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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. 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

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. (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.

  11. 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

  12. 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

  13. 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.

  14. 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

  15. 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

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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).

  6. 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

  7. 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.

  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. 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.

  10. (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.

  11. 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

  12. 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.

  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. 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.

  16. 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%.

  17. 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.

  18. [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.

  19. 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

  20. 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.

  1. Pollution of Flooded Arable Soils with Heavy Metals and Polycyclic Aromatic Hydrocarbons (PAHs).

    PubMed

    Ciesielczuk, Tomasz; Kusza, Grzegorz; Poluszyńska, Joanna; Kochanowska, Katarzyna

    2014-01-01

    Soils that are exposed to floodwaters because of shallow groundwater and periodical wetlands are, to a large extent, exposed to contamination by organic and inorganic compounds. These are mainly compounds that have drifted along with the inflow of heavily laden floodwater and are produced within the soil profile by the anaerobic transformation of organic matter. Heavy metals and polycyclic aromatic hydrocarbon (PAH) compounds are absorbed by the soil of the floodwaters, and moving in the soil profile, they pose a threat to groundwater. What is more, after a flood, they may be absorbed by the crops. This paper focuses on the effects of Odra River (Poland) floods, heavy metals, and PAHs on soil and the possibilities of the migration of these pollutants into the soil profile. In the tested sludge samples of floodwater and soil, there were no abnormal concentrations of heavy metals, but the flooding time positively affected the amount listed in the test samples. Concentrations of PAHs increased, but they also exceeded the standards for arable soils in the case of single compounds.

  2. 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

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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).

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. 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

  20. 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

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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.

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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.

  16. 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

  17. 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

  18. 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

  19. 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.

  20. 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

  1. 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.

  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 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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

  18. 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

  19. 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

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  10. 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.

  11. 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

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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

  1. 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.

  2. 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

  3. 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

  4. 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

  5. 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.

  6. 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.

  7. 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.

  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. 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

  10. 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

  11. 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.

  12. 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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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. 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.

  15. 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

  16. 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.

  17. 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

  18. [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.

  19. 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.

  20. 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.

  1. 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].

  2. 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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  4. 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)

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. [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.

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. 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

  20. 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

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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)

  8. 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.

  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. 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

  11. "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.

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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…

  16. Quantification of peptide m/z distributions from 13C-labeled cultures with high resolution mass spectrometry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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-...

  17. Vitamin K absorption and kinetics in human subjects after consumption of 13C-labeled phylloquinone from kale

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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%).

  3. 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.

  4. 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.

  5. 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...

  6. Plant adaptation to acid soils: the molecular basis for crop aluminum resistance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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 ...

  7. 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

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. [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.

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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.

  19. Transformation of forest soils in Iowa (the United States) under the impact of the long-term agricultural development

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  20. 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.

  1. Litter decay controlled by temperature, not soil properties, affecting future soil carbon.

    PubMed

    Gregorich, Edward G; Janzen, Henry; Ellert, Benjamin H; Helgason, Bobbi L; Qian, Budong; Zebarth, Bernie J; Angers, Denis A; Beyaert, Ronald P; Drury, Craig F; Duguid, Scott D; May, William E; McConkey, Brian G; Dyck, Miles F

    2017-04-01

    Widespread global changes, including rising atmospheric CO2 concentrations, climate warming and loss of biodiversity, are predicted for this century; all of these will affect terrestrial ecosystem processes like plant litter decomposition. Conversely, increased plant litter decomposition can have potential carbon-cycle feedbacks on atmospheric CO2 levels, climate warming and biodiversity. But predicting litter decomposition is difficult because of many interacting factors related to the chemical, physical and biological properties of soil, as well as to climate and agricultural management practices. We applied (13) C-labelled plant litter to soil at ten sites spanning a 3500-km transect across the agricultural regions of Canada and measured its decomposition over five years. Despite large differences in soil type and climatic conditions, we found that the kinetics of litter decomposition were similar once the effect of temperature had been removed, indicating no measurable effect of soil properties. A two-pool exponential decay model expressing undecomposed carbon simply as a function of thermal time accurately described kinetics of decomposition. (R(2)  = 0.94; RMSE = 0.0508). Soil properties such as texture, cation exchange capacity, pH and moisture, although very different among sites, had minimal discernible influence on decomposition kinetics. Using this kinetic model under different climate change scenarios, we projected that the time required to decompose 50% of the litter (i.e. the labile fractions) would be reduced by 1-4 months, whereas time required to decompose 90% of the litter (including recalcitrant fractions) would be reduced by 1 year in cooler sites to as much as 2 years in warmer sites. These findings confirm quantitatively the sensitivity of litter decomposition to temperature increases and demonstrate how climate change may constrain future soil carbon storage, an effect apparently not influenced by soil properties.

  2. Rice (Oryza sativa L) plantation affects the stability of biochar in paddy soil.

    PubMed

    Wu, Mengxiong; Feng, Qibo; Sun, Xue; Wang, Hailong; Gielen, Gerty; Wu, Weixiang

    2015-05-05

    Conversion of rice straw into biochar for soil amendment appears to be a promising method to increase long-term carbon sequestration and reduce greenhouse gas (GHG) emissions. The stability of biochar in paddy soil, which is the major determining factor of carbon sequestration effect, depends mainly on soil properties and plant functions. However, the influence of plants on biochar stability in paddy soil remains unclear. In this study, bulk and surface characteristics of the biochars incubated without rice plants were compared with those incubated with rice plants using a suite of analytical techniques. Results showed that although rice plants had no significant influence on the bulk characteristics and decomposition rates of the biochar, the surface oxidation of biochar particles was enhanced by rice plants. Using (13)C labeling we observed that rice plants could significantly increase carbon incorporation from biochar into soil microbial biomass. About 0.047% of the carbon in biochar was incorporated into the rice plants during the whole rice growing cycle. These results inferred that root exudates and transportation of biochar particles into rice plants might decrease the stability of biochar in paddy soil. Impact of plants should be considered when predicting carbon sequestration potential of biochar in soil systems.

  3. Drought effects on allocation of recent carbon: from beech leaves to soil CO2 efflux.

    PubMed

    Ruehr, Nadine K; Offermann, Christine A; Gessler, Arthur; Winkler, Jana Barbro; Ferrio, Juan Pedro; Buchmann, Nina; Barnard, Romain L

    2009-12-01

    *Recent studies have highlighted a direct, fast transfer of recently assimilated C from the tree canopy to the soil. However, the effect of environmental changes on this flux remains largely unknown. *We investigated the effects of drought on the translocation of recently assimilated C, by pulse-labelling 1.5-yr-old beech tree mesocosms with (13)CO(2). (13)C signatures were then measured daily for 1 wk in leaves, twigs, coarse and fine root water-soluble and total organic matter, phloem organic matter, soil microbial biomass and soil CO(2) efflux. *Drought reduced C assimilation and doubled the residence time of recently assimilated C in leaf biomass. In phloem organic matter, the (13)C label peaked immediately after labelling then decayed exponentially in the control treatment, while under drought it peaked 4 d after labelling. In soil microbial biomass, the label peaked 1 d after labelling in the control treatment, whereas under drought no peak was measured. Two days after labelling, drought decreased the contribution of recently assimilated C to soil CO(2) efflux by 33%. *Our study showed that drought reduced the coupling between canopy photosynthesis and belowground processes. This will probably affect soil biogeochemical cycling, with potential consequences including slower soil nitrogen cycling and changes in C-sequestration potential under future climate conditions.

  4. Multisubstrate Isotope Labeling and Metagenomic Analysis of Active Soil Bacterial Communities

    PubMed Central

    Verastegui, Y.; Cheng, J.; Engel, K.; Kolczynski, D.; Mortimer, S.; Lavigne, J.; Montalibet, J.; Romantsov, T.; Hall, M.; McConkey, B. J.; Rose, D. R.; Tomashek, J. J.; Scott, B. R.

    2014-01-01

    ABSTRACT Soil microbial diversity represents the largest global reservoir of novel microorganisms and enzymes. In this study, we coupled functional metagenomics and DNA stable-isotope probing (DNA-SIP) using multiple plant-derived carbon substrates and diverse soils to characterize active soil bacterial communities and their glycoside hydrolase genes, which have value for industrial applications. We incubated samples from three disparate Canadian soils (tundra, temperate rainforest, and agricultural) with five native carbon (12C) or stable-isotope-labeled (13C) carbohydrates (glucose, cellobiose, xylose, arabinose, and cellulose). Indicator species analysis revealed high specificity and fidelity for many uncultured and unclassified bacterial taxa in the heavy DNA for all soils and substrates. Among characterized taxa, Actinomycetales (Salinibacterium), Rhizobiales (Devosia), Rhodospirillales (Telmatospirillum), and Caulobacterales (Phenylobacterium and Asticcacaulis) were bacterial indicator species for the heavy substrates and soils tested. Both Actinomycetales and Caulobacterales (Phenylobacterium) were associated with metabolism of cellulose, and Alphaproteobacteria were associated with the metabolism of arabinose; members of the order Rhizobiales were strongly associated with the metabolism of xylose. Annotated metagenomic data suggested diverse glycoside hydrolase gene representation within the pooled heavy DNA. By screening 2,876 cloned fragments derived from the 13C-labeled DNA isolated from soils incubated with cellulose, we demonstrate the power of combining DNA-SIP, multiple-displacement amplification (MDA), and functional metagenomics by efficiently isolating multiple clones with activity on carboxymethyl cellulose and fluorogenic proxy substrates for carbohydrate-active enzymes. PMID:25028422

  5. Cold- and Growing-Season Microbial Substrate Use in Arctic Tundra Soil

    NASA Astrophysics Data System (ADS)

    Schimel, J.; McMahon, S.

    2006-12-01

    Microbial communities will play a critical role in determining arctic ecosystem response to warming due to global climate change since decomposition, which is responsible for both CO2 evolution and plant nutrient availability, is a microbially-mediated process. Microorganisms living in tundra soil have access to two broad categories of carbon compounds via decomposition: complex polymers such as cellulose, lignin, protein and soil organic matter, and simple monomers such as glucose, phenolics and amino acids. Thermodynamically, labile substrates are easier to degrade because the activation energy of the reaction is lower than for more recalcitrant polymers. Thus, metabolic processes involving simple compounds are more likely under frozen conditions during the cold season. To test this theory, we incubated soils collected at Toolik Lake, Alaska before and after snowmelt and freeze-up with a variety of 13C-labelled substrates to track microbial carbon use during cold- and growing-season conditions. Surprisingly, tussock soils respired more protein-derived carbon under frozen pre-thaw conditions than late growing-season conditions. Organic shrub soils respired more glutamic acid-derived carbon under all conditions. Since nitrogen is more abundant in shrub than tussock soils, microbes in the shrub soil can afford to respire glutamic acid as an energy source rather than incorporate it into microbial biomass as a nitrogen source. This study indicates that winter substrate use may not follow predictions made strictly on a thermodynamic basis and hints at the complex nature of cold-tolerant microorganisms.

  6. Drought effects on allocation of recent carbon: From beech leaves to soil CO2 efflux

    NASA Astrophysics Data System (ADS)

    Ruehr, N. K.; Offermann, C. A.; Gessler, A.; Winkler, J. B.; Buchmann, N. C.; Barnard, R. L.

    2009-12-01

    Recent studies have highlighted a direct and fast transfer of recently-assimilated carbon from tree canopy to roots and soil microorganisms. However, the response of this carbon flux to environmental conditions remains largely unknown. In the present study, we investigated drought effects on translocation of recently-assimilated carbon, by pulse-labelling 1.5-year old beech tree mesocosms with 13CO2. During the first week after pulse-labelling, 13C signatures were measured daily in leaves, twigs, coarse and fine root water-soluble and total organic matter, phloem organic matter, soil microbial biomass, as well as in soil CO2 efflux. Drought reduced C assimilation and doubled the residence time of recently-assimilated C in leaf biomass. In phloem organic matter, the 13C label peaked immediately after labelling then decayed exponentially in the control treatment, while under drought the peak occurred 4 days after labelling. In soil microbial biomass, the label peaked 1 day after labelling in the control treatment, whereas under drought no peak was measured. The contribution of recently assimilated C to soil CO2 efflux was decreased by 33% in the drought treatment 2 days after labelling. Thus, our study showed that drought reduced both magnitude and velocity of the coupling between canopy photosynthesis and belowground processes in beech mesocosms. This will likely affect soil biogeochemical cycling, with potential consequences including slower soil nitrogen cycling and changes in carbon sequestration potential under future climate conditions.

  7. Changes in herbivore control in arable fields by detrital subsidies depend on predator species and vary in space.

    PubMed

    von Berg, Karsten; Thies, Carsten; Tscharntke, Teja; Scheu, Stefan

    2010-08-01

    Prey from the decomposer subsystem may help sustain predator populations in arable fields. Adding organic residues to agricultural systems may therefore enhance pest control. We investigated whether resource addition (maize mulch) strengthens aboveground trophic cascades in winter wheat fields. Evaluating the flux of the maize-borne carbon into the food web after 9 months via stable isotope analysis allowed differentiating between prey in predator diets originating from the above- and belowground subsystems. Furthermore, we recorded aphid populations in predator-reduced and control plots of no-mulch and mulch addition treatments. All analyzed soil dwelling species incorporated maize-borne carbon. In contrast, only 2 out of 13 aboveground predator species incorporated maize carbon, suggesting that these 2 predators forage on prey from the above- and belowground systems. Supporting this conclusion, densities of these two predator species were increased in the mulch addition fields. Nitrogen isotope signatures suggested that these generalist predators in part fed on Collembola thereby benefiting indirectly from detrital resources. Increased density of these two predator species was associated by increased aphid control but the identity of predators responsible for aphid control varied in space. One of the three wheat fields studied even lacked aphid control despite of mulch-mediated increased density of generalist predators. The results suggest that detrital subsidies quickly enter belowground food webs but only a few aboveground predator species include prey out of the decomposer system into their diet. Variation in the identity of predator species benefiting from detrital resources between sites suggest that, depending on locality, different predator species are subsidised by prey out of the decomposer system and that these predators contribute to aphid control. Therefore, by engineering the decomposer subsystem via detrital subsidies, biological control by

  8. Modelling impacts of climate change on arable crop diseases: progress, challenges and applications.

    PubMed

    Newbery, Fay; Qi, Aiming; Fitt, Bruce Dl

    2016-08-01

    Combining climate change, crop growth and crop disease models to predict impacts of climate change on crop diseases can guide planning of climate change adaptation strategies to ensure future food security. This review summarises recent developments in modelling climate change impacts on crop diseases, emphasises some major challenges and highlights recent trends. The use of multi-model ensembles in climate change modelling and crop modelling is contributing towards measures of uncertainty in climate change impact projections but other aspects of uncertainty remain largely unexplored. Impact assessments are still concentrated on few crops and few diseases but are beginning to investigate arable crop disease dynamics at the landscape level.

  9. Soil carbon sequestration by three perennial legume pastures is greater in deeper soil layers than in the surface soil

    NASA Astrophysics Data System (ADS)

    Guan, X.-K.; Turner, N. C.; Song, L.; Gu, Y.-J.; Wang, T.-C.; Li, F.-M.

    2016-01-01

    Soil organic carbon (SOC) plays a vital role as both a sink for and source of atmospheric carbon. Revegetation of degraded arable land in China is expected to increase soil carbon sequestration, but the role of perennial legumes on soil carbon stocks in semiarid areas has not been quantified. In this study, we assessed the effect of alfalfa (Medicago sativa L.) and two locally adapted forage legumes, bush clover (Lespedeza davurica S.) and milk vetch (Astragalus adsurgens Pall.) on the SOC concentration and SOC stock accumulated annually over a 2 m soil profile. The results showed that the concentration of SOC in the bare soil decreased slightly over the 7 years, while 7 years of legume growth substantially increased the concentration of SOC over the 0-2.0 m soil depth. Over the 7-year growth period the SOC stocks increased by 24.1, 19.9 and 14.6 Mg C ha-1 under the alfalfa, bush clover and milk vetch stands, respectively, and decreased by 4.2 Mg C ha-1 in the bare soil. The sequestration of SOC in the 1-2 m depth of the soil accounted for 79, 68 and 74 % of the SOC sequestered in the 2 m deep soil profile under alfalfa, bush clover and milk vetch, respectively. Conversion of arable land to perennial legume pasture resulted in a significant increase in SOC, particularly at soil depths below 1 m.

  10. The impact of agricultural intensification and land-use change on the European arable flora

    PubMed Central

    Storkey, J.; Meyer, S.; Still, K. S.; Leuschner, C.

    2012-01-01

    The impact of crop management and agricultural land use on the threat status of plants adapted to arable habitats was analysed using data from Red Lists of vascular plants assessed by national experts from 29 European countries. There was a positive relationship between national wheat yields and the numbers of rare, threatened or recently extinct arable plant species in each country. Variance in the relative proportions of species in different threat categories was significantly explained using a combination of fertilizer and herbicide use, with a greater percentage of the variance partitioned to fertilizers. Specialist species adapted to individual crops, such as flax, are among the most threatened. These species have declined across Europe in response to a reduction in the area grown for the crops on which they rely. The increased use of agro-chemicals, especially in central and northwestern Europe, has selected against a larger group of species adapted to habitats with intermediate fertility. There is an urgent need to implement successful conservation strategies to arrest the decline of this functionally distinct and increasingly threatened component of the European flora. PMID:21993499

  11. A First Look at the Turnover Dynamics of Low Molecular Weight Organic Carbon in Shallow and Deep Soils of Coastal Prairie Grassland Ecosystem

    NASA Astrophysics Data System (ADS)

    Mcfarland, J. W.; Lawrence, C. R.; Haw, M.; Waldrop, M. P.

    2015-12-01

    The functional importance of low molecular weight organic compounds (LMWOC) is in disproportion to their abundance within soil organic carbon (SOC) pools. They are critical in driving microbial metabolism, though microbial utilization of LMWOC is likely dependent on C chemistry. Studies of C turnover in soils tend to focus in shallower horizons despite that for many ecosystems a substantial fraction of SOC resides below 1 m. In this study, we examined the fate of two important components of soluble SOC, sugars and carboxylic acids, through a soil profile extending to 150 cm. Our objective was to evaluate the turnover of LMWOC under varying physical, biological, and chemical conditions through the soil column. Our study area is part of a soil chronosequence near Santa Cruz, CA. From the side wall of a soil pit we installed intact soil collars and injected 13C-labeled glucose (GLU), 13C-labeled oxalic acid (OA), or deionized water (control) into the A, B (argillic) , and B/C (mottled) horizons at depths of 25, 75, and 125 cm, respectively. We sampled soil gas for 13CO2 intensively at graduated sampling intervals (6 hours to 2 weeks). The entire experiment was also replicated in the laboratory. We measured dissolved organic C (DOC) and microbial biomass C (MBC), and calculated total recovery of 13C in atmospheric and soil pools. Measures of DOC indicated a significant priming effect in the deepest (mottled) horizon and an increase in MBC in the argillic and mottled horizons. In all instances residence time was significantly lower for GLU than OA and increased with depth for both substrates. Mass balance calculations from the laboratory component indicated stronger retention for GLU than OA for the upper soils; however, this trend reversed below the argillic horizon. We hypothesize the greater retention of OA in the deepest (mottled) soil horizon may result from enhanced organo-metal complexation (e.g., between OA and dissolved Fe or Al). This hypothesis is consistent

  12. Soil organic phosphorus in soils under different land use systems in northeast Germany

    NASA Astrophysics Data System (ADS)

    Slazak, Anna; Freese, Dirk; Hüttl, Reinhard F.

    2010-05-01

    Phosphorus (P) is commonly known as a major plant nutrient, which can act as a limiting factor for plant growth in many ecosystems, including different land use systems. Organic P (Po), transformations in soil are important in determining the overall biological availability of P and additionally Po depletion is caused by land cultivation. It is expected that changes of land use modifies the distribution of soil P among the various P-pools (Ptotal, Plabile, Po), where the Plabile forms are considered to be readily available to plants and Po plays an important role with P nutrition supply for plants. The aim of the study was to measure the different soil P pools under different land use systems. The study was carried out in northeast of Brandenburg in Germany. Different land use systems were studied: i) different in age pine-oak mixed forest stands, ii) silvopastoral land, iii) arable lands. Samples were taken from two mineral soil layers: 0-10 and 10-20 cm. Recently, a variety of analytical methods are available to determine specific Po compounds in soils. The different P forms in the soil were obtained by a sequential P fractionation by using acid and alkaline extractants, which mean that single samples were subjected to increasingly stronger extractants, consequently separating the soil P into fractions based on P solubility. The soil Ptotal for the forest stands ranged from 100 to 183 mg kg -1 whereas Po from 77 to 148 mg kg -1. The Po and Plabile in both soil layers increased significantly with increase of age-old oak trees. The most available-P fraction was Plabile predominate in the oldest pine-oak forest stand, accounting for 29% of soil Ptotal. For the silvopasture and arable study sites the Ptotal content was comparable. However, the highest value of Ptotal was measured in the 30 years old silvopastoral system with 685 mg kg-1 and 728 mg kg-1 at 0-10 cm and 10-20 cm depth, respectively than in arable lands. The results have shown that the 30 years old

  13. Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils

    DOE PAGES

    Eichorst, Stephanie A.; Strasser, Florian; Woyke, Tanja; ...

    2015-08-31

    The combined approach of incubating environmental samples with stable isotope-labeled substrates followed by single-cell analyses through high-resolution secondary ion mass spectrometry (NanoSIMS) or Raman microspectroscopy provides insights into the in situ function of microorganisms. This approach has found limited application in soils presumably due to the dispersal of microbial cells in a large background of particles. We developed a pipeline for the efficient preparation of cell extracts from soils for subsequent single-cell methods by combining cell detachment with separation of cells and soil particles followed by cell concentration. The procedure was evaluated by examining its influence on cell recoveries andmore » microbial community composition across two soils. This approach generated a cell fraction with considerably reduced soil particle load and of sufficient small size to allow single-cell analysis by NanoSIMS, as shown when detecting active N2-fixing and cellulose-responsive microorganisms via 15N2 and 13C-UL-cellulose incubations, respectively. The same procedure was also applicable for Raman microspectroscopic analyses of soil microorganisms, assessed via microcosm incubations with a 13C-labeled carbon source and deuterium oxide (D2O, a general activity marker). Lastly, the described sample preparation procedure enables single-cell analysis of soil microorganisms using NanoSIMS and Raman microspectroscopy, but should also facilitate single-cell sorting and sequencing.« less

  14. Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils

    PubMed Central

    Eichorst, Stephanie A.; Strasser, Florian; Woyke, Tanja; Schintlmeister, Arno; Wagner, Michael; Woebken, Dagmar

    2015-01-01

    The combined approach of incubating environmental samples with stable isotope-labeled substrates followed by single-cell analyses through high-resolution secondary ion mass spectrometry (NanoSIMS) or Raman microspectroscopy provides insights into the in situ function of microorganisms. This approach has found limited application in soils presumably due to the dispersal of microbial cells in a large background of particles. We developed a pipeline for the efficient preparation of cell extracts from soils for subsequent single-cell methods by combining cell detachment with separation of cells and soil particles followed by cell concentration. The procedure was evaluated by examining its influence on cell recoveries and microbial community composition across two soils. This approach generated a cell fraction with considerably reduced soil particle load and of sufficient small size to allow single-cell analysis by NanoSIMS, as shown when detecting active N2-fixing and cellulose-responsive microorganisms via 15N2 and 13C-UL-cellulose incubations, respectively. The same procedure was also applicable for Raman microspectroscopic analyses of soil microorganisms, assessed via microcosm incubations with a 13C-labeled carbon source and deuterium oxide (D2O, a general activity marker). The described sample preparation procedure enables single-cell analysis of soil microorganisms using NanoSIMS and Raman microspectroscopy, but should also facilitate single-cell sorting and sequencing. PMID:26324854

  15. Reintroduction of rare arable plants by seed transfer. What are the optimal sowing rates?

    PubMed

    Lang, Marion; Prestele, Julia; Fischer, Christina; Kollmann, Johannes; Albrecht, Harald

    2016-08-01

    During the past decades, agro-biodiversity has markedly declined and some species are close to extinction in large parts of Europe. Reintroduction of rare arable plant species in suitable habitats could counteract this negative trend. The study investigates optimal sowing rates of three endangered species (Legousia speculum-veneris (L.) Chaix, Consolida regalis Gray, and Lithospermum arvense L.), in terms of establishment success, seed production, and crop yield losses.A field experiment with partial additive design was performed in an organically managed winter rye stand with study species added in ten sowing rates of 5-10,000 seeds m(-2). They were sown as a single species or as a three-species mixture (pure vs. mixed sowing) and with vs. without removal of spontaneous weeds. Winter rye was sown at a fixed rate of 350 grains m(-2). Performance of the study species was assessed as plant establishment and seed production. Crop response was determined as grain yield.Plant numbers and seed production were significantly affected by the sowing rate, but not by sowing type (pure vs. mixed sowing of the three study species), and weed removal. All rare arable plant species established and reproduced at sowing rates >25 seeds m(-2), with best performance of L. speculum-veneris. Negative density effects occurred to some extent for plant establishment and more markedly for seed production.The impact of the three study species on crop yield followed sigmoidal functions. Depending on the species, a yield loss of 10% occurred at >100 seeds m(-2). Synthesis and applications: The study shows that reintroduction of rare arable plants by seed transfer is a suitable method to establish them on extensively managed fields, for example, in organic farms with low nutrient level and without mechanical weed control. Sowing rates of 100 seeds m(-2) for C. regalis and L. arvense, and 50 seeds m(-2) for L. speculum-veneris are recommended, to achieve successful establishment

  16. Soil 13C Dynamics in Aggregates Across a Soil Profile Under an Established Miscanthus System

    NASA Astrophysics Data System (ADS)

    Dondini, M.; Groenigen, K. J.; Jones, M.

