Dual isotope and isotopomer signatures of nitrous oxide from fungal denitrification--a pure culture study

Mitigated N2O emissions from submerged-plant-covered aquatic ecosystems on the Changjiang River Delta

Submerged plants affect nitrogen cycling in aquatic ecosystems. However, whether and how submerged plants change nitrous oxide (N2O) production mechanism and emissions flux remains controversial. Current research primarily focuses on the feedback from N2O release to variation of substrate level and microbial communities. It is deficient in connecting the relative contribution of individual N2O production processes (i.e., the N2O partition). Here, we attempted to offer a comprehensive understanding of the N2O mitigation mechanism in aquatic ecosystems on the Changjiang River Delta according to stable isotopic techniques, metagenome-assembly genome analysis, and statistical analysis. We found that the submerged plant reduced 45 % of N2O emissions by slowing down the dissolved inorganic nitrogen conversion velocity to N2O in sediment (Vf-[DIN]sed). It was attributed to changing the N2O partition and suppressing the potential capacity of net N2O production (i.e., nor/nosZ). The dominated production processes showed a shift with increasing excess N2O. Meanwhile, distinct shift thresholds of planted and unplanted habitats reflected different mechanisms of stimulated N2O production. The hotspot zone of N2O production corresponded to high nor/nosZ and unsaturated oxygen (O2) in unplanted habitat. In contrast, planted habitat hotspot has lower nor/nosZ and supersaturated O2. O2 from photosynthesis critically impacted the activities of N2O producers and consumers. In summary, the presence of submerged plants is beneficial to mitigate N2O emissions from aquatic ecosystems.

Hydrologic Connectivity Regulates Riverine N2O Sources and Dynamics

Indirect nitrous oxide (N2O) emissions from streams and rivers are a poorly constrained term in the global N2O budget. Current models of riverine N2O emissions place a strong focus on denitrification in groundwater and riverine environments as a dominant source of riverine N2O, but do not explicitly consider direct N2O input from terrestrial ecosystems. Here, we combine N2O isotope measurements and spatial stream network modeling to show that terrestrial-aquatic interactions, driven by changing hydrologic connectivity, control the sources and dynamics of riverine N2O in a mesoscale river network within the U.S. Corn Belt. We find that N2O produced from nitrification constituted a substantial fraction (i.e., >30%) of riverine N2O across the entire river network. The delivery of soil-produced N2O to streams was identified as a key mechanism for the high nitrification contribution and potentially accounted for more than 40% of the total riverine emission. This revealed large terrestrial N2O input implies an important climate-N2O feedback mechanism that may enhance riverine N2O emissions under a wetter and warmer climate. Inadequate representation of hydrologic connectivity in observations and modeling of riverine N2O emissions may result in significant underestimations.

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.

Sources and transformations of riverine nitrogen across a coastal-plain river network of eastern China: New insights from multiple stable isotopes

Riverine nitrogen pollution is ubiquitous and attracts considerable global attention. Nitrate is commonly the dominant total nitrogen (TN) constituent in surface and ground waters; thus, stable isotopes of nitrate (δ15N/δ18O-NO3-) are widely used to differentiate nitrate sources. However, δ15N/δ18O-NO3- approach fails to present a holistic perspective of nitrogen pollution for many coastal-plain river networks because diverse nitrogen species contribute to high TN loads. In this study, multiple isotopes, namely, δ15N/δ18O-NO3-, δ18O-H2O, δ15N-NH4+, δ15N-PN, and δ15Nbulk/δ18O/SP-N2O in the Wen-Rui Tang River, a typical coastal-plain river network of Eastern China, were investigated to identify transformation processes and sources of nitrogen. Then, a stable isotope analysis in R (SIAR) model-TN source apportionment method was developed to quantify the contributions of different nitrogen sources to riverine TN loads. Results showed that nitrogen pollution in the river network was serious with TN concentrations ranging from 1.71 to 8.09 mg/L (mean ± SD: 3.77 ± 1.39 mg/L). Ammonium, nitrate, and suspended particulate nitrogen were the most prominent nitrogen components during the study period, constituting 45.4 %, 28.9 %, and 19.9 % of TN, respectively. Multiple hydrochemical and isotopic analysis identified nitrification as the dominant N cycling process. Biological assimilation and denitrification were minor N cycling processes, whereas ammonia volatilization was deemed negligible. Isotopic evidence and SIAR modeling revealed municipal sewage was the dominant contributor to nitrogen pollution. Based on quantitative estimates from the SIAR model, nitrogen source contributions to the Wen-Rui Tang River watershed followed: municipal sewage (40.6 %) ≈ soil nitrogen (39.5 %) > nitrogen fertilizer (9.7 %) > atmospheric deposition (2.8 %) during wet season; and municipal sewage (59.1 %) > soil nitrogen (30.4 %) > nitrogen fertilizer (4.1 %) > atmospheric deposition (1.0 %) during dry season. This study provides a deeper understanding of nitrogen dynamics in eutrophic coastal-plain river networks, which informs strategies for efficient control and remediation of riverine nitrogen pollution.

