Nitrogen isotope effects induced by anammox bacteria

Lateral redox variability in ca. 1.9 Ga marine environments indicated by organic carbon and nitrogen isotope compositions

The stepwise oxygenation of Earth's surficial environment is thought to have shaped the evolutionary history of life. Microfossil records and molecular clocks suggest eukaryotes appeared during the Paleoproterozoic, perhaps shortly after the Great Oxidation Episode at ca. 2.43 Ga. The mildly oxygenated atmosphere and surface oceans likely contributed to the early evolution of eukaryotes. However, the principal trigger for the eukaryote appearance and a potential factor for their delayed expansion (i.e., intermediate ocean redox conditions until the Neoproterozoic) remain poorly understood, largely owing to a lack of constraints on marine and terrestrial nutrient cycling. Here, we analyzed redox-sensitive element contents and organic carbon and nitrogen isotope compositions of relatively low metamorphic-grade (greenschist facies) black shales preserved in the Flin Flon Belt of central Canada to examine open-marine redox conditions and biological activity around the ca. 1.9 Ga Flin Flon oceanic island arc. The black shale samples were collected from the Reed Lake area in the eastern part of the Flin Flon Belt, and the depositional site was likely distal from the Archean cratons. The black shales have low Al/Ti ratios and are slightly depleted in light rare-earth elements relative to the post-Archean average shale, which is consistent with a limited contribution from felsic igneous rocks in Archean upper continental crust. Redox conditions have likely varied between suboxic and euxinic at the depositional site of the studied section, as suggested by variable U/Al and Mo/Al ratios. Organic carbon and nitrogen isotope compositions of the black shales are approximately -23‰ and +13.7‰, respectively, and these values are systematically higher than those of broadly coeval continental margin deposits (approximately -30‰ for δ13Corg and +5‰ for δ15Nbulk). These elevated values are indicative of high productivity that led to enhanced denitrification (i.e., a high denitrification rate relative to nitrogen influx at the depositional site). Similar geochemical patterns have also been observed in the modern Peruvian oxygen minimum zone where dissolved nitrogen compounds are actively lost from the reservoir via denitrification and anammox, but the large nitrate reservoir of the deep ocean prevents exhaustion of the surface nitrate pool. Nitrogen must have been widely bioavailable in the ca. 1.9 Ga oceans, and its supply to upwelling zones must have supported habitable environments for eukaryotes, even in the middle of oceans around island arcs.

Microbial nitrogen transformations tracked by natural abundance isotope studies and microbiological methods: A review

Nitrogen is an essential nutrient in the environment that exists in multiple oxidation states in nature. Numerous microbial processes are involved in its transformation. Knowledge about very complex N cycling has been growing rapidly in recent years, with new information about associated isotope effects and about the microbes involved in particular processes. Furthermore, molecular methods that are able to detect and quantify particular processes are being developed, applied and combined with other analytical approaches, which opens up new opportunities to enhance understanding of nitrogen transformation pathways. This review presents a summary of the microbial nitrogen transformation, including the respective isotope effects of nitrogen and oxygen on different nitrogen-bearing compounds (including nitrates, nitrites, ammonia and nitrous oxide), and the microbiological characteristics of these processes. It is supplemented by an overview of molecular methods applied for detecting and quantifying the activity of particular enzymes involved in N transformation pathways. This summary should help in the planning and interpretation of complex research studies applying isotope analyses of different N compounds and combining microbiological and isotopic methods in tracking complex N cycling, and in the integration of these results in modelling approaches.

Characteristics of dissolved organic matter contribute to Geogenic ammonium enrichment in coastal versus alluvial-lacustrine aquifers

Elevated concentration levels of geogenic ammonium in groundwater arise from the mineralization of nitrogen-containing natural organic matter in various geological settings worldwide, especially in alluvial-lacustrine and coastal environments. However, the difference in enrichment mechanisms of geogenic ammonium between these two types of aquifers remains poorly understood. To address this knowledge gap, we investigated two representative aquifer systems in central Yangtze (Dongting Lake Plain, DTP) and southern China (Pearl River Delta, PRD) with contrasting geogenic ammonium contents. The use of optical and molecular characterization of DOM combined with hydrochemistry and stable carbon isotopes has revealed differences in DOM between the two types of aquifer systems and revealed contrasting controls of DOM on ammonium enrichment. The results indicated higher humification and degradation of DOM in DTP groundwater, characterized by abundant highly unsaturated compounds. The degradation of DOM and nitrogen-containing DOM was dominated by highly unsaturated compounds and CHO+N molecular formulas in highly unsaturated compounds, respectively. In contrast, the DOM in PRD groundwater was more biogenic, less degraded, and contained more aliphatic compounds in addition to highly unsaturated compounds. The degradation of DOM and nitrogen-containing DOM was dominated by aliphatic compounds and polyphenols and CHO+N molecular formulas in highly unsaturated compounds and polyphenols, respectively. As DOM degraded, the ammonium production efficiency of DOM decreased, contributing to lower ammonium concentrations in DTP groundwater. In addition, the CHO+N(SP) molecular formulas were mainly of microbial-derived and gradually accumulated with DOM degradation. In this study, we conducted the first comprehensive investigation into the patterns of groundwater ammonium enrichment based on DOM differences in various geological settings.

Physiological Influence of Fe and Cu Availability on Nitrogen Isotope Fractionation during Ammonia Oxidation

Microbially mediated cycling processes play central roles in regulating the speciation and availability of nitrogen, a vital nutrient with wide implications for agriculture, water quality, wastewater treatment, ecosystem health, and climate change. Ammonia oxidation, the first and rate-limiting step of nitrification, is carried out by bacteria (AOB) and archaea (AOA) that require the trace metal micronutrients copper (Cu) and iron (Fe) for growth and metabolic catalysis. While stable isotope analyses for constraining nitrogen cycling are commonly used, it is unclear whether metal availability may modulate expression of stable isotope fractionation during ammonia oxidation, by varying growth or through regulation of metabolic metalloenzymes. We present the first study examining the influence of Fe and Cu availability on the kinetic nitrogen isotope effect in ammonia oxidation (15εAO). We report a general independence of 15εAO from the growth rate in AOB, except at a low temperature (10 °C). With AOA Nitrosopumilus maritimus SCM1, however, 15εAO decreases nonlinearly at lower oxidation rates. We examine assumptions involved in the interpretation of 15εAO values and suggest these dynamics may arise from physiological constraints that push the system toward isotopic equilibrium. These results suggest important links between isotope fractionation and environmental constraints on physiology in these key N cycling microorganisms.

Unignorable enzyme-specific isotope fractionation for nitrate source identification in aquatic ecosystem

Nitrate contamination in aquatic systems is a widespread problem across the world. The isotopic composition (δ15N, δ18O) of nitrate and their isotope effect (15ε, 18ε) can facilitate the identification of the source and transformation of nitrate. Although previous researches claimed the isotope fractionations may change the original δ15N/δ18O values and further bias identification of nitrate sources, isotope effect was often ignored due to its complexity. To fill the gap between the understanding and application, it is crucial to develop a deep understanding of isotopic fractionation based on available evidence. In this regard, this study summarized the available methods to determine isotope effects, thereby systematically comparing the magnitude of isotope effects (15ε and 18ε) in nitrification, denitrification and anammox. We found that the enzymatic reaction plays the key role in isotope fractionations, which is significantly affected by the difference in the affinity, substrate channel properties and redox potential of active site. Due to the overlapping of microbial processes and accumulation of uncertainties, the significant isotope effects at small scales inevitably decrease in large-scale ecosystems. However, the proportionality of N and O isotope fractionation (δ18O/δ15N; 18ε/15ε) associated with nitrate reduction generally follows enzyme-specific proportionalities (i.e., Nar, 0.95; Nap, 0.57; eukNR, 0.98) in aquatic ecosystems, providing enzyme-specific constant factors for the identification of nitrate transformation. With these results, this study finally discussed feasible source portioning methods when considering the isotope effect and aimed to improve the accuracy in nitrate source identification.

