Advanced spectroscopic, microscopic, and tomographic characterization techniques to study biogeochemical interfaces in soil

Rennert, Thilo; Totsche, Kai Uwe; Heister, Katja; Kersten, Michael; Thieme, Jürgen

doi:10.1007/s11368-011-0417-5

Cited by 35 publications

(21 citation statements)

References 150 publications

(145 reference statements)

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“…3), consistent either with environmental exposure, such as weather or the proximity of a tree root, being important, or with a patchy distribution of the yeast. It is well known that resources are patchily distributed in soils (Hodge, 2006;Rennert, 2012) and the same is true for the microbial life, which tends to live in aggregates and to form spots of activity (Nunan et al, 2003;Ling et al, 2011). This variation offers the possibility that a larger survey might reveal the factors affecting S. paradoxus abundance, and, therefore, provide information about the resources that the yeast exploits.…”

Section: Seasonal Changes In Saccharomyces Abundance and Distributionmentioning

confidence: 99%

A systematic forest survey showing an association of Saccharomyces paradoxus with oak leaf litter

Kowallik

Greig

2016

Environ Microbiol Rep

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SummaryAlthough we understand the genetics of the laboratory model yeast Saccharomyces cerevisiae very well, we know little about the natural ecology and environment that shaped its genome. Most isolates of Saccharomyces paradoxus, the wild relative of S. cerevisiae, come from oak trees, but it is not known whether this is because oak is their primary habitat. We surveyed leaf litter in a forest in Northern Germany and found a strong correlation between isolation success of wild Saccharomyces and the proximity of the nearest oak. We compared the four most common tree genera and found Saccharomyces most frequently in oak litter. Interestingly, we show that Saccharomyces is much more abundant in oak leaf litter than on oak bark, suggesting that it grows in litter or soil rather than on the surfaces of oaks themselves. The distribution and abundance of Saccharomyces over the course of a year shows that oak leaf litter provides a stable habitat for the yeast, although there was significant tree-to-tree variation. Taken together, our results suggest that leaf litter rather than tree surfaces provide the better habitat for wild Saccharomyces, with oak being the preferred tree genus. 99.5% of all strains (633/636) isolated were S. paradoxus.

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Section: Seasonal Changes In Saccharomyces Abundance and Distributionmentioning

confidence: 99%

A systematic forest survey showing an association of Saccharomyces paradoxus with oak leaf litter

Kowallik

Greig

2016

Environ Microbiol Rep

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“…The combination of high spatial resolution (down to 50 nm), high sensitivity (parts per million, ppm, in elemental imaging) and high mass resolution has made this instrument one of the most sensitive tools for spatially resolved elemental and isotopic analysis of complex surfaces. Although most applications of NanoSIMS are related to imaging of biological materials [114][115][116][117][118][119] and soil aggregates, several groups explored the potential of this technique for chemical characterisation of ambient particles. For example, McIntire et al demonstrated the utility of NanoSIMS in studying the three-dimensional (3D) structure of complex organic particles [120].…”

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confidence: 99%

New mass spectrometry techniques for studying physical chemistry of atmospheric heterogeneous processes

Laskin

Nizkorodov

2013

International Reviews in Physical Chemistry

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Ambient particles and droplets have a significant effect on climate, visibility and human health. Once formed, they undergo continuous transformations through condensation and evaporation of water, uptake of low-volatility organic molecules and photochemical reactions involving various gaseous and condensed-phase species in the atmosphere. These transformations determine the physical and chemical properties of airborne particles, such as their ability to absorb and scatter solar radiation and nucleate cloud droplets. The complexity, heterogeneity and size of ambient particles make it challenging to understand the kinetics and mechanisms of their formation and chemical transformations. Mass spectrometry (MS) is a powerful analytical technique that enables detailed chemical characterisation of both small and large molecules in complex matrices. This capability makes MS a promising tool for studying chemical transformations of particles and droplets in the atmosphere. This review is focused on new and emerging experimental MS-based approaches for understanding the kinetics and mechanisms of such transformations. Some of the techniques discussed herein are best suited for ambient samples, while the others work best in laboratory applications. However, in combination, they provide a comprehensive arsenal of methods for characterisation of particles and droplets. In addition, we emphasise the role of fundamental physical chemistry studies in the development of new methods for chemical analysis of ambient particles and droplets.

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“…2), the boundary voxels are equally partitioned into full void or solid voxels. This is justified because of the use of monochromatic synchrotron radiation, where the absorption coefficient for each voxel remains the same independent of the projection angle and hence propagation pathway to that voxel through the sample (Rennert et al 2011). This simple approach enabled us to convert the whole raw grey-scale image into a reliable binary blackand-white image representing voids and solids as shown in Fig.…”

Section: Image Processingmentioning

confidence: 99%

3D simulation of the permeability tensor in a soil aggregate on basis of nanotomographic imaging and LBE solver

et al. 2011

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Purpose: The purpose of this hydropedological work is to investigate the feasibility of a method to calculate permeability of soil peds on the matrix pore scale resolution. This paper focuses on imaging of the intra-aggregate microstructure and, based on the three-dimensional (3D) images, quantification of the pore network connectivity and permeability tensor. Finally, lattice Boltzmann equation (LBE) simulations of Navier-Stokes flow in the thus derived pore network allow to compute the heterogeneous 3D flow velocity field. Materials and methods: Nanotomographic X-ray absorption mode imaging of a single soil ped has been performed at the TOMCAT beamline of the Swiss Light Source synchrotron facility with 0.74 µm spatial resolution. Segmentation of the 3D Nano-CT images into solid phase and pore space allowed to study the statistical properties of the connected pore network. The thus derived pore network data were used as direct input for the software package GeoDict integrated with a LBE algorithm to perform saturated water flow modeling. Results and discussion: The soil ped features quantified from the tomographic images were pore and grain size distributions (PSD, GSD), porosity, percolation tensor in x, y, z-direction and percolation pathways (macropores). The PSD frequency has a peak in the range 3-8 µm (mesopores) contributing 50% of the total. In general, the matrix pore structure and, hence, saturated flow field velocity of our sample is highly anisotropic. LBE-simulated pore scale fluid flow is used to ultimately determine gross parameters (coefficients) of Darcy's law such as the saturated hydraulic conductivity, Ks. The thus simulated Ks=105±24 cm day(-1) of a single soil ped (mean of three ROIs and directions) is one order of magnitude higher than the value of Ks=12±2 cm day(-1) predicted by a classical pedotranfer function approach. This Ks underestimation by PTF is typical for macropore flow. Conclusions: Integration of 3D image evaluation with the LBE approach as an essential step toward understanding the highly heterogeneous intra-aggregate microstructure is now possible on the submicron scale. Modeling the resulting anisotropic fluid advection field is, however, just a first step for 3D models of biogeochemical reactions at soil interfaces on this pore scale

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Advanced spectroscopic, microscopic, and tomographic characterization techniques to study biogeochemical interfaces in soil

Cited by 35 publications

References 150 publications

A systematic forest survey showing an association of Saccharomyces paradoxus with oak leaf litter

A systematic forest survey showing an association of Saccharomyces paradoxus with oak leaf litter

New mass spectrometry techniques for studying physical chemistry of atmospheric heterogeneous processes

3D simulation of the permeability tensor in a soil aggregate on basis of nanotomographic imaging and LBE solver

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