Correlative SIP-FISH-Raman-SEM-NanoSIMS links identity, morphology, biochemistry, and physiology of environmental microbes

Schaible, George; Hatzenpichler, Roland S.; Cliff, John B.; Kohtz, Anthony

doi:10.1038/s43705-022-00134-3

Title: Correlative SIP-FISH-Raman-SEM-NanoSIMS links identity, morphology, biochemistry, and physiology of environmental microbes

Journal Article · Thu Jun 30 00:00:00 EDT 2022 · ISME Communications

DOI:https://doi.org/10.1038/s43705-022-00134-3· OSTI ID:1883223

Schaible, George ^[1]; Hatzenpichler, Roland S. ^[2];

^[3]; Kohtz, Anthony ^[1]

Montana State University
MONTANA STATE UNIVERSITY
BATTELLE (PACIFIC NW LAB)

Microscopic and spectroscopic techniques are commonly applied to study microbial cells but are typically used on separate samples, resulting in population-level datasets that are integrated across different cells with little spatial resolution. To address this shortcoming, we developed a workflow that correlates several microscopic and spectroscopic techniques to generate an in depth analysis of individual cells. By combining stable isotope probing (SIP), fluorescence in situ hybridization (FISH), scanning electron microscopy (SEM), confocal Raman microspectroscopy (Raman), and nano-scale secondary ion mass spectrometry (NanoSIMS), we illustrate how individual cells can be thoroughly interrogated to obtain information about their taxonomic identity, structure, physiology, and metabolic activity. Analysis of an artificial community demonstrated that our correlative approach was able to resolve the activity of single cells using heavy water SIP in conjunction with Raman and/or NanoSIMS and establish their taxonomy and morphology using FISH and SEM. We then applied this workflow to a sample of yet uncultured multicellular magnetotactic bacteria. In addition to establishing their identity and activity, backscatter electron microscopy (BSE), NanoSIMS, and energy-dispersive X-ray spectroscopy (EDS) were employed to characterize the magnetosomes within the cells. By integrating these techniques, we demonstrate a cohesive approach to thoroughly study environmental microbes at single cell resolution.

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Research Organization:: Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC05-76RL01830

OSTI ID:: 1883223

Report Number(s):: PNNL-SA-172171

Journal Information:: ISME Communications, Vol. 2

Country of Publication:: United States

Language:: English

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