title: Flow cytometry combined with viSNE for the analysis of microbial biofilms and detection of microplastics.
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.
authors.affiliation: Department of Environmental Toxicology, Eawag-Swiss Federal Institute for Aquatic Science and Technology, 8600 Dübendorf, Switzerland.
authors.forename: Linn
authors.initials: L
authors.lastname: Sgier
authors.affiliation: ETHZ-Department of Biology, Institute of Molecular Health Sciences, 8093 Zürich, Switzerland.
authors.forename: Remo
authors.identifier: 0000-0002-8955-2842
authors.initials: R
authors.lastname: Freimann
authors.affiliation: Department of Environmental Toxicology, Eawag-Swiss Federal Institute for Aquatic Science and Technology, 8600 Dübendorf, Switzerland.
authors.forename: Anze
authors.initials: A
authors.lastname: Zupanic
authors.affiliation: Department of Environmental Toxicology, Eawag-Swiss Federal Institute for Aquatic Science and Technology, 8600 Dübendorf, Switzerland.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Kroll
mesh_terms: D018441:Biofilms; D005434:Flow Cytometry; D059013:Microbial Consortia; D010969:Plastics / Q000032:analysis*; D045483:Rivers / Q000382:microbiology*; D059010:Single-Cell Analysis / Q000379:methods*
chemical_list: D010969:Plastics