Acidification Offset Warming-Induced Increase in N2O Production in Estuarine and Coastal Sediments

Global warming and acidification, induced by a substantial increase in anthropogenic CO2 emissions, are expected to have profound impacts on biogeochemical cycles. However, underlying mechanisms of nitrous oxide (N2O) production in estuarine and coastal sediments remain rarely constrained under warming and acidification. Here, the responses of sediment N2O production pathways to warming and acidification were examined using a series of anoxic incubation experiments. Denitrification and N2O production were largely stimulated by the warming, while N2O production decreased under the acidification as well as the denitrification rate and electron transfer efficiency. Compared to warming alone, the combination of warming and acidification decreased N2O production by 26 ± 4%, which was mainly attributed to the decline of the N2O yield by fungal denitrification. Fungal denitrification was mainly responsible for N2O production under the warming condition, while bacterial denitrification predominated N2O production under the acidification condition. The reduced site preference of N2O under acidification reflects that the dominant pathways of N2O production were likely shifted from fungal to bacterial denitrification. In addition, acidification decreased the diversity and abundance of nirS-type denitrifiers, which were the keystone taxa mediating the low N2O production. Collectively, acidification can decrease sediment N2O yield through shifting the responsible production pathways, partly counteracting the warming-induced increase in N2O emissions, further reducing the positive climate warming feedback loop.

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.

Increased Nitrogen Loading Facilitates Nitrous Oxide Production through Fungal and Chemodenitrification in Estuarine and Coastal Sediments

Estuarine and coastal environments are assumed to contribute to nitrous oxide (N₂O) emissions under increasing nitrogen loading. However, isotopic and molecular mechanisms underlying N₂O production pathways under elevated nitrogen concentration remain poorly understood. Here we used microbial inhibition, isotope mass balance, and molecular approaches to investigate N₂O production mechanisms in estuarine and coastal sediments through a series of anoxic incubations. Site preference of the N₂O molecule increased due to increasing nitrate concentration, suggesting the changes in N₂O production pathways. Enhanced N₂O production under high nitrate concentration was not mediated by bacterial denitrification, but instead was mainly regulated by fungal denitrification. Elevated nitrate concentration increased the contribution of fungal denitrification to N₂O production by 11-25%, whereas it decreased bacterial N₂O production by 16-33%. Chemodenitrification was also enhanced by high nitrate concentration, contributing to 13-28% of N₂O production. Elevated nitrate concentration significantly mediated nirK-type denitrifiers structure and abundance, which are the keystone taxa driving N₂O production. Collectively, these results suggest that increasing nitrate concentration can shift N₂O production pathways from bacterial to fungal and chemodenitrification, which are mainly responsible for the enhanced N₂O production and have widespread implications for N₂O projections under ongoing nitrogen pollution in estuarine and coastal ecosystems.

Sources of nitrous oxide emissions from hydroponic tomato cultivation: Evidence from stable isotope analyses

Introduction

Hydroponic vegetable cultivation is characterized by high intensity and frequent nitrogen fertilizer application, which is related to greenhouse gas emissions, especially in the form of nitrous oxide (N₂O). So far, there is little knowledge about the sources of N₂O emissions from hydroponic systems, with the few studies indicating that denitrification could play a major role.

Methods

Here, we use evidence from an experiment with tomato plants (Solanum lycopersicum) grown in a hydroponic greenhouse setup to further shed light into the process of N₂O production based on the N₂O isotopocule method and the ¹⁵N tracing approach. Gas samples from the headspace of rock wool substrate were collected prior to and after ¹⁵N labeling at two occasions using the closed chamber method and analyzed by gas chromatography and stable isotope ratio mass spectrometry.

Results

The isotopocule analyses revealed that either heterotrophic bacterial denitrification (bD) or nitrifier denitrification (nD) was the major source of N₂O emissions, when a typical nutrient solution with a low ammonium concentration (1-6 mg L^-1) was applied. Furthermore, the isotopic shift in ¹⁵N site preference and in δ¹⁸O values indicated that approximately 80-90% of the N₂O produced were already reduced to N₂ by denitrifiers inside the rock wool substrate. Despite higher concentrations of ammonium present during the ¹⁵N labeling (30-60 mg L^-1), results from the ¹⁵N tracing approach showed that N₂O mainly originated from bD. Both, ¹⁵N label supplied in the form of ammonium and ¹⁵N label supplied in the form of nitrate, increased the ¹⁵N enrichment of N₂O. This pointed to the contribution of other processes than bD. Nitrification activity was indicated by the conversion of small amounts of ¹⁵N-labeled ammonium into nitrate.

Discussion/Conclusion

Comparing the results from N₂O isotopocule analyses and the ¹⁵N tracing approach, likely a combination of bD, nD, and coupled nitrification and denitrification (cND) was responsible for the vast part of N₂O emissions observed in this study. Overall, our findings help to better understand the processes underlying N₂O and N₂ emissions from hydroponic tomato cultivation, and thereby facilitate the development of targeted N₂O mitigation measures.

Influences of carbon sources on N2O production during denitrification in freshwaters: Activity, isotopes and functional microbes

Denitrification is one of the major sources of N₂O in freshwaters. Diverse forms of organic compounds act as the electron donors for microbial denitrification. However, the influences of carbon sources on N₂O production, N₂O reduction, isotope fractionation and functional microbes during denitrification were largely unknown. In this study, five forms of carbon sources (i.e. acetate, citrate, glucose, cellobiose and leucine) were used to enrich denitrifiers in freshwater sediments. N₂O conversion in the enrichments was investigated by a combination of inhibition technique, natural stable isotope method and metagenomics. Acetylene was effective in inhibiting N₂O reduction without influencing the isotopic characteristics during N₂O production. Glucose led to the least N₂O production and reduction, in accordance with the lowest abundance of both NO and N₂O reductases in this enrichment. δ¹⁸O and site preference value (SP, =δ¹⁵N^α-δ¹⁵N^β) of N₂O were sensitive to discriminate the five carbon sources, except when comparing acetate and leucine. Isotopic values of N₂O were not significantly different in these two enrichments due to the similarity of NO reductases - Pseudomonas-type cNorB. Specifically, the enrichment with cellobiose produced N₂O with the lowest δ¹⁸O values (39.4‰±1.1‰), due to Alicycliphilus with both cNorB and qNorB. The enrichment with glucose led to the highest SP values (8.9‰±8.6‰), caused by Thiobacillus-type cNorB. Our results demonstrated the link between carbon sources, N₂O production and reduction, isotopic signatures, microbial populations and enzymes during denitrification in freshwaters.

