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  • 1
    Electronic Resource
    Electronic Resource
    [s.l.] : Nature Publishing Group
    Nature 371 (1994), S. 405-408 
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Renewed interest in DOC was sparked by a series of reports of elevated concentrations determined by the high-temperature combustion (HTC) method14'16 suggesting the presence of a previously unmeasured and chemically refractory pool. Although these elevated DOC values have since proven to be ...
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    [s.l.] : Nature Publishing Group
    Nature 372 (1994), S. 537-540 
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] The Bermuda Atlantic Time-series Study (BATS; part of the US Joint Global Ocean Flux Study (JGOFS)) has sampled the Sargasso Sea (31° 50' N, 64° 10' W) biweekly to monthly since October 1988. The programme includes measurements of most components of the carbon cycle using ...
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  • 3
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    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Publication Date: 2022-10-31
    Description: Dataset: MO - biogeochemical and microbial field surveys
    Description: Biogeochemical and microbial field surveys from the BATS site, Bermuda from R/V Atlantic Explorer cruises from 2009-2013. This dataset includes water samples collected from 2009-2013 at the Bermuda Hydrostation that were analyzed for DOC, POC, bacterial abundance, leucine, and thymidine incorporation. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/543314
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-0802004
    Keywords: Hydrography ; Bacteria ; Organic matter ; Sargasso Sea
    Repository Name: Woods Hole Open Access Server
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  • 4
    Publication Date: 2022-05-26
    Description: Dataset: Data Set 1B: Bioavailability of dissolved organic carbon produced by Thalassiosira weissflogii grown under different pCO2 and temperature conditions - Experiment OA5
    Description: Bioavailability of dissolved organic carbon produced by Thalassiosira weissflogii grown under different pCO2 and temperature conditions from UCSB Marine Science Institute Passow Lab from 2009 to 2010. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/471701
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1041038
    Repository Name: Woods Hole Open Access Server
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  • 5
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    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Publication Date: 2022-05-26
    Description: Dataset: MO - sugars
    Description: Sugar concentrations and dissolved combined neutral sugar (DCNS) dynamics were measured from samples for DCNS collected monthly to bimonthly between 2001 and 2004 at the BATS study site aboard the R/V Weatherbird II, Western Sargasso Sea. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/543771
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-0802004
    Keywords: Sargasso Sea ; Dissolved combined neutral sugars (DCNS) ; Dissolved Organic Matter (DOM)
    Repository Name: Woods Hole Open Access Server
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  • 6
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Maas, A. E., Liu, S., Bolanos, L. M., Widner, B., Parsons, R., Kujawinski, E. B., Blanco-Bercial, L., & Carlson, C. A. Migratory zooplankton excreta and its influence on prokaryotic communities. Frontiers in Marine Science, 7, (2020): 573268, doi:10.3389/fmars.2020.573268.
    Description: Particulate organic matter (POM) (fecal pellets) from zooplankton has been demonstrated to be an important nutrient source for the pelagic prokaryotic community. Significantly less is known about the chemical composition of the dissolved organic matter (DOM) produced by these eukaryotes and its influence on pelagic ecosystem structure. Zooplankton migrators, which daily transport surface-derived compounds to depth, may act as important vectors of limiting nutrients for mesopelagic microbial communities. In this role, zooplankton may increase the DOM remineralization rate by heterotrophic prokaryotes through the creation of nutrient rich “hot spots” that could potentially increase niche diversity. To explore these interactions, we collected the migratory copepod Pleuromamma xiphias from the northwestern Sargasso Sea and sampled its excreta after 12–16 h of incubation. We measured bulk dissolved organic carbon (DOC), dissolved free amino acids (DFAA) via high performance liquid chromatography and dissolved targeted metabolites via quantitative mass spectrometry (UPLC-ESI-MSMS) to quantify organic zooplankton excreta production and characterize its composition. We observed production of labile DOM, including amino acids, vitamins, and nucleosides. Additionally, we harvested a portion of the excreta and subsequently used it as the growth medium for mesopelagic (200 m) bacterioplankton dilution cultures. In zooplankton excreta treatments we observed a four-fold increase in bacterioplankton cell densities that reached stationary growth phase after five days of dark incubation. Analyses of 16S rRNA gene amplicons suggested a shift from oligotrophs typical of open ocean and mesopelagic prokaryotic communities to more copiotrophic bacterial lineages in the presence of zooplankton excreta. These results support the hypothesis that zooplankton and prokaryotes are engaged in complex and indirect ecological interactions, broadening our understanding of the microbial loop.
