Comparison of methods for simultaneous identification of bacterial species and determination of metabolic activity by protein‐based stable isotope probing (Protein‐SIP) experiments

We developed a concept for analysing carbon and nitrogen fluxes in microbial communities by employing protein‐based stable isotope probing (Protein‐SIP) in metabolic labelling experiments with stable isotope labelled substrates. For identification of microbial species intact protein profiling (IPP) can be used, whereas the assessment of their metabolic activity is achieved by shotgun mass mapping (SMM). Microbial cultures were grown on substrates containing ¹³C or ¹⁵N. For identification of species we tested both the IPP and the SMM approaches. Mass spectra (MALDI‐MS) were taken from mixtures of either intact proteins or peptides from tryptic digestion for generating species‐specific peak patterns. In the case of SMM, the fragmentation of peptides was additionally used to obtain sequence information for species identification. Mass spectra of peptide sequences allow calculation of the amount of ¹³C or ¹⁵N incorporation within peptides for determining metabolic activity of the specific species. The comparison of IPP and SMM revealed a higher robustness of species identification by SMM. In addition, the assessment of incorporation levels of ¹³C and ¹⁵N into peptides by SMM revealed a lower uncertainty (0.5–0.8 atom %) compared to IPP (6.4–8.9 atom %). The determination of metabolic activity and function of individual species by Protein‐SIP can help to analyse carbon and nitrogen fluxes within microbial communities. Copyright © 2009 John Wiley & Sons, Ltd.     

A novel method for the study of the biophysical interface in soils using nano-scale secondary ion mass spectrometry

The spatial location of microorganisms and their activity within the soil matrix have major impacts on biological processes such as nutrient cycling. However, characterizing the biophysical interface in soils is hampered by a lack of techniques at relevant scales. A novel method for studying the distribution of microorganisms that have incorporated isotopically labelled substrate ('active' microorganisms) in relation to the soil microbial habitat is provided by nano-scale secondary ion mass spectrometry (NanoSIMS). Pseudomonas fluorescens are ubiquitous in soil and were therefore used as a model for 'active' microorganisms in soil. Batch cultures (NCTC 10038) were grown in a minimal salt medium containing 15N-ammonium sulphate (15/14N ratio of 1.174), added to quartz-based white sand or soil (coarse textured sand), embedded in Araldite 502 resin and sectioned for NanoSIMS analysis. The 15N-enriched P. fluorescens could be identified within the soil structure, demonstrating that the NanoSIMS technique enables the study of spatial location of microbial activity in relation to the heterogeneous soil matrix. This technique is complementary to the existing techniques of digital imaging analysis of soil thin sections and scanning electron microscopy. Together with advanced computer-aided tomography of soils and mathematical modelling of soil heterogeneity, NanoSIMS may be a powerful tool for studying physical and biological interactions, thereby furthering our understanding of the biophysical interface in soils.     

Incorporation of carbon and nitrogen atoms into proteins measured by protein-based stable isotope probing (Protein-SIP)

The identification of metabolically active microbial key players is fundamental for understanding the structure and functions of contaminant-degrading communities. The metabolic activity can be analysed by feeding the microbial culture with stable-isotope-labelled substrates and subsequently tracing their incorporation into the biomass. In this paper we present a method which is able to detect the incorporation of stable isotopes from the substrate into the proteins of a benzene-metabolising microorganism. Pseudomonas putida strain ML2 was grown under aerobic conditions with the substrates (12)C-benzene, (13)C-benzene or (15)N-ammonium and (12)C-benzene. Proteins of these cultures were resolved by two-dimensional gel electrophoresis (2-DE) and corresponding protein spots were subjected to matrix-assisted laser ionization/desorption mass spectrometric (MALDI-MS) analysis. The proteins of the (12)C-sample were identified by peptide mass fingerprinting (PMF) as well as by tandem mass spectrometric (MS/MS) measurements. The (13)C- or (15)N-content of the peptides from the labelling experiments was determined by MALDI-MS/MS. The incorporation of heavy isotopes into the proteins from cultures grown on (13)C-benzene and (15)N-ammonium was determined based on the mass differences between labelled and non-labelled peptides as well as on the isotopic distribution of the y(1)-ion of arginine. The method we present here principally allows the unravelling of the carbon and nitrogen flow not only in pure cultures, but also in microbial communities consisting of many microbial species. Copyright (c) 2008 John Wiley & Sons, Ltd.     