Age, metabolisms, and potential origin of dominant anammox bacteria in the global oxygen-deficient zones

Anammox bacteria inhabiting oxygen-deficient zones (ODZs) are a major functional group mediating fixed nitrogen loss in the global ocean. However, many basic questions regarding the diversity, broad metabolisms, origin, and adaptive mechanisms of ODZ anammox bacteria remain unaddressed. Here we report two novel metagenome-assembled genomes of anammox bacteria affiliated with the Scalindua genus, which represent most, if not all, of the anammox bacteria in the global ODZs. Metagenomic read-recruiting and comparison with historical data show that they are ubiquitously present in all three major ODZs. Beyond the core anammox metabolism, both organisms contain cyanase, and the more dominant one encodes a urease, indicating most ODZ anammox bacteria can utilize cyanate and urea in addition to ammonium. Molecular clock analysis suggests that the evolutionary radiation of these bacteria into ODZs occurred no earlier than 310 million years ago, ~1 billion years after the emergence of the earliest modern-type ODZs. Different strains of the ODZ Scalindua species are also found in benthic sediments, and the first ODZ Scalindua is likely derived from the benthos. Compared to benthic strains of the same clade, ODZ Scalindua uniquely encodes genes for urea utilization but has lost genes related to growth arrest, flagellum synthesis, and chemotaxis, presumably for adaptation to thrive in the global ODZ waters. Our findings expand the known metabolisms and evolutionary history of the bacteria controlling the global nitrogen budget.

Dissolved N2O concentrations in oil palm plantation drainage in a peat swamp of Malaysia

Oil palm plantations in Southeast Asia are the largest supplier of palm oil products and have been rapidly expanding in the last three decades even in peat-swamp areas. Oil palm plantations on peat ecosystems have a unique water management system that lowers the water table and, thus, may yield indirect N₂O emissions from the peat drainage system. We conducted two seasons of spatial monitoring for the dissolved N₂O concentrations in the drainage and adjacent rivers of palm oil plantations on peat swamps in Sarawak, Malaysia, to evaluate the magnitude of indirect N₂O emissions from this ecosystem. In both the dry and wet seasons, the mean and median dissolved N₂O concentrations exhibited over-saturation in the drainage water, i.e., the oil palm plantation drainage may be a source of N₂O to the atmosphere. In the wet season, the spatial distribution of dissolved N₂O showed bimodal peaks in both the unsaturated and over-saturated concentrations. The bulk δ¹⁵N of dissolved N₂O was higher than the source of inorganic N in the oil palm plantation (i.e., N fertilizer and soil organic nitrogen) during both seasons. An isotopocule analysis of the dissolved N₂O suggested that denitrification was a major source of N₂O, followed by N₂O reduction processes that occurred in the drainage water. The δ¹⁵N and site preference mapping analysis in dissolved N₂O revealed that a significant proportion of the N₂O produced in peat and drainage is reduced to N₂ before being released into the atmosphere.

Iron-mediated anaerobic ammonium oxidation recorded in the early Archean ferruginous ocean

The nitrogen isotopic composition of organic matter is controlled by metabolic activity and redox speciation and has therefore largely been used to uncover the early evolution of life and ocean oxygenation. Specifically, positive δ¹⁵ N values found in well-preserved sedimentary rocks are often interpreted as reflecting the stability of a nitrate pool sustained by water column partial oxygenation. This study adds much-needed data to the sparse Paleoarchean record, providing carbon and nitrogen concentrations and isotopic compositions for more than fifty samples from the 3.4 Ga Buck Reef Chert sedimentary deposit (BRC, Barberton Greenstone Belt). In the overall anoxic and ferruginous conditions of the BRC depositional environment, these samples yield positive δ¹⁵ N values up to +6.1‰. We argue that without a stable pool of nitrates, these values are best explained by non-quantitative oxidation of ammonium via the Feammox pathway, a metabolic co-cycling between iron and nitrogen through the oxidation of ammonium in the presence of iron oxides. Our data contribute to the understanding of how the nitrogen cycle operated under reducing, anoxic, and ferruginous conditions, which are relevant to most of the Archean. Most importantly, they invite to carefully consider the meaning of positive δ¹⁵ N signatures in Archean sediments.

Nitrate limitation in early Neoproterozoic oceans delayed the ecological rise of eukaryotes

The early Neoproterozoic Era witnessed the initial ecological rise of eukaryotes at ca. 800 Ma. To assess whether nitrate availability played an important role in this evolutionary event, we measured nitrogen isotope compositions (δ¹⁵N) of marine carbonates from the early Tonian (ca. 1000 Ma to ca. 800 Ma) Huaibei Group in North China. The data reported here fill a critical gap in the δ¹⁵N record and indicate nitrate limitation in early Neoproterozoic oceans. A compilation of Proterozoic sedimentary δ¹⁵N data reveals a stepwise increase in δ¹⁵N values at ~800 Ma. Box model simulations indicate that this stepwise increase likely represents a ~50% increase in marine nitrate availability. Limited nitrate availability in early Neoproterozoic oceans may have delayed the ecological rise of eukaryotes until ~800 Ma when increased nitrate supply, together with other environmental and ecological factors, may have contributed to the transition from prokaryote-dominant to eukaryote-dominant marine ecosystems.

Microbial Denitrification: Active Site and Reaction Path Models Predict New Isotopic Fingerprints

The study of isotopic fingerprints in nitrate (δ15N, δ18O, Δ17O) has enabled pivotal insights into the global nitrogen cycle and revealed new knowledge gaps. Measuring populations of isotopic homologs of intact NO3 - ions (isotopologues) shows promise to advance the understanding of nitrogen cycling processes; however, we need new theory and predictions to guide laboratory experiments and field studies. We investigated the hypothesis that the isotopic composition of the residual nitrate pool is controlled by the N-O bond-breaking step in Nar dissimilatory nitrate reductase using molecular models of the enzyme active sites and associated kinetic isotope effects (KIEs). We integrated the molecular model results into reaction path models representing the reduction of nitrate under either closed-system or steady-state conditions. The predicted intrinsic KIE (15ε and 18ε) of the Nar active site matches observed fractionations in both culture and environmental studies. This is what would be expected if the isotopic composition of marine nitrate were controlled by dissimilatory nitrate reduction by Nar. For a closed system, the molecular models predict a pronounced negative 15N-18O clumping anomaly in residual nitrate. This signal could encode information about the amount of nitrate consumed in a closed system and thus constrain initial nitrate concentration and its isotopic composition. Similar clumped isotope anomalies can potentially be used to distinguish whether a system is open or closed to new nitrate addition. These mechanistic predictions can be tested and refined in combination with emerging ESI-Orbitrap measurements.

Dual isotopes of nitrite in the Amundsen Sea in summer

Nitrite (NO₂^-) is a key intermediate in the nitrogen (N) cycle, and its transformation is accomplished by microbial communities. However, due to few studies on the nitrite cycle, a clear assessment of the contribution to the marine biogeochemical cycle is missing. Here, we present data on nitrogen and oxygen isotopic composition of NO₂^- in the Amundsen Sea in summer, and explore the biogeochemical processes that influence the NO₂^- cycle. Extremely low δ¹⁵N_NO2 and abnormally high δ¹⁸O_NO2 were found in the upper waters of the Amundsen Sea, with δ¹⁵N_NO2 as low as -58.4 ‰ and δ¹⁸O_NO2 as high as 44.4 ‰. Enzymatic isotopic exchange reactions between nitrate and nitrite have been proposed to be responsible for these isotopic anomalies. The mirror-symmetrical variation between δ¹⁵N_NO2 and δ¹⁸O_NO2 suggests that the isotopic fractionation effects of nitrogen and oxygen are opposite in isotope exchange reactions. Dual isotopes of nitrite indicate that ammonia oxidation is the main source of nitrite, thus nitrification plays an important role in the formation of primary nitrite maximum in the upper Amundsen Sea. The nitrogen and oxygen isotopic compositions of nitrite provide support for clarifying multiple processes of marine nitrogen cycle.

Distinct oxygen isotope fractionations driven by different electron donors during microbial nitrate reduction in lake sediments

Microbial nitrate reduction can be driven by organic carbon oxidation, as well as by inorganic electron donors, such as reduced forms of sulfur and iron. An apparent inverse oxygen isotope fractionation effect was observed during nitrate reduction in sediment incubations from five sampling sites of a freshwater lake, Hongze Lake, China. Incubations with organic and inorganic electron donor additions were performed. Especially, the inverse oxygen isotope effect was intensified after glucose addition, whereas the incubations with sulfide and Fe²⁺ showed normal fractionation factors. Nitrate reductase encoding genes, napA and narG, were analysed with metagenomics. Higher napA/narG ratios were associated with higher oxygen fractionation factors. The most abundant clade (59%) of NapA in the incubation with glucose was affiliated with Rhodocyclales. In contrast, it only accounted for 8%-9% of NapA in the incubations with sulfide and Fe²⁺ . Differences in nitrate reductases might explain different oxygen isotope effects. Our findings also suggested that large variance of O-nitrate isotope fractionations might have to be considered in the interpretation of natural isotope records.

