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J W Van Groenigen - One of the best experts on this subject based on the ideXlab platform.
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nitrifier denitrification can be a source of n2o from soil a revised approach to the dual Isotope Labelling Method
European Journal of Soil Science, 2010Co-Authors: D M Kool, N Wrage, O Oenema, Sophie Zechmeisterboltenstern, Michael Pfeffer, D J Brus, J W Van GroenigenAbstract:Nitrifier denitrification (i.e. nitrite reduction by ammonia oxidizers) is one of the biochemical pathways of nitrous oxide (N2O) production. It is increasingly suggested that this pathway may contribute substantially to N2O production in soil, the major source of this greenhouse gas. However, although monoculture studies recognize its potential, Methodological drawbacks prohibit conclusive proof that nitrifier denitrification occurs in actual soils. Here we suggest and apply a new isotopic approach to identify its presence in soil. In incubation experiments with 12 soils, N2O production was studied using oxygen (O) and nitrogen (N) Isotope tracing, accounting for O exchange. Microbial biomass C and N and phospholipid fatty acid (PLFA) patterns were analysed to explain potential differences in N2O production pathways. We found that in at least five of the soils nitrifier denitrification must have contributed to N2O production. Moreover, it may even have been responsible for all NH4+-derived N2O in most soils. In contrast, N2O as a by-product of ammonia oxidation contributed very little to total production. Microbial biomass C and N and PLFA-distinguished microbial community composition were not indicative of differences in N2O production pathways. Overall, we show that combined O and N Isotope tracing may still provide a powerful tool to understand N2O production pathways, provided that O exchange is accounted for. We conclude that nitrifier denitrification can indeed occur in soils, and may in fact be responsible for the greater proportion of total nitrifier-induced N2O production.
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a novel dual Isotope Labelling Method for distinguishing between soil sources of n2o
Rapid Communications in Mass Spectrometry, 2005Co-Authors: N Wrage, J W Van Groenigen, O Oenema, Elizabeth M BaggsAbstract: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.
Mari Yotsuyamashita - One of the best experts on this subject based on the ideXlab platform.
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metabolomic study of saxitoxin analogues and biosynthetic intermediates in dinoflagellates using 15 n labelled sodium nitrate as a nitrogen source
Scientific Reports, 2019Co-Authors: Yuko Cho, Shigeki Tsuchiya, Takuo Omura, Kazuhiko Koike, Hiroshi Oikawa, Keiichi Konoki, Yasukatsu Oshima, Mari YotsuyamashitaAbstract:A stable-Isotope-Labelling Method using 15N-labelled sodium nitrate as a nitrogen source was developed for the toxic dinoflagellate Alexandrium catenella. The labelled saxitoxin analogues (STXs), their precursor, and the biosynthetic intermediates were analyzed by column-switching high-resolution hydrophilic interaction liquid chromatography with mass spectrometry. The low contents on Day 0, high 15N incorporation % of Int-C'2 and Int-E' suggested that their turn-over rates are high and that the sizes of the pool of these compounds are smaller than those of the other intermediates. The experimentally determined isotopomer distributions showed that arginine, Int-C'2, 11-hydroxy-Int-C'2, Int-E', GTX5, GTX4, C1, and C2, each existed as a combination of three populations that consisted of the non-labelled molecules and the labelled isotopomers representing molecules newly synthesized by incorporation of 15N assimilated from the medium with two different incorporation rates. The order of 15N incorporation % values of the labelled populations predicted by this model largely agreed with the proposed biosynthetic route. The stable-Isotope-Labelling Method will be useful for understanding the complex mechanism of nitrogen flux in STX-producing dinoflagellates.
N Wrage - One of the best experts on this subject based on the ideXlab platform.
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nitrifier denitrification can be a source of n2o from soil a revised approach to the dual Isotope Labelling Method
European Journal of Soil Science, 2010Co-Authors: D M Kool, N Wrage, O Oenema, Sophie Zechmeisterboltenstern, Michael Pfeffer, D J Brus, J W Van GroenigenAbstract:Nitrifier denitrification (i.e. nitrite reduction by ammonia oxidizers) is one of the biochemical pathways of nitrous oxide (N2O) production. It is increasingly suggested that this pathway may contribute substantially to N2O production in soil, the major source of this greenhouse gas. However, although monoculture studies recognize its potential, Methodological drawbacks prohibit conclusive proof that nitrifier denitrification occurs in actual soils. Here we suggest and apply a new isotopic approach to identify its presence in soil. In incubation experiments with 12 soils, N2O production was studied using oxygen (O) and nitrogen (N) Isotope tracing, accounting for O exchange. Microbial biomass C and N and phospholipid fatty acid (PLFA) patterns were analysed to explain potential differences in N2O production pathways. We found that in at least five of the soils nitrifier denitrification must have contributed to N2O production. Moreover, it may even have been responsible for all NH4+-derived N2O in most soils. In contrast, N2O as a by-product of ammonia oxidation contributed very little to total production. Microbial biomass C and N and PLFA-distinguished microbial community composition were not indicative of differences in N2O production pathways. Overall, we show that combined O and N Isotope tracing may still provide a powerful tool to understand N2O production pathways, provided that O exchange is accounted for. We conclude that nitrifier denitrification can indeed occur in soils, and may in fact be responsible for the greater proportion of total nitrifier-induced N2O production.