Diffusion technique for 15N and inorganic N analysis of low-N aqueous solutions and Kjeldahl digests

Diffusion of ammonia is a common sample preparation method for the stable isotope analysis of inorganic nitrogen in aqueous solution. Classical diffusion methods usually require 6-12 days of diffusion and often focus on (15)N/(14)N analysis only. More recent studies have discussed whether complete N recovery was necessary for the precise analysis of stable N isotope ratios. In this paper we present a newly revised diffusion technique that allows correct and simultaneous determination of total N and (15)N at% from aqueous solutions and Kjeldahl digests, with N concentrations down to sub-0.5-mg N L(-1) levels, and it is tested under different conditions of (15)N isotope labelling. With the modification described, the diffusion time was reduced to 72 h, while the ratios of measured and expected (15)N at% were greater than 99% and the simultaneous recovery of total N was >95%. Analysis of soil microbial biomass N and its (15)N/(14)N ratio is one of the most important applications of this diffusion technique. An experiment with soil extracts spiked with (15)N-labelled yeast showed that predigestion was necessary to prevent serious N loss during Kjeldahl digestion of aqueous samples (i.e. soil extracts). The whole method of soil microbial biomass N preparation for (15)N/(14)N analysis included chloroform fumigation, predigestion, Kjeldahl digestion and diffusion. An experiment with soil spiked with (15)N-labelled yeast was carried out to evaluate the method. Results showed a highly significant correlation of recovered and added N, with the same recovery rate (0.21) of both total N and (15)N. A k(N) value of 0.25 was obtained based on the data. In conclusion, the diffusion method works for soil extracts and microbial biomass N determination and hence could be useful in many types of soil/water studies.     

Recent advances in polyhydroxyalkanoate production by mixed aerobic cultures: from the substrate to the final product

Numerous bacteria have been found to exhibit the capacity for intracellular polyhydroxyalkanoates (PHA) accumulation. Current methods for PHA production at the industrial scale are based on their synthesis from microbial isolates in either their wild form or by recombinant strains. High production costs are associated with these methods; thus, attempts have been made to develop more cost-effective processes. Reducing the cost of the carbon substrates (e.g., through feeding renewable wastes) and increasing the efficiency of production technologies (including both fermentation and downstream extraction and recovery) are two such examples of these attempts. PHA production processes based on mixed microbial cultures are being investigated as a possible technology to decrease production costs, since no sterilization is required and bacteria can adapt quite well to the complex substrates that may be present in waste material. PHA accumulation by mixed cultures has been found under various operational conditions and configurations at both bench-scale and full-scale production. The process known as "feast and famine" or as "aerobic dynamic feeding" seems to have a high potential for PHA production by mixed cultures. Enriched cultures submitted to a transient carbon supply can synthesize PHA at levels comparable to those of pure cultures. Indeed, the intracellular PHA content can reach around 70% of the cell dry weight, suggesting that this process could be competitive with pure culture PHA production when fully developed. Basic and applied research of the PHA production process by mixed cultures has been carried out in the past decade, focusing on areas such as microbial characterization, process configuration, reactor operational strategies, process modeling and control, and polymer characterization. This paper presents a review of the PHA production process with mixed cultures, encompassing the findings reported in the literature as well as our own experimental results in relation to each of these areas.     

