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  • Artikel  (211)
  • Bacteria
  • Dissolved organic carbon
  • Springer  (166)
  • Iranian Fisheries Science Research Institute  (36)
  • Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu  (7)
  • American Chemical Society
  • Molecular Diversity Preservation International
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  • 1
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    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Publikationsdatum: 2022-10-31
    Beschreibung: Dataset: qPCR
    Beschreibung: These data include the quantification of specific microbial taxa within the sediments collected during Integrated Ocean Drilling Program (IODP) Expedition 347: Baltic Sea. DNA was extracted from the interior of frozen whole round cores sampled from Little Belt, Anholt Loch, Landsort Deep, and Bornholm Basin at The University of Tennessee. For a more detailed description of drill sites, access the data set, "IODP-347 drill site locations". Primers specifically targeting the 16S rRNA gene of bacteria, archaea, anaerobic methane oxidizers (ANME-1), and Miscellaneous Crenarchaeota Group (MCG; taxonomically reassigned as the Bathyarchaeota phylum of Archaea) were used to assess abundance of these microbial groups. Abundance data was generated using quantitative-PCR (qPCR) and a non-specific, intercalating DNA stain, SYBR Green. Values were compared against a standard curve to generate copies/uL. These data were collected by Alex Shumaker as part of Dr. Karen Lloyd and Dr. Andrew Steen’s project funded by the National Science Foundation entitled, "Quantifying the contribution of the deep biosphere in the marine sediment carbon cycle using deep-sea sediment cores from the Baltic Sea". For a complete list of measurements, refer to the supplemental document 'Field_names.pdf', and a full dataset description is included in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: http://www.bco-dmo.org/dataset/641358
    Beschreibung: NSF Division of Ocean Sciences (NSF OCE) OCE-1431598
    Schlagwort(e): qPCR ; Bacteria ; Archaea ; Baltic Sea ; Marine sediment
    Repository-Name: Woods Hole Open Access Server
    Materialart: Dataset
    Standort Signatur Erwartet Verfügbarkeit
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  • 2
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    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Publikationsdatum: 2022-10-31
    Beschreibung: Dataset: Inferno vent plume proteins-Av1
    Beschreibung: Proteins identified from the black smoker chimney Inferno hydrothermal vent plume waters at Axial Seamount, an active volcano along the Juan de Fuca Ridge spreading center, were identified using tandem mass spectrometry (MS/MS). These data are reported as Supplementary Table 3 and discussed in the on-line publication “Sulfur oxidizers dominate carbon fixation at a biogeochemical hot spot in the dark ocean” by Mattes, et al., 2013. doi for that publication: 10.1038/ismej.2013.113. This is the first of two replicate datasets. For a complete list of measurements, refer to the supplemental document 'Field_names.pdf', and a full dataset description is included in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: http://www.bco-dmo.org/dataset/627835
    Beschreibung: NSF Ocean Sciences (NSF OCE) OCE-1232840
    Schlagwort(e): Bacteria ; Proteomics ; Hydrothermal
    Repository-Name: Woods Hole Open Access Server
    Materialart: Dataset
    Standort Signatur Erwartet Verfügbarkeit
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  • 3
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    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Publikationsdatum: 2022-10-31
    Beschreibung: Dataset: MO - biogeochemical and microbial field surveys
    Beschreibung: 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
    Beschreibung: NSF Division of Ocean Sciences (NSF OCE) OCE-0802004
    Schlagwort(e): Hydrography ; Bacteria ; Organic matter ; Sargasso Sea
    Repository-Name: Woods Hole Open Access Server
    Materialart: Dataset
    Standort Signatur Erwartet Verfügbarkeit
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  • 4
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    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Publikationsdatum: 2022-10-31
    Beschreibung: Dataset: Diatom Matrix RNAseq
    Beschreibung: Transcriptome data for bacteria Ruegeria pomeroyi DSS-3, Stenotrophomonas sp. SKA14, Polaribacter dokdonensis MED152, and Dokdonia MED134 collected eight hours after individual inoculation into a diatom Thalassiosira psuedonana culture. The sequence data description for PRHNA448168 is at https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA448168. 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/818765
    Beschreibung: NSF Division of Integrative Organismal Systems (NSF IOS) IOS-1656311
