CARD-FISH cell counts of taxonomic bacterial groups from different microbiomes in Fram Strait used to evalute primer sets

• Main Authors: Fadeev, Eduard, Cardozo-Mino, Magda Guadalupe, Rapp, Josephine Z, Bienhold, Christina, Salter, Ian, Salman-Carvalho, Verena, Molari, Massimiliano, Tegetmeyer, Halina E, Buttigieg, Pier Luigi, Boetius, Antje
• Format: Dataset
• Language: English
• Published: PANGAEA - Data Publisher for Earth & Environmental Science 2021
• Subjects: CARD-FISH; cell counts; Fram Strait; Event label; Type; DEPTH, ice/snow; DEPTH, water; 2-4-Amidinophenyl-1H-indole-6-carboxamidine; Alteromonas, cells; Alteromonas; Bacteroidetes, cells; Bacteroidetes; Polaribacter, cells; Polaribacter; Gammaproteobacteria, cells; Gammaproteobacteria; SAR11 clade; CTD/Rosette with Underwater Vision Profiler; Ice station; Giant box corer; PS99.2; Polarstern; Arctic; Arctic Ocean
• Online Access: https://dx.doi.org/10.1594/pangaea.928720; https://doi.pangaea.de/10.1594/PANGAEA.928720

Samples in this dataset were collected at the long-term ecological research (LTER) site HAUSGARTEN in Fram Strait, and the central Arctic Ocean. On board, the samples were fixed with formalin in a final concentration of 2% for 10 – 12 hours, then filtered onto 0.2 µm polycarbonate Nucleopore Track-Etched filters, and stored at -20°C for further analysis. Cell abundances of the groups Alteromonas, Bacteroidia, Polaribacter, Gammaproteobacteria and the SAR11 clade were asses using CAtalyzed reporter deposition Fluorescence In Situ Hybridization (CARD-FISH) following the protocol established by (Pernthaler et al., 2002). The filters were evaluated microscopically under an automated microscope (Zeder et al., 2011). Cell enumeration was performed with the software Automated Cell Measuring and Enumeration Tool (ACMETool3, 2018-11-09; Zeder et al., 2011). Cells were counted as objects according to manually defined parameters separately for the DAPI and FISH channels.