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Sample records for 13c-labelled arable soils

  1. Mineral fertilization did not affect decay of old lignin and SOC in a 13C-labeled arable soil over 36 years

    NASA Astrophysics Data System (ADS)

    Hofmann, A.; Heim, A.; Gioacchini, P.; Miltner, A.; Gehre, M.; Schmidt, M. W. I.

    2009-07-01

    Retardation of soil organic carbon (SOC) decay after nitrogen addition to litter or soil has been suggested in several recent studies and has been attributed to a retardation in lignin decay. With our study we tested the long-term effect of mineral fertilization (N+P) on the decay of the SOC component lignin in arable soil. To achieve this, we tracked 13C-labeled lignin and SOC in an arable soil that is part of a 36-year field experiment (conversion from C3 to C4 crops) with two mineral fertilization levels. We could show that fertilization neither retarded nor enhanced the decay of old SOC or lignin over a period of 36 years, proposing that decay of lignin was less sensitive to fertilization than previously suggested. However, for new, C4-derived lignin there were indications that decay might have been enhanced by the fertilization treatment, whereas decay of new SOC was unaffected.

  2. Enhancing Phospholipid Fatty Acid Profiling of Soil Bacterial Communities via Substrate- Specific 13C-labelling

    NASA Astrophysics Data System (ADS)

    Evershed, R. P.; Maxfield, P. J.; Bingham, E. M.; Dildar, N.; Brennand, E. L.; Hornibrook, E.

    2008-12-01

    A range of culture-independent methods, has recently emerged to study environmental microorganisms in situ[1]. One such method is phospholipid fatty acid (PLFA) analysis, wherein these ubiquitous membrane lipids provide a powerful tool for the study of unculturable soil microorganisms. PLFA analyses have been used to investigate the impacts of a wide range of environmental factors on the soil microbial community. An acknowledged shortcoming of the PLFAs approach is the lack the chemotaxonoic specificity, which restricts the ability of the method to probe the activities of specific functional groups of the microbial community selectively. However, the selectivity of PLFAs analyses can be enhanced by incubating soils with 13C- labelled substrates followed by gas chromatography-combustion-isotope ratio mass spectrometry to reveal the specific PLFAs incorporating the 13C-label. The application of this approach will be demonstrated through our recent work on methanotrophic bacteria in soils. We applied this approach initially to mineral soils[2] and then extended chemotaxonomic assessments by using a combination of 13C-labelled PLFAs and hopanoids [3]. We have used this approach to explore the properties of high affinity methanotrophs in a range of environments, investigating the relationship between methane oxidation rates and the nature and magnitude of the methanotrophic community for the first time[4,5] More recently we extended the technique using a novel time series 13C-labelling of PLFAs[6] to estimate the rate and progression of 13C- label incorporation and turnover of methanotrophic populations. This modified approach has been used to investigate the impacts of various environmental variables, e.g. soil type, vegetation cover and land use, on the methanotrophic biomass[7.8]. The unique nature of the 13CH4 as a gaseous substate/carbon source means that can be readily introduced into soils via a specific subset of the soil microbial biomass, thereby offering many

  3. The use of 13-C-labelled polyaromatic hydrocarbons in soil bound residue formation

    SciTech Connect

    Richnow, H.H.; Seifert, R.; Hefter, J.

    1996-12-31

    The formation of non-extractable residues during biodegradation and humification processes in soils and sediments represent a major sink for organic contaminants. We studied the mode of incorporation of polycyclic aromatic hydrocarbons (PAM) and their metabolites into macromolecular organic matter during microbial degradation applying {sup 13}C-labelled compounds. Mineralization rates were determined by measuring the {sup 13}CO{sub 2} production. An incorporation of {sup 13}C-PAH-fragments into humic material could be traced by isotopic analysis of the bulk organic matter. Furthermore, selective chemical degradation reactions were applied to analyze the precise chemical structure of covalently bound {sup 13}C-labelled PAH fragments in soil humic substances. Structural assignments by GC-MS combined with isotope measurements on the bulk organic carbon and the molecular level (IRM-GC-MS) provide useful information on the fate of xenobiotics within the soil. The results are discussed in the context of long-term risk assessment of bioremediated soils.

  4. Microbial metabolism in soil at low temperatures: Mechanisms unraveled by position-specific 13C labeling

    NASA Astrophysics Data System (ADS)

    Bore, Ezekiel

    2016-04-01

    Microbial transformation of organic substances in soil is the most important process of the C cycle. Most of the current studies base their information about transformation of organic substances on incubation studies under laboratory conditions and thus, we have a profound knowledge on SOM transformations at ambient temperatures. However, metabolic pathway activities at low temperature are not well understood, despite the fact that the processes are relevant for many soils globally and seasonally. To analyze microbial metabolism at low soil temperatures, isotopomeres of position-specifically 13C labeled glucose were incubated at three temperature; 5, -5 -20 oC. Soils were sampled after 1, 3 and 10 days and additionally after 30 days for samples at -20 °C. The 13C from individual molecule position was quantifed in respired CO2, bulk soil, extractable organic C and extractable microbial biomass by chloroform fumigation extraction (CFE) and cell membranes of microbial communities classified by 13C phospholipid fatty acid (PLFA) analysis. 13CO2 released showed a dominance of the flux from C-1 position at 5 °C. Consequently, at 5 °C, pentose phosphate pathway activity is a dominant metabolic pathway of glucose metabolization. In contrast to -5 °C and -20 oC, metabolic behaviors completely switched towards a preferential respiration of the glucose C-4 position. With decreasing temperature, microorganism strongly shifted towards metabolization of glucose via glycolysis which indicates a switch to cellular maintenance. High recoveries of 13C in extractable microbial biomass at -5 °C indicates optimal growth condition for the microorganisms. PLFA analysis showed high incorporation of 13C into Gram negative bacteria at 5 °C but decreased with temperature. Gram positive bacteria out-competed Gram negatives with decreasing temperature. This study revealed a remarkable microbial activity at temperatures below 0 °C, differing significantly from that at ambient

  5. Anaerobic Methane Oxidation in Soils - revealed using 13C-labelled methane tracers

    NASA Astrophysics Data System (ADS)

    Riekie, G. J.; Baggs, E. M.; Killham, K. S.; Smith, J. U.

    2008-12-01

    In marine sediments, anaerobic methane oxidation is a significant biogeochemical process limiting methane flux from ocean to atmosphere. To date, evidence for anaerobic methane oxidation in terrestrial environments has proved elusive, and its significance is uncertain. In this study, an isotope dilution method specifically designed to detect the process of anaerobic methane oxidation in methanogenic wetland soils is applied. Methane emissions of soils from three contrasting permanently waterlogged sites in Scotland are investigated in strictly anoxic microcosms to which 13C- labelled methane is added, and changes in the concentration and 12C/13C isotope ratios of methane and carbon dioxide are subsequently measured and used to calculate separate the separate components of the methane flux. The method used takes into account the 13C-methane associated with methanogenesis, and the amount of methane dissolved in the soil. The calculations make no prior assumptions about the kinetics of methane production or oxidation. The results indicate that methane oxidation can take place in anoxic soil environments. The clearest evidence for anaerobic methane oxidation is provided by soils from a minerotrophic fen site (pH 6.0) in Bin Forest underlain by ultra-basic and serpentine till. In the fresh soil anoxic microcosms, net consumption methane was observed, and the amount of headspace 13C-CO2 increased at a greater rate than the 12+13C-CO2, further proof of methane oxidation. A net increase in methane was measured in microcosms of soil from Murder Moss, an alkaline site, pH 6.5, with a strong calcareous influence. However, the 13C-CH4 data provided evidence of methane oxidation, both in the disappearance of C- CH4 and appearance of smaller quantities of 13C-CO2. The least alkaline (pH 5.5) microcosms, of Gateside Farm soil - a granitic till - exhibited net methanogenesis and the changes in 13C-CH4 and 13C-CO2 here followed the pattern expected if no methane is consumed

  6. Respiration of 13C-labeled substrates added to soil in the field and subsequent 16S rRNA gene analysis of 13C-labeled soil DNA.

    PubMed

    Padmanabhan, P; Padmanabhan, S; DeRito, C; Gray, A; Gannon, D; Snape, J R; Tsai, C S; Park, W; Jeon, C; Madsen, E L

    2003-03-01

    Our goal was to develop a field soil biodegradation assay using (13)C-labeled compounds and identify the active microorganisms by analyzing 16S rRNA genes in soil-derived (13)C-labeled DNA. Our biodegradation approach sought to minimize microbiological artifacts caused by physical and/or nutritional disturbance of soil associated with sampling and laboratory incubation. The new field-based assay involved the release of (13)C-labeled compounds (glucose, phenol, caffeine, and naphthalene) to soil plots, installation of open-bottom glass chambers that covered the soil, and analysis of samples of headspace gases for (13)CO(2) respiration by gas chromatography/mass spectrometry (GC/MS). We verified that the GC/MS procedure was capable of assessing respiration of the four substrates added (50 ppm) to 5 g of soil in sealed laboratory incubations. Next, we determined background levels of (13)CO(2) emitted from naturally occurring soil organic matter to chambers inserted into our field soil test plots. We found that the conservative tracer, SF(6), that was injected into the headspace rapidly diffused out of the soil chamber and thus would be of little value for computing the efficiency of retaining respired (13)CO(2). Field respiration assays using all four compounds were completed. Background respiration from soil organic matter interfered with the documentation of in situ respiration of the slowly metabolized (caffeine) and sparingly soluble (naphthalene) compounds. Nonetheless, transient peaks of (13)CO(2) released in excess of background were found in glucose- and phenol-treated soil within 8 h. Cesium-chloride separation of (13)C-labeled soil DNA was followed by PCR amplification and sequencing of 16S rRNA genes from microbial populations involved with (13)C-substrate metabolism. A total of 29 full sequences revealed that active populations included relatives of Arthrobacter, Pseudomonas, Acinetobacter, Massilia, Flavobacterium, and Pedobacter spp. for glucose

  7. The effect of biochar amendment on the soil microbial community - PLFA analyses and 13C labeling results

    NASA Astrophysics Data System (ADS)

    Watzinger, A.; Feichtmair, S.; Rempt, F.; Anders, E.; Wimmer, B.; Kitzler, B.; Zechmeister-Boltenstern, S.; Horacek, M.; Zehetner, F.; Kloss, S.; Richoz, S.; Soja, G.

    2012-04-01

    The effects of biochar amendment on plant growth and on the chemical / physical soil characteristics are well explored but only few studies have investigated the impact on soil microorganisms. The response of the soil microbial community to biochar amendment was investigated by phospholipid fatty acid (PLFA) analysis in (i) a large scale pot experiment, (ii) a small scale pot experiment using 13C labeled biochar and (iii) an incubation study using 13C labeled biochar. In the large scale pot experiment, three different agricultural soils from Austria (Planosol, Cambisol, Chernozem) and four different types of biochar were investigated. In total, 25 treatments with 5 replicates each were set up and monitored over a year. The results from the pot experiments showed no significant influence of biochar amendment on the total microbial biomass in the first 100 days after biochar addition. However, discriminant analysis showed a distinction of biochar and control soils as well as a strong effect of the pyrolysis temperature on the microbial composition. The effect of biochar was dependent on the type of soil. In the Planosol, some PLFAs were affected positively, especially when adding biochar with a low pyrolysis temperature, in the first month. In the long term, microbial community composition altered. Growth of fungi and gram negative bacteria was enhanced. In the Chernozem, PLFAs from various microbial groups decreased in the long term. Variability in the incubation study was low. Consequently, many PLFAs were significantly affected by biochar amendment. Again, in the Planosol, gram negative bacteria, actinomycetes and, after 2 weeks, gram positive bacteria increased under biochar amendment whereas in the chernozem total microbial biomass and gram positive bacteria were negatively affected in the long term. The 13C labeling studies confirmed the low degradability of the biochar, i.e. no alteration of the content and the δ13C in the soil organic matter within 100 days

  8. Probing metabolic processes of intact soil microbial communities using position-specific 13C-labeled glucose

    NASA Astrophysics Data System (ADS)

    Fairbanks, D. E.; Hungate, B. A.; KOCH, G. W.; Schwartz, E.; Dijkstra, P.

    2012-12-01

    Soils represent one of the largest carbon pools in the terrestrial biosphere and fluxes into or out of this pool may feedback to current climate change. Understanding the mechanisms behind microbial processes regulating C cycling, microbial turnover, and soil organic matter stabilization is hindered by our lack of understanding of the details of microbial physiology in soils. Position-specific 13C labeled metabolic tracers are proposed as a new way to probe microbial community energy production, biosynthesis, C use efficiency (the proportion of substrate incorporated into microbial biomass), and enables the determination of C fluxes through the various C metabolic pathways. We determined the 13CO2 production from microbial communities within a one hour time frame by adding six isotopomers (1-13C, 2-13C, 3-13C, 4-13C, 5-13C, 6-13C) of glucose in parallel incubations using a young volcanic soil (Pinyon-juniper wood, near Sunset Crater, Flagstaff, Arizona). We compared the measured rates of position-specific 13CO2 production with modeled results based on glucose (1-13C and U-13C) and pyruvate (1-13C and 2,3-13C) incubations. These labeling and modeling techniques may improve our ability to analyze the biochemistry and ecophysiology of intact soil microbial communities.

  9. Changes in microbial structure and functional communities at different soil depths during 13C labelled root litter degradation

    NASA Astrophysics Data System (ADS)

    Sanaullah, Muhammad; Baumann, Karen; Chabbi, Abad; Dignac, Marie-France; Maron, Pierre-Alain; Kuzyakov, Yakov; Rumpel, Cornelia

    2014-05-01

    Soil organic matter turnover depends on substrate quality and microbial activity in soil but little is known about how addition of freshly added organic material modifies the diversity of soil microbial communities with in a soil profile. We took advantage of a decomposition experiment, which was carried out at different soil depths under field conditions and sampled litterbags with 13C-labelled wheat roots, incubated in subsoil horizons at 30, 60 and 90 cm depth for up to 36 months. The effect of root litter addition on microbial community structure, diversity and activity was studied by determining total microbial biomass, PLFA signatures, molecular tools (DNA genotyping and pyrosequencing of 16S and 18S rDNAs) and extracellular enzyme activities. Automated ribosomal intergenic spacer analysis (ARISA) was also carried out to determine the differences in microbial community structure. We found that with the addition of root litter, total microbial biomass as well as microbial community composition and structure changed at different soil depths and change was significantly higher at top 30cm soil layer. Moreover, in the topsoil, population of both gram-positive and gram-negative bacteria increased with root litter addition over time, while subsoil horizons were relatively dominated by fungal community. Extra-cellular enzyme activities confirmed relatively higher fungal community at subsoil horizons compared with surface soil layer with bacteria dominant microbial population. Bacterial-ARISA profiling illustrated that the addition of root litter enhanced the abundance of Actinobacteria and Proteobacteria, at all three soil depths. These bacteria correspond to copiotrophic attributes, which can preferentially consume of labile soil organic C pools. While disappearance of oligotrophic Acidobacteria confirmed the shifting of microbial communities due to the addition of readily available substrate. We concluded that root litter mixing altered microbial community

  10. Using 13C-labeled benzene and Raman gas spectroscopy to investigate respiration and biodegradation kinetics following soil contamination

    NASA Astrophysics Data System (ADS)

    Jochum, Tobias; Popp, Juergen; Frosch, Torsten

    2016-04-01

    Soil and groundwater contamination with benzene can cause serious environmental damages. However, many soil microorganisms are capable to adapt and known to strongly control the fate of organic contamination. Cavity enhanced Raman gas spectroscopy (CERS) was applied to investigate the short-term response of indigenous soil bacteria to a sudden surface contamination with benzene regarding the temporal variations of gas products and their exchange rates with the adjacent atmosphere. 13C-labeled benzene was spiked on a silty-loamy soil column (sampled from Hainich National Park, Germany) in order to track and separate the changes in heterotrophic soil respiration - involving 12CO2 and O2 - from the microbial process of benzene degradation, which ultimately forms 13CO2.1 The respiratory quotient (RQ) of 0.98 decreased significantly after the spiking and increased again within 33 hours to a value of 0.72. This coincided with maximum 13CO2 concentration rates (0.63 μ mol m-2 s-1), indicating highest benzene degradation at 33 hours after the spiking event. The diffusion of benzene in the headspace and the biodegradation into 13CO2 were simultaneously monitored and 12 days after the benzene spiking no measurable degradation was detected anymore.1 The RQ finally returned to a value of 0.96 demonstrating the reestablished aerobic respiration. In summary, this study shows the potential of combining Raman gas spectroscopy and stable isotopes to follow soil microbial biodegradation dynamics while simultaneously monitoring the underlying respiration behavior. Support by the Collaborative Research Center 1076 Aqua Diva is kindly acknowledged. We thank Beate Michalzik for soil analysis and discussion. 1. T. Jochum, B. Michalzik, A. Bachmann, J. Popp and T. Frosch, Analyst, 2015, 140, 3143-3149.

  11. Carbon Metabolism of Soil microorganisms at Low Temperatures: Position-Specific 13C Labeled Glucose Reveals the Story

    NASA Astrophysics Data System (ADS)

    Apostel, C.; Bore, E. K.; Halicki, S.; Kuzyakov, Y.; Dippold, M.

    2015-12-01

    Metabolic pathway activities at low temperature are not well understood, despite the fact that the processes are relevant for many soils globally and seasonally. To analyze soil metabolism at low temperature, isotopomeres of position-specifically 13C labeled glucose were applied at three temperature levels; +5, -5 -20 oC. In additon, one sterilization treatment with sodium azide at +5 oC was also performed. Soils were incubated for 1, 3 and 10 days while soil samples at -20 oC were additionally sampled after 30 days. The 13C from individual molecule position in respired CO2 was quantifed. Incorporation of 13C in bulk soil, extractable microbial biomass by chloroform fumigation extraction (CFE) and cell membranes of different microbial communities classified by 13C phospholipid fatty acid analysis (PLFA) was carried out. Our 13CO2 data showed a dominance of C-1 respiration at +5 °C for treatments with and without sodium azide, but total respiration for sodium azide inhibited treatments increased by 14%. In contrast, at -5 and -20 oC metabolic behavior showed intermingling of preferential respiration of the glucose C-4 and C-1 positions. Therefore, at +5 °C, pentose phosphate pathway activity is a dominant metabolic pathway used by microorganisms to metabolize glucose. The respiration increase due to NaN3 inhibition was attributed to endoenzymes released from dead organisms that are stabilized at the soil matrix and have access to suitable substrate and co-factors to permit their funtions. Our PLFA analysis showed that incorporation of glucose 13C was higher in Gram negative bacteria than other microbial groups as they are most competitive for LMWOS. Only a limited amount of microbial groups maintained their glucose utilizing activity at -5 and -20 °C and they strongly shifted towards a metabolization of glucose via both glycolysis and pentose phosphate pathways indicating both growth and cellular maintenance. This study revealed a remarkable microbial acitivity

  12. Combining position-specific 13C labeling with compound-specific isotope analysis: first steps towards soil fluxomics

    NASA Astrophysics Data System (ADS)

    Dippold, Michaela; Kuzyakov, Yakov

    2015-04-01

    Understanding the soil organic matter (SOM) dynamics is one of the most important challenges in soil science. Transformation of low molecular weight organic substances (LMWOS) is a key step in biogeochemical cycles because 1) all high molecular substances pass this stage during their decomposition and 2) only LMWOS will be taken up by microorganisms. Previous studies on LMWOS were focused on determining net fluxes through the LMWOS pool, but they rarely identified transformations. As LMWOS are the preferred C and energy source for microorganisms, the transformations of LMWOS are dominated by biochemical pathways of the soil microorganisms. Thus, understanding fluxes and transformations in soils requires a detailed knowledge on the biochemical pathways and its controlling factors. Tracing C fate in soil by isotopes became on of the most applied and promising biogeochemistry tools. Up to now, studies on LMWOS were nearly exclusively based on uniformly labeled organic substances i.e. all C atoms in the molecules were labeled with 13C or 14C. However, this classical approach did not allow the differentiation between use of intact initial substances in any process, or whether they were transformed to metabolites. The novel tool of position-specific labeling enables to trace molecule atoms separately and thus to determine the cleavage of molecules - a prerequisite for metabolic tracing. Position-specific labeling of LMWOS and quantification of 13CO2 and 13C in bulk soil enabled following the basic metabolic pathways of soil microorganisms. However, only the combination of position-specific 13C labeling with compound-specific isotope analysis of microbial biomarkers and metabolites allowed 1) tracing specific anabolic pathways in diverse microbial communities in soils and 2) identification of specific pathways of individual functional microbial groups. So, these are the prerequisites for soil fluxomics. Our studies combining position-specific labeled glucose with amino

  13. Metabolic Response of Soil Microorganisms to Frost: A New Perspective from Position-specific 13C Labeling

    NASA Astrophysics Data System (ADS)

    Bore, E. K.; Apostel, C.; Halicki, S.; Dippold, M. A.; Kuzyakov, Y.

    2016-12-01

    Cold adapted organisms and their biomolecules have received considerable attention in the last few decades, particularly in light of the perceived biotechnological potential. Mostly, these studies are based on pure isolated cultures from permafrost or permafrost samples with inherently adapted microbes. However, microbial activities in agricultural soils that are predominantly exposed to freeze conditions during winter in temperate ecosystems remain unclear. To analyze microbial metabolism at low soil temperatures, isotopomeres of position-specifically 13C labeled glucose were incubated at three temperature; 5 (control), -5 -20 oC. Soils were sampled after 1, 3 and 10 days (and after 30 days for samples at -20 °C). 13C was quantifed in CO2, bulk soil, microbial biomass and dissolved organic carbon (DOC). Highest 13C recovery in CO2 was obtained from C-1 position in control soil. Consequently, metabolic activity was dominated by pentose phosphate pathway at 5 °C. In contrast, metabolic behaviors switched towards a preferential respiration of the glucose C-4 position at -5 and -20 °C. High 13C recovery from C-4 position confirms previous studies suggesting that fermentation increases at subzero temperature. A 3-fold higher 13C recovery in microbial biomass at -5 °C than under control conditions points towards synthesis of intracellular antifreeze metabolites such as glycerol and ethanol and it is consistent with fermentative metabolism. A 5-fold higher 13C in bulk soil than microbial biomass at -20 °C does not reflect non-metabolized glucose because 13C recovery in DOC was less than 0.4% at day 1. Therefore, high 13C recovery in bulk soil at -20 °C was attributed to extracellular metabolites secreted to overcome frost. The shift in antifreeze mechanisms with temperature was brought about by shift in microbial community structure as indicated by incorporation into 13C into PLFA which was 2-fold higher in gram negative bacteria under control than frozen

  14. Utilization of low molecular weight organics by soil microorganisms: combination of 13C-labelling with PLFA analysis

    NASA Astrophysics Data System (ADS)

    Gunina, Anna; Dippold, Michaela; Kuzyakov, Yakov

    2014-05-01

    Microbial metabolisation is the main transformation pathway of low molecular weight organic substances (LMWOS), but detailed knowledge concerning the fate of LMWOS in soils is strongly limited. Considering that various LMWOS classes enter biochemical cycles at different steps, we hypothesise that the percentage of their LMWOS-Carbon (C) used for microbial biomass (MB) production and consequently medium-term stabilisation in soil is different. We traced the three main groups of LMWOS: amino acids, sugars and carboxylic acids, by uniformly labelled 13C-alanine, -glutamate, -glucose, -ribose, -acetate and -palmitate. Incorporation of 13C from these LMWOS into MB (fumigation-extraction method) and into phospholipid fatty acids (PLFAs) (Bligh-Dyer extraction, purification and GC-C-IRMS measurement) was investigated under field conditions 3 d and 10 d after LMWOS application. The activity of microbial utilization of LMWOS for cell membrane construction was estimated by replacement of PLFA-C with 13C. Decomposition of LMWOS-C comprised 20-65% of the total label, whereas incorporation of 13C into MB amounted to 20-50% of initially applied 13C on day three and was reduced to 5-30% on day 10. Incorporation of 13C-labelled LMWOS into MB followed the trend sugars > carboxylic acids > amino acids. Differences in microbial utilisation between LMWOS were observed mainly at day 10. Thus, instead of initial rapid uptake, further metabolism within microbial cells accounts for the individual fate of C from different LMWOS in soils. Incorporation of 13C from each LMWOS into each PLFA occurred, which reflects the ubiquitous ability of all functional microbial groups for LMWOS utilization. The preferential incorporation of palmitate can be attributed to its role as a direct precursor for many fatty acids (FAs) and PLFA formation. Higher incorporation of alanine and glucose compared to glutamate, ribose and acetate reflect the preferential use of glycolysis-derived substances in the FAs

  15. Dynamic secondary ion mass spectrometry (SIMS) imaging of microbial populations utilizing 13C-labeled substrates in pure culture and in soil

    PubMed Central

    Pumphrey, Graham M.; Hanson, Buck T.; Chandra, Subhash; Madsen, Eugene L.

    2008-01-01

    Summary We demonstrate that dynamic secondary ion mass spectrometry (SIMS)-based ion microscopy can provide a means of measuring 13C assimilation into individual bacterial cells grown on 13C-labeled organic compounds in the laboratory and in field soil. We grew pure cultures of Pseudomonas putida NCIB 9816-4 in minimal media with known mixtures of 12C- and 13C-glucose and analyzed individual cells via SIMS imaging. Individual cells yielded signals of masses 12, 13, 24, 25, 26, and 27 as negative secondary ions indicating the presence of 12C−, 13C−, 24(12C2)−, 25(12C13C)−, 26(12C14N)−, and 27(13C14N)− ions, respectively. We verified that ratios of signals taken from the same cells only changed minimally during a ∼4.5-min period of primary O2+ beam sputtering by the dynamic SIMS instrument in microscope detection mode. There was a clear relationship between mass 27 and 26 signals in Psuedomonas putida cells grown in media containing varying proportions of 12C- to 13C-glucose: a standard curve was generated to predict 13C-enrichment in unknown samples. We then used two strains of Pseudomonas putida able to grow on either all or only a part of a mixture of 13C-labeled and unlabeled carbon sources to verify that differential 13C signals measured by SIMS were due to 13C assimilation into cell biomass. Finally, we made three key observations after applying SIMS ion microscopy to soil samples from a field experiment receiving 12C- or 13C-phenol: (i) cells enriched in 13C were heterogeneously distributed among soil populations; (ii) 13C-labeled cells were detected in soil that was dosed a single time with 13C-phenol; and (iii) in soil that received 12 doses of 13C-phenol, 27% of the cells in the total community were more than 90% 13C-labeled. PMID:18811644

  16. Priming effect of 13C-labelled wheat straw in no-tillage soil under drying and wetting cycles in the Loess Plateau of China

    PubMed Central

    Liu, Enke; Wang, Jianbo; Zhang, Yanqing; Angers, Denis A.; Yan, Changrong; Oweis, Theib; He, Wenqing; Liu, Qin; Chen, Baoqing

    2015-01-01

    The objectives of this study were to determine the effects of drying and wetting (DW) cycles on soil organic carbon (SOC) mineralisation and on the priming effect (PE) induced by the addition of 13C-labelled wheat straw to long-term no-tillage (NT) and conventional-tillage (CT) soils. We observed that the SOC mineralisation rate in rewetted soils was greater than that in soils that were kept at constant water content. The proportion of CO2 derived from the straw declined dramatically during the first 10 days. The priming direction was first positive, and then became slightly negative. The PE was higher under DW cycles than under constant water content. There was no significant effect of the tillage system on the SOC mineralisation rate or PE. The data indicate that the DW cycles had a significant effect on the SOC mineralisation rate and on the PE, demonstrating a positive combined effect between wheat straw and moisture fluctuations. Further research is needed to study the role of microbial communities and C pools in affecting the SOC mineralisation response to DW cycles. PMID:26345303

  17. A method for (13)C-labeling of metabolic carbohydrates within French bean leaves (Phaseolus vulgaris L.) for decomposition studies in soils.

    PubMed

    Girardin, Cyril; Rasse, Daniel P; Biron, Philippe; Ghashghaie, Jaleh; Chenu, Claire

    2009-06-01

    The molecular composition of plant residues is suspected to largely govern the fate of their constitutive carbon (C) in soils. Labile compounds, such as metabolic carbohydrates, are affected differently from recalcitrant and structural compounds by soil-C stabilisation mechanisms. Producing (13)C-enriched plant residues with specifically labeled fractions would help us to investigate the fate in soils of the constitutive C of these compounds. The objective of the present research was to test (13)C pulse chase labeling as a method for specifically enriching the metabolic carbohydrate components of plant residues, i.e. soluble sugars and starch. Bean plants were exposed to a (13)CO(2)-enriched atmosphere for 0.5, 1, 2, 3 and 21 h. The major soluble sugars were then determined on water-soluble extracts, and starch on HCl-hydrolysable extracts. The results show a quick differential labeling between water-soluble and water-insoluble compounds. For both groups, (13)C-labeling increased linearly with time. The difference in delta(13)C signature between water-soluble and insoluble fractions was 7 per thousand after 0.5 h and 70 per thousand after 21 h. However, this clear isotopic contrast masked a substantial labeling variability within each fraction. By contrast, metabolic carbohydrates on the one hand (i.e. soluble sugars + starch) and other fractions (essentially cell wall components) on the other hand displayed quite homogeneous signatures within fractions, and a significant difference in labeling between fractions: delta(13)C = 414 +/- 3.7 per thousand and 56 +/- 5.5 per thousand, respectively. Thus, the technique generates labeled plant residues displaying contrasting (13)C-isotopic signatures between metabolic carbohydrates and other compounds, with homogenous signatures within each group. Metabolic carbohydrates being labile compounds, our findings suggest that the technique is particularly appropriate for investigating the effect of compound lability on the long

  18. Incorporation of 13C labeled Pinus ponderosa needle and fine root litter into soil organic matter measured by Py-GC/MS-C-IRMS

    NASA Astrophysics Data System (ADS)

    Mambelli, S.; Gleixner, G.; Dawson, T. E.; Bird, J. A.; Torn, M. S.

    2006-12-01

    Developing effective strategies for enhancing C storage in soils requires understanding the influence of plant C quality. In turn, plant C quality impacts the decay continuum between plant residue and humified, stable SOM. This remains one of the least understood aspects of soil biogeochemistry. We investigated the initial phase of incorporation of 13C labeled Pinus ponderosa needle and fine root litter into SOM. The two litter types were placed in separate microcosms in the A horizon in a temperate conifer soil. Curie-point pyrolysis-gas chromatography coupled with on-line mass spectrometry and isotope ratio mass spectrometry (Py-GC/MS-C- IRMS) were used to determine the identity and the 13C enrichment of pyrolysis products (fragments of carbohydrates, lignin, proteins and lipids). We compared the two initial litter types, needles and fine roots, to samples of the bulk soil (A horizon, < 2mm) and soil humin fraction (from chemical solubility) obtained from each microcosm 1.5y after litter addition. Pyrolysis of plant material and SOM produced 56 suitable products for isotopic analysis; of them, 15 occurred in both the litter and bulk soil, 7 in both the litter and the humin fraction and 9 in both bulk soil and the humin fraction. The pyrolysis products found in common in the plant and soil were related either to polysaccharides or were non-specific and could have originated from various precursors. The data suggest that the majority of plant inputs, both from needles or fine roots, were degraded very rapidly. In the humin fraction, the most recalcitrant pool of C in soil, with a measured turnover time of 260y (this soil), only products from the fragmentation of polysaccharides and alkyl-benzene compounds were found. Comparisons of the enrichment normalized by input level suggest little difference between the incorporation of C from needles versus fine roots into SOM. The most enriched fragments in the humin fraction were products from polysaccharides degradation

  19. Incorporation of 13C labelled root-shoot residues in soil in the presence of Lumbricus terrestris: An isotopic and molecular approach

    NASA Astrophysics Data System (ADS)

    Vidal, Alix; Alexis, Marie; Nguyen Tu, Thanh Tu; Anquetil, Christelle; Vaury, Véronique; Derenne, Sylvie; Quenea, Katell

    2016-04-01

    Litter from plant biomass deposited on soil surface can either be mineralized; releasing CO2 to the atmosphere, or transferred into the soil as organic compounds. Both pathways depend on biotic factors such as litter characteristics and the of soil organism activity. During the last decades, many studies have focused on the origin of organic matter, with a particular attention to the fate of root and shoot litter. It is generally admitted that roots decompose at a slower rate than shoots, resulting in a higher carbon sequestration in soil for compounds originating from roots. Earthworms play a central role in litter decomposition and carbon cycling, ingesting both organic and mineral compounds which are mixed, complexed and dejected in the form of casts at the soil surface or along earthworm burrows. The simultaneous impact of earthworms and root-shoot on soil carbon cycling is still poorly understood. This study aimed at (1) defining the rate of incorporation of root and shoot litter with or without earthworms and (2) characterizing the molecular composition of soil organic matter upon litter decomposition, after one year of experimentation. A mesocosm experiment was set up to follow the incorporation of 13C labelled Ryegrass root and shoot litter in the soil, in the presence of anecic earthworms (Lumbricus terrestris). Soil samples were collected at 0-20 and 40-60 cm, as well as surface casts, at the beginning and after 1, 2, 4, 8, 24 and 54 weeks of experiment. Organic carbon content and δ13C values were determined for all the samples with Elemental Analysis - Isotope Ratio Mass Spectrometry. Lipid-free soil and cast samples after 54 weeks of incubation were analyzed with Pyrolysis-Gas Chromatography-Mass Spectrometry. Pyrolysis products were grouped into six classes: polysaccharides, lignin derived compounds, phenols, N-compounds, aliphatic compounds and sterols. Each pyrolysis product was quantified thanks to its peak area, relative to the total area of the

  20. Molecular Investigation of the Short-term Sequestration of Natural Abundance 13C -labelled Cow Dung in the Surface Horizons of a Temperate Grassland Soil

    NASA Astrophysics Data System (ADS)

    Dungait, J.; Bol, R.; Evershed, R. P.

    2004-12-01

    An adequate understanding of the carbon (C) sequestration potential of grasslands requires that the quantity and residence times of C inputs be measured. Herbivore dung is largely comprised of plant cell wall material, a significant source of stable C in intensively grazed temperate grassland ecosystems that contributes to the soil carbon budget. Our work uses compound-specific isotope analysis to identify the pattern of input of dung-derived compounds from natural abundance 13C/-labelled cow dung into the surface horizons of a temperate grassland soil over one year. C4 dung (δ 13C \\-12.6 ‰ ) from maize fed cows was applied to a temperate grassland surface (δ 13C \\-29.95 ‰ ) at IGER-North Wyke (Devon, UK), and dung remains and soil cores beneath the treatments collected at ŧ = 7, 14, 28, 56, 112, 224 and 372 days. Bulk dung carbon present in the 0\\-1 cm and 1\\-5 cm surface horizons of a grassland soil over one year was estimated using Δ 13C between C4 dung and C3 dung, after Bol {\\et al.} (2000). The major biochemical components of dung were quantified using proximate forage fibre analyses, after Goering and Van Soest (1970) and identified using `wet' chemical and GC-MS methods. Plant cell wall polysaccharides and lignin were found to account for up to 67 {%} of dung dry matter. Hydrolysed polysaccharides were prepared as alditol acetates for analyses (after Docherty {\\et al.}, 2001), and a novel application of an off-line pyrolysis method applied to measure lignin-derived phenolic compounds (after Poole & van Bergen, 2002). This paper focuses on major events in the incorporation of dung carbon, estimated using natural abundance 13C&-slash;labelling technique. This revealed a major bulk input of dung carbon after a period of significant rainfall with a consequent decline in bulk soil δ 13C values until the end of the experiment (Dungait {\\et al.}, submitted). Findings will be presented revealing contribution of plant cell wall polysaccharides and

  1. Investigation of the degradation of 13C-labeled fungal biomass in soil - fate of carbon in a soil bioreactor system

    NASA Astrophysics Data System (ADS)

    Schweigert, Michael; Fester, Thomas; Miltner, Anja; Kaestner, Matthias

    2015-04-01

    Nutrient balances and degradation processes in boreal forests are mainly influenced by interactions of plant roots and ectomycorrhizal fungi. Plants benefit from nitrogen compounds provided by their symbiotic interaction partner. In return ectomycorrhiza are provided by large amounts of carbon from the plants which is used for the synthesis of hyphal networks in soil and for metabolic activity for nutrient uptake. Therefore, ectomycorrhizal fungi play a major role in ecosystems of boreal forests and are consequently an important sink for carbon by building large amount of mycelia. Recently, it has been shown that microbial biomass residues contribute significantly to soil organic matter formation. This suggests that also residues of ectomycorrhizal fungi may be an important source for soil organic matter formation in forest soils where these fungi are abundant. However, the fate of ectomycorrhizal biomass residues in soils is unknown. We therefore investigated the fate of ectomycorrhizal biomass in soil in a soil bioreactor system to quantify the contribution of this material to soil organic matter formation. As a model organism, we selected Laccaria bicolor, which was labelled by growing the fungus on 13C glucose. The stable isotope-labeled biomass was then homogenized and incubated in a podzol from a typical forest site in Central Germany. The fate of the labeled biomass was traced by analyzing the amount of 13C mineralized and the amount remaining in the soil. The fungal biomass carbon was mineralized rather rapidly during the first 50 days. Then the mineralization rate slowed down, but mineralization continued until the end of the experiment, when approximately 40% of the 13C was mineralized and 60% remained in soil. In addition, we analyzed biomolecules such as fatty acids to trace the incorporation of the L. bicolor-derived biomass carbon into other microorganisms and to identify potential primary consumers of fungal biomass. By these analyses, we found a

  2. Investigation of the degradation of 13C-labeled fungal biomass in soil - fate of carbon in a soil bioreactor system

    NASA Astrophysics Data System (ADS)

    Schweigert, Michael; Fester, Thomas; Miltner, Anja; Kästner, Matthias

    2014-05-01

    Nutrient balances and degradation processes in boreal forests are mainly influenced by interactions of plant roots and ectomycorrhizal fungi. Plants benefit from nitrogen compounds provided by their symbiotic interaction partner. In return ectomycorrhiza are provided by large amounts of carbon from the plants which is used for the synthesis of hyphal networks in soil and for metabolic activity for nutrient uptake. Therefore ectomycorrhizal fungi play a major role in ecosystems of boreal forests and are consequently an important sink for carbon by building large amounts of mycelia. Recently, it has been shown that microbial biomass residues contribute significantly to soil organic matter formation. This suggests that also residues of ectomycorrhizal fungi may be an important source for soil organic matter formation in forest soils where these fungi are abundant. However, the fate of ectomycorrhizal biomass residues in soils is unknown. We therefore investigated the fate of ectomycorrhizal biomass in soil in a bioreactor system to quantify the contribution of this material to soil organic matter formation. As a model organism, we selected Laccaria bicolor, which was labelled by growing the fungus on 13C glucose. The stable isotope-labeled biomass was then homogenized and incubated in a podzol from a typical forest site in Central Germany. The fate of the labeled biomass was traced by analyzing the amount of 13C mineralized and the amount remaining in the soil. The fungal biomass carbon was mineralized rather rapidly during the first 25 days. Then the mineralization rate slowed down, but mineralization continued until the end of the experiment, when approximately 40% of the 13C was mineralized and 60% remained in soil. In addition, we analyzed biomolecules such as fatty acids to trace the incorporation of the L. bicolor-derived biomass carbon into other microorganisms and to identify potential primary consumers of fungal biomass. By these analyses, we found a

  3. Spatial and temporal distribution of 13C labelled plant residues in soil aggregates and Lumbricus terrestris surface casts: A combination of Transmission Electron Microscopy and Nanoscale Secondary Ion Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Vidal, Alix; Remusat, Laurent; Watteau, Françoise; Derenne, Sylvie; Quenea, Katell

    2016-04-01

    Earthworms play a central role in litter decomposition, soil structuration and carbon cycling. They ingest both organic and mineral compounds which are mixed, complexed with mucus and dejected in form of casts at the soil surface and along burrows. Bulk isotopic or biochemical technics have often been used to study the incorporation of litter in soil and casts, but they could not reflect the complex interaction between soil, plant and microorganisms at the microscale. However, the heterogeneous distribution of organic carbon in soil structures induces contrasted microbial activity areas. Nano-scale secondary ion mass spectrometry (NanoSIMS), which is a high spatial resolution method providing elemental and isotopic maps of organic and mineral materials, has recently been applied in soil science (Herrmann et al., 2007; Vogel et al., 2014). The combination of Nano-scale secondary ion mass spectrometry (NanoSIMS) and Transmission Electron Microscopy (TEM) has proven its potential to investigate labelled residues incorporation in earthworm casts (Vidal et al., 2016). In line of this work, we studied the spatial and temporal distribution of plant residues in soil aggregates and earthworm surface casts. This study aimed to (1) identify the decomposition states of labelled plant residues incorporated at different time steps, in casts and soil, (2) identify the microorganisms implied in this decomposition (3) relate the organic matter states of decomposition with their 13C signature. A one year mesocosm experiment was set up to follow the incorporation of 13C labelled Ryegrass (Lolium multiflorum) litter in a soil in the presence of anecic earthworms (Lumbricus terrestris). Soil and surface cast samples were collected after 8 and 54 weeks, embedded in epoxy resin and cut into ultra-thin sections. Soil was fractionated and all and analyzed with TEM and NanoSIMS, obtaining secondary ion images of 12C, 16O, 12C14N, 13C14N and 28Si. The δ13C maps were obtained using the 13C14

  4. Synthesis of Site-Specifically (13)C Labeled Linoleic Acids.

    PubMed

    Offenbacher, Adam R; Zhu, Hui; Klinman, Judith P

    2016-10-12

    Soybean lipoxygenase-1 (SLO-1) catalyzes the C-H abstraction from the reactive carbon (C-11) in linoleic acid as the first and rate-determining step in the formation of alkylhydroperoxides. While previous labeling strategies have focused on deuterium labeling to ascertain the primary and secondary kinetic isotope effects for this reaction, there is an emerging interest and need for selectively enriched (13)C isotopologues. In this report, we present synthetic strategies for site-specific (13)C labeled linoleic acid substrates. We take advantage of a Corey-Fuchs formyl to terminal (13)C-labeled alkyne conversion, using (13)CBr4 as the labeling source, to reduce the number of steps from a previous fatty acid (13)C synthetic labeling approach. The labeled linoleic acid substrates are useful as nuclear tunneling markers and for extracting active site geometries of the enzyme-substrate complex in lipoxygenase.

  5. Variability of 13C-labeling in plant leaves.

    PubMed

    Nguyen Tu, Thanh Thuy; Biron, Philippe; Maseyk, Kadmiel; Richard, Patricia; Zeller, Bernd; Quénéa, Katell; Alexis, Marie; Bardoux, Gérard; Vaury, Véronique; Girardin, Cyril; Pouteau, Valérie; Billiou, Daniel; Bariac, Thierry

    2013-09-15

    Plant tissues artificially labeled with (13)C are increasingly used in environmental studies to unravel biogeochemical and ecophysiological processes. However, the variability of (13)C-content in labeled tissues has never been carefully investigated. Hence, this study aimed at documenting the variability of (13)C-content in artificially labeled leaves. European beech and Italian ryegrass were subjected to long-term (13)C-labeling in a controlled-environment growth chamber. The (13)C-content of the leaves obtained after several months labeling was determined by isotope ratio mass spectrometry. The (13)C-content of the labeled leaves exhibited inter- and intra-leaf variability much higher than those naturally occurring in unlabeled plants, which do not exceed a few per mil. This variability was correlated with labeling intensity: the isotope composition of leaves varied in ranges of ca 60‰ and 90‰ for experiments that led to average leaf (13)C-content of ca +15‰ and +450‰, respectively. The reported variability of isotope composition in (13)C-enriched leaves is critical, and should be taken into account in subsequent experimental investigations of environmental processes using (13)C-labeled plant tissues. Copyright © 2013 John Wiley & Sons, Ltd.

  6. Accumulation of cadmium and uranium in arable soils in Switzerland.

    PubMed

    Bigalke, Moritz; Ulrich, Andrea; Rehmus, Agnes; Keller, Armin

    2017-02-01

    Mineral phosphorus (P) fertilizers contain contaminants that are potentially hazardous to humans and the environment. Frequent mineral P fertilizer applications can cause heavy metals to accumulate and reach undesirable concentrations in agricultural soils. There is particular concern about Cadmium (Cd) and Uranium (U) accumulation because these metals are toxic and can endanger soil fertility, leach into groundwater, and be taken up by crops. We determined total Cd and U concentrations in more than 400 topsoil and subsoil samples obtained from 216 agricultural sites across Switzerland. We also investigated temporal changes in Cd and U concentrations since 1985 in soil at six selected Swiss national soil monitoring network sites. The mean U concentrations were 16% higher in arable topsoil than in grassland topsoil. The Cd concentrations in arable and grassland soils did not differ, which we attribute to soil management practices and Cd sources other than mineral P fertilizers masking Cd inputs from mineral P fertilizers. The mean Cd and U concentrations were 58% and 9% higher, respectively, in arable topsoil than in arable subsoil, indicating that significant Cd and U inputs to arable soils occurred in the past. Geochemical mass balances confirmed this, indicating an accumulation of 52% for Cd and 6% for U. Only minor temporal changes were found in the Cd concentrations in topsoil from the six soil-monitoring sites, but U concentrations in topsoil from three sites had significantly increased since 1985. Sewage sludge and atmospheric deposition were previously important sources of Cd to agricultural soils, but today mineral P fertilizers are the dominant sources of Cd and U. Future Cd and U inputs to agricultural soils may be reduced by using optimized management practices, establishing U threshold values for mineral P fertilizers and soils, effectively enforcing threshold values, and developing and using clean recycled P fertilizers.

  7. NMR structure analysis of uniformly 13C-labeled carbohydrates.

    PubMed

    Fontana, Carolina; Kovacs, Helena; Widmalm, Göran

    2014-06-01

    In this study, a set of nuclear magnetic resonance experiments, some of them commonly used in the study of (13)C-labeled proteins and/or nucleic acids, is applied for the structure determination of uniformly (13)C-enriched carbohydrates. Two model substances were employed: one compound of low molecular weight [(UL-(13)C)-sucrose, 342 Da] and one compound of medium molecular weight ((13)C-enriched O-antigenic polysaccharide isolated from Escherichia coli O142, ~10 kDa). The first step in this approach involves the assignment of the carbon resonances in each monosaccharide spin system using the anomeric carbon signal as the starting point. The (13)C resonances are traced using (13)C-(13)C correlations from homonuclear experiments, such as (H)CC-CT-COSY, (H)CC-NOESY, CC-CT-TOCSY and/or virtually decoupled (H)CC-TOCSY. Based on the assignment of the (13)C resonances, the (1)H chemical shifts are derived in a straightforward manner using one-bond (1)H-(13)C correlations from heteronuclear experiments (HC-CT-HSQC). In order to avoid the (1) J CC splitting of the (13)C resonances and to improve the resolution, either constant-time (CT) in the indirect dimension or virtual decoupling in the direct dimension were used. The monosaccharide sequence and linkage positions in oligosaccharides were determined using either (13)C or (1)H detected experiments, namely CC-CT-COSY, band-selective (H)CC-TOCSY, HC-CT-HSQC-NOESY or long-range HC-CT-HSQC. However, due to the short T2 relaxation time associated with larger polysaccharides, the sequential information in the O-antigen polysaccharide from E. coli O142 could only be elucidated using the (1)H-detected experiments. Exchanging protons of hydroxyl groups and N-acetyl amides in the (13)C-enriched polysaccharide were assigned by using HC-H2BC spectra. The assignment of the N-acetyl groups with (15)N at natural abundance was completed by using HN-SOFAST-HMQC, HNCA, HNCO and (13)C-detected (H)CACO spectra.

  8. Survey of phthalate pollution in arable soils in China.

    PubMed

    Hu, Xiao-yu; Wen, Bei; Shan, Xiao-quan

    2003-08-01

    The problem of pollution by phthalates is of global concern due to their widespread occurrence, toxicity and endocrine disruption properties. The contamination by phthalates such as dimethyl phthalate (DMP), diethyl phthalate (DEP), di-n-butyl phthalate (DBP) and di(2-ethylhexyl) phthalate (DEHP) in 23 arable soils throughout China was investigated to evaluate the present pollution situation. The survey results demonstrated that phthalates were ubiquitous pollutants in soils in China. The total concentrations of phthalates differed from one location to another, and ranged from 0.89 to 10.03 mg kg(-1) with a median concentration of 3.43 mg kg(-1). Among the phthalates, DEHP was dominant and detected in all 23 soils. DEP and DBP were also in abundance, and DMP was rarely detected. Similar contamination patterns were observed in all 23 soils. A distinct feature of phthalate pollution in China was that the average concentration in northern China was higher than that in southern China. In addition, a close relationship was observed between the concentration of phthalates in soils and the consumption of agricultural film. The correlation showed that the application of agriculture film might be a significant pollution source of phthalates in arable soils of China. The potential risk of phthalates in soils was assessed on the basis of current guide values and limits.

  9. Spatial Distribution of Fungal Communities in an Arable Soil.

    PubMed

    Moll, Julia; Hoppe, Björn; König, Stephan; Wubet, Tesfaye; Buscot, François; Krüger, Dirk

    2016-01-01

    Fungi are prominent drivers of ecological processes in soils, so that fungal communities across different soil ecosystems have been well investigated. However, for arable soils taxonomically resolved fine-scale studies including vertical itemization of fungal communities are still missing. Here, we combined a cloning/Sanger sequencing approach of the ITS/LSU region as marker for general fungi and of the partial SSU region for arbuscular mycorrhizal fungi (AMF) to characterize the microbiome in different maize soil habitats. Four compartments were analyzed over two annual cycles 2009 and 2010: a) ploughed soil in 0-10 cm, b) rooted soil in 40-50 cm, c) root-free soil in 60-70 cm soil depth and d) maize roots. Ascomycota was the most dominant phylum across all compartments. Fungal communities including yeasts and AMF differed strongly between compartments. Inter alia, Tetracladium, the overall largest MOTU (molecular operational taxonomic unit), occurred in all compartments, whereas Trichosporon dominated all soil compartments. Sequences belonging to unclassified Helotiales were forming the most abundant MOTUs exclusively present in roots. This study gives new insights on spatial distribution of fungi and helps to link fungal communities to specific ecological properties such as varying resources, which characterize particular niches of the heterogeneous soil environment.

  10. Spatial Distribution of Fungal Communities in an Arable Soil

    PubMed Central

    Moll, Julia; Hoppe, Björn; König, Stephan; Wubet, Tesfaye; Buscot, François; Krüger, Dirk

    2016-01-01

    Fungi are prominent drivers of ecological processes in soils, so that fungal communities across different soil ecosystems have been well investigated. However, for arable soils taxonomically resolved fine-scale studies including vertical itemization of fungal communities are still missing. Here, we combined a cloning/Sanger sequencing approach of the ITS/LSU region as marker for general fungi and of the partial SSU region for arbuscular mycorrhizal fungi (AMF) to characterize the microbiome in different maize soil habitats. Four compartments were analyzed over two annual cycles 2009 and 2010: a) ploughed soil in 0–10 cm, b) rooted soil in 40–50 cm, c) root-free soil in 60–70 cm soil depth and d) maize roots. Ascomycota was the most dominant phylum across all compartments. Fungal communities including yeasts and AMF differed strongly between compartments. Inter alia, Tetracladium, the overall largest MOTU (molecular operational taxonomic unit), occurred in all compartments, whereas Trichosporon dominated all soil compartments. Sequences belonging to unclassified Helotiales were forming the most abundant MOTUs exclusively present in roots. This study gives new insights on spatial distribution of fungi and helps to link fungal communities to specific ecological properties such as varying resources, which characterize particular niches of the heterogeneous soil environment. PMID:26840453

  11. Database of Polish arable mineral soils: a review

    NASA Astrophysics Data System (ADS)

    Bieganowski, A.; Witkowska-Walczak, B.; Gliñski, J.; Sokołowska, Z.; Sławiński, C.; Brzezińska, M.; Włodarczyk, T.

    2013-09-01

    The database of Polish arable mineral soils is presented. The database includes a lot of information about the basic properties of soils and their dynamic characteristics. It was elaborated for about 1 000 representative profiles of soils in Poland The database concerns: particle size distribution, organic carbon content, acidity-pH, specific surface area, hydrophobicity - solidliquid contact angle, static and dynamic hydrophysical properties, oxidation-reduction properties and selected biological (microbiological) properties of soils. Knowledge about soil characteristics is indispensable for description, interpretation and prediction of the course of physical, chemical and biological processes, and modelling these processes requires representative data. The utility of simulation and prediction models describing phenomena which take place in the soil-plant-atmosphere system greatly depends on the precision of data concerning characteristics of soil. On the basis of this database, maps of chosen soil properties are constructed. The aim of maps is to provide specialists in agriculture, ecology, and environment protection with an opportunity to gain knowledge of soil properties and their spatial and seasonal variability.

  12. A method to trace root-respired CO2 using a 13C label

    NASA Astrophysics Data System (ADS)

    Cooperdock, S.; Breecker, D.; Litvak, M. E.

    2014-12-01

    In order to partition total soil respiration into root respiration and decomposition under ambient conditions in desert soils, the following method was developed using 13C-labeled CO2 in a modern juniper savannah in central New Mexico. The labeled CO2 was mixed with ambient air and pumped into a small (2.5 m diameter and 1.4 m tall) juniper tree canopy . 10 L of the 13CO2 was sufficient to generate a stream of air at 20 L/min for 1 hour with a CO2 concentration of 540 ppm and a δ13C value of approximately 35,000‰. Plastic tarpaulins were used as a wind block. The 13CO2 -labeled air was applied to the canopy during peak photosynthesis between 10 and 11 am on June 30 2014 during which canopy air CO2 was elevated by approximately 10 ppm over ambient and had δ13C values ranging from 50 to 1000 ‰. Over the next three days, gas and tissue samples were collected in order to trace the 13C label through the juniper tree. Leaf and root samples collected from the labeled tree and from several control trees were loaded into exetainer vials, flushed with CO2-free air and incubated in the dark for 5 hours in order to measure the carbon isotope composition of respired CO2. Samples of soil pore space gas were collected from wells under the labeled tree and a control tree and were transported to the laboratory in He-flushed exetainer vials. The δ13C values of CO2 in the soil gas samples and in the headspace of incubation vials were measured using an isotope ratio mass spectrometer. The δ13C values of foliar respiration were significantly higher than those of the control (by 3.6‰, p < 0.01) one and two days after labeling and δ13C values of root-respired CO2 were significantly higher (by 0.7‰, p = 0.01) than those of the control three days after labeling. In addition, δ13C values of soil respired CO2, determined from measurements of soil pore space CO2 at 50 cm three days after labeling, were significantly higher (by 0.7‰, p < 0.03)) for the labeled tree than control

  13. Synthesis and solid-state NMR structural characterization of 13C-labeled graphite oxide.

    PubMed

    Cai, Weiwei; Piner, Richard D; Stadermann, Frank J; Park, Sungjin; Shaibat, Medhat A; Ishii, Yoshitaka; Yang, Dongxing; Velamakanni, Aruna; An, Sung Jin; Stoller, Meryl; An, Jinho; Chen, Dongmin; Ruoff, Rodney S

    2008-09-26

    The detailed chemical structure of graphite oxide (GO), a layered material prepared from graphite almost 150 years ago and a precursor to chemically modified graphenes, has not been previously resolved because of the pseudo-random chemical functionalization of each layer, as well as variations in exact composition. Carbon-13 (13C) solid-state nuclear magnetic resonance (SSNMR) spectra of GO for natural abundance 13C have poor signal-to-noise ratios. Approximately 100% 13C-labeled graphite was made and converted to 13C-labeled GO, and 13C SSNMR was used to reveal details of the chemical bonding network, including the chemical groups and their connections. Carbon-13-labeled graphite can be used to prepare chemically modified graphenes for 13C SSNMR analysis with enhanced sensitivity and for fundamental studies of 13C-labeled graphite and graphene.

  14. Origin of acetaldehyde during milk fermentation using (13)C-labeled precursors.

    PubMed

    Ott, A; Germond, J E; Chaintreau, A

    2000-05-01

    Acetaldehyde formation by Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus during fermentation of cow's milk was investigated using (13)C-labeled glucose, L-threonine, and pyruvate with a recent static-and-trapped-headspace technique that does not require derivatization of acetaldehyde prior to gas chromatography-mass spectrometry. Over 90% and almost 100% of acetaldehyde originated from glucose during fermentation by L. delbrueckii subsp. bulgaricus and S. thermophilus, respectively, taking into account both singly and doubly labeled acetaldehyde. As both microorganisms showed threonine aldolase activity and formed labeled acetaldehyde from (13)C-labeled threonine during the fermentation of milk, this amino acid should also contribute to the acetaldehyde produced.

  15. Phosphorus Containing Water Dispersible Nanoparticles in Arable Soil.

    PubMed

    Jiang, Xiaoqian; Bol, Roland; Nischwitz, Volker; Siebers, Nina; Willbold, Sabine; Vereecken, Harry; Amelung, Wulf; Klumpp, Erwin

    2015-11-01

    Due to the limited solubility of phosphorus (P) in soil, understanding its binding in fine colloids is vital to better forecast P dynamics and losses in agricultural systems. We hypothesized that water-dispersible P is present as nanoparticles and that iron (Fe) plays a crucial role for P binding to these nanoparticles. To test this, we isolated water-dispersible fine colloids (WDFC) from an arable topsoil (Haplic Luvisol, Germany) and assessed colloidal P forms after asymmetric flow field-flow fractionation coupled with ultraviolet and an inductively coupled plasma mass spectrometer, with and without removal of amorphous and crystalline Fe oxides using oxalate and dithionite, respectively. We found that fine colloidal P was present in two dominant sizes: (i) in associations of organic matter and amorphous Fe (Al) oxides in nanoparticles <20 nm, and (ii) in aggregates of fine clay, organic matter and Fe oxides (more crystalline Fe oxides) with a mean diameter of 170 to 225 nm. Solution P-nuclear magnetic resonance spectra indicated that the organically bound P predominantly comprised orthophosphate-monoesters. Approximately 65% of P in the WDFC was liberated after the removal of Fe oxides (especially amorphous Fe oxides). The remaining P was bound to larger-sized WDFC particles and Fe bearing phyllosilicate minerals. Intriguingly, the removal of Fe by dithionite resulted in a disaggregation of the nanoparticles, evident in higher portions of organically bound P in the <20 nm nanoparticle fraction, and a widening of size distribution pattern in larger-sized WDFC fraction. We conclude that the crystalline Fe oxides contributed to soil P sequestration by (i) acting as cementing agents contributing to soil fine colloid aggregation, and (ii) binding not only inorganic but also organic P in larger soil WDFC particles. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

  16. 13C-labelled microdialysis studies of cerebral metabolism in TBI patients☆

    PubMed Central

    Carpenter, Keri L.H.; Jalloh, Ibrahim; Gallagher, Clare N.; Grice, Peter; Howe, Duncan J.; Mason, Andrew; Timofeev, Ivan; Helmy, Adel; Murphy, Michael P.; Menon, David K.; Kirkpatrick, Peter J.; Carpenter, T. Adrian; Sutherland, Garnette R.; Pickard, John D.; Hutchinson, Peter J.

    2014-01-01

    Human brain chemistry is incompletely understood and better methodologies are needed. Traumatic brain injury (TBI) causes metabolic perturbations, one result of which includes increased brain lactate levels. Attention has largely focussed on glycolysis, whereby glucose is converted to pyruvate and lactate, and is proposed to act as an energy source by feeding into neurons’ tricarboxylic acid (TCA) cycle, generating ATP. Also reportedly upregulated by TBI is the pentose phosphate pathway (PPP) that does not generate ATP but produces various molecules that are putatively neuroprotective, antioxidant and reparative, in addition to lactate among the end products. We have developed a novel combination of 13C-labelled cerebral microdialysis both to deliver 13C-labelled substrates into brains of TBI patients and recover the 13C-labelled metabolites, with high-resolution 13C NMR analysis of the microdialysates. This methodology has enabled us to achieve the first direct demonstration in humans that the brain can utilise lactate via the TCA cycle. We are currently using this methodology to make the first direct comparison of glycolysis and the PPP in human brain. In this article, we consider the application of 13C-labelled cerebral microdialysis for studying brain energy metabolism in patients. We set this methodology within the context of metabolic pathways in the brain, and 13C research modalities addressing them. PMID:24361470

  17. (13)C-labelled microdialysis studies of cerebral metabolism in TBI patients.

    PubMed

    Carpenter, Keri L H; Jalloh, Ibrahim; Gallagher, Clare N; Grice, Peter; Howe, Duncan J; Mason, Andrew; Timofeev, Ivan; Helmy, Adel; Murphy, Michael P; Menon, David K; Kirkpatrick, Peter J; Carpenter, T Adrian; Sutherland, Garnette R; Pickard, John D; Hutchinson, Peter J

    2014-06-16

    Human brain chemistry is incompletely understood and better methodologies are needed. Traumatic brain injury (TBI) causes metabolic perturbations, one result of which includes increased brain lactate levels. Attention has largely focussed on glycolysis, whereby glucose is converted to pyruvate and lactate, and is proposed to act as an energy source by feeding into neurons' tricarboxylic acid (TCA) cycle, generating ATP. Also reportedly upregulated by TBI is the pentose phosphate pathway (PPP) that does not generate ATP but produces various molecules that are putatively neuroprotective, antioxidant and reparative, in addition to lactate among the end products. We have developed a novel combination of (13)C-labelled cerebral microdialysis both to deliver (13)C-labelled substrates into brains of TBI patients and recover the (13)C-labelled metabolites, with high-resolution (13)C NMR analysis of the microdialysates. This methodology has enabled us to achieve the first direct demonstration in humans that the brain can utilise lactate via the TCA cycle. We are currently using this methodology to make the first direct comparison of glycolysis and the PPP in human brain. In this article, we consider the application of (13)C-labelled cerebral microdialysis for studying brain energy metabolism in patients. We set this methodology within the context of metabolic pathways in the brain, and (13)C research modalities addressing them.

  18. Spatial patterns of soil organic carbon stocks in Estonian arable soils

    NASA Astrophysics Data System (ADS)

    Suuster, Elsa; Astover, Alar; Kõlli, Raimo; Roostalu, Hugo; Reintam, Endla; Penu, Priit

    2010-05-01

    Soil organic carbon (SOC) determines ecosystem functions, influencing soil fertility, soil physical, chemical and biological properties and crop productivity. Therefore the spatial pattern of SOC stocks and its appropriate management is important at various scales. Due to climate change and the contribution of carbon store in the soils, the national estimates of soil carbon stocks should be determined. Estonian soils have been well studied and mapped at a scale 1:10,000. Previous studies have estimated SOC stocks based on combinations of large groups of Estonian soils and the mean values of the soil profile database, but were not embedded into the geo-referenced databases. These studies have estimated SOC stocks of Estonian arable soils 122.3 Tg. Despite of available soil maps and databases, this information is still very poorly used for spatial soil modelling. The aim of current study is to assess and model spatial pattern of SOC stocks of arable soils on a pilot area Tartu County (area 3089 sq km). Estonian digital soil map and soil monitoring databases are providing a good opportunity to assess SOC stocks at various scales. The qualitative nature of the initial data from a soil map prohibits any straightforward use in modelling. Thus we have used several databases to construct models and linkages between soil properties that can be integrated into soil map. First step was to reorganize the soil map database (44,046 mapping units) so it can be used as an input to modelling. Arable areas were distinguished by a field layer of Agricultural Registers and Information Board, which provides precise information of current land use as it is the basis of paying CAP subsidies. The estimates of SOC content were found by using the arable land evaluation database of Tartu from the Estonian Land Board (comprising 950 sq km and 31,226 fields), where each soil type was assessed separately and average SOC content grouped by texture was derived. SOC content of epipedon varies in

  19. 13C isotope effects on 1H chemical shifts: NMR spectral analysis of 13C-labelled D-glucose and some 13C-labelled amino acids.

    PubMed

    Tiainen, Mika; Maaheimo, Hannu; Soininen, Pasi; Laatikainen, Reino

    2010-02-01

    The one- and two-bond (13)C isotope shifts, typically -1.5 to -2.5 ppb and -0.7 ppb respectively, in non-cyclic aliphatic systems and up to -4.4 ppb and -1.0 ppb in glucose cause effects that need to be taken into account in the adaptive NMR spectral library-based quantification of the isotopomer mixtures. In this work, NMR spectral analyses of some (13)C-labelled amino acids, D-glucose and other small compounds were performed in order to obtain rules for prediction of the (13)C isotope effects on (1)H chemical shifts. It is proposed that using the additivity rules, the isotope effects can be predicted with a sufficient accuracy for amino acid isotopomer applications. For glucose the effects were found strongly non-additive. The complete spectral analysis of fully (13)C-labelled D-glucose made it also possible to assign the exocyclic proton signals of the glucose. Copyright 2009 John Wiley & Sons, Ltd.

  20. Enhancement of Late Successional Plants on Ex-Arable Land by Soil Inoculations

    PubMed Central

    Carbajo, Vanesa; den Braber, Bowy; van der Putten, Wim H.; De Deyn, Gerlinde B.

    2011-01-01

    Restoration of species-rich grasslands on ex-arable land can help the conservation of biodiversity but faces three big challenges: absence of target plant propagules, high residual soil fertility and restoration of soil communities. Seed additions and top soil removal can solve some of these constraints, but restoring beneficial biotic soil conditions remains a challenge. Here we test the hypotheses that inoculation of soil from late secondary succession grasslands in arable receptor soil enhances performance of late successional plants, especially after top soil removal but pending on the added dose. To test this we grew mixtures of late successional plants in arable top (organic) soil or in underlying mineral soil mixed with donor soil in small or large proportions. Donor soils were collected from different grasslands that had been under restoration for 5 to 41 years, or from semi-natural grassland that has not been used intensively. Donor soil addition, especially when collected from older restoration sites, increased plant community biomass without altering its evenness. In contrast, addition of soil from semi-natural grassland promoted plant community evenness, and hence its diversity, but reduced community biomass. Effects of donor soil additions were stronger in mineral than in organic soil and larger with bigger proportions added. The variation in plant community composition was explained best by the abundances of nematodes, ergosterol concentration and soil pH. We show that in controlled conditions inoculation of soil from secondary succession grassland into ex-arable land can strongly promote target plant species, and that the role of soil biota in promoting target plant species is greatest when added after top soil removal. Together our results point out that transplantation of later secondary succession soil can promote grassland restoration on ex-arable land. PMID:21760929

  1. Ancient manuring practices pollute arable soils at the St Kilda World Heritage Site, Scottish North Atlantic.

    PubMed

    Meharg, Andrew A; Deacon, Clare; Edwards, Kevin J; Donaldson, Margaret; Davidson, Donald A; Spring, Christian; Scrimgeour, Charles M; Feldmann, Jörg; Rabb, A

    2006-09-01

    The impact of ancient fertilization practices on the biogeochemistry of arable soils on the remote Scottish island of Hirta, St Kilda was investigated. The island was relatively unusual in that the inhabitants exploited seabird colonies for food, enabling high population densities to be sustained on a limited, and naturally poor, soil resource. A few other Scottish islands, the Faeroes and some Icelandic Islands, had similar cultural dependence on seabirds. Fertilization with human and animal waste streams (mainly peat ash and bird carcases) on Hirta over millennia has led to over-deepened, nutrient-rich soils (plaggen). This project set out to examine if this high rate of fertilization had adversely impacted the soil, and if so, to determine which waste streams were responsible. Arable soils were considerably elevated in Pb and Zn compared to non-arable soils. Using Pb isotope signatures and analysis of the waste streams, it was determined that this pollution came from peat and turf ash (Pb and Zn) and from bird carcases (Zn). This was also confirmed by (13)C and (15)N analysis of the profiles which showed that soil organic matter was highly enriched in marine-derived C and N compared to non-arable soils. The pollution of such a remote island may be typical of other 'bird culture' islands, and peat ash contamination of marginal arable soils at high latitudes may be widespread in terms of geographical area, but less intense at specific locations due to lower population densities than on Hirta.

  2. 13C-labeled D-ribose: chemi-enzymic synthesis of various isotopomers.

    PubMed

    Serianni, A S; Bondo, P B

    1994-04-01

    Current interest in the use of heteronuclear multidimensional NMR methods to assess the structures, conformations and/or dynamics of oligonucleotides in solution has created an immediate need for nucleosides and their derivatives labeled in various ways with stable isotopes (13C, 2H, 15N and/or 17,18O). This short review focuses exclusively on chemienzymic methods to introduce one or more 13C labels into D-ribose, a precursor to ribo- and 2'-deoxyribonucleosides. It will be demonstrated that five convenient reactions, applied in specific sequences, provide access to 26 of the 32 13C-labeled isotopomers of D-ribose in acceptable yields. While not explicitly discussed herein, these same reactions, appropriately modified, can also be used to insert one or more 2H and/or 17,18O isotopes into this aldopentose.

  3. A Method to Constrain Genome-Scale Models with 13C Labeling Data

    PubMed Central

    García Martín, Héctor; Kumar, Vinay Satish; Weaver, Daniel; Ghosh, Amit; Chubukov, Victor; Mukhopadhyay, Aindrila; Arkin, Adam; Keasling, Jay D.

    2015-01-01

    Current limitations in quantitatively predicting biological behavior hinder our efforts to engineer biological systems to produce biofuels and other desired chemicals. Here, we present a new method for calculating metabolic fluxes, key targets in metabolic engineering, that incorporates data from 13C labeling experiments and genome-scale models. The data from 13C labeling experiments provide strong flux constraints that eliminate the need to assume an evolutionary optimization principle such as the growth rate optimization assumption used in Flux Balance Analysis (FBA). This effective constraining is achieved by making the simple but biologically relevant assumption that flux flows from core to peripheral metabolism and does not flow back. The new method is significantly more robust than FBA with respect to errors in genome-scale model reconstruction. Furthermore, it can provide a comprehensive picture of metabolite balancing and predictions for unmeasured extracellular fluxes as constrained by 13C labeling data. A comparison shows that the results of this new method are similar to those found through 13C Metabolic Flux Analysis (13C MFA) for central carbon metabolism but, additionally, it provides flux estimates for peripheral metabolism. The extra validation gained by matching 48 relative labeling measurements is used to identify where and why several existing COnstraint Based Reconstruction and Analysis (COBRA) flux prediction algorithms fail. We demonstrate how to use this knowledge to refine these methods and improve their predictive capabilities. This method provides a reliable base upon which to improve the design of biological systems. PMID:26379153

  4. Biochar decelerates soil organic nitrogen cycling but stimulates soil nitrification in a temperate arable field trial.

    PubMed

    Prommer, Judith; Wanek, Wolfgang; Hofhansl, Florian; Trojan, Daniela; Offre, Pierre; Urich, Tim; Schleper, Christa; Sassmann, Stefan; Kitzler, Barbara; Soja, Gerhard; Hood-Nowotny, Rebecca Clare

    2014-01-01

    Biochar production and subsequent soil incorporation could provide carbon farming solutions to global climate change and escalating food demand. There is evidence that biochar amendment causes fundamental changes in soil nutrient cycles, often resulting in marked increases in crop production, particularly in acidic and in infertile soils with low soil organic matter contents, although comparable outcomes in temperate soils are variable. We offer insight into the mechanisms underlying these findings by focusing attention on the soil nitrogen (N) cycle, specifically on hitherto unmeasured processes of organic N cycling in arable soils. We here investigated the impacts of biochar addition on soil organic and inorganic N pools and on gross transformation rates of both pools in a biochar field trial on arable land (Chernozem) in Traismauer, Lower Austria. We found that biochar increased total soil organic carbon but decreased the extractable organic C pool and soil nitrate. While gross rates of organic N transformation processes were reduced by 50-80%, gross N mineralization of organic N was not affected. In contrast, biochar promoted soil ammonia-oxidizer populations (bacterial and archaeal nitrifiers) and accelerated gross nitrification rates more than two-fold. Our findings indicate a de-coupling of the soil organic and inorganic N cycles, with a build-up of organic N, and deceleration of inorganic N release from this pool. The results therefore suggest that addition of inorganic fertilizer-N in combination with biochar could compensate for the reduction in organic N mineralization, with plants and microbes drawing on fertilizer-N for growth, in turn fuelling the belowground build-up of organic N. We conclude that combined addition of biochar with fertilizer-N may increase soil organic N in turn enhancing soil carbon sequestration and thereby could play a fundamental role in future soil management strategies.

  5. Biochar Decelerates Soil Organic Nitrogen Cycling but Stimulates Soil Nitrification in a Temperate Arable Field Trial

    PubMed Central

    Prommer, Judith; Wanek, Wolfgang; Hofhansl, Florian; Trojan, Daniela; Offre, Pierre; Urich, Tim; Schleper, Christa; Sassmann, Stefan; Kitzler, Barbara; Soja, Gerhard; Hood-Nowotny, Rebecca Clare

    2014-01-01

    Biochar production and subsequent soil incorporation could provide carbon farming solutions to global climate change and escalating food demand. There is evidence that biochar amendment causes fundamental changes in soil nutrient cycles, often resulting in marked increases in crop production, particularly in acidic and in infertile soils with low soil organic matter contents, although comparable outcomes in temperate soils are variable. We offer insight into the mechanisms underlying these findings by focusing attention on the soil nitrogen (N) cycle, specifically on hitherto unmeasured processes of organic N cycling in arable soils. We here investigated the impacts of biochar addition on soil organic and inorganic N pools and on gross transformation rates of both pools in a biochar field trial on arable land (Chernozem) in Traismauer, Lower Austria. We found that biochar increased total soil organic carbon but decreased the extractable organic C pool and soil nitrate. While gross rates of organic N transformation processes were reduced by 50–80%, gross N mineralization of organic N was not affected. In contrast, biochar promoted soil ammonia-oxidizer populations (bacterial and archaeal nitrifiers) and accelerated gross nitrification rates more than two-fold. Our findings indicate a de-coupling of the soil organic and inorganic N cycles, with a build-up of organic N, and deceleration of inorganic N release from this pool. The results therefore suggest that addition of inorganic fertilizer-N in combination with biochar could compensate for the reduction in organic N mineralization, with plants and microbes drawing on fertilizer-N for growth, in turn fuelling the belowground build-up of organic N. We conclude that combined addition of biochar with fertilizer-N may increase soil organic N in turn enhancing soil carbon sequestration and thereby could play a fundamental role in future soil management strategies. PMID:24497947

  6. Dynamics of organic carbon stock of Estonian arable and grassland peat soils

    NASA Astrophysics Data System (ADS)

    Kauer, Karin; Tammik, Kerttu; Penu, Priit

    2016-04-01

    Peat soils represent globally a major reserve of soil organic carbon (SOC). Estimation of changes in SOC stocks is important for understanding soil carbon sequestration and dynamics of greenhouse gas emissions. The aim of this study was to estimate the SOC stock of Estonian agricultural peat soils and SOC stock change depending on land use type (arable land and long-term grasslands (over 5 years)). The soils were classified as Histosols according to WRB classification. Generally the arable land was used for growing cereals, oilseed rape, legumes and used as ley in crop rotation. The main technique of soil cultivation was ploughing. During 2002-2015 the soil samples of 0-20 cm soil layer (one average soil sample per 1-5 ha) were collected. The SOC content was measured by NIRS method. The SOC stock was calculated by assuming that soil mean bulk density is 0.3 g cm-3. The SOC stock change in arable land was estimated during 3-13 years (N=91) and in grassland 4-13 year (N=163). The average SOC content of peat soils varied from 150.6 to 549.0 mg g-1. The initial SOC stock of arable land was 271.3 t ha-1 and of grassland 269.3 t ha-1. The SOC stock declined in arable peat soils faster (-2.57 t ha-1 y-1) compared to the changes in grassland peat soils (-0.67 t ha-1 y-1). According to the length of the study period the SOC stock change per year varied from -5.14 to 6.64 t ha-1 y-1 in grasslands and from -14.78 to 0.83 t ha-1 y-1 in arable land, although there was no clear relationship between the SOC stock change and the length of the study period. More detailed information about the properties of agricultural land and land use history is needed to analyse the causes of the SOC stock changes in agricultural peat soils. However, from the current research we can conclude that the SOC stock of arable and grassland peat soils is declining during the cultivation. These decreases are important to specify when considering the role of peat soils in atmospheric greenhouse gas

  7. The dissolved organic matter as a potential soil quality indicator in arable soils of Hungary.

    PubMed

    Filep, Tibor; Draskovits, Eszter; Szabó, József; Koós, Sándor; László, Péter; Szalai, Zoltán

    2015-07-01

    Although several authors have suggested that the labile fraction of soils could be a potential soil quality indicator, the possibilities and limitations of using the dissolved organic matter (DOM) fraction for this purpose have not yet been investigated. The objective of this study was to evaluate the hypothesis that DOM is an adequate indicator of soil quality. To test this, the soil quality indices (SQI) of 190 arable soils from a Hungarian dataset were estimated, and these values were compared to DOM parameters (DOC and SUVA254). A clear difference in soil quality was found between the soil types, with low soil quality for arenosols (average SQI 0.5) and significantly higher values for gleysols, vertisols, regosols, solonetzes and chernozems. The SQI-DOC relationship could be described by non-linear regression, while a linear connection was observed between SQI and SUVA. The regression equations obtained for the dataset showed only one relatively weak significant correlation between the variables, for DOC (R (2) = 0.157(***); n = 190), while non-significant relationships were found for the DOC and SUVA254 values. However, an envelope curve operated with the datasets showed the robust potential of DOC to indicate soil quality changes, with a high R (2) value for the envelope curve regression equation. The limitations to using the DOM fraction of soils as a quality indicator are due to the contradictory processes which take place in soils in many cases.