Denitrification and N2O Emission in Estuarine Sediments in Response to Ocean Acidification: From Process to Mechanism

Global estuarine ecosystems are experiencing severe nitrogen pollution and ocean acidification (OA) simultaneously. Sedimentary denitrification is an important way of reactive nitrogen removal but at the same time leads to the emission of large amounts of nitrous oxide (N₂O), a potent greenhouse gas. It is known that OA in estuarine regions could impact denitrification and N₂O production; however, the underlying mechanism is still underexplored. Here, sediment incubation and pure culture experiments were conducted to explore the OA impacts on microbial denitrification and the associated N₂O emissions in estuarine sediments. Under neutral (in situ) conditions, fungal N₂O emission dominated in the sediment, while the bacterial and fungal sources had a similar role under acidification. This indicated that acidification decreased the sedimentary fungal denitrification and likely inhibited the activity of fungal denitrifiers. To explore molecular mechanisms, a denitrifying fungal strain of Penicillium janthinellum was isolated from the sediments. By using deuterium-labeled single-cell Raman spectroscopy and isobaric tags for relative and absolute quantitation proteomics, we found that acidification inhibited electron transfers in P. janthinellum and downregulated expressions of the proteins related to energy production and conservation. Two collaborative pathways of energy generation in the P. janthinellum were further revealed, that is, aerobic oxidative phosphorylation and TCA cycle and anoxic pyruvate fermentation. This indicated a distinct energy supply strategy from bacterial denitrification. Our study provides insights into fungi-mediated nitrogen cycle in acidifying aquatic ecosystems.

Estuarine plastisphere as an overlooked source of N2O production

“Plastisphere”, microbial communities colonizing plastic debris, has sparked global concern for marine ecosystems. Microbiome inhabiting this novel human-made niche has been increasingly characterized; however, whether the plastisphere holds crucial roles in biogeochemical cycling remains largely unknown. Here we evaluate the potential of plastisphere in biotic and abiotic denitrification and nitrous oxide (N₂O) production in estuaries. Biofilm formation provides anoxic conditions favoring denitrifiers. Comparing with surrounding bulk water, plastisphere exhibits a higher denitrifying activity and N₂O production, suggesting an overlooked N₂O source. Regardless of plastisphere and bulk water, bacterial and fungal denitrifications are the main regulators for N₂O production instead of chemodenitrification. However, the contributions of bacteria and fungi in the plastisphere are different from those in bulk water, indicating a distinct N₂O production pattern in the plastisphere. These findings pinpoint plastisphere as a N₂O source, and provide insights into roles of the new biotope in biogeochemical cycling in the Anthropocene.

The roles of marine plastisphere in global nitrogen cycling are largely unknown. Here, the authors indicate that the plastisphere could act as a potential source of N2O production, which is mainly regulated by the biotic denitrification

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.

Isotopic assessment of soil N2O emission from a sub-tropical agricultural soil under varying N-inputs

Nitrogen fertilizers result in high crop productivity but also enhance the emission of N₂O, an environmentally harmful greenhouse gas. Only approximately a half of the applied nitrogen is utilized by crops and the rest is either vaporized, leached, or lost as NO, N₂O and N₂ via soil microbial activity. Thus, improving the nitrogen use efficiency of cropping systems has become a global concern. Factors such as types and rates of fertilizer application, soil texture, moisture level, pH, and microbial activity/diversity play important roles in N₂O production. Here, we report the results of N₂O production from a set of chamber experiments on an acidic sandy-loam agricultural soil under varying levels of an inorganic N-fertilizer, urea. Stable isotope technique was employed to determine the effect of increasing N-fertilizer levels on N₂O emissions and identify the microbial processes involved in fertilizer N-transformation that give rise to N₂O. We monitored the isotopic changes in both substrate (ammonium and nitrate) and the product N₂O during the entire course of the incubation experiments. Peak N₂O emissions of 122 ± 98 μg N₂O-N m^-2 h^-1, 338 ± 49 μg N₂O-N m^-2 h^-1 and 739 ± 296 μg N₂O-N m^-2 h^-1 were observed for urea application rate of 40, 80, and 120 μg N g^-1. The duration of emissions also increased with urea levels. The concentration and isotopic compositions of the substrates and product showed time-bound variation. Combining the observations of isotopic effects in δ¹⁵N, δ¹⁸O, and ¹⁵N site preference, we inferred co-occurrence of several microbial N₂O production pathways with nitrification and/or fungal denitrification as the dominant processes responsible for N₂O emissions. Besides this, dominant signatures of bacterial denitrification were observed in a second N₂O emission pulse in intermediate urea-N levels. Signature of N₂O consumption by reduction could be traced during declining emissions in treatment with high urea level.

