On Wednesday 11th May 2022 we organized a webinar about the use of nanoSIMS in Earth Sciences. NanoSIMS is a technique that allows us to image isotopic and elemental composition of samples on a sub-micrometer spatial scale (down to 50 nm), and in this webinar we showcased how these capabilities help us investigate geological and biogeochemical processes. Our aim is to stimulate future collaborations among scientists interested in this type of research.

Please find below the presentations given during the webinar.


Brief introduction to the nanoSIMS facility by Lubos Polerecky, head of the facility.

Use of nanoSIMS to identify and trace microbial processes and interactions

The combination of stable isotope probing (SIP) and nanoSIMS has increasingly been used in microbiology field over the past 15 years. The SIP-nanoSIMS approach is highly sensitive and allows tracing and quantifying metabolic rates at the level of single-cells, based on the assimilation of isotopically-labelled substrates into the cell biomass. It allows us to explore biological interactions between uncultured microorganisms, especially in the context of spatial and trophic relationships in biological systems where exchanges of nutrients can be extremely rapid, e.g., symbiotic or syntrophic interactions. Generally, SIP-nanoSIMS can answer questions that are out of reach for conventional approaches, ranging from microbe-host and microbe-microbe interactions (including single-cell ecophysiology) to cell-cell nutrient or metabolite exchanges, and interactions between cells and their organic/inorganic matrix. However, the wider application of this approach in microbiology field is currently hampered by the necessity of custom made, sample dependent preparation work-flows for correct identification and quantification of cellular processes and interactions within a spatial context. During this presentation, Niculina Musat (Helmholtz Centre for Environmental Research, Germany) discussed a few case studies on the application of SIP-nanoSIMS to trace microbial processes and interactions, including:

  1. tracing the flow of carbon in the rhizosphere
  2. studying the capability of microbial colonizers of plastics to degrade antibiotics
  3. tracing the nutrient and water flow between fungi and microbial cells

Together, these case studies illustrate the necessity of thoughtful consideration and design of suitable sample preparation as well as the necessity of using correlative analyses to add a new level of resolution to the microbial identity-function conundrum.

Ecophysiology of multicellular cable bacteria – insights from SIP-nanoSIMS

Cable bacteria are filamentous bacteria that evolved an ingenious division of labour in which redox transformations in distant cells are coupled via long-distance electron transport. Cells in deeper sediment layers oxidize hydrogen sulfide, the electrons generated are then transported via “wires” along the longitudinal axis of the filament towards cells residing in the oxic zone, where they are used to reduce oxygen. To investigate the cellular physiology and the interactions among cells within a filament, the metabolic activity of single cells was tracked by nanoSIMS after probing with different stable isotopes (13C, 15N and 18O). Nicole Geerlings (Utrecht University) showed how these SIP-nanoSIMS analyses provided important insights into the division of labour, growth, cell cycle, and polyphosphate dynamics in multicellular cable bacteria.

Use of nanoSIMS to investigate geological processes

NanoSIMS is one of the few techniques suitable for the detection and quantification of volatiles and trace elements in natural and experimental samples at the micron scale. Laurent Remusat (National Museum of Natural History, France) presented two case to show the advances that nanoSIMS can bring to the understanding of crucial geological processes: element partitioning during planetary differentiation and crustal melting.