  8. Biosynthesis of curdlan from culture media containing 13C-labeled glucose as the carbon source.

    PubMed

    Kai, A; Ishino, T; Arashida, T; Hatanaka, K; Akaike, T; Matsuzaki, K; Kaneko, Y; Mimura, T

    1993-02-24

    13C-Labeled curdlans were biosynthesized by Agrobacterium sp. (ATCC 31749) from culture media containing D-(1-13C)glucose, D-(6-13C)glucose, or D-(2-13C)glucose as the carbon source, and their structures were analyzed by 13C NMR spectroscopy. The labeling was mainly found in the original position, that is, C-1, C-6, or C-2, indicating direct polymerization of introduced glucose. In addition, C-3 in curdlan obtained from D-(1-13C)glucose, C-1 in curdlan obtained from D-(6-13C)glucose, and C-1 and C-3 in curdlan obtained from D-(2-13)glucose were labeled. From analysis of this labeling, the biosynthesis of curdlan was interpreted as involving five routes: (1) direct synthesis from glucose; (2) rearrangement (1-13C-->3-13C); and (3) isomerization (6-13C-->1-13C) of cleaved trioses by the Embden-Meyerhof pathway, followed by neogenesis of glucose and formation of curdlan; (4) from fructose 6-phosphate formed in the pentose cycle (2-13C-->1-13C, 3-13C); and (5) neogenesis of glucose from fragments produced in various pathways of glycolysis. The 13C-labeling at C-6 and C-2 in the starting glucoses is well preserved in the C-6 carbon and the C-1 to C-3 carbons, respectively, in the curdlan produced.

  9. Heavy metals relationship in arable and greenhouse soils of SE Spain using a geostatistical analysis

    NASA Astrophysics Data System (ADS)

    Gil, Carlos; Joaquin Ramos-Miras, Jose; Rodríguez Martín, Jose Antonio; Boluda, Rafael; Roca, Núria; Bech, Jaume

    2013-04-01

    This study compares heavy metals contents and the main edaphic parameters in greenhouse soils from the W Almería region one of the most productive agricultural systems in Europe, with agricultural soils (arable soils) in western Andalusia, SW Spain. Heavy metals input in agricultural soils mainly occur through pesticides and phytosanitary control products. The hazardousness of the studied elements (Cr, Ni, Pb, Cu, Zn and Cd) is particularly relevant in soils used for intensive greenhouse farming where such agricultural practices, which centre on maximising production, end up with products that finally enter the human food chain directly. Here we explore a total of 199 greenhouse soils and 142 arable soils, representing two scales of variation in this Mediterranean area. Despite their similar edaphic characteristics, the main differences between arable soils and greenhouse soils lie in nutrients contents (P and K) and in certain heavy metals (Cd, Pb and Zn), which reflect widespread use of pesticides in greenhouse farming. One of the most toxic metals is Cd given its mobility, whose concentrations triple in greenhouse soils, although it does not exceed the limits set by Spanish legislation. We conclude that despite anthropic heavy metals input, the association patterns of these elements were similar on the two spatial variability scales. Cd, Pb and Zn contents, and partly those of Cu, are related with agricultural practices. On the short spatial scale, grouping these heavy metals shows very high contents in greenhouse soils in the central northern area of the W Almería region. On the other hand, the associations of Cr and Ni suggest a lithogenic influence combined with a pedogenic effect on spatial maps. This natural origin input becomes more marked on the long spatial scale (arable soils) where the main Cr and Ni contents are found in the vicinity of the Gádor Mountain Range.

  10. Remediation of degraded arable steppe soils in Moldova using vetch as green manure

    NASA Astrophysics Data System (ADS)

    Wiesmeier, M.; Lungu, M.; Hübner, R.; Cerbari, V.

    2015-01-01

    In the Republic of Moldova, non-sustainable arable farming led to severe degradation and erosion of fertile steppe soils (Chernozems). As a result, the Chernozems lost about 40% of their initial amounts of soil organic carbon (SOC). Aim of this study was to remediate degraded arable soils and promote carbon sequestration by implementation of cover cropping and green manuring in Moldova. Thereby, the suitability of the legume hairy vetch (Vicia sativa) as cover crop under the dry, continental climate of Moldova was examined. At two experimental sites, the effect of cover cropping on chemical and physical soil properties as well as on yields of subsequent main crops was determined. The results showed a significant increase of SOC after incorporation of hairy vetch due to a high above- and belowground biomass production that was related with a high input of carbon and nitrogen. A calculation of SOC stocks based on equivalent soil masses revealed a sequestration of around 3 t C ha-1 yr-1 as a result of hairy vetch cover cropping. The buildup of SOC was associated with an improvement of the soil structure as indicated by a distinct decrease of bulk density and a relative increase of macroaggregates at the expense of microaggregates and clods. As a result, yields of subsequent main crops increased by around 20%. Our results indicated that hairy vetch is a promising cover crop to remediate degraded steppe soils, control soil erosion and sequestrate substantial amounts of atmospheric C in arable soils of Moldova.

  11. SoilBioHedge, harnessing hedgerow soil biodiversity for restoration of arable soil quality and resilience to climatic extremes and land use changes: The impacts of arable to ley conversion on soil hydrological properties

    NASA Astrophysics Data System (ADS)

    Grayson, Richard; Holden, Joseph; Chapman, Pippa; Hunt, Sarah; Leake, Jonathan

    2017-04-01

    Modern agricultural practices pose a significant threat to soil security. Continuous conventional cultivation has been observed to deplete soil organic matter, degrade soil structure, reduce water drainage and water holding capacity, increase nitrate leaching, damage the ecosystem engineer earthworm and mycorrhiza populations and increase the susceptibility of soil and crops to the impacts of climatic stress through decreased resilience to flood and drought conditions. The SoilBioHedge project aims to determine the effectiveness of using grass-clover leys linking hedgerows to arable fields in restoring functional biodiversity, soil quality and resilience to drought and excess rainfall in arable farming. Paired 70m long ley strips have been inserted in to 4 fields. Within each field one ley is connected to the margin while in the other a small 1m fallow area and a steel mesh barrier inserted to bedrock is being used to disconnect the ley and margin and prevent macrofaunal movement from the margin to the ley. As part of the SoilBioHedge project we are undertaking a range of analyses to establish the impacts of arable to ley conversion on key hydrological properties of agricultural soils. Soil moisture is being continuously monitored at three depths at 48 separate locations, in addition monthly manual measurements are being taken at 1158 locations. Arable-to-ley conversion is expected to increase soil macrofaunal activity especially in locations closer to hedgerows, enhancing macropore development. Therefore the proportion of water percolating into macropores, mesopores and micropores is being measured using tension infiltrometers which also allow the calculation of saturated hydraulic conductivity. Soil cores have been extracted to examine impacts on bulk and particle density and subsequently porosity, with hydraulic conductivity being measured using a lab permeameter. Here we present the results of these analyses over the first 24 months of the project. This

  12. Synthesis and NMR studies of (13)C-labeled vitamin D metabolites.

    PubMed

    Okamura, William H; Zhu, Gui-Dong; Hill, David K; Thomas, Richard J; Ringe, Kerstin; Borchardt, Daniel B; Norman, Anthony W; Mueller, Leonard J

    2002-03-08

    Isotope-labeled drug molecules may be useful for probing by NMR spectroscopy the conformation of ligand associated with biological hosts such as membranes and proteins. Triple-labeled [7,9,19-(13)C(3)]-vitamin D(3) (56), its 25-hydroxylated and 1 alpha,25-dihydroxylated metabolites (58 and 68, respectively), and other labeled materials have been synthesized via coupling of [9-(13)C]-Grundmann's ketone 39 or its protected 25-hydroxy derivative 43 with labeled A ring enyne fragments 25 or 26. The labeled CD-ring fragment 39 was prepared by a sequence involving Grignard addition of [(13)C]-methylmagnesium iodide to Grundmann's enone 28, oxidative cleavage, functional group modifications leading to seco-iodide 38, and finally a kinetic enolate S(N)2 cycloalkylation. The C-7,19 double labeling of the A-ring enyne was achieved by the Corey-Fuchs/Wittig processes on keto aldehyde 11. By employing these labeled fragments in the Wilson-Mazur route, the C-7,9,19 triple-(13)C-labeled metabolites 56, 58, and 68 as well as other (13)C-labeled metabolites have been prepared. In an initial NMR investigation of one of the labeled metabolites prepared in this study, namely [7,9,19-(13)C(3)]-25-hydroxyvitamin D(3) (58), the three (13)C-labeled carbons of the otherwise water insoluble steroid could be clearly detected by (13)C NMR analysis at 0.1 mM in a mixture of CD(3)OD/D(2)O (60/40) or in aqueous dimethylcyclodextrin solution and at 2 mM in 20 mM sodium dodecyl sulfate (SDS) aqueous micellar solution. In the SDS micellar solution, a double half-filter NOESY experiment revealed that the distance between the H(19Z) and H(7) protons is significantly shorter than that of the corresponding distance calculated from the solid state (X-ray) structure of the free ligand. The NMR data in micelles reveals that 58 exists essentially completely in the alpha-conformer with the 3 beta-hydroxyl equatorially oriented, just as in the solid state. The shortened distance (H(19Z))-H(7)) in micellar

  13. Remediation of degraded arable steppe soils in Moldova using vetch as green manure

    NASA Astrophysics Data System (ADS)

    Wiesmeier, M.; Lungu, M.; Hübner, R.; Cerbari, V.

    2015-05-01

    In the Republic of Moldova, non-sustainable arable farming led to severe degradation and erosion of fertile steppe soils (Chernozems). As a result, the Chernozems lost about 40% of their initial amounts of soil organic carbon (SOC). The aim of this study was to remediate degraded arable soils and promote carbon sequestration by implementation of cover cropping and green manuring in Moldova. Thereby, the suitability of the legume hairy vetch (Vicia sativa) as cover crop under the dry continental climate of Moldova was examined. At two experimental sites, the effect of cover cropping on chemical and physical soil properties as well as on yields of subsequent main crops was determined. The results showed a significant increase of SOC after incorporation of hairy vetch mainly due to increases of aggregate-occluded and mineral-associated OC. This was related to a high above- and belowground biomass production of hairy vetch associated with a high input of carbon and nitrogen into arable soils. A calculation of SOC stocks based on equivalent soil masses revealed a sequestration of around 3 t C ha-1yr-1 as a result of hairy vetch cover cropping. The buildup of SOC was associated with an improvement of the soil structure as indicated by a distinct decrease of bulk density and a relative increase of macroaggregates at the expense of microaggregates and clods. As a result, yields of subsequent main crops increased by around 20%. Our results indicated that hairy vetch is a promising cover crop to remediate degraded steppe soils, control soil erosion and sequester substantial amounts of atmospheric C in arable soils of Moldova.

  14. Chiral Recognition by Dissolution DNP NMR Spectroscopy of (13)C-Labeled dl-Methionine.

    PubMed

    Monteagudo, Eva; Virgili, Albert; Parella, Teodor; Pérez-Trujillo, Míriam

    2017-05-02

    A method based on d-DNP NMR spectroscopy to study chiral recognition is described for the first time. The enantiodifferentiation of a racemic metabolite in a millimolar aqueous solution using a chiral solvating agent was performed. Hyperpolarized (13)C-labeled dl-methionine enantiomers were differently observed with a single-scan (13)C NMR experiment, while the chiral auxiliary at thermal equilibrium remained unobserved. The method developed entails a step forward in the chiral recognition of small molecules by NMR spectroscopy, opening new possibilities in situations where the sensitivity is limited, for example, when a low concentration of analyte is available or when the measurement of an insensitive nucleus, like (13)C, is required. The advantages and current limitations of the method, as well as future perspectives, are discussed.

  15. Increased Resolution of Aromatic Cross Peaks Using Alternate 13C Labeling and TROSY

    PubMed Central

    Milbradt, Alexander G.; Arthanari, Haribabu; Takeuchi, Koh; Boeszoermenyi, Andras; Hagn, Franz; Wagner, Gerhard

    2016-01-01

    For typical globular proteins, contacts involving aromatic side chains would constitute the largest number of distance constraints that could be used to define the structure of proteins and protein complexes based on NOE contacts. However, the 1H NMR signals of aromatic side chains are often heavily overlapped, which hampers extensive use of aromatic NOE cross peaks. Some of this overlap can be overcome by recording 13C-dispersed NOESY spectra. However, the resolution in the carbon dimension is rather low due to the narrow dispersion of the carbon signals, large one-bond carbon-carbon (C-C) couplings, and line broadening due to chemical shift anisotropy (CSA). Although it has been noted that the CSA of aromatic carbons could be used in TROSY experiments for enhancing resolution, this has not been used much in practice because of complications arising from large aromatic one-bond C-C couplings, and 3D or 4D carbon dispersed NOESY are typically recorded at low resolution hampering straightforward peak assignments. Here we show that the aromatic TROSY effect can optimally be used when employing alternate 13C labeling using 2-13C glycerol, 2-13C pyruvate, or 3-13C pyruvate as carbon source. With the elimination of the strong one-bond C-C coupling, the TROSY effect can easily be exploited. We show that 1H-13C TROSY spectra of alternately 13C labeled samples can be recorded at high resolution, and we employ 3D NOESY aromatic-TROSY spectra to obtain valuable intramolecular and intermolecular cross peaks on a protein complex. PMID:25957757

  16. Roots rather than shoot residues drive soil arthropod communities of arable fields.

    PubMed

    Scheunemann, Nicole; Digel, Christoph; Scheu, Stefan; Butenschoen, Olaf

    2015-12-01

    Soil food webs are driven by plant-derived carbon (C) entering the soil belowground as rhizodeposits or aboveground via leaf litter, with recent research pointing to a higher importance of the former for driving forest soil food webs. Using natural abundance stable isotopes of wheat (C3 plant) and maize (C4 plant), we followed and quantified the incorporation of shoot residue- and root-derived maize C into the soil animal food web of an arable field for 1 year, thereby disentangling the importance of shoot residue- versus root-derived resources for arable soil food webs. On average, shoot residue-derived resources only contributed less than 12% to soil arthropod body C, while incorporation of root-derived resources averaged 26% after 2 months of maize crop and increased to 32% after 1 year. However, incorporation of root-derived maize C did not consistently increase with time: rather, it increased, decreased or remained constant depending on species. Further, preference of shoot residue- or root-derived resources was also species-specific with about half the species incorporating mainly root-derived C, while only a few species preferentially incorporated shoot residue-derived C, and about 40% incorporated both shoot residue- as well as root-derived C. The results highlight the predominant importance of root-derived resources for arable soil food webs and suggest that shoot residues only form an additional resource of minor importance. Variation in the use of plant-derived C between soil arthropod species suggests that the flux of C through soil food webs of arable systems can only be disentangled by adopting a species-specific approach.

  17. Erodibility of arable soils in Georgia during the period of storm runoff

    NASA Astrophysics Data System (ADS)

    Gogichaishvili, G. P.

    2012-02-01

    The erodibility of arable soils in Georgia varies from 1.0 to 2.9 t/ha per unit of the rainfall erosivity index. The well-structured brown forest and yellow-brown soils with a high humus content are the most resistant to erosion. The soils in the dry areas of Georgia (gray-cinnamon and cinnamon soils) are the most susceptible to erosion. The first map of the soil erodibility was composed that illustrates the spatial distribution pattern of this parameter in the Georgia territory.

  18. Diurnal changes of PM10-emission from arable soils in NE-Germany

    NASA Astrophysics Data System (ADS)

    Hoffmann, Carsten; Funk, Roger

    2015-06-01

    Repeated loss of fine soil particles by dust emission from arable fields caused by tillage operations, decline soil fertility and reduce air quality. The objective of this study was to quantify the diurnal dynamic of topsoil moisture and the connected PM10-emission of 15 different soils from arable fields around Berlin. As typical for the young moraine landscape in NE Germany, soils from glacial (sand and loam dominated), aeolian (silt loam), and fluvial (organic) sediments were selected. Soil samples were placed outside under hot summer and clear sky conditions for 24 h to reproduce the natural dynamic of soil surface moisture, including dew uptake during the night and evaporation during the day. Dynamic of PM10 emissions of all soils were then measured nine times per day in a stationary wind tunnel. Glacial and fluvial sands showed lowest fine dust emission potential (PM10pot) between 89 and 415 μg PM10 g-1 soil, while PM10pot of loess soils were higher (369-1215 μg PM10 g-1 soil). During the night, the moisture of all samples increased slightly by dew uptake, and fine dust emissions of soil samples were reduced up to 51% directly after sunrise. Highest average reductions in PM10 emissions were found for glacial and fluvial loams. Some hours after sunrise, all soil samples heated up and quickly dried again. Under minimal moisture conditions, highest fine dust emissions were measured between 10 a.m. and 3 p.m.

  19. Measuring and modeling C flux rates through the central metabolic pathways in microbial communities using position-specific 13C-labeled tracers

    NASA Astrophysics Data System (ADS)

    Dijkstra, P.; van Groenigen, K.; Hagerty, S.; Salpas, E.; Fairbanks, D. E.; Hungate, B. A.; KOCH, G. W.; Schwartz, E.

    2012-12-01

    The production of energy and metabolic precursors occurs in well-known processes such as glycolysis and Krebs cycle. We use position-specific 13C-labeled metabolic tracers, combined with models of microbial metabolic organization, to analyze the response of microbial community energy production, biosynthesis, and C use efficiency (CUE) in soils, decomposing litter, and aquatic communities. The method consists of adding position-specific 13C -labeled metabolic tracers to parallel soil incubations, in this case 1-13C and 2,3-13C pyruvate and 1-13C and U-13C glucose. The measurement of CO2 released from the labeled tracers is used to calculate the C flux rates through the various metabolic pathways. A simplified metabolic model consisting of 23 reactions is solved using results of the metabolic tracer experiments and assumptions of microbial precursor demand. This new method enables direct estimation of fundamental aspects of microbial energy production, CUE, and soil organic matter formation in relatively undisturbed microbial communities. We will present results showing the range of metabolic patterns observed in these communities and discuss results from testing metabolic models.

  20. Synthesis and applications of selectively {sup 13}C-labeled RNA

    SciTech Connect

    SantaLucia, J. Jr.; Shen, L.X.; Lewis, H.; Cai, Z.; Tinoci, I. Jr.

    1994-12-01

    Spectral overlap is a substantial problem in NMR studies of RNA molecules >30 nucleotides. To overcome this difficulty, we synthesized selectively {sup 13}C-labeled RNAs and adapted several isotope-edited two- and three-dimensional NMR experiments originally developed for protein studies. We optimized protocols for synthesis of multi-gram quantities of CTP, UTp, ATP, and GTP using a combination of synthetic organic and enzymatic methods. Uracil is prepared in 40 to 50% yield from {sup 13}C-cyanide in two steps. Using acetyl- tribenzoyl-ribose and standard chemistry uracil is then attached to the sugar (90% yield). The tribenzoyl-uridine intermediate is converted into uridine or cytidine quantitatively, depending on the deblocking protocol. Labeled purines are synthesized using simple pyrimidine precursors and reacting with {sup 13}C-formic acid (80% yield). Purine nucleosides are then synthesized using uridine phosphorylase and purine nucleoside phosphorylase. The nucleosides were converted to NMPs by treatment with POC1{sub 3} in triethylphosphate. We converted NMPs to NTPs by standard enzymatic methods. Selectively labeled RNAs were synthesized by run-off transcription using {sup 13}C-labeled NTPs. Several different strategies help solve over-lap problems in larger RNAs. Isotope-edited two-dimensional NMR experiments such as {omega}1-1/2 X-filtered NOESY simplify NMR spectra by dividing the normal NOESY spectrum into two subspectra-one involving NOEs from protons bound to {sup 12}C and one from protons bound to {sup 13}C. For example, we labeled A and U residues of a 34-nucleotide pseudoknot, and the {sup 12}C subspectrum of the 1/2 X-filtered NOESY contained NOEs only from G and C residues (along with adenine 2H); the {sup 13}C subspectrum contained NOEs only from A and U residues. Each subspectrum has less overlap than the NOESY of an unlabeled sample; the editing strategy allows each resonance to be identified by residue type (A, C, G, or U).

  1. Microbial biodiversity in arable soils is affected by agricultural practices

    NASA Astrophysics Data System (ADS)

    Wolińska, Agnieszka; Górniak, Dorota; Zielenkiewicz, Urszula; Goryluk-Salmonowicz, Agata; Kuźniar, Agnieszka; Stępniewska, Zofia; Błaszczyk, Mieczysław

    2017-04-01

    The aim of the study was to examine the differences in microbial community structure as a result of agricultural practices. Sixteen samples of cultivated and the same number of non-cultivated soils were selected. Gel bands were identified using the GelCompar software to create the presence-absence matrix, where each band represented a bacterial operational taxonomic unit. The data were used for principal-component analysis and additionally, the Shannon- Weaver index of general diversity, Simpson index of dominance and Simpson index of diversity were calculated. Denaturing gradient gel electrophoresis profiles clearly indicated differentiation of tested samples into two clusters: cultivated and non-cultivated soils. Greater numbers of dominant operational taxonomic units (65) in non-cultivated soils were noted compared to cultivated soils (47 operational taxonomic units). This implies that there was a reduction of dominant bacterial operational taxonomic units by nearly 30% in cultivated soils. Simpson dominance index expressing the number of species weighted by their abundance amounted to 1.22 in cultivated soils, whereas a 3-fold higher value (3.38) was observed in non-cultivated soils. Land-use practices seemed to be a important factors affected on biodiversity, because more than soil type determined the clustering into groups.

  2. Biosynthetic production of universally (13)C-labelled polyunsaturated fatty acids as reference materials for natural health product research.

    PubMed

    Le, Phuong Mai; Fraser, Catherine; Gardner, Graeme; Liang, Wei-Wan; Kralovec, Jaroslav A; Cunnane, Stephen C; Windust, Anthony J

    2007-09-01

    Long-chain polyunsaturated fatty acids (LCPUFA) including eicosapentaenoic acid (EPA, 20:5n-3) and docosahexaenoic acid (DHA, 22:6n-3) have become important natural health products with numerous proven benefits related to brain function and cardiovascular health. Not only are omega-3 fatty acids available in a plethora of dietary supplements, but they are also increasingly being incorporated as triglycerides into conventional foods, including bread, milk, yoghurt and confectionaries. Recently, transgenic oil seed crops and livestock have been developed that enhance omega-3 fatty acid content. This diverse array of matrices presents a difficult analytical challenge and is compounded further by samples generated through clinical research. Stable isotope (13)C-labelled LCPUFA standards offer many advantages as research tools because they may be distinguished from their naturally abundant counterparts by mass spectrometry and directly incorporated as internal standards into analytical procedures. Further, (13)C-labelled LCPUFAs are safe to use as metabolic tracers to study uptake and metabolism in humans. Currently, (13)C-labelled LCPUFAs are expensive, available in limited supply and not in triglyceride form. To resolve these issues, marine heterotrophic microorganisms are being isolated and screened for LCPUFA production with a view to the efficient biosynthetic production of U-(13)C-labelled fatty acids using U-(13)C glucose as a carbon source. Of 37 isolates obtained, most were thraustochytrids, and either DHA or omega-6 docosapentaenoic acid (22:5n-6) were produced as the major LCPUFA. The marine protist Hyalochlorella marina was identified as a novel source of EPA and omega-3 docosapentaenoic acid (22:5n-3). As proof of principle, gram-level production of (13)C-labelled DHA has been achieved with high chemical purity ( >99%) and high (13)C incorporation levels (>90%), as confirmed by NMR and MS analyses. Finally, U-(13)C-DHA was enzymatically re-esterified to

  3. Sparse (13)C labelling for solid-state NMR studies of P. pastoris expressed eukaryotic seven-transmembrane proteins.

    PubMed

    Liu, Jing; Liu, Chang; Fan, Ying; Munro, Rachel A; Ladizhansky, Vladimir; Brown, Leonid S; Wang, Shenlin

    2016-05-01

    We demonstrate a novel sparse (13)C labelling approach for methylotrophic yeast P. pastoris expression system, towards solid-state NMR studies of eukaryotic membrane proteins. The labelling scheme was achieved by co-utilizing natural abundance methanol and specifically (13)C labelled glycerol as carbon sources in the expression medium. This strategy improves the spectral resolution by 1.5 fold, displays site-specific labelling patterns, and has advantages for collecting long-range distance restraints for structure determination of large eukaryotic membrane proteins by solid-state NMR.

  4. Uniformly sup 13 C-labeled algal protein used to determine amino acid essentiality in vivo

    SciTech Connect

    Berthold, H.K.; Hachey, D.L.; Reeds, P.J.; Klein, P.D. ); Thomas, O.P. ); Hoeksema, S. )

    1991-09-15

    The edible alga Spirulina platensis was uniformly labeled with {sup 13}C by growth in an atmosphere of pure {sup 13}CO{sub 2}. The labeled biomass was then incorporated into the diet of a laying hen for 27 days. The isotopic enrichment of individual amino acids in egg white and yolk proteins, as well as in various tissues of the hen at the end of the feeding period, was analyzed by negative chemical ionization gas chromatography/mass spectrometry. The amino acids of successive eggs showed one of two exclusive enrichment patterns: complete preservation of the intact carbon skeleton or extensive degradation and resynthesis. The same observation was made in tissue proteins. These patterns were cleanly divided according to known nutritional amino acid essentiality/nonessentiality but revealed differences in labeling among the nonessential amino acids: most notable was that proline accretion was derived entirely from the diet. Feeding uniformly {sup 13}C-labeled algal protein and recovering and analyzing de novo-synthesized protein provides a useful method to examine amino acid metabolism and determine conditional amino acid essentially in vivo.

  5. (13)C-Labeling the carbon-fixation pathway of a highly efficient artificial photosynthetic system.

    PubMed

    Liu, Chong; Nangle, Shannon N; Colón, Brendan C; Silver, Pamela A; Nocera, Daniel G

    2017-03-15

    Interfacing the CO2-fixing microorganism, Ralstonia eutropha, to the energy derived from hydrogen produced by water splitting is a viable approach to achieving renewable CO2 reduction at high efficiencies. We employ (13)C-labeling to report on the nature of CO2 reduction in the inorganic water splitting|R. eutropha hybrid system. Accumulated biomass in a reactor under a (13)C-enriched CO2 atmosphere may be sampled at different time points during CO2 reduction. Converting the sampled biomass into gaseous CO2 allows the (13)C/(12)C ratio to be determined by gas chromatography-mass spectrometry. After 2 hours of inoculation and the initiation of water splitting, the microbes adapted and began to convert CO2 into biomass. The observed time evolution of the (13)C/(12)C ratio in accumulated biomass is consistent with a Monod model for carbon fixation. Carbon dioxide produced by catabolism was found to be minimal. This rapid response of the bacteria to a hydrogen input and to subsequent CO2 reduction at high efficiency are beneficial to achieving artificial photosynthesis for the storage of renewable energy.

  6. Uniformly 13C-labeled algal protein used to determine amino acid essentiality in vivo.

    PubMed

    Berthold, H K; Hachey, D L; Reeds, P J; Thomas, O P; Hoeksema, S; Klein, P D

    1991-09-15

    The edible alga Spirulina platensis was uniformly labeled with 13C by growth in an atmosphere of pure 13CO2. The labeled biomass was then incorporated into the diet of a laying hen for 27 days. The isotopic enrichment of individual amino acids in egg white and yolk proteins, as well as in various tissues of the hen at the end of the feeding period, was analyzed by negative chemical ionization gas chromatography/mass spectrometry. The amino acids of successive eggs showed one of two exclusive enrichment patterns: complete preservation of the intact carbon skeleton or extensive degradation and resynthesis. The same observation was made in tissue proteins. These patterns were cleanly divided according to known nutritional amino acid essentiality/nonessentiality but revealed differences in labeling among the nonessential amino acids: most notable was that proline accretion was derived entirely from the diet. Feeding uniformly 13C-labeled algal protein and recovering and analyzing de novo-synthesized protein provides a useful method to examine amino acid metabolism and determine conditional amino acid essentially in vivo.

  7. Uniformly 13C-labeled algal protein used to determine amino acid essentiality in vivo.

    PubMed Central

    Berthold, H K; Hachey, D L; Reeds, P J; Thomas, O P; Hoeksema, S; Klein, P D

    1991-01-01

    The edible alga Spirulina platensis was uniformly labeled with 13C by growth in an atmosphere of pure 13CO2. The labeled biomass was then incorporated into the diet of a laying hen for 27 days. The isotopic enrichment of individual amino acids in egg white and yolk proteins, as well as in various tissues of the hen at the end of the feeding period, was analyzed by negative chemical ionization gas chromatography/mass spectrometry. The amino acids of successive eggs showed one of two exclusive enrichment patterns: complete preservation of the intact carbon skeleton or extensive degradation and resynthesis. The same observation was made in tissue proteins. These patterns were cleanly divided according to known nutritional amino acid essentiality/nonessentiality but revealed differences in labeling among the nonessential amino acids: most notable was that proline accretion was derived entirely from the diet. Feeding uniformly 13C-labeled algal protein and recovering and analyzing de novo-synthesized protein provides a useful method to examine amino acid metabolism and determine conditional amino acid essentially in vivo. Images PMID:11607211

  8. Timing and magnitude of C partitioning through a young loblolly pine (Pinus taeda L.) stand using 13C labeling and shade treatments

    DOE PAGES

    Warren, Jeffrey M.; Iversen, Colleen M.; Garten, Jr., Charles T.; ...

    2011-12-30

    The dynamics of rapid changes in carbon (C) partitioning within forest ecosystems are not well understood, which limits improvement of mechanistic models of C cycling. Our objective was to inform model processes by describing relationships between C partitioning and accessible environmental or physiological measurements, with a special emphasis on short-term C flux through a forest ecosystem. We exposed eight 7-year-old loblolly pine (Pinus taeda L.) trees to air enriched with 13CO2 and then implemented adjacent light shade (LS) and heavy shade (HS) treatments in order to manipulate C uptake and flux. The impacts of shading on photosynthesis, plant water potential,more » sap flow, basal area growth, root growth, and soil CO2 efflux rate (CER) were assessed for each tree over a three-week period. The progression of the 13C label was concurrently tracked from the atmosphere through foliage, phloem, roots, and surface soil CO2 efflux. The HS treatment significantly reduced C uptake, sap flow, stem growth and fine root standing crop, and resulted in greater residual soil water content to 1 m depth. Sap flow was strongly correlated with CER on the previous day, but not the current day, with no apparent treatment effect on the relationship. Although there were apparent reductions in new C flux belowground, the heavy shade treatment did not noticeably reduce the magnitude of belowground autotrophic and heterotrophic respiration based on surface soil CO2 efflux rate (CER), which was overwhelmingly driven by soil temperature and moisture. The 13C label was immediately detected in foliage on label day (half-life = 0.5 d), progressed through phloem by day 2 (half-life = 4.7 d), roots by day 2-4, and subsequently was evident as respiratory release from soil which peaked between days 3-6. The δ13C of soil CO2 efflux was strongly correlated with phloem 13C on the previous day, or two days earlier. While the 13C label was readily tracked through the ecosystem, the fate of root

  9. Changes in soil organic matter over 70 years in continuous arable and ley-arable rotations on a sandy loam soil in England.

    PubMed

    Johnston, A E; Poulton, P R; Coleman, K; Macdonald, A J; White, R P

    2017-05-01

    The sequestration in soil of organic carbon (SOC) derived from atmospheric carbon dioxide (CO2) by replacing arable crops with leys, has been measured over 70 years on a sandy loam soil. The experiment was designed initially to test the effect of leys on the yields of arable crops. A 3-year grazed grass with clover (grass + clover) ley in a 5-year rotation with arable crops increased percentage organic carbon (%OC) in the top 25 cm of the soil from 0.98 to 1.23 in 28 years, but with little further increase during the next 40 years with all-grass leys given fertilizer nitrogen (N). In this second period, OC inputs were balanced by losses, suggesting that about 1.3% OC might be near the equilibrium content for this rotation. Including 3-year lucerne (Medicago sativa) leys had little effect on %OC over 28 years, but after changing to grass + clover leys, %OC increased to 1.24 during the next 40 years. Eight-year leys (all grass with N or grass + clover) in 10-year rotations with arable crops were started in the 1970s, and after three rotations %OC had increased to ca. 1.40 in 2000-2009. Over 70 years, %OC declined from 0.98 to 0.94 in an all-arable rotation with mainly cereals and to 0.82 with more root crops. Applications of 38 t ha(-1) farmyard manure (FYM) every fifth year increased %OC by 0.13% by the mid-1960s when applications ceased. Soil treated with FYM still contained 0.10% more OC in 2000-2009. Changes in the amount of OC have been modelled with RothC-26.3 and estimated inputs of C for selected rotations. Little of the OC input during the 70 years has been retained; most was retained in the grazed ley rotation, but 9 t ha(-1) only of a total input of 189 t ha(-1). In other rotations more than 98% of the total OC input was lost. Despite large losses of C, annual increases in OC of 4‰ are possible on this soil type with the inclusion of grass or grass + clover leys or the application of FYM, but only for a limited

  10. Solid-phase material connectivity in the soil catenas in the arable landscapes

    NASA Astrophysics Data System (ADS)

    Koshovskii, Timur; Zhidkin, Andrei; Gennadiev, Alexandr

    2017-04-01

    Transport of soil solid-phase material at the arable slopes lead to connectivity between different landscape positions. But there is lack of knowledge about distance and real extent of connectivity of soils within catenas. The aim of this research was - the large-scale estimation of connectivity within arable part of catenas by applying soil solid-phase marker of material movement. The studied catchment is located in the forest-steppe zone (near Plavsk city, Tula region, Russia), and had an area of 0.96 sq.km. Lengths of slopes were 300 - 700 meters; steepness of slopes was from 1 to 7 degrees in arable part and exceeded 18 degrees in the grass part. Nine catenas were studied within the catchment; they had dispersed form near outfall and converge form near valley head. Soil samples were taken along catenas with step 100-25 m from the depths 0-25 and 25-50 cm. The quantitative analysis of the content of spherical magnetic particles (SMPs) was conducted in soil samples. SMPs were used for estimation the soil solid-phase material transport during 100-120 year, as these particles were falling out from the atmosphere on the soil surface since 1860 after burning of coal in steam locomotives. Present-day uneven distribution of SMPs in the catchment is a result of soil erosion and deposition processes. The comparison of SMPs storage in non-eroded sites with slopes allowed estimating the mid-year displacement of solid-phase material mass in each sample point. Multiplying the soil erosion rate by the area of soil erosion gave the idea of the total removal of material from catena's part. In this research studied only arable part of the watershed. The volume of material transported through the plot was calculated for each catena's position. The following results were obtained. The extent and structure of the connectivity differed in the studied catenas within the same catchment area. On the wellhead slopes of southern exposition, the soil solid phase material, eroded from the

  11. Bacterial communities associated with Chenopodium album and Stellaria media seeds from arable soils.

    PubMed

    van Overbeek, Leonard S; Franke, Angelinus C; Nijhuis, Els H M; Groeneveld, Roel M W; da Rocha, Ulisses Nunes; Lotz, Lambertus A P

    2011-08-01

    The bacterial community compositions in Chenopodium album and Stellaria media seeds recovered from soil (soil weed seedbank), from bulk soil, and from seeds harvested from plants grown in the same soils were compared. It was hypothesized that bacterial communities in soil weed seedbanks are distinct from the ones present in bulk soils. For that purpose, bacterial polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) fingerprints, made from DNA extracts of different soils and seed fractions, were analyzed by principal component analysis. Bacterial fingerprints from C. album and S. media seeds differed from each other and from soil. Further, it revealed that bacterial fingerprints from soil-recovered and plant-harvested seeds from the same species clustered together. Hence, it was concluded that microbial communities associated with seeds in soil mostly originated from the mother plant and not from soil. In addition, the results indicated that the presence of a weed seedbank in arable soils can increase soil microbial diversity. Thus, a change in species composition or size of the soil weed seedbank, for instance, as a result of a change in crop management, could affect soil microbial diversity. The consequence of increased diversity is yet unknown, but by virtue of identification of dominant bands in PCR-DGGE fingerprints as Lysobacter oryzae (among four other species), it became clear that bacteria potentially antagonizing phytopathogens dominate in C. album seeds in soil. The role of these potential antagonists on weed and crop plant growth was discussed.

  12. Monitoring electron donor metabolism under variable electron acceptor conditions using 13C-labeled lactate

    NASA Astrophysics Data System (ADS)

    Bill, M.; Conrad, M. E.; Yang, L.; Beller, H. R.; Brodie, E. L.

    2010-12-01

    Three sets of flow-through columns constructed with aquifer sediment from Hanford (WA) were used to study reduction of Cr(VI) to poorly soluble Cr(III) under denitrifying, sulfate-reducing/fermentative, and iron-reducing conditions with lactate as the electron donor. In order to understand the relationship between electron donors and biomarkers, and to determine the differences in carbon isotope fractionation resulting from different microbial metabolic processes, we monitored the variation in carbon isotopes in dissolved inorganic carbon (DIC), in total organic carbon (TOC), and in lactate, acetate and propionate. The greatest enrichment in 13C in columns was observed under denitrifying conditions. The δ13C of DIC increased by ~1750 to ~2000‰ fifteen days after supplementation of natural abundance lactate with a 13C-labeled lactate tracer (for an influent δ13C of ~2250‰ for the lactate) indicating almost complete oxidation of the electron donor. The denitrifying columns were among the most active columns and had the highest cell counts and the denitrification rate was highly correlated with Cr(VI) reduction rate. δ13C values of DIC ranged from ~540 to ~1170‰ for iron-reducing conditions. The lower enrichment in iron columns was related to the lower biological activity observed with lower yields of RNA and cell numbers in the column effluents. The carbon isotope shift in the sulfate-reducing ~198 to ~1960‰ for sulfate-reducing conditions reflecting the lower levels of the lactate in these columns. Additionally, in two of the sulfate columns, almost complete fermentation of the lactate occurred, producing acetate and propionate with the labeled carbon signature, but relatively smaller amounts of inorganic carbon. For all electron-accepting conditions, TOC yielded similar δ13C values as lactate stock solutions. Differences in C use efficiency, metabolic rate or metabolic pathway contributed to the differing TOC δ13C to DIC δ13C ratios between treatments

  13. Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils.

    PubMed

    Girvan, Martina S; Bullimore, Juliet; Pretty, Jules N; Osborn, A Mark; Ball, Andrew S

    2003-03-01

    Degradation of agricultural land and the resulting loss of soil biodiversity and productivity are of great concern. Land-use management practices can be used to ameliorate such degradation. The soil bacterial communities at three separate arable farms in eastern England, with different farm management practices, were investigated by using a polyphasic approach combining traditional soil analyses, physiological analysis, and nucleic acid profiling. Organic farming did not necessarily result in elevated organic matter levels; instead, a strong association with increased nitrate availability was apparent. Ordination of the physiological (BIOLOG) data separated the soil bacterial communities into two clusters, determined by soil type. Denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism analyses of 16S ribosomal DNA identified three bacterial communities largely on the basis of soil type but with discrimination for pea cropping. Five fields from geographically distinct soils, with different cropping regimens, produced highly similar profiles. The active communities (16S rRNA) were further discriminated by farm location and, to some degree, by land-use practices. The results of this investigation indicated that soil type was the key factor determining bacterial community composition in these arable soils. Leguminous crops on particular soil types had a positive effect upon organic matter levels and resulted in small changes in the active bacterial population. The active population was therefore more indicative of short-term management changes.

  14. Humus form development of former arable soils under forest and fallow systems

    NASA Astrophysics Data System (ADS)

    Marcinkonis, Saulius

    2010-05-01

    Soil humus is a multi-component organic media and most dynamic part of soil, even humus amount itself under natural vegetation is relatively stable and predetermined by climatic conditions and landscape. Soil cultivation including common farming practices - mechanical soil tillage, use of mineral fertilizers (especially nitrogen) and ameliorants aimed to increase crop production. Agricultural soils beside many environmentally unfavorable more or less controlled processes of soil degradation (nutrient leaching, soil erosion) have unstable level and quality of soil humus (qualitative composition). These humus fluctuations are controlled through organic matter development processes - accelerating or inhabitation of mineralization and humification. During last decades economical drivers in Lithuania stimulated land uses changes (LUC) in less-favored farming areas with regions attributing to large proportions of low fertile soils, hilly landscape and ecological vulnerability. Prevailed types of LUC - arable land to grassland, land afforestration or land abandonment prompt agro ecosystems to return to land primeval state (under natural vegetation) and initial humus level through self-regulation. But listed transformations having own process drivers and prevailing soil humus development directions. Experimental field at the Voke branch of LIA was established (in 1995) and studies conducted with the aim to monitor soil properties transformation, to explore variation of soil quality under different stages of renaturalisation. The experiment was designed with four sites (treatments) on former arable land: 1) left as a cropland site (control) (I); 2) transformed to grassland (II); 3) uncultivated or transformed to fallow (III) and 4) pine afforested site (IV). Assuming 10 years of experimental results (1995-2004) it was concluded that transition of agricultural land characterized as complex of factors having strong effect on energy and nutrients turnover, however soil testing

  15. Economical synthesis of 13C-labeled opiates, cocaine derivatives and selected urinary metabolites by derivatization of the natural products.

    PubMed

    Karlsen, Morten; Liu, Huiling; Johansen, Jon Eigill; Hoff, Bård Helge

    2015-03-25

    The illegal use of opiates and cocaine is a challenge world-wide, but some derivatives are also valuable pharmaceuticals. Reference samples of the active ingredients and their metabolites are needed both for controlling administration in the clinic and to detect drugs of abuse. Especially, (13)C-labeled compounds are useful for identification and quantification purposes by mass spectroscopic techniques, potentially increasing accuracy by minimizing ion alteration/suppression effects. Thus, the synthesis of [acetyl-(13)C4]heroin, [acetyl-(13)C4-methyl-(13)C]heroin, [acetyl-(13)C2-methyl-(13)C]6-acetylmorphine, [N-methyl-(13)C-O-metyl-(13)C]codeine and phenyl-(13)C6-labeled derivatives of cocaine, benzoylecgonine, norcocaine and cocaethylene was undertaken to provide such reference materials. The synthetic work has focused on identifying (13)C atom-efficient routes towards these derivatives. Therefore, the (13)C-labeled opiates and cocaine derivatives were made from the corresponding natural products.

  16. [Spatial variation of soil properties and quality evaluation for arable Ustic Cambosols in central Henan Province].

    PubMed

    Zhang, Xue-Lei; Feng, Wan-Wan; Zhong, Guo-Min

    2011-01-01

    A GIS-based 500 m x 500 m soil sampling point arrangement was set on 248 points at Wenshu Town of Yuzhou County in central Henan Province, where the typical Ustic Cambosols locates. By using soil digital data, the spatial database was established, from which, all the needed latitude and longitude data of the sampling points were produced for the field GPS guide. Soil samples (0-20 cm) were collected from 202 points, of which, bulk density measurement were conducted for randomly selected 34 points, and the ten soil property items used as the factors for soil quality assessment, including organic matter, available K, available P, pH, total N, total P, soil texture, cation exchange capacity (CEC), slowly available K, and bulk density, were analyzed for the other points. The soil property items were checked by statistic tools, and then, classified with standard criteria at home and abroad. The factor weight was given by analytic hierarchy process (AHP) method, and the spatial variation of the major 10 soil properties as well as the soil quality classes and their occupied areas were worked out by Kriging interpolation maps. The results showed that the arable Ustic Cambosols in study area was of good quality soil, over 95% of which ranked in good and medium classes and only less than 5% were in poor class.

  17. Ecotoxicological Impact of the Bioherbicide Leptospermone on the Microbial Community of Two Arable Soils

    PubMed Central

    Romdhane, Sana; Devers-Lamrani, Marion; Barthelmebs, Lise; Calvayrac, Christophe; Bertrand, Cédric; Cooper, Jean-François; Dayan, Franck E.; Martin-Laurent, Fabrice

    2016-01-01

    The ecotoxicological impact of leptospermone, a β-triketone bioherbicide, on the bacterial community of two arable soils was investigated. Soil microcosms were exposed to 0 × (control), 1 × or 10 × recommended dose of leptospermone. The β-triketone was moderately adsorbed to both soils (i.e.,: Kfa ~ 1.2 and Koc ~ 140 mL g−1). Its dissipation was lower in sterilized than in unsterilized soils suggesting that it was mainly influenced by biotic factors. Within 45 days, leptospermone disappeared almost entirely from one of the two soils (i.e., DT50 < 10 days), while 25% remained in the other. The composition of the microbial community assessed by qPCR targeting 11 microbial groups was found to be significantly modified in soil microcosms exposed to leptospermone. Pyrosequencing of 16S rRNA gene amplicons showed a shift in the bacterial community structure and a significant impact of leptospermone on the diversity of the soil bacterial community. Changes in the composition, and in the α- and β-diversity of microbial community were transient in the soil able to fully dissipate the leptospermone, but were persistent in the soil where β-triketone remained. To conclude the bacterial community of the two soils was sensitive to leptospermone and its resilience was observed only when leptospermone was fully dissipated. PMID:27252691

  18. Galacto-oligosaccharides have prebiotic activity in a dynamic in vitro colon model using a (13)C-labeling technique.

    PubMed

    Maathuis, Annet J H; van den Heuvel, Ellen G; Schoterman, Margriet H C; Venema, Koen

    2012-07-01

    Galacto-oligosaccharides (GOS) are considered to be prebiotic, although the contribution of specific members of the microbiota to GOS fermentation and the exact microbial metabolites that are produced upon GOS fermentation are largely unknown. We aimed to determine this using uniformly (13)C-labeled GOS. The normal (control) medium and unlabeled or (13)C-labeled GOS was added to a dynamic, validated, in vitro model of the large-intestine containing an adult-type microbiota. Liquid-chromatography MS was used to measure the incorporation of (13)C label into metabolites. 16S-rRNA stable isotope probing coupled to a phylogenetic micro-array was used to determine label incorporation in microbial biomass. The primary members within the complex microbiota that were directly involved in GOS fermentation were shown to be Bifidobacterium longum, B. bifidum, B. catenulatum, Lactobacillus gasseri, and L. salivarius, in line with the prebiotic effect of GOS, although some other species incorporated (13)C label also. GOS fermentation led to an increase in acetate (+49%) and lactate (+23%) compared with the control. Total organic acid production was 8.50 and 7.52 mmol/g of carbohydrate fed for the GOS and control experiments, respectively. At the same time, the cumulative production of putrefactive metabolites (branched-chain fatty acids and ammonia) was reduced by 55%. Cross-feeding of metabolites from primary GOS fermenters to other members of the microbiota was observed. Our findings support a prebiotic role for GOS and its potential to act as a synbiotic in combination with certain probiotic strains.

  19. Metagenomic Analysis of Some Potential Nitrogen-Fixing Bacteria in Arable Soils at Different Formation Processes.

    PubMed

    Wolińska, Agnieszka; Kuźniar, Agnieszka; Zielenkiewicz, Urszula; Banach, Artur; Izak, Dariusz; Stępniewska, Zofia; Błaszczyk, Mieczysław

    2017-01-01

    The main goal of the study was to determine the diversity of the potential nitrogen-fixing (PNF) bacteria inhabiting agricultural (A) soils versus wastelands serving as controls (C). The soils were classified into three groups based on the formation process: autogenic soils (Albic Luvisols, Brunic Arenosols, Haplic Phaeozem) formed on loess material, hydrogenic soils (Mollic Gleysols, Eutric Fluvisol, Eutric Histosol) formed under the effect of stagnant water and lithogenic soils (Rendzina Leptosols) formed on limestone. In order to determine the preferable conditions for PNF bacteria, the relationships between the soil chemical features and bacterial operational taxonomic units (OTUs) were tested. Additionally, the nitrogen content and fertilisation requirement of the lithogenic (LG), autogenic (AG) and hydrogenic (HG) soils were discussed. The composition of the bacterial communities was analysed with the next-generation sequencing (NGS) by the Ion Torrent™ technology. The sequences were clustered into OTU based on a 99 % similarity threshold. The arable soils tested were distinctly dominated by β-Proteobacteria representatives of PNF bacteria belonging to the genus Burkholderia. Bacteria from the α-Proteobacteria class and Devosia genus were subdominants. A free-living Cyanobacteria population dominated in A rather than in C soils. We have found that both soil agricultural management and soil formation processes are the most conducive factors for PNF bacteria, as a majority of these microorganisms inhabit the AG group of soils, whilst the LG soils with the lowest abundance of PNF bacteria revealed the need for additional mineral fertilisation. Our studies have also indicated that there are close relationships between soil classification with respect to soil formation processes and PNF bacteria preference for occupation of soil niches.

  20. Assessment of the production of 13C labeled compounds from phototrophic microalgae at laboratory scale.

    PubMed

    Acién Fernández, Francisco G; Alías, Celeste Brindley; García-Malea López, María C; Fernández Sevilla, José M; Ibáñez González, María J; Gómez, Rafael Núñez; Molina Grima, Emilio

    2003-07-01

    An integrated process for the indoor production of 13C labeled polyunsaturated fatty acids (PUFAs) from Phaeodactylum tricornutum is presented. The core of the process is a bubble column photobioreactor operating with recirculation of the exhaust gas using a low-pressure compressor. Oxygen accumulation in the system is avoided by bubbling the exhaust gas from the reactor in a sodium sulfite solution before returning to it. To achieve a high 13C enrichment in the biomass obtained, the culture medium is initially stripped of carbon, and labeled 13CO(2) is automatically injected on-demand during operation for pH control and carbon supply. The reactor was operated in both batch and semicontinuous modes. In semicontinuous mode, the reactor was operated at a dilution rate of 0.01 h(-1), resulting in a biomass productivity of 0.1 g l(-1) per day. The elemental analysis of the inlet and outlet flows of the reactor showed that 64.9% of carbon was turned into microalgal biomass, 34.9% remained in the supernatant mainly as inorganic compounds. Only 3.8% of injected carbon was effectively fixed as the target labeled product (EPA). Regarding the isotopic composition of fatty acids, results showed that fatty acids were not labeled in the same proportion, the higher the number of carbons the lower the percentage of 13C. Isotopic composition of EPA ranged from 36.5 to 53.5%, as a function of the methodology used (GC-MS, EA-IRMS or gas chromatography-combustion-isotope ratio mass spectrometry (GC-IRMS)). The low carbon uptake efficiency combined with the high cost of 13CO(2) make necessary to redefine the designed culture system to increase the efficiency of the conversion of 13CO(2) into the target product. Therefore, the possibility of removing 12C from the fresh medium, and recovering and recirculating the inorganic carbon in the supernatant and the organic carbon from the EPA depleted biomass was studied. The inorganic carbon of the fresh medium was removed by acidification and

  1. The fate of (13)C-labelled and non-labelled inulin predisposed to large bowel fermentation in rats.

    PubMed

    Butts, Christine A; Paturi, Gunaranjan; Tavendale, Michael H; Hedderley, Duncan; Stoklosinski, Halina M; Herath, Thanuja D; Rosendale, Douglas; Roy, Nicole C; Monro, John A; Ansell, Juliet

    2016-04-01

    The fate of stable-isotope (13)C labelled and non-labelled inulin catabolism by the gut microbiota was assessed in a healthy rat model. Sprague-Dawley male rats were randomly assigned to diets containing either cellulose or inulin, and were fed these diets for 3 days. On day (d) 4, rats allocated to the inulin diet received (13)C-labelled inulin. The rats were then fed the respective non-labelled diets (cellulose or inulin) until sampling (d4, d5, d6, d7, d10 and d11). Post feeding of (13)C-labelled substrate, breath analysis showed that (13)C-inulin cleared from the host within a period of 36 hours. Faecal (13)C demonstrated the clearance of inulin from gut with a (13)C excess reaching maximum at 24 hours (d5) and then declining gradually. There were greater variations in caecal organic acid concentrations from d4 to d6, with higher concentrations of acetic, butyric and propionic acids observed in the rats fed inulin compared to those fed cellulose. Inulin influenced caecal microbial glycosidase activity, increased colon crypt depth, and decreased the faecal output and polysaccharide content compared to the cellulose diet. In summary, the presence of inulin in the diet positively influenced large bowel microbial fermentation.

  2. Use of 13C-Labeled Substrates to Determine Relative Methane Production Rates in Hypersaline Microbial Communities

    NASA Astrophysics Data System (ADS)

    Kelley, C. A.; Bebout, B.; Chanton, J.

    2015-12-01

    Rates and pathways of methane production were determined from photosynthetic soft microbial mats and gypsum-encrusted endoevaporites collected in hypersaline environments from California, Mexico and Chile, as well as an organic-rich mud from a pond in the El Tatio volcanic fields, Chile. Samples (mud, homogenized soft mats and endoevaporites) were incubated anaerobically with deoxygenated site water, and the increase in methane concentration through time in the headspaces of the incubation vials was used to determine methane production rates. To ascertain the substrates used by the methanogens, 13C-labeled methylamines, methanol, dimethylsulfide, acetate or bicarbonate were added to the incubations (one substrate per vial) and the stable isotopic composition of the resulting methane was measured. The vials amended with 13C-labeled methylamines produced the most 13C-enriched methane, generally followed by the 13C-labeled methanol-amended vials. The stable isotope data and the methane production rates were used to determine first order rate constants for each of the substrates at each of the sites. Estimates of individual substrate use revealed that the methylamines produced 55 to 92% of the methane generated, while methanol was responsible for another 8 to 40%.

  3. Biochemical synthesis of uniformly (13)C-labeled diterpene hydrocarbons and their bioconversion to diterpenoid phytoalexins in planta.

    PubMed

    Ye, Zhongfeng; Nakagawa, Kazuya; Natsume, Masahiro; Nojiri, Hideaki; Kawaide, Hiroshi; Okada, Kazunori

    2017-06-01

    Phytocassanes and momilactones are the major diterpenoid phytoalexins inductively produced in rice as bioactive substances. Regardless of extensive studies on the biosynthetic pathways of these phytoalexins, bioconversion of diterpene hydrocarbons is not shown in planta. To elucidate the entire biosynthetic pathways of these phytoalexins, uniformly (13)C-labeled ent-cassadiene and syn-pimaradiene were enzymatically synthesized with structural verification by GC-MS and (13)C-NMR. Application of the (13)C-labeled substrates on rice leaves led to the detection of (13)C-labeled metabolites using LC-MS/MS. Further application of this method in the moss Hypnum plumaeforme and the nearest out-group of Oryza species Leersia perrieri, respectively, resulted in successful bioconversion of these labeled substrates into phytoalexins in these plants. These results demonstrate that genuine biosynthetic pathways from these diterpene hydrocarbons to the end product phytoalexins occur in these plants and that enzymatically synthesized [U-(13)C20] diterpene substrates are a powerful tool for chasing endogenous metabolites without dilution with naturally abundant unlabeled compounds.

  4. VARIABLE RATE APPLICATION OF SOIL HERBICIDES IN ARABLE CROPS: FROM THEORY TO PRACTICE.

    PubMed

    Heijting, S; Kempenaar, C

    2014-01-01

    Soil herbicides are applied around crop emergence and kill germinating weeds in the surface layer of the soil. These herbicides play an important role in the chemical management of weeds in major arable crops. From an environmental point of view there is a clear need for smarter application of these chemicals. This paper presents research done in The Netherlands on Variable Rate Application (VRA) of soil herbicides by taking into account spatial variation of the soil. Herbicides adsorbed to soil parameters such as clay or organic matter are not available for herbicidal activity. Decision Support Rules (DSR) describe the relation between the soil parameter and herbicide dosage needed for effectively controlling weeds. Research methods such as greenhouse trials, models and on farm research to develop DSR are discussed and results are presented. Another important ingredient for VRA of soil herbicides is an accurate soil map of the field. Sampling and subsequent interpolation is costly. Soil scans measuring a proxy that is subsequently translated into soil properties such as clay fraction and soil organic matter content offer a quicker way to achieve such maps but validation is needed. DSR is applied to the soil map to get the variable dosage map. The farmer combines this map with the routing, spray volume and spray boom width in the Farm Management Information System (FMIS), resulting in a task file. This task file can subsequently be read by the board computer resulting in a VRA spray map. Reduction in soil herbicide depends on the DSR, the spatial variation and pattern of the soil, the spatial configuration of the routing and the technical advances of the spray equipment. Recently, within the framework the Programma Precisie Landbouw, first steps were made to test and implement this in practice. Currently, theory and practice of VRA of soil herbicides is developed within the research program IJKakker in close cooperation with pioneering farmers in The Netherlands.

  5. Potential carbon sequestration of European arable soils estimated by modelling a comprehensive set of management practices.

    PubMed

    Lugato, Emanuele; Bampa, Francesca; Panagos, Panos; Montanarella, Luca; Jones, Arwyn

    2014-11-01

    Bottom-up estimates from long-term field experiments and modelling are the most commonly used approaches to estimate the carbon (C) sequestration potential of the agricultural sector. However, when data are required at European level, important margins of uncertainty still exist due to the representativeness of local data at large scale or different assumptions and information utilized for running models. In this context, a pan-European (EU + Serbia, Bosnia and Herzegovina, Montenegro, Albania, Former Yugoslav Republic of Macedonia and Norway) simulation platform with high spatial resolution and harmonized data sets was developed to provide consistent scenarios in support of possible carbon sequestration policies. Using the CENTURY agroecosystem model, six alternative management practices (AMP) scenarios were assessed as alternatives to the business as usual situation (BAU). These consisted of the conversion of arable land to grassland (and vice versa), straw incorporation, reduced tillage, straw incorporation combined with reduced tillage, ley cropping system and cover crops. The conversion into grassland showed the highest soil organic carbon (SOC) sequestration rates, ranging between 0.4 and 0.8 t C ha(-1)  yr(-1) , while the opposite extreme scenario (100% of grassland conversion into arable) gave cumulated losses of up to 2 Gt of C by 2100. Among the other practices, ley cropping systems and cover crops gave better performances than straw incorporation and reduced tillage. The allocation of 12 to 28% of the European arable land to different AMP combinations resulted in a potential SOC sequestration of 101-336 Mt CO2 eq. by 2020 and 549-2141 Mt CO2 eq. by 2100. Modelled carbon sequestration rates compared with values from an ad hoc meta-analysis confirmed the robustness of these estimates. © 2014 John Wiley & Sons Ltd.

  6. The use of soil gypsum concentration as an indicator of arable land degradation

    NASA Astrophysics Data System (ADS)

    Robledo, Irene; Marqués Pérez, Maria Jose; Hernandez, Zulimar; Carral, Pilar; Crittenden, Stephen; Sastre, Blanca; Bienes, Ramón

    2017-04-01

    Gypsiferous soils are frequent in arid and semi-arid areas. These soils can be used for farming but shallow soils and steep slopes are detrimental to establishing their profitability. Tillage of sloping land increases risk of soil erosion processes that lead to diminished thickness of the richer topsoil layer. Topsoil loss exposes subsoil layers with higher gypsum concentration. This increased gypsum concentration can influence the potential biomass production and agricultural suitability of gypsiferous soils. In the literature, soils having more than 15% gypsum tend to have weak soil structure and inhibited root growth. Consequently, there is a need to diagnose these eroded soils and to develop a soil protection strategy for arable land if continued soil loss is to be abated and productivity is to be restored or maintained. Indicators to establish the level of degradation are needed, particularly ones that are easy to measure. We hypothesize that pale soil colours indicate proximity to soil conditions linked to high concentrations of gypsum that are detrimental to plant growth. Spain leads the list of European countries having gypsiferous soils, with an area of approximately 35 000 sq km covered. Gypsiferous soils analysed in this study are located at the centre of Spain, where average temperature is 16°C and soils receive around 400 mm of rainfall per year. Sampling was conducted in various areas of a sloping agricultural land with olive trees. Topsoil disturbed samples were randomly collected, in addition, six 70 cm deep soil core were collected. Two soil cores at the top, two in the middle, and two at the bottom slope areas were taken. Colour and gypsum concentration were analysed in the soil samples and also for sub-samples each 5 cm of the core samples. Gypsum was analysed by chemical and thermogravimetric methods. Other parameters like aggregate stability, electrical conductivity, water retention, and bulk density were also analysed. Gypsum concentration

  7. Communities of arbuscular mycorrhizal fungi in arable soils are not necessarily low in diversity.

    PubMed

    Hijri, Isabelle; Sýkorová, Zuzana; Oehl, Fritz; Ineichen, Kurt; Mäder, Paul; Wiemken, Andres; Redecker, Dirk

    2006-07-01

    Communities of arbuscular mycorrhizal fungi (AMF) in five agricultural field sites of different management intensities were studied. Variable regions of the ribosomal RNA genes were used to detect and identify AMF directly within colonized roots. Roots from a continuous maize monoculture showed low AMF diversity, in agreement with previous reports on molecular diversity of AMF in agricultural soils. In contrast, a substantially higher diversity of AMF was found throughout the long term 'DOK' field experiment, where organic and conventional agricultural practices have been compared side by side since 1978. In this experiment, a 7-year crop rotation is performed under lower levels of inorganic fertilizer input and chemical pest control. These results are in good agreement with analyses of the spore community previously conducted in these field sites. In a third site, an organically managed leek field with soil of very high phosphate content reflecting the highly intensive conventional field history and intensive tillage, we detected a low-diversity community comparable to the maize monoculture. In addition to fungi from Glomus group A, which have previously been reported to dominate arable soils, we regularly found members of the genera Scutellospora, Paraglomus and Acaulospora. The genus Acaulospora was shown to occur more frequently early in the growing season, suggesting that the life history strategy of AMF may influence the active community at a given time. These data show that the diversity of AMF is not always low in arable soils. Furthermore, low-input agriculture involving crop rotation may provide better conditions to preserve AMF diversity, by preventing the selection for the few AMF taxa tolerating high nutrient levels.

  8. Survival of free-living Acholeplasma in aerated pig manure slurry revealed by 13C-labeled bacterial biomass probing

    PubMed Central

    Hanajima, Dai; Aoyagi, Tomo; Hori, Tomoyuki

    2015-01-01

    Many studies have been performed on microbial community succession and/or predominant taxa during the composting process; however, the ecophysiological roles of microorganisms are not well understood because microbial community structures are highly diverse and dynamic. Bacteria are the most important contributors to the organic-waste decomposition process, while decayed bacterial cells can serve as readily digested substrates for other microbial populations. In this study, we investigated the active bacterial species responsible for the assimilation of dead bacterial cells and their components in aerated pig manure slurry by using 13C-labeled bacterial biomass probing. After 3 days of forced aeration, 13C-labeled and unlabeled dead Escherichia coli cell suspensions were added to the slurry. The suspensions contained 13C-labeled and unlabeled bacterial cell components, possibly including the cell wall and membrane, as well as intracellular materials. RNA extracted from each slurry sample 2 h after addition of E. coli suspension was density-resolved by isopycnic centrifugation and analyzed by terminal restriction fragment length polymorphism, followed by cloning and sequencing of bacterial 16S rRNA genes. In the heavy isotopically labeled RNA fraction, the predominant 13C-assimilating population was identified as belonging to the genus Acholeplasma, which was not detected in control heavy RNA. Acholeplasma spp. have limited biosynthetic capabilities and possess a wide variety of transporters, resulting in their metabolic dependence on external carbon and energy sources. The prevalence of Acholeplasma spp. was further confirmed in aerated pig manure slurry from four different pig farms by pyrosequencing of 16S rRNA genes; their relative abundance was ∼4.4%. Free-living Acholeplasma spp. had a competitive advantage for utilizing dead bacterial cells and their components more rapidly relative to other microbial populations, thus allowing the survival and prevalence

  9. A chemical synthesis of a multiply (13) C-labeled hexasaccharide: a high-mannose N-glycan fragment.

    PubMed

    Zhang, Wenhui; Pan, Qingfeng; Serianni, Anthony S

    2016-12-01

    As covalent modifiers of proteins, high-mannose N-glycans are important in maintaining protein structure and function in vivo. The conformations of these glycans can be studied by nuclear magnetic resonance spectroscopy using spin-spin couplings (J-couplings; scalar couplings) and other nuclear magnetic resonance parameters that are sensitive to the geometries of their constituent glycosidic linkages and other mobile elements in their structures. These analyses often require (13) C-labeling at specific carbon atoms, especially when measurements of (13) C-(13) C J-couplings are of interest. The selection of particular (13) C isotopomers of a glycan depends on the type of question under scrutiny. A chemical synthesis of a mannose-containing hexasaccharide, α[1-(13) C]Man(1→2)α[1,2-(13) C2 ]Man(1→6)[α[1-(13) C]Man(1→2)α[1,2-(13) C2 ]Man(1→3)]α[1,2-(13) C2 ]Man(1→6)βManOCH3 , which is a nested fragment of the high-mannose N-glycans of human glycoproteins and contains eight (13) C-enriched carbon sites, is described in this report. The selected (13) C isotopomer was chosen to maximize the measurement of J-couplings sensitive to linkage conformations. This work demonstrates that chemical syntheses of multiply (13) C-labeled oligosaccharides are technically feasible and practical using present synthetic methods. The availability of this and other multiply (13) C-labeled mannose-containing oligosaccharides will promote future studies of their conformations in solution and in the bound state. Copyright © 2016 John Wiley & Sons, Ltd.

  10. Restoration of species-rich grasslands on ex-arable land: seed addition outweighs soil fertility reduction

    SciTech Connect

    Kardol, Paul

    2008-01-01

    A common practice in biodiversity conservation is restoration of former species-rich grassland on ex-arable land. Major constraints for grassland restoration are high soil fertility and limited dispersal ability of plant species to target sites. Usually, studies focus on soil fertility or on methods to introduce plant seeds. However, the question is whether soil fertility reduction is always necessary for getting plant species established on target sites. In a three-year field experiment with ex-arable soil with intensive farming history, we tested single and combined effects of soil fertility reduction and sowing mid-successional plant species on plant community development and soil biological properties. A controlled microcosm study was performed to test short-term effects of soil fertility reduction measures on biomass production of mid-successional species. Soil fertility was manipulated by adding carbon (wood or straw) to incorporate plant-available nutrients into organic matter, or by removing nutrients through top soil removal (TSR). The sown species established successfully and their establishment was independent of carbon amendments. TSR reduced plant biomass, and effectively suppressed arable weeds, however, created a desert-like environment, inhibiting the effectiveness of sowing mid-successional plant species. Adding straw or wood resulted in short-term reduction of plant biomass, suggesting a temporal decrease in plant-available nutrients by microbial immobilisation. Straw and wood addition had little effects on soil biological properties, whereas TSR profoundly reduced numbers of bacteria, fungal biomass and nematode abundance. In conclusion, in ex-arable soils, on a short term sowing is more effective for grassland restoration than strategies aiming at soil fertility reduction.

  11. Assessment of sampling and analytical uncertainty of trace element contents in arable field soils.

    PubMed

    Buczko, Uwe; Kuchenbuch, Rolf O; Ubelhör, Walter; Nätscher, Ludwig

    2012-07-01

    Assessment of trace element contents in soils is required in Germany (and other countries) before sewage sludge application on arable soils. The reliability of measured element contents is affected by measurement uncertainty, which consists of components due to (1) sampling, (2) laboratory repeatability (intra-lab) and (3) reproducibility (between-lab). A complete characterization of average trace element contents in field soils should encompass the uncertainty of all these components. The objectives of this study were to elucidate the magnitude and relative proportions of uncertainty components for the metals As, B, Cd, Co, Cr, Mo, Ni, Pb, Tl and Zn in three arable fields of different field-scale heterogeneity, based on a collaborative trial (CT) (standardized procedure) and two sampling proficiency tests (PT) (individual sampling procedure). To obtain reference values and estimates of field-scale heterogeneity, a detailed reference sampling was conducted. Components of uncertainty (sampling person, sampling repetition, laboratory) were estimated by variance component analysis, whereas reproducibility uncertainty was estimated using results from numerous laboratory proficiency tests. Sampling uncertainty in general increased with field-scale heterogeneity; however, total uncertainty was mostly dominated by (total) laboratory uncertainty. Reproducibility analytical uncertainty was on average by a factor of about 3 higher than repeatability uncertainty. Therefore, analysis within one single laboratory and, for heterogeneous fields, a reduction of sampling uncertainty (for instance by larger numbers of sample increments and/or a denser coverage of the field area) would be most effective to reduce total uncertainty. On the other hand, when only intra-laboratory analytical uncertainty was considered, total sampling uncertainty on average prevailed over analytical uncertainty by a factor of 2. Both sampling and laboratory repeatability uncertainty were highly variable

  12. Gram-scale synthesis and efficient purification of 13C-labeled levoglucosan from 13C glucose.

    PubMed

    Alexander, Lisa; Hoyt, Caroline; Michalczyk, Ryszard; Wu, Ruilian; Thorn, Dave L; Silks, L A Pete

    2013-01-01

    (13)C-Labeled levoglucosan has been synthesized and purified in good yield, and on the gram scale in one step from commercially available (13)C glucose. This one-step protocol uses 2-chloro-1,3-dimethylimidazolinium chloride that serves to selectively activate the anomeric carbon toward substitution reactions. The labeled glucose is then smoothly converted to the anhydroglucose. Purification is efficiently achieved on large scale by chromatography on silica gel. Published 2012. This article is a US Government work and is in the public domain in the USA.

  13. Biosynthesis of pyrroloquinoline quinone. 1. Identification of biosynthetic precursors using /sup 13/C labeling and NMR spectroscopy

    SciTech Connect

    Houck, D.R.; Hanners, J.L.; Unkefer, C.J.

    1988-09-28

    The biosynthesis of pyrroloquinoline quinone (PQQ) in the methylotropic bacterium methylobacterium AM1 has been investigated using /sup 13/C-labelling of the products and NMR spectroscopy. The data indicated that the quinoline portion of PQQ is formed by a novel condensation of N-1, C-2, -3, and -4 of glutamate with a symmetrical six-carbon ring derived from the shikimate pathway. It is postulated that tyrosine is the shikimate-derived percursor, since pyrrole could be formed by the internal cyclization of the amino acid backbone. 18 references, 2 figures, 2 tables.

  14. Thallium in French agrosystems--I. Thallium contents in arable soils.

    PubMed

    Tremel, A; Masson, P; Sterckeman, T; Baize, D; Mench, M

    1997-01-01

    The thallium (Tl) content of the upper horizons of 244 French soils was determined as the first step towards the creation of a reference data bank for total Tl content of arable soils. Forty soil samples were collected in the vicinity of potential anthropogenic sources of Tl, but the remainder came from rural areas. The distribution of Tl concentrations in soils was characterized by a median value of 0.29 mg Tl kg(-1) and a 90th percentile value of 1.54 mg Tl kg(-1). Very high pedogeochemical contents were found (up to 55 mg Tl kg(-1)) but none could be attributed to obvious anthropogenic pollution. Areas of very high Tl concentration belong to an epihercynian transgression zone with a contact between a sedimentary basin and a crystalline massif. This contact is associated with stratified mineralizations (Zn, Pb, F, Sb, Ba, Tl and pyrites). High Tl concentrations were common in limestone, marl or granite derived soils, and the Tl in limestones or marls is probably concentrated in the sulfides contained in these rocks because Tl has a high affinity to S. In granites, Tl may be in the micas and feldspars because Tl+ can replace K+ in these minerals. Silty or clay-silty soils showed the highest concentrations. These granulometric fractions contain the majority of the minerals, which are supposed to be the major hosts of Tl in soils, i.e. clay minerals, oxides and micas. Tl in the soils was positively correlated with Ba, V, Pb, Fe, Ni, Cd, Zn, Co, As and especially Mn. A significant proportion of Tl may be in the Mn oxides: in oxidizing conditions, Tl(III) could enter the Mn oxides by sorption, or Tl(I) could replace K(I) in the oxide.

  15. Reliable Identification of Cross-Linked Products in Protein Interaction Studies by 13C-Labeled p-Benzoylphenylalanine

    NASA Astrophysics Data System (ADS)

    Pettelkau, Jens; Ihling, Christian H.; Frohberg, Petra; van Werven, Lars; Jahn, Olaf; Sinz, Andrea

    2014-09-01

    We describe the use of the 13C-labeled artificial amino acid p-benzoyl-L-phenylalanine (Bpa) to improve the reliability of cross-linked product identification. Our strategy is exemplified for two protein-peptide complexes. These studies indicate that in many cases the identification of a cross-link without additional stable isotope labeling would result in an ambiguous assignment of cross-linked products. The use of a 13C-labeled photoreactive amino acid is considered to be preferred over the use of deuterated cross-linkers as retention time shifts in reversed phase chromatography can be ruled out. The observation of characteristic fragment ions additionally increases the reliability of cross-linked product assignment. Bpa possesses a broad reactivity towards different amino acids and the derived distance information allows mapping of spatially close amino acids and thus provides more solid structural information of proteins and protein complexes compared to the longer deuterated amine-reactive cross-linkers, which are commonly used for protein 3D-structure analysis and protein-protein interaction studies.

  16. Input and behavior of polycyclic aromatic hydrocarbons in arable, fallow, and forest soils of the taiga zone (Tver oblast)

    NASA Astrophysics Data System (ADS)

    Zhidkin, A. P.; Gennadiev, A. N.; Koshovskii, T. S.

    2017-03-01

    Contents of 11 most prevalent polycyclic aromatic hydrocarbons (PAHs) in snow and soils of arable, fallow, and forest areas significantly remote from impact technogenic sources of polyarenes have been examined in the Torzhok district of Tver oblast. From the analysis of snow samples, the volumes and composition of PAHs coming from the atmosphere onto the areas of different land use have been determined. Light hydrocarbons prevail in PAHs. They make up 65-70% of total PAHs; their share in soils reaches almost 95%. An increase in the content of PAHs is revealed in fallow soils compared to arable and afforested areas. A direct relationship is revealed between the lateral distribution of total PAHs and the content of organic carbon. The distribution of total PAHs is surface-accumulative in forest soils, mainly uniform in arable soils, and deepaccumulative in fallow soils. PAH groups characterized by similar radial distributions and ratios between their reserves in snow and soils are distinguished: (1) fluorene and phenanthrene, (2) biphenyl and naphthalene, (3) benzo(a)anthracene, chrysene, perylene, and benzo[ a]pyrene, and (4) anthracene and benzo[ ghi]pyrene.

  17. Observing 13C labelling kinetics in CO2 respired by a temperate grassland ecosystem.

    PubMed

    Gamnitzer, Ulrike; Schäufele, Rudi; Schnyder, Hans

    2009-10-01

    * The kinetic characteristics of the main sources of ecosystem respiration are quite unknown, partly because of methodological constraints. Here, we present a new open-top chamber (OTC) apparatus for continuous 13C/12C labelling and measurement of ecosystem CO2 fluxes, and report the tracer kinetics of nighttime respiration of a temperate grassland. * The apparatus includes four dynamic flow-through OTCs, a unit mixing CO2-free air with 13C-depleted CO2, and a CO2 analyser and an online isotope ratio mass spectrometer. * The concentration (367 +/- 6.5 micromol mol(-1)) and carbon isotopic composition, delta13C, (-46.9 +/- 0.4 per thousand) of CO2 in the OTCs were stable during photosynthesis as a result of high air through flux and minimal incursion through the buffered vent. Soil CO2 efflux was not affected by pressure effects during respiration measurements. The labelling kinetics of respiratory CO2 measured in the field agreed with that of excised soil + vegetation blocks measured in a laboratory-based system. The kinetics fitted a two-source system (r(2) = 0.97), with a rapidly labelled source (half-life 2.6 d) supplying 48% of respiration, and the other source (52%) releasing no tracer during 14 d of labelling. * Of the two sources supplying ecosystem respiration, one was closely connected to current photosynthesis (approximately autotrophic respiration) and the other was provided by decomposition of structural plant biomass (approximately heterotrophic respiration).

  18. Wettability, soil organic matter and structure-properties of typical chernozems under the forest and under the arable land

    NASA Astrophysics Data System (ADS)

    Bykova, Galina; Umarova, Aminat; Tyugai, Zemfira; Milanovskiy, Evgeny; Shein, Evgeny

    2017-04-01

    Intensive tillage affects the properties of soil: decrease in content of soil organic matter and in hydrophobicity of the soil's solid phase, the reduction of amount of water stable aggregates - all this leads to deterioration of the structure of the soil and affects the process of movement of moisture in the soil profile. One of the hypotheses of soil's structure formation ascribes the formation of water stable aggregates with the presence of hydrophobic organic substances on the surface of the soil's solid phase. The aim of this work is to study the effect of tillage on properties of typical chernozems (pachic Voronic Chernozems, Haplic Chernozems) (Russia, Kursk region), located under the forest and under the arable land. The determination of soil-water contact angle was performed by a Drop Shape Analyzer DSA100 (Krüss GmbH, Germany) by the static sessile drop method. For all samples the content of total and organic carbon by dry combustion in oxygen flow and the particle size distribution by the laser diffraction method on the device Analysette 22 comfort, FRITCH, Germany were determined. The estimation of aggregate composition was performed by dry sieving (AS 200, Retsch, Germany), the content of water stable aggregates was estimated by the Savvinov method. There was a positive correlation between the content of organic matter and soil's wettability in studied soils, a growth of contact angle with the increasing the content of organic matter. Under the forest the content of soil organic matter was changed from 6,41% on the surface up to 1,9% at the depth of 100 cm. In the Chernozem under the arable land the organic carbon content in arable horizon is almost two times less. The maximum of hydrophobicity (78.1o) was observed at the depth of 5 cm under the forest. In the profile under the arable land the contact angle value at the same depth was 50o. The results of the structure analysis has shown a decrease in the content of agronomically valuable and water

  19. Earthworm impact on the global warming potential of a no-tillage arable soil

    NASA Astrophysics Data System (ADS)

    Nieminen, M.; Hurme, T.; Mikola, J.; Regina, K.; Nuutinen, V.

    2015-04-01

    We studied the effect of the deep-burrowing earthworm Lumbricus terrestris on the greenhouse gas (GHG) fluxes and global warming potential (GWP) of arable no-till soil using both field measurements and a controlled 15 week laboratory experiment. In the field, the emissions of nitrous oxide (N2O) and carbon dioxide (CO2) were on average 43 and 32% higher in areas occupied by L. terrestris (the presence judged by the surface midden) than in adjacent, unoccupied areas (with no midden). The fluxes of methane (CH4) were variable and had no consistent difference between the midden and non-midden areas. Removing the midden did not affect soil N2O and CO2 emissions. The laboratory results were consistent with the field observations in that the emissions of N2O and CO2 were on average 27 and 13% higher in mesocosms with than without L. terrestris. Higher emissions of N2O were most likely due to the higher content of mineral nitrogen and soil moisture under the middens, whereas L. terrestris respiration fully explained the observed increase in CO2 emissions. The activity of L. terrestris increased the GWP of field and laboratory soil by 50 and 18%, but only 6 and 2% of this increase was due to the enhanced N2O emission. Our results suggest that high N2O emissions commonly observed in no-tillage soils can partly be explained by the abundance of L. terrestris under no-till management and that L. terrestris can markedly regulate the climatic effects of different cultivation practises.

