Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils

Eichorst, Stephanie A.; Strasser, Florian; Woyke, Tanja; Schintlmeister, Arno; Wagner, Michael; Woebken, Dagmar; Haggblom, Max

doi:10.1093/femsec/fiv106

Title: Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils

Journal Article · Mon Aug 31 00:00:00 EDT 2015 · FEMS Microbiology Ecology (Online)

DOI:https://doi.org/10.1093/femsec/fiv106· OSTI ID:1342958

Eichorst, Stephanie A. ^[1]; Strasser, Florian ^[1]; Woyke, Tanja ^[2]; Schintlmeister, Arno ^[1]; Wagner, Michael ^[1]; Woebken, Dagmar ^[1]; Haggblom, Max ^[3]

Univ. of Vienna, Vienna (Austria)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Rutgers Univ., New Brunswick, NJ (United States)

The combined approach of incubating environmental samples with stable isotope-labeled substrates followed by single-cell analyses through high-resolution secondary ion mass spectrometry (NanoSIMS) or Raman microspectroscopy provides insights into the in situ function of microorganisms. This approach has found limited application in soils presumably due to the dispersal of microbial cells in a large background of particles. We developed a pipeline for the efficient preparation of cell extracts from soils for subsequent single-cell methods by combining cell detachment with separation of cells and soil particles followed by cell concentration. The procedure was evaluated by examining its influence on cell recoveries and microbial community composition across two soils. This approach generated a cell fraction with considerably reduced soil particle load and of sufficient small size to allow single-cell analysis by NanoSIMS, as shown when detecting active N2-fixing and cellulose-responsive microorganisms via ¹⁵N2 and ¹³C-UL-cellulose incubations, respectively. The same procedure was also applicable for Raman microspectroscopic analyses of soil microorganisms, assessed via microcosm incubations with a ¹³C-labeled carbon source and deuterium oxide (D2O, a general activity marker). Lastly, the described sample preparation procedure enables single-cell analysis of soil microorganisms using NanoSIMS and Raman microspectroscopy, but should also facilitate single-cell sorting and sequencing.

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Research Organization:: USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1342958

Journal Information:: FEMS Microbiology Ecology (Online), Vol. 91, Issue 10; ISSN 1574-6941

Publisher:: Federation of European Microbiological SocietiesCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 83 works

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