Browsing by Author "Schmidt, Hannes"
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Item Open Access Bacterial distribution in soil microhabitats at different spatial scales(Cranfield University, 2018-08-08 16:11) Otten, Wilfred; Eickhorst, Thilo; Juyal, Archana; Falconer, Ruth; Hapca, Simona; Schmidt, Hannes; C Baveye, PhilippeThe data underpin the results described in the Geoderma paper by Juyal et al (2018) https://doi.org/10.1016/j.geoderma.2018.07.031 entitled 'Combination of techniques to quantify the distribution of bacteria in their soil microhabitats at different spatial scales'. The data are represented in an Excel file and show counts of bacteria in individual sections of soil blocks and their corresponding pore geometry as determined by Xray CT at three different spatial scales. The data underpin the summary data described in the paper where a detailed method description is also provided.Item Open Access Bypass and hyperbole in soil science: a perspective from the next generation of soil scientists(Wiley, 2020-11-23) Portell, Xavier; Sauzet, Ophélie; Balseiro-Romero, María; Benard, Pascal; Cardinael, Rémi; Couradeau, Estelle; Danra, Dieudonné D.; Evans, Daniel L.; Fry, Ellen L.; Hammer, Edith C.; Mamba, Danielle; Merino‐Martín, Luis; Mueller, Carsten W.; Paradelo, Marcos; Rees, Frédéric; Rossi, Lorenzo M. W.; Schmidt, Hannes; Schnee, Laura S.; Védère, Charlotte; Vidal, AlixItem Open Access Combination of techniques to quantify the distribution of bacteria in their soil microhabitats at different spatial scales(Elsevier, 2018-04-08) Juyal, Archana; Otten, Wilfred; Falconer, Ruth; Hapca, Simona; Schmidt, Hannes; Baveye, Philippe C.; Eickhorst, ThiloTo address a number of issues of great societal concern at the moment, like the sequestration of carbon, information is direly needed about interactions between soil architecture and microbial dynamics. Unfortunately, soils are extremely complex, heterogeneous systems comprising highly variable and dynamic micro-habitats that have significant impacts on the growth and activity of inhabiting microbiota. Data remain scarce on the influence of soil physical parameters characterizing the pore space on the distribution and diversity of bacteria. In this context, the objective of the research described in this article was to develop a method where X-ray microtomography, to characterize the soil architecture, is combined with fluorescence microscopy to visualize and quantify bacterial distributions in resin-impregnated soil sections. The influence of pore geometry (at a resolution of 13.4 μm) on the distribution of Pseudomonas fluorescens was analysed at macro- (5.2 mm × 5.2 mm), meso- (1 mm × 1 mm) and microscales (0.2 mm × 0.2 mm) based on an experimental setup simulating different soil architectures. The cell density of P. fluorescens was 5.59 x 107(SE 2.6 x 106) cells g−1 soil in 1–2 mm and 5.84 x 107(SE 2.4 x 106) cells g−1 in 2–4 mm size aggregates soil. Solid-pore interfaces influenced bacterial distribution at micro- and macroscale, whereas the effect of soil porosity on bacterial distribution varied according to three observation scales in different soil architectures. The influence of soil porosity on the distribution of bacteria in different soil architectures was observed mainly at the macroscale, relative to micro- and mesoscales. Experimental data suggest that the effect of pore geometry on the distribution of bacteria varied with the spatial scale, thus highlighting the need to consider an “appropriate spatial scale” to understand the factors that regulate the distribution of microbial communities in soils. The results obtained to date also indicate that the proposed method is a significant step towards a full mechanistic understanding of microbial dynamics in structured soils.Item Open Access Emergent properties of microbial activity in heterogeneous soil microenvironments: different research approaches are slowly converging, yet major challenges remain(Frontiers Media, 2018-08-27) Baveye, Philippe C.; Otten, Wilfred; Kravchenko, Alexandra; Balseiro-Romero, María; Beckers, Éléonore; Chalhoub, Maha; Darnault, Christophe; Eickhorst, Thilo; Garnier, Patricia; Hapca, Simona; Kiranyaz, Serkan; Monga, Olivier; Mueller, Carsten W.; Nunan, Naoise; Pot, Valérie; Schlüter, Steffen; Schmidt, Hannes; Vogel, Hans-JörgOver the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the bulk, macroscopic parameters (e.g., granulometry, pH, soil organic matter, and biomass contents) commonly used to characterize soils provide insufficient information to describe quantitatively the activity of soil microorganisms and some of its outcomes, like the emission of greenhouse gasses. Clearly, new, more appropriate macroscopic parameters are needed, which reflect better the spatial heterogeneity of soils at the microscale (i.e., the pore scale) that is commensurate with the habitat of many microorganisms. For a long time, spectroscopic and microscopic tools were lacking to quantify processes at that scale, but major technological advances over the last 15 years have made suitable equipment available to researchers. In this context, the objective of the present article is to review progress achieved to date in the significant research program that has ensued. This program can be rationalized as a sequence of steps, namely the quantification and modeling of the physical-, (bio)chemical-, and microbiological properties of soils, the integration of these different perspectives into a unified theory, its upscaling to the macroscopic scale, and, eventually, the development of new approaches to measure macroscopic soil characteristics. At this stage, significant progress has been achieved on the physical front, and to a lesser extent on the (bio)chemical one as well, both in terms of experiments and modeling. With regard to the microbial aspects, although a lot of work has been devoted to the modeling of bacterial and fungal activity in soils at the pore scale, the appropriateness of model assumptions cannot be readily assessed because of the scarcity of relevant experimental data. For significant progress to be made, it is crucial to make sure that research on the microbial components of soil systems does not keep lagging behind the work on the physical and (bio)chemical characteristics. Concerning the subsequent steps in the program, very little integration of the various disciplinary perspectives has occurred so far, and, as a result, researchers have not yet been able to tackle the scaling up to the macroscopic level. Many challenges, some of them daunting, remain on the path ahead. Fortunately, a number of these challenges may be resolved by brand new measuring equipment that will become commercially available in the very near future.