Look@NanoSIMS – a tool for the analysis of nanoSIMS data in environmental microbiology

Polerecký, Lùbos; Adam, Birgit; Milucka, Jana; Musat, Niculina; Vágner, Tomáš; Kuypers, Marcel M. M.

doi:10.1111/j.1462-2920.2011.02681.x

Cited by 196 publications

(166 citation statements)

References 22 publications

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“…For 13 C: 12 C ratio mosaic images, images were first uploaded individually to obtain the 13 C: 12 C ratio distribution and uploaded in the MosaicJ plugin for the mosaic creation. The interactive regions of interest (ROIs) definition tool of Look@NanoSIMS program (Polerecky et al, 2012) was used to draw ROIs on selected 12 C 14 N images, in order to obtain their isotopic composition. ROIs were drawn either by using the threshold function according to 12 C 14 N counts (microbes and hyphae), the freehand drawing option (plant cell walls) or by drawing ellipses (resin spots).…”

Section: Nanosims Analysesmentioning

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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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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Section: Nanosims Analysesmentioning

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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“…Isotope ratio images were created as the ratio of a sum of total counts for each pixel over all recorded planes with respect to the investigated isotope. Regions of interest around cell structures were circled and calculated using the automated threshold feature based on the look@nanosims software (Polerecky et al, 2012). Cell dimensions were determined based on regions of interest.…”

Section: Nanosims Measurementsmentioning

confidence: 99%

The effect of nutrients on carbon and nitrogen fixation by the UCYN-A–haptophyte symbiosis

et al. 2014

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Symbiotic relationships between phytoplankton and N 2 -fixing microorganisms play a crucial role in marine ecosystems. The abundant and widespread unicellular cyanobacteria group A (UCYN-A) has recently been found to live symbiotically with a haptophyte. Here, we investigated the effect of nitrogen (N), phosphorus (P), iron (Fe) and Saharan dust additions on nitrogen (N 2 ) fixation and primary production by the UCYN-A-haptophyte association in the subtropical eastern North Atlantic Ocean using nifH expression analysis and stable isotope incubations combined with single-cell measurements. N 2 fixation by UCYN-A was stimulated by the addition of Fe and Saharan dust, although this was not reflected in the nifH expression. CO 2 fixation by the haptophyte was stimulated by the addition of ammonium nitrate as well as Fe and Saharan dust. Intriguingly, the single-cell analysis using nanometer scale secondary ion mass spectrometry indicates that the increased CO 2 fixation by the haptophyte in treatments without added fixed N is likely an indirect result of the positive effect of Fe and/or P on UCYN-A N 2 fixation and the transfer of N 2 -derived N to the haptophyte. Our results reveal a direct linkage between the marine carbon and nitrogen cycles that is fuelled by the atmospheric deposition of dust. The comparison of single-cell rates suggests a tight coupling of nitrogen and carbon transfer that stays balanced even under changing nutrient regimes. However, it appears that the transfer of carbon from the haptophyte to UCYN-A requires a transfer of nitrogen from UCYN-A. This tight coupling indicates an obligate symbiosis of this globally important diazotrophic association.

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“…The depth of the removed material was estimated to 120-600 nm, without considering the material removed during pre-sputtering (Lechene et al, 2006). The data were analyzed with the Look@NanoSIMS software (Polerecky et al, 2012). For each field analyzed, individual scans were accumulated and drift corrected.…”

Section: Fluorescence In Situ Hybridizationmentioning

confidence: 99%

Anaerobic degradation of propane and butane by sulfate-reducing bacteria enriched from marine hydrocarbon cold seeps

et al. 2012

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The short-chain, non-methane hydrocarbons propane and butane can contribute significantly to the carbon and sulfur cycles in marine environments affected by oil or natural gas seepage. In the present study, we enriched and identified novel propane and butane-degrading sulfate reducers from marine oil and gas cold seeps in the Gulf of Mexico and Hydrate Ridge. The enrichment cultures obtained were able to degrade simultaneously propane and butane, but not other gaseous alkanes. They were cold-adapted, showing highest sulfate-reduction rates between 16 and 20 1C. Analysis of 16S rRNA gene libraries, followed by whole-cell hybridizations with sequence-specific oligonucleotide probes showed that each enrichment culture was dominated by a unique phylotype affiliated with the Desulfosarcina-Desulfococcus cluster within the Deltaproteobacteria. These phylotypes formed a distinct phylogenetic cluster of propane and butane degraders, including sequences from environments associated with hydrocarbon seeps. Incubations with 13 C-labeled substrates, hybridizations with sequence-specific probes and nanoSIMS analyses showed that cells of the dominant phylotypes were the first to become enriched in 13 C, demonstrating that they were directly involved in hydrocarbon degradation. Furthermore, using the nanoSIMS data, carbon assimilation rates were calculated for the dominant cells in each enrichment culture.

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Look@NanoSIMS – a tool for the analysis of nanoSIMS data in environmental microbiology

Cited by 196 publications

References 22 publications

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

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

The effect of nutrients on carbon and nitrogen fixation by the UCYN-A–haptophyte symbiosis

Anaerobic degradation of propane and butane by sulfate-reducing bacteria enriched from marine hydrocarbon cold seeps

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