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a novel dual Isotope Labelling Method for distinguishing between soil sources of n2o
Rapid Communications in Mass Spectrometry, 2005Co-Authors: N Wrage, J W Van Groenigen, O Oenema, Elizabeth M BaggsAbstract: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.
Christopher G Proud - One of the best experts on this subject based on the ideXlab platform.
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Differing effects of rapamycin and mTOR kinase inhibitors on protein synthesis
Biochemical Society Transactions, 2011Co-Authors: Valentina Iadevaia, Christopher G ProudAbstract:mTOR (mammalian target of rapamycin) forms two distinct types of complex, mTORC (mTOR complex) 1 and 2. Rapamycin inhibits some of the functions of mTORC1, whereas newly developed mTOR kinase inhibitors interfere with the actions of both types of complex. We have explored the effects of rapamycin and mTOR kinase inhibitors on general protein synthesis and, using a new stable Isotope-Labelling Method, the synthesis of specific proteins. In HeLa cells, rapamycin only had a modest effect on total protein synthesis, whereas mTOR kinase inhibitors decreased protein synthesis by approx. 30%. This does not seem to be due to the ability of mTOR kinase inhibitors to block the binding of eIFs (eukaryotic initiation factors) eIF4G and eIF4E. Analysis of the effects of the inhibitors on the synthesis of specific proteins showed a spectrum of behaviours. As expected, synthesis of proteins encoded by mRNAs that contain a 5′-TOP (5′-terminal oligopyrimidine tract) was impaired by rapamycin, but more strongly by mTOR kinase inhibition. Several proteins not known to be encoded by 5′-TOP mRNAs also showed similar behaviour. Synthesis of proteins encoded by ‘non-TOP’ mRNAs was less inhibited by mTOR kinase inhibitors and especially by rapamycin. The implications of our findings are discussed.
O Oenema - One of the best experts on this subject based on the ideXlab platform.
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nitrifier denitrification can be a source of n2o from soil a revised approach to the dual Isotope Labelling Method
European Journal of Soil Science, 2010Co-Authors: D M Kool, N Wrage, O Oenema, Sophie Zechmeisterboltenstern, Michael Pfeffer, D J Brus, J W Van GroenigenAbstract:Nitrifier denitrification (i.e. nitrite reduction by ammonia oxidizers) is one of the biochemical pathways of nitrous oxide (N2O) production. It is increasingly suggested that this pathway may contribute substantially to N2O production in soil, the major source of this greenhouse gas. However, although monoculture studies recognize its potential, Methodological drawbacks prohibit conclusive proof that nitrifier denitrification occurs in actual soils. Here we suggest and apply a new isotopic approach to identify its presence in soil. In incubation experiments with 12 soils, N2O production was studied using oxygen (O) and nitrogen (N) Isotope tracing, accounting for O exchange. Microbial biomass C and N and phospholipid fatty acid (PLFA) patterns were analysed to explain potential differences in N2O production pathways. We found that in at least five of the soils nitrifier denitrification must have contributed to N2O production. Moreover, it may even have been responsible for all NH4+-derived N2O in most soils. In contrast, N2O as a by-product of ammonia oxidation contributed very little to total production. Microbial biomass C and N and PLFA-distinguished microbial community composition were not indicative of differences in N2O production pathways. Overall, we show that combined O and N Isotope tracing may still provide a powerful tool to understand N2O production pathways, provided that O exchange is accounted for. We conclude that nitrifier denitrification can indeed occur in soils, and may in fact be responsible for the greater proportion of total nitrifier-induced N2O production.
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a novel dual Isotope Labelling Method for distinguishing between soil sources of n2o
Rapid Communications in Mass Spectrometry, 2005Co-Authors: N Wrage, J W Van Groenigen, O Oenema, Elizabeth M BaggsAbstract: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.