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  • 1
    Language: English
    In: Chemosphere, January 2018, Vol.191, pp.607-615
    Description: Spreading organic waste products (OWP) issued from sewage sludge or manures into soil may disseminate antibiotics with unknown risks for human health and environment. Our objectives were to compare the fate of two sulfonamides, sulfamethoxazole (SMX) and its metabolite N-acetyl-sulfamethoxazole (N-ac-SMX), and one fluoroquinolone, ciprofloxacin (CIP), in an unamended soil, and two soils regularly amended since 1998 with a sewage sludge and green waste compost and with farmyard manure respectively. Incubations of soil spiked with C labelled SMX or N-ac-SMX (0.02 mg kg ) or CIP (0.15 mg kg ) allowed a quantification of radiolabeled molecules in the mineralized, easily, hardly and non-extractable fractions after 3 and 156 days. Nature of C molecules was also analyzed by HPLC in extractable fractions after 3 and 156 days. SMX and N-ac-SMX dissipation was fast and due to i) mineralization (∼10% of recovered C after 156 days) or incomplete degradation (production of metabolites), ii) adsorption, even if both sulfonamides present low Kd (〈3 L kg ) and iii) formation of non-extractable residues (NER), representing more than 50% of recovered radioactivity. N-ac-SMX was more mineralized than SMX, and formed more progressively NER, after a step of deacetylation. Adsorption of CIP was fast and formed mainly NER (〉72%) whereas its mineralization was negligible. Repeated applications of OWP tend to enhance adsorption of antibiotics and lower their degradation, through the quantity and quality of the built up soil organic matter. If applications of sewage sludge compost favor adsorption and inhibit mineralization, applications of manure boost the formation of non-extractable residues.
    Keywords: Soil ; Antibiotic ; Metabolite ; Organic Waste Products ; Biodegradation ; Adsorption ; Chemistry ; Ecology
    ISSN: 0045-6535
    E-ISSN: 1879-1298
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  • 2
    Language: English
    In: Soil Biology and Biochemistry, April 2016, Vol.95, pp.180-188
    Description: Organic matter (OM) is known to affect the behaviour of pesticides in soil (transfer, degradation, retention). In cultivated soils, crops residues and compost incorporation by ploughing results in a heterogeneous OM distribution in soil with the formation of spots with a mm to dm size. This study aimed to compare the impact of OM (straw and compost) addition and its spatial distribution in soil on the total mineralization and the fate of isoproturon (IPU) in cm repacked soil cores. OM was homogeneously or heterogeneously (in small spots or in a larger spot) distributed in the soil cores. C IPU was uniformly added at the regular agronomic dose to the soil and OM. We followed total carbon mineralization, C IPU mineralization, and extractable and non-extractable C residues during a 43-days incubation. We analysed the fate of C at the core scale, and characterised what happened separately on soil and spots of OM after their separation. The results showed that i) the addition of exogenous OM stimulated microbial respiration, but the effect was similar regardless of the spatial distribution of OM in soil (13.9%–19.5% of the total organic carbon); ii) IPU degradation was negligible in OM but was significantly stimulated when OM was added to soil (compared to soil incubated alone) up to a factor of 2; iii) the fate of IPU was impacted by the OM spatial distribution in soil locally and at the core scale and degradation and mineralization was maximal when compost was homogeneously distributed in soil; and iv) these effects were different for maize straw and compost. The nature of OM and its spatial distribution that can be impacted by agricultural practices seem to be important factors to be considered to better understand the fate of pesticides in soil and their transfer to superficial or underground water.
    Keywords: Crop Residues ; Compost ; Spatial Distribution ; Microbial Respiration ; Pesticide Biodegradation ; Cultivated Soil ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 3
    Language: English
    In: Soil Biology and Biochemistry, September 2010, Vol.42(9), pp.1640-1642
    Description: A miniaturised method developed to measure the mineralisation of C-labelled organic compounds in small soil samples is presented. Soil samples (〈0.5 g) were placed in wells of microtiter plates with CO traps (NaOH-soaked glass microfiber filters) and amended with C-labelled substrate. The microtiter plate was covered with a seal and placed in a microplate clamp system to ensure that each well was airtight. After incubation, the CO traps were transferred to tightly sealed glass phials under CO -free atmosphere and the C-labelled CO was released by addition of H PO . The CO was measured by micro-GC and its isotopic signature was determined using a GC-IRMS. The qualitative and quantitative efficiency of the microplate system was demonstrated by comparison with direct measurement of CO in the headspace of phials in which similarly treated soil samples had been incubated. The two methods showed similar mineralisation rates for added C-substrates but the apparent mineralisation of soil organic matter was greater with the microtiter plate method. The microplate system presented here is suitable for studying the mineralisation of different kinds of C-labelled substrates in small soil samples and allows analysis of functional and molecular characteristics on the same micro-samples.
