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  • 1
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    Taxonomic and Functional Analyses of Marine Microbial Polysaccharide Utilisation (2017)
    In:  (PhD/ Doctoral thesis), Universität Bremen, Bremen, Germany, 220 pp
    Details
    Publication Date: 2020-02-06
    Type: Thesis , NonPeerReviewed
    Format: text
    Location Call Number Limitation Availability
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    OceanRep: Thesis - not published by a publisher
  • 2
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    Short term changes in polysaccharide utilisation during a spring phytoplankton bloom on Helgoland (2019)
    PANGAEA
    Details
    Publication Date: 2023-07-06
    Description: Spring phytoplankton blooms contribute significantly to global marine primary production. A large fraction of the bloom derived organic matter is available to heterotrophic bacteria in the form of polysaccharides. We analyzed changes in the modes of polysaccharide utilization (selfish uptake and extracellular hydrolysis) during a spring phytoplankton bloom using fluorescently labelled polysaccharide incubations coupled with 16s rRNA sequencing and fluorescence in situ hybridization. We found that in the early bloom phases there was high selfish activity of simple polysaccharides (laminarin) and low extracellular hydrolysis rates of a limited range of polysaccharides. During the course of the bloom both the selfish uptake and extracellular hydrolysis rates increased but only for a limited range of substrates. At the late bloom phase a wide range of substrate was extracellularly hydrolyzed and the level of selfish uptake decreased. We found that during a spring phytoplankton bloom the mode of substrate utilization depended on both the substrates structural complexity and the composition of the heterotrophic community related to the bloom phase.
    Keywords: Alteromonadales, substrate stained; Alteromonadales, targeted with ALT1413 oligonucleiotide FISH-Probe; Bacterioplankton; Bacteroidetes, substrate stained; Bacteroidetes, targeted with CF319a oligonucliotide FISH-Probe; DATE/TIME; DEPTH, water; Device type; Experiment day; Fluorescence in situ hybridization (FISH); German Bight, North Sea; HelgolandRoads_site; Kabeltonne; Microbial abundance, cells; Sample code/label; Sample ID; Size; Substrate type; Volume
    Type: Dataset
    Format: text/tab-separated-values, 1448 data points
    Location Call Number Limitation Availability
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    DATA PANGAEA
  • 3
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    A biogeographical study of microbial substrate utilisation in the Atlantic Ocean (2018)
    PANGAEA
    In:  Supplement to: Reintjes, Greta; Arnosti, Carol; Fuchs, Bernhard M; Amann, Rudolf (2019): Selfish, sharing and scavenging bacteria in the Atlantic Ocean: a biogeographical study of bacterial substrate utilisation. The ISME Journal, 13(5), 1119-1132, https://doi.org/10.1038/s41396-018-0326-3
    Details
    Publication Date: 2023-07-10
    Description: A large fraction of the organic matter fixed in the oceans is transformed and remineralised by marine heterotrophic microorganisms. They, therefore, play a critical role in the marine carbon cycle. In this study, we set out to identify the roles played by individual heterotrophic bacteria in the degradation of high molecular weight polysaccharides. At five sites in the Atlantic Ocean, we investigated the processing of organic matter in microbial communities by tracking the changes in community composition (fluorescence in situ hybridisation (FISH), 16S rRNA tag sequencing) in substrate incubation using a defined concentration of a known fluorescently labelled polysaccharide (FLA-laminarin, FLA-xylan, and FLA-chondroitin sulfate). Additionally, we tracked the dynamics of substrate processing (selfish uptake and extracellular hydrolysis) within the microbial communities between sites. We found that the same substrate was processed in different ways by different members of a pelagic microbial community which points to significant follow-on effects for carbon cycling.
