Optical microsensors for analysis of microbial communities

Methods Enzymol. 2005;397:166-99. doi: 10.1016/S0076-6879(05)97010-9.


Fiber-optic microprobes connected to sensitive light meters are ideal tools to resolve the steep gradients of light intensity and spectral composition that prevail in aggregates and surface-associated microbial communities in sediments, biofilms, and microbial mats. They allow for a detailed mapping of light fields and enable insights to the complex optical properties of such highly light-scattering and -absorbing microbial systems. Used in combination with microsensors for chemical species, fiber-optic irradiance microprobes allow for detailed studies of photosynthesis regulation and of the photobiology of microbial phototrophs in intact samples under ambient microenvironmental conditions of the natural habitat. Fiber-optic microprobes connected to sensitive fluorometers enable microscale fluorescence measurements, which can be used to map (i) diffusivity and flow; (ii) distribution of photosynthetic microbes, via their photopigment autofluorescence; and (iii) activity of oxygenic photosynthesis via variable chlorophyll fluorescence measurements. Furthermore, by immobilizing optical indicator dyes on the end of optical fibers, fiber-optic microsensors for temperature, salinity, and chemical species such as oxygen, pH, and CO2 can be realized.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biofilms
  • Biosensing Techniques / instrumentation
  • Biosensing Techniques / methods
  • Diffusion
  • Environmental Microbiology*
  • Fiber Optic Technology* / instrumentation
  • Fluorescence
  • Fluorometry
  • Geologic Sediments / microbiology
  • Light
  • Light-Harvesting Protein Complexes / analysis
  • Luminescence
  • Microchemistry / instrumentation
  • Optical Fibers
  • Photosynthesis
  • Rheology / instrumentation
  • Scattering, Radiation
  • Surface Properties


  • Light-Harvesting Protein Complexes