Submicron scale imaging of soil organic matter dynamics using NanoSIMS – From single particles to intact aggregates

Mueller, Carsten W.; Kölbl, Angelika; Hoeschen, Carmen; Hillion, F.; Heister, Katja; Herrmann, Anke M.; Kögel‐Knabner, Ingrid

doi:10.1016/j.orggeochem.2011.06.003

Cited by 92 publications

(94 citation statements)

References 32 publications

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“…8c), a zone devoid of secondary ion signal appeared at the center of the silica surface. This was probably due to charging (Mueller et al, 2012) and/or to topographic heterogeneity (Winterholler et al, 2008). As silica was more resistant to polishing than the epoxy, silica surfaces were often convex (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…They are separated according to their mass and an image of the intensity of the secondary ion beam is made for a selected mass (http:// www.cameca.com/instruments-for-research/sims.aspx. Over the past few years, the NanoSIMS technique has increasingly been used in geosciences to investigate the elemental and isotopic composition of organic and inorganic materials (Herrmann et al, 2007;Hatton et al, 2012;Mueller et al, 2012Mueller et al, , 2013. The NanoSIMS technique however has only scarcely been used for measuring secondary ion emission from amorphous silica.…”

Section: Methodsmentioning

confidence: 99%

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New highlights of phytolith structure and occluded carbon location: 3-D X-ray microscopy and NanoSIMS results

et al. 2015

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Abstract. Phytoliths contain occluded organic compounds called phytC. Recently, phytC content, nature, origin, paleoenvironmental meaning and impact in the global C cycle have been the subject of increasing debate. Inconsistencies were fed by the scarcity of in situ characterizations of phytC in phytoliths. Here we reconstructed at high spatial resolution the 3-D structure of harvested grass short cell (GSC) phytoliths using 3-D X-ray microscopy. While this technique has been widely used for 3-D reconstruction of biological systems it has never been applied in high-resolution mode to silica particles. Simultaneously, we investigated the location of phytC using nanoscale secondary ion mass spectrometry (NanoSIMS). Our data evidenced that the silica structure contains micrometric internal cavities. These internal cavities were sometimes observed isolated from the outside. Their opening may be an original feature or may result from a beginning of dissolution of silica during the chemical extraction procedure, mimicking the progressive dissolution process that can happen in natural environments. The phytC that may originally occupy the cavities is thus susceptible to rapid oxidation. It was not detected by the NanoSIMS technique. However, another pool of phytC, continuously distributed in and protected by the silica structure, was observed. Its N / C ratio (0.27) is in agreement with the presence of amino acids. These findings constitute a basis to further characterize the origin, occlusion process, nature and accessibility of phytC, as a prerequisite for assessing its significance in the global C cycle.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

New highlights of phytolith structure and occluded carbon location: 3-D X-ray microscopy and NanoSIMS results

et al. 2015

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“…Larger soil aggregates including root fragments (approximately 1 cm −3 ) were sampled. Two samples from each cylinder, i.e., four samples in total, were chemically fixed using Karnovsky fixative (Morris, 1965) and dehydrated in graded acetone series and embedded in araldite resin (Araldite 502) until complete polymerization, according to the method described by Mueller et al (2012). Samples were cut and polished to obtain intact rhizosphere cross sections.…”

Section: Sample Processingmentioning

confidence: 99%

“…In order to analyze the fine soil fraction containing microaggregates and fungal hyphae, a fungal hypha was extracted from cylinder 1, which showed a higher percentage of hyphal root colonization (Table 1). This sample was prepared on a silica wafer according to Mueller et al (2012). Briefly, 1 mg of dried soil from the chemically fixed and dried rhizosphere was dispersed in 10 mL of analytical water ACS.…”

Section: Sample Processingmentioning

confidence: 99%

Linking 3D Soil Structure and Plant-Microbe-Soil Carbon Transfer in the Rhizosphere

Vidal

Hirte

Bender

et al. 2018

Front. Environ. Sci.

