Glycerol dialkyl glycerol tetraethers (GDGT) lipids and CARD-FISH data from suspended particulate matter from the central Baltic Sea

During expedition EMB201 in the Baltic Sea we investigated the local producers of glycerol dialkyl glycerol tetraethers (GDGT) and their thriving depth by a combined 16S rRNA gene amplicon sequencing/ CARD-FISH and lipidomic approach. Water samples were taken in December 2018 by a pump-CTD, a giant water sampler and with Niskin bottles at the surface, suboxic and sulfidic zones of the Landsort Deep, Fårö Basin and East Gotland Basin. This data set contains the CARD-FISH and lipidomics data, while the 16S rRNA gene sequencing data is available on ENA. Cell abundance was analysed in an aliquot of 40 ml filtered (pore size 0.22 micro m) sea water fixed with particle-free formaldehyde. Archaeal cells on the filters were specifically hybridized via catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH) using the Cren537 probe. Cells on the hybridized filter were counter-stained with 40,6-diamidin-2-phenylindol (DAPI). For lipid analysis, 150–600 L sea water were filtered with a flow rate of 1.5 L min-1 on pre-ashed, 142-mm-diameter, 0.7µm pore size glass fibre GF/F filters, and frozen at –20 °C. The filters were lyophilized before different extraction methods were used to obtain intact and core GDGTs by ultra-sonification in different solvent mixtures. The combined supernatants were phase separated before analysis by high performance liquid chromatography coupled to tandem mass spectrometry (HPLC-MS2) for intact polar lipids and by high performance liquid chromatography coupled to atmospheric pressure chemical ionization mass spectrometry (HPLC APCI-MS; ThermoScientific) for core GDGTs.