    Schlagwort(e): Phytoplankton ; Bacteria ; Co-cultures ; Transcriptomes ; RNAseq
    Repository-Name: Woods Hole Open Access Server
    Materialart: Dataset
    Standort Signatur Erwartet Verfügbarkeit
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  • 5
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    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Publikationsdatum: 2022-10-31
    Beschreibung: Dataset: BLOOFINZ-GoM flow cytometry abundance
    Beschreibung: Phytoplankton and bacteria abundance from flow cytometry from samples collected in the Gulf of Mexico on R/V Nancy Foster cruises NF1704 and NF1802 in May 2017 and May 2018 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/835414
    Beschreibung: NSF Division of Ocean Sciences (NSF OCE) OCE-1851558, National Oceanic and Atmospheric Administration (NOAA) NA16NMF4320058
    Schlagwort(e): Phytoplankton ; Bacteria ; Prochlorococcus ; Synechococcus ; Gulf of Mexico
    Repository-Name: Woods Hole Open Access Server
    Materialart: Dataset
    Standort Signatur Erwartet Verfügbarkeit
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  • 6
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    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Publikationsdatum: 2022-10-31
    Beschreibung: Dataset: Coral Associated Microbes on Mo'orean Coral Reefs
    Beschreibung: Three species of coral, plus water and sediment, were sampled at 21 sites around the island of Mo’orea, French Polynesia during the dry and rainy seasons in 2017 and 2018. Coral associated microbes (bacteria and archaea) were investigated and their community composition characterized through sequencing of the 16S rRNA gene. 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/845039
    Beschreibung: NSF Division of Ocean Sciences (NSF OCE) OCE-1635798, NSF Division of Ocean Sciences (NSF OCE) OCE-1635913
    Schlagwort(e): Bacteria ; Archaea ; Moorea Coral Reef LTER ; Holobiont ; Microbiome ; Earth Microbiome Project
    Repository-Name: Woods Hole Open Access Server
    Materialart: Dataset
    Standort Signatur Erwartet Verfügbarkeit
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  • 7
    Publikationsdatum: 2022-10-31
    Beschreibung: Dataset: CTD Profile Casts
    Beschreibung: CTD Depth Profile Cast Data for the InVirT-2019-BATS (Bermuda Atlantic Time Series) project taken in the on board of the R/V Atlantic Explorer AE1926 in 2019. 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/835593
    Beschreibung: NSF Division of Ocean Sciences (NSF OCE) OCE-1829636
    Schlagwort(e): Bermuda Atlantic Time Series ; BATS ; Virus ; Phage ; Metatranscriptomics ; Bacteria ; Diel ; Sargasso Sea
    Repository-Name: Woods Hole Open Access Server
    Materialart: Dataset
    Standort Signatur Erwartet Verfügbarkeit
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  • 8
    Publikationsdatum: 2022-10-26
    Beschreibung: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Walsh, A. N., Reddy, C. M., Niles, S. F., McKenna, A. M., Hansel, C. M., & Ward, C. P. Plastic formulation is an emerging control of its photochemical fate in the ocean. Environmental Science & Technology, 55(18), (2021): 12383–12392, https://doi.org/10.1021/acs.est.1c02272.
    Beschreibung: Sunlight exposure is a control of long-term plastic fate in the environment that converts plastic into oxygenated products spanning the polymer, dissolved, and gas phases. However, our understanding of how plastic formulation influences the amount and composition of these photoproducts remains incomplete. Here, we characterized the initial formulations and resulting dissolved photoproducts of four single-use consumer polyethylene (PE) bags from major retailers and one pure PE film. Consumer PE bags contained 15–36% inorganic additives, primarily calcium carbonate (13–34%) and titanium dioxide (TiO2; 1–2%). Sunlight exposure consistently increased production of dissolved organic carbon (DOC) relative to leaching in the dark (3- to 80-fold). All consumer PE bags produced more DOC during sunlight exposure than the pure PE (1.2- to 2.0-fold). The DOC leached after sunlight exposure increasingly reflected the 13C and 14C isotopic composition of the plastic. Ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry revealed that sunlight exposure substantially increased the number of DOC formulas detected (1.1- to 50-fold). TiO2-containing bags photochemically degraded into the most compositionally similar DOC, with 68–94% of photoproduced formulas in common with at least one other TiO2-containing bag. Conversely, only 28% of photoproduced formulas from the pure PE were detected in photoproduced DOC from the consumer PE. Overall, these findings suggest that plastic formulation, especially TiO2, plays a determining role in the amount and composition of DOC generated by sunlight. Consequently, studies on pure, unweathered polymers may not accurately represent the fates and impacts of the plastics entering the ocean.
