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 ce...
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| creator | Kroll, Alexandra Sgier, Linn Zupanic, Anze Freimann, Remo |
| description | 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. |
| doi_str_mv | 10.25678/0000ee |
| format | Dataset |
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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.</description><identifier>DOI: 10.25678/0000ee</identifier><language>eng</language><publisher>Eawag: Swiss Federal Institute of Aquatic Science and Technology</publisher><subject>Achnanthes spec ; Achnanthidium minutissimum ; Achnanthidium spec ; algae ; Amphora spec ; Anabaena spec ; Bangia atropurpurea ; batch ; biofilm ; Botryococcus braunii ; Botryococcus spec ; calcium ; carbon ; Chamaesiphon polonicus ; Chlorella spec ; chloride ; clustering ; Cocconeis placentula var. Euglypta ; Cocconeis spec ; community structure ; Craticula accomoda ; Cyclotella meneghiniana ; Cyclotella spec ; Cymatopleura solea ; Cymbella spec ; Denticula tenuis ; Diatoma spec ; Diatoma vulgaris ; dissoved phosphorus ; DOC ; Eolimna minima ; flow cytometry ; flow-through ; Fragilaria perminuta ; Gomphonema olivaceum ; Gomphonema parvulum ; Gomphonema truncatum ; Gyrosigma attenuatum ; Lab ; magnesium ; Melosira varians ; Meridion circulare ; Merismopedia glauca ; Microcystis aeruginosa ; microplastics ; Mougotia spec ; Navicula spec ; nitrate ; Nitzschia palea ; Nitzschia spec ; nutrients ; Oedogonium spec ; organic matter ; organic phosphorus ; orthosilicic acid ; oxygen ; periphyton ; Phormidium autumnale ; Phormidium spec ; phosphorus ; potassium ; Protozoa ; Pseudanabaena galeata ; Rhoicosphenia abbreviata ; River ; Scenedesmus acuminatus ; Scenedesmus bijugatus ; Scenedesmus bimorphus ; sodium ; Stauroneis smithii ; Stigeoclonium aestivale ; sulfate ; Surirella brebissonii ; Surirella spec ; Synedra spec ; Tabellaria flocculosa ; TOC ; total phosphorus ; Ulnaria ulna ; Ulothrix mucosa ; Ulothrix spec ; WWTP</subject><creationdate>2018</creationdate><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><orcidid>0000-0003-3303-9086</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>780,1894</link.rule.ids><linktorsrc>$$Uhttps://commons.datacite.org/doi.org/10.25678/0000ee$$EView_record_in_DataCite.org$$FView_record_in_$$GDataCite.org$$Hfree_for_read</linktorsrc></links><search><creatorcontrib>Kroll, Alexandra</creatorcontrib><creatorcontrib>Sgier, Linn</creatorcontrib><creatorcontrib>Zupanic, Anze</creatorcontrib><creatorcontrib>Freimann, Remo</creatorcontrib><title>Data for: Flow cytometry combined with viSNE for the analysis of microbial biofilms and detection of microplastics</title><description>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.</description><subject>Achnanthes spec</subject><subject>Achnanthidium minutissimum</subject><subject>Achnanthidium spec</subject><subject>algae</subject><subject>Amphora spec</subject><subject>Anabaena spec</subject><subject>Bangia atropurpurea</subject><subject>batch</subject><subject>biofilm</subject><subject>Botryococcus braunii</subject><subject>Botryococcus spec</subject><subject>calcium</subject><subject>carbon</subject><subject>Chamaesiphon polonicus</subject><subject>Chlorella spec</subject><subject>chloride</subject><subject>clustering</subject><subject>Cocconeis placentula var. Euglypta</subject><subject>Cocconeis spec</subject><subject>community structure</subject><subject>Craticula accomoda</subject><subject>Cyclotella meneghiniana</subject><subject>Cyclotella spec</subject><subject>Cymatopleura solea</subject><subject>Cymbella spec</subject><subject>Denticula tenuis</subject><subject>Diatoma spec</subject><subject>Diatoma vulgaris</subject><subject>dissoved phosphorus</subject><subject>DOC</subject><subject>Eolimna minima</subject><subject>flow cytometry</subject><subject>flow-through</subject><subject>Fragilaria