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Physiology and Distribution of Anaerobic Oxidation of Methane by Archaeal Methanotrophs
Published in Chiara Cassarini, Anaerobic Oxidation of Methane Coupled to the Reduction of Different Sulfur Compounds as Electron Acceptors in Bioreactors, 2019
NanoSIMS (Nanometer-scale secondary ion mass spectrometry) miniaturized SIMS instrumentation with a sub micrometer spatial resolution has been used for ANME studies. It allows observation of single cell morphology in combination with FISH and quantitative analysis of the elemental and isotopic composition of cells with high sensitivity and precision (Behrens et al., 2008; Musat et al., 2008; Polerecky et al., 2012). FISH-NanoSIMS has been used in ANME studies detailing nitrogen fixation by ANME-2d archaea (Dekas et al., 2009) and sulfur metabolism in ANME-2 cells (Milucka et al., 2012). Normally highly enriched microbial communities are incubated with isotopic labeled substrates and the fate of the substrates is detected by specifically designed NanoSIMS equipment. FISH-NanoSIMS is often complemented by advanced microscopic observations such as scanning (SEM) or transmission (TEM) electron microscopy or atomic force microscopy (AFM) (Polerecky et al., 2012). Recently it was described how combining FISH-NanoSIMS with SIP can be used to link identity, function and metabolic activity at cellular level and therefore showing the metabolic interactions within consortia (Musat et al., 2016).
Physiology and Distribution of Anaerobic Oxidation of Methane by Archaeal Methanotrophs
Published in Susma Bhattarai Gautam, Performance Assessment and Enrichment of Anaerobic Methane Oxidising Microbial Communities from Marine Sediments in Bioreactors, 2018
SIMS miniaturized instrumentation with a sub micrometer spatial resolution (NanoSIMS) has been used for ANME studies. It allows observation of single cell morphology in combination with FISH and quantitative analysis of the elemental and isotopic composition of cells with high sensitivity and precision (Behrens et al., 2008; Musat et al., 2008; Polerecky et al., 2012). FISH-NanoSIMS has been used in ANME studies detailing nitrogen fixation by ANME-2d archaea (Dekas et al., 2009) and sulfur metabolism in ANME-2 cells (Milucka et al., 2012). Normally highly enriched microbial communities are incubated with isotopic labeled substrates and the fate of the substrates is detected by specifically designed NanoSIMS equipment. FISH-NanoSIMS is often complemented by advanced microscopic observations such as scanning (SEM) or transmission (TEM) electron microscopy or atomic force microscopy (AFM) (Polerecky et al., 2012).
SIMS method and examples of applications in coral biomineralization
Published in Elaine DiMasi, Laurie B. Gower, Biomineralization Sourcebook, 2014
Claire Rollion-Bard, Dominique Blamart
We have shown that SIMS (or more generally, in situ) measurements can give us some information about the processes of biomineralization, and that the bulk data represent an average of all the different mechanisms present at the interface calicoblastic cells and coral skeleton, that is, pH variation, kinetic e ects, amorphous precursors, etc. Nevertheless, it is important to note that some geochemical signatures cannot be measured by SIMS, and this technique represents then also a bulk analysis. To go deeper into the biomineralization processes and the impact of these processes on geochemical proxies, a technique with a higher spatial resolution is needed. The NanoSIMS is the instrument dedicated to high spatial resolution. The basic principles are the same as the SIMS, but as the primary beam is perpendicular to the sample, the size of the beam is smaller, typically about 100–500 nm. With this type of instrument, it is possible, for example, to study the formation dynamics of different parts of the coral skeleton and to determine the growth rate of CoC and bers (Brahmi et al., 2012), or to examine the distribution of Mg and Sr into the coral skeleton (Meibom et al., 2004) or in foraminifera. This study showed that the Mg distribution is strongly dependent on the microstructure of the coral and corresponds to the layered organization of aragonite bers surrounding the centers of calci cation (Meibom et al., 2004). From this study, it was proposed that Mg may be biologically used to control the growth of the coral. This kind of technique can be also adapted to the measurements of elements on cells (Pernice et al., 2012), and so on the calcifying interface of the coral (i.e., calicoblastic cells— coral skeleton—space between these two components). This interface between cells and skeleton is the key space to understand, to have a better view of the different processes of biomineralization, and to reconcile the calci cation model derived from biology and geochemistry communities. Two major points are still under discussion not only between biologists and geochemists, but also between geochemists themselves. The two questions are: what is the thickness of the space between the skeleton and the tissues, and what is the nature of the so-called extra calcifying fluid (ECF), if this fluid exists. At the moment, in almost all geochemical models, the ECF is thick and is constituted of seawater. Indeed, geochemical models are based on aqueous solution chemistry to precipitate carbonates in a large free space, applying, for example, Rayleigh distillation (Gagnon et al., 2008). This space between the newly formed skeleton and the calicoblastic cells, where ECF is found, is believed to be in the range of 1.5 cm thick if Rayleigh geochemical model is applied (Meibom et al., 2008). This unrealistic large space is at the opposite to the biologists' observations, where the ECF appears, by microscopy, thinner than the calicoblastic cells, which are 1 m thick (Barnes, 1972), or even does not exist
Probing the nature of soil organic matter
Published in Critical Reviews in Environmental Science and Technology, 2022
Zhe (Han) Weng, Johannes Lehmann, Lukas Van Zwieten, Stephen Joseph, Braulio S. Archanjo, Bruce Cowie, Lars Thomsen, Mark J. Tobin, Jitraporn Vongsvivut, Annaleise Klein, Casey L. Doolette, Helen Hou, Carsten W. Mueller, Enzo Lombi, Peter M. Kopittke
Technical background: Nanoscale secondary ion mass spectrometry (NanoSIMS) is an analytical technique that provides information of the microscale (∼50–100 nm spatial resolution) elemental and isotopic composition of a material (Herrmann et al., 2007; Hoppe et al., 2013; Mueller et al., 2013). A primary ion beam (either Cs+ or O−) is accelerated onto the sample surface which releases secondary ion particles. These ions are separated according to their mass to charge ratio in a sector mass spectrometer. The primary ion beam can be focused to a spot of sample to achieve a lateral resolution of up to 50 nm, with scanned area typically between 5 × 5 μm up to 30 × 30 μm (Mueller et al., 2012; Steffens et al., 2017).