Stable isotopes (δ13C, δ15N) and biomarkers as indicators of the hydrological regime of fens in a European east-west transect

Peatland degradation is tightly connected to hydrological changes and microbial metabolism. To better understand these metabolism processes, more information is needed on how microbial communities and substrate cycling are affected by changing hydrological regimes. These activities should be imprinted in stable isotope bulk values (δ ¹⁵N, δ ¹³C) due to specific isotopic fractionation by different microbial communities, their metabolic pathways and nutrient sources. We hypothesize that stable isotope values and microbial abundance are correlated and act as indicators of different hydrological regimes. We sampled an East-West transect across European fens in 14 areas and conducted a stable isotope (δ ¹³C, δ ¹⁵N) and membrane fatty acid (mFA) analysis. Within each area an undrained, drained and rewetted site was selected. Rewetted sites were separated based on when rewetting occurred. We found differences in the upper layers of all sites in microbial-derived mFAs and stable isotope values corresponding to hydrological regimes. The highest and lowest quantities of microbial-derived mFAs were measured in undrained and drained sites, respectively. Fungal-derived mFAs were especially lower in drained sites. Simultaneously, δ¹⁵N stable isotope values were highest in drained sites. In addition, stable isotope values and microbial-derived mFAs showed distinct depth trends. In undrained sites stable isotopes values slightly increased with depth. In drained sites, δ¹⁵N values decreased downwards, whereas δ¹³C values increased. Overall microbial-derived mFAs decreased with depth. These patterns presumably result from anoxic conditions and high peat recalcitrance in the deeper layers. In sites with short time of rewetting, the microbial-derived mFAs and stable isotope values were similar to values of drained sites, while with increasing rewetting time values shifted to those of undrained sites. We conclude that biomarkers indicate that stable isotope values reflect specific microbial metabolic processes, which differ with hydrological regimes, and thus could indicate both drainage and rewetting in fens.

Feammox in alluvial-lacustrine aquifer system: Nitrogen/iron isotopic and biogeochemical evidences

Groundwater nitrogen contamination is becoming increasingly serious worldwide, and natural nitrogen attenuation processes such as anaerobic ammonium oxidation coupled to iron reduction ("Feammox") play an important role in mitigating contamination. Although there has been intensive study of Feammox in soils and sediments, still lacks research on this process in groundwater. This study makes effort to demonstrate the occurrence of Feammox in groundwater by combining information from Fe/N isotope composition, the quantitative polymerase chain reaction (qPCR) assay, and 16S rRNA gene sequencing. Poyang Lake Plain of Yangtze River in central China was selected as the case study area. The critical evidences that indicate Feammox in groundwater include favorable hydrogeochemical conditions of the alluvia-lacustrine aquifer systems, the simultaneous enrichment of ¹⁵N in ammonium and ⁵⁶Fe, the relative high abundance of Acidimicrobiaceae bacterium A6, and the joint elevation of the abundance of the Feammox bacteria and the concentration of Fe(III). Redundancy analysis (RDA) indicated that Geothrix and Rhodobacter may participate directly or cooperatively in the Feammox process. Ammonium-oxidizing archaea (AOA) involved in ammonium-oxidizing or Feammox process may be stimulated by Fe(III) under a low oxygen concentration and weakly acidic condition. Anammox may be indirectly enhanced by products of the nitrogen transformation processes involving Feammox bacteria and AOA. Fe(III) concentration is an important environmental factor affecting the abundance of functional microorganisms related to nitrogen cycling and the composition of ammonium-oxidizing and iron-reducing microbes. Specific geological background (such as the widespread red soils) and anthropogenic input of ammonium, iron, and acidic substances may jointly promote Feammox in groundwater.

Phylogenomic evidence for the Origin of Obligately Anaerobic Anammox Bacteria around the Great Oxidation Event

The anaerobic ammonium oxidation (anammox) bacteria can transform ammonium and nitrite to dinitrogen gas, and this obligate anaerobic process accounts for up to half of the global nitrogen loss in surface environments. Yet its origin and evolution, which may give important insights into the biogeochemistry of early Earth, remain enigmatic. Here, we performed a comprehensive phylogenomic and molecular clock analysis of anammox bacteria within the phylum Planctomycetes. After accommodating the uncertainties and factors influencing time estimates, which include implementing both a traditional cyanobacteria-based and a recently developed mitochondria-based molecular dating approach, we estimated a consistent origin of anammox bacteria at early Proterozoic and most likely around the so-called Great Oxidation Event (GOE; 2.32–2.5 Ga) which fundamentally changed global biogeochemical cycles. We further showed that during the origin of anammox bacteria, genes involved in oxidative stress adaptation, bioenergetics, and anammox granules formation were recruited, which might have contributed to their survival on an increasingly oxic Earth. Our findings suggest the rising levels of atmospheric oxygen, which made nitrite increasingly available, was a potential driving force for the emergence of anammox bacteria. This is one of the first studies that link the GOE to the evolution of obligate anaerobic bacteria.

Tracing sources and transformations of ammonium during river bank filtration by means of column experiments

Ammonium is an undesirable substance in the abstracted water of riverbank filtration (RBF) schemes, due mainly to the complications it causes during post-treatment (e. g. during chlorination). During RBF, ammonium can be formed in the riverbed by mineralization of organic nitrogen. Column experiments with riverbed sediments and river water from the Elbe were performed to evaluate the controls on ammonium concentrations during riverbed infiltration. Concentrations of ammonium went from <0.1 mgN/l in the feed water up to 1 mgN/l in the columns effluent. Higher temperatures and lower infiltration rates led to increased ammonium concentrations in the effluent. This shows higher susceptibility to ammonium increases of RBF settings in warmer climates and points to potential threats of climate change to water quality at RBF sites. In the later phases of the experiments, after the columns have been flushed their pore volumes several times, ammonium concentrations continually decreased. This behavior was attributed to the partial consumption of easily degradable organic material in the sediments, leading to lesser reducing conditions and lower mineralization rates. Based on operation with varied nitrate concentrations (0-11 mgN/l) and ¹⁵N isotopic measurements, dissimilatory nitrate reduction to ammonium (DNRA) was not shown to be relevant in the formation of ammonium. Anaerobic ammonium oxidation (anammox), however, was hypothesized to be an important sink of ammonium inside the columns, which indicates that rivers with high nitrate concentrations, such as the Elbe, may have a buffer of protection against ammonium formation during RBF.

Effect of sulfur sources on the competition between denitrification and DNRA

The fate of nitrogen is controlled by the competition between nitrate reduction pathways. Denitrification removes nitrogen in the system to the atmosphere, whereas dissimilatory nitrate reduction to ammonia (DNRA) retains nitrate in the form of ammonia. Different microbes specialize in the oxidation of different electron donors, thus electron donors might influence the outcomes of the competition. Here, we investigated the fate of nitrate with five forms of sulfur as electron donors. Chemoautotrophic nitrate reduction did not continue after the passages of the enrichments with sulfide, sulfite and pyrite. Nitrate reduction rate was the highest in the enrichment with thiosulfate. Denitrification was stimulated and no DNRA was observed with thiosulfate, while both denitrification and DNRA were stimulated with elemental sulfur. Metagenomes of the enrichments were assembled and binned into ten genomes. The enriched populations with thiosulfate included Thiobacillus, Lentimicrobium, Sulfurovum and Hydrogenophaga, all of which contained genes involved in sulfur oxidation. Elemental sulfur-based DNRA was performed by Thiobacillus (with NrfA and NirB) and Nocardioides (with only NirB). Our study established a link between sulfur sources, nitrate reduction pathways and microbial populations.