perminuta</subject><subject>Gomphonema olivaceum</subject><subject>Gomphonema parvulum</subject><subject>Gomphonema truncatum</subject><subject>Gyrosigma attenuatum</subject><subject>Lab</subject><subject>magnesium</subject><subject>Melosira varians</subject><subject>Meridion circulare</subject><subject>Merismopedia glauca</subject><subject>Microcystis aeruginosa</subject><subject>microplastics</subject><subject>Mougotia spec</subject><subject>Navicula spec</subject><subject>nitrate</subject><subject>Nitzschia palea</subject><subject>Nitzschia spec</subject><subject>nutrients</subject><subject>Oedogonium spec</subject><subject>organic matter</subject><subject>organic phosphorus</subject><subject>orthosilicic acid</subject><subject>oxygen</subject><subject>periphyton</subject><subject>Phormidium autumnale</subject><subject>Phormidium spec</subject><subject>phosphorus</subject><subject>potassium</subject><subject>Protozoa</subject><subject>Pseudanabaena galeata</subject><subject>Rhoicosphenia abbreviata</subject><subject>River</subject><subject>Scenedesmus acuminatus</subject><subject>Scenedesmus bijugatus</subject><subject>Scenedesmus bimorphus</subject><subject>sodium</subject><subject>Stauroneis smithii</subject><subject>Stigeoclonium aestivale</subject><subject>sulfate</subject><subject>Surirella brebissonii</subject><subject>Surirella spec</subject><subject>Synedra spec</subject><subject>Tabellaria flocculosa</subject><subject>TOC</subject><subject>total phosphorus</subject><subject>Ulnaria ulna</subject><subject>Ulothrix mucosa</subject><subject>Ulothrix spec</subject><subject>WWTP</subject><fulltext>true</fulltext><rsrctype>dataset</rsrctype><creationdate>2018</creationdate><recordtype>dataset</recordtype><sourceid>PQ8</sourceid><recordid>eNqNjrkOwjAQBd1QIED8wnZUQABxiBYSUdFAHzn2WlnJjiN7ReS_Jxyi5jVTvClGiOkqW6y3u_1hmfVDHIpwlizB-HCEwvoOVGLvkEMC5V1FDWroiGt40O2avzzgGkE20qZIEbwBRyr4iqSFirwh62J_a9DIqJh883NaKyOTimMxMNJGnHw5ErMiv58uc92nKGIs20BOhlSusvJdW35qN_-bT_bKS80</recordid><startdate>2018</startdate><enddate>2018</enddate><creator>Kroll, Alexandra</creator><creator>Sgier, Linn</creator><creator>Zupanic, Anze</creator><creator>Freimann, Remo</creator><general>Eawag: Swiss Federal Institute of Aquatic Science and Technology</general><scope>DYCCY</scope><scope>PQ8</scope><orcidid>https://orcid.org/0000-0003-3303-9086</orcidid></search><sort><creationdate>2018</creationdate><title>Data for: Flow cytometry combined with viSNE for the analysis of microbial biofilms and detection of microplastics</title><author>Kroll, Alexandra ; Sgier, Linn ; Zupanic, Anze ; Freimann, Remo</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-datacite_primary_10_25678_0000ee3</frbrgroupid><rsrctype>datasets</rsrctype><prefilter>datasets</prefilter><language>eng</language><creationdate>2018</creationdate><topic>Achnanthes spec</topic><topic>Achnanthidium minutissimum</topic><topic>Achnanthidium spec</topic><topic>algae</topic><topic>Amphora spec</topic><topic>Anabaena spec</topic><topic>Bangia atropurpurea</topic><topic>batch</topic><topic>biofilm</topic><topic>Botryococcus braunii</topic><topic>Botryococcus spec</topic><topic>calcium</topic><topic>carbon</topic><topic>Chamaesiphon polonicus</topic><topic>Chlorella spec</topic><topic>chloride</topic><topic>clustering</topic><topic>Cocconeis placentula var. Euglypta</topic><topic>Cocconeis spec</topic><topic>community structure</topic><topic>Craticula accomoda</topic><topic>Cyclotella meneghiniana</topic><topic>Cyclotella spec</topic><topic>Cymatopleura solea</topic><topic>Cymbella spec</topic><topic>Denticula tenuis</topic><topic>Diatoma spec</topic><topic>Diatoma vulgaris</topic><topic>dissoved phosphorus</topic><topic>DOC</topic><topic>Eolimna minima</topic><topic>flow cytometry</topic><topic>flow-through</topic><topic>Fragilaria perminuta</topic><topic>Gomphonema olivaceum</topic><topic>Gomphonema parvulum</topic><topic>Gomphonema