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  • Ecology
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  • 1
    Language: English
    In: Journal of Plant Nutrition and Soil Science, August 2017, Vol.180(4), pp.425-429
    Description: The microbial habitat is rarely studied in soil microbial ecology even though microbial cells are exposed and adapt to their local environmental conditions. The physical environment also constrains interactions among organisms. The nature of microbial communities and their functioning can only be fully understood if their habitat is accounted for. Here, I describe the soil microbial habitat and show how our understanding of microbial functioning has been shaped by this line of investigation.
    Keywords: Diffusion ; Functional Redundancy ; Microbial Communities ; Micro‐Habitat ; Microscale
    ISSN: 1436-8730
    E-ISSN: 1522-2624
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  • 2
    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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  • 3
    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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  • 4
    Language: English
    In: African Journal of Ecology, 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...
    Keywords: Environmental Sciences ; Life Sciences ; Plant-Soil Inter-Actions ; Above-Ground-Below-Ground Interactions ; Attractiveness ; Competition ; Diversity ; Floral Display ; Nectar ; Plant-Plant Interactions ; Plant-Pollinator Interactions ; Environmental Sciences ; Biology ; Zoology ; Ecology
    ISSN: 0141-6707
    ISSN: 00220477
    E-ISSN: 1365-2028
    E-ISSN: 13652745
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  • 5
    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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  • 6
    In: Functional Ecology, December 2014, Vol.28(6), pp.1523-1533
    Description: A major question in ecology is to know how ecosystem function is affected by the number of species. After two decades of research, the nature, shape, and causes of the relationships between biodiversity and ecosystem functioning remain unresolved. Huston ([Huston, M.A., 1997]) suggested that a statistical ‘sampling effect’ for a few dominant species produced the patterns observed in experiments, while Tilman et al. ([Tilman, D., 1997a]) argued that the observed responses were due to the number of species rather than the properties of a few. Here, we present a general, theoretical and parsimonious model using combinatorial probabilities to describe the assembly effect as a probabilistic process. Our basic assumption is that community function is determined by random drawing from a fixed species pool composed of three classes of species. The species classes differ in their effect on community function and are ordered in a simple dominance hierarchy (subordinate, dominant and super‐dominant species). Community function is determined by prevalent dominance rules: the dominance by the majority of species mimics the effect of dominant species, i.e. the function is determined by the dominant or super‐dominant species class the most numerous within the community; the dominance by the presence of species mimics the effect of keystone species, i.e. the function is determined by the species that is ranked highest in the dominance hierarchy. The model produces significant fits to four experimental data sets obtained for plant and microbial communities, including monotonic and hump‐shaped curves. The results indicate that the model gave good fits under both the dominance rules in any data set, suggesting that the random sampling effect provides a parsimonious explanation for the various relationships observed in diversity‐ecosystem functioning experiments. The model describes a random assembly process that produces variation in ecosystem functioning in response to number of species selected from a regional species pool composed of several classes of species differing in their ecosystem effects and relative dominance. This simple model reproduces all shapes of diversity‐ecosystem functioning relationships reported in the experimental literature. The results suggest that the multi‐faceted response of ecosystems to biodiversity may be nothing more than manifestations of random assembly effects and variation in species properties. Lay
    Keywords: Assembly Process ; Biological Interactions ; Dominance ; Keystone ; Modelling ; Probability ; Sampling Effect ; Theoretical Ecology
    ISSN: 0269-8463
    E-ISSN: 1365-2435
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  • 7
    Language: English
    In: Microbial Ecology, 2015, Vol.70(3), pp.809-818
    Description: Many studies have assessed the responses of soil microbial functional groups to increases in atmospheric CO 2 or N deposition alone and more rarely in combination. However, the effects of elevated CO 2 and N on the (de)coupling between different microbial functional groups (e.g., different groups of nitrifiers) have been barely studied, despite potential consequences for ecosystem functioning. Here, we investigated the short-term combined effects of elevated CO 2 and N supply on the abundances of the four main microbial groups involved in soil nitrification: ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (belonging to the genera Nitrobacter and Nitrospira ) in grassland mesocosms. AOB and AOA abundances responded differently to the treatments: N addition increased AOB abundance, but did not alter AOA abundance. Nitrobacter and Nitrospira abundances also showed contrasted responses to the treatments: N addition increased Nitrobacter abundance, but decreased Nitrospira abundance. Our results support the idea of a niche differentiation between AOB and AOA, and between Nitrobacter and Nitrospira . AOB and Nitrobacter were both promoted at high N and C conditions (and low soil water content for Nitrobacter ), while AOA and Nitrospira were favored at low N and C conditions (and high soil water content for Nitrospira ). In addition, Nitrobacter abundance was positively correlated to AOB abundance and Nitrospira abundance to AOA abundance. Our results suggest that the couplings between ammonia and nitrite oxidizers are influenced by soil N availability. Multiple environmental changes may thus elicit rapid and contrasted responses between and among the soil ammonia and nitrite oxidizers due to their different ecological requirements.