  20. Soil organic carbon accumulation in afforested/abandoned arable fields in Taiwan

    NASA Astrophysics Data System (ADS)

    Lin, Yi-Han; Cheng, Chih-Hsin; Huang, Yu-Hsuan

    2016-04-01

    Afforestation or abandonment of arable fields has been proposed as a way to increase terrestrial carbon storage and mitigate anthropogenic carbon emissions. When the arable fields are afforested or abandoned, the accumulation in soil organic carbon (SOC) is a key pool to sequestrate carbon. However, high uncertainties still exist in the tropics and subtropics because of fast SOC turnover rates and variable land use managements in these areas. In this study, a total of eleven sites with afforested/abandoned age over 15 years and elevation ranging from 16 to 2,056 m were investigated. We examined the increments of SOC by comparing with the adjacent tilled (e.g. croplands) and non-tilled (e.g. tea plantation or orchards) fields in two sampling layers, 0 - 10 and 10 - 20 cm in depth. In addition, density fractionation of SOC was also conducted in order to differentiate SOC into light fraction, intra-aggregate fraction, and heavy fraction to gain more information about the mechanism of SOC sequestration. Our results indicated that the increments of SOC concentration and stock varied with elevation, land use management, and soil depth. For the sites with elevation below 500 m, the SOC concentration and stock in the abandoned fields were 14.3 ± 0.9 mg C g-1 and 14.6 ± 4.6 Mg C ha-1 higher than the adjacent tilled fields, and 10.2 ± 6.3 mg C g-1and 6.4 ± 6.2 Mg C ha-1 higher than the adjacent non-tilled fields for surface 0-10 cm. For the sites with elevation above 500 m, the SOC concentration in the abandoned arable fields were 22.8 ± 12.8 mg C g-1 higher than the adjacent tilled fields, but the SOC stock might not be different due to high stone content in abandoned field. Moreover, the SOC concentration and stock in abandoned field were not different or even less than non-tilled fields where organic amendments were frequently applied. The increments of SOC for 10-20 cm soils were less evident than those for surface 0-10 cm soils, and the differences were only

  1. The biosynthetic pathway of curcuminoid in turmeric (Curcuma longa) as revealed by 13C-labeled precursors.

    PubMed

    Kita, Tomoko; Imai, Shinsuke; Sawada, Hiroshi; Kumagai, Hidehiko; Seto, Haruo

    2008-07-01

    In order to investigate the biosynthesis of curcuminoid in rhizomes of turmeric (Curcuma longa), we established an in vitro culture system of turmeric plants for feeding (13)C-labeled precursors. Analyses of labeled desmethoxycurcumin (DMC), an unsymmetrical curcuminoid, by (13)C-NMR, revealed that one molecule of acetic acid or malonic acid and two molecules of phenylalanine or phenylpropanoids, but not tyrosine, were incorporated into DMC. The incorporation efficiencies of the same precursors into DMC and curcumin were similar, and were in the order malonic acid > acetic acid, and cinnamic acid > p-coumaric acid > ferulic acid. These results suggest the possibility that the pathway to curcuminoids utilized two cinnamoyl CoAs and one malonyl CoA, and that hydroxy- and methoxy-functional groups on the aromatic rings were introduced after the formation of the curcuminoid skeleton.

  2. Enzymatic (13)C labeling and multidimensional NMR analysis of miltiradiene synthesized by bifunctional diterpene cyclase in Selaginella moellendorffii.

    PubMed

    Sugai, Yoshinori; Ueno, Yohei; Hayashi, Ken-ichiro; Oogami, Shingo; Toyomasu, Tomonobu; Matsumoto, Sadamu; Natsume, Masahiro; Nozaki, Hiroshi; Kawaide, Hiroshi

    2011-12-16

    Diterpenes show diverse chemical structures and various physiological roles. The diversity of diterpene is primarily established by diterpene cyclases that catalyze a cyclization reaction to form the carbon skeleton of cyclic diterpene. Diterpene cyclases are divided into two types, monofunctional and bifunctional cyclases. Bifunctional diterpene cyclases (BDTCs) are involved in hormone and defense compound biosyntheses in bryophytes and gymnosperms, respectively. The BDTCs catalyze the successive two-step type-B (protonation-initiated cyclization) and type-A (ionization-initiated cyclization) reactions of geranylgeranyl diphosphate (GGDP). We found that the genome of a lycophyte, Selaginella moellendorffii, contains six BDTC genes with the majority being uncharacterized. The cDNA from S. moellendorffii encoding a BDTC-like enzyme, miltiradiene synthase (SmMDS), was cloned. The recombinant SmMDS converted GGDP to a diterpene hydrocarbon product with a molecular mass of 272 Da. Mutation in the type-B active motif of SmMDS abolished the cyclase activity, whereas (+)-copalyl diphosphate, the reaction intermediate from the conversion of GGDP to the hydrocarbon product, rescued the cyclase activity of the mutant to form a diterpene hydrocarbon. Another mutant lacking type-A activity accumulated copalyl diphosphate as the reaction intermediate. When the diterpene hydrocarbon was enzymatically synthesized from [U-(13)C(6)]mevalonate, all carbons were labeled with (13)C stable isotope (>99%). The fully (13)C-labeled product was subjected to (13)C-(13)C COSY NMR spectroscopic analyses. The direct carbon-carbon connectivities observed in the multidimensional NMR spectra demonstrated that the hydrocarbon product by SmMDS is miltiradiene, a putative biosynthetic precursor of tanshinone identified from the Chinese medicinal herb Salvia miltiorrhiza. Hence, SmMDS functions as a bifunctional miltiradiene synthase in S. moellendorffii. In this study, we demonstrate that one

  3. A Comprehensive Metabolic Profile of Cultured Astrocytes Using Isotopic Transient Metabolic Flux Analysis and 13C-Labeled Glucose

    PubMed Central

    Amaral, Ana I.; Teixeira, Ana P.; Håkonsen, Bjørn I.; Sonnewald, Ursula; Alves, Paula M.

    2011-01-01

    Metabolic models have been used to elucidate important aspects of brain metabolism in recent years. This work applies for the first time the concept of isotopic transient 13C metabolic flux analysis (MFA) to estimate intracellular fluxes in primary cultures of astrocytes. This methodology comprehensively explores the information provided by 13C labeling time-courses of intracellular metabolites after administration of a 13C-labeled substrate. Cells were incubated with medium containing [1-13C]glucose for 24 h and samples of cell supernatant and extracts collected at different time points were then analyzed by mass spectrometry and/or high performance liquid chromatography. Metabolic fluxes were estimated by fitting a carbon labeling network model to isotopomer profiles experimentally determined. Both the fast isotopic equilibrium of glycolytic metabolite pools and the slow labeling dynamics of TCA cycle intermediates are described well by the model. The large pools of glutamate and aspartate which are linked to the TCA cycle via reversible aminotransferase reactions are likely to be responsible for the observed delay in equilibration of TCA cycle intermediates. Furthermore, it was estimated that 11% of the glucose taken up by astrocytes was diverted to the pentose phosphate pathway. In addition, considerable fluxes through pyruvate carboxylase [PC; PC/pyruvate dehydrogenase (PDH) ratio = 0.5], malic enzyme (5% of the total pyruvate production), and catabolism of branched-chained amino acids (contributing with ∼40% to total acetyl-CoA produced) confirmed the significance of these pathways to astrocytic metabolism. Consistent with the need of maintaining cytosolic redox potential, the fluxes through the malate–aspartate shuttle and the PDH pathway were comparable. Finally, the estimated glutamate/α-ketoglutarate exchange rate (∼0.7 μmol mg prot−1 h−1) was similar to the TCA cycle flux. In conclusion, this work demonstrates the potential of

  4. Future rainfall patterns will reduce arthropod abundance in model arable agroecosystems with different soil types

    NASA Astrophysics Data System (ADS)

    Zaller, Johann; Simmer, Laura; Tabi Tataw, James; Formayer, Herbert; Hösch, Johannes; Baumgarten, Andreas

    2013-04-01

    Climate change scenarios for eastern Austria predict a seasonal shift in precipitation patterns with fewer but heavier rainfall events and longer drought periods during the growing season and more precipitation during winter. This is expected to alter arthropods living in natural and agricultural ecosystems with consequences for several ecosystem functions and services. In order to better understand the effects of future rainfall patterns on aboveground arthropods inhabiting an agroecosystem, we conducted an experiment where we simulated rainfall patterns in model arable systems with three different soil types. Experiments were conducted in winter wheat cultivated in a lysimeter facility near Vienna, Austria, where three different soil types (calcaric phaeozem, calcic chernozem and gleyic phaeozem) were subjected to long-term current vs. predicted rainfall patterns according to regionalized climate change projections for 2071-2100. Aboveground arthropods were assessed by suction sampling in April, May and June 2012. We found significant differences in mean total arthropod abundances between the sampling dates with 20 ± 2 m-2, 90 ± 20 m-2 and 289 ± 54 m-2 in April, May and June, respectively. Across all three sampling dates, future rainfall patterns significantly reduced the abundance of Araneae (-43%), Auchenorrhyncha (-39%), Coleoptera (-48%), Carabidae (-41%), Chrysomelidae (-64%), Collembola (-58%), Diptera (-75%) and Neuroptera (-73%). Generally, different soil types had no effect on the abundance of arthropods. The diversity of arthropod communities was unaffected by rainfall patterns or soil types. Correlation analyses of arthropod abundances with crop biomass, weed density and abundance suggest that rainfall effects indirectly affected arthropods via changes on crops and weeds. In conclusion, these results show that future rainfall patterns will have detrimental effects on the abundance of a variety of aboveground arthropods in winter wheat with potential

  5. Influence of mineral characteristics and long-term arable and forest land use on stocks, composition, and stability of soil organic matter

    NASA Astrophysics Data System (ADS)

    Kaiser, Michael; Ellerbrock, Ruth H.; Wulf, Monika; Dultz, Stefan; Hierath, Christina; Michael, Sommer

    2013-04-01

    A land use change from arable to forest is discussed as an option to sequester carbon and mitigate climate change but land use specific mechanisms responsible for soil organic matter stabilization are still poorly understood. In this study we aimed to analyze the impact of soil mineral characteristics on organic carbon (OC) stocks and on the composition as well as on the stability of mineral associated organic matter (OM) of arable and forest topsoils. We selected seven soil types of different mineral characteristics. Topsoil samples of each soil type were taken from a deciduous forest and an adjacent arable site, which have been continuously used for more than 100 years. The sequentially extracted Na-pyrophosphate soluble OM fractions (OM(PY)), representing mineral associated OM, were analyzed on their OC and 14C content and characterized by infrared spectroscopy. We found land use effects on the soil OC stocks and OC amounts separated by OM(PY) (OCPY) (forest > arable) as well as on the stability of OM(PY) (arable > forest). For the forest and arable topsoils, a linear relationship was found between the stocks of OC and exchangeable Ca. Only for the near neutral arable topsoils, correlation analyses indicate increasing OCPY contents with an increase in oxalate soluble Fe and Al, exchangable Ca, and Na-pyrophosphate soluble Mg and Fe contents. The stability of OM(PY) of the arable topsoils seems to increase with the specific surface area of the mineral phase and the content of exchangeable Ca. For the acidic forest topsoils, the stability of OM(PY) seems to increase with increasing pH, the C=O group content of OM(PY) and, the Na-pyrophosphate soluble Mg contents. The results indicate cation bridging of OM to mineral surfaces in near neutral arable soils and OM-crosslinking in acidic forest soil as important mechanisms for the stabilization of OM(PY).

  6. Structural properties of dissolved organic carbon in deep soil horizons of an arable and temporarily grassland.

    NASA Astrophysics Data System (ADS)

    Lavaud, A.; Chabbi, A.; Croue, J. P.

    2009-04-01

    It is commonly accepted that dissolved organic carbon (DOC) is the bio-available fraction of the largest amount of soil organic matter (SOM), even if it does represent only a very small proportion. Because most of the studies on DOC dynamics were mainly restricted to forest soils, studies on the factors governing the dynamics of DOC in deep soil horizons (>1 m) in arable system are still very little limited. The objective of this work is to better define the proportion of DOC in deep soil horizons and indicate their main characteristics and structural properties. The study was conducted on the long term observatory for environmental research- biogeochemical cycles and biodiversity Lusignan site). DOC collected using lysimeters plates inserted to a depth of 105 cm was fractionated into 3 fractions using the two column array of XAD-8 and XAD-4 resins. The HPO (hydrophobic) fraction (i.e. humic substances) isolated from the XAD-8 resin, the TPH (Transphilic) fraction from the XAD-4 resin and the HPI (hydrophilic) fraction which corresponds to the DOC that does not adsorbed onto the two resins under the acid condition used (pH 2). DOM adsorbed onto the resins is recovered with a 75%/25% acetonitrile/water mixture and lyophilized. Depend on the amount of material; the chemical composition of DOC was performed using UV254 nm, fluorescence EEM, NMR and HPSEC/UV/COD. The results show that the concentration and structural properties of DOC in deep soil horizon were similar to those of groundwater (low SUVA (1.2 m-1.L.mg C-1), structures composed mainly of low molecular weight). Because of the relatively recent establishment of the treatment, the monitoring of the dynamics of the DOC concentrations did not show significant differences between arable and grassland. However, the temporal dynamic shows a slight increase in the DOC content regardless of the of land use. DOC concentrations between winter and the middle of spring tend to double going from 1 to 2.5 mg / L and then

  7. Laccase activity is proportional to the abundance of bacterial laccase-like genes in soil from subtropical arable land.

    PubMed

    Feng, Shuzhen; Su, Yirong; Dong, Mingzhe; He, Xunyang; Kumaresan, Deepak; O'Donnell, Anthony G; Wu, Jinshui; Chen, Xiangbi

    2015-12-01

    Laccase enzymes produced by both soil bacteria and fungi play important roles in refractory organic matter turnover in terrestrial ecosystems. We investigated the abundance and diversity of fungal laccase genes and bacterial laccase-like genes in soil from subtropical arable lands, and identified which microbial group was associated with laccase activity. Compared with fungal laccase genes, the bacterial laccase-like genes had greater abundance, richness and Shannon-Wiener diversity. More importantly, laccase activity can be explained almost exclusively by the bacterial laccase-like genes, and their abundance had significant linear relationship with laccase activity. Thus, bacterial laccase-like gene has great potential to be used as a sensitive indicator of laccase enzyme for refractory organic matter turnover in subtropical arable lands.

  8. Differences in ice nucleation behavior of arable and desert soil dust in deposition nucleation regime

    NASA Astrophysics Data System (ADS)

    Ullrich, Romy; Vogel, Franziska; Möhler, Ottmar; Höhler, Kristina; Schiebel, Thea

    2017-04-01

    Soil dust from arid and semi-arid regions is one of the most abundant aerosol types in the atmosphere with emission rates of about 1600 Tg per year (Andreae et al. (2009)). Therewith, soil dust plays an important role for the atmospheric radiative transfer and also for the formation of clouds. Soil dust refers to dust sampled from agricultural used areas, to dust from bare soil as well as to dust from desert regions. By mass-spectrometric measurements of the chemical composition of ice residuals, mineral dust as component of soil dust was found to be the major heterogeneous ice nucleating particle (INP) type (e.g. Cziczo et al. (2013)), in particular in the upper troposphere. Also in laboratory studies the ice nucleation efficiency of the different soil dusts was investigated. It was shown that desert dusts (Ullrich et al. (2017)) as well as soil dusts from arable regions (O'Sullivan et al. (2014), Tobo et al. (2014)) are efficient INP. However, there is still a lack of data for ice nucleation on soil dusts for temperatures below about 220 K. With the AIDA (Aerosol Interactions and Dynamics in the Atmosphere) cloud chamber, we are able to characterize the ice nucleation efficiency for different aerosol types to temperatures down to 180 K and high ice supersaturations. In order to extend the already existing AIDA data base for deposition nucleation on desert dusts and agricultural soil dusts, new experiments were done in the upper tropospheric temperature regime. This contribution will show the results of the new experiments with desert dust in comparison to existing data for higher temperatures. The first data analysis confirms the temperature dependent trend of the ice nucleation activity as discussed and parameterized in a recent paper by Ullrich et al. (2017). Furthermore, the update and extension of the recently published parameterization of deposition nucleation for desert dust to lower temperatures will be discussed. The experiments with agricultural soil

  9. Response of rhizosphere microbial community structure and diversity to heavy metal co-pollution in arable soil.

    PubMed

    Deng, Linjing; Zeng, Guangming; Fan, Changzheng; Lu, Lunhui; Chen, Xunfeng; Chen, Ming; Wu, Haipeng; He, Xiaoxiao; He, Yan

    2015-10-01

    Due to the emerging environmental issues related to heavy metals, concern about the soil quality of farming lands near manufacturing district is increasing. Investigating the function of soil microorganisms exposed to long-term heavy metal contamination is meaningful and important for agricultural soil utilization. This article studied the potential influence of several heavy metals on microbial biomass, activity, abundance, and community composition in arable soil near industrial estate in Zhuzhou, Hunan province, China. The results showed that soil organic contents (SOC) were significantly positive correlated with heavy metals, whereas dehydrogenase activity (DHA) was greatly depressed by the heavy metal stress. Negative correlation was found between heavy metals and basal soil respiration (BSR), and no correlation was found between heavy metals and microbial biomass content (MBC). The quantitative PCR (QPCR) and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis could suggest that heavy metal pollution has significantly decreased abundance of bacteria and fungi and also changed their community structure. The results could contribute to evaluate heavy metal pollution level in soil. By combining different environmental parameters, it would promote the better understanding of heavy metal effect on the size, structure, and activity of microbial community in arable soil.

  10. Production of Hydrolysable Tannin-Like Structures During the Microbial Demethylation of lignin: An Assessment Using13C-Labeled Tetramethylammonium Hydroxide Thermochemolysis.

    NASA Astrophysics Data System (ADS)

    Filley, T.; Blanchette, R.; Nierop, K.; Gamblin, D.

    2003-12-01

    Phenolic compounds in soils are important mediators of microbial activity, metal mobility, soil redox, and soil organic matter building processes. Direct tannin input and the microbial decomposition of lignin in litter and soil are important contributors to this pool of phenols. The ability to accurately assess the relative differences in lignin decay (which are initiated by demethylation and side chain oxidation) among synapyl, coniferyl, and p-coumaryl components of detrital lignin requires the ability to determine microbial demethylation within the complex soil residues. Differentiating between hydrolysable tannins and contributions from advanced lignin decay can be problematic for many of the most common molecular techniques such as alkaline CuO oxidation, pyrolysis GC, and tetramethylammonium hydroxide thermochemolysis because of either the masking effects of derivatizing agents, oxidative damage to ortho-phenols or low volatility of lignin monomers. In this study we investigate lignin demethylation and polyhydroxyl-aromatic production in BC and C horizons of sandy forest soils dominated by oak, the A horizon from a red spruce forest, and controlled microbial inoculation studies of woody tissue using in-line 13C-labeled tetramethylammonium hydroxide thermochemolysis. Both white-rot and brown-rot decay resulted in syringyl demethylation, with the latter exhibiting more aggressive demethylation chemistry, while coniferyl monomer demethylation was essentially restricted to brown-rot decay. In a typical brown-rot sequence demethylation of syringyl components occurs more rapidly than coniferyl units within the same tissue and lower molecular weight fragments are likewise more demethylated than lignin monomers containing the full glycerol side chain. Demethylation of both methoxyl groups in the syringyl monomer is evident in soil horizons as well as laboratory inoculations. The latter may suggest demethylation after lignin depolymerization. Low molecular weight

  11. The use of 13C labeling to enhance the sensitivity of 13C solid-state CPMAS NMR to study polymorphism in low dose solid formulations.

    PubMed

    Booy, Kees-Jan; Wiegerinck, Peter; Vader, Jan; Kaspersen, Frans; Lambregts, Dorette; Vromans, Herman; Kellenbach, Edwin

    2005-02-01

    (13)C labeling was used to enhance the sensitivity of (13)C solid-state NMR to study the effect of tabletting on the polymorphism of a steroidal drug. The steroidal drug Org OD 14 was (13)C labeled and formulated into tablets containing only 0.5-2.5% active ingredient. The tablets were subsequently studied by solid-state (13)C CPMAS NMR. The crystalline form present in tablets could readily be analyzed in tablets. No change in crystalline form was observed as a result of formulation or in subsequent stability studies. Solid-state NMR in combination with (13)C labeling can, in suitable cases, be used as a strategy to study the effect of formulation on the polymorphism of low dose drugs.

  12. Soil pH effect on phosphate induced cadmium precipitation in Arable soil.

    PubMed

    Hong, Chang Oh; Owens, Vance N; Kim, Yong Gyun; Lee, Sang Mong; Park, Hyean Cheal; Kim, Keun Ki; Son, Hong Joo; Suh, Jeong Min; Kim, Pil Joo

    2014-07-01

    The objective of this study was to determine soil pH conditions that allow cadmium (Cd) to precipitate as Cd minerals in phosphate (P) amended soil. Cadmium immobilization could be attributed primarily to Cd adsorption due to increase in pH and negative charge. Soil pH might not affect Cd precipitation as Cd3(PO4)2 by direct reaction of Cd and P in the studied soil, even when soil pH increased up to 9.0. However, Cd might precipitate as CdCO3 with increasing pH up to 9.0 in P untreated soil and up to 8.0 in P treated soil depending on CO2 level.

  13. Enantiomer signature and carbon isotope evidence for the migration and transformation of DDTs in arable soils across China

    NASA Astrophysics Data System (ADS)

    Niu, Lili; Xu, Chao; Zhu, Siyu; Bao, Huiming; Xu, Yang; Li, Hongyi; Zhang, Zhijian; Zhang, Xichang; Qiu, Jiguo; Liu, Weiping

    2016-12-01

    Due to the adverse impact of DDTs on ecosystems and humans, a full fate assessment deems a comprehensive study on their occurrence in soils over a large region. Through a sampling campaign across China, we measured the concentrations, enantiomeric fractions (EFs), compound-specific carbon isotope composition of DDT and its metabolites, and the microbial community in related arable soils. The geographically total DDT concentrations are higher in eastern than western China. The EFs and δ13C of o,p’-DDT in soils from western China show smaller deviations from those of racemic/standard compound, indicating the DDT residues there mainly result from atmospheric transport. However, the sources of DDT in eastern China are mainly from historic application of technical DDTs and dicofol. The inverse dependence of o,p’-DDT and p,p’-DDE on temperature evidences the transformation of parent DDT to its metabolites. Initial usage, abiotic parameters and microbial communities are found to be the main factors influencing the migration and transformation of DDT isomers and their metabolites in soils. In addition, a prediction equation of DDT concentrations in soils based on stepwise multiple regression analysis is developed. Results from this study offer insights into the migration and transformation pathways of DDTs in Chinese arable soils, which will allow data-based risk assessment on their use.

  14. Responses of plasmid-mediated quinolone resistance genes and bacterial taxa to (fluoro)quinolones-containing manure in arable soil.

    PubMed

    Xiong, Wenguang; Sun, Yongxue; Ding, Xueyao; Zhang, Yiming; Zhong, Xiaoxia; Liang, Wenfei; Zeng, Zhenling

    2015-01-01

    The aim of the present study was to investigate the fate of plasmid-mediated quinolone resistance (PMQR) genes and the disturbance of soil bacterial communities posed by (fluoro)quinolones (FQNs)-containing manure in arable soil. Representative FQNs (enrofloxacin (ENR), ciprofloxacin (CIP) and norfloxacin (NOR)), PMQR genes (qepA, oqxA, oqxB, aac(6')-Ib-cr and qnrS) and bacterial communities in untreated soil, +manure and +manure+FQNs groups were analyzed using culture independent methods. The significantly higher abundance of oqxA, oqxB and aac(6')-Ib-cr, and significantly higher abundance of qnrS in +manure group than those in untreated soil disappeared at day 30 and day 60, respectively. All PMQR genes (oqxA, oqxB, aac(6')-Ib-cr and qnrS) dissipated 1.5-1.7 times faster in +manure group than those in +manure+FQNs group. The disturbance of soil bacterial communities posed by FQNs-containing manure was also found. The results indicated that significant effects of PMQR genes (oqxA, oqxB, aac(6')-Ib and qnrS) on arable soils introduced by manure disappeared 2 month after manure application. FQNs introduced by manure slowed down the dissipation of PMQR genes. The presence of high FQNs provided a selective advantage for species affiliated to the phylum including Acidobacteria, Verrucomicrobia and Planctomycetes while suppressing Proteobacteria and Actinobacteria.

  15. Enantiomer signature and carbon isotope evidence for the migration and transformation of DDTs in arable soils across China

    PubMed Central

    Niu, Lili; Xu, Chao; Zhu, Siyu; Bao, Huiming; Xu, Yang; Li, Hongyi; Zhang, Zhijian; Zhang, Xichang; Qiu, Jiguo; Liu, Weiping

    2016-01-01

    Due to the adverse impact of DDTs on ecosystems and humans, a full fate assessment deems a comprehensive study on their occurrence in soils over a large region. Through a sampling campaign across China, we measured the concentrations, enantiomeric fractions (EFs), compound-specific carbon isotope composition of DDT and its metabolites, and the microbial community in related arable soils. The geographically total DDT concentrations are higher in eastern than western China. The EFs and δ13C of o,p’-DDT in soils from western China show smaller deviations from those of racemic/standard compound, indicating the DDT residues there mainly result from atmospheric transport. However, the sources of DDT in eastern China are mainly from historic application of technical DDTs and dicofol. The inverse dependence of o,p’-DDT and p,p’-DDE on temperature evidences the transformation of parent DDT to its metabolites. Initial usage, abiotic parameters and microbial communities are found to be the main factors influencing the migration and transformation of DDT isomers and their metabolites in soils. In addition, a prediction equation of DDT concentrations in soils based on stepwise multiple regression analysis is developed. Results from this study offer insights into the migration and transformation pathways of DDTs in Chinese arable soils, which will allow data-based risk assessment on their use. PMID:27922096

  16. Linking autotrophic activity in environmental samples with specific bacterial taxa by detection of 13C-labelled fatty acids.

    PubMed

    Knief, Claudia; Altendorf, Karlheinz; Lipski, André

    2003-11-01

    A method for the detection of physiologically active autotrophic bacteria in complex microbial communities was developed based on labelling with the stable isotope 13C. Labelling of autotrophic nitrifying, sulphur-oxidizing and iron-oxidizing populations was performed in situ by incubation with NaH[13C]O3. Incorporated label into fatty acid methyl esters (FAMEs) was detected and quantified using gas chromatography-mass spectrometry in single ion monitoring mode. Before the analyses of different environmental samples, the protocol was evaluated in pure culture experiments. In different environmental samples a selective labelling of fatty acids demonstrated which microbial taxa were responsible for the respective chemolithoautotrophic activity. The most strongly labelled fatty acids of a sample from a sulphide treating biofilter from an animal rendering plant were cis-7-hexadecenoic acid (16:1 cis7) and 11-methyl hexadecanoic acid (16:0 11methyl), which are as-yet not known for any sulphide-oxidizing autotroph. The fatty acid labelling pattern of an experimental biotrickling filter sample supplied with dimethyl disulphide clearly indicated the presence and activity of sulphide-oxidizing bacteria of the genus Thiobacillus. For a third environmental sample from an acid mining lake sediment, the assignment of autotrophic activity to bacteria of the genus Leptospirillum but not to Acidithiobacillus could be made by this method, as the fatty acid patterns of these bacteria show clear differences.

  17. Determination of sup 13 C labeling pattern of citric acid cycle intermediates by gas chromatography-mass spectrometry

    SciTech Connect

    Di Donato, L.; Montgomery, J.A.; Des Rosiers, C.; David, F.; Garneau, M.; Brunengraber, H. )

    1990-02-26

    Investigations of the regulation of the citric acid cycle require determination of labeling patterns of cycle intermediates. These were assayed to date, using infusion of: (i) ({sup 14}C)tracer followed by chemical degradation of intermediates and (ii) ({sup 13}C)tracer followed by NMR analysis of intermediates. The authors developed a strategy to analyze by GC-MS the ({sup 13}C) labeling pattern of {mu}mole samples of citrate (CIT), isocitrate (ICIT), 2-ketoglutarate (2-KG), glutamate (GLU) and glutamine (GLN). These are enzymatically or chemically converted to 2-KG, ICIT, 4-aminobutyrate (GABA) and 2-hydroxyglutarate (2-OHG). GC-MS analyses of TMS or TBDMS derivatives of these compounds yield the enrichment of each carbon. The authors confirmed the identity of each fragment using the spectra of (1-{sup 13}C), (5-{sup 13}C), (2,3,3,4,4-{sup 2}H{sub 5})glutamate and (1-{sup 13}C), (1,4-{sup 13}C)GABA.

  18. Root and nodule growth in Pisum sativum L. in relation to photosynthesis: analysis using 13C-labelling.

    PubMed

    Voisin, A S; Salon, C; Jeudy, C; Warembourg, F R

    2003-10-01

    The effect of the nitrogen source (gaseous nitrogen, N2, or nitrate ions, NO3-) on the use of carbon (C) for root and nodule growth of pea (Pisum sativum L.) was investigated using 13C-labelling of assimilated CO2 at various stages of growth. Nitrate supply and growing conditions (sowing dates, air CO2 concentration) were varied to alter photosynthetic rates. Nodules are the sink with the highest demand for C in both the vegetative and flowering stages, growing at the expense of shoot and root in the vegetative stage, but only at the expense of roots at flowering. Until flowering, the addition of C into root and nodule biomass was linearly related to pre-existing biomass, thus determining net sink strengths which decreased with root and nodule age. Nodule growth patterns did not depend on the N source, whereas root growth was increased by nitrate when nodule biomass was low. At seed filling, the increase in C of biomass of the root system was no longer related to pre-existing biomass and C was preferentially diverted to roots of plants assimilating nitrate, or to nodules for plants fixing N2.

  19. Tracing metabolic pathways of lipid biosynthesis in ectomycorrhizal fungi from position-specific 13C-labelling in glucose.

    PubMed

    Scandellari, Francesca; Hobbie, Erik A; Ouimette, Andrew P; Stucker, Valerie K

    2009-12-01

    Six position-specific (13)C-labelled isotopomers of glucose were supplied to the ectomycorrhizal fungi Suillus pungens and Tricholoma flavovirens. From the resulting distribution of (13)C among fungal PLFAs, the overall order and contribution of each glucose atom to fatty acid (13)C enrichment was: C6 (approximately 31%) > C5 (approximately 25%) > C1 (approximately 18%) > C2 (approximately 18%) > C3 (approximately 8%) > C4 (approximately 1%). These data were used to parameterize a metabolic model of the relative fluxes from glucose degradation to lipid synthesis. Our data revealed that a higher amount of carbon is directed to glycolysis than to the oxidative pentose phosphate pathway (60% and 40% respectively) and that a significant part flows through these pathways more than once (73%) due to the reversibility of some glycolysis reactions. Surprisingly, 95% of carbon cycled through glyoxylate prior to incorporation into lipids, possibly to consume the excess of acetyl-CoA produced during fatty acid turnover. Our approach provides a rigorous framework for analysing lipid biosynthesis in fungi. In addition, this approach could ultimately improve the interpretation of isotopic patterns at natural abundance in field studies.

  20. High resolution 4D HPCH experiment for sequential assignment of (13)C-labeled RNAs via phosphodiester backbone.

    PubMed

    Saxena, Saurabh; Stanek, Jan; Cevec, Mirko; Plavec, Janez; Koźmiński, Wiktor

    2015-11-01

    The three-dimensional structure determination of RNAs by NMR spectroscopy requires sequential resonance assignment, often hampered by assignment ambiguities and limited dispersion of (1)H and (13)C chemical shifts, especially of C4'/H4'. Here we present a novel through-bond 4D HPCH NMR experiment involving phosphate backbone where C4'-H4' correlations are resolved along the (1)H3'-(31)P spectral planes. The experiment provides high peak resolution and effectively removes ambiguities encountered during assignments. Enhanced peak dispersion is provided by the inclusion of additional (31)P and (1)H3' dimensions and constant-time evolution of chemical shifts. High spectral resolution is obtained by using non-uniform sampling in three indirect dimensions. The experiment fully utilizes the isotopic (13)C-labeling with evolution of C4' carbons. Band selective (13)C inversion pulses are used to achieve selectivity and prevent signal dephasing due to the C4'-C3' and C4'-C5' homonuclear couplings. Multiple quantum line narrowing is employed to minimize sensitivity loses. The 4D HPCH experiment is verified and successfully applied to a non-coding 34-nt RNA consisting typical structure elements and a 14-nt RNA hairpin capped by cUUCGg tetraloop.

  1. Metabolic network analysis of Bacillus clausii on minimal and semirich medium using (13)C-labeled glucose.

    PubMed

    Christiansen, Torben; Christensen, Bjarke; Nielsen, Jens

    2002-04-01

    Using (13)C-labeled glucose fed to the facultative alkalophilic Bacillus clausii producing the alkaline serine protease Savinase, the intracellular fluxes were quantified in continuous cultivation and in batch cultivation on a minimal medium. The flux through the pentose phosphate pathway was found to increase with increasing specific growth rate but at a much lower level than previously reported for Bacillus subtilis. Two futile cycles in the pyruvate metabolism were included in the metabolic network. A substantial flux in the futile cycle involving malic enzyme was estimated, whereas only a very small or zero flux through PEP carboxykinase was estimated, indicating that the latter enzyme was not active during growth on glucose. The uptake of the amino acids in a semirich medium containing 15 of the 20 amino acids normally present in proteins was estimated using fully labeled glucose in batch cultivations. It was found that leucine, isoleucine, and phenylalanine were taken up from the medium and not synthesized de novo from glucose. In contrast, serine and threonine were completely synthesized from other metabolites and not taken up from the medium. Valine, proline, and lysine were partly taken up from the medium and partly synthesized from glucose. The metabolic network analysis was extended to include analysis of growth on the semirich medium containing amino acids, and the metabolic flux distribution on this medium was estimated and compared with growth on minimal medium.

  2. Effective Estimation of Dynamic Metabolic Fluxes Using 13C Labeling and Piecewise Affine Approximation: From Theory to Practical Applicability

    PubMed Central

    Schumacher, Robin; Wahl, S. Aljoscha

    2015-01-01

    The design of microbial production processes relies on rational choices for metabolic engineering of the production host and the process conditions. These require a systematic and quantitative understanding of cellular regulation. Therefore, a novel method for dynamic flux identification using quantitative metabolomics and 13C labeling to identify piecewise-affine (PWA) flux functions has been described recently. Obtaining flux estimates nevertheless still required frequent manual reinitalization to obtain a good reproduction of the experimental data and, moreover, did not optimize on all observables simultaneously (metabolites and isotopomer concentrations). In our contribution we focus on measures to achieve faster and robust dynamic flux estimation which leads to a high dimensional parameter estimation problem. Specifically, we address the following challenges within the PWA problem formulation: (1) Fast selection of sufficient domains for the PWA flux functions, (2) Control of over-fitting in the concentration space using shape-prescriptive modeling and (3) robust and efficient implementation of the parameter estimation using the hybrid implicit filtering algorithm. With the improvements we significantly speed up the convergence by efficiently exploiting that the optimization problem is partly linear. This allows application to larger-scale metabolic networks and demonstrates that the proposed approach is not purely theoretical, but also applicable in practice. PMID:26690237

  3. Asymmetry of (13)C labeled 3-pyruvate affords improved site specific labeling of RNA for NMR spectroscopy.

    PubMed

    Thakur, Chandar S; Dayie, T Kwaku

    2011-12-01

    Selective isotopic labeling provides an unparalleled window within which to study the structure and dynamics of RNAs by high resolution NMR spectroscopy. Unlike commonly used carbon sources, the asymmetry of (13)C-labeled pyruvate provides selective labeling in both the ribose and base moieties of nucleotides using E. coli variants, that until now were not feasible. Here we show that an E. coli mutant strain that lacks succinate and malate dehydrogenases (DL323) and grown on [3-(13)C]-pyruvate affords ribonucleotides with site specific labeling at C5' (~95%) and C1' (~42%) and minimal enrichment elsewhere in the ribose ring. Enrichment is also achieved at purine C2 and C8 (~95%) and pyrimidine C5 (~100%) positions with minimal labeling at pyrimidine C6 and purine C5 positions. These labeling patterns contrast with those obtained with DL323 E. coli grown on [1, 3-(13)C]-glycerol for which the ribose ring is labeled in all but the C4' carbon position, leading to multiplet splitting of the C1', C2' and C3' carbon atoms. The usefulness of these labeling patterns is demonstrated with a 27-nt RNA fragment derived from the 30S ribosomal subunit. Removal of the strong magnetic coupling within the ribose and base leads to increased sensitivity, substantial simplification of NMR spectra, and more precise and accurate dynamic parameters derived from NMR relaxation measurements. Thus these new labels offer valuable probes for characterizing the structure and dynamics of RNA that were previously limited by the constraint of uniformly labeled nucleotides.

  4. Identification of aquatically available carbon from algae through solution-state NMR of whole (13)C-labelled cells.

    PubMed

    Akhter, Mohammad; Dutta Majumdar, Rudraksha; Fortier-McGill, Blythe; Soong, Ronald; Liaghati-Mobarhan, Yalda; Simpson, Myrna; Arhonditsis, George; Schmidt, Sebastian; Heumann, Hermann; Simpson, André J

    2016-06-01

    Green algae and cyanobacteria are primary producers with profound impact on food web functioning. Both represent key carbon sources and sinks in the aquatic environment, helping modulate the dissolved organic matter balance and representing a potential biofuel source. Underlying the impact of algae and cyanobacteria on an ecosystem level is their molecular composition. Herein, intact (13)C-labelled whole cell suspensions of Chlamydomonas reinhardtii, Chlorella vulgaris and Synechocystis were studied using a variety of 1D and 2D (1)H/(13)C solution-state nuclear magnetic resonance (NMR) spectroscopic experiments. Solution-state NMR spectroscopy of whole cell suspensions is particularly relevant as it identifies species that are mobile (dissolved or dynamic gels), 'aquatically available' and directly contribute to the aquatic carbon pool upon lysis, death or become a readily available food source on consumption. In this study, a wide range of metabolites and structural components were identified within the whole cell suspensions. In addition, significant differences in the lipid/triacylglyceride (TAG) content of green algae and cyanobacteria were confirmed. Mobile species in algae are quite different from those in abundance in 'classic' dissolved organic matter (DOM) indicating that if algae are major contributors to DOM, considerable selective preservation of minor components (e.g. sterols) or biotransformation would have to occur. Identifying the metabolites and dissolved components within algal cells by NMR permits future studies of carbon transfer between species and through the food chain, whilst providing a foundation to better understand the role of algae in the formation of DOM and the sequestration/transformation of carbon in aquatic environments.

  5. Biomineralization of 1,4-dioxane in Pure Culture, Microcosm, and Column Studies Using 13C Labeling

    NASA Astrophysics Data System (ADS)

    Rolston, H. M.; Azizian, M.; Hyman, M. R.; Semprini, L.

    2016-12-01

    1,4-dioxane (1,4-D), a probable human carcinogen at low (< 1ppb) concentrations, is a widely occurring groundwater contaminant due to its use as a stabilizer for chlorinated solvents. Aerobic cometabolism, the use of a primary substrate to induce the production of microbial enzymes capable of transforming contaminants into innocuous products, is a promising in-situ treatment strategy for 1,4-D because it has the potential to mineralize trace 1,4-D concentrations to carbon dioxide (CO2). Previous work has confirmed the bacterium Rhodococcus rhodochrous (strain ATCC 21198) will transform 1,4-D when grown on isobutane. In this study, 13C uniformly labeled 1,4-D was used to determine the extent to which strain ATCC 21198 biomineralizes 1,4-D to CO2. Batch experiments have been conducted with pure culture 21198 and in microcosms constructed with aquifer sediments. The rate of resting cell transformation of 1,4-D by ATCC 21198 was over 100 times faster than the rate of CO2 accumulation, indicating the presence of intermediates that were slowly mineralized to CO2 . In microcosms, the use of isobutane as a primary substrate effectively stimulated the native microbial community to transform 1,4-D. Microcosms were also bioaugmented with ATCC 21198. After an initial lag and subsequent additions of isobutane, transformation rates in the native microcosms approached those of the bioaugmented microcosms. Cometabolically active microbes survived several periods of starvation in all microcosms, and nutrient amendment allowed for sustained transformation rates. 13C labeled 1,4-D is currently being used to determine the rates and extents of biomineralization in the microcosms. Column studies are also being conducted to evaluate cometabolism and biominerazation potential of isobutane as a biostimulant and 21198 for bioaugmentation under geochemical and flow conditions more representative of in-situ bioremediation.

  6. The impact of management and climate on soil nitric oxide fluxes from arable land in the Southern Ukraine

    NASA Astrophysics Data System (ADS)

    Medinets, Sergiy; Gasche, Rainer; Skiba, Ute; Medinets, Volodymyr; Butterbach-Bahl, Klaus

    2016-07-01

    NO fluxes from soils are a significant source for tropospheric NOx, though global and regional estimates of the soil source strength are constrained by the paucity of measurements. In a continuous 18 month effort (2012-2014) soil NO fluxes from an intensively managed arable site in the black soil region of the Southern Ukraine (Odessa region) were measured using an automated dynamic chamber system. Measurements revealed three periods of peak NO emissions (fertigation, re-wetting of soils, and to a lower extend during winter), with a pulse emission peak during soil re-wetting in summer of 88.4 μg N m-2 h-1. The mean annual NO flux was 5.1 ± 8.9 μg N m-2 h-1 and total annual NO emissions were 0.44 ± 0.78 kg N ha-1 yr-1. The fertilizer induced emission factor for NO was 0.63% under beetroot. The combined effect of soil temperature, soil moisture and soil DIN (NH4+ and NO3-) concentrations were identified as drivers of the temporal and spatial variability of soil NO fluxes. This work shows that long-term measurements are needed for estimating annual fluxes and the importance of soils as a source for tropospheric NOx as the contribution of different seasons and crop growing periods to the annual budget differed markedly.

  7. Stabilization of glucose-C in microbial cell membranes (PLFA) and cell walls (amino sugars) evaluated by 13C-labelling in a field experiment

    NASA Astrophysics Data System (ADS)

    Gunina, Anna; Kuzyakov, Yakov; Glaser, Bruno

    2015-04-01

    Microorganisms control carbon (C) cycle and strongly contribute to formation of soil organic matter. Strong differences in the turnover of microbial groups and cellular compounds complicate the assessment of their contribution to microbial food webs and C sequestration in soil in situ. The uptake and incorporation of 13C labeled glucose by microbial groups were traced during 50 days after the labeling under field conditions. 13C was analysed: i) in the cytosolic pool by chloroform fumigation extraction, ii) in cell membranes by phospholipid fatty acids (PLFA), iii) in cell walls by amino sugars, and iv) remaining in bulk soil. This allowed tracing C in microbial groups as well as cellular compounds. Mean residence times (MRT) of C in PLFA and the cytosol were 47 and 150 days, respectively. Such long cytosol MRT depends on its heterogeneous composition, which includes high and low molecular weight organics. Amino sugars were mainly originated from microbial residues and thus, observation periods higher than 1 year are required for estimation of their MRT. Relative 13C incorporation (13C portion in total pool C) was the highest for PLFAs (~1.5% at day 3), whereas 13C content of the cytosol and amino sugars was one and two orders of magnitude less, respectively. Relative 13C incorporation into amino sugars of living microorganisms showed only 0.57% on day 3. Therefore, the turnover of cell membrane components is two times faster than that of cell walls, even in living microorganisms. Both PLFAs and amino sugars showed that glucose C was preferentially used by bacteria. 13C incorporation into bacterial cell walls and membranes decreased with time, but increased or remained constant for fungi, reflecting faster turnover of bacteria than fungi. Consequently, bacteria contribute more to the decomposition of low molecular weight organics, whereas fungi consume bacterial products or necromass and contribute more to long-term C stabilisation. Thus, tracing of 13C in cellular

  8. Soil bacterial and fungal communities across a pH gradient in an arable soil.

    PubMed

    Rousk, Johannes; Bååth, Erland; Brookes, Philip C; Lauber, Christian L; Lozupone, Catherine; Caporaso, J Gregory; Knight, Rob; Fierer, Noah

    2010-10-01

    Soils collected across a long-term liming experiment (pH 4.0-8.3), in which variation in factors other than pH have been minimized, were used to investigate the direct influence of pH on the abundance and composition of the two major soil microbial taxa, fungi and bacteria. We hypothesized that bacterial communities would be more strongly influenced by pH than fungal communities. To determine the relative abundance of bacteria and fungi, we used quantitative PCR (qPCR), and to analyze the composition and diversity of the bacterial and fungal communities, we used a bar-coded pyrosequencing technique. Both the relative abundance and diversity of bacteria were positively related to pH, the latter nearly doubling between pH 4 and 8. In contrast, the relative abundance of fungi was unaffected by pH and fungal diversity was only weakly related with pH. The composition of the bacterial communities was closely defined by soil pH; there was as much variability in bacterial community composition across the 180-m distance of this liming experiment as across soils collected from a wide range of biomes in North and South America, emphasizing the dominance of pH in structuring bacterial communities. The apparent direct influence of pH on bacterial community composition is probably due to the narrow pH ranges for optimal growth of bacteria. Fungal community composition was less strongly affected by pH, which is consistent with pure culture studies, demonstrating that fungi generally exhibit wider pH ranges for optimal growth.

  9. Lateral Distribution of Polycyclic Aromatic Hydrocarbons and Spherical Magnetic Particles within Soil Catenas of the Arable Watershed (Tver Region, Russia)

    NASA Astrophysics Data System (ADS)

    Koshovskii, Timur; Zhidkin, Andrei; Gennadiev, Alexander

    2015-04-01

    Polycyclic aromatic hydrocarbons (PAHs) are very dangerous substances because of their carcinogenic properties. It is important to know the features of PAHs transport and accumulation in soils, especially on agricultural lands. Unfortunately this scientific problem is studied not enough. It is known that predominantly PAHs in soils are sorbed on solid phase particles [2], so redistribution of PAHs should be carried out with transport of soil solid phase matter. For the purpose of assessment of connections between PAHs and soil solid phase transport the lateral distribution of PAHs and spherical magnetic particles (SMP) as tracers of soil solid phase migration has been compared. SMP is the component of fly ash which is used last two decades for quantitative assessment of soil erosion [1]. Studies were conducted in small watershed of south-taiga zone in European part of Russia in Tver region. The watershed has 53 ha, steep slopes, less 50, convex and convexo-concave shapes with ridges and runnels. The watershed lands were plowed up for the last 350-400 years until 1995 year. Predominant soils are Umbric Albeluvisols. Soil samples were selected at four soil catenas (30 points with average distance about 70 meters). Two catenas were on opposite slopes near the road, and other two catenas were located on the opposite slopes (250-400 m from the road). It is revealed that average concentration of PAHs in studied soils are 105 ng/g, and varies from 11 to 770 ng/g, with coefficient of variation 143%. Lateral distribution of PAHs and SMP differs within different catenas, because of various factors influence on PAHs concentrations: 1) amounts of PAHs income, depending on the distance from the source; 2) homogenization of PAHs concentrations within arable layer because of mixing the soil matter due to plowing; 3) vertical transport of PAHs in subarable layers is also connected with plowing and bioturbation; 4) rates of decomposition of PAHs in arable layer, depending on

  10. Structural properties of dissolved organic carbon in deep horizons of an arable soil.

    NASA Astrophysics Data System (ADS)

    Lavaud, A.; Croué, Jp; Berwick, L.; Steffens, M.; Chabbi, A.

    2010-05-01

    The objective of this work is to quantity the DOC that percolates in deep horizons of an arable soil, and to characterize the structural properties of the main fractions. The study was conducted on the long term observatory for environmental research- biogeochemical cycles and biodiversity Lusignan site-France. DOC collected using lysimeter plates inserted to a depth of 105 cm was fractionated into 3 fractions using the two column array of XAD-8 and XAD-4 resins. The HPO (hydrophobic) fraction (i.e. humic substances) isolated from the XAD-8 resin, the TPH (Transphilic) fraction from the XAD-4 resin and the HPI (hydrophilic) fraction which corresponds to the DOC that does not adsorbed onto the two resins under the acid condition used (pH 2). DOM adsorbed onto the resins is recovered with a 75%/25% acetonitrile/water mixture and lyophilized. The hydrophilic fraction is purified according the protocol proposed by Aiken and Leenheer (1993). The isolated fractions were subjected to several characterization tools: UV/Vis, fluorescence EEM, HPSEC/UV/DOC, 13C NMR, 14C dating, FT-IR, pyrolysis, thermochemolysis and MSSV GC/MS. The DOC content ranged from 1 to 2.5 mg / L between winter and the middle of spring and then to 4-5 mg / L in summer time. For all isolated fractions HPSEC analyses indicated the predominance of low molecular structures with a low aromatic character. Fluorescence EEM confirmed the non-humic character of the DOM. 13C-NMR spectra showed that the aromatic character decreased from HPO to TPH, and HPI character. Molecular size follows the same trend. HPI DOM was found to be strongly enriched in carboxyl groups. The 14C concentration of the HPO fraction corresponds to an apparent calibrated age around AD 1500. For the same fraction isolated from the 0 - 30 cm horizon, the measured 14C concentration 131.9 pMC corresponds to that in the atmosphere around AD 1978. Significant input of terpenoid derived organic matter was confirmed in the HPO fraction of DOC

  11. Retrobiosynthetic NMR studies with 13C-labeled glucose. Formation of gallic acid in plants and fungi.

    PubMed

    Werner, I; Bacher, A; Eisenreich, W

    1997-10-10

    The biosynthesis of gallic acid was studied in cultures of the fungus Phycomyces blakesleeanus and in leaves of the tree Rhus typhina. Fungal cultures were grown with [1-13C]glucose or with a mixture of unlabeled glucose and [U-13C6]glucose. Young leaves of R. typhina were kept in an incubation chamber and were supplied with a solution containing a mixture of unlabeled glucose and [U-13C6]glucose via the leaf stem. Isotope distributions in isolated gallic acid and aromatic amino acids were analyzed by one-dimensional 1H and 13C NMR spectroscopy. A quantitative analysis of the complex isotopomer composition of metabolites was obtained by deconvolution of the 13C13C coupling multiplets using numerical simulation methods. This approach required the accurate analysis of heavy isotope chemical shift effects in a variety of different isotopomers and the analysis of long range 13C13C coupling constants. The resulting isotopomer patterns were interpreted using a retrobiosynthetic approach based on a comparison between the isotopomer patterns of gallic acid and tyrosine. The data show that both in the fungus and in the plant all carbon atoms of gallic acid are biosynthetically equivalent to carbon atoms of shikimate. Notably, the carboxylic group of gallic acid is derived from the carboxylic group of an early intermediate of the shikimate pathway and not from the side chain of phenylalanine or tyrosine. It follows that the committed precursor of gallic acid is an intermediate of the shikimate pathway prior to prephenate or arogenate, most probably 5-dehydroshikimate. A formation of gallic acid via phenylalanine, the lignin precursor, caffeic acid, or 3,4, 5-trihydroxycinnamic acid can be ruled out as major pathways in the fungus and in young leaves of R. typhina. The incorporation of uniformly 13C-labeled glucose followed by quantitative NMR analysis of isotopomer patterns is suggested as a general method for biosynthetic studies. As shown by the plant experiment, this

  12. Atmospheric CO2 level affects plants' carbon use efficiency: insights from a 13C labeling experiment on sunflower stands

    NASA Astrophysics Data System (ADS)

    Gong, Xiaoying; Schäufele, Rudi; Schnyder, Hans

    2015-04-01

    The increase of atmospheric CO2 concentration has been shown to stimulate plant photosynthesis and (to a lesser extent) growth, thereby acting as a possible sink for the additional atmospheric CO2. However, this effect is dependent on the efficiency with which plants convert atmospheric carbon into biomass carbon, since a considerable proportion of assimilated carbon is returned to the atmosphere via plant respiration. As a core parameter for carbon cycling, carbon use efficiency of plants (CUE, the ratio of net primary production to gross primary production) quantifies the proportion of assimilated carbon that is incorporated into plant biomass. CUE has rarely been assessed based on measurements of complete carbon balance, due to methodological difficulties in measuring respiration rate of plants in light. Moreover, foliar respiration is known to be inhibited in light, thus foliar respiration rate is generally lower in light than in dark. However, this phenomenon, termed as inhibition of respiration in light (IRL), has rarely been assessed at the stand-scale and been incorporated into the calculation of CUE. Therefore, how CUE responses to atmospheric CO2 levels is still not clear. We studied CUE of sunflower stands grown at sub-ambient CO2 level (200 μmol mol-1) and elevated CO2 level (1000 μmol mol-1) using mesocosm-scale gas exchange facilities which enabled continuous measurements of 13CO2/12CO2 exchange. Appling steady-state 13C labeling, fluxes of respiration and photosynthesis in light were separated, and tracer kinetic in respiration was analyzed. This study provides the first data on CUE at a mesocosm-level including respiration in light in different CO2 environments. We found that CUE of sunflower was lower at an elevated CO2 level than at a sub-ambient CO2 level; and the ignorance of IRL lead to erroneous estimations of CUE. Variation in CUE at atmospheric CO2 levels was attributed to several mechanisms. In this study, CO2 enrichment i) affected the

  13. Assessment of pesticide residues in two arable soils from the semi-arid and subtropical regions of China.

    PubMed

    Wang, Ligang; Zhao, Zhenhua; Jiang, Xin; Wu, Jinshui; Martens, Dieter

    2005-10-01

    The residues of 31 chlorinated hydrocarbons (CHCs), 25 chlorophenols (CPs), 30 organophosphorus (OP) and pyrethroid (PRT) in two arable soils from the semi-arid and subtropical regions of China were assessed. Data obtained indicate that the main compounds of CHC pesticide residues in the semi-arid soil were 4,4'-DDE (25.3 ng/g) and beta-HCH (14.1 ng/g), which totally accounted to about 90% of total CHC residues detected. The total content of CHC residues detected in the subtropical soil was only 3.1 ng/g, of which approximately 50% was beta-HCH. However, the total content of CP residues in both of the soils was about 11 ng/g. In the semi-arid soil, only parathion-methyl amongst the 30 compounds of OP and PRT residues was detected (32.5 ng/g), whilst malathion and parathion-methyl (8.7 and 17.7 ng/g, respectively) detected in the subtropical soil. Based on these results, it was suggested the environmental risk of pesticide residues ranked in an order as CHCs (mainly as 4,4'-DDE, beta-HCH) > OP (parathion-methyl) > CPs for the semi-arid soil, and as OPs (parathion-methyl and malathion) > CPs > CHCs (beta-HCH) for the subtropical soil.

  14. Changes in soil water balance following afforestation of former arable soils in Denmark as evaluated using the DAISY model

    NASA Astrophysics Data System (ADS)

    Salazar, Osvaldo; Hansen, Søren; Abrahamsen, Per; Hansen, Karin; Gundersen, Per

    2013-03-01

    SummaryLand use change alters water and element cycles, but the changes in these cycles after conversion, for example, from cropland to forest are not fully described in hydrological and nutrient transport models, which usually describe either cropland or forest stands. In the European Union future afforestation is likely to occur on abandoned cropland, and evaluation of the future impacts of this land use change will require projections with models that include combined cropland-forest modules. This study used the agro-based DAISY model (Version 4.93) to investigate changes in the soil water balance over four decades following afforestation of a homogeneous area of former arable land on a sandy loam in Denmark. Hydrological data collected during nine hydrological years (April 2001-March 2010) were used to test the DAISY model. Monthly data on soil water content at 0-90 cm used for calibration were available from April 2001 to December 2002 for six monoculture stands of oak (age 8, 22 and 31 years) and Norway spruce (age 4, 13 and 32 years). Model performance was evaluated by considering uncertainties in model inputs using the Generalised Likelihood Uncertainty Estimation (GLUE) procedure. The GLUE estimates obtained (uncertainty bands 5% and 95%) agreed satisfactorily with measured monthly soil water content during the calibration period (April 2001-December 2002). Similarly, in the oldest oak stand, long-term monitoring observations and predictions of monthly water content were in satisfactory agreement during the period January 2003-March 2010). Sensitivity analysis showed that the DAISY model was most sensitive to the potential evapotranspiration factor and soil hydraulic parameters included in the Campbell model. Simulation results during nine hydrological years showed that 16-25% of incoming precipitation led to water recharge in the spruce stands, while the corresponding range for oak stands was 25-27%. A 35-year DAISY simulation revealed that Norway spruce

  15. Influence of long-term land use (arable and forest) and soil mineralogy on organic carbon stocks as well as composition and stability of soil organic matter

    NASA Astrophysics Data System (ADS)

    Kaiser, M.; Ellerbrock, R. H.; Wulf, M.; Dultz, S.; Hierath, C.; Sommer, M.

    2009-04-01

    The function of soils to sequester organic carbon (OC) and their related potential to mitigate the greenhouse effect is strongly affected by land use and soil mineralogy. This study is aimed to clarify long-term impacts of arable and forest land use as well as soil mineralogy on topsoil soil organic carbon (SOC) stocks as well as soil organic matter (SOM) composition and stability. Topsoil samples were taken from deciduous forest and adjacent arable sites (within Germany) that are continuously used for more than 100 years. The soils are different in genesis (Albic and Haplic Luvisol (AL, HL), Colluvic and Haplic Regosol (CR, HR), Haplic and Vertic Cambisol (HC, VC), Haplic Stagnosol (HSt)). First, particulate and water soluble organic matter were separated from the topsoil samples (Ap and Ah horizons). From the remaining solid extraction residues the Na-pyrophosphate soluble organic matter fractions (OM(PY)) were extracted, analysed for its OC content (OC(PY)) and characterized by FTIR spectroscopy and 14C analyses. The SOC stocks calculated for 0-40 cm depth are in general larger for the forest as compared to the adjacent arable soils (except VC). The largest difference between forest and arable topsoils was detected for the HR site (5.9 kg m-2) and seemed to be caused by a two times larger stock of exchangeable Ca of the forest topsoil. For the arable topsoils multiple regression analyses indicate a strong influence of clay, oxalate soluble Al and pyrophosphate soluble Mg on the content of OC(PY) weighted with its C=O content. Such relation is not found for the forest topsoils. Further, a positive relation between Δ14C values of OM(PY) and the following independent variables: (i) specific mineral surface area, (ii) relative C=O group content in OM(PY) and (iii) soil pH is found for the arable topsoils (pH 6.7 - 7.5) suggesting an increase in OM(PY) stability with increasing interactions between OM(PY) and soil mineral surfaces via cation bridging. A similar

  16. Effect of the natural reforestation of an arable land on the organic matter composition in soddy-podzolic soils

    NASA Astrophysics Data System (ADS)

    Erokhova, A. A.; Makarov, M. I.; Morgun, E. G.; Ryzhova, I. M.

    2014-11-01

    The dynamics of the organic matter composition in soddy-podzolic soils during the natural reforestation of an arable land in the southern taiga zone have been discussed. It has been shown that the contents of the total and labile carbon in the old plow horizon increase with the age of the fallow in the chronosequence of soils established in the Parfen'evo district of Kostroma oblast. The parameters characterizing the labile soil organic matter include the contents of the carbon extractable by mild chemical extractants (distilled water, 0.1 M K2SO4 solution, 0.1 M neutral Na4P2O7 solution), the microbial biomass, and the light fraction. The granulo-densimetric fractionation has shown that the contents of carbon in the light and organomineral fractions of the soil vary in the course of the postagrogenic succession. The content of the clay-fraction carbon increases and its portion in the total carbon of the soil decreases at the transition from the plowland to the forest. The reforestation of agrosoddy-podzolic soils enhances the physical protection of the soil organic matter due to the increase in the portion of microaggregate carbon.

  17. Oribatida (Acari) in grassy arable fallows are more affected by soil properties than habitat age and plant species☆

    PubMed Central

    Wissuwa, Janet; Salamon, Jörg-Alfred; Frank, Thomas

    2013-01-01

    Oribatid mites are one of the numerically dominant arthropod groups in soils. They play an important role in soil food webs via regulating the decomposition of organic matter and propagating microorganisms within the soil. To our knowledge, the influence of different plant functional groups on oribatid mites has not been studied in abandoned farmland with undisturbed succession before. The density and assemblage structure of oribatid mites in nine grassy arable fallows relative to three habitat age classes (2–3, 6–8, 12–15 years) and three selected plant species (legume: Medicago sativa, forb: Taraxacum officinale, grass: Bromus sterilis) were investigated in soil associated with single plants. Mite density declined marginally not significant with habitat age because of high abundances of the ubiquitous species Tectocepheus velatus sarekensis and Punctoribates punctum in young and mid-aged fallows and their subsequent decline in old fallows. Oribatid mite density and species assemblage were not affected by plant species. Only P. punctum had significantly higher densities in B. sterilis samples than in T. officinale samples due to a higher amount of fine roots. Distance-based linear models revealed that 65% of the variation in mite assemblage was explained by soil properties, soil type, exposition and geographic position, while habitat age was of minor importance. Canonical correspondence analysis revealed that the mite assemblage was best explained by soil organic and microbial carbon, water content and pH. PMID:26109839

  18. Oribatida (Acari) in grassy arable fallows are more affected by soil properties than habitat age and plant species.

    PubMed

    Wissuwa, Janet; Salamon, Jörg-Alfred; Frank, Thomas

    2013-11-01

    Oribatid mites are one of the numerically dominant arthropod groups in soils. They play an important role in soil food webs via regulating the decomposition of organic matter and propagating microorganisms within the soil. To our knowledge, the influence of different plant functional groups on oribatid mites has not been studied in abandoned farmland with undisturbed succession before. The density and assemblage structure of oribatid mites in nine grassy arable fallows relative to three habitat age classes (2-3, 6-8, 12-15 years) and three selected plant species (legume: Medicago sativa, forb: Taraxacum officinale, grass: Bromus sterilis) were investigated in soil associated with single plants. Mite density declined marginally not significant with habitat age because of high abundances of the ubiquitous species Tectocepheus velatus sarekensis and Punctoribates punctum in young and mid-aged fallows and their subsequent decline in old fallows. Oribatid mite density and species assemblage were not affected by plant species. Only P. punctum had significantly higher densities in B. sterilis samples than in T. officinale samples due to a higher amount of fine roots. Distance-based linear models revealed that 65% of the variation in mite assemblage was explained by soil properties, soil type, exposition and geographic position, while habitat age was of minor importance. Canonical correspondence analysis revealed that the mite assemblage was best explained by soil organic and microbial carbon, water content and pH.

  19. Effect of almond shell biochar addition on the hydro-physical properties of an arable Central Valley soil

    NASA Astrophysics Data System (ADS)

    Lopez, V.; Ghezzehei, T. A.

    2014-12-01

    Biochar is composed of any carbonaceous matter pyrolyzed under low oxygen exposure. Its use as a soil amendment to address soil infertility has been accelerated by studies reporting positive effects of enhanced nutrient retention, cation exchange capacity, microbial activity, and vegetative growth over time. Biochar has also been considered as a carbon sequestration method because of its reported environmental persistence. While the aforementioned effects are positive benefits of biochar's use, its impact on soil physical properties and water flow are equally important in maintaining soil fertility. This study aims to show how soil physical and hydraulic properties change over time with biochar addition. To address these aims, we conducted a 9 week microcosm incubation experiment with local arable loamy sand soils amended with biochar. Biochar was created from locally collected almond shells and differs by pyrolysis temperatures (350°C, 700°C) and size (<250 μm, 1-2mm). Additionally, biochar was applied to soil at a low (10 t/ha) or high (60 t/ha) rates. Changes in soil water flow properties were analyzed by infiltration or pressure cell experiments immediately after creating our soil-biochar mixtures. These experiments were repeated during and after the incubation period to observe if and how flow is altered over time. Following incubation and hydraulic experiments, a water drop penetration time (WDPT) test was conducted to observe any alterations in surface hydrophobicity. Changes in soil physical properties were analyzed by determining content of water stable aggregates remaining after wet sieving. This series of experiments is expected to provide a greater understanding on the impact biochar addition on soil physical and hydraulic properties. Furthermore, it provides insight into whether or not converting local agricultural waste into biochar for soil use will be beneficial, especially in agricultural systems undergoing climate stress.

  20. Streamlined pentafluorophenylpropyl column liquid chromatography-tandem quadrupole mass spectrometry and global (13)C-labeled internal standards improve performance for quantitative metabolomics in bacteria.

    PubMed

    Yang, Song; Sadilek, Martin; Lidstrom, Mary E

    2010-11-19

    Streamlined quantitative metabolomics in central metabolism of bacteria would be greatly facilitated by a high-efficiency liquid chromatography (LC) method in conjunction with accurate quantitation. To achieve this goal, a methodology for LC-tandem quadrupole mass spectrometry (LC-MS/MS) involving a pentafluorophenylpropyl (PFPP) column and culture-derived global (13)C-labeled internal standards (I.Ss.) has been developed and compared to hydrophilic interaction liquid chromatography (HILIC)-MS/MS and published combined two-dimensional gas chromatography and LC methods. All 50 tested metabolite standards from 5 classes (amino acids, carboxylic acids, nucleotides, acyl-CoAs and sugar phosphates) displayed good chromatographic separation and sensitivity on the PFPP column. In addition, many important critical pairs such as isomers/isobars (e.g. isoleucine/leucine, methylsuccinic acid/ethylmalonic acid and malonyl-CoA/3-hydroxybutyryl-CoA) and metabolites of similar structure (e.g. malate/fumarate) were resolved better on the PFPP than on the HILIC column. Compared to only one (13)C-labeled I.S., the addition of global (13)C-labeled I.Ss. improved quantitative linearity and accuracy. PFPP-MS/MS with global (13)C-labeled I.Ss. allowed the absolute quantitation of 42 metabolite pool sizes in Methylobacterium extorquens AM1. A comparison of metabolite level changes published previously for ethylamine (C2) versus succinate (C4) cultures of M. extorquens AM1 indicated a good consistency with the data obtained by PFPP-MS/MS, suggesting this single approach has the capability of providing comprehensive metabolite profiling similar to the combination of methods. The more accurate quantification obtained by this method forms a fundamental basis for flux measurements and can be used for metabolism modeling in bacteria in future studies. Published by Elsevier B.V.

  1. Application of Metabolic 13C Labeling in Conjunction with High-Field Nuclear Magnetic Resonance Spectroscopy for Comparative Conformational Analysis of High Mannose-Type Oligosaccharides

    PubMed Central

    Kamiya, Yukiko; Yanagi, Kotaro; Kitajima, Toshihiko; Yamaguchi, Takumi; Chiba, Yasunori; Kato, Koichi

    2013-01-01

    High mannose-type oligosaccharides are enzymatically trimmed in the endoplasmic reticulum, resulting in various processing intermediates with exposed glycotopes that are recognized by a series of lectins involved in glycoprotein fate determination in cells. Although recent crystallographic data have provided the structural basis for the carbohydrate recognition of intracellular lectins, atomic information of dynamic oligosaccharide conformations is essential for a quantitative understanding of the energetics of carbohydrate–lectin interactions. Carbohydrate NMR spectroscopy is useful for characterizing such conformational dynamics, but often hampered by poor spectral resolution and lack of recombinant techniques required to produce homogeneous glycoforms. To overcome these difficulties, we have recently developed a methodology for the preparation of a homogeneous high mannose-type oligosaccharide with 13C labeling using a genetically engineered yeast strain. We herein successfully extended this method to result in the overexpression of 13C-labeled Man9GlcNAc2 (M9) with a newly engineered yeast strain with the deletion of four genes involved in N-glycan processing. This enabled high-field NMR analyses of 13C-labeled M9 in comparison with its processing product lacking the terminal mannose residue ManD2. Long-range NOE data indicated that the outer branches interact with the core in both glycoforms, and such foldback conformations are enhanced upon the removal of ManD2. The observed conformational variabilities might be significantly associated with lectins and glycan-trimming enzymes. PMID:24970159

  2. Fast Volumetric Spatial-Spectral MR Imaging of Hyperpolarized 13C-Labeled Compounds using Multiple Echo 3D bSSFP

    PubMed Central

    Perman, William H.; Bhattacharya, Pratip; Leupold, Jochen; Lin, Alexander P.; Harris, Kent C.; Norton, Valerie A.; Hovener, Jan B.; Ross, Brian D.

    2010-01-01

    PURPOSE The goal of this work was to develop a fast 3D chemical shift imaging technique for the non-invasive measurement of hyperpolarized 13C-labeled substrates and metabolic products at low concentration. MATERIALS AND METHODS Multiple echo 3D balanced steady state MR imaging (ME-3DbSSFP) was performed in vitro on a syringe containing hyperpolarized [1,3,3-2H3; 1-13C]2-hydroxyethylpropionate (HEP) adjacent to a 13C-enriched acetate phantom, and in vivo on a rat before and after IV injection of hyperpolarized HEP at 1.5 T. Chemical shift images of the hyperpolarized HEP were derived from the multiple echo data by Fourier transformation along the echoes on a voxel by voxel basis for each slice of the 3D data set. RESULTS ME-3DbSSFP imaging was able to provide chemical shift images of hyperpolarized HEP in vivo, and in a rat with isotropic 7 mm spatial resolution, 93 Hz spectral resolution and 16 second temporal resolution for a period greater than 45 seconds. CONCLUSION Multiple echo 3D bSSFP imaging can provide chemical shift images of hyperpolarized 13C-labeled compounds in vivo with relatively high spatial resolution and moderate spectral resolution. The increased signal-to-noise ratio (SNR) of this 3D technique will enable the detection of hyperpolarized 13C-labeled metabolites at lower concentrations as compared to a 2D technique. PMID:20171034

  3. Response of microbial community of organic-matter-impoverished arable soil to long-term application of soil conditioner derived from dynamic rapid fermentation of food waste.

    PubMed

    Hou, Jiaqi; Li, Mingxiao; Mao, Xuhui; Hao, Yan; Ding, Jie; Liu, Dongming; Xi, Beidou; Liu, Hongliang

    2017-01-01

    Rapid fermentation of food waste can be used to prepare soil conditioner. This process consumes less time and is more cost-effective than traditional preparation technology. However, the succession of the soil microbial community structure after long-term application of rapid fermentation-derived soil conditioners remains unclear. Herein, dynamic rapid fermentation (DRF) of food waste was performed to develop a soil conditioner and the successions and diversity of bacterial communities in an organic-matter-impoverished arable soil after six years of application of DRF-derived soil conditioner were investigated. Results showed that the treatment increased soil organic matter (SOM) accumulation and strawberry yield by 5.3 g/kg and 555.91 kg/ha, respectively. Proteobacteria, Actinobacteria, Acidobacteria, and Firmicutes became the dominant phyla, occupying 65.95%-77.52% of the bacterial sequences. Principal component analysis (PCA) results showed that the soil bacterial communities were largely influenced by the treatment. Redundancy analysis (RDA) results showed that the relative abundances of Gemmatimonadetes, Chloroflexi, Verrucomicrobia, Nitrospirae, and Firmicutes were significantly correlated with soil TC, TN, TP, NH4+-N, NO3--N, OM, and moisture. These communities were all distributed in the soil samples collected in the sixth year of application. Long-term treatment did not enhance the diversity of bacterial species but significantly altered the distribution of major functional bacterial communities in the soils. Application of DRF-derived soil conditioner could improve the soil quality and optimize the microbial community, ultimately enhancing fruit yields.

  4. Effect of Phosphate Addition on Cadmium Precipitation and Adsorption in Contaminated Arable Soil with a Low Concentration of Cadmium.

    PubMed

    Kim, Sung Un; Owens, Vance N; Kim, Yong Gyun; Lee, Sang Mong; Park, Hyean Cheal; Kim, Keun Ki; Son, Hong Joo; Hong, Chang Oh

    2015-11-01

    The objectives of this study were to determine (1) the phosphorus (P) level required to induce cadmium (Cd) precipitation in a contaminated arable soil with low concentrations of Cd and (2) the primary mechanism of Cd immobilization at different P levels. Phosphorus was added at levels of 0 800, 1600, and 16,000 mg P kg(-1) to a soil containing 5.57 mg Cd kg(-1). The concentration of 1 M NH4OAc extractable Cd decreased significantly with P levels up to 1600 mg kg(-1) due to an increase in soil pH and negative charge of soil (p<0.001). A further decrease in 1 M NH4OAc extractable Cd concentration was noted when P was increased to 16,000 mg P kg(-1) and may have been the result of Cd precipitation. This study suggest that adding P at high levels may help in the formation of geochemically stable Cd minerals in soil containing low levels of this heavy metal.

  5. Effects of a copper-tolerant grass (Agrostis capillaris) on the ecosystem of a copper-contaminated arable soil

    SciTech Connect

    Boon, G.T.; Bouwman, L.A.; Bloem, J.; Roemkens, P.F.A.M.

    1998-10-01

    To test how a dysfunctioning ecosystem of a severely metal-polluted soil responds to renewed plant growth, a pot experiment was conducted with soil from an experimental arable field with pH and copper gradients imposed 13 years ago. In this experiment, four pH/copper combinations from this field were either planted with a pH- and copper-resistant grass cultivar or remained fallow. During a 10-week period, the dynamics of the microbial activity and of the abundances of bacteria, protozoa. and nematodes were measured, as were the dynamics of several chemical soil parameters. After 13 years of copper, which had resulted in severely reduced crop growth, no effects were observed on bacterial numbers, respiration, or protozoan numbers, but bacterial growth was strongly reduced in the low pH plots, and even more so in low pH plots enriched with copper. Of the organisms, only nematodes were negatively affected under conditions of high copper load at low pH. In these plots, numbers belonging to all feeding categories were strongly reduced. Planting of a copper-tolerant grass variety, Agrostis capillaris L. var. Parys Mountain, resulted within 10 weeks in faster bacterial growth and more protozoa and bacterivorous nematodes in comparison with fallow controls; these effects were markedly strongest in the acidic, copper-enriched soils. During incubation, fungivorous nematodes increased in all treatments, in fallow and in planted pots and in the pots with high-copper, low-pH soil. The results of this experiment suggest that introduction of plant growth is one of the major causes of increased biological activity in acidic contaminated soils. Planting such soils with metal-tolerant plant species can reestablish the necessary food base to support soil organism growth, and this can lead to numerous positive effects, reversing the loss of soil functions due to the high copper levels under acidic conditions.

  6. Quantification of the fate of mesotrione applied alone or in a herbicide mixture in two Brazilian arable soils.

    PubMed

    Mendes, Kassio Ferreira; Martins, Bianca Assis Barbosa; Dos Reis, Marcelo Rodrigues; Pimpinato, Rodrigo Floriano; Tornisielo, Valdemar Luiz

    2017-03-01

    The effects of mesotrione, S-metolachlor, and terbuthylazine, applied in mixture, on soil biodegradation remain insufficiently researched. However, herbicide mixtures have been a common practice in agricultural systems in the last years. Understanding the fate of soil-applied herbicides may help on planning weed management tactics towards more sustainable and efficient weed control. Therefore, this study evaluated the fate of mesotrione alone and in mixture with S-metolachlor and terbuthylazine when applied to two contrasting arable Brazilian soils. Mineralization and degradation experiments were conducted using (14)C-mesotrione alone or in mixture. From the 49-day laboratory incubation data, increased mineralization half-life of mesotrione was observed for the mixture of herbicides, ranging from a 4-day increase for the sandy loam soil to a 1-day increase in the sandy clay texture soils. Mesotrione degradation rate had a twofold increase in the sandy loam compared to the sandy clay soil. Two metabolites can be identified from mesotrione degradation, 4-methyl-sulfonyl-2-nitrobenzoic acid (MNBA) and 2-amino-4-methylsulfonyl benzoic acid (AMBA). Indices for the score of ubiquity in groundwater indicated mesotrione possesses leaching potential for both soils. Applying mesotrione alone or in mixture did not influence the amount of bound residues from mesotrione. However, mesotrione degradation rate was influenced by soil texture regardless if applied alone or in mixture. Mesotrione biotransformation was relatively quick, indicating that this herbicide has low persistence and, consequently, low residual effect on crops and weeds when present in similar soils to this present study.

  7. Effects of agricultural tillage practise on green house gas balance of an arable soil in a long term field experiment

    NASA Astrophysics Data System (ADS)

    Munch, Jean Charles; Schilling, Rolf; Ruth, Bernhard; Fuss, Roland

    2010-05-01

    Soils are an important part of the global carbon cycle. A large proportion of global carbon dioxide (CO2) emissions is released from soils, though carbon sequestration occurs. Nitrous oxide (N2O) emissions of soils are also believed to contribute significantly to the green house effect as well as the stratospheric ozone depletion. An important source of N2O emissions is denitrification of nitrate from nitrogen fertilized soils. Although it is desirable to minimize these emissions while maintaining high crop yields it is still poorly understood how green house gas emissions may be steered by agricultural management practise, i.e. tillage and fertilization systems . In an ongoing long term field experiment at the research farm Scheyern, Bavaria, a arable field with one homogenous soil formation was transformed into plots in a randomized design 14 years ago. Since then, they are managed using conventional tillage (CT) and no tillage (NT) as well as low and high fertilization. A conventional crop rotation is maintained on the field. Starting 2007, CO2 and N2O emissions were monitored continuously for 2.5 years. Furthermore water content, temperature and redox potential were measured in-situ as they are major factors on microbial activity and denitrification. Soil was sampled from the Ap horizons of the plots about twice a month and extracts from these soil samples were analyzed for dissolved organic carbon (DOC), ammonium, nitrate/nitrite, and dissolved organic nitrogen (DON). According to the results soil density and hydrology are clearly affected by tillage practise. DOC is more affected by tillage while concentration of nitrogen species is controlled mainly by fertilization. There are distinct differences in redox potential between CT and NT plots with CT plots having more anaerobic periods. CO2 and N2O emissions exhibit a clear seasonal pattern and are affected by both tillage system and fertilization

  8. Different impacts of manure and chemical fertilizers on bacterial community structure and antibiotic resistance genes in arable soils.

