such thermophilic NOB can be enriched using modified mineral media inoculated with samples from a wastewater side-stream reactor operated at 39.5°C. Distinct cultivation conditions resulted in quick and reproducible high enrichment of two different strains of Nitrolancea, closely related to Nl. hollandica. The same cultivation approach was applied to a complex nitrite-oxidizing pre-enrichment at 42°C inoculated with biomass from a geothermal spring in the Copahue volcano area in Neuquen, Argentina. Here, an additional distinct representative of the genus Nitrolancea was obtained. This novel species had 16S rRNA and nitrite oxidoreductase alpha subunit (nxrA) gene sequence identities to Nl. hollandica of 98.5% and 97.2%, respectively. A genomic average nucleotide identity between the Argentinian strain and Nl. hollandica of 91.9% indicates that it indeed represents a distinct species. All Nitrolancea cultures formed lancet-shaped cells identical to Nl. hollandica and revealed similar physiological features, including the capability to grow at high nitrite concentrations. Growth was optimal at temperatures of 35–37°C and was strongly enhanced by ammonium supplementation. Genomic comparisons revealed that the four Nitrolancea strains share 2399 out of 3387 orthologous gene clusters and encode similar key functions. Our results define general growth conditions that enable the selective enrichment of Nitrolancea from artificial and natural environments. In most natural habitats these NOB apparently are of low abundance and their proliferation depends on the balanced presence of nitrite and ammonium, with an optimal incubation temperature of 37°C.

Abstract The genus Nitrospira is considered to be the most widespread and abundant group of nitrite-oxidizing bacteria in many natural and man-made ecosystems. However, the ecophysiological versatility within this phylogenetic group remains highly understudied, mainly due to the lack of pure cultures and genomic data. To further expand our understanding of this biotechnologically important genus, we analyzed the high quality draft genome of “Nitrospira lenta” strain BS10, a sublineage II Nitrospira that was isolated from a municipal wastewater treatment plant in Hamburg, Germany. The genome of “N. lenta” has a size of 3,756,190 bp and contains 3968 genomic objects, of which 3907 are predicted protein-coding sequences. Thorough genome annotation allowed the reconstruction of the “N. lenta” core metabolism for energy conservation and carbon fixation. Comparative analyses indicated that most metabolic features are shared with N. moscoviensis and “N. defluvii”, despite their ecological niche differentiation and phylogenetic distance. In conclusion, the genome of “N. lenta” provides important insights into the genomic diversity of the genus Nitrospira and provides a foundation for future comparative genomic studies that will generate a better understanding of the nitrification process.

Nitritation, the oxidation of ammonia to nitrite without subsequent oxidation to nitrate, is a starting step for nitrite-based nitrogen removal approaches. This process can be induced by maintaining specific operating conditions that facilitate ammonia oxidation but deteriorate nitrite oxidation. In recent years, a number of publications have demonstrated the ability of cell immobilization to maintain nitritation and an oxygen-limiting strategy was suggested to be a key to the success of the approach. However, several aspects related to the success and failure of such systems remains unclear and requires further in-depth clarification. This review provides current information on the utilization of cell immobilization in nitritation reactors. Common operating strategies that promote nitritation by controlling environmental conditions are summarized in the first part of the review. The application of cell immobilization, including cell attachment, cell granulation, and cell entrapment systems, as well as microenvironments, and microbial distributions within cell immobilization matrices, are elaborated in the middle part of the review. Problems encountered in the operation of nitritation reactors using cell immobilization are discussed as opportunities for further research at the end of the review. [ABSTRACT FROM AUTHOR]