    Keywords: Global change ; Grasslands ; Nitrification ; Ammonia oxidizers ; Nitrite oxidizers ; Niche differentiation
    ISSN: 0095-3628
    E-ISSN: 1432-184X
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  • 8
    Language: English
    In: Environmental Science and Pollution Research, 2011, Vol.18(9), pp.1574-1584
    Description: Introduction: Composting may enhance bioremediation of PAH-contaminated soils by providing organic substrates that stimulate the growth of potential microbial degraders. However, the influence of added organic matter (OM) together with the microbial activities on the dissipation of PAHs has not yet been fully assessed. Materials and methods: An in-vessel composting-bioremediation experiment of a contaminated soil amended with fresh wastes was carried out. Four different experimental conditions were tested in triplicate during 60 days using laboratory-scale reactors: treatment S (100% soil), W (100% wastes), SW (soil/waste mixture), and SWB (soil/waste mixture with inoculation of degrading microorganisms). Results and discussion: A dry mass loss of 35 plus or minus 5% was observed in treatments with organic wastes during composting in all the treatments except treatment S. The dissipation of the 16 USEPA-listed PAHs was largely enhanced from no significant change to 50.5 plus or minus 14.8% (for SW)/63.7 plus or minus 10.0% (for SWB). More obvious dissipation was observed when fresh wastes were added at the beginning of composting to the contaminated soil, without significant difference between the inoculated and non-inoculated treatments. Phospholipid fatty acid (PLFA) profiling showed that fungi and G-bacteria dominated at the beginning of experiment and were probably involved in PAH dissipation. Subsequently, greater relative abundances of G+bacteria were observed as PAH dissipation slowed down. Conclusions: The results suggest that improving the composting process with optimal organic compositions may be a feasible remediation strategy in PAH-contaminated soils through stimulation of active microbial populations.
    Keywords: Composting ; Contaminated soil ; PAHs ; Bioremediation ; Microbial communities ; PLFAs
    ISSN: 0944-1344
    E-ISSN: 1614-7499
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  • 9
    Language: English
    In: Geoderma, 2006, Vol.133(3), pp.398-407
    Description: We investigated the utility of combining micro-scale computed tomography (micro-CT), image analysis and geostatistics to quantify pore geometry at spatial scales ranging from 4.4 μm to 2 mm. To facilitate this, we investigated soil taken from an old permanent upland pasture known to support very high levels of microbial diversity and that had not been cultivated for many centuries. Aggregates (〈 3 mm in diameter) from three treatments (control, sewage sludge amended and biocide treated) derived from the site were imaged using synchrotron-based computed microtomography. Image analysis was used to determine aggregate porosity and pore shape parameters, and semivariance analysis was used to measure the spatial correlation of pore space within the three land treatments. For all plots high porosities were observed (c. 30%) at scales below 3 mm. High variations of porosity were also observed, ranging from 22% to 47%, but no significant differences among treatments were found. No significant differences among treatments were found in the distribution of pores within aggregates, as revealed by semivariance analysis, or in pore shape parameters. No treatment effects were observed. However, the work presented here shows that the combination of approaches adopted has great potential for quantifying the soil microbial physical habitat. Future work, should investigate the use of these novel techniques in more controlled soil ecosystems to provide an exciting new way of understanding the soil-microbe interactions at appropriate scales.
    Keywords: X-Ray Computer Tomography ; Aggregates ; Microscale ; Agriculture
    ISSN: 0016-7061
    E-ISSN: 1872-6259
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  • 10
    Language: English
    In: European Journal of Soil Biology, September 2013, Vol.58, pp.81-90
    Description: Soil microbial communities live in the soil pore network and therefore the access they have to organic substrate, oxygen and water depends on how this network is structured. In this experimental study, the relationship between soil structure and soil organic matter dynamics was investigated by measuring the kinetics of organic carbon decomposition in samples that varied in the physical structure of the soil pore network. Soil cores with different structures (undisturbed, sieved and disaggregated by agitation in water), but with the same bulk density, were incubated and the mineralisation of native and added ( C-labelled substrates, fructose and vanillin) organic carbon was measured for a period of 127 days. The incubation was commenced after the immediate effects of the perturbations caused by the soil structural treatments had dissipated. At the end of the incubation, the microbial biomass and microbial community structure were determined. It was found that the respiration kinetics were not related to soil structural parameters, which were determined using X-ray micro-CT. The structure treatments had no significant effect on the mineralisation of soil or added organic carbon, despite the significantly different physical environments. However, the microbial community structure of the undisturbed and dispersed samples were significantly different. These results indicate that neither decomposer access to organic substrate nor the environmental conditions in which decomposition occurred were impaired by the soil structure treatments and suggest that the controls on carbon dynamics may take place at scales below those that were manipulated in this experiment.
    Keywords: Soil Organic Carbon ; Mineralisation ; Carbon Dynamics ; Soil Structure ; X-Ray Micro-Computed Tomography ; Microbial Habitat ; Biology ; Zoology ; Ecology
    ISSN: 1164-5563
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