    PubMed

    Liu, Peng; Jia, Shuyu; He, Xiwei; Zhang, Xuxiang; Ye, Lin

    2017-09-04

    Both manure and chemical fertilizers are widely used in modern agriculture. However, the impacts of different fertilizers on bacterial community structure and antibiotic resistance genes (ARGs) in arable soils still remain unclear. In this study, high-throughput sequencing and quantitative PCR were employed to investigate the bacterial community structure, ARGs and mobile genetic elements (MGEs) influenced by the application of different fertilizers, including chemical fertilizers, piggery manure and straw ash. The results showed that the application of fertilizers could significantly change the soil bacterial community and the abundance of Gaiella under phylum Actinobacteria was significantly reduced from 12.9% in unfertilized soil to 4.1%-7.4% in fertilized soil (P < 0.05). It was also found that the application of manure could cause a transient effect on soil resistome composition and the relative abundance of ARGs increased from 7.37 ppm to 32.10 ppm. The abundance of aminoglycoside, sulfonamide and tetracycline resistance genes greatly increased after manure fertilization and then gradually returned to normal levels with the decay of some intestinal bacteria carrying ARGs. In contrast, the application of chemical fertilizers and straw ash significantly changed the bacterial community structure but exerted little effect on soil resistome. Overall, the results of this study illustrated the different effects of different fertilizers on the soil resistome and revealed that the changes of soil resistome induced by manure application mainly resulted from alteration of bacteria community rather than the horizontal gene transfer. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Statistical test for tolerability of effects of an antifungal biocontrol strain on fungal communities in three arable soils.

    PubMed

    Antweiler, Kai; Schreiter, Susanne; Keilwagen, Jens; Baldrian, Petr; Kropf, Siegfried; Smalla, Kornelia; Grosch, Rita; Heuer, Holger

    2017-03-01

    A statistical method was developed to test for equivalence of microbial communities analysed by next-generation sequencing of amplicons. The test uses Bray-Curtis distances between the microbial community structures and is based on a two-sample jackknife procedure. This approach was applied to investigate putative effects of the antifungal biocontrol strain RU47 on fungal communities in three arable soils which were analysed by high-throughput ITS amplicon sequencing. Two contrasting workflows to produce abundance tables of operational taxonomic units from sequence data were applied. For both, the developed test indicated highly significant equivalence of the fungal communities with or without previous exposure to RU47 for all soil types, with reference to fungal community differences in conjunction with field site or cropping history. However, minor effects of RU47 on fungal communities were statistically significant using highly sensitive multivariate tests. Nearly all fungal taxa responding to RU47 increased in relative abundance indicating the absence of ecotoxicological effects. Use of the developed equivalence test is not restricted to evaluate effects on soil microbial communities by inoculants for biocontrol, bioremediation or other purposes, but could also be applied for biosafety assessment of compounds like pesticides, or genetically engineered plants. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  10. Offsetting global warming-induced elevated greenhouse gas emissions from an arable soil by biochar application.

    PubMed

    Bamminger, Chris; Poll, Christian; Marhan, Sven

    2017-08-17

    Global warming will likely enhance greenhouse gas (GHG) emissions from soils. Due to its slow decomposability, biochar is widely recognized as effective in long-term soil carbon (C) sequestration and in mitigation of soil GHG emissions. In a long-term soil warming experiment (+2.5 °C, since July 2008) we studied the effect of applying high-temperature Miscanthus biochar (0, 30 t/ha, since August 2013) on GHG emissions and their global warming potential (GWP) during 2 years in a temperate agroecosystem. Crop growth, physical and chemical soil properties, temperature sensitivity of soil respiration (Rs ), and metabolic quotient (qCO2 ) were investigated to yield further information about single effects of soil warming and biochar as well as on their interactions. Soil warming increased total CO2 emissions by 28% over 2 years. The effect of warming on soil respiration did not level off as has often been observed in less intensively managed ecosystems. However, the temperature sensitivity of soil respiration was not affected by warming. Overall, biochar had no effect on most of the measured parameters, suggesting its high degradation stability and its low influence on microbial C cycling even under elevated soil temperatures. In contrast, biochar × warming interactions led to higher total N2 O emissions, possibly due to accelerated N-cycling at elevated soil temperature and to biochar-induced changes in soil properties and environmental conditions. Methane uptake was not affected by soil warming or biochar. The incorporation of biochar-C into soil was estimated to offset warming-induced elevated GHG emissions for 25 years. Our results highlight the suitability of biochar for C sequestration in cultivated temperate agricultural soil under a future elevated temperature. However, the increased N2 O emissions under warming limit the GHG mitigation potential of biochar. © 2017 John Wiley & Sons Ltd.

  11. The association of soil organic matter with mineral surfaces depends on clay content in an arable Cambisol

    NASA Astrophysics Data System (ADS)

    Schweizer, Steffen A.; Angelika, Koelbl; Hoeschen, Carmen; Mueller, Carsten W.; Koegel-Knabner, Ingrid

    2017-04-01

    The amount and distribution of mineral-associated soil organic matter (MOM) depends on the availability of adsorptive mineral surface area. In soils with low content of fine-sized mineral particles, the available mineral surface is limited in comparison to soils with high content of fine-sized mineral particles. Accordingly, the spatial distribution of MOM from soils with various contents of fine-sized mineral particles should reflect different structural organization of organo-mineral associations. In this study, we analyzed MOM and further indicators of its binding in the topsoil (020 cm) of an arable Cambisol. The sampled site showed a gradient in the content of clay-sized particles (6-35 %) under similar soil management and biomass input. We obtained fine silt-sized (26.3 μm) and clay-sized (0.22 μm) mineral-associated (>1.6 g cm3) fractions from a combined density and size fractionation. We measured solid-state 13C nuclear magnetic resonance spectra and analyzed the specific surface area of the fractions by N2-BET with and without NaOCl oxidation. The spatial distribution of MOM was determined by nanoscale secondary ion mass spectrometry (NanoSIMS) at a lateral resolution of approximately 100 nm. We found that the mineral-associated carbon concentration of the fine silt and clay-sized fractions decreased from 80 to 40 mg g-1 when the content of clay-sized particles increased from 6 to 15 %. In the clay-rich soils the mineral-associated carbon remained constant at approximately 40 mg g-1 for higher contents of clay-sized particles from 15 to 30 %. In addition, the 12C and 12C14N ion distributions obtained from NanoSIMS indicated a much higher coverage of mineral surface with MOM in the sandy soils than in the clay-rich soils. Our data shows that both the concentration and coverage of MOM is increased in soils with a lower content of fine-sized mineral particles, when the input of organic material to the soil is similar.

  12. Impact of earthworm Lumbricus terrestris living sites on the greenhouse gas balance of no-till arable soil

    NASA Astrophysics Data System (ADS)

    Nieminen, M.; Hurme, T.; Mikola, J.; Regina, K.; Nuutinen, V.

    2015-09-01

    We studied the effect of the deep-burrowing earthworm Lumbricus terrestris on the greenhouse gas (GHG) fluxes and global warming potential (GWP) of arable no-till soil using both field measurements and a controlled 15-week laboratory experiment. In the field, the emissions of nitrous oxide (N2O) and carbon dioxide (CO2) were on average 43 and 32 % higher in areas occupied by L. terrestris (the presence judged by the surface midden) than in adjacent, unoccupied areas (with no midden). The fluxes of methane (CH4) were variable and had no consistent difference between the midden and non-midden areas. Removing the midden did not affect soil N2O and CO2 emissions. The laboratory results were consistent with the field observations in that the emissions of N2O and CO2 were on average 27 and 13 % higher in mesocosms with than without L. terrestris. Higher emissions of N2O were most likely due to the higher content of mineral nitrogen and soil moisture under the middens, whereas L. terrestris respiration fully explained the observed increase in CO2 emissions in the laboratory. In the field, the significantly elevated macrofaunal densities in the vicinity of middens likely contributed to the higher emissions from areas occupied by L. terrestris. The activity of L. terrestris increased the GWP of field and laboratory soil by 50 and 18 %, but only 6 and 2 % of this increase was due to the enhanced N2O emission. Our results suggest that high N2O emissions commonly observed in no-till soils can partly be explained by the abundance of L. terrestris under no-till management and that L. terrestris can markedly regulate the climatic effects of different cultivation practises.

  13. Probing the origin of acetyl-CoA and oxaloacetate entering the citric acid cycle from the 13C labeling of citrate released by perfused rat hearts.

    PubMed

    Comte, B; Vincent, G; Bouchard, B; Des Rosiers, C

    1997-10-17

    We present a strategy for simultaneous assessment of the relative contributions of anaplerotic pyruvate carboxylation, pyruvate decarboxylation, and fatty acid oxidation to citrate formation in the perfused rat heart. This requires perfusing with a mix of 13C-substrates and determining the 13C labeling pattern of a single metabolite, citrate, by gas chromatography-mass spectrometry. The mass isotopomer distributions of the oxaloacetate and acetyl moieties of citrate allow calculation of the flux ratios: (pyruvate carboxylation)/(pyruvate decarboxylation), (pyruvate carboxylation)/(citrate synthesis), (pyruvate decarboxylation)/(citrate synthesis) (pyruvate carboxylation)/(fatty acid oxidation), and (pyruvate decarboxylation)/(fatty acid oxidation). Calculations, based on precursor-product relationship, are independent of pool size. The utility of our method was demonstrated for hearts perfused under normoxia with [U-13C3](lactate + pyruvate) and [1-13C]octanoate under steady-state conditions. Under these conditions, effluent and tissue citrate were similarly enriched in all 13C mass isotopomers. The use of effluent citrate instead of tissue citrate allows probing substrate fluxes through the various reactions non-invasively in the intact heart. The methodology should also be applicable to hearts perfused with other 13C-substrates, such as 1-13C-labeled long chain fatty acid, and under various conditions, provided that assumptions on which equations are developed are valid.

  14. In vivo, large-scale preparation of uniformly (15)N- and site-specifically (13)C-labeled homogeneous, recombinant RNA for NMR studies.

    PubMed

    Le, My T; Brown, Rachel E; Simon, Anne E; Dayie, T Kwaku

    2015-01-01

    Knowledge of how ribonucleic acid (RNA) structures fold to form intricate, three-dimensional structures has provided fundamental insights into understanding the biological functions of RNA. Nuclear magnetic resonance (NMR) spectroscopy is a particularly useful high-resolution technique to investigate the dynamic structure of RNA. Effective study of RNA by NMR requires enrichment with isotopes of (13)C or (15)N or both. Here, we present a method to produce milligram quantities of uniformly (15)N- and site-specifically (13)C-labeled RNAs using wild-type K12 and mutant tktA Escherichia coli in combination with a tRNA-scaffold approach. The method includes a double selection protocol to obtain an E. coli clone with consistently high expression of the recombinant tRNA-scaffold. We also present protocols for the purification of the tRNA-scaffold from a total cellular RNA extract and the excision of the RNA of interest from the tRNA-scaffold using DNAzymes. Finally, we showcase NMR applications to demonstrate the benefit of using in vivo site-specifically (13)C-labeled RNA. © 2015 Elsevier Inc. All rights reserved.

  15. Application of 13C-labeling and 13C-13C COSY NMR experiments in the structure determination of a microbial natural product.

    PubMed

    Kwon, Yun; Park, Sunghyouk; Shin, Jongheon; Oh, Dong-Chan

    2014-08-01

    The elucidation of the structures of complex natural products bearing many quaternary carbons remains challenging, even in this advanced spectroscopic era. (13)C-(13)C COSY NMR spectroscopy shows direct couplings between (13)C and (13)C, which comprise the backbone of a natural product. Thus, this type of experiment is particularly useful for natural products bearing consecutive quaternary carbons. However, the low sensitivity of (13)C-based NMR experiments, due to the low natural abundance of the (13)C nucleus, is problematic when applying these techniques. Our efforts in the (13)C labeling of a microbial natural product, cyclopiazonic acid (1), by feeding (13)C-labeled glucose to the fungal culture, enabled us to acquire (13)C-(13)C COSY NMR spectra on a milligram scale that clearly show the carbon backbone of the compound. This is the first application of (13)C-(13)C COSY NMR experiments for a natural product. The results suggest that (13)C-(13)C COSY NMR spectroscopy can be routinely used for the structure determination of microbial natural products by (13)C-enrichment of a compound with (13)C-glucose.

  16. Chemo-Enzymatic Synthesis of (13)C Labeled Complex N-Glycans As Internal Standards for the Absolute Glycan Quantification by Mass Spectrometry.

    PubMed

    Echeverria, Begoña; Etxebarria, Juan; Ruiz, Nerea; Hernandez, Álvaro; Calvo, Javier; Haberger, Markus; Reusch, Dietmar; Reichardt, Niels-Christian

    2015-11-17

    Methods for the absolute quantification of glycans are needed in glycoproteomics, during development and production of biopharmaceuticals and for the clinical analysis of glycan disease markers. Here we present a strategy for the chemo-enzymatic synthesis of (13)C labeled N-glycan libraries and provide an example for their use as internal standards in the profiling and absolute quantification of mAb glycans by matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry. A synthetic biantennary glycan precursor was (13)C-labeled on all four amino sugar residues and enzymatically derivatized to produce a library of 15 glycan isotopologues with a mass increment of 8 Da over the natural products. Asymmetrically elongated glycans were accessible by performing enzymatic reactions on partially protected UV-absorbing intermediates, subsequent fractionation by preparative HPLC, and final hydrogenation. Using a preformulated mixture of eight internal standards, we quantified the glycans in a monoclonal therapeutic antibody with excellent precision and speed.

  17. Response of microbial community of organic-matter-impoverished arable soil to long-term application of soil conditioner derived from dynamic rapid fermentation of food waste

    PubMed Central

    Hou, Jiaqi; Li, Mingxiao; Mao, Xuhui; Hao, Yan; Ding, Jie; Liu, Dongming; Liu, Hongliang

    2017-01-01

    Rapid fermentation of food waste can be used to prepare soil conditioner. This process consumes less time and is more cost-effective than traditional preparation technology. However, the succession of the soil microbial community structure after long-term application of rapid fermentation-derived soil conditioners remains unclear. Herein, dynamic rapid fermentation (DRF) of food waste was performed to develop a soil conditioner and the successions and diversity of bacterial communities in an organic-matter-impoverished arable soil after six years of application of DRF-derived soil conditioner were investigated. Results showed that the treatment increased soil organic matter (SOM) accumulation and strawberry yield by 5.3 g/kg and 555.91 kg/ha, respectively. Proteobacteria, Actinobacteria, Acidobacteria, and Firmicutes became the dominant phyla, occupying 65.95%–77.52% of the bacterial sequences. Principal component analysis (PCA) results showed that the soil bacterial communities were largely influenced by the treatment. Redundancy analysis (RDA) results showed that the relative abundances of Gemmatimonadetes, Chloroflexi, Verrucomicrobia, Nitrospirae, and Firmicutes were significantly correlated with soil TC, TN, TP, NH4+-N, NO3−-N, OM, and moisture. These communities were all distributed in the soil samples collected in the sixth year of application. Long-term treatment did not enhance the diversity of bacterial species but significantly altered the distribution of major functional bacterial communities in the soils. Application of DRF-derived soil conditioner could improve the soil quality and optimize the microbial community, ultimately enhancing fruit yields. PMID:28419163

  18. Short-term ecological risks of depositing contaminated sediment on arable soil.

    PubMed

    Peijnenburg, Willie; de Groot, Arthur; Jager, Tjalling; Posthuma, Leo

    2005-01-01

    Sediments act as sinks of suspended material from surface water. Dredging of regional waters and subsequent disposal of the sediment on soil may lead to contamination of the soil, in some cases resulting in exceedance of soil quality standards. Soil quality standards are based on total concentrations. Total levels, however, do not always give an indication of adverse effects in soil ecosystems. Instead, truly bioavailable concentrations should be used as indicators. In this study we aim to test a set of suited indicators. We carried out partition and accumulation assays with metals and polycyclic aromatic hydrocarbons (PAHs) in soils and mixtures of soil and sediment, as well as a limited number of toxicity bioassays. We also investigated the rate of disappearance of PAHs from mixtures of sediments and soils. The experiments confirm that total levels indeed are not indicative of truly occurring toxic effects: mixing of highly contaminated sediments with soil hardly gave rise to either additional accumulation of metals and PAHs or excess toxicity. This indicates that the bioavailability of the metals and PAHs present in the sediment is limited. This general finding is confirmed by the low rate of disappearance of PAHs from the mixtures. It is concluded that inclusion of the aspects of bioavailability, mixture toxicity, and degradation, in the way described in this report, will solve the major limitations of the current methodology of classification of contaminated sediments.

  19. Speciation and distribution of P associated with Fe and Al oxides in aggregate-sized fraction of an arable soil

    NASA Astrophysics Data System (ADS)

    Jiang, X.; Bol, R.; Willbold, S.; Vereecken, H.; Klumpp, E.

    2015-07-01

    To maximize crop productivity fertilizer P is generally applied to arable soils, a significant proportion of which becomes stabilized by mineral components and in part subsequently becomes unavailable to plants. However, little is known about the relative contributions of the different organic and inorganic P bound to Fe/Al oxides in the smaller soil particles. The alkaline (NaOH-Na2EDTA) extraction with solution 31P-nuclear magnetic resonance (31P-NMR) spectroscopy is considered as a reliable method for extracting and quantifying organic P and (some) inorganic P. However, any so-called residual P after the alkaline extraction has remained unidentified. Therefore, in the present study, the amorphous (a) and crystalline (c) Fe/Al oxide minerals and related P in soil aggregate-sized fractions (> 20, 2-20, 0.45-2 and < 0.45 μm) were specifically extracted by oxalate (a-Fe/Al oxides) and dithionite (DCB, both a- and c-Fe/Al oxides). These soil aggregate-sized fractions with and without the oxalate and DCB pre-treatments were then sequentially extracted by alkaline extraction prior to solution 31P-NMR spectroscopy. This was done to quantify the various chemical P forms which were associated with a- and c-Fe/Al oxides both in alkaline extraction and in the residual P of different soil aggregate-sized fractions. The results showed that overall P contents increased with decreasing size of the soil aggregate-sized fractions. However, the relative distribution and speciation of varying P forms were found to be independent of soil aggregate-size. The majority of alkaline extractable P was in the a-Fe/Al oxide fraction (42-47 % of total P), most of which was orthophosphate (36-41 % of total P). Furthermore, still significant amounts of particularly monoester P were bound to the oxides. Intriguingly, however, Fe/Al oxides were not the main bonding sites for pyrophosphate. Residual P contained similar amounts of total P associated with both a- (10-13 % of total P) and c

  20. Speciation and distribution of P associated with Fe and Al oxides in aggregate-sized fraction of an arable soil

    NASA Astrophysics Data System (ADS)

    Jiang, X.; Bol, R.; Willbold, S.; Vereecken, H.; Klumpp, E.

    2015-11-01

    To maximize crop productivity fertilizer P is generally applied to arable soils, a significant proportion of which becomes stabilized by mineral components and in part subsequently becomes unavailable to plants. However, little is known about the relative contributions of the different organic and inorganic P bound to Fe/Al oxides in the smaller soil particles. Alkaline (NaOH-Na2EDTA) extraction with solution 31P-nuclear magnetic resonance (31P-NMR) spectroscopy is considered a reliable method for extracting and quantifying organic P and (some) inorganic P. However, any so-called residual P after the alkaline extraction has remained unidentified. Therefore, in the present study, the amorphous (a) and crystalline (c) Fe/Al oxide minerals and related P in soil aggregate-sized fractions (> 20, 2-20, 0.45-2 and < 0.45 μm) were specifically extracted by oxalate (a-Fe/Al oxides) and dithionite-citrate-bicarbonate (DCB, both a- and c-Fe/Al oxides). These soil aggregate-sized fractions with and without the oxalate and DCB pre-treatments were then sequentially extracted by alkaline extraction prior to solution 31P-NMR spectroscopy. This was done to quantify the P associated with a- and c-Fe/Al oxides in both alkaline extraction and the residual P of different soil aggregate-sized fractions. The results showed that overall P contents increased with decreasing size of the soil aggregate-sized fractions. However, the relative distribution and speciation of varying P forms were found to be independent of soil aggregate-size. The majority of alkaline-extractable P was in the a-Fe/Al oxide fraction (42-47 % of total P), most of which was ortho-phosphate (36-41 % of total P). Furthermore, still significant amounts of particularly monoester P were bound to these oxides. Intriguingly, however, Fe/Al oxides were not the main bonding sites for pyrophosphate. Residual P contained similar amounts of total P associated with both a- (11-15 % of total P) and c-Fe oxides (7-13 % of total P

  1. Soil types will alter the response of arable agroecosystems to future rainfall patterns

    NASA Astrophysics Data System (ADS)

    Zaller, J. G.; Schwarz, T.; Hall, R.; Ziss, E.; von Hohberg und Buchwald, C.; Hösch, J.; Baumgarten, A.

    2012-04-01

    Regional climate change scenarios for eastern Austria (pannonian region) predict fewer but heavier rains during the vegetation period without substantial changes in the total annual amount of rainfall. While many studies investigated the effects of rainfall patterns on ecosystem properties, very little is known on how different soil types might alter ecosystem responses. In order to test this, we conducted an experiment at the AGES lysimeter station using 18 3 m2 lysimeters where we simultaneously manipulated rainfall patterns according to regional climate scenarios (current vs. prognosticated rain) on the three main soil types of the region (sandy calcaric phaeozem, gleyic phaeozem and calcic chernozem). Lysimeters were cultivated according to good farming practice using crop varieties and crop rotations typically for the region. Here, we present results of the response of field peas (Pisum sativum) on important agricultural parameters. Lysimeters under progn. rain showed lower crop cover than under curr. rain while soil types had no effect. Total aboveground biomass production (comprising crops plus weeds) was significantly lower under progn. rain; sandy calcaric phaeozem showed the lowest plant biomass. Pea yields under progn. rain were substantially lower than under curr. rain; again, yields under sandy soils were lower than under the other two soil types. Root growth was significantly higher in progn. rain than in curr. rain; there was a trend towards less root growth in the gleyic soils. Mycorrhization of roots was not influenced by soil types, however under progn. rain colonization rates were lower than under curr. rain. Weed establishment and growth was increased under progn. rain in gleyic soils but decreased in the other soil types. Weed biomass was not affected by rainfall, however sandy soils had less weed biomass than the other soil types. Abundance of the insect pest pea moth (Cydia nigricana) was almost twice as high under progn. rain than under curr

  2. Modelling soil borne fungal pathogens of arable crops under climate change

    NASA Astrophysics Data System (ADS)

    Manici, L. M.; Bregaglio, S.; Fumagalli, D.; Donatelli, M.

    2014-12-01

    Soil-borne fungal plant pathogens, agents of crown and root rot, are seldom considered in studies on climate change and agriculture due both to the complexity of the soil system and to the incomplete knowledge of their response to environmental drivers. A controlled chamber set of experiments was carried out to quantify the response of six soil-borne fungi to temperature, and a species-generic model to simulate their response was developed. The model was linked to a soil temperature model inclusive of components able to simulate soil water content also as resulting from crop water uptake. Pathogen relative growth was simulated over Europe using the IPCC A1B emission scenario derived from the Hadley-CM3 global climate model. Climate scenarios of soil temperature in 2020 and 2030 were compared to the baseline centred in the year 2000. The general trend of the response of soil-borne pathogens shows increasing growth in the coldest areas of Europe; however, a larger rate of increase is shown from 2020 to 2030 compared to that of 2000 to 2020. Projections of pathogens of winter cereals indicate a marked increase of growth rate in the soils of northern European and Baltic states. Fungal pathogens of spring sowing crops show unchanged conditions for their growth in soils of the Mediterranean countries, whereas an increase of suitable conditions was estimated for the areals of central Europe which represent the coldest limit areas where the host crops are currently grown. Differences across fungal species are shown, indicating that crop-specific analyses should be ran.

  3. Modeling greenhouse gas emissions and nutrient transport in managed arable soils with a fully coupled hydrology-biogeochemical modeling system

    NASA Astrophysics Data System (ADS)

    Haas, Edwin; Klatt, Steffen; Kiese, Ralf; Butterbach-Bahl, Klaus; Kraft, Philipp; Breuer, Lutz

    2015-04-01

    The use of mineral nitrogen fertilizer sustains the global food production and therefore the livelihood of human kind. The rise in world population will put pressure on the global agricultural system to increase its productivity leading most likely to an intensification of mineral nitrogen fertilizer use. The fate of excess nitrogen and its distribution within landscapes is manifold. Process knowledge on the site scale has rapidly grown in recent years and models have been developed to simulate carbon and nitrogen cycling in managed ecosystems on the site scale. Despite first regional studies, the carbon and nitrogen cycling on the landscape or catchment scale is not fully understood. In this study we present a newly developed modelling approach by coupling the fully distributed hydrology model CMF (catchment modelling framework) to the process based regional ecosystem model LandscapeDNDC for the investigation of hydrological processes and carbon and nitrogen transport and cycling, with a focus on nutrient displacement and resulting greenhouse gas emissions in various virtual landscapes / catchment to demonstrate the capabilities of the modelling system. The modelling system was applied to simulate water and nutrient transport at the at the Yanting Agro-ecological Experimental Station of Purple Soil, Sichuan province, China. The catchment hosts cypress forests on the outer regions, arable fields on the sloping croplands cultivated with wheat-maize rotations and paddy rice fields in the lowland. The catchment consists of 300 polygons vertically stratified into 10 soil layers. Ecosystem states (soil water content and nutrients) and fluxes (evapotranspiration) are exchanged between the models at high temporal scales (hourly to daily) forming a 3-dimensional model application. The water flux and nutrients transport in the soil is modelled using a 3D Richards/Darcy approach for subsurface fluxes with a kinematic wave approach for surface water runoff and the

  4. Soil organic carbon dynamics under long-term fertilizations in arable land of northern China

    NASA Astrophysics Data System (ADS)

    Zhang, W. J.; Wang, X. J.; Xu, M. G.; Huang, S. M.; Liu, H.; Peng, C.

    2010-02-01

    Soil carbon sequestration is a complex process influenced by agricultural practices, climate and soil conditions. This paper reports a study of long-term fertilization impacts on soil organic carbon (SOC) dynamic from six long-term experiments. The experiment sites are located from warm-temperate zone with a double-cropping system of corn (Zea mays L.) - wheat (Triticum Aestivium L.) rotation, to mild-temperate zones with mono-cropping systems of continuous corn, or a three-year rotation of corn-wheat-wheat. Mineral fertilizer applications result in an increasing trend in SOC except in the arid and semi-arid areas with the mono-cropping systems. Additional manure application is important to maintain SOC level in the arid and semi-arid areas. Carbon conversion rate is significant lower in the warm-temperate zone with double cropping system (6.8%-7.7%) than that in the mild-temperate areas with mono-cropping systems (15.8%-31.0%). The conversion rate is significantly correlated with annual precipitation and active accumulative temperature, i.e., higher conversion rate under lower precipitation and/or temperature conditions. Moreover, soil high in clay content has higher conversion rate than soils low in clay content. Soil carbon sequestration rate ranges from 0.07 to 1.461 t ha-1 year-1 in the upland of northern China. There is significantly linear correlation between soil carbon sequestration and carbon input at most sites, indicating that these soils are not carbon-saturated thus have potential to migrate more CO2 from atmosphere.

  5. Spatio-temporal distribution and emergence of beetles in arable fields in relation to soil moisture.

    PubMed

    Holland, J M; Thomas, C F G; Birkett, T; Southway, S

    2007-02-01

    Predatory beetles contribute to the control of crop pests and are an important food resource for farmland birds. Many of these beetle species overwinter as larvae within agricultural soils, however, their spatio-temporal emergence patterns are poorly understood, even though such knowledge can assist with their management for biocontrol. Soil moisture is considered to be a key factor influencing oviposition site selection and larval survival. The time, density and spatial pattern of Carabidae and Staphylidae emergence was therefore measured across two fields and compared to soil moisture levels in the previous winter and adult distribution in the previous July. The mean density of Carabidae and Staphylidae that emerged between April and harvest within each field was 157 and 86 m-2, indicating that soils are an important over-wintering habitat for beneficial invertebrates and should be managed sympathetically if numbers are to be increased. Of the species that were sufficiently numerous to allow their spatial pattern to be analysed, all showed a heterogeneous emergence pattern, although patches with high emergence were stable over the sampling period. The distribution of eight species was influenced by soil moisture levels in the previous winter and eight species, although not the same, were spatially associated with the distribution of adults in the previous summer suggesting that the females selected oviposition areas with the appropriate soil wetness.

  6. Direct uptake of organically derived carbon by grass roots and allocation in leaves and phytoliths: 13C labeling evidence

    NASA Astrophysics Data System (ADS)

    Alexandre, Anne; Balesdent, Jérôme; Cazevieille, Patrick; Chevassus-Rosset, Claire; Signoret, Patrick; Mazur, Jean-Charles; Harutyunyan, Araks; Doelsch, Emmanuel; Basile-Doelsch, Isabelle; Miche, Hélène; Santos, Guaciara M.

    2016-03-01

    In the rhizosphere, the uptake of low-molecular-weight carbon (C) and nitrogen (N) by plant roots has been well documented. While organic N uptake relative to total uptake is important, organic C uptake is supposed to be low relative to the plant's C budget. Recently, radiocarbon analyses demonstrated that a fraction of C from the soil was occluded in amorphous silica micrometric particles that precipitate in plant cells (phytoliths). Here, we investigated whether and to what extent organically derived C absorbed by grass roots can feed the C occluded in phytoliths. For this purpose we added 13C- and 15N-labeled amino acids (AAs) to the silicon-rich hydroponic solution of the grass Festuca arundinacea. The experiment was designed to prevent C leakage from the labeled nutritive solution to the chamber atmosphere. After 14 days of growth, the 13C and 15N enrichments (13C excess and 15N excess) in the roots, stems and leaves as well as phytoliths were measured relative to a control experiment in which no labeled AAs were added. Additionally, the 13C excess was measured at the molecular level, in AAs extracted from roots and stems and leaves. The net uptake of labeled AA-derived 13C reached 4.5 % of the total AA 13C supply. The amount of AA-derived 13C fixed in the plant was minor but not nil (0.28 and 0.10 % of total C in roots and stems/leaves, respectively). Phenylalanine and methionine that were supplied in high amounts to the nutritive solution were more 13C-enriched than other AAs in the plant. This strongly suggested that part of AA-derived 13C was absorbed and translocated into the plant in its original AA form. In phytoliths, AA-derived 13C was detected. Its concentration was on the same order of magnitude as in bulk stems and leaves (0.15 % of the phytolith C). This finding strengthens the body of evidences showing that part of organic compounds occluded in phytoliths can be fed by C entering the plant through the roots. Although this experiment was done in

  7. Redox dependent changes at the heme propionates in cytochrome c oxidase from Paracoccus denitrificans: direct evidence from FTIR difference spectroscopy in combination with heme propionate 13C labeling.

    PubMed

    Behr, J; Hellwig, P; Mäntele, W; Michel, H

    1998-05-19

    Specific isotope labeling at the carboxyl groups of the four heme propionates of cytochrome c oxidase from Paracoccus denitrificans was used in order to assign signals observed in electrochemically induced redox Fourier transform infrared (FTIR) difference spectra of this enzyme. For this purpose, the hemA gene of the P. denitrificans strain PD1222, coding for 5-aminolevulinate synthase, was deleted by partial replacement with a kanamycin resistance cartridge, resulting in a stable 5-aminolevulinic acid (ALA) auxotrophy. Normal growth of this deficient strain and cytochrome c oxidase yield comparable to that of P. dentrificans wild-type strain PD1222 could be obtained by supplementation with 0.1 mM ALA in the growth medium. Visible spectra and reduced-minus-oxidized FTIR spectra showed that the purified cytochrome c oxidase had spectral characteristics identical to those of the wild-type enzyme. The decrease of a negative signal at 1676 cm-1 in the reduced-minus-oxidized FTIR difference spectra of the 13C-labeled cytochrome c oxidase in comparison to those of the unlabeled protein allowed the assignment of this signal to a COOH vibration mode of at least one of the four heme propionates. Moreover, a negative band at approximately 1570 cm-1 shifted to smaller wavenumbers in the spectra of the 13C-labeled enzyme in comparison to the spectra of the unlabeled enzyme and was thus assigned to contributions from an antisymmetric COO- mode of one or more of the four heme propionates. Additionally, a positive signal at 1538 cm-1 shifted to approximately 1500 cm-1 in the spectra of the isotopically labeled protein and was therefore assigned to at least one antisymmetric COO- mode of the heme propionates. A negative signal at 1390 cm-1, which has been shifted to 1360 cm-1 in the spectra of the 13C-labeled enzyme, is due to a symmetric COO- mode from at least one heme propionate. These results suggest that at least two of the four heme propionates in cytochrome c oxidase

  8. Direct uptake of organic carbon by grass roots and allocation in leaves and phytoliths: 13C labeling evidence

    NASA Astrophysics Data System (ADS)

    Alexandre, A.; Balesdent, J.; Cazevieille, P.; Chevassus-Rosset, C.; Signoret, P.; Mazur, J.-C.; Harutyunyan, A.; Doelsch, E.; Basile-Doelsch, I.; Miche, H.; Santos, G. M.

    2015-12-01

    In the rhizosphere, the uptake of low molecular weight carbon (C) and nitrogen (N) by plant roots has been well documented. While organic N uptake relatively to total uptake is important, organic C uptake is supposed to be low relatively to the plant's C budget. Recently, radiocarbon analyses demonstrated that a fraction of C from the soil was occluded in amorphous silica micrometric particles that precipitate in plant cells (phytoliths). Here, we investigated whether and in which extent organic C absorbed by grass roots, under the form of either intact amino acids (AAs) or microbial metabolites, can feed the organic C occluded in phytoliths. For this purpose we added 13C- and 15N-labeled AAs to the silicon-rich hydroponic solution of the grass Festuca arundinacea. The experiment was designed to prevent C leakage from the labeled nutritive solution to the chamber atmosphere. After 14 days of growth, the 13C and 15N enrichments (13C-excess and 15N-excess) in the roots, stems and leaves, and phytoliths, as well as the 13C-excess in AAs extracted from roots and stems and leaves, were quantified relatively to a control experiment in which no labelled AAs were added. The net uptake of 13C derived from the labeled AAs supplied to the nutritive solution (AA-13C) by Festuca arundinacea represented 4.5 % of the total AA-13C supply. AA-13C fixed in the plant represented only 0.13 % of total C. However, the experimental conditions may have underestimated the extent of the process under natural and field conditions. Previous studies showed that 15N and 13C can be absorbed by the roots in several organic and inorganic forms. In the present experiment, the fact that phenylalanine and methionine, that were supplied in high amount to the nutritive solution, were more 13C-enriched than other AAs in the roots and stems and leaves strongly suggested that part of AA-13C was absorbed and translocated in its original AA form. The concentration of AA-13C represented only 0.15 % of the

  9. Quantitation of a spin polarization-induced nuclear Overhauser effect (SPINOE) between a hyperpolarized (13) C-labeled cell metabolite and water protons.

    PubMed

    Marco-Rius, Irene; Bohndiek, Sarah E; Kettunen, Mikko I; Larkin, Timothy J; Basharat, Meer; Seeley, Colm; Brindle, Kevin M

    2014-01-01

    The spin polarization-induced nuclear Overhauser effect (SPINOE) describes the enhancement of spin polarization of solvent nuclei by the hyperpolarized spins of a solute. In this communication we demonstrate that SPINOEs can be observed between [1,4-(13) C2 ]fumarate, hyperpolarized using the dissolution dynamic nuclear polarization technique, and solvent water protons. We derive a theoretical expression for the expected enhancement and demonstrate that this fits well with experimental measurements. Although the magnitude of the effect is relatively small (around 2% measured here), the SPINOE increases at lower field strengths, so that at clinically relevant magnetic fields (1.5-3 T) it may be possible to track the passage through the circulation of a bolus containing a hyperpolarized (13) C-labeled substrate through the increase in solvent water (1) H signal. © 2014 The Authors. Contrast Media & Molecular Imaging published by John Wiley and Sons, Ltd.

  10. Quantitation of a spin polarization-induced nuclear Overhauser effect (SPINOE) between a hyperpolarized 13C-labeled cell metabolite and water protons

    PubMed Central

    Marco-Rius, Irene; Bohndiek, Sarah E; Kettunen, Mikko I; Larkin, Timothy J; Basharat, Meer; Seeley, Colm; Brindle, Kevin M

    2014-01-01

    The spin polarization-induced nuclear Overhauser effect (SPINOE) describes the enhancement of spin polarization of solvent nuclei by the hyperpolarized spins of a solute. In this communication we demonstrate that SPINOEs can be observed between [1,4-13C2]fumarate, hyperpolarized using the dissolution dynamic nuclear polarization technique, and solvent water protons. We derive a theoretical expression for the expected enhancement and demonstrate that this fits well with experimental measurements. Although the magnitude of the effect is relatively small (around 2% measured here), the SPINOE increases at lower field strengths, so that at clinically relevant magnetic fields (1.5–3 T) it may be possible to track the passage through the circulation of a bolus containing a hyperpolarized 13C-labeled substrate through the increase in solvent water 1H signal. © 2014 The Authors. Contrast Media & Molecular Imaging published by John Wiley and Sons, Ltd. PMID:24523064

  11. Use of 13C Labeled Carbon Tetrachloride to Demonstrate the Transformation to Carbon Dioxide under Anaerobic Conditions in a Continuous Flow Column

    NASA Astrophysics Data System (ADS)

    Semprini, L.; Azizian, M.

    2012-12-01

    The demonstration of transformation of chlorinated aliphatic compounds (CAHs) in the subsurface is a challenge, especially when the products are carbon dioxide (CO2) and chloride ion. The groundwater contaminant carbon tetrachloride (CT) is of particular interest since a broad range of transformation products can be potentially formed under anaerobic conditions. The ability to demonstrate the transformation of CT to CO2 as a non toxic endproduct, is also of great interest. Results will be presented from a continuous flow column study where 13C labeled CT was used to demonstrate its transformation to CO2. The column was packed with a quartz sand and bioaugmented the Evanite Culture (EV) that is capable of transforming tetrachloroethene (PCE) to ethene. The column was continously fed a synthetic groundwater that was amended with PCE (0.10 mM) and either formate (1.5 mM) or lactate (1.1 mM), which ferments to produce hydrogen (H2) as the ultimate electron donor. Earlier CT transformation studies with the column, in the absence of sulfate reduction, and with formate added as a donor found CT (0.015 mM) was over 98% transformed with about 20% converted to chloroform (CF) (0.003 mM) and with a transient detection of chloromethane (CM). Methane and carbon disulfide, as potential products, were not detected. Neither CT nor CF inhibited the reductive dehalogenation of PCE to ethene. A series of transient studies conducted after these initial CT transformation tests, but in the absence of CT, showed formate remained an effective substrate for maintaining sulfate reduction and PCE transformation. Lactate, which was effectively fermented prior to CT addition, was not effectively fermented, with propionate accumulating as a fermentation product. When lactate was added, PCE was mainly transformed to cis-dichloroethene (cis-DCE) and VC, and sulfate reduction did not occur. In order to restore effective lactate fermentation the column was then bioaugmented with an EV culture that

  12. Structure and Metabolic-Flow Analysis of Molecular Complexity in a (13) C-Labeled Tree by 2D and 3D NMR.

    PubMed

    Komatsu, Takanori; Ohishi, Risa; Shino, Amiu; Kikuchi, Jun

    2016-05-10

    Improved signal identification for biological small molecules (BSMs) in a mixture was demonstrated by using multidimensional NMR on samples from (13) C-enriched Rhododendron japonicum (59.5 atom%) cultivated in air containing (13) C-labeled carbon dioxide for 14 weeks. The resonance assignment of 386 carbon atoms and 380 hydrogen atoms in the mixture was achieved. 42 BSMs, including eight that were unlisted in the spectral databases, were identified. Comparisons between the experimental values and the (13) C chemical shift values calculated by density functional theory supported the identifications of unlisted BSMs. Tracing the (13) C/(12) C ratio by multidimensional NMR spectra revealed faster and slower turnover ratios of BSMs involved in central metabolism and those categorized as secondary metabolites, respectively. The identification of BSMs and subsequent flow analysis provided insight into the metabolic systems of the plant.

  13. Specific 13C labeling of leucine, valine and isoleucine methyl groups for unambiguous detection of long-range restraints in protein solid-state NMR studies

    NASA Astrophysics Data System (ADS)

    Fasshuber, Hannes Klaus; Demers, Jean-Philippe; Chevelkov, Veniamin; Giller, Karin; Becker, Stefan; Lange, Adam

    2015-03-01

    Here we present an isotopic labeling strategy to easily obtain unambiguous long-range distance restraints in protein solid-state NMR studies. The method is based on the inclusion of two biosynthetic precursors in the bacterial growth medium, α-ketoisovalerate and α-ketobutyrate, leading to the production of leucine, valine and isoleucine residues that are exclusively 13C labeled on methyl groups. The resulting spectral simplification facilitates the collection of distance restraints, the verification of carbon chemical shift assignments and the measurement of methyl group dynamics. This approach is demonstrated on the type-three secretion system needle of Shigella flexneri, where 49 methyl-methyl and methyl-nitrogen distance restraints including 10 unambiguous long-range distance restraints could be collected. By combining this labeling scheme with ultra-fast MAS and proton detection, the assignment of methyl proton chemical shifts was achieved.

  14. Probing pyruvate metabolism in normal and mutant fibroblast cell lines using 13C-labeled mass isotopomer analysis and mass spectrometry.

    PubMed

    Riazi, Roya; Khairallah, Maya; Cameron, Jessie M; Pencharz, Paul B; Des Rosiers, Christine; Robinson, Brian H

    2009-12-01

    Fibroblast cell lines are frequently used to diagnose genetic mitochondrial defects in children. The effect of enzyme deficiency on overall flux rate through metabolic pathways is, however, not generally considered. We have transposed an experimental paradigm that was developed for isolated perfused organs using (13)C-labeled substrates and (13)C-isotopomer analysis to probe pyruvate mitochondrial metabolism in cultured human fibroblast cell lines with normal or genetically mutant pyruvate decarboxylation (PDC) or carboxylation (PC) activity. Cells were incubated with 1mM [U-(13)C]pyruvate, and the (13)C-molar percent enrichment (MPE) of intracellular pyruvate, citrate, malate (as a surrogate of oxaloacetate) and aspartate was assessed by mass spectrometry. We estimated various flux ratios relevant to metabolic pathways involved in energy production, namely pyruvate formation, PDC, PC, and citrate recycling in the citric acid cycle (CAC). In all cell lines, exogenous pyruvate was predominately decarboxylated (PC/PDC ratios 0.01-0.3). PC-deficient cell lines displayed an expected negligible contribution of PC flux to oxaloacetate formation for citrate synthesis (PC/CS), which was associated with a greater contribution of PDC to acetyl-CoA formation (PDC/CS), and greater recycling of (13)C-labeled citrate into the CAC. In PDH-deficient cell lines, metabolic flux alterations were most apparent in cells with more than 50% reduction in enzyme activity. This led to an unexpected lower PC/CS flux ratio, while the PDC/CS flux ratio was unchanged. These data illustrate the usefulness of this approach in identifying unexpected metabolic consequences of genetic defects related to pyruvate metabolism.

  15. 13C-labeled gluconate tracing as a direct and accurate method for determining the pentose phosphate pathway split ratio in Penicillium chrysogenum.

    PubMed

    Kleijn, Roelco J; van Winden, Wouter A; Ras, Cor; van Gulik, Walter M; Schipper, Dick; Heijnen, Joseph J

    2006-07-01

    In this study we developed a new method for accurately determining the pentose phosphate pathway (PPP) split ratio, an important metabolic parameter in the primary metabolism of a cell. This method is based on simultaneous feeding of unlabeled glucose and trace amounts of [U-13C]gluconate, followed by measurement of the mass isotopomers of the intracellular metabolites surrounding the 6-phosphogluconate node. The gluconate tracer method was used with a penicillin G-producing chemostat culture of the filamentous fungus Penicillium chrysogenum. For comparison, a 13C-labeling-based metabolic flux analysis (MFA) was performed for glycolysis and the PPP of P. chrysogenum. For the first time mass isotopomer measurements of 13C-labeled primary metabolites are reported for P. chrysogenum and used for a 13C-based MFA. Estimation of the PPP split ratio of P. chrysogenum at a growth rate of 0.02 h(-1) yielded comparable values for the gluconate tracer method and the 13C-based MFA method, 51.8% and 51.1%, respectively. A sensitivity analysis of the estimated PPP split ratios showed that the 95% confidence interval was almost threefold smaller for the gluconate tracer method than for the 13C-based MFA method (40.0 to 63.5% and 46.0 to 56.5%, respectively). From these results we concluded that the gluconate tracer method permits accurate determination of the PPP split ratio but provides no information about the remaining cellular metabolism, while the 13C-based MFA method permits estimation of multiple fluxes but provides a less accurate estimate of the PPP split ratio.

  16. Occurrence of Chlorotriazine herbicides and their transformation products in arable soils.

    PubMed

    Scherr, Kerstin E; Bielská, Lucie; Kosubová, Petra; Dinisová, Petra; Hvězdová, Martina; Šimek, Zdeněk; Hofman, Jakub

    2017-03-01

    Chlorotriazine herbicides (CTs) are widely used pest control chemicals. In contrast to groundwater contamination, little attention has been given to the circumstances of residue formation of parent compounds and transformation products in soils. Seventy-five cultivated floodplain topsoils in the Czech Republic were sampled in early spring of 2015, corresponding to a minimum of six months (current-use terbuthylazine, TBA) and a up to a decade (banned atrazine, AT and simazine, SIM) after the last herbicide application. Soil residues of parent compounds and nine transformation products were quantified via multiple residue analysis using liquid chromatography - tandem mass spectrometry of acetonitrile partitioning extracts (QuEChERS). Using principal component analysis (PCA), their relation to soil chemistry, crops and environmental parameters was determined. Of the parent compounds, only TBA was present in more than one sample. In contrast, at least one CT transformation product, particularly hydroxylated CTs, was detected in 89% of the sites, or 54% for banned triazines. Deethylated and bi-dealkylated SIM or AT residues were not detectable. PCA suggests the formation and/or retention of CT hydroxy-metabolite residues to be related to low soil pH, and a direct relation between TBA and soil organic carbon, and between deethyl-TBA and clay or Ca contents, respectively, the latter pointing towards distinct sorption mechanisms. The low historic application of simazine contrasted by the high abundance of its residues, and the co-occurrence with AT residues suggests the post-ban application of AT and SIM banned triazines as a permitted impurity of TBA formulations as a recent, secondary source. The present data indicate that topsoils do not contain abundant extractable residues of banned parent chlorotriazines, and are thus likely not the current source for related ground- and surface water contamination. In contrast, topsoils might pose a long-term source of TBA and CT

  17. Specificity of Cs-137 redistribution in toposequence of arable soils cultivated after the Chernobyl accident

    NASA Astrophysics Data System (ADS)

    Korobova, Elena; Romanov, Sergey; Baranchukov, Vladimir; Berezkin, Victor; Moiseenko, Fedor; Kirov, Sergey

    2017-04-01

    Investigations performed after the Chernobyl accident showed high spatial variation of radionuclide contamination of the soil cover in elementary landscape geochemical systems (ELGS) that characterize catena's structure. Our studies of Cs-137 distribution along and cross the slopes of local ridges in natural forested key site revealed a cyclic character of variation of the radionuclide surface activity along the studied transections (Korobova et al, 2008; Korobova, Romanov, 2009; 2011). We hypothesized that the observed pattern reflects a specific secondary migration of Cs-137 with water, and that this process could have taken place in any ELGS. To test this hypothesis a detailed field measurement of Cs-137 surface activity was performed in ELGS in agricultural area cultivated after the Chernobyl accident but later withdrawn from land-use. In situ measurements carried out by field gamma-spectrometry were accompanied by soil core sampling at the selected points. Soil samples were taken in increments of 2 cm down to 20 cm and of 5 cm down to 40 cm. The samples were analyzed for Cs-137 in laboratory using Canberra gamma-spectrometer with HP-Ge detector. Obtained results confirmed the fact of area cultivation down to 20 cm that was clearly traced by Cs-137 profile in soil columns. At the same time, the measurements also showed a cyclic character of Cs-137 variation in a sequence of ELGS from watershed to the local depression similar to that found in woodland key site. This proved that the observed pattern is a natural process typical for matter migration in ELGS independently of the vegetation type and ploughing. Therefore, spatial aspect is believed to be an important issue for development of adequate technique for a forecast of contamination of agricultural production and remediation of the soil cover on the local scale within the contaminated areas. References Korobova, E.M., Romanov, S.L., 2009. A Chernobyl 137Cs contamination study as an example for the spatial

  18. Carbon dynamics with prolonged arable cropping soils in the Dano district (Southwest Burkina-Faso)

    NASA Astrophysics Data System (ADS)

    Hounkpatin, Ozias; Welp, Gerhard; Amelung, Wulf

    2016-04-01

    The conversion of natural ecosystems into agricultural land affects the atmospheric CO2 concentration whose increase contributes to global warming. In the low activity clay soils (LAC) of the tropics, farming is largely dependent on the level of soil organic carbon (SOC) for sustainable crop production. In this study, we investigated the changes in SOC in Plinthosols along a cultivation chronosequence in the Dano district (Southwest Burkina-Faso). The chronosequence consisted of undisturbed savannah (Y0) and 11 agricultural fields with short and long histories of cultivation ranging from 1-year-old cropland to 29-year-old cropland (Y29). About 14 soil profiles were described and soil composite samples were taken per horizon. Particulate organic matter (POM) was fractionated according to particle size: fraction 2000 - 250 μm (POM1), 250 μm - 53 μm (POM2), 53 μm - 20 μm (POM3), and < 20 μm (nonPOM). Our results revealed that the extent of change in SOC stock varied with depth and the age of the cropland. The impact of cultivation was greater in the top 10 cm with a decrease in SOC stock of 21 t C/ha after 29 years of cropping indicating that about 60% of the initial stock in the native vegetation had been released. The SOC content and stock in the different POM fractions followed the following pattern: non POM > POM1 > POM3 > POM2 carbon no matter the duration of land use. However, SOC losses occurred not only in the labile C pools but also in the stabile nonPOM fraction with increasing duration of agricultural land use. Compared to the initial carbon content in the Y0 field, about 59% of carbon content loss occurred in the POM1 (> 250 μm), 53% in the POM2 (250 - 53 μm), 52 % in the POM3 (53 - 20 μm) and 47% in the nonPOM fraction (< 20 μm) after 11 years of cultivation while 79 % occurred in the POM1 C, 75% in the POM2C, 78 % in the POM3 C and 67% in the nonPOM C after 29 years of cultivation. Though most carbon was found as nonPOM, indicating that organo

  19. Impact of manure-related DOM on sulfonamide transport in arable soils

    NASA Astrophysics Data System (ADS)

    Zhou, Dan; Thiele-Bruhn, Sören; Arenz-Leufen, Martina Gesine; Jacques, Diederik; Lichtner, Peter; Engelhardt, Irina

    2016-09-01

    Field application of livestock manure introduces colloids and veterinary antibiotics, e.g. sulfonamides (SAs), into farmland. The presence of manure colloids may potentially intensify the SAs-pollution to soils and groundwater by colloid-facilitated transport. Transport of three SAs, sulfadiazine (SDZ), sulfamethoxypyridazine (SMPD), and sulfamoxole (SMOX), was investigated in saturated soil columns with and without manure colloids from sows and farrows, weaners, and fattening pigs. Experimental results showed that colloid-facilitated transport of SMOX was significant in the presence of manure colloids from fattening pigs with low C/N ratio, high SUVA280 nm and protein C, while manure colloids from sows and farrows and weaners had little effect on SMOX transport. In contrast, only retardation was observed for SDZ and SMPD when manure colloids were present. Breakthrough curves (BTCs) of colloids and SAs were replicated well by a newly developed numerical model that considers colloid-filtration theory, competitive kinetic sorption, and co-transport processes. Model results demonstrate that mobile colloids act as carriers for SMOX, while immobile colloids block SMOX from sorbing onto the soil. The low affinity of SMOX to sorb on immobile colloids prevents aggregation and also promotes SMOX's colloid-facilitated transport. Conversely, the high affinity of SDZ and SMPD to sorb on all types of immobile colloids retarded their transport. Thus, manure properties play a fundamental role in increasing the leaching risk of hydrophobic sulfonamides.

  20. Drying-rewetting cycles affect fungal and bacterial growth differently in an arable soil.

    PubMed

    Bapiri, Azadeh; Bååth, Erland; Rousk, Johannes

    2010-08-01

    Drying and rewetting is a frequent physiological stress for soil microbial communities; a stress that is predicted to grow more influential with future climate change. We investigated the effect of repeated drying-rewetting cycles on bacterial (leucine incorporation) and fungal (acetate in ergosterol incorporation) growth, on the biomass concentration and composition (PLFA), and on the soil respiration. Using different plant material amendments, we generated soils with different initial fungal:bacterial compositions that we exposed to 6-10 repetitions of a drying-rewetting cycle. Drying-rewetting decreased bacterial growth while fungal growth remained unaffected, resulting in an elevated fungal:bacterial growth ratio. This effect was found irrespective of the initial fungal:bacterial biomass ratio. Many drying-rewetting cycles did not, however, affect the fungal:bacterial growth ratio compared to few cycles. The biomass response of the microbial community differed from the growth response, with fungal and total biomass only being slightly negatively affected by the repeated drying-rewetting. The discrepancy between growth- and biomass-based assessments underscores that microbial responses to perturbations might previously have been misrepresented with biomass-based assessments. In light of this, many aspects of environmental microbial ecology may need to be revisited with attention to what measure of the microbial community is relevant to study.

  1. Geographical features of the distribution and renewal of easily decomposable organic matter in virgin and arable zonal soils of European Russia

    NASA Astrophysics Data System (ADS)

    Borisov, B. A.; Ganzhara, N. F.

    2008-09-01

    A decrease in the depth of organic surface horizons (forest litters and steppe mats), the reserves of organic matter in them, and an increase in their renewal rate were noted for virgin and fallow soils when going from the southern taiga to the dry steppe zone. Zonal changes in the content and reserve of easily decomposable soil organic matter showed a similar tendency: these parameters regularly decreased from soddy-podzolic soils of the southern taiga to chestnut and light chestnut soils of the dry steppe. An exception from this series is provided by fallow chernozems of the steppe zone noted for the lowest content and reserve of labile organic matter in the series of soils studied. Similar, although less pronounced, tendencies were observed for the arable soils.

  2. Biogeochemistry of Ni and Pb in a periodically flooded arable soil: Fractionation and redox-induced (im)mobilization.

    PubMed

    Antić-Mladenović, Svetlana; Frohne, Tina; Kresović, Mirjana; Stärk, Hans-Joachim; Tomić, Zorica; Ličina, Vlado; Rinklebe, Jörg

    2017-01-15

    The redox-induced (im)mobilization of nickel (Ni) and lead (Pb) under pre-definite redox conditions and their binding forms were studied in a periodically flooded, slightly acidic arable soil enriched with serpentine minerals at the Velika Morava River valley, Serbia. The total contents of Ni and Pb were 152 and 109 mg kg(-1), respectively. Geochemical fractionation of Ni, combined with mineralogical analysis, confirmed its geogenic origin in the soil. Potentially mobile fractions were the dominating binding forms of Pb; thus, indicating anthropogenic sources as prevailing. Risk assessment indicated a low risk of Ni and Pb transfer from soil to other environmental constituents. However, the results imply that geogenic metals might pose higher environmental risk than those from anthropogenic origin, in dependence of their total concentrations and contents in the specific solid-phase fractions. Flooding of the soil was simulated in an automated biogeochemical microcosm system, which allows a control and a continuous measurements of redox potential (EH) and pH. Subsequently, the EH was increased in steps of approximately 100 mV from anoxic to oxic conditions. Concurrently, the concentrations of soluble Ni, Pb, iron (Fe), manganese (Mn), dissolved organic carbon (DOC), and sulfates were measured. The EH was brought from low to high values (-220 to 520 mV) and correlated negative with soluble Ni, Pb, Fe, Mn and DOC. Soluble Ni ranged from 125 to 228 μg l(-1) while Pb ranged from 3.0 to 21.4 μg l(-1). Concentrations of both metals in solution were high at low EH and decreased with increasing EH. Nickel immobilization may be attributed to sorption to or co-precipitation with re-oxidized Fe-Mn (hydr)oxides, whereas Pb, in addition, might be immobilized via precipitation with inorganic ligands, such as carbonates and phosphates. The results imply that Ni and Pb solubility might also be related to the formation of metal-DOC complexes. The detected dynamic and

  3. Studies on organic and in-organic biostimulants in bioremediation of diesel-contaminated arable soil.

    PubMed

    Nwankwegu, Amechi S; Orji, Michael U; Onwosi, Chukwudi O

    2016-11-01

    In this study, use of inorganic fertilizer (N.P.K) was compared with organic manure (compost) in the bioremediation of diesel-polluted agricultural soil over a two-month period. Renewal by enhanced natural attenuation was used as control. The results revealed that total petroleum hydrocarbon removal from polluted soil was 71.40 ± 5.60% and 93.31 ± 3.60% for N.P.K and compost amended options, respectively. The control (natural attenuation) had 57.90 ± 3.98% of total petroleum hydrocarbon removed. Experimental data fitted second order kinetic model adequately for compost amended option. The fertilizer amended option was found to be 1.04 times slower (k2 = 4.00 ± 1.40 × 10(-7)gmg(-1)d(-1), half-life = 28.15 d) than compost amended option (k2 = 1.39 ± 0.54 × 10(-5) gmg(-1)d(-1), half-life = 8.10 d) but 1.21 times (20.6%) faster than the control (k2 = 2.57 ± 0.16 × 10(-7) gmg(-1)d(-1), half-life = 43.81 d). The hydrocarbon utilizers isolated from the diesel contaminated soil were: Bacillus nealsoni, Micrococcus luteus, Aspergillus awamori, and Fusarium proliferatum. The phytotoxicity test showed that germination indices for natural attenuation (control), fertilizer (NPK) and compost amended options were 34%, 56%, and 89%, respectively. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Redox-controlled release dynamics of thallium in periodically flooded arable soil.

    PubMed

    Antić-Mladenović, Svetlana; Frohne, Tina; Kresović, Mirjana; Stärk, Hans-Joachim; Savić, Dubravka; Ličina, Vlado; Rinklebe, Jörg

    2017-07-01

    To our knowledge, this is the first work to mechanistically study the impact of the redox potential (EH) and principal factors, such as pH, iron (Fe), manganese (Mn), dissolved organic carbon (DOC), dissolved inorganic carbon (DIC), chlorides (Cl(-)) and sulfates (SO4(2-)), on the release dynamics of thallium (Tl) in periodically flooded soil. We simulated flooding using an automated biogeochemical microcosm system that allows for systematical control of pre-defined redox windows. The EH value was increased mechanistically at intervals of approximately 100 mV from reducing (-211 mV) to oxidizing (475 mV) conditions. Soluble Tl levels (0.02-0.28 μg L(-1)) increased significantly with increases in EH (r = 0.80, p < 0.01, n = 30). Thallium mobilization was found to be related to several simultaneous processes involving the gradual oxidation of Tl-bearing sulfides, reductive dissolution of Fe-Mn oxides and desorption from mineral sorbents. Manganese oxides did not appear to have a considerable effect on Tl retention under oxidizing conditions. Before conducting the microcosm experiment, Tl geochemical fractionation was assessed using the modified BCR sequential extraction procedure. The BCR revealed a majority of Tl in the residual fraction (77.7%), followed by reducible (13.3%) and oxidizable fractions (5.9%). By generating high levels of Tl toxicity at low doses, Tl released under oxidizing conditions may pose an environmental threat. In the future, similar studies should be conducted on various soils along with a determination of the Tl species and monitoring of the Tl content in plants to achieve more detailed insight into soluble Tl behavior. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Incorporation of plant carbon into the soil animal food web of an arable system.

    PubMed

    Albers, Derk; Schaefer, Matthias; Scheu, Stefan

    2006-01-01

    We used stable isotopes to examine the incorporation of plant carbon into the belowground food web of an agricultural system. Plots were established and planted with maize (Zea mays) in a rye field (Secale cereale) near Göttingen (northern Germany) in May 1999. In October 1999, April 2000, and October 2000, meso- and macrofauna and maize and rye litter were collected in each plot and analyzed for 13C and 15N content. 15N signatures suggested that the soil animal species analyzed span three trophic levels with the trophic position of species varying little in time. The species investigated formed a continuum from primary to secondary decomposers to predators. On average, predator species differed from primary and secondary decomposers by 3.9 sigma15N suggesting that they fed on a mixed diet of both decomposer groups. The combined analysis of 13C and 15N signatures allowed us to identify links between prey and consumer species. In October 1999, shortly after maize residues had been incorporated into the plots, maize-born carbon was present in each of the animal species investigated, including top predators. The incorporation of maize carbon into the belowground food web increased during the following 12 months but the concentration of maize-born carbon never exceeded 50% in any of the species. Furthermore, the ranks of the incorporation of maize-born carbon of the species changed little. The results suggest that the belowground food web relies heavily on carbon originating from plant residues from before the recent two growing seasons. In most species the amount of maize-born carbon increased continuously; however, in some species it decreased during winter, suggesting that these species switched to a diet based more on C3 plants during winter, or predominantly metabolized carbon incorporated during the last growing season. The study documents that the combined analysis of 13C and 15N signatures in soil invertebrate species, after replacement of C3 by C4 plants, is

  6. Disentangling the root- and detritus-based food chain in the micro-food web of an arable soil by plant removal

    PubMed Central

    Glavatska, Olena; Müller, Karolin; Butenschoen, Olaf; Schmalwasser, Andreas; Kandeler, Ellen; Scheu, Stefan; Totsche, Kai Uwe

    2017-01-01

    Soil food web structure and function is primarily determined by the major basal resources, which are living plant tissue, root exudates and dead organic matter. A field experiment was performed to disentangle the interlinkage of the root-and detritus-based soil food chains. An arable site was cropped either with maize, amended with maize shoot litter or remained bare soil, representing food webs depending on roots, aboveground litter and soil organic matter as predominant resource, respectively. The soil micro-food web, i.e. microorganisms and nematodes, was investigated in two successive years along a depth transect. The community composition of nematodes was used as model to determine the changes in the rhizosphere, detritusphere and bulk soil food web. In the first growing season the impact of treatments on the soil micro-food web was minor. In the second year plant-feeding nematodes increased under maize, whereas after harvest the Channel Index assigned promotion of the detritivore food chain, reflecting decomposition of root residues. The amendment with litter did not foster microorganisms, instead biomass of Gram-positive and Gram-negative bacteria as well as that of fungi declined in the rooted zone. Likely higher grazing pressure by nematodes reduced microbial standing crop as bacterial and fungal feeders increased. However, populations at higher trophic levels were not promoted, indicating limited flux of litter resources along the food chain. After two years of bare soil microbial biomass and nematode density remained stable, pointing to soil organic matter-based resources that allow bridging periods with deprivation. Nematode communities were dominated by opportunistic taxa that are competitive at moderate resource supply. In sum, removal of plants from the system had less severe effects than expected, suggesting considerable food web resilience to the disruption of both the root and detrital carbon channel, pointing to a legacy of organic matter

  7. Disentangling the root- and detritus-based food chain in the micro-food web of an arable soil by plant removal.

    PubMed

    Glavatska, Olena; Müller, Karolin; Butenschoen, Olaf; Schmalwasser, Andreas; Kandeler, Ellen; Scheu, Stefan; Totsche, Kai Uwe; Ruess, Liliane

    2017-01-01

    Soil food web structure and function is primarily determined by the major basal resources, which are living plant tissue, root exudates and dead organic matter. A field experiment was performed to disentangle the interlinkage of the root-and detritus-based soil food chains. An arable site was cropped either with maize, amended with maize shoot litter or remained bare soil, representing food webs depending on roots, aboveground litter and soil organic matter as predominant resource, respectively. The soil micro-food web, i.e. microorganisms and nematodes, was investigated in two successive years along a depth transect. The community composition of nematodes was used as model to determine the changes in the rhizosphere, detritusphere and bulk soil food web. In the first growing season the impact of treatments on the soil micro-food web was minor. In the second year plant-feeding nematodes increased under maize, whereas after harvest the Channel Index assigned promotion of the detritivore food chain, reflecting decomposition of root residues. The amendment with litter did not foster microorganisms, instead biomass of Gram-positive and Gram-negative bacteria as well as that of fungi declined in the rooted zone. Likely higher grazing pressure by nematodes reduced microbial standing crop as bacterial and fungal feeders increased. However, populations at higher trophic levels were not promoted, indicating limited flux of litter resources along the food chain. After two years of bare soil microbial biomass and nematode density remained stable, pointing to soil organic matter-based resources that allow bridging periods with deprivation. Nematode communities were dominated by opportunistic taxa that are competitive at moderate resource supply. In sum, removal of plants from the system had less severe effects than expected, suggesting considerable food web resilience to the disruption of both the root and detrital carbon channel, pointing to a legacy of organic matter

  8. Biokinetics of (13)C in the human body after oral administration of (13)C-labeled glucose as an index for the biokinetics of (14)C.

    PubMed

    Masuda, Tsuyoshi; Tako, Yasuhiro; Matsushita, Kensaku; Takeda, Hiroshi; Endo, Masahiro; Nakamura, Yuji; Hisamatsu, Shun'ichi

    2016-09-01

    The retention of (13)C in the human body after oral administration of (13)C-labeled glucose was studied in three healthy volunteer subjects to estimate the 50 year cumulative body burden for (13)C as an index of the committed dose of the radioisotope (14)C. After administration of (13)C-labeled glucose, the volunteers ingested controlled diets with a fixed number of calories for 112 d. Samples of breath and urine were collected up to 112 d after administration. Samples of feces were collected up to 14 d after administration. Hair samples were obtained at 119 d after administration and analyzed as a representative index of the rate of excretion of organic (13)C via pathways such as skin cell exfoliation and mucus secretion. All samples were analyzed for (13)C/(12)C atomic ratio to determine the rate of excretion via each pathway. We then constructed a metabolic model with a total of four pathways (breath, urine, feces, and other) comprising seven compartments. We determined the values of the biokinetic parameters in the model by using the obtained excretion data. From 74% to 94% of the (13)C administered was excreted in breath, whereas  <2% was excreted in urine and feces. In the other pathway, the excretion rate constant in the compartment with the longest residence time stretched to hundreds of days but the rate constant for each subject was not statistically significant (P value  >  0.1). In addition, the dataset for one of the three subjects was markedly different from those of the other two. When we estimated the 50 year cumulative body burden for (13)C by using our model and we included non-statistically significant parameters, a considerable cumulative body burden was found in the compartments excreting to the other pathway. Although our results on the cumulative body burden of (13)C from orally administered carbon as glucose were inconclusive, we found that the compartments excreting to the other pathway had a markedly long residence time and

  9. Biogenic Volatile Organic Compound and Respiratory CO2 Emissions after 13C-Labeling: Online Tracing of C Translocation Dynamics in Poplar Plants

    PubMed Central

    Ghirardo, Andrea; Gutknecht, Jessica; Zimmer, Ina; Brüggemann, Nicolas; Schnitzler, Jörg-Peter

    2011-01-01

    Background Globally plants are the primary sink of atmospheric CO2, but are also the major contributor of a large spectrum of atmospheric reactive hydrocarbons such as terpenes (e.g. isoprene) and other biogenic volatile organic compounds (BVOC). The prediction of plant carbon (C) uptake and atmospheric oxidation capacity are crucial to define the trajectory and consequences of global environmental changes. To achieve this, the biosynthesis of BVOC and the dynamics of C allocation and translocation in both plants and ecosystems are important. Methodology We combined tunable diode laser absorption spectrometry (TDLAS) and proton transfer reaction mass spectrometry (PTR-MS) for studying isoprene biosynthesis and following C fluxes within grey poplar (Populus x canescens) saplings. This was achieved by feeding either 13CO2 to leaves or 13C-glucose to shoots via xylem uptake. The translocation of 13CO2 from the source to other plant parts could be traced by 13C-labeled isoprene and respiratory 13CO2 emission. Principal Finding In intact plants, assimilated 13CO2 was rapidly translocated via the phloem to the roots within 1 hour, with an average phloem transport velocity of 20.3±2.5 cm h−1. 13C label was stored in the roots and partially reallocated to the plants' apical part one day after labeling, particularly in the absence of photosynthesis. The daily C loss as BVOC ranged between 1.6% in mature leaves and 7.0% in young leaves. Non-isoprene BVOC accounted under light conditions for half of the BVOC C loss in young leaves and one-third in mature leaves. The C loss as isoprene originated mainly (76–78%) from recently fixed CO2, to a minor extent from xylem-transported sugars (7–11%) and from photosynthetic intermediates with slower turnover rates (8–11%). Conclusion We quantified the plants' C loss as respiratory CO2 and BVOC emissions, allowing in tandem with metabolic analysis to deepen our understanding of ecosystem C flux. PMID:21387007

  10. Evidence of polycyclic aromatic hydrocarbon biodegradation in a contaminated aquifer by combined application of in situ and laboratory microcosms using (13)C-labelled target compounds.

    PubMed

    Bahr, Arne; Fischer, Anko; Vogt, Carsten; Bombach, Petra

    2015-02-01

    The number of approaches to evaluate the biodegradation of polycyclic aromatic hydrocarbons (PAHs) within contaminated aquifers is limited. Here, we demonstrate the applicability of a novel method based on the combination of in situ and laboratory microcosms using (13)C-labelled PAHs as tracer compounds. The biodegradation of four PAHs (naphthalene, fluorene, phenanthrene, and acenaphthene) was investigated in an oxic aquifer at the site of a former gas plant. In situ biodegradation of naphthalene and fluorene was demonstrated using in situ microcosms (BACTRAP(®)s). BACTRAP(®)s amended with either [(13)C6]-naphthalene or [(13)C5/(13)C6]-fluorene (50:50) were incubated for a period of over two months in two groundwater wells located at the contaminant source and plume fringe, respectively. Amino acids extracted from BACTRAP(®)-grown cells showed significant (13)C-enrichments with (13)C-fractions of up to 30.4% for naphthalene and 3.8% for fluorene, thus providing evidence for the in situ biodegradation and assimilation of those PAHs at the field site. To quantify the mineralisation of PAHs, laboratory microcosms were set up with BACTRAP(®)-grown cells and groundwater. Naphthalene, fluorene, phenanthrene, or acenaphthene were added as (13)C-labelled substrates. (13)C-enrichment of the produced CO2 revealed mineralisation of between 5.9% and 19.7% for fluorene, between 11.1% and 35.1% for acenaphthene, between 14.2% and 33.1% for phenanthrene, and up to 37.0% for naphthalene over a period of 62 days. Observed PAH mineralisation rates ranged between 17 μg L(-1) d(-1) and 1639 μg L(-1) d(-1). The novel approach combining in situ and laboratory microcosms allowed a comprehensive evaluation of PAH biodegradation at the investigated field site, revealing the method's potential for the assessment of PAH degradation within contaminated aquifers.

  11. Biogenic volatile organic compound and respiratory CO2 emissions after 13C-labeling: online tracing of C translocation dynamics in poplar plants.

    PubMed

    Ghirardo, Andrea; Gutknecht, Jessica; Zimmer, Ina; Brüggemann, Nicolas; Schnitzler, Jörg-Peter

    2011-02-28

    Globally plants are the primary sink of atmospheric CO(2), but are also the major contributor of a large spectrum of atmospheric reactive hydrocarbons such as terpenes (e.g. isoprene) and other biogenic volatile organic compounds (BVOC). The prediction of plant carbon (C) uptake and atmospheric oxidation capacity are crucial to define the trajectory and consequences of global environmental changes. To achieve this, the biosynthesis of BVOC and the dynamics of C allocation and translocation in both plants and ecosystems are important. We combined tunable diode laser absorption spectrometry (TDLAS) and proton transfer reaction mass spectrometry (PTR-MS) for studying isoprene biosynthesis and following C fluxes within grey poplar (Populus x canescens) saplings. This was achieved by feeding either (13)CO(2) to leaves or (13)C-glucose to shoots via xylem uptake. The translocation of (13)CO(2) from the source to other plant parts could be traced by (13)C-labeled isoprene and respiratory (13)CO(2) emission. In intact plants, assimilated (13)CO(2) was rapidly translocated via the phloem to the roots within 1 hour, with an average phloem transport velocity of 20.3±2.5 cm h(-1). (13)C label was stored in the roots and partially reallocated to the plants' apical part one day after labeling, particularly in the absence of photosynthesis. The daily C loss as BVOC ranged between 1.6% in mature leaves and 7.0% in young leaves. Non-isoprene BVOC accounted under light conditions for half of the BVOC C loss in young leaves and one-third in mature leaves. The C loss as isoprene originated mainly (76-78%) from recently fixed CO(2), to a minor extent from xylem-transported sugars (7-11%) and from photosynthetic intermediates with slower turnover rates (8-11%). We quantified the plants' C loss as respiratory CO(2) and BVOC emissions, allowing in tandem with metabolic analysis to deepen our understanding of ecosystem C flux.

  12. Effects of sulfachlorpyridazine in MS.3-arable land: a multispecies soil system for assessing the environmental fate and effects of veterinary medicines.

    PubMed

    Boleas, Sara; Alonso, Carmen; Pro, Javier; Babín, M Mar; Fernández, Carlos; Carbonell, Gregoria; Tarazona, José V

    2005-04-01

    A multispecies soil system (MS.3) has been used to evaluate the ecological effects of veterinary pharmaceuticals in soil as a result of routine agricultural practices. Different experimental conditions were tested and the variation of the different parameters was evaluated for a final design. A protocol for the MS.3-arable land is presented here. Emergence of seedlings, plant elongation and biomass, earthworm mortality, and soil microbial enzymatic activities have been selected as toxicological endpoints for soil organisms. Toxicity tests were conducted with the leachate on aquatic organisms (in vitro fish cell lines, daphnids, and algae). The system was used for assessing the effects of the antimicrobial sulfachlorpyridazine that was tested in triplicate at concentrations of 0.01, 1, and 100 mg/kg. The chemical was mixed uniformly with a 20-cm depth soil column to resemble the distribution of manure within arable soil. Reversible and nonreversible effects on soil enzymatic activities were observed at 1 and 100 mg/kg, respectively. Earthworms were not affected. Significant reduction of plant elongation and biomass was observed at the highest concentration. Degradation and leaching contributed to the dissipation of sulfachlorpyridazine from the soil column. The undiluted leachate was highly toxic to Daphnia magna. The parent chemical was assumed responsible for the leachate toxicity although the role of mobile metabolites could not be excluded fully. No significant effects were observed for green algae Chlorella vulgaris and for the rainbow trout established cell lines RTG-2 (rainbow trout gonads) and RTL-WI (rainbow trout liver). The MS.3 system offers a cost-effective experimental approach to measure simultaneously fate and effects of chemicals on a realistic soil system under controlled laboratory conditions. The advantages of using MS.3-effect endpoints are discussed.

  13. Influence of conventional biochar and ageing biochar application to arable soil on soil fertility and plant yield

    NASA Astrophysics Data System (ADS)

    Dvořáčková, Helena; Záhora, Jaroslav; Elbl, Jakub; Kynický, Jindřich; Hladký, Jan; Brtnický, Martin

    2017-04-01

    Biochar represents very controversial material which is product of pyrolysis. According to many studies biochar has positive effect on physical and chemical properties such as pH, conductivity, aggregates stability etc. Unfortunately biochar is product of combustion, so it can content toxic substance as are aromatic compound. These substances may have a negative effect on yield and microbial activities in soil. Our aim was eliminated concentration of toxic compound but preserved positive effect of biochar on soil properties. We was ageing/ activating of biochar in water environment and for soil inoculum we used native soil from landscape. Moreover two types of biochar was tested by pot experiment with seven variants, where conventional biochar from residual biomass and ageing biochar were applied in different doses: 10 t/ha, 20t/ha and 50 t/ha. Pots were placed in green house for 90 days and after the end of experiment the following parameters of soil fertility, health and quality were evaluated: content of soil organic matter, arbuscular mycorrhizal colonisation of Lactuca sativa L. roots, leaching of mineral nitrogen, changes in plant available nutrient content, EC and pH. Above all the total yield of indicator plant was observed. The significant (P < 0.05) differences in plant yield and soil properties were found. The application of conventional biochar didn't have positive effect on plant yield in comparison with ageing biochar. The positive effect of ageing biochar addition on soil fertility was directly proportional to the dose which were applied - increasing in dose of ageing biochar resulted in increase of plant yield. Moreover the special experimental containers were used, where we was able to monitor the development of root in soil with and without addition of biochar (conventional or ageing). The positive influence of ageing biochar addition into soil on development of Lactuca sativa L. roots was observed.