Nucleobase Modifiers Identify TET Enzymes as Bifunctional DNA Dioxygenases Capable of Direct N‐Demethylation

TET family enzymes are known for oxidation of the 5‐methyl substituent on 5‐methylcytosine (5mC) in DNA. 5mC oxidation generates the stable base 5‐hydroxymethylcytosine (5hmC), starting an indirect, multi‐step process that ends with reversion of 5mC to unmodified cytosine. While probing the nucleobase determinants of 5mC recognition, we discovered that TET enzymes are also proficient as direct N‐demethylases of cytosine bases. We find that N‐demethylase activity can be readily observed on substrates lacking a 5‐methyl group and, remarkably, TET enzymes can be similarly proficient in either oxidation of 5mC or demethylation of N4‐methyl substituents. Our results indicate that TET enzymes can act as both direct and indirect demethylases, highlight the active‐site plasticity of these Fe^II/α‐ketoglutarate‐dependent dioxygenases, and suggest activity on unexplored substrates that could reveal new TET biology.     

Controlled fabrication of nanopillar arrays as active substrates for surface-enhanced Raman spectroscopy

Highly ordered gold nanopillar arrays were fabricated using anodized aluminum oxide (AAO) templates. Nanopillars with a dimension of 110 +/- 15 nm in vertical height and 75 +/- 10 nm in base diameter were formed with a density of 150 microm(-2). The ordered nanopillar arrays give reproducible surface-enhanced Raman scattering (SERS) at a detection limit of 10(-8) M using thionine as probing molecules. The enhancement by the Au nanopillar arrays was comparable with or better than that of dispersed gold nanoparticle SERS substrates. This work demonstrates a new technique for producing highly ordered and reproducible SERS substrates potentially applicable for chemical and biological assay.     

Microcalorimetric study of the biodegradation of cellulolytic compounds

Microcalorimetry can be used as a tool for the analysis of microbial growth on soluble or insoluble substrates. Modern apparatus allows studies under aerobic or anaerobic growth culture conditions. The heat quantity evolved during any microbial growth is dependent on catabolic and anabolic reactions according to:△H _met=(1-α)△H _cat+α△H _an In this relationship, δH_met, δH_cat, and δH_an are the enthalpy variations associated with metabolic, catabolic, and anabolic reactions, respectively, and a represents the molar fraction of the energy source that is incorporated into cellular carbon. The value of α is strongly influenced by culture conditions. Under anaerobic conditions, the α coefficient is low and does not exceed 0.2. Under aerobic conditions, α can reach a value as high as 0.6. Some experimental results were presented and discussed. Modern microcalorimeters record the power evolved by microbial growth as a function of time. The curves obtained are called power-time curves. These curves can be used for the determination of growth parameters. However, power-time curves allow visualization of some catabolic phenomena that are not related to growth because they occur during the stationary growth phase. Some examples were shown. More recently, microcalorimetry has been used for studies of degradation of insoluble substrates, such as lignocellulosic compounds, by pure or mixed cultures of microbes. The results obtained with pure cultures of bacteria growing on cellulose were interpreted using the same relationships that have been used for studies on soluble sugars. It was possible to show the influence of the structure of the cellulose on the kinetics of its degradation. The results obtained with mixed cultures were difficult to interprete at the present time. The power-time curves are very complex, showing many heat peaks that cannot be related to any known physiological phenomena. However, the total heat evolved during lignocellulosic fermentation by mixed cultures is proportional to the quantity of sugar fermented; this was demonstrated and discussed. Thus it can be concluded that microcalorimetry can be used for the estimation of the biodegradability of any solid substrate. This technique can also be used for evaluation of the efficiency of the pretreatments of lignocellulosic compounds that are done to increase the biodegradability of these substrates. Recent data will be shown.     

A label-free electrochemical test for DNA-binding activities of tumor suppressor protein p53 using immunoprecipitation at magnetic beads

In this paper we extend the application area of the label-free structure-sensitive electrochemical DNA sensing with mercury-based electrodes which is for the first time used, in combination with immunoprecipitation at magnetic beads (MB), for the probing of DNA interactions with tumor suppressor protein p53. The technique relies on capture of the p53-DNA complexes at MB via anti-p53 antibodies, followed by salt-induced dissociation of linear DNA from the complex and its voltammetric detection. Competitive binding of p53 to various plasmid DNA substrates, including lin or scDNAs with or without a specific target site, can easily be followed by ex situ electrochemical analysis of DNA recovered from the immunoprecipitated complexes. Compared to gel electrophoresis which is usually applied to analyze different plasmid DNA forms and their complexes with proteins, the electrochemical detection is faster and allows simpler quantitation of DNA containing free ends at submicrogram levels. We demonstrate applicability of the proposed technique to monitor different DNA-binding activities of wild type and mutant p53 proteins.     

