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  • 1
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    Microbial Communities in the East and West Fram Strait During Sea Ice Melting Season (2018)
    Frontiers
    In:  Frontiers in Marine Science, 5 . Art.Nr. 429.
    Details
    Publication Date: 2021-02-08
    Description: Climate models project that the Arctic Ocean may experience ice-free summers by the second half of this century. This may have severe repercussions on phytoplankton bloom dynamics and the associated cycling of carbon in surface waters. We currently lack baseline knowledge of the seasonal dynamics of Arctic microbial communities, which is needed in order to better estimate the effects of such changes on ecosystem functioning. Here we present a comparative study of polar summer microbial communities in the ice-free (eastern) and ice-covered (western) hydrographic regimes at the LTER HAUSGARTEN in Fram Strait, the main gateway between the Arctic and North Atlantic Oceans. Based on measured and modeled biogeochemical parameters, we tentatively identified two different ecosystem states (i.e., different phytoplankton bloom stages) in the distinct regions. Using Illumina tag-sequencing, we determined the community composition of both free-living and particle-associated bacteria as well as microbial eukaryotes in the photic layer. Despite substantial horizontal mixing by eddies in Fram Strait, pelagic microbial communities showed distinct differences between the two regimes, with a proposed early spring (pre-bloom) community in the ice-covered western regime (with higher representation of SAR11, SAR202, SAR406 and eukaryotic MALVs) and a community indicative of late summer conditions (post-bloom) in the ice-free eastern regime (with higher representation of Flavobacteria, Gammaproteobacteria and eukaryotic heterotrophs). Co-occurrence networks revealed specific taxon-taxon associations between bacterial and eukaryotic taxa in the two regions. Our results suggest that the predicted changes in sea ice cover and phytoplankton bloom dynamics will have a strong impact on bacterial community dynamics and potentially on biogeochemical cycles in this region.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
    Format: text
    Format: text
    DOI: 10.3389/fmars.2018.00429
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 2
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    Submesoscale physicochemical dynamics directly shape bacterioplankton community structure in space and time (2021)
    Association for the Sciences of Limnology and Oceanography
    Details
    Publication Date: 2024-02-07
    Description: Submesoscale eddies and fronts are important components of oceanic mixing and energy fluxes. These phenomena occur in the surface ocean for a period of several days, on scales between a few hundred meters and few tens of kilometers. Remote sensing and modeling suggest that eddies and fronts may influence marine ecosystem dynamics, but their limited temporal and spatial scales make them challenging for observation and in situ sampling. Here, the study of a submesoscale filament in summerly Arctic waters (depth 0–400 m) revealed enhanced mixing of Polar and Atlantic water masses, resulting in a ca. 4 km wide and ca. 50 km long filament with distinct physical and biogeochemical characteristics. Compared to the surrounding waters, the filament was characterized by a distinct phytoplankton bloom, associated with depleted inorganic nutrients, elevated chlorophyll a concentrations, as well as twofold higher phyto- and bacterioplankton cell abundances. High-throughput 16S rRNA gene sequencing of bacterioplankton communities revealed enrichment of typical phytoplankton bloom-associated taxonomic groups (e.g., Flavobacteriales) inside the filament. Furthermore, linked to the strong water subduction, the vertical export of organic matter to 400 m depth inside the filament was twofold higher compared to the surrounding waters. Altogether, our results show that physical submesoscale mixing can shape distinct biogeochemical conditions and microbial communities within a few kilometers of the ocean. Hence, the role of submesoscale features in polar waters for surface ocean biodiversity and biogeochemical processes need further investigation, especially with regard to the fate of sea ice in the warming Arctic Ocean.
    Type: Article , PeerReviewed
    Format: text
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 3
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    CARD-FISH cell counts of taxonomic bacterial groups from different microbiomes in Fram Strait used to evalute primer sets (2021)
    PANGAEA
    Details
    Publication Date: 2023-02-12
    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.
