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Berlin Brandenburg

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  • 1
    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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  • 2
    Language: English
    In: Soil Biology and Biochemistry, October 2018, Vol.125, pp.1-9
    Description: Earthworms contribute to numerous ecosystem services provided by soils. Most of the studies focusing on the contributions of earthworms on leaf litter decomposition were conducted by comparing distinct ecological categories (epigeic, epi-anecic, anecic strict and endogeic), whereas their specific contributions within a given ecological category remains largely unknown. In this context, the aim of this study was to determine the contribution of four epi-anecic earthworm species ( , and to the leaf litter decomposition of three plant species ( and ) with contrasted litter traits located at both the soil surface and at a depth of 10 cm. Fungal and bacterial communities inhabiting epi-anecic earthworm burrows were also assessed using T-RFLP analysis. Epi-anecic earthworms improved the leaf litter mass loss solely at the soil surface, while leaf litter mass loss was mainly due to microbial activity at 10 cm deep. Leaf litter mass loss was positively correlated to the initial biomass of the epi-anecic earthworms and the intensity of this relationship was dependent on litter type. Interestingly, seemed to have a higher contribution to surface leaf litter mass loss that was linked to a stimulation of the fungal communities in its burrows. Fungal communities were thus impacted by both the litter type and the epi-anecic earthworm identity whereas soil bacterial diversity and richness were stimulated in the earthworm burrows whatever the epi-anecic earthworm species considered. Overall, epi-anecic earthworms contributed to enhance the diversity of the drilospheric microbiota.
    Keywords: Lumbricidae ; Leaf Litter ; Burrows ; Fungi ; Bacteria ; Temperate Grassland ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 3
    Language: English
    In: Biodegradation, 2013, Vol.24(2), pp.203-213
    Description: Assessing in situ microbial abilities of soils to degrade pesticides is of great interest giving insight in soil filtering capability, which is a key ecosystem function limiting pollution of groundwater. Quantification of pesticide-degrading gene expression by reverse transcription quantitative PCR (RT-qPCR) was tested as a suitable indicator to monitor pesticide biodegradation performances in soil. RNA extraction protocol was optimized to enhance the yield and quality of RNA recovered from soil samples to perform RT-qPCR assays. As a model, the activity of atrazine-degrading communities was monitored using RT-qPCRs to estimate the level of expression of atzD in five agricultural soils showing different atrazine mineralization abilities. Interestingly, the relative abundance of atzD mRNA copy numbers was positively correlated to the maximum rate and to the maximal amount of atrazine mineralized. Our findings indicate that the quantification of pesticide-degrading gene expression may be suitable to assess biodegradation performance in soil and monitor natural attenuation of pesticide.
    Keywords: mRNA ; RT-qPCR ; Atrazine ; Soil RNA extraction ; Natural attenuation
    ISSN: 0923-9820
    E-ISSN: 1572-9729
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  • 4
    Language: English
    In: PLoS ONE, 2018, Vol.13(12), p.e0209089
    Description: Agriculture is undergoing important changes in order to meet sustainable soil management with respect to biodiversity (namely agroecology). Within this context, alternative solutions to mineral fertilizers such as agricultural biostimulants are thus promoted and being developed. The mechanisms...
    Keywords: Life Sciences ; Agricultural Sciences ; Soil Study ; Environmental Sciences ; Biodiversity and Ecology ; Sciences (General) ; Environmental Sciences
    ISSN: 1932-6203
    ISSN: PLOS ONE
    E-ISSN: 1932-6203
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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: Agriculture, Ecosystems and Environment, 01 December 2017, Vol.250, pp.25-36
    Description: We investigated whether perennial soil organic amendments of pig slurry (PS) and methanized pig slurry (MPS) affect active bacterial communities and change the diversity and the C-flux of Volatile Organic Compounds (VOCs) emitted by soils compared to control plots without any fertilization (C). The long term effects of the fertilization history of the amendments and the short term impact of the organic inputs were both investigated by measuring VOCs emissions using a Proton Transfer Reaction-Mass Spectrometer (PTR-MS) and by analyzing active bacterial diversity by MiSeq Illumina sequencing just before and up to 64 days following the inputs. Soil VOCs emissions (diversity and fluxes) naturally varied with temperature and rainfall variations, irrespective of manure inputs. No effect of the 5-yr fertilization history was observed on bacterial communities’ composition and on soil VOCs emissions. However, both manure inputs (PS and MPS) were associated with an inoculation of γ- ( sp. and/or sp.) to the soil on top of which PS inputs activated native soil sp. (Firmicutes). VOCs spectra was mainly dominated by methanol and acetonitrile, the acetonitrile emissions not depending on the organic practices. C-VOCs fluxes from the soil to the atmosphere varied from 12 to 76 μg of C-VOCs h m in the control plots. Pig slurry and methanized pig slurry differentially impacted soil VOCs emissions: PS inputs doubled the C-VOC fluxes due to high emission of methanol while MPS inputs reduced VOCs fluxes even less than the control unamended plots, which is of great interest in the context of mitigating greenhouse gases in agriculture. Our results suggest that soil fluxes could, under certain conditions, not be marginal compared to plant fluxes and be potentially driven by new land-uses in agriculture.
