N and O isotope fractionation in nitrate during chemolithoautotrophic denitrification by Sulfurimonas gotlandica

Active microbial communities facilitate carbon turnover in brine pools found in the deep Southeastern Mediterranean Sea

Discharge of gas-rich brines fuels productive chemosynthetic ecosystems in the deep sea. In these salty, methanic and sulfidic brines, microbial communities adapt to specific niches along the physicochemical gradients. However, the molecular mechanisms that underpin these adaptations are not fully known. Using metagenomics, we investigated the dense (∼106 cell ml-1) microbial communities that occupy small deep-sea brine pools found in the Southeastern Mediterranean Sea (1150 m water depth, ∼22 °C, ∼60 PSU salinity, sulfide, methane, ammonia reaching millimolar levels, and oxygen usually depleted), reaching high productivity rates of 685 μg C L-1 d-1 ex-situ. We curated 266 metagenome-assembled genomes of bacteria and archaea from the several pools and adjacent sediment-water interface, highlighting the dominance of a single Sulfurimonas, which likely fuels its autotrophy using sulfide oxidation or inorganic sulfur disproportionation. This lineage may be dominant in its niche due to genome streamlining, limiting its metabolic repertoire, particularly by using a single variant of sulfide: quinone oxidoreductase. These primary producers co-exist with ANME-2c archaea that catalyze the anaerobic oxidation of methane. Other lineages can degrade the necromass aerobically (Halomonas and Alcanivorax), or anaerobically through fermentation of macromolecules (e.g., Caldatribacteriota, Bipolaricaulia, Chloroflexota, etc). These low-abundance organisms likely support the autotrophs, providing energy-rich H2, and vital organics such as vitamin B12.

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.

Impact of organic carbon on sulfide-driven autotrophic denitrification: Insights from isotope fractionation and functional genes

Additional organics are generally supplemented in the sulfide-driven autotrophic denitrification system to accelerate the denitrification rate and reduce sulfate production. In this study, different concentrations of sodium acetate (NaAc) were added to the sulfide-driven autotrophic denitrification reactor, and the S0 accumulation increased from 7.8% to 100% over a 120-day operation period. Batch experiments revealed a threefold increase in total nitrogen (TN) removal rate at an Ac--C/N ratio of 2.8 compared to a ratio of 0.5. Addition of organic carbon accelerated denitrification rate and nitrite consumption, which shortened the emission time of N2O, but increased the N2O production rate. The lowest N2O emissions were achieved at the Ac--C/N ratio of 1.3. Stable isotope fractionation is a powerful tool for evaluating different reaction pathways, with the 18ε/15ε values in nitrate reduction ranging from 0.5 to 1.0. This study further confirmed that isotope fractionation can reveal denitrifying nutrient types, with the 18ε (isotopic enrichment factor of oxygen)/15ε (isotopic enrichment factor of nitrogen) value approaching 1.0 for autotrophic denitrification and 0.5 for heterotrophic denitrification. Additionally, the 18ε/15ε values can indicate changes in nitrate reductase. There is a positive correlation between the 18ε/15ε values and the abundance of the functional gene napA, and a negative correlation with the abundance of the gene narG. Moreover, 18ε and 15ε were associated with changes in kinetic parameters during nitrate reduction. In summary, the combination of functional gene analysis and isotope fractionation effectively revealed the complexities of mixotrophic denitrification systems, providing insights for optimizing denitrification processes.

Optimized start-up strategies for elemental sulfur packing bioreactor achieving effective autotrophic denitrification

The start-up efficiency of the elemental sulfur packing bioreactor (S0PB) is constrained by the slow growth kinetics of autotrophic microorganisms, which is essentially optimized. This study aims to optimize start-up procedures and offer scientific guidance for the practical applications of S0PB. Through comparing the start-up efficiencies under various conditions related to inoculation, backwashing, and EBCT, it was found that these conditions did not significantly influence start-up time, but they did impact denitrification performance in detail. Using activated sludge as the inoculum was not recommended as the 2.5 ± 0.2 mg-N/L higher nitrite accumulation and 26.0 ± 5.1 % lower TN removal rate, compared to self-enrichment. Starting with a long-to-short EBCT (1 → 0.33 h) achieved higher nitrate removal of 11.5 ± 0.6 mg-N/L and eliminated nitrite accumulation compared to constantly short EBCT (0.33 h) conditions. Daily and postponed backwashing were suggested for long-to-short EBCT and constantly short EBCT start-up, respectively. Enrichment of Sulfurimonas was beneficial for the effective nitrite reduction process.