    Keywords: 2-(4-Amidinophenyl)-1H-indole-6-carboxamidine; Alteromonas; Alteromonas, cells; ARK-XXX/1.2; Bacteroidetes; Bacteroidetes, cells; CARD-FISH; cell counts; CTD/Rosette with Underwater Vision Profiler; CTD-RO_UVP; DEPTH, ice/snow; DEPTH, water; EG_I; EG_IV; Event label; Fram Strait; Gammaproteobacteria; Gammaproteobacteria, cells; Giant box corer; GKG; ICE; Ice station; North Greenland Sea; Polaribacter; Polaribacter, cells; Polarstern; PS99/043-3; PS99/048-15; PS99/051-2; PS99/053-8; PS99.2; SAR11 clade; Type
    Type: Dataset
    Format: text/tab-separated-values, 48 data points
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    DATA PANGAEA
  • 4
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    CTD measurements from the Mediterranean Sea during the MicroB3 Summer School in May 2014 (2014)
    PANGAEA
    Details
    Publication Date: 2023-04-01
    Keywords: [CABLE]+[sbe19]+[NISKIN]; Cast-1; Cast-2; Conductivity; CTD; CTD (sbe19) and Niskin bottles (8-L or 12-L) triggered with messengers; Date/Time of event; DEPTH, water; Event label; Fluorescence, chlorophyll; Latitude of event; Longitude of event; Mediterranean Sea, north of Crete; MicroB3; MicroB3_SummerSchool_20140527T0942; MicroB3_SummerSchool_20140527T1505; MicroB3 - Microbial Biodiversity, Bioinformatics and Biotechnology; MicroB3 Summer School 2014; Philia; Pressure, water; Radiation, photosynthetically active; Salinity; Temperature, water
    Type: Dataset
    Format: text/tab-separated-values, 2430 data points
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    DATA PANGAEA
  • 5
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    Mesocosms analysis from water samples of the Mediterranean Sea during the MicroB3 Summer School in May 2014 (2014)
    PANGAEA
    Details
    Publication Date: 2023-04-01
    Keywords: Ammonium; Bacteria; Chlorophyll a; DEPTH, water, experiment; Event label; Mesocosms_T2_Control; Mesocosms_T2_Nitrate+Phosphate; Mesocosms_T2_Phosphate; MicroB3_SummerSchool_Mesocosms_C; MicroB3_SummerSchool_Mesocosms_NH-PO; MicroB3_SummerSchool_Mesocosms_PO; MicroB3 Summer School 2014; pH; Philia; Phosphate; Picoeukaryotes, autotrophic; Prochlorococcus; Salinity; Synechococcus; Temperature, water
    Type: Dataset
    Format: text/tab-separated-values, 30 data points
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    DATA PANGAEA
  • 6
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    Flow cytometry analysis from water samples of the Mediterranean Sea during the MicroB3 Summer School in May 2014 (2014)
    PANGAEA
    Details
    Publication Date: 2023-04-01
    Keywords: [CABLE]+[sbe19]+[NISKIN]; Ammonium; Bacteria; Cast-1; Cast-2; Chlorophyll a; CTD (sbe19) and Niskin bottles (8-L or 12-L) triggered with messengers; Date/Time of event; DEPTH, water; Event label; Flow cytometry; Latitude of event; Longitude of event; Mediterranean Sea, north of Crete; MicroB3; MicroB3_SummerSchool_20140527T0942; MicroB3_SummerSchool_20140527T1505; MicroB3 - Microbial Biodiversity, Bioinformatics and Biotechnology; MicroB3 Summer School 2014; Philia; Phosphate; Picoeukaryotes, autotrophic; Prochlorococcus; Salinity; Synechococcus; Temperature, water
    Type: Dataset
    Format: text/tab-separated-values, 27 data points
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    DATA PANGAEA
  • 7
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    CARD-FISH cell counts of taxonomic bacterial and archaeal groups in Fram Strait during PS99.2 (2019)
    PANGAEA
    Details
    Publication Date: 2023-07-10
    Description: With CARD-FISH we quantified 16 microbial taxonomic groups in different water depths, from surface to the deep sea. We investigated 11 stations in LTER-HAUSGARTEN and adjacent stations in Fram Strait.