    2008-12-01

    Soils are the largest pool of terrestrial organic carbon (C), containing nearly three times the amount of C as the atmosphere. Environmental changes that affect soil C dynamics could slow down the rise in atmospheric CO2 and associated warming by promoting soil C storage. Our capacity to predict the consequences for global change therefore depends on a better understanding of the distribution and controls of soil organic C and how vegetation change may affect SOC distributions. One land cover change of particular interest involves the establishment of bio energy crop stands. The full mitigation potential of bio energy crops cannot be considered without taking into account their effect on soil C dynamics. Miscanthus, a perennial C4 grass from Eastern Asia, has recently received considerable interest as a bio-energy crop. For that reason, we analyzed the C content and the 13C signatures across the soil profile in a 14 year old Miscanthus system, established on former arable land. We combined SOM fractionation techniques by size and density, allowing us to investigate small shifts in soil C stores that would be significant in the long term, but that might not be detected by conventional methodologies. The 13C signal of the various SOM fractions allowed us to distinguish between Miscanthus-derived vs. native soil organic C. Soils under Miscanthus contained 796 g C/m2 in the 0-15 cm layer, and 1233g C/m2 in the 15- 30 cm layer. These values are significantly higher than soil C contents in the arable land. Macroaggregates under Miscanthus contain more than twice as much C compared to arable land, showing a decrease in soil C content with decreasing aggregate size. These differences are largely caused by soil C storage in the microaggregate within macroaggregates fraction. Under Miscanthus, this fraction contains 440 g C/m2 and 488 g C/m2 at 0-15 cm and 15-30 cm respectively, while under the arable land it has mean values of 174 g C/m2 and 353 g C/m2. Our data suggest a

  17. Distribution of selenium and cadmium in soil-rice system of selenium-rich area in Hainan, China.

    PubMed

    Wang, Dengfeng; Wei, Zhiyuan; Tang, Shumei; Qi, Zhiping

    2014-09-01

    Rice, which is the staple food in East Asia, is a source of Selenium (Se) and Cadmium (Cd). The distribution of Se and Cd in soil-rice system is significant to human nutrition and public health. This study is to explore the distribution of Se and Cd in arable land soils and their distribution in polished rice and stalks of Se-rich area. A total of 63 soil samples and 126 rice samples (63 groups of rice grains and stalk samples) were collected from West Hainan Island to determine Se and Cd concentrations. The results suggested the concentration of Se in soil was higher than average level in China, and Cd content was lower than the agricultural land-use threshold of China. The distribution of Se and Cd in arable land soil was primarily determined by diagenesis and mineralization. Se and Cd were more inclined to accumulate in stalks than rice grains, and the contents in polished rice were correlated with that in stalk. Acidification of arable land soil will threaten human nutrition and health for the bioaccumulation factor of Se in polished rice decreased significantly with the decrease of soil pH, while that of Cd in polished rice increased significantly. Therefore, application of lime or alkaline fertilizers in arable land soil of Se-rich area can promote the accumulation of Se in polished rice but reduced the intake of Cd in rice crops.

  18. Reducing pesticide use while preserving crop productivity and profitability on arable farms.

    PubMed

    Lechenet, Martin; Dessaint, Fabrice; Py, Guillaume; Makowski, David; Munier-Jolain, Nicolas

    2017-03-01

    Achieving sustainable crop production while feeding an increasing world population is one of the most ambitious challenges of this century(1). Meeting this challenge will necessarily imply a drastic reduction of adverse environmental effects arising from agricultural activities(2). The reduction of pesticide use is one of the critical drivers to preserve the environment and human health. Pesticide use could be reduced through the adoption of new production strategies(3-5); however, whether substantial reductions of pesticide use are possible without impacting crop productivity and profitability is debatable(6-17). Here, we demonstrated that low pesticide use rarely decreases productivity and profitability in arable farms. We analysed the potential conflicts between pesticide use and productivity or profitability with data from 946 non-organic arable commercial farms showing contrasting levels of pesticide use and covering a wide range of production situations in France. We failed to detect any conflict between low pesticide use and both high productivity and high profitability in 77% of the farms. We estimated that total pesticide use could be reduced by 42% without any negative effects on both productivity and profitability in 59% of farms from our national network. This corresponded to an average reduction of 37, 47 and 60% of herbicide, fungicide and insecticide use, respectively. The potential for reducing pesticide use appeared higher in farms with currently high pesticide use than in farms with low pesticide use. Our results demonstrate that pesticide reduction is already accessible to farmers in most production situations. This would imply profound changes in market organization and trade balance.

  19. Quality of fresh organic matter affects priming of soil organic matter and substrate utilization patterns of microbes

    PubMed Central

    Wang, Hui; Boutton, Thomas W.; Xu, Wenhua; Hu, Guoqing; Jiang, Ping; Bai, Edith

    2015-01-01

    Changes in biogeochemical cycles and the climate system due to human activities are expected to change the quantity and quality of plant litter inputs to soils. How changing quality of fresh organic matter (FOM) might influence the priming effect (PE) on soil organic matter (SOM) mineralization is still under debate. Here we determined the PE induced by two 13C-labeled FOMs with contrasting nutritional quality (leaf vs. stalk of Zea mays L.). Soils from two different forest types yielded consistent results: soils amended with leaf tissue switched faster from negative PE to positive PE due to greater microbial growth compared to soils amended with stalks. However, after 16 d of incubation, soils amended with stalks had a higher PE than those amended with leaf. Phospholipid fatty acid (PLFA) results suggested that microbial demand for carbon and other nutrients was one of the major determinants of the PE observed. Therefore, consideration of both microbial demands for nutrients and FOM supply simultaneously is essential to understand the underlying mechanisms of PE. Our study provided evidence that changes in FOM quality could affect microbial utilization of substrate and PE on SOM mineralization, which may exacerbate global warming problems under future climate change. PMID:25960162

  20. Quality of fresh organic matter affects priming of soil organic matter and substrate utilization patterns of microbes

    NASA Astrophysics Data System (ADS)

    Wang, Hui; Boutton, Thomas W.; Xu, Wenhua; Hu, Guoqing; Jiang, Ping; Bai, Edith

    2015-05-01

    Changes in biogeochemical cycles and the climate system due to human activities are expected to change the quantity and quality of plant litter inputs to soils. How changing quality of fresh organic matter (FOM) might influence the priming effect (PE) on soil organic matter (SOM) mineralization is still under debate. Here we determined the PE induced by two 13C-labeled FOMs with contrasting nutritional quality (leaf vs. stalk of Zea mays L.). Soils from two different forest types yielded consistent results: soils amended with leaf tissue switched faster from negative PE to positive PE due to greater microbial growth compared to soils amended with stalks. However, after 16 d of incubation, soils amended with stalks had a higher PE than those amended with leaf. Phospholipid fatty acid (PLFA) results suggested that microbial demand for carbon and other nutrients was one of the major determinants of the PE observed. Therefore, consideration of both microbial demands for nutrients and FOM supply simultaneously is essential to understand the underlying mechanisms of PE. Our study provided evidence that changes in FOM quality could affect microbial utilization of substrate and PE on SOM mineralization, which may exacerbate global warming problems under future climate change.

  1. Quality of fresh organic matter affects priming of soil organic matter and substrate utilization patterns of microbes.

    PubMed

    Wang, Hui; Boutton, Thomas W; Xu, Wenhua; Hu, Guoqing; Jiang, Ping; Bai, Edith

    2015-05-11

    Changes in biogeochemical cycles and the climate system due to human activities are expected to change the quantity and quality of plant litter inputs to soils. How changing quality of fresh organic matter (FOM) might influence the priming effect (PE) on soil organic matter (SOM) mineralization is still under debate. Here we determined the PE induced by two (13)C-labeled FOMs with contrasting nutritional quality (leaf vs. stalk of Zea mays L.). Soils from two different forest types yielded consistent results: soils amended with leaf tissue switched faster from negative PE to positive PE due to greater microbial growth compared to soils amended with stalks. However, after 16 d of incubation, soils amended with stalks had a higher PE than those amended with leaf. Phospholipid fatty acid (PLFA) results suggested that microbial demand for carbon and other nutrients was one of the major determinants of the PE observed. Therefore, consideration of both microbial demands for nutrients and FOM supply simultaneously is essential to understand the underlying mechanisms of PE. Our study provided evidence that changes in FOM quality could affect microbial utilization of substrate and PE on SOM mineralization, which may exacerbate global warming problems under future climate change.

  2. Potential of temperate agricultural soils for carbon sequestration: A meta-analysis of land-use effects.

    PubMed

    Kämpf, Immo; Hölzel, Norbert; Störrle, Maria; Broll, Gabriele; Kiehl, Kathrin

    2016-10-01

    Restoring depleted soil organic carbon (SOC) stocks of arable land to remove carbon from the atmosphere and offset fossil fuel emissions is a promising strategy for the mitigation of climate change. In agroecosystems conservational tillage practices and the abandonment of formerly plowed fields (ex-arable land) are shown to have the highest potential to sequester SOC. Nevertheless reported sequestration rates vary and the effects of environmental site conditions remain poorly understood. Our results are based on a meta-analysis of 273 paired SOC estimates from 65 publications which included only mineral soils from the temperate zone. SOC stocks of ex-arable grasslands with an average of 14years since abandonment were 18% larger compared to the SOC of arable land. Likewise, SOC stocks of never-plowed grassland plots were 11% larger than the SOC stocks of abandoned fields. The average sequestration rate was 0.72t Cha(-1)yr(-1). Semi-arid and sub-humid climate as well as low initial SOC stocks positively affected proportional SOC gains suggesting that the recovery of carbon stocks is not limited by low primary production. Therefore, the northward shift of cultivation areas in the temperate zone will lead to the abandonment of soils with high SOC recovery potential. However, if native soils are opened up elsewhere to compensate for yield losses due to abandonment the surplus of SOC in ex-arable land can easily be overcompensated by cultivation losses.

  3. Nitrous oxide and nitrate concentration in under-drainage from arable fields subject to diffuse pollution mitigation measures

    NASA Astrophysics Data System (ADS)

    Hama-Aziz, Zanist; Hiscock, Kevin; Adams, Christopher; Reid, Brian

    2016-04-01

    Atmospheric nitrous oxide concentrations are increasing by 0.3% annually and a major source of this greenhouse gas is agriculture. Indirect emissions of nitrous oxide (e.g. from groundwater and surface water) account for about quarter of total nitrous oxide emissions. However, these indirect emissions are subject to uncertainty, mainly due to the range in reported emission factors. It's hypothesised in this study that cover cropping and implementing reduced (direct drill) cultivation in intensive arable systems will reduce dissolved nitrate concentration and subsequently indirect nitrous oxide emissions. To test the hypothesis, seven fields with a total area of 102 ha in the Wensum catchment in eastern England have been chosen for experimentation together with two fields (41 ha) under conventional cultivation (deep inversion ploughing) for comparison. Water samples from field under-drainage have been collected for nitrate and nitrous oxide measurement on a weekly basis from April 2013 for two years from both cultivation areas. A purge and trap preparation line connected to a Shimadzu GC-8A gas chromatograph fitted with an electron capture detector was used for dissolved nitrous oxide analysis. Results revealed that with an oilseed radish cover crop present, the mean concentration of nitrate, which is the predominant form of N, was significantly depleted from 13.9 mg N L-1 to 2.5 mg N L-1. However, slightly higher mean nitrous oxide concentrations under the cover crop of 2.61 μg N L-1 compared to bare fields of 2.23 μg N L-1 were observed. Different inversion intensity of soil tended to have no effect on nitrous oxide and nitrate concentrations. The predominant production mechanism for nitrous oxide was nitrification process and the significant reduction of nitrate was due to plant uptake rather than denitrification. It is concluded that although cover cropping might cause a slight increase of indirect nitrous oxide emission, it can be a highly effective

  4. Plant roots alter microbial potential for mediation of soil organic carbon decomposition

    NASA Astrophysics Data System (ADS)

    Firestone, M.; Shi, S.; Herman, D.; He, Z.; Zhou, J.

    2014-12-01

    Plant root regulation of soil organic carbon (SOC) decomposition is a key controller of terrestrial C-cycling. Although many studies have tested possible mechanisms underlying plant "priming" of decomposition, few have investigated the microbial mediators of decomposition, which can be greatly influenced by plant activities. Here we examined effects of Avena fatua roots on decomposition of 13C-labeled root litter in a California grassland soil over two simulated growing-seasons. The presence of plant roots consistently suppressed rates of litter decomposition. Reduction of inorganic nitrogen (N) concentration in soil reduced but did not completely relieve this suppressive effect. The presence of plants significantly altered the abundance, composition and functional potential of microbial communities. Significantly higher signal intensities of genes capable of degrading low molecular weight organic compounds (e.g., glucose, formate and malate) were observed in microbial communities from planted soils, while microorganisms in unplanted soils had higher relative abundances of genes involved in degradation of some macromolecules (e.g., hemicellulose and lignin). Additionally, compared to unplanted soils, microbial communities from planted soils had higher signal intensities of proV and proW, suggesting microbial osmotic stress in planted soils. Possible mechanisms for the observed inhibition of decomposition are 1) microbes preferentially using simple substrates from root exudates and 2) soil drying by plant evapotranspiration impairing microbial activity. We propose a simple data-based model suggesting that the impacts of roots, the soil environment, and microbial community composition on decomposition processes result from impacts of these factors on the soil microbial functional gene potential.

  5. Input of easily available organic C and N stimulates microbial decomposition of soil organic matter in arctic permafrost soil.

    PubMed

    Wild, Birgit; Schnecker, Jörg; Alves, Ricardo J Eloy; Barsukov, Pavel; Bárta, Jiří; Capek, Petr; Gentsch, Norman; Gittel, Antje; Guggenberger, Georg; Lashchinskiy, Nikolay; Mikutta, Robert; Rusalimova, Olga; Santrůčková, Hana; Shibistova, Olga; Urich, Tim; Watzka, Margarete; Zrazhevskaya, Galina; Richter, Andreas

    2014-08-01

    Rising temperatures in the Arctic can affect soil organic matter (SOM) decomposition directly and indirectly, by increasing plant primary production and thus the allocation of plant-derived organic compounds into the soil. Such compounds, for example root exudates or decaying fine roots, are easily available for microorganisms, and can alter the decomposition of older SOM ("priming effect"). We here report on a SOM priming experiment in the active layer of a permafrost soil from the central Siberian Arctic, comparing responses of organic topsoil, mineral subsoil, and cryoturbated subsoil material (i.e., poorly decomposed topsoil material subducted into the subsoil by freeze-thaw processes) to additions of (13)C-labeled glucose, cellulose, a mixture of amino acids, and protein (added at levels corresponding to approximately 1% of soil organic carbon). SOM decomposition in the topsoil was barely affected by higher availability of organic compounds, whereas SOM decomposition in both subsoil horizons responded strongly. In the mineral subsoil, SOM decomposition increased by a factor of two to three after any substrate addition (glucose, cellulose, amino acids, protein), suggesting that the microbial decomposer community was limited in energy to break down more complex components of SOM. In the cryoturbated horizon, SOM decomposition increased by a factor of two after addition of amino acids or protein, but was not significantly affected by glucose or cellulose, indicating nitrogen rather than energy limitation. Since the stimulation of SOM decomposition in cryoturbated material was not connected to microbial growth or to a change in microbial community composition, the additional nitrogen was likely invested in the production of extracellular enzymes required for SOM decomposition. Our findings provide a first mechanistic understanding of priming in permafrost soils and suggest that an increase in the availability of organic carbon or nitrogen, e.g., by increased plant

  6. Input of easily available organic C and N stimulates microbial decomposition of soil organic matter in arctic permafrost soil

    PubMed Central

    Wild, Birgit; Schnecker, Jörg; Alves, Ricardo J. Eloy; Barsukov, Pavel; Bárta, Jiří; Čapek, Petr; Gentsch, Norman; Gittel, Antje; Guggenberger, Georg; Lashchinskiy, Nikolay; Mikutta, Robert; Rusalimova, Olga; Šantrůčková, Hana; Shibistova, Olga; Urich, Tim; Watzka, Margarete; Zrazhevskaya, Galina; Richter, Andreas

    2014-01-01

    Rising temperatures in the Arctic can affect soil organic matter (SOM) decomposition directly and indirectly, by increasing plant primary production and thus the allocation of plant-derived organic compounds into the soil. Such compounds, for example root exudates or decaying fine roots, are easily available for microorganisms, and can alter the decomposition of older SOM (“priming effect”). We here report on a SOM priming experiment in the active layer of a permafrost soil from the central Siberian Arctic, comparing responses of organic topsoil, mineral subsoil, and cryoturbated subsoil material (i.e., poorly decomposed topsoil material subducted into the subsoil by freeze–thaw processes) to additions of 13C-labeled glucose, cellulose, a mixture of amino acids, and protein (added at levels corresponding to approximately 1% of soil organic carbon). SOM decomposition in the topsoil was barely affected by higher availability of organic compounds, whereas SOM decomposition in both subsoil horizons responded strongly. In the mineral subsoil, SOM decomposition increased by a factor of two to three after any substrate addition (glucose, cellulose, amino acids, protein), suggesting that the microbial decomposer community was limited in energy to break down more complex components of SOM. In the cryoturbated horizon, SOM decomposition increased by a factor of two after addition of amino acids or protein, but was not significantly affected by glucose or cellulose, indicating nitrogen rather than energy limitation. Since the stimulation of SOM decomposition in cryoturbated material was not connected to microbial growth or to a change in microbial community composition, the additional nitrogen was likely invested in the production of extracellular enzymes required for SOM decomposition. Our findings provide a first mechanistic understanding of priming in permafrost soils and suggest that an increase in the availability of organic carbon or nitrogen, e.g., by increased

  7. Variability of soil microbial properties: effects of sampling, handling and storage.

    PubMed

    Cernohlávková, Jitka; Jarkovský, Jirí; Nesporová, Michala; Hofman, Jakub

    2009-11-01

    We investigated the effect of soil spatial variability within the sampling site scale, the effects of sample sieving (1, 2 and 4mm), and storage conditions up to 32 weeks (wet at 4 degrees C, -20 degrees C and air dried) on microbial biomass C, respiration, ammonification and nitrification activities in arable, grassland and forest soil. In general, all results were dependent on soil type. Arable soil showed the highest spatial variability, followed by grassland and forest soil. Sieving did not cause large differences; however, higher biomass C and respiration activity were observed in the 1mm than in the 4mm fraction. Storage at 4 degrees C seemed to be the most appropriate up to 8 weeks showing only minor changes of microbial parameters. Freezing of soils resulted in large increase of respiration. Dried storage indicated disruption of microbial communities even after 2 weeks.

  8. Microbial carbon mineralization in tropical lowland and montane forest soils of Peru

    PubMed Central

    Whitaker, Jeanette; Ostle, Nicholas; McNamara, Niall P.; Nottingham, Andrew T.; Stott, Andrew W.; Bardgett, Richard D.; Salinas, Norma; Ccahuana, Adan J. Q.; Meir, Patrick

    2014-01-01

    Climate change is affecting the amount and complexity of plant inputs to tropical forest soils. This is likely to influence the carbon (C) balance of these ecosystems by altering decomposition processes e.g., “positive priming effects” that accelerate soil organic matter mineralization. However, the mechanisms determining the magnitude of priming effects are poorly understood. We investigated potential mechanisms by adding 13C labeled substrates, as surrogates of plant inputs, to soils from an elevation gradient of tropical lowland and montane forests. We hypothesized that priming effects would increase with elevation due to increasing microbial nitrogen limitation, and that microbial community composition would strongly influence the magnitude of priming effects. Quantifying the sources of respired C (substrate or soil organic matter) in response to substrate addition revealed no consistent patterns in priming effects with elevation. Instead we found that substrate quality (complexity and nitrogen content) was the dominant factor controlling priming effects. For example a nitrogenous substrate induced a large increase in soil organic matter mineralization whilst a complex C substrate caused negligible change. Differences in the functional capacity of specific microbial groups, rather than microbial community composition per se, were responsible for these substrate-driven differences in priming effects. Our findings suggest that the microbial pathways by which plant inputs and soil organic matter are mineralized are determined primarily by the quality of plant inputs and the functional capacity of microbial taxa, rather than the abiotic properties of the soil. Changes in the complexity and stoichiometry of plant inputs to soil in response to climate change may therefore be important in regulating soil C dynamics in tropical forest soils. PMID:25566230

  9. Microbial carbon mineralization in tropical lowland and montane forest soils of Peru.

    PubMed

    Whitaker, Jeanette; Ostle, Nicholas; McNamara, Niall P; Nottingham, Andrew T; Stott, Andrew W; Bardgett, Richard D; Salinas, Norma; Ccahuana, Adan J Q; Meir, Patrick

    2014-01-01

    Climate change is affecting the amount and complexity of plant inputs to tropical forest soils. This is likely to influence the carbon (C) balance of these ecosystems by altering decomposition processes e.g., "positive priming effects" that accelerate soil organic matter mineralization. However, the mechanisms determining the magnitude of priming effects are poorly understood. We investigated potential mechanisms by adding (13)C labeled substrates, as surrogates of plant inputs, to soils from an elevation gradient of tropical lowland and montane forests. We hypothesized that priming effects would increase with elevation due to increasing microbial nitrogen limitation, and that microbial community composition would strongly influence the magnitude of priming effects. Quantifying the sources of respired C (substrate or soil organic matter) in response to substrate addition revealed no consistent patterns in priming effects with elevation. Instead we found that substrate quality (complexity and nitrogen content) was the dominant factor controlling priming effects. For example a nitrogenous substrate induced a large increase in soil organic matter mineralization whilst a complex C substrate caused negligible change. Differences in the functional capacity of specific microbial groups, rather than microbial community composition per se, were responsible for these substrate-driven differences in priming effects. Our findings suggest that the microbial pathways by which plant inputs and soil organic matter are mineralized are determined primarily by the quality of plant inputs and the functional capacity of microbial taxa, rather than the abiotic properties of the soil. Changes in the complexity and stoichiometry of plant inputs to soil in response to climate change may therefore be important in regulating soil C dynamics in tropical forest soils.