Distinguishing N2O and N2 ratio and their microbial source in soil fertilized for vegetable production using a stable isotope method

Vegetable production systems with excessive nitrogen fertilizer result in severe N₂O emission. It is pivotal to identify the source of N₂O for reducing N₂O emission, but estimating microbial pathways of N₂O production is very difficult due to the existence of N₂O reduction. A promising tool can address this problem by using δ¹⁸O and δ¹⁵N^SP of N₂O to construct a dual isotopocule plot. For ascertaining the microbial pathways of N₂O production and consumption in soil fertilized for vegetable production, four treatments were set up: urea (U), half urea and half organic fertilizer (UO), organic fertilizer (O) and no fertilizer (NF), and the experiment was carried out continuously for two years. The δ¹⁸O vs. δ¹⁵N^SP plot method indicated that the nitrification/fungal denitrification was a dominant in N₂O emission, and the U treatment was the highest, followed by OU, O and NF in the both years. Among the different treatments, furthermore, the N₂O flux had the same trend, whereas the extent of N₂O reduction showed an opposite trend. Overall, inorganic fertilizer enhances nitrification/fungal denitrification and hinders reduction of N₂O to N₂, resulting in a larger amount of N₂O emission. However, organic fertilizer increases the contribution of denitrification and greatly improves the extent of N₂O reduction, which helps to reduce N₂O emission. Therefore, organic fertilizer is crucial to reducing N₂O emission by enhancing N₂O reduction and should be properly applied in production practice.

Nitrite isotope characteristics and associated soil N transformations

Nitrite (NO₂⁻) is a crucial compound in the N soil cycle. As an intermediate of nearly all N transformations, its isotopic signature may provide precious information on the active pathways and processes. NO₂⁻ analyses have already been applied in ¹⁵N tracing studies, increasing their interpretation perspectives. Natural abundance NO₂⁻ isotope studies in soils were so far not applied and this study aims at testing if such analyses are useful in tracing the soil N cycle. We conducted laboratory soil incubations with parallel natural abundance and ¹⁵N treatments, accompanied by isotopic analyses of soil N compounds (NO₃⁻, NO₂⁻, NH₄⁺). The double ¹⁵N tracing method was used as a reference method for estimations of N transformation processes based on natural abundance nitrite dynamics. We obtained a very good agreement between the results from nitrite isotope model proposed here and the ¹⁵N tracing approach. Natural abundance nitrite isotope studies are a promising tool to our understanding of soil N cycling.

Isolation of cold-adapted nitrate-reducing fungi that have potential to increase nitrate removal in woodchip bioreactors

AIMS

The aim of this study was to obtain cold-adapted denitrifying fungi that could be used for bioaugmentation in woodchip bioreactors to remove nitrate from agricultural subsurface drainage water.

METHODS AND RESULTS

We isolated a total of 91 nitrate-reducing fungal strains belonging to Ascomycota and Mucoromycota from agricultural soil and a woodchip bioreactor under relatively cold conditions (5 and 15°C). When these strains were incubated with ¹⁵ N-labelled nitrate, ²⁹ N₂ was frequently produced, suggesting the occurrence of co-denitrification (microbially mediated nitrosation). Two strains also produced ³⁰ N₂ , indicating their ability to reduce N₂ O. Of the 91 nitrate-reducing fungal strains, fungal nitrite reductase gene (nirK) and cytochrome P450 nitric oxide reductase gene (p450nor) were detected by PCR in 34 (37%) and 11 (12%) strains, respectively. Eight strains possessed both nirK and p450nor, further verifying their denitrification capability. In addition, most strains degraded cellulose under denitrification condition.

CONCLUSIONS

Diverse nitrate-reducing fungi were isolated from soil and a woodchip bioreactor. These fungi reduced nitrate to gaseous N forms at relatively low temperatures. These cold-adapted, cellulose-degrading and nitrate-reducing fungi could support themselves and other denitrifiers in woodchip bioreactors.

SIGNIFICANCE AND IMPACT OF THE STUDY

The cold-adapted, cellulose-degrading and nitrate-reducing fungi isolated in this study could be useful to enhance nitrate removal in woodchip bioreactors under low-temperature conditions.

Dynamics and resilience of soil mycobiome under multiple organic and inorganic pulse disturbances

Disturbances in soil can cause short-term soil changes, consequently changes in microbial community what may result in long-lasting ecological effects. Here, we evaluate how multiple pulse disturbances effect the dynamics and resilience of fungal community, and the co-occurrence of fungal and bacterial communities in a 389 days field experiment. We used soil under sugarcane cultivation as soil ecosystem model, and organic residue (vinasse - by-product of sugarcane ethanol production) combined or not with inorganic (organic residue applied 30 days before or together with mineral N fertilizer) amendments as disturbances. Application of organic residue alone as a single disturbance or 30 days prior to a second disturbance with mineral N resulted in similar changes in the fungal community. The simultaneous application of organic and mineral N as a single pulse disturbance had the greatest impact on the fungal community. Organic amendment increased the abundance of saprotrophs, fungal species capable of denitrification, and fungi described to have copiotrophic and oligotrophic lifestyles. Furthermore, the changes in the fungal community were not correlated with the changes in the bacterial community. The fungal community was neither resistant nor resilient to organic and inorganic disturbances over the one-year sampling period. Our findings provide insights on the immediate and delayed responses of the fungal community over one year to disturbance by organic and inorganic amendments.

Microbial and isotopomer analysis of N2O generation pathways in ammonia removal biofilters

Ammonia removal biofilters can be a potential source of nitrous oxide (N₂O) production as a result of microbial nitrification and denitrification. In this study, these two N₂O generation pathways was quantified using isotopic site preference values (SP, 33‰ for nitrification and 0‰ for denitrification) in a 204-d operation. Tests with two moisture conditions (45% and 55%) and three inlet NH₃ concentrations (35, 18 and 0 ppmv) were performed. A 55+% NH₃ removal efficiency was achieved in biofilters with 35 and 18 ppmv ammonia supply, but no significant difference (p > 0.05) was found between the moisture treatments. Results showed that biofilters were clearly net sources of N₂O, and biofilters with higher moisture content generated significantly (p < 0.05) higher N₂O concentration. The N₂O generation did not stop even after the biofilters were terminated. The percentage of inlet NH₃-N converted into N₂O-N were 5.2%, 8.5% for biofilters with 45% moisture content, and 14.8%, 10.8% for those with 55% moisture content. Gene abundance of amoA and nosZ in packing materials (taken on days 64, 107, 140, 180 and 204) increased due to NH₃ input reaching the highest on day 140 and then decreased in response to reduced NH₃ supply on day 180 and 204. The changes of SP values suggested a shift between nitrification and denitrification with regard to N₂O generation. Overall, the nitrification was the dominant pathway for N₂O generation, but uncertainty exits as well. This study confirmed that NH₃-loaded biofilters were net sources of N₂O, and use of SP-N₂O may be helpful in better understanding the processes responsible for such emissions.