Nitrite-oxidizing bacteria (NOB) are ubiquitous and abundant microorganisms that play key roles in global nitrogen and carbon biogeochemical cycling. Despite recent advances in understanding NOB physiology and taxonomy, there are currently very few cultured NOB or representative NOB genome sequences from marine environments. In this study, we employed enrichment culturing and genomic approaches in order to shed light on the phylogeny and metabolic capacity of marine NOB. We successfully enriched two marine NOB (designated MSP and DJ) and obtained a high-quality metagenome-assembled genome (MAG) from each organism. The maximum nitrite oxidation rates of the MSP and DJ enrichment cultures were 13.8 (0.1 mM nitrite as optimum) and 30.0 µM (0.3 mM nitrite) nitrite per day, respectively. Each enrichment culture exhibited different tolerance to varying nitrite and salt concentrations. Based on phylogenomic position and overall genome relatedness indices, both NOB MAGs were proposed as novel taxa within the Nitrospinota and Nitrospirota phyla. Functional predictions indicated that both NOB MAGs shared many highly conserve metabolic features with other NOB. Both NOB MAGs encoded proteins for hydrogen and organic compound metabolism and defense mechanisms for oxidative stress. Additionally, these organisms may have the genetic potential to produce cobalamin (an essential enzyme cofactor that is limiting in many environments) and thus may play an important role in recycling cobalamin in marine sediment. Overall, this study appreciably expands our understanding of the Nitrospinota and Nitrospirota phyla, and suggests that these NOB may play important biogeochemical roles in marine habitats. [ABSTRACT FROM AUTHOR]

A simple and greener electrochemical sensing platform towards nitrite measurement using amine modified Zr‐terephthalate and MWCNTs has been demonstrated. The characterization of the composite material has been carried out using spectroscopic and voltammetric techniques. The composite material overcomes the inherent drawbacks of MOFs like lower conductivity and stability in aqueous medium. The MWCNTs/Zr−ATA composite modified electrode showed better electrocatalytic activity in nitrite quantification with good linearity in the concentration range 2–440 μM with detection limit 0.22 μM and sensitivity of 0.657 μA μM−1 cm−2. The fabricated electrode has been applied to quantify nitrite from root nodule samples. [ABSTRACT FROM AUTHOR]

To understand how and to what extent single or multiple perturbations can alter the relationships between the abundances of different nitrifier groups and nitrification, soil microcosms were exposed to six disturbance treatments: a heat shock, cold shock, or control conditions applied to undisturbed soils or to soils that had previously been subjected to a first heat shock. We monitored the recovery of the abundances of four main nitrifier groups (ammonia-oxidizing archaea and bacteria, AOA and AOB, respectively, and Nitrobacter and Nitrospira nitrite oxidizers) as well as nitrification activity for 25 days. AOA were sensitive to cold shocks, whereas AOB were not; the latter were sensitive to heat shock. Despite the variations, both groups were resilient to the first disturbance. In contrast, Nitrobacter was affected by both disturbances, whereas Nitrospira was resistant to both shocks. Prior exposure to a heat shock affected each group's responses as well as the relationships between them. For example, AOB were more vulnerable to heat shock in pre-exposed soils, whereas under the same circumstances, AOA were resilient. Nitrification activity was resistant to the first disturbances, but a legacy effect was observed, and nitrification was highest in Heat-Heat and lowest in Heat-Cold treatments. Overall, our study shows that within soil nitrifiers, temporal patterns and legacy effects interact to result in complex disturbance responses. [ABSTRACT FROM AUTHOR]

Gold nanoparticles (AuNPs) decorated bimetallic CuNi-based hollow nanoarchitecture (CNHN) are reported for the first time as a nonenzymatic sensor for the quantification of nitrite in neutral solution. The CNHN was prepared via a convenient calcining routine using the bimetallic CuNi-MOFs as a coprecursor. The unique chemical structure of hollow CNHN with high specific surface area and abundant terminal amino groups effectively avoid the aggregation of AuNPs and facilitate the subsequent adsorption of nitrite. The Au/CNHN exhibited high electrocatalytic activity towards nitrite oxidation due to the synergetic catalytic effect of AuNPs and CNHN. Chronoamperometric detection of nitrite at the Au/CNHN/GCE achieved a lower linear calibration range of 0.05 to 1.15 mM, with an LOD of 0.017 μM compared with previous reports. The proposed method obtained satisfactory recoveries for nitrite determination in practical applications, which was verified by UV-Vis spectrophotometry. The prepared sensor based on Au/CNHN featured favorable selectivity and stability, which provides a promising approach for real sample analysis. [ABSTRACT FROM AUTHOR]

