Improved detection of soil microorganisms using fluorescence in situ hybridization (FISH) and catalyzed reporter deposition (CARD-FISH)

Eickhorst, Thilo; Tippkötter, Rolf

doi:10.1016/j.soilbio.2008.03.024

Cited by 112 publications

(65 citation statements)

References 45 publications

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“…The results moreover suggest the presence of extracellular RNA as part of the observed EPS. An explanation for extracellular staining could be that some of the intracellular RNA leaked out of the permeabilised cell membranes during the CARD-FISH procedure (Eickhorst and Tippkötter 2008) or the death of cells. Bombach et al (2010) performed confocal laser scanning microscopy on stained (SYTO 60) samples on BioSep beads, which were previously incubated in laboratory microcosms containing an enrichment culture from a BTEX contaminated aquifer.…”

Section: Visualisation Of Active Microbial Biomassmentioning

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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Section: Visualisation Of Active Microbial Biomassmentioning

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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“…FISH combined with catalyzed reporter deposition (CARD-FISH) is a powerful tool in modern microbial ecology (29). CARD-FISH allows the specific direct detection of target populations in their natural environments, such as soil, sediment, and the rhizosphere (30)(31)(32)(33). In addition, CARD-FISH has been used to analyze methanogens in anaerobic sludge (34) and methanotrophs in the soil covering an aged municipal landfill (35).…”

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confidence: 99%

Metaproteomic Identification of Diazotrophic Methanotrophs and Their Localization in Root Tissues of Field-Grown Rice Plants

Bao

Okubo

Kubota

et al. 2014

Appl Environ Microbiol

108

105

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dIn a previous study by our group, CH 4 oxidation and N 2 fixation were simultaneously activated in the roots of wild-type rice plants in a paddy field with no N input; both processes are likely controlled by a rice gene for microbial symbiosis. The present study examined which microorganisms in rice roots were responsible for CH 4 oxidation and N 2 fixation under the field conditions. Metaproteomic analysis of root-associated bacteria from field-grown rice (Oryza sativa Nipponbare) revealed that nitrogenase complex-containing nitrogenase reductase (NifH) and the alpha subunit (NifD) and beta subunit (NifK) of dinitrogenase were mainly derived from type II methanotrophic bacteria of the family Methylocystaceae, including Methylosinus spp. Minor nitrogenase proteins such as Methylocella, Bradyrhizobium, Rhodopseudomonas, and Anaeromyxobacter were also detected. Methane monooxygenase proteins (PmoCBA and MmoXYZCBG) were detected in the same bacterial group of the Methylocystaceae. Because these results indicated that Methylocystaceae members mediate both CH 4 oxidation and N 2 fixation, we examined their localization in rice tissues by using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). The methanotrophs were localized around the epidermal cells and vascular cylinder in the root tissues of the field-grown rice plants. Our metaproteomics and CARD-FISH results suggest that CH 4 oxidation and N 2 fixation are performed mainly by type II methanotrophs of the Methylocystaceae, including Methylosinus spp., inhabiting the vascular bundles and epidermal cells of rice roots.

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“…1995 ;Pernthaler et al . 2002 ;Wilhartitz et al ., 2007 ;Eickhorst and Tippkötter, 2008 ;Shiraishi et al ., 2008 ;Schramm and Amann 2008 RISA/ribosomal intergenic spacer Fast and large numbers of samples possible. Automatic approach possible.…”

Section: Referencementioning

confidence: 99%

Molecular methods for studying biocorrosion

Graeber

Boehm

Kuever

2014

Understanding Biocorrosion

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Improved detection of soil microorganisms using fluorescence in situ hybridization (FISH) and catalyzed reporter deposition (CARD-FISH)

Cited by 112 publications

References 45 publications

Methods for visualising active microbial benzene degraders in in situ microcosms

Methods for visualising active microbial benzene degraders in in situ microcosms

Metaproteomic Identification of Diazotrophic Methanotrophs and Their Localization in Root Tissues of Field-Grown Rice Plants

Molecular methods for studying biocorrosion

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