  10. Unearthing the ecology of soil microorganisms using a high resolution DNA-SIP approach to explore cellulose and xylose metabolism in soil

    DOE PAGES

    Pepe-Ranney, Charles; Campbell, Ashley N.; Koechli, Chantal N.; ...

    2016-05-12

    We explored microbial contributions to decomposition using a sophisticated approach to DNA Stable Isotope Probing (SIP). Our experiment evaluated the dynamics and ecological characteristics of functionally defined microbial groups that metabolize labile and structural C in soils. We added to soil a complex amendment representing plant derived organic matter substituted with either 13C-xylose or 13C-cellulose to represent labile and structural C pools derived from abundant components of plant biomass. We found evidence for 13C-incorporation into DNA from 13C-xylose and 13C-cellulose in 49 and 63 operational taxonomic units (OTUs), respectively. The types of microorganisms that assimilated 13C in the 13C-xylose treatmentmore » changed over time being predominantly Firrnicutes at day 1 followed by Bacteroidetes at day 3 and then Actinobacteria at day 7. These 13C-labeling dynamics suggest labile C traveled through different trophic levels. In contrast, microorganisms generally metabolized cellulose-C after 14 days and did not change to the same extent in phylogenetic composition over time. Furthermore, microorganisms that metabolized cellulose-C belonged to poorly characterized but cosmopolitan soil lineages including Verrucomicrobia, Chlorotlexi, and Planctomycetes.« less

  11. Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil.

    PubMed

    Pepe-Ranney, Charles; Campbell, Ashley N; Koechli, Chantal N; Berthrong, Sean; Buckley, Daniel H

    2016-01-01

    We explored microbial contributions to decomposition using a sophisticated approach to DNA Stable Isotope Probing (SIP). Our experiment evaluated the dynamics and ecological characteristics of functionally defined microbial groups that metabolize labile and structural C in soils. We added to soil a complex amendment representing plant derived organic matter substituted with either (13)C-xylose or (13)C-cellulose to represent labile and structural C pools derived from abundant components of plant biomass. We found evidence for (13)C-incorporation into DNA from (13)C-xylose and (13)C-cellulose in 49 and 63 operational taxonomic units (OTUs), respectively. The types of microorganisms that assimilated (13)C in the (13)C-xylose treatment changed over time being predominantly Firmicutes at day 1 followed by Bacteroidetes at day 3 and then Actinobacteria at day 7. These (13)C-labeling dynamics suggest labile C traveled through different trophic levels. In contrast, microorganisms generally metabolized cellulose-C after 14 days and did not change to the same extent in phylogenetic composition over time. Microorganisms that metabolized cellulose-C belonged to poorly characterized but cosmopolitan soil lineages including Verrucomicrobia, Chloroflexi, and Planctomycetes.

  12. Unearthing the Ecology of Soil Microorganisms Using a High Resolution DNA-SIP Approach to Explore Cellulose and Xylose Metabolism in Soil

    PubMed Central

    Pepe-Ranney, Charles; Campbell, Ashley N.; Koechli, Chantal N.; Berthrong, Sean; Buckley, Daniel H.

    2016-01-01

    We explored microbial contributions to decomposition using a sophisticated approach to DNA Stable Isotope Probing (SIP). Our experiment evaluated the dynamics and ecological characteristics of functionally defined microbial groups that metabolize labile and structural C in soils. We added to soil a complex amendment representing plant derived organic matter substituted with either 13C-xylose or 13C-cellulose to represent labile and structural C pools derived from abundant components of plant biomass. We found evidence for 13C-incorporation into DNA from 13C-xylose and 13C-cellulose in 49 and 63 operational taxonomic units (OTUs), respectively. The types of microorganisms that assimilated 13C in the 13C-xylose treatment changed over time being predominantly Firmicutes at day 1 followed by Bacteroidetes at day 3 and then Actinobacteria at day 7. These 13C-labeling dynamics suggest labile C traveled through different trophic levels. In contrast, microorganisms generally metabolized cellulose-C after 14 days and did not change to the same extent in phylogenetic composition over time. Microorganisms that metabolized cellulose-C belonged to poorly characterized but cosmopolitan soil lineages including Verrucomicrobia, Chloroflexi, and Planctomycetes. PMID:27242725

  13. Indirect nitrous oxide emissions from surface water bodies in a lowland arable catchment: a significant contribution to agricultural greenhouse gas budgets?

    PubMed

    Outram, Faye N; Hiscock, Kevin M

    2012-08-07

    In the UK agriculture is by far the largest source of nitrous oxide (N(2)O) emissions. Direct N(2)O emissions as a result of nitrogen (N) application to soils have been well documented in the UK, whereas indirect emissions produced in surface waters and groundwaters from leached N are much less understood with limited data to support IPCC emission factors. Indirect emissions were studied in surface waters in the Upper Thurne, a lowland drained arable catchment in eastern England. All surface waters were found to have dissolved N(2)O concentrations above that expected if in equilibrium with ambient concentrations, demonstrating all surface waters were acting as a source of N(2)O. The drainage channels represented 86% of the total indirect N(2)O flux, followed by wetland areas, 11%, and the river, 3%. The dense drainage network was found to have the highest dissolved N(2)O concentrations of all the water bodies studied with a combined N(2)O flux of 16 kg N(2)O-N per day in March 2007. Such indirect fluxes are comparable to direct fluxes per hectare and represent a significant proportion of the total N(2)O flux for this catchment. Separate emission factors were established for the three different surface water types within the same catchment, suggesting that the one emission factor used in the Intergovernmental Panel on Climate Change (IPCC) methodology for predicting all indirect N(2)O emissions is inappropriate.

  14. Partitioning in trees and soil (PiTS) - a experimental approach to improve knowledge of forest carbon dynamics

    SciTech Connect

    Warren, Jeffrey; Garten Jr, Charles T; Iversen, Colleen M; Norby, Richard J; Thornton, Peter E; Weston, David; Gu, Lianhong; Brice, Deanne Jane; Childs, Joanne; Evans, R

    2012-01-01

    Summary 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 belowground C flux. We exposed eight 7-year-old loblolly pine 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. A soil pit was dug adjacent to the trees to provide greater access belowground. The impacts of shading on photosynthesis, plant water potential, sap flow, basal area growth, root growth, and soil C exchange 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 soil CO2 efflux. The HS treatment significantly reduced C uptake, sap flow, stem growth and 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. 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 13C of soil CO2 efflux was strongly correlated with phloem 13C on the previous day, or two days earlier. These data detail the timing and relative magnitude of C flux through a young pine stand in relation to environmental conditions. Refinement of belowground sampling will be necessary to adequately separate and quantify the flux of recently fixed C into roots, and fate of that new C as respiratory, mycorrhizal or exudative release, storage or partitioning

  15. Microbial respiration and natural attenuation of benzene contaminated soils investigated by cavity enhanced Raman multi-gas spectroscopy.

    PubMed

    Jochum, Tobias; Michalzik, Beate; Bachmann, Anne; Popp, Jürgen; Frosch, Torsten

    2015-05-07

    Soil and groundwater contamination with benzene can cause serious environmental damage. However, many soil microorganisms are capable to adapt and are known to strongly control the fate of organic contamination. Innovative cavity enhanced Raman multi-gas spectroscopy (CERS) was applied to investigate the short-term response of the soil micro-flora to sudden surface contamination with benzene regarding the temporal variations of gas products and their exchange rates with the adjacent atmosphere. (13)C-labeled benzene was spiked on a silty-loamy soil column in order to track and separate the changes in heterotrophic soil respiration - involving (12)CO2 and O2- from the natural attenuation process of benzene degradation to ultimately form (13)CO2. The respiratory quotient (RQ) decreased from a value 0.98 to 0.46 directly after the spiking and increased again within 33 hours to a value of 0.72. This coincided with the maximum (13)CO2 concentration rate (0.63 μmol m(-2) s(-1)), indicating the highest benzene degradation at 33 hours after the spiking event. The diffusion of benzene in the headspace and the biodegradation into (13)CO2 were simultaneously monitored and 12 days after the benzene spiking no measurable degradation was detected anymore. The RQ finally returned to a value of 0.96 demonstrating the reestablished aerobic respiration.

  16. Monitoring microbial biomass and respiration in different soils from the Czech Republic--a summary of results.

    PubMed

    Hofman, Jakub; Dusek, Ladislav; Klánová, Jana; Bezchlebová, Jitka; Holoubek, Ivan

    2004-03-01

    The microbial biomass (Cbio), respiration (basal respiration (BR) and potential respiration (PR)), and derived indices for 520 independent soil samples of 117 different soils from the Czech Republic were statistically analysed. The broad range of soil samples allowed the stepwise breakdown of the database into six reasonable categories of soil: arable soils, loamy grassland soils, sandy grassland soils with weak organic matter content, sandy grassland soils with moderate organic matter content, forest soils with moderate organic matter content, and forest organic soils with rich organic matter content. Because soil microbiology lacks benchmarking values, the ranges of the microbial characteristics for these categories were stated and are presented here. The separation into soil groups narrowed the ranges enough to be useful for comparative purposes. The groups displayed significant differences in basal microbial parameters. The lowest microbial biomass was found in arable soils and grassland sandy soils with weak organic matter content. The highest microbial biomass was shown by loamy grassland soils and organic forest soils. Respiration displayed similar results to the microbial biomass. The derived indices revealed less significant differences confirming their inner-standard nature. The relationships between the soil contamination and microbial parameters were not explored because of the confounding effect of soil organic matter. However, it was not shown by the category of grassland sandy soils with weak organic matter content suggesting they could be especially suitable for the biomonitoring of harmful effects of chemicals on soil microorganisms.

  17. A specialist-generalist classification of the arable flora and its response to changes in agricultural practices

    PubMed Central

    2010-01-01

    Background Theory in ecology points out the potential link between the degree of specialisation of organisms and their responses to disturbances and suggests that this could be a key element for understanding the assembly of communities. We evaluated this question for the arable weed flora as this group has scarcely been the focus of ecological studies so far and because weeds are restricted to habitats characterised by very high degrees of disturbance. As such, weeds offer a case study to ask how specialization relates to abundance and distribution of species in relation to the varying disturbance regimes occurring in arable crops. Results We used data derived from an extensive national monitoring network of approximately 700 arable fields scattered across France to quantify the degree of specialisation of 152 weed species using six different ecological methods. We then explored the impact of the level of disturbance occurring in arable fields by comparing the degree of specialisation of weed communities in contrasting field situations. The classification of species as specialist or generalist was consistent between different ecological indices. When applied on a large-scale data set across France, this classification highlighted that monoculture harbour significantly more specialists than crop rotations, suggesting that crop rotation increases abundance of generalist species rather than sets of species that are each specialised to the individual crop types grown in the rotation. Applied to a diachronic dataset, the classification also shows that the proportion of specialist weed species has significantly decreased in cultivated fields over the last 30 years which suggests a biotic homogenization of agricultural landscapes. Conclusions This study shows that the concept of generalist/specialist species is particularly relevant to understand the effect of anthropogenic disturbances on the evolution of plant community composition and that ecological theories

  18. Soil erosion survey using remote sensing images

    NASA Astrophysics Data System (ADS)

    Jakab, Gergely; Kertész, Ádám; Madarász, Balázs; Pálinkás, Melinda; Tóth, Adrienn

    2016-04-01

    Soil erosion is one of the most effective soil degradation processes reducing crop production on arable fields significantly. It also leads to serious environmental hazards such as eutrophication, mud and flesh floods. Beyond the processes there is an urgent need to survey and descript the current degree of erosion of arable lands in order to provide adequate land use techniques and mitigate the harmful effects. Surveying soil erosion is a very time consuming process since soil loss and deposition take place next to each other resulting a rather diverse erosion pattern even within a plot. Remote sensing is a possible way to determine the degree of soil erosion without special efforts taken in the field. The application of images can provide high resolution erosion maps of almost any type of arable fields. The method is based on the identification of the origin of the surface soil layer, i.e. whether it represents an originally deeper laying horizon (e.g. B horizon), or the parent material. A case study was carried out on a Cambisol formed on loess parent material. The soil and the parent rock have various reflectance spectra in the visible range, so this strip was used for the investigations. For map creation "training sites" were used in ArcMap environment. The obtained results suggest that the method is highly effective and useful, however, other properties like moisture content and plant cover can limit automated application. In this case new training sites are needed. The study was supported by the National Research, Development and Innovation Office (NKFIH),), project Nr. 108755 and the support is gratefully acknowledged here. G. Jakab was supported by the János Bolyai Fellowship.

  19. Trophic links between functional groups of arable plants and beetles are stable at a national scale.

    PubMed

    Brooks, David R; Storkey, Jonathan; Clark, Suzanne J; Firbank, Les G; Petit, Sandrine; Woiwod, Ian P

    2012-01-01

    1. There is an urgent need to accurately model how environmental change affects the wide-scale functioning of ecosystems, but advances are hindered by a lack of knowledge of how trophic levels are linked across space. It is unclear which theoretical approach to take to improve modelling of such interactions, but evidence is gathering that linking species responses to their functional traits can increase understanding of ecosystem dynamics. Currently, there are no quantitative studies testing how this approach might improve models of multiple, trophically interacting species, at wide spatial scales. 2. Arable weeds play a foundational role in linking food webs, providing resources for many taxa, including carabid beetles that feed on their seeds and weed-associated invertebrate prey. Here, we model associations between weeds and carabids across farmland in Great Britain (GB), to test the hypothesis that wide-scale trophic links between these groups are structured by their species functional traits. 3. A network of c. 250 arable fields, covering four crops and most lowland areas of GB, was sampled for weed, carabid and invertebrate taxa over 3 years. Data sets of these groups were closely matched in time and space, and each contained numerous species with a range of eco-physiological traits. The consistency of trophic linkages between multiple taxa sharing functional traits was tested within multivariate and log-linear models. 4. Robust links were established between the functional traits of taxa and their trophic interactions. Autumn-germinating, small-seeded weeds were associated with smaller, spring-breeding carabids, more specialised in seed feeding, whereas spring-germinating, large-seeded weeds were associated with a range of larger, autumn-breeding omnivorous carabids. These relationships were strong and dynamic, being independent of changes in invertebrate food resources and consistent across sample dates, crops and regions of GB. 5. We conclude that, in at

  20. Different effects of plant-derived dissolved organic matter (DOM) and urea on the priming of soil organic carbon.

    PubMed

    Qiu, Qingyan; Wu, Lanfang; Ouyang, Zhu; Li, Binbin; Xu, Yanyan

    2016-03-01

    Soil organic carbon (SOC) mineralization is important for the regulation of the global climate and soil fertility. Decomposition of SOC may be significantly affected by the supply of plant-derived labile carbon (C). To investigate the impact of plant-derived dissolved organic matter (DOM) and urea (N) additions on the decomposition of native SOC as well as to elucidate the underlying mechanisms of priming effects (PEs), a batch of incubation experiments was conducted for 250 days by application of (13)C-labeled plant-derived DOM and urea to soils. The direction of PE induced by the addition of DOM was different from the addition of N, i.e. it switched from negative to positive in DOM-amended soils, whereas in the N-treated soil it switched from positive to negative. Adding DOM alone was favorable for soil C sequestration (59 ± 5 mg C per kg soil), whereas adding N alone or together with DOM accelerated the decomposition of native SOC, causing net C losses (-62 ± 4 and -34 ± 31 mg C per kg soil, respectively). These findings indicate that N addition and its interaction with DOM are not favorable for soil C sequestration. Adding DOM alone increased the level of dissolved organic carbon (DOC), but it did not increase the level of soil mineral N. Changes in the ratio of microbial biomass carbon (MBC) to microbial biomass nitrogen (MBN) and microbial metabolic quotient (qCO2) after the addition of DOM and N suggest that a possible shift in the microbial community composition may occur in the present study. Adding DOM with or without N increased the activities of β-glucosidase and urease. Changes in the direction and magnitude of PE were closely related to changes in soil C and N availability. Soil C and N availability might influence the PE through affecting the microbial biomass and extracellular enzyme activity as well as causing a possible shift in the microbial community composition.

  1. Direct incorporation of fatty acids into microbial phospholipids in soils: Position-specific labeling tells the story

    NASA Astrophysics Data System (ADS)

    Dippold, Michaela A.; Kuzyakov, Yakov

    2016-02-01

    Fatty acids have been used as plant and microbial biomarkers, and knowledge about their transformation pathways in soils and sediments is crucial for interpreting fatty acid signatures, especially because the formation, recycling and decomposition processes are concurrent. We analyzed the incorporation of free fatty acids into microbial fatty acids in soil by coupling position-specific 13C labeling with compound-specific 13C analysis. Position-specifically and uniformly 13C labeled palmitate were applied in an agricultural Luvisol. Pathways of fatty acids were traced by analyzing microbial utilization of 13C from individual molecule positions of palmitate and their incorporation into phospholipid fatty acids (PLFA). The fate of palmitate 13C in the soil was characterized by the main pathways of microbial fatty acid metabolism: Odd positions (C-1) were preferentially oxidized to CO2 in the citric acid cycle, whereas even positions (C-2) were preferentially incorporated into microbial biomass. This pattern is a result of palmitate cleavage to acetyl-CoA and its further use in the main pathways of C metabolism. We observed a direct, intact incorporation of more than 4% of the added palmitate into the PLFA of microbial cell membranes, indicating the important role of palmitate as direct precursor for microbial fatty acids. Palmitate 13C was incorporated into PLFA as intact alkyl chain, i.e. the C backbone of palmitate was not cleaved, but palmitate was incorporated either intact or modified (e.g. desaturated, elongated or branched) according to the fatty acid demand of the microbial community. These modifications of the incorporated palmitate increased with time. Future PLFA studies must therefore consider the recycling of existing plant and microbial-derived fatty acids. This study demonstrates the intact uptake and recycling of free fatty acids such as palmitate in soils, as well as the high turnover and transformation of cellular PLFA. Knowledge about the intact

  2. Estimating reduction of nitrogen leaching from arable land and the related costs.

    PubMed

    Larsson, Martin H; Kyllmar, Katarina; Jonasson, Lars; Johnsson, Holger

    2005-11-01

    The EU Water Framework Directive will require river-basin management plans in order to achieve good ecological status and find the most cost-efficient nitrogen (N) leaching abatement measures. Detailed scenario calculations based on modeling methods will be valuable in this regard. This paper describes the approach and an application with a coefficient method based on the simulation model SOILNDB for quantification of N leaching from arable land and for prediction of the effect of abatement scenarios for the Rönneå catchment (1900 km2) in southern Sweden. Cost calculations for the different measures were also performed. The results indicate that the individual measures-cover crop and spring plowing, late termination of ley and fallow, and spring application of manure-would only reduce N leaching by between 5% and 8%. If all measures were combined and winter crops replaced by their corresponding spring variants, a 21% reduction in N leaching would be possible. However, this would require total fulfillment of the suggested measures.

  3. Ex situ cultivation affects genetic structure and diversity in arable plants.

    PubMed

    Brütting, C; Hensen, I; Wesche, K

    2013-05-01

    Worldwide, botanical gardens cultivate around 80,000 taxa, corresponding to approximately one-quarter of all vascular plants. Most cultivated taxa are, however, held in a small number of collections, and mostly only in small populations. Lack of genetic exchange and stochastic processes in small populations make them susceptible to detrimental genetic effects, which should be most severe in annual species, as sowing cycles are often short. In order to assess whether ex situ cultivation affects genetic diversity of annuals, five annual arable species with similar breeding systems were assessed with 42 in situ populations being compared to 20 ex situ populations using a random amplified polymorphic DNA (RAPD) analysis approach. Population sizes tended to be lower under ex situ cultivation and levels of genetic diversity also tended to be lower in four of the five species, with differences being significant in only two. Ex situ populations showed incomplete representation of alleles found in the wild. The duration of cultivation did not indicate any effect on genetic diversity. This implies that cultivation strategies resulted in different genetic structures in the garden populations. Although not unequivocally pronounced, differences nonetheless imply that conservation strategies in the involved gardens may need improvement. One option is cold storage of seeds, a practice that is not currently followed in the studied ex situ collections. This may reflect that the respective gardens focus on displaying living plant populations.

  4. Environmental and economic impacts of decision-making at an arable farm: an integrative modeling approach.

    PubMed

    Lindgren, Urban; Elmquist, Helena

    2005-06-01

    This study examines the dependency between physical and anthropogenic systems in arable farming. The dynamic simulation model, which has its methodological origins in the modeling traditions of environmental systems analysis and microsimulation, reproduces the mutual links between the physical flows (e.g. energy, materials, emissions, and products), the farmer as a decision-making agent, and structural conditions influencing the farm. In running the model, the intention is to answer the question: What are the impacts on profitability and the environment (i.e. greenhouse gas effects, eutrophication, acidification, and energy use) of variations in prices, subsidies, the farmer's environmental values, and the farmer's skill in making production allocation choices? The results of the model simulations indicate, for example, that in terms of economic performance, a farmer can choose between two relatively sustainable strategies--either to specialize in organic production (thereby benefiting from higher subsidies and output prices), or to focus on conventional cultivation and use of pesticides and fertilizers (thereby benefiting from large yields). Regarding environmental impacts, there was no clear-cut divide between organic and conventional farming due to difficulties in allocating the use of manure. This finding is essentially related to the choice of system boundary, which is thoroughly discussed in the paper.

  5. Spatial Heterogeneity of Leaf Area Index (LAI) and Its Temporal Course on Arable Land: Combining Field Measurements, Remote Sensing and Simulation in a Comprehensive Data Analysis Approach (CDAA).

    PubMed

    Reichenau, Tim G; Korres, Wolfgang; Montzka, Carsten; Fiener, Peter; Wilken, Florian; Stadler, Anja; Waldhoff, Guido; Schneider, Karl

    2016-01-01

    The ratio of leaf area to ground area (leaf area index, LAI) is an important state variable in ecosystem studies since it influences fluxes of matter and energy between the land surface and the atmosphere. As a basis for generating temporally continuous and spatially distributed datasets of LAI, the current study contributes an analysis of its spatial variability and spatial structure. Soil-vegetation-atmosphere fluxes of water, carbon and energy are nonlinearly related to LAI. Therefore, its spatial heterogeneity, i.e., the combination of spatial variability and structure, has an effect on simulations of these fluxes. To assess LAI spatial heterogeneity, we apply a Comprehensive Data Analysis Approach that combines data from remote sensing (5 m resolution) and simulation (150 m resolution) with field measurements and a detailed land use map. Test area is the arable land in the fertile loess plain of the Rur catchment on the Germany-Belgium-Netherlands border. LAI from remote sensing and simulation compares well with field measurements. Based on the simulation results, we describe characteristic crop-specific temporal patterns of LAI spatial variability. By means of these patterns, we explain the complex multimodal frequency distributions of LAI in the remote sensing data. In the test area, variability between agricultural fields is higher than within fields. Therefore, spatial resolutions less than the 5 m of the remote sensing scenes are sufficient to infer LAI spatial variability. Frequency distributions from the simulation agree better with the multimodal distributions from remote sensing than normal distributions do. The spatial structure of LAI in the test area is dominated by a short distance referring to field sizes. Longer distances that refer to soil and weather can only be derived from remote sensing data. Therefore, simulations alone are not sufficient to characterize LAI spatial structure. It can be concluded that a comprehensive picture of LAI spatial

  6. Relationships between soil physicochemical, microbiological properties, and nutrient release in buffer soils compared to field soils.

