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  • 1
    Language: English
    In: Soil Biology and Biochemistry, Feb, 2013, Vol.57, p.950(3)
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.soilbio.2012.08.026 Byline: Pascal Jouquet (a), Pierre-Alain Maron (b), Virginie Nowak (b), Toan Tran Duc (c) Abstract: This study aimed at testing the capability of microbial community structure and abundance to be used as bioindicators of the origin of earthworm cast aggregates. Compact surface casts produced by Amynthas khami and surrounding aggregates lacking visible signs of biological activity (control) were left to disaggregate by natural rainfall and separated into four size classes (5-2, 2-0.5, 0.5-0.25 and 〈0.25 mm). The genetic structure and the abundance of the bacterial and fungal communities were characterized using B- and F-ARISA fingerprinting approach and quantitative PCR directly from DNA extracted from soil. Bacteria and to a lesser extent fungi were more abundant in casts than in control aggregates for all the size fractions. In addition, PCA carried out from B- and F-ARISA confirmed the different microbial properties between cast and control aggregates for all the aggregate size fractions. In conclusion, this study confirms the cryptic properties of earthworm casts when fragmented by the rain and the relevance of bacterial and fungal abundance and diversity as biological indicators of the origin of soil aggregates. Author Affiliation: (a) Institute of Research for Development (IRD), UMR 211 Bioemco, Centre IRD Ile de France, 32 Av. Henry Varagnat, 93143 Bondy, France (b) National Institute of Research in Agronomy (INRA), UMR MSE, Universite de Bourgogne, 17 rue de Sully, 21065 Dijon, France (c) Soils and Fertilizers Research Institute (SFRI), Dong Ngac, Tu Liem, Hanoi, Viet Nam Article History: Received 4 May 2012; Revised 1 August 2012; Accepted 27 August 2012
    ISSN: 0038-0717
    Source: Cengage Learning, Inc.
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  • 2
    Language: English
    In: Soil Biology and Biochemistry, Nov, 2013, Vol.66, p.69(9)
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.soilbio.2013.07.001 Byline: Aurore Kaisermann, Adelaide Roguet, Naoise Nunan, Pierre-Alain Maron, Nicholas Ostle, Jean-Christophe Lata Abstract: Soil microorganisms are responsible for organic matter decomposition processes that regulate soil carbon storage and mineralisation to CO.sub.2. Climate change is predicted to increase the frequency of drought events, with uncertain consequences for soil microbial communities. In this study we tested the hypothesis that agricultural management used to enhance soil carbon stocks would increase the stability of microbial community structure and activity in response to water-stress. Soil was sampled from a long-term field trial with three soil carbon management systems and was used in a laboratory study of the effect of a dry-wet cycle on organic C mineralisation and microbial community structure. After a drying-rewetting event, soil microcosms were maintained wet and microbial community structure and abundance as well as microbial respiration were measured for four weeks. The results showed that the NO-TILL management system, with the highest soil organic matter content and respiration rate, had a distinct bacterial community structure relative to the conventional and the TILL without fertiliser systems. In all management systems, the rewetting event clearly modified microbial community structure and activity. Both returned to their pre-drought state after 28 days. However, the magnitude of variation of C mineralisation was lower (i.e. the resistance to stress was higher) in the NO-TILL system. The genetic structure of the NO-TILL bacterial communities was most modified by water-stress and exhibited a slower recovery rate. This suggests that land use management can increase microbial functional resistance to drought stress via the establishment of bacterial communities with particular metabolic capacities. Nevertheless, the resilience rates of C mineralisation were similar among management regimes, suggesting that similar mechanisms occur, maybe due to a common soil microbial community legacy. Author Affiliation: (a) Laboratoire Bioemco, CNRS/UPMC, 46 rue d'Ulm, 75230 Paris Cedex 5, France (b) Laboratoire Bioemco, CNRS/UPMC, Batiment EGER Campus AgroParisTech, F-78850 Thiverval Grignon, France (c) UMR 1347 Agroecology INRA - AgroSup Dijon - University of Burgundy, 17, rue Sully, B.V. 86510, 21065 Dijon Cedex, France (d) Platform GenoSol, UMR Agroecology INRA - AgroSup Dijon - University of Burgundy, 17, rue Sully, B.V. 86510, 21065 Dijon Cedex, France (e) Centre for Ecology and Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster LA1 4AP, UK Article History: Received 14 May 2013; Accepted 1 July 2013
    Keywords: Global Temperature Changes ; No-tillage ; Soil Carbon
    ISSN: 0038-0717
    Source: Cengage Learning, Inc.
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  • 3
    Language: English
    In: Soil biology & biochemistry, 2013, Vol.57, pp.950-952
    Description: This study aimed at testing the capability of microbial community structure and abundance to be used as bioindicators of the origin of earthworm cast aggregates. Compact surface casts produced by Amynthas khami and surrounding aggregates lacking visible signs of biological activity (control) were left to disaggregate by natural rainfall and separated into four size classes (5–2, 2–0.5, 0.5–0.25 and 〈0.25 mm). The genetic structure and the abundance of the bacterial and fungal communities were characterized using B- and F-ARISA fingerprinting approach and quantitative PCR directly from DNA extracted from soil. Bacteria and to a lesser extent fungi were more abundant in casts than in control aggregates for all the size fractions. In addition, PCA carried out from B- and F-ARISA confirmed the different microbial properties between cast and control aggregates for all the aggregate size fractions. In conclusion, this study confirms the cryptic properties of earthworm casts when fragmented by the rain and the relevance of bacterial and fungal abundance and diversity as biological indicators of the origin of soil aggregates. ; p. 950-952.
    Keywords: Biodiversity ; Amynthas ; Soil Aggregates ; Fungal Communities ; Bioactive Properties ; Earthworms ; Fungi ; Indicator Species ; Bacteria ; Dna ; Community Structure ; Rain ; Worm Casts ; Quantitative Polymerase Chain Reaction
    ISSN: 0038-0717
    Source: AGRIS (Food and Agriculture Organization of the United Nations)
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  • 4
    Language: English
    In: Soil Biology and Biochemistry, February 2013, Vol.57, pp.950-952
    Description: This study aimed at testing the capability of microbial community structure and abundance to be used as bioindicators of the origin of earthworm cast aggregates. Compact surface casts produced by and surrounding aggregates lacking visible signs of biological activity (control) were left to disaggregate by natural rainfall and separated into four size classes (5–2, 2–0.5, 0.5–0.25 and 〈0.25 mm). The genetic structure and the abundance of the bacterial and fungal communities were characterized using B- and F-ARISA fingerprinting approach and quantitative PCR directly from DNA extracted from soil. Bacteria and to a lesser extent fungi were more abundant in casts than in control aggregates for all the size fractions. In addition, PCA carried out from B- and F-ARISA confirmed the different microbial properties between cast and control aggregates for all the aggregate size fractions. In conclusion, this study confirms the cryptic properties of earthworm casts when fragmented by the rain and the relevance of bacterial and fungal abundance and diversity as biological indicators of the origin of soil aggregates. ► Earthworms ( ) create casts on the soil surface. ► Earthworm casts have cryptic properties when fragmented by the rain. ► Bacteria and to a lesser extent fungi were more abundant in casts than in control surrounding aggregates. ► Earthworm casts are characterized by specific soil microbial communities. ► Bacterial and fungal abundance and diversity can be considered as biological indicators of the origin of soil aggregates.
    Keywords: Earthworm ; Biogenic Aggregates ; Physicogenic Aggregates ; Microbial Diversity ; Amynthas Khami ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 5
    Language: English
    In: PLoS ONE, 01 January 2013, Vol.8(10), p.e76991
    Description: Understanding the ecology of pathogenic organisms is important in order to monitor their transmission in the environment and the related health hazards. We investigated the relationship between soil microbial diversity and the barrier effect against Listeria monocytogenes invasion. By using...
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 6
    Language: English
    In: Science of the Total Environment, 15 September 2018, Vol.636, pp.1333-1343
    Description: Volatile Organic Compounds (VOCs) are reactive compounds essential to atmospheric chemistry. They are mainly emitted by living organisms, and mostly by plants. Soil microbes also contribute to emissions of VOCs. However, these emissions have not yet been characterised in terms of quality and quantity. Furthermore, long-term organic matter amendments are known to affect the microbial content of soils, and hence the quantity and quality of VOC emissions. This study investigates which and how much of these VOCs are emitted from soil amended with organic waste products (OWPs). Four OWPs were investigated: municipal solid waste compost (MSW), green waste and sludge co-compost (GWS), bio-waste compost (BIOW) and farmyard manure (FYM). These OWPs have been amended every two years since 1998 until now at a rate of ~4 tC ha . A soil receiving no organic inputs was used as a reference (CN). VOCs emissions were measured under laboratory conditions using a Proton Transfer Reaction-Quadrupole ion guide Time of Flight-Mass Spectrometry (PTR-QiToF-MS). A laboratory system was set up made of two Pyrex chambers, one for samples and the second empty, to be used as a blank. Our results showed that total VOC emissions were higher in BIOW than in MSW. Further findings outlined that the most emitted compounds were acetone, butanone and acetaldehyde in all treatments, suggesting a common production mechanism for these compounds, meaning they were not affected by the OWP amendment. We isolated 21 VOCs that had statistically different emissions between the treatments and could therefore be considered as good markers of soil biological functioning. Our results suggest that organic matter and pH jointly influenced total VOC emissions. In conclusion, OWPs in soil affect the type of VOC emissions and the total flux also depends on the pH of the soil and the quantity of organic matter.
    Keywords: VOC ; Soil ; Organic Waste Products ; Ptr-Qitof-MS ; Vocs Fluxes ; Environmental Sciences ; Biology ; Public Health
    ISSN: 0048-9697
    E-ISSN: 1879-1026
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  • 7
    Language: English
    In: 2012, Vol.7(9), p.e44279
    Description: Soil DNA extraction has become a critical step in describing microbial biodiversity. Historically, ascertaining overarching microbial ecological theories has been hindered as independent studies have used numerous custom and commercial DNA extraction procedures. For that reason, a standardized soil DNA extraction method (ISO-11063) was previously published. However, although this ISO method is suited for molecular tools such as quantitative PCR and community fingerprinting techniques, it has only been optimized for examining soil bacteria. Therefore, the aim of this study was to assess an appropriate soil DNA extraction procedure for examining bacterial, archaeal and fungal diversity in soils of contrasting land-use and physico-chemical properties. Three different procedures were tested: the ISO-11063 standard; a custom procedure (GnS-GII); and a modified ISO procedure (ISOm) which includes a different mechanical lysis step (a FastPrep ®-24 lysis step instead of the recommended bead-beating). The efficacy of each method was first assessed by estimating microbial biomass through total DNA quantification. Then, the abundances and community structure of bacteria, archaea and fungi were determined using real-time PCR and terminal restriction fragment length polymorphism approaches. Results showed that DNA yield was improved with the GnS-GII and ISOm procedures, and fungal community patterns were found to be strongly dependent on the extraction method. The main methodological factor responsible for differences between extraction procedure efficiencies was found to be the soil homogenization step. For integrative studies which aim to examine bacteria, archaea and fungi simultaneously, the ISOm procedure results in higher DNA recovery and better represents microbial communities.
    Keywords: Research Article ; Biology ; Microbiology
    E-ISSN: 1932-6203
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  • 8
    Language: English
    In: Soil Biology and Biochemistry, November 2013, Vol.66, pp.69-77
    Description: Soil microorganisms are responsible for organic matter decomposition processes that regulate soil carbon storage and mineralisation to CO . Climate change is predicted to increase the frequency of drought events, with uncertain consequences for soil microbial communities. In this study we tested the hypothesis that agricultural management used to enhance soil carbon stocks would increase the stability of microbial community structure and activity in response to water-stress. Soil was sampled from a long-term field trial with three soil carbon management systems and was used in a laboratory study of the effect of a dry–wet cycle on organic C mineralisation and microbial community structure. After a drying–rewetting event, soil microcosms were maintained wet and microbial community structure and abundance as well as microbial respiration were measured for four weeks. The results showed that the NO-TILL management system, with the highest soil organic matter content and respiration rate, had a distinct bacterial community structure relative to the conventional and the TILL without fertiliser systems. In all management systems, the rewetting event clearly modified microbial community structure and activity. Both returned to their pre-drought state after 28 days. However, the magnitude of variation of C mineralisation was lower ( the resistance to stress was higher) in the NO-TILL system. The genetic structure of the NO-TILL bacterial communities was most modified by water-stress and exhibited a slower recovery rate. This suggests that land use management can increase microbial functional resistance to drought stress the establishment of bacterial communities with particular metabolic capacities. Nevertheless, the resilience rates of C mineralisation were similar among management regimes, suggesting that similar mechanisms occur, maybe due to a common soil microbial community legacy.
    Keywords: Global Change ; Bacterial Community Structure ; C Mineralisation ; Stability ; Agricultural Land Use ; Drying–Rewetting ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 9
    Language: English
    In: Soil Biology and Biochemistry, December 2016, Vol.103, pp.28-38
    Description: Contrasting microbial community composition and activity at different soil depths may affect root litter decomposition. These effects have up to now been investigated mainly in laboratory studies, which may not be able to take into account complex conditions. Our study aimed to analyze the composition and activity of microbial communities after addition of C labeled wheat root litter to a loamy soil under grassland at 30, 60 and 90 cm depths, during a three-year field experiment. We investigated the dynamics of bacterial and fungal abundances and community structures by DNA genotyping and pyrosequencing of 16S and 18S rDNAs. The genetic structures of bacterial and fungal communities were evaluated by automated ribosomal intergenetic spacer analysis. The functions of these communities were analysed by determination of extracellular enzyme activities and viable microbial communities involved in C labeled organic matter decomposition studied by C PLFAs. The abundance of fungal and bacterial communities (16S and 18S rDNAs and PLFA) and the potential activities of enzymes involved in the C- and N-cycles were significantly higher at the top 30 cm compared with deeper soil throughout the experiment. Both were stimulated by fresh litter input. A trend to decreasing bacterial and fungal richness was noted after root litter addition at 30 cm, while richness of bacteria at 90 cm and those of fungi at 60 and 90 cm increased. Moreover, root litter addition caused a reduction of the Shannon Weaver Diversity index and a shift in microbial community structure at all three depths, which was more pronounced for bacteria at 30 and 60 cm and for fungi at 90 cm. The changes during litter degradation resulted in similar dynamics of most enzyme activities at all depths. Chitinase activity was enhanced after 29 months compared to initial conditions indicating the availability of high amounts of microbial detritus. The degrading microbial community as assessed by C PLFA showed similar temporal dynamics at all three depths. Fungal contribution to this community decreased during later stages of litter degradation, while the contribution of Gram+ bacteria increased. We conclude that litter addition led to convergence of microbial communities of top- and subsoil through stimulation of copiotrophic populations. Soil microbial community structures are thus connected with the amount of fresh litter input. Enzyme activities and C PLFA reflect to some extent the changes occurring during degradation, i.e. exhaustion of fresh plant material and accumulation of detritus.
    Keywords: Wheat Root ; Top- and Subsoil ; Extra-Cellular Enzyme Activities ; Plfa ; DNA ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 10
    Language: English
    In: Soil biology & biochemistry, 2013, Vol.66, pp.69-77
    Description: Soil microorganisms are responsible for organic matter decomposition processes that regulate soil carbon storage and mineralisation to CO₂. Climate change is predicted to increase the frequency of drought events, with uncertain consequences for soil microbial communities. In this study we tested the hypothesis that agricultural management used to enhance soil carbon stocks would increase the stability of microbial community structure and activity in response to water-stress. Soil was sampled from a long-term field trial with three soil carbon management systems and was used in a laboratory study of the effect of a dry–wet cycle on organic C mineralisation and microbial community structure. After a drying–rewetting event, soil microcosms were maintained wet and microbial community structure and abundance as well as microbial respiration were measured for four weeks. The results showed that the NO-TILL management system, with the highest soil organic matter content and respiration rate, had a distinct bacterial community structure relative to the conventional and the TILL without fertiliser systems. In all management systems, the rewetting event clearly modified microbial community structure and activity. Both returned to their pre-drought state after 28 days. However, the magnitude of variation of C mineralisation was lower (i.e. the resistance to stress was higher) in the NO-TILL system. The genetic structure of the NO-TILL bacterial communities was most modified by water-stress and exhibited a slower recovery rate. This suggests that land use management can increase microbial functional resistance to drought stress via the establishment of bacterial communities with particular metabolic capacities. Nevertheless, the resilience rates of C mineralisation were similar among management regimes, suggesting that similar mechanisms occur, maybe due to a common soil microbial community legacy. ; p. 69-77.
    Keywords: Soil Bacteria ; Carbon Sequestration ; Drought Tolerance ; No-Tillage ; Soil Organic Matter ; Organic Matter ; Field Experimentation ; Bacterial Communities ; Soil Ecology ; Climate Change ; Carbon Dioxide ; Drought ; Water Stress ; Agricultural Management ; Carbon Sinks ; Carbon ; Land Use Planning ; Management Systems ; Mineralization ; Stress Tolerance ; Respiratory Rate ; Community Structure ; Conventional Tillage ; Soil
    ISSN: 0038-0717
    Source: AGRIS (Food and Agriculture Organization of the United Nations)
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