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.

Optimization of the chemolithotrophic denitrification of ion exchange concentrate using hydrogen-based membrane biofilm reactors

A H2-based membrane biofilm reactor (MBfR) was used to remove nitrate from a synthetic ion-exchange brine made up of 23.8 g L-1 NaCl. To aid the selection of the best nitrate management strategy, our research was based on the integrated analysis of ionic exchange and MBfR processes, including a detailed cost analysis. The nitrate removal flux was not affected if key nutrients were present in the feed solution including potassium and sodium bicarbonate. Operating pH was maintained between 7 and 8. By using a H2 pressure of 15 psi, a hydraulic retention time (HRT) of 4 h, and a surface loading rate of 13.6 ± 0.2 g N m-2 d-1, the average nitrate removal flux was 3.3 ± 0.6 g N m-2 d-1. At HRTs of up to 24 h, the system was able to maintain a removal flux of 1.6 ± 0.2 g N m-2 d-1. Microbial diversity analysis showed that the consortium was dominated by the genera Sulfurimonas and Marinobacter. The estimated cost for a 200 m3/h capacity, coupled ion exchange (IX) + MBfR treatment plant is 0.43 USD/m3. This is a sustainable and competitive alternative to an IX-only plant for the same flowrate. The proposed treatment option allows for brine recycling and reduces costs by 55% by avoiding brine disposal expenses.

Metagenomic 16S rDNA reads of in situ preserved samples revealed microbial communities in the Yongle blue hole

Our knowledge on biogeochemistry and microbial ecology of marine blue holes is limited due to challenges in collecting multilayered water column and oxycline zones. In this study, we collected samples from 16 water layers in Yongle blue hole (YBH) located in the South China Sea using the in situ microbial filtration and fixation (ISMIFF) apparatus. The microbial communities based on 16S rRNA metagenomic reads for the ISMIFF samples showed high microbial diversity and consistency among samples with similar dissolved oxygen levels. At the same depth of the anoxic layer, the ISMIFF samples were dominated by sulfate-reducing bacteria from Desulfatiglandales (17.96%). The sulfide concentration is the most significant factor that drives the division of microbial communities in YBH, which might support the prevalence of sulfate-reducing microorganisms in the anoxic layers. Our results are different from the microbial community structures of a Niskin sample of this study and the reported samples collected in 2017, in which a high relative abundance of Alteromonadales (26.59%) and Thiomicrospirales (38.13%), and Arcobacteraceae (11.74%) was identified. We therefore demonstrate a new profile of microbial communities in YBH probably due to the effect of sampling and molecular biological methods, which provides new possibilities for further understanding of the material circulation mechanism of blue holes and expanding anoxic marine water zones under global warming.

Denitrification fractionates N and O isotopes of nitrate following a ratio independent of carbon sources in freshwaters

The stable isotope technique has been used in tracking nitrogen cycling processes, but the isotopic characteristics are influenced by environmental conditions. To better understand the variability of nitrate isotopes in nature, we investigated the influence of organic carbon sources on isotope fractionation characteristics during microbial denitrification. Denitrifying cultures were inoculated with freshwater samples and enriched with five forms of organic compounds, that is, acetate, citrate, glucose, cellobiose, and leucine. Though the isotope enrichment factors of nitrogen and oxygen (15 ε and 18 ε) changed with carbon sources, 18 ε/15 ε always followed a proportionality near 1. Genome-centred metagenomics revealed the enrichment of a few populations, such as Pseudomonas, Enterobacter, and Atlantibacter, most of which contained both NapA- and NarG-type nitrate reductases. Metatranscriptome showed that both NapA and NarG were expressed but to different extents in the enrichments. Furthermore, isotopic data collected from a deep reservoir was analysed. The results showed δ18 O- and δ15 N-nitrate did not correlate in the surface water where nitrification was active, but 18 ε/15 ε followed a proportionality of 1.05 ± 011 in deeper waters (≥ 12 m) where denitrification controlled the nitrate isotope. The independence of 18 ε/15 ε from carbon sources provides an opportunity to determine heterotrophic denitrification and helps the interpretation of nitrate isotopes in freshwaters.