Quantifying N2O reduction to N2 during denitrification in soils via isotopic mapping approach: Model evaluation and uncertainty analysis

The last step of denitrification, i.e. the reduction of N₂O to N₂, has been intensively studied in the laboratory to understand the denitrification process, predict nitrogen fertiliser losses, and to establish mitigation strategies for N₂O. However, assessing N₂ production via denitrification at large spatial scales is still not possible due to lack of reliable quantitative approaches. Here, we present a novel numerical "mapping approach" model using the δ¹⁵N^sp/δ¹⁸O slope that has been proposed to potentially be used to indirectly quantify N₂O reduction to N₂ at field or larger spatial scales. We evaluate the model using data obtained from seven independent soil incubation studies conducted under a He-O₂ atmosphere. Furthermore, we analyse the contribution of different parameters to the uncertainty of the model. The model performance strongly differed between studies and incubation conditions. Re-evaluation of the previous data set demonstrated that using soils-specific instead of default endmember values could largely improve model performance. Since the uncertainty of modelled N₂O reduction was relatively high, further improvements to estimate model parameters to obtain more precise estimations remain an on-going matter, e.g. by determination of soil-specific isotope fractionation factors and isotopocule endmember values of N₂O production processes using controlled laboratory incubations. The applicability of the mapping approach model is promising with an increasing availability of real-time and field based analysis of N₂O isotope signatures.

Nitrous oxide effluxes from plants as a potentially important source to the atmosphere

The global budget for nitrous oxide (N₂ O), an important greenhouse gas and probably dominant ozone-depleting substance emitted in the 21^st century, is far from being fully understood. Cycling of N₂ O in terrestrial ecosystems has traditionally exclusively focused on gas exchange between the soil surface (nitrification-denitrification processes) and the atmosphere. Terrestrial vegetation has not been considered in the global budget so far, even though plants are known to release N₂ O. Here, we report the N₂ O emission rates of 32 plant species from 22 different families measured under controlled laboratory conditions. Furthermore, the first isotopocule values (δ¹⁵ N, δ¹⁸ O and δ¹⁵ N^sp ) of N₂ O emitted from plants were determined. A robust relationship established between N₂ O emission and CO₂ respiration rates, which did not alter significantly over a broad range of changing environmental conditions, was used to quantify plant-derived emissions on an ecosystem scale. Stable isotope measurements (δ¹⁵ N, δ¹⁸ O and δ¹⁵ N^sp ) of N₂ O emitted by plants clearly show that the dual isotopocule fingerprint of plant-derived N₂ O differs from that of currently known microbial or chemical processes. Our work suggests that vegetation is a natural source of N₂ O in the environment with a large fraction released by a hitherto unrecognized process.

Biochar amendment suppresses N2 O emissions but has no impact on 15 N site preference in an anaerobic soil

RATIONALE

Biochar amendments often decrease N₂ O gas production from soil, but the mechanisms and magnitudes are still not well characterized since N₂ O can be produced via several different microbial pathways. We evaluated the influence of biochar amendment on N₂ O emissions and N₂ O isotopic composition, including ¹⁵ N site preference (SP) under anaerobic conditions.

METHODS

An agricultural soil was incubated with differing levels of biochar. Incubations were conducted under anaerobic conditions for 10 days with and without acetylene, which inhibits N₂ O reduction to N₂ . The N₂ O concentrations were measured every 2 days, the SPs were determined after 5 days of incubation, and the inorganic nitrogen concentrations were measured after the incubation.

RESULTS

The SP values with acetylene were consistent with N₂ O production by bacterial denitrification and those without acetylene were consistent with bacterial denitrification that included N₂ O reduction to N₂ . There was no effect of biochar on N₂ O production in the presence of acetylene between day 3 and day 10. However, in the absence of acetylene, soils incubated with 4% biochar produced less N₂ O than soils with no biochar addition. Different amounts of biochar amendment did not change the SP values.

CONCLUSIONS

Our study used N₂ O emission rates and SP values to understand biochar amendment mechanisms and demonstrated that biochar amendment reduces N₂ O emissions by stimulating the last step of denitrification. It also suggested a possible shift in N₂ O-reducing microbial taxa in 4% biochar samples.

Phylogenomics Reveal the Dynamic Evolution of Fungal Nitric Oxide Reductases and Their Relationship to Secondary Metabolism