    Keywords: Abundance; Alteromonadales, substrate stained; Alteromonadales, targeted with ALT1413 oligonucleiotide FISH-Probe; AMT22-46; ATM22; ATM22_JC079_CTD-24; ATM22_JC079_CTD-38; ATM22_JC079_CTD-57; ATM22_JC079_CTD-8; Bacteroidetes, substrate stained; Bacteroidetes, targeted with CF319a oligonucliotide FISH-Probe; Catenovulum, substrate stained; Catenovulum, targets with CAT653 oligonucleotide FISH-Probe; CTD/Rosette; CTD-RO; Date/Time of event; DEPTH, water; Event label; Experiment day; Fluorescence in situ hybridization (FISH); James Cook; JC079; JC079-04; JC079-12; JC079-19; JC079-28; JC079-46; Latitude of event; Longitude of event; Microbial abundance, cells; Optional event label; Planctomycetes, substrate stained; Planctomycetes, targeted with PLA46 oligonucliotide FISH-Probe; Sample ID; Substrate type
    Type: Dataset
    Format: text/tab-separated-values, 3490 data points
    Location Call Number Limitation Availability
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    DATA PANGAEA
  • 4
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    On-board sequencing of the microbial community of the South Pacific Gyre (2017)
    PANGAEA
    Details
    Publication Date: 2024-02-02
    Description: Fluorescence in situ hybridization (FISH) with 16S rRNA-targeted oligonucleotide probes was used to investigate the phylogenetic composition of the seven most abundant bacterial clades (determined by 16S rRNA tag sequencing) of the South Pacific Gyre (SPG). Seawater samples were collected aboard the RV Sonne SO-245 "UltraPac"cruise from Antofagasta, Chile (17.12.2015) to Wellington, New Zealand (28.01.2016). A total of 15 stations were sampled at multiple depths from surface (20 m) to ~5000 m. Total cell counts (TCC, by DAPI staining) and FISH were carried out as described in Bennke et al. (2016). DAPI and FISH stained cells were visualised and counted automatically using a fully automated image acquisition and cell enumeration system (Bennke et al., 2016). The cellular abundance of SAR11 clade, Prochlorococcus, AEGEAN-169 marine group, SAR86, SAR202, SAR324 and SAR406 were enumerated and are shown here in total (cell ml-1) and relative abundance (% TCC). For this study, a new probe specific for the AEGEAN-169 clade was designed and tested, based on the latest SILVA 16S rRNA database (refnr 128). We found that the microbial community within the SPG was highly similar to that of other oceanic gyres and showed a pronounced vertical distribution pattern. Two major differences which we observed, in comparison to previous studies of both the SPG and other oceanic Gyres, was a high abundance of the AEGEAN-169 marine group, a sister group of the SAR11 clade, and a low abundance of Prochlorococcus specifically in the surface waters of the central gyre.
    Keywords: Accession number, genetics; AEGEAN-169 marine group, targeted with the AEGEAN-169 mix oligonucleotide FISH-probes; Catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH); CTD/Rosette; CTD-RO; DEPTH, water; Event label; Flow cytometry; Microbial abundance, cells; Number; Prochlorococcus, targeted with PRO405 oligonucleotide FISH-probe; SAR11 mix oligonucleotide FISH-probes targeting SAR11 clade; SAR202 clade, targeted with SAR202-312R oligonucleotide FISH-probe; SAR324 clade, targeted with SAR324-1412 oligonucleotide FISH-probe; SAR406 clade, targeted with SAR406-97 oligonucleotide FISH-probe; SAR86 clade, targeted with SAR86-1245 oligonucleotide FISH-probe; SO245; SO245_10-1; SO245_1-1; SO245_11-1; SO245_12-2; SO245_13-1; SO245_14-2; SO245_15-13; SO245_2-2; SO245_3-1; SO245_4-1; SO245_5-1; SO245_6-1; SO245_7-4; SO245_8-1; SO245_9-1; Sonne_2; South Pacific Ocean; Station label; UltraPac, GEOTRACES
    Type: Dataset
    Format: text/tab-separated-values, 2922 data points
    Location Call Number Limitation Availability
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    DATA PANGAEA
  • 5
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    Microbial community composition and polysaccharide processing potential in the South Pacific Gyre (2020)
    PANGAEA
    Details
    Publication Date: 2024-02-02