Novel Insight into Microbially Mediated Nitrate-Reducing Fe(II) Oxidation by Acidovorax sp. Strain BoFeN1 Using Dual N-O Isotope Fractionation

Microbially mediated nitrate reduction coupled with Fe(II) oxidation (NRFO) plays an important role in the Fe/N interactions in pH-neutral anoxic environments. However, the relative contributions of the chemical and microbial processes to NRFO are still unclear. In this study, N-O isotope fractionation during NRFO was investigated. The ratios of O and N isotope enrichment factors (18ε:15ε)-NO3- indicated that the main nitrate reductase functioning in Acidovorax sp. strain BoFeN1 was membrane-bound dissimilatory nitrate reductase (Nar). N-O isotope fractionation during chemodenitrification [Fe(II) + NO2-], microbial nitrite reduction (cells + NO2-), and the coupled process [cells + NO2- + Fe(II)] was explored. The ratios of (18ε:15ε)-NO2- were 0.58 ± 0.05 during chemodenitrification and -0.41 ± 0.11 during microbial nitrite reduction, indicating that N-O isotopes can be used to distinguish chemical from biological reactions. The (18ε:15ε)-NO2- of 0.70 ± 0.05 during the coupled process was close to that obtained for chemodenitrification, indicating that chemodenitrification played a more important role than biological reactions during the coupled process. The results of kinetic modeling showed that the relative contribution of chemodenitrification was 99.3% during the coupled process, which was consistent with that of isotope fractionation. This study provides a better understanding of chemical and biological mechanisms of NRFO using N-O isotopes and kinetic modeling.

Deep denitrification: Stream and groundwater biogeochemistry reveal contrasted but connected worlds above and below

Excess nutrients from agricultural and urban development have created a cascade of ecological crises around the globe. Nutrient pollution has triggered eutrophication in most freshwater and coastal ecosystems, contributing to a loss in biodiversity, harm to human health, and trillions in economic damage every year. Much of the research conducted on nutrient transport and retention has focused on surface environments, which are both easy to access and biologically active. However, surface characteristics of watersheds, such as land use and network configuration, often do not explain the variation in nutrient retention observed in rivers, lakes, and estuaries. Recent research suggests subsurface processes and characteristics may be more important than previously thought in determining watershed-level nutrient fluxes and removal. In a small watershed in western France, we used a multi-tracer approach to compare surface and subsurface nitrate dynamics at commensurate spatiotemporal scales. We combined 3-D hydrological modeling with a rich biogeochemical dataset from 20 wells and 15 stream locations. Water chemistry in the surface and subsurface showed high temporal variability, but groundwater was substantially more spatially variable, attributable to long transport times (10-60 years) and patchy distribution of the iron and sulfur electron donors fueling autotrophic denitrification. Isotopes of nitrate and sulfate revealed fundamentally different processes dominating the surface (heterotrophic denitrification and sulfate reduction) and subsurface (autotrophic denitrification and sulfate production). Agricultural land use was associated with elevated nitrate in surface water, but subsurface nitrate concentration was decoupled from land use. Dissolved silica and sulfate are affordable tracers of residence time and nitrogen removal that are relatively stable in surface and subsurface environments. Together, these findings reveal distinct but adjacent and connected biogeochemical worlds in the surface and subsurface. Characterizing how these worlds are linked and decoupled is critical to meeting water quality targets and addressing water issues in the Anthropocene.