    PubMed

    Stutter, Marc I; Richards, Samia

    2012-01-01

    The retention of nutrients in narrow, vegetated riparian buffer strips (VBS) is uncertain and underlying processes are poorly understood. Evidence suggests that buffer soils are poor at retaining dissolved nutrients, especially phosphorus (P), necessitating management actions if P retention is not to be compromised. We sampled 19 buffer strips and adjacent arable field soils. Differences in nutrient retention between buffer and field soils were determined using a combined assay for release of dissolved P, N, and C forms and particulate P. We then explored these differences in relation to changes in soil bulk density (BD), moisture, organic matter by loss on ignition (OM), and altered microbial diversity using molecular fingerprinting (terminal restriction fragment length polymorphism [TRFLP]). Buffer soils had significantly greater soil OM (89% of sites), moisture content (95%), and water-soluble nutrient concentrations for dissolved organic C (80%), dissolved organic N (80%), dissolved organic P (55%), and soluble reactive P (70%). Buffer soils had consistently smaller bulk densities than field soils. Soil fine particle release was generally greater for field than buffer soils. Significantly smaller soil bulk density in buffer soils than in adjacent fields indicated increased porosity and infiltration in buffers. Bacterial, archaeal, and fungal communities showed altered diversity between the buffer and field soils, with significant relationships with soil BD, moisture, OM, and increased solubility of buffer nutrients. Current soil conditions in VBS appear to be leading to potentially enhanced nutrient leaching via increasing solubility of C, N, and P. Manipulating soil microbial conditions (by management of soil moisture, vegetation type, and cover) may provide options for increasing the buffer storage for key nutrients such as P without increasing leaching to adjacent streams.

  7. Pyrogenic and Fresh Organic Matter Effects on Soil Microbial Communities

    NASA Astrophysics Data System (ADS)

    Whitman, T.; Buckley, D. H.; Lehmann, J.

    2014-12-01

    Soils hold a globally important stock of carbon (C) and can act as both a C source and sink, depending on management and environmental conditions. Pyrogenic organic matter (PyOM) is produced naturally during fires, and contains relatively stable forms of C. Its intentional production has also been proposed as a mechanism for C management (in such cases PyOM is often referred to as "biochar"). However, the impact of natural or anthropogenic PyOM production on soils is complex and depends on many factors. In particular, PyOM additions to soils may have effects on plant growth and on native soil C cycling. The response of the soil microbial community to PyOM additions is likely key to understanding these interactions, but remains poorly characterized. We studied soil C dynamics and soil microbial communities in a field study with 350°C PyOM from 13C-labelled corn stover, a C3-derived soil, and C4 plants (sudangrass). PyOM additions only temporarily increased total soil CO2 fluxes, dramatically less than the increase associated with the addition of corn stover, which likely increased SOC losses. We used high-throughput sequencing of the 16S region on the MiSeq platform to characterize the initial, 12-day and 82-day soil bacterial communiities. We used three-part stable isotopic partitioning after two months to distinguish 334% higher root-derived CO2 fluxes in the plots with PyOM additions than those without, and 45% lower PyOM-C derived CO2 fluxes in the plots with plants present. The 84% increase in estimated cumulative soil CO2 emissions with stover additions was accompanied by a significant shift in the soil bacterial community on days 12 and 82, while the PyOM additions only resulted in significant changes to the overall community on day 82. We investigate which taxa are driving these community shifts, and how they may relate to the soil CO2 fluxes.

  8. Effect of application method, manure characteristics, weather and field conditions on ammonia volatilization from manure applied to arable land

    NASA Astrophysics Data System (ADS)

    Huijsmans, J. F. M.; Hol, J. M. G.; Vermeulen, G. D.

    To predict ammonia (NH 3) volatilization from field-applied manure, factors affecting volatilization following manure application need to be known. A database of field measurements in the Netherlands was analysed to identify these factors and to quantify their effects on the volatilization of NH 3 from liquid pig manure applied and incorporated on arable land. The combination and the statistical analysis of these data, together with the models that were designed, yielded valuable information about the factors that influence NH 3 volatilization, and about the magnitude of their effects when applying and incorporating manure on arable land. Factors analysed were application method, characteristics of the manure, weather and field conditions. The mean total volatilization, expressed as % of the total ammoniacal nitrogen (TAN) applied, was 68% for surface spreading, 17% for surface incorporation and 2% for deep placement. The volatilization rate increased with an increase in TAN content of the manure, manure application rate and air temperature. Wind speed had a substantial effect on the volatilization rate, only when manure was surface applied or surface incorporated. The results show that useful prediction of ammonia volatilization following manure application on arable land in the Netherlands is feasible on the basis of information about application method, characteristics of the manure and weather conditions.

  9. Influence of Litter Diversity on Dissolved Organic Matter Release and Soil Carbon Formation in a Mixed Beech Forest

    PubMed Central

    Scheibe, Andrea; Gleixner, Gerd

    2014-01-01

    We investigated the effect of leaf litter on below ground carbon export and soil carbon formation in order to understand how litter diversity affects carbon cycling in forest ecosystems. 13C labeled and unlabeled leaf litter of beech (Fagus sylvatica) and ash (Fraxinus excelsior), characterized by low and high decomposability, were used in a litter exchange experiment in the Hainich National Park (Thuringia, Germany). Litter was added in pure and mixed treatments with either beech or ash labeled with 13C. We collected soil water in 5 cm mineral soil depth below each treatment biweekly and determined dissolved organic carbon (DOC), δ13C values and anion contents. In addition, we measured carbon concentrations and δ13C values in the organic and mineral soil (collected in 1 cm increments) up to 5 cm soil depth at the end of the experiment. Litter-derived C contributes less than 1% to dissolved organic matter (DOM) collected in 5 cm mineral soil depth. Better decomposable ash litter released significantly more (0.50±0.17%) litter carbon than beech litter (0.17±0.07%). All soil layers held in total around 30% of litter-derived carbon, indicating the large retention potential of litter-derived C in the top soil. Interestingly, in mixed (ash and beech litter) treatments we did not find a higher contribution of better decomposable ash-derived carbon in DOM, O horizon or mineral soil. This suggest that the known selective decomposition of better decomposable litter by soil fauna has no or only minor effects on the release and formation of litter-derived DOM and soil organic matter. Overall our experiment showed that 1) litter-derived carbon is of low importance for dissolved organic carbon release and 2) litter of higher decomposability is faster decomposed, but litter diversity does not influence the carbon flow. PMID:25486628

  10. Influence of litter diversity on dissolved organic matter release and soil carbon formation in a mixed beech forest.

    PubMed

    Scheibe, Andrea; Gleixner, Gerd

    2014-01-01

    We investigated the effect of leaf litter on below ground carbon export and soil carbon formation in order to understand how litter diversity affects carbon cycling in forest ecosystems. 13C labeled and unlabeled leaf litter of beech (Fagus sylvatica) and ash (Fraxinus excelsior), characterized by low and high decomposability, were used in a litter exchange experiment in the Hainich National Park (Thuringia, Germany). Litter was added in pure and mixed treatments with either beech or ash labeled with 13C. We collected soil water in 5 cm mineral soil depth below each treatment biweekly and determined dissolved organic carbon (DOC), δ13C values and anion contents. In addition, we measured carbon concentrations and δ13C values in the organic and mineral soil (collected in 1 cm increments) up to 5 cm soil depth at the end of the experiment. Litter-derived C contributes less than 1% to dissolved organic matter (DOM) collected in 5 cm mineral soil depth. Better decomposable ash litter released significantly more (0.50±0.17%) litter carbon than beech litter (0.17±0.07%). All soil layers held in total around 30% of litter-derived carbon, indicating the large retention potential of litter-derived C in the top soil. Interestingly, in mixed (ash and beech litter) treatments we did not find a higher contribution of better decomposable ash-derived carbon in DOM, O horizon or mineral soil. This suggest that the known selective decomposition of better decomposable litter by soil fauna has no or only minor effects on the release and formation of litter-derived DOM and soil organic matter. Overall our experiment showed that 1) litter-derived carbon is of low importance for dissolved organic carbon release and 2) litter of higher decomposability is faster decomposed, but litter diversity does not influence the carbon flow.

  11. Amino acid transporter mutants of Arabidopsis provides evidence that a non-mycorrhizal plant acquires organic nitrogen from agricultural soil.

    PubMed

    Ganeteg, Ulrika; Ahmad, Iftikhar; Jämtgård, Sandra; Aguetoni-Cambui, Camila; Inselsbacher, Erich; Svennerstam, Henrik; Schmidt, Susanne; Näsholm, Torgny

    2017-03-01

    Although organic nitrogen (N) compounds are ubiquitous in soil solutions, their potential role in plant N nutrition has been questioned. We performed a range of experiments on Arabidopsis thaliana genetically modified to enhance or reduce root uptake of amino acids. Plants lacking expression of the Lysine Histidine Transporter 1 (LHT1) displayed significantly lower contents of (13) C and (15) N label and of U-(13) C5 ,(15) N2 L-glutamine, as determined by liquid chromatography-mass spectrometry when growing in pots and supplied with dually labelled L-glutamine compared to wild type plants and LHT1-overexpressing plants. Slopes of regressions between accumulation of (13) C-labelled carbon and (15) N-labelled N were higher for LHT1-overexpressing plants than wild type plants, while plants lacking expression of LHT1 did not display a significant regression between the two isotopes. Uptake of labelled organic N from soil tallied with that of labelled ammonium for wild type plants and LHT1-overexpressing plants but was significantly lower for plants lacking expression of LHT1. When grown on agricultural soil plants lacking expression of LHT1 had the lowest, and plants overexpressing LHT1 the highest C/N ratios and natural δ(15) N abundance suggesting their dependence on different N pools. Our data show that LHT1 expression is crucial for plant uptake of organic N from soil.

  12. Bacterial colonization of a fumigated alkaline saline soil.

    PubMed

    Bello-López, Juan M; Domínguez-Mendoza, Cristina A; de León-Lorenzana, Arit S; Delgado-Balbuena, Laura; Navarro-Noya, Yendi E; Gómez-Acata, Selene; Rodríguez-Valentín, Analine; Ruíz-Valdiviezo, Victor M; Luna-Guido, Marco; Verhulst, Nele; Govaerts, Bram; Dendooven, Luc

    2014-07-01

    After chloroform fumigating an arable soil, the relative abundance of phylotypes belonging to only two phyla (Actinobacteria and Firmicutes) and two orders [Actinomycetales and Bacillales (mostly Bacillus)] increased in a subsequent aerobic incubation, while it decreased for a wide range of bacterial groups. It remained to be seen if similar bacterial groups were affected when an extreme alkaline saline soil was fumigated. Soil with electrolytic conductivity between 139 and 157 dS m(-1), and pH 10.0 and 10.3 was fumigated and the bacterial community structure determined after 0, 1, 5 and 10 days by analysis of the 16S rRNA gene, while an unfumigated soil served as control. The relative abundance of the Firmicutes increased in the fumigated soil (52.8%) compared to the unfumigated soil (34.2%), while that of the Bacteroidetes decreased from 16.2% in the unfumigated soil to 8.8% in the fumigated soil. Fumigation increased the relative abundance of the genus Bacillus from 14.7% in the unfumigated soil to 25.7%. It was found that phylotypes belonging to the Firmicutes, mostly of the genus Bacillus, were dominant in colonizing the fumigated alkaline saline as found in the arable soil, while the relative abundance of a wide range of bacterial groups decreased.

  13. The role of ectomycorrhizae of Arolla pine in mediating soil priming

    NASA Astrophysics Data System (ADS)

    Menyailo, Oleg; Matvienko, Anastasia; Cheng, Chih-Hsin

    2015-04-01

    Ectomycorhizae is playing a vital role in soil C cycle. However, the role is controversial. Mycorrhizae could be a major source of soil C promoting C sequestration. On the other hand, mycorrhizal fungi could compete with soil free-living microorganisms for resources, accelerating their decomposition of soil organic matter, therefore leading to soil C losses. We studied the contribution of ectomycorrhizae of Arolla pine, a popular tree species in Siberia, in soil priming, a short term changes in decomposition of soil organic matter after addition of glucose. We used in-growth mesh collars where mycorrhizal hyphae could or could not grow in. We applied 13C labeled glucose and measured evolution of CO2 thereafter, and determined 13C-CO2 using Picarro 2131 iCO2 analyzer. The CO2 produced from soil was enriched 13C only during the first 48 hours, thereafter the enrichment declined to the natural abundance level. The maximum δ13C-CO2 was observed during the first 20 min after glucose amendment. It is surprising that not more than 3% of applied C-glucose was recovered as C-CO2 suggesting extremely high C use efficiency (97%). The glucose addition caused CO2 flux to increase by 25-30% during the first two days, the amount of primed C-CO2 was 7 times higher than emitted from applied C. The presence of mycorrhizae shifted both CUE and the priming. Mycorrhizae apparently competed with heterotrophs reducing their CUE by factor of 2, and increasing the priming by factor of 1.5. Overall, mycorrhizae could amplify the priming effect increasing C losses. However, the most part of applied C was incorporated into microbial biomass, resulting at least at the short time scale in net C sequestration. Future studies should be directed to understanding of the long-term fate of C incorporated into microbial biomass.

  14. The Role of Actinobacteria in Biochar Decomposition in a Mediterranean Grassland Soil

    NASA Astrophysics Data System (ADS)

    Brodie, E. L.; Lim, H.; Bill, M.; Castanha, C.; Conrad, M. E.; Schmidt, M. W.; Abiven, S.; Jansson, J. K.; Torn, M. S.

    2012-12-01

    Biochar addition to soil has been proposed as an attractive approach for carbon sequestration, particularly in concert with bioenergy biomass production and conversion. Biochar, partially combusted organic material, is assumed to be recalcitrant in soil but studies show significant variation in residence times. The controls on biochar C stabilization are likely complex interactions among the substrate, microbial activities, and the soil chemical and physical environment. However, there is a lack of understanding regarding the impact of biochar on soil microbial populations, the organisms that may be responsible for its mineralization or the factors regulating the rate of biochar mineralization. In this study we amended a Mediterranean grassland soil (Ultic Haploxeralf) with biochar (dried chestnut pyrolized at 450°C for 5h) or non-pyrolized oak at ratios of either 1:9 or 1:2 relative to native organic carbon. Both wood and biochar resulted in a significant and dose dependent alteration of microbial community composition within 1 week relative to controls. The rate of change of microbial composition was slower for biochar than for non-pyrolized wood but in both cases Actinobacteria showed significant enrichment relative to controls. From the same grassland soils, we then isolated bacteria capable of subsisting on biochar as a sole C or N source, many of which were Actinobacteria. We selected one Streptomyces isolate and confirmed using 13C-labeled biochar that this strain was capable of biochar mineralization, and show that mineralization was accelerated in the presence of an additional carbon source. We also detected significant abiotic CO2 loss from biochar during incubations. This study demonstrates that some soil Actinobacteria can subsist on biochar as a sole C source, mineralizing it to CO2, our data also shows that priming of biochar decomposition can occur. Overall this highlights the important roles that microbial composition and resource availability may

  15. Anaerobic mineralization of indigenous organic matters and methanogenesis in tropical wetland soils

    SciTech Connect

    Miyajima, Toshihiro; Wada, Eitaro; Hanba, Yuko T.; Vijarnsorn, P.

    1997-09-01

    Tropical wetlands are one of the largest natural sources in the global methane budget due to high biological activities and the anaerobiosis in soil. We studied mineralization and gas production during the early stage of anaerobic decomposition of indigenous organic matters in soils of Narathiwat, southern Thailand, to clarify the significance of the substrate quality in controlling decomposition and methanogenesis in some different tropical wetland soils. The optimal temperature of decomposition was around 35{degrees}C, while methanogenesis did not proceed at 45{degrees}C. During the first 50 days of anaerobic incubation, 5 {approximately} 63% (carbon basis) of indigeneous plant leaves were mineralized. The mineralization rate was strongly and negatively correlated with the lignin and/or fiber contents, but not the C/N ratio, of the substrate plant materials. Difference in {delta}{sup 13}C between the substrate, indicating that H{sub 2} as opposed to acetate becomes a more important metabolic intermediate in the anaerobic food web when the decomposition rate is limited by substrate recalcitrance. Thus, the CH{sub 4} isotope signature may be used to evaluate the importance of new vs. old organic matter as CH{sub 4} isotope signature may be used to evaluate the importance of new vs. old organic matter as CH{sub 4} source in natural soils. The mineralization rate was higher, and the isotopic difference between the substrate and CH{sub 4} was smaller when plant materials were incubated with sulfate-contaminated soils than with native peat soils. The isotopic difference between the substrate and CH{sub 4} was significantly different between native peat soils. Results of a tracer experiment using {sup 13}C-labeled substrates indicated that these differences could be ascribed to difference in the mode of acetate metabolism between soils. 49 refs., 8 figs., 7 tabs.

  16. Active Ammonia Oxidizers in an Acidic Soil Are Phylogenetically Closely Related to Neutrophilic Archaeon

    PubMed Central

    Wang, Baozhan; Zheng, Yan; Huang, Rong; Zhou, Xue; Wang, Dongmei; He, Yuanqiu

    2014-01-01

    All cultivated ammonia-oxidizing archaea (AOA) within the Nitrososphaera cluster (former soil group 1.1b) are neutrophilic. Molecular surveys also indicate the existence of Nitrososphaera-like phylotypes in acidic soil, but their ecological roles are poorly understood. In this study, we present molecular evidence for the chemolithoautotrophic growth of Nitrososphaera-like AOA in an acidic soil with pH 4.92 using DNA-based stable isotope probing (SIP). Soil microcosm incubations demonstrated that nitrification was stimulated by urea fertilization and accompanied by a significant increase in the abundance of AOA rather than ammonia-oxidizing bacteria (AOB). Real-time PCR analysis of amoA genes as a function of the buoyant density of the DNA gradient following the ultracentrifugation of the total DNA extracted from SIP microcosms indicated a substantial growth of soil AOA during nitrification. Pyrosequencing of the total 16S rRNA genes in the “heavy” DNA fractions suggested that archaeal communities were labeled to a much greater extent than soil AOB. Acetylene inhibition further showed that 13CO2 assimilation by nitrifying communities depended solely on ammonia oxidation activity, suggesting a chemolithoautotrophic lifestyle. Phylogenetic analysis of both 13C-labeled amoA and 16S rRNA genes revealed that most of the active AOA were phylogenetically closely related to the neutrophilic strains Nitrososphaera viennensis EN76 and JG1 within the Nitrososphaera cluster. Our results provide strong evidence for the adaptive growth of Nitrososphaera-like AOA in acidic soil, suggesting a greater metabolic versatility of soil AOA than previously appreciated. PMID:24375137

  17. Assessment of vertical soil solid phase transport (pedoturbations) in different types of land use by magnetic tracer method (Belgorod region, Russia)

    NASA Astrophysics Data System (ADS)

    Zhidkin, Andrey

    2015-04-01

    New method of quantitative assessments of vertical soil solid phase transport (pedoturbations) is based on redistribution of spherical magnetic particles (SMP) in soil profiles. SMP - are fly ash components, which mainly produce during coal burning. The main sources of SMP on studied object were locomotives on the railroads, which used coal at the turn of the XIX century. SMP income into the soil only from the atmosphere, very stable for destructions, can be preserved in soils for centuries, and have the same size and weight as the soil matter. So SMP redistribution reflects soil solid phase transport. SMP used as tracers of soil erosion (Olson et.al., 2013), but for the first time applied for quantitative assessments of pedoturbations. In Belgorod region of Russia studied vertical distribution of SMP in soils in different types of land use: a) arable chernozem about 160-year plowing, b) arable chernozem 120-year plowing, c) dark-gray forest soil, which didn't plow at least last 150 years. All three sites are located nearby for the same physical-geography conditions. Distribution of SMP studied layer by layer (thickness of the layer 7 cm) from the top to 70 cm depth, in triplicate soil columns in every land use type (totally 90 soil samples). The period of SMP kept in studied soils is about 115 years. Revealed the different depth of SMP penetration (burial) in soil profiles for this period: 49 cm in the soil of 160-year arable land, 58 cm in the soil of 120-year arable land and 68 cm in the virgin forest soil. Different depth of SMP penetration is connected with different activity of pedoturbations, which differs according to the composition of soil flora and fauna, root activity, and animal mixing work. It is supposed that in the arable land single cropping can reduce the thickness of the active layer and as a result the zone of active pedoturbation depth. Based on SMP distribution counted rates of vertical soil solid phase transport, which are equaled: 31 t

  18. Effect of above-ground plant species on soil microbial community structure and its impact on suppression of Rhizoctonia solani AG3.

    PubMed

    Garbeva, P; Postma, J; van Veen, J A; van Elsas, J D

    2006-02-01

    The extent of soil microbial diversity is seen to be critical to the maintenance of soil health and quality. Different agricultural practices are able to affect soil microbial diversity and thus the level of suppressiveness of plant diseases. In a 4-year field experiment, we investigated the microbial diversity of soil under different agricultural regimes. We studied permanent grassland, grassland turned into arable land, long-term arable land and arable land turned into grassland. The diversity of microbial communities was described by using cultivation-based and cultivation-independent methods. Both types of methods revealed differences in the diversities of soil microbial communities between different treatments. The treatments with higher above-ground biodiversity generally maintained higher levels of microbial diversity. Moreover, a positive correlation between suppression of Rhizoctonia solani AG3 and microbial diversity was observed. Permanent (species-rich) grassland and grassland turned into maize stimulated higher microbial diversities and higher levels of suppressiveness of R. solani AG3 compared with the long-term arable land. Effects of agricultural practices on Bacillus and Pseudomonas communities were also observed and clear correlations between the levels of suppressiveness and the diversities of these bacterial groups were found. This study highlighted the importance of agricultural management regime for soil microbial community structure and diversity as well as the level of soil suppressiveness.

  19. Soil carbon sequestration by three perennial legume pastures is greater in deeper soil layers than in the surface soil

    NASA Astrophysics Data System (ADS)

    Guan, X.-K.; Turner, N. C.; Song, L.; Gu, Y.-J.; Wang, T.-C.; Li, F.-M.

    2015-07-01

    Soil organic carbon (SOC) plays a vital role as both a sink for and source of atmospheric carbon. Revegetation of degraded arable land in China is expected to increase soil carbon sequestration, but the role of perennial legumes on soil carbon stocks in semiarid areas has not been quantified. In this study, we assessed the effect of alfalfa (Medicago sativa L.) and two locally adapted forage legumes, bush clover (Lespedeza davurica S.) and milk vetch (Astragalus adsurgens Pall.) on the SOC concentration and SOC stock accumulated annually over a 2 m soil profile, and to estimate the long-term potential for SOC sequestration in the soil under the three forage legumes. The results showed that the concentration of SOC of the bare soil decreased slightly over the 7 years, while 7 years of legume growth substantially increased the concentration of SOC over the 0-2.0 m soil depth measured. Over the 7 year growth period the SOC stocks increased by 24.1, 19.9 and 14.6 Mg C ha-1 under the alfalfa, bush clover and milk vetch stands, respectively, and decreased by 4.2 Mg C ha-1 under bare soil. The sequestration of SOC in the 1-2 m depth of soil accounted for 79, 68 and 74 % of SOC sequestered through the upper 2 m of soil under alfalfa, bush clover and milk vetch, respectively. Conversion of arable land to perennial legume pasture resulted in a significant increase in SOC, particularly at soil depths below 1 m.

  20. Utilization of Soil C and N by Microbial Groups in the Presence of Living Roots

    NASA Astrophysics Data System (ADS)

    Bird, J.; Herman, D.; Firestone, M.