The most abundant known nitrite-oxidizing bacteria in the marine water column belong to the phylum Nitrospinota . Despite their importance in marine nitrogen cycling and primary production, there are only few cultured representatives that all belong to the class Nitrospinia . Moreover, although Nitrospinota were traditionally thought to be restricted to marine environments, metagenome-assembled genomes have also been recovered from groundwater. Over the recent years, metagenomic sequencing has led to the discovery of several novel classes of Nitrospinota (UBA9942, UBA7883, 2-12-FULL-45-22, JACRGO01, JADGAW01), which remain uncultivated and have not been analyzed in detail. Here, we analyzed a nonredundant set of 98 Nitrospinota genomes with focus on these understudied Nitrospinota classes and compared their metabolic profiles to get insights into their potential role in biogeochemical element cycling. Based on phylogenomic analysis and average amino acid identities, the highly diverse phylum Nitrospinota could be divided into at least 33 different genera, partly with quite distinct metabolic capacities. Our analysis shows that not all Nitrospinota are nitrite oxidizers and that members of this phylum have the genomic potential to use sulfide and hydrogen for energy conservation. This study expands our knowledge of the phylogeny and potential ecophysiology of the phylum Nitrospinota and offers new avenues for the isolation and cultivation of these elusive bacteria., Competing Interests: The authors declare that they have no conflict of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

Chemolithoautotrophic nitrifiers are model groups for linking phylogeny, evolution, and ecophysiology. Ammonia-oxidizing bacteria (AOB) typically dominate the first step of ammonia oxidation at high ammonium supply rates, ammonia-oxidizing archaea (AOA) and complete ammonia-oxidizing Nitrospira (comammox) are often active at lower supply rates or during AOB inactivity, and nitrite-oxidizing bacteria (NOB) complete canonical nitrification. Soil virus communities are dynamic but contributions to functional processes are largely undetermined. In addition, characterizing viruses infecting hosts with low relative abundance, such as nitrifiers, may be constrained by vast viral diversity, partial genome recovery, and difficulties in host linkage. Here, we describe a targeted incubation study that aimed to determine whether growth of different nitrifier groups in soil is associated with active virus populations and if process-focused analyses facilitate characterization of high-quality virus genomes. dsDNA viruses infecting different nitrifier groups were enriched in situ via differential host inhibition. Growth of each nitrifier group was consistent with predicted inhibition profiles and concomitant with the abundance of their viruses. These included 61 high-quality/complete virus genomes 35-173 kb in length with minimal similarity to validated families. AOA viruses lacked ammonia monooxygenase sub-unit C (amoC) genes found in marine AOA viruses but some encoded AOA-specific multicopper oxidase type 1 (MCO1), previously implicated in copper acquisition, and suggesting a role in supporting energy metabolism of soil AOA. Findings demonstrate focused incubation studies facilitate characterization of active host-virus interactions associated with specific processes and viruses of soil AOA, AOB, and NOB are dynamic and potentially influence nitrogen cycling processes., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

• The response of Anammox process to Cr(VI) stress were evaluated. • Cr(VI) inhibition mechanism on Anammox was investigated for the first time. • Intracellular Cr(VI) reduction dominated with the percentage of 99.78%. • Nitrite oxidation to nitrate was unexpectedly observed. The toxicity of hexavalent chromium (Cr(VI)) is one of the challenges in implementing Anammox process to ammonium-rich wastewater treatment. However, the response of Anammox process to Cr(VI) stress and the inhibition mechanism remain unclear. Here, two Anammox UASB reactors were operated for 285 days under different Cr(VI) stresses. The results showed Anammox performance was not affected at low Cr(VI) concentration (i.e., 0–0.5 mg L−1), but was severely inhibited at 0.8 mg L−1. Attempts to domesticate Anammox process to higher Cr(VI) by lowering nitrogen loading rate were failed. Examination of Cr(VI) fate showed the occurrence of extracellular and intracellular Cr(VI) reduction to Cr(III). The inhibition was ascribed to the significant intracellular Cr(VI) reduction, accounting for 99.78% of the total Cr(VI) reduction. Moreover, under long-term Cr(VI) exposure, most nitrite was oxidized to nitrate. But microbial community showed no enrichment of Cr(VI) reducing bacteria and other nitrogen transformation-related bacteria. [ABSTRACT FROM AUTHOR]