Effect of increased carbon load on denitrification efficiency and nitrate isotope enrichment factors in subsurface wastewater infiltration system

Denitrification plays a dominant role in nitrate removal in subsurface wastewater infiltration system (SWIS). However, the effect of increased carbon (C) load on denitrification efficiency in the SWIS remain unclear. In this study, we used analyses of stable isotopes of nitrogen (N) and oxygen (O) in nitrate to investigate the N and O isotope enrichment factors (¹⁵ ε and ¹⁸ ε) and quantified N losses via denitrification in SWIS. The results demonstrated that an increase in C loads positively affected the pollutant removal performance of SWIS. The natural abundance of ¹⁵ N and ¹⁸ O increased with decreasing nitrate concentration from 12.5 to 7.3 mg/L, accompanied by increased ¹⁵ ε and ¹⁸ ε from -8.7‰ to -10.6‰ and -5.9‰ to -8.2‰, respectively, as the C load increased from 18 to 36 g/(m²  d). The contribution of denitrification to nitrate removal was 62%, 71%, and 77% when C loads were 18, 27, and 36 g/(m²  d), respectively, indicating that increased C loads could improve the nitrate removal through denitrification in SWIS. PRACTITIONER POINTS: Increasing C loads positively affected the nitrate removal performance of SWIS. N and O isotope enrichment factors of nitrate increased with the enhancement of influent C load. A C load of 36 g/(m²  d) is recommended in SWIS to improve the N removal performance and denitrification efficiency.

Nitrate removal rates, isotopic fractionation, and denitrifying bacteria in a woodchip-based permeable reactive barrier system: a long-term column experiment

This study evaluated the effectiveness of using organic carbon materials (i.e., woodchips) to remove nitrate from groundwater. The results of our flow-through column experiment, which was conducted over 1.6 years, suggested that denitrifying bacteria reduce nitrate by using it as an electron acceptor and woodchips as an electron donor. The nitrate removal rates were sufficiently high (0.39-1.04 mmol L-1 day-1) during the operation of the column. Denitrification process was supported by fractionation of nitrogen and oxygen isotopes (δ15N and δ18O), with the δ15N and δ18O values enriched from 7.4‰ and 22.3‰ to 21.2‰ and 30.4‰, respectively. Enrichment factors ([Formula: see text]) for 15 N and 18O were calculated using the Rayleigh fractionation model, with values of - 13.2‰ for ε15N and - 7.1‰ for ε18O. The fractionation ratio of 15 N to 18O was 1.9:1, confirming denitrification. The most abundant bacterial genera in the soil used for inoculation were Enterobacter (86.7%), Nitrospira (1.8%), and Arthrobacter (1.5%), while those in the column effluent were Macrococcus (37.1%), Escherichia (14.7%), and Shigella (14.6%), indicating that bacterial communities changed in response to geochemical conditions in the column. This study suggests that nitrate in groundwater can be effectively removed using woodchip-based passive treatment systems and that information on isotopic fractionation and denitrifying bacteria can be key tools to understand denitrification.

Denitrification kinetics during aquifer storage and recovery of drainage water from agricultural land

An aquifer storage transfer and recovery (ASTR) system was studied in which tile drainage water (TDW) was injected with relatively high NO₃ (about 14 mg/L) concentrations originating from fertilizers. Here we present the evolution of denitrification kinetics at 6 different depths in the aquifer before, and during ASTR operation. First-order denitrification rate constants increased over time before and during the first days of ASTR operation, likely due to microbial adaptation of the native bacterial community and/or bioaugmentation of the aquifer by denitrifying bacteria present in injected TDW. Push-pull tests were performed in the native aquifer before ASTR operation. Obtained first-order denitrification rate constants were negligible (0.00-0.03 d^-1) at the start, but increased to 0.17-0.83 d^-1 after a lag-phase of about 6 days. During the first days of ASTR operation in autumn 2019, the arrival of injected TDW was studied at 2.5 m distance from the injection well. First-order denitrification rate constants increased again over time (maximum >1 d^-1). Three storage periods without injection were monitored in winter 2019, fall 2020, and spring 2021 during ASTR operation. First-order rate constants ranged between 0.12 and 0.61 d^-1. Denitrification coupled to pyrite oxidation occurred at all depths, but other oxidation processes were indicated as well. NO₃ concentration trends resembled Monod kinetics but were fitted also to a first-order decay rate model to facilitate comparison. Rate constants during the storage periods were substantially lower than during injection, probably due to a reduction in the exchange rate between aquifer solid phases and injected water during the stagnant conditions. Denitrification rate constants deviated maximally a factor 5 over time and depth for all in-situ measurement approaches after the lag-phase. The combination of these in-situ approaches enabled to obtain more detailed insights in the evolution of denitrification kinetics during AS(T)R.

