NanoSIP: NanoSIMS Applications for Microbial Biology

Pett-Ridge, Jennifer; Weber, Peter K.

doi:10.1007/978-1-0716-1585-0_6

NanoSIP: NanoSIMS Applications for Microbial Biology

Journal Article · Sun Oct 31 00:00:00 EDT 2021 · Methods in Molecular Biology

DOI:https://doi.org/10.1007/978-1-0716-1585-0_6· OSTI ID:2425900

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Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

High-resolution imaging with secondary ion mass spectrometry (nanoSIMS) has become a standard method in systems biology and environmental biogeochemistry and is broadly used to decipher ecophysiological traits of environmental microorganisms, metabolic processes in plant and animal tissues, and cross-kingdom symbioses. When combined with stable isotope-labeling—an approach we refer to as nanoSIP—nanoSIMS imaging offers a distinctive means to quantify net assimilation rates and stoichiometry of individual cell-sized particles in both low- and high-complexity environments. While the majority of nanoSIP studies in environmental and microbial biology have focused on nitrogen and carbon metabolism (using ¹⁵N and ¹³C tracers), multiple advances have pushed the capabilities of this approach in the past decade. The development of a high-brightness oxygen ion source has enabled high-resolution metal analyses that are easier to perform, allowing quantification of metal distribution in cells and environmental particles. New preparation methods, tools for automated data extraction from large data sets, and analytical approaches that push the limits of sensitivity and spatial resolution have allowed for more robust characterization of populations ranging from marine archaea to fungi and viruses. Further, NanoSIMS studies continue to be enhanced by correlation with orthogonal imaging and ‘omics approaches; when linked to molecular visualization methods, such as in situ hybridization and antibody labeling, these techniques enable in situ function to be linked to microbial identity and gene expression. Here we present an updated description of the primary materials, methods, and calculations used for nanoSIP, with an emphasis on recent advances in nanoSIMS applications, key methodological steps, and potential pitfalls.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA); USDOE Office of Science (SC), Biological and Environmental Research (BER); USDOE Laboratory Directed Research and Development (LDRD) Program

Grant/Contract Number:: AC52-07NA27344

OSTI ID:: 2425900

Report Number(s):: LLNL--JRNL-814027; 1021335

Journal Information:: Methods in Molecular Biology, Journal Name: Methods in Molecular Biology Vol. 2349; ISSN 1064-3745

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

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Calculation of Single Cell Assimilation Rates From SIP-NanoSIMS-Derived Isotope Ratios: A Comprehensive Approach Stryhanyuk, Hryhoriy; Calabrese, Federica; Kümmel, Steffen Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02342	journal	October 2018
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Characterizing Chemoautotrophy and Heterotrophy in Marine Archaea and Bacteria With Single-Cell Multi-isotope NanoSIP Dekas, Anne E.; Parada, Alma E.; Mayali, Xavier Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02682	journal	December 2019
Quantitation and Comparison of Phenotypic Heterogeneity Among Single Cells of Monoclonal Microbial Populations Calabrese, Federica; Voloshynovska, Iryna; Musat, Florin Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.02814	journal	December 2019

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NanoSIP: NanoSIMS Applications for Microbial Biology

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