    Description: Funding for this research was provided by Simons Foundation International as part of the BIOS-SCOPE project to AM, LB-B, CC, and EK.
    Keywords: DOC ; Dissolved metabolites ; Diel vertical migration ; Biogeochemistry ; Copepod
    Repository Name: Woods Hole Open Access Server
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  • 7
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Saw, J. H. W., Nunoura, T., Hirai, M., Takaki, Y., Parsons, R., Michelsen, M., Longnecker, K., Kujawinski, E. B., Stepanauskas, R., Landry, Z., Carlson, C. A., & Giovannoni, S. J. Pangenomics analysis reveals diversification of enzyme families and niche specialization in globally abundant SAR202 bacteria. Mbio, 11(1), (2020): e02975-19, doi:10.1128/mBio.02975-19.
    Description: It has been hypothesized that the abundant heterotrophic ocean bacterioplankton in the SAR202 clade of the phylum Chloroflexi evolved specialized metabolisms for the oxidation of organic compounds that are resistant to microbial degradation via common metabolic pathways. Expansions of paralogous enzymes were reported and implicated in hypothetical metabolism involving monooxygenase and dioxygenase enzymes. In the proposed metabolic schemes, the paralogs serve the purpose of diversifying the range of organic molecules that cells can utilize. To further explore SAR202 evolution and metabolism, we reconstructed single amplified genomes and metagenome-assembled genomes from locations around the world that included the deepest ocean trenches. In an analysis of 122 SAR202 genomes that included seven subclades spanning SAR202 diversity, we observed additional evidence of paralog expansions that correlated with evolutionary history, as well as further evidence of metabolic specialization. Consistent with previous reports, families of flavin-dependent monooxygenases were observed mainly in the group III SAR202 genomes, and expansions of dioxygenase enzymes were prevalent in those of group VII. We found that group I SAR202 genomes encode expansions of racemases in the enolase superfamily, which we propose evolved for the degradation of compounds that resist biological oxidation because of chiral complexity. Supporting the conclusion that the paralog expansions indicate metabolic specialization, fragment recruitment and fluorescent in situ hybridization (FISH) with phylogenetic probes showed that SAR202 subclades are indigenous to different ocean depths and geographical regions. Surprisingly, some of the subclades were abundant in surface waters and contained rhodopsin genes, altering our understanding of the ecological role of SAR202 species in stratified water columns. IMPORTANCE The oceans contain an estimated 662 Pg C in the form of dissolved organic matter (DOM). Information about microbial interactions with this vast resource is limited, despite broad recognition that DOM turnover has a major impact on the global carbon cycle. To explain patterns in the genomes of marine bacteria, we propose hypothetical metabolic pathways for the oxidation of organic molecules that are resistant to oxidation via common pathways. The hypothetical schemes we propose suggest new metabolic pathways and classes of compounds that could be important for understanding the distribution of organic carbon throughout the biosphere. These genome-based schemes will remain hypothetical until evidence from experimental cell biology can be gathered to test them. Our findings also fundamentally change our understanding of the ecology of SAR202 bacteria, showing that metabolically diverse variants of these cells occupy niches spanning all depths and are not relegated to the dark ocean.
    Description: We thank the captain, crew, ROV and CTD operation teams, and science party of the JAMSTEC RV Kairei cruises KR11-11, KR12-19, and KR14-01. We thank the staff of the Bigelow Laboratory for Ocean Sciences’ Single Cell Genomics Center for the generation of single-cell genomic data. We thank Mark Dasenko from the Center for Genome Research and Biocomputing at Oregon State University for sequencing six of the Illumina SAG libraries. We thank the captain, crew and CTD operations team of the RV Atlantic Explorer (cruise AE1712). T.N. was supported in part by a Grant-in-Aid for Scientific Research (B) (30070015) from the Japan Society for the Promotion of Science (JSPS). The mass spectrometry samples were analyzed at the WHOI FT-MS Users’ Facility; funding for data collection and analysis came from the National Science Foundation (NSF Grant OCE-1154320 to E.B.K. and K.L.). This work was funded by Simons Foundation International as part of the BIOS-SCOPE initiative (S.J.G., C.A.C., and E.B.K.), and by NSF grants OCE-1335810 and DEB-1441717 to R.S. This work was funded by National Science Foundation grant OCE-1436865.