    Keywords: 13c-Labelling ; Co2 Trap ; Acid Release ; Mineralisation ; Microbial Scale ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 4
    Language: English
    In: Soil Biology and Biochemistry, September 2015, Vol.88, pp.90-100
    Description: The biodegradation of organic compounds in soil is a key process that has major implications for different ecosystem services such as soil fertility, air and water quality, and climate regulation. Due to the complexity of soil, the distributions of organic compounds and microorganisms are heterogeneous on sub-cm scales, and biodegradation is therefore partly controlled by the respective localizations of organic substrates and degraders. If they are not co-localized, transfer processes become crucial for the accessibility and availability of the substrate to degraders. This spatial interaction is still poorly understood, leading to poor predictions of organic compound dynamics in soils. The objectives of this work were to better understand how the mm-scale distribution of a model pesticide, 2,4-dichlorophenoxyacetic acid (2,4-D), and its degraders drives the fate of 2,4-D at the cm soil core scale. We constructed cm-scale soil cores combining sterilized and “natural” soil aggregates in which we controlled the initial distributions of 2,4-D and soil microorganisms with the following spatial distributions: i) a homogeneous distribution of microorganisms and 2,4-D at the core-scale, ii) a co-localized distribution of microorganisms and 2,4-D in a single spot (360 mm ) and iii) a disjoint localization of microorganisms and 2,4-D in 2 soil spots (360 mm ) separated by 2 cm. Two sets of experiments were performed: one used radiolabeled C-2,4-D to study the fate of 2,4-D, and the other used C-2,4-D to follow the dynamics of degraders. Microcosms were incubated at 20 °C and at field capacity (−31.6 kPa). At the core scale, we followed 2,4-D mineralization over time. On three dates, soil cores with microorganisms and 2,4-D localized in soil spots, were cut out in slices and then in 360 mm soil cubes. The individual soil cubes were then independently analysed for extractable and non-extractable C and for degraders (quantitative PCR of genes). Knowing the initial position of each soil cube allowed us to establish 3D maps of 2,4-D residues and degraders in soil. The results indicated that microorganisms and pesticide localizations in soil are major driving factors of i) pesticide biodegradation, by regulating the accessibility of 2,4-D to degrading microorganisms (by diffusion); and ii) the formation of non-extractable residues (NER). These results also emphasized the dominant role of microorganisms in the formation and localization of biogenic NER at a mm-scale. To conclude, these results demonstrate the importance of considering micro-scale processes to better understand the fate of pesticides and more generally of soil organic substrates at upper scales in soil and suggest that such spatial heterogeneity should not be neglected when predicting the fate of organic compounds in soils.
    Keywords: Pesticide ; Spatial Heterogeneity ; Biodegradation ; Biogenic and Abiotic Non-Extractable Residues ; Diffusion ; Mm and Cm-Scale ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 5
    Language: English
    In: Soil biology & biochemistry, 2010, Vol.42, pp.1640-1642
    Description: A miniaturised method developed to measure the mineralisation of 13C-labelled organic compounds in small soil samples is presented. Soil samples (〈0.5 g) were placed in wells of microtiter plates with CO2 traps (NaOH-soaked glass microfiber filters) and amended with 13C-labelled substrate. The microtiter plate was covered with a seal and placed in a microplate clamp system to ensure that each well was airtight. After incubation, the CO2 traps were transferred to tightly sealed glass phials under CO2-free atmosphere and the 13C-labelled CO2 was released by addition of H3PO4. The CO2 was measured by micro-GC and its isotopic signature was determined using a GC-IRMS. The qualitative and quantitative efficiency of the microplate system was demonstrated by comparison with direct measurement of CO2 in the headspace of phials in which similarly treated soil samples had been incubated. The two methods showed similar mineralisation rates for added 13C-substrates but the apparent mineralisation of soil organic matter was greater with the microtiter plate method. The microplate system presented here is suitable for studying the mineralisation of different kinds of 13C-labelled substrates in small soil samples and allows analysis of functional and molecular characteristics on the same micro-samples. ; Includes references ; p. 1640-1642.