Fungi expressing P450nor, an unconventional nitric oxide (NO) reducing cytochrome P450, are considered significant contributors to environmental nitrous oxide (N₂O) emissions. Despite extensive efforts, fungal contributions to N₂O emissions remain uncertain. For example, the majority of N₂O emitted from antibiotic-amended soil microcosms is attributed to fungal activity, yet axenic fungal cultures do not couple N-oxyanion respiration to growth and these fungi produce only minor quantities of N₂O. To assist in reconciling these conflicting observations and produce a benchmark genomic analysis of fungal denitrifiers, genes underlying denitrification were examined in >700 fungal genomes. Of 167 p450nor—containing genomes identified, 0, 30, and 48 also harbored the denitrification genes narG, napA, or nirK, respectively. Compared with napA and nirK, p450nor was twice as abundant and exhibited 2–5-fold more gene duplications, losses, and transfers, indicating a disconnect between p450nor presence and denitrification potential. Furthermore, cooccurrence of p450nor with genes encoding NO-detoxifying flavohemoglobins (Spearman r = 0.87, p = 1.6e⁻¹⁰) confounds hypotheses regarding P450nor’s primary role in NO detoxification. Instead, ancestral state reconstruction united P450nor with actinobacterial cytochrome P450s (CYP105) involved in secondary metabolism (SM) and 19 (11%) p450nor-containing genomic regions were predicted to be SM clusters. Another 40 (24%) genomes harbored genes nearby p450nor predicted to encode hallmark SM functions, providing additional contextual evidence linking p450nor to SM. These findings underscore the potential physiological implications of widespread p450nor gene transfer, support the undiscovered affiliation of p450nor with fungal SM, and challenge the hypothesis of p450nor’s primary role in denitrification.

Estimating N2 O processes during grassland renewal and grassland conversion to maize cropping using N2 O isotopocules

RATIONALE

Enhanced nitrous oxide (N₂ O) emissions can occur following grassland break-up for renewal or conversion to maize cropping, but knowledge about N₂ O production pathways and N₂ O reduction to N₂ is very limited. A promising tool to address this is the combination of mass spectrometric analysis of N₂ O isotopocules and an enhanced approach for data interpretation.

METHODS

The isotopocule mapping approach was applied to field data using a δ¹⁵ N^sp_N2O and δ¹⁸ O_N2O map to simultaneously determine N₂ O production pathways contribution and N₂ O reduction for the first time. Based on the isotopic composition of N₂ O produced and literature values for specific N₂ O pathways, it was possible to distinguish: (i) heterotrophic bacterial denitrification and/or nitrifier denitrification and (ii) nitrification and/or fungal denitrification and the contribution of N₂ O reduction.

RESULTS

The isotopic composition of soil-emitted N₂ O largely resembled the known end-member values for bacterial denitrification. The isotopocule mapping approach indicated different effects of N₂ O reduction on the isotopic composition of soil-emitted N₂ O for the two soils under study. Differing N₂ O production pathways in different seasons were not observed, but management events and soil conditions had a significant impact on pathway contribution and N₂ O reduction. N₂ O reduction data were compared with a parallel ¹⁵ N-labelling experiment.

CONCLUSIONS

The field application of the isotopocule mapping approach opens up new prospects for studying N₂ O production and consumption of N₂ O in soil simultaneously based on mass spectrometric analysis of natural abundance N₂ O. However, further studies are needed in order to properly validate the isotopocule mapping approach.

Relative Contribution of nirK- and nirS- Bacterial Denitrifiers as Well as Fungal Denitrifiers to Nitrous Oxide Production from Dairy Manure Compost

The relative contribution of fungi, bacteria, and nirS and nirK denirifiers to nitrous oxide (N₂O) emission with unknown isotopic signature from dairy manure compost was examined by selective inhibition techniques. Chloramphenicol (CHP), cycloheximide (CYH), and diethyl dithiocarbamate (DDTC) were used to suppress the activity of bacteria, fungi, and nirK-possessing denitrifiers, respectively. Produced N₂O were surveyed to isotopocule analysis, and its ¹⁵N site preference (SP) and δ¹⁸O values were compared. Bacteria, fungi, nirS, and nirK gene abundances were compared by qPCR. The results showed that N₂O production was strongly inhibited by CHP addition in surface pile samples (82.2%) as well as in nitrite-amended core samples (98.4%), while CYH addition did not inhibit the N₂O production. N₂O with unknown isotopic signature (SP = 15.3-16.2‰), accompanied by δ¹⁸O (19.0-26.8‰) values which were close to bacterial denitrification, was also suppressed by CHP and DDTC addition (95.3%) indicating that nirK denitrifiers were responsible for this N₂O production despite being less abundant than nirS denitrifiers. Altogether, our results suggest that bacteria are important for N₂O production with different SP values both from compost surface and pile core. However, further work is required to decipher whether N₂O with unknown isotopic signature is mostly due to nirK denitrifiers that are taxonomically different from the SP-characterized strains and therefore have different SP values rather than also being interwoven with the contribution of the NO-detoxifying pathway and/or of co-denitrification.

Use of oxygen isotopes to differentiate between nitrous oxide produced by fungi or bacteria during denitrification

RATIONALE

Fungal denitrifiers can contribute substantially to N₂ O emissions from arable soil and show a distinct site preference for N₂ O (SP(N₂ O)). This study sought to identify another process-specific isotopic tool to improve precise identification of N₂ O of fungal origin by mass spectrometric analysis of the N₂ O produced.

METHODS

Three pure bacterial and three fungal species were incubated under denitrifying conditions in treatments with natural abundance and stable isotope labelling to analyse the N₂ O produced. Combining different applications of isotope ratio mass spectrometry enabled us to estimate the oxygen (O) exchange accelerated by denitrifying enzymes and the ongoing microbial pathway in parallel. This experimental set-up allowed the determination of δ¹⁸ O(N₂ O) values and isotopic fractionation of O, as well as SP(N₂ O) values, as a perspective to differentiate between microbial denitrifiers.

RESULTS

Oxygen exchange during N₂ O production was lower for bacteria than for fungi, differed between species, and depended also on incubation time. Apparent O isotopic fractionation during denitrification was in a similar range for bacteria and fungi, but application of the fractionation model indicated that different enzymes in bacteria and fungi were responsible for O exchange. This difference was associated with different isotopic fractionation for bacteria and fungi.