Effect of S2O32--S addition on Anammox coupling sulfur autotrophic denitrification and mechanism analysis using N and O dual isotope effects

Anaerobic ammonia oxidation (Anammox) coupling sulfur autotrophic denitrification is an effective method for the advanced nitrogen removal from the wastewater with limited carbon source. The influence of S₂O₃^2--S addition on Anammox coupling sulfur autotrophic denitrification was investigated by adding different concentrations of S₂O₃^2--S (0, 39, 78, 156 and 312 mg/L) to the Anammox system. The contribution of sulfur autotrophic denitrification and Anammox to nitrogen removal at S₂O₃^2--S concentrations of 156 mg/L was 75% ∼83% and 17%∼25%, respectively, and the mixed system achieved completely nitrogen removal. However, Anammox bioactivity was completely inhibited at S₂O₃^2--S concentrations up to 312 mg/L, and only sulfur autotrophic denitrification occurred. The isotopic effects of NO₂^--N (δ¹⁵N_NO2 and δ¹⁸O_NO2) and NO₃^--N (δ¹⁵N_NO3 and δ¹⁸O_NO3) during Anammox coupling sulfur autotrophic denitrification showed a gradual decrease trend with the increase of S₂O₃^2--S addition. The ratios of δ¹⁵N_NO2:δ¹⁸O_NO2 and δ¹⁵N_NO3:δ¹⁸O_NO3 was maintained at 1.30-2.41 and 1.36-2.52, respectively, which revealed that Anammox was dominant nitrogen removal pathway at S₂O₃^2--S concentrations less than 156 mg/L. Microbial diversity gradually decreased with the increase of S₂O₃^2--S. The S₂O₃^2--S addition enhanced the S₂O₃^2--driven autotrophic denitrification and weakened the Anammox, leading to a gradually decreasing trend of the proportion of Candidatus Brocadia as Anammox bacteria from the initial 27% to 4% (S₂O₃^2--S of 156 mg/L). Yet Norank-f-Hydrogenophilaceae (more than 50%) and Thiobacillus (54%) as functional bacteria of autotrophic denitrification obviously increased. The appropriate amount of S₂O₃^2--S addition promoted the performance of Anammox coupling sulfur autotrophic denitrification achieved completely nitrogen removal.

Determination of 15N/14N of Ammonium, Nitrite, Nitrate, Hydroxylamine, and Hydrazine Using Colorimetric Reagents and Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS)

In the nitrogen (N) cycle, nitrogenous compounds are chemically and biologically converted to various aqueous and gaseous N species. The ¹⁵N-labeling approach is a powerful culture-dependent technique to obtain insights into the complex nitrogen transformation reactions that occur in cultures. In the ¹⁵N-labeling approach, the fates of supplemented ¹⁵N- and/or unlabeled gaseous and aqueous compounds are tracked by mass spectrometry (MS) analysis, whereas MS analysis of aqueous N species requires laborious sample preparation steps and is performed using isotope-ratio mass spectrometry, which requires an expensive mass spectrometer. We developed a simple and high-throughput MS method for determining the ¹⁵N atoms percent of NH₄⁺, NO₂^-, NO₃^-, NH₂OH, and N₂H₄, where liquid samples (<0.5 mL) were mixed with colorimetric reagents (naphthylethylenediamine for NO₂^-, indophenol for NH₄⁺, and p-aminobenzaldehyde for N₂H₄), and the mass spectra of the formed N complex dyes were obtained by matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) MS. NH₂OH and NO₃^- were chemically converted to NO₂^- by iodine oxidation and copper/hydrazine reduction reaction, respectively, prior to the above colorimetric reaction. The intensity of the isotope peak (M + 1 or M + 2) increased when the N complex dye was formed by coupling with a ¹⁵N-labeled compound, and a linear relationship was found between the determined ¹⁵N/¹⁴N peak ratio and ¹⁵N atom% for the tested N species. The developed method was applied to bacterial cultures to examine their N-transformation reactions, enabling us to observe the occurrence of NO₂^- oxidation and NO₃^- reduction in a hypoxic Nitrobacter winogradskyi culture. IMPORTANCE ¹⁵N/¹⁴N analysis for aqueous N species is a powerful tool for obtaining insights into the global N cycle, but the procedure is cumbersome and laborious. The combined use of colorimetric reagents and MALDI-TOF MS, designated color MALDI-TOF MS, enabled us to determine the ¹⁵N atom% of common aqueous N species without laborious sample preparation and chromatographic separation steps; for instance, the ¹⁵N atom% of NO₂^- can be determined from >1,000 liquid samples daily at <$1 (U.S.) per 384 samples for routine analysis. This convenient MS method is a powerful tool that will advance our ability to explore the N-transformation reactions that occur in various environments and biological samples.

Contrasting sources and fate of nitrogen compounds in different groundwater systems in the Central Yangtze River Basin

Although groundwater nitrogen pollution has been widely studied, the control of hydrogeological conditions on behavior of nitrogen compounds has been poorly understood. In this study, multiple stable isotopes (N/C/H/O), spectral characteristics of DOM coupled with water chemistry were used to reveal the sources and fate of nitrate and ammonium in three subareas with different hydrogeological conditions in the Central Yangtze River Basin. We identified three contrasting patterns of nitrogen sources and fate in groundwater controlled by different aquifer features. In a reducing porous aquifer mainly composed of carbonate minerals overlain by a thick low-permeability layer, the NH₄-N concentration is high (mean 4.12 mg/L) but with quite low NO₃-N concentration (mean 0.28 mg/L). The high ammonium is mainly from intense degradation of organic matter (OM), while denitrification at a higher rate results in nitrate removal. Feammox may be favored owing to abundant humics acting as the electron shuttle. In a weakly reducing to oxidizing porous aquifer mainly composed of aluminosilicate minerals overlain by a varying thickness of low-permeability layer, high ammonium occurs in a weakly reducing condition and is affected by both anthropogenic input and OM degradation, while high nitrate occurs in a more oxidizing condition and could be mainly from soil nitrogen, manure or sewage. Feammox may be also favored due to more acidic environment formed by weathering of aluminosilicate minerals, fluctuating redox condition and low abundance of labile organic carbon, while denitrification occurs at a slower rate coupled with concurrent re-oxidation of nitrite to nitrate. In an oxidizing porous - fissured aquifer system overlain by a thin low-permeability layer, the concentrations of ammonium and nitrate are both low, possibly due to strong hydrodynamic and flushing condition, although slightly higher concentration of nitrate exhibit similar sources and fate with the weakly reducing to oxidizing porous aquifer mentioned above.

Septic systems drive nutrient enrichment of groundwaters and eutrophication in the urbanized Indian River Lagoon, Florida

Effluent from septic systems can pollute groundwater and surface waters in coastal watersheds. These effects are unknown for the highly urbanized central Indian River Lagoon (CIRL), Florida, where septic systems represent > 50% of wastewater disposal. To better understand these impacts, water quality was assessed along both canals and a tributary that drain into the CIRL. Dissolved nutrient concentrations were higher near septic systems than in natural areas. δ¹⁵N values of groundwater (+7.2‰), surface water (+5.5‰), and macrophytes (+9.7‰) were within the range for wastewater (>+3‰), as were surface water concentrations of the artificial sweetener sucralose (100 to 1700 ng/L) and fecal indicator bacteria density. These results indicate that septic systems are promoting eutrophication in the CIRL by contributing nutrient pollution to surface water via groundwater. This study demonstrates the need to reduce reliance on septic systems in urbanized coastal communities to improve water quality and subsequently mitigate harmful algal blooms.

Nitrogen fixation and denitrification activity differ between coral- and algae-dominated Red Sea reefs

Coral reefs experience phase shifts from coral- to algae-dominated benthic communities, which could affect the interplay between processes introducing and removing bioavailable nitrogen. However, the magnitude of such processes, i.e., dinitrogen (N2) fixation and denitrification levels, and their responses to phase shifts remain unknown in coral reefs. We assessed both processes for the dominant species of six benthic categories (hard corals, soft corals, turf algae, coral rubble, biogenic rock, and reef sands) accounting for > 98% of the benthic cover of a central Red Sea coral reef. Rates were extrapolated to the relative benthic cover of the studied organisms in co-occurring coral- and algae-dominated areas of the same reef. In general, benthic categories with high N2 fixation exhibited low denitrification activity. Extrapolated to the respective reef area, turf algae and coral rubble accounted for > 90% of overall N2 fixation, whereas corals contributed to more than half of reef denitrification. Total N2 fixation was twice as high in algae- compared to coral-dominated areas, whereas denitrification levels were similar. We conclude that algae-dominated reefs promote new nitrogen input through enhanced N2 fixation and comparatively low denitrification. The subsequent increased nitrogen availability could support net productivity, resulting in a positive feedback loop that increases the competitive advantage of algae over corals in reefs that experienced a phase shift.