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.

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.

Unchanged nitrate and nitrite isotope fractionation during heterotrophic and Fe(II)-mixotrophic denitrification suggest a non-enzymatic link between denitrification and Fe(II) oxidation

Natural-abundance measurements of nitrate and nitrite (NO_x) isotope ratios (δ¹⁵N and δ¹⁸O) can be a valuable tool to study the biogeochemical fate of NO_x species in the environment. A prerequisite for using NO_x isotopes in this regard is an understanding of the mechanistic details of isotope fractionation (¹⁵ε, ¹⁸ε) associated with the biotic and abiotic NO_x transformation processes involved (e.g., denitrification). However, possible impacts on isotope fractionation resulting from changing growth conditions during denitrification, different carbon substrates, or simply the presence of compounds that may be involved in NO_x reduction as co-substrates [e.g., Fe(II)] remain uncertain. Here we investigated whether the type of organic substrate, i.e., short-chained organic acids, and the presence/absence of Fe(II) (mixotrophic vs. heterotrophic growth conditions) affect N and O isotope fractionation dynamics during nitrate (NO₃^–) and nitrite (NO₂^–) reduction in laboratory experiments with three strains of putative nitrate-dependent Fe(II)-oxidizing bacteria and one canonical denitrifier. Our results revealed that ¹⁵ε and ¹⁸ε values obtained for heterotrophic (¹⁵ε-NO₃^–: 17.6 ± 2.8‰, ¹⁸ε-NO₃^–:18.1 ± 2.5‰; ¹⁵ε-NO₂^–: 14.4 ± 3.2‰) vs. mixotrophic (¹⁵ε-NO₃^–: 20.2 ± 1.4‰, ¹⁸ε-NO₃^–: 19.5 ± 1.5‰; ¹⁵ε-NO₂^–: 16.1 ± 1.4‰) growth conditions are very similar and fall within the range previously reported for classical heterotrophic denitrification. Moreover, availability of different short-chain organic acids (succinate vs. acetate), while slightly affecting the NO_x reduction dynamics, did not produce distinct differences in N and O isotope effects. N isotope fractionation in abiotic controls, although exhibiting fluctuating results, even expressed transient inverse isotope dynamics (¹⁵ε-NO₂^–: –12.4 ± 1.3 ‰). These findings imply that neither the mechanisms ordaining cellular uptake of short-chain organic acids nor the presence of Fe(II) seem to systematically impact the overall N and O isotope effect during NO_x reduction. The similar isotope effects detected during mixotrophic and heterotrophic NO_x reduction, as well as the results obtained from the abiotic controls, may not only imply that the enzymatic control of NO_x reduction in putative NDFeOx bacteria is decoupled from Fe(II) oxidation, but also that Fe(II) oxidation is indirectly driven by biologically (i.e., via organic compounds) or abiotically (catalysis via reactive surfaces) mediated processes co-occurring during heterotrophic denitrification.