    Keywords: Manure Fertilization ; Soil Living Bacteria ; Soil C-Vocs Fluxes ; Field Gas Sampling ; Methanization Process ; Agriculture ; Environmental Sciences
    ISSN: 0167-8809
    E-ISSN: 1873-2305
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  • 7
    Language: English
    In: Agriculture, Ecosystems and Environment, 01 March 2018, Vol.255, pp.119-120
    Keywords: Agriculture ; Environmental Sciences
    ISSN: 0167-8809
    E-ISSN: 1873-2305
    Source: ScienceDirect Journals (Elsevier)
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  • 8
    Language: English
    In: Molecular Ecology, 2010, Vol.19(4), pp.749-759
    Description: One of the various ecosystemic services sustained by soil is pollutant degradation mediated by adapted soil bacteria. The pathways of atrazine biodegradation have been elucidated but in situ expression of the genes involved in atrazine degradation has yet to be demonstrated in soil. Expression...
    Keywords: Environmental Sciences ; Biodiversity and Ecology ; Atrazine ; Atz Mrna ; Earthworms ; Soil Bioturbation ; Transcriptional Analysis ; Environmental Sciences ; Biology ; Ecology
    ISSN: 0962-1083
    E-ISSN: 1365-294X
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  • 9
    In: The ISME Journal, 2010, Vol.5(6), p.1048
    Description: In soil, the way biotic parameters impact the relationship between bacterial diversity and function is still unknown. To understand these interactions better, we used RNA-based stable-isotope probing to study the diversity of active atrazine-degrading bacteria in relation to atrazine degradation and to explore the impact of earthworm-soil engineering with respect to this relationship. Bulk soil, burrow linings and earthworm casts were incubated with (13)C-atrazine. The pollutant degradation was quantified by liquid chromatography-mass spectrometry for 8 days, whereas active atrazine degraders were identified at 2 and 8 days by sequencing the 16S ribosomal RNA in the (13)C-RNA fractions from the three soil microsites. An original diversity of atrazine degraders was found. Earthworm soil engineering greatly modified the taxonomic composition of atrazine degraders with dominance of α-, β- and γ-proteobacteria in burrow linings and of Actinobacteria in casts. Earthworm soil bioturbation increased the γ-diversity of atrazine degraders over the soil microsites generated. Atrazine degradation was enhanced in burrow linings in which primary atrazine degraders, closely related to Pelomonas aquatica, were detected only 2 days after atrazine addition. Atrazine degradation efficiency was not linearly related to the species richness of degraders but likely relied on keystone species. By enhancing soil heterogeneity, earthworms sustained high phylogenetic bacterial diversity and exerted a biotic control on the bacterial diversity-function relationships. Our findings call for future investigations to assess the ecological significance of biotic controls on the relationships between diversity and function on ecosystem properties and services (for example, soil detoxification) at larger scales.
    Keywords: Biology;
    ISSN: 1751-7362
    E-ISSN: 17517370
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  • 10
    In: FEMS Microbiology Ecology, 2013, Vol. 84(1), pp.165-175
    Description: The shorter reads generated by high-throughput sequencing has led to a focus on either the ITS1 or the ITS2 sublocus in fungal diversity analyses. Our study aimed to determine how making this choice would influence the datasets obtained and our vision of environmental fungal diversity. DNA was extracted from different environmental samples (water, sediments and soil) and the total internal transcribed spacer (ITS) locus was amplified. 454-sequencing was performed targeting both ITS1 and ITS2. No significant differences in the number of sequences, operational taxonomic units (OTUs) and in the dominant OTUs were detected but less diversity was observed in the ITS2 dataset. In the soil samples, differences in the fungal taxonomic identification were observed, with more Basidiomycota in the ITS1 dataset and more Ascomycota in the ITS2 dataset. Only one-third of the OTUs were detected in both datasets which could be due to (1) more short sequences removed in the ITS2 dataset, (2) different taxonomic affiliation depending on the sublocus used as BLASTn query and/or (3) selectivity in how a primer amplifies the true community. Although ITS1 and ITS2 datasets led to similar results at the fungal community level, for further in-depth diversity analysis this study suggests the analysis of both ITS regions, as they provided different information and were complementary.
    Keywords: 454 Pyrosequencing ; Community Structure ; Species Richness ; Sørensen Index ; Minimum Read Length
    ISSN: 01686496
    E-ISSN: 1574-6941
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