Enzyme-Specific Coupling of Oxygen and Nitrogen Isotope Fractionation of the Nap and Nar Nitrate Reductases

Dissimilatory nitrate reduction (DNR) to nitrite is the first step in denitrification, the main process through which bioavailable nitrogen is removed from ecosystems. DNR is catalyzed by both cytosolic (Nar) and periplasmic (Nap) nitrate reductases and fractionates the stable isotopes of nitrogen (¹⁴N, ¹⁵N) and oxygen (¹⁶O, ¹⁸O), which is reflected in residual environmental nitrate pools. Data on the relationship between the pattern in oxygen vs nitrogen isotope fractionation (¹⁸ε/¹⁵ε) suggests that systematic differences exist between marine and terrestrial ecosystems that are not fully understood. We examined the ¹⁸ε/¹⁵ε of nitrate-reducing microorganisms that encode Nar, Nap, or both enzymes, as well as gene deletion mutants of Nar and Nap to test the hypothesis that enzymatic differences alone could explain the environmental observations. We find that the distribution of ¹⁸ε/¹⁵ε fractionation ratios of all examined nitrate reductases forms two distinct peaks centered around an ¹⁸ε/¹⁵ε proportionality of 0.55 (Nap) and 0.91 (Nar), with the notable exception of the Bacillus Nar reductases, which cluster isotopically with the Nap reductases. Our findings may explain differences in ¹⁸ε/¹⁵ε fractionation between marine and terrestrial systems and challenge current knowledge about Nar ¹⁸ε/¹⁵ε signatures.

Nitrogen isotope effects can be used to diagnose N transformations in wastewater anammox systems

Anaerobic ammonium oxidation (anammox) plays an important role in aquatic systems as a sink of bioavailable nitrogen (N), and in engineered processes by removing ammonium from wastewater. The isotope effects anammox imparts in the N isotope signatures (¹⁵N/¹⁴N) of ammonium, nitrite, and nitrate can be used to estimate its role in environmental settings, to describe physiological and ecological variations in the anammox process, and possibly to optimize anammox-based wastewater treatment. We measured the stable N-isotope composition of ammonium, nitrite, and nitrate in wastewater cultivations of anammox bacteria. We find that the N isotope enrichment factor ¹⁵ε for the reduction of nitrite to N₂ is consistent across all experimental conditions (13.5‰ ± 3.7‰), suggesting it reflects the composition of the anammox bacteria community. Values of ¹⁵ε for the oxidation of nitrite to nitrate (inverse isotope effect, - 16 to - 43‰) and for the reduction of ammonium to N₂ (normal isotope effect, 19-32‰) are more variable, and likely controlled by experimental conditions. We argue that the variations in the isotope effects can be tied to the metabolism and physiology of anammox bacteria, and that the broad range of isotope effects observed for anammox introduces complications for analyzing N-isotope mass balances in natural systems.

Multiple isotopic compositions reveal complex nitrogen cycling in a subtropical estuary

Nitrogen (N) pollution and the resulting eutrophication can have deleterious consequences on estuaries, such as hypoxia, fish kills, and loss of biotic diversity. An understanding of N sources and cycling in estuaries is fundamental to determining how to effectively manage these ecologically and commercially important areas. We applied a multiple-isotopic approach to examine the transformations and sources of the N pools in the Pearl River Estuary (PRE) during winter. The surface water in the West PRE was characterized by low salinity and high NO₃^-, while that in the east had high salinity and low NO₃^-. The NO₃^- in the West PRE was largely regulated by a conservative mixing process. In contrast, assimilation and nitrification dominated in the East PRE, which was attributed to the long water-residence time. For the first time, the source contributions of NO₃^- and NH₄⁺ were estimated by isotope mixing models. Our results suggest that river discharge and nitrification contributed 81% and 12% to the NO₃^- pool, respectively. A major portion (68%) of the NH₄⁺ was from river discharge, with the remainder likely from sewage and the aquitard-aquifer system. Our study demonstrates that internal nitrification can potentially be of pivotal importance in determining the NO₃^- level in an estuary and its export to coastal waters.

Nitrogen and Oxygen Isotope Signatures of Nitrogen Compounds during Anammox in the Laboratory and a Wastewater Treatment Plant

Isotopic fractionation factors against ¹⁵N and ¹⁸O during anammox (anaerobic ammonia oxidization by nitrite) are critical for evaluating the importance of this process in natural environments. We performed batch incubation experiments with an anammox-dominated biomass to investigate nitrogen (N) and oxygen (O) isotopic fractionation factors during anammox and also examined apparent isotope fractionation factors during anammox in an actual wastewater treatment plant. We conducted one incubation experiment with high δ¹⁸O of water to investigate the effects of water δ¹⁸O. The N isotopic fractionation factors estimated from incubation experiments and the wastewater treatment plant were similar to previous values. We also found that the N isotopic effect (¹⁵ε_NXR of -77.8 to -65.9‰ and ¹⁵Δ_NXR of -31.3 to -30.4‰) and possibly O isotopic effect (¹⁸ε_NXR of -20.6‰) for anaerobic nitrite oxidation to nitrate were inverse. We applied the estimated isotopic fractionation factors to the ordinary differential equation model to clarify whether anammox induces deviations in the δ¹⁸O vs δ¹⁵N of nitrate from a linear trajectory of 1, similar to heterotrophic denitrification. Although this deviation has been attributed to nitrite oxidation, the O isotopic fractionation factor for anammox is crucial for obtaining a more detailed understanding of the mechanisms controlling this deviation. In our model, anammox induced the trajectory of the δ¹⁸O vs δ¹⁵N of nitrate during denitrification to less than one, which strongly indicates that this deviation is evidence of nitrite oxidation by anammox under denitrifying conditions.

The key role of Geobacter in regulating emissions and biogeochemical cycling of soil-derived greenhouse gases

In the past two decades, more and more attentions have been paid to soil-derived greenhouse gases (GHGs) including carbon dioxide (CO₂), methane (CH₄) and nitrous oxide (N₂O) because there are signs that they have rising negative impacts on the sustainability of the earth surface system. Farmlands, particularly paddy soils, have been regarded as the most important emitter of GHGs (nearly 17%) due to a large influx of fertilization and the abundance in animals, plants and microorganisms. Geobacter, as an electroactive microorganism widely occurred in soil, has been well studied on electron transport mechanisms and the direct interspecies electron transfer. These studies on Geobacter illustrate that it has the ability to be involved in the pathways of soil GHG emissions through redox reactions under anaerobic conditions. In this review, production mechanisms of soil-derived GHGs and the amount of these GHGs produced had been first summarized. The cycling process of CH₄ and N₂O was described from the view of microorganisms and discussed the co-culture relationships between Geobacter and other microorganisms. Furthermore, the role of Geobacter in the production of soil-derived GHGs is defined by biogeochemical cycling. The complete view on the effect of Geobacter on the emission of soil-derived GHGs has been shed light on, and appeals further investigation.

Trace Metal Availability Affects Greenhouse Gas Emissions and Microbial Functional Group Abundance in Freshwater Wetland Sediments

We investigated the effects of trace metal additions on microbial nitrogen (N) and carbon (C) cycling using freshwater wetland sediment microcosms amended with micromolar concentrations of copper (Cu), molybdenum (Mo), iron (Fe), and all combinations thereof. In addition to monitoring inorganic N transformations (NO₃ ^-, NO₂ ^-, N₂O, NH₄ ⁺) and carbon mineralization (CO₂, CH₄), we tracked changes in functional gene abundance associated with denitrification (nirS, nirK, nosZ), dissimilatory nitrate reduction to ammonium (DNRA; nrfA), and methanogenesis (mcrA). With regards to N cycling, greater availability of Cu led to more complete denitrification (i.e., less N₂O accumulation) and a higher abundance of the nirK and nosZ genes, which encode for Cu-dependent reductases. In contrast, we found sparse biochemical evidence of DNRA activity and no consistent effect of the trace metal additions on nrfA gene abundance. With regards to C mineralization, CO₂ production was unaffected, but the amendments stimulated net CH₄ production and Mo additions led to increased mcrA gene abundance. These findings demonstrate that trace metal effects on sediment microbial physiology can impact community-level function. We observed direct and indirect effects on both N and C biogeochemistry that resulted in increased production of greenhouse gasses, which may have been mediated through the documented changes in microbial community composition and shifts in functional group abundance. Overall, this work supports a more nuanced consideration of metal effects on environmental microbial communities that recognizes the key role that metal limitation plays in microbial physiology.