truncatum</topic><topic>Gyrosigma attenuatum</topic><topic>Lab</topic><topic>magnesium</topic><topic>Melosira varians</topic><topic>Meridion circulare</topic><topic>Merismopedia glauca</topic><topic>Microcystis aeruginosa</topic><topic>microplastics</topic><topic>Mougotia spec</topic><topic>Navicula spec</topic><topic>nitrate</topic><topic>Nitzschia palea</topic><topic>Nitzschia spec</topic><topic>nutrients</topic><topic>Oedogonium spec</topic><topic>organic matter</topic><topic>organic phosphorus</topic><topic>orthosilicic acid</topic><topic>oxygen</topic><topic>periphyton</topic><topic>Phormidium autumnale</topic><topic>Phormidium spec</topic><topic>phosphorus</topic><topic>potassium</topic><topic>Protozoa</topic><topic>Pseudanabaena galeata</topic><topic>Rhoicosphenia abbreviata</topic><topic>River</topic><topic>Scenedesmus acuminatus</topic><topic>Scenedesmus bijugatus</topic><topic>Scenedesmus bimorphus</topic><topic>sodium</topic><topic>Stauroneis smithii</topic><topic>Stigeoclonium aestivale</topic><topic>sulfate</topic><topic>Surirella brebissonii</topic><topic>Surirella spec</topic><topic>Synedra spec</topic><topic>Tabellaria flocculosa</topic><topic>TOC</topic><topic>total phosphorus</topic><topic>Ulnaria ulna</topic><topic>Ulothrix mucosa</topic><topic>Ulothrix spec</topic><topic>WWTP</topic><toplevel>online_resources</toplevel><creatorcontrib>Kroll, Alexandra</creatorcontrib><creatorcontrib>Sgier, Linn</creatorcontrib><creatorcontrib>Zupanic, Anze</creatorcontrib><creatorcontrib>Freimann, Remo</creatorcontrib><collection>DataCite (Open Access)</collection><collection>DataCite</collection></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext_linktorsrc</fulltext></delivery><addata><au>Kroll, Alexandra</au><au>Sgier, Linn</au><au>Zupanic, Anze</au><au>Freimann, Remo</au><format>book</format><genre>unknown</genre><ristype>DATA</ristype><title>Data for: Flow cytometry combined with viSNE for the analysis of microbial biofilms and detection of microplastics</title><date>2018</date><risdate>2018</risdate><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.</abstract><pub>Eawag: Swiss Federal Institute of Aquatic Science and Technology</pub><doi>10.25678/0000ee</doi><orcidid>https://orcid.org/0000-0003-3303-9086</orcidid><oa>free_for_read</oa></addata></record> |
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| identifier | DOI: 10.25678/0000ee |
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| subjects | Achnanthes spec Achnanthidium minutissimum Achnanthidium spec algae Amphora spec Anabaena spec Bangia atropurpurea batch biofilm Botryococcus braunii Botryococcus spec calcium carbon Chamaesiphon polonicus Chlorella spec chloride clustering Cocconeis placentula var. Euglypta Cocconeis spec community structure Craticula accomoda Cyclotella meneghiniana Cyclotella spec Cymatopleura solea Cymbella spec Denticula tenuis Diatoma spec Diatoma vulgaris dissoved phosphorus DOC Eolimna minima flow cytometry flow-through Fragilaria perminuta Gomphonema olivaceum Gomphonema parvulum Gomphonema truncatum Gyrosigma attenuatum Lab magnesium Melosira varians Meridion circulare Merismopedia glauca Microcystis aeruginosa microplastics Mougotia spec Navicula spec nitrate Nitzschia palea Nitzschia spec nutrients Oedogonium spec organic matter organic phosphorus orthosilicic acid oxygen periphyton Phormidium autumnale Phormidium spec phosphorus potassium Protozoa Pseudanabaena galeata Rhoicosphenia abbreviata River Scenedesmus acuminatus Scenedesmus bijugatus Scenedesmus bimorphus sodium Stauroneis smithii Stigeoclonium aestivale sulfate Surirella brebissonii Surirella spec Synedra spec Tabellaria flocculosa TOC total phosphorus Ulnaria ulna Ulothrix mucosa Ulothrix spec WWTP |
| title | Data for: Flow cytometry combined with viSNE for the analysis of microbial biofilms and detection of microplastics |
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