    2007-12-01

    The effects of living plant roots and N on belowground C dynamics were examined in a CA annual grassland soil (Haploxeralf) during a 2-y greenhouse study. The fate of 13C-labeled plant roots ( Avena barbata L.) and soil were followed under planted and unplanted conditions; and with and without N addition (20 kg N ha-1 season-1). The treatments were applied during 2 growing seasons and each growing season was followed by a dry, fallow period (~ 150-d long). Living roots increased the turnover rate and loss of belowground 13 C during and after 2 seasons compared with unplanted soils. After 2 seasons, planted soils had 21% less belowground 13C present than in unplanted soils. However, total soil C increased in planted soils by 4.6% compared to unplanted after 2 seasons. N additions decreased belowground 13C turnover during the first treatment season in both planted and unplanted soils, however no effect of N on soil C was observed thereafter. Planted soils had larger microbial biomass and the community structure differed compared with unplanted soils. Planted soils had higher proportions of gram (-) bacteria, while unplanted soils had higher proportions of gram (+) bacteria, actinomycetes, and fungi. New root and exudate C supplied from living roots increased the turnover of microbial assimilated 13C compared with unplanted for all microbial groups. This greater turnover of belowground 13C was especially significant for gram (-) bacteria, which were stimulated in the planted soil. In contrast, the activity among microbial groups in unplanted soils was similar to that prior to the initiation of the treatments and soil wet-up. Our findings suggest that A. barbata roots increased soil C levels over time because root and exudate C inputs are significant, however that C increase will be moderated by an overall faster C mineralization rate of belowground C. Increased N deposition may slow soil C losses, however, they appear minor and temporary at the rates applied and for

  1. Ecological Intensification Through Pesticide Reduction: Weed Control, Weed Biodiversity and Sustainability in Arable Farming

    NASA Astrophysics Data System (ADS)

    Petit, Sandrine; Munier-Jolain, Nicolas; Bretagnolle, Vincent; Bockstaller, Christian; Gaba, Sabrina; Cordeau, Stéphane; Lechenet, Martin; Mézière, Delphine; Colbach, Nathalie

    2015-11-01

    Amongst the biodiversity components of agriculture, weeds are an interesting model for exploring management options relying on the principle of ecological intensification in arable farming. Weeds can cause severe crop yield losses, contribute to farmland functional biodiversity and are strongly associated with the generic issue of pesticide use. In this paper, we address the impacts of herbicide reduction following a causal framework starting with herbicide reduction and triggering changes in (i) the management options required to control weeds, (ii) the weed communities and functions they provide and (iii) the overall performance and sustainability of the implemented land management options. The three components of this framework were analysed in a multidisciplinary project that was conducted on 55 experimental and farmer's fields that included conventional, integrated and organic cropping systems. Our results indicate that the reduction of herbicide use is not antagonistic with crop production, provided that alternative practices are put into place. Herbicide reduction and associated land management modified the composition of in-field weed communities and thus the functions of weeds related to biodiversity and production. Through a long-term simulation of weed communities based on alternative (?) cropping systems, some specific management pathways were identified that delivered high biodiversity gains and limited the negative impacts of weeds on crop production. Finally, the multi-criteria assessment of the environmental, economic and societal sustainability of the 55 systems suggests that integrated weed management systems fared better than their conventional and organic counterparts. These outcomes suggest that sustainable management could possibly be achieved through changes in weed management, along a pathway starting with herbicide reduction.

  2. Ecological Intensification Through Pesticide Reduction: Weed Control, Weed Biodiversity and Sustainability in Arable Farming.

    PubMed

    Petit, Sandrine; Munier-Jolain, Nicolas; Bretagnolle, Vincent; Bockstaller, Christian; Gaba, Sabrina; Cordeau, Stéphane; Lechenet, Martin; Mézière, Delphine; Colbach, Nathalie

    2015-11-01

    Amongst the biodiversity components of agriculture, weeds are an interesting model for exploring management options relying on the principle of ecological intensification in arable farming. Weeds can cause severe crop yield losses, contribute to farmland functional biodiversity and are strongly associated with the generic issue of pesticide use. In this paper, we address the impacts of herbicide reduction following a causal framework starting with herbicide reduction and triggering changes in (i) the management options required to control weeds, (ii) the weed communities and functions they provide and (iii) the overall performance and sustainability of the implemented land management options. The three components of this framework were analysed in a multidisciplinary project that was conducted on 55 experimental and farmer's fields that included conventional, integrated and organic cropping systems. Our results indicate that the reduction of herbicide use is not antagonistic with crop production, provided that alternative practices are put into place. Herbicide reduction and associated land management modified the composition of in-field weed communities and thus the functions of weeds related to biodiversity and production. Through a long-term simulation of weed communities based on alternative (?) cropping systems, some specific management pathways were identified that delivered high biodiversity gains and limited the negative impacts of weeds on crop production. Finally, the multi-criteria assessment of the environmental, economic and societal sustainability of the 55 systems suggests that integrated weed management systems fared better than their conventional and organic counterparts. These outcomes suggest that sustainable management could possibly be achieved through changes in weed management, along a pathway starting with herbicide reduction.

  3. Complementary effects of soil organism and plant propagule introductions in restoration of species-rich grassland communities.

    SciTech Connect

    Kardol, Paul; Bezemer, T Martijn; van der Putten, Wim H.

    2009-01-01

    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.

  4. Responses of soil microeukaryotic communities to short-term fumigation-incubation revealed by MiSeq amplicon sequencing

    PubMed Central

    Chen, Lin; Xu, Jianming; Feng, Youzhi; Wang, Juntao; Yu, Yongjie; Brookes, Philip C.

    2015-01-01

    In soil microbiology, there is a “paradox” of soil organic carbon (SOC) mineralization, which is that even though chloroform fumigation destroys majority of the soil microbial biomass, SOC mineralization continues at the same rate as in the non-fumigated soil during the incubation period. Soil microeukaryotes as important SOC decomposers, however, their community-level responses to chloroform fumigation are not well understood. Using the 18S rRNA gene amplicon sequencing, we analyzed the composition, diversity, and C-metabolic functions of a grassland soil and an arable soil microeukaryotic community in response to fumigation followed by a 30-day incubation. The grassland and arable soil microeukaryotic communities were dominated by the fungal Ascomycota (80.5–93.1% of the fungal sequences), followed by the protistan Cercozoa and Apicomplexa. In the arable soil fungal community, the predominance of the class Sordariomycetes was replaced by the class Eurotiomycetes after fumigation at days 7 and 30 of the incubation. Fumigation changed the microeukaryotic α-diversity in the grassland soil at days 0 and 7, and β-diversity in the arable soil at days 7 and 30. Network analysis indicated that after fumigation fungi were important groups closely related to other taxa. Most phylotypes (especially Sordariomycetes, Dothideomycetes, Coccidia, and uncultured Chytridiomycota) were inhibited, and only a few were positively stimulated by fumigation. Despite the inhibited Sordariomycetes, the fumigated communities mainly consisted of Eurotiomycetes and Sordariomycetes (21.9 and 36.5% relative frequency, respectively), which are able to produce hydrolytic enzymes associated with SOC mineralization. Our study suggests that fumigation not only decreases biomass size, but modulates the composition and diversity of the soil microeukaryotic communities, which are capable of driving SOC mineralization by release of hydrolytic enzymes during short-term fumigation-incubation. PMID

  5. Identification of biomass utilizing bacteria in a carbon-depleted glacier forefield soil by the use of 13C DNA stable isotope probing.

    PubMed

    Zumsteg, Anita; Schmutz, Stefan; Frey, Beat

    2013-06-01

    As Alpine glaciers are retreating rapidly, bare soils with low organic C and N contents are becoming exposed. Carbon availability is a key factor regulating microbial diversity and ecosystem functioning in these soils. The aim of this study was to investigate how bacterial activity, community structure and composition are influenced by organic carbon availability. Bare soils were supplied with (13)C-labelled fungal (Penicillium sp.) and green algal (Chlorella sp.) biomass and the CO2 evolution and its δ(13)C signature were monitored up to 60 days. These organisms have previously been isolated near the glacier terminus. DNA stable isotope probing followed by T-RFLP profiling and sequencing of 16S rRNA genes was employed to identify consumers able to assimilate carbon from these biomass amendments. Higher respiration and higher bacterial activity indicated a more efficient utilization of algal cells than fungal cells. Flavobacterium sp. predominantly incorporated fungal-derived C, whereas the algal-derived C was mainly incorporated by Acidobacteria and Proteobacteria. This study emphasizes the important role of both fungal and algal biomass in increasing the carbon pool in recently deglaciated bare soils, as only 20% of the added C was respired as CO2, and the rest, we presume, remained in the soil.

  6. Integrating microbial diversity in soil carbon dynamic models parameters

    NASA Astrophysics Data System (ADS)

    Louis, Benjamin; Menasseri-Aubry, Safya; Leterme, Philippe; Maron, Pierre-Alain; Viaud, Valérie

    2015-04-01

    Faced with the numerous concerns about soil carbon dynamic, a large quantity of carbon dynamic models has been developed during the last century. These models are mainly in the form of deterministic compartment models with carbon fluxes between compartments represented by ordinary differential equations. Nowadays, lots of them consider the microbial biomass as a compartment of the soil organic matter (carbon quantity). But the amount of microbial carbon is rarely used in the differential equations of the models as a limiting factor. Additionally, microbial diversity and community composition are mostly missing, although last advances in soil microbial analytical methods during the two past decades have shown that these characteristics play also a significant role in soil carbon dynamic. As soil microorganisms are essential drivers of soil carbon dynamic, the question about explicitly integrating their role have become a key issue in soil carbon dynamic models development. Some interesting attempts can be found and are dominated by the incorporation of several compartments of different groups of microbial biomass in terms of functional traits and/or biogeochemical compositions to integrate microbial diversity. However, these models are basically heuristic models in the sense that they are used to test hypotheses through simulations. They have rarely been confronted to real data and thus cannot be used to predict realistic situations. The objective of this work was to empirically integrate microbial diversity in a simple model of carbon dynamic through statistical modelling of the model parameters. This work is based on available experimental results coming from a French National Research Agency program called DIMIMOS. Briefly, 13C-labelled wheat residue has been incorporated into soils with different pedological characteristics and land use history. Then, the soils have been incubated during 104 days and labelled and non-labelled CO2 fluxes have been measured at ten

  7. Flux response of glycolysis and storage metabolism during rapid feast/famine conditions in Penicillium chrysogenum using dynamic (13)C labeling.

    PubMed

    de Jonge, Lodewijk; Buijs, Nicolaas A A; Heijnen, Joseph J; van Gulik, Walter M; Abate, Alessandro; Wahl, S Aljoscha

    2014-03-01

    The scale-up of fermentation processes frequently leads to a reduced productivity compared to small-scale screening experiments. Large-scale mixing limitations that lead to gradients in substrate and oxygen availability could influence the microorganism performance. Here, the impact of substrate gradients on a penicillin G producing Penicillium chrysogenum cultivation was analyzed using an intermittent glucose feeding regime. The intermittent feeding led to fluctuations in the extracellular glucose concentration between 400 μM down to 6.5 μM at the end of the cycle. The intracellular metabolite concentrations responded strongly and showed up to 100-fold changes. The intracellular flux changes were estimated on the basis of dynamic (13) C mass isotopomer measurements during three cycles of feast and famine using a novel hybrid modeling approach. The flux estimations indicated a high turnover of internal and external storage metabolites in P. chrysogenum under feast/famine conditions. The synthesis and degradation of storage requires cellular energy (ATP and UTP) in competition with other cellular functions including product formation. Especially, 38% of the incoming glucose was recycled once in storage metabolism. This result indicated that storage turnover is increased under dynamic cultivation conditions and contributes to the observed decrease in productivity compared to reference steady-state conditions.

  8. The pharmacokinetics and metabolism of 14C/13C-labeled ortho-phenylphenol formation following dermal application to human volunteers.

    PubMed

    Timchalk, C; Selim, S; Sangha, G; Bartels, M J

    1998-08-01

    1. The pharmacokinetics and metabolism of uniformly labeled 14C/13C-ortho-phenylphenol (OPP) were followed in six human male volunteers given a single 8 h dermal dose of 6 microg OPP/kg body weight formulated as a 0.4% (w/v) solution in isopropyl alcohol. The application site was covered with a non-occlusive dome allowing free movement of air, but preventing the loss of radioactivity due to physical contact. At 8 h post-exposure the non-occlusive dome was removed, the dose site was wiped with isopropyl alcohol containing swabs and the skin surface repeatedly stripped with tape. Blood specimens, urine, and feces were collected from each volunteer over a 5 day post-exposure period and were analyzed for radioactivity and metabolites (urine only). 2. Following dermal application, peak plasma levels of radioactivity were obtained within 4 h post-exposure and rapidly declined with virtually all of the absorbed dose rapidly excreted into the urine within 24 h post-exposure. A one-compartment pharmacokinetic model was used to describe the time-course of OPP absorption and clearance in male human volunteers. Approximately 43% of the dermally applied dose was absorbed through the skin with an average absorption half-life of 10 h. Once absorbed the renal clearance of OPP was rapid with an average half-life of 0.8 h. The rate limiting step for renal clearance was the relatively slower rate of dermal absorption; therefore the pharmacokinetics of OPP in humans was described by a 'flip-flop' single compartment model. Overall, the pharmacokinetics were similar between individuals, and the model parameters were in excellent agreement with the experimental data. 3. Approximately 73% of the total urinary radioactivity was accounted for as free OPP, OPP-sulfate and OPP-glucuronide conjugates. The sulfate conjugate was the major metabolite (approximately 69%). Therefore, total urinary OPP equivalents (acid-labile conjugates+free OPP) can be used to estimate the systemically absorbed dose of OPP. 4. The rapid excretion of OPP and metabolites into the urine following dermal exposure indicates that OPP is unlikely to accumulate in humans upon repeated exposure. Based on these data, blood and/or urinary OPP concentration (acid-labile conjugates) could be utilized to quantify the amount of OPP absorbed by humans under actual use conditions.

  9. Intraseasonal carbon sequestration and allocation in larch trees growing on permafrost in Siberia after (13)C labeling (two seasons of 2013-2014 observation).

    PubMed

    Masyagina, Oxana; Prokushkin, Anatoly; Kirdyanov, Alexander; Artyukhov, Aleksey; Udalova, Tatiana; Senchenkov, Sergey; Rublev, Aleksey

    2016-12-01

    This research is an attempt to study seasonal translocation patterns of photoassimilated carbon within trees of one of the high latitudes widespread deciduous conifer species Larix gmelinii (Rupr. Rupr). For this purpose, we applied whole-tree labeling by (13)CO2, which is a powerful and effective tool for tracing newly developed assimilates translocation to tissues and organs of a tree. Experimental plot has been established in a mature 105-year-old larch stand located within the continuous permafrost area near Tura settlement (Central Siberia, 64°17'13″N, 100°11'55″E, 148 m a.s.l.). Measurements of seasonal photosynthetic activity and foliage parameters (i.e., leaf length, area, biomass, etc.), and sampling were arranged from early growing season (June 8, 2013; May 14, 2014) until yellowing and senescence of needles (September 17, 2013; September 14, 2014). Labeling by (13)C of the tree branch (June 2013, for 3 branch replicates in 3 different trees) and the whole tree was conducted at early (June 2014), middle (July 2014), and late (August 2013) phase of growing season (for different trees in 3 replicates each time) by three pulses [(CO2)max = 3000-4000 ppmv, (13)CO2 (30 % v/v)]. We found at least two different patterns of carbon translocation associated with larch CO2 assimilation depending on needle phenology. In early period of growing season (June), (13)C appearing in newly developed needles is a result of remobilized storage material use for growth purposes. Then approximately at the end of June, growth processes is switching to storage processes lasting to the end of growing season.

  10. Pentose cycling and the distribution of 13C in trehalose during glucogenesis from 13C-labelled substrates in an insect.

    PubMed

    Thompson, S N; Scales, V M; Bochardt, D B

    1995-07-26

    Redistribution of 13C in trehalose (Tre) due to pentose cycling was observed in vivo in Manduca sexta during glucogenesis from [3-13C]alanine (Ala) and [2-13C]glycerol (Gly). The extent of cycling was affected by dietary composition. Larvae maintained on a low-carbohydrate diet (LCD) exhibited approximately 13% cycling, while those on a complete-balanced diet (CBD) or low-fat diet (LFD) displayed much higher rates of cycling. Significant incorporation of 13C via reversal of the non-oxidative phase was evident on all diets but was greatest on the CBD and LFD. In contrast to conclusions from previous studies with insects, the present results indicate that under normal conditions the pentose pathway is not the principal source of triose phosphates for oxidative catabolism during larval development.

  11. Multidimensional solid-state NMR studies of the structure and dynamics of pectic polysaccharides in uniformly 13C-labeled Arabidopsis primary cell walls

    SciTech Connect

    Dick-Perez, Marilu; Wang, Tuo; Salazar, Andre; Zabotina, Olga A.; Hong, Mei

    2012-07-08

    Plant cell wall (CW) polysaccharides are responsible for the mechanical strength and growth of plant cells; however, the high-resolution structure and dynamics of the CW polysaccharides are still poorly understood because of the insoluble nature of these molecules. Here, we use 2D and 3D magic-angle-spinning (MAS) solid-state NMR (SSNMR) to investigate the structural role of pectins in the plant CW. Intact and partially depectinated primary CWs of Arabidopsis thaliana were uniformly labeled with 13C and their NMR spectra were compared. Recent 13C resonance assignment of the major polysaccharides in Arabidopsis thaliana CWs allowed us to determine the effects of depectination on the intermolecular packing and dynamics of the remaining wall polysaccharides. 2D and 3D correlation spectra show the suppression of pectin signals, confirming partial pectin removal by chelating agents and sodium carbonate. Importantly, higher cross peaks are observed in 2D and 3D 13C spectra of the depectinated CW, suggesting higher rigidity and denser packing of the remaining wall polysaccharides compared with the intact CW. 13C spin–lattice relaxation times and 1H rotating-frame spin–lattice relaxation times indicate that the polysaccharides are more rigid on both the nanosecond and microsecond timescales in the depectinated CW. Taken together, these results indicate that pectic polysaccharides are highly dynamic and endow the polysaccharide network of the primary CW with mobility and flexibility, which may be important for pectin functions. This study demonstrates the capability of multidimensional SSNMR to determine the intermolecular interactions and dynamic structures of complex plant materials under near-native conditions. Copyright © 2012 John Wiley & Sons, Ltd.

  12. (13)C-labeled biochemical probes for the study of cancer metabolism with dynamic nuclear polarization-enhanced magnetic resonance imaging.

    PubMed

    Salamanca-Cardona, Lucia; Keshari, Kayvan R

    2015-01-01

    In recent years, advances in metabolic imaging have become dependable tools for the diagnosis and treatment assessment in cancer. Dynamic nuclear polarization (DNP) has recently emerged as a promising technology in hyperpolarized (HP) magnetic resonance imaging (MRI) and has reached clinical relevance with the successful visualization of [1-(13)C] pyruvate as a molecular imaging probe in human prostate cancer. This review focuses on introducing representative compounds relevant to metabolism that are characteristic of cancer tissue: aerobic glycolysis and pyruvate metabolism, glutamine addiction and glutamine/glutamate metabolism, and the redox state and ascorbate/dehydroascorbate metabolism. In addition, a brief introduction of probes that can be used to trace necrosis, pH changes, and other pathways relevant to cancer is presented to demonstrate the potential that HP MRI has to revolutionize the use of molecular imaging for diagnosis and assessment of treatments in cancer.

  13. Analyses of the bifid shunt and carbohydrate metabolism in Bifidobacterium spp. using **13C-labeled substrates and gas chromatography-mass spectrometry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bifidobacteria are Gram-positive, anaerobic bacteria whose presence in the gastrointestinal tract (GIT) is widely considered as a positive influence on human health. This is especially true in the early development of the infant GIT. Analyses of the genome sequence of Bifidobacterium longum sugges...

  14. {sup 13}C-enrichment at carbons 8 and 2 of uric acid after {sup 13}C-labeled folate dose in man

    SciTech Connect

    Baggott, Joseph E.; Gorman, Gregory S.; Morgan, Sarah L.; Tamura, Tsunenobu . E-mail: tamurat@uab.edu

    2007-09-21

    To evaluate folate-dependent carbon incorporation into the purine ring, we measured {sup 13}C-enrichment independently at C{sub 2} and C{sub 8} of urinary uric acid (the final catabolite of purines) in a healthy male after an independent oral dose of [6RS]-5-[{sup 13}C]-formyltetrahydrofolate ([6RS]-5-H{sup 13}CO-H{sub 4}folate) or 10-H{sup 13}CO-7,8-dihydrofolate (10-H{sup 13}CO-H{sub 2}folate). The C{sub 2} position was {sup 13}C-enriched more than C{sub 8} after [6RS]-5-H{sup 13}CO-H{sub 4}folate, and C{sub 2} was exclusively enriched after 10-H{sup 13}CO-H{sub 2}folate. The enrichment of C{sub 2} was greater from [6RS]-5-H{sup 13}CO-H{sub 4}folate than 10-H{sup 13}CO-H{sub 2}folate using equimolar bioactive doses. Our data suggest that formyl C of [6RS]-10-H{sup 13}CO-H{sub 4}folate was not equally utilized by glycinamide ribotide transformylase (enriches C{sub 8}) and aminoimidazolecarboxamide ribotide (AICAR) transformylase (enriches C{sub 2}), and the formyl C of 10-H{sup 13}CO-H{sub 2}folate was exclusively used by AICAR transformylase. 10-HCO-H{sub 2}folate may function in vivo as the predominant substrate for AICAR transformylase in humans.

  15. Selective 13C labeling of nucleotides for large RNA NMR spectroscopy using an E. coli strain disabled in the TCA cycle

    PubMed Central

    Thakur, Chandar S.; Sama, Jacob N.; Jackson, Melantha E.; Chen, Bin

    2010-01-01

    Escherichia coli (E. coli) is an ideal organism to tailor-make labeled nucleotides for biophysical studies of RNA. Recently, we showed that adding labeled formate enhanced the isotopic enrichment at protonated carbon sites in nucleotides. In this paper, we show that growth of a mutant E. coli strain DL323 (lacking succinate and malate dehydrogenases) on 13C-2-glycerol and 13C-1,3-glycerol enables selective labeling at many useful sites for RNA NMR spectroscopy. For DL323 E. coli grown in 13C-2-glycerol without labeled formate, all the ribose carbon atoms are labeled except the C3′ and C5′ carbon positions. Consequently the C1′, C2′ and C4′ positions remain singlet. In addition, only the pyrimidine base C6 atoms are substantially labeled to ~96% whereas the C2 and C8 atoms of purine are labeled to ~5%. Supplementing the growth media with 13C-formate increases the labeling at C8 to ~88%, but not C2. Not unexpectedly, addition of exogenous formate is unnecessary for attaining the high enrichment levels of ~88% for the C2 and C8 purine positions in a 13C-1,3-glycerol based growth. Furthermore, the ribose ring is labeled in all but the C4′ carbon position, such that the C2′ and C3′ positions suffer from multiplet splitting but the C5′ position remains singlet and the C1′ position shows a small amount of residual C1′–C2′ coupling. As expected, all the protonated base atoms, except C6, are labeled to ~90%. In addition, labeling with 13C-1,3-glycerol affords an isolated methylene ribose with high enrichment at the C5′ position (~90%) that makes it particularly attractive for NMR applications involving CH2-TROSY modules without the need for decoupling the C4′ carbon. To simulate the tumbling of large RNA molecules, perdeuterated glycerol was added to a mixture of the four nucleotides, and the methylene TROSY experiment recorded at various temperatures. Even under conditions of slow tumbling, all the expected carbon correlations were observed, which indicates this approach of using nucleotides obtained from DL323 E. coli will be applicable to high molecular weight RNA systems. PMID:21057854

  16. Folate is absorbed across the human colon: evidence by using enteric-coated caplets containing 13C-labeled [6S]-5-formyltetrahydrofolate1, 2, 3, 4

    PubMed Central

    Lakoff, Alanna; Fazili, Zia; Aufreiter, Susanne; Pfeiffer, Christine M; Connolly, Bairbie; Gregory, Jesse F; Pencharz, Paul B; O’Connor, Deborah L

    2016-01-01

    Background Folate intakes that do not meet or greatly exceed requirements may be associated with negative health outcomes. A better understanding of contributors that influence the input side will help establish dietary guidance that ensures health benefits without associated risks. Colonic microbiota produce large quantities of folate, and [13C5]5-formyltetrahydrofolate infused during colonoscopy is absorbed. However, it is unclear if significant quantities of folate are absorbed in an intact microbiome. Objective We determined whether and how much of a physiologic dose of [13C5]5-formyltetrahydrofolate delivered in a pH-sensitive enteric caplet to an intact colonic microbiome is absorbed. Design Healthy adults ingested a specially designed pH-sensitive acrylic copolymer–coated barium sulfate caplet that contained 855 nmol (400 μg) [13C5]5-formyltetrahydrofolate. After a washout period ≥4 wk, subjects received an intravenous injection of the same compound (214 nmol). Serially collected blood samples before and after each test dose were analyzed by using a microbiological assay and liquid chromatography–tandem mass spectrometry. Results Caplet disintegration in the colon was observed by fluoroscopic imaging for 6 subjects with a mean (±SD) complete disintegration time of 284 ± 155 min. The mean (±SEM) rate of appearance of [13C5]5-methyltetrahydrofolate in plasma was 0.33 ± 0.09 (caplet) and 5.8 ± 1.2 (intravenous) nmol/h. Likely because of the significant time in the colon, the mean apparent absorption across the colon was 46%. Conclusions Folate is absorbed across the colon in humans with an undisturbed microbiome. This finding and previous observations of the size of the colonic depot of folate and its potential for manipulation by diet (eg, dietary fiber, oligosaccharides, and probiotics) suggest that an individual’s dietary folate requirement may differ depending on the consumption of dietary constituents that affect the size and composition of their gastrointestinal microbiota. In addition, a systematic investigation of the role of colonic folate on gastrointestinal development and the prevention of colorectal cancer is warranted. This trial was registered at clinicaltrials.gov as NCT00941174. PMID:25332326

  17. The content of macro- and microelements and the phosphatase activity of soils under a varied plant cultivation technology

    NASA Astrophysics Data System (ADS)

    Bartkowiak, A.; Lemanowicz, J.; Kobierski, M.