  14. Manipulation of temperature and precipitation alter CO2 and N2O fluxes from an arable soil

    NASA Astrophysics Data System (ADS)

    Poll, Christian; Marhan, Sven; Kandeler, Ellen

    2010-05-01

    Carbon cycling in terrestrial ecosystems provides a feedback mechanism to climate change by releasing or sequestering additional atmospheric CO2. However, the response of terrestrial carbon cycling to the interactive effects of a changing temperature and precipitation regime is still unclear. A field experiment was established in summer 2008 to manipulate soil temperature and precipitation on an arable field. The plots are covered by roofs, which are closed with a UV-transparent greenhouse film during summer. Roof control plots (without roof) were additionally established to account for the impact of the roof on the micro-environmental conditions (only Ambient precipitation). Each treatment is replicated four times. Soil temperature is increased by 2.5°C in 4 cm depth using heating cables, which are placed on the surface. Temperature probes in 4 cm depth are connected to a datalogger, which controls the electricity supply of the heating system. Each ambient and elevated temperature plot has a size of 4 x 1 m² and is divided into 4 subplots according to the following precipitation manipulation treatments: a) ambient, b) precipitation amount decreased by 25% during summer and increased by 25% during winter, c) drought periods increased by 50% during summer, d) combination of b and c. Each subplot is surrounded by a PVC barrier to a depth of 0.5 m to avoid lateral water movement between subplots and the surrounding soil. The experimental plots were planted with spring wheat (Triticum aestivum) in 2009. Plants were harvested in August and aboveground biomass was determined. We measured the CO2 and N2O fluxes weekly using the closed chamber method. After mid of October, the closure time was increased from 30 to 60 min to account for low gas fluxes. First results indicate that the manipulation of climatic factors (soil temperature, precipitation) induced short-term effects one year after start of the field experiment. Aboveground wheat biomass was increased by elevated

  15. Vertical distribution of soil organic carbon originated from a prior peatland in Greece and impacts on the landscape, after conversion to arable land

    NASA Astrophysics Data System (ADS)

    Kayrotis, Theodore; Charoulis, A.; Vavoulidou, E.; Tziouvalekas, M.

    2010-05-01

    The vertical distribution and the status of soil organic carbon (Corg.) in 66 surface and subsurface soil samples were investigated. These soils originated mainly from organic deposits of Philippoi (northern Greece) have been classified as Histosols and belong to the suborder of Saprists. The present study consisted of an area of 10,371 ha where about 90% of the soils are organic. The main crops are maize (Zea mays L.), sugar beets (Beta vulgaris L.), tobacco (Nicotiana tabacum L.), cotton (Gossypium hirsutum L.), tomatoes (Lycopersicon esculentum Mill.), and wheat (Triticum aestivum L.).The surface horizons consist mainly of well-humified organic materials mixed with mineral soil particles. Usually, they have moderate or insufficient drainage regime and conditions become favorable for microbial growth. Microbes decompose and transform the soil organic compounds into mineral forms, which are then available as nutrients for the crop. The organic matter was derived primarily from Cyperaceae (Cladium mariscus, various Carex species, etc.) and from decomposed residues of arable crops. The dominant features of these soils are the high content of organic matter and the obvious stratification of soil horizons. In contrast, most arable soils in Greece are characterized by low organic matter content. The stratification differentiates the physical and chemical properties and the groundwater table even during dry summers lies at depths,150 cm beneath surface. The Corg. content was high and varied greatly among the examined samples. In the surface layers ranged between 3.57 and 336.50 g kg2 (mean 199.26 g kg2) and between 22.10 and 401.10 g kg2 in the subsurface horizons (mean 258.89 g kg2). It can be argued that surface layers are drier and part of soil organic matter was seriously affected by the process of oxidation. At drier sites, soil subsidence was appeared as a consequence of soil organic matter oxidation. Increased contents were found in the northern part of the

  16. Accurate measurements of 13C-13C distances in uniformly 13C-labeled proteins using multi-dimensional four-oscillating field solid-state NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Straasø, Lasse Arnt; Nielsen, Jakob Toudahl; Bjerring, Morten; Khaneja, Navin; Nielsen, Niels Chr.

    2014-09-01

    Application of sets of 13C-13C internuclear distance restraints constitutes a typical key element in determining the structure of peptides and proteins by magic-angle-spinning solid-state NMR spectroscopy. Accurate measurements of the structurally highly important 13C-13C distances in uniformly 13C-labeled peptides and proteins, however, pose a big challenge due to the problem of dipolar truncation. Here, we present novel two-dimensional (2D) solid-state NMR experiments capable of extracting distances between carbonyl (13C') and aliphatic (13Caliphatic) spins with high accuracy. The method is based on an improved version of the four-oscillating field (FOLD) technique [L. A. Straasø, M. Bjerring, N. Khaneja, and N. C. Nielsen, J. Chem. Phys. 130, 225103 (2009)] which circumvents the problem of dipolar truncation, thereby offering a base for accurate extraction of internuclear distances in many-spin systems. The ability to extract reliable accurate distances is demonstrated using one- and two-dimensional variants of the FOLD experiment on uniformly 13C,15N-labeled-L-isoleucine. In a more challenging biological application, FOLD 2D experiments are used to determine a large number of 13C'-13Caliphatic distances in amyloid fibrils formed by the SNNFGAILSS fibrillating core of the human islet amyloid polypeptide with uniform 13C,15N-labeling on the FGAIL fragment.

  17. Determination of the Orientation and Dynamics of Ergosterol in Model Membranes Using Uniform 13C Labeling and Dynamically Averaged 13C Chemical Shift Anisotropies as Experimental Restraints

    PubMed Central

    Soubias, O.; Jolibois, F.; Massou, S.; Milon, A.; Réat, V.

    2005-01-01

    A new strategy was established to determine the average orientation and dynamics of ergosterol in dimyristoylphosphatidylcholine model membranes. It is based on the analysis of chemical shift anisotropies (CSAs) averaged by the molecular dynamics. Static 13C CSA tensors were computed by quantum chemistry, using the gauge-including atomic-orbital approach within Hartree-Fock theory. Uniformly 13C-labeled ergosterol was purified from Pichia pastoris cells grown on labeled methanol. After reconstitution into dimyristoylphosphatidylcholine lipids, the complete 1H and 13C assignment of ergosterol's resonances was performed using a combination of magic-angle spinning two-dimensional experiments. Dynamically averaged CSAs were determined by standard side-band intensity analysis for isolated 13C resonances (C3 and ethylenic carbons) and by off-magic-angle spinning experiments for other carbons. A set of 18 constraints was thus obtained, from which the sterol's molecular order parameter and average orientation could be precisely defined. The validity of using computed CSAs in this strategy was verified on cholesterol model systems. This new method allowed us to quantify ergosterol's dynamics at three molar ratios: 16 mol % (Ld phase), 30 mol % (Lo phase), and 23 mol % (mixed phases). Contrary to cholesterol, ergosterol's molecular diffusion axis makes an important angle (14°) with the inertial axis of the rigid four-ring system. PMID:15923221

  18. Combining asymmetric 13C-labeling and isotopic filter/edit NOESY: a novel strategy for rapid and logical RNA resonance assignment.

    PubMed

    LeBlanc, Regan M; Longhini, Andrew P; Le Grice, Stuart F J; Johnson, Bruce A; Dayie, Theodore K

    2017-09-19

    Although ∼98% of the human genomic output is transcribed as non-protein coding RNA, <2% of the protein data bank structures comprise RNA. This huge structural disparity stems from combined difficulties of crystallizing RNA for X-ray crystallography along with extensive chemical shift overlap and broadened linewidths associated with NMR of RNA. While half of the deposited RNA structures in the PDB were solved by NMR methods, the usefulness of NMR is still limited by the high cost of sample preparation and challenges of resonance assignment. Here we propose a novel strategy for resonance assignment that combines new strategic 13C labeling technologies with filter/edit type NOESY experiments to greatly reduce spectral complexity and crowding. This new strategy allowed us to assign important non-exchangeable resonances of proton and carbon (1', 2', 2, 5, 6 and 8) nuclei using only one sample and <24 h of NMR instrument time for a 27 nt model RNA. The method was further extended to assigning a 6 nt bulge from a 61 nt viral RNA element justifying its use for a wide range RNA chemical shift resonance assignment problems. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. Evaluation of biodegradability of phenol and bisphenol A during mesophilic and thermophilic municipal solid waste anaerobic digestion using 13C-labeled contaminants.

    PubMed

    Limam, Intissar; Mezni, Mohamed; Guenne, Angéline; Madigou, Céline; Driss, Mohamed Ridha; Bouchez, Théodore; Mazéas, Laurent

    2013-01-01

    In this paper, the isotopic tracing using (13)C-labeled phenol and bisphenol A was used to study their biodegradation during anaerobic digestion of municipal solid waste. Microcosms were incubated anaerobically at 35 °C (mesophilic conditions) and 55 °C (thermophilic conditions) without steering. A continuous follow-up of the production of biogas (CH(4) and CO(2)), was carried out during 130 d until the establishment of stable methanogenesis. Then (13)C(12)-BPA, and (13)C(6)-phenol were injected in microcosms and the follow-up of their degradation was performed simultaneously by gas chromatography isotope-ratio mass spectrometry (GC-IRMS) and gas chromatography mass spectrometry (GC-MS). Moreover, Carbon-13 Nuclear Magnetic Resonance ((13)C-NMR) Spectroscopy is used in the identification of metabolites. This study proves that the mineralization of phenol to CO(2) and CH(4) occurs during anaerobic digestion both in mesophilic and thermophilic conditions with similar kinetics. In mesophilic condition phenol degradation occurs through the benzoic acid pathway. In thermophilic condition it was not possible to identify the complete metabolic pathway as only acetate was identified as metabolite. Our results suggest that mineralization of phenol under thermophilic condition is instantaneous explaining why metabolites are not observed as they do not accumulate. No biodegradation of BPA was observed.

  20. A Comparison between Radiolabeled Fluorodeoxyglucose Uptake and Hyperpolarized 13C-Labeled Pyruvate Utilization as Methods for Detecting Tumor Response to Treatment12

    PubMed Central

    Witney, Timothy H; Kettunen, Mikko I; Day, Samuel E; Hu, De-en; Neves, Andre A; Gallagher, Ferdia A; Fulton, Sandra M; Brindle, Kevin M

    2009-01-01

    Detection of early tumor responses to treatment can give an indication of clinical outcome. Positron emission tomography measurements of the uptake of the glucose analog, [18F] 2-fluoro-2-deoxy-d-glucose (FDG), have demonstrated their potential for detecting early treatment response in the clinic. We have shown recently that 13C magnetic resonance spectroscopy and spectroscopic imaging measurements of the uptake and conversion of hyperpolarized [1-13C]pyruvate into [1-13C]lactate can be used to detect treatment response in a murine lymphoma model. The present study compares these magnetic resonance measurements with changes in FDG uptake after chemotherapy. A decrease in FDG uptake was found to precede the decrease in flux of hyperpolarized 13C label between pyruvate and lactate, both in tumor cells in vitro and in tumors in vivo. However, the magnitude of the decrease in FDG uptake and the decrease in pyruvate to lactate flux was comparable at 24 hours after drug treatment. In cells, the decrease in FDG uptake was shown to correlate with changes in plasma membrane expression of the facilitative glucose transporters, whereas the decrease in pyruvate to lactate flux could be explained by an increase in poly(ADP-ribose) polymerase activity and subsequent depletion of the NAD(H) pool. These results show that measurement of flux between pyruvate and lactate may be an alternative to FDG-positron emission tomography for imaging tumor treatment response in the clinic. PMID:19484146

  1. C4'/H4' selective, non-uniformly sampled 4D HC(P)CH experiment for sequential assignments of (13)C-labeled RNAs.

    PubMed

    Saxena, Saurabh; Stanek, Jan; Cevec, Mirko; Plavec, Janez; Koźmiński, Wiktor

    2014-11-01

    A through bond, C4'/H4' selective, "out and stay" type 4D HC(P)CH experiment is introduced which provides sequential connectivity via H4'(i)-C4'(i)-C4'(i-1)-H4'(i-1) correlations. The (31)P dimension (used in the conventional 3D HCP experiment) is replaced with evolution of better dispersed C4' dimension. The experiment fully utilizes (13)C-labeling of RNA by inclusion of two C4' evolution periods. An additional evolution of H4' is included to further enhance peak resolution. Band selective (13)C inversion pulses are used to achieve selectivity and prevent signal dephasing due to the of C4'-C3' and C4'-C5' homonuclear couplings. For reasonable resolution, non-uniform sampling is employed in all indirect dimensions. To reduce sensitivity losses, multiple quantum coherences are preserved during shared-time evolution and coherence transfer delays. In the experiment the intra-nucleotide peaks are suppressed whereas inter-nucleotide peaks are enhanced to reduce the ambiguities. The performance of the experiment is verified on a fully (13)C, (15)N-labeled 34-nt hairpin RNA comprising typical structure elements.

  2. Determination of the orientation and dynamics of ergosterol in model membranes using uniform 13C labeling and dynamically averaged 13C chemical shift anisotropies as experimental restraints.

    PubMed

    Soubias, O; Jolibois, F; Massou, S; Milon, A; Réat, V

    2005-08-01

    A new strategy was established to determine the average orientation and dynamics of ergosterol in dimyristoylphosphatidylcholine model membranes. It is based on the analysis of chemical shift anisotropies (CSAs) averaged by the molecular dynamics. Static (13)C CSA tensors were computed by quantum chemistry, using the gauge-including atomic-orbital approach within Hartree-Fock theory. Uniformly (13)C-labeled ergosterol was purified from Pichia pastoris cells grown on labeled methanol. After reconstitution into dimyristoylphosphatidylcholine lipids, the complete (1)H and (13)C assignment of ergosterol's resonances was performed using a combination of magic-angle spinning two-dimensional experiments. Dynamically averaged CSAs were determined by standard side-band intensity analysis for isolated (13)C resonances (C(3) and ethylenic carbons) and by off-magic-angle spinning experiments for other carbons. A set of 18 constraints was thus obtained, from which the sterol's molecular order parameter and average orientation could be precisely defined. The validity of using computed CSAs in this strategy was verified on cholesterol model systems. This new method allowed us to quantify ergosterol's dynamics at three molar ratios: 16 mol % (Ld phase), 30 mol % (Lo phase), and 23 mol % (mixed phases). Contrary to cholesterol, ergosterol's molecular diffusion axis makes an important angle (14 degrees) with the inertial axis of the rigid four-ring system.

  3. Two-dimensional IR spectroscopy and segmental 13C labeling reveals the domain structure of human γD-crystallin amyloid fibrils

    PubMed Central

    Moran, Sean D.; Woys, Ann Marie; Buchanan, Lauren E.; Bixby, Eli; Decatur, Sean M.; Zanni, Martin T.

    2012-01-01

    The structural eye lens protein γD-crystallin is a major component of cataracts, but its conformation when aggregated is unknown. Using expressed protein ligation, we uniformly 13C labeled one of the two Greek key domains so that they are individually resolved in two-dimensional (2D) IR spectra for structural and kinetic analysis. Upon acid-induced amyloid fibril formation, the 2D IR spectra reveal that the C-terminal domain forms amyloid β-sheets, whereas the N-terminal domain becomes extremely disordered but lies in close proximity to the β-sheets. Two-dimensional IR kinetics experiments show that fibril nucleation and extension occur exclusively in the C-terminal domain. These results are unexpected because the N-terminal domain is less stable in the monomer form. Isotope dilution experiments reveal that each C-terminal domain contributes two or fewer adjacent β-strands to each β-sheet. From these observations, we propose an initial structural model for γD-crystallin amyloid fibrils. Because only 1 μg of protein is required for a 2D IR spectrum, even poorly expressing proteins can be studied under many conditions using this approach. Thus, we believe that 2D IR and protein ligation will be useful for structural and kinetic studies of many protein systems for which IR spectroscopy can be straightforwardly applied, such as membrane and amyloidogenic proteins. PMID:22328156

  4. Two-dimensional IR spectroscopy and segmental 13C labeling reveals the domain structure of human γD-crystallin amyloid fibrils.

    PubMed

    Moran, Sean D; Woys, Ann Marie; Buchanan, Lauren E; Bixby, Eli; Decatur, Sean M; Zanni, Martin T

    2012-02-28

    The structural eye lens protein γD-crystallin is a major component of cataracts, but its conformation when aggregated is unknown. Using expressed protein ligation, we uniformly (13)C labeled one of the two Greek key domains so that they are individually resolved in two-dimensional (2D) IR spectra for structural and kinetic analysis. Upon acid-induced amyloid fibril formation, the 2D IR spectra reveal that the C-terminal domain forms amyloid β-sheets, whereas the N-terminal domain becomes extremely disordered but lies in close proximity to the β-sheets. Two-dimensional IR kinetics experiments show that fibril nucleation and extension occur exclusively in the C-terminal domain. These results are unexpected because the N-terminal domain is less stable in the monomer form. Isotope dilution experiments reveal that each C-terminal domain contributes two or fewer adjacent β-strands to each β-sheet. From these observations, we propose an initial structural model for γD-crystallin amyloid fibrils. Because only 1 μg of protein is required for a 2D IR spectrum, even poorly expressing proteins can be studied under many conditions using this approach. Thus, we believe that 2D IR and protein ligation will be useful for structural and kinetic studies of many protein systems for which IR spectroscopy can be straightforwardly applied, such as membrane and amyloidogenic proteins.

  5. Multidimensional High-Resolution Magic Angle Spinning and Solution-State NMR Characterization of 13C-labeled Plant Metabolites and Lignocellulose

    PubMed Central

    Mori, Tetsuya; Tsuboi, Yuuri; Ishida, Nobuhiro; Nishikubo, Nobuyuki; Demura, Taku; Kikuchi, Jun

    2015-01-01

    Lignocellulose, which includes mainly cellulose, hemicellulose, and lignin, is a potential resource for the production of chemicals and for other applications. For effective production of materials derived from biomass, it is important to characterize the metabolites and polymeric components of the biomass. Nuclear magnetic resonance (NMR) spectroscopy has been used to identify biomass components; however, the NMR spectra of metabolites and lignocellulose components are ambiguously assigned in many cases due to overlapping chemical shift peaks. Using our 13C-labeling technique in higher plants such as poplar samples, we demonstrated that overlapping peaks could be resolved by three-dimensional NMR experiments to more accurately assign chemical shifts compared with two-dimensional NMR measurements. Metabolites of the 13C-poplar were measured by high-resolution magic angle spinning NMR spectroscopy, which allows sample analysis without solvent extraction, while lignocellulose components of the 13C-poplar dissolved in dimethylsulfoxide/pyridine solvent were analyzed by solution-state NMR techniques. Using these methods, we were able to unambiguously assign chemical shifts of small and macromolecular components in 13C-poplar samples. Furthermore, using samples of less than 5 mg, we could differentiate between two kinds of genes that were overexpressed in poplar samples, which produced clearly modified plant cell wall components. PMID:26143886

  6. Metabolite channeling and compartmentation in the human cell line AGE1.HN determined by 13C labeling experiments and 13C metabolic flux analysis.

    PubMed

    Niklas, Jens; Sandig, Volker; Heinzle, Elmar

    2011-12-01

    This study focused on analyzing active pathways and the metabolic flux distribution in human neuronal AGE1.HN cells that is a desirable basis for a rational design and optimization of producing cell lines and production processes for biopharmaceuticals. (13)C-labeling experiments and (13)C metabolic flux analysis were conducted using glucose, glutamine, alanine and lactate tracers in parallel experiments. Connections between cytosolic and mitochondrial metabolite pools were verified, e.g., flux from TCA cycle metabolite (13)C to glycolytic metabolites. It was also found that lactate and alanine are produced from the same pyruvate pool and that consumed alanine is mainly directly metabolized and secreted as lactate. Activity of the pentose phosphate pathway was low being around 2.3% of the glucose uptake flux. This might be compensated in AGE1.HN by high mitochondrial malic enzyme flux producing NADPH. Mitochondrial pyruvate transport was almost zero. Instead pyruvate carbons were channeled via oxaloacetate into the TCA cycle which was mainly fed via α-ketoglutarate and oxaloacetate during the investigated phase. The data indicate that further optimization of this cell line should focus on the improved substrate usage which can be accomplished by an improved connectivity between glycolytic and mitochondrial pyruvate pools or by better control of the substrate uptake.

  7. Incorporation of {sup 13}C-labeled intermediates into developing lignin revealed by analytical pyrolysis and CuO oxidation in combination with IRM-GC-MS

    SciTech Connect

    Eglinton, T.I.; Goni, M.A.; Boon, J.J.

    1995-12-31

    Tissue samples from Ginkgo shoots (Ginkgo biloba L.) and Rice grass (Oryzasitiva sp.) incubated in the presence of {sup 13}C-labeled substrates such as coniferin (postulated to be biosynthetic intermediates in lignin biosynthesis) were studied using thermal and chemical dissociation methods in combination with molecular-level isotopic measurements. The aim of the study was (1) to investigate dissociation mechanisms, and (2) to examine and quantify the proportions of labeled material incorporated within each sample. Isotopic analysis of specific dissociation products revealed the presence of the label in its original positions, and only within lignin-derived (phenolic) products. Moreover, the distribution and isotopic composition of the dissociation products strongly suggest an origin from newly-formed lignin. These results clearly indicate that there is no {open_quotes}scrambling{close_quotes} of carbon atoms as a result of the dissociation process, thereby lending support to this analytical approach. In addition, the data provide confidence in the selective labeling approach for elucidation of the structure and biosynthesis of lignin.

  8. Impacts of proline on the central metabolism of an industrial erythromycin-producing strain Saccharopolyspora erythraea via (13)C labeling experiments.

    PubMed

    Hong, Ming; Huang, Mingzhi; Chu, Ju; Zhuang, Yingping; Zhang, Siliang

    2016-08-10

    Saccharopolyspora erythraea E3 is an important industrial strain for erythromycin production and knowledge on its metabolism is limited. In the present work, (13)C labeling experiments were conducted to characterize the metabolism of S. erythraea E3. We found that S. erythraea E3 was difficult to grow on minimal medium with glucose as sole carbon source and the addition of proline remarkably improved the cell growth. The activity of EMP pathway was very low and ED pathway was alternatively the main glucose utilization pathway. The addition of proline resulted in remarkable changes in the fluxes of central metabolism. The fluxes in PP pathway, in TCA cycle and in ED pathway were 90% higher, 64% and 31% lower on Glc/Pro than on Glc, respectively. The maintenance energy on Glc/Pro was 58.4% lower than that on Glc. The energy charge was lower on Glc than on Glc/Pro, indicating that the cells on Glc suffered from energy burden. This study elucidates the impacts of proline on the central metabolism of S. erythraea and deepens the understanding of its metabolism.

  9. Characterization of uniformly and atom-specifically 13C-labeled heparin and heparan sulfate polysaccharide precursors using 13C NMR spectroscopy and ESI mass spectrometry

    PubMed Central

    Nguyen, Thao K. N.; Tran, Vy M.; Victor, Xylophone V.; Skalicky, Jack J.; Kuberan, Balagurunathan

    2010-01-01

    The biological actions of heparin and heparan sulfate, two structurally related glycosaminoglycans, depend on the organization of the complex heparanome. Due to the structural complexity of the heparanome, the sequence of variably sulfonated uronic acid and glucosamine residues is usually characterized by the analysis of smaller oligosaccharide and disaccharide fragments. Even characterization of smaller heparin/heparan sulfate oligosaccharide or disaccharide fragments using simple 1D 1H NMR spectroscopy is often complicated by the extensive signal overlap. 13C NMR signals, on the other hand, overlap less and therefore, 13C NMR spectroscopy can greatly facilitate the structural elucidation of the complex heparanome and provide finer insights into the structural basis for biological functions. This is the first report of the preparation of anomeric carbon-specific 13C-labeled heparin/heparan sulfate precursors from the Escherichia coli K5 strain. Uniformly 13C- and 15N-labeled precursors were also produced and characterized by 13C NMR spectroscopy. Mass spectrometric analysis of enzymatically fragmented disaccharides revealed that anomeric carbon-specific labeling efforts resulted in a minor loss/scrambling of 13C in the precursor backbone, whereas uniform labeling efforts resulted in greater than 95% 13C isotope enrichment in the precursor backbone. These labeled precursors provided high-resolution NMR signals with great sensitivity and set the stage for studying the heparanome–proteome interactions. PMID:20832774

  10. Structure formation and its consequences for soil strength, mass flow processes and carbon sequestration in unsaturated arable and forest soils

    NASA Astrophysics Data System (ADS)

    Horn, Rainer

    2014-05-01

    The aim of this lecture is to clarify the process of aggregate formation and the following effects on physical and chemical properties of structured soils both on a bulk soil scale, for single aggregates, as well as for homogenized material. Aggregate formation and aggregate strength depend on swelling and shrinkage processes and on biological activity and kinds of organic exudates as well as on the intensity, number and time of swelling and drying events. Such aggregates are denser than the bulk soil. The intra-aggregate pore distribution consists not only of finer pores but these are also more tortuous. Therefore, water fluxes in aggregated soils are mostly multidimensional and the corresponding water fluxes in the intra- aggregate pore system are much smaller. The aggregate formation also affects the aeration and the gaseous composition of in the intra- aggregate pore space. Depending on the kind and intensity of aggregation, the intra-aggregate pores can be completely anoxic, while the inter-aggregate pores are already completely aerated. The possibility to predict physical properties on these various scales depends on the rigidity of the pore system. In general this rigidity depends on the above-mentioned physical and chemical processes both with respect to intensity and frequency. The consequences of aggregate formation on soil strength can be quantified by frame shear as well as rheometrical tests.

  11. Health risks of thallium in contaminated arable soils and food crops irrigated with wastewater from a sulfuric acid plant in western Guangdong province, China.

    PubMed

    Wang, Chunlin; Chen, Yongheng; Liu, Juan; Wang, Jin; Li, Xiangping; Zhang, Yongbo; Liu, Yimin

    2013-04-01

    Thallium (Tl) contamination in soils poses a significant threat to human health due to the high toxicity of Tl and its ready assimilation by crops. Consumption of food crops contaminated with Tl is a major food chain route for human exposure. The health risks of Tl in contaminated food crops irrigated with wastewater from a sulfuric acid factory were investigated in this paper. Results indicate that long-term Tl-containing wastewater irrigation resulted in Tl contamination of arable soils and crops. The pollution load index values indicated that the arable soils were moderately enriched with Tl. Tl was highly accumulated in the crops. The content of Tl in the edible plant portions of crops ranged from 1.2 mg/kg to 104.8 mg/kg, exceeding the recommended permissible limits for food crops. The daily intake of metals (DIM) values of Tl for both adults and children via the consumption of the food crops except soya beans were higher than the reference oral dose (RfD) limit recommend by the United States environmental protection agency (US-EPA). Health risk index (HRI) values were generally higher than 1, indicating that health risks associated with Tl exposure are significant and assumed to be dangerous to the health of local villagers. Therefore, much attention should be paid to avoid consumption of these Tl-contaminated crops that can cause great potential risks.

  12. Synthesis of /sup 13/C-labeled standards for use in coal liquefaction studies. II. Dissolving metal reactions applied to naphthalenes and indoles: effect of sonication

    SciTech Connect

    Pickering, R.E.

    1986-01-01

    High yield syntheses of /sup 13/C-labeled standards for later use in coal liquefaction studies are described. An alternate route for the synthesis of 1-cyclohexanone-1-/sup 13/C is discussed. Naphthalene and 2,3-dimethylnaphthalene were reduced with metal-amine solutions. The effect of sonication on product distribution was investigated. The effect of different amine solvent and different metals also was studied. A series of indoles were reduced with lithium and ethylenediamine to study the effect of sonication. To aid identification of some reduction products, independent syntheses were conducted. Naphthalenol-1-/sup 13/C, phenol-1-/sup 13/C, 1-indanone-1-/sup 13/C, 3,4-dihydro-2(1H)-quinolinone-2-/sup 13/C, 1,2,3,4-tetrahydroquinoline-2-/sup 13/C and carbazole-9a-/sup 13/C were synthesized in good yield. The carbonation of 1,5-pentanedimagnesium bromide was shown to be a viable alternative route for the synthesis of 1-cyclohexanone-1-/sup 13/C. Sonication was found to be an efficient agitation method for the reductive dimerization or the reductive amination of naphthalene and 2,3-dimethylnaphthalene. The product distribution was found to be dependent on the selection of the amine solvent. Sodium was shown to be a better reagent for reductive dimerization than potassium, lithium, calcium, or magnesium. The synthesis of 6,6',7,7'-tetramethyl-,1'-binaphthyl, 6,6',7,7'-tetramethyl-1,2'-binaphthyl, 6,6',7,7'-tetramethyl-2,2'-binaphthyl and some of their hydro-derivatives are described. The reduction of indoles with lithium-ethylenediamine was found to be influenced by sonication which significant increased the yield of the 4,5,6,7-tetrahydro-derivative. N-Substituted indoles were shown to undergo reductive cleavage with lithium-ethylenediamine while being treated with ultrasound.

  13. Non-targeted determination of (13)C-labeling in the Methylobacterium extorquens AM1 metabolome using the two-dimensional mass cluster method and principal component analysis.

    PubMed

    Reaser, Brooke C; Yang, Song; Fitz, Brian D; Parsons, Brendon A; Lidstrom, Mary E; Synovec, Robert E

    2016-02-05

    A novel analytical workflow is presented for the analysis of time-dependent (13)C-labeling of the metabolites in the methylotrophic bacterium Methylobacterium extorquens AM1 using gas chromatography time-of-flight mass spectrometry (GC-TOFMS). Using (13)C-methanol as the substrate in a time course experiment, the method provides an accurate determination of the number of carbons converted to the stable isotope. The method also extracts a quantitative isotopic dilution time course profile for (13)C uptake of each metabolite labeled that could in principle be used to obtain metabolic flux rates. The analytical challenges encountered require novel analytical platforms and chemometric techniques. GC-TOFMS offers advanced separation of mixtures, identification of individual components, and high data density for the application of advanced chemometrics. This workflow combines both novel and traditional chemometric techniques, including the recently reported two-dimensional mass cluster plot method (2D m/z cluster plot method) as well as principal component analysis (PCA). The 2D m/z cluster plot method effectively indexed all metabolites present in the sample and deconvoluted metabolites at ultra-low chromatographic resolution (RS≈0.04). Using the pure mass spectra extracted, two PCA models were created. Firstly, PCA was used on the first and last time points of the time course experiment to determine and quantify the extent of (13)C uptake. Secondly, PCA modeled the full time course in order to quantitatively extract the time course profile for each metabolite. The 2D m/z cluster plot method found 152 analytes (metabolites and reagent peaks), with 54 pure analytes, and 98 were convoluted, with 65 of the 98 requiring mathematical deconvolution. Of the 152 analytes surveyed, 83 were metabolites determined by the PCA model to have incorporated (13)C while 69 were determined to be either metabolites or reagent peaks that remained unlabeled.

  14. Modelling of nitrate leaching from arable land into unsaturated soil and chalk 2. Model confirmation and application to agricultural and sewage sludge management

    NASA Astrophysics Data System (ADS)

    Andrews, R. J.; Lloyd, J. W.; Lerner, D. N.

    1997-12-01

    A layered deterministic N-leaching model, IMPACT, has been calibrated using data from two study sites on the unconfined Chalk aquilfer of East Anglia, UK. The model predicts nitrogen species movement resulting from the application of sewage sludges and fertilizers to arable land for different vegetation-soil-hydrogeological conditions. One site received sludge in the form of digested sewage cake (DSC) for the first time during the study period, whilst the other site had over 15 years history of liquid undigested sludge (LUS) applications at 3 year intervals. Site data included: 3-monthly concentration profiles at 0.3 m intervals to depths of up to 6 m for N-species and chloride; unsaturated potential measurements; water level and saturated groundwater solute concentrations, fertilizer and sludge input; daily recharge, and soil/chalk type and moisture content. The observed average movement rate for nitrate peaks in the Lower Chalk, measured at one site, was 0.2 m year -2. Leachate peaks were not observed annually but approximately every third year, being associated with large sludge applications and ploughing of grass crops. Significant correlation between observed and modelled nitrate profiles in soil and chalk were obtained which demonstrated applications. The relationship between crop demand, application times of fertilizers and sludge, nitrate availability and recharge was shown strongly to control the shape of nitrate profiles in the soil and chalk and the quantity of nitrate leached tochalk. The change in hydrogeological conditions at the soil-chalk contact and associated potential for denitrification was also shown to exert a significant control on the shape of the nitrate profile. Following calibration, different arable crop and sludge application regimes were examined for a 6 year period and ranked according to their nitrate leaching risk. Of the modelled cereal farming scenarios, the crop/sludge regime giving the least nitrate leaching was a late autumn

  15. A method to assess ecosystem services developed from soil attributes with stakeholders and data of four arable farms.

    PubMed

    Rutgers, M; van Wijnen, H J; Schouten, A J; Mulder, C; Kuiten, A M P; Brussaard, L; Breure, A M

    2012-01-15

    Ecosystem-service indicators and related accounting units are crucial for the development of decision frameworks for sustainable land management systems. With a management concept using ecosystem services, land-use expectations can be linked to quantifiable soil features in a defendable and transparent way. A method to define a set of site-specific ecosystem services and indication system for quantification was set-up and run. First, we interviewed a wide group of land users profiting from ecosystem services of the soil at four arable farms in the polder Hoeksche Waard (S-SE of Rotterdam, the Netherlands). Subsequently, site-specific ecosystem services were defined and weighted according to land use expectations at different spatial and temporal scales. Second, a practical set of indicators was taken from 'Best Professional Judgment' and used to quantify the performance of the ecosystem services for these four farms. The indicators were derived from biotic and abiotic soil parameters. The performance of ecosystem services was related to a reference situation (MEP: maximum ecological potential) with the same land use and soil type combination (i.e., arable fields on silt loam) taken from the database of our national soil survey. In many cases, the performance of ecosystem services was relatively poor if compared to MEP. However, the performances of natural attenuation and/or climate-related services were better. In addition, the different management of these farms (i.e. conventional, intensive and organic farming) was reflected in the performance of the ecosystem services of their soils. Third, land management measures to improve the targeted ecosystem services were incorporated in the outlined method, but not worked out with illustrative field data in this study. Together with concordant data, we show opportunities for a quantification of ecosystem services to improve land-users' awareness and to

  16. Linking an economic model for European agriculture with a mechanistic model to estimate nitrogen and carbon losses from arable soils in Europe

    NASA Astrophysics Data System (ADS)

    Leip, A.; Marchi, G.; Koeble, R.; Kempen, M.; Britz, W.; Li, C.

    2008-01-01

    A comprehensive assessment of policy impact on greenhouse gas (GHG) emissions from agricultural soils requires careful consideration of both socio-economic aspects and the environmental heterogeneity of the landscape. We developed a modelling framework that links the large-scale economic model for agriculture CAPRI (Common Agricultural Policy Regional Impact assessment) with the biogeochemistry model DNDC (DeNitrification DeComposition) to simulate GHG fluxes, carbon stock changes and the nitrogen budget of agricultural soils in Europe. The framework allows the ex-ante simulation of agricultural or agri-environmental policy impacts on a wide range of environmental problems such as climate change (GHG emissions), air pollution and groundwater pollution. Those environmental impacts can be analyzed in the context of economic and social indicators as calculated by the economic model. The methodology consists of four steps: (i) definition of appropriate calculation units that can be considered as homogeneous in terms of economic behaviour and environmental response; (ii) downscaling of regional agricultural statistics and farm management information from a CAPRI simulation run into the spatial calculation units; (iii) designing environmental model scenarios and model runs; and finally (iv) aggregating results for interpretation. We show the first results of the nitrogen budget in croplands in fourteen countries of the European Union and discuss possibilities to improve the detailed assessment of nitrogen and carbon fluxes from European arable soils.

  17. Thallium contamination in arable soils and vegetables around a steel plant-A newly-found significant source of Tl pollution in South China.

    PubMed

    Liu, Juan; Luo, Xuwen; Wang, Jin; Xiao, Tangfu; Chen, Diyun; Sheng, Guodong; Yin, Meiling; Lippold, Holger; Wang, Chunlin; Chen, Yongheng

    2017-05-01

    Thallium (Tl) is a highly toxic rare element. Severe Tl poisoning can cause neurological brain damage or even death. The present study was designed to investigate contents of Tl and other associated heavy metals in arable soils and twelve common vegetables cultivated around a steel plant in South China, a newly-found initiator of Tl pollution. Potential health risks of these metals to exposed population via consumption of vegetables were examined by calculating hazard quotients (HQ). The soils showed a significant contamination with Tl at a mean concentration of 1.34 mg/kg. The Tl levels in most vegetables (such as leaf lettuce, chard and pak choy) surpassed the maximum permissible level (0.5 mg/kg) according to the environmental quality standards for food in Germany. Vegetables like leaf lettuce, chard, pak choy, romaine lettuce and Indian beans all exhibited bioconcentration factors (BCF) and transfer factors (TF) for Tl higher than 1, indicating a hyperaccumulation of Tl in these plants. Although the elevated Tl levels in the vegetables at present will not immediately pose significant non-carcinogenic health risks to residents, it highlights the necessity of a permanent monitoring of Tl contamination in the steel-making areas. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Heavy metals and health risk assessment of arable soils and food crops around Pb-Zn mining localities in Enyigba, southeastern Nigeria

    NASA Astrophysics Data System (ADS)

    Obiora, Smart C.; Chukwu, Anthony; Davies, Theophilus C.

    2016-04-01

    This study determined the heavy metals concentration in arable soils and associated food crops around the Pb-Zn mines in Enyigba, Nigeria, and metal transfer factors were calculated. Air-dried samples of the soils and food crops were analyzed for 8 known nutritional and toxic heavy metals by Inductively Coupled Plasma - Mass Spectrometer (ICP-MS) method. Eighty seven percent of all the 20 sampled soils contain Pb in excess of the maximum allowable concentration (MAC) set by Canadian Environmental Quality Guideline (CCME) and European Union (EU) Standard, while Zn in thirty-one percent of the samples exceeded the CCME for MAC of 200 mg/kg. All the food crops, with the exception of yam tuber, contain Pb which exceeded the 0.43 mg/kg and 0.3 mg/kg MAC standards of EU and WHO/FAO respectively, with the leafy vegetables accumulating more Pb than the tubers. The metal transfer factors in the tubers and the leafy vegetables were in the order: Mo > Cu > Zn > Mn > As > Cd > Cr > Ni > Pb and Cd > Cu > Zn > Mn > Mo > As > Ni > Pb > Cr, respectively. Risk assessment studies revealed no health risk in surrounding populations for most of the heavy metals. However, Pb had a high health risk index (HRI) of 1.1 and 1.3, in adults and children, respectively for cassava tuber; Pb had HRI > 1 in lemon grass while Mn also had HRI > 1 in all the leafy vegetables for both adult and children. This high level of HRI for Pb and Mn is an indication that consumers of the food crops contaminated by these metals are at risk of health problems such as Alzheimers' disease and Manganism, associated with excessive intake of these metals. Further systematic monitoring of heavy metal fluxes in cultivable soils around the area of these mines is recommended.

  19. Seasonal variation of N2O and CH4 fluxes in differently managed arable soils in southern Germany

    NASA Astrophysics Data System (ADS)

    Flessa, H.; DöRsch, P.; Beese, F.

    1995-11-01

    Agricultural practices are assumed to contribute significantly to the increase in atmospheric nitrous oxide (N2O) concentrations observed in the last decades, and they might influence the consumption of atmospheric methane (CH4) by soil. The aim of this study was to quantify the effects of management intensity, soil type, and frost periods on the emission of N2O and the consumption of CH4 in rotations in southern Germany. Fluxes of N2O and CH4 were monitored over 12 months, using a closed chamber technique. The extensively managed system was cropped to sunflower and fertilized with farmyard manure (12 t ha-1). The intensively managed field was planted with spring wheat and fertilized with a total of 190 kg N ha-1 given as calcium ammonium nitrate (30 kg N) and urea-NH4NO3 solution (160 kg N). Variation in the N2O emissions with time was extremely high, with flux rates ranging from 0 to 2700 μg m-2 h-1. The N2O fluxes were influenced by soil properties, management practices, and weather. The highest release rates were measured in the winter during thawing of the frozen soil. During the growing season, N2O emission was highest after heavy precipitation. No strong relationship was found between N2O emission rates and soil factors such as soil temperature, soil moisture, and soil nitrate content. Annual fluxes of N2O from the extensively managed field were 9.4 and 12.9 kg N2O-N ha-1 yr-1 for a sandy soil and a clay soil, respectively. Total N2O-N losses from the intensively fertilized field amounted to 9.6 kg ha-1 yr-1 for a silty soil with a tendency to waterlogging during wintertime and to 16.8 kg ha yr-1 for a loamy colluvial soil. Up to 46% of the annual N2O evolution was emitted during December and January when frost/thaw cycles induced extremely high N2O production. The application of urea-NH4NO3 solution significantly increased N2O emission rates. Of the 160 kg N applied, 2.9 kg N or 1.8% was lost as N2O within a period of 8 weeks. Rates of CH4-C uptake varied

  20. Fate of the herbicides glyphosate, glufosinate-ammonium, phenmedipham, ethofumesate and metamitron in two Finnish arable soils.

    PubMed

    Laitinen, Pirkko; Siimes, Katri; Eronen, Liisa; Rämö, Sari; Welling, Leena; Oinonen, Seija; Mattsoff, Leona; Ruohonen-Lehto, Marja

    2006-06-01

    The fate of five herbicides (glyphosate, glufosinate-ammonium, phenmedipham, ethofumesate and metamitron) was studied in two Finnish sugar beet fields for 26 months. Soil types were sandy loam and clay. Two different herbicide-tolerant sugar beet cultivars and three different herbicide application schedules were used. Meteorological data were collected throughout the study and soil properties were thoroughly analysed. An extensive data set of herbicide residue concentrations in soil was collected. Five different soil depths were sampled. The study was carried out using common Finnish agricultural practices and represents typical sugar beet cultivation conditions in Finland. The overall observed order of persistence was ethofumesate > glyphosate > phenmedipham > metamitron > glufosinate-ammonium. Only ethofumesate and glyphosate persisted until the subsequent spring. Seasonal variation in herbicide dissipation was very high and dissipation ceased almost completely during winter. During the 2 year experiment no indication of potential groundwater pollution risk was obtained, but herbicides may cause surface water pollution. Copyright (c) 2006 Society of Chemical Industry

  1. Long-term application of fresh and composted manure increase tetracycline resistance in the arable soil of eastern China.

    PubMed

    Peng, Shuang; Wang, Yiming; Zhou, Beibei; Lin, Xiangui

    2015-02-15

    The aim of this study was to compare the occurrence, abundance, and diversity of tetracycline resistance genes (tet) in agricultural soils after 6 years' application of fresh or composted swine manure. Soil samples were collected from fresh or composted manure-treated farmland at three depths (0-5 cm, 5-10 cm, and 10-20 cm). Nine classes of tet genes [tetW, tetB(P), tetO, tetS, tetC, tetG, tetZ, tetL, and tetX] were detected; tetG, tetZ, tetL, and tetB(P) were predominant in the manure-treated soil. The abundances of tetB(P), tetW, tetC, and tetO were reduced, while tetG and tetL were increased by fertilizing with composted versus fresh manure; thus, the total abundance of tet genes was not significantly reduced by compost manuring. tetG was the most abundant gene in manure-treated soil; the predominant tetG genotypes shared high homology with pathogenic bacteria. The tetG isolates were more diverse in soils treated with fresh versus composted manure, although the residual tet genes in composted manure remain a pollutant and produce a different influence on the tet gene resistome in field soil. Copyright © 2014 Elsevier B.V. All rights reserved.

  2. Carbon Stocks in Physically-Protected Soil Organic Matter Pools of European Forests, Grasslands and Arable Lands

    NASA Astrophysics Data System (ADS)

    Cotrufo, M.; Del Galdo, I.; Marzaioli, F.; Rubino, M.; Terrasi, F.

    2006-12-01

    Soils represent the largest stock of C in most terrestrial ecosystems: a large research effort worldwide is devoted to quantify these stocks and their mean residence time, and to model changes in response to future scenarios of climate and land use. As a consequence, a fairly good understanding of the processes controlling C flows from the plant roots and littering into soil organic matter pools and, eventually, back to the atmosphere has been achieved. Yet, the characterization of functionally meaningful soil organic matter pools, which can be measured and applied in models remains an unfulfilled goal. Results will be presented on the organic carbon stocks of soils from the CARBOEUROPE network. Soil samples collected at 3 broad-leaved and 3 coniferous forests, 3 croplands and 3 pastures, along a depth gradient, were separated by size and density, and the isolated fractions analysed for C content and isotopic composition. The data set will be interpreted in terms of soil mineralogical properties, site climate and land use. Additionally, the stable C isotope values of physically-protected C pools from this dataset and the stable and radioactive C isotope datasets originated from other key isotope labelling studies, will be used to characterize the fractions isolated and to provide a mechanistic understanding of C flows among them

  3. Preferential Colonization of Solanum tuberosum L. Roots by the Fungus Glomus intraradices in Arable Soil of a Potato Farming Area▿

    PubMed Central

    Cesaro, Patrizia; van Tuinen, Diederik; Copetta, Andrea; Chatagnier, Odile; Berta, Graziella; Gianinazzi, Silvio; Lingua, Guido

    2008-01-01

    The symbiosis between plant roots and arbuscular mycorrhizal (AM) fungi has been shown to affect both the diversity and productivity of agricultural communities. In this study, we characterized the AM fungal communities of Solanum tuberosum L. (potato) roots and of the bulk soil in two nearby areas of northern Italy, in order to verify if land use practices had selected any particular AM fungus with specificity to potato plants. The AM fungal large-subunit (LSU) rRNA genes were subjected to nested PCR, cloning, sequencing, and phylogenetic analyses. One hundred eighty-three LSU rRNA sequences were analyzed, and eight monophyletic ribotypes, belonging to Glomus groups A and B, were identified. AM fungal communities differed between bulk soil and potato roots, as one AM fungal ribotype, corresponding to Glomus intraradices, was much more frequent in potato roots than in soils (accounting for more than 90% of sequences from potato samples and less than 10% of sequences from soil samples). A semiquantitative heminested PCR with specific primers was used to confirm and quantify the AM fungal abundance observed by cloning. Overall results concerning the biodiversity of AM fungal communities in roots and in bulk soils from the two studied areas suggested that potato roots were preferentially colonized by one AM fungal species, G. intraradices. PMID:18676711

  4. Preferential colonization of Solanum tuberosum L. roots by the fungus Glomus intraradices in arable soil of a potato farming area.

    PubMed

    Cesaro, Patrizia; van Tuinen, Diederik; Copetta, Andrea; Chatagnier, Odile; Berta, Graziella; Gianinazzi, Silvio; Lingua, Guido

    2008-09-01

    The symbiosis between plant roots and arbuscular mycorrhizal (AM) fungi has been shown to affect both the diversity and productivity of agricultural communities. In this study, we characterized the AM fungal communities of Solanum tuberosum L. (potato) roots and of the bulk soil in two nearby areas of northern Italy, in order to verify if land use practices had selected any particular AM fungus with specificity to potato plants. The AM fungal large-subunit (LSU) rRNA genes were subjected to nested PCR, cloning, sequencing, and phylogenetic analyses. One hundred eighty-three LSU rRNA sequences were analyzed, and eight monophyletic ribotypes, belonging to Glomus groups A and B, were identified. AM fungal communities differed between bulk soil and potato roots, as one AM fungal ribotype, corresponding to Glomus intraradices, was much more frequent in potato roots than in soils (accounting for more than 90% of sequences from potato samples and less than 10% of sequences from soil samples). A semiquantitative heminested PCR with specific primers was used to confirm and quantify the AM fungal abundance observed by cloning. Overall results concerning the biodiversity of AM fungal communities in roots and in bulk soils from the two studied areas suggested that potato roots were preferentially colonized by one AM fungal species, G. intraradices.

  5. Assessing microbial utilization of free versus sorbed Alanine by using position-specific 13C labeling and 13C-PLFA analysis

    NASA Astrophysics Data System (ADS)

    Herschbach, Jennifer; Apostel, Carolin; Spielvogel, Sandra; Kuzyakov, Yakov; Dippold, Michaela

    2016-04-01

    Microbial utilization is a key transformation process of soil organic matter (SOM). Sorption of low molecular weight organic substances (LMWOS) to soil mineral surfaces blocks or delays microbial uptake and therefore mineralization of LMWOS to CO2, as well as all other biochemical transformations. We used position-specific labeling, a tool of isotope applications novel to soil science, combined with 13C-phospholipid fatty acid (PLFA) analysis, to assess microbial utilization of sorbed and non-sorbed Alanine in soil. Alanine has various functional groups enabling different sorption mechanisms via its positive charge (e.g. to clay minerals by cation exchange), as well as via its negative charge (e.g. to iron oxides by ligand exchange). To assess changes in the transformation pathways caused by sorption, we added uniformly and position-specifically 13C and 14C labeled Alanine to the Ap of a loamy Luvisol in a short-term (10 days) incubation experiment. To allow for sorption of the tracer solution to an aliquot of this soil, microbial activity was minimized in this subsample by sterilizing the soil by γ-radiation. After shaking, the remaining solutions were filtered and the non-sorbed Alanine was removed with Millipore water and then added to non-sterilized soil. For the free Alanine treatment, solutions with Alanine of similar amount and isotopic composition were prepared, added to the soil and incubated as well. The respired CO2 was trapped in NaOH and its 14C-activity was determined at increasing times intervals. Microbial utilization of Alanine's individual C positions was evaluated in distinct microbial groups classified by 13C-PLFA analysis. Sorption to soil minerals delayed respiration to CO2 and reduced initial respiration rate by 80%. Irrespective of sorption, the highest amount was respired from the carboxylic position (C-1), whereas the amino-bound (C-2) and the methylic position (C-3) were preferentially incorporated into PLFA of microorganisms due to the

  6. Effect of Conversion from Natural Grassland to Arable Land on Soil Carbon Reserve in the Argentinean Rolling Pampas

    NASA Astrophysics Data System (ADS)

    Andriulo, A. E.; Irizar, A. B.; Mary, B.; Wilson, M. G.

    2012-04-01

    The evaluation of the effect of land use change on accumulation of soil organic carbon (SOC) requires reliable data obtained from georeferenced sites with land use history records. The purpose of this study was to evaluate long term changes in the reserves of SOC in a typical Argiudol of the Pergamino series after the introduction of agriculture. Measures of soil organic carbon concentration and bulk density of Ap and A12 horizons were carried out in three sites of the Pergamino County (N of Buenos Aires province): a reference field with untilled pristine soil (33° 57' S; 60° 34' W), a field with 31 years (1980-2011) of agriculture (31Y) located next to the former, and a third field (33° 46' S; 60° 37' W) with 80 years (1910/1990) of agriculture (80Y). 31Y has been under continuous soybean cultivation with conventional tillage (CT) that consists of moldboard plow or double disk harrowing. At 80K the cultivation sequence was: 44 years of corn + 9 years of flax + 2 years of wheat + 17 years of wheat/soybean double cropping + 1 year of lentil; mostly under CT, some years under chisel plow during the 70's and a few years under zero tillage in soybean after wheat sown with conventional tillage during the 80's. Before the introduction of mechanical harvesting (1947) crop residues were burnt as well as the wheat stubble during the conventional double cropping period (1970-1980). Soil texture (23±1% clay, with predominance of illite) and field slopes (<0.5%) were similar in the three sites. Nitrogen and phosphorus fertilization rates were minimal due to the low crop response. The results are expressed in Mg ha-1 for an A soil horizon mass of 2500 Mg ha-1. The introduction of agriculture decreased SOC stock: 31Y varied from 68.3 to 40.1 Mg ha-1 (41.3% loss) and 80Y from 68.3 to 47.2 Mg ha-1 (30% loss). The SOC loss was the result of the mineralization of a large amount labile SOC present in the pristine soil and low annual additions of carbon issued from crop residue

  7. Effects of long-term differential fertilization on eukaryotic microbial communities in an arable soil: a multiple barcoding approach.

    PubMed

    Lentendu, Guillaume; Wubet, Tesfaye; Chatzinotas, Antonis; Wilhelm, Christian; Buscot, François; Schlegel, Martin

    2014-07-01

    To understand the fine-scale effects of changes in nutrient availability on eukaryotic soil microorganisms communities, a multiple barcoding approach was used to analyse soil samples from four different treatments in a long-term fertilization experiment. We performed PCR amplification on soil DNA with primer pairs specifically targeting the 18S rRNA genes of all eukaryotes and three protist groups (Cercozoa, Chrysophyceae-Synurophyceae and Kinetoplastida) as well as the ITS gene of fungi and the 23S plastid rRNA gene of photoautotrophic microorganisms. Amplicons were pyrosequenced, and a total of 88,706 quality filtered reads were clustered into 1232 operational taxonomic units (OTU) across the six data sets. Comparisons of the taxonomic coverage achieved based on overlapping assignment of OTUs revealed that half of the eukaryotic taxa identified were missed by the universal eukaryotic barcoding marker. There were only little differences in OTU richness observed between organic- (farmyard manure), mineral- and nonfertilized soils. However, the community compositions appeared to be strongly structured by organic fertilization in all data sets other than that generated using the universal eukaryotic 18S rRNA gene primers, whereas mineral fertilization had only a minor effect. In addition, a co-occurrence based network analysis revealed complex potential interaction patterns between OTUs from different trophic levels, for example between fungivorous flagellates and fungi. Our results demonstrate that changes in pH, moisture and organic nutrients availability caused shifts in the composition of eukaryotic microbial communities at multiple trophic levels. © 2014 John Wiley & Sons Ltd.

  8. 13C nuclear magnetic resonance and gas chromatography-mass spectrometry studies of carbon metabolism in the actinomycin D producer Streptomyces parvulus by use of 13C-labeled precursors.

    PubMed

    Inbar, L; Lapidot, A

    1991-12-01

    Fructose and glutamate metabolism was monitored in cell suspensions of streptomyces parvulus by 13C nuclear magnetic resonance. The experiments were performed for cells grown with various 13C sources in a growth medium containing D-[U-13C]fructose, L-[13C]glutamate, or L-[U-13C]aspartate and with nonlabeled precursors to compare intracellular pools in S. parvulus cells at different periods of the cell life cycle. The transport of fructose into the cells was biphasic in nature; during rapid transport, mannitol, fructose, and glucose 6-phosphate were accumulated intracellularly, whereas during the passive diffusion of fructose, the intracellular carbohydrate pool comprised mainly trehalose (1,1'-alpha-alpha-D-glucose). The regulation of fructokinase activity by the intracellular intermediates may play an important role in fructose catabolism in S. parvulus. Transaldolase activity in S. parvulus was determined from the 13C nuclear magnetic resonance labeling pattern of trehalose carbons obtained from cells grown in medium containing either L-[U-13C]aspartate or L-[U-13C]glutamate. Only carbons 4, 5, and 6 of the disaccharide were labeled. Isotopomer analysis of the trehalose carbons led us to conclude that the flux through the reverse glycolytic pathway, condensation of glyceraldehyde 3-phosphate with dihydroxyacetone phosphate, makes at best a minor contribution to the 13C-labeled glucose units observed in trehalose. The pentose pathway and transaldolase activity can explain the labeling pattern of 4,5,6-13C3 of trehalose. Moreover, the transfer of the 13C label of L-[U-13C]aspartate into the different isotopomers of trehalose C4, C5, and C6 by the transaldolase activity allowed us to calculate the relative fluxes from oxaloacetate via gluconeogenesis and through the tricarboxylic acid cycle. The ratio of the two fluxes is approximately 1. However, the main carbon source for trehalose synthesis in S. parvulus is fructose and not glutamate or aspartate. The 13C

  9. Do cover crops enhance N₂O, CO₂ or CH₄ emissions from soil in Mediterranean arable systems?

    PubMed

    Sanz-Cobena, A; García-Marco, S; Quemada, M; Gabriel, J L; Almendros, P; Vallejo, A

    2014-01-01

    This study evaluates the effect of planting three cover crops (CCs) (barley, Hordeum vulgare L.; vetch, Vicia villosa L.; rape, Brassica napus L.) on the direct emission of N₂O, CO₂ and CH₄ in the intercrop period and the impact of incorporating these CCs on the emission of greenhouse gas (GHG) from the forthcoming irrigated maize (Zea mays L.) crop. Vetch and barley were the CCs with the highest N₂O and CO₂ losses (75 and 47% increase compared with the control, respectively) in the fallow period. In all cases, fluxes of N₂O were increased through N fertilization and the incorporation of barley and rape residues (40 and 17% increase, respectively). The combination of a high C:N ratio with the addition of an external source of mineral N increased the fluxes of N₂O compared with -Ba and -Rp. The direct emissions of N₂O were lower than expected for a fertilized crop (0.10% emission factor, EF) compared with other studies and the IPCC EF. These results are believed to be associated with a decreased NO₃(-) pool due to highly denitrifying conditions and increased drainage. The fluxes of CO₂ were in the range of other fertilized crops (i.e., 1118.71-1736.52 kg CO₂-Cha(-1)). The incorporation of CC residues enhanced soil respiration in the range of 21-28% for barley and rape although no significant differences between treatments were detected. Negative CH₄ fluxes were measured and displayed an overall sink effect for all incorporated CC (mean values of -0.12 and -0.10 kg CH₄-Cha(-1) for plots with and without incorporated CCs, respectively). © 2013 Elsevier B.V. All rights reserved.

  10. Modeling the effects of different N fertilizer rates on N2O emissions and nitrate leaching from arable soils in Korea

    NASA Astrophysics Data System (ADS)

    Kim, Y.; Berger, S.; Tenhunen, J. D.; Gebauer, G.; Kiese, R.

    2012-12-01

    Process-based biogeochemical models can be used to predict the impact of various agricultural management practices on plant nitrogen use efficiency and nitrogen losses to the environment such as greenhouse gas emissions and nitrate leaching by analyzing the interactions between management practices, primary drivers such as climate, soil properties, crop types, etc., and biogeochemical reactions. In this study we applied the Landscape-DNDC model, which combines and uniforms functions of the agricultural-DNDC and the Forest-DNDC for simulation of C and N turnover, GHG emissions, nitrate leaching, and plant growth for a Korean arable field cultivated with radish (Raphanus sativus L.). The annual average temperature is app. 8.5°C and the annual precipitation is app. 1,500 mm. According to farmers practice the study field received a basal fertilizer application of app. 200 kg N ha-1 before setting up four fertilizer treatments i.e. additionally 50, 150, 250 and 350 kg N ha-1. All N treatment plots were tilled a week after application of specific N fertilizer in order to make row and interrow. Just before radish seeding rows were covered with black plastic mulch which was removed after harvest. In spite the widespread usage of black mulch in Korea or even Asia; so far biogeochemical models do not consider impacts of mulch on soil environmental conditions and soil biogeochemistry. Based on field measurements we adjusted input information and used only half of the annual precipitation and the maximum temperature for simulation of row conditions, whereas the actual weather data were used for the interrow simulations. Simulated N2O emissions agreed well with measurements; however peak emissions after fertilization were slightly underestimated in row and interrow. Annual N2O emissions of the fertilizer treatments increased with increasing fertilization rates from around 1.5 to 3 kg N ha-1 in the row and lower emissions of app. 1.5 kg N ha-1 (for all N treatments) in the

  11. Significant alteration of soil bacterial communities and organic carbon decomposition by different long-term fertilization management conditions of extremely low-productivity arable soil in South China.

    PubMed

    Xun, Weibing; Zhao, Jun; Xue, Chao; Zhang, Guishan; Ran, Wei; Wang, Boren; Shen, Qirong; Zhang, Ruifu

    2016-06-01

    Different fertilization managements of red soil, a kind of Ferralic Cambisol, strongly affected the soil properties and associated microbial communities. The association of the soil microbial community and functionality with long-term fertilization management in the unique low-productivity red soil ecosystem is important for both soil microbial ecology and agricultural production. Here, 454 pyrosequencing analysis of 16S recombinant ribonucleic acid genes and GeoChip4-NimbleGen-based functional gene analysis were used to study the soil bacterial community composition and functional genes involved in soil organic carbon degradation. Long-term nitrogen-containing chemical fertilization-induced soil acidification and fertility decline and significantly altered the soil bacterial community, whereas long-term organic fertilization and fallow management improved the soil quality and maintained the bacterial diversity. Short-term quicklime remediation of the acidified soils did not change the bacterial communities. Organic fertilization and fallow management supported eutrophic ecosystems, in which copiotrophic taxa increased in relative abundance and have a higher intensity of labile-C-degrading genes. However, long-term nitrogen-containing chemical fertilization treatments supported oligotrophic ecosystems, in which oligotrophic taxa increased in relative abundance and have a higher intensity of recalcitrant-C-degrading genes but a lower intensity of labile-C-degrading genes. Quicklime application increased the relative abundance of copiotrophic taxa and crop production, although these effects were utterly inadequate. This study provides insights into the interaction of soil bacterial communities, soil functionality and long-term fertilization management in the red soil ecosystem; these insights are important for improving the fertility of unique low-productivity red soil.

  12. Effectiveness Of Miraba an Indigenous Soil and Water Conservation Measures On Reducing Runoff And Soil Loss In Arable Land Of Western Usambara Mountains

    NASA Astrophysics Data System (ADS)

    Msita, H. B.; Kimaro, D. N.; Mtakwa, P. W.; Msanya, B. M.; Dondyene, S.; Poesen, J.; Deckers, J.

    2012-04-01

    Soil erosion by water is rampant mainly in mountainous areas of Tanzania leading to environmental hazards, low land productivity, low income and increased poverty. Despite the severity of the soil erosion problem, there is not much quantitative data on the erosion effects and effectiveness of indigenous soil and water conservation (SWC) measures. The consequence is that indigenous knowledge in SWC planning is ignored. The on-farm field experiment was conducted for three years in Migambo village, Lushoto district in Tanzania, to determine the effectiveness of improved Miraba (IM) an indigenous soil erosion control measure on reducing runoff and soil loss. Management practices were tested viz: control that is without any soil conservation measure (C), Miraba alone (M), Miraba with farmyard manure and mulching (MFM) replicated three times in CRD setting. Maize (Zea mays) and beans (Phaseolus vulgaris) were used as test crops, due to their importance as food crops and the high erosion rates on fields with these crops. The crops were planted in rotation, maize and beans in short and long rains respectively. Gerlach troughs and runoff plots were used to evaluate the physical effectiveness. Results show significant effects of IM against control on crop yields, soil loss, surface runoff and moisture retention. MFM is the most effective measure in reducing soil and water losses followed by MF and M. The results further showed that these management practices can be implemented to reduce soil erosion and nutrient losses in the study area and areas with similar ecological setting. To facilitate adoption of these practices further research works is recommended for identifying economically feasible indigenous SWC measures under different biophysical and socio-economic conditions.

  13. Metabolic flux analysis of recombinant Pichia pastoris growing on different glycerol/methanol mixtures by iterative fitting of NMR-derived (13)C-labelling data from proteinogenic amino acids.

    PubMed

    Jordà, Joel; de Jesus, Sérgio S; Peltier, Solenne; Ferrer, Pau; Albiol, Joan

    2014-01-25

    The yeast Pichia pastoris has emerged as one of the most promising yeast cell factories for the production of heterologous proteins. The readily available genetic tools and the ease of high-cell density cultivations using methanol or glycerol/methanol mixtures are among the key factors for this development. Previous studies have shown that the use of mixed feeds of glycerol and methanol seem to alleviate the metabolic burden derived from protein production, allowing for higher specific and volumetric process productivities. However, initial studies of glycerol/methanol co-metabolism in P. pastoris by classical metabolic flux analyses using (13)C-derived Metabolic Flux Ratio (METAFoR) constraints were hampered by the reduced labelling information obtained when using C3:C1 substrate mixtures in relation to the conventional C6 substrate, that is, glucose. In this study, carbon flux distributions through the central metabolic pathways in glycerol/methanol co-assimilation conditions have been further characterised using biosynthetically directed fractional (13)C labelling. In particular, metabolic flux distributions were obtained under 3 different glycerol/methanol ratios and growth rates by iterative fitting of NMR-derived (13)C-labelling data from proteinogenic amino acids using the software tool (13)CFlux2. Specifically, cells were grown aerobically in chemostat cultures fed with 80:20, 60:40 and 40:60 (w:w) glycerol/methanol mixtures at two dilutions rates (0.05 hour(-1) and 0.16 hour(-1)), allowing to obtain additional data (biomass composition and extracellular fluxes) to complement pre-existing datasets. The performed (13)C-MFA reveals a significant redistribution of carbon fluxes in the central carbon metabolism as a result of the shift in the dilution rate, while the ratio of carbon sources has a lower impact on carbon flux distribution in cells growing at the same dilution rate. At low growth rate, the percentage of methanol directly dissimilated to CO2 ranges

  14. Linear ion trap MS(n) of enzymatically synthesized 13C-labeled fructans revealing differentiating fragmentation patterns of β (1-2) and β (1-6) fructans and providing a tool for oligosaccharide identification in complex mixtures.

    PubMed

    Harrison, Scott; Xue, Hong; Lane, Geoff; Villas-Boas, Silas; Rasmussen, Susanne

    2012-02-07

    Fructans are polymeric carbohydrates, which play important roles as plant reserve carbohydrates and stress protectants, and are beneficial for human health and animal production. Fructans are formed by the addition of β-d-fructofuranosyl units to sucrose, leading to very complex mixtures of 1-kestose based inulins, 6-kestose linked levans, and 6G-kestose derived neoseries inulins and levans in cool season grasses such as Lolium perenne. The identification of isomeric fructan oligomers in chromatographic analysis of crude plant extracts is often hampered by the lack of authentic standards, and unambiguous peak assignment usually requires time-consuming analyses of purified fructan oligomers. We have developed a LC-MS(n) method for the separation and detection of fructan isomers and present here evidence for specific MS(n) fragmentation patterns associated with β 1-2 (inulins) and β 2-6 (levans) fructans. LC-MS(n) analysis of (13)C labeled fructan oligomers produced by L. perenne fructosyltransferases expressed in yeast has enabled us to account for the observed fragmentation patterns in terms of preferential cleavage of the glycosidic bond between O- and fructose C2 in both inulins and levans and to differentiate reducing-end from nonreducing end cross ring cleavages in levans. We propose that higher order MS fragmentation patterns can be used to distinguish between the two major classes of fructan, i.e., inulins and levans, without the need for authentic standards.

  15. De novo biosynthesis of linoleic acid and its conversion to the hydrocarbon (Z,Z)-6,9-heptadecadiene in the astigmatid mite, Carpoglyphus lactis: incorporation experiments with 13C-labeled glucose.

    PubMed

    Shimizu, Nobuhiro; Naito, Michiya; Mori, Naoki; Kuwahara, Yasumasa

    2014-02-01

    De novo biosynthesis of linoleic acid (LA) and its conversion to (Z,Z)-6,9-heptadecadiene were examined in Carpoglyphus lactis (Acarina, Carpoglyphidae). Experiments involving (13)C-administration using [1-(13)C]-d-glucose revealed that (13)C atoms were incorporated into LA of total lipid extracted from the mite, resulting in labeling of all even-numbered carbons. This result demonstrated that LA was produced from (13)C-labeled acetyl-CoA, which is indicative of direct de novo biosynthesis. In these feeding experiments involving [1-(13)C]-D-glucose, (13)C atoms were also incorporated into (Z,Z)-6,9-heptadecadiene, which is one of the major secretory components in the mite. The labeling pattern of (Z,Z)-6,9-heptadecadiene at odd-numbered carbons agreed well with that of LA after loss of the carboxyl carbon. It was concluded that the mites could stably convert LA into (Z,Z)-6,9-heptadecadiene without the dietary requirement of this essential fatty acid.

  16. Uniform {sup 15}N- and {sup 15}N/{sup 13}C-labeling of proteins in mammalian cells and solution structure of the amino terminal fragment of u-PA

    SciTech Connect

    Hansen, A.P.; Petros, A.M.; Meadows, R.P.; Mazar, A.P.; Nettesheim, D.G.; Pederson, T.M.; Fesik, S.W.

    1994-12-01

    Urokinase-type plasminogen activator (u-PA) is a 54-kDa glycoprotein that catalyzes the conversion of plasminogen to plasmin, a broad-specificity protease responsible for the degradation of fibrin clots and extracellular matrix components. The u-PA protein consists of three individual modules: a growth factor domain (GFD), a kringle, and a serine protease domain. The amino terminal fragment (ATF) includes the GFD-responsible for u-PA binding to its receptor-and the kringle domains. This protein was expressed and uniformly {sup 15}N-and {sup 15}N/{sup 13}C-labeled in mammalian cells by methods that will be described. In addition, we present the three-dimensional structure of ATF that was derived from 1299 NOE-derived distance restraints along with the {phi} angle and hydrogen bonding restraints. Although the individual domains in the structures were highly converged, the two domains are structurally independent. The overall structures of the individual domains are very similar to the structures of homologous proteins. However, important structural differences between the growth factor domain of u-PA and other homologous proteins were observed in the region that has been implicated in binding the urokinase receptor. These results may explain, in part, why other growth factors show no appreciable affinity for the urokinase receptor.

  17. Use of {sup 13}C NMR to assess the biodegradation of 1-{sup 13}C-labeled acenaphthene in the presence of creosote polynuclear hydrocarbons (PAHs) and naphthalene by mixed bacterial cultures

    SciTech Connect

    Selifonov, S.A.; Bortiatynski, J.M.; Nanny, M.A.; Hatcher, P.G.

    1996-10-01

    1-{sup 13}C-acenaphthene mixed with creosote PAH`s or naphthalene was incubated with bacterial strains known to degrade naphthalene, phenanthrene and acenaphthene. After incubation, the reaction mixtures were extracted with organic solvent, and the biodegradation products were identified by {sup 13}C NMR. An accumulation of intermediate degradation products was identified and attributed to the non-specific action of naphthalene catabolic pathways of the mixed bacterial cultures. An acenaphthene degrading strain, Pseudomonas sp. strain A2279 was added to the nixed bacterial cultures to minimize the formation of the observed dead-end products. The {sup 13}C NMR spectra obtained from the experiments in which strain A2279 was present clearly showed the complete biodegradation of 1-{sup 13}C-acenaphthene without the accumulation of {sup 13}C-labeled products. This set of experiments clearly demonstrates the utility of {sup 13}C NMR as an effective tool for the assessment of the biodegradation of PAH`s such as 1-{sup 13}C-acenaphthene by various microbial strains.

  18. Accurate measurements of {sup 13}C-{sup 13}C distances in uniformly {sup 13}C-labeled proteins using multi-dimensional four-oscillating field solid-state NMR spectroscopy

    SciTech Connect

    Straasø, Lasse Arnt; Nielsen, Jakob Toudahl; Bjerring, Morten; Nielsen, Niels Chr.; Khaneja, Navin

    2014-09-21

    Application of sets of {sup 13}C-{sup 13}C internuclear distance restraints constitutes a typical key element in determining the structure of peptides and proteins by magic-angle-spinning solid-state NMR spectroscopy. Accurate measurements of the structurally highly important {sup 13}C-{sup 13}C distances in uniformly {sup 13}C-labeled peptides and proteins, however, pose a big challenge due to the problem of dipolar truncation. Here, we present novel two-dimensional (2D) solid-state NMR experiments capable of extracting distances between carbonyl ({sup 13}C′) and aliphatic ({sup 13}C{sub aliphatic}) spins with high accuracy. The method is based on an improved version of the four-oscillating field (FOLD) technique [L. A. Straasø, M. Bjerring, N. Khaneja, and N. C. Nielsen, J. Chem. Phys. 130, 225103 (2009)] which circumvents the problem of dipolar truncation, thereby offering a base for accurate extraction of internuclear distances in many-spin systems. The ability to extract reliable accurate distances is demonstrated using one- and two-dimensional variants of the FOLD experiment on uniformly {sup 13}C,{sup 15}N-labeled-L-isoleucine. In a more challenging biological application, FOLD 2D experiments are used to determine a large number of {sup 13}C′-{sup 13}C{sub aliphatic} distances in amyloid fibrils formed by the SNNFGAILSS fibrillating core of the human islet amyloid polypeptide with uniform {sup 13}C,{sup 15}N-labeling on the FGAIL fragment.

  19. hNCOcanH pulse sequence and a robust protocol for rapid and unambiguous assignment of backbone ((1)H(N), (15)N and (13)C') resonances in (15)N/(13)C-labeled proteins.

    PubMed

    Kumar, Dinesh; Hosur, Ramakrishna V

    2011-09-01

    A three-dimensional nuclear magnetic resonance (NMR) pulse sequence named as hNCOcanH has been described to aid rapid sequential assignment of backbone resonances in (15)N/(13)C-labeled proteins. The experiment has been derived by a simple modification of the previously described HN(C)N pulse sequence [Panchal et al., J. Biomol. NMR 20 (2001) 135-147]; t2 evolution is used to frequency label (13)C' rather than (15)N (similar trick has also been used in the design of hNCAnH pulse sequence from hNcaNH [Frueh et al., JACS, 131 (2009) 12880-12881]). The modification results in a spectrum equivalent to HNCO, but in addition to inter-residue correlation peaks (i.e. Hi , Ci-1), the spectrum also contains additional intra-residue correlation peaks (i.e. Hi-1 , Ci-1) in the direct proton dimension which has maximum resolution. This is the main strength of the experiment and thus, even a small difference in amide (1) H chemical shifts (5-6 Hz) can be used for establishing a sequential connectivity. This experiment in combination with the HNN experiment described previously [Panchal et al., J. Biomol. NMR 20 (2001) 135-147] leads to a more robust assignment protocol for backbone resonances ((1) H(N) , (15)N) than could be derived from the combination of HNN and HN(C)N experiments [Bhavesh et al., Biochemistry, 40 (2001) 14727-14735]. Further, this new protocol enables assignment of (13)C' resonances as well. We believe that the experiment and the protocol presented here will be of immense value for structural-and functional-proteomics research by NMR. Performance of this experiment has been demonstrated using (13)C/(15)N labeled ubiquitin. Copyright © 2011 John Wiley & Sons, Ltd.

  20. An automated GCxGC-TOF-MS protocol for batch-wise extraction and alignment of mass isotopomer matrixes from differential 13C-labelling experiments: a case study for photoautotrophic-mixotrophic grown Chlamydomonas reinhardtii cells.

    PubMed

    Kempa, Stefan; Hummel, Jan; Schwemmer, Thorsten; Pietzke, Matthias; Strehmel, Nadine; Wienkoop, Stefanie; Kopka, Joachim; Weckwerth, Wolfram

    2009-02-01

    Two dimensional gas chromatography coupled to time-of-flight mass spectrometry (GCxGC-TOF-MS) is a promising technique to overcome limits of complex metabolome analysis using one dimensional GC-TOF-MS. Especially at the stage of data export and data mining, however, convenient procedures to cope with the complexity of GCxGC-TOF-MS data are still in development. Here, we present a high sample throughput protocol exploiting first and second retention index for spectral library search and subsequent construction of a high dimensional data matrix useful for statistical analysis. The method was applied to the analysis of (13)C-labelling experiments in the unicellular green alga Chlamydomonas reinhardtii. We developed a rapid sampling and extraction procedure for Chlamydomonas reinhardtii laboratory strain (CC503), a cell wall deficient mutant. By testing all published quenching protocols we observed dramatic metabolite leakage rates for certain metabolites. To circumvent metabolite leakage, samples were directly quenched and analyzed without separation of the medium. The growth medium was adapted to this rapid sampling protocol to avoid interference with GCxGC-TOF-MS analysis. To analyse batches of samples a new software tool, MetMax, was implemented which extracts the isotopomer matrix from stable isotope labelling experiments together with the first and second retention index (RI1 and RI2). To exploit RI1 and RI2 for metabolite identification we used the Golm metabolome database (GMD [1] with RI1/RI2-reference spectra and new search algorithms. Using those techniques we analysed the dynamics of (13)CO(2) and (13)C-acetate uptake in Chlamydomonas reinhardtii cells in two different steady states namely photoautotroph and mixotroph growth conditions.

  1. Modeling the Emergence of Three Arable Bedstraw (Galium) Species

    USDA-ARS?s Scientific Manuscript database

    Seedling emergence was modelled for three arable species of bedstraw (Galium), which may coexist in winter cereal fields, using multi-year field data from Spain. The relationships between cumulative emergence and both growing degree days (GDD) and hydrothermal time (HTT) in soil were analyzed as sig...

  2. Modeling greenhouse gas emissions (CO2, N2O, CH4) from managed arable soils with a fully coupled hydrology-biogeochemical modeling system simulating water and nutrient transport and associated carbon and nitrogen cycling at catchment scale

    NASA Astrophysics Data System (ADS)

    Klatt, Steffen; Haas, Edwin; Kraus, David; Kiese, Ralf; Butterbach-Bahl, Klaus; Kraft, Philipp; Plesca, Ina; Breuer, Lutz; Zhu, Bo; Zhou, Minghua; Zhang, Wei; Zheng, Xunhua; Wlotzka, Martin; Heuveline, Vincent

    2014-05-01

    The use of mineral nitrogen fertilizer sustains the global food production and therefore the livelihood of human kind. The rise in world population will put pressure on the global agricultural system to increase its productivity leading most likely to an intensification of mineral nitrogen fertilizer use. The fate of excess nitrogen and its distribution within landscapes is manifold. Process knowledge on the site scale has rapidly grown in recent years and models have been developed to simulate carbon and nitrogen cycling in managed ecosystems on the site scale. Despite first regional studies, the carbon and nitrogen cycling on the landscape or catchment scale is not fully understood. In this study we present a newly developed modelling approach by coupling the fully distributed hydrology model CMF (catchment modelling framework) to the process based regional ecosystem model LandscapeDNDC for the investigation of hydrological processes and carbon and nitrogen transport and cycling, with a focus on nutrient displacement and resulting greenhouse gas emissions in a small catchment at the Yanting Agro-ecological Experimental Station of Purple Soil, Sichuan province, China. The catchment hosts cypress forests on the outer regions, arable fields on the sloping croplands cultivated with wheat-maize rotations and paddy rice fields in the lowland. The catchment consists of 300 polygons vertically stratified into 10 soil layers. Ecosystem states (soil water content and nutrients) and fluxes (evapotranspiration) are exchanged between the models at high temporal scales (hourly to daily) forming a 3-dimensional model application. The water flux and nutrients transport in the soil is modelled using a 3D Richards/Darcy approach for subsurface fluxes with a kinematic wave approach for surface water runoff and the evapotranspiration is based on Penman-Monteith. Biogeochemical processes are modelled by LandscapeDNDC, including soil microclimate, plant growth and biomass allocation

  3. Changes in the agrochemical properties of major arable soils in the south of the Far East of Russia under the impact of their long-term agricultural use

    NASA Astrophysics Data System (ADS)

    Burdukovskii, M. L.; Golov, V. I.; Kovshik, I. G.