Sources and cycling of nitrogen revealed by stable isotopes in a highly populated large temperate coastal embayment

The identification of nitrogen sources and cycling processes is critical to the management of nitrogen pollution. Here, we used both stable (δ¹⁵N-NO₃^-, δ¹⁸O-NO₃^-, δ¹⁵N-NH₄⁺) and radiogenic (²²²Rn) isotopes together with nitrogen concentrations to evaluate the relative importance of point (i.e. sewage) and diffuse sources (i.e. agricultural-derived NO₃^- from groundwater, drains and creeks) in driving nitrogen dynamic in a shallow coastal embayment, Port Phillip Bay (PPB) in Victoria, Australia. This study is an exemplar of nitrogen-limited coastal systems around the world where nitrogen contamination is prevalent and where constraining it may be challenging. In addition to surrounding land use, we found that the distributions of NO₃^- and NH₄⁺ in the bay were closely linked to the presence of drift algae. Highest NO₃^- and NH₄⁺ concentrations were 315 μmol L^-1 and 2140 μmol L^-1, respectively. Based on the isotopic signatures of NO₃^- (δ¹⁵N: 0.17 to 21‰; δ¹⁸O: 3 to 26‰) and NH₄⁺ (δ¹⁵N: 30 to 39‰) in PPB, the high nitrogen concentrations were attributed to three major sources which varied between winter and summer; (1) nitrified sewage effluent and drift algae derived NH₄⁺ mainly during winter, (2) NO₃^- mixture from atmospheric deposition, drains and creeks predominantly observed during summer and (3) groundwater and sewage derived NO₃^- during both surveys. The isotopic composition of NO₃^- also suggested the removal of agriculture-derived NO₃^- through denitrification was prevalent during transport. This study highlights the role of terrestrial-coastal interactions on nitrogen dynamics and illustrates the importance of submarine groundwater discharge as a prominent pathway of diffuse NO₃^- inputs. Quantifying the relative contributions of multiple NO₃^- input pathways, however, require more extensive efforts and is an important avenue for future research.

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.

Community diversity metrics, interactions, and metabolic functions of bacteria associated with municipal solid waste landfills at different maturation stages

Municipal landfills are hot spots of dynamic bioprocesses facilitated by complex interactions of a multifaceted microbiome, whose functioning in municipal landfills at different maturing stages is poorly understood. This study determined bacterial community composition, interaction conetworks, metabolic functions, and controlling physicochemical properties in two landfills aged 14 and 36 years. High throughput sequencing revealed a similar distribution of bacterial diversity, evenness, and richness in the 14‐ and 36‐year‐old landfills in the 0–90 cm depth. At deeper layers (120–150 cm), the 14‐year‐old landfill had significantly greater bacterial diversity and richness indicating that it is a more active microcosm than the 36‐year‐old landfill, where phylum Epsilonbacteraeota was overwhelmingly dominant. The taxonomic and functional diversity in the 14‐year‐old landfill was further reflected by the abundant presence of indicator genera Pseudomonas,Lutispora,Hydrogenspora, and Sulfurimonas coupled with the presence of biomarker enzymes associated with carbon (C), nitrogen (N), and sulfur (S) metabolism. Furthermore, canonical correspondence analysis revealed that bacteria in the 14‐year‐old landfill were positively correlated with high C, N, S, and phosphorus resulting in positive cooccurrence interactions. In the 36‐year‐old landfill, negative coexclusion interactions populated by members of N fixing Rhizobiales were dominant, with metabolic functions and biomarker enzymes predicting significant N fixation that, as indicated by interaction network, potentially inhibited ammonia‐intolerant bacteria. Overall, our findings show that diverse bacterial community in the 14‐year‐old landfill was dominated by copiotrophs associated with positive conetworks, whereas the 36‐year‐old landfill was dominated by lithotrophs linked to coexclusion interactions that greatly reduced bacterial diversity and richness.

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.

Controls on the Isotopic Composition of Nitrite (δ15N and δ18O) during Denitrification in Freshwater Sediments