The reduced graphene oxide – polyaniline – Arsenomolybdate (rGO-Pani-AsM) composite modified glassy carbon electrode (GCE) interface has been demonstrated as a sensitive electrochemical interface for nitrite sensing. The synthesized composite has been characterized by spectroscopic and electrochemical techniques such as X-ray diffraction (XRD), Fourier transform Infra-red spectroscopy (FTIR), Raman spectroscopy, scanning electron microscopy (SEM), cyclic voltammetry (CV) and square wave voltammetry (SWV). The rGO-Pani-AsM composite exhibited higher oxidative current and reduced over potentials in the electrochemical oxidation of nitrite than bare glassy carbon electrode. The proposed sensor exhibited linearity in the concentration range 25–7500 μM with a limit of detection (LOD) of 10.71 μM and sensitivity of 0.803 μA μM−1 cm−2. The analytical utility of the proposed sensor has been examined by applying it to real sample analysis such as packed beverages, cucumber extract and water samples. Schematic representation of synthesis, fabrication of composite modified electrode and its electrochemical sensing towards nitrite quantification. Image 1 • Reduced graphene oxide–polyaniline-arsenomolybdate composite is used as nitrite sensor. • It has been characterized using FTIR, Raman, XRD, SEM and electrochemical techniques. • Modified electrode showed an excellent electrocatalytic activity in nitrite oxidation. • Nitrite measurement with wide linearity 25–7500 μM and detection limit of 10.71 μM. • The proposed sensor has been successfully applied to real sample matrices. [ABSTRACT FROM AUTHOR]

ABSTRACT K. Kitzinger et al. (mBio 9:e01186-18, 2018, https://doi.org/10.1128/mBio.01186-18) report the first isolation of a novel nitrite-oxidizing bacterium, “Candidatus Nitrotoga,” and provide the first detailed information on the physiology, phylogeny, and characterization of the nitrite-oxidizing system of this genus. The isolate was derived from a wastewater treatment system and exhibits adaptation and tolerance to relatively high levels of nitrite. The origin of its nitrite oxidoreductase is distinct from other known nitrite oxidoreductase (NXR) systems, having arisen either in this organism or by horizontal gene transfer. In contrast to many earlier-characterized nitrite oxidizers, it displays substantial metabolic plasticity in its mode of energetic metabolism with capabilities to use both hydrogen and sulfite as electron donors.

Abstract This study report a new method for simultaneously determining microbial ammonia oxidation rate (V a) and nitrite oxidation rate (V n) in water and sediment. This method is based on mathematical modeling analysis for the time series variation of DIN (nitrite, nitrate, and ammonium) in an incubation system without an inhibitor. Compared to the traditional methods with specific inhibitors, this method is not affected by inhibitors and can determine both instantaneous and average V a and V n accurately and simultaneously. Practical application indicated that this method can well determine the dynamic variations in V a and V n in both water and sediment samples. Highlights • Developed a new method for determining microbial nitrification rate. • This method can determine both instantaneous and average rates accurately. • This method is based on mathematical modeling analysis. [ABSTRACT FROM AUTHOR]

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Purpose: Nitrification, the microbial oxidation of ammonia to nitrate via nitrite, is a pivotal component of the biogeochemical nitrogen cycle. Nitrification was conventionally assumed as a two-step process in which ammonia oxidation was thought to be catalyzed by ammonia-oxidizing archaea (AOA) and bacteria (AOB), as well as nitrite oxidation by nitrite-oxidizing bacteria (NOB). This long-held assumption of labour division between the two functional groups, however, was challenged by the recent unexpected discovery of complete ammonia oxidizers within the Nitrospira genus that are capable of converting ammonia to nitrate in a single organism (comammox). This breakthrough raised fundamental questions on the niche specialization and differentiation of comammox organisms with other canonical nitrifying prokaryotes in terrestrial ecosystems. Materials and methods: This article provides an overview of the recent insights into the genomic analysis, physiological characterization and environmental investigation of the comammox organisms, which have dramatically changed our perspective on the aerobic nitrification process. By using quantitative PCR analysis, we also compared the abundances of comammox Nitrospira clade A and clade B, AOA, AOB and NOB in 300 forest soil samples from China spanning a wide range of soil pH. Results and discussion: Comammox Nitrospira are environmentally widespread and numerically abundant in natural and engineered habitats. Physiological data, including ammonia oxidation kinetics and metabolic versatility, and comparative genomic analysis revealed that comammox organisms might functionally outcompete other canonical nitrifiers under highly oligotrophic conditions. These findings highlight the necessity in future studies to re-evaluate the niche differentiation between ammonia oxidizers and their relative contribution to nitrification in various terrestrial ecosystems by including comammox Nitrospira in such comparisons. Conclusions: The discovery of comammox and their broad environmental distribution added a new dimension to our knowledge of the biochemistry and physiology of nitrification and has far-reaching implications for refined strategies to manipulate nitrification in terrestrial ecosystems and to maximize agricultural productivity and sustainability. [ABSTRACT FROM AUTHOR]