Application of an enrichment culture of the marine anammox bacterium "Ca. Scalindua sp. AMX11" for nitrogen removal under moderate salinity and in the presence of organic carbon

Seawater can be directly used for toilet flushing in coastal areas to reduce our dependence on desalination and freshwater resources. The presence of high-salt content in the generated wastewater from seawater toilet flushing could limit the performance of conventional biological nitrogen removal processes. Anaerobic ammonium oxidation (anammox) process is regarded as one of the most energy-efficient process for nitrogen removal from N-rich waste streams. In this study, we demonstrated the application of a novel marine anammox bacterium (Candidatus Scalindua sp. AMX11) in a membrane bioreactor (MBR) to treat moderate-saline (∼1.2% salinity) and N-rich organic (2 mM acetate) solution, prepared using real seawater. The MBR showed stable performance with nitrogen removal rate of 0.3 kg-N m^-3 d^-1 at >90% N-removal efficiency. Furthermore, results of ¹⁵N stable isotope experiments revealed that anammox bacteria was mainly responsible for respiratory ammonification through NO₃^- reduction to NH₄⁺ via NO₂^-, and the by-products of respiratory ammonification were used as substrates by anammox bacteria. The dominant role of anammox bacteria in nitrogen removal under saline and organic conditions was further confirmed by genome-centric combined metagenomics and meta-transcriptomic approach. Taken together, these results highlight the potential application of marine anammox bacteria for treating saline wastewater generated from seawater toilet flushing practices.

Tracking the dynamic ecological history of a tropical urban estuary as it responds to human pressures

Coastal cities in tropical areas are often low-lying and vulnerable to the effects of flooding and storms. San Juan, Puerto Rico is a good example of this. It is built around a lagoon-channel complex called the San Juan Bay Estuary (SJBE). A critical channel in the estuary, the Caño Martín Peña, has filled in and now frequently floods the surrounding communities with sewage-enriched waters, causing a series of human health and ecological problems. Sediment core analyses indicate that portions of the SJBE now function as settling basins. High urban and sewage runoff to the Caño contributes nitrogen (N), but stable isotope and sediment nutrient analyses indicate that this runoff may also enhance conditions for coupled sulfate reduction-nitrogen fixation. The amount of 'new' bioavailable N created from inert atmospheric N₂ gas may meet or exceed that from the runoff into the Caño Martín Peña. The ecological consequences of this appear to extend beyond the ponded channel, potentially contributing to the poor water quality of the SJBE, greater than contaminated runoff alone.

Exploring cycad foliage as an archive of the isotopic composition of atmospheric nitrogen

Molecular nitrogen (N₂ ) constitutes the majority of Earth's modern atmosphere, contributing ~0.79 bar of partial pressure (pN₂ ). However, fluctuations in pN₂ may have occurred on 10⁷ -10⁹  year timescales in Earth's past, perhaps altering the isotopic composition of atmospheric nitrogen. Here, we explore an archive that may record the isotopic composition of atmospheric N₂ in deep time: the foliage of cycads. Cycads are ancient gymnosperms that host symbiotic N₂ -fixing cyanobacteria in modified root structures known as coralloid roots. All extant species of cycads are known to host symbionts, suggesting that this N₂ -fixing capacity is perhaps ancestral, reaching back to the early history of cycads in the late Paleozoic. Therefore, if the process of microbial N₂ fixation records the δ¹⁵ N value of atmospheric N₂ in cycad foliage, the fossil record of cycads may provide an archive of atmospheric δ¹⁵ N values. To explore this potential proxy, we conducted a survey of wild cycads growing in a range of modern environments to determine whether cycad foliage reliably records the isotopic composition of atmospheric N₂ . We find that neither biological nor environmental factors significantly influence the δ¹⁵ N values of cycad foliage, suggesting that they provide a reasonably robust record of the δ¹⁵ N of atmospheric N₂ . Application of this proxy to the record of carbonaceous cycad fossils may not only help to constrain changes in atmospheric nitrogen isotope ratios since the late Paleozoic, but also could shed light on the antiquity of the N₂ -fixing symbiosis between cycads and cyanobacteria.

Dual nitrogen and oxygen isotope fractionation during anaerobic ammonium oxidation by anammox bacteria

Natural abundance of stable nitrogen (N) and oxygen (O) isotopes are invaluable biogeochemical tracers for assessing the N transformations in the environment. To fully exploit these tracers, the N and O isotope effects (¹⁵ε and ¹⁸ε) associated with the respective nitrogen transformation processes must be known. However, the N and O isotope effects of anaerobic ammonium oxidation (anammox), one of the major fixed N sinks and NO₃^- producers, are not well known. Here, we report the dual N and O isotope effects associated with anammox by three different anammox bacteria including "Ca. Scalindua japonica", a putative marine species, which were measured in continuous enrichment culture experiments. All three anammox species yielded similar N isotope effects of NH₄⁺ oxidation to N₂ (¹⁵ε_NH4→N2) ranging from 30.9‰ to 32.7‰ and inverse kinetic isotope effects of NO₂^- oxidation to NO₃^- (¹⁵ε_NO2→NO3 = -45.3‰ to -30.1‰). In contrast, ¹⁵ε_NO2→N2 (NO₂^- reduction to N₂) were significantly different among three species, which is probably because individual anammox bacteria species might possess different types of nitrite reductase. We also report the combined O isotope effects for NO₂^- oxidation (¹⁸E_NO2→NO3) by anammox bacteria. These obtained dual N and O isotopic effects could provide significant insights into the contribution of anammox bacteria to the fixed N loss and NO₂^- reoxidation (N recycling) in various natural environments.

In Situ Quantification of Biological N2 Production Using Naturally Occurring 15N15N

We describe an approach for determining biological N₂ production in soils based on the proportions of naturally occurring ¹⁵N¹⁵N in N₂. Laboratory incubation experiments reveal that biological N₂ production, whether by denitrification or anaerobic ammonia oxidation, yields proportions of ¹⁵N¹⁵N in N₂ that are within 1‰ of that predicted for a random distribution of ¹⁵N and ¹⁴N atoms. This relatively invariant isotopic signature contrasts with that of the atmosphere, which has ¹⁵N¹⁵N proportions in excess of the random distribution by 19.1 ± 0.1‰. Depth profiles of gases in agricultural soils from the Kellogg Biological Station Long-Term Ecological Research site show biological N₂ accumulation that accounts for up to 1.6% of the soil N₂. One-dimensional reaction-diffusion modeling of these soil profiles suggests that subsurface N₂ pulses leading to surface emission rates as low as 0.3 mmol N₂ m^-2 d^-1 can be detected with current analytical precision, decoupled from N₂O production.

The Effect of a Tropical Climate on Available Nutrient Resources to Springs in Ophiolite-Hosted, Deep Biosphere Ecosystems in the Philippines

Springs hosted in ophiolites are often affected by serpentinization processes. The characteristically low DIC and high CH4 and H2 gas concentrations of serpentinizing ecosystems have led to interest in hydrogen based metabolisms in these subsurface biomes. However, a true subsurface signature can be difficult to identify in surface expressions such as serpentinizing springs. Here, we explore carbon and nitrogen resources in serpentinization impacted springs in the tropical climate of the Zambales and Palawan ophiolites in the Philippines, with a focus on surface vs. subsurface processes and exogenous vs. endogenous nutrient input. Isotopic signatures in spring fluids, biomass, and carbonates were examined to identify sources and sinks of carbon and nitrogen, carbonate geochemistry, and the effect of seasonal precipitation. Seasonality affected biomass production in both low flow and high flow spring systems. Changes in meteorological precipitation affected δ13CDIC and δ13CDOC values of the spring fluids, which reflected seasonal gain/loss of atmospheric influence and changes in exogenous DOC input. The primary carbon source in high flow systems was variable, with DOC contributing to biomass in many springs, and a mix of DIC and carbonates contributing to biomass in select locations. However, primary carbon resources in low flow systems may depend more on endogenous than exogenous carbon, even in high precipitation seasons. Isotopic evidence for nitrogen fixation was identified, with seasonal influence only seen in low flow systems. Carbonate formation was found to occur as a mixture of recrystallization/recycling of older carbonates and rapid mineral precipitation (depending on the system), with highly δ13C and δ18O depleted carbonates occurring in many locations. Subsurface signatures (e.g., low DOC influence on Cbiomass) were most apparent in the driest seasons and lowest flow systems, indicating locations where metabolic processes divorced from surface influences (including hydrogen based metabolisms) are most likely to be occurring.