The microbial reduction of nitrate, via nitrite into gaseous di-nitrogen (denitrification) plays a major role in nitrogen removal from aquatic ecosystems. Natural abundance stable isotope measurements can reveal insights into the dynamics of production and consumption of nitrite during denitrification. In this study, batch experiments with environmental bacterial communities were used to investigate variations of concentrations and isotope compositions of both nitrite and nitrate under anoxic conditions. To this end, denitrification experiments were carried out with nitrite or nitrate as sole electron acceptors at two substrate levels respectively. For experiments with nitrate as substrate, where the intermediate compound nitrite is both substrate and product of denitrification, calculations of the extent of isotope fractionation were conducted using a non-steady state model capable of tracing chemical and isotope kinetics during denitrification. This study showed that nitrogen isotope fractionation was lower during the use of nitrite as substrate (ε = −4.2 and −4.5‰ for both treatments) as compared to experiments where nitrite was produced as an intermediate during nitrate reduction (ε = −10 and −15‰ for both treatments). This discrepancy might be due to isotopic fractionation within the membrane of denitrifiers. Moreover, our results confirmed previously observed rapid biotic oxygen isotope exchange between nitrite and water.

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 δ¹³C_DIC and δ¹³C_DOC 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 C_biomass) 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.

Broad Phylogenetic Diversity Associated with Nitrogen Loss through Sulfur Oxidation in a Large Public Marine Aquarium

Denitrification by sulfur-oxidizing bacteria is an effective nitrate removal strategy in engineered aquatic systems. However, the community taxonomic and metabolic diversity of sulfur-driven denitrification (SDN) systems, as well as the relationship between nitrate removal and SDN community structure, remains underexplored. This is particularly true for SDN reactors applied to marine aquaria, despite the increasing use of this technology to supplement filtration. We applied 16S rRNA gene, metagenomic, and metatranscriptomic analyses to explore the microbial basis of SDN reactors operating on Georgia Aquarium's Ocean Voyager, the largest indoor closed-system seawater exhibit in the United States. The exhibit's two SDN systems vary in water retention time and nitrate removal efficiency. The systems also support significantly different microbial communities. These communities contain canonical SDN bacteria, including a strain related to Thiobacillus thioparus that dominates the system with the higher water retention time and nitrate removal but is effectively absent from the other system. Both systems contain a wide diversity of other microbes whose metagenome-assembled genomes contain genes of SDN metabolism. These include hundreds of strains of the epsilonproteobacterium Sulfurimonas, as well as gammaproteobacterial sulfur oxidizers of the Thiotrichales and Chromatiales, and a relative of Sedimenticola thiotaurini with complete denitrification potential. The SDN genes are transcribed and the taxonomic richness of the transcript pool varies markedly among the enzymatic steps, with some steps dominated by transcripts from noncanonical SDN taxa. These results indicate complex and variable SDN communities that may involve chemical dependencies among taxa as well as the potential for altering community structure to optimize nitrate removal.IMPORTANCE Engineered aquatic systems such as aquaria and aquaculture facilities have large societal value. Ensuring the health of animals in these systems requires understanding how microorganisms contribute to chemical cycling and waste removal. Focusing on the largest seawater aquarium in the United States, we explore the microbial communities in specialized reactors designed to remove excess nitrogen through the metabolic activity of sulfur-consuming microbes. We show that the diversity of microbes in these reactors is both high and highly variable, with distinct community types associated with significant differences in nitrogen removal rate. We also show that the genes encoding the metabolic steps of nitrogen removal are distributed broadly throughout community members, suggesting that the chemical transformations in this system are likely a result of microbes relying on other microbes. These results provide a framework for future studies exploring the contributions of different community members, both in waste removal and in structuring microbial biodiversity.

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.

High nitrogen isotope fractionation of nitrate during denitrification in four forest soils and its implications for denitrification rate estimates