    Keywords: Archaea, targed with ARCH915 oligonucleotide FISH-probe; ARK-XXX/1.2; Bacteria, targed with EUB338(I-III) oligonucleotide FISH-probe; Bacteroidetes, targeted with CF968 oligonucleotides FISH-probe; CARD-FISH; Catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH); cell counts; Chloroflexi, targeted with CFX1223 and GNSB941 oligonucleotides FISH-probe; Crenarchaeota marine group I, targeted with Cren554 oligonucleotide FISH-probe; CTD/Rosette; CTD/Rosette with Underwater Vision Profiler; CTD-RO; CTD-RO_UVP; Deltaproteobacteria, targeted with the DELTA495 mix oligonucleotide FISH-probes; DEPTH, water; EG_I; EG_IV; Event label; Fluorescence determination of DAPI stain; Fram Strait; Gammaproteobacteria, targeted with Gam42a oligonucleotide FISH-probe; HG_I; HG_II; HG_IV; HG_IX; HG_V; HG_VII; Microbial abundance, cells; N3; N4; N5; North Greenland Sea; Opitutales, targeted with OPI346 oligonucleotides FISH-probe; Polaribacter, targeted with POL740 oligonucleotides FISH-probe; Polarstern; PS99/042-1; PS99/042-11; PS99/044-1; PS99/046-1; PS99/048-1; PS99/048-11; PS99/051-2; PS99/053-2; PS99/054-1; PS99/055-1; PS99/055-7; PS99/057-1; PS99/059-2; PS99/066-2; PS99/066-5; PS99.2; Pseudoalteromonas, targeted with PSA184 oligonucleotide FISH-probe; Rhodobacteraceae, targeted with ROS536 oligonucleotides FISH-probe; SAR11 mix oligonucleotide FISH-probes targeting SAR11 clade; SAR202 clade, targeted with SAR202-312R oligonucleotide FISH-probe; SAR324 Marine group B, targeted with SAR324-R-625 oligonucleotide FISH-probe; SAR406 clade, targeted with SAR406-97 oligonucleotide FISH-probe; seawater; Verrucomicrobiales, targeted with EUB338 III oligonucleotides FISH-probe
    Type: Dataset
    Format: text/tab-separated-values, 748 data points
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    DATA PANGAEA
  • 8
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    Abundance of Prokaryotes in deep-sea sediments analyzed by CARD-FISH (2017)
    PANGAEA
    Details
    Publication Date: 2024-04-13
    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.
    Keywords: ABYSS; Analytical method; ANT-XXIX/8; ANT-XXV/3; ANT-XXVIII/3; Arctic Ocean; ARK-XXIX/2.2; ARK-XXVII/3; ARK-XXVIII/2; Assessment of bacterial life and matter cycling in deep-sea surface sediments; AT26-23-05; AT26-23-12; Catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH); Comment; Date/Time of event; Depth, bottom/max; DEPTH, sediment/rock; Depth, top/min; EGI; Elevation of event; Environmental feature; Epifluorescence microscopy after DAPI staining; Event label; Gammaproteobacteria; Gammaproteobacteria, cells; GeoB12202-1; GeoB12202-2; HGI; HGIV; HGIX; HGVI; HYDROMAR-III; J2-255; J2-258; J2-261; Japan Trench Bacteria clone 255 marine benthic group; JPI-OCEANS; Latitude of event; Longitude of event; M74/2; M74/2_962-1; M74/2_962-2; Maria S. Merian; Meteor (1986); MSM04/3; MSM04/3_251-ROV; MSM04/3_259-ROV; MSM04/3_271-ROV; MUC; MultiCorer; Multicorer with television; North Greenland Sea; PC; Piston corer; PLA; Plankton net; Polarstern; Prokaryotes; PS73/127-7; PS73 LOHAFEX; PS79; PS79/086-28; PS79/141-9; PS79/177-3; PS80/225-1; PS80/350-1; PS80 IceArc; PS81; PS81/606-1; PS85; PS85/436-1; PS85/454-3; PS85/460-4; PS85/464-1; PS85/465-4; PS85/470-3; PS93/067-2; PS93.2; Reference/source; Remote operated vehicle; Replicates; ROV; Sample ID; Sample type; SO242/2; SO242/2_147-148; SO242/2_194-1; SO242/2_198_MUC; Sonne_2; South Atlantic Ocean; South Pacific Ocean, Peru Basin; tropical/subtropical North Atlantic; TVMUC
    Type: Dataset
    Format: text/tab-separated-values, 648 data points
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    DATA PANGAEA
  • 9
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    Comparison of two common 16S rRNA primers (V3-V4 and V4-V5) for studies of Arctic microbial communities (2021)
    In:  EPIC3Frontiers in Microbiology
    Details
    Publication Date: 2021-05-21