Limitations in detection of 15N incorporation by mass spectrometry in protein-based stable isotope probing (protein-SIP)

The method of protein-based stable isotope probing (protein-SIP) has previously been shown to allow the modeling of carbon fluxes in microbial communities, thus tackling one of the key questions in microbial ecology. The method allows the analysis of stable isotope distribution in peptides, revealing metabolic activities of the species present in an ecosystem. Besides carbon, an application of protein-SIP with nitrogen is of interest for resolving the nitrogen fluxes in microbial communities. Thus, the sensitivity and reliability of a protein-SIP approach employing ¹⁵N was analyzed. For this, cultivations of Pseudomonas fluorescens ATCC 17483 with different ratios of ¹⁴N/¹⁵N were performed, from 10 % down to 0.1 % ¹⁵N. After incubation leading to complete labeling of biomass, proteins were extracted and separated by one-dimensional gel electrophoresis, followed by tryptic digest and UPLC Orbitrap MS/MS analysis. ¹⁵N relative isotope abundance (RIA) was calculated based on isotopic patterns from identified peptides in mass spectra. Proteomics data have been deposited to ProteomeXchange with identifier PXD000127. The distribution of ¹⁵N RIA values among peptides was analyzed in samples with different ¹⁵N amount, and potential causes for variations within individual samples of either technical or biological origin were investigated. Using a number of 50 peptides, significant differences (p?≤?0.05) in ¹⁵N incorporation were found between samples of different ¹⁵N RIA down to 0.1 %. The study demonstrates that protein-SIP using ¹⁵N is sufficiently sensitive for quantitative investigation of microbial activity in nitrogen cycling processes.     

A suite of sensitive chemical methods to determine the δ15N of ammonium, nitrate and total dissolved N in soil extracts

Natural ¹⁵N abundances (δ¹⁵N values) of different soil nitrogen pools deliver crucial information on the soil N cycle for the analysis of biogeochemical processes. Here we report on a complete suite of methods for sensitive δ¹⁵N analysis in soil extracts. A combined chemical reaction of vanadium(III) chloride (VCl₃) and sodium azide under acidic conditions is used to convert nitrate into N₂O, which is subsequently analyzed by purge‐and‐trap isotope ratio mass spectrometry (PTIRMS) with a cryo‐focusing unit. Coupled with preparation steps (microdiffusion for collection of ammonium, alkaline persulfate oxidation to convert total dissolved N (TDN) or ammonium into nitrate) this allows the determination of the δ¹⁵N values of nitrate, ammonium and total dissolved N (dissolved organic N, microbial biomass N) in soil extracts with the same basic protocol. The limits of quantification for δ¹⁵N analysis with a precision of 0.5‰ were 12.4 µM for ammonium, 23.7 µM for TDN, 16.5 µM for nitrate and 22.7 µM for nitrite. Copyright © 2010 John Wiley & Sons, Ltd.     

Biological solubilization of untreated north dakota lignite by a mixed bacterial and a mixed bacterial/fungal culture

Four microbial cultures, two pure and two mixed, were examined for their abilities to solubilize chemically treated (oxidized) lignites, thermally treated (wet-carbonized) lignite, and untreated lignites. Extensive solubilization of oxidized lignites and limited solubilization of untreated North Dakota lignite was observed by three of the four cultures tested. Solubilization of wet-carbonized (a technique to reduce equilibrium moisture and oxygen contents) lignite was not demonstrated. The increase in solubilization correlated with the increase in the oxygen content of lignite and the pH of culture broths. These results also suggest that microbial solubilization of coal may involve nonlignin degrading organisms capable of producing alkaline conditions in the presence of coal.

