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  • Microorganisms
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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
    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 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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  • 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: Soil Biology and Biochemistry, April 2014, Vol.71, pp.21-30
    Description: Temporal dynamics create unique and often ephemeral conditions that can influence soil microbial biogeography at different spatial scales. This study investigated the relation between decimeter to meter spatial variability of soil microbial community structure, plant diversity, and soil properties at six dates from April through November. We also explored the robustness of these interactions over time. An historically unfertilized, unplowed grassland in southwest Germany was selected to characterize how seasonal variability in the composition of plant communities and substrate quality changed the biogeography of soil microorganisms at the plot scale (10 m × 10 m). Microbial community spatial structure was positively correlated with the local environment, i.e. physical and chemical soil properties, in spring and autumn, while the density and diversity of plants had an additional effect in the summer period. Spatial relationships among plant and microbial communities were detected only in the early summer and autumn periods when aboveground biomass increase was most rapid and its influence on soil microbial communities was greatest due to increased demand by plants for nutrients. Individual properties exhibited varying degrees of spatial structure over the season. Differential responses of Gram positive and Gram negative bacterial communities to seasonal shifts in soil nutrients were detected. We concluded that spatial distribution patterns of soil microorganisms change over a season and that chemical soil properties are more important controlling factors than plant density and diversity. Finer spatial resolution, such as the mm to cm scale, as well as taxonomic resolution of microbial groups, could help determine the importance of plant species density, composition, and growth stage in shaping microbial community composition and spatial patterns.
    Keywords: Microbial Community Composition ; Spatial Patterns ; Grassland Soils ; Plfas ; Mantel Statistic ; Variogram ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 7
    In: FEMS Microbiology Letters, 2017, Vol. 364(9)
    Description: Nitrogen (N) addition is known to affect soil microbial communities, but the interactive effects of N addition with other drivers of global change remain unclear. The impacts of multiple global changes on the structure of microbial communities may be mediated by specific microbial groups with different life-history strategies. Here, we investigated the combined effects of elevated CO 2 and N addition on soil microbial communities using PLFA profiling in a short-term grassland mesocosm experiment. We also examined the linkages between the relative abundance of r- and K-strategist microorganisms and resistance of the microbial community structure to experimental treatments. N addition had a significant effect on microbial community structure, likely driven by concurrent increases in plant biomass and in soil labile C and N. In contrast, microbial community structure did not change under elevated CO 2 or show significant CO 2 × N interactions. Resistance of soil microbial community structure decreased with increasing fungal/bacterial ratio, but showed a positive relationship with the Gram-positive/Gram-negative bacterial ratio. Our findings suggest that the Gram-positive/Gram-negative bacteria ratio may be a useful indicator of microbial community resistance and that K-strategist abundance may play a role in the short-term stability of microbial communities under global change. Elevated CO 2 alone or in combination with N addition does not affect soil microbial community structure in grassland mesocosms.
    Keywords: Global Change ; Grassland ; Fungal/Bacterial Ratio ; Plfa
    ISSN: 03781097
    E-ISSN: 1574-6968
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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: Environmental Pollution, 2009, Vol.157(11), pp.2985-2993
    Description: The biodegradation of nonextractable residues (NER) of pesticides in soil is still poorly understood. The aim of this study was to evaluate the influence of NER ageing and fresh soil addition on the microbial communities responsible for their mineralisation. Soil containing either 15 or...
    Keywords: Environmental Sciences ; Environmental and Society ; Pesticides ; Nonextractable Residues ; 13c Labelling ; Soil Microbial Communities ; Biodegradation  ; Engineering ; Environmental Sciences ; Anatomy & Physiology
    ISSN: 0269-7491
    E-ISSN: 1873-6424
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