    Description: Microbial communities of the Arctic Ocean are poorly characterized in comparison to other aquatic environments as to their horizontal, vertical and temporal turnover. However, the Arctic marine ecosystem harbors unique microbial communities, which are adapted to harsh environmental conditions, such as near-freezing temperatures and extreme seasonality. The gene for the small ribosomal subunit (16S rRNA) is commonly used to study microbial communities in their natural environment. Several primer sets for this marker gene have been extensively tested across various sample-sets, typically originating from low-latitude environments. Yet, an explicit evaluation of their performance in representing the microbial communities of the Arctic Ocean is currently lacking. To select a suitable primer set for studying microbiomes of various Arctic marine habitats (sea ice, surface and deep ocean, sinking aggregates, and deep-sea sediment), we have conducted a performance comparison between two widely used primer sets, targeting different hypervariable regions of the 16S rRNA gene (V3-V4 and V4-V5). We observed that both primer sets were highly similar in representing the total microbial community composition down to a genus rank, which was also confirmed independently by subgroup-specific CARD-FISH counts. The V3-V4 primer set revealed higher internal diversity sensitivity in various taxonomic groups (e.g., Flavobacteriaceae). On the other hand, the V4-V5 primer set provides concurrent coverage of the archaeal domain, a relevant component that comprises 8-17% of sequences of the deep ocean and sediment Arctic microbial communities. Altogether, our comparison suggests that the use of the V4-V5 primer set is more suitable for studying microbial community dynamics of the Arctic marine environment.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 10
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    Towards an integrated microbial observatory in the Arctic Ocean (2016)
    In:  EPIC3YouMares7, Uni Hamburg, Germany, 2016-09-11-2016-09-13
    Details
    Publication Date: 2017-01-26
    Description: The Fram Strait separates Northeast Greenland from the Svalbard Archipelago, and is the only deep connection to the Arctic Ocean. Therefore, this strait is the only gateway for direct exchange of intermediate and deep waters between the Arctic Ocean and the North Atlantic. Two main currents influence the exchanges: i) the West Spitsbergen Current, bringing Atlantic waters northwards, and ii) the East Greenland Current, which carries cold Arctic waters and ice southwards. These two currents consist of water masses with different origin, generate distinct physical and chemical conditions between the eastern and western parts of the strait, which effects the biological characteristics in this region. Oceanographic observations in the Fram Strait have been carried out for ~15 years with microbial research in the water column focusing mainly on eukaryotes, while very little exploratory work was conducted on pelagic Bacteria and Archaea. Here we present a preliminary report of the first extensive survey across the waters of the Fram Strait focused on Bacterial and Archaeal domains, conducted as part of the Arctic long-term observatory HAUSGARTEN annual expedition in summer 2016. Besides the investigation of “who is out there”, the observations gained in this survey will be integrated with other biological and physical data of the long-term observatory framework and will provide an essential step towards the understanding of the biochemical dynamics in the Fram Strait. In addition, on a long-term plan this project will contribute to the microbial observatory work as part of the FRAM Helmholtz research infrastructure and EU AtlantOS program.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Conference , notRev
    Format: application/pdf
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