biostudies-literatureEichorst SAEuropean Research CouncilMarie Curiefiv106https://www.ebi.ac.uk/biostudies/studies/S-EPMC4629873biostudies-literatureUnknown91(10)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 generatedFEMS microbiology ecologyAdvancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils.PMC46298732943433217430080Woebken DStrasser FWagner MEichorst SAWoyke TSchintlmeister AfalseAdvancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils.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 generated2015-01-01T00:00:00Z2015 Oct2025-04-22T21:18:47.19Z2019-03-27T02:01:11ZS-EPMC46298732632485410.1093/femsec/fiv106