CONCLUSIONS

δ¹⁸ O(N₂ O) values depend on isotopic fractionation and isotopic fractionation may differ between processes and organism groups. By comparing SP(N₂ O) values, O exchange and the isotopic signature of precursors, we propose here a novel tool for differentiating between different sources of N₂ O.

Evidence for fungal and chemodenitrification based N2O flux from nitrogen impacted coastal sediments

Although increasing atmospheric nitrous oxide (N₂O) has been linked to nitrogen loading, predicting emissions remains difficult, in part due to challenges in disentangling diverse N₂O production pathways. As coastal ecosystems are especially impacted by elevated nitrogen, we investigated controls on N₂O production mechanisms in intertidal sediments using novel isotopic approaches and microsensors in flow-through incubations. Here we show that during incubations with elevated nitrate, increased N₂O fluxes are not mediated by direct bacterial activity, but instead are largely catalysed by fungal denitrification and/or abiotic reactions (e.g., chemodenitrification). Results of these incubations shed new light on nitrogen cycling complexity and possible factors underlying variability of N₂O fluxes, driven in part by fungal respiration and/or iron redox cycling. As both processes exhibit N₂O yields typically far greater than direct bacterial production, these results emphasize their possibly substantial, yet widely overlooked, role in N₂O fluxes, especially in redox-dynamic sediments of coastal ecosystems.

Isotopocule analysis of biologically produced nitrous oxide in various environments

Natural abundance ratios of isotopocules, molecules that have the same chemical constitution and configuration, but that only differ in isotope substitution, retain a record of a compound's origin and reactions. A method to measure isotopocule ratios of nitrous oxide (N₂ O) has been established by using mass analysis of molecular ions and fragment ions. The method has been applied widely to environmental samples from the atmosphere, ocean, fresh water, soils, and laboratory-simulation experiments. Results show that isotopocule ratios, particularly the ¹⁵ N-site preference (difference between isotopocule ratios ¹⁴ N¹⁵ N¹⁶ O/¹⁴ N¹⁴ N¹⁶ O and ¹⁵ N¹⁴ N¹⁶ O/¹⁴ N¹⁴ N¹⁶ O), have a wide range that depends on their production and consumption processes. Observational and laboratory studies of N₂ O related to biological processes are reviewed and discussed to elucidate complex material cycles of this trace gas, which causes global warming and stratospheric ozone depletion. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:135-160, 2017.

Chemical formation of hybrid di-nitrogen calls fungal codenitrification into question

Removal of excess nitrogen (N) can best be achieved through denitrification processes that transform N in water and terrestrial ecosystems to di-nitrogen (N₂) gas. The greenhouse gas nitrous oxide (N₂O) is considered an intermediate or end-product in denitrification pathways. Both abiotic and biotic denitrification processes use a single N source to form N₂O. However, N₂ can be formed from two distinct N sources (known as hybrid N₂) through biologically mediated processes of anammox and codenitrification. We questioned if hybrid N₂ produced during fungal incubation at neutral pH could be attributed to abiotic nitrosation and if N₂O was consumed during N₂ formation. Experiments with gas chromatography indicated N₂ was formed in the presence of live and dead fungi and in the absence of fungi, while N₂O steadily increased. We used isotope pairing techniques and confirmed abiotic production of hybrid N₂ under both anoxic and 20% O₂ atmosphere conditions. Our findings question the assumptions that (1) N₂O is an intermediate required for N₂ formation, (2) production of N₂ and N₂O requires anaerobiosis, and (3) hybrid N₂ is evidence of codenitrification and/or anammox. The N cycle framework should include abiotic production of N₂.

Influence of Lumbricus terrestris and Folsomia candida on N2 O formation pathways in two different soils - with particular focus on N2 emissions

RATIONALE

The gaseous N losses mediated by soil denitrifiers are generally inferred by measuring N₂ O fluxes, but should include associated N₂ emissions, which may be affected by abiotic soil characteristics and biotic interactions. Soil fauna, particularly anecic earthworms and euedaphic collembola, alter the activity of denitrifiers, creating hotspots for denitrification. These soil fauna are abundant in perennial agroecosystems intended to contribute to more sustainable production of bioenergy.

METHODS

Two microcosm experiments were designed to evaluate gaseous N emissions from a silty loam and a sandy soil, both provided with litter from the bioenergy crop Silphium perfoliatum (cup-plant) and inoculated with an anecic earthworm (Lumbricus terrestris), which was added alone or together with an euedaphic collembola (Folsomia candida). In experiment 1, litter-derived N flux was determined by adding ¹⁵ N-labelled litter, followed by mass spectrometric analysis of N₂ and N₂ O isotopologues. In experiment 2, the δ¹⁸ O values and ¹⁵ N site preference of N₂ O were determined by isotope ratio mass spectrometry to reveal underlying N₂ O formation pathways.

RESULTS

Lumbricus terrestris significantly increased litter-derived N₂ emissions in the loamy soil, from 174.5 to 1019.3 μg N₂ -N kg^-1 soil, but not in the sandy soil (non-significant change from 944.7 to 1054.7 μg N₂ -N kg^-1 soil). Earthworm feeding on plant litter resulted in elevated N₂ O emissions in both soils, derived mainly from turnover of the soil mineral N pool during denitrification. Folsomia candida did not affect N losses but showed a tendency to redirect N₂ O formation pathways from fungal to bacterial denitrification. The N₂ O/(N₂  + N₂ O) product ratio was predominantly affected by abiotic soil characteristics (loamy soil: 0.14, sandy soil: 0.26).

CONCLUSIONS

When feeding on S. perfoliatum litter, the anecic L. terrestris, but not the euedaphic F. candida, has the potential to cause substantial N losses. Biotic interactions between the species are not influential, but abiotic soil characteristics have an effect. The coarse-textured sandy soil had lower gaseous N losses attributable to anecic earthworms. Copyright © 2016 John Wiley & Sons, Ltd.