    2015-12-01

    The paper presents the results of the analyses of selected physicochemical properties and the activity of alkaline and acid phosphatase in the soils which differed in terms of plant cultivation technology. Profile sI represented arable land in the crop rotation with cereals dominating (medium intensive technology), without irrigation, while profile sII—represented arable land with vegetable crops cultivation (intensive technology), intensively fertilized and irrigated. The content of available phosphorus in the two soil profiles investigated ranged from 6.6 to 69.1 mg/kg. The highest contents of phosphorus available to plants were reported in the plough horizon of both soils, while the abundance of potassium and magnesium was highest in the illuvial horizon of both soils. The soil profiles investigated showed a significant variation in terms of the cultivation technologies applied. The contents of plant-available Cu and Zn in soil were low and they resulted in the inhibition of neither alkaline nor acid phosphatase. The intensive vegetable crops cultivation technology decreased the content of organic matter and increased the content of the nutrients in soil. Using the Ward method, it was found that relatively similar physicochemical and chemical properties were reported for the genetic horizons of both soil profiles, especially Ap horizon of the soil representing arable land with intensive cultivation of vegetable crops.

  18. The fate of eroded soil organic carbon along a European transect - controls after deposition in terrestrial and aquatic systems

    NASA Astrophysics Data System (ADS)

    Kirkels, Frédérique; Cammeraat, Erik; Kalbitz, Karsten; Van Oost, Kristof; Ellerbrock, Ruth; Folain, Stéphane; Gerke, Horst; Heckrath, Goswin; Kögel-Knabner, Ingrid; Kuhn, Nikolaus; Quinton, John; Salvador-Blanes, Sébastien; Sommer, Michael; Steffens, Markus

    2014-05-01

    The potential fate of eroded soil organic carbon (SOC) after deposition is key to understand carbon cycling in eroding landscapes. Globally, large quantities of sediments and SOC are redistributed by soil erosion on agricultural land, particularly after heavy precipitation events. Deposition of eroded SOC takes place on downslope soils within the catchment and in adjacent inland waters, i.e. substantial amounts of SOC are transferred from terrestrial to aquatic ecosystems. However, the net effect on C exchange between soils, atmosphere and inland waters is unknown. We hypothesize that the turnover of deposited C is significantly affected by soil and organic matter properties, and whether deposition occurs in terrestrial or aquatic environments. We sampled topsoils from 10 agricultural sites along a European transect, spanning a wide range of SOC and soil characteristics (e.g. texture, aggregation, C content, etc.). Turnover of SOC was determined for terrestrial and aquatic depositional conditions in a 10-week incubation study. Moreover, we studied the impact of labile carbon inputs ('priming') on SOC stability using 13C labelled cellulose. We evaluated potentially important controls on the fate of SOC such as amounts and composition of soil organic matter (SOM), distribution of SOC in density fractions and aggregates as well as soil physical and chemical properties. NMR analysis provided an in-depth characterization of SOM quality, showing large similarities in chemical composition among the sites. The role of the microbial biomass was specifically assessed in relation to SOC turnover. The results of our study broadly enhanced our knowledge about controls on SOC decomposition/stabilization after its deposition in terrestrial and aquatic environments. We envisage that our quantitative relationships will contribute to obtain better estimates of the impact of soil erosion on carbon budgets and reduce uncertainties in the linkage between terrestrial and aquatic carbon

  19. Measurement of δ13C values of soil amino acids by GC-C-IRMS using trimethylsilylation: a critical assessment.

    PubMed

    Rubino, Mauro; Milin, Sylvie; D'Onofrio, Antonio; Signoret, Patrick; Hatté, Christine; Balesdent, Jérôme

    2014-01-01

    In this study, we evaluated trimethylsilyl (TMS) derivatives as derivatization reagents for the compound-specific stable carbon isotope analysis of soil amino acids by gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS). We used non-proteinogenic amino acids to show that the extraction-derivatization-analysis procedure provides a reliable method to measure δ(13)C values of amino acids extracted from soil. However, we found a number of drawbacks that significantly increase the final total uncertainty. These include the following: production of multiple peaks for each amino acid, identified as di-, tri- and tetra-TMS derivatives; a number of TMS-carbon (TMS-C) atoms added lower than the stoichiometric one, possibly due to incomplete combustion; different TMS-C δ(13)C for di-, tri- and tetra-TMS derivatives. For soil samples, only four amino acids (leucine, valine, threonine and serine) provide reliable δ(13)C values with a total average uncertainty of 1.3 ‰. We conclude that trimethylsilyl derivatives are only suitable for determining the (13)C incorporation in amino acids within experiments using (13)C-labelled tracers but cannot be applied for amino acids with natural carbon isotope abundance until the drawbacks described here are overcome and the measured total uncertainty significantly decreased.

  20. Mixing of an anthracene-contaminated soil: a simple but efficient remediation technique?

    PubMed

    Delgado-Balbuena, Laura; Aguilar-Chávez, Ángel R; Luna-Guido, Marco L; Dendooven, Luc

    2013-10-01

    Contamination of soils with polycyclic aromatic hydrocarbons (PAHs) is a serious problem in petroleum producing countries, such as México, and environment-friendly easy to apply techniques are required to accelerate the removal of the contaminants. Removal of anthracene was monitored in an arable and a pasture soil regularly mixed or amended with organic material, a non-ionic surfactant (Surfynol(®) 485) or earthworms (Eisenia fetida (Savigny, 1826)). In both soils the same results were obtained although the removal of anthracene was faster from the pasture than from the arable soil. The fastest removal of anthracene was obtained when the soil was mixed every 7 days and no contaminant was detected in both soils after 56 days. The second fastest removal of anthracene was obtained when earthworms were added to soil and no contaminant was detected in both soils after 112 days. Application of organic material that served as feed for the earthworms also accelerated the removal of the contaminant compared to the unamended soil, but application of the surfactant inhibited the dissipation of the contaminant. Only 37% of the spiked anthracene was removed from soil when surfactant was applied, while 62% was dissipated in the unamended soil after 112 days. It was found that simply mixing a soil removed anthracene faster than when earthworms were applied, while the application of the surfactant inhibited the removal of anthracene by the autochthonous soil microorganisms.

  1. Co-adaptation of seed dormancy and flowering time in the arable weed Capsella bursa-pastoris (shepherd's purse)

    PubMed Central

    Toorop, Peter E.; Campos Cuerva, Rafael; Begg, Graham S.; Locardi, Bruna; Squire, Geoff R.; Iannetta, Pietro P. M.

    2012-01-01

    Background and Aims The duration of the plant life cycle is an important attribute that determines fitness and coexistence of weeds in arable fields. It depends on the timing of two key life-history traits: time from seed dispersal to germination and time from germination to flowering. These traits are components of the time to reproduction. Dormancy results in reduced and delayed germination, thus increasing time to reproduction. Genotypes in the arable seedbank predominantly have short time to flowering. Synergy between reduced seed dormancy and reduced flowering time would create stronger contrasts between genotypes, offering greater adaptation in-field. Therefore, we studied differences in seed dormancy between in-field flowering time genotypes of shepherd's purse. Methods Genotypes with early, intermediate or late flowering time were grown in a glasshouse to provide seed stock for germination tests. Secondary dormancy was assessed by comparing germination before and after dark-incubation. Dormancy was characterized separately for seed myxospermy heteromorphs, observed in each genotype. Seed carbon and nitrogen content and seed mass were determined as indicators of seed filling and resource partitioning associated with dormancy. Key Results Although no differences were observed in primary dormancy, secondary dormancy was weaker among the seeds of early-flowering genotypes. On average, myxospermous seeds showed stronger secondary dormancy than non-myxospermous seeds in all genotypes. Seed filling was similar between the genotypes, but nitrogen partitioning was higher in early-flowering genotypes and in non-myxospermous seeds. Conclusions In shepherd's purse, early flowering and reduced seed dormancy coincide and appear to be linked. The seed heteromorphism contributes to variation in dormancy. Three functional groups of seed dormancy were identified, varying in dormancy depth and nitrate response. One of these groups (FG-III) was distinct for early

  2. Two Bee-Pollinated Plant Species Show Higher Seed Production when Grown in Gardens Compared to Arable Farmland

    PubMed Central

    Cussans, John; Goulson, David; Sanderson, Roy; Goffe, Louis; Darvill, Ben; Osborne, Juliet L.

    2010-01-01

    Background Insect pollinator abundance, in particular that of bees, has been shown to be high where there is a super-abundance of floral resources; for example in association with mass-flowering crops and also in gardens where flowering plants are often densely planted. Since land management affects pollinator numbers, it is also likely to affect the resultant pollination of plants growing in these habitats. We hypothesised that the seed or fruit set of two plant species, typically pollinated by bumblebees and/or honeybees might respond in one of two ways: 1) pollination success could be reduced when growing in a floriferous environment, via competition for pollinators, or 2) pollination success could be enhanced because of increased pollinator abundance in the vicinity. Methodology/Principal Findings We compared the pollination success of experimental plants of Glechoma hederacea L. and Lotus corniculatus L. growing in gardens and arable farmland. On the farms, the plants were placed either next to a mass-flowering crop (oilseed rape, Brassica napus L. or field beans, Vicia faba L.) or next to a cereal crop (wheat, Triticum spp.). Seed set of G. hederacea and fruit set of L. corniculatus were significantly higher in gardens compared to arable farmland. There was no significant difference in pollination success of G. hederacea when grown next to different crops, but for L. corniculatus, fruit set was higher in the plants growing next to oilseed rape when the crop was in flower. Conclusions/Significance The results show that pollination services can limit fruit set of wild plants in arable farmland, but there is some evidence that the presence of a flowering crop can facilitate their pollination (depending on species and season). We have also demonstrated that gardens are not only beneficial to pollinators, but also to the process of pollination. PMID:20668704

  3. Priming of soil organic matter decomposition in cryoturbated Arctic soils

    NASA Astrophysics Data System (ADS)

    Richter, A.; Wild, B.; Schnecker, J.; Rusalimova, O.

    2012-12-01

    The Arctic is subjected to particularly high rates of warming, with profound consequences for the carbon cycle: on the one hand plant productivity and C storage in plant biomass have been shown to increase strongly in many parts of the Arctic, on the other hand, increasing rates of soil organic matter (SOM) decomposition have been reported. One of the possibilities that could reconcile these observations is, that increased plant growth may lead to increased root exudation rates, which are known to stimulate microbial turnover of organic matter under certain circumstances, in a process termed "priming" of SOM. Two mechanisms have been brought forward that may be responsible for priming: first, easily assimilable material exuded by plant roots may help microbes to overcome their energy limitation and second, this input of labile carbon could lead to a nitrogen limitation of the microbial community and lead to nitrogen mining, i.e. decomposition of N-rich SOM. We here report on an incubation study with arctic soil investigating potential priming of SOM decomposition in organic topsoil horizons, cryoturbated organic matter and subsoil mineral horizons of tundra soil from the Taymyr peninsula in Siberia. We used arctic soils, that are characterized by cryoturbation (mixing of soil layers due to freezing and thawing), for this study. Turbated cryosols store more than 580 Gt C globally, a significant proportion of which is stored in the cryoturbated organic matter. We hypothesized that an increased availability of labile compounds would increase SOM decomposition rates, and that this effect would be strongest in horizons with a low natural availability of labile C, i.e. in the mineral subsoil. We amended soils with 13C labelled glucose, cellulose, amino acids or proteins, and measured the mineralization of SOM C as well as microbial community composition and potential activities of extracellular enzymes. Our results demonstrate that topsoil organic, cryoturbated and

  4. Hydrogen dynamics in soil organic matter as determined by 13C and 2H labeling experiments

    NASA Astrophysics Data System (ADS)

    Paul, Alexia; Hatté, Christine; Pastor, Lucie; Thiry, Yves; Siclet, Françoise; Balesdent, Jérôme

    2016-12-01

    Understanding hydrogen dynamics in soil organic matter is important to predict the fate of 3H in terrestrial environments. One way to determine hydrogen fate and to point out processes is to examine the isotopic signature of the element in soil. However, the non-exchangeable hydrogen isotopic signal in soil is complex and depends on the fate of organic compounds and microbial biosyntheses that incorporate water-derived hydrogen. To decipher this complex system and to understand the close link between hydrogen and carbon cycles, we followed labeled hydrogen and labeled carbon throughout near-natural soil incubations. We performed incubation experiments with three labeling conditions: 1 - 13C2H double-labeled molecules in the presence of 1H2O; 2 - 13C-labeled molecules in the presence of 2H2O; 3 - no molecule addition in the presence of 2H2O. The preservation of substrate-derived hydrogen after 1 year of incubation (ca. 5 % in most cases) was lower than the preservation of substrate-derived carbon (30 % in average). We highlighted that 70 % of the C-H bonds are broken during the degradation of the molecule, which permits the exchange with water hydrogen. Added molecules are used more for trophic resources. The isotopic composition of the non-exchangeable hydrogen was mainly driven by the incorporation of water hydrogen during microbial biosynthesis. It is linearly correlated with the amount of carbon that is degraded in the soil. The quantitative incorporation of water hydrogen in bulk material and lipids demonstrates that non-exchangeable hydrogen exists in both organic and mineral-bound forms. The proportion of the latter depends on soil type and minerals. This experiment quantified the processes affecting the isotopic composition of non-exchangeable hydrogen, and the results can be used to predict the fate of tritium in the ecosystem or the water deuterium signature in organic matter.

  5. The priming effect of soluble carbon inputs in organic and mineral soils from a temperate forest.

    PubMed

    Wang, Hui; Xu, Wenhua; Hu, Guoqing; Dai, Weiwei; Jiang, Ping; Bai, Edith

    2015-08-01

    The priming effect (PE) is one of the most important interactions between C input and output in soils. Here we aim to quantify patterns of PE in response to six addition rates of (13)C-labeled water-soluble C (WSC) and determine if these patterns are different between soil organic and mineral layers in a temperate forest. Isotope mass balance was used to distinguish WSC derived from SOC-derived CO2 respiration. The relative PE was 1.1-3.3 times stronger in the mineral layer than in the organic layer, indicating higher sensitivity of the mineral layer to WSC addition. However, the magnitude of cumulative PE was significantly higher in the organic layer than in the mineral layer due to higher SOC in the organic layer. With an increasing WSC addition rate, cumulative PE increased for both layers, but tended to level off when the addition rate was higher than 400 mg C kg(-1) soil. This saturation effect indicates that stimulation of soil C loss by exogenous substrate would not be as drastic as the increase of C input. In fact, we found that the mineral layer with an WSC addition rate of 160-800 mg C kg(-1) soil had net C storage although positive PE was observed. The addition of WSC basically caused net C loss in the organic layer due to the high magnitude of PE, pointing to the importance of the organic layer in C cycling of forest ecosystems. Our findings provide a fundamental understanding of PE on SOC mineralization of forest soils and warrant further in situ studies of PE in order to better understand C cycling under global climate change.

  6. Microbial biomass as a significant source of soil organic matter

    NASA Astrophysics Data System (ADS)

    Miltner, Anja; Kindler, Reimo; Schweigert, Michael; Achtenhagen, Jan; Bombach, Petra; Fester, Thomas; Kästner, Matthias

    2014-05-01

    Soil organic matter (SOM) plays an important role for soil fertility and in the global carbon cycle. SOM management should be based on knowledge about the chemical composition as well as the spatial distribution of SOM and its individual components in soils. Both parameters strongly depend on the direct precursors of SOM. In the past, microbial biomass has been neglected as a potential source of SOM, mainly because of its small pool size. Recent studies, however, show that a substantial portion of SOM is derived from microbial biomass residues. We therefore investigated the fate of microbial biomass residues in soils by means of incubation experiments with 13C-labelled microbial biomass. For our studies, we selected model organisms representing the three types of soil microorganisms and their characteristic cell wall structures: Escherichia coli (a Gram-negative bacterium), Bacillus subtilis (a Gram-positive bacterium) and Laccaria bicolor (an ectomycorrhizal fungus). We labelled the organisms by growing them on 13C glucose and incubated them in soil. During incubation, we followed the mineralisation of the labelled C, its incorporation into microbial biomass, and its transformation to non-living SOM. We found that 50-65% of the microbial biomass C remained in the soil during incubation. However, only a small part remained in the microbial biomass, the majority was transformed to SOM. In particular, proteins seemed to be rather stable in our experiments. In addition, we used scanning electron microscopy to identify microbial residues in soils and, for comparison, in artificial groundwater microcosms. Scanning electron micrographs showed a low number of intact cells, but mainly fragments of about 200-500 nm size. Similar fragments were found in artificial groundwater microcosms where the only possible origin was microbial biomass residues. Based on the results obtained, we provide a mechanistic model which explains how microbial biomass residues are formed and

  7. Soil nitrogen status as a regulator of carbon substrate flows through microbial communities with elevated CO2

    NASA Astrophysics Data System (ADS)

    Ziegler, Susan E.; Billings, Sharon A.

    2011-03-01

    To assess how microbial processing of organic C inputs to forest soils may be influenced by elevated CO2 and altered N dynamics, we followed the fate of 13C-labeled substrates in soils from the Duke Free Air Carbon Enrichment site where differences in soil N status have been imposed by 7 years of N amendments. Heterotrophic respiration and δ13C of respired CO2-C and phospholipid fatty acids (PLFA) were measured to track activities of microbial groups and estimate a relative measure of substrate use efficiency (PLFA-based SUE). Results indicate an increased proportion of fungal and actinomycete activity in elevated CO2 soils, which varied with substrate. The negative effect of N on vanillin phenolic-C incorporation into actinomycete PLFA suggests legacies of fertilization can mitigate increased C flow into actinomycetes with elevated CO2. Further, the fourfold increase in PLFA-based SUE for vanillin phenolic-C in elevated CO2 soils that received N suggests future enhanced N limitation in elevated CO2 soils may promote enhanced respiratory loss relative to incorporation of some C-substrates into microbial biomass. These short-term incubations did not reveal greater loss of soil organic carbon via respiration or shifts in SUE with elevated CO2. However, observed relative increases in activity of actinomycetes and fungi with elevated CO2 and mitigation of this effect on actinomycetes with N amendments suggests that elevated CO2 and predicted N limitation may alter the fate of slow-turnover soil organic matter (SOM) in two competing ways. Investigations need to focus on how these microorganisms may increase slow-turnover substrate use while possibly enhancing the prevalence of microbial cell wall structures that can serve as precursors of stabilized SOM.

  8. Assessing anthropogenic sources of mercury in soil in Wanshan Hg mining area, Guizhou, China.

    PubMed

    Dai, Zhihui; Feng, Xinbin; Zhang, Chao; Wang, Jingfu; Jiang, Taiming; Xiao, Houjun; Li, Yu; Wang, Xun; Qiu, Guangle

    2013-11-01

    Long-term mining and smelting activities brought a series of environmental issues into soils in Wanshan mercury (Hg) mining area (WMMA), Guizhou, China. Several studies have been published on the concentrations of Hg in local soils, but a comprehensive assessment of the mass of Hg in soil induced by anthropogenic activities, as presented in this paper, has not been previously conducted. Three districts of WMMA were chosen as the study areas. We summarized previous published data and sampled 14 typical soil profiles to analyze the spatial and vertical distributions of Hg in soil in the study areas. The regional geologic background, direct and indirect Hg deposition, and Hg-polluted irrigation water were considered as the main sources of Hg contaminations in local soils. Furthermore, the enrichment factor (EF) method was applied to assess the extent of anthropogenic input of Hg to soil. Titanium (Ti) was chosen to be the reference element to calculate the EF. Generally, the elevated values of EF were observed in the upper soil layers and close to mine wastes. The total budget of Hg in soil contributed from anthropogenic sources was estimated to be 1,227 t in arable soil and 75 t in natural soil. Our data showed that arable soil was the major sink of anthropogenic Hg in the study area.

  9. Bacteria-to-Archaea ratio depending on soil depth and agrogenic impact

    NASA Astrophysics Data System (ADS)

    Semenov, Mikhail; Manucharova, Natalia; Kuzyakov, Yakov

    2014-05-01

    Archaeal communities and their potential roles in the soil ecosystem are affected by a number of soil proprerties and environmental factors. Competitive interactions between Archaea and Bacteria play a particular role in spread and abundance of these two domains. Therefore, the goal of the study was to evaluate the Bacteria-to-Archaea ratio in different soils. The research was carried out at field and natural ecosystems of European part of Russia. Samples were collected within the soil profiles (3-6 horizons) of chernozem and kastanozem with distinctly different agrogenic impact. In situ hybridization with fluorescently labeled rRNA-targeted oligonucleotide probes (FISH) was used to determine the abundance of metabolically active cells of Archaea and Bacteria. The Cmic, Corg, C/N, DNA content and growth characteristics have been analyzed as well. Determination of number of metabolically active cells in chernozem under arable land and forest revealed that abundance of Archaea in topsoil under forest was higher more than 2 times comparing with arable land, but leveled off in the deeper horizons. Plowing of Chernozem decreased amount of archaeal and bacterial active cells simultaneously, however, Bacteria were more resistant to agrogenic impact than Archaea. Determination of the taxonomic composition within Bacteria domain showed a significant decrease in the abundance of phylogenetic groups Firmicutes and Actinobacteria in the topsoil under arable land comparing to the forest, which is the main reason for the declining of the total amount of prokaryotic cells. In kastanozem significant change in the number of metabolically active cells due to plowing was detected only within 40 cm soil layer, and this effect disappeared in lower horizons. The number of Archaea was higher in the upper horizons of arable as compared to virgin soil. Conversely, the number of Bacteria in the upper layers of the soil after plowing kastanozem decreased. Relationship between soil organic

  10. Herbicide impact on the growth and reproduction of characteristic and rare arable weeds of winter cereal fields.

    PubMed

    Rotchés-Ribalta, Roser; Boutin, Céline; Blanco-Moreno, José M; Carpenter, David; Sans, F Xavier

    2015-07-01

    The decline of arable species characteristic of winter cereal fields has often been attributed to different factors related to agricultural intensification but most importantly to herbicide use. Herbicide phytotoxicity is most frequently assessed using short-term endpoints, primarily aboveground biomass. However, short-term sensitivity is usually not sufficient to detect actual effects because plants may or may not recover over time following sublethal herbicide exposures. Therefore, it is important to assess the long-term effects of herbicide applications. Annual species rely on renewable seed production to ensure their persistence; hence, assessment of herbicide sensitivity is more accurately estimated through effects on reproduction. Here we aim to assess the phytotoxicity of two commonly used herbicides: tribenuron and 2,4-D on eight plant species belonging to four families, each with one rare and one more common species. Specifically we examined the pattern of sensitivity using short-term and long-term endpoints (total aboveground biomass, total seed biomass and number of seeds) of these species; we determined the levels of and time to recovery in terms of stem length and fruit number, and assessed whether their rarity relates to their sensitivity to herbicide application. Our results suggest that although differences in herbicide sensitivity are not a direct cause of rarity for all species, it may be an important driver of declining arable plants.