The genomes of many bacteria that participate in nitrogen cycling through the process of nitrification contain putative genes associated with acylhomoserine lactone (AHL) quorum sensing (QS). AHL QS or bacterial cell-cell signaling is a method of bacterial communication and gene regulation and may be involved in nitrogen oxide fluxes or other important phenotypes in nitrifying bacteria. Here, we carried out a broad survey of AHL production in nitrifying bacteria in three steps. First, we analyzed the evolutionary history of AHL synthase and AHL receptor homologs in sequenced genomes and metagenomes of nitrifying bacteria to identify AHL synthase homologs in ammonia-oxidizing bacteria (AOB) of the genus Nitrosospira and nitrite-oxidizing bacteria (NOB) of the genera Nitrococcus, Nitrobacter, and Nitrospira. Next, we screened cultures of both AOB and NOB with uncharacterized AHL synthase genes and AHL synthase-negative nitrifiers by a bioassay. Our results suggest that an AHL synthase gene is required for, but does not guarantee, cell density-dependent AHL production under the conditions tested. Finally, we utilized mass spectrometry to identify the AHLs produced by the AOB Nitrosospira multiformis and Nitrosospira briensis and the NOB Nitrobacter vulgaris and Nitrospira moscoviensis as N-decanoyl-L-homoserine lactone (C10-HSL), N-3-hydroxy-tetradecanoyl-L-homoserine lactone (3-OH-C14-HSL), a monounsaturated AHL (C10:1-HSL), and N-octanoyl-L-homoserine lactone (C8-HSL), respectively. Our survey expands the list of AHL-producing nitrifiers to include a representative of Nitrospira lineage II and suggests that AHL production is widespread in nitrifying bacteria. IMPORTANCE Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite by nitrifying microorganisms, plays an important role in environmental nitrogen cycling from agricultural fertilization to wastewater treatment. The genomes of many nitrifying bacteria contain genes associated with bacterial cell-cell signaling or quorum sensing (QS). QS is a method of bacterial communication and gene regulation that is well studied in bacterial pathogens, but less is known about QS in environmental systems. Our previous work suggested that QS might be involved in the regulation of nitrogen oxide gas production during nitrite metabolism. This study characterized putative QS signals produced by different genera and species of nitrifiers. Our work lays the foundation for future experiments investigating communication between nitrifying bacteria, the purpose of QS in these microorganisms, and the manipulation of QS during nitrification. [ABSTRACT FROM AUTHOR]

Nitrite oxidation is an essential step in transformations of fixed nitrogen. The physiology of nitrite oxidizing bacteria (NOB) implies that the rates of nitrite oxidation should be controlled by concentration of their substrate, nitrite, and the terminal electron acceptor, oxygen. The sensitivities of nitrite oxidation to oxygen and nitrite concentrations were investigated using 15N tracer incubations in the Eastern Tropical North Pacific. Nitrite stimulated nitrite oxidation under low in situ nitrite conditions, following Michaelis-Menten kinetics, indicating that nitrite was the limiting substrate. The nitrite half-saturation constant ( K s = 0.254 ± 0.161 μM) was 1-3 orders of magnitude lower than in cultivated NOB, indicating higher affinity of marine NOB for nitrite. The highest rates of nitrite oxidation were measured in the oxygen depleted zone (ODZ), and were partially inhibited by additions of oxygen. This oxygen sensitivity suggests that ODZ specialist NOB, adapted to low-oxygen conditions, are responsible for apparently anaerobic nitrite oxidation. [ABSTRACT FROM AUTHOR]

