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

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 carbonDOC, calcium) and detection of microplastic contamination. The method can potentially be applied to other biofilm types, e.g. for inferring community structure for environmental and industrial research and monitoring.

Dataset extent

Data and Resources


This Data Package

Kroll, A., Sgier, L., Zupanic, A., & Freimann, R. (2018). Data for: Flow cytometry combined with viSNE for the analysis of microbial biofilms and detection of microplastics [Data set]. Eawag: Swiss Federal Institute of Aquatic Science and Technology.

The associated article

Sgier, L., R. Freimann, A. Zupanic, and A. Kroll (2016), Flow cytometry combined with viSNE for the analysis of microbial biofilms and detection of microplastics, Nature Communications, 7(1), doi:10.1038/ncomms11587.


Open Data Open Data
  • Kroll, Alexandra
  • Sgier, Linn
  • Zupanic, Anze
  • Freimann, Remo
Keywords DOC,TOC,biofilm,clustering,community structure,dissoved phosphorus,flow cytometry,organic phosphorus,periphyton,total phosphorus,nutrients,organic matter,algae,microplastics
  • concentration
  • electric_conductivity
  • pH
  • temperature
Substances (scientific names)
  • calcium
  • carbon
  • chloride
  • magnesium
  • nitrate
  • orthosilicic acid
  • oxygen
  • phosphorus
  • potassium
  • sodium
  • sulfate
Taxa (scientific names)
  • Achnanthes spec
  • Achnanthidium minutissimum
  • Achnanthidium spec
  • Amphora spec
  • Anabaena spec
  • Bangia atropurpurea
  • Botryococcus braunii
  • Botryococcus spec
  • Chamaesiphon polonicus
  • Chlorella spec
  • Cocconeis placentula var. Euglypta
  • Cocconeis spec
  • Craticula accomoda
  • Cyclotella meneghiniana
  • Cyclotella spec
  • Cymatopleura solea
  • Cymbella spec
  • Cymbella spec
  • Denticula tenuis
  • Diatoma spec
  • Diatoma vulgaris
  • Eolimna minima
  • Fragilaria perminuta
  • Gomphonema truncatum
  • Gomphonema olivaceum
  • Gomphonema parvulum
  • Gyrosigma attenuatum
  • Melosira varians
  • Meridion circulare
  • Merismopedia glauca
  • Microcystis aeruginosa
  • Mougotia spec
  • Navicula spec
  • Nitzschia palea
  • Nitzschia spec
  • Oedogonium spec
  • Phormidium autumnale
  • Phormidium spec
  • Protozoa
  • Pseudanabaena galeata
  • Rhoicosphenia abbreviata
  • Scenedesmus acuminatus
  • Scenedesmus bijugatus
  • Scenedesmus bimorphus
  • Stauroneis smithii
  • Stigeoclonium aestivale
  • Surirella brebissonii
  • Surirella spec
  • Synedra spec
  • Tabellaria flocculosa
  • Ulnaria ulna
  • Ulothrix mucosa
  • Ulothrix spec
  • batch
  • flow-through
  • Lab
  • River
  • WWTP
  • 2014-10-15 TO 2014-11-05
  • 2015-03-18
Review Level none
Curator Zupanic, Anze
DOI 10.25678/0000ee