  11. Spatial Heterogeneity of Leaf Area Index (LAI) and Its Temporal Course on Arable Land: Combining Field Measurements, Remote Sensing and Simulation in a Comprehensive Data Analysis Approach (CDAA)

    PubMed Central

    Korres, Wolfgang; Montzka, Carsten; Fiener, Peter; Wilken, Florian; Stadler, Anja; Waldhoff, Guido; Schneider, Karl

    2016-01-01

    The ratio of leaf area to ground area (leaf area index, LAI) is an important state variable in ecosystem studies since it influences fluxes of matter and energy between the land surface and the atmosphere. As a basis for generating temporally continuous and spatially distributed datasets of LAI, the current study contributes an analysis of its spatial variability and spatial structure. Soil-vegetation-atmosphere fluxes of water, carbon and energy are nonlinearly related to LAI. Therefore, its spatial heterogeneity, i.e., the combination of spatial variability and structure, has an effect on simulations of these fluxes. To assess LAI spatial heterogeneity, we apply a Comprehensive Data Analysis Approach that combines data from remote sensing (5 m resolution) and simulation (150 m resolution) with field measurements and a detailed land use map. Test area is the arable land in the fertile loess plain of the Rur catchment on the Germany-Belgium-Netherlands border. LAI from remote sensing and simulation compares well with field measurements. Based on the simulation results, we describe characteristic crop-specific temporal patterns of LAI spatial variability. By means of these patterns, we explain the complex multimodal frequency distributions of LAI in the remote sensing data. In the test area, variability between agricultural fields is higher than within fields. Therefore, spatial resolutions less than the 5 m of the remote sensing scenes are sufficient to infer LAI spatial variability. Frequency distributions from the simulation agree better with the multimodal distributions from remote sensing than normal distributions do. The spatial structure of LAI in the test area is dominated by a short distance referring to field sizes. Longer distances that refer to soil and weather can only be derived from remote sensing data. Therefore, simulations alone are not sufficient to characterize LAI spatial structure. It can be concluded that a comprehensive picture of LAI spatial

  12. Soil water retention dynamics in Luvisols at contrasting slope positions in lysimeter monoliths from an eroded soil landscape

    NASA Astrophysics Data System (ADS)

    Herbrich, Marcus; Gerke, Horst H.; Sommer, Michael

    2015-04-01

    Modeling water flow and solute transport in variably saturated soils requires the proper description of the soil water retention curve. The problem is that under field conditions, water retention may be hysteretic or otherwise changing in time due to changing soil properties. In arable soil landscapes, these changes may depend on the erosion history which created spatial patterns of soil properties such as texture and organic matter content and differences in crop development. The objective of this study was to analyze the dynamics in field-measured water retention data for Luvisols in 10 cm, 30 cm and 50 cm soil depth (Ap, E, and Bt horizons) at two contrasting at slope positions characterized by different degrees of soil erosion under intensive agricultural cultivation. Drying and wetting water retention was obtained from tensiometer/MPS and TDR data in depths representing same soil horizons. For comparison, we used drying retention data obtained from soil cores using the evaporation method (Hyprop). Drying data were fitted to the unconstrained water retention function proposed by van Genuchten (1980) and the bimodal model of Durner (1994). For wetting data, hydraulic model parameters were determined by using the Pedroso-Williams model (2010). The water contents of wetting and drying branches were dynamically changing. These changes in water retention were different for several horizons of the more eroded Luvisol as compared to the less eroded one. Differences in water retention dynamics could be related to soil tillage and the erosion history at the different slope positions. The water differences in retention could be explained by hysteresis and temporal changes in soil water repellency. Field and lab retention data differed as reported earlier. The results suggest that estimation of soil water retention curves without resorting to time-consuming field measurements remains challenging. The results suggest that for erosion-affected arable soils of the hummocky

  13. Microbial Decomposition of Extracellular DNA in Clay Soils

    NASA Astrophysics Data System (ADS)

    Morrissey, E. M.; McHugh, T. A.; Schwartz, E.; Preteska, L.; Hayer, M.; Hungate, B. A.

    2014-12-01

    Genomic analysis of soil communities can only be useful in predicting ecosystem processes if the genetic data gathered is representative of the microbial community. Consequently, extracellular DNA (eDNA) represents a pool of unexpressed genetic information that may skew genomic analyses. To date, our understanding of the representation of eDNA in metagenomic data and its decomposition in soil is very limited. To address this deficit, we performed a laboratory experiment wherein soils were amended with eDNA and/or clay minerals in a full factorial design. Specifically, the decomposition of 13C labeled E. coli DNA was monitored over a 30-day period in control, Kaolinite-amended, and Montmorillonite-amended soils. The amount of added eDNA carbon (C) remaining in the soil declined exponentially over time, with the majority of decomposition occurring in the first two weeks. Kaolinite significantly decreased eDNA decomposition rates and retained a higher fraction of eDNA-C (~70% remaining) than unamended and Montmorillonite-soils (~40% remaining) after 30 days. Phylogenetic (16S rRNA) sequencing of DNA extracted over the course of the incubation period enabled detection of the added eDNA. The relative abundance of added E. coli DNA decreased ~10-100 fold over 30 days. These results indicate that while a significant fraction of eDNA-C remained in the soil, this carbon was likely no longer in the form of intact strands of DNA amenable to sequencing. In addition, the eDNA affected the composition of the bacterial community. Specifically, the relative abundance of Planctomycetes and TM7 were elevated in soils that received eDNA regardless of clay addition, suggesting these phyla may be particularly effective at degrading eDNA and using it for growth. In conclusion these results indicate that the representation of eDNA in metagenomic sequence data declines rapidly, likely due to fragmentation. However, a fraction of eDNA material was resistant to decomposition, suggesting a

  14. Degradation pathway and field-scale DT50 determination of Boscalid in a sandy Soil

    NASA Astrophysics Data System (ADS)

    Karlsson, Anneli S.; Weihermüller, Lutz; Tappe, Wolfgang; Mukherjee, Santanu; Spielvogel, Sandra

    2016-04-01

    The research on environmental fate of pesticides has received increasing attention within the last decades and the persistence of several compounds in soil matrices is well documented. However, the fate of the new fungicide Boscalid (introduced in 2003) is not yet completely investigated. The aim of this study was to analyze the environmental fate of Boscalid in a sandy soil. Three years after the second application on a cropland site in Kaldenkirchen, Germany, 65 undisturbed soil samples from the plough layer were derived. Boscalid residues were extracted using Accelerated Solvent Extraction (ASE) and measured with UPLC-MS/MS. The Boscalid residues ranged between 0.12 and 0.53 μg kg-1with a field mean of 0.20 ± 0.09 μg kg-1. These results differed considerably from the predicted field concentration of 16.89 μg kg-1 (calculated from the application rate) and half-lives (DT50) of 104-182 days compared to 345 days reported in literature. Adjusting the extraction efficiency to 20% could not explain the large difference. Therefore, an incubation study with 14C-labeled Boscalid was conducted to measure the DT50 under controlled conditions. Here, the DT50 values were in the range of values stated in literature (297-337 days compared to 345 days) but still much larger than the DT50 based on the field-study values (104-182 days). Our results indicate that Boscalid dissipation under field conditions is much faster at agricultural sites with sandy soil type as expected from laboratory incubation experiments. Future experiments with Boscalid will be conducted in two different soils with different particle size. A laboratory experiment with uniformly 13C-labeled Boscalid will provide insight into the uptake and incorporation in microbial biomass.

  15. Relevance of nonfunctional linear polyacrylic acid for the biodegradation of superabsorbent polymer in soils.

    PubMed

    Bai, Mo; Wilske, Burkhard; Buegger, Franz; Esperschütz, Jürgen; Bach, Martin; Frede, Hans-Georg; Breuer, Lutz

    2015-04-01

    Biodegradability is a desired characteristic for synthetic soil amendments. Cross-linked polyacrylic acid (PAA) is a synthetic superabsorbent used to increase the water availability for plant growth in soils. About 4% within products of cross-linked PAA remains as linear polyacrylic acid (PAAlinear). PAAlinear has no superabsorbent function but may contribute to the apparent biodegradation of the overall product. This is the first study that shows specifically the biodegradation of PAAlinear in agricultural soil. Two (13)C-labeled PAAlinear of the average molecular weights of 530, 400, and 219,500 g mol(-1) were incubated in soil. Mineralization of PAAlinear was measured directly as the (13)CO2 efflux from incubation vessels using an automatic system, which is based on (13)C-sensitive wavelength-scanned cavity ring-down spectroscopy. After 149 days, the PAAlinear with the larger average molecular weight and chain length showed about half of the degradation (0.91% of the initial weight) of the smaller PAAlinear (1.85%). The difference in biodegradation was confirmed by the δ(13)C signature of the microbial biomass (δ(13)Cmic), which was significantly enriched in the samples with short PAAlinear (-13‰ against reference Vienna Pee Dee Belemnite,VPDB) as compared to those with long PAAlinear (-16‰ VPDB). In agreement with other polymer studies, the results suggest that the biodegradation of PAAlinear in soil is determined by the average molecular weight and occurs mainly at terminal sites. Most importantly, the study outlines that the size of PAA that escapes cross-linking can have a significant impact on the overall biodegradability of a PAA-based superabsorbent.

  16. Fertilizer addition lessens the flux of microbial carbon to higher trophic levels in soil food webs of grassland.

    PubMed

    Lemanski, Kathleen; Scheu, Stefan

    2014-10-01

    Roots and root-derived C compounds are increasingly recognised as important resources for soil animal food webs. We used (13)C-labelled glucose as a model C compound representing root exudates to follow the incorporation of root-derived C into the soil animal food web of a temperate grassland over a period of 52 weeks. We investigated variations in glucose C incorporation with fertilizer addition and sward composition, i.e. variations in plant functional groups. The approach allowed the differentiation of trophic chains based on primary decomposers feeding on litter and phytophagous species feeding on roots (i.e. not incorporating glucose C) from those based on secondary decomposers feeding on microorganisms (thereby assimilating glucose C). Each of the studied soil animal species incorporated glucose C, indicating that the majority of grassland soil animal species rely on microorganisms as food resources with microorganisms being fuelled by root exudates. However, incorporation of glucose C into soil animal species varied markedly with species identity, suggesting that detritivorous microarthropods complement each other in channelling microbial C through soil food webs. Fertilizer addition markedly reduced the concentration of glucose C in most soil animal species as well as the absolute transfer of glucose C into oribatid mites as major secondary decomposers. The results suggest that fertilizer addition shifts the basis of the decomposer food web towards the use of unlabelled resources, presumably roots, i.e. towards a herbivore system, thereby lessening the link between microorganisms and microbial grazers and hampering the propagation of microbial C to higher trophic levels.

  17. Microbial food web mapping: linking carbon cycling and community structure in soils through pyrosequencing enabled stable isotope probing

    SciTech Connect

    Buckley, Daniel H.

    2015-03-15

    Soil represents a massive reservoir of active carbon and climate models vary dramatically in predicting how this carbon will respond to climate change over the coming century. A major cause of uncertainty is that we still have a very limited understand the microorganisms that dominate the soil carbon cycle. The vast majority of soil microbes cannot be cultivated in the laboratory and the diversity of organisms and enzymes that participate in the carbon cycle is staggeringly complex. We have developed a new toolbox for exploring the carbon cycle and the metabolic and ecological characteristics of uncultivated microorganisms. The high-resolution nucleic acid stable isotope probing approach that we have developed makes it possible to characterize microbial carbon cycling dynamics in soil. The approach allows us to track multiple 13C-labeled substrates into thousands of microbial taxa over time. Using this approach we have discovered several major lineages of uncultivated microorganisms that participate in cellulose metabolism and are found widely in soils (including Verrucomicrobia and Chloroflexi, which have not previously been implicated as major players in the soil carbon cycle). Furthermore, isotopic labelling of nucleic acids enables community genomics and permits genome fragment binning for a majority of these cellulolytic microorganisms allowing us to explore the metabolic underpinnings of cellulose degradation. This approach has allowed us to describe unexpected dynamics of carbon metabolism with different microbial taxa exhibiting characteristic patterns of carbon substrate incorporation, indicative of distinct ecological strategies. The data we describe allows us to characterize the activity of novel microorganisms as they occur in the environment and these data provide a basis for understanding how the physiological traits of discrete microorganisms sum to govern the complex responses of the soil carbon cycle.

  18. Intrinsic and induced isoproturon catabolic activity in dissimilar soils and soils under dissimilar land use.

    PubMed

    Reid, Brian J; Papanikolaou, Niki D; Wilcox, Ronah K

    2005-02-01

    The catabolic activity with respect to the systemic herbicide isoproturon was determined in soil samples by (14)C-radiorespirometry. The first experiment assessed levels of intrinsic catabolic activity in soil samples that represented three dissimilar soil series under arable cultivation. Results showed average extents of isoproturon mineralisation (after 240 h assay time) in the three soil series to be low. A second experiment assessed the impact of addition of isoproturon (0.05 microg kg(-1)) into these soils on the levels of catabolic activity following 28 days of incubation. Increased catabolic activity was observed in all three soils. A third experiment assessed levels of intrinsic catabolic activity in soil samples representing a single soil series managed under either conventional agricultural practice (including the use of isoproturon) or organic farming practice (with no use of isoproturon). Results showed higher (and more consistent) levels of isoproturon mineralisation in the soil samples collected from conventional land use. The final experiment assessed the impact of isoproturon addition on the levels of inducible catabolic activity in these soils. The results showed no significant difference in the case of the conventional farm soil samples while the induction of catabolic activity in the organic farm soil samples was significant.

  19. Evaluating Soil Moisture Status Using an e-Nose

    PubMed Central

    Bieganowski, Andrzej; Jaromin-Glen, Katarzyna; Guz, Łukasz; Łagód, Grzegorz; Jozefaciuk, Grzegorz; Franus, Wojciech; Suchorab, Zbigniew; Sobczuk, Henryk

    2016-01-01

    The possibility of distinguishing different soil moisture levels by electronic nose (e-nose) was studied. Ten arable soils of various types were investigated. The measurements were performed for air-dry (AD) soils stored for one year, then moistened to field water capacity and finally dried within a period of 180 days. The volatile fingerprints changed during the course of drying. At the end of the drying cycle, the fingerprints were similar to those of the initial AD soils. Principal component analysis (PCA) and artificial neural network (ANN) analysis showed that e-nose results can be used to distinguish soil moisture. It was also shown that different soils can give different e-nose signals at the same moistures. PMID:27338404

  20. Soil compaction and structural morphology under tractor wheelings

    NASA Astrophysics Data System (ADS)

    Shanahan, Peter; Quinton, John; Binley, Andrew; Silgram, Martyn

    2010-05-01

    Compaction of cultivated soils is a major problem for agriculture in terms of yield decline and sustainable soil resource management. Tramline wheelings exacerbate runoff and increase erosion from arable land. The UK Department for Environment, Food and Rural Affairs (Defra) LINK Project - a joint venture between agri-business, land managers and research groups - is currently evaluating a number of methods for alleviating compaction in tractor wheelings across a range of soil types in England. Using innovative applications of agri-geophysics (e.g. ground penetrating radar, electrical resistivity, acoustics and x-ray tomography), this current project aims to determine relationships between properties derived from geophysical methods (e.g. soil moisture, porosity), soil compaction and structural morphology. Such relationships are important for a clearer understanding of hydrological and biogeochemical processes in compacted soils, to address land management practices and develop cost-effective mitigation measures. Our poster will present some early results of this study.

  1. Multiple DNA extractions coupled with stable-isotope probing of anthracene-degrading bacteria in contaminated soil.

    PubMed

    Jones, Maiysha D; Singleton, David R; Sun, Wei; Aitken, Michael D

    2011-05-01

    In many of the DNA-based stable-isotope probing (SIP) studies published to date in which soil communities were investigated, a single DNA extraction was performed on the soil sample, usually using a commercial DNA extraction kit, prior to recovering the (13)C-labeled (heavy) DNA by density-gradient ultracentrifugation. Recent evidence suggests, however, that a single extraction of a soil sample may not lead to representative recovery of DNA from all of the organisms in the sample. To determine whether multiple DNA extractions would affect the DNA yield, the eubacterial 16S rRNA gene copy number, or the identification of anthracene-degrading bacteria, we performed seven successive DNA extractions on the same aliquot of contaminated soil either untreated or enriched with [U-(13)C]anthracene. Multiple extractions were necessary to maximize the DNA yield and 16S rRNA gene copy number from both untreated and anthracene-enriched soil samples. Sequences within the order Sphingomonadales, but unrelated to any previously described genus, dominated the 16S rRNA gene clone libraries derived from (13)C-enriched DNA and were designated "anthracene group 1." Sequences clustering with Variovorax spp., which were also highly represented, and sequences related to the genus Pigmentiphaga were newly associated with anthracene degradation. The bacterial groups collectively identified across all seven extracts were all recovered in the first extract, although quantitative PCR analysis of SIP-identified groups revealed quantitative differences in extraction patterns. These results suggest that performing multiple DNA extractions on soil samples improves the extractable DNA yield and the number of quantifiable eubacterial 16S rRNA gene copies but have little qualitative effect on the identification of the bacterial groups associated with the degradation of a given carbon source by SIP.

  2. Dynamics of PAHs and derived organic compounds in a soil-plant mesocosm spiked with (13)C-phenanthrene.

    PubMed

    Cennerazzo, Johanne; de Junet, Alexis; Audinot, Jean-Nicolas; Leyval, Corinne

    2017-02-01

    Polycyclic Aromatic Hydrocarbons (PAHs) are ubiquitous and persistent soil pollutants. Their fate and the influence of the plant rhizosphere on their dynamics has been extensively studied, but studies mainly focused on their dissipation rate. We conducted a plant-soil mesocosm experiment to study the fate and distribution of PAHs or derived compounds in the extractable fraction, the residual soil, the shoot biomass and the root biomass. The experiment was conducted for 21 days using ryegrass and a forest soil spiked with (13)C-labeled phenanthrene (PHE), using combined IRMS and NanoSIMS for analyses. Almost 90% of the initial extractable PHE content was dissipated within 3 weeks, but no rhizospheric effect was highlighted on PHE dissipation. More than 40% of (13)C-PHE was still in the soil at the end of the experiment, but not as PHE or PAH-derived compounds. Therefore it was under the form of new compounds (metabolites) and/or had been incorporated into the microbial biomass. About 0.36% of the initial (13)C-PHE was recovered in the root and shoot tissues, representing similar (13)C enrichment (E(13)C) as in the soil (E(13)C ≈ 0.04 at.%). Using NanoSIMS, (13)C was also localized at the microscale in the roots and their close environment. Global (13)C enrichment confirmed the results obtained by IRMS. Some hotspots of (13)C enrichment were found, with a high (32)S/(12)C(14)N ratio. Comparing the ratios, sizes and shapes of these hotspots suggested that they could be bacteria.

  3. Identification and isolation of active N2O reducers in rice paddy soil.

    PubMed

    Ishii, Satoshi; Ohno, Hiroki; Tsuboi, Masahiro; Otsuka, Shigeto; Senoo, Keishi

    2011-12-01

    Dissolved N(2)O is occasionally detected in surface and ground water in rice paddy fields, whereas little or no N(2)O is emitted to the atmosphere above these fields. This indicates the occurrence of N(2)O reduction in rice paddy fields; however, identity of the N(2)O reducers is largely unknown. In this study, we employed both culture-dependent and culture-independent approaches to identify N(2)O reducers in rice paddy soil. In a soil microcosm, N(2)O and succinate were added as the electron acceptor and donor, respectively, for N(2)O reduction. For the stable isotope probing (SIP) experiment, (13)C-labeled succinate was used to identify succinate-assimilating microbes under N(2)O-reducing conditions. DNA was extracted 24  h after incubation, and heavy and light DNA fractions were separated by density gradient ultracentrifugation. Denaturing gradient gel electrophoresis and clone library analysis targeting the 16S rRNA and the N(2)O reductase gene were performed. For culture-dependent analysis, the microbes that elongated under N(2)O-reducing conditions in the presence of cell-division inhibitors were individually captured by a micromanipulator and transferred to a low-nutrient medium. The N(2)O-reducing ability of these strains was examined by gas chromatography/mass spectrometry. Results of the SIP analysis suggested that Burkholderiales and Rhodospirillales bacteria dominated the population under N(2)O-reducing conditions, in contrast to the control sample (soil incubated with only (13)C-succinate). Results of the single-cell isolation technique also indicated that the majority of the N(2)O-reducing strains belonged to the genera Herbaspirillum (Burkholderiales) and Azospirillum (Rhodospirillales). In addition, Herbaspirillum strains reduced N(2)O faster than Azospirillum strains. These results suggest that Herbaspirillum spp. may have an important role in N(2)O reduction in rice paddy soils.

  4. The interaction between soil erosion and soil organisms in temperate agroecosystems: nematode redistribution in tramlines

    NASA Astrophysics Data System (ADS)

    Baxter, Craig; Rowan, John S.; McKenzie, Blair M.; Neilson, Roy

    2014-05-01

    Arable agriculture presents a unique set of challenges, and one of the most important is soil erosion. Whilst policy and practice look towards sustainable intensification of production to ensure food security, fundamental gaps in our understanding still exist. The physical processes involved in the detachment, transport and deposition of soil are well characterised but further research considering chemical and nutrient transport, fertiliser and pesticide losses, and environmental impacts to downstream environments is still required. Furthermore the interaction between soil erosion and soil organisms have largely been ignored, even though soil organisms serve a myriad of functions essential in the provision of soil ecosystem goods and services. Here we present the findings of a field-scale experiment into soil biotic redistribution undertaken at the James Hutton Institute's Balruddery Farm, Scotland (Link Tramlines Project XDW8001). Farm vehicle-tyre wheelings left in arable fields (tramlines) to enable crop spraying during the crop growth cycle have been identified as key transport pathways for sediment and associated nutrients. We tested the hypothesis that soil organisms were also transported by tramline erosion. During the winter of 2012/13 an experiment was undertaken to measure soil organism export from unbound hillslope plots subject to four different tramline treatments set out in a randomised block design. We used soil nematodes as a model organism as they are ubiquitous and sensitive to disturbance and an established indicator taxa of biological and physico-chemical changes in soil. Tramline treatments included a control tyre (conventional tractor tyre), a control tyre with a sown tramline, a low pressure tyre with sown tramline, and a control tyre with a spiked harrow. Post-event sampling of rainfall events was undertaken, and a range of variables measured in the laboratory. The spiked harrow treatment produced the greatest overall reductions in nematode

  5. Mapping vegetation patterns in arable land using the models STICS and DAISY

    NASA Astrophysics Data System (ADS)

    Heuer, Antje; Casper, Markus

    2010-05-01

    Several statistical methods exist to detect spatial and / or temporal variability with regard to ecological data-analysis: Semivariance-analysis, Trend surface analysis, Kriging, Voronoi polygons, Moran's I and Mantel-test, to mention just some of them. In this contribution, we concentrate on spatial vegetation patterns within the soil-vegetation-atmosphere (SVAT) system. Using variography, spatial analysis with a geographic information system and self-organizing maps, spatial patterns of yield have been isolated in an agro-ecosystem (see poster contribution EGU 2009, EGU2009-8948). Data were derived from two agricultural plots, each about 5 hectare, in the area of Newel, located in Western Palatinate, Germany. The plots have been conventionally cultivated with a crop rotation of winter rape, winter wheat and spring barley. The aim of the present study is to find out if the existing natural spatial patterns can be mapped by means of SVAT models. If so, the discretization of a landscape according to its spatial patterns could be the basis for parameterization of SVAT models in order to model soil-vegetation-atmosphere interaction over a large area, that is for up-scaling. For this purpose the SVAT models STICS (developed by INRA, France) and DAISY (developed at Tåstrup University, Denmark) are applied. After a wide sensitivity analysis both models are parameterized with field data according to the given situation of each of the detected spatial patterns. The results of the simulation per representative location of a pattern are validated first with field data concerning yield, soil water content and soil nitrogen; besides, above ground dry matter, root depth and specific stress indices are used for validation. The conclusions that can be made with regard to up-scaling are discussed in detail. In a second step the results of the STICS model are compared with those of the DAISY model to analyse the models' behaviour, to get further knowledge about the inner structure

  6. Using Smoke Injection in Drains to Identify Potential Preferential Pathways in a Drained Arable Field

    NASA Astrophysics Data System (ADS)

    Nielsen, M. H.; Petersen, C. T.; Hansen, S.