In this study, we investigated how co-occurrence patters of ammonia and nitrite oxidizers, which drive autotrophic nitrification, are influenced by tree species composition as well as soil pH in different forest soils. We expected that a decline of ammonia oxidizers in coniferous forests, as a result of excreted nitrification inhibitors and at acidic sites with low availability of ammonia, would reduce the abundance of nitrite-oxidizing bacteria (NOB). To detect shifts in co-occurrence patterns, the abundance of key players was measured at 50 forest plots with coniferous respectively deciduous vegetation and different soil pH levels in the region Schwäbische Alb (Germany). We found ammonia-oxidizing archaea (AOA) and Nitrospira-like NOB (NS) to be dominating in numbers over their counterparts across all forest types. AOA co-occurred mostly with NS, while bacterial ammonia oxidizers (AOB) were correlated with Nitrobacter-like NOB (NB). Co-occurrence patterns changed from tight significant relationships of all ammonia and nitrite oxidizers in deciduous forests to a significant relationship of AOB and NB in coniferous forests, where AOA abundance was reduced. Surprisingly, no co-occurrence structures between ammonia and nitrite oxidizers could be determined at acidic sites, although abundances were correlated to the respective nitrogen pools. This raises the question whether interactions with heterotrophic nitrifiers may occur, which needs to be addressed in future studies. [ABSTRACT FROM AUTHOR]

The Arabian Sea is home to one of the three main oceanic oxygen deficient zones (ODZs). We present paired nitrogen (N) and oxygen (O) isotope measurements of nitrate (NO 3 - ) and nitrite (NO 2 - ) from the central Arabian Sea in order to understand the effects of N biogeochemistry on the distribution of these species in the low oxygen waters. Within the ODZ, NO 2 - accumulated in a secondary NO 2 - maximum (SNM), though the shape and magnitude of the SNM, along with the isotopic composition of NO 3 - and NO 2 - , were highly dependent on the location within the ODZ. We also explored water mass mixing within the Arabian Sea as an explanatory factor in the distribution of NO 2 - in the SNM. The intrusion of Persian Gulf Water at depth may influence the shape of the NO 2 - peak by introducing small amounts of dissolved oxygen (O 2 ), favoring NO 2 - oxidation. There was also evidence that vertical mixing may play a role in shaping the top of the SNM peak. Finally, we present evidence for NO 2 - oxidation and NO 2 - reduction co-occurring within the ODZ, as has been previously suggested in the Arabian Sea, as well as in other ODZs. The decoupling of the N and O isotopes of NO 3 - , deviating from the expected 1:1 ratio for dissimilatory NO 3 - reduction, indicates that NO 2 - oxidation has a significant influence on the isotopic composition of NO 3 - . Additionally, the N isotopes of NO 2 - were generally fit well by Rayleigh curves for NO 2 - oxidation. However, the removal of dissolved inorganic nitrogen (DIN) within the domain reflects the importance of NO 2 - reduction to N 2 . [ABSTRACT FROM AUTHOR]

Shortcut nitrification can be successfully achieved by dosing methanoic acid in the sequencing batch reactor (SBR) system. While processing stable shortcut nitrification, influent pH value was kept at 7.5-8.5. However, dissolved oxygen and temperature were not controlled in the SBR. When influent NH4+−N was 50 mg/L, NH4+−N removal efficiency reached 98.77% and 98.92% in the reactor when we dosed 0.25 and 0.35 mL/L methanoic acid. Moreover, when we dosed 0.25 and 0.35 mL/L methanoic acid in the reactor, NO2−−N removal reached 77.88% and 79.63% of the NO2−−N/(NO2−−N + NO3−−N) in the effluent, respectively. We also discovered that when we dosed 0.35 mL/L methanoic acid, effluent NH4+−N was more volatile. Scanning electron microscopy showed that the main composition of the activated sludge was bacilli and coccus bacteria. High throughput sequencing analysis revealed that after methanoic acid was dosed, the dominant bacteria were Blastocatella, Brevundimonas, Ferruginibacter, Paracoccus, Pseudoxanthomonas, and Thermomonas. Methanoic acid can be used to control the development and maintenance for shortcut nitrification. [ABSTRACT FROM AUTHOR]