    Beschreibung: Funding was provided by the Seaver Institute, the Gerstner Family Foundation, Woods Hole Oceanographic Institution, and the National Science Foundation Graduate Research Fellowship Program (A.N.W.). The Ion Cyclotron Resonance user facility at the National High Magnetic Field Laboratory is supported by the National Science Foundation Division of Chemistry and Division of Materials Research through DMR-1644779 and the State of Florida.
    Schlagwort(e): Plastic pollution ; Marine debris ; Additives ; Dissolved organic carbon ; Photochemical oxidation ; FT-ICR-MS ; Titanium dioxide
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
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  • 9
    Publikationsdatum: 2022-05-27
    Beschreibung: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gosselin, K. M., Nelson, R. K., Spivak, A. C., Sylva, S. P., Van Mooy, B. A. S., Aeppli, C., Sharpless, C. M., O’Neil, G. W., Arrington, E. C., Reddy, C. M., & Valentine, D. L. Production of two highly abundant 2-methyl-branched fatty acids by blooms of the globally significant marine cyanobacteria Trichodesmium erythraeum. ACS Omega, 6(35), (2021): 22803–22810, https://doi.org/10.1021/acsomega.1c03196.
    Beschreibung: The bloom-forming cyanobacteria Trichodesmium contribute up to 30% to the total fixed nitrogen in the global oceans and thereby drive substantial productivity. On an expedition in the Gulf of Mexico, we observed and sampled surface slicks, some of which included dense blooms of Trichodesmium erythraeum. These bloom samples contained abundant and atypical free fatty acids, identified here as 2-methyldecanoic acid and 2-methyldodecanoic acid. The high abundance and unusual branching pattern of these compounds suggest that they may play a specific role in this globally important organism.
    Beschreibung: This work was funded with grants from the National Science Foundation grants OCE-1333148, OCE-1333162, and OCE-1756254 and the Woods Hole Oceanographic Institution (IR&D). GCxGC analysis made possible by WHOI’s Investment in Science Fund.
    Schlagwort(e): Lipids ; Alkyls ; Bacteria ; Genetics ; Chromatography
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Erwartet Verfügbarkeit
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  • 10
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Authors 2009. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License. The definitive version was published in Functional & Integrative Genomics 10 (2010): 97-110, doi:10.1007/s10142-009-0142-y.
    Beschreibung: Bacteria of the genus Shewanella can thrive in different environments and demonstrate significant variability in their metabolic and ecophysiological capabilities including cold and salt tolerance. Genomic characteristics underlying this variability across species are largely unknown. In this study, we address the problem by a comparison of the physiological, metabolic, and genomic characteristics of 19 sequenced Shewanella species. We have employed two novel approaches based on association of a phenotypic trait with the number of the trait-specific protein families (Pfam domains) and on the conservation of synteny (order in the genome) of the trait-related genes. Our first approach is top-down and involves experimental evaluation and quantification of the species’ cold tolerance followed by identification of the correlated Pfam domains and genes with a conserved synteny. The second, a bottom-up approach, predicts novel phenotypes of the species by calculating profiles of each Pfam domain among their genomes and following pair-wise correlation of the profiles and their network clustering. Using the first approach, we find a link between cold and salt tolerance of the species and the presence in the genome of a Na+/H+ antiporter gene cluster. Other cold-tolerance-related genes include peptidases, chemotaxis sensory transducer proteins, a cysteine exporter, and helicases. Using the bottom-up approach, we found several novel phenotypes in the newly sequenced Shewanella species, including degradation of aromatic compounds by an aerobic hybrid pathway in Shewanella woodyi, degradation of ethanolamine by Shewanella benthica, and propanediol degradation by Shewanella putrefaciens CN32 and Shewanella sp. W3-18-1.
    Beschreibung: This research was supported by the U.S. Department of Energy (DOE) Office of Biological and Environmental Research under the Genomics: GTL Program via the Shewanella Federation consortium.
    Schlagwort(e): Phenotypic trait ; Bacteria ; Molecular mechanisms of cold tolerance ; Shewanella ; Protein families
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/pdf
    Format: application/vnd.ms-excel
    Standort Signatur Erwartet Verfügbarkeit
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