Fungi Contribute Critical but Spatially Varying Roles in Nitrogen and Carbon Cycling in Acid Mine Drainage

The ecosystem roles of fungi have been extensively studied by targeting one organism and/or biological process at a time, but the full metabolic potential of fungi has rarely been captured in an environmental context. We hypothesized that fungal genome sequences could be assembled directly from the environment using metagenomics and that transcriptomics and proteomics could simultaneously reveal metabolic differentiation across habitats. We reconstructed the near-complete 27 Mbp genome of a filamentous fungus, Acidomyces richmondensis, and evaluated transcript and protein expression in floating and streamer biofilms from an acid mine drainage (AMD) system. A. richmondensis transcripts involved in denitrification and in the degradation of complex carbon sources (including cellulose) were up-regulated in floating biofilms, whereas central carbon metabolism and stress-related transcripts were significantly up-regulated in streamer biofilms. These findings suggest that the biofilm niches are distinguished by distinct carbon and nitrogen resource utilization, oxygen availability, and environmental challenges. An isolated A. richmondensis strain from this environment was used to validate the metagenomics-derived genome and confirm nitrous oxide production at pH 1. Overall, our analyses defined mechanisms of fungal adaptation and identified a functional shift related to different roles in carbon and nitrogen turnover for the same species of fungi growing in closely located but distinct biofilm niches.

Fungal denitrification: Bipolaris sorokiniana exclusively denitrifies inorganic nitrogen in the presence and absence of oxygen

Fungi may play an important role in the production of the greenhouse gas nitrous oxide (N2O). Bipolaris sorokiniana is a ubiquitous saprobe found in soils worldwide, yet denitrification by this fungal strain has not previously been reported. We aimed to test if B. sorokiniana would produce N2O and CO2 in the presence of organic and inorganic forms of nitrogen (N) under microaerobic and anaerobic conditions. Nitrogen source (organic-N, inorganic-N, no-N control) significantly affected N2O and CO2 production both in the presence and absence of oxygen, which contrasts with bacterial denitrification. Inorganic N addition increased denitrification of N2O (from 0 to 0.3 μg N20-N h(-1) g(-1) biomass) and reduced respiration of CO2 (from 0.1 to 0.02 mg CO2 h(-1) g(-1) biomass). Isotope analyses indicated that nitrite, rather than ammonium or glutamine, was transformed to N2O. Results suggest the source of N may play a larger role in fungal N2O production than oxygen status.

Isotopic evidence for nitrous oxide production pathways in a partial nitritation-anammox reactor

Nitrous oxide (N2O) production pathways in a single stage, continuously fed partial nitritation-anammox reactor were investigated using online isotopic analysis of offgas N2O with quantum cascade laser absorption spectroscopy (QCLAS). N2O emissions increased when reactor operating conditions were not optimal, for example, high dissolved oxygen concentration. SP measurements indicated that the increase in N2O was due to enhanced nitrifier denitrification, generally related to nitrite build-up in the reactor. The results of this study confirm that process control via online N2O monitoring is an ideal method to detect imbalances in reactor operation and regulate aeration, to ensure optimal reactor conditions and minimise N2O emissions. Under normal operating conditions, the N2O isotopic site preference (SP) was much higher than expected - up to 40‰ - which could not be explained within the current understanding of N2O production pathways. Various targeted experiments were conducted to investigate the characteristics of N2O formation in the reactor. The high SP measurements during both normal operating and experimental conditions could potentially be explained by a number of hypotheses: i) unexpectedly strong heterotrophic N2O reduction, ii) unknown inorganic or anammox-associated N2O production pathway, iii) previous underestimation of SP fractionation during N2O production from NH2OH, or strong variations in SP from this pathway depending on reactor conditions. The second hypothesis - an unknown or incompletely characterised production pathway - was most consistent with results, however the other possibilities cannot be discounted. Further experiments are needed to distinguish between these hypotheses and fully resolve N2O production pathways in PN-anammox systems.

Isotope fractionation factors controlling isotopocule signatures of soil-emitted N₂O produced by denitrification processes of various rates

RATIONALE

This study aimed (i) to determine the isotopic fractionation factors associated with N2O production and reduction during soil denitrification and (ii) to help specify the factors controlling the magnitude of the isotope effects. For the first time the isotope effects of denitrification were determined in an experiment under oxic atmosphere and using a novel approach where N2O production and reduction occurred simultaneously.

METHODS

Soil incubations were performed under a He/O2 atmosphere and the denitrification product ratio [N2O/(N2 + N2O)] was determined by direct measurement of N2 and N2O fluxes. N2O isotopocules were analyzed by mass spectrometry to determine δ(18)O, δ(15)N and (15)N site preference within the linear N2O molecule (SP). An isotopic model was applied for the simultaneous determination of net isotope effects (η) of both N2O production and reduction, taking into account emissions from two distinct soil pools.

RESULTS

A clear relationship was observed between (15)N and (18)O isotope effects during N2O production and denitrification rates. For N2O reduction, diverse isotope effects were observed for the two distinct soil pools characterized by different product ratios. For moderate product ratios (from 0.1 to 1.0) the range of isotope effects given by previous studies was confirmed and refined, whereas for very low product ratios (below 0.1) the net isotope effects were much smaller.

CONCLUSIONS

The fractionation factors associated with denitrification, determined under oxic incubation, are similar to the factors previously determined under anoxic conditions, hence potentially applicable for field studies. However, it was shown that the η(18)O/η(15)N ratios, previously accepted as typical for N2O reduction processes (i.e., higher than 2), are not valid for all conditions.