Methods for visualising active microbial benzene degraders in in situ microcosms

Abstract

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 13C-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 13C-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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Acknowledgments

We gratefully acknowledge funding for this study by the Helmholtz Centre for Environmental Research—UFZ, the German Research Council (project DynaCARB, MI 598/2-2, within the framework of the SPP 1315: Biogeochemical Interfaces in soil) and the European Union (FP7, Contract no. 213161 ModelPROBE). Furthermore, we thank Johann Lugmeier (TU München) for performing the NanoSIMS measurements.

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Correspondence to Christian Schurig.

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Schurig, C., Mueller, C.W., Höschen, C. et al. Methods for visualising active microbial benzene degraders in in situ microcosms. Appl Microbiol Biotechnol 99, 957–968 (2015). https://doi.org/10.1007/s00253-014-6037-4

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Keywords

  • NanoSIMS
  • 13C
  • Microbial activity
  • In situ microcosms
  • DP-BACTRAPs
  • Benzene