ALBERT

Description: This data was collected as part of the Polarstern PS113 expedition to obtain insights into primary productivity on a latitudinal transect in the Atlantic Ocean. In-situ experiments of stable isotope (13C) uptake were conducted on board in triplicates of 1L pre-acid washed polycarbonate bottles. In detail, samples were spiked with Na13CO3 at a final 13C concentration of 200 µmol L-1. Experiments were terminated after 24h incubation and filter on a 0.7 precombusted polycarbonate filter. Samples were snap fronzen and stored at -80°C while at sea. Prior analysis, samples were acid fumed and dried. Samples were analysed on a PDZ Europa ANCA-GSL elemental analyzer interfaced to a PDZ Europa 20-20 isotope ratio mass spectrometer (Sercon Ltd., Cheshire, UK) by the Isotopic Laboratory at the UC Davis, California campus. This data reflects high-resolution spatial variations in primary productivity.

Description: This data set was collected in support of an investigation of the variability of particulate organic matter content and composition across a high-resoultion latitudinal transect across the Atlantic Ocean during the PS113 expedition. 4L of seawater from the clean ships' underway system were filtered on a 0.7 µm pre-combusted GFF filter. Samples were snap-frozen and stored at -80°C while at sea. Samples were acid fumed and dried before analyses. Particulate organic carbon and particulate nitrogen contents were measured using an Euro EA elemental analyzer (CHNS; EuroVector, Italy). This data reflects high-resolution spatial variabilites in particulate organic carbon and particulate nitrogen concentrations in surface waters accompanied by few samples from higher depths (0 - 400 m).

Description: This data was collected to investigate spatial differences in dissolved inorganic nutrient concentrations in surface waters of the Atlantic Ocean as part of the PS113 expedition. Water samples for dissolved inorganic nutrient concentrations including Nitrate, Silicate and Phosphate were filtered through a 0.2 µm syringe filter and stored at -80°C while at sea. Nutrient concentrations were assayed on an Evolution 3 Alliance Autoanalyser and calibrations were corrected for concentrations using certified reference material (CRM) 7602a (JAMSTEC; JAPAN) and MERCK STD (NIST-Standard). Concentrations were calculated by means of standard colorimetric techniques (Grasshoff, Kremling, & Ehrhardt, 2009).

Description: The present study aimed at a first characterization of the enigmatic JTB255 marine benthic group in deep-sea sediments, by: i) confirming the abundance and ubiquitous distribution of JTB255 in deep-sea sediments globally, ii) refining the phylogenetic positioning of the JTB255 clade within the \u03b3-Proteobacteria, iii) distinguishing potential ecotypes within the JTB255 clade, iv) providing first insights into the metabolic potential of deep-sea representatives of this clade. Therefore, two single cell genomes from Arctic HAUSGARTEN deep-se surface sediments were obtained and CARD-FISH counts of total cells, y-Proteobacteria and the JTB255 marine benthic group performed.

Description: 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.

Description: Marine microorganisms adapt to their habitat by structural modification of their membrane lipids. This concept is the basis of numerous molecular proxies used for paleoenvironmental reconstruction. Archaeal tetraether lipids from ubiquitous marine planktonic archaea are particularly abundant, well preserved in the sedimentary record and utilized in several molecular proxies. We here introduce the direct, extraction-free analysis of these compounds in intact sediment core sections using laser desorption ionization (LDI) coupled to Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). LDI FTICR-MS can detect the target lipids in single sub-mm sized spots on sediment sections, equivalent to a sample mass in the nanogram range, and could thus pave the way for biomarker-based reconstruction of past environments and ecosystems at subannual to decadal resolution. We demonstrate that ratios of selected archaeal tetraethers acquired by LDI FTICR-MS are highly correlated with values obtained by conventional LC/MS protocols. The ratio of the major archaeal lipids, caldarchaeol and crenarchaeol, analyzed in a 6.2-cm intact section of Mediterranean sapropel S1 at 250-µm resolution (~4-year temporal resolution), provides an unprecedented view of the fine-scale patchiness of sedimentary biomarker distributions and the processes involved in proxy signal formation. Temporal variations of this lipid ratio indicate a strong influence of the 200-yr de Vries solar cycle on reconstructed sea surface temperatures with possible amplitudes of several degrees, and suggest signal amplification by a complex interplay of ecological and hydrological factors. Laser-based biomarker analysis of geological samples has the potential to revolutionize molecular stratigraphic studies of paleoenvironments.

