GLORIA

GEOMAR Library Ocean Research Information Access

X
feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
Filter
Document type
Keywords
Publisher
Years
  • 1
    facet.materialart.
    Unknown
    Seawater carbonate chemistry and processes during experiments with Emiliania huxleyi, 2008 (2008)
    PANGAEA
    In:  Supplement to: Iglesias-Rodriguez, Debora; Halloran, P R; Rickaby, Rosalind E M; Hall, Ian R; Colmenero-Hidalgo, Elena; Gittins, J R; Green, Darryl R H; Tyrrell, Toby; Gibbs, Samantha J; von Dassow, Peter; Rehm, E; Armbrust, E Virginia; Boessenkool, K P (2008): Phytoplankton calcification in a high-CO2 world. Science, 320(5874), 336-340, https://doi.org/10.1126/science.1154122
    Details
    Publication Date: 2024-03-15
    Description: Ocean acidification in response to rising atmospheric CO2 partial pressures is widely expected to reduce calcification by marine organisms. From the mid-Mesozoic, coccolithophores have been major calcium carbonate producers in the world's oceans, today accounting for about a third of the total marine CaCO3 production. Here, we present laboratory evidence that calcification and net primary production in the coccolithophore species Emiliania huxleyi are significantly increased by high CO2 partial pressures. Field evidence from the deep ocean is consistent with these laboratory conclusions, indicating that over the past 220 years there has been a 40% increase in average coccolith mass. Our findings show that coccolithophores are already responding and will probably continue to respond to rising atmospheric CO2 partial pressures, which has important implications for biogeochemical modeling of future oceans and climate.
    Keywords: Alkalinity, total; Aragonite saturation state; Bicarbonate ion; Biomass/Abundance/Elemental composition; Calcification/Dissolution; Calcification rate of calcium carbonate per algae cell; Calcite saturation state; Calcium carbonate in cell; Calculated; Calculated using seacarb after Nisumaa et al. (2010); Carbon, inorganic, dissolved; Carbon/Nitrogen ratio; Carbonate ion; Carbonate system computation flag; Carbon dioxide; Chromista; Counting; Element analyser, Thermo Finnigan flash EA 1112; Emiliania huxleyi; EPOCA; EUR-OCEANS; European network of excellence for Ocean Ecosystems Analysis; European Project on Ocean Acidification; Experimental treatment; Flow cytometry; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Growth/Morphology; Growth rate; Haptophyta; Laboratory experiment; Laboratory strains; North Atlantic; OA-ICC; Ocean Acidification International Coordination Centre; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); Particulate organic carbon, per cell; Particulate organic carbon production per cell; Pelagos; pH; Phytoplankton; Potentiometric titration, VINDTA (marianda); Primary production/Photosynthesis; Salinity; Single species; Temperature, water
    Type: Dataset
    Format: text/tab-separated-values, 1237 data points
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    DATA PANGAEA
  • 2
    facet.materialart.
    Unknown
    The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing (2014)
    PUBLIC LIBRARY SCIENCE
    In:  EPIC3PLoS Biology, PUBLIC LIBRARY SCIENCE, 12(6), pp. e1001889, ISSN: 1544-9173
    Details
    Publication Date: 2014-07-01
    Description: Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 3
    facet.materialart.
    Unknown
    Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus (2017)
    Nature Publishing Group
    In:  EPIC3Nature, Nature Publishing Group, 541, pp. 536-540, ISSN: 0028-0836
    Details
    Publication Date: 2019-03-08
    Description: The Southern Ocean houses a diverse and productive community of organisms. Unicellular eukaryotic diatoms are the main primary producers in this environment, where photosynthesis is limited by low concentrations of dissolved iron and large seasonal fluctuations in light, temperature and the extent of sea ice. How diatoms have adapted to this extreme environment is largely unknown. Here we present insights into the genome evolution of a cold-adapted diatom from the Southern Ocean, Fragilariopsis cylindrus based on a comparison with temperate diatoms. We find that approximately 24.7 per cent of the diploid F. cylindrus genome consists of genetic loci with alleles that are highly divergent from those of temperate diatoms (15.1 megabases of the total genome size of 61.1 megabases). These divergent alleles were differentially expressed across environmental conditions, including darkness, low iron, freezing, elevated temperature and increased CO2. Alleles with the largest ratio of non-synonymous to synonymous nucleotide substitutions also show the most pronounced condition-dependent expression, suggesting a correlation between diversifying selection and allelic differentiation. Divergent alleles may be involved in adaptation to environmental fluctuations in the Southern Ocean.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 4
    facet.materialart.