    2016-10-01

    Agrochemical properties of meadow-brown (Gleyic Cambisols (Clayic, Aric)) and meadow-chernozemic (Luvic Gleyic Chernic Phaeozems (Loamic, Aric, Pachic)) soils under the impact of long-term application of mineral and organic fertilizers were studied. The investigations were performed at the agrochemical experimental stations of the Primorskii region and Amur oblast founded in 1941 and 1962, respectively. It was shown that the long-term crop cultivation without fertilizers or with great rates of mineral fertilizers and lime resulted in the soil dehumification, a rise in the soil acidity, and a decrease of the content of exchangeable bases. These processes were slowed down by the application of organic fertilizers. Agrochemical parameters of meadow-chernozemic and floodplain meadow (Fluvic Phaeozems (Loamic, Aric, Oxyaquic)) soils of Amur oblast (Russia) and the Heilongjiang border province (China) were compared.

  4. Spatial and temporal diversification of crops dynamics in soil erosion modelling. A case study in the arable land of the upper Enziwigger River, Switzerland.

    NASA Astrophysics Data System (ADS)

    Borrelli, Pasquale; Meusburger, Katrin; Panagos, Panos; Ballabio, Cristiano; Alewell, Christine

    2017-04-01

    Accelerated soil erosion by water is a widespread phenomenon that affects several Mediterranean and Alpine landscapes causing on-site and off-site environmental impacts. Recognized in the EU Thematic Strategy for Soil Protection as one of the major threats to European soils (COM(2006)231), accelerated soil erosion is a major concern in landscape management and conservation planning (UN SDG 2.4). Agriculture and associated land-use change is the primary cause of accelerated soil erosion. This, because the soil displacement by water erosion mainly occurs when bare-sloped soil surfaces are exposed to the effect of rainfall and overland flow. The Revised Universal Soil Loss Equation (RUSLE) and other RUSLE-based models (which account for more than 90% of current worldwide modelling applications) describe the effect of the vegetation in the so called cover and management factor (C). The C-factor is generally the most challenging modelling component to compute over large study sites. To run a GIS-based RUSLE modelling for a study site greater than few hectares, the use of a simplified approach to assess the C-factor is inevitably necessary. In most of the cases, the C-factor values are assigned to the different land-use classes according to i) the C-values proposed in the literature, and ii) through land-use classifications based on vegetation indices (VI). In previous national (Land Use Policy, 50, 408-421, 2016) and pan-European (Environmental Science & Policy, 54, 438-447, 2015) studies, we computed regional C-values through weighted average operations combining crop statistics with remote sensing and GIS modelling techniques. Here, we present the preliminary results of an object-oriented change detection approach that we are testing to acquire spatial as well temporal crops dynamics at field-scale level in complex agricultural systems.

  5. Responses of bacterial communities in arable soils in a rice-wheat cropping system to different fertilizer regimes and sampling times.

    PubMed

    Zhao, Jun; Ni, Tian; Li, Yong; Xiong, Wu; Ran, Wei; Shen, Biao; Shen, Qirong; Zhang, Ruifu

    2014-01-01

    Soil physicochemical properties, soil microbial biomass and bacterial community structures in a rice-wheat cropping system subjected to different fertilizer regimes were investigated in two seasons (June and October). All fertilizer regimes increased the soil microbial biomass carbon and nitrogen. Both fertilizer regime and time had a significant effect on soil physicochemical properties and bacterial community structure. The combined application of inorganic fertilizer and manure organic-inorganic fertilizer significantly enhanced the bacterial diversity in both seasons. The bacterial communities across all samples were dominated by Proteobacteria, Acidobacteria and Chloroflexi at the phylum level. Permutational multivariate analysis confirmed that both fertilizer treatment and season were significant factors in the variation of the composition of the bacterial community. Hierarchical cluster analysis based on Bray-Curtis distances further revealed that bacterial communities were separated primarily by season. The effect of fertilizer treatment is significant (P = 0.005) and accounts for 7.43% of the total variation in bacterial community. Soil nutrients (e.g., available K, total N, total P and organic matter) rather than pH showed significant correlation with the majority of abundant taxa. In conclusion, both fertilizer treatment and seasonal changes affect soil properties, microbial biomass and bacterial community structure. The application of NPK plus manure organic-inorganic fertilizer may be a sound fertilizer practice for sustainable food production.

  6. Responses of Bacterial Communities in Arable Soils in a Rice-Wheat Cropping System to Different Fertilizer Regimes and Sampling Times

    PubMed Central

    Zhao, Jun; Ni, Tian; Li, Yong; Xiong, Wu; Ran, Wei; Shen, Biao; Shen, Qirong; Zhang, Ruifu

    2014-01-01

    Soil physicochemical properties, soil microbial biomass and bacterial community structures in a rice-wheat cropping system subjected to different fertilizer regimes were investigated in two seasons (June and October). All fertilizer regimes increased the soil microbial biomass carbon and nitrogen. Both fertilizer regime and time had a significant effect on soil physicochemical properties and bacterial community structure. The combined application of inorganic fertilizer and manure organic-inorganic fertilizer significantly enhanced the bacterial diversity in both seasons. The bacterial communities across all samples were dominated by Proteobacteria, Acidobacteria and Chloroflexi at the phylum level. Permutational multivariate analysis confirmed that both fertilizer treatment and season were significant factors in the variation of the composition of the bacterial community. Hierarchical cluster analysis based on Bray-Curtis distances further revealed that bacterial communities were separated primarily by season. The effect of fertilizer treatment is significant (P = 0.005) and accounts for 7.43% of the total variation in bacterial community. Soil nutrients (e.g., available K, total N, total P and organic matter) rather than pH showed significant correlation with the majority of abundant taxa. In conclusion, both fertilizer treatment and seasonal changes affect soil properties, microbial biomass and bacterial community structure. The application of NPK plus manure organic-inorganic fertilizer may be a sound fertilizer practice for sustainable food production. PMID:24465530

  7. Heavy metal contamination of arable soil and corn plant in the vicinity of a zinc smelting factory and stabilization by liming.

    PubMed

    Hong, Chang Oh; Gutierrez, Jessie; Yun, Sung Wook; Lee, Yong Bok; Yu, Chan; Kim, Pil Joo

    2009-02-01

    The heavy metal contamination in soils and cultivated corn plants affected by zinc smelting activities in the vicinity of a zinc smelting factory in Korea was studied. Soils and corn plants were sampled at the harvesting stage and analyzed for cadmium (Cd) and zinc (Zn) concentration, as well as Cd and Zn fraction and other chemical properties of soils. Cd and Zn were highly accumulated in the surface soils (0-20 cm), at levels higher than the Korean warning criteria (Cd, 1.5; Zn, 300 mg kg(-1)), with corresponding mean values of 1.7 and 407 mg kg(-1), respectively, but these metals decreased significantly with increasing soil depth and distance from the factory, implying that contaminants may come from the factory through aerosol dynamics (Hong et al., Kor J Environ Agr 26(3):204-209, 2007a; Environ Contam Toxicol 52:496-502, 2007b) and not from geological sources. The leaf part had higher Cd and Zn concentrations, with values of 9.5 and 1733 mg kg(-1), compared to the stem (1.6 and 547 mg kg(-1)) and grain (0.18 and 61 mg kg(-1)) parts, respectively. Cd and Zn were higher in the oxidizable fraction, at 38.5% and 46.9% of the total Cd (2.6 mg kg(-1)) and Zn (407 mg kg(-1)), but the exchangeable + acidic fraction of Cd and Zn as the bioavailable phases was low, 0.2 and 50 mg kg(-1), respectively. To study the reduction of plant Cd and Zn uptake by liming, radish (Raphanus sativa L.) was cultivated in one representative field among the sites investigated, and Ca(OH)(2) was applied at rates of 0, 2, 4, and 8 mg ha(-1). Plant Cd and Zn concentrations and NH(4)OAc extractable Cd and Zn concentrations of soil decreased significantly with increasing Ca(OH)(2) rate, since it markedly increases the cation exchange capacity of soil induced by increased pH. As a result, liming in this kind of soil could be an effective countermeasure in reducing the phytoextractability of Cd and Zn.

  8. Archaeal abundance across a pH gradient in an arable soil and its relationship to bacterial and fungal growth rates.

    PubMed

    Bengtson, Per; Sterngren, Anna E; Rousk, Johannes

    2012-08-01

    Soil pH is one of the most influential factors for the composition of bacterial and fungal communities, but the influence of soil pH on the distribution and composition of soil archaeal communities has yet to be systematically addressed. The primary aim of this study was to determine how total archaeal abundance (quantitative PCR [qPCR]-based estimates of 16S rRNA gene copy numbers) is related to soil pH across a pH gradient (pH 4.0 to 8.3). Secondarily, we wanted to assess how archaeal abundance related to bacterial and fungal growth rates across the same pH gradient. We identified two distinct and opposite effects of pH on the archaeal abundance. In the lowest pH range (pH 4.0 to 4.7), the abundance of archaea did not seem to correspond to pH. Above this pH range, there was a sharp, almost 4-fold decrease in archaeal abundance, reaching a minimum at pH 5.1 to 5.2. The low abundance of archaeal 16S rRNA gene copy numbers at this pH range then sharply increased almost 150-fold with pH, resulting in an increase in the ratio between archaeal and bacterial copy numbers from a minimum of 0.002 to more than 0.07 at pH 8. The nonuniform archaeal response to pH could reflect variation in the archaeal community composition along the gradient, with some archaea adapted to acidic conditions and others to neutral to slightly alkaline conditions. This suggestion is reinforced by observations of contrasting outcomes of the (competitive) interactions between archaea, bacteria, and fungi toward the lower and higher ends of the examined pH gradient.

  9. Archaeal Abundance across a pH Gradient in an Arable Soil and Its Relationship to Bacterial and Fungal Growth Rates

    PubMed Central

    Sterngren, Anna E.; Rousk, Johannes

    2012-01-01

    Soil pH is one of the most influential factors for the composition of bacterial and fungal communities, but the influence of soil pH on the distribution and composition of soil archaeal communities has yet to be systematically addressed. The primary aim of this study was to determine how total archaeal abundance (quantitative PCR [qPCR]-based estimates of 16S rRNA gene copy numbers) is related to soil pH across a pH gradient (pH 4.0 to 8.3). Secondarily, we wanted to assess how archaeal abundance related to bacterial and fungal growth rates across the same pH gradient. We identified two distinct and opposite effects of pH on the archaeal abundance. In the lowest pH range (pH 4.0 to 4.7), the abundance of archaea did not seem to correspond to pH. Above this pH range, there was a sharp, almost 4-fold decrease in archaeal abundance, reaching a minimum at pH 5.1 to 5.2. The low abundance of archaeal 16S rRNA gene copy numbers at this pH range then sharply increased almost 150-fold with pH, resulting in an increase in the ratio between archaeal and bacterial copy numbers from a minimum of 0.002 to more than 0.07 at pH 8. The nonuniform archaeal response to pH could reflect variation in the archaeal community composition along the gradient, with some archaea adapted to acidic conditions and others to neutral to slightly alkaline conditions. This suggestion is reinforced by observations of contrasting outcomes of the (competitive) interactions between archaea, bacteria, and fungi toward the lower and higher ends of the examined pH gradient. PMID:22706045

  10. Measurement and simulation of the effect of compaction on the pore structure and saturated hydraulic conductivity of grassland and arable soil

    NASA Astrophysics Data System (ADS)

    Matthews, G. P.; Laudone, G. M.; Gregory, A. S.; Bird, N. R. A.; Matthews, A. G. de G.; Whalley, W. R.

    2010-05-01

    Measurements have been made of the effect of compaction on water retention, saturated hydraulic conductivity, and porosity of two English soils: North Wyke (NW) grassland clay topsoil and Broadbalk silty topsoil, fertilized inorganically (PKMg) or with farmyard manure (FYM). As expected, the FYM topsoil had greater porosity and greater water retention than PKMg topsoil, and the NW clay topsoil retained more water at each matric potential than the silty topsoils. Compaction had a clear effect on water retention at matric potentials wetter than -10 kPa for the PKMg and FYM soils, corresponding to voids greater than 30 μm cylindrical diameter, whereas smaller voids appeared to be unaffected. The Pore-Cor void network model has been improved by including a Euler beta distribution to describe the sizes of the narrow interconnections, termed throats. The model revealed a change from bimodal to unimodal throat size distributions on compaction, as well as a reduction in sizes overall. It also matched the water retention curves more closely than van Genuchten fits and correctly predicted changes in saturated hydraulic conductivity better than those predicted by a prior statistical approach. However, the changes in hydraulic conductivity were masked by the stochastic variability of the model. Also, an artifact of the model, namely its inability to pack small features close together, caused incorrect increases in pore sizes on compaction. These deficiencies in the model demonstrate the need for an explicitly dual porous network model to account for the effects of compaction in soil.

  11. Landscape assessment of spatial Cs-137 connectivity patterns in arable land with gray loamy soils in the Bryansk Region (landscapes of the Opolje)

    NASA Astrophysics Data System (ADS)

    Linnik, Vitaly; Sokolov, Alexander; Saveliev, Anatoly; Mironenko, Iya

    2017-04-01

    As a result of the Chernobyl accident in 1986 landscapes of the Bryansk Region (Russia) were contaminated by Cs-137. In 1993 air-gamma survey with 100 m resolution was done in contaminated areas of the region, which revealed significant spatial heterogeneity of Cs-137 contamination. The initial "spotting" of contamination Cs-137, which in the spring of 1986 represented multi-scale complex patterns of contamination, was substantially transformed by 1993 as a result of erosion processes of various intensity. The purpose of this research was to obtain estimates of the transformation of initial Cs-137 patterns as influenced by different landscape factors. The study is based on the concept of sediment and hydrological connectivity. We apply GIS-based models considering lateral soil migration to analyze sediment cascade system. The study area is a test plot that has grey loamy soils (landscapes of the Opolje) with a size 10x16 km in the central part of the Bryansk Region, with more than 80% of the area under cultivation. Elevation levels are in the range of 140-210 m. Because of plowing, intense erosion processes have taken place. The slope angles in the lower parts of slopes reach 2-3 degrees. Maximum slopes in gullies reach 11,5 degrees. Cs-137 levels of contamination vary from 3,6 kBq/m2 to 35 3,6 kBq/m2. Over the past few decades the Cs-137 technique has been applied to determine net soil redistribution rates. It is applicable for medium long term (30 to 40 years) soil redistribution estimates. In this technique, the anthropogenic radionuclide Cs-137 is used as a sediment tracer from upland erosion studies to catchment sediment budgets, as well as to depositional areas in colluvial positions, valleys, river terraces, floodplains. The soil movement is primarily driven by water flow due to the gravity. The effect of gravity can be easily approximated using DEM derivatives. Cs-137 patterns have been investigated to estimate landscape connectivity and soil redistribution

  12. Recycling vs. stabilisation of soil sugars - a long-term laboratory incubation experiment

    NASA Astrophysics Data System (ADS)

    Basler, A.; Dippold, M.; Helfrich, M.; Dyckmans, J.

    2015-06-01

    Independent of its chemical structure carbon (C) persists in soil for several decades, controlled by stabilisation and recycling. To disentangle the importance of the two factors on the turnover dynamics of soil sugars, an important compound of soil organic matter (SOM), a three year incubation experiment was conducted on a silty loam soil under different types of land use (arable land, grassland and forest) by adding 13C-labeled glucose. The compound specific isotope analysis of soil sugars was used to examine the dynamics of different sugars during incubation. Sugar dynamics were dominated by a pool of high mean residence times (MRT) indicating that recycling plays an important role for sugars. However, this was not substantially affected by soil C content. Six months after label addition the contribution of the label was much higher for microbial biomass than for CO2 production for all examined soils, corroborating that substrate recycling was very effective within the microbial biomass. Two different patterns of tracer dynamics could be identified for different sugars: while fucose (fuc) and mannose (man) showed highest label contribution at the beginning of the incubation with a subsequent slow decline, galactose (gal) and rhamnose (rha) were characterised by slow label incorporation with subsequently constant levels, which indicates that recycling is dominating the dynamics of these sugars. This may correspond to (a) different microbial growing strategies (r and K-strategist) or (b) location within or outside the cell membrane (lipopolysaccharides vs. exopolysaccharides) and thus be subject of different re-use within the microbial food web. Our results show how the microbial community recycles substrate very effectively and that high losses of substrate only occur during initial stages after substrate addition.

  13. An incubation system to trace carbon fluxes in soil - First experimental

    NASA Astrophysics Data System (ADS)

    Thiessen*, Stefany; Gleixner, Gerd; Reichstein, Markus

    2010-05-01

    Soils contain the largest carbon pool in terrestrial ecosystems and it is widely assumed that a considerable fraction of this pool might be mobilized by global warming. Numerous investigations have proven that soil respiration is a mixture of several source, like root rhizosphere and soil organic matter (SOM) degradation. However, little is still known about soil carbon dynamics and the influence of microbes on this process. We developed an incubation system to perform multitracer experiments to quantify the contribution of microorganisms to carbon turnover from different carbon sources. A natural 13C label was used to mark carbon sources. The old carbon in the SOM held a depleted 13C3 signal and newly added C was enriched in 13C4. Accordingly, in the experiment we quantified the relative respiration of carbon from added sugars and soil organic matter by microbial groups, with additional application of fungicide (cycloheximide). A root free arable soil was divided into three sets, all with depleted C3 soil, but varied in terms of the added material: one with C4 glucose, a second with C4 glucose combined with fungicide and the last one with water application only, as control. To characterize microbial communities and estimate microbial biomass we extract phospholipid fatty acids (PLFA). Furthermore, by measuring the isotopic ratio of the PLFA it was also possible to identify microorganisms that metabolised the traced material. Preliminary results showed that the glucose application stimulated microbial growth in the beginning, but afterwards the microbial biomass decreased again over time. However, a change in the microbial community composition could not be observed, regardless to the kind of added material. Nevertheless, the respiration response slowed down after the fungicide application, and a second respiration pulse was induced by this application. This was probably due to reactivation of the fungi, after the effect of the fungicide expired.

  14. Formation of nonextractable soil residues: A stable isotope approach

    SciTech Connect

    Richnow, H.H.; Eschenback, A.; Mahro, B.; Kaestner, M.; Annweiler, E.; Seifert, R.; Michaelis, W.

    1999-11-01

    Stable carbon isotopic measurements were employed to characterize the transformation of a {sup 13}C-labeled polycyclic aromatic hydrocarbon (PAH), anthracene, in a closed soil bioreactor system. The {sup 13}C-label was used to calculate a carbon mass balance including mineralization and the formation of nonextractable soil-bound residues. Similar results were obtained from {sup 13}C-labeled carbon and {sup 14}C-labeled carbon mass balance calculations for separate batch experiments with labeled anthracene. In concentration ranges typical for real PAH-contaminated sites, the sensitivity of the {sup 13}C tracer method meets the requirements of classical radiotracer experiments. Therefore, the authors balancing method based on stable isotope-labeled chemicals may supplement or substitute radiotracer experiments under many circumstances. One major advantage of using stable isotope-labeled tracers is the possible application in transformation studies where the use of radioactive substances is of environmental concern. The transformation of {sup 13}C-labeled PAH into nonextractable residues clearly depends on the metabolic activity of the soil microflora and occurs during an early phase of biodegradation. Successive contamination of the soil by anthracene leads to a progressive adaptation of the microflora to a complete mineralization of anthracene in the soil. The extent of residue formation is controlled by the capability of the microflora to degrade the contaminant. Results of long-term experiments indicate that nonextractable residues are relatively stable over time.

  15. Adverse weather impacts on arable cropping systems

    NASA Astrophysics Data System (ADS)

    Gobin, Anne

    2016-04-01

    Damages due to extreme or adverse weather strongly depend on crop type, crop stage, soil conditions and management. The impact is largest during the sensitive periods of the farming calendar, and requires a modelling approach to capture the interactions between the crop, its environment and the occurrence of the meteorological event. The hypothesis is that extreme and adverse weather events can be quantified and subsequently incorporated in current crop models. Since crop development is driven by thermal time and photoperiod, a regional crop model was used to examine the likely frequency, magnitude and impacts of frost, drought, heat stress and waterlogging in relation to the cropping season and crop sensitive stages. Risk profiles and associated return levels were obtained by fitting generalized extreme value distributions to block maxima for air humidity, water balance and temperature variables. The risk profiles were subsequently confronted with yields and yield losses for the major arable crops in Belgium, notably winter wheat, winter barley, winter oilseed rape, sugar beet, potato and maize at the field (farm records) to regional scale (statistics). The average daily vapour pressure deficit (VPD) and reference evapotranspiration (ET0) during the growing season is significantly lower (p < 0.001) and has a higher variability before 1988 than after 1988. Distribution patterns of VPD and ET0 have relevant impacts on crop yields. The response to rising temperatures depends on the crop's capability to condition its microenvironment. Crops short of water close their stomata, lose their evaporative cooling potential and ultimately become susceptible to heat stress. Effects of heat stress therefore have to be combined with moisture availability such as the precipitation deficit or the soil water balance. Risks of combined heat and moisture deficit stress appear during the summer. These risks are subsequently related to crop damage. The methodology of defining

  16. Flash Flooding and 'Muddy Floods' on Arable Land

    NASA Astrophysics Data System (ADS)

    Boardman, J.

    2012-04-01

    Flash flooding is often associated with upland, grazed catchments. It does, however, occur in lowland arable-dominated areas. In southern England, notable examples have occurred at Rottingdean (Brighton) in 1987, at Faringdon (Oxfordshire) in 1993 and at Breaky Bottom vineyard (near Brighton) in 1987 and 2000. All resulted in damage to nearby property. Runoff was largely from recently cultivated ground. The characteristics of such floods are: Rapid runoff from bare soil surfaces. Saturated excess overland flow is likely in the early parts of storms but high intensity rainfall on loamy soils results in crusting and Hortonian overland flow; High rates of erosion; Sediment transport to downvalley sites causing property damage ('muddy flooding'). Muddy floods are known from several areas of Europe e.g. Belgium, northern France, South Limburg (Netherlands) and Slovakia (Boardman et al 2006). In other areas they occur but have gone unreported or are classified under different terms. The necessary conditions for occurrence are areas of arable land which is bare at times of the year when there is a risk of storms. For muddy floods to cause damage (and hence be reported), vulnerable property must lie downstream from such areas of arable land. In some areas the incidence of muddy floods relates to autumn and early winter rainfall and winter cereal crops (e.g. southern England). In continental Europe, flooding is more common in summer and is associated with convectional storms and land uses including sugar beet, maize and potatoes. Predictions of increased numbers of high-intensity storms with future climate change, suggest that arable areas will continue to generate both flash floods and muddy floods.

  17. Microbial carbon recycling - an underestimated process controlling soil carbon dynamics - Part 1: A long-term laboratory incubation experiment

    NASA Astrophysics Data System (ADS)

    Basler, A.; Dippold, M.; Helfrich, M.; Dyckmans, J.

    2015-10-01

    Independent of its chemical structure carbon (C) persists in soil for several decades, controlled by stabilization and recycling. To disentangle the importance of the two factors on the turnover dynamics of soil sugars, an important compound of soil organic matter (SOM), a 3-year incubation experiment was conducted on a silty loam soil under different types of land use (arable land, grassland and forest) by adding 13C-labelled glucose. The compound-specific isotope analysis of soil sugars was used to examine the dynamics of different sugars during incubation. Sugar dynamics were dominated by a pool of high mean residence times (MRT) indicating that recycling plays an important role for sugars. However, this was not substantially affected by soil C content. Six months after label addition the contribution of the label was much higher for microbial biomass than for CO2 production for all examined land use types, corroborating that substrate recycling was very effective within the microbial biomass. Two different patterns of tracer dynamics could be identified for different sugars: while fucose and mannose showed highest label contribution at the beginning of the incubation with a subsequent slow decline, galactose and rhamnose were characterized by slow label incorporation with subsequently constant levels, which indicates that recycling is dominating the dynamics of these sugars. This may correspond to (a) different microbial growing strategies (r and K-strategist) or (b) location within or outside the cell membrane (lipopolysaccharides vs. exopolysaccharides) and thus be subject of different re-use within the microbial food web. Our results show how the microbial community recycles substrate very effectively and that high losses of substrate only occur during initial stages after substrate addition. This study indicates that recycling is one of the major processes explaining the high MRT observed for many SOM fractions and thus is crucial for understanding the

  18. Resource Utilization by Native and Invasive Earthworms and Their Effects on Soil Carbon and Nitrogen Dynamics in Puerto Rican Soils

    Treesearch

    Ching-Yu Huang; Grizelle Gonzalez; Paul F. Hendrix

    2016-01-01

    Resource utilization by earthworms affects soil C and N dynamics and further colonization of invasive earthworms. By applying 13C-labeled Tabebuia heterophylla leaves and 15N-labeled Andropogon glomeratus grass, we investigated resource utilization by three earthworm species (...

  19. The good, the bad or the ugly: Microbial biomass of biogas residues as a contributor to soil carbon cycle

    NASA Astrophysics Data System (ADS)

    Coban, H.; Miltner, A.; Kaestner, M.

    2013-12-01

    Loss of soil organic matter is a recent problem in soils all over the world. This can be related to enhanced mineralization of the soil organic matter due to land use change, which is a source of anthropogenic carbon dioxide increase. For example, the carbon input from plant residues is reduced because of the increased cultivation of bioenergy crops. In order to avoid soil degradation, application of biogas residues is a common practice in such areas. Biogas residues are side products of biogas production and contain microbial biomass. Application of these residues as soil additive influences the soil microorganisms as well as the carbon cycle. We study this effect by incubating 13C-labeled biogas residues in an arable soil from the Static Fertilization Experiment in Bad Lauchstaedt, Germany. Labeled residues were produced via labeling of active microbial biomass by addition of KH13CO3 to biogas reactors. High enrichment in the various phospholipid fatty acids proved the successful labeling of the biomass. The labeled biogas residues are being long-term incubated in the soil. During incubation, we monitor the fate of the carbon by analyzing the label in phospholipid fatty acids, amino acids as well as carbon dioxide. This allows us to trace the fate of the biogas residues-derived C in soil and to quantify the effect on the transformation of the natural soil organic matter (e.g. negative effects such as priming effects). Also, microbial community dynamics will be determined using molecular biology tools such as denaturing gradient gel electrophoresis (DGGE) and real-time quantitative PCR (Q-PCR). In order to prevent potentially negative effects, various additives such as charred biomaterials, clays and chopped bark will be tested to improve the carbon storage in soil. In conclusion, this study investigates the fate and impact of biogas residues used as a soil additive on the soil microbial community and amount of soil organic matter. It is aimed to understand and

  20. Optimization of Sample Points for Monitoring Arable Land Quality by Simulated Annealing while Considering Spatial Variations

    PubMed Central

    Wang, Junxiao; Wang, Xiaorui; Zhou, Shenglu; Wu, Shaohua; Zhu, Yan; Lu, Chunfeng

    2016-01-01

    With China’s rapid economic development, the reduction in arable land has emerged as one of the most prominent problems in the nation. The long-term dynamic monitoring of arable land quality is important for protecting arable land resources. An efficient practice is to select optimal sample points while obtaining accurate predictions. To this end, the selection of effective points from a dense set of soil sample points is an urgent problem. In this study, data were collected from Donghai County, Jiangsu Province, China. The number and layout of soil sample points are optimized by considering the spatial variations in soil properties and by using an improved simulated annealing (SA) algorithm. The conclusions are as follows: (1) Optimization results in the retention of more sample points in the moderate- and high-variation partitions of the study area; (2) The number of optimal sample points obtained with the improved SA algorithm is markedly reduced, while the accuracy of the predicted soil properties is improved by approximately 5% compared with the raw data; (3) With regard to the monitoring of arable land quality, a dense distribution of sample points is needed to monitor the granularity. PMID:27706051

  1. Converting highly productive arable cropland in Europe to grassland: -a poor candidate for carbon sequestration.

    PubMed

    Gosling, Paul; van der Gast, Christopher; Bending, Gary D

    2017-09-05

    Sequestration of atmospheric CO2 as organic carbon by agricultural soils (SOC) is promoted as a climate change mitigation option. IPCC provides guidelines for determining carbon stocks and sequestration potential, incentivising policy changes towards management of farmland for carbon sequestration. However, the basis of the assumption that agricultural soils can sequester significant atmospheric CO2 has been questioned. We sought to determine the potential for conversion of arable cropland to grassland to sequester carbon in the short to medium term and potential limiting factors. There were no differences in SOC stocks in the top 30 cm between grassland up to 17 years old and arable cropland at 14 sites across the UK. However, SOC showed different distribution patterns, being concentrated in the top 10 cm under grassland. Soil microbial communities were significantly different between arable and grassland, with higher biomass and lesser dominance by bacteria in grassland soils. A land use conversion experiment showed these changes occurred within one year of land use change. Failure of grassland soils to accumulate SOC was attributed to reduced available soil nitrogen, resulting in low productivity. The implications of these results for carbon sequestration in soils as a climate change mitigation strategy are discussed.

  2. Magnetic Measurements as a Useful Tool for the Evaluation of Spatial Variability of the Arable Horizon Thickness

    NASA Astrophysics Data System (ADS)

    Fattakhova, Leysan; Shinkarev, Alexandr; Ryzhikh, Lyudmila; Kosareva, Lina

    2017-04-01

    In normal practice, the thickness of the arable horizon is determined on the basis of field morphological descriptions, allowing the subjectivity of perception and judgment at the crucial role of experience of the researcher. The subject of special interest are independent analytical and technically relatively simple in design approaches to the diagnosis of the lower boundary of the blended plowing the profiles part. Theoretical premises to use spectrophotometry and magnetometry to arable horizon depth diagnose is based on the concept of regular color and magnetic properties vertical differentiation in a profile of virgin soils. This work is devoted to the comparative assessment of the possibility to objectively and reliably diagnose the lower boundary of the arable horizon in gray forest soils by determining the color characteristics and the magnetic susceptibility of their layer-wise samples. It was shown with arable gray forest soil (Cutanic Luvisols (Anthric)) as example that the magnetic susceptibility profile distribution curves can provide more reliable and objective assessment of the arable horizon thickness spatial variability than the profile curves of the color characteristics in the CIELAB coordinates. Therefore, magnetic measurements can be a useful tool for the tillage erosion estimation in the monitoring of soil characteristics in connection with the development of precision agriculture technologies and the organizing of agricultural field plot experiments.

  3. Cover crops support ecological intensification of arable cropping systems

    PubMed Central

    Wittwer, Raphaël A.; Dorn, Brigitte; Jossi, Werner; van der Heijden, Marcel G. A.

    2017-01-01

    A major challenge for agriculture is to enhance productivity with minimum impact on the environment. Several studies indicate that cover crops could replace anthropogenic inputs and enhance crop productivity. However, so far, it is unclear if cover crop effects vary between different cropping systems, and direct comparisons among major arable production systems are rare. Here we compared the short-term effects of various cover crops on crop yield, nitrogen uptake, and weed infestation in four arable production systems (conventional cropping with intensive tillage and no-tillage; organic cropping with intensive tillage and reduced tillage). We hypothesized that cover cropping effects increase with decreasing management intensity. Our study demonstrated that cover crop effects on crop yield were highest in the organic system with reduced tillage (+24%), intermediate in the organic system with tillage (+13%) and in the conventional system with no tillage (+8%) and lowest in the conventional system with tillage (+2%). Our results indicate that cover crops are essential to maintaining a certain yield level when soil tillage intensity is reduced (e.g. under conservation agriculture), or when production is converted to organic agriculture. Thus, the inclusion of cover crops provides additional opportunities to increase the yield of lower intensity production systems and contribute to ecological intensification. PMID:28157197

  4. Cover crops support ecological intensification of arable cropping systems

    NASA Astrophysics Data System (ADS)

    Wittwer, Raphaël A.; Dorn, Brigitte; Jossi, Werner; van der Heijden, Marcel G. A.

    2017-02-01

    A major challenge for agriculture is to enhance productivity with minimum impact on the environment. Several studies indicate that cover crops could replace anthropogenic inputs and enhance crop productivity. However, so far, it is unclear if cover crop effects vary between different cropping systems, and direct comparisons among major arable production systems are rare. Here we compared the short-term effects of various cover crops on crop yield, nitrogen uptake, and weed infestation in four arable production systems (conventional cropping with intensive tillage and no-tillage; organic cropping with intensive tillage and reduced tillage). We hypothesized that cover cropping effects increase with decreasing management intensity. Our study demonstrated that cover crop effects on crop yield were highest in the organic system with reduced tillage (+24%), intermediate in the organic system with tillage (+13%) and in the conventional system with no tillage (+8%) and lowest in the conventional system with tillage (+2%). Our results indicate that cover crops are essential to maintaining a certain yield level when soil tillage intensity is reduced (e.g. under conservation agriculture), or when production is converted to organic agriculture. Thus, the inclusion of cover crops provides additional opportunities to increase the yield of lower intensity production systems and contribute to ecological intensification.

  5. Carbon use efficiency (CUE) and biomass turnover of soil microbial communities as affected by bedrock, land management and soil temperature and moisture

    NASA Astrophysics Data System (ADS)

    Zheng, Qing; Hu, Yuntao; Richter, Andreas; Wanek, Wolfgang

    2017-04-01

    Soil microbial carbon use efficiency (CUE), defined as the proportion of organic C taken up that is allocated to microbial growth, represents an important synthetic representation of microbial community C metabolism that describes the flux partitioning between microbial respiration and growth. Therefore, studying microbial CUE is critical for the understanding of soil C cycling. Microbial CUE is thought to vary with environmental conditions (e.g. temperature and soil moisture). Microbial CUE is thought to decrease with increasing temperature and declining soil moisture, as the latter may trigger stress responses (e.g. the synthesis of stress metabolites), which may consequently lower microbial community CUE. However, these effects on microbial CUE have not been adequately measured so far due to methodological restrictions. The most widely used methods for microbial CUE estimation are based on tracing 13C-labeled substrates into microbial biomass and respiratory CO2, approaches that are known to overestimate microbial CUE of native organic matter in soil. Recently, a novel substrate-independent approach based on the measurement of (i) respiration rates and (ii) the incorporation rates of 18O from labelled water into newly formed microbial DNA has been developed in our laboratory for measuring microbial CUE. This approach overcomes the shortcomings of previously used methods and has already been shown to yield realistic estimations of soil microbial CUE. This approach can also be applied to concurrently measure microbial biomass turnover rates, which also influence the sequestration of soil organic C. Microbial turnover rates are also thought to be impacted by environmental factors, but rarely have been directly measured so far. Here, we aimed at determining the short-term effects of environmental factors (soil temperature and soil moisture) on microbial CUE and microbial biomass turnover rates based on the novel 18O approach. Soils from three land-use types (arable

  6. Estimation of soil-to-plant transfer factors of radiocesium in 99 wild plant species grown in arable lands 1 year after the Fukushima 1 Nuclear Power Plant accident.

    PubMed

    Yamashita, Jun; Enomoto, Takashi; Yamada, Masao; Ono, Toshiro; Hanafusa, Tadashi; Nagamatsu, Tomohiro; Sonoda, Shoji; Yamamoto, Yoko

    2014-01-01

    One year after the deposition of radionuclides from the Fukushima 1 Nuclear Power Plant (A formal name is Fukushima Daiichi Nuclear Power Station) in March 2011, radiocesium (¹³⁴Cs, ¹³⁷Cs) concentrations ([Cs]) were comprehensively investigated in the wild plants of 99 species most of which were annual or summer green perennial herbs and started to grow from April 2012 at the heavily contaminated fields of paddy (three study sites) and upland (one study site) in Fukushima Prefecture. The survey was conducted three times (April, July and October) in the year. In each site, soils (soil cores of 5-cm depth) and plants (aerial shoots) were collected for determination of [Cs] on a dry weight basis, and then the transfer factor (TF) of radiocesium from soil to plant ([Cs]plant/[Cs]soil) was estimated in each species. The [Cs] values of both soils and plants largely varied. However, some species exhibited relatively high TF values (more than 0.4) (e.g., Athyrium yokoscense, Dryopteris tokyoensis, and Cyperus brevifolius), while others exhibited almost negligible values (less than 0.01) (e.g., Salix miyabeana, Humulus scandens, and Elymus tsukushiensis). In addition, judging from the 11 species grown in both paddy and upland fields, TF values were generally higher in the paddy fields. The estimation of phytoextraction efficiency of soil radiocesium by weed communities in the paddy fields suggests that the weed community is not a practical candidate for phytoremediation technique.

  7. Modeling Central Carbon Metabolic Processes in Soil Microbial Communities: Comparing Measured With Modeled

    NASA Astrophysics Data System (ADS)

    Dijkstra, P.; Fairbanks, D.; Miller, E.; Salpas, E.; Hagerty, S.

    2013-12-01

    Understanding the mechanisms regulating C cycling is hindered by our inability to directly observe and measure the biochemical processes of glycolysis, pentose phosphate pathway, and TCA cycle in intact and complex microbial communities. Position-specific 13C labeled metabolic tracer probing is proposed as a new way to study microbial community energy production, biosynthesis, C use efficiency (the proportion of substrate incorporated into microbial biomass), and enables the quantification of C fluxes through the central C metabolic network processes (Dijkstra et al 2011a,b). We determined the 13CO2 production from U-13C, 1-13C, 2-13C, 3-13C, 4-13C, 5-13C, and 6-13C labeled glucose and 1-13C and 2,3-13C pyruvate in parallel incubations in three soils along an elevation gradient. Qualitative and quantitative interpretation of the results indicate a high pentose phosphate pathway activity in soils. Agreement between modeled and measured CO2 production rates for the six C-atoms of 13C-labeled glucose indicate that the metabolic model used is appropriate for soil community processes, but that improvements can be made. These labeling and modeling techniques may improve our ability to analyze the biochemistry and (eco)physiology of intact microbial communities. Dijkstra, P., Blankinship, J.C., Selmants, P.C., Hart, S.C., Koch, G.W., Schwartz, E., Hungate, B.A., 2011a. Probing C flux patterns of soil microbial metabolic networks using parallel position-specific tracer labeling. Soil Biology & Biochemistry 43, 126-132. Dijkstra, P., Dalder, J.J., Selmants, P.C., Hart, S.C., Koch, G.W., Schwartz, E., Hungate, B.A., 2011b. Modeling soil metabolic processes using isotopologue pairs of position-specific 13C-labeled glucose and pyruvate. Soil Biology & Biochemistry 43, 1848-1857.

  8. Mathematical modeling of water fluxes in arable chernozems under different land use

    NASA Astrophysics Data System (ADS)

    Arkhangel'skaya, T. A.; Khokhlova, O. S.; Myakshina, T. N.

    2016-07-01

    The hydrologic regimes of arable chernozems were simulated for two plots located within a watershed. For the last fifty years continuous corn monoculture was practiced in one plot, and permanent bare fallow was practiced in the other plot. Carbonates are detected from a depth of 140-160 cm under corn and from 70-80 cm under bare fallow. The objective of the simulation study was to test the validity of the hypothesis that the shallower depth to carbonates under bare fallow is related to carbonate rise due to changes in the hydrologic regime of bare soil compared to soil under vegetation. Mathematical modeling using the HYDRUS-1D software and the FAO56 method confirmed that the hydrologic regimes of arable chernozems within the two plots are different. The soil water content under bare fallow is generally higher than that under corn. The downward soil water fluxes for the two plots are comparable. The upward soil water fluxes under bare fallow significantly exceed those under corn and affect a thicker soil layer. The changes in the hydrologic regimes of chernozems under bare fallow favor the upward movement of carbonates through both the direct transfer by upward water fluxes and the diffusion of ions.

  9. Continuous measurements of N2O emissions from arable fields

    NASA Astrophysics Data System (ADS)

    Wallman, Magdalena; Lammirato, Carlo; Rütting, Tobias; Delin, Sofia; Weslien, Per; Klemedtsson, Leif

    2017-04-01

    Agriculture represents 59 % of the anthropogenic nitrous oxide (N2O) emissions, according to the IPCC (Ciais et al. 2013). N2O emissions are typically irregular and vary widely in time and space, which makes it difficult to get a good representation of the emissions (Henault et al. 2012), particularly if measurements have low frequency and/or cover only a short time period. Manual measurements are, for practical reasons, often short-term and low-frequent, or restricted to periods where emissions are expected to be high, e.g. after fertilizing. However, the nature of N2O emissions, being largely unpredictable, calls for continuous or near-continuous measurements over long time periods. So far, rather few long-term, high resolution measurements of N2O emissions from arable fields are reported; among them are Flessa et al. (2002) and Senapati et al. (2016). In this study, we have a two-year data set (2015-2017) with hourly measurements from ten automatic chambers, covering unfertilized controls as well as different nitrogen fertilizer treatments. Grain was produced on the field, and effects of tillage, harvest and other cropping measures were covered. What we can see from the experiment is that (a) the unfertilized control plots seem to follow the same emission pattern as the fertilized plots, at a level similar to the standard mineral fertilized plots (120 kg N ha-1 yr-1) and (b) freeze/thaw emissions are comparable in size to emissions after fertilizing. These two findings imply that the importance of fertilizing to the overall N2O emissions from arable soils may be smaller than previously expected. References: Ciais, P., C. Sabine, G. Bala, L. Bopp, V. Brovkin, J. Canadell et al. 2013: Carbon and Other Biogeochemical Cycles. In: Climate Change 2013: The Physical Science Basis. Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change [Stocker, T.F., D. Qin, G.-K. Plattner, M. Tignor, S.K. Allen, J. Boschung et

  10. Process-oriented Simulation of Runoff Generation on Arable Fields Using a Physically Based Hydrological Model

    NASA Astrophysics Data System (ADS)

    Winter, F.; Disse, M.

    2011-12-01

    In Germany, aside from technical flood protection and forecasting, modern flood protection strategies include distributed flood control measures. On arable fields these measures comprise of increasing infiltration ability due to different tillage practices such as conservational tillage or no-tillage. Tillage practices have a significant effect on the runoff generation process. Bare soils are prone to forming soil crusts during extreme rainfall events especially on Loessial soils that are abundant in Central European landscapes, and soil crusts promote surface runoff and erosion. Due to the impact of raindrops, the topsoil aggregates are broken and form a layer of a few millimeters to centimeters with very low hydraulic conductivity. One way to describe this process is by using a modified Horton infiltration equation. WaSiM-ETH is a physically based hydrological modeling system developed by SCHULLA (1997) to analyze the spatial and temporal distributed flow processes in complex catchments. In order to investigate the effect of soil crusts on runoff generation on arable fields, WaSiM-ETH was extended by adding a silting module which is able to simulate the process of soil crust formation. It has been shown that sprinkler experiments could be simulated more efficiently with the model extension than with the simulation of runoff generation according to the Mualem-van-Genuchten parameterization. This effect is extended to a lower mesoscale agricultural catchment for a number of different high intensity storm events. Finally, scenario setups show the potential of surface water retention for different tillage practices. Literature: SCHULLA, J. (1997): Hydrologische Modellierung von Flussgebieten zur Abschätzung der Folgen von Klimaänderungen, Dissertation, ETH Zürich, 161. S. (in German) http://www.unibw.de/ifw/WWR-en/forschung-en/einflussbewirtschaftung-en?set_language=en

  11. Managing Bioenergy Production on Arable Field Margins for Multiple Ecosystem Services: Challenges and Opportunities

    NASA Astrophysics Data System (ADS)

    Ferrarini, Andrea; Serra, Paolo; Amaducci, Stefano; Trevisan, Marco; Puglisi, Edoardo

    2013-04-01

    Growing crops for bioenergy is increasingly viewed as conflicting with food production. However, energy use continues to rise and food production requires fuel inputs, which have increased with intensification. The debate should shift from "food or fuel" to the more challenging target: how the increasing demand for food and energy can be met in the future, particularly when water and land availability will be limited. As for food crops, also for bioenergy crops it is questioned whether it is preferable to manage cultivation to enhance ecosystem services ("land sharing" strategy) or to grow crops with lower ecosystem services but higher yield, thereby requiring less land to meet bioenergy demand ("land sparing" strategy). Energy crop production systems differ greatly in the supply of ecosystem services. The use of perennial biomass (e.g. Switchgrass, Mischantus, Giant reed) for energy production is considered a promising way to reduce net carbon emissions and mitigate climate change. In addition, regulating and supporting ecosystem services could be provided when specific management of bioenergy crops is implemented. The idea of HEDGE-BIOMASS* project is to convert the arable field margins to bioenergy crop production fostering a win-win strategy at landscape level. Main objective of the project is to improve land management to generate environmental benefits and increase farmer income. The various options available in literature for an improved field boundary management are presented. The positive/unknown/negative effects of growing perennial bioenergy crops on field margins will be discussed relatively to the following soil-related ecosystem services: (I) biodiversity conservation and enhancement, (II) soil nutrient cycling, (III) climate regulation (reduction of GHG emissions and soil carbon sequestration/stabilization, (IV) water regulation (filtering and buffering), (V) erosion regulation, (VI) pollination and pest regulation. From the analysis of available

  12. Assessing and analysing the impact of land take pressures on arable land

    NASA Astrophysics Data System (ADS)

    Aksoy, Ece; Gregor, Mirko; Schröder, Christoph; Löhnertz, Manuel; Louwagie, Geertrui

    2017-06-01

    Land, and in particular soil, is a finite and essentially non-renewable resource. Across the European Union, land take, i.e. the increase of settlement area over time, annually consumes more than 1000 km2 of which half is actually sealed and hence lost under impermeable surfaces. Land take, and in particular soil sealing, has already been identified as one of the major soil threats in the 2006 European Commission Communication Towards a Thematic Strategy on Soil Protection and the Soil Thematic Strategy and has been confirmed as such in the report on the implementation of this strategy. The aim of this study is to relate the potential of land for a particular use in a given region with the actual land use. This allows evaluating whether land (especially the soil dimension) is used according to its (theoretical) potential. To this aim, the impact of several land cover flows related to urban development on soils with good, average, and poor production potentials were assessed and mapped. Thus, the amount and quality (potential for agricultural production) of arable land lost between the years 2000 and 2006 was identified. In addition, areas with high productivity potential around urban areas, indicating areas of potential future land use conflicts for Europe, were identified.

  13. Field scale studies on the spatial variability of soil quality indicators in Washington State, USA

    USDA-ARS?s Scientific Manuscript database

    Arable lands are needed for sustainable agricultural systems to support an ever growing human population. Soil quality needs to be defined to assure the new arable land is sustainable. To evaluate soil quality a number of soil attributes will need to be measured, evaluated and integrated into a soi...

  14. Arsenic Content in Arable Land of the Ząbkowice District

    NASA Astrophysics Data System (ADS)

    Kaszubkiewicz, Jarosław; Pora, Ewa; Kawałko, Dorota; Jezierski, Paweł

    2014-06-01

    The aim of this study was to determine the content of arsenic in soils used for agriculture in the Ząbkowicki district. The content of arsenic in collected soil samples ranged 1.1-569.5 mg·kg-1. The standard for arable lands of Group B has been exceeded in 24 out of 231 test points. The highest concentrations occurred in the Złoty Stok commune. This is due to the output of arsenic and gold in this area. Exceeding the standard also occurred in neighboring communes: Kamieniec Ząbkowicki and Ziębice. This is due to the blowing and washing pollutions form the source of contamination, the arsenic mines in the Złoty Stok commune.

  15. Simulating the impacts of land use in northwest Europe on Net Ecosystem Exchange (NEE): the role of arable ecosystems, grasslands and forest plantations in climate change mitigation.

    PubMed

    Abdalla, Mohamed; Saunders, Matthew; Hastings, Astley; Williams, Mike; Smith, Pete; Osborne, Bruce; Lanigan, Gary; Jones, Mike B

    2013-11-01

    In this study, we compared measured and simulated Net Ecosystem Exchange (NEE) values from three wide spread ecosystems in the southeast of Ireland (forest, arable and grassland), and investigated the suitability of the DNDC (the DeNitrification-DeComposition) model to estimate present and future NEE. Although, the field-DNDC version overestimated NEE at temperatures >5 °C, forest-DNDC under-estimated NEE at temperatures >5 °C. The results suggest that the field/forest DNDC models can successfully estimate changes in seasonal and annual NEE from these ecosystems. Differences in NEE were found to be primarily land cover specific. The annual NEE was similar for the grassland and arable sites, but due to the contribution of exported carbon, the soil carbon increased at the grassland site and decreased at the arable site. The NEE of the forest site was an order of magnitude larger than that of the grassland or arable ecosystems, with large amounts of carbon stored in woody biomass and the soil. The average annual NEE, GPP and Reco values over the measurement period were -904, 2379 and 1475 g C m(-2) (forest plantations), -189, 906 and 715 g C m(-2) (arable systems) and -212, 1653 and 1444 g C m(-2) (grasslands), respectively. The average RMSE values were 3.8 g C m(-2) (forest plantations), 0.12 g C m(-2) (arable systems) and 0.21 g C m(-2) (grasslands). When these models were run with climate change scenarios to 2060, predictions show that all three ecosystems will continue to operate as carbon sinks. Further, climate change may decrease the carbon sink strength in the forest plantations by up to 50%. This study supports the use of the DNDC model as a valid tool to predict the consequences of climate change on NEE from different ecosystems.

  16. Peatlands under cultivation for arable crops; a new area estimate for Ireland

    NASA Astrophysics Data System (ADS)

    Donlan, Jennifer; Byrne, Ken

    2015-04-01

    Peatlands cover 20% of the Irish landscape and store between 53% and 61% of total soil carbon stocks. Eighty percent of these have been drained for peat cutting, afforestation and conversion to agricultural use. As a signatory to the United Nations framework Convention on Climate Change, Ireland is required to make an annual inventory of greenhouse gas emissions and sinks in the agricultural sector. While guidelines on the compilation of such inventories are provided by the IPCC 2006 Guidelines, reporting at higher Tiers requires the collection of national specific information including the accuracy of inventories. Total land area (including accuracy estimates) and national emission factors are lacking for agricultural activity on drained organic soils i.e. converted peatlands. Locations of organic (peat) soils under cultivation were identified using a map overlay analysis and existing geographic data on peat habitats and agricultural activities. The result was 3688 ha of land cultivated for arable crops overlaid areas classified as peatland. A design-based accuracy assessment and probability sampling method were chosen to assess the accuracy of the overlay. The focus of the analysis was on the accuracy of the peat data. The agricultural data was considered quite robust, so it was used to limit the area included in the assessment. Ground truthing was carried out at randomly chosen locations within areas mapped as 1) areas cultivated for arable crops and 2) peat habitats or a 100m buffer surrounding those areas. Sixty-nine sites were sampled and an error matrix was constructed comparing the map classification at the sample location to the samples taken there. The overall accuracy was 77%. There was a high producer's accuracy (84%) and a low user's accuracy (28%) for the peat category. Area estimate of peatlands under cultivation for arable crops was 1235 ± 784 ha. Future policies will require the identification of strategies to reduce greenhouse gas emissions and

  17. Properties of the Hubert-Arable Adjusted Rand Index

    ERIC Educational Resources Information Center

    Steinley, Douglas

    2004-01-01

    This article provides an investigation of cluster validation indices that relates 4 of the indices to the L. Hubert and P. Arable (1985) adjusted Rand index--the cluster validation measure of choice (G. W. Milligan & M. C. Cooper, 1986). It is shown how these other indices can be "roughly" transformed into the same scale as the adjusted Rand…

  18. Dedicated biomass crops can enhance biodiversity in the arable landscape.

    PubMed

    Haughton, Alison J; Bohan, David A; Clark, Suzanne J; Mallott, Mark D; Mallott, Victoria; Sage, Rufus; Karp, Angela

    2016-11-01

    Suggestions that novel, non-food, dedicated biomass crops used to produce bioenergy may provide opportunities to diversify and reinstate biodiversity in intensively managed farmland have not yet been fully tested at the landscape scale. Using two of the largest, currently available landscape-scale biodiversity data sets from arable and biomass bioenergy crops, we take a taxonomic and functional trait approach to quantify and contrast the consequences for biodiversity indicators of adopting dedicated biomass crops on land previously cultivated under annual, rotational arable cropping. The abundance and community compositions of biodiversity indicators in fields of break and cereal crops changed when planted with the dedicated biomass crops, miscanthus and short rotation coppiced (SRC) willow. Weed biomass was consistently greater in the two dedicated biomass crops than in cereals, and invertebrate abundance was similarly consistently higher than in break crops. Using canonical variates analysis, we identified distinct plant and invertebrate taxa and trait-based communities in miscanthus and SRC willows, whereas break and cereal crops tended to form a single, composite community. Seedbanks were shown to reflect the longer term effects of crop management. Our study suggests that miscanthus and SRC willows, and the management associated with perennial cropping, would support significant amounts of biodiversity when compared with annual arable crops. We recommend the strategic planting of these perennial, dedicated biomass crops in arable farmland to increase landscape heterogeneity and enhance ecosystem function, and simultaneously work towards striking a balance between energy and food security.

  19. [Profile distribution and storage of soil organic carbon in a black soil as affected by land use types].

    PubMed

    Hao, Xiang-xiang; Han, Xiao-zeng; Li, Lu-jun; Zou, Wen-xiu; Lu, Xin-chun; Qiao, Yun-fa

    2015-04-01

    Taking soils in a long-term experimental field over 29 years with different land uses types, including arable land, bare land, grassland and larch forest land as test materials, the distribution and storage of soil organic carbon (SOC) in the profile (0-200 cm) in typical black soil (Mollisol) region of China were investigated. The results showed that the most significant differences in SOC content occurred in the 0-10 cm surface soil layer among all soils with the order of grassland > arable land > larch forest land > bare land. SOC contents at 10-120 cm depth were lower in arable land as compared with the other land use types. Compared with arable land, grassland could improve SOC content obviously. SOC content down to a depth of 60 cm in grassland was significantly higher than that in arable land. The content of SOC at 0-10 cm in bare land was significantly lower than that in arable land. Although there were no significant differences in SOC content at 0-20 cm depth between larch forestland and arable land, the SOC contents at 20-140 cm depth were generally higher in larch forestland than that in arable land. In general, SOC content showed a significantly negative relationship with soil pH, bulk density, silt and clay content and an even stronger significantly positive relationship with soil total N content and sand content. The SOC storage in arable land at 0-200 cm depth was significantly lower than that in the other three land use types, which was 13.6%, 11.4% and 10.9% lower than in grassland, bare land and larch forest land, respectively. Therefore, the arable land of black soil has a great potential for sequestering C in soil and improving environmental quality.

  20. Soil warming alters microbial substrate use in alpine soils.

    PubMed

    Streit, Kathrin; Hagedorn, Frank; Hiltbrunner, David; Portmann, Magdalena; Saurer, Matthias; Buchmann, Nina; Wild, Birgit; Richter, Andreas; Wipf, Sonja; Siegwolf, Rolf T W

    2014-04-01

    Will warming lead to an increased use of older soil organic carbon (SOC) by microbial communities, thereby inducing C losses from C-rich alpine soils? We studied soil microbial community composition, activity, and substrate use after 3 and 4 years of soil warming (+4 °C, 2007-2010) at the alpine treeline in Switzerland. The warming experiment was nested in a free air CO2 enrichment experiment using depleted (13)CO2 (δ(13)C = -30‰, 2001-2009). We traced this depleted (13)C label in phospholipid fatty acids (PLFA) of the organic layer (0-5 cm soil depth) and in C mineralized from root-free soils to distinguish substrate ages used by soil microorganisms: fixed before 2001 ('old'), from 2001 to 2009 ('new') or in 2010 ('recent'). Warming induced a sustained stimulation of soil respiration (+38%) without decline in mineralizable SOC. PLFA concentrations did not reveal changes in microbial community composition due to soil warming, but soil microbial metabolic activity was stimulated (+66%). Warming decreased the amount of new and recent C in the fungal biomarker 18:2ω6,9 and the amount of new C mineralized from root-free soils, implying a shift in microbial substrate use toward a greater use of old SOC. This shift in substrate use could indicate an imbalance between C inputs and outputs, which could eventually decrease SOC storage in this alpine ecosystem.

  1. Insecticides and arable weeds: effects on germination and seedling growth.

    PubMed

    Hanley, M E; Whiting, M D

    2005-05-01

    The decline of many arable weed species in Northern Europe has been attributed to the intensification of modern agriculture and in particular, increasing pesticide use. In this study, we examined the effect of two insecticides, dimethoate and deltamethrin, on the germination and seedling growth of six arable weed species. Although germination was unaffected by insecticide application, seedling growth of four species was decreased by exposure to deltamethrin (Capsella bursa-pastoris and Poa annua), dimethoate (Agrostemma githago), or by both insecticides together (Urtica urens). While increased herbicide use, seed cleaning, and changing sowing times may be of primary importance in explaining the reduction of northern Europe's arable weed flora, our results indicate that insecticide use may also be a contributory factor. Moreover, those species that exhibit apparent tolerance of the insecticides tested, particularly the grass Avena fatua, may benefit from continued insecticide use. The ability to tolerate these agrochemicals, in tandem with reduced herbivory and competition from plants, whose growth is reduced by insecticide application, is likely to confer a significant competitive advantage on insecticide-resistant weed species.

  2. Microbial utilization of rice straw and its derived biochar in a paddy soil.

    PubMed

    Pan, Fuxia; Li, Yaying; Chapman, Stephen James; Khan, Sardar; Yao, Huaiying

    2016-07-15

    The application of straw and biochar to soil has received great attention because of their potential benefits such as fertility improvement and carbon (C) sequestration. The abiotic effects of these materials on C and nitrogen (N) cycling in the soil ecosystem have been previously investigated, however, the effects of straw or its derived biochar on the soil microbial community structure and function are not well understood. For this purpose, a short-term incubation experiment was conducted using (13)C-labeled rice straw and its derived biochar ((13)C-labeled biochar) to deepen our understanding about soil microbial community dynamics and function in C sequestration and greenhouse gas emission in the acidic paddy soil amended with these materials. Regarding microbial function, biochar and straw applications increased CO2 emission in the initial stage of incubation and reached the highest level (0.52 and 3.96mgCkg(-1)soilh(-1)) at 1d and 3d after incubation, respectively. Straw amendment significantly (p<0.01) increased respiration rate, total phospholipid fatty acids (PLFAs) and (13)C-PLFA as compared to biochar amendment and the control. The amount and percent of Gram positive bacteria, fungi and actinomycetes were also significantly (p<0.05) higher in (13)C-labeled straw amended soil than the (13)C-labeled biochar amended soil. According to the (13)C data, 23 different PLFAs were derived from straw amended paddy soil, while only 17 PLFAs were derived from biochar amendments. The profile of (13)C-PLFAs derived from straw amendment was significantly (p<0.01) different from biochar amendment. The PLFAs18:1ω7c and cy17:0 (indicators of Gram negative bacteria) showed high relative abundances in the biochar amendment, while 10Me18:0, i17:0 and 18:2ω6,9c (indicators of actinomycetes, Gram positive bacteria and fungi, respectively) showed high relative abundance in the straw amendments. Our results suggest that the function, size and structure of the microbial

  3. Dynamics of denitrification and ammonification activities in the abandoned and intensely cultivated gray forest soils (Tula oblast)

    NASA Astrophysics Data System (ADS)

    Emer, N. R.; Kostina, N. V.; Golichenkov, M. V.; Netrusov, A. I.

    2017-04-01

    The results of experimental study of daily dynamics of denitrification activity and the activity and population density of ammonifiers in the abandoned (converted to long-term fallow) and intensely cultivated gray forest soils (Luvic Retic Greyzemic Phaeozems (Aric)) are discussed. The potential denitrification activity in the arable soil is higher than that in the fallow soil, whereas the actual denitrification activity in the arable soil is lower. Data on the dynamics of ammonification do not show reliable differences between the activities of ammonifiers in the arable and fallow soils, though the number of ammonifying bacteria is considerably higher in the arable soil. Differences in daily dynamics of the numbers of ammonifiers in the fallow and arable soils are shown.

  4. Stable-Isotope Probing Identifies Uncultured Planctomycetes as Primary Degraders of a Complex Heteropolysaccharide in Soil

    PubMed Central

    Wang, Xiaoqing; Sharp, Christine E.; Jones, Gareth M.; Grasby, Stephen E.; Brady, Allyson L.

    2015-01-01

    The exopolysaccharides (EPSs) produced by some bacteria are potential growth substrates for other bacteria in soil. We used stable-isotope probing (SIP) to identify aerobic soil bacteria that assimilated the cellulose produced by Gluconacetobacter xylinus or the EPS produced by Beijerinckia indica. The latter is a heteropolysaccharide comprised primarily of l-guluronic acid, d-glucose, and d-glycero-d-mannoheptose. 13C-labeled EPS and 13C-labeled cellulose were purified from bacterial cultures grown on [13C]glucose. Two soils were incubated with these substrates, and bacteria actively assimilating them were identified via pyrosequencing of 16S rRNA genes recovered from 13C-labeled DNA. Cellulose C was assimilated primarily by soil bacteria closely related (93 to 100% 16S rRNA gene sequence identities) to known cellulose-degrading bacteria. However, B. indica EPS was assimilated primarily by bacteria with low identities (80 to 95%) to known species, particularly by different members of the phylum Planctomycetes. In one incubation, members of the Planctomycetes made up >60% of all reads in the labeled DNA and were only distantly related (<85% identity) to any described species. Although it is impossible with SIP to completely distinguish primary polysaccharide hydrolyzers from bacteria growing on produced oligo- or monosaccharides, the predominance of Planctomycetes suggested that they were primary degraders of EPS. Other bacteria assimilating B. indica EPS included members of the Verrucomicrobia, candidate division OD1, and the Armatimonadetes. The results indicate that some uncultured bacteria in soils may be adapted to using complex heteropolysaccharides for growth and suggest that the use of these substrates may provide a means for culturing new species. PMID:25934620

  5. Absorption and distribution kinetics of the 13C-labeled tomato carotenoid phytoene in healthy adults

    USDA-ARS?s Scientific Manuscript database

    Phytoene is a tomato carotenoid which may contribute to the apparent health benefits of tomato consumption. While phytoene is a less prominent tomato carotenoid than lycopene, it is a major carotenoid in various human tissues. Phytoene distribution to plasma lipoproteins and tissues differs from lyc...

  6. Methanogenic capabilities of ANME-archaea deduced from (13) C-labelling approaches.

    PubMed

    Bertram, Sebastian; Blumenberg, Martin; Michaelis, Walter; Siegert, Michael; Krüger, Martin; Seifert, Richard

    2013-08-01

    Anaerobic methanotrophic archaea (ANME) are ubiquitous in marine sediments where sulfate dependent anaerobic oxidation of methane (AOM) occurs. Despite considerable progress in the understanding of AOM, physiological details are still widely unresolved. We investigated two distinct microbial mat samples from the Black Sea that were dominated by either ANME-1 or ANME-2. The (13) C lipid stable isotope probing (SIP) method using labelled substances, namely methane, bicarbonate, acetate, and methanol, was applied, and the substrate-dependent methanogenic capabilities were tested. Our data provide strong evidence for a versatile physiology of both, ANME-1 and ANME-2. Considerable methane production rates (MPRs) from CO2 -reduction were observed, particularly from ANME-2 dominated samples and in the presence of methane, which supports the hypothesis of a co-occurrence of methanotrophy and methanogenesis in the AOM systems (AOM/MPR up to 2:1). The experiments also revealed strong methylotrophic capabilities through (13) C-assimilation from labelled methanol, which was independent of the presence of methane. Additionally, high MPRs from methanol were detected in both of the mat samples. As demonstrated by the (13) C-uptake into lipids, ANME-1 was found to thrive also under methane free conditions. Finally, C35 -isoprenoid hydrocarbons were identified as new lipid biomarkers for ANME-1, most likely functioning as a hydrogen sink during methanogenesis.

  7. Production and NMR signal optimization of hyperpolarized 13C-labeled amino acids

    NASA Astrophysics Data System (ADS)

    Parish, Christopher; Niedbalski, Peter; Ferguson, Sarah; Kiswandhi, Andhika; Lumata, Lloyd

    Amino acids are targeted nutrients for consumption by cancers to sustain their rapid growth and proliferation. 13C-enriched amino acids are important metabolic tracers for cancer diagnostics using nuclear magnetic resonance (NMR) spectroscopy. Despite this diagnostic potential, 13C NMR of amino acids however is hampered by the inherently low NMR sensitivity of the 13C nuclei. In this work, we have employed a physics technique known as dynamic nuclear polarization (DNP) to enhance the NMR signals of 13C-enriched amino acids. DNP works by transferring the high polarization of electrons to the nuclear spins via microwave irradiation at low temperature and high magnetic field. Using a fast dissolution method in which the frozen polarized samples are dissolved rapidly with superheated water, injectable solutions of 13C-amino acids with highly enhanced NMR signals (by at least 5,000-fold) were produced at room temperature. Factors that affect the NMR signal enhancement levels such as the choice of free radical polarizing agents and sample preparation will be discussed along with the thermal mixing physics model of DNP. The authors would like to acknowledge the support by US Dept of Defense Award No. W81XWH-14-1-0048 and Robert A. Welch Foundation Grant No. AT-1877.

  8. Isotopomer studies of gluconeogenesis and the Krebs cycle with 13C-labeled lactate.

    PubMed

    Katz, J; Wals, P; Lee, W N

    1993-12-05

    Fasted rats were intragastrically infused with either [2,3-13C]lactate or [1,2,3-13C]lactate. The infusate also contained 14C-labeled lactate and [3-3H]glucose. Glucose, alanine, glutamate, and glutamine were isolated from liver and blood. There was near complete equilibration of lactate and alanine, and the relative specific activities and relative enrichments were the same in blood and liver. Glucose was cleaved enzymatically to lactate. The compounds were examined by gas chromatography-mass spectroscopy. From the mass isotopomer spectra of the lactate, glutamate, and glutamine and their cleavage fragments the positional isotopomer composition of these compounds was obtained. The enrichment and isotopomer pattern in the lactate from cleaved glucose represents that in phosphoenolpyruvate (PEP). When [1,2,3-13C]lactate was infused the mass isotopomer spectrum of glutamates consisted only of compounds containing either one, two, or three 13C carbons per molecule (m1, m2, and m3). There was little 13C in C-4 and C-5 of glutamate. The rate of pyruvate decarboxylation is low, and 3-4% of the acetyl-CoA flux in the Krebs cycle is contributed by lactate carbon. The major isotopomers in lactate, alanine, and PEP were m3 and m2 with 13C in C-2 and C-3. The predominant isotopomer in PEP from [2,3-13C]lactate was m2 with 13C in C-2 and C-3. There was much more of m1 isotopomer with 13C in C-3 and C-2 than the m1 isotopomer with 13C in C-1. There was very little m3, the isotopomer with 13C in all three carbons. Most of the 13C in C-3 and C-4 of glucose and C-1 of glutamate was introduced via 13CO2 fixation. From the isotopomer distribution and the rate of glucose turnover we deduced, applying the analysis described in the "Appendix," the absolute rates of gluconeogenic pathways, recycling of PEP and the Cori cycle, and flux in the Krebs cycle. The flux from oxaloacetate (OAA)-->PEP was seven times that of OAA-->citrate, and about half of PEP was recycled to pyruvate via pyruvate kinase. The mass isotopomer patterns in glutamate and glutamine were similar but differed from those of lactate and glucose. It appears that the glutamates are derived from alpha-ketoglutarate from a different Krebs cycle pool than PEP. The flux from OAA to PEP in this pool was two to three times that of OAA to citrate.(ABSTRACT TRUNCATED AT 400 WORDS)

  9. Magnetic resonance imaging of pH in vivo using hyperpolarized 13C-labelled bicarbonate.

    PubMed

    Gallagher, Ferdia A; Kettunen, Mikko I; Day, Sam E; Hu, De-En; Ardenkjaer-Larsen, Jan Henrik; Zandt, René in 't; Jensen, Pernille R; Karlsson, Magnus; Golman, Klaes; Lerche, Mathilde H; Brindle, Kevin M

    2008-06-12

    As alterations in tissue pH underlie many pathological processes, the capability to image tissue pH in the clinic could offer new ways of detecting disease and response to treatment. Dynamic nuclear polarization is an emerging technique for substantially increasing the sensitivity of magnetic resonance imaging experiments. Here we show that tissue pH can be imaged in vivo from the ratio of the signal intensities of hyperpolarized bicarbonate (H(13)CO(3)(-)) and (13)CO(2) following intravenous injection of hyperpolarized H(13)CO(3)(-). The technique was demonstrated in a mouse tumour model, which showed that the average tumour interstitial pH was significantly lower than the surrounding tissue. Given that bicarbonate is an endogenous molecule that can be infused in relatively high concentrations into patients, we propose that this technique could be used clinically to image pathological processes that are associated with alterations in tissue pH, such as cancer, ischaemia and inflammation.

  10. Computational Platform for Flux Analysis Using 13C-Label Tracing- Phase I SBIR Final Report

    SciTech Connect

    Van Dien, Stephen J.

    2005-04-12

    Isotopic label tracing is a powerful experimental technique that can be combined with metabolic models to quantify metabolic fluxes in an organism under a particular set of growth conditions. In this work we constructed a genome-scale metabolic model of Methylobacterium extorquens, a facultative methylotroph with potential application in the production of useful chemicals from methanol. A series of labeling experiments were performed using 13C-methanol, and the resulting distribution of labeled carbon in the proteinogenic amino acids was determined by mass spectrometry. Algorithms were developed to analyze this data in context of the metabolic model, yielding flux distributions for wild-type and several engineered strains of M. extorquens. These fluxes were compared to those predicted by model simulation alone, and also integrated with microarray data to give an improved understanding of the metabolic physiology of this organism.

  11. 13C labeling analysis of sugars by high resolution-mass spectrometry for metabolic flux analysis.

    PubMed

    Acket, Sébastien; Degournay, Anthony; Merlier, Franck; Thomasset, Brigitte

    2017-02-14

    Metabolic flux analysis is particularly complex in plant cells because of highly compartmented metabolism. Analysis of free sugars is interesting because it provides data to define fluxes around hexose, pentose, and triose phosphate pools in different compartment. In this work, we present a method to analyze the isotopomer distribution of free sugars labeled with carbon 13 using a liquid chromatography-high resolution mass spectrometry, without derivatized procedure, adapted for Metabolic flux analysis. Our results showed a good sensitivity, reproducibility and better accuracy to determine isotopic enrichments of free sugars compared to our previous methods [5, 6].

  12. Metabolic Flux Elucidation for Large-Scale Models Using 13C Labeled Isotopes

    PubMed Central

    Suthers, Patrick F.; Burgard, Anthony P.; Dasika, Madhukar S.; Nowroozi, Farnaz; Van Dien, Stephen; Keasling, Jay D.; Maranas, Costas D.

    2007-01-01

    A key consideration in metabolic engineering is the determination of fluxes of the metabolites within the cell. This determination provides an unambiguous description of metabolism before and/or after engineering interventions. Here, we present a computational framework that combines a constraint-based modeling framework with isotopic label tracing on a large-scale. When cells are fed a growth substrate with certain carbon positions labeled with 13C, the distribution of this label in the intracellular metabolites can be calculated based on the known biochemistry of the participating pathways. Most labeling studies focus on skeletal representations of central metabolism and ignore many flux routes that could contribute to the observed isotopic labeling patterns. In contrast, our approach investigates the importance of carrying out isotopic labeling studies using a more comprehensive reaction network consisting of 350 fluxes and 184 metabolites in Escherichia coli including global metabolite balances on cofactors such as ATP, NADH, and NADPH. The proposed procedure is demonstrated on an E. coli strain engineered to produce amorphadiene, a precursor to the anti-malarial drug artemisinin. The cells were grown in continuous culture on glucose containing 20% [U-13C]glucose; the measurements are made using GC-MS performed on 13 amino acids extracted from the cells. We identify flux distributions for which the calculated labeling patterns agree well with the measurements alluding to the accuracy of the network reconstruction. Furthermore, we explore the robustness of the flux calculations to variability in the experimental MS measurements, as well as highlight the key experimental measurements necessary for flux determination. Finally, we discuss the effect of reducing the model, as well as shed light onto the customization of the developed computational framework to other systems. PMID:17632026

  13. Structural analysis of uniformly (13)C-labelled solids from selective angle measurements at rotational resonance.

    PubMed

    Patching, Simon G; Edwards, Rachel; Middleton, David A

    2009-08-01

    We demonstrate that individual H-C-C-H torsional angles in uniformly labelled organic solids can be estimated by selective excitation of (13)C double-quantum coherences under magic-angle spinning at rotational resonance. By adapting a straightforward one-dimensional experiment described earlier [T. Karlsson, M. Eden, H. Luhman, M.H. Levitt, J. Magn. Reson. 145 (2000) 95-107], a double-quantum filtered spectrum selective for Calpha and Cbeta of uniformly labelled L-[(13)C,(15)N]valine is obtained with 25% efficiency. The evolution of Calpha-Cbeta double-quantum coherence under the influence of the dipolar fields of bonded protons is monitored to provide a value of the Halpha-Calpha-Cbeta-Hbeta torsional angle that is consistent with the crystal structure. In addition, double-quantum filtration selective for C6 and C1' of uniformly labelled [(13)C,(15)N]uridine is achieved with 12% efficiency for a (13)C-(13)C distance of 2.5A, yielding a reliable estimate of the C6-H and C1'-H projection angle defining the relative orientations of the nucleoside pyrimidine and ribose rings. This procedure will be useful, in favourable cases, for structural analysis of fully labelled small molecules such as receptor ligands that are not readily synthesised with labels placed selectively at structurally diagnostic sites.

  14. Structural analysis of uniformly 13C-labelled solids from selective angle measurements at rotational resonance

    NASA Astrophysics Data System (ADS)

    Patching, Simon G.; Edwards, Rachel; Middleton, David A.

    2009-08-01

    We demonstrate that individual H-C-C-H torsional angles in uniformly labelled organic solids can be estimated by selective excitation of 13C double-quantum coherences under magic-angle spinning at rotational resonance. By adapting a straightforward one-dimensional experiment described earlier [T. Karlsson, M. Eden, H. Luhman, M.H. Levitt, J. Magn. Reson. 145 (2000) 95-107], a double-quantum filtered spectrum selective for Cα and Cβ of uniformly labelled L-[ 13C, 15N]valine is obtained with 25% efficiency. The evolution of Cα-Cβ double-quantum coherence under the influence of the dipolar fields of bonded protons is monitored to provide a value of the Hα-Cα-Cβ-Hβ torsional angle that is consistent with the crystal structure. In addition, double-quantum filtration selective for C6 and C1' of uniformly labelled [ 13C, 15N]uridine is achieved with 12% efficiency for a 13C- 13C distance of 2.5 Å, yielding a reliable estimate of the C6-H and C1'-H projection angle defining the relative orientations of the nucleoside pyrimidine and ribose rings. This procedure will be useful, in favourable cases, for structural analysis of fully labelled small molecules such as receptor ligands that are not readily synthesised with labels placed selectively at structurally diagnostic sites.

  15. Distinct germination response of endangered and common arable weeds to reduced water potential.

    PubMed

    Rühl, A T; Eckstein, R L; Otte, A; Donath, T W

    2016-01-01

    Arable weeds are one of the most endangered species groups in Europe. Modern agriculture and intensive land-use management are the main causes of their dramatic decline. However, besides the changes in land use, climate change may further challenge the adaptability of arable weeds. Therefore, we investigated the response pattern of arable weeds to different water potential and temperature regimes during the phase of germination. We expected that endangered arable weeds would be more sensitive to differences in water availability and temperature than common arable weeds. To this end, we set up a climate chamber experiment where we exposed seeds of five familial pairs of common and endangered arable weed species to different temperatures (5/15, 10/20 °C) and water potentials (0.0 to -1.2 MPa). The results revealed a significant relationship between the reaction of arable weed species to water availability and their Red List status. The effects of reduced water availability on total germination, mean germination time and synchrony were significantly stronger in endangered than in common arable weeds. Therefore, global climate change may present a further threat to the survival of endangered arable weed species. © 2015 German Botanical Society and The Royal Botanical Society of the Netherlands.

  16. Differential priming of soil carbon driven by soil depth and root impacts on carbon availability

    SciTech Connect

    de Graaff, Marie-Anne; Jastrow, Julie D.; Gillette, Shay; Johns, Aislinn; Wullschleger, Stan D.

    2013-11-15

    Enhanced root-exudate inputs can stimulate decomposition of soil carbon (C) by priming soil microbial activity, but the mechanisms controlling the magnitude and direction of the priming effect remain poorly understood. With this study we evaluated how differences in soil C availability affect the impact of simulated root exudate inputs on priming. We conducted a 60-day laboratory incubation with soils collected (60 cm depth) from under six switchgrass (Panicum virgatum) cultivars. Differences in specific root length (SRL) among cultivars were expected to result in small differences in soil C inputs and thereby create small differences in the availability of recent labile soil C; whereas soil depth was expected to create large overall differences in soil C availability. Soil cores from under each cultivar (roots removed) were divided into depth increments of 0–10, 20–30, and 40–60 cm and incubated with addition of either: (1) water or (2) 13C-labeled synthetic root exudates (0.7 mg C/g soil). We measured CO2 respiration throughout the experiment. The natural difference in 13C signature between C3 soils and C4 plants was used to quantify cultivar-induced differences in soil C availability. Amendment with 13C-labeled synthetic root-exudate enabled evaluation of SOC priming. Our experiment produced three main results: (1) switchgrass cultivars differentially influenced soil C availability across the soil profile; (2) small differences in soil C availability derived from recent root C inputs did not affect the impact of exudate-C additions on priming; but (3) priming was greater in soils from shallow depths (relatively high total soil C and high ratio of labile-to-stable C) compared to soils from deep depths (relatively low total soil C and low ratio of labile-to-stable C). These findings suggest that the magnitude of the priming effect is affected, in part, by the ratio of root exudate C inputs to total soil C and that the impact of changes in exudate inputs on

  17. Autotrophic ammonia oxidation by soil thaumarchaea

    PubMed Central

    Zhang, Li-Mei; Offre, Pierre R.; He, Ji-Zheng; Verhamme, Daniel T.; Nicol, Graeme W.; Prosser, James I.

