Interoperable vocabulary for marine microbial flow cytometry

被引:13
|
作者
Thyssen, Melilotus [1 ]
Gregori, Gerald [1 ]
Creach, Veronique [2 ]
Lahbib, Soumaya [1 ]
Dugenne, Mathilde [3 ]
Aardema, Hedy M. [4 ]
Artigas, Luis-Felipe [5 ]
Huang, Bangqin [6 ]
Barani, Aude [1 ]
Beaugeard, Laureen [7 ]
Bellaaj-Zouari, Amel [8 ]
Beran, Alfred [9 ]
Casotti, Raffaella [10 ]
Del Amo, Yolanda [11 ]
Denis, Michel [1 ]
Dubelaar, George B. J. [12 ]
Endres, Sonja [13 ]
Haraguchi, Lumi [14 ]
Karlson, Bengt [15 ]
Lambert, Christophe [16 ]
Louchart, Arnaud [5 ]
Marie, Dominique [17 ]
Moncoiffe, Gwenaelle [18 ]
Pecqueur, David [19 ]
Ribalet, Francois [20 ]
Rijkeboer, Machteld [21 ]
Silovic, Tina [22 ]
Silva, Ricardo [23 ]
Marro, Sophie [3 ]
Sosik, Heidi M. [24 ]
Sourisseau, Marc [25 ]
Tarran, Glen [26 ]
Van Oostende, Nicolas [27 ]
Zhao, Li [28 ]
Zheng, Shan [28 ]
机构
[1] Univ Toulon & Var, Aix Marseille Univ, CNRS, IRD,MIO, Marseille, France
[2] Ctr Environm Fisheries & Aquaculture, Lowestoft, Suffolk, England
[3] Sorbonne Univ, CNRS, UMR 7093, Lab Oceanog Villefranche Sur Mer LOV, Villefranche Sur Mer, France
[4] Max Plank Inst Chem, Dept Climate Geochem, Mainz, Germany
[5] Univ Lille, Univ Littoral Cote Opale, IRD, CNRS,UMR 8187,LOG, Wimereux, France
[6] Xiamen Univ, State Key Lab Marine Environm Sci, Natl Observat & Res Stn Taiwan Strait Marine Ecos, Xiamen, Peoples R China
[7] Univ La Rochelle, Lab LIENSs Littoral Environm & Soc, CNRS, UMR 7266, La Rochelle, France
[8] INSTM, Salammbo, Tunisia
[9] Natl Inst Oceanog & Appl Geophys OGS, Phys Oceanog Grp, Trieste, Italy
[10] Stn Zool Anton Dohrn, Dept Integrat Marine Ecol, Naples, Italy
[11] Univ Bordeaux, CNRS, UMR 5805, EPOC, Arcachon, France
[12] Cytobuoy Bv, Woerden, Netherlands
[13] Helmholtz Ctr Polar & Marine Res, Alfred Wegener Inst, Project Polarstern 2, Bremerhaven, Germany
[14] Finnish Environm Inst, Marine Res Ctr, Helsinki, Finland
[15] Swedish Meteorol & Hydrol Inst, Oceanog Res, Vastra Frolunda, Sweden
[16] Univ Brest, CNRS, IRD, Ifremer,LEMAR, Plouzane, France
[17] UPMC Univ Paris 06, Sorbonne Univ, CNRS, UMR 7144, Roscoff, France
[18] British Oceanog Data Ctr, Natl Oceanog Ctr, Liverpool, Merseyside, England
[19] Sorbonne Univ, CNRS, Observ Oceanol Banyuls S Mer, Banyuls Sur Mer, France
[20] Univ Washington, Sch Oceanog, Seattle, WA USA
[21] Rijkswaterstaat RWS, Lab Hydrobiol Anal, Lelystad, Netherlands
[22] Mercator Ocean Int, Ramonville St Agne, France
[23] Inst Nacl Invest & Desarrollo Pesquero INIDEP, Buenos Aires, DF, Argentina
[24] Woods Hole Oceanog Inst, Biol Dept, Woods Hole, MA USA
[25] IFREMER, Pelagos Lab, DYNECO, Plouzane, France
[26] Plymouth Marine Lab, Plymouth, Devon, England
[27] Princeton Univ, Dept Geosci, Princeton, NJ USA
[28] Chinese Acad Sci, Inst Oceanol, Key Lab Marine Ecol & Environm Sci, Qingdao, Peoples R China
基金
欧盟地平线“2020”; 美国国家科学基金会;
关键词
flow cytometry; marine microorganisms; standardization; vocabulary; FAIR principle interoperable vocabulary for marine flow cytometry; PHYTOPLANKTON COMMUNITY STRUCTURE; NW MEDITERRANEAN SEA; COASTAL WATERS; LIGHT SCATTER; DYNAMICS; GROWTH; PICOPLANKTON; DIVERSITY; BLOOM; NANOPHYTOPLANKTON;
D O I
10.3389/fmars.2022.975877
中图分类号
X [环境科学、安全科学];
学科分类号
08 ; 0830 ;
摘要
The recent development of biological sensors has extended marine plankton studies from conducting laboratory bench work to in vivo and real-time observations. Flow cytometry (FCM) has shed new light on marine microorganisms since the 1980s through its single-cell approach and robust detection of the smallest cells. FCM records valuable optical properties of light scattering and fluorescence from cells passing in a single file in front of a narrow-collimated light source, recording tens of thousands of cells within a few minutes. Depending on the instrument settings, the sampling strategy, and the automation level, it resolves the spatial and temporal distribution of microbial marine prokaryotes and eukaryotes. Cells are usually classified and grouped on cytograms by experts and are still lacking standards, reducing data sharing capacities. Therefore, the need to make FCM data sets FAIR (Findability, Accessibility, Interoperability, and Reusability of digital assets) is becoming critical. In this paper, we present a consensus vocabulary for the 13 most common marine microbial groups observed with FCM using blue and red-light excitation. The authors designed a common layout on two-dimensional log-transformed cytograms reinforced by a decision tree that facilitates the characterization of groups. The proposed vocabulary aims at standardising data analysis and definitions, to promote harmonisation and comparison of data between users and instruments. This represents a much-needed step towards FAIRification of flow cytometric data collected in various marine environments.
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页数:13
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