Dynamic interaction between basin redox and the biogeochemical nitrogen cycle in an unconventional Proterozoic petroleum system

Precambrian hydrocarbons and their corresponding source rocks are distinctly different from their Phanerozoic counterparts, having been deposited in persistently anoxic environments in ecosystems dominated by bacteria. Here, we show that cyclic enrichment of organic matter in the world’s oldest hydrocarbon play (ca. 1.38 Ga), is not associated with flooding surfaces and is unrelated to variations in mineralogy or changes in the relative rate of clastic to biogenic sedimentation—factors typically attributed to organic enrichment in Phanerozoic shales. Instead, the cyclic covariation of total organic carbon, δ¹⁵N, δ¹³C and molybdenum are explained by the feedback between high levels of primary productivity, basin redox and the biogeochemical nitrogen cycle. These factors are important in constraining productivity in the marine biosphere, the development of Precambrian hydrocarbon source rocks, and more generally in understanding oxygenation of the ocean and atmosphere through Earth history; as all are ultimately related to organic carbon burial.

Efficient recycling of nutrients in modern and past hypersaline environments

The biogeochemistry of hypersaline environments is strongly influenced by changes in biological processes and physicochemical parameters. Although massive evaporation events have occurred repeatedly throughout Earth history, their biogeochemical cycles and global impact remain poorly understood. Here, we provide the first nitrogen isotopic data for nutrients and chloropigments from modern shallow hypersaline environments (solar salterns, Trapani, Italy) and apply the obtained insights to δ¹⁵N signatures of the Messinian salinity crisis (MSC) in the late Miocene. Concentrations and δ¹⁵N of chlorophyll a, bacteriochlorophyll a, nitrate, and ammonium in benthic microbial mats indicate that inhibition of nitrification suppresses denitrification and anammox, resulting in efficient ammonium recycling within the mats and high primary productivity. We also suggest that the release of ¹⁵N-depleted NH_3(gas) with increasing salinity enriches ammonium ¹⁵N in surface brine (≈34.0‰). Such elevated δ¹⁵N is also recorded in geoporphyrins isolated from sediments of the MSC peak (≈20‰), reflecting ammonium supply sufficient for sustaining phototrophic primary production. We propose that efficient nutrient supply combined with frequent bottom-water anoxia and capping of organic-rich sediments by evaporites of the Mediterranean MSC could have contributed to atmospheric CO₂ reduction during the late Miocene.

Role of APS reductase in biogeochemical sulfur isotope fractionation

Sulfur isotope fractionation resulting from microbial sulfate reduction (MSR) provides some of the earliest evidence of life, and secular variations in fractionation values reflect changes in biogeochemical cycles. Here we determine the sulfur isotope effect of the enzyme adenosine phosphosulfate reductase (Apr), which is present in all known organisms conducting MSR and catalyzes the first reductive step in the pathway and reinterpret the sedimentary sulfur isotope record over geological time. Small fractionations may be attributed to low sulfate concentrations and/or high respiration rates, whereas fractionations greater than that of Apr require a low chemical potential at that metabolic step. Since Archean sediments lack fractionation exceeding the Apr value of 20‰, they are indicative of sulfate reducers having had access to ample electron donors to drive their metabolisms. Large fractionations in post-Archean sediments are congruent with a decline of favorable electron donors as aerobic and other high potential metabolic competitors evolved.

Anoxic nitrogen cycling in a hydrocarbon and ammonium contaminated aquifer

Nitrogen fate and transport through contaminated groundwater systems, where N is both ubiquitous and commonly limits pollutant attenuation, must be re-evaluated given evidence for new potential microbial N pathways. We addressed this by measuring the isotopic composition of dissolved inorganic N (DIN = NH₄⁺, NO₂^-, and NO₃^-) and N functional gene abundances (amoA, nirK, nirS, hszA) from 20 to 38 wells across an NH₄⁺, hydrocarbon, and SO₄^2- contaminated aquifer. In-situ N attenuation was confirmed on three sampling dates (0, +6, +12 months) by the decreased [DIN] (4300 - 40 μM) and increased δ¹⁵N-DIN (5‰-33‰) over the flow path. However, the assumption of negligible N attenuation within the plume was complicated by the presence of alternative electron acceptors (SO₄^2-, Fe³⁺), both oxidizing and reducing functional genes, and N oxides within this anoxic zone. Active plume N cycling was corroborated using an NO₂^- dual isotope based model, which found the fastest (∼10 day) NO₂^- turnover within the N and electron donor rich central plume. Findings suggest that N cycling is not always O₂ limited within chemically complex contaminated aquifers, though this cycling may recycle the N species rather than attenuate N.

Coupling of ocean redox and animal evolution during the Ediacaran-Cambrian transition

The late Ediacaran to early Cambrian interval witnessed extraordinary radiations of metazoan life. The role of the physical environment in this biological revolution, such as changes to oxygen levels and nutrient availability, has been the focus of longstanding debate. Seemingly contradictory data from geochemical redox proxies help to fuel this controversy. As an essential nutrient, nitrogen can help to resolve this impasse by establishing linkages between nutrient supply, ocean redox, and biological changes. Here we present a comprehensive N-isotope dataset from the Yangtze Basin that reveals remarkable coupling between δ¹⁵N, δ¹³C, and evolutionary events from circa 551 to 515 Ma. The results indicate that increased fixed nitrogen supply may have facilitated episodic animal radiations by reinforcing ocean oxygenation, and restricting anoxia to near, or even at the sediment–water interface. Conversely, sporadic ocean anoxic events interrupted ocean oxygenation, and may have led to extinctions of the Ediacaran biota and small shelly animals.

The late Ediacaran to early Cambrian interval witnessed extraordinary radiations of metazoan life, in which the role of physical environment remains debated. Here, Wang et al. show that increased nutrient nitrogen availability may have exerted an important control on both macroevolution and ocean oxygenation.

Extreme enrichment in atmospheric 15N15N

Molecular nitrogen (N₂) comprises three-quarters of Earth's atmosphere and significant portions of other planetary atmospheres. We report a 19 per mil (‰) excess of ¹⁵N¹⁵N in air relative to a random distribution of nitrogen isotopes, an enrichment that is 10 times larger than what isotopic equilibration in the atmosphere allows. Biological experiments show that the main sources and sinks of N₂ yield much smaller proportions of ¹⁵N¹⁵N in N₂. Electrical discharge experiments, however, establish ¹⁵N¹⁵N excesses of up to +23‰. We argue that ¹⁵N¹⁵N accumulates in the atmosphere because of gas-phase chemistry in the thermosphere (>100 km altitude) on time scales comparable to those of biological cycling. The atmospheric ¹⁵N¹⁵N excess therefore reflects a planetary-scale balance of biogeochemical and atmospheric nitrogen chemistry, one that may also exist on other planets.

Isotopic constraints on water source mixing, network leakage and contamination in an urban groundwater system

Water supply in developing countries is prone to large water losses due to leaky distribution networks and defective sewers, which may affect groundwater quality and quantity in urban areas and result in complex subsurface mixing dynamics. In this study, a multi-stable isotope approach was used to investigate spatiotemporal fluctuations of surface and sub-surface water source partitioning and mixing, and to assess nitrogen (N) contamination in the urban water cycle of As-Salt, Jordan. Water import from the King Abdullah Canal (KAC), mains waters from the network, and wastewater are characterized by distinct isotopic signatures, which allowed us to quantify city effluents into the groundwater. Temporal variations in isotopic signatures of polluted groundwater are explained by seasonally fluctuating inflow, and dilution by water that originates from Lake Tiberias and enters the urban water cycle via the KAC. Isotopic analysis (N and O) and comparison between groundwater nitrate and nitrate from mains water, water imports and wastewater confirmed that septic waste from leaky sewers is the main contributor of nitrate contamination. The nitrate of strongly contaminated groundwater was characterized by highest δ¹⁵N_NO3 values (13.3±1.8‰), whereas lowest δ¹⁵N_NO3 values were measured in unpolluted groundwater (6.9‰). Analogously, nitrate concentration and isotopic ratios were used for source partitioning and qualitatively confirmed δD_H2O and δ¹⁸O_H2O-based estimates. Dual water isotope endmember mixing calculations suggest that city effluents from leaky networks and sewers contribute 30-64% to the heavily polluted groundwater. Ternary mixing calculations including also chloride revealed that 5-18% of the polluted groundwater is wastewater. Up to two thirds of the groundwater originates from mains, indicating excessive water loss from the network, and calling for improved water supply management.

