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Per Persson. Photo.

Per Persson


Per Persson. Photo.

Shining new light into soil systems : Spectroscopy in microfluidic soil chips reveals microbial biogeochemistry


  • Milda Pucetaite
  • Pelle Ohlsson
  • Per Persson
  • Edith Hammer

Summary, in English

Microfluidic soil chips render optical access to the naturally opaque soil systems and enable direct investigation of microbial growth and interactions in micro-structurally and chemically controlled environments. However, chemical analyses of these interactions at high spatial and temporal resolution are still lacking. Here we propose that the use of advanced microspectroscopy techniques, namely infrared absorption, Raman scattering and synchrotron radiation based X-ray microspectroscopy, in microfluidic soil chips would make it possible to approach these phenomena. They allow monitoring biogeochemical processes in and around soil microbial cells growing in the reproducibly designed microenvironments within the chips at (sub)micrometer scale. Complementary use of several of the microspectroscopy techniques is beneficial for obtaining information about both molecular and elemental composition, oxidation states and local structure of the elements in the sample. Ultimately, we argue that microspectroscopy in microfluidic chips can lead to relevant breakthroughs in frontier research areas in soil science, such as (1) analysis of chemical responses of microbes to environmental triggers at micro-scale spatial resolution, (2) phenotypical identification and phylogenetic classification of single cells of soil microbes in situ, (3) determining spatially and time resolved effects of heavy metals and organic pollutants, including microplastics, on soils and (4) spatially resolved analysis of soil organic matter dynamics for better understanding of soil carbon storage. Tailoring the chip design to achieve optical transparency to the radiation type used by the different microspectroscopy methods is crucial to achieve this; therefore, we expect that this perspective will inspire the scientific community to use the proposed approaches and thus push both the technical development of the microspectroscopy suitable soil chips and the research frontier in soil science.


  • Centre for Environmental and Climate Science (CEC)
  • BECC: Biodiversity and Ecosystem services in a Changing Climate
  • Department of Biomedical Engineering
  • Microbial Ecology

Publishing year





Soil Biology and Biochemistry



Document type

Journal article




  • Soil Science
  • Microbiology


  • Microbial biogeochemistry
  • Microbial interactions
  • Microfluidics
  • Soil chip
  • Vibrational microspectroscopy
  • X-ray microspectroscopy




  • How do microbes “tuck away” carbon? The role of microbes in physical soil organic carbon stabilization

Research group

  • Microbial Ecology


  • ISSN: 0038-0717