Fungal oxygen exchange between denitrification intermediates and water

First investigation and absolute calibration of clumped isotopes in N2 O by mid-infrared laser spectroscopy

RATIONALE

Unravelling the biogeochemical cycle of the potent greenhouse gas nitrous oxide (N₂ O) is an underdetermined problem in environmental sciences due to the multiple source and sink processes involved, which complicate mitigation of its emissions. Measuring the doubly isotopically substituted molecules (isotopocules) of N₂ O can add new opportunities to fingerprint and constrain its cycle.

METHODS

We present a laser spectroscopic technique to selectively and simultaneously measure the eight most abundant isotopocules of N₂ O, including three doubly substituted species - so called "clumped isotopes". For the absolute quantification of individual isotopocule abundances, we propose a new calibration scheme that combines thermal equilibration of a working standard gas with a direct mole fraction-based approach.

RESULTS

The method is validated for a large range of isotopic composition values by comparison with other established methods (laser spectroscopy using conventional isotopic scale and isotope ratio mass spectrometry). Direct intercomparison with recently developed ultrahigh-resolution mass spectrometry shows clearly the advantages of the new laser technique, especially with respect to site specificity of isotopic substitution in the N₂ O molecule.

CONCLUSIONS

Our study represents a new methodological basis for the measurements of both singly substituted and clumped N₂ O isotopes. It has a high potential to stimulate future research in the N₂ O community by establishing a new class of reservoir-insensitive tracers and molecular-scale insights.

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.

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.

Measurement of rare isotopologues of nitrous oxide by high-resolution multi-collector mass spectrometry

RATIONALE

Bulk and position-specific stable isotope characterization of nitrous oxide represents one of the most powerful tools for identifying its environmental sources and sinks. Constraining (14) N(15) N(18) O and (15) N(14) N(18) O will add two new dimensions to our ability to uniquely fingerprint N2 O sources.

METHODS

We describe a technique to measure six singly and doubly substituted isotopic variants of N2 O, constraining the values of δ(15) N, δ(18) O, ∆(17) O, (15) N site preference, and the clumped isotopomers (14) N(15) N(18) O and (15) N(14) N(18) O. The technique uses a Thermo MAT 253 Ultra, a high-resolution multi-collector gas source isotope ratio mass spectrometer. It requires 8-10 hours per sample and ~10 micromoles or more of pure N2 O.

RESULTS

We demonstrate the precision and accuracy of these measurements by analyzing N2 O brought to equilibrium in its position-specific and clumped isotopic composition by heating in the presence of a catalyst. Finally, an illustrative analysis of biogenic N2 O from a denitrifying bacterium suggests that its clumped isotopic composition is controlled by kinetic isotope effects in N2 O production.

CONCLUSIONS

We developed a method for measuring six isotopic variants of N2 O and tested it with analyses of biogenic N2 O. The added isotopic constraints provided by these measurements will enhance our ability to apportion N2 O sources.

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.

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.

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

RATIONALE

The contribution of fungal denitrification to the emission of the greenhouse gas nitrous oxide (N2O) from soil has not yet been sufficiently investigated. The intramolecular (15)N site preference (SP) of N2O could provide a tool to distinguish between N2O produced by bacteria or fungi, since in previous studies fungi exhibited much higher SP values than bacteria.

METHODS

To further constrain isotopic evidence of fungal denitrification, we incubated six soil fungal strains under denitrifying conditions, with either NO3(-) or NO2(-) as the electron acceptor, and measured the isotopic signature (δ(18)O, δ(15)Nbulk and SP values) of the N2O produced. The nitrogen isotopic fractionation was calculated and the oxygen isotope exchange associated with particular fungal enzymes was estimated.

RESULTS

Five fungi of the order Hypocreales produced N2O with a SP of 35.1 ± 1.7 ‰ after 7 days of anaerobic incubation independent of the electron acceptor, whereas one Sordariales species produced N2O from NO2(-) only, with a SP value of 21.9 ± 1.4 ‰. Smaller isotope effects of (15)Nbulk were associated with larger N2O production. The δ(18)O values were influenced by oxygen exchange between water and denitrification intermediates, which occurred primarily at the nitrite reduction step.

CONCLUSIONS

Our results confirm that SP of N2O is a promising tool to differentiate between fungal and bacterial N2O from denitrification. Modelling of oxygen isotope fractionation processes indicated that the contribution of the NO2(-) and NO reduction steps to the total oxygen exchange differed among the various fungal species studied. However, more information is needed about different biological orders of fungi as they may differ in denitrification enzymes and consequently in the SP and δ(18)O values of the N2O produced.