Applications of single-cell methods in terrestrial ecosystems

Technology / method development

Soils encompass a large area on Earth, which is home to a multitude of our planet’s biodiversity including a vast number of bacterial, archaeal and fungal taxa. This microbial diversity is crucial for driving various biogeochemical cycles, yet our understanding of the participants and their activity remains rudimentary at best. The functions of microorganisms in soil have been extensively studied on an ecosystem or community level with activity assays or in combination with stable isotopes. Little attention, however, has been paid to the single-cell level that can provide valuable information on metabolic heterogeneity within a population of cells.

Investigations at the single-cell scale through high-resolution secondary ion mass spectrometry (NanoSIMS) or Raman microspectroscopy in combination with stable isotope incubations provide insights into the function of microorganisms. Yet this approach has found limited application in soils most likely due to the fact that microbial cells are dispersed in a large background of particles, complicating these analyses. We are developing strategies for the efficient application of single-cell methods to soil samples by combining cell detachment, separation of cells and soil particles, and subsequent cell concentration. These sample preparation are being evalulated for NanoSIMS and Raman microspectroscopic analyses of soil cells, assessed with 13C-labeled carbon source, 15N- labeled substrates and deuterium oxide (D2O, a general activity marker) to soil microcosms. In summary, these sample preparation procedures should enable single-cell analysis of soil microorganisms using NanoSIMS and Raman microspectroscopy, but should facilitate other methods such as single-cell sorting and sequencing.


This project is funded by the FWF, Austrian Science Fund (project No. P 26392-B20).


This project has received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no 321742.



Selected Publications:

Angel R, Panhölzl C, Gabriel R, Herbold C, Wanek W, Richter A, Eichorst SA and Woebken D. (2018) Applicaiton of stable-isotope labelling techniques for the detection of active diazotrophs. Environ Microbiol 20: 44-61.{doi:10.1111/1462-2920.13954}

Eichorst SA, Strasser F, Woyke T, Schintlmeister A, Wagner M, and Woebken D. (2015) Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils. FEMS Microbiol Ecology 91: fiv106. {doi:10.1093/femsec/fiv106}

Eichorst SA and Woeben D. (2014) Investigation of microorganisms at the single-cell level using Raman Microspectroscopy and Nanometer-scale Secondary Ion Mass Spectrometry. In Molecular Methods and Applications in Microbiology. Eds., TL Skovhus, S Caffrey, CRJ Hubert. Caister Academic Press, Norfolk, UK.