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 (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.

Novel Sample Preparation Technique To Improve Spectromicroscopic Analyses of Micrometer-Sized Particles

“…The sputter damage on the particle was different on each of the three fragments, indicating different sputter rates on heterogeneous structures that vary in chemical composition or local material density. Such kinds of granular accretions as visible on regions 2 and 3 (Figure b) have been previously reported for soft organic material …”

NanoSIMS imaging of extracellular electron transport processes during microbial iron(III) reduction

“…NanoSIMS, often in combination with stable isotope labelling, has been used previously to study a range of microorganisms and microbial processes, including benzene degrading communities (Schurig et al . 2015 ), periplasmic encrustation in nitrate-reducing Fe(II)-oxidising bacteria (Miot et al . 2015 ), anaerobic phototrophy (Musat et al .…”

Application of stable isotope tools for evaluating natural and stimulated biodegradation of organic pollutants in field studies

“…Recent developments in the field of in situ microcosms in combination with protein-SIP and nano-scale secondary ion mass spectrometry (NanoSIMS) show promise to identify and visualise key microbial players and metabolic pathways [52,53], which might help to design successful biostimulation strategies.…”