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Flow cytometry combined with viSNE for the analysis of microbial biofilms and detection of microplastics

Author

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  • Linn Sgier

    (Eawag—Swiss Federal Institute for Aquatic Science and Technology)

  • Remo Freimann

    (Institute of Molecular Health Sciences)

  • Anze Zupanic

    (Eawag—Swiss Federal Institute for Aquatic Science and Technology)

  • Alexandra Kroll

    (Eawag—Swiss Federal Institute for Aquatic Science and Technology)

Abstract

Biofilms serve essential ecosystem functions and are used in different technical applications. Studies from stream ecology and waste-water treatment have shown that biofilm functionality depends to a great extent on community structure. Here we present a fast and easy-to-use method for individual cell-based analysis of stream biofilms, based on stain-free flow cytometry and visualization of the high-dimensional data by viSNE. The method allows the combined assessment of community structure, decay of phototrophic organisms and presence of abiotic particles. In laboratory experiments, it allows quantification of cellular decay and detection of survival of larger cells after temperature stress, while in the field it enables detection of community structure changes that correlate with known environmental drivers (flow conditions, dissolved organic carbon, calcium) and detection of microplastic contamination. The method can potentially be applied to other biofilm types, for example, for inferring community structure for environmental and industrial research and monitoring.

Suggested Citation

  • Linn Sgier & Remo Freimann & Anze Zupanic & Alexandra Kroll, 2016. "Flow cytometry combined with viSNE for the analysis of microbial biofilms and detection of microplastics," Nature Communications, Nature, vol. 7(1), pages 1-10, September.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms11587
    DOI: 10.1038/ncomms11587
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    Cited by:

    1. Cheryl Qian Ying Yong & Suresh Valiyaveettil & Bor Luen Tang, 2020. "Toxicity of Microplastics and Nanoplastics in Mammalian Systems," IJERPH, MDPI, vol. 17(5), pages 1-24, February.

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