Description: Bacteria play a crucial role in the marine carbon cycle. To better understand the impacts of ocean warming and acidification on marine carbon cycling, natural analogues for future ocean conditions have gained increasing popularity. Here, we investigated three contrasting oceanographic settings in the Galapagos Archipelago regarding their suitability to represent future ocean conditions in research on organic carbon pools and bacterioplankton communities. Compared to a reference site representative of ambient pH and temperature (Cowley Islet; CoI), we studied a submarine CO2 vent at Roca Redonda (RoR), and an upwelling site at Bolivar Channel (BoC) subjected to a weak El-Nino event at the time of sampling in October 2014. At each site, we collected data from five (four at RoR) spatially independent subsites. Physical water parameters were measured in situ using a Eureka Manta probe. Inorganic nutrient concentrations were determined on a continuous flow injection analyzer. Particulate (POC) and dissolved organic carbon (DOC) were quantified as difference in filter weight after filtration using pre-combusted GFF filters and via the high-temperature combustion technique, respectively. Transparent exopolymers (TEP) were determined using the xanthan equivalent method. This data is available in the 'water chemistry' data set and is directly linked to the sequence data obtained from free-living and particle-attached bacterial communities (ENA PRJEB27168). The table of operational taxonomic units (OTUs) and their assigned taxonomy that were generated after the bioinformatic sequence processing are likewise included in this data submission. Additional to the environmental sampling, a rolling tank experiment was conducted to assess the potential of the water to form larger marine aggregates. Estimated aggregate volume in the rolling tank from each subsite is available in the 'Aggregates analysis' data set. All scripts (R and bash code) that were used for the analysis of the data deposited here and on ENA are attached to the submission. Both RoR and BoC exhibited temperatures elevated by 1 - 1.5°C compared to the reference site. RoR further experienced reduced pH between 6.8 and 7.4. We observed pronounced differences in organic carbon pools (POC, DOC, TEP) at each of the three sites, with highest particulate organic carbon concentrations and aggregate formation at BoC. Bacterioplankton at BoC was dominated by opportunistic copiotrophic taxa, such as Alteromonas and Roseobacter, known for phytoplankton blooms, as opposed to oligotrophic taxa dominating the reference site, such as SAR 11. We presume that bacterial communities were rather influenced by the availability of organic carbon than directly by pH or temperature. Our results highlight the difficulty of establishing natural analogues, and suggest that at the time of sampling the selected sites were not suitable to represent future ocean conditions. Nevertheless, we provide a comprehensive characterization of organic carbon pools and bacterioplankton communities around the Galapagos Archipelago.

Description: We fixed 0.5 g aliquots of sediment with a 4% formaldehyde solution for 2-4 h, washed the fixed sediments three times with 1x phosphate-buffered saline (PBS), before storing them in 50% ethanol/PBS at -20°C. For water samples, we fixed 10 ml (for samples from the deep chlorophyll maximum and 100 m water depth) and 30 ml (for meso- and bathypelagic samples) with formaldehyde to a final concentration of 2-4% for 2-4 h, then filtered over a 0.22 µm polycarbonate filter, and stored samples at -20°C. We performed total cell counts as described by Schauer et al. (2011, doi:10.1111/j.1462-2920.2011.02530.x) using the nucleic acid dye 4'-6-diamidino-2-phenylindole (DAPI). A minimum of 1,000 cells in 20 independent grids were counted using a Zeiss Axio Imager M1 epifluorescence microscope equipped with a 100x/1.25 oil plan-apochromat objective. We used Catalyzed Reporter Deposition-Fluorescence In Situ Hybridization (CARD-FISH) according to Ishii et al. (2004) to count Gammaproteobacteria and JTB255 cells. We used the GAM42a oligonucleotide probe and the BET42a competitor probe to target members of the Gammaproteobacteria (Manz et al., 1992, doi:10.1016/S0723-2020(11)80121-9). We designed the JTB819a and JTB897 probes to target 16S rRNA gene sequences assigned to JTB255 in SILVA release 128 and the cJTB897 competitor probe to target all non-JTB255 16S sequences in SILVA release 128 that have a single mismatch to JTB819a and JTB897 probes. We obtained total gammaproteobacterial and JTB255 cell counts from duplicate filters derived from each sampling site.