    Keywords: SAR202 ; Biological carbon pump ; Carbon sequestration ; Dissolved organic matter ; Enolase ; Marine carbon cycle ; Recalcitrant organic matter
    Repository Name: Woods Hole Open Access Server
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  • 8
    Publication Date: 2022-10-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Liu, S., Longnecker, K., Kujawinski, E., Vergin, K., Bolaños, L., Giovannoni, S., Parsons, R., Opalk, K., Halewood, E., Hansell, D., Johnson, R., Curry, R., & Carlson, C. Linkages among dissolved organic matter export, dissolved metabolites, and associated microbial community structure response in the northwestern Sargasso Sea on a seasonal scale. Frontiers in Microbiology, 13, (2022): 833252, https://doi.org/10.3389/fmicb.2022.833252.
    Description: Deep convective mixing of dissolved and suspended organic matter from the surface to depth can represent an important export pathway of the biological carbon pump. The seasonally oligotrophic Sargasso Sea experiences annual winter convective mixing to as deep as 300 m, providing a unique model system to examine dissolved organic matter (DOM) export and its subsequent compositional transformation by microbial oxidation. We analyzed biogeochemical and microbial parameters collected from the northwestern Sargasso Sea, including bulk dissolved organic carbon (DOC), total dissolved amino acids (TDAA), dissolved metabolites, bacterial abundance and production, and bacterial community structure, to assess the fate and compositional transformation of DOM by microbes on a seasonal time-scale in 2016–2017. DOM dynamics at the Bermuda Atlantic Time-series Study site followed a general annual trend of DOC accumulation in the surface during stratified periods followed by downward flux during winter convective mixing. Changes in the amino acid concentrations and compositions provide useful indices of diagenetic alteration of DOM. TDAA concentrations and degradation indices increased in the mesopelagic zone during mixing, indicating the export of a relatively less diagenetically altered (i.e., more labile) DOM. During periods of deep mixing, a unique subset of dissolved metabolites, such as amino acids, vitamins, and benzoic acids, was produced or lost. DOM export and compositional change were accompanied by mesopelagic bacterial growth and response of specific bacterial lineages in the SAR11, SAR202, and SAR86 clades, Acidimicrobiales, and Flavobacteria, during and shortly following deep mixing. Complementary DOM biogeochemistry and microbial measurements revealed seasonal changes in DOM composition and diagenetic state, highlighting microbial alteration of the quantity and quality of DOM in the ocean.
    Description: This project was funded by the Simons Foundation International’s BIOS-SCOPE program and US National Science Foundation (NSF OCE-1756105 for BATS cruises).
    Keywords: Dissolved organic matter ; Amino acids ; Metabolites ; Bacterioplankton ; Sargasso Sea ; Seasonal ; Mixing
    Repository Name: Woods Hole Open Access Server
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  • 9
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    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Publication Date: 2022-05-26
    Description: Dataset: MO - virioplankton abund-FISH probe
    Description: Virioplankton abundances were measured from samples collected from January 2000 to December 2011 as part of the larger BATS program aboard the R/V Weatherbird II or the R/V Atlantic Explorer. Supporting data provided by the BATS time-series program and are available at (http://bats.bios.edu/). This dataset reports abundances quantified using FISH (Fluorescence in situ hybridization). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/543828
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-0802004
    Keywords: Fluorescence In Situ Hybridization (FISH) ; Cyanobacteria ; Eubacteria ; SAR11 ; Bacteriodetes ; Rhodobacteraceae ; Sargasso Sea
    Repository Name: Woods Hole Open Access Server
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  • 10
    Publication Date: 2022-05-26
    Description: Dataset: MO - virioplankton abundance
    Description: Virioplankton abundances were measured from samples collected from January 2000 to December 2011 at the Bermuda Atlantic Time Series Station (BATS), Western Sargasso Sea, as part of the larger BATS program aboard the R/V Weatherbird II or the R/V Atlantic Explorer. Supporting data provided by the BATS time-series program and are available at (http://bats.bios.edu/). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/543808
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-0802004
    Keywords: Virioplankton ; Sargasso Sea
    Repository Name: Woods Hole Open Access Server
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