     

A 15N-aided artificial atmosphere gas flow technique for online determination of soil N2 release using the zeolite Köstrolith SX6

N2 is one of the major gaseous nitrogen compounds released by soils due to N-transformation processes. Since it is also the major constituent of the earth's atmosphere (78.08% vol.), the determination of soil N2 release is still one of the main methodological challenges with respect to a complete evaluation of the gaseous N-loss of soils. Commonly used approaches are based either on a C2H2 inhibition technique, an artificial atmosphere or a 15N-tracer technique, and are designed either as closed systems (non-steady state) or gas flow systems (steady state). The intention of this work has been to upgrade the current gas flow technique using an artificial atmosphere for a 15N-aided determination of the soil N2 release simultaneously with N2O. A 15N-aided artificial atmosphere gas flow approach has been developed, which allows a simultaneous online determination of N2 as well as N2O fluxes from an open soil system (steady state). Fluxes of both gases can be determined continuously over long incubation periods and with high sampling frequency. The N2 selective molecular sieve K?strolith SX6 was tested successfully for the first time for dinitrogen collection. The presented paper mainly focuses on N2 flux determination. For validation purposes soil aggregates of a Haplic Phaeozem were incubated under aerobic (21 and 6 vol.% O2) and anaerobic conditions. Significant amounts of N2 were released only during anaerobic incubation (0.4 and 640.2 pmol N2 h(-1) g(-1) dry soil). However, some N2 formation also occurred during aerobic incubation. It was also found that, during ongoing denitrification, introduced [NO3]- will be more strongly delivered to microorganisms than the original soil [NO3]-.     

Short-Time Effects of Pure and Formulated Herbicides on Soil Microbial Activity and Biomass

The short-time of six pure herbicides (atrazine, terbuthylazine, rimsulfuron, primisulfuron-methyl, glyphosate and gluphosinate-ammonium) with respect to the corresponding commercial formulations on microbial activity and biomass of sandy loam soil were investigated. Application rates were: agricultural rate, 20 and 200 µg a.i. g m 1 soil. Application at normal agricultural rates did not lead to significant effects on soil microbial activity, whereas soil microbial activity was markedly stimulated when pure and commercial formulations of the six herbicides were applied at 20 µg a.i. g m 1 soil. The addition of 200 µg a.i. g m 1 soil of four pure herbicides (atrazine, terbuthylazine, rimsulfuron, primisulfuron-methjyl) led to a significant decrease of soil microbial activity. Commercial formulations characterized by a higher relative a.i. concentration (atrazine and primisulfuron-methyl) approximately determined the same decreasing effect of the pure compound, whereas herbicide formulations with a lower relative a.i. concentration (terbuthylazine and rimsulfuron) produced a significant increase in soil microbial activity.     

A review of stable isotope techniques for N2O source partitioning in soils: recent progress, remaining challenges and future considerations

Nitrous oxide is produced in soil during several processes, which may occur simultaneously within different micro-sites of the same soil. Stable isotope techniques have a crucial role to play in the attribution of N(2)O emissions to different microbial processes, through estimation (natural abundance, site preference) or quantification (enrichment) of processes based on the (15)N and (18)O signatures of N(2)O determined by isotope ratio mass spectrometry. These approaches have the potential to become even more powerful when linked with recent developments in secondary isotope mass spectrometry, with microbial ecology, and with modelling approaches, enabling sources of N(2)O to be considered at a wide range of scales and related to the underlying microbiology. Such source partitioning of N(2)O is inherently challenging, but is vital to close the N(2)O budget and to better understand controls on the different processes, with a view to developing appropriate management practices for mitigation of N(2)O. In this respect, it is essential that as many of the contributing processes as possible are considered in any study aimed at source attribution, as mitigation strategies for one process may not be appropriate for another. To aid such an approach, here the current state of the art is critically examined, remaining challenges are highlighted, and recommendations are made for future direction.     

