ArticleFrontiers in microbiology2018
Calculation of Single Cell Assimilation Rates From SIP-NanoSIMS-Derived Isotope Ratios: A Comprehensive Approach.
Article in Frontiers in microbiology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Restoration of deuterium marker for multi-isotope mapping of cellular metabolic activity.Scientific reports · 2026Article
- Fungal parasites infecting NNature communications · 2026Article
- Dissolved inorganic carbon supports robust anabolism and methanogenesis in actively serpentinizing rocks.bioRxiv : the preprint server for biology · 2025Article
- In Situ Metabolic Rates of Alkane-Degrading Sulphate-Reducing Bacteria in Hydrocarbon Seep Sediments Revealed by Combining CARD-FISH, NanoSIMS, and Mathematical Modelling.Environmental microbiology · 2025Article
- Single-cell measurement of microbial growth rate with Raman microspectroscopy.FEMS microbiology ecology · 2024Article
- Urea assimilation and oxidation support activity of phylogenetically diverse microbial communities of the dark ocean.The ISME journal · 2024Article
- Gold-FISH enables targeted NanoSIMS analysis of plant-associated bacteria.The New phytologist · 2023Article
- One Cell at a Time: Advances in Single-Cell Methods and Instrumentation for Discovery in Aquatic Microbiology.Frontiers in microbiology · 2022Article
- Microfluidic Single-Cell Analytics.Advances in biochemical engineering/biotechnology · 2022Article
- NanoSIP: NanoSIMS Applications for Microbial Biology.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Using Stable Isotope Probing and Raman Microspectroscopy To Measure Growth Rates of Heterotrophic Bacteria.Applied and environmental microbiology · 2021Article
- Isotopic tracing reveals single-cell assimilation of a macroalgal polysaccharide by a few marine Flavobacteria and Gammaproteobacteria.The ISME journal · 2021Article
- Light and depth dependency of nitrogen fixation by the non-photosynthetic, symbiotic cyanobacterium UCYN-A.Environmental microbiology · 2021Article
- Cytoklepty in the plankton: A host strategy to optimize the bioenergetic machinery of endosymbiotic algae.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Characterizing the "fungal shunt": Parasitic fungi on diatoms affect carbon flow and bacterial communities in aquatic microbial food webs.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Chemical Analysis of Single Cells and Organelles.Analytical chemistry · 2021Review
- Calculation and Interpretation of Substrate Assimilation Rates in Microbial Cells Based on Isotopic Composition Data Obtained by nanoSIMS.Frontiers in microbiology · 2021Article
- Article
- Quantitation and Comparison of Phenotypic Heterogeneity Among Single Cells of Monoclonal Microbial Populations.Frontiers in microbiology · 2019Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The nanoSIMS-based chemical microscopy has been introduced in biology over a decade ago. The spatial distribution of elements and isotopes analyzed by nanoSIMS can be used to reconstruct images of biological samples with a resolution down to tens of nanometers, and can be also interpreted quantitatively. Currently, a unified approach for calculation of single cell assimilation rates from nanoSIMS-derived changes in isotope ratios is missing. Here we present a comprehensive concept of assimilation rate calculation with a rigorous mathematical model based on quantitative evaluation of nanoSIMS-derived isotope ratios. We provide a detailed description of data acquisition and treatment, including the selection and accumulation of nanoSIMS scans, defining regions of interest and extraction of isotope ratios. Next, we present alternative methods to determine the cellular volume and the density of the element under scrutiny. Finally, to compensate for alterations of original isotopic ratios, our model considers corrections for sample preparation methods (e.g., air dry, chemical fixation, permeabilization, hybridization), and when known, for the stable isotope fractionation associated with utilization of defined growth substrates. As proof of concept we implemented this protocol to quantify the assimilation of
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