    Keywords: Soil Organic Carbon ; Laboratory Techniques ; Isotope Labeling ; New Methods ; Methodology ; Stable Isotopes ; Soil Sampling ; Carbon Dioxide ; Gas Chromatography ; Gas Emissions ; Headspace Analysis ; Soil Microorganisms ; Carbon ; Mineralization ; Phosphoric Acid ; Sample Size ; Microtiter Plates ; Miniaturized Methods
    ISSN: 0038-0717
    Source: AGRIS (Food and Agriculture Organization of the United Nations)
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  • 6
    Language: English
    In: Soil Biology and Biochemistry, December 2018, Vol.127, pp.137-147
    Description: Complex interactions between biodegradation and mass transfer of organic compounds drive the fate of pesticides in soil ecosystems. We hypothesized that, at the small-scale, co-location of degraders and pollutants in soils may be a prerequisite for efficient biodegradation of these chemicals. In non-co-localized micro-environments, however, diffusive and advective solute transport as well as active transport of microbial degraders towards their corresponding substrate may improve the accessibility of microbial substrates. The objective of this study was to test whether water flow can accelerate microbial pesticide degradation by facilitating the encounter of spatially separated pesticides and bacterial degraders at the millimeter scale. Combining natural and sterilized soil aggregates, we built soil cores with different spatial localizations of the pesticide 2,4-dichlorophenoxyacetic acid (2,4-D) and microbial degraders: (i) homogeneous distribution of microorganisms and 2,4-D throughout the soil core, (ii) co-localized microorganisms and 2,4-D in a mm soil location, and iii) separated microorganisms and 2,4-D in two mm soil locations spaced 1 cm apart. Following the fate of C labelled 2,4-D (mineralization, extractable and non-extractable residues) as well as the abundance of bacterial 2,4-D degraders harboring the gene over an incubation period of 24 days, we observed decreased biodegradation of 2,4-D with increasing spatial separation between substrate and bacterial degraders. We found evidence that advection is a key process controlling the accessibility of 2,4-D and pesticide degraders. Advective solute transport induced leaching of about 50% of the initially applied 2,4-D regardless of initial spatial distribution patterns. Simultaneously, advective transport of 2,4-D and bacterial degraders triggered their re-encounter and compensated for the leaching-induced separation of initially co-localized microorganisms and 2,4-D. This resulted in effective biodegradation of 2,4-D, comparable to the homogeneous treatment. Similarly, advective transport processes brought substrate and degraders into contact if both were initially separated. Thus, advection more effectively removed bioaccessibility limitations to pesticide degradation than diffusive transport alone. These results emphasize the importance of considering spatial microbial ecology as well as biogeophysics at the mm scale to better understand the fate of pesticides at larger scales in soil.
    Keywords: Accessibility ; Biodegradation ; Mm Scale ; Biogenic and Abiotic Non Extractable Residues ; Advection and Diffusion Transport ; Tfda Genes ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 7
    Language: English
    In: Ecological Modelling, 24 January 2017, Vol.344, pp.48-61
    Description: We investigate the temporal constraints of 2,4-D degradation by spatially distributed soil microorganisms. Based on a complementary set of laboratory experiments ( ), we determine the characteristic temporal scales of the involved chemical, biological and diffusion processes from the calibration of a biochemical transport model. Reversible sorption is the fastest process with characteristic sorption and desorption rates = 0.09 d and = 4.4 d respectively, but remains limited to a minor amount of pesticides. Microbial mineralization is slower and is well described by a Monod formulation ( = 0.6 d , μgC/g , = 0.5) complemented by the characteristic accommodation rate = 0.93 d , the microbial mortality rate = 0.06 d and the recycling coefficient for dead biomass . Irreversible abiotic attachment and 2,4-D diffusion are the slowest processes, with the estimated attachment rate = 0.01 d and diffusion coefficient = 6.10 m /d. We use the calibrated biochemical transport model to explore the influence of the initial 2,4-D repartition and of the water potential. When added next to the microorganisms, pesticides that are not diffused away are efficiently degraded in the first few days. The pesticides diffused away are diluted, sorbed and hardly get back to the microorganisms, limiting the overall degradation. In this case degradation is more efficient for smaller diffusion and water content conditions. When initially separated, pesticides diffuse slowly everywhere in the soil core. The small part reaching the microorganisms is not efficiently degraded due to a low biological activity. The larger part becomes abiotically trapped before reaching the degraders. We hypothesize that transport mechanisms like pesticide convection or microbial mobility might be more decisive than pesticide diffusion to establish contact between pesticides and microorganisms.