Organic matter flow in the food web at a temperate heath under multifactorial climate change

The rising atmospheric CO(2) concentration, increasing temperature and changed patterns of precipitation currently expose terrestrial ecosystems to altered environmental conditions. This may affect belowground nutrient cycling through its intimate relationship with the belowground decomposers. Three climate change factors (elevated CO(2), increased temperature and drought) were investigated in a full factorial field experiment at a temperate heathland location. The combined effect of biotic and abiotic factors on nitrogen and carbon flows was traced in plant root → litter → microbe → detritivore/omnivore → predator food-web for one year after amendment with (15)N(13)C(2)-glycine. Isotope ratio mass spectrometry (IRMS) measurement of (15)N/(14)N and (13)C/(12)C in soil extracts and functional ecosystem compartments revealed that the recovery of (15)N sometimes decreased through the chain of consumption, with the largest amount of bioactive (15)N label pool accumulated in the microbial biomass. The elevated CO(2) concentration at the site for 2 years increased the biomass, the (15)N enrichment and the (15)N recovery in detritivores. This suggests that detritivore consumption was controlled by both the availability of the microbial biomass, a likely major food source, and the climatic factors. Furthermore, the natural abundance δ(13)C of enchytraeids was significantly altered in CO(2)-fumigated plots, showing that even small changes in δ(13)C-CO(2) can be used to detect transfer of carbon from primary producers to detritivores. We conclude that, in the short term, the climate change treatments affected soil organism activity, possibly with labile carbohydrate production controlling the microbial and detritivore biomass, with potential consequences for the decomposition of detritus and nutrient cycling. Hence, there appears to be a strong coupling of responses in carbon and nitrogen cycling at this temperate heath.     

A technique to recover tracer as carboxyl-carbon and alpha-nitrogen from amino acids in soil hydrolysates

Isotope analysis of biochemical compounds provides an unequivocal means for detecting assimilation of tracer C and N into microbial biomass. A diffusion method recently developed to determine amino acid-N by ninhydrin oxidation of soil hydrolysates was modified to permit simultaneous collection of the CO2 liberated during this oxidation. In the technique described herein, this is accomplished after removal of (NH4+ + amino sugar)-N, by performing ninhydrin oxidation at 90 degrees C for 7 h in a 1.9 L Mason jar sealed with a lid equipped to support a petri dish containing 5 mL 0.2N NaOH. Recoveries of carboxyl-C and alpha-N ranged from 98 to 101% in evaluations with standard solutions of amino acids, whereas these recoveries exceeded 90% for 14C and 94% for 15N when soil hydrolysates amended with labeled amino acids were analyzed.     

Evaluation of methods to measure differential 15N labeling of soil and root N pools for studies of root exudation

To study patterns of root exudation, the effectiveness of different techniques for in situ 15N labeling of Brassica napus, Centaurea jacea and Lolium perenne with ammonium nitrate was tested. Stem infiltration was found to effectively label plants with thicker stems, whereas, for grass species, cutting and immersing the leaf tips into 15N solution proved to be most effective. A microdiffusion technique to isolate ammonium, combined with conventional cation-exchange chromatography to separate nitrate from amino-N compounds thereafter, was found suitable for separation of the N fractions of plant and soil extracts for 15N determination. All three species were then cultivated in nutrient solution and labeled with 15NH4 15NO3 by stem feeding for 42 hours. Kinetics of 15N labeling of bulk roots and shoots as well as hot water extractable material were assessed, and up to 1.1 at% 15N excess (APE) was found in nutrient solutions. The main amino acids exuded by L. perenne were glycine, serine, alanine and aspartic acid. To assess the suitability of this set of methods to study root exudation in field settings, L. perenne was grown without fertiliser addition in pots containing low-nutrient soil. Plants were 15N labeled via tip immersion and 15N and N concentrations were analysed in shoots, roots and soils during a 48-h interval. Shoots reached 1.25 APE, roots and soil 0.10 and 0.005 APE, respectively. Between 4% (48 h) and 6% (24 h) of total plant 15N was exuded by roots into the soil. In roots amino acids comprised the largest proportion of the soluble 15N pool, whereas soil 15N levels were similar for amino acids and ammonium, exceeding those of nitrate. Mechanisms for the shift within N fractions from roots to soils are briefly discussed.     