    2014-12-01

    Macropores forming a continuous pathway between the soil surface and subsurface drains favour the transport of many contaminants from agricultural fields to surface waters. The smoke injection method presented by Shipitalo and Gibbs (2000) used for demonstrating and quantifying such pathways has been further developed and used on a drained Danish sandy loam. In order to identify the preferential pathways to drains, smoke was injected in three 1.15 m deep tile drains (total drain length 93 m), and smoke emitting macropores (SEMP) at the soil surface were counted and characterized as producing either strong or weak plumes compared to reference plumes from 3 and 6 mm wide tubes. In the two situations investigated in the present study - an early spring and an autumn situation, smoke only penetrated the soil surface layer via earthworm burrows located in a 1.0 m wide belt directly above the drain lines. However, it is known from previous studies that desiccation fractures in a dry summer situation also can contribute to the smoke pattern. The distance between SEMP measured along the drain lines was on average 0.46 m whereas the average spacing between SEMP with strong plumes was 2.3 m. Ponded water was applied in 6 cm wide rings placed above 52 burrows including 17 reference burrows which did not emit smoke. Thirteen pathways in the soil were examined using dye tracer and profile excavation. SEMP with strong plumes marked the entrance of highly efficient transport pathways conducting surface applied water and dye tracer into the drain. However, no single burrow was traced all the way from the surface into the drain, the dye patterns branched off in a network of other macropores. Water infiltration rates were significantly higher (P < 0.05) in SEMP with strong plumes (average rate: 247 mL min-1 n = 19) compared to SEMP with weak plumes (average rate: 87 mL min-1 n = 16) and no plumes (average rate: 56 mL min-1 n = 17). The results suggest that the smoke injection method

  7. Role of antecedent conditions on nitrogen and phosphorus mobilisation observed in a lowland arable catchment in eastern England: insights from high-frequency monitoring

    NASA Astrophysics Data System (ADS)

    Outram, Faye; Hiscock, Kevin; Dugdale, Stephen; Lovett, Andrew

    2015-04-01

    In order to reduce annual riverine loadings of nutrients which are responsible for degradation of ecosystems downstream and in near coastal areas, it is important to first understand the mobilisation and pathways responsible for transporting them from source to river and how these pathways vary in space and time. The Blackwater tributary of the River Wensum in Norfolk, England, has been equipped with a sensor network as part of the Demonstration Test Catchments project, which has the aim of reducing pollution from agriculture to river systems whilst maintaining food security by the trial of mitigation measures on working farms at the sub-catchment level. The River Wensum is a lowland chalk catchment with intensive arable agriculture and high occurrence of tile drainage on heavier soils. Three hydrological years of high-frequency data have been gathered in the Blackwater since October 2011, including rainfall, half hourly measurements of discharge and groundwater level coupled with hydrochemical parameters including nitrate, total phosphorus (TP) and total reactive phosphorus (TRP). In the three years of data collection, there were distinct departures from long-term rainfall averages as the winter of 2011-12 was extremely dry following a drought from the previous hydrological year, followed by a summer which was unseasonably wet, which continued into the following winter. The relationship between rainfall, storage and discharge was found to be complex, which in turn had an impact on the dominant controls transporting nutrients from the landscape to the river network. Thirty three storms occurred throughout the three year period which have been analysed in the context of the range of hydrometeorological conditions observed throughout the dataset. Discharge-concentration hysteretic responses of nitrogen, TP and TRP have been used alongside statistical analysis of storm characteristics including antecedent hydrological conditions. The nitrate storm response showed

  8. Foundations of Soil Organic Matter Stabilization: Tracing the Influence of Mineralogy on the Initial Sorption of Root-Derived Carbon

    NASA Astrophysics Data System (ADS)

    Neurath, R.; Nico, P. S.; Pett-Ridge, J.; Firestone, M.

    2014-12-01

    Soils are the largest terrestrial carbon (C) reservoir, storing 2,300 Gt C globally, with the largest C input allocated by plant roots. Many root-derived C inputs are low molecular weight compounds (exudates), although complex C compounds from sloughed off cells and decaying roots also contribute precursors to the soil organic matter (SOM) pool. Root-derived compounds are metabolized by microorganisms, using extracellular enzymes to degrade the more complex C compounds. Thus, products of microbial use of root C may be free in soil solution or occur as microbial cell material. Products of root decomposition are stabilized in soil when C compounds are protected from degradation by (i) chemical recalcitrance, (ii) physical protection by aggregation, or (iii) physical-chemical protection by sorption to mineral surfaces. Previous studies show that sorption of SOM to soil minerals can stabilize C compounds for up to thousands of years. We examined the influence of soil mineralogy on sorption of root-derived C. We hypothesized that differences in specific surface area (SSA) and chemical reactivity of four mineral types: goethite, kaolinite, quartz, as well as native minerals extracted from field soil, are significant controls on the rate, quantity, and composition of mineral-sorbed SOM. Soils were collected at the UC Hopland Research and Extension Center in Hopland, CA and planted in soil microcosms with the common annual grass A. barbata; seeds collected from the field site. Microcosms were incubated in a sealed chamber under 13CO2 (99 atom%) for 8 weeks. Plant photosynthesized-C is allocated to the soil via roots, and with the 13C label, allows us to trace the fate of plant-derived C in the soil. Minerals, which were isolated in 18 μm mesh to exclude roots but not microorganisms, were extracted and measured for total C and 13C atom% after a 12 week growing season of A. barbata. Preliminary FTIR and 13C-NMR analysis show differences in the chemical composition of

  9. Effects of assimilate supply on root and microbial components of soil respiration in a mountain grassland.

    NASA Astrophysics Data System (ADS)

    Schmitt, M.; Siegwolf, R.; Ekblad, A.; Pfahringer, N.; Bahn, M.

    2012-04-01

    Soil respiration is the main source of carbon emitted from terrestrial ecosystems. Soil CO2 originates from multiple processes, comprising respiration by plant roots, mycorrhizae and microbes in the rhizosphere, as well as respiration due to soil organic matter (SOM) decomposition. Thus, components of soil respiration have different controls and show varying responses to changing environmental conditions and to the supply of fresh assimilates from photosynthesis. For grasslands there is still little information available as to what extent root and microbial respiration respond to reduced or enhanced assimilate supply. The aim of this study was to assess effects of assimilate supply on root and microbial components of soil respiration in a temperate mountain grassland. Root and microbial components were separated and quantified by applying the Substrate Induced Respiration method (SIR) in situ using a δ13C labelled sucrose solution, and analysing δ13C of the subsequently respired CO2. Assimilate supply was modified by clipping and shading treatments, which strongly reduced photosynthetic C supply, and by applying a sucrose solution 8 days after clipping and shading. We tested the hypotheses that (1) due to a reduction of assimilate supply, soil respiration would be lower in the clipped and shaded than in the control treatment, that (2) the microbial contribution to soil respiration would be lower in the assimilate-limited than in the control treatments, and that (3) priming effects following the addition of sucrose would be stronger in shaded and mowed treatments than in control plots. Our results showed that clipping and shading reduced soil respiration significantly. Whilst the microbial contribution to soil respiration was 61% in control plots, it amounted to only 50-48% in clipped and shaded plots, respectively. Sucrose application did not affect root respiration in any of the plots, but generally stimulated microbial respiration. The measured priming effect

  10. Impact of a pesticide cocktail (fenhexamid, folpel, deltamethrin) on the abundance of Glomeromycota in two agricultural soils.

    PubMed

    Rivera-Becerril, Facundo; van Tuinen, Diederik; Chatagnier, Odile; Rouard, Nadine; Béguet, Jérémie; Kuszala, Catherine; Soulas, Guy; Gianinazzi-Pearson, Vivienne; Martin-Laurent, Fabrice

    2017-01-15

    Pesticide contamination of the environment can result from agricultural practices. Persistence of pesticide residues is a threat to the soil biota including plant roots and beneficial microorganisms, which support an important number of soil ecosystem services. Arbuscular mycorrhizal fungi (AMF) are key symbiotic microorganisms contributing to plant nutrition. In the present study, we assessed whether AMF could indicate eventual side effects of pesticides when directly applied to field soils. We evaluated the ecotoxicological impact of a cocktail of three commonly used agricultural pesticides (fenhexamid, folpel, deltamethrin) on the abundance and composition of the AMF community in vineyard (Montagne de Saint-Emilion) and arable (Martincourt) soils subjected to different agricultural practices. The dissipation of applied pesticides was monitored by multiresidual analyses to determine the scenario of exposure of the AMF community. Diversity analysis before application of the pesticide cocktail showed that the AMF communities of vineyard soils, subjected to mechanical weeding or grass cover, and of the arable soil subjected to intensive agriculture, were dominated by Glomerales. Ribotypes specific to each soil and to each agricultural practice in the same soil were found, with the highest abundance and diversity of AMF being observed in the vineyard soil with a grass-cover. The abundance of the global AMF community (Glomeromycota) and of three taxa of AMF (Funneliformis mosseae, Claroideoglomus etunicatum/C. claroideum) was evaluated after pesticide application. The abundance of Glomeromycota decreased in both soils after pesticide application while the abundance of Claroideoglomus and F. mosseae decreased only in the arable soil. These results show that higher doses of pesticide exposure did not affect the global abundance, but altered the composition, of the AMF community. Resilience of the AMF community composition was observed only in the vineyard soil, where F

  11. Soil factors exhibit greater influence than bacterial inoculation on alfalfa growth and nitrogen fixation.

    PubMed

    Neumann, Ute; Kosier, Bob; Jahnke, Joachim; Priefer, Ursula B; Al-Halbouni, Djamila

    2011-09-01

    In order to study the effects of soil factors and bacterial inoculation on alfalfa (Medicago sativa), plants were inoculated with Ensifer meliloti L33 and Azospirillum brasilense Sp7 in pot experiments using two different soils separately as well as in a mixture. One soil was contaminated with chemical waste products; the other was an arable soil. Soil factors, including the availability of macro- and micronutrients as well as carbon and nitrogen contents, were found to exhibit a much greater influence on the growth of alfalfa than any of the inoculations. In contaminated soil, the shoot and root growth of alfalfa was decreased and nodules were diminished and ineffective. Bacterial inoculations did not significantly improve this hostile growth environment. However, in a mixture (44% arable, 22% contaminated soil, 34% vermiculite), growth conditions for alfalfa were improved so that shoot dry weight and nodule numbers increased up to 100- and 20-fold, respectively, compared with the contaminated soil. For the strain L33, its persistence in the rhizosphere was correlated to the presence of its host plant, but its dynamics were influenced by competition with indigenous rhizobia. The strain Sp7, once provided with a suitable soil, was not dependent on the plant's rhizosphere, but it enhanced the performance of L33 and native rhizobia.

  12. Detecting climate-change responses of plants and soil organic matter using isotopomers

    NASA Astrophysics Data System (ADS)

    Schleucher, Jürgen; Ehlers, Ina; Segura, Javier; Haei, Mahsa; Augusti, Angela; Köhler, Iris; Zuidema, Pieter; Nilsson, Mats; Öquist, Mats

    2015-04-01

    lack of biomass increases. Isotopomer patterns are a rich source of metabolic information, which can be retrieved from archives of plant material covering centuries and millennia, the time scales relevant for climate change. Boreal soils contain a huge carbon pool that may be particularly vulnerable to climate change. Biological activity persists in soils under frozen conditions, but it is largely unknown what controls it, and whether it differs from unfrozen conditions. In an incubation experiment, we traced the metabolism of 13C-labeled cellulose by soil microorganisms. NMR analysis revealed that the 13C label was converted both to respired CO2 and to phospholipid fatty acids, indicating that the polymeric substrate cellulose entered both catabolic and anabolic pathways. Both applications demonstrate a fundamental advantage of isotopomer analysis, namely that their abundances directly reflect biochemical processes. This allows obtaining metabolic information on millennial time scales, thus bridging between plant-physiology and paleo sciences. It may also be key to characterizing SOM with sufficient resolution to understand current biogeochemical fluxes involving SOM and to identify molecular components and organisms that are key for SOM turnover.

  13. Transport and reduction of nitrate in clayey till underneath forest and arable land

    NASA Astrophysics Data System (ADS)

    Jørgensen, Peter R.; Urup, Johanne; Helstrup, Tina; Jensen, Marina B.; Eiland, Finn; Vinther, Finn P.

    2004-09-01

    Transport and reduction of nitrate in a typically macroporous clayey till were examined at variable flow rate and nitrate flux. The experiments were carried out using saturated, large diameter (0.5 m), undisturbed soil columns (LUC), from a forest and nearby agricultural sites. Transport of nitrate was controlled by flow along the macropores (fractures and biopores) in the columns. Nitrate reduction (denitrification) determined under active flow mainly followed first order reactions with half-lives ( t1/2) increasing with depth (1.5-3.5 m) from 7 to 35 days at the forest site and 1-7 h at the agricultural site. Nitrate reduction was likely due to microbial degradation of accumulated organic matter coupled with successive consumption of O 2 and NO 3- in the macropore water followed by reductive dissolution of Fe and Mn from minerals along the macropores. Concentrations of total organic carbon measured in soil samples were near identical at the two study sites and consequently not useful as indicator for the observed differences in nitrate reduction. Instead the high reduction rates at the agricultural site were positively correlated with elevated concentration of water-soluble organic carbon and nitrate-removing bacteria relative to the forest site. After high concentrations of water-soluble organic carbon in the columns from the agricultural site were leached they lost their elevated reduction rates, which, however, was successfully re-established by infiltration of new reactive organics represented by pesticides. Simulations using a calibrated discrete fracture matrix diffusion (DFMD) model could reasonably reproduce the denitrification and resulting flux of nitrate observed during variable flow rate from the columns.

  14. Soil and plant factors driving the community of soil-borne microorganisms across chronosequences of secondary succession of chalk grasslands with a neutral pH.

    PubMed

    Kuramae, Eiko; Gamper, Hannes; van Veen, Johannes; Kowalchuk, George

    2011-08-01

    Although soil pH has been shown to be an important factor driving microbial communities, relatively little is known about the other potentially important factors that shape soil-borne microbial community structure. This study examined plant and microbial communities across a series of neutral pH fields (pH=7.0-7.5) representing a chronosequence of secondary succession after former arable fields were taken out of production. These fields ranged from 17 to >66 years since the time of abandonment, and an adjacent arable field was included as a reference. Hierarchical clustering analysis, nonmetric multidimensional scaling and analysis of similarity of 52 different plant species showed that the plant community composition was significantly different in the different chronosequences, and that plant species richness and diversity increased with time since abandonment. The microbial community structure, as analyzed by phylogenetic microarrays (PhyloChips), was significantly different in arable field and the early succession stage, but no distinct microbial communities were observed for the intermediate and the late succession stages. The most determinant factors in shaping the soil-borne microbial communities were phosphorous and NH(4)(+). Plant community composition and diversity did not have a significant effect on the belowground microbial community structure or diversity.

  15. Bacteria capable of degrading anthracene, phenanthrene, and fluoranthene as revealed by DNA based stable-isotope probing in a forest soil.

    PubMed

    Song, Mengke; Jiang, Longfei; Zhang, Dayi; Luo, Chunling; Wang, Yan; Yu, Zhiqiang; Yin, Hua; Zhang, Gan

    2016-05-05

    Information on microorganisms possessing the ability to metabolize different polycyclic aromatic hydrocarbons (PAHs) in complex environments helps in understanding PAHs behavior in natural environment and developing bioremediation strategies. In the present study, stable-isotope probing (SIP) was applied to investigate degraders of PAHs in a forest soil with the addition of individually (13)C-labeled phenanthrene, anthracene, and fluoranthene. Three distinct phylotypes were identified as the active phenanthrene-, anthracene- and fluoranthene-degrading bacteria. The putative phenanthrene degraders were classified as belonging to the genus Sphingomona. For anthracene, bacteria of the genus Rhodanobacter were the putative degraders, and in the microcosm amended with fluoranthene, the putative degraders were identified as belonging to the phylum Acidobacteria. Our results from DNA-SIP are the first to directly link Rhodanobacter- and Acidobacteria-related bacteria with anthracene and fluoranthene degradation, respectively. The results also illustrate the specificity and diversity of three- and four-ring PAHs degraders in forest soil, contributes to our understanding on natural PAHs biodegradation processes, and also proves the feasibility and practicality of DNA-based SIP for linking functions with identity especially uncultured microorganisms in complex microbial biota.

  16. Tracing fresh assimilates through Larix decidua exposed to elevated CO₂ and soil warming at the alpine treeline using compound-specific stable isotope analysis.

    PubMed

    Streit, Kathrin; Rinne, Katja T; Hagedorn, Frank; Dawes, Melissa A; Saurer, Matthias; Hoch, Günter; Werner, Roland A; Buchmann, Nina; Siegwolf, Rolf T W

    2013-02-01

    How will carbon source-sink relations of 35-yr-old larch trees (Larix decidua) at the alpine treeline respond to changes in atmospheric CO(2) and climate? We evaluated the effects of previously elevated CO(2) concentrations (9 yr, 580 ppm, ended the previous season) and ongoing soil warming (4 yr, + 4°C). Larch branches were pulse labeled (50 at% (13)CO(2)) in July 2010 to trace fresh assimilates through tissues (buds, needles, bark and wood) and non-structural carbon compounds (NCC; starch, lipids, individual sugars) using compound-specific isotope analysis. Nine years of elevated CO(2) did not lead to increased NCC concentrations, nor did soil warming increase NCC transfer velocities. By contrast, we found slower transfer velocities and higher NCC concentrations than reported in the literature for lowland larch. As a result of low dilution with older carbon, sucrose and glucose showed the highest maximum (13)C labels, whereas labels were lower for starch, lipids and pinitol. Label residence times in needles were shorter for sucrose and starch (c. 2 d) than for glucose (c. 6 d). Although our treatments showed no persistent effect on larch carbon relations, low temperature at high altitudes clearly induced a limitation of sink activities (growth, respiration, root exudation), expressed in slower carbon transfer and higher NCC concentrations.

  17. [Forecast of collective radiation dose decrease of the population of Belarus as the result of optimization of moveable potassium contents in soils contaminated by 137Cs].

    PubMed

    Putiatin, Iu V; Adianova, O B

    2010-01-01

    Results of study on an efficiency of potassium moveable content for decrease of a collective dose from 137Cs to the population of Belarus are presented. On the basis of the "cost-benefit" analysis it is shown, that expenses for decreasing averted collective dose due to increase of potassium contents on arable lands amounts to more than 80 thousand US dollars per 1 man.-Sv depending on density of soil contamination of rural districts by 137Cs. It is found that high effect (costs less than 40 thousand US dollars per 1 man.-Sv on hectare of arable land) on averted collective dose from 137Cs at cultivation of cereals can be expected at an optimization of mobile potassium contents in sod-podzolic loamy sand soils with density of 137Cs contamination more than 925 kBq/m2, sand soils--more than 1184, light loam soils--more than 629 kBq/m2.

  18. Chemodestructive fractionation of soil organic matter

    NASA Astrophysics Data System (ADS)

    Popov, A. I.; Rusakov, A. V.

    2016-06-01

    The method of chemodestructive fractionation is suggested to assess the composition of soil organic matter. This method is based on determination of the resilience of soil organic matter components and/or different parts of organic compounds to the impact of oxidizing agents. For this purpose, a series of solutions with similar concentration of the oxidant (K2Cr2O7), but with linearly increasing oxidative capacity was prepared. Chemodestructive fractionation showed that the portion of easily oxidizable (labile) organic matter in humus horizons of different soil types depends on the conditions of soil formation. It was maximal in hydromorphic soils of the taiga zone and minimal in automorphic soils of the dry steppe zone. The portion of easily oxidizable organic matter in arable soils increased with an increase in the rate of organic fertilizers application. The long-lasting agricultural use of soils and burying of the humus horizons within the upper one-meter layer resulted in the decreasing content of easily oxidizable organic matter. It was found that the portion of easily oxidizable organic matter decreases by the mid-summer or fall in comparison with the spring or early summer period.

  19. Multisubstrate isotope labeling and metagenomic analysis of active soil bacterial communities.

    PubMed

    Verastegui, Y; Cheng, J; Engel, K; Kolczynski, D; Mortimer, S; Lavigne, J; Montalibet, J; Romantsov, T; Hall, M; McConkey, B J; Rose, D R; Tomashek, J J; Scott, B R; Charles, T C; Neufeld, J D

    2014-07-15

    Soil microbial diversity represents the largest global reservoir of novel microorganisms and enzymes. In this study, we coupled functional metagenomics and DNA stable-isotope probing (DNA-SIP) using multiple plant-derived carbon substrates and diverse soils to characterize active soil bacterial communities and their glycoside hydrolase genes, which have value for industrial applications. We incubated samples from three disparate Canadian soils (tundra, temperate rainforest, and agricultural) with five native carbon ((12)C) or stable-isotope-labeled ((13)C) carbohydrates (glucose, cellobiose, xylose, arabinose, and cellulose). Indicator species analysis revealed high specificity and fidelity for many uncultured and unclassified bacterial taxa in the heavy DNA for all soils and substrates. Among characterized taxa, Actinomycetales (Salinibacterium), Rhizobiales (Devosia), Rhodospirillales (Telmatospirillum), and Caulobacterales (Phenylobacterium and Asticcacaulis) were bacterial indicator species for the heavy substrates and soils tested. Both Actinomycetales and Caulobacterales (Phenylobacterium) were associated with metabolism of cellulose, and Alphaproteobacteria were associated with the metabolism of arabinose; members of the order Rhizobiales were strongly associated with the metabolism of xylose. Annotated metagenomic data suggested diverse glycoside hydrolase gene representation within the pooled heavy DNA. By screening 2,876 cloned fragments derived from the (13)C-labeled DNA isolated from soils incubated with cellulose, we demonstrate the power of combining DNA-SIP, multiple-displacement amplification (MDA), and functional metagenomics by efficiently isolating multiple clones with activity on carboxymethyl cellulose and fluorogenic proxy substrates for carbohydrate-active enzymes. Importance: The ability to identify genes based on function, instead of sequence homology, allows the discovery of genes that would not be identified through sequence alone. This

  20. "Lou soil", a fertile anthropogenic soil with thousands of years of cultivating history

    NASA Astrophysics Data System (ADS)

    Zhou, J.; Liang, B.; Yan, J.; Zhao, W.

    2012-12-01

    in a warming earth. Our micro-plot experiment with 15N-labeled fertilizer in the long-term fertilizer trial found that the use efficiency of N fertilizer (NUE) in MNPK soil was higher than the NPK soil and NF soil in both wheat-summer fallow and winter wheat and summer corn rotation system. However, the N fertilizer losses in MNPK soil was lower than the NPK soil and NF soil in the two systems. We concluded that the long-term combined application of manure and inorganic fertilizers improves N synchrony between the supply and crop demand, and reduces its loss. Since the 1980s, however, the application of manure to arable fields has declined in Guanzhong Plain, and in other parts of China, due to the increasing use of inorganic fertilizers, and labor co