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106

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Plant roots are major transmitters of atmospheric carbon into soil. The rhizosphere, the soil volume around living roots influenced by root activities, represents hotspots for organic carbon (OC) inputs, microbial activity, and carbon turnover. Rhizosphere processes remain poorly understood and the observation of key mechanisms for carbon transfer and protection in intact rhizosphere microenvironments are challenging. We deciphered the fate of photosynthesis-derived OC in intact wheat rhizosphere, combining stable isotope labeling at field scale with high-resolution 3D-imaging. We used nano-scale secondary ion mass spectrometry and focus ion beam-scanning electron microscopy to generate insights into rhizosphere processes at nanometer scale. In immature wheat roots, the carbon circulated through the apoplastic pathway, via cell walls, from the stele to the cortex. The carbon was transferred to substantial microbial communuties, mainly represented by bacteria surrounding peripheral root cells. Iron oxides formed bridges between roots and bigger mineral particles, such as quartz, and surrounded bacteria in microaggregates close to the root surface. Some microaggregates were also intimately associated with the fungal hyphae surface. Based on these results, we propose a conceptual model depicting the fate of carbon at biogeochemical interfaces in the rhizosphere, at the forefront of growing roots. We observed complex interplays between vectors (roots, fungi, bacteria), transferring plant-derived OC into root-free soil and stabilizing agents (iron oxides, root and microorganism products), potentially protecting plant-derived OC within microaggregates in the rhizosphere.

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“…While studies have already employed NanoSIMS to elucidate the identity of microbes and establish a link to their activity in water samples by means of isotope enrichment alone (Popa et al 2007) or combined with a FISH approach applying halogenated dyes (HISH-SIMS; Musat et al 2008;Morono et al 2011;Alonso et al 2012), the potential of the instrument for studies in porous media such as soils or aquifers is currently not fully explored (e.g. Herrmann et al 2007a, b;Behrens et al 2012;Mueller et al 2012). This is partly due to the limitations of the NanoSIMS method, which prohibits analysing samples with pronounced topography, e.g.…”

Section: Introductionmentioning

confidence: 99%

Methods for visualising active microbial benzene degraders in in situ microcosms

Schurig

Mueller

Höschen

et al. 2014

Appl Microbiol Biotechnol

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Natural attenuation maybe a cost-efficient option for bioremediation of contaminated sites but requires knowledge about the activity of degrading microbes under in situ conditions. In order to link microbial activity to the spatial distribution of contaminant degraders, we combined the recently improved in situ microcosm approach, so-called 'direct-push bacterial trap' (DP-BACTRAP), with nano-scale secondary ion mass spectrometry (NanoSIMS) analysis on samples from contaminated constructed wetlands. This approach is based on initially sterile microcosms amended with (13)C-labelled benzene as a source of carbon and energy for microorganisms. The microcosms were introduced directly in the constructed wetland, where they were colonised by indigenous microorganisms from the sediment. After incubation in the field, the samples were analysed by NanoSIMS, scanning electron microscopy (SEM) and fluorescence microscopy in order to visualise (13)C-labelled microbial biomass on undisturbed samples from the microcosms. With the approach developed, we successfully visualised benzene-degrading microbes on solid materials with high surface area by means of NanoSIMS. Moreover, we could demonstrate the feasibility of NanoSIMS analysis of unembedded porous media with a highly complex topography, which was frequently reasoned to not lead to sufficient results.

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Submicron scale imaging of soil organic matter dynamics using NanoSIMS – From single particles to intact aggregates

Cited by 92 publications

References 32 publications

New highlights of phytolith structure and occluded carbon location: 3-D X-ray microscopy and NanoSIMS results

New highlights of phytolith structure and occluded carbon location: 3-D X-ray microscopy and NanoSIMS results

Linking 3D Soil Structure and Plant-Microbe-Soil Carbon Transfer in the Rhizosphere

Methods for visualising active microbial benzene degraders in in situ microcosms

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