Denitrification is a major process contributing to the removal of nitrogen (N) from ecosystems, but its rate is difficult to quantify. The natural abundance of isotopes can be used to identify the occurrence of denitrification and has recently been used to quantify denitrification rates at the ecosystem level. However, the technique requires an understanding of the isotopic enrichment factor associated with denitrification, which few studies have investigated in forest soils. Here, soils collected from two tropical and two temperate forests in China were incubated under anaerobic or aerobic laboratory conditions for two weeks to determine the N and oxygen (O) isotope enrichment factors during denitrification. We found that at room temperature (20°C), NO₃^- was reduced at a rate of 0.17 to 0.35μgNg^-1h^-1, accompanied by the isotope fractionation of N (¹⁵ε) and O (¹⁸ε) of 31‰ to 65‰ (48.3±2.0‰ on average) and 11‰ to 39‰ (18.9±1.7‰ on average), respectively. The N isotope effects were, unexpectedly, much higher than reported in the literature for heterotrophic denitrification (typically ranging from 5‰ to 30‰) and in other environmental settings (e.g., groundwater, marine sediments and agricultural soils). In addition, the ratios of Δδ¹⁸O:Δδ¹⁵N ranged from 0.28 to 0.60 (0.38±0.02 on average), which were lower than the canonical ratios of 0.5 to 1 for denitrification reported in other terrestrial and freshwater systems. We suggest that the isotope effects of denitrification for soils may vary greatly among regions and soil types and that gaseous N losses may have been overestimated for terrestrial ecosystems in previous studies in which lower fractionation factors were applied.

Success of chemolithoautotrophic SUP05 and Sulfurimonas GD17 cells in pelagic Baltic Sea redox zones is facilitated by their lifestyles as K- and r-strategists

Chemolithoautotrophic sulfur-oxidizing and denitrifying Gamma- (particularly the SUP05 cluster) and Epsilonproteobacteria (predominantly Sulfurimonas subgroup GD17) are assumed to compete for substrates (electron donors and acceptors) in marine pelagic redox gradients. To elucidate their ecological niche separation we performed ³⁴ S⁰ , ¹⁵ NO3- and H¹³ CO3- stable-isotope incubations with water samples from Baltic Sea suboxic, chemocline and sulfidic zones followed by combined phylogenetic staining and high-resolution secondary ion mass spectrometry of single cells. SUP05 cells were small-sized (0.06-0.09 µm³ ) and most abundant in low-sulfidic to suboxic zones, whereas Sulfurimonas GD17 cells were significantly larger (0.26-0.61 µm³ ) and most abundant at the chemocline and below. Together, SUP05 and GD17 cells accumulated up to 48% of the labelled substrates but calculation of cell volume-specific rates revealed that GD17 cells incorporated labelled substrates significantly faster throughout the redox zone, thereby potentially outcompeting SUP05 especially at high substrate concentrations. Thus, in synopsis with earlier described features of SUP05/GD17 we conclude that their spatially overlapping association in stratified sulfidic zones is facilitated by their different lifestyles: whereas SUP05 cells are streamlined, non-motile K-strategists adapted to low substrate concentrations, GD17 cells are motile r-strategists well adapted to fluctuating substrate and redox conditions.

Coupled molecular and isotopic evidence for denitrifier controls over terrestrial nitrogen availability

Denitrification removes ecologically available nitrogen (N) from the biosphere and influences both the pace and magnitude of global climate change. Disagreements exist over the degree to which this microbial process influences N-availability patterns across Earth's ecosystems. We combine natural stable isotope methods with qPCR to investigate how denitrifier gene abundance is related to variations in nitrate (NO3-) pool sizes across diverse terrestrial biomes and conditions. We analyze NO3- isotope composition (15N/14N, 18O/16O) and denitrifier gene nirS in 52 soil samples from different California ecosystems, spanning desert, chaparral, oak-woodland/savanna and forest. δ15N-NO3- correlates positively with δ18O-NO3- (P⩽0.03) and nirS abundance (P=0.00002) across sites, revealing the widespread importance of isotopic discrimination by soil denitrifiers. Furthermore, NO3- concentrations correlate negatively to nirS (P=0.002) and δ15N-NO3- (P=0.003) across sites. We also observe these spatial relationships in short-term (7-day), in situ soil-incubation experiments; NO3--depletion strongly corresponds with increased nirS, nirS/16 rRNA, and enrichment of heavy NO3- isotopes over time. Overall, these findings suggest that microbial denitrification can consume plant-available NO3- to low levels at multiple time scales, contributing to N-limitation patterns across sites, particularly in moist, carbon-rich soils. Furthermore, our study provides a new approach for understanding the relationships between microbial gene abundance and terrestrial ecosystem functioning.

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.