    Keywords: Pesticide Degradation ; Spatial Heterogeneity ; Reactive Transport Model ; Diffusion-Controlled Microbial Activity ; 2,4-D ; Environmental Sciences ; Ecology
    ISSN: 0304-3800
    E-ISSN: 1872-7026
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  • 8
    Language: English
    In: Agriculture, Ecosystems and Environment, 16 September 2016, Vol.232, pp.165-178
    Description: The objective was to develop a multi-criteria tool to compare fertilizing practices either based on mineral fertilizer (CONT + N) or repeated applications of exogenous organic matter (EOM) and considering the positive but also the negative impacts of these practices. Three urban composts (a municipal solid waste or MSW, a co-compost of sewage sludge and green waste (GWS), and biowaste (BIO)) and a farmyard manure (FYM) have been applied biennially over 14 years. Soils and crops were sampled repeatedly and 〉100 parameters measured. The development of different quality indices (QI) was used to provide a quantitative tool for assessing the overall effects of recycling different types of EOM. A minimum data set was determined and 7 indices of soil and crop quality were calculated using linear scoring functions: soil fertility, soil biodiversity, soil biological activities, soil physical properties, soil contamination (⿿available⿿ and ⿿total⿿) and crop productivity. All QI varied between 0 and 1, 1 being the best score. EOM amendments significantly increased soil biodiversity, biological activities and physical properties with intensity generally depending on their characteristics. FYM was the most efficient EOM to improve soil biological properties. EOM application lead to similar yields as mineral fertilizers but grain quality was slightly decreased. Thus, mineral fertilizers remained more efficient at improving crop productivity index (QI = 0.88) than EOM although BIO was not significantly different than CONT + N. All EOM improved soil fertility but only BIO was significantly higher (QI = 0.86). EOM added a range of nutrients but an excess of P (e.g. GWS) can negatively impact the soil fertility index. EOM negatively affected the soil contamination index when considering total concentrations but decreased available fractions and consequently the risks of transfer. BIO was the most efficient EOM for most indices including improving the index of ⿿available⿿ soil contamination. This study demonstrated the positive impact of repeated EOM applications on soil and crop quality in a loamy soil.
    Keywords: Compost ; Farmyard Manure ; Mineral Fertilizer ; Long Term Effect ; Quality Index ; Aggregated Method ; Agriculture ; Environmental Sciences
    ISSN: 0167-8809
    E-ISSN: 1873-2305
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  • 9
    In: FEMS Microbiology Ecology, 2012, Vol. 81(3), pp.673-683
    Description: The impact of the soil matric potential on the relationship between the relative abundance of degraders and their activity and on the spatial distribution of both at fine scales was determined to understand the role of environmental conditions in the degradation of organic substrates. The mineralization of 13 C-glucose and 13 C-2,4-dichlorophenoxyacetic acid (2,4-D) was measured at different matric potentials (−0.001, −0.01 and −0.316 MPa) in 6 × 6 × 6 mm 3 cubes excised from soil cores. At the end of the incubation, total bacterial and 2,4-D degrader abundances were determined by quantifying the 16S rRNA and the tfdA genes, respectively. The mineralization of 2,4-D was more sensitive to changes in matric potential than was that of glucose. The amount and spatial structure of 2,4-D mineralization decreased with matric potential, whilst the spatial variability increased. On the other hand, the spatial variation of glucose mineralization was less affected by changes in matric potential. The relationship between the relative abundance of 2,4-D degraders and 2,4-D mineralization was significantly affected by matric potential: the relative abundance of tfdA needed to be higher to reach a given level of 2,4-D mineralization in dryer than in moister conditions. The data show how microbial interactions with their microhabitat can have an impact on soil processes at larger scales.
    Keywords: 2, 4 - D ; Relative Abundance Of Degraders ; Water Content ; Glucose ; Organic Substrate Mineralization ; Spatial Variability
    ISSN: 01686496
    E-ISSN: 1574-6941
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  • 10
    Language: English
    In: Advances in Water Resources, September 2015, Vol.83, pp.123-136
    Description: Soil structure and interactions between biotic and abiotic processes are increasingly recognized as important for explaining the large uncertainties in the outputs of macroscopic SOM decomposition models. We present a numerical analysis to assess the role of meso- and macropore topology on the biodegradation of a soluble carbon substrate in variably water saturated and pure diffusion conditions . Our analysis was built as a complete factorial design and used a new 3D pore-scale model, LBioS, that couples a diffusion lattice-Boltzmann model and a compartmental biodegradation model. The scenarios combined contrasted modalities of four factors: meso- and macropore space geometry, water saturation, bacterial distribution and physiology. A global sensitivity analysis of these factors highlighted the role of physical factors in the biodegradation kinetics of our scenarios. Bacteria location explained 28% of the total variance in substrate concentration in all scenarios, while the interactions among location, saturation and geometry explained up to 51% of it.
    Keywords: Biodegradation ; Lattice-Boltzmann Method ; Pore-Scale Heterogeneity ; Spatial Distribution ; Substrate Diffusion ; Microbial Habitats ; Engineering
    ISSN: 0309-1708
    E-ISSN: 1872-9657
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