    Description: The South Pacific Gyre (SPG) covers 10% of the ocean's surface and is considered a marine biological desert. However, recent investigations have shown that primary production occurs throughout its deep euphotic zone and that this fuels the regeneration of nutrients and the recycling of organic matter. We set out to investigate the SPG's microbial communities' heterotrophic capability to utilize polysaccharides, an important marine organic matter component. Using fluorescently labeled polysaccharide (FLA-PS) incubations (Reintjes, et al., 2017), we analyzed the initial step of organic matter degradation by measuring both the rate of external hydrolysis and the rate of direct uptake of polysaccharides by marine microorganisms. Furthermore, we investigated the change in bacterial abundance and diversity during the FLA-PS incubations using direct cell counts and 16S rRNA sequencing. The presented dataset contains the microbial diversity, total cellular abundance, and direct FLA-PS uptake results generated during the FLA-PS incubations performed with six polysaccharides (laminarin, xylan, chondroitin sulfate, arabinogalactan, fucoidan, and pullulan) over 18 days. The incubations were performed with seawater from the epipelagic and bathypelagic (75 m, 160 m, 1250 m, and 2800 m) in the central gyre, and seawater from the epipelagic (75 m) at two stations adjacent to the gyre. Our study found that the SPG's microbial community showed remarkably high extracellular enzyme activities, and a considerable fraction of the microorganisms were capable of the direct uptake (selfish-uptake) of FLA-PS. Interestingly, a wide variety of bacteria were capable of cycling HMW organic matter using distinct polysaccharide processing mechanisms in the SPG. This research shows that the SPG features not only organisms capable of existing on the fine edge of minimal substrate concentrations but also those capable of taking advantage of abrupt changes in physical conditions and substrate availability
    Keywords: activity; Basis of event; Campaign of event; CTD/Rosette; CTD-RO; Date/Time of event; Day of experiment; DEPTH, water; Event label; Extracellular Enzyme Activity; FLA-PS; Fluorescence in situ hybridization (FISH); Fluorescently labeled polysaccharides (FLA-PS); Gyre; heterotrophy; Latitude of event; Location of event; Longitude of event; metabolism; microbial; Microbial abundance, cells; Pacific; polysaccharide; Sample ID; Sample method; SO245; SO245_2-2; SO245_6-1; SO245_8-1; Sonne_2; South Pacific Ocean; Substrate type; UltraPac, GEOTRACES; Volume
    Type: Dataset
    Format: text/tab-separated-values, 1618 data points
    Location Call Number Limitation Availability
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    DATA PANGAEA
  • 6
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    Microbial community composition and bacterioplankton at time series station Helgoland Roads, North Sea (2016)
    PANGAEA
    Details
    Publication Date: 2024-02-23
    Description: A process of global importance in carbon cycling is the remineralization of algae biomass by heterotrophic bacteria, most notably during massive marine algae blooms. Such blooms can trigger secondary blooms of planktonic bacteria that consist of swift successions of distinct bacterial clades, most prominently members of the Flavobacteriia, Gammaproteobacteria and the alphaproteobacterial Roseobacter clade. This study explores such successions during spring phytoplankton blooms in the southern North Sea (German Bight) for four consecutive years. The surface water samples were taken at Helgoland Island about 40 km offshore in the southeastern North Sea in the German Bight at the station 'Kabeltonne' (54° 11.3' N, 7° 54.0' E) between the main island and the minor island, Düne (German for 'dune') using small research vessels (http://www.awi.de/en/expedition/ships/more-ships.html). Water depths at this site fluctuate from 6 to 10 m over the tidal cycle. Samples were processed as described previously (Teeling et al., 2012; doi:10.7554/eLife.11888.001) in the laboratory of the Biological Station Helgoland within less than two hours after sampling. Assessment of absolute cell numbers and bacterioplankton community composition was carried out as described previously (Thiele et al., 2011; doi:10.1016/B978-0-444-53199-5.00056-7). To obtain total cell numbers, DNA of formaldehyde fixed cells filtered on 0.2 mm pore sized filters was stained with 4',6-diamidino-2-phenylindole (DAPI). Fluorescently labeled cells were subsequently counted on filter sections using an epifluores-cence microscope. Likewise, bacterioplankton community composition was assessed by catalyzedreporter deposition fluorescence in situ hybridization (CARD-FISH) of formaldehyde fixed cells on 0.2 mm pore sized filters.