Kinetic 15N-isotope effects on algal growth

Stable isotope labeling is a standard technique for tracing material transfer in molecular, ecological and biogeochemical studies. The main assumption in this approach is that the enrichment with a heavy isotope has no effect on the organism metabolism and growth, which is not consistent with current theoretical and empirical knowledge on kinetic isotope effects. Here, we demonstrate profound changes in growth dynamics of the green alga Raphidocelis subcapitata grown in 15N-enriched media. With increasing 15N concentration (0.37 to 50 at%), the lag phase increased, whereas maximal growth rate and total yield decreased; moreover, there was a negative relationship between the growth and the lag phase across the treatments. The latter suggests that a trade-off between growth rate and the ability to adapt to the high 15N environment may exist. Remarkably, the lag-phase response at 3.5 at% 15N was the shortest and deviated from the overall trend, thus providing partial support to the recently proposed Isotopic Resonance hypothesis, which predicts that certain isotopic composition is particularly favorable for living organisms. These findings confirm the occurrence of KIE in isotopically enriched algae and underline the importance of considering these effects when using stable isotope labeling in field and experimental studies.

Onset of the aerobic nitrogen cycle during the Great Oxidation Event

The rise of oxygen on the early Earth (about 2.4 billion years ago) caused a reorganization of marine nutrient cycles, including that of nitrogen, which is important for controlling global primary productivity. However, current geochemical records lack the temporal resolution to address the nature and timing of the biogeochemical response to oxygenation directly. Here we couple records of ocean redox chemistry with nitrogen isotope (¹⁵N/¹⁴N) values from approximately 2.31-billion-year-old shales of the Rooihoogte and Timeball Hill formations in South Africa, deposited during the early stages of the first rise in atmospheric oxygen on the Earth (the Great Oxidation Event). Our data fill a gap of about 400 million years in the temporal ¹⁵N/¹⁴N record and provide evidence for the emergence of a pervasive aerobic marine nitrogen cycle. The interpretation of our nitrogen isotope data in the context of iron speciation and carbon isotope data suggests biogeochemical cycling across a dynamic redox boundary, with primary productivity fuelled by chemoautotrophic production and a nitrogen cycle dominated by nitrogen loss processes using newly available marine oxidants. This chemostratigraphic trend constrains the onset of widespread nitrate availability associated with ocean oxygenation. The rise of marine nitrate could have allowed for the rapid diversification and proliferation of nitrate-using cyanobacteria and, potentially, eukaryotic phytoplankton.

Enhanced Nitrogen Loss by Eddy-Induced Vertical Transport in the Offshore Peruvian Oxygen Minimum Zone

The eastern tropical South Pacific (ETSP) upwelling region is one of the ocean’s largest sinks of fixed nitrogen, which is lost as N₂ via the anaerobic processes of anammox and denitrification. One-third of nitrogen loss occurs in productive shelf waters stimulated by organic matter export as a result of eastern boundary upwelling. Offshore, nitrogen loss rates are lower, but due to its sheer size this area accounts for ~70% of ETSP nitrogen loss. How nitrogen loss and primary production are regulated in the offshore ETSP region where coastal upwelling is less influential remains unclear. Mesoscale eddies, ubiquitous in the ETSP region, have been suggested to enhance vertical nutrient transport and thereby regulate primary productivity and hence organic matter export. Here, we investigated the impact of mesoscale eddies on anammox and denitrification activity using ¹⁵N-labelled in situ incubation experiments. Anammox was shown to be the dominant nitrogen loss process, but varied across the eddy, whereas denitrification was below detection at all stations. Anammox rates at the eddy periphery were greater than at the center. Similarly, depth-integrated chlorophyll paralleled anammox activity, increasing at the periphery relative to the eddy center; suggestive of enhanced organic matter export along the periphery supporting nitrogen loss. This can be attributed to enhanced vertical nutrient transport caused by an eddy-driven submesoscale mechanism operating at the eddy periphery. In the ETSP region, the widespread distribution of eddies and the large heterogeneity observed in anammox rates from a compilation of stations suggests that eddy-driven vertical nutrient transport may regulate offshore primary production and thereby nitrogen loss.

Nitrite isotopes as tracers of marine N cycle processes

Nitrite (NO₂^-) is a key intermediate in the marine nitrogen (N) cycle. It is produced and consumed throughout the ocean by the dominant processes driving the distribution, availability and speciation of N. However, the accumulation of nitrite is typically confined to depths near the base of the sunlit euphotic zone and in oxygen-deficient zones. These features are known as the primary and secondary nitrite maximum (PNM and SNM), respectively. The processes controlling nitrite accumulation in these features are not fully understood, but are thought to depend on the microbial community composition and its response to environmental conditions. A variety of approaches have been applied to understanding these features since their discovery, with the stable N and oxygen (O) isotope measurements of nitrite being added to this toolkit most recently. Large variations in nitrite N isotope ratios (¹⁵N/¹⁴N) and dramatic depletions in ¹⁵N contrast with more consistent nitrite O isotope ratios (¹⁸O/¹⁶O) in the SNM. These signals provide unique information about the mechanisms of nitrite consumption in the SNM. By contrast, nitrite in the PNM shows less variation in ¹⁵N/¹⁴N, but variations in ¹⁸O/¹⁶O that provide insight into the mechanisms and rates of N cycling there. This review presents a synthesis of nitrite isotope measurements in the marine environment, highlighting the insights that have been gained from these measurements.This article is part of the themed issue 'Biological and climatic impacts of ocean trace element chemistry'.

Isotopic overprinting of nitrification on denitrification as a ubiquitous and unifying feature of environmental nitrogen cycling

Natural abundance nitrogen and oxygen isotopes of nitrate (δ¹⁵N_NO3 and δ¹⁸O_NO3) provide an important tool for evaluating sources and transformations of natural and contaminant nitrate (NO₃^-) in the environment. Nevertheless, conventional interpretations of NO₃^- isotope distributions appear at odds with patterns emerging from studies of nitrifying and denitrifying bacterial cultures. To resolve this conundrum, we present results from a numerical model of NO₃^- isotope dynamics, demonstrating that deviations in δ¹⁸O_NO3 vs. δ¹⁵N_NO3 from a trajectory of 1 expected for denitrification are explained by isotopic over-printing from coincident NO₃^- production by nitrification and/or anammox. The analysis highlights two driving parameters: (i) the δ¹⁸O of ambient water and (ii) the relative flux of NO₃^- production under net denitrifying conditions, whether catalyzed aerobically or anaerobically. In agreement with existing analyses, dual isotopic trajectories >1, characteristic of marine denitrifying systems, arise predominantly under elevated rates of NO₂^- reoxidation relative to NO₃^- reduction (>50%) and in association with the elevated δ¹⁸O of seawater. This result specifically implicates aerobic nitrification as the dominant NO₃^- producing term in marine denitrifying systems, as stoichiometric constraints indicate anammox-based NO₃^- production cannot account for trajectories >1. In contrast, trajectories <1 comprise the majority of model solutions, with those representative of aquifer conditions requiring lower NO₂^- reoxidation fluxes (<15%) and the influence of the lower δ¹⁸O of freshwater. Accordingly, we suggest that widely observed δ¹⁸O_NO3 vs. δ¹⁵N_NO3 trends in freshwater systems (<1) must result from concurrent NO₃^- production by anammox in anoxic aquifers, a process that has been largely overlooked.

Electron Shuttles Enhance Anaerobic Ammonium Oxidation Coupled to Iron(III) Reduction

Anaerobic ammonium oxidation coupled to iron(III) reduction, termed Feammox, is a newly discovered nitrogen cycling process. However, little is known about the roles of electron shuttles in the Feammox reactions. In this study, two forms of Fe(III) (oxyhydr)oxide ferrihydrite (ex situ ferrihydrite and in situ ferrihydrite) were used in dissimilatory Fe(III) reduction (DIR) enrichments from paddy soil. Evidence for Feammox in DIR enrichments was demonstrated using the (15)N-isotope tracing technique. The extent and rate of both the (30)N2-(29)N2 and Fe(II) formation were enhanced when amended with electron shuttles (either 9,10-anthraquinone-2,6-disulfonate (AQDS) or biochar) and further simulated when these two shuttling compounds were combined. Although the Feammox-associated Fe(III) reduction accounted for only a minor proportion of total Fe(II) formation compared to DIR, it was estimated that the potentially Feammox-mediated N loss (0.13-0.48 mg N L(-1) day(-1)) was increased by 17-340% in the enrichments by the addition of electron shuttles. The addition of electron shuttles led to an increase in the abundance of unclassified Pelobacteraceae, Desulfovibrio, and denitrifiers but a decrease in Geobacter. Overall, we demonstrated a stimulatory effect of electron shuttles on Feammox that led to higher N loss, suggesting that electron shuttles might play a crucial role in Feammox-mediated N loss from soils.