    Unknown
    The evolution of silicon transporters in diatoms (2016)
    John Wiley & Sons
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Phycology 52 (2016): 716–731, doi:10.1111/jpy.12441.
    Description: Diatoms are highly productive single-celled algae that form an intricately patterned silica cell wall after every cell division. They take up and utilize silicic acid from seawater via silicon transporter (SIT) proteins. This study examined the evolution of the SIT gene family to identify potential genetic adaptations that enable diatoms to thrive in the modern ocean. By searching for sequence homologs in available databases, the diversity of organisms found to encode SITs increased substantially and included all major diatom lineages and other algal protists. A bacterial-encoded gene with homology to SIT sequences was also identified, suggesting that a lateral gene transfer event occurred between bacterial and protist lineages. In diatoms, the SIT genes diverged and diversified to produce five distinct clades. The most basal SIT clades were widely distributed across diatom lineages, while the more derived clades were lineage-specific, which together produced a distinct repertoire of SIT types among major diatom lineages. Differences in the predicted protein functional domains encoded among SIT clades suggest that the divergence of clades resulted in functional diversification among SITs. Both laboratory cultures and natural communities changed transcription of each SIT clade in response to experimental or environmental growth conditions, with distinct transcriptional patterns observed among clades. Together, these data suggest that the diversification of SITs within diatoms led to specialized adaptations among diatoms lineages, and perhaps their dominant ability to take up silicic acid from seawater in diverse environmental conditions.
    Description: Gordon and Betty Moore Foundation Grant Numbers: GBMF2637, GBMF3776; University of Washington; National Science Foundation Grant Number: OCE-1205233
    Keywords: Diatoms ; Gene family ; Molecular evolution ; Nutrients ; Silicon ; Transporter
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 5
    facet.materialart.
    Unknown
    Daily changes in phytoplankton lipidomes reveal mechanisms of energy storage in the open ocean (2018)
    Nature Publishing Group
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature Communications 9 (2018): 5179, doi:10.1038/s41467-018-07346-z.
    Description: Sunlight is the dominant control on phytoplankton biosynthetic activity, and darkness deprives them of their primary external energy source. Changes in the biochemical composition of phytoplankton communities over diel light cycles and attendant consequences for carbon and energy flux in environments remain poorly elucidated. Here we use lipidomic data from the North Pacific subtropical gyre to show that biosynthesis of energy-rich triacylglycerols (TAGs) by eukaryotic nanophytoplankton during the day and their subsequent consumption at night drives a large and previously uncharacterized daily carbon cycle. Diel oscillations in TAG concentration comprise 23 ± 11% of primary production by eukaryotic nanophytoplankton representing a global flux of about 2.4 Pg C yr−1. Metatranscriptomic analyses of genes required for TAG biosynthesis indicate that haptophytes and dinoflagellates are active members in TAG production. Estimates suggest that these organisms could contain as much as 40% more calories at sunset than at sunrise due to TAG production.
    Description: This work was supported by a grant from the Simons Foundation, and is a contribution of the Simons Collaboration on Ocean Processes and Ecology (SCOPE award # 329108, B.A.S.V.M.). K.W.B. was further supported by the Postdoctoral Scholarship Program at Woods Hole Oceanographic Institution & U.S. Geological Survey.
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 6
    facet.materialart.
    Unknown
    Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities (2021)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Coesel, S. N., Durham, B. P., Groussman, R. D., Hu, S. K., Caron, D. A., Morales, R. L., Ribalet, F., & Armbrust, E. V. Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities. Proceedings of the National Academy of Sciences of the United States of America, 118(6), (2021): e2011038118, https://doi.org/10.1073./pnas.2011038118.
