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

Research datakeyboard_double_arrow_right Dataset 01 Jan 2018 English Publisher:ZenodoFunded by:SNSF | Fate and effects of engin..., FCT | LA 8, FCT | LA 11 +2 projects

Authors: Kroll, Alexandra; Sgier, Linn; Zupanic, Anze; Freimann, Remo;

doi: 10.25678/0000ee

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

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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 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.

Related Organizations

Swiss Federal Institute of Aquatic Science and Technology
Switzerland

Keywords

Achnanthes spec, Craticula accomoda, chloride, Gomphonema parvulum, Fragilaria perminuta, Melosira varians, sulfate, Merismopedia glauca, magnesium, DOC, Cymatopleura solea, orthosilicic acid, biofilm, Scenedesmus bimorphus, batch, Eolimna minima, Bangia atropurpurea, Scenedesmus acuminatus, Diatoma spec, Surirella spec, Chlorella spec, Nitzschia palea, Surirella brebissonii, Oedogonium spec, phosphorus, TOC, sodium, Diatoma vulgaris, Ulothrix spec, organic matter, River, algae, Achnanthidium spec, Navicula spec, Mougotia spec, potassium, Phormidium autumnale, dissoved phosphorus, Nitzschia spec, Botryococcus braunii, Phormidium spec, Gyrosigma attenuatum, Scenedesmus bijugatus, flow-through, community structure, Denticula tenuis, clustering, Stigeoclonium aestivale, Cocconeis placentula var. Euglypta, Stauroneis smithii, microplastics, Anabaena spec, Botryococcus spec, periphyton, Cocconeis spec, Chamaesiphon polonicus, Gomphonema olivaceum, nitrate, nutrients, Tabellaria flocculosa, Cyclotella meneghiniana, Cymbella spec, Microcystis aeruginosa, Protozoa, Gomphonema truncatum, Achnanthidium minutissimum, WWTP, Lab, organic phosphorus, Synedra spec, calcium, carbon, flow cytometry, Ulothrix mucosa, Ulnaria ulna, Cyclotella spec, Amphora spec, Pseudanabaena galeata, total phosphorus, Meridion circulare, oxygen, Rhoicosphenia abbreviata

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