Chapter 14 : Nano-Secondary Ions Mass Spectrometry (nanoSIMS) Coupled with In Situ Hybridization for Ecological Research

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This chapter focuses on the application of nano-secondary ions mass spectrometry (nanoSIMS) coupled to in situ hybridization for tracking isotopically labeled cells within complex microbial communities and the importance of nanoSIMS-derived methodologies in analyzing the metabolic and phylogenetic diversity of microorganisms in the environment. The coupling of nanoSIMS and in situ hybridization allows simultaneous quantification of substrate uptake and phylogenetic identification of an individual microbial cell in a single nanoSIMS scan. Halogens such as fluorine, bromine, or iodine are used as markers for the Identification of the cells and are specifically introduced into the cells via in situ hybridization. The broad application of fluorescence in situ hybridization (FISH) on a wide variety of samples offers a big advantage for any combined method that uses FISH or in situ hybridization-related techniques for the phylogenetic identification of single cells. The chapter outlines FISH-based Identification and in situ hybridization using halogen-containing tyramides coupled to nanoSIMS, with focus on the usefulness of both approaches and the problems that can emerge. The first application of the halogen-based identification and nanoSIMS in the natural environment was performed on individual cells of the anaerobic, phototrophic bacteria inhabiting the oligotrophic, meromictic alpine Lake Cadagno. The study focused on quantification of the metabolic activities of three different bacterial species, , , and. Moreover, a remarkable variability in metabolic rates of individual cells of the same species was measured, showing for the first time that a microbial population is a heterogeneous group of physiologically distinct individuals.

Citation: Musat N, Adam B, Kuypers M. 2011. Nano-Secondary Ions Mass Spectrometry (nanoSIMS) Coupled with In Situ Hybridization for Ecological Research, p 295-303. In Murrell J, Whiteley A (ed), Stable Isotope Probing and Related Technologies. ASM Press, Washington, DC. doi: 10.1128/9781555816896.ch14
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