The natural abundance of 13C, 15N, 34S and 14C in archived (1923-2000) plant and soil samples from the Askov long-term experiments on animal manure and mineral fertilizer

The Askov field experiment (Denmark), established in 1894, provides a unique opportunity to examine long-term effects of animal manure and mineral fertilizer on soil organic matter quality and turnover. This sandy loam soil is classified as Alfisol (Typic Hapludalf). Soil C, N, S, 13C, 15N, 34S and 14C contents were measured in a selection of archived soil samples (1923, 1938, 1945, 1953, 1964, 1976, 1985, 1996 and 2000) from unfertilized (O), animal manure (1 AM) and mineral fertilizer (1 NPK) treatments. These treatments are imbedded in a four-course crop rotation of winter cereals, root crops, spring cereals and a clover/grass mixture. The contents of C, N, S, 13C, 15N and 34S in selected crop samples (1953-1996) and in contemporary samples of animal feed and manure were also determined. Temporal soil nutrient and isotope trends between fertilizer treatments were significantly different, except for S content in 1 AM and 1 NPK. The total soil C and S was higher in 1 AM and 1 NPK than in the O treatment. The total soil N content (1 AM>1 NPK>O) and the delta15N content (1 AM>1 NPK and O) were also different. Analyses of plant, animal feed and manures confirmed that differences in soil 15N values were related to delta15N values of added source inputs. Soil and crop delta13C values were similar, but manures had slightly lower values. The variation of soil delta34S (and total S) from 1923 to 1996 was larger in the O than 1 AM and 1 NPK plots reflecting changes in atmospheric S inputs. The total contents of soil C, N and S were significantly correlated, but their isotopic signatures were not, suggesting that the C, N, S turnovers in soil are subject to different controls. The 14C content was generally higher in the 1 AM than 1 NPK and O, with bomb-14C incorporation modelling indicating that mean residence time (MRT) was ca. 170 years in the 1 AM, but closer to 250-290 years in the 1 NPK and O treatments. The measured trends in soil C and 14C during 1923-1996 were successfully modelled using the RothC model. The OM accumulation in the Askov soils was generally dominated by microbial decomposition products rather than by recalcitrant components of the various inputs.     

A novel dual-isotope labelling method for distinguishing between soil sources of N2O

We present a novel 18O-15N-enrichment method for the distinction between nitrous oxide (N2O) from nitrification, nitrifier denitrification and denitrification based on a method with single- and double-15N-labelled ammonium nitrate. We added a new treatment with 18O-labelled water to quantify N2O from nitrifier denitrification. The theory behind this is that ammonia oxidisers use oxygen (O2) from soil air for the oxidation of ammonia (NH3), but use H2O for the oxidation of the resulting hydroxylamine (NH2OH) to nitrite (NO2-). Thus, N2O from nitrification would therefore be expected to reflect the 18O signature of soil O2, whereas the 18O signature of N2O from nitrifier denitrification would reflect that of both soil O2 and H2O. It was assumed that (a) there would be no preferential removal of 18O or 16O during nitrifier denitrification or denitrification, (b) the 18O signature of the applied 18O-labelled water would remain constant over the experimental period, and (c) any O exchange between H(2)18O and NO3- would be negligible under the chosen experimental conditions. These assumptions were tested and validated for a silt loam soil at 50% water-filled pore space (WFPS) following application of 400 mg N kg-1 dry soil. We compared the results of our new method with those of a conventional inhibition method using 0.02% v/v acetylene (C2H2) and 80% v/v O2 in helium. Both the 18O-15N-enrichment and inhibitor methods identified nitrifier denitrification to be a major source of N2O, accounting for 44 and 40%, respectively, of N2O production over 24 h. However, compared to our 18O-15N-method, the inhibitor method overestimated the contribution from nitrification at the expense of denitrification, probably due to incomplete inhibition of nitrifier denitrification and denitrification by large concentrations of O2 and a negative effect of C2H2 on denitrification. We consider our new 18O-15N-enrichment method to be more reliable than the use of inhibitors; it enables the distinction between more soil sources of N2O than was previously possible and has provided the first direct evidence of the significance of nitrifier denitrification as a source of N2O in fertilised arable soil.