    Description: The 24-h cycle of light and darkness governs daily rhythms of complex behaviors across all domains of life. Intracellular photoreceptors sense specific wavelengths of light that can reset the internal circadian clock and/or elicit distinct phenotypic responses. In the surface ocean, microbial communities additionally modulate nonrhythmic changes in light quality and quantity as they are mixed to different depths. Here, we show that eukaryotic plankton in the North Pacific Subtropical Gyre transcribe genes encoding light-sensitive proteins that may serve as light-activated transcription factors, elicit light-driven electrical/chemical cascades, or initiate secondary messenger-signaling cascades. Overall, the protistan community relies on blue light-sensitive photoreceptors of the cryptochrome/photolyase family, and proteins containing the Light-Oxygen-Voltage (LOV) domain. The greatest diversification occurred within Haptophyta and photosynthetic stramenopiles where the LOV domain was combined with different DNA-binding domains and secondary signal-transduction motifs. Flagellated protists utilize green-light sensory rhodopsins and blue-light helmchromes, potentially underlying phototactic/photophobic and other behaviors toward specific wavelengths of light. Photoreceptors such as phytochromes appear to play minor roles in the North Pacific Subtropical Gyre. Transcript abundance of environmental light-sensitive protein-encoding genes that display diel patterns are found to primarily peak at dawn. The exceptions are the LOV-domain transcription factors with peaks in transcript abundances at different times and putative phototaxis photoreceptors transcribed throughout the day. Together, these data illustrate the diversity of light-sensitive proteins that may allow disparate groups of protists to respond to light and potentially synchronize patterns of growth, division, and mortality within the dynamic ocean environment.
    Description: This work was supported by a grant from the Simons Foundation (SCOPE Award 329108 [to E.V.A.]) and XSEDE Grant Allocation OCE160019 (to R.D.G.).
    Keywords: Photoreceptors ; Microbial eukaryotes ; Oligotrophic gyre ; Diel cycles ; Metatranscriptomics
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 7
    facet.materialart.
    Unknown
    Cryptic carbon and sulfur cycling between surface ocean plankton (2015)
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2014. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 112 (2015): 453-457, doi:10.1073/pnas.1413137112 .
    Description: About half the carbon fixed by phytoplankton in the ocean is taken up and metabolized by marine bacteria, a transfer that is mediated through the seawater dissolved organic carbon (DOC) pool. The chemical complexity of marine DOC, along with a poor understanding of which compounds form the basis of trophic interactions between bacteria and phytoplankton, have impeded efforts to identify key currencies of this carbon cycle link. Here, we used transcriptional patterns in a bacterial-diatom model system based on vitamin B12 auxotrophy as a sensitive assay for metabolite exchange between marine plankton. The most highly upregulated genes (up to 374-fold) by a marine Roseobacter clade bacterium when co-cultured with the diatom Thalassiosira pseudonana were those encoding the transport and catabolism of 2,3- dihydroxypropane-1-sulfonate (DHPS). This compound has no currently recognized role in the marine microbial food web. As the genes for DHPS catabolism have limited distribution among bacterial taxa, T. pseudonana may use this novel sulfonate for targeted feeding of beneficial associates. Indeed, DHPS was both a major component of the T. pseudonana cytosol and an abundant microbial metabolite in a diatom bloom in the eastern North Pacific Ocean. Moreover, transcript analysis of the North Pacific samples provided evidence of DHPS catabolism by Roseobacter populations. Other such biogeochemically important metabolites may be common in the ocean but difficult to discriminate against the complex chemical background of seawater. Bacterial transformation of this diatom-derived sulfonate represents a new and likely sizeable link in both the marine carbon and sulfur cycles.
    Description: This research was partially funded by NSF grants OCE-1356010 to M.A.M., OCE-1205233 to E.V.A., OCE-0928424 to E.B.K., and OCE-1233964 to S.R.C., and by the Gordon and Betty Moore Foundation grants 538.01 to M.A.M. and 537.01 to E.V.A.
    Description: 2015-06-29
    Keywords: Diatