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  • 1
    In: PLoS ONE, 2014, Vol.9(1)
    Description: Despite an exceptional number of bacterial cells and species in soils, bacterial diversity seems to have little effect on soil processes, such as respiration or nitrification, that can be affected by interactions between bacterial cells. The aim of this study is to understand how bacterial cells are distributed in soil to better understand the scaling between cell-to-cell interactions and what can be measured in a few milligrams, or more, of soil. Based on the analysis of 744 images of observed bacterial distributions in soil thin sections taken at different depths, we found that the inter-cell distance was, on average 12.46 µm and that these inter-cell distances were shorter near the soil surface (10.38 µm) than at depth (〉18 µm), due to changes in cell densities. These images were also used to develop a spatial statistical model, based on Log Gaussian Cox Processes, to analyse the 2D distribution of cells and construct realistic 3D bacterial distributions. Our analyses suggest that despite the very high number of cells and species in soil, bacteria only interact with a few other individuals. For example, at bacterial densities commonly found in bulk soil (10 8 cells g −1 soil), the number of neighbours a single bacterium has within an interaction distance of ca. 20 µm is relatively limited (120 cells on average). Making conservative assumptions about the distribution of species, we show that such neighbourhoods contain less than 100 species. This value did not change appreciably as a function of the overall diversity in soil, suggesting that the diversity of soil bacterial communities may be species-saturated. All in all, this work provides precise data on bacterial distributions, a novel way to model them at the micrometer scale as well as some new insights on the degree of interactions between individual bacterial cells in soils.
    Keywords: Research Article ; Agriculture ; Biology ; Earth Sciences ; Mathematics
    E-ISSN: 1932-6203
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  • 2
    Language: English
    In: Soil Biology and Biochemistry, February 2011, Vol.43(2), pp.280-286
    Description: Microbial communities exist and are active in a complex 3-D physical framework which can cause a variety of micro-environments to develop that are more or less suitable for microbial growth, activity and survival. If there is a significant microbial biogeography at the pore scale in soil, then the relationship between microbial diversity and ecosystem function is likely to be affected by micro-environmental variations at the pore scale. In this laboratory study we show that there is a significant pore-scale microbial biogeography by labelling microbial communities in different pore size classes of undisturbed soil cores with C-labelled fructose (a soluble, labile substrate). This was achieved by adding the substrate solution to the samples at different matric potentials (−100 kPa, −3.15 kPa and −1 kPa; placing the substrate in pores with maximum diameter of 0.97, 9.7 and 97 μm, respectively) and incubating the samples for two weeks. The mineralisation of soil organic carbon and fructose was measured as CO and C–CO , respectively, in the jar headspace throughout the incubation. At the end of incubation we analysed the total microbial community structure using PLFA. The structure of microbial communities in different pore size classes was measured by PLFA stable isotope probing. Total PLFA profiles suggested that there was little effect of the incubation conditions on microbial community structure. However, labelled PLFA profiles showed that microbial community structure differed significantly among pore size classes, the differences being due primarily to variations in the abundance of mono-unsaturated lipids (Gram-biomarkers) and of the fungal biomarker (C18:2(9,12)). This is the first evidence for a significant microbial biogeography at the pore scale in undisturbed soil cores. ► Non-random variation in microbial community structure at pore scale. ► Gram-bacterial and fungal abundance change at pore scale. ► Different regions of the soil pore system can be targetted using combination of C-labelled substrate and moisture release curve.
    Keywords: Stable Isotope Probing ; Undisturbed Cores ; Matric Potential ; Plfa ; Pore Scale ; Biogeography ; 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 & 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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  • 5
    Language: English
    In: Soil Biology and Biochemistry, April 2014, Vol.71, pp.1-12
    Description: Thermal acclimation of soil organic matter (SOM) decomposition is frequently observed and has often been attributed to substrate depletion under warming, but other mechanisms, such as changes in microbial community structure and functioning, have received less attention. In order to determine whether shifts in microbial community structure and functioning are involved in thermal acclimation of SOM decomposition, a laboratory incubation experiment was conducted using an artificial forest soil. Samples were first subjected to different temperatures of 5, 15, and 25 °C during a 72-day pre-incubation period and then half of the microcosms from each pre-incubation temperature were incubated at 5 or 25 °C for a period of 11 days. Substantial thermal acclimation of SOM decomposition was observed, with the SOM decomposition in soils pre-incubated at higher temperatures being less sensitive to temperature. Along with the reduced temperature sensitivity in response to warming, significant changes in microbial community PLFAs, microbial biomass carbon (MBC), and the potential activities of 11 enzymes were also observed. Nevertheless, shifts in microbial community PLFAs and particular enzyme activities provided the most explanatory power for the decreased temperature sensitivity with warming, as revealed by a multivariate regression analysis. The microbial community structure shifts were mainly manifested as an increase in the relative abundance of Gram-positive bacteria and decreases in the relative abundances of Gram-negative bacteria and fungi. Microbial communities pre-incubated under lower temperatures experienced greater shifts in their structure. Substrate depletion did not occur in this short-term incubation experiment, since neither total organic carbon (TOC) nor dissolved organic carbon (DOC) decreased with increasing temperature. Our results suggest that shifts in microbial community structure and functioning may underlie the thermal acclimation of SOM decomposition and should be taken into account when predicting the response of soil CO efflux to global warming.
    Keywords: Heterotrophic Respiration ; Acclimatization ; Microbial Adaptation ; Phospholipid Fatty Acids (Plfas) ; Substrate Availability ; Carbon Cycling ; Temperate Forest ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 6
    Language: English
    In: Environmental science & technology, 15 April 2014, Vol.48(8), pp.4344-52
    Description: Energy is continuously transformed in environmental systems through the metabolic activities of living organisms, but little is known about the relationship between the two. In this study, we tested the hypothesis that microbial energetics are controlled by microbial community composition in terrestrial ecosystems. We determined the functional diversity profiles of the soil biota (i.e., multiple substrate-induced respiration and microbial energetics) in soils from an arable ecosystem with contrasting long-term management regimes (54 years). These two functional profiling methods were then related to the soils' microbial community composition. Using isothermal microcalorimetry, we show that direct measures of energetics provide a functional link between energy flows and the composition of below-ground microbial communities at a high taxonomic level (Mantel R = 0.4602, P = 0.006). In contrast, this link was not apparent when carbon dioxide (CO2) was used as an aggregate measure of microbial metabolism (Mantel R = 0.2291, P = 0.11). Our work advocates that the microbial energetics approach provides complementary information to soil respiration for investigating the involvement of microbial communities in below-ground carbon dynamics. Empirical data of our proposed microbial energetics approach can feed into carbon-climate based ecosystem feedback modeling with the suggested conceptual ecological model as a base.
    Keywords: Carbon Cycle ; Ecosystem ; Temperature ; Calorimetry -- Methods
    ISSN: 0013936X
    E-ISSN: 1520-5851
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  • 7
    Language: English
    In: Science of the Total Environment, 15 November 2017, Vol.598, pp.938-948
    Description: The concentration, degree of contamination and pollution of 7 trace elements (TEs) along an urban pressure gradient were measured in 180 lawn and wood soils of the Paris region (France). Iron (Fe), a major element, was used as reference element. Copper (Cu), cadmium (Cd), lead (Pb) and zinc (Zn) were of anthropogenic origin, while arsenic (As), chromium (Cr) and nickel (Ni) were of natural origin. Road traffic was identified as the main source of anthropogenic TEs. In addition, the industrial activity of the Paris region, especially cement plants, was identified as secondary source of Cd. Soil characteristics (such as texture, organic carbon (OC) and total nitrogen (tot N) contents) tell the story of the soil origins and legacies along the urban pressure gradient and often can explain TE concentrations. The history of the land-use types was identified as a factor that allowed understanding the contamination and pollution by TEs. Urban wood soils were found to be more contaminated and polluted than urban lawns, probably because woods are much older than lawns and because of the legacy of the historical management of soils in the Paris region (Haussmann period). Lawn soils are similar to the fertile agricultural soils and relatively recently (mostly from the 1950s onwards) imported from the surrounding of Paris, so that they may be less influenced by urban conditions in terms of TE concentrations. Urban wood soils are heavily polluted by Cd, posing a high risk to the biological communities. The concentration of anthropogenic TEs increased from the rural to the urban areas, and the concentrations of most anthropogenic TEs in urban areas were equivalent to or above the regulatory reference values, raising the question of longer-term monitoring.
    Keywords: Trace Elements ; Urban-Rural Gradient ; Soils ; Green Spaces ; Lawns ; Forests ; Environmental Sciences ; Biology ; Public Health
    ISSN: 0048-9697
    E-ISSN: 1879-1026
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  • 8
    Language: English
    In: Journal of Ecology, 1 May 2011, Vol.99(3), pp.828-837
    Description: 1. Declines in availability of plant resources to pollinators are a major cause of pollinator loss. The management of plant communities to enhance floral resources is often proposed as a way to sustain pollinator populations. Nectar, the main energetic resource for pollinators, plays a central role in behaviour and composition of pollinator communities. Abiotic and biotic factors are known to influence nectar traits at both the species and community levels, but the impact of plant community composition itself has never been investigated. 2. Below-ground interactions in plant communities can induce changes in plant development through (i) plant-derived litter amendment of the soil and (ii) competition for soil resources between plants. We tested how plant below-ground interactions affect above-ground nectar traits involved in plant attractiveness to pollinators. 3. A short-term pot experiment was carried out with three temperate grassland species Mimulus guttatus, Lamium amplexicaule, and Medicago sativa, showing distinct litter stoichiometry and competitive abilities for soil resources. Litter amendment (none, mono and tri-specific litter) and plant interaction treatments (monocultures, two- and three-species mixtures) were crossed in a factorial design. 4. Litter amendment to the soil led to an increase in total nectar sugar content in L. amplexicaule plants but not in the two other species. We also found that the presence of M. guttatus, a competitive species, reduced the total nectar sugar content in L. amplexicaule through a concomitant decrease in nectar volume per flower and in floral display size, but not in other species. Species-specific responses of nectar traits to variation in soil nitrogen availability were thus observed, suggesting consequences for plant species and community attractiveness to pollinators. However, we did not find evidence that the legume M. sativa affected nectar traits of any neighbouring plants. 5. Synthesis. Our results demonstrate that litter inputs and competition between plants for soil resources can alter nectar traits linked to plant attractiveness to pollinators. This supports the idea that below-ground plant—plant interactions for soil resources can influence above-ground plant— plant interactions for pollination services. This offers promising perspectives in studying the role of below-ground—above-ground interactions on higher trophic levels.
    Keywords: Biological sciences -- Biology -- Botany ; Biological sciences -- Biology -- Botany ; Applied sciences -- Materials science -- Materials ; Biological sciences -- Agriculture -- Agricultural sciences ; Biological sciences -- Biology -- Botany ; Biological sciences -- Biochemistry -- Biomolecules ; Biological sciences -- Ecology -- Human ecology ; Biological sciences -- Ecology -- Natural resources ; Environmental studies -- Environmental sciences -- Developmental biology ; Biological sciences -- Biology -- Developmental biology
    ISSN: 00220477
    E-ISSN: 13652745
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  • 9
    Language: English
    In: 한국토양비료학회 학술발표회 초록집, 2014, Vol.2014(6), pp.338-338
    Keywords: Bacterial Distribution ; Soil ; Spatial Statistics ; Bacterial Diversity ; Thin Section
    Source: DBpia - 디비피아 (Nurimedia)
    Source: DBpia (Nurimedia)
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  • 10
    Language: English
    In: Biology and Fertility of Soils, 2013, Vol.49(7), pp.939-948
    Description: Soil organisms are of fundamental importance for many soil functions, such as organic matter decomposition, nutrient cycling and energy flow. Most research suggests that soil microbial communities are functionally redundant, meaning that there is little relationship between microbial diversity and soil functions. However, the activity of biological communities is known to be affected by their physical environment. Here, the effects of changes in microbial diversity and soil structure on organic C (OC) mineralisation were investigated. Sterile soil samples that had been subjected to different physical perturbations were inoculated with microbial communities with different levels of diversity. The samples were incubated for a period of 127 days and the mineralisation of native and added ( 13 C-labelled substrates, fructose and vanillin) OC was measured. It was hypothesised that the magnitude of the effect of changes in soil structure on OC mineralisation would increase as diversity decreased. The diversity treatment had a small but significant effect on the mineralisation of SOC and of the added substrates. The soil structure treatment had a significant effect only on the mineralisation of the added substrate C. There was no interaction between diversity and soil structure treatments, indicating that the relationship between diversity and OC decomposition was not dependent on the soil physical environment.
    Keywords: Soil microbial diversity ; Soil structure ; Soil organic carbon mineralisation ; Carbon dynamics
    ISSN: 0178-2762
    E-ISSN: 1432-0789
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