    Keywords: Actinobacteria, targeted with HGC69a oligonucleotides FISH-probe; Alphaproteobacteria, targeted with ALF968 oligonucleotides FISH-probe; Alteromonas/Colwellia, targeted with Alt1413 oligonucleotide FISH-probe; Archaea, targed with ARCH915 oligonucleotide FISH-probe; Bacteria, targed with EUB338(I-III) oligonucleotide FISH-probe; Bacterioplankton; Balneatrix, targeted with Bal731 oligonucleotides FISH-probe; Betaproteobacteria, targeted with BET42a oligonucleotides FISH-probe; Catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH); Crenarchaeota marine group I, targeted with Cren554 oligonucleotide FISH-probe; Cytophaga-Flavobacterium cluster, targeted with CF319a oligonucleotide FISH-probe; DATE/TIME; DEPTH, water; Epifluorescence microscopy after DAPI staining; Euryarchaeota marine group II, targeted with Eury806 oligonucleotide FISH-probe; Formosa, targeted with FORM181A oligonucleotides FISH-probe; Formosa, targeted with FORM181B oligonucleotides FISH-probe; Gammaproteobacteria, targeted with Gam42a oligonucleotide FISH-probe; German Bight, North Sea; Glaciecola, targeted with Glac227 oligonucleotides FISH-probe; HelgolandRoads_bacterioplankton_2009-2012; Julian day; Kabeltonne; Marinoscillum, targeted with CYT-734 oligonucleotides FISH-probe; NAC11-7 clade, targeted with NAC11-7-1030 oligonucleotides FISH-probe; Non-bacteria control, targeted with NON338 oligonucleotides FISH-probe; NOR5 clade, targeted with NOR5-730 oligonucleotides FISH-probe; NS3a clade, targeted with NS3a-840 oligonucleotides FISH-probe; NS5 clade, targeted with NS5/DE2-471 oligonucleotides FISH-probe; NS5 clade, targeted with NS5/VIS1-575 oligonucleotides FISH-probe; NS9 clade, targeted with NS9-664 oligonucleotides FISH-probe; OM182 clade, targeted with OM182-707 oligonucleotides FISH-probe; Pirellula group D, targeted with PirD1039 oligonucleotides FISH-probe; Planctomyce group A, targeted with PlaA1228 oligonucleotides FISH-probe; Planctomycete group B, targeted with uPlaB440 oligonucleotides FISH-probe; Planctomycetes, targeted with Pla46 oligonucleotide FISH-probe; Polaribacter, targeted with POL740 oligonucleotides FISH-probe; Pseudoalteromonas, targeted with PSA184 oligonucleotide FISH-probe; Reinekea, targeted with REI731 oligonucleotides FISH-probe; Roseobacter clade, targeted with RCA1000 oligonucleotides FISH-probe; Roseobacter clade, targeted with ROS537 oligonucleotides FISH-probe; SAR11 clade, targeted with SAR11-441 oligonucleotide FISH-probe; SAR11 clade, targeted with SAR11-486 oligonucleotides FISH-probe; SAR324 clade, targeted with SAR324-1412 oligonucleotide FISH-probe; SAR86 clade, targeted with SAR86-1245 oligonucleotide FISH-probe; SAR92 clade, targeted with SAR92-627 oligonucleotides FISH-probe; Ulvibacter, targeted with ULV995 oligonucleotides FISH-probe; Vibrio, targeted with GV841 oligonucleotide FISH-probe; VIS6 clade, targeted with VIS6-814 oligonucleotides FISH-probe
    Type: Dataset
    Format: text/tab-separated-values, 5239 data points
    Location Call Number Limitation Availability
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    DATA PANGAEA
  • 7
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    Short-term changes in polysaccharide utilization mechanisms of marine bacterioplankton during a spring phytoplankton bloom (2020)
    In:  EPIC3Journal of Sea Research
    Details
    Publication Date: 2020-08-03
    Description: Spring phytoplankton blooms in temperate environments contribute disproportionately to global marine productivity. Bloom-derived organic matter, much of it occurring as polysaccharides, fuels biogeochemical cycles driven by interacting autotrophic and heterotrophic communities. We tracked changes in the mode of polysaccharide utilization by heterotrophic bacteria during the course of a diatom-dominated bloom in the German Bight, North Sea. Polysaccharides can be taken up in a ‘selfish’ mode, where initial hydrolysis is coupled to transport into the periplasm, such that little to no low-molecular weight (LMW) products are externally released to the environment. Alternatively, polysaccharides hydrolyzed by cell-surface attached or free extracellular enzymes (external hydrolysis) yield LMW products available to the wider bacterioplankton community. In the early bloom phase, selfish activity was accompanied by low extracellular hydrolysis rates of a few polysaccharides. As the bloom progressed, selfish uptake increased markedly, and external hydrolysis rates increased, but only for a limited range of substrates. The late bloom phase was characterized by high external hydrolysis rates of a broad range of polysaccharides and reduced selfish uptake of polysaccharides, except for laminarin. Substrate utilization mode is related both to substrate structural complexity and to the bloom-stage dependent composition of the heterotrophic bacterial community.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 8