    2010-01-01

    Nitrification plays a central role in the global nitrogen cycle and is responsible for significant losses of nitrogen fertilizer, atmospheric pollution by the greenhouse gas nitrous oxide, and nitrate pollution of groundwaters. Ammonia oxidation, the first step in nitrification, was thought to be performed by autotrophic bacteria until the recent discovery of archaeal ammonia oxidizers. Autotrophic archaeal ammonia oxidizers have been cultivated from marine and thermal spring environments, but the relative importance of bacteria and archaea in soil nitrification is unclear and it is believed that soil archaeal ammonia oxidizers may use organic carbon, rather than growing autotrophically. In this soil microcosm study, stable isotope probing was used to demonstrate incorporation of 13C-enriched carbon dioxide into the genomes of thaumarchaea possessing two functional genes: amoA, encoding a subunit of ammonia monooxygenase that catalyses the first step in ammonia oxidation; and hcd, a key gene in the autotrophic 3-hydroxypropionate/4-hydroxybutyrate cycle, which has been found so far only in archaea. Nitrification was accompanied by increases in archaeal amoA gene abundance and changes in amoA gene diversity, but no change was observed in bacterial amoA genes. Archaeal, but not bacterial, amoA genes were also detected in 13C-labeled DNA, demonstrating inorganic CO2 fixation by archaeal, but not bacterial, ammonia oxidizers. Autotrophic archaeal ammonia oxidation was further supported by coordinate increases in amoA and hcd gene abundance in 13C-labeled DNA. The results therefore provide direct evidence for a role for archaea in soil ammonia oxidation and demonstrate autotrophic growth of ammonia oxidizing archaea in soil. PMID:20855593

  18. Identification of soil bacteria able to degrade phenanthrene bound to a hydrophobic sorbent in situ.

    PubMed

    Regonne, Raïssa Kom; Martin, Florence; Mbawala, Augustin; Ngassoum, Martin Benoît; Jouanneau, Yves

    2013-09-01

    Efficient bioremediation of PAH-contaminated sites is limited by the hydrophobic character and poor bioavailability of pollutants. In this study, stable isotope probing (SIP) was implemented to track bacteria that can degrade PAHs adsorbed on hydrophobic sorbents. Temperate and tropical soils were incubated with (13)C-labeled phenanthrene, supplied by spiking or coated onto membranes. Phenanthrene mineralization was faster in microcosms with PAH-coated membranes than in microcosms containing spiked soil. Upon incubation with temperate soil, phenanthrene degraders found in the biofilms that formed on coated membranes were mainly identified as Sphingomonadaceae and Actinobacteria. In the tropical soil, uncultured Rhodocyclaceae dominated degraders bound to membranes. Accordingly, ring-hydroxylating dioxygenase sequences recovered from this soil matched PAH-specific dioxygenase genes recently found in Rhodocyclaceae. Hence, our SIP approach allowed the detection of novel degraders, mostly uncultured, which differ from those detected after soil spiking, but might play a key role in the bioremediation of PAH-polluted soils.

  19. Can the application of biochar during arable and forestry plantation create an ongoing carbon sink and increase plant productivity?

    NASA Astrophysics Data System (ADS)

    Bell, M. J.; Worrall, F.

    2009-04-01

    This study is based at the National Trust Wallington estate in Northumberland, NE England, an agricultural estate where land-management options are being considered in an attempt to enhance current land carbon stocks. The aim of this research is to identify if biochar (charcoal produced from biomass) can provide an opportunity to create a perpetual carbon sink as apposed to a transitionary sink associated with other land-use changes currently under consideration? The main issues under investigation are: can biochar be ploughed into arable soils to create a long term carbon sink? Can biochar be ploughed into organic rich forest soils to create a long term carbon sink? Will the application of biochar increase crop productivity, increasing photosynthesis and carbon sequestration further still? In order for the estate to become carbon neutral through biochar application alone it was calculated that 3312 Kg/ha/year of biochar would need to be applied to the current area of arable land. This however is based on the assumption that all of the biochar added is stable and will remain in the soil, and assumes that addition does not lead to increased CO2 emissions from the organic matter already present. This study presents the results of weekly soil respiration measurements currently being made on 24 lysimeters filled with arable and forestry soils and 4 levels of charcoal treatment. Levels of treatment were chosen to assess the impact of applying biochar on a yearly basis and any negative impacts which may result from very high eventual concentrations. The following levels of charcoal were applied: 0 Kg/hectare, 6250 Kg/hectare, 62500 Kg/hectare, 87 500 Kg/hectare. The lysimeters containing 0 Kg/ha act as a control, the lysimeters containing 6250 Kg/hectare allow assessment of the impacts of 2 years of addition, 62 500Kg/ha the impact of 18 years of addition, and 87 500kg/ha the impact of 26 years of addition. The study will also present the results of plant productivity

  20. [Regulation of acidity of arable lands contaminated by Sr-90: analysis of cost of the averted doses of irradiation of population of Belarus].

    PubMed

    Putiatin, Iu V; Adianova, O B

    2010-01-01

    Results of researches on study of efficiency of soil acidity optimization on decrease of a collective doze from 90Sr to the population of Belarus are presented. On the basis of the "cost--benefit" analysis it is shown, that the savings for averted collective doze due to optimization of soil acidity of arable lands on cereals amount to 21-170 thousand US dollars per 1 man.-Sv depending on density of 90Sr soil contamination of districts of Belarus. It is established, that high effect on averting of collective doze 90Sr at cultivation of cereals can be expected at liming of sod-podsolic loamy sand soils with contamination density of 90Sr more than 12 kBq/m2, sand soils more than 16 kBq/m2, light loam soils more than 17 kBq/m2, at present time share of these lands in Belarus is about half from the area of the arable lands contaminated with radiostrontium - 86 thousand hectares.

  1. Changes in Root Decomposition Rates Across Soil Depths

    NASA Astrophysics Data System (ADS)

    Hicks Pries, C.; Porras, R. C.; Castanha, C.; Torn, M. S.

    2016-12-01

    Over half of global soil organic carbon (SOC) is stored in subsurface soils (>30 cm). Turnover times of soil organic carbon (SOC) increases with depth as evidenced by radiocarbon ages of 1,000 to more than 10,000 years in many deep soil horizons but the reasons for this increase are unclear. Many factors that potentially control SOC decomposition change with depth such as increased protection of SOC in aggregates or organo-mineral complexes and increased spatial heterogeneity of SOC "hotspots" like roots, which limit the accessibility of SOC to microbes. Lower concentrations of organic matter at depth may inhibit microbial activity due to energy limitation, and the microbial community itself changes with depth. To investigate how SOC decomposition differs with depth, we inserted a 13C-labeled fine root substrate into three depths (15, 50, and 90 cm) in a coniferous forest Alfisol and measured the root carbon remaining in particulate (>2 mm), bulk (< 2mm), free light, and mineral soil fractions over 2.5 years. We also characterized how the microbial community and SOC changed with depth. Initial rates of decomposition were unaffected by soil depth—50% of root carbon was lost from all depths within the first year. However, after 2.5 years, decomposition rates were affected by soil depth with only 15% of the root carbon remaining at 15 cm while 35% remained at 90 cm. Microbial communities, based on phospholipid fatty acid analysis, changed with depth—fungal biomarkers decreased whereas actinomycetes biomarkers increased. However, the preferences of different microbial groups for the 13C-labeled root carbon were consistent with depth. In contrast, the amount of mineral-associated SOC did not change with depth. Thus, decreased decomposition rates in this deep soil are not due to mineral associations limiting SOC availability, but may instead be due to changes in microbial communities, particularly in the microbes needed to carry out the later stages of root

  2. Cellulose utilization in forest litter and soil: identification of bacterial and fungal decomposers.

    PubMed

    Stursová, Martina; Zifčáková, Lucia; Leigh, Mary Beth; Burgess, Robert; Baldrian, Petr

    2012-06-01

    Organic matter decomposition in the globally widespread coniferous forests has an important role in the carbon cycle, and cellulose decomposition is especially important in this respect because cellulose is the most abundant polysaccharide in plant litter. Cellulose decomposition was 10 times faster in the fungi-dominated litter of Picea abies forest than in the bacteria-dominated soil. In the soil, the added (13)C-labelled cellulose was the main source of microbial respiration and was preferentially accumulated in the fungal biomass and cellulose induced fungal proliferation. In contrast, in the litter, bacterial biomass showed higher labelling after (13)C-cellulose addition and bacterial biomass increased. While 80% of the total community was represented by 104-106 bacterial and 33-59 fungal operational taxonomic units (OTUs), 80% of the cellulolytic communities of bacteria and fungi were only composed of 8-18 highly abundant OTUs. Both the total and (13)C-labelled communities differed substantially between the litter and soil. Cellulolytic bacteria in the acidic topsoil included Betaproteobacteria, Bacteroidetes and Acidobacteria, whereas these typically found in neutral soils were absent. Most fungal cellulose decomposers belonged to Ascomycota; cellulolytic Basidiomycota were mainly represented by the yeasts Trichosporon and Cryptococcus. Several bacteria and fungi demonstrated here to derive their carbon from cellulose were previously not recognized as cellulolytic.

  3. Microbial respiration activities correlated to sequentially separated, particulate and water-soluble organic matter fractions from arable and forest topsoils

    NASA Astrophysics Data System (ADS)

    Kaiser, M.; Wirth, S.; Ellerbrock, R.; Sommer, M.

    2009-12-01

    Michael Kaiser1, Stephan Wirth2, Ruth H. Ellerbrock3, Michael Sommer3,4 1University of California Merced, Natural Science, 4225 N. Hospital Rd., Atwater, CA 95301 2,3 Leibniz-Center for Agricultural Research (ZALF) e. V. 2 Institute of Landscape Matter Dynamics 3 Institute of Soil Landscape Research Eberswalder Str. 84, D-15374 Muencheberg, Germany 4University of Potsdam, Institute of Geoecology, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany Microbial respiration activities correlated to sequentially separated, particulate and water-soluble organic matter fractions from arable and forest topsoils Microbial decomposition of soil organic matter (SOM) accounts for roughly half of CO2 evolution from vegetated soil surfaces and plays a crucial role in the ability of soil to mitigate the greenhouse effect. The separation and identification of labile (i.e., easily decomposable) organic matter (OM) fractions from bulk SOM is of particular importance for a mechanistic understanding of microbial decomposition processes and for predicting the response of SOM to changes in land use, management, and climate. This work aimed to reveal differences in the relevance of particulate as well as water-soluble organic matter (OM) fractions from topsoils to the easily biodegradable soil organic matter (SOM). We selected eight paired sites with quite different soil types (Udorthent, Paleudalf, Glossudalf, Aquept, Hapludalf, Aquert, Udert, Haplorthod) and soil properties (e.g., clay content: 28 to 564 g kg-1). For each of these sites, we took samples from adjacent arable and forest topsoils. Physically uncomplexed, macro-, and micro-aggregate-occluded organic particle, as well as water-soluble OM fractions were sequentially separated by a combination of electrostatic attraction, ultrasonic treatment, density separation, sieving, and water extraction. The easily biodegradable SOM of the topsoil samples was determined by measuring microbial respiration during a short-term incubation

  4. Eddy Covariance Measurements of Methane Fluxes over Arable Land in Southern Ontario

    NASA Astrophysics Data System (ADS)

    Brown, S. E.; Wagner-Riddle, C.

    2013-12-01

    Aerobic soils are the only biological sink for atmospheric methane. Although the sinks are relatively small (~ -1 to -5 ng/m2s), this can translate to a significant quantity of methane consumption over large areas. The degree of sink strength can vary over time and space with changing soil moisture and texture, as well as variations in agricultural practices. Chamber measurements currently provide the majority of information on methane flux values for arable land. Improvements in high-frequency trace gas instrumentation allows for easier eddy covariance flux measurements for methane, thus providing the opportunity for flux measurements over a larger integrated area than chambers. A Picarro G2311-f gas analyzer was recently acquired to measure CH4 and CO2 fluxes for a corn field in Southern Ontario treated with manure. The analyzer employs cavity ring-down spectroscopy to measure gas concentrations and integrates sonic anemometry for eddy covariance measurements. Since methane flux values are small for agricultural soils, noise tests assessed the detection limits of the Picarro system in order to differentiate between instrument noise and fluxes close to zero. A spectral response test characterized the analyzer's capacity to resolve flux values by using a random noise generator to simulate different sized eddies passing by an eddy covariance system. Measurements of CH4 and CO2 commenced in spring of 2013 and continued throughout the growing season and post-harvest. Models will be developed to gap-fill the time series to calculate the net CO2 and CH4 budgets for the corn field. Results from the instrument characterization tests and preliminary results from the flux measurements will be presented.

  5. Partitioning CO2 effluxes from an Atlantic pine forest soil between endogenous soil organic matter and recently incorporated 13C-enriched plant material.

    PubMed

    Fernandez, Irene; Cabaneiro, Ana; González-Prieto, Serafín J

    2006-04-15

    Soil CO2 effluxes from recently added 13C-labeled phytomass versus endogenous soil organic matter (SOM) were studied in an acid soil from Atlantic pine forests (NW Spain). After several cultures to incorporate fresh 13C-enriched Lolium perenne to a Humic Cambisol with predominance of humus--Al over humus--Fe complexes, potential soil C mineralization was determined by laboratory aerobic incubation (84 days). Isotopic 13C analyses of SOM fractions were assessed to know in which organic compartments the 13C was preferentially incorporated. Although in the 13C-labeled soil the C mineralization coefficient totalized less than 3% of soil C, the 13C mineralization coefficient exceeded 14%, indicating a greater lability of the newly incorporated organic matter. Organic compounds coming from added phytomass showed a higher lability and contributed considerably to the total soil CO2 effluxes (52% of total soil CO2 evolved during the first decomposition stages and 27% at the end), even though added-C comprised less than 4% of total soil C. Good determination coefficients, when values of CO2--C released were fitted to a first-order double exponential kinetic model, support the existence of two C pools of different lability. Kinetic parameters obtained with this model indicated that phytomass addition augmented the biodegradability of the labile pool (instantaneous mineralization rate k increased from 0.07 d(-1) to 0.12 d(-1)) but diminished that of the recalcitrant pool (instantaneous mineralization rate h decreased from 2.7 x 10(-4) d(-1) to 1.6 x 10(-4) d(-1)). Consequently, the differentiation between both SOM pools increased, showing the importance of SOM quality on CO2 emissions from this kind of soil to the atmosphere.

  6. Rapid recovery of cyanobacterial pigments in desiccated biological soil crusts following addition of water.

    PubMed

    Abed, Raeid M M; Polerecky, Lubos; Al-Habsi, Amal; Oetjen, Janina; Strous, Marc; de Beer, Dirk

    2014-01-01

    We examined soil surface colour change to green and hydrotaxis following addition of water to biological soil crusts using pigment extraction, hyperspectral imaging, microsensors and 13C labeling experiments coupled to matrix-assisted laser desorption and ionization time of flight-mass spectrometry (MALD-TOF MS). The topsoil colour turned green in less than 5 minutes following water addition. The concentrations of chlorophyll a (Chl a), scytonemin and echinenon rapidly increased in the top <1 mm layer while in the deeper layer, their concentrations remained low. Hyperspectral imaging showed that, in both wet and dehydrated crusts, cyanobacteria formed a layer at a depth of 0.2-0.4 mm and this layer did not move upward after wetting. 13C labeling experiments and MALDI TOF analysis showed that Chl a was already present in the desiccated crusts and de novo synthesis of this molecule started only after 2 days of wetting due to growth of cyanobacteria. Microsensor measurements showed that photosynthetic activity increased concomitantly with the increase of Chl a, and reached a maximum net rate of 92 µmol m-2 h-1 approximately 2 hours after wetting. We conclude that the colour change of soil crusts to green upon water addition was not due to hydrotaxis but rather to the quick recovery and reassembly of pigments. Cyanobacteria in crusts can maintain their photosynthetic apparatus intact even under prolonged periods of desiccation with the ability to resume their photosynthetic activities within minutes after wetting.

  7. Rapid Recovery of Cyanobacterial Pigments in Desiccated Biological Soil Crusts following Addition of Water

    PubMed Central

    Abed, Raeid M. M.; Polerecky, Lubos; Al-Habsi, Amal; Oetjen, Janina; Strous, Marc; de Beer, Dirk

    2014-01-01

    We examined soil surface colour change to green and hydrotaxis following addition of water to biological soil crusts using pigment extraction, hyperspectral imaging, microsensors and 13C labeling experiments coupled to matrix-assisted laser desorption and ionization time of flight-mass spectrometry (MALD-TOF MS). The topsoil colour turned green in less than 5 minutes following water addition. The concentrations of chlorophyll a (Chl a), scytonemin and echinenon rapidly increased in the top <1 mm layer while in the deeper layer, their concentrations remained low. Hyperspectral imaging showed that, in both wet and dehydrated crusts, cyanobacteria formed a layer at a depth of 0.2–0.4 mm and this layer did not move upward after wetting. 13C labeling experiments and MALDI TOF analysis showed that Chl a was already present in the desiccated crusts and de novo synthesis of this molecule started only after 2 days of wetting due to growth of cyanobacteria. Microsensor measurements showed that photosynthetic activity increased concomitantly with the increase of Chl a, and reached a maximum net rate of 92 µmol m−2 h−1 approximately 2 hours after wetting. We conclude that the colour change of soil crusts to green upon water addition was not due to hydrotaxis but rather to the quick recovery and reassembly of pigments. Cyanobacteria in crusts can maintain their photosynthetic apparatus intact even under prolonged periods of desiccation with the ability to resume their photosynthetic activities within minutes after wetting. PMID:25375172

  8. The underestimated importance of belowground carbon input for forest soil animal food webs.

    PubMed

    Pollierer, Melanie M; Langel, Reinhard; Körner, Christian; Maraun, Mark; Scheu, Stefan

    2007-08-01

    The present study investigated the relative importance of leaf and root carbon input for soil invertebrates. Experimental plots were established at the Swiss Canopy Crane (SCC) site where the forest canopy was enriched with (13)C depleted CO(2) at a target CO(2) concentration of c. 540 p.p.m. We exchanged litter between labelled and unlabelled areas resulting in four treatments: (i) leaf litter and roots labelled, (ii) only leaf litter labelled, (iii) only roots labelled and (iv) unlabelled controls. In plots with only (13)C-labelled roots most of the soil invertebrates studied were significantly depleted in (13)C, e.g. earthworms, chilopods, gastropods, diplurans, collembolans, mites and isopods, indicating that these taxa predominantly obtain their carbon from belowground input. In plots with only (13)C-labelled leaf litter only three taxa, including, e.g. juvenile Glomeris spp. (Diplopoda), were significantly depleted in (13)C suggesting that the majority of soil invertebrates obtain its carbon from roots. This is in stark contrast to the view that decomposer food webs are based on litter input from aboveground.

  9. Fate of brominated flame retardants and organochlorine pesticides in urban soil: volatility and degradation.

    PubMed

    Wong, Fiona; Kurt-Karakus, Perihan; Bidleman, Terry F

    2012-03-06

    As the uses of polybrominated diphenyl ethers (BDEs) are being phased out in many countries, soils could become a secondary emission source to the atmosphere. It is also anticipated that the demand for alternative brominated flame retardants (BFRs) will grow, but little is known about their environmental fate in soils. In this study, the volatility and degradation of BFRs and organochlorine pesticides (OCPs) in soil was investigated. A low organic carbon (5.6%) urban soil was spiked with a suite of BFRs and OCPs, followed by incubation under laboratory condition for 360 days. These included BDE- 17, -28, -47, -99; α- and β-1,2-dibromo-4-(1,2-dibromoethyl)cyclohexane (TBECH), β-1,2,5,6-tetrabromocyclooctane (TBCO), and 2,3-dibromopropyl-2,4,6-tribromophenyl ether (DPTE), OCPs: α-hexachlorocyclohexane (α-HCH) and (13)C(6)-α-HCH, trans-chlordane (TC), and (13)C(10)-TC. The volatility of spiked chemicals was investigated using a fugacity meter to measure the soil-air partition coefficient (K(SA)). K(SA) of some spiked BFRs and OCPs increased from Day 10 to 60 or 90 and leveled off afterward. This suggests that the volatility of BFRs and OCPs decreases over time as the chemicals become more strongly bound to the soil. Degradation of alternative BFRs (α- and β-TBECH, β-TBCO, DPTE), BDE-17, and α-HCH ((13)C-labeled and nonlabeled) was evident in soils over 360 days, but no degradation was observed for the BDE-28, -47, -99, and TC ((13)C-labeled and nonlabeled). A method to separate the enantiomers of α-TBECH and β-TBCO was developed and their degradation, along with α-HCH ((13)C-labeled and nonlabeled) was enantioselective. This is the first study which reports the enantioselective degradation of chiral BFRs in soils. Discrepancies between the enantiomer fraction (EF) of chemicals extracted from the soil by dichloromethane (DCM) and air were found. It is suggested that DCM removes both the sequestered and loosely bound fractions of chemicals in soil, whereas

  10. Reconciling pesticide reduction with economic and environmental sustainability in arable farming.

    PubMed

    Lechenet, Martin; Bretagnolle, Vincent; Bockstaller, Christian; Boissinot, François; Petit, Marie-Sophie; Petit, Sandrine; Munier-Jolain, Nicolas M

    2014-01-01

    Reducing pesticide use is one of the high-priority targets in the quest for a sustainable agriculture. Until now, most studies dealing with pesticide use reduction have compared a limited number of experimental prototypes. Here we assessed the sustainability of 48 arable cropping systems from two major agricultural regions of France, including conventional, integrated and organic systems, with a wide range of pesticide use intensities and management (crop rotation, soil tillage, cultivars, fertilization, etc.). We assessed cropping system sustainability using a set of economic, environmental and social indicators. We failed to detect any positive correlation between pesticide use intensity and both productivity (when organic farms were excluded) and profitability. In addition, there was no relationship between pesticide use and workload. We found that crop rotation diversity was higher in cropping systems with low pesticide use, which would support the important role of crop rotation diversity in integrated and organic strategies. In comparison to conventional systems, integrated strategies showed a decrease in the use of both pesticides and nitrogen fertilizers, they consumed less energy and were frequently more energy efficient. Integrated systems therefore appeared as the best compromise in sustainability trade-offs. Our results could be used to re-design current cropping systems, by promoting diversified crop rotations and the combination of a wide range of available techniques contributing to pest management.

  11. The arable ecosystem as battleground for emergence of new human pathogens.

    PubMed

    van Overbeek, Leonard S; van Doorn, Joop; Wichers, Jan H; van Amerongen, Aart; van Roermund, Herman J W; Willemsen, Peter T J

    2014-01-01

    Disease incidences related to Escherichia coli and Salmonella enterica infections by consumption of (fresh) vegetables, sprouts, and occasionally fruits made clear that these pathogens are not only transmitted to humans via the "classical" routes of meat, eggs, and dairy products, but also can be transmitted to humans via plants or products derived from plants. Nowadays, it is of major concern that these human pathogens, especially the ones belonging to the taxonomical family of Enterobacteriaceae, become adapted to environmental habitats without losing their virulence to humans. Adaptation to the plant environment would lead to longer persistence in plants, increasing their chances on transmission to humans via consumption of plant-derived food. One of the mechanisms of adaptation to the plant environment in human pathogens, proposed in this paper, is horizontal transfer of genes from different microbial communities present in the arable ecosystem, like the ones originating from soil, animal digestive track systems (manure), water and plants themselves. Genes that would confer better adaptation to the phytosphere might be genes involved in plant colonization, stress resistance and nutrient acquisition and utilization. Because human pathogenic enterics often were prone to genetic exchanges via phages and conjugative plasmids, it was postulated that these genetic elements may be hold key responsible for horizontal gene transfers between human pathogens and indigenous microbes in agroproduction systems. In analogy to zoonosis, we coin the term phytonosis for a human pathogen that is transmitted via plants and not exclusively via animals.

  12. Reconciling Pesticide Reduction with Economic and Environmental Sustainability in Arable Farming

    PubMed Central

    Lechenet, Martin; Bretagnolle, Vincent; Bockstaller, Christian; Boissinot, François; Petit, Marie-Sophie; Petit, Sandrine; Munier-Jolain, Nicolas M.

    2014-01-01

    Reducing pesticide use is one of the high-priority targets in the quest for a sustainable agriculture. Until now, most studies dealing with pesticide use reduction have compared a limited number of experimental prototypes. Here we assessed the sustainability of 48 arable cropping systems from two major agricultural regions of France, including conventional, integrated and organic systems, with a wide range of pesticide use intensities and management (crop rotation, soil tillage, cultivars, fertilization, etc.). We assessed cropping system sustainability using a set of economic, environmental and social indicators. We failed to detect any positive correlation between pesticide use intensity and both productivity (when organic farms were excluded) and profitability. In addition, there was no relationship between pesticide use and workload. We found that crop rotation diversity was higher in cropping systems with low pesticide use, which would support the important role of crop rotation diversity in integrated and organic strategies. In comparison to conventional systems, integrated strategies showed a decrease in the use of both pesticides and nitrogen fertilizers, they consumed less energy and were frequently more energy efficient. Integrated systems therefore appeared as the best compromise in sustainability trade-offs. Our results could be used to re-design current cropping systems, by promoting diversified crop rotations and the combination of a wide range of available techniques contributing to pest management. PMID:24887494

  13. The arable ecosystem as battleground for emergence of new human pathogens

    PubMed Central

    van Overbeek, Leonard S.; van Doorn, Joop; Wichers, Jan H.; van Amerongen, Aart; van Roermund, Herman J. W.; Willemsen, Peter T. J.

    2014-01-01

    Disease incidences related to Escherichia coli and Salmonella enterica infections by consumption of (fresh) vegetables, sprouts, and occasionally fruits made clear that these pathogens are not only transmitted to humans via the “classical” routes of meat, eggs, and dairy products, but also can be transmitted to humans via plants or products derived from plants. Nowadays, it is of major concern that these human pathogens, especially the ones belonging to the taxonomical family of Enterobacteriaceae, become adapted to environmental habitats without losing their virulence to humans. Adaptation to the plant environment would lead to longer persistence in plants, increasing their chances on transmission to humans via consumption of plant-derived food. One of the mechanisms of adaptation to the plant environment in human pathogens, proposed in this paper, is horizontal transfer of genes from different microbial communities present in the arable ecosystem, like the ones originating from soil, animal digestive track systems (manure), water and plants themselves. Genes that would confer better adaptation to the phytosphere might be genes involved in plant colonization, stress resistance and nutrient acquisition and utilization. Because human pathogenic enterics often were prone to genetic exchanges via phages and conjugative plasmids, it was postulated that these genetic elements may be hold key responsible for horizontal gene transfers between human pathogens and indigenous microbes in agroproduction systems. In analogy to zoonosis, we coin the term phytonosis for a human pathogen that is transmitted via plants and not exclusively via animals. PMID:24688484

  14. The effects of soil management on subsoil organic matter

    NASA Astrophysics Data System (ADS)

    Gregory, Andrew; Coleman, Kevin; Jenkinson, David; Powlson, David; Poulton, Paul; Whitmore, Andrew

    2010-05-01

    Soil management has a clear effect on the organic matter (OM) content of soils in agricultural systems. For instance, grassland soils tend to have a greater OM content than arable soils due to the difference in the management of the surface vegetation between the two systems. Our knowledge of this is largely restricted to the topsoil however, as this is the part of the profile that is most obviously influenced by the inputs and losses of OM. How agricultural management at the surface affects OM contents in the subsoil is rarely considered, let alone understood. We present the state of our current knowledge of the effect of soil management on subsoil OM based on measurements made on soils from some of the established field experiments at Rothamsted Research, UK. We have examined subsoil OM data collected by us and other scientists at Rothamsted representing different timescales: long-term (Broadbalk wilderness and arable, Geescroft wilderness, and Park Grass: 130 years), medium-term (Highfield ley-arable: 40-60 years), and short-term (Highfield and Geescroft reversion: 2 years). Samples to depths of up to 96 cm in the profile were collected from the field experiments periodically between 1870 and 2009 and analysed for C and N. Both C and N increased in soils converted from arable to long-term woodland and grassland throughout the profile. The C:N ratio also increased in comparison to long-term arable soils which suggested either the preferential accumulation of C or the preferential decomposition of N at depth in grassland and woodland soils, or the converse at depth in the arable soils. Small increases in C and N in both long-term grassland and arable soils were also apparent. In the medium-term, differences in the pattern of soil C and N with depth were found, with homogenisation in the cultivated layer in arable and fallow soils and a more gradual decrease with depth in the grassland soil. In general, differences between soils subjected to different management

  15. Phylogenetically Distinct Phylotypes Modulate Nitrification in a Paddy Soil

    PubMed Central

    Zhao, Jun; Wang, Baozhan

    2015-01-01

    Paddy fields represent a unique ecosystem in which regular flooding occurs, allowing for rice cultivation. However, the taxonomic identity of the microbial functional guilds that catalyze soil nitrification remains poorly understood. In this study, we provide molecular evidence for distinctly different phylotypes of nitrifying communities in a neutral paddy soil using high-throughput pyrosequencing and DNA-based stable isotope probing (SIP). Following urea addition, the levels of soil nitrate increased significantly, accompanied by an increase in the abundance of the bacterial and archaeal amoA gene in microcosms subjected to SIP (SIP microcosms) during a 56-day incubation period. High-throughput fingerprints of the total 16S rRNA genes in SIP microcosms indicated that nitrification activity positively correlated with the abundance of Nitrosospira-like ammonia-oxidizing bacteria (AOB), soil group 1.1b-like ammonia-oxidizing archaea (AOA), and Nitrospira-like nitrite-oxidizing bacteria (NOB). Pyrosequencing of 13C-labeled DNA further revealed that 13CO2 was assimilated by these functional groups to a much greater extent than by marine group 1.1a-associated AOA and Nitrobacter-like NOB. Phylogenetic analysis demonstrated that active AOB communities were closely affiliated with Nitrosospira sp. strain L115 and the Nitrosospira multiformis lineage and that the 13C-labeled AOA were related to phylogenetically distinct groups, including the moderately thermophilic “Candidatus Nitrososphaera gargensis,” uncultured fosmid 29i4, and acidophilic “Candidatus Nitrosotalea devanaterra” lineages. These results suggest that a wide variety of microorganisms were involved in soil nitrification, implying physiological diversification of soil nitrifying communities that are constantly exposed to environmental fluctuations in paddy fields. PMID:25724959

  16. Life cycle assessment of energy self-sufficiency systems based on agricultural residues for organic arable farms.

    PubMed

    Kimming, M; Sundberg, C; Nordberg, A; Baky, A; Bernesson, S; Norén, O; Hansson, P-A

    2011-01-01

    The agricultural industry today consumes large amounts of fossil fuels. This study used consequential life cycle assessment (LCA) to analyse two potential energy self-sufficient systems for organic arable farms, based on agricultural residues. The analysis focused on energy balance, resource use and greenhouse gas (GHG) emissions. A scenario based on straw was found to require straw harvest from 25% of the farm area; 45% of the total energy produced from the straw was required for energy carrier production and GHG emissions were reduced by 9% compared with a fossil fuel-based reference scenario. In a scenario based on anaerobic digestion of ley, the corresponding figures were 13%, 24% and 35%. The final result was sensitive to assumptions regarding, e.g., soil carbon content and handling of by-products.

  17. Glyphosate applications on arable fields considerably coincide with migrating amphibians.

    PubMed

    Berger, Gert; Graef, Frieder; Pfeffer, Holger

    2013-01-01

    Glyphosate usage is increasing worldwide and the application schemes of this herbicide are currently changing. Amphibians migrating through arable fields may be harmed by Glyphosate applied to field crops. We investigated the population-based temporal coincidence of four amphibian species with Glyphosate from 2006 to 2008. Depending on a) age- and species-specific main migration periods, b) crop species, c) Glyphosate application mode for crops, and d) the presumed DT50 value (12 days or 47 days) of Glyphosate, we calculated up to 100% coincidence with Glyphosate. The amphibians regularly co-occur with pre-sowing/pre-emerging Glyphosate applications to maize in spring and with stubble management prior to crop sowing in late summer and autumn. Siccation treatment in summer coincides only with early pond-leaving juveniles. We suggest in-depth investigations of both acute and long-term effects of Glyphosate applications on amphibian populations not only focussed on exposure during aquatic periods but also terrestrial life stages.

  18. Weed vegetation ecology of arable land in Salalah, Southern Oman

    PubMed Central

    El-Sheikh, Mohamed A.

    2013-01-01

    This paper applies multivariate statistical methods to a data set of weed relevés from arable fields in two different habitat types of coastal and mountainous escarpments in Southern Oman. The objectives were to test the effect of environmental gradients, crop plants and time on weed species composition, to rank the importance of these particular factors, and to describe the patterns of species composition and diversity associated with these factors. Through the application of TWINSPAN, DCA and CCA programs on data relating to 102 species recorded in 28 plots and farms distributed in the study area, six plant communities were identified: I- Dichanthium micranthum, II- Cynodon dactylon–D. micranthum, III- Convolvulus arvensis, IV- C. dactylon–Sonchus oleraceus, V- Amaranthus viridis and VI- Suaeda aegyptiaca–Achyranthes aspera. The ordination process (CCA) provided a sequence of plant communities and species diversity that correlated with some anthropogenic factors, physiographic variables and crop types. Therefore, length of time since farm construction, disturbance levels and altitude are the most important factors related to the occurrence of the species. The perennial species correlated with the more degraded mountain areas of new farm stands, whereas most of the annuals correlated with old lowland and less disturbed farms. PMID:23961246

  19. Weed vegetation ecology of arable land in Salalah, Southern Oman.

    PubMed

    El-Sheikh, Mohamed A

    2013-07-01

    This paper applies multivariate statistical methods to a data set of weed relevés from arable fields in two different habitat types of coastal and mountainous escarpments in Southern Oman. The objectives were to test the effect of environmental gradients, crop plants and time on weed species composition, to rank the importance of these particular factors, and to describe the patterns of species composition and diversity associated with these factors. Through the application of TWINSPAN, DCA and CCA programs on data relating to 102 species recorded in 28 plots and farms distributed in the study area, six plant communities were identified: I- Dichanthium micranthum, II- Cynodon dactylon-D. micranthum, III- Convolvulus arvensis, IV- C. dactylon-Sonchus oleraceus, V- Amaranthus viridis and VI- Suaeda aegyptiaca-Achyranthes aspera. The ordination process (CCA) provided a sequence of plant communities and species diversity that correlated with some anthropogenic factors, physiographic variables and crop types. Therefore, length of time since farm construction, disturbance levels and altitude are the most important factors related to the occurrence of the species. The perennial species correlated with the more degraded mountain areas of new farm stands, whereas most of the annuals correlated with old lowland and less disturbed farms.

  20. Soils

    Treesearch

    Emily Moghaddas; Ken Hubbert

    2014-01-01

    When managing for resilient forests, each soil’s inherent capacity to resist and recover from changes in soil function should be evaluated relative to the anticipated extent and duration of soil disturbance. Application of several key principles will help ensure healthy, resilient soils: (1) minimize physical disturbance using guidelines tailored to specific soil types...

  1. Soil

    USDA-ARS?s Scientific Manuscript database

    Soil is a diverse natural material characterized by solid, liquid, and gas phases that impart unique chemical, physical, and biological properties. Soil provides many key functions, including supporting plant growth and providing environmental remediation. Monitoring key soil properties and processe...

  2. Probing soil C metabolism in response to temperature: results from experiments and modeling

    NASA Astrophysics Data System (ADS)

    Dijkstra, P.; Dalder, J.; Blankinship, J.; Selmants, P. C.; Schwartz, E.; Koch, G. W.; Hart, S.; Hungate, B. A.

    2010-12-01

    C use efficiency (CUE) is one of the least understood aspects of soil C cycling, has a very large effect on soil respiration and C sequestration, and decreases with elevated temperature. CUE is directly related to substrate partitioning over energy production and biosynthesis. The production of energy and metabolic precursors occurs in well-known processes such as glycolysis and Krebs cycle. We have developed a new stable isotope approach using position-specific 13C-labeled metabolic tracers to measure these fundamental metabolic processes in intact soil communities (1). We use this new approach, combined with models of soil metabolic flux patterns, to analyze the response of microbial energy production, biosynthesis, and CUE to temperature. The method consists of adding small but precise amounts of position-specific 13C -labeled metabolic tracers to parallel soil incubations, in this case 1-13C and 2,3-13C pyruvate and 1-13C and U-13C glucose. The measurement of CO2 released from the labeled tracers is used to calculate the C flux rates through various metabolic pathways. A simplified metabolic model consisting of 23 reactions is iteratively solved using results of the metabolic tracer experiments and information on microbial precursor demand under different temperatures. This new method enables direct study of fundamental aspects of microbial energy production, C use efficiency, and soil organic matter formation in response to temperature. (1) Dijkstra P, Blankinship JC, Selmants PC, Hart SC, Koch GW, Schwarz E and Hungate BA. Probing metabolic flux patterns of soil microbial communities using parallel position-specific tracer labeling. Soil Biology and Biochemistry (accepted)

  3. Estimation of Arable Land Loss in Shandong Province, China based on BFAST Model

    NASA Astrophysics Data System (ADS)

    Liu, Y.

    2016-12-01

    With the rapid development of national economy and rise of industrialization, China has been one of the countries which has the fastest urbanization process. From 2001 to 2005, China lost over 2000 km2 fertile arable land every year because of urban expansion. Arable land area declining continuously poses a threat to China's food security. Land survey is the direct way to statistic the arable land status, which lasts long time and needs mounts of financial support. Remote sensing is a perfect way to survey land use and its dynamics at large scale. This paper aims to evaluate the detailed status of agricultural land loss of Shandong Province, China by using BFAST (Breaks for Additive Seasonal and Trend) model. First, the 30m spatial resolution global land cover products GlobeLand30 in 2000 and 2010 are used to locate pixels transforming from agricultural land to artificial cover during this period. Within a MODIS pixel (250m) area, if over half of GlobeLand30 pixels have changed from arable land to artificial cover, then the responding MODIS pixel is classified as changed area, whose phenology reflected by NDVI time series curve will also change. Then, BFAST is used to detect the break point which represents the time of change occurred using MODIS NDVI time series data. From 2002 to 2010, Shandong Province lost its 1063.03 km2 arable land in total. Arable land loss has a declining trend in each year and most loss occurred in 2002 and 2003. Spatially, cities which has higher level of economic development in central and eastern regions lost more arable land. Finally, compare this result with statistical data from China's national Bureau of Statistics, there is a strong positive relationship.

  4. The Bio-accessibility of Synthetic Fe-Organo Complexes in Subsurface Soil with Elevated Temperature: a Proxy for the Vulnerability of Mineral Associated Carbon to Warming Rachel C. Porras, Peter S. Nico, and Margaret Torn Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA

    NASA Astrophysics Data System (ADS)

    Porras, R. C.; Hicks Pries, C.

    2015-12-01

    Globally, subsurface soils (>30 cm) represent an important reservoir of soil organic carbon (SOC). However, the vulnerability of this deep SOC and, in particular mineral-associated SOC, to warming, and its potential to amplify the effects of climate change is highly uncertain. To gain insight into the bio-accessibility and temperature sensitivity of mineral-associated organic C, we conducted a series of incubations using soils collected from three depths (0-10, 50-60, and 80-90 cm) under coniferous forest. The soils are moderately acidic (mean pH=6.5) sandy, mixed, mesic Ultic Haploxeralfs. To understand how mechanisms controlling SOC bio-accessibilty or temperature sensitivity differ with depth and with the properties of Fe-organo complexes (i.e.,degree of crystallinity, amount of reactive surface area, or surface saturation), we used a 13C labeled glucose substrate to prepare synthetic Fe-organo complexes spanning a range of crystallinity and mineral surface saturation. The synthetic Fe-organo complexes were then added to soil from three depths. The soils containing the 13C labeled Fe-organo adduct were incubated at two temperatures (ambient and +4°C) and respired 13CO2 was measured and used to estimate flux rates. Differences in measured 13CO2 fluxes as a function of depth, surface loading, and mineral properties are discussed in terms of their implications for the temperature sensitivity of mineral protected organic carbon in subsurface soils.

  5. Short rotation coppice improve the phosphorus (P) supply of arable land through translocation of P from subsoil to topsoil

    NASA Astrophysics Data System (ADS)

    Doering, K.; Kaupenjohann, M.

    2011-12-01

    Even if the agricultural use of P will not increase during the next decades, the stock of phosphorous (P) in global mineral deposits is predicted to last for only less than 50 to 100 years. This will cause a much more severe problem than the shortage of fossil energy because P as an element essential to all life is not substitutable through any other material. Thus, efforts have to be made to close the P-cycle and it will in the near future be no more justifiable to disperse P or dump it at places where it cannot be recovered from. Additionally, new resources of P have to be explored to cover increasing P demand and to compensate for inevitable losses. Subsoil, which is hardly explored by arable crops may contain such P reserves. Deep rooting perennial plants like trees have access to these P resources and may be used to introduce subsoil P into the agricultural P cycle. Using literature data we followed the question to what extent the introduction of short rotation coppice of energy - Populus, Salix and Robinia into the agricultural crop rotation could support the P supply to annual food crops. Leaf litter of Populs, Salix and Robinia will transfer 3 to 13, 5 to 12 and 5 to 12 kg P and ha-1 a-1 to the soil surface, respectively. The large variation is mainly explained by site conditions (soil and climate). Assuming that 30 % of the nutrient requirement of the trees is assimilated from the subsoil, 1 to 5 kg of P ha-1 a-1 may be translocated to the topsoil. The knowledge about root content of P of the three tree species is very scarce. Based on information about other broadleaf trees, we consider that root litter may transfer amounts of P to the topsoil similar to leaf litter. Thus, in total the annual translocation of subsoil-P to the topsoil may range between 2 to 10 kg ha-1 in short rotation plantations. These amounts are far below the annual P removal from soils through food crops which may range from 20 to 40 kg P ha-1 a-1. Therefore subsoil P cannot replace P

  6. Nutrient production from dairy cattle manure and loading on arable land

    PubMed Central

    You, Byung-Gu; Choi, Yoon-Seok; Ra, Changsix

    2017-01-01

    Objective Along with increasing livestock products via intensive rearing, the accumulation of livestock manure has become a serious issue due to the fact that there is finite land for livestock manure recycling via composting. The nutrients from livestock manure accumulate on agricultural land and the excess disembogues into streams causing eutrophication. In order to systematically manage nutrient loading on agricultural land, quantifying the amount of nutrients according to their respective sources is very important. However, there is a lack of research concerning nutrient loss from livestock manure during composting or storage on farms. Therefore, in the present study we quantified the nutrients from dairy cattle manure that were imparted onto agricultural land. Methods Through investigation of 41 dairy farms, weight reduction and volatile solids (VS), total nitrogen (TN), and total phosphorus (TP) changes of dairy cattle manure during the storage and composting periods were analyzed. In order to support the direct investigation and survey on site, the three cases of weight reduction during the storing and composting periods were developed according to i) experiment, ii) reference, and iii) theoretical changes in phosphorus content (ΔP = 0). Results The data revealed the nutrient loading coefficients (NLCs) of VS, TN, and TP on agricultural land were 1.48, 0.60, and 0.66, respectively. These values indicated that the loss of nitrogen and phosphorus was 40% and 34%, respectively, and that there was an increase of VS since bedding materials were mixed with excretion in the barn. Conclusion As result of nutrient-footprint analyses, the amounts of TN and TP particularly entered on arable land have been overestimated if applying the nutrient amount in fresh manure. The NLCs obtained in this study may assist in the development of a database to assess the accurate level of manure nutrient loading on soil and facilitate systematic nutrient management. PMID:27492346

  7. Microbial Diversity Indexes Can Explain Soil Carbon Dynamics as a Function of Carbon Source.

    PubMed

    Louis, Benjamin P; Maron, Pierre-Alain; Menasseri-Aubry, Safya; Sarr, Amadou; Lévêque, Jean; Mathieu, Olivier; Jolivet, Claudy; Leterme, Philippe; Viaud, Valérie

    2016-01-01

    Mathematical models do not explicitly represent the influence of soil microbial diversity on soil organic carbon (SOC) dynamics despite recent evidence of relationships between them. The objective of the present study was to statistically investigate relationships between bacterial and fungal diversity indexes (richness, evenness, Shannon index, inverse Simpson index) and decomposition of different pools of soil organic carbon by measuring dynamics of CO2 emissions under controlled conditions. To this end, 20 soils from two different land uses (cropland and grassland) were incubated with or without incorporation of 13C-labelled wheat-straw residue. 13C-labelling allowed us to study residue mineralisation, basal respiration and the priming effect independently. An innovative data-mining approach was applied, based on generalized additive models and a predictive criterion. Results showed that microbial diversity indexes can be good covariates to integrate in SOC dynamics models, depending on the C source and the processes considered (native soil organic carbon vs. fresh wheat residue). Specifically, microbial diversity indexes were good candidates to help explain mineralisation of native soil organic carbon, while priming effect processes seemed to be explained much more by microbial composition, and no microbial diversity indexes were found associated with residue mineralisation. Investigation of relationships between diversity and mineralisation showed that higher diversity, as measured by the microbial diversity indexes, seemed to be related to decreased CO2 emissions in the control soil. We suggest that this relationship can be explained by an increase in carbon yield assimilation as microbial diversity increases. Thus, the parameter for carbon yield assimilation in mathematical models could be calculated as a function of microbial diversity indexes. Nonetheless, given limitations of the methods used, these observations should be considered with caution and

  8. Microbial Diversity Indexes Can Explain Soil Carbon Dynamics as a Function of Carbon Source

    PubMed Central

    Maron, Pierre-Alain; Menasseri-Aubry, Safya; Sarr, Amadou; Lévêque, Jean; Mathieu, Olivier; Jolivet, Claudy; Leterme, Philippe; Viaud, Valérie

    2016-01-01

    Mathematical models do not explicitly represent the influence of soil microbial diversity on soil organic carbon (SOC) dynamics despite recent evidence of relationships between them. The objective of the present study was to statistically investigate relationships between bacterial and fungal diversity indexes (richness, evenness, Shannon index, inverse Simpson index) and decomposition of different pools of soil organic carbon by measuring dynamics of CO2 emissions under controlled conditions. To this end, 20 soils from two different land uses (cropland and grassland) were incubated with or without incorporation of 13C-labelled wheat-straw residue. 13C-labelling allowed us to study residue mineralisation, basal respiration and the priming effect independently. An innovative data-mining approach was applied, based on generalized additive models and a predictive criterion. Results showed that microbial diversity indexes can be good covariates to integrate in SOC dynamics models, depending on the C source and the processes considered (native soil organic carbon vs. fresh wheat residue). Specifically, microbial diversity indexes were good candidates to help explain mineralisation of native soil organic carbon, while priming effect processes seemed to be explained much more by microbial composition, and no microbial diversity indexes were found associated with residue mineralisation. Investigation of relationships between diversity and mineralisation showed that higher diversity, as measured by the microbial diversity indexes, seemed to be related to decreased CO2 emissions in the control soil. We suggest that this relationship can be explained by an increase in carbon yield assimilation as microbial diversity increases. Thus, the parameter for carbon yield assimilation in mathematical models could be calculated as a function of microbial diversity indexes. Nonetheless, given limitations of the methods used, these observations should be considered with caution and

  9. Labile carbon retention compensates for CO2 released by priming in forest soils.

    PubMed

    Qiao, Na; Schaefer, Douglas; Blagodatskaya, Evgenia; Zou, Xiaoming; Xu, Xingliang; Kuzyakov, Yakov

    2014-06-01

    Increase of belowground C allocation by plants under global warming or elevated CO2 may promote decomposition of soil organic carbon (SOC) by priming and strongly affects SOC dynamics. The specific effects by priming of SOC depend on the amount and frequency of C inputs. Most previous priming studies have investigated single C additions, but they are not very representative for litterfall and root exudation in many terrestrial ecosystems. We evaluated effects of (13)C-labeled glucose added to soil in three temporal patterns: single, repeated, and continuous on dynamics of CO2 and priming of SOC decomposition over 6 months. Total and (13)C labeled CO2 were monitored to analyze priming dynamics and net C balance between SOC loss caused by priming and the retention of added glucose-C. Cumulative priming ranged from 1.3 to 5.5 mg C g(-1) SOC in the subtropical, and from -0.6 to 5.5 mg C g(-1) SOC in the tropical soils. Single addition induced more priming than repeated and continuous inputs. Therefore, single additions of high substrate amounts may overestimate priming effects over the short term. The amount of added glucose C remaining in soil after 6 months (subtropical: 8.1-11.2 mg C g(-1) SOC or 41-56% of added glucose; tropical: 8.7-15.0 mg C g(-1) SOC or 43-75% of glucose) was substantially higher than the net C loss due to SOC decomposition including priming effect. This overcompensation of C losses was highest with continuous inputs and lowest with single inputs. Therefore, raised labile organic C input to soils by higher plant productivity will increase SOC content even though priming accelerates decomposition of native SOC. Consequently, higher continuous input of C belowground by plants under warming or elevated CO2 can increase C stocks in soil despite accelerated C cycling by priming in soils.

  10. Prediction of soil organic carbon concentration and soil bulk density of mineral soils for soil organic carbon stock estimation

    NASA Astrophysics Data System (ADS)

    Putku, Elsa; Astover, Alar; Ritz, Christian

    2016-04-01

    Soil monitoring networks provide a powerful base for estimating and predicting nation's soil status in many aspects. The datasets of soil monitoring are often hierarchically structured demanding sophisticated data analyzing methods. The National Soil Monitoring of Estonia was based on a hierarchical data sampling scheme as each of the monitoring site was divided into four transects with 10 sampling points on each transect. We hypothesized that the hierarchical structure in Estonian Soil Monitoring network data requires a multi-level mixed model approach to achieve good prediction accuracy of soil properties. We used this database to predict soil bulk density and soil organic carbon concentration of mineral soils in arable land using different statistical methods: median approach, linear regression and mixed model; additionally, random forests for SOC concentration. We compared the prediction results and selected the model with the best prediction accuracy to estimate soil organic carbon stock. The mixed model approach achieved the best prediction accuracy in both soil organic carbon (RMSE 0.22%) and bulk density (RMSE 0.09 g cm-3) prediction. Other considered methods under- or overestimated higher and lower values of soil parameters. Thus, using these predictions we calculated the soil organic carbon stock of mineral arable soils and applied the model to a specific case of Tartu County in Estonia. Average estimated SOC stock of Tartu County is 54.8 t C ha-1 and total topsoil SOC stock 1.8 Tg in humus horizon.

  11. An econometric analysis of changes in arable land utilization using multinomial logit model in Pinggu district, Beijing, China.

    PubMed

    Xu, Yueqing; McNamara, Paul; Wu, Yanfang; Dong, Yue

    2013-10-15

    Arable land in China has been decreasing as a result of rapid population growth and economic development as well as urban expansion, especially in developed regions around cities where quality farmland quickly disappears. This paper analyzed changes in arable land utilization during 1993-2008 in the Pinggu district, Beijing, China, developed a multinomial logit (MNL) model to determine spatial driving factors influencing arable land-use change, and simulated arable land transition probabilities. Land-use maps, as well as social-economic and geographical data were used in the study. The results indicated that arable land decreased significantly between 1993 and 2008. Lost arable land shifted into orchard, forestland, settlement, and transportation land. Significant differences existed for arable land transitions among different landform areas. Slope, elevation, population density, urbanization rate, distance to settlements, and distance to roadways were strong drivers influencing arable land transition to other uses. The MNL model was proved effective for predicting transition probabilities in land use from arable land to other land-use types, thus can be used for scenario analysis to develop land-use policies and land-management measures in this metropolitan area.

  12. "Death in soil" or what can we learn from groundwater for the genesis of soil organic matter

    NASA Astrophysics Data System (ADS)

    Kaestner, M.; Miltner, A.; Bombach, P.; Schmidt-Brücken, B.

    2009-04-01

    Soil microorganisms do not only catalyze the transformation of plant residues to soil organic matter, but also serve as considerable carbon source for the formation of refractory soil organic matter by providing cell fragments as structural interfacial surfaces in soil systems. After incubation of 13C-labeled Gram negative bacteria in soil for 224 days, we could show that 44% of the bulk carbon remained in soil. 30 - 35 % of the remaining bulk C from Gram negative microbial biomass was stabilized in non-living soil organic matter (SOM). Surprisingly, the added labeled biomass proteins remained in soil almost completely which clearly indicates the stabilization of proteins in cell aggregations being more resistant to biodegradation than free proteins and amino acids. Scanning electron micrographs of the soil showed very rarely intact cells but highly abundant patchy organic cover material of 20 to 50 nm2 size on the mineral surfaces. A possible mechanism for this stabilization and the observed material could be found by analyses of microbial communities and biofilms developing on Biosep? beads within in situ microcosms exposed to contaminated aquifers. Scanning electron micrographs of the developing biofilms on the beads showed the formation of such patchy material found in the soil by fragmentation of empty bacterial cell envelopes (cell walls) and all stages of decay. The fragmentation of these cell walls provided a mechanistic explanation for the observed stabilisation, the genesis of SOM derived from dead bacterial cells, and the enzyme activity always found associated to SOM.

  13. Autotrophic growth of nitrifying community in an agricultural soil

    PubMed Central

    Xia, Weiwei; Zhang, Caixia; Zeng, Xiaowei; Feng, Youzhi; Weng, Jiahua; Lin, Xiangui; Zhu, Jianguo; Xiong, Zhengqin; Xu, Jian; Cai, Zucong; Jia, Zhongjun

    2011-01-01

    The two-step nitrification process is an integral part of the global nitrogen cycle, and it is accomplished by distinctly different nitrifiers. By combining DNA-based stable isotope probing (SIP) and high-throughput pyrosequencing, we present the molecular evidence for autotrophic growth of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) in agricultural soil upon ammonium fertilization. Time-course incubation of SIP microcosms indicated that the amoA genes of AOB was increasingly labeled by 13CO2 after incubation for 3, 7 and 28 days during active nitrification, whereas labeling of the AOA amoA gene was detected to a much lesser extent only after a 28-day incubation. Phylogenetic analysis of the 13C-labeled amoA and 16S rRNA genes revealed that the Nitrosospira cluster 3-like sequences dominate the active AOB community and that active AOA is affiliated with the moderately thermophilic Nitrososphaera gargensis from a hot spring. The higher relative frequency of Nitrospira-like NOB in the 13C-labeled DNA suggests that it may be more actively involved in nitrite oxidation than Nitrobacter-like NOB. Furthermore, the acetylene inhibition technique showed that 13CO2 assimilation by AOB, AOA and NOB occurs only when ammonia oxidation is not blocked, which provides strong hints for the chemolithoautotrophy of nitrifying community in complex soil environments. These results show that the microbial community of AOB and NOB dominates the nitrification process in the agricultural soil tested. PMID:21326337

  14. How does different arable management affect potential N mineralisation?

    NASA Astrophysics Data System (ADS)

    Spiegel, Heide; Sandén, Taru; Dersch, Georg; Baumgarten, Andreas

    2017-04-01

    The production of food and animal feed on agricultural soils and an increasing need to generate biomass for material and energy use on the limited resource soil require optimal nutrient storage and cycling. Especially nitrogen (N) should be managed as accurate as possible to ensure beneficial yields and product qualities and to avoid adverse environmental effects, e.g. N leaching into waters and gaseous losses into the atmosphere. One biological indicator to assess the site specific potential to release N is the "potential N mineralisation". This parameter can be measured by routine analysis with the anaerobic incubation method (KEENEY, 1982), modified according to KANDELER (1993) on dried soils. The results of the potential N mineralisation measurements can be classified (high: > 70 mg N kg-1 7 d-1, medium and low: 35-70 mg and ≤ 35 N kg-1 7d-1, respectively) according to the Austrian guidelines for appropriate fertilisation (BMLFUW, 2017). The results of this biological soil parameter provide information about soil fertility and the nutrient status to the farmers and can be used to adjust N fertilisation recommendations. Furthermore, AGES runs long-term field experiments since several decades. We have evaluated the effects of different agricultural management, such as organic and mineral fertilisation and tillage, on the potential N mineralisation at different sites in Austria. Our results indicate that the potential N mineralisation increases significantly after long-term organic fertilisation (farmyard manure (FYM)), after long-term incorporation of crop residues and the reduction of tillage.

  15. Tracking the influence of global change on soil organic C: opportunities and challenges

    NASA Astrophysics Data System (ADS)

    Billings, S. A.; Ziegler, S. E.; Li, J.

    2009-12-01

    Anthropogenic global changes such as rising atmospheric CO2 and temperatures likely will enhance multiple flows of carbon (C) between terrestrial ecosystems and the atmosphere. Understanding the changes these perturbations exert on soil organic C (SOC) pools and fluxes is critical for predicting climate, yet approaches for quantifying changes in SOC cycling suffer from deficiencies. We outline opportunities and challenges of employing stable isotopes in short- and longer-term studies to track soil change, using two forests as case studies. Relatively short-term lab studies employing isotopically labeled compounds can help us elucidate mechanisms of SOC stabilization and loss, but added substrate represents a small fraction of the complex suite of compounds in situ and can induce priming effects. By replacing inputs to a soil profile with labeled photosynthate, we can trace realistic substrates through the soil profile, but the time required for the substrate to become incorporated into all soil organic matter (SOM) fractions is longer than most study periods. These pros and cons are exemplified by two studies. First, tracing 13C-labeled photosynthate applied to temperate pine forest soils for ~10 y demonstrated unequal distribution of 13C label among SOC components, but we discerned likely enhanced activity of microorganisms that turnover recalcitrant SOC compounds in forests exposed to elevated CO2. Here, we describe data consistent with this, emanating from laboratory incubations in which 13C labeled, individual compounds were applied to elevated CO2 and control soils. We demonstrate increased fungal and actinomycete activity with elevated CO2. Here, short-term, lab experiments with simple 13C compounds strengthen longer-term in situ studies. We also employed knowledge gained from these studies to assess how warming will alter flows of SOC. Along a climate transect in boreal forests with similar vegetation and soil types, we applied 13C-labeled photosynthate to

  16. Impact of heat and drought stress on arable crop production in Belgium

    NASA Astrophysics Data System (ADS)

    Gobin, A.

    2012-06-01

    Modelling approaches are needed to accelerate understanding of adverse weather impacts on crop performances and yields. The aim was to elicit biometeorological conditions that affect Belgian arable crop yield, commensurate with the scale of climatic impacts. The regional crop model REGCROP (Gobin, 2010) enabled to examine changing weather patterns in relation to the crop season and crop sensitive stages of six arable crops: winter wheat, winter barley, winter rapeseed, potato, sugar beet and maize. The sum of vapour pressure deficit during the growing season is the single best predictor of arable yields, with R2 ranging from 0.55 for sugar beet to 0.76 for wheat. Drought and heat stress, in particular during the sensitive crop stages, occur at different times in the crop season and significantly differ between two climatic periods, 1947-1987 and 1988-2008. Though average yields have risen steadily between 1947 and 2008, there is no evidence that relative tolerance to stress has improved.

  17. Litter input decreased the response of soil organic matter decomposition to warming in two subtropical forest soils

    NASA Astrophysics Data System (ADS)

    Wang, Qingkui; He, Tongxin; Liu, Jing

    2016-09-01

    Interaction effect of temperature and litter input on SOM decomposition is poor understood, restricting accurate prediction of the dynamics and stocks of soil organic carbon under global warming. To address this knowledge gap, we conducted an incubation experiment by adding 13C labeled leaf-litter into a coniferous forest (CF) soil and a broadleaved forest (BF) soil. In this experiment, response of the temperature sensitivity (Q10) of SOM decomposition to the increase in litter input was investigated. The temperature dependences of priming effect (PE) and soil microbial community were analyzed. The Q10 for CF soil significantly decreased from 2.41 in no-litter treatment to 2.05 in litter-added treatment and for BF soil from 2.14 to 1.82, suggesting that litter addition decreases the Q10. PE in the CF soil was 24.9% at 20 °C and 6.2% at 30 °C, and in the BF soil the PE was 8.8% at 20 °C and ‑7.0% at 30 °C, suggesting that PE decreases with increasing temperature. Relative PE was positively related to the concentrations of Gram-negative bacterial and fungal PLFAs. This study moves a step forward in understanding warming effect on forest carbon cycling by highlighting interaction effect of litter input and warming on soil carbon cycling.

  18. Litter input decreased the response of soil organic matter decomposition to warming in two subtropical forest soils

    PubMed Central

    Wang, Qingkui; He, Tongxin; Liu, Jing

    2016-01-01

    Interaction effect of temperature and litter input on SOM decomposition is poor understood, restricting accurate prediction of the dynamics and stocks of soil organic carbon under global warming. To address this knowledge gap, we conducted an incubation experiment by adding 13C labeled leaf-litter into a coniferous forest (CF) soil and a broadleaved forest (BF) soil. In this experiment, response of the temperature sensitivity (Q10) of SOM decomposition to the increase in litter input was investigated. The temperature dependences of priming effect (PE) and soil microbial community were analyzed. The Q10 for CF soil significantly decreased from 2.41 in no-litter treatment to 2.05 in litter-added treatment and for BF soil from 2.14 to 1.82, suggesting that litter addition decreases the Q10. PE in the CF soil was 24.9% at 20 °C and 6.2% at 30 °C, and in the BF soil the PE was 8.8% at 20 °C and −7.0% at 30 °C, suggesting that PE decreases with increasing temperature. Relative PE was positively related to the concentrations of Gram-negative bacterial and fungal PLFAs. This study moves a step forward in understanding warming effect on forest carbon cycling by highlighting interaction effect of litter input and warming on soil carbon cycling. PMID:27644258

  19. Litter input decreased the response of soil organic matter decomposition to warming in two subtropical forest soils.

    PubMed

    Wang, Qingkui; He, Tongxin; Liu, Jing

    2016-09-20

    Interaction effect of temperature and litter input on SOM decomposition is poor understood, restricting accurate prediction of the dynamics and stocks of soil organic carbon under global warming. To address this knowledge gap, we conducted an incubation experiment by adding (13)C labeled leaf-litter into a coniferous forest (CF) soil and a broadleaved forest (BF) soil. In this experiment, response of the temperature sensitivity (Q10) of SOM decomposition to the increase in litter input was investigated. The temperature dependences of priming effect (PE) and soil microbial community were analyzed. The Q10 for CF soil significantly decreased from 2.41 in no-litter treatment to 2.05 in litter-added treatment and for BF soil from 2.14 to 1.82, suggesting that litter addition decreases the Q10. PE in the CF soil was 24.9% at 20 °C and 6.2% at 30 °C, and in the BF soil the PE was 8.8% at 20 °C and -7.0% at 30 °C, suggesting that PE decreases with increasing temperature. Relative PE was positively related to the concentrations of Gram-negative bacterial and fungal PLFAs. This study moves a step forward in understanding warming effect on forest carbon cycling by highlighting interaction effect of litter input and warming on soil carbon cycling.

  20. Labile soil carbon inputs mediate the soil microbial community composition and plant residue decomposition rates

    SciTech Connect

    De Graaff, Marie-Anne; Classen, Aimee T; Castro Gonzalez, Hector F; Schadt, Christopher Warren

    2010-01-01

    Root carbon (C) inputs may regulate decomposition rates in soil, and in this study we ask: how do labile C inputs regulate decomposition of plant residues, and soil microbial communities? In a 14 d laboratory incubation, we added C compounds often found in root exudates in seven different concentrations (0, 0.7, 1.4, 3.6, 7.2, 14.4 and 21.7 mg C g{sup -1} soil) to soils amended with and without {sup 13}C-labeled plant residue. We measured CO{sub 2} respiration and shifts in relative fungal and bacterial rRNA gene copy numbers using quantitative polymerase chain reaction (qPCR). Increased labile C input enhanced total C respiration, but only addition of C at low concentrations (0.7 mg C g{sup -1}) stimulated plant residue decomposition (+2%). Intermediate concentrations (1.4, 3.6 mg C g{sup -1}) had no impact on plant residue decomposition, while greater concentrations of C (> 7.2 mg C g{sup -1}) reduced decomposition (-50%). Concurrently, high exudate concentrations (> 3.6 mg C g{sup -1}) increased fungal and bacterial gene copy numbers, whereas low exudate concentrations (< 3.6 mg C g{sup -1}) increased metabolic activity rather than gene copy numbers. These results underscore that labile soil C inputs can regulate decomposition of more recalcitrant soil C by controlling the activity and relative abundance of fungi and bacteria.

  1. Correspondence of ectomycorrhizal diversity and colonisation of willows (Salix spp.) grown in short rotation coppice on arable sites and adjacent natural stands.

    PubMed

    Hrynkiewicz, Katarzyna; Toljander, Ylva K; Baum, Christel; Fransson, Petra M A; Taylor, Andy F S; Weih, Martin

    2012-11-01

    Willows (Salix spp.) are mycorrhizal tree species sometimes cultivated as short rotation coppice (SRC) on arable sites for energy purposes; they are also among the earliest plants colonising primary successional sites in natural stands. The objective of this study was to analyse the degree of colonisation and diversity of ectomycorrhizal (EM) communities on willows grown as SRC in arable soils and their adjacent natural or naturalized stands. Arable sites usually lack ectomycorrhizal host plants before the establishment of SRC, and adjacent natural or naturalized willow stands were hypothesized to be a leading source of ectomycorrhizal inoculum for the SRC. Three test sites including SRC stands (Salix viminalis, Salix dasyclados, and Salix schwerinii) and adjacent natural or naturalized (Salix caprea, Salix fragilis, and Salix × mollissima) stands in central Sweden were investigated on EM colonisation and morphotypes, and the fungal partners of 36 of the total 49 EM fungi morphotypes were identified using molecular tools. The frequency of mycorrhizas in the natural/naturalized stands was higher (two sites) or lower (one site) than in the corresponding cultivated stands. Correspondence analysis revealed that some EM taxa (e.g. Agaricales) were mostly associated with cultivated willows, while others (e.g. Thelephorales) were mostly found in natural/naturalized stands. In conclusion, we found strong effects of sites and willow genotype on EM fungi formation, but poor correspondence between the EM fungi abundance and diversity in SRC and their adjacent natural/naturalized stands. The underlying mechanism might be selective promotion of some EM fungi species by more effective spore dispersal.

  2. Dynamics of Maize Carbon Contribution to Soil Organic Carbon in Association with Soil Type and Fertility Level

    PubMed Central

    Pei, Jiubo; Li, Hui; Li, Shuangyi; An, Tingting; Farmer, John; Fu, Shifeng; Wang, Jingkuan

    2015-01-01

    Soil type and fertility level influence straw carbon dynamics in the agroecosystems. However, there is a limited understanding of the dynamic processes of straw-derived and soil-derived carbon and the influence of the addition of straw carbon on soil-derived organic carbon in different soils associated with different fertility levels. In this study, we applied the in-situ carborundum tube method and 13C-labeled maize straw (with and without maize straw) at two cropland (Phaeozem and Luvisol soils) experimental sites in northeast China to quantify the dynamics of maize-derived and soil-derived carbon in soils associated with high and low fertility, and to examine how the addition of maize carbon influences soil-derived organic carbon and the interactions of soil type and fertility level with maize-derived and soil-derived carbon. We found that, on average, the contributions of maize-derived carbon to total organic carbon in maize-soil systems during the experimental period were differentiated among low fertility Luvisol (from 62.82% to 42.90), high fertility Luvisol (from 53.15% to 30.00%), low fertility Phaeozem (from 58.69% to 36.29%) and high fertility Phaeozem (from 41.06% to 16.60%). Furthermore, the addition of maize carbon significantly decreased the remaining soil-derived organic carbon in low and high fertility Luvisols and low fertility Phaeozem before two months. However, the increasing differences in soil-derived organic carbon between both soils with and without maize straw after two months suggested that maize-derived carbon was incorporated into soil-derived organic carbon, thereby potentially offsetting the loss of soil-derived organic carbon. These results suggested that Phaeozem and high fertility level soils would fix more maize carbon over time and thus were more beneficial for protecting soil-derived organic carbon from maize carbon decomposition. PMID:25774529

  3. Dynamics of maize carbon contribution to soil organic carbon in association with soil type and fertility level.

    PubMed

    Pei, Jiubo; Li, Hui; Li, Shuangyi; An, Tingting; Farmer, John; Fu, Shifeng; Wang, Jingkuan

    2015-01-01

    Soil type and fertility level influence straw carbon dynamics in the agroecosystems. However, there is a limited understanding of the dynamic processes of straw-derived and soil-derived carbon and the influence of the addition of straw carbon on soil-derived organic carbon in different soils associated with different fertility levels. In this study, we applied the in-situ carborundum tube method and 13C-labeled maize straw (with and without maize straw) at two cropland (Phaeozem and Luvisol soils) experimental sites in northeast China to quantify the dynamics of maize-derived and soil-derived carbon in soils associated with high and low fertility, and to examine how the addition of maize carbon influences soil-derived organic carbon and the interactions of soil type and fertility level with maize-derived and soil-derived carbon. We found that, on average, the contributions of maize-derived carbon to total organic carbon in maize-soil systems during the experimental period were differentiated among low fertility Luvisol (from 62.82% to 42.90), high fertility Luvisol (from 53.15% to 30.00%), low fertility Phaeozem (from 58.69% to 36.29%) and high fertility Phaeozem (from 41.06% to 16.60%). Furthermore, the addition of maize carbon significantly decreased the remaining soil-derived organic carbon in low and high fertility Luvisols and low fertility Phaeozem before two months. However, the increasing differences in soil-derived organic carbon between both soils with and without maize straw after two months suggested that maize-derived carbon was incorporated into soil-derived organic carbon, thereby potentially offsetting the loss of soil-derived organic carbon. These results suggested that Phaeozem and high fertility level soils would fix more maize carbon over time and thus were more beneficial for protecting soil-derived organic carbon from maize carbon decomposition.

  4. Rapid determination of soil quality and earthworm impacts on soil microbial communities using fluorescence-based respirometry

    NASA Astrophysics Data System (ADS)

    Prendergast-Miller, Miranda T.; Thurston, Josh; Taylor, Joe; Helgason, Thorunn; Ashauer, Roman; Hodson, Mark E.

    2017-04-01

    We applied a fluorescence-based respirometry method currently devised for aquatic ecotoxicology studies to rapidly measure soil microbial oxygen consumption as a function of soil quality. In this study, soil was collected from an arable wheat field and the field margin. These two soil habitats are known to differ in their soil quality due to differences in their use and management as well as plant, microbial and earthworm community. The earthworm Lumbricus terrestris was incubated in arable or margin soil for three weeks. After this initial phase, a transfer experiment was then conducted to test the hypothesis that earthworm 'migration' alters soil microbial community function and diversity. In this transfer experiment, earthworms incubated in margin soil were transferred to arable soil. The converse transfer (i.e. earthworms incubated in arable soil) was also conducted. Soils of each type with no earthworms were also incubated as controls. After a further four week incubation, the impact of earthworm migration on the soil microbial community was tested by measuring oxygen consumption. Replicated soil slurry subsamples were aliquoted into individual respirometer wells (600 μl volume) on a glass 24-well microplate (Loligo Systems, Denmark) fitted with non-invasive, reusable oxygen sensor spots. The sealed microplate was then attached to an oxygen fluorescence sensor (SDR SensorDish Reader, PreSens, Germany). Oxygen consumption was measured in real-time over a 2 hr period following standard operating procedures. Soil microbial activity was measured with and without an added carbon source (glucose or cellulose, 50 mg C L-1). Using this system, we were able to differentiate between soil type, earthworm treatment and C source. Earthworm-driven impacts on soil microbial oxygen consumption were also supported by changes in soil microbial community structure and diversity revealed using DNA-based sequencing techniques. This method provides a simple and rapid system for

  5. Biodegradability of a polyacrylate superabsorbent in agricultural soil.

    PubMed

    Wilske, Burkhard; Bai, Mo; Lindenstruth, Beate; Bach, Martin; Rezaie, Zahra; Frede, Hans-Georg; Breuer, Lutz

    2014-01-01

    Superabsorbent polymers (SAP) are used, inter alia, as soil amendment to increase the water holding capacity of soils. Biodegradability of soil conditioners has become a desired key characteristic to protect soil and groundwater resources. The present study characterized the biodegradability of one acrylate based SAP in four agricultural soils and at three temperatures. Mineralisation was measured as the (13)CO₂ efflux from (13)C-labelled SAP in soil incubations. The SAP was either single-labelled in the carboxyl C-atom or triple-labelled including additionally the two C-atoms interlinked in the SAP backbone. The dual labelling allowed estimating the degradation of the polyacrylate main chain. The (13)CO₂ efflux from samples was measured using an automated system including wavelength-scanned cavity ring-down spectroscopy. Based on single-labelled SAP, the mean degradation after 24 weeks varied between 0.45% in loamy sand and 0.82% in loam. However, the differences between degradation rates in different soils were not significant due to a large intra-replicate variability. Similarly, mean degradation did not differ significantly between effective temperature regimes of 20° and 30 °C after 12 weeks. Results from the triple-labelled SAP were lower as compared to their single-labelled variant. Detailed results suggest that the polyacrylate main chain degraded in the soils, if at all, at rates of 0.12-0.24 % per 6 months.

  6. The capacity of soil particles for spontaneous formation of macroaggregates after a wetting-drying cycle

    NASA Astrophysics Data System (ADS)

    Kholodov, V. A.

    2013-06-01

    The capacity of soil particles for spontaneous formation of aggregates >0.25 mm was studied in a laboratory experiment. The particles from soil aggregates (3-1 mm) (initially aggregated particles, APs) and initially free particles (FPs) of <0.25 mm in size were isolated from the soddy-podzolic and chernozemic soils under fallow and from the arable soddy-podzolic soil. The aggregates of 3-1 mm were ground and passed through a 0.25-mm sieve. Then, the aggregates and free particles were poured with water and dried, and the content of the formed aggregates and their water stability were determined; in the samples from the arable soddy-podzolic soil, the organic carbon content was also determined in the newly formed aggregates. The FPs from the untilled soils formed almost no aggregates. At the same time, the APs from these soils manifested the ability for the spontaneous formation of aggregates, including water-stable aggregates. In the arable soddy-podzolic soil, on the contrary, both FPs and APs demonstrated the capacity for spontaneous self-organization into aggregates. The water stability of the self-organized aggregates from the arable soil was similar regardless of their source (APs or FPs). It was supposed that the ability of the FPs from the arable soil to form macroaggregates reflects the mechanical degradation of the aggregates in the soil: tillage results in the degradation of the aggregates, and the particles capable of spontaneously aggregation temporarily fall in the fraction of <0.25 mm. The water-stable aggregates produced from the APs or FPs of the arable soil contained more organic carbon (1.89%) in comparison with the water-stable aggregates separated from the initial 3- to 1-mm aggregates of this soil (1.31%).

  7. Effects of fungicides mancozeb and dinocap on carbon and nitrogen mineralization in soils.

    PubMed

    Cernohlávková, Jitka; Jarkovský, Jirí; Hofman, Jakub

    2009-01-01

    In our study, effects of fungicides mancozeb and dinocap on C and N mineralization were measured in arable and grassland soil. The soils were treated with these fungicides at the application and 10 times lower doses and then incubated at 20 degrees C for 2 weeks. Carbon mineralization (basal and substrate-induced respiration) and nitrogen mineralization (potential ammonification and nitrification) were evaluated 1 and 14 days after the treatment. After 14 days, ammonification was decreased to 48% and 83% at dinocap application dose in arable and grassland soil, respectively. Application dose of mancozeb caused significant decrease of nitrification to 11.2% and 5.6% in arable and grassland soil, respectively. Basal respiration and substrate-induced growth were rather stimulated by fungicides, especially at lower application doses. To conclude, potential risk may exist to soil microorganisms and their activities in soils treated routinely by mancozeb or dinocap.

  8. Decadally cycling soil carbon is more sensitive to warming than faster-cycling soil carbon.

    PubMed

    Lin, Junjie; Zhu, Biao; Cheng, Weixin

    2015-12-01

    The response of soil organic carbon (SOC) pools to globally rising surface temperature crucially determines the feedback between climate change and the global carbon cycle. However, there is a lack of studies investigating the temperature sensitivity of decomposition for decadally cycling SOC which is the main component of total soil carbon stock and the most relevant to global change. We tackled this issue using two decadally (13) C-labeled soils and a much improved measuring system in a long-term incubation experiment. Results indicated that the temperature sensitivity of decomposition for decadally cycling SOC (>23 years in one soil and >55 years in the other soil) was significantly greater than that for faster-cycling SOC (<23 or 55 years) or for the entire SOC stock. Moreover, decadally cycling SOC contributed substantially (35-59%) to the total CO2 loss during the 360-day incubation. Overall, these results indicate that the decomposition of decadally cycling SOC is highly sensitive to temperature change, which will likely make this large SOC stock vulnerable to loss by global warming in the 21st century and beyond.

  9. Soils

    Treesearch

    John R. Jones; Norbert V. DeByle

    1985-01-01

    Edaphic and climatic characteristics of a site quite well define the quality of that site for plant growth. The importance of soil characteristics to the growth and well-being of aspen in the West is apparent from observations by many authors, from inferences resulting from work with other trees and agricultural crops, and from detailed study of aspen soils and site...