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    Short‐term changes in polysaccharide utilization mechanisms of marine bacterioplankton during a spring phytoplankton bloom (2020)
    In:  EPIC3Environmental Microbiology, 22(5), pp. 1884-1900, ISSN: 1462-2912
    Details
    Publication Date: 2020-07-22
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 9
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    On-Site Analysis of Bacterial Communities of the Ultraoligotrophic South Pacific Gyre (2019)
    AMER SOC MICROBIOLOGY
    In:  EPIC3Applied and Environmental Microbiology, AMER SOC MICROBIOLOGY, ISSN: 0099-2240
    Details
    Publication Date: 2020-02-14
    Description: The South Pacific Gyre (SPG) covers 10% of the ocean’s surface and is often regarded as a marine biological desert. To gain an on-site overview of the remote, ultraoligotrophic microbial community of the SPG, we developed a novel onboard analysis pipeline, which combines next-generation sequencing with fluorescence in situ hybridization and automated cell enumeration. We tested the pipeline during the SO-245 “UltraPac” cruise from Chile to New Zealand and found that the overall microbial community of the SPG was highly similar to those of other oceanic gyres. The SPG was dominated by 20 major bacterial clades, including SAR11, SAR116, the AEGEAN-169 marine group, SAR86, Prochlorococcus, SAR324, SAR406, and SAR202. Most of the bacterial clades showed a strong vertical (20 m to 5,000 m), but only a weak longitudinal (80°W to 160°W), distribution pattern. Surprisingly, in the central gyre, Prochlorococcus, the dominant photosynthetic organism, had only low cellular abundances in the upper waters (20 to 80 m) and was more frequent around the 1% irradiance zone (100 to 150 m). Instead, the surface waters of the central gyre were dominated by the SAR11, SAR86, and SAR116 clades known to harbor light-driven proton pumps. The alphaproteobacterial AEGEAN-169 marine group was particularly abundant in the surface waters of the central gyre, indicating a potentially interesting adaptation to ultraoligotrophic waters and high solar irradiance. In the future, the newly developed community analysis pipeline will allow for on-site insights into a microbial community within 35 h of sampling, which will permit more targeted sampling efforts and hypothesis-driven research.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 10
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    Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms (2016)
    eLife Sciences Publications, Ltd
    In:  EPIC3eLIFE, eLife Sciences Publications, Ltd
    Details
    Publication Date: 2019-03-08
    Description: A process of global importance in carbon cycling is the remineralization of algae biomass by heterotrophic bacteria, most notably during massive marine algae blooms. Such blooms can trigger secondary blooms of planktonic bacteria that consist of swift successions of distinct bacterial clades, most prominently members of the Flavobacteriia, Gammaproteobacteria and the alphaproteobacterial Roseobacter clade. We investigated such successions during spring phytoplankton blooms in the southern North Sea (German Bight) for four consecutive years. Dense sampling and high-resolution taxonomic analyses allowed the detection of recurring patterns down to the genus level. Metagenome analyses also revealed recurrent patterns at the functional level, in particular with respect to algal polysaccharide degradation genes. We demonstrate that even though there is substantial inter-annual variation between spring phytoplankton blooms, the accompanying succession of bacterial clades is not a purely stochastic process, but also governed by deterministic principles such as substrate-induced forcing.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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