  10. Subsoil carbon accumulation on an arable Mollisol is retention dominated, in contrast to input driven carbon dynamics in topsoil

    NASA Astrophysics Data System (ADS)

    Beem-Miller, Jeffrey; Lehmann, Johannes

    2017-04-01

    The majority of the world's soil organic carbon (OC) stock is stored below 30 cm in depth, yet sampling for soil OC assessment rarely goes below 30 cm. Recent studies suggest that subsoil OC is distinct from topsoil OC in quantity and quality: subsoil OC concentrations are typically much lower and turnover times are much longer, but the mechanisms involved in retention and input of OC to the subsoil are not well understood. Improving our understanding of subsoil OC is essential for balancing the global carbon budget and confronting the challenge of global climate change. This study was undertaken to assess the relationship between OC stock and potential drivers of OC dynamics, including both soil properties and environmental covariates, in topsoil (0 to 30 cm) versus subsoil (30 to 75 cm). The performance of commonly used depth functions in predicting OC stock from 0 to 75 cm was also assessed. Depth functions are a useful tool for extrapolating OC stock below the depth of sampling, but may poorly model "hot spots" of OC accumulation, and be inadequate for modelling the distinct dynamics of topsoil and subsoil OC when applied with a single functional form. We collected two hundred soil cores on an arable Mollisol, sectioned into five depth increments (0-10, 10-20, 20-30, 30-50, and 50-75 cm), and performed the following analyses on each depth increment: concentration of OC, inorganic C, permanganate oxidizable carbon (POXC), and total N, as well as texture, pH, and bulk density; a digital elevation model was used to calculate elevation, slope, curvature, and soil topographic wetness index. We found that topsoil OC stocks were significantly correlated (p < 0.05) with terrain variables, texture, and pH, while subsoil OC stock was only significantly correlated with topsoil OC stock and soil pH. Total OC stock was highly spatially variable, and the relationship between surface soil properties, terrain variables, and subsoil OC stock was spatially variable as well. Hot

  11. Interactions among roots, mycorrhizas and free-living microbial communities differentially impact soil carbon processes

    DOE PAGES

    Moore, Jessica A. M.; Jiang, Jiang; Patterson, Courtney M.; ...

    2015-10-20

    Plant roots, their associated microbial community and free-living soil microbes interact to regulate the movement of carbon from the soil to the atmosphere, one of the most important and least understood fluxes of terrestrial carbon. Our inadequate understanding of how plant-microbial interactions alter soil carbon decomposition may lead to poor model predictions of terrestrial carbon feedbacks to the atmosphere. Roots, mycorrhizal fungi and free-living soil microbes can alter soil carbon decomposition through exudation of carbon into soil. Exudates of simple carbon compounds can increase microbial activity because microbes are typically carbon limited. When both roots and mycorrhizal fungi are presentmore » in the soil, they may additively increase carbon decomposition. However, when mycorrhizas are isolated from roots, they may limit soil carbon decomposition by competing with free-living decomposers for resources. We manipulated the access of roots and mycorrhizal fungi to soil insitu in a temperate mixed deciduous forest. We added 13C-labelled substrate to trace metabolized carbon in respiration and measured carbon-degrading microbial extracellular enzyme activity and soil carbon pools. We used our data in a mechanistic soil carbon decomposition model to simulate and compare the effects of root and mycorrhizal fungal presence on soil carbon dynamics over longer time periods. Contrary to what we predicted, root and mycorrhizal biomass did not interact to additively increase microbial activity and soil carbon degradation. The metabolism of 13C-labelled starch was highest when root biomass was high and mycorrhizal biomass was low. These results suggest that mycorrhizas may negatively interact with the free-living microbial community to influence soil carbon dynamics, a hypothesis supported by our enzyme results. Our steady-state model simulations suggested that root presence increased mineral-associated and particulate organic carbon pools, while mycorrhizal

  12. Comparison of energetic productivity in differently renaturalized arable land

    NASA Astrophysics Data System (ADS)

    Kazlauskaite-Jadzevice, Asta; Marcinkonis, Saulius; Baksiene, Eugenija

    2014-05-01

    Soil renaturalization or ecological recovery has been studied from local to global scales. On a global scale - it's one of the ways of carbon fixation, preservation of natural diversity, locally - renaturalization processes help to solve problems of damaged (eroded and polluted) and infertile soils areas. Efficient land use can improve soil structure and therefore be attractive as a renewable energy resource that can encourage thermal energy, fuel production and installation of new technologies. Soil renaturalization is very important not only in that it helps to decrease the impact on the environment, but it can produce higher energy value of biomass at a lower cost. The aim of this study is to evaluate and compare different renaturalization methods through analyzing biomass yields and chemical composition (pine afforested, fallowing, manage grassland - Alfalfa and cropland) carried out during almost two decades (1995 - 2012). The four stationary experimental sites were set up in 1995 in Vilnius district, Lithuania. Common sandy soils prevail in the region, and the agronomic value of soil is very low. All sites were arranged in one row (the divided sides is 400 m2 each). Managed grassland and cropland areas were subdivided into fertilized and unfertilized subplots. The size of the subdivided plots was 200 m2 each. Gross productions (straw, grain, hay, pine biomass) was recalculated into total energy amount (in the calculationswere used K. Neringa and R. Siman equation) expressed in MJ and the site's productivity data compared. Gross productions total energy amount of pine afforestration was recalculated into trees volume using diameter (DBH), height and density of pines. Observed data suggest that the difference between fertilized and unfertilized plots in the cropland site was on average 1.62 times and made up an average of 20 339 MJ y-1 ha-1. The grassland site was characterized by higher productivity and a bigger difference of total energy between fertilized

  13. Synthesis and incorporation of 13C-labeled DNA building blocks to probe structural dynamics of DNA by NMR

    PubMed Central

    Nußbaumer, Felix; Juen, Michael Andreas; Gasser, Catherina; Kremser, Johannes; Müller, Thomas; Tollinger, Martin

    2017-01-01

    Abstract We report the synthesis of atom-specifically 13C-modified building blocks that can be incorporated into DNA via solid phase synthesis to facilitate investigations on structural and dynamic features via NMR spectroscopy. In detail, 6-13C-modified pyrimidine and 8-13C purine DNA phosphoramidites were synthesized and incorporated into a polypurine tract DNA/RNA hybrid duplex to showcase the facile resonance assignment using site-specific labeling. We also addressed micro- to millisecond dynamics in the mini-cTAR DNA. This DNA is involved in the HIV replication cycle and our data points toward an exchange process in the lower stem of the hairpin that is up-regulated in the presence of the HIV-1 nucleocapsid protein 7. As another example, we picked a G-quadruplex that was earlier shown to exist in two folds. Using site-specific 8-13C-2′deoxyguanosine labeling we were able to verify the slow exchange between the two forms on the chemical shift time scale. In a real-time NMR experiment the re-equilibration of the fold distribution after a T-jump could be monitored yielding a rate of 0.012 min−1. Finally, we used 13C-ZZ-exchange spectroscopy to characterize the kinetics between two stacked X-conformers of a Holliday junction mimic. At 25°C, the refolding process was found to occur at a forward rate constant of 3.1 s−1 and with a backward rate constant of 10.6 s−1.

  14. Fate of xylem-transported 11C- and 13C-labeled CO2 in leaves of poplar.

    PubMed

    Bloemen, Jasper; Bauweraerts, Ingvar; De Vos, Filip; Vanhove, Christian; Vandenberghe, Stefaan; Boeckx, Pascal; Steppe, Kathy

    2015-04-01

    In recent studies, assimilation of xylem-transported CO2 has gained considerable attention as a means of recycling respired CO2 in trees. However, we still lack a clear and detailed picture on the magnitude of xylem-transported CO2 assimilation, in particular within leaf tissues. To this end, detached poplar leaves (Populus × canadensis Moench 'Robusta') were allowed to take up a dissolved (13)CO2 label serving as a proxy of xylem-transported CO2 entering the leaf from the branch. The uptake rate of the (13)C was manipulated by altering the vapor pressure deficit (VPD) (0.84, 1.29 and 1.83 kPa). Highest tissue enrichments were observed under the highest VPD. Among tissues, highest enrichment was observed in the petiole and the veins, regardless of the VPD treatment. Analysis of non-labeled leaves showed that some (13)C diffused from the labeled leaves and was fixed in the mesophyll of the non-labeled leaves. However, (13)C leaf tissue enrichment analysis with elemental analysis coupled to isotope ratio mass spectrometry was limited in spatial resolution at the leaf tissue level. Therefore, (11)C-based CO2 labeling combined with positron autoradiography was used and showed a more detailed spatial distribution within a single tissue, in particular in secondary veins. Therefore, in addition to (13)C, (11) C-based autoradiography can be used to study the fate of xylem-transported CO2 at leaf level, allowing the acquisition of data at a yet unprecedented resolution.

  15. Human lactation: oxidation and maternal transfer of dietary (13)C-labelled α-linolenic acid into human milk.

    PubMed

    Demmelmair, Hans; Kuhn, Angelika; Dokoupil, Katharina; Hegele, Verena; Sauerwald, Thorsten; Koletzko, Berthold

    2016-06-01

    The origin of fatty acids in milk has not been elucidated in detail. We investigated the contribution of dietary α-linolenic acid (ALA) to human milk fat, its oxidation and endogenous conversion to long-chain polyunsaturated fatty acids. Ten lactating women were given (13)C-ALA orally, and breath and milk samples were collected for a five-day period, while dietary intakes were assessed. 37.5 ± 2.7 % (M ± SE) of the tracer was recovered in breath-CO2, and 7.3 ± 1.1 % was directly transferred into milk. About 0.25 % of the tracer was found in milk long-chain polyunsaturated fatty acids. Combining intake and milk data, we estimate that about 65 % of milk ALA is directly derived from maternal diet. Thus, the major portion of milk ALA is directly derived from the diet, but dietary ALA does not seem to contribute much as a precursor to milk n-3 long-chain polyunsaturated fatty acids within the studied time period.

  16. Accurate determinations of one-bond 13C-13C couplings in 13C-labeled carbohydrates

    NASA Astrophysics Data System (ADS)

    Azurmendi, Hugo F.; Freedberg, Darón I.

    2013-03-01

    Carbon plays a central role in the molecular architecture of carbohydrates, yet the availability of accurate methods for 1DCC determination has not been sufficiently explored, despite the importance that such data could play in structural studies of oligo- and polysaccharides. Existing methods require fitting intensity ratios of cross- to diagonal-peaks as a function of the constant-time (CT) in CT-COSY experiments, while other methods utilize measurement of peak separation. The former strategies suffer from complications due to peak overlap, primarily in regions close to the diagonal, while the latter strategies are negatively impacted by the common occurrence of strong coupling in sugars, which requires a reliable assessment of their influence in the context of RDC determination. We detail a 13C-13C CT-COSY method that combines a variation in the CT processed with diagonal filtering to yield 1JCC and RDCs. The strategy, which relies solely on cross-peak intensity modulation, is inspired in the cross-peak nulling method used for JHH determinations, but adapted and extended to applications where, like in sugars, large one-bond 13C-13C couplings coexist with relatively small long-range couplings. Because diagonal peaks are not utilized, overlap problems are greatly alleviated. Thus, one-bond couplings can be determined from different cross-peaks as either active or passive coupling. This results in increased accuracy when more than one determination is available, and in more opportunities to measure a specific coupling in the presence of severe overlap. In addition, we evaluate the influence of strong couplings on the determination of RDCs by computer simulations. We show that individual scalar couplings are notably affected by the presence of strong couplings but, at least for the simple cases studied, the obtained RDC values for use in structural calculations were not, because the errors introduced by strong couplings for the isotropic and oriented phases are very similar and therefore cancel when calculating the difference to determine 1DCC values.

  17. Quantification of peptide m/z distributions from 13C-labeled cultures with high-resolution mass spectrometry.

    PubMed

    Allen, Doug K; Goldford, Joshua; Gierse, James K; Mandy, Dominic; Diepenbrock, Christine; Libourel, Igor G L

    2014-02-04

    Isotopic labeling studies of primary metabolism frequently utilize GC/MS to quantify (13)C in protein-hydrolyzed amino acids. During processing some amino acids are degraded, which reduces the size of the measurement set. The advent of high-resolution mass spectrometers provides a tool to assess molecular masses of peptides with great precision and accuracy and computationally infer information about labeling in amino acids. Amino acids that are isotopically labeled during metabolism result in labeled peptides that contain spatial and temporal information that is associated with the biosynthetic origin of the protein. The quantification of isotopic labeling in peptides can therefore provide an assessment of amino acid metabolism that is specific to subcellular, cellular, or temporal conditions. A high-resolution orbital trap was used to quantify isotope labeling in peptides that were obtained from unlabeled and isotopically labeled soybean embryos and Escherichia coli cultures. Standard deviations were determined by estimating the multinomial variance associated with each element of the m/z distribution. Using the estimated variance, quantification of the m/z distribution across multiple scans was achieved by a nonlinear fitting approach. Observed m/z distributions of uniformly labeled E. coli peptides indicated no significant differences between observed and simulated m/z distributions. Alternatively, amino acid m/z distributions obtained from GC/MS were convolved to simulate peptide m/z distributions but resulted in distinct profiles due to the production of protein prior to isotopic labeling. The results indicate that peptide mass isotopologue measurements faithfully represent mass distributions, are suitable for quantification of isotope-labeling-based studies, and provide additional information over existing methods.

  18. Structure of uniaxially aligned 13C labeled silk fibroin fibers with solid state 13C-NMR

    NASA Astrophysics Data System (ADS)

    Demura, Makoto; Yamazaki, Yasunobu; Asakura, Tetsuo; Ogawa, Katsuaki

    1998-01-01

    Carbon-13 isotopic labeling of B. mori silk fibroin was achieved biosynthetically with [1- 13C] glycine in order to determine the carbonyl bond orientation angle of glycine sites with the silk fibroin. Angular dependence of 13C solid state NMR spectra of uniaxially oriented silk fibroin fiber block sample due to the carbonyl 13C chemical shift anisotropy was simulated according to the chemical shift transformation with Euler angles, αF and βF, from principal axis system (PAS) to fiber axis system (FAS). The another Euler angles, αDCO and βDCO, for transformation from PAS to the molecular symmetry axis were determined from the [1- 13C] glycine sequence model compounds for the silk fibroin. By the combination of these Euler angles, the carbonyl bond orientation angle with respect to FAS of the [1- 13C] glycine sites of the silk fibroin was determined to be 90 ± 5°. This value is in agreement with the X-ray diffraction and our previous solid state NMR data of B. mori silk fibroin fiber (a typical β-pleated sheet) within experimental error.

  19. Metabolomic profiling of 13C-labelled cellulose digestion in a lower termite: insights into gut symbiont function

    PubMed Central

    Tokuda, Gaku; Tsuboi, Yuuri; Kihara, Kumiko; Saitou, Seikou; Moriya, Sigeharu; Lo, Nathan; Kikuchi, Jun

    2014-01-01

    Termites consume an estimated 3–7 billion tonnes of lignocellulose annually, a role in nature which is unique for a single order of invertebrates. Their food is digested with the help of microbial symbionts, a relationship that has been recognized for 200 years and actively researched for at least a century. Although DNA- and RNA-based approaches have greatly refined the details of the process and the identities of the participants, the allocation of roles in space and time remains unclear. To resolve this issue, a pioneer study is reported using metabolomics to chart the in situ catabolism of 13C-cellulose fed to the dampwood species Hodotermopsis sjostedti. The results confirm that the secretion of endogenous cellulases by the host may be significant to the digestive process and indicate that a major contribution by hindgut bacteria is phosphorolysis of cellodextrins or cellobiose. This study provides evidence that essential amino acid acquisition by termites occurs following the lysis of microbial tissue obtained via proctodaeal trophallaxis. PMID:25009054

  20. Reduced mitochondrial malate dehydrogenase activity has a strong effect on photorespiratory metabolism as revealed by 13C labelling

    PubMed Central

    Lindén, Pernilla; Keech, Olivier; Stenlund, Hans; Gardeström, Per; Moritz, Thomas

    2016-01-01

    Mitochondrial malate dehydrogenase (mMDH) catalyses the interconversion of malate and oxaloacetate (OAA) in the tricarboxylic acid (TCA) cycle. Its activity is important for redox control of the mitochondrial matrix, through which it may participate in regulation of TCA cycle turnover. In Arabidopsis, there are two isoforms of mMDH. Here, we investigated to which extent the lack of the major isoform, mMDH1 accounting for about 60% of the activity, affected leaf metabolism. In air, rosettes of mmdh1 plants were only slightly smaller than wild type plants although the fresh weight was decreased by about 50%. In low CO2 the difference was much bigger, with mutant plants accumulating only 14% of fresh weight as compared to wild type. To investigate the metabolic background to the differences in growth, we developed a 13CO2 labelling method, using a custom-built chamber that enabled simultaneous treatment of sets of plants under controlled conditions. The metabolic profiles were analysed by gas- and liquid- chromatography coupled to mass spectrometry to investigate the metabolic adjustments between wild type and mmdh1. The genotypes responded similarly to high CO2 treatment both with respect to metabolite pools and 13C incorporation during a 2-h treatment. However, under low CO2 several metabolites differed between the two genotypes and, interestingly most of these were closely associated with photorespiration. We found that while the glycine/serine ratio increased, a concomitant altered glutamine/glutamate/α-ketoglutarate relation occurred. Taken together, our results indicate that adequate mMDH activity is essential to shuttle reductants out from the mitochondria to support the photorespiratory flux, and strengthen the idea that photorespiration is tightly intertwined with peripheral metabolic reactions. PMID:26889011

  1. Evidence of the photosynthetic origin of monoterpenes emitted by quercus ilex L. leaves by {sup 13}C labeling

    SciTech Connect

    Loreto, F.; Ciccioli, P.; Cecinato, A.; Brancaleoni, E. |

    1996-04-01

    The carbon of the four main monoterpenes emitted by Quercus ilex L. leaves was completely labeled with {sup 13}C after a 20-min feeding with 99% {sup 13}CO{sub 2}. This labeling time course is comparable with the labeling time course of isoprene, the terpenoid emitted by other Quercus species and synthesized in leaf chloroplasts. It is also comparable with that of phosphoglyceric acid. Our experiment therefore provides evidence that monoterpenes emitted by Q. ilex are formed photosynthesis intermediates and may share the same synthetic pathway with isoprene. By analyzing the rate and the distribution of labeling in the different fragments, we looked for evidence of differential carbon labeling in the {alpha}-pinene emitted. However, the labeling pattern was quite uniform in the different fragments, suggesting that the carbon skeleton of the emitted monoterpenes comes from a unique carbon source. 16 refs., 3 figs., 1 tab.

  2. Spatially tracking 13C labeled substrate (bicarbonate) accumulation in microbial communities using laser ablation isotope ratio mass spectrometry

    SciTech Connect

    Moran, James J.; Doll, Charles G.; Bernstein, Hans C.; Renslow, Ryan S.; Cory, Alexandra B.; Hutchison, Janine R.; Lindemann, Stephen R.; Fredrickson, Jim K.

    2014-08-25

    This is a manuscript we would like to submit for publication in Environmental Microbiology Reports. This manuscript contains a description of a laser ablation isotope ratio mass spectrometry methodology developed at PNNL and applied to a microbial system at a PNNL project location – Hot Lake, Washington. I will submit a word document containing the entire manuscript with this Erica input request form.

  3. The interactions with solvent, heat stability, and 13C-labelling of alamethicin, an ion-channel-forming peptide.

    PubMed

    Yee, A A; Marat, K; O'Neil, J D

    1997-01-15

    The peptide alamethicin was labelled with 13C and 15N by growing the fungus Trichoderma viride in a medium containing [U-13C] glucose and K15NO3. Spin-echo difference spectroscopy showed that 13C was incorporated to a level of about 50% and 15N to about 98%. Incorporation of 13C into the peptide provided residue-specific probes of the interactions with solvent and heat stability of this ion-channel-forming peptide. All of the carbonyl carbons and the alpha-carbons of the alpha-aminoisobutyric acid [Ala(Me)] residues of alamethicin in methanol were assigned using two-dimensional and three-dimensional heteronuclear correlation experiments. Measurements of 1JC'N revealed hydrogen bonding with solvent at residues 1 and 19 at the ends of the peptide and at Gly11 in the middle. The data also support the thesis [see Juranic, N., Ilich, P. K. & Macara, S. (1995) J. Am. Chem. Soc. 117, 405-410 that intramolecular hydrogen bonds in proteins and peptides are weaker than hydrogen bonds to solvent. The sensitivity of alamethicin carbonyl and proton chemical shifts to perturbation by dimethyl sulfoxide correlates well with the calculated solvent accessibilities of the carbonyls in the crystal structures and reveals residues in the middle of the peptide and at the C-terminus which interact with solvent. Taken together with the 1JC'N measurements, the data support a model in which hydrogen bonding to solvent at the Gly11/Leu12 amide could provide a site of hydration in the interior of the alamethicin channel structure. The temperature dependencies of the carbonyl chemical shifts support the suggestion that the peptide is flexible in the regions where solvent interacts with the backbone of the peptide. The linear temperature dependence of the carbonyl chemical shifts and molar ellipticity indicate that, due to steric constraints at the Ala(Me) residues, the peptide folding/unfolding transition is non-cooperative and that the peptide is remarkably heat stable.

  4. Vitamin K absorption and kinetics in human subjects after consumption of 13C-labelled phylloquinone from kale.

    PubMed

    Novotny, Janet A; Kurilich, Anne C; Britz, Steven J; Baer, David J; Clevidence, Beverly A

    2010-09-01

    The absorption and plasma disappearance of vitamin K were investigated by uniformly labelling phylloquinone in kale with carbon-13, and by feeding the kale to study subjects. Seven healthy volunteers ingested a single 400 g serving of kale with 30 g vegetable oil. The kale provided 156 nmol of phylloquinone. Serial plasma samples were collected and analysed for the appearance of 13C-phylloquinone by HPLC-MS. Six of the subjects showed significant amounts of labelled phylloquinone in plasma, though one subject's plasma was not consistently enriched above the detection limit, and this subject's baseline plasma phylloquinone level was the lowest in the group. After ingestion of the labelled kale, plasma 13C-phylloquinone concentration increased rapidly to a peak between 6 and 10 h, and then rapidly decreased. Average peak plasma concentration for the six subjects with detectable 13C-phylloquinone was 2.1 nmol/l. Plasma concentration-time data were analysed by compartmental modelling. Modelling results demonstrated a mean (n 6) bioavailability of phylloquinone from kale to be 4.7%. Plasma and tissue half-times for phylloquinone were found to be 8.8 and 215 h, respectively.

  5. Bioconversion of (13)C-labeled microalgal phytosterols to cholesterol by the Northern Bay scallop, Argopecten irradians irradians.

    PubMed

    Giner, José-Luis; Zhao, Hui; Dixon, Mark S; Wikfors, Gary H

    2016-02-01

    Bivalve mollusks lack de novo cholesterol biosynthesis capabilities and therefore rely upon dietary sources of sterols for rapid growth. Microalgae that constitute the main source of nutrition for suspension-feeding bivalves contain a diverse array of phytosterols, in most cases lacking cholesterol. Rapid growth of bivalves on microalgal diets with no cholesterol implies that some phytosterols can satisfy the dietary requirement for cholesterol through metabolic conversion to cholesterol, but such metabolic pathways have not been rigorously demonstrated. In the present study, stable isotope-labeled phytosterols were used to supplement a unialgal diet of Rhodomonas sp. and their biological transformation to cholesterol within scallop tissues was determined using (13)C-NMR spectroscopy. Scallops efficiently dealkylated ∆(5) C29 (24-ethyl) sterols to cholesterol, and the only C28 sterol that was dealkylated efficiently possessed the 24(28)-double bond. Non-metabolized dietary phytosterols accumulated in the soft tissues. Observed formation of ∆(5,7) sterols (provitamin D) from ∆(5) sterols may represent initiation of steroid hormone (possibly ecdysone) biosynthesis. These findings provide a key component necessary for formulation of nutritionally complete microalgal diets for hatchery production of seed for molluscan aquaculture.

  6. Deuteration of Hyperpolarized (13) C-Labeled Zymonic Acid Enables Sensitivity-Enhanced Dynamic MRI of pH.

    PubMed

    Hundshammer, Christian; Düwel, Stephan; Köcher, Simone S; Gersch, Malte; Feuerecker, Benedikt; Scheurer, Christoph; Haase, Axel; Glaser, Steffen J; Schwaiger, Markus; Schilling, Franz

    2017-09-20

    Aberrant pH is characteristic of many pathologies such as ischemia, inflammation or cancer. Therefore, a non-invasive and spatially resolved pH determination is valuable for disease diagnosis, characterization of response to treatment and the design of pH-sensitive drug-delivery systems. We recently introduced hyperpolarized [1,5-(13) C2 ]zymonic acid (ZA) as a novel MRI probe of extracellular pH utilizing dissolution dynamic polarization (DNP) for a more than 10000-fold signal enhancement of the MRI signal. Here we present a strategy to enhance the sensitivity of this approach by deuteration of ZA yielding [1,5-(13) C2 , 3,6,6,6-D4 ]zymonic acid (ZAd ), which prolongs the liquid state spin lattice relaxation time (T1 ) by up to 39 % in vitro. Measurements with ZA and ZAd on subcutaneous MAT B III adenocarcinoma in rats show that deuteration increases the signal-to-noise ratio (SNR) by up to 46 % in vivo. Furthermore, we demonstrate a proof of concept for real-time imaging of dynamic pH changes in vitro using ZAd , potentially allowing for the characterization of rapid acidification/basification processes in vivo. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Monitoring CO[subscript 2] Fixation Using GC-MS Detection of a [superscript 13]C-Label

    ERIC Educational Resources Information Center

    Hammond, Daniel G.; Bridgham, April; Reichert, Kara; Magers, Martin

    2010-01-01

    Much of our understanding of metabolic pathways has resulted from the use of chemical and isotopic labels. In this experiment, a heavy isotope of carbon, [superscript 13]C, is used to label the product of the well-known RuBisCO enzymatic reaction. This is a key reaction in photosynthesis that converts inorganic carbon to organic carbon; a process…

  8. Assimilation of xylem-transported 13C-labelled CO2 in leaves and branches of sycamore (Platanus occidentalis L.).

    PubMed

    McGuire, M A; Marshall, J D; Teskey, R O

    2009-01-01

    Previous reports have shown that CO(2) dissolved in xylem sap in tree stems can move upward in the transpiration stream. To determine the fate of this dissolved CO(2), the internal transport of respired CO(2) at high concentration from the bole of the tree was simulated by allowing detached young branches of sycamore (Platanus occidentalis L.) to transpire water enriched with a known quantity of (13)CO(2) in sunlight. Simultaneously, leaf net photosynthesis and CO(2) efflux from woody tissue were measured. Branch and leaf tissues were subsequently analysed for (13)C content to determine the quantity of transported (13)CO(2) label that was fixed. Treatment branches assimilated an average of 35% (SE=2.4) of the (13)CO(2) label taken up in the treatment water. The majority was fixed in the woody tissue of the branches, with smaller amounts fixed in the leaves and petioles. Overall, the fixation of internally transported (13)CO(2) label by woody tissues averaged 6% of the assimilation of CO(2) from the atmosphere by the leaves. Woody tissue assimilation rates calculated from measurements of (13)C differed from rates calculated from measurements of CO(2) efflux in the lower branch but not in the upper branch. The results of this study showed unequivocally that CO(2) transported in xylem sap can be fixed in photosynthetic cells in the leaves and branches of sycamore trees and provided evidence that recycling of xylem-transported CO(2) may be an important means by which trees reduce the carbon cost of respiration.

  9. Monitoring CO[subscript 2] Fixation Using GC-MS Detection of a [superscript 13]C-Label

    ERIC Educational Resources Information Center

    Hammond, Daniel G.; Bridgham, April; Reichert, Kara; Magers, Martin

    2010-01-01

    Much of our understanding of metabolic pathways has resulted from the use of chemical and isotopic labels. In this experiment, a heavy isotope of carbon, [superscript 13]C, is used to label the product of the well-known RuBisCO enzymatic reaction. This is a key reaction in photosynthesis that converts inorganic carbon to organic carbon; a process…

  10. Fungal carbon sources in a pine forest: evidence from a 13C-labeled global change experiment

    Treesearch

    Erik A. Hobbie; Kirsten S. Hofmockel; Linda T.A. Van Diepen; Erik A. Lilleskov; Andrew P. Oiumette; Adrien C. Finzi

    2014-01-01

    We used natural abundance 13C:12C (δ13C) and 8 yr of labeling with 13C-depleted CO2 in a Pinus taeda Free Air CO2 Enrichment (FACE) experiment to investigate carbon sources of saprotrophic fungi, ectomycorrhizal...

  11. Vitamin K absorption and kinetics in human subjects after consumption of 13C-labeled phylloquinone from kale

    USDA-ARS?s Scientific Manuscript database

    The absorption and plasma elimination of vitamin K was investigated by uniformly labeling phylloquinone in kale with carbon-13 and feeding the kale to study subjects. Seven healthy volunteers ingested a single 400 g serving of kale with 30 g vegetable oil. The kale provided 156 nmol of phylloquino...

  12. Quantification of peptide m/z distributions from 13C-labeled cultures with high resolution mass spectrometry

    USDA-ARS?s Scientific Manuscript database

    With the introduction of orbital trap mass spectrometers molecular masses can be determined with great precision and accuracy. In addition, orbital trap spectrometers (Orbitraps) are sensitive and possess a linear dynamic range of multiple orders of magnitude. These qualities make the Orbitrap well-...

  13. Weak coupling between magnetically inequivalent spins: The deceptively simple, complicated spectrum of a 13C-labeled trimethylated amine

    NASA Astrophysics Data System (ADS)

    le Paige, Ulric B.; Smits, Bauke; 't Hart, Peter; Lefeber, Fons; Martin, Nathaniel I.; van Ingen, Hugo

    2017-05-01

    Magnetic inequivalence of nuclear spins is well known to cause additional splittings that complicate spectral analysis. Here, we present an extraordinary case of magnetic inequivalence, manifested in the 13-spin system of a 13C,15N-labeled trimethylated amine. All methyl group protons are chemically equivalent due to the molecular symmetry, but not all are magnetically equivalent as they have different 1JCH and 3JCH couplings. In general, spectra of such a large spin system can be expected to be extremely complicated by the presence of hundreds if not thousands of extra lines, caused by the strong coupling between inequivalent nuclei. Surprisingly, the 1H spectrum presented consists of very few lines, in a pattern of the utmost simplicity. Using sub-spectral analysis we show that this is due to weak coupling between the magnetically inequivalent nuclei, as a consequence of the particular combination of coupling constants. We find that the 4JHH geminal methyl coupling constant is 0.43 Hz and 2JCC is ∼0 Hz. In addition, we demonstrate that homo-decoupling can be used to transform the spin system to a set of fully equivalent spins, resulting in disappearance of 4JHH-splittings. We believe this curious case is a highly instructive example of magnetic inequivalence. The spectra may be considered deceptively simple, as fewer lines are observed than one would anticipate. At the same time, the spectra are deceptively complicated, as they can very well be approximated by intuitive reasoning.

  14. Absorption and Distribution Kinetics of the 13C-Labeled Tomato Carotenoid Phytoene in Healthy Adults1234

    PubMed Central

    Riedl, Kenneth M; Rogers, Randy B; Grainger, Elizabeth M; Erdman, John W; Clinton, Steven K

    2016-01-01

    Background: Phytoene is a tomato carotenoid that may contribute to the apparent health benefits of tomato consumption. Although phytoene is a less prominent tomato carotenoid than lycopene, it is a major carotenoid in various human tissues. Phytoene distribution to plasma lipoproteins and tissues differs from lycopene, suggesting the kinetics of phytoene and lycopene differ. Objective: The objective of this study was to characterize the kinetic parameters of phytoene absorption, distribution, and excretion in adults, to better understand why biodistribution of phytoene differs from lycopene. Methods: Four adults (2 males, 2 females) maintained a controlled phytoene diet (1–5 mg/d) for 42 d. On day 14, each consumed 3.2 mg 13C-phytoene, produced using tomato cell suspension culture technology. Blood samples were collected at 0, 1–15, 17, 21, and 24 h and 2, 3, 4, 7, 10, 14, 17, 21, and 28 d after 13C-phytoene consumption. Plasma-unlabeled and plasma-labeled phytoene concentrations were determined using ultra-HPLC–quadrupole time-of-flight-mass spectrometry, and data were fit to a 7-compartment carotenoid kinetic model using WinSAAM 3.0.7 software. Results: Subjects were compliant with a controlled phytoene diet, consuming a mean ± SE of 2.5 ± 0.6 mg/d, resulting in a plasma unlabeled phytoene concentration of 71 ± 14 nmol/L. A maximal plasma 13C-phytoene concentration of 55.6 ± 5.9 nM was achieved 19.8 ± 9.2 h after consumption, and the plasma half-life was 2.3 ± 0.2 d. Compared with previous results for lycopene, phytoene bioavailability was nearly double at 58% ± 19%, the clearance rate from chylomicrons was slower, and the rates of deposition into and utilization by the slow turnover tissue compartment were nearly 3 times greater. Conclusions: Although only differing from lycopene by 4 double bonds, phytoene exhibits markedly different kinetic characteristics in human plasma, providing insight into metabolic processes contributing to phytoene enrichment in plasma and tissues compared with lycopene. This trial was registered at clinicaltrials.gov as NCT01692340. PMID:26674763

  15. Selective {sup 2}H and {sup 13}C labeling in NMR analysis of solution protein structure and dynamics

    SciTech Connect

    LeMaster, D.M.

    1994-12-01

    Preparation of samples bearing combined isotope enrichment patterns has played a central role in the recent advances in NMR analysis of proteins in solution. In particular, uniform {sup 13}C, {sup 15}N enrichment has made it possible to apply heteronuclear multidimensional correlation experiments for the mainchain assignments of proteins larger than 30 KDa. In contrast, selective labeling approaches can offer advantages in terms of the directedness of the information provided, such as chirality and residue type assignments, as well as through enhancements in resolution and sensitivity that result from editing the spectral complexity, the relaxation pathways and the scalar coupling networks. In addition, the combination of selective {sup 13}C and {sup 2}H enrichment can greatly facilitate the determination of heteronuclear relaxation behavior.

  16. The application of 13C-labeled tetramethylammonium hydroxide (13C-TMAH) thermochemolysis to study fungal degradation of wood

    Treesearch

    T.R. Filley; P.G. Hatcher; W.C. Shortle

    2000-01-01

    This paper presents the results from an assessment of the application of a new molecular analytical procedure, 13C-TMAH thermochemolysis, to study the chemical modification of lignin by white-rot and brown-rot fungi. This technique differs from other molecular chemolysis procedures (e.g. TMAH thermochemolysis and CuO alkaline oxidation) as it...

  17. Accurate determinations of one-bond 13C-13C couplings in 13C-labeled carbohydrates.

    PubMed

    Azurmendi, Hugo F; Freedberg, Darón I

    2013-03-01

    Carbon plays a central role in the molecular architecture of carbohydrates, yet the availability of accurate methods for (1)D(CC) determination has not been sufficiently explored, despite the importance that such data could play in structural studies of oligo- and polysaccharides. Existing methods require fitting intensity ratios of cross- to diagonal-peaks as a function of the constant-time (CT) in CT-COSY experiments, while other methods utilize measurement of peak separation. The former strategies suffer from complications due to peak overlap, primarily in regions close to the diagonal, while the latter strategies are negatively impacted by the common occurrence of strong coupling in sugars, which requires a reliable assessment of their influence in the context of RDC determination. We detail a (13)C-(13)C CT-COSY method that combines a variation in the CT processed with diagonal filtering to yield (1)J(CC) and RDCs. The strategy, which relies solely on cross-peak intensity modulation, is inspired in the cross-peak nulling method used for J(HH) determinations, but adapted and extended to applications where, like in sugars, large one-bond (13)C-(13)C couplings coexist with relatively small long-range couplings. Because diagonal peaks are not utilized, overlap problems are greatly alleviated. Thus, one-bond couplings can be determined from different cross-peaks as either active or passive coupling. This results in increased accuracy when more than one determination is available, and in more opportunities to measure a specific coupling in the presence of severe overlap. In addition, we evaluate the influence of strong couplings on the determination of RDCs by computer simulations. We show that individual scalar couplings are notably affected by the presence of strong couplings but, at least for the simple cases studied, the obtained RDC values for use in structural calculations were not, because the errors introduced by strong couplings for the isotropic and oriented phases are very similar and therefore cancel when calculating the difference to determine (1)D(CC) values.

  18. CORRELATIONS BETWEEN PESTICIDE TRANSFORMATION RATE AND MICROBIAL RESPIRATION ACTIVITY IN SOIL OF DIFFERENT ECOSYSTEMS

    EPA Science Inventory

    Cecil sandy loam soils (ultisol) from forest (coniferous and deciduous), pasture, and arable ecosystems were sampled (0-10 cm) in the vicinity of Athens, GA, USA. Soil from each site was subdivided into three portions, consisting of untreated soil (control) as well as live and s...

  19. Plant adaptation to acid soils: the molecular basis for crop aluminum resistance

    USDA-ARS?s Scientific Manuscript database

    Aluminum (Al) toxicity on acid soils is a significant limitation to crop production worldwide, as approximately 50% of the world’s potentially arable soils are acidic. Because acid soils are such an important constraint to agriculture, understanding the mechanisms and genes conferring resistance to ...

  20. CORRELATIONS BETWEEN PESTICIDE TRANSFORMATION RATE AND MICROBIAL RESPIRATION ACTIVITY IN SOIL OF DIFFERENT ECOSYSTEMS

    EPA Science Inventory

    Cecil sandy loam soils (ultisol) from forest (coniferous and deciduous), pasture, and arable ecosystems were sampled (0-10 cm) in the vicinity of Athens, GA, USA. Soil from each site was subdivided into three portions, consisting of untreated soil (control) as well as live and s...

  1. Identification of degradation routes of metamitron in soil microcosms using (13)C-isotope labeling.

    PubMed

    Wang, Shizong; Miltner, Anja; Nowak, Karolina M

    2017-01-01

    Metamitron is one of the most commonly used herbicide in sugar beet and flower bulb cultures. Numerous laboratory and field studies on sorption and degradation of metamitron were performed. Detailed biodegradation studies in soil using (13)C-isotope labeling are still missing. Therefore, we aimed at providing a detailed turnover mass balance of (13)C6-metamitron in soil microcosms over 80 days. In the biotic system, metamitron mineralized rapidly, and (13)CO2 finally constituted 60% of the initial (13)C6-metamitron equivalents. In abiotic control experiments CO2 rose to only 7.4% of the initial (13)C6-metamitron equivalents. The (13)C label from (13)C6-metamitron was incorporated into microbial amino acids that were ultimately stabilized in the soil organic matter forming presumably harmless biogenic residues. Finally, (13)C label from (13)C6-metamitron was distributed between the (13)CO2 and the (13)C-biogenic residues indicating nearly complete biodegradation. The parallel increase of (13)C-alanine, (13)C-glutamate and (13)CO2 indicates that metamitron was initially biodegraded via the desamino-metamitron route suggesting its relevance in the growth metabolism. In later phases of biodegradation, the "Rhodococcus route" was indicated by the low (13)CO2 evolution and the high relevance of the pyruvate pathway, which aims at biomolecule synthesis and seems to be related to starvation. This is a first report on the detailed degradation route of metamitron in soil. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. Simulation and validation of greenhouse gas emissions and SOC stock changes in arable land using the ECOSSE model

    NASA Astrophysics Data System (ADS)

    Khalil, M. I.; Richards, M.; Osborne, B.; Williams, M.; Müller, C.

    2013-12-01

    Model simulations of C and N dynamics, based on country-specific agricultural and environmental conditions, can provide information for compiling national greenhouse gas (GHG) inventories, as well as insights into potential mitigation options. A multi-pool dynamic model, ‘ECOSSE’ (v5 modified), was used to simulate coupled GHGs and soil organic carbon (SOC) stock changes. It was run for an equivalent time frame of 8 years with inputs from conventionally-tilled arable land cropped with spring barley receiving N fertilizer as calcium ammonium nitrate at 135-159 kg N ha-1 and crop residues (3 t ha-1 yr-1). The simulated daily N2O fluxes were consistent with the measured values, with R2 of 0.33 (p < 0.05) and the total error and bias differences were within 95% confidence levels. The measured seasonal N2O losses were 0.39-0.60% of the N applied, with a modelled estimate of 0.23-0.41%. In contrast, the measured annual N2O loss (integrated) was 0.35% and the corresponding simulated value of 0.45% increased to 0.59% when the sum of the daily fluxes was taken into account. This indicates intermittent gas samplings may miss the peak fluxes. On an 8-year average the modelled N2O emission factor (EF) was 0.53 ± 0.03%. The model successfully predicted the daily heterotrophic respiration (RH), with an R2 of 0.45 (p < 0.05) and the total error and bias differences were within the 95% confidence intervals. The simulated and measured total RH (3149 versus 3072 kg C ha-1 yr-1) was within the cropland average values previously reported. The total measured CH4 fluxes indicated that the unfertilized treatments were a small source (-2.29 g C ha-1 yr-1), whilst the fertilized treatments were a sink (+3.64). In contrast, the simulated values suggested a sink (26.61-31.37 g C ha-1 yr-1), demonstrating fertilizer-induced decreases in CH4 oxidation. On average, based on the simulated SOC content a loss of 516 kg C ha-1 yr-1 was indicated, which is within the uncertainty range for

  3. Partitioning of CH4 and CO2 Production Originating from Rice Straw, Soil and Root Organic Carbon in Rice Microcosms

    PubMed Central

    Yuan, Quan; Pump, Judith; Conrad, Ralf

    2012-01-01

    Flooded rice fields are an important source of the greenhouse gas CH4. Possible carbon sources for CH4 and CO2 production in rice fields are soil organic matter (SOM), root organic carbon (ROC) and rice straw (RS), but partitioning of the flux between the different carbon sources is difficult. We conducted greenhouse experiments using soil microcosms planted with rice. The soil was amended with and without 13C-labeled RS, using two 13C-labeled RS treatments with equal RS (5 g kg−1 soil) but different δ13C of RS. This procedure allowed to determine the carbon flux from each of the three sources (SOM, ROC, RS) by determining the δ13C of CH4 and CO2 in the different incubations and from the δ13C of RS. Partitioning of carbon flux indicated that the contribution of ROC to CH4 production was 41% at tillering stage, increased with rice growth and was about 60% from the booting stage onwards. The contribution of ROC to CO2 was 43% at tillering stage, increased to around 70% at booting stage and stayed relatively constant afterwards. The contribution of RS was determined to be in a range of 12–24% for CH4 production and 11–31% for CO2 production; while the contribution of SOM was calculated to be 23–35% for CH4 production and 13–26% for CO2 production. The results indicate that ROC was the major source of CH4 though RS application greatly enhanced production and emission of CH4 in rice field soil. Our results also suggest that data of CH4 dissolved in rice field could be used as a proxy for the produced CH4 after tillering stage. PMID:23162678

  4. Plant species controls on atmospheric CH4 oxidation by soil

    NASA Astrophysics Data System (ADS)

    Menyailo, O. V.; Abraham, W.; Conrad, R.

    2009-12-01

    Plant species exert strong effects on ecosystem functions and one of the emerging, and difficult to test hypotheses, is that plants alter soil functions through changing the community structure of soil microorganisms. We tested the hypothesis for atmospheric CH4 oxidation by using soil samples from a Siberian afforestation experiment and exposing them to 13C-CH4. We determined the activity of the soil methanotrophs under different tree species at three levels of initial CH4 concentration (30, 200 and 1000 ppm) thus distinguishing the activities of low- and high-affinity methanotrophs. Half of the samples were incubated with 13C-enriched CH4 (99.9%) and half with 12C-CH4. This allowed an estimation of the amount of 13C incorporated into individual PLFAs and determination of PLFAs of methanotrophs involved in CH4 oxidation at the different CH4 concentrations. Tree species strongly altered the activity of atmospheric CH4 oxidation without appearing to change the composition of high-affinity methanotrophs as evidenced by PLFA 13C labeling. The low diversity of atmospheric CH4 oxidizers, presumably belonging to the UCSα group, may explain the lack of tree species effects on the composition of soil methanotrophs. We submit that the observed tree species effects on atmospheric CH4 oxidation indicate an effect on biomass or cell-specific activities rather than by a community change and this may be related to the impact of the tree species on soil N cycling.

  5. Soil microbial response to photo-degraded C60 fullerenes.

    PubMed

    Berry, Timothy D; Clavijo, Andrea P; Zhao, Yingcan; Jafvert, Chad T; Turco, Ronald F; Filley, Timothy R

    2016-04-01

    Recent studies indicate that while unfunctionalized carbon nanomaterials (CNMs) exhibit very low decomposition rates in soils, even minor surface functionalization (e.g., as a result of photochemical weathering) may accelerate microbial decay. We present results from a C60 fullerene-soil incubation study designed to investigate the potential links between photochemical and microbial degradation of photo-irradiated C60. Irradiating aqueous (13)C-labeled C60 with solar-wavelength light resulted in a complex mixture of intermediate products with decreased aromaticity. Although addition of irradiated C60 to soil microcosms had little effect on net soil respiration, excess (13)C in the respired CO2 demonstrates that photo-irradiating C60 enhanced its degradation in soil, with ∼ 0.78% of 60 day photo-irradiated C60 mineralized. Community analysis by DGGE found that soil microbial community structure was altered and depended on the photo-treatment duration. These findings demonstrate how abiotic and biotic transformation processes can couple to influence degradation of CNMs in the natural environment.

  6. Degradation and Microbial Uptake of C60 Fullerols in Contrasting Agricultural Soils.

    PubMed

    Berry, Timothy D; Filley, Timothy R; Clavijo, Andrea P; Bischoff Gray, Marianne; Turco, Ronald

    2017-02-07

    The environmental fate of functionalized carbon nanomaterials (CNM) remains poorly understood. Using (13)C-labeled nanomaterial we present the results of a study investigating the mineralization and microbial uptake of surface-functionalized C60 (fullerols) in agricultural soils with contrasting properties. Soil microcosms rapidly mineralized fullerol C, as determined by (13)C-content in the respired CO2, with higher fullerol mineralization in an organic, clay-rich soil versus a silty, low C soil (∼56.3% vs ∼30.9% fullerol C mineralized over 65 days). By tracking the enriched (13)C from fullerol into microbial phospholipid fatty acids (PLFA) we also report, for the first time, the incorporation of nanomaterial-derived C into soil microbial biomass, primarily by fungi and Gram-negative bacteria. While more fullerol C was incorporated into PLFA in the organic C-rich soil (0.77% vs 0.19% of PLFA C), this soil incorporated fullerol C into biomass less efficiently than the silty, low C soil (0.13% and 0.84% of assimilated fullerol C, respectively). These results demonstrate that, in contrast to pristine C60, surface functionalized C60 are unlikely to accumulate in surface soils and are readily mineralized by a range of soil microorganisms.

  7. Stabilization of microbial biomass in soils: Implications for SOM formation and xenobiotics degradation

    NASA Astrophysics Data System (ADS)

    Miltner, A.; Kindler, R.; Achtenhagen, J.; Nowak, K.; Girardi, C.; Kästner, M.

    2012-04-01

    Soil organic matter (SOM) plays an important role in soils. It is the carbon source and the habitat of many soil microorganisms, its quality and quantity thus affect soil microbial activity. Therefore, the amount and composition of SOM determines soil quality, but SOM formation and stabilization are not yet sufficiently understood. Recently, microbial biomass residues could be identified as a significant source of SOM. We incubated 13C-labelled bacterial cells for 224 days in an agricultural soil and traced the fate of the 13C label of bacterial biomass in soil by isotopic analysis. The data were combined to a mass balance, and the biomass residues were visualized by scanning electron microscopy (SEM). A high percentage of the biomass-derived carbon (in particular from proteins) remained in soil, mainly in the non-living part of SOM, after extended incubation. The SEM micrographs only rarely showed intact cells. Instead, organic patchy fragments of 200-500 nm size were abundant. These fragments were associated with all stages of cell envelope decay and fragmentation, indicating specific disintegration processes of cell walls. Similar fragments developed on initially clean and sterile in situ microcosms during exposure in groundwater, thus providing clear evidence for their microbial origin. Microbial cell envelope fragments thus contribute significantly to SOM formation. A significant contribution of cell envelope fragments to SOM formation provides a simple explanation for the development of the small, nano-scale patchy organic materials observed in soil electron micrographs. It also suggests that microstructures of microbial cells and of small plant debris provide the molecular architecture of SOM attached to particle surfaces. This origin and macromolecular architecture of SOM is consistent with most observations on SOM, e.g. the abundance of microbial-derived biomarkers, the low C/N ratio, the water repellency and the stabilization of microbial biomass. The

  8. Effects of habitat age and plant species on predatory mites (Acari, Mesostigmata) in grassy arable fallows in Eastern Austria.

    PubMed

    Wissuwa, Janet; Salamon, Jörg-Alfred; Frank, Thomas

    2012-07-01

    Density, diversity and assemblage structure of Mesostigmata (cohorts Gamasina and Uropodina) were investigated in nine grassy arable fallows according to a factorial design with age class (2-3, 6-8, 12-15 years) and plant species (legume: Medicago sativa, herb: Taraxacum officinale, grass: Bromus sterilis) as factors. The response of Mesostigmata to habitat age and plant species was explored because this group belongs to the dominant acarine predators playing a crucial role in soil food webs and being important as biological control agents. To our knowledge, this combination of factors has never been studied before for Mesostigmata. A further rarely applied aspect of the present study is the micro-scale approach investigating the Mesostigmata assemblage of the soil associated with single plants. Four plots were randomly chosen at each fallow in May 2008. At each plot plant roots and the adjacent soil of five randomly selected plant individuals per plant species were dug out with steel cylinders for heat extraction of soil fauna and measurement of environmental parameters. In total, 83 mite taxa were identified, with 50 taxa being new to Austria. GLM analysis revealed a significant effect of plant species on mite density, with significantly more mites in B. sterilis than in T. officinale samples, and M. sativa samples being intermediate. This was in contrast to the assumption that the mite density is highest in M. sativa samples due to the propagation of plant quality effects to higher trophic levels. These results were probably caused by a higher amount of fine roots in grass samples leading to high densities of Collembola, which are preferred prey of predatory mites. Mite density did not significantly differ between the three age classes. A canonical analysis of principal coordinates (CAP) showed that the mite assemblage exhibited a weak yet significant separation between plant species, and a highly significant separation between age classes. Accordingly

  9. [Characteristics of nutrient loss by runoff in sloping arable land of yellow-brown under different rainfall intensities].

    PubMed

    Chen, Ling; Liu, De-Fu; Song, Lin-Xu; Cui, Yu-Jie; Zhang, Gei

    2013-06-01

    In order to investigate the loss characteristics of N and P through surface flow and interflow under different rainfall intensities, a field experiment was conducted on the sloping arable land covered by typical yellow-brown soils inXiangxi River watershed by artificial rainfall. The results showed that the discharge of surface flow, total runoff and sediment increased with the increase of rain intensity, while the interflow was negatively correlated with rain intensity under the same total rainfall. TN, DN and DP were all flushed at the very beginning in surface flow underdifferent rainfall intensities; TP fluctuated and kept consistent in surface flow without obvious downtrend. While TN, DN and DP in interflow kept relatively stable in the whole runoff process, TP was high at the early stage, then rapidly decreased with time and kept steady finally. P was directly influenced by rainfall intensity, its concentration in the runoff increased with the increase of the rainfall intensity, the average concentration of N and P both exceeded the threshold of eutrophication of freshwater. The higher the amount of P loss was, the higher the rain intensity. The change of N loss was the opposite. The contribution rate of TN loss carried by surface flow increased from 36.5% to 57.6% with the increase of rainfall intensity, but surface flow was the primary form of P loss which contributed above 90.0%. Thus, it is crucial to control interflow in order to reduce N loss. In addition, measures should be taken to effectively manage soil erosion to mitigate P loss. The proportion of dissolved nitrogen in surface flow elevated with the decrease of rainfall intensity, but in interflow, dissolved form was predominant. P was exported mainly in the form of particulate under different rainfall intensities and runoff conditions.

  10. Possible changes to arable crop yields by 2050

    PubMed Central

    Jaggard, Keith W.; Qi, Aiming; Ober, Eric S.

    2010-01-01

    By 2050, the world population is likely to be 9.1 billion, the CO2 concentration 550 ppm, the ozone concentration 60 ppb and the climate warmer by ca 2°C. In these conditions, what contribution can increased crop yield make to feeding the world? CO2 enrichment is likely to increase yields of most crops by approximately 13 per cent but leave yields of C4 crops unchanged. It will tend to reduce water consumption by all crops, but this effect will be approximately cancelled out by the effect of the increased temperature on evaporation rates. In many places increased temperature will provide opportunities to manipulate agronomy to improve crop performance. Ozone concentration increases will decrease yields by 5 per cent or more. Plant breeders will probably be able to increase yields considerably in the CO2-enriched environment of the future, and most weeds and airborne pests and diseases should remain controllable, so long as policy changes do not remove too many types of crop-protection chemicals. However, soil-borne pathogens are likely to be an increasing problem when warmer weather will increase their multiplication rates; control is likely to need a transgenic approach to breeding for resistance. There is a large gap between achievable yields and those delivered by farmers, even in the most efficient agricultural systems. A gap is inevitable, but there are large differences between farmers, even between those who have used the same resources. If this gap is closed and accompanied by improvements in potential yields then there is a good prospect that crop production will increase by approximately 50 per cent or more by 2050 without extra land. However, the demands for land to produce bio-energy have not been factored into these calculations. PMID:20713388

  11. Possible changes to arable crop yields by 2050.

    PubMed

    Jaggard, Keith W; Qi, Aiming; Ober, Eric S

    2010-09-27

    By 2050, the world population is likely to be 9.1 billion, the CO(2) concentration 550 ppm, the ozone concentration 60 ppb and the climate warmer by ca 2 degrees C. In these conditions, what contribution can increased crop yield make to feeding the world? CO(2) enrichment is likely to increase yields of most crops by approximately 13 per cent but leave yields of C4 crops unchanged. It will tend to reduce water consumption by all crops, but this effect will be approximately cancelled out by the effect of the increased temperature on evaporation rates. In many places increased temperature will provide opportunities to manipulate agronomy to improve crop performance. Ozone concentration increases will decrease yields by 5 per cent or more. Plant breeders will probably be able to increase yields considerably in the CO(2)-enriched environment of the future, and most weeds and airborne pests and diseases should remain controllable, so long as policy changes do not remove too many types of crop-protection chemicals. However, soil-borne pathogens are likely to be an increasing problem when warmer weather will increase their multiplication rates; control is likely to need a transgenic approach to breeding for resistance. There is a large gap between achievable yields and those delivered by farmers, even in the most efficient agricultural systems. A gap is inevitable, but there are large differences between farmers, even between those who have used the same resources. If this gap is closed and accompanied by improvements in potential yields then there is a good prospect that crop production will increase by approximately 50 per cent or more by 2050 without extra land. However, the demands for land to produce bio-energy have not been factored into these calculations.

  12. Change We Can Fight Over: The Relationship between Arable Land Supply and Substate Conflict

    DTIC Science & Technology

    2010-01-01

    resource scarcities will supposedly lead to armed violence between competing non-state actors and/or states. Each of the steps in this process must be...validated conclusively in order for us to predict that climate change will increase the frequency of armed conflict in the future. Thus, recent empirical...critical natural resource, arable land, and the likelihood of both civil war and substate armed conflict in general between 1965 and 1999. In so doing

  13. Changes in the Bacterial Community Structure of Remediated Anthracene-Contaminated Soils

    PubMed Central

    Delgado-Balbuena, Laura; Bello-López, Juan M.; Navarro-Noya, Yendi E.; Rodríguez-Valentín, Analine; Luna-Guido, Marco L.; Dendooven, Luc

    2016-01-01

    Mixing soil or adding earthworms (Eisenia fetida (Savigny, 1826)) accelerated the removal of anthracene, a polycyclic aromatic hydrocarbon, from a pasture and an arable soil, while a non-ionic surfactant (Surfynol® 485) inhibited the removal of the contaminant compared to the untreated soil. It was unclear if the treatments affected the soil bacterial community and consequently the removal of anthracene. Therefore, the bacterial community structure was monitored by means of 454 pyrosequencing of the 16S rRNA gene in the pasture and arable soil mixed weekly, amended with Surfynol® 485, E. fetida or organic material that served as food for the earthworms for 56 days. In both soils, the removal of anthracene was in the order: mixing soil weekly (100%) > earthworms applied (92%) > organic material applied (77%) > untreated soil (57%) > surfactant applied (34%) after 56 days. There was no clear link between removal of anthracene from soil and changes in the bacterial community structure. On the one hand, application of earthworms removed most of the contaminant from the arable soil and had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of the Acidobacteria, Chloroflexi and Gemmatimonadetes, and an increase in that of the Proteobacteria compared to the unamended soil. Mixing the soil weekly removed all anthracene from the arable soil, but had little or no effect on the bacterial community structure. On the other hand, application of the surfactant inhibited the removal of anthracene from the arable soil compared to the untreated soil, but had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of Cytophagia (Bacteroidetes), Chloroflexi, Gemmatimonadetes and Planctomycetes and an increase in that of the Flavobacteria (Bacteroidetes) and Proteobacteria. Additionally, the removal of anthracene was similar in the different treatments of both the arable and pasture soil, but the

  14. Changes in the Bacterial Community Structure of Remediated Anthracene-Contaminated Soils.

    PubMed

    Delgado-Balbuena, Laura; Bello-López, Juan M; Navarro-Noya, Yendi E; Rodríguez-Valentín, Analine; Luna-Guido, Marco L; Dendooven, Luc

    2016-01-01

    Mixing soil or adding earthworms (Eisenia fetida (Savigny, 1826)) accelerated the removal of anthracene, a polycyclic aromatic hydrocarbon, from a pasture and an arable soil, while a non-ionic surfactant (Surfynol® 485) inhibited the removal of the contaminant compared to the untreated soil. It was unclear if the treatments affected the soil bacterial community and consequently the removal of anthracene. Therefore, the bacterial community structure was monitored by means of 454 pyrosequencing of the 16S rRNA gene in the pasture and arable soil mixed weekly, amended with Surfynol® 485, E. fetida or organic material that served as food for the earthworms for 56 days. In both soils, the removal of anthracene was in the order: mixing soil weekly (100%) > earthworms applied (92%) > organic material applied (77%) > untreated soil (57%) > surfactant applied (34%) after 56 days. There was no clear link between removal of anthracene from soil and changes in the bacterial community structure. On the one hand, application of earthworms removed most of the contaminant from the arable soil and had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of the Acidobacteria, Chloroflexi and Gemmatimonadetes, and an increase in that of the Proteobacteria compared to the unamended soil. Mixing the soil weekly removed all anthracene from the arable soil, but had little or no effect on the bacterial community structure. On the other hand, application of the surfactant inhibited the removal of anthracene from the arable soil compared to the untreated soil, but had a strong effect on the bacterial community structure, i.e. a decrease in the relative abundance of Cytophagia (Bacteroidetes), Chloroflexi, Gemmatimonadetes and Planctomycetes and an increase in that of the Flavobacteria (Bacteroidetes) and Proteobacteria. Additionally, the removal of anthracene was similar in the different treatments of both the arable and pasture soil, but the

  15. Long-term Priming-induced Changes in Permafrost Soil Organic Matter Decomposition

    NASA Astrophysics Data System (ADS)

    Pegoraro, E.; Bracho, R. G.; Schuur, E.

    2016-12-01

    Warming of tundra ecosystems due to climate change is predicted to thaw permafrost and increase plant biomass and litter input to soil. Additional input of easily decomposable carbon can stimulate microbial activity, consequently increasing soil organic matter decomposition rates. This phenomenon, known as the priming effect, can exacerbate the effects of climate change by releasing more CO2 from permafrost soils; however, the extent to which it could decrease soil carbon stocks in the Arctic is unknown. Most priming incubation studies are conducted for a short period of time, making it difficult to assess if priming is a short-term phenomenon, or could persist over the long-term. We incubated permafrost soil from a moist acidic tundra site in Healy, Alaska for 456 days at 15° C. Soil from surface and deep layers were amended with three pulses of uniformly 13C labeled glucose, a fast decomposing substrate, every 152 days. We also quantified the proportion of old carbon respired by measuring 14CO2. Substrate addition resulted in higher respiration rates in glucose amended soils; however, positive priming was only observed in deep layers, where on average 9%, 57%, and 25% more soil-derived C was respired at 45-55, 65-75, and 75-85 cm depth increments for the duration of the experiment. This suggests that microbes in deep layers are limited in energy, and the addition of easily decomposable carbon increases native soil organic matter decomposition.

  16. Soil structural quality assessment for soil protection regulation

    NASA Astrophysics Data System (ADS)

    Johannes, Alice; Boivin, Pascal

    2017-04-01

    Soil quality assessment is rapidly developing worldwide, though mostly focused on the monitoring of arable land and soil fertility. Soil protection regulations assess soil quality differently, focusing on priority pollutants and threshold values. The soil physical properties are weakly considered, due to lack of consensus and experimental difficulties faced with characterization. Non-disputable, easy to perform and inexpensive methods should be available for environmental regulation to be applied, which is unfortunately not the case. As a consequence, quantitative soil physical protection regulation is not applied, and inexpensive soil physical quality indicators for arable soil management are not available. Overcoming these limitations was the objective of a research project funded by the Swiss federal office for environment (FOEN). The main results and the perspectives of application are given in this presentation. A first step of the research was to characterize soils in a good structural state (reference soils) under different land use. The structural quality was assessed with field expertise and Visual Evaluation of the Soil Structure (VESS), and the physical properties were assessed with Shrinkage analysis. The relationships between the physical properties and the soil constituents were linear and highly determined. They represent the reference properties of the corresponding soils. In a second step, the properties of physically degraded soils were analysed and compared to the reference properties. This allowed defining the most discriminant parameters departing the different structure qualities and their threshold limits. Equivalent properties corresponding to these parameters but inexpensive and easy to determine were defined and tested. More than 90% of the samples were correctly classed with this method, which meets, therefore, the requirements for practical application in regulation. Moreover, result-oriented agri-environmental schemes for soil quality

  17. Microbial communities in pyrene amended soil-compost mixture and fertilized soil.

    PubMed

    Adam, Iris K U; Duarte, Márcia; Pathmanathan, Jananan; Miltner, Anja; Brüls, Thomas; Kästner, Matthias

    2017-12-01

    Polycyclic aromatic hydrocarbons are distributed ubiquitously in the environment and form metabolites toxic to most organisms. Organic amendment of PAH contaminated soil with compost and farmyard manure has proven to be efficient for PAH bioremediation mediated by native microorganisms, even though information on the identity of PAH degraders in organic-amended soil is still scarce. Here we provide molecular insight into the bacterial communities in soil amended with compost or farmyard manure for which the degradation mass balances of (13)C-labeled pyrene have been recently published and assess the relevant bacterial genera capable of degrading pyrene as a model PAH. We performed statistical analyses of bacterial genera abundance data based on total DNA and RNA (for comparison) extracted from the soil samples. The results revealed complex pyrene degrading communities with low abundance of individual degraders instead of a limited number of abundant key players. The bacterial degrader communities of the soil-compost mixture and soil fertilized with farmyard manure differed considerably in composition albeit showing similar degradation kinetics. Additional analyses were carried out on enrichment cultures and enabled the reconstruction of several nearly complete genomes, thus allowing to link microcosm and enrichment experiments. However, pyrene mineralizing bacteria enriched from the compost or unfertilized soil-compost samples did not dominate pyrene degradation in the soils. Based on the present findings, evaluations of PAH degrading microorganisms in complex soil mixtures with high organic matter content should not target abundant key degrading species, since the specific degraders may be highly diverse, of low abundance, and masked by high bacterial background.

  18. Transformation of forest soils in Iowa (the United States) under the impact of the long-term agricultural development

    USDA-ARS?s Scientific Manuscript database

    The evolution of automorphic cultivated soils of the Fayette series (the order of Alfisols)—close analogues of gray forest soils in the European part of Russia—was studied by the method of agrosoil chro_nosequences in the lower reaches of the Iowa River. It was found that the old_arable soils are ch...

  19. Relationship between carbon and nitrogen mineralization in a subtropical soil

    NASA Astrophysics Data System (ADS)

    Li, Qianru; Sun, Yue; Zhang, Xinyu; Xu, Xingliang; Kuzyakov, Yakov

    2014-05-01

    In most soils, more than 90% nitrogen is bonded with carbon in organic forms. This indicates that carbon mineralization should be closely coupled with nitrogen mineralization, showing a positive correlation between carbon and nitrogen mineralization. To test this hypothesis above, we conducted an incubation using a subtropical soil for 10 days at 15 °C and 25 °C. 13C-labeled glucose and 15N-labeled ammonium or nitrate was used to separate CO2 and mineral N released from mineralization of soil organic matter and added glucose or inorganic nitrogen. Phospholipid fatty acid (PLFA) and four exoenzymes (i.e. β-1,4- Glucosaminidase, chitinase, acid phosphatase, β-1,4-N- acetyl glucosamine glycosidase) were also analyzed to detect change in microbial activities during the incubation. Our results showed that CO2 release decreased with increasing nitrogen mineralization rates. Temperature did not change this relationship between carbon and nitrogen mineralization. Although some changes in PLFA and the four exoenzymes were observed, these changes did not contribute to changes in carbon and nitrogen mineralization. These findings indicates that carbon and nitrogen mineralization in soil are more complicated than as previously expected. Future investigation should focus on why carbon and nitrogen mineralization are coupled in a negative correlation not in a positive correlation in many soils for a better understanding of carbon and nitrogen transformation during their mineralization.

  20. Impact of cultivation year, nitrogen fertilization rate and irrigation water quality on soil salinity and soil nitrogen in saline-sodic paddy fields in Northeast China

    USDA-ARS?s Scientific Manuscript database

    Saline-sodic soils are a valuable potential arable land resource, and are widely distributed in the western Songnen Plain of Northeast China. Reclaiming and planting rice is an effective and feasible approach for improving saline-sodic soil and increasing food production. Assessment of the effective...

  1. Soil Fungal:Bacterial Ratios Are Linked to Altered Carbon Cycling

    PubMed Central

    Malik, Ashish A.; Chowdhury, Somak; Schlager, Veronika; Oliver, Anna; Puissant, Jeremy; Vazquez, Perla G. M.; Jehmlich, Nico; von Bergen, Martin; Griffiths, Robert I.; Gleixner, Gerd

    2016-01-01

    Despite several lines of observational evidence, there is a lack of consensus on whether higher fungal:bacterial (F:B) ratios directly cause higher soil carbon (C) storage. We employed RNA sequencing, protein profiling and isotope tracer techniques to evaluate whether differing F:B ratios are associated with differences in C storage. A mesocosm 13C labeled foliar litter decomposition experiment was performed in two soils that were similar in their physico-chemical properties but differed in microbial community structure, specifically their F:B ratio (determined by PLFA analyses, RNA sequencing and protein profiling; all three corroborating each other). Following litter addition, we observed a consistent increase in abundance of fungal phyla; and greater increases in the fungal dominated soil; implicating the role of fungi in litter decomposition. Litter derived 13C in respired CO2 was consistently lower, and residual 13C in bulk SOM was higher in high F:B soil demonstrating greater C storage potential in the F:B dominated soil. We conclude that in this soil system, the increased abundance of fungi in both soils and the altered C cycling patterns in the F:B dominated soils highlight the significant role of fungi in litter decomposition and indicate that F:B ratios are linked to higher C storage potential. PMID:27555839

  2. Aging of organochlorine pesticides and polychlorinated biphenyls in muck soil: volatilization, bioaccessibility, and degradation.

    PubMed

    Wong, Fiona; Bidleman, Terry F

    2011-02-01

    An organic rich muck soil which is highly contaminated with native organochlorine pesticide (OCs) was spiked with known amounts of (13)C-labeled OCs and nonlabeled polychlorinated biphenyls (PCBs). Spiked soils were aged under indoor, outdoor, and sterile conditions and the change in volatility, surrogate bioaccessibility, and degradation of chemicals was monitored periodically over 730 d. Volatility was measured using a fugacity meter to characterize the soil-air partition coefficient (K(SA) = C(SOIL)/C(AIR)). The fraction of bioaccessible residues was estimated by comparing recoveries of chemical with a mild extractant, hydroxylpropyl-β-cyclodextrin (HPCD) vs a harsh extractant, DCM. K(SA) of the spiked OCs in the nonsterile (Indoor, Outdoor) soils were initially lower and approached the K(SA) of native OCs over time, showing reduction of volatility upon aging. HPCD extractability of spiked OCs and PCBs were negatively correlated with K(SA), which suggests that volatility can be used as a surrogate for bioaccessibility. Degradation of endosulfans, PCB 8 and 28 was observed in the nonsterile soils, and (13)C(6)-α-HCH showed selective degradation of the (+) enantiomer. Enantiomer fractions (EF) in air and HPCD extracts were lower than in nonsterile soils, suggesting greater sequestering of the (+) enantiomer in the soil during microbial degradation.

  3. The sustainable arable land use pattern under the tradeoff of agricultural production, economic development, and ecological protection-an analysis of Dongting Lake basin, China.

    PubMed

    Yin, Guanyi; Liu, Liming; Jiang, Xilong

    2017-09-20

    To find a solution regarding sustainable arable land use pattern in the important grain-producing area during the rapid urbanization process, this study combined agricultural production, locational condition, and ecological protection to determine optimal arable land use. Dongting Lake basin, one of the major grain producing areas in China, was chosen as the study area. The analysis of land use transition, the calculation of arable land barycenter, the landscape indices of arable land patches, and the comprehensive evaluation of arable land quality(productivity, economic location, and ecological condition) were adopted in this study. The results showed that (1) in 1990-2000, the arable land increased by 11.77%, and the transformation between arable land and other land use types actively occurred; in 2000-2010, the arable land decreased by 0.71%, and more ecological area (forestland, grassland, and water area) were disturbed and transferred into arable land; (2) urban expansion of the Changsha-Zhuzhou-Xiangtan city cluster (the major economy center of this area) induced the northward movement of the arable land barycenter; (3) the landscape fragmentation and decentralization degree of arable land patches increased during 1990-2010; (4) potential high-quality arable land is located in the zonal area around Dongting Lake, which contains the Li County, Linli County, Jinshi County, Taoyuan County, Taojiang County, Ningxiang County, Xiangxiang County, Shaoshan County, Miluo County, and Zhuzhou County. The inferior low-quality arable land is located in the northwestern Wuling mountainous area, the southeastern hilly area, and the densely populated big cities and their surrounding area. In the optimized arable land use pattern, the high-quality land should be intensively used, and the low-quality arable land should be reduced used or prohibitively used. What is more, it is necessary to quit the arable land away from the surrounding area of cities appropriately, in order to

  4. Priming-induced Changes in Permafrost Soil Organic Matter Decomposition

    NASA Astrophysics Data System (ADS)

    Pegoraro, E.; Schuur, E.; Bracho, R. G.

    2015-12-01

    Warming of tundra ecosystems due to climate change is predicted to thaw permafrost and increase plant biomass and litter input to soil. Additional input of easily decomposable carbon can alter microbial activity by providing a much needed energy source, thereby accelerating soil organic matter decomposition. This phenomenon, known as the priming effect, can increase CO2 flux from soil to the atmosphere. However, the extent to which this mechanism can decrease soil carbon stocks in the Arctic is unknown. This project assessed priming effects on permafrost soil collected from a moist acidic tundra site in Healy, Alaska. We hypothesized that priming would increase microbial activity by providing microbes with a fresh source of carbon, thereby increasing decomposition of old and slowly decomposing carbon. Soil from surface and deep layers were amended with multiple pulses of uniformly 13C labeled glucose and cellulose, and samples were incubated at 15° C to quantify whether labile substrate addition increased carbon mineralization. We quantified the proportion of old carbon mineralization by measuring 14CO2. Data shows that substrate addition resulted in higher respiration rates in amended soils; however, priming was only observed in deep layers, where 30% more soil-derived carbon was respired compared to control samples. This suggests that microbes in deep layers are limited in energy, and the addition of labile carbon increases native soil organic matter decomposition, especially in soil with greater fractions of slowly decomposing carbon. Priming in permafrost could exacerbate the effects of climate change by increasing mineralization rates of carbon accumulated over the long-term in deep layers. Therefore, quantifying priming effect in permafrost soils is imperative to understanding the dynamics of carbon turnover in a warmer world.

  5. Effects of different mechanized soil fertilization methods on corn soil fertility under continuous cropping

    NASA Astrophysics Data System (ADS)

    Shi, Qingwen; Wang, Huixin; Bai, Chunming; Wu, Di; Song, Qiaobo; Gao, Depeng; Dong, Zengqi; Cheng, Xin; Dong, Qiping; Zhang, Yahao; Mu, Jiahui; Chen, Qinghong; Liao, Wenqing; Qu, Tianru; Zhang, Chunling; Zhang, Xinyu; Liu, Yifei; Han, Xiaori

    2017-05-01

    Experiments for mechanized soil fertilization for corns were conducted in Faku demonstration zone. On this basis, we studied effects on corn soil fertility under continuous cropping due to different mechanized soil fertilization methods. Our study would serve as a theoretical basis further for mechanized soil fertilization improvement and soil quality improvement in brown soil area. Based on the survey of soil physical characteristics during different corn growth periods, we collected soil samples from different corn growth periods to determine and make statistical analysis accordingly. Stalk returning to field with deep tillage proved to be the most effective on available nutrient improvement for arable soil in the demonstration zone. Different mechanized soil fertilization methods were remarkably effective on total phosphorus improvement for arable soil in the demonstration zone, while less effective on total nitrogen or total potassium, and not so effective on C/N ratio in soil. Stalk returning with deep tillage was more favorable to improve content of organic matter in soil, when compared with surface application, and organic granular fertilizer more favorable when compared with decomposed cow dung for such a purpose, too.

  6. The impact of pyrogenic C on soil functioning : a study using ancient killn soil as a model system

    NASA Astrophysics Data System (ADS)

    Rumpel, Cornelia; Naisse, Christophe; Thi Ngo, Phuong; Davasse, Bernard; Girardin, Cyril; Chabbi, Abad

    2016-04-01

    The long-term effect of pyrogenic C on the physicochemical and biological functioning of soils is poorly understood. We used ancient killn soils as model systems in order to investigate soil properties after four centuries of pyrogenic C addition. In particular we were interested in the effect of the pyrogenic C amendment on the (micro-)biological functioning of the soil. We analysed for physicochemical properties, C mineralisation as well as C dynamics following input of 13C labelled charcoal and plant residues. Our results show compared to soil without any addition, that pyrogenic C amendment led in the long term to more rapid decomposition of the new materials. The decomposition rate was increased by about 17%. In contrast,a negative priming effect reduced soil organic carbon mineralization by about 30%. Soil physicochemical poperties, i.e. clay content, cation exchange and nutrient availability were durably improved in soil amended with pyrogenic C four centuries ago. These changes probably promoted higher microbial activity and thus intense mineralization when new plant litter was added. On the contrary, charcoal was degraded at a similar rate compared to soil without pyrogenic C amendment. Thus no specific adaptation of microorganism to charcoal degradation was observed even after several centuries. The negative priming effect induced by charcoal additiion can be due to a physical protection of the soluble carbon fraction at the surfaces of new charcoal. In contrast, the negative priming effect induced by plant residue input may be more likely due to a shift of substrate utilisation by microbial communities evolving in a nutrient-rich environment. Our results demonstrate that pyrogenic C addition modifies the carbon dynamic of soils in the long-term. We propose a conceptual model accounting for the alterations of soil functioning in the long term after pyrogenic C addition.

  7. Nutrient losses by surface run-off following the application of organic manures to arable land. 2. Phosphorus.

    PubMed

    Smith, K A; Jackson, D R; Withers, P J

    2001-01-01

    Phosphorus (P) surface run-off losses were studied following organic manure applications to land, utilising a purpose-built facility on a sloping site in Herefordshire under arable tillage. Different rates and timing of cattle slurry, farm yard manure (FYM) and inorganic nitrogen (N) and P fertiliser were compared, over a 4-year period (1993-97). N losses from the same studies are reported in a separate paper. The application of cattle FYM and, especially slurry, to the silty clay loam soil increased both particulate and soluble P loss in surface water flow. Losses via subsurface flow (30 cm interflow) were consistently much lower than via surface water movement and were generally unaffected by treatment. Increased application of slurry solids increased all forms of P loss via surface run-off; the results suggested that a threshold for greatly increased risk of P losses via this route, as for N, occurred at ca. 2.5-3.0 t/ha solids loading. This approximates to the 50 m3/ha application rate limit suggested for slurry within UK 'good agricultural practice'. The studies also provided circumstantial evidence of the sealing of the soil surface by slurry solids as the major mechanism by which polluting surface run-off may occur following slurry application on susceptible soils. Losses of total and soluble P, recorded for each of the 4 years of experiments, reached a maximum of only up to 2 kg/ha total P (TP), even after slurry applications initiating run-off. Whilst these losses are insignificant in agronomic terms, peak concentrations of P (up to 30,000 micrograms/l TP) in surface water during a run-off event, could be of considerable concern in sensitive catchments. Losses of slurry P via surface run-off could make a significant contribution to accelerated eutrophication on entry to enclosed waters, particularly when combined with high concentrations of NO3(-)-N. Restricting slurry application rates to those consistent with good agronomic practice, and within the

  8. Nutrient losses by surface run-off following the application of organic manures to arable land. 1. Nitrogen.

    PubMed

    Smith, K A; Jackson, D R; Pepper, T J

    2001-01-01

    Research was conducted on nitrogen (N) surface run-off losses following organic manure applications to land, utilising a purpose-built facility on a sloping site in Herefordshire under arable tillage. Different rates and timing of cattle slurry, farmyard manure and inorganic N and phosphorus (P) fertiliser were compared, over a 4-year period (1993-97). P losses from the same studies are reported in a separate paper. The application of cattle slurries to the silty clay loam soil increased the loss of solids and NH4(+)-N in surface water flow compared to control plots receiving inorganic fertiliser only, or no treatment, but had little effect on NO3(-)-N losses by this route. Results were consistent with other observations that rainfall events immediately after manure applications are particularly likely to be associated with nutrient run-off losses. Losses via subsurface flow (30 cm interflow) were consistently much lower than via surface water movement and were generally unaffected by treatment. Increasing slurry application rate and, in particular, slurry solids loading, increased solids and NH4(-)-N losses via surface run-off. The threshold, above which the risk of losses via surface run-off appeared to be greatly increased, was ca. 2.5-3.0 t/ha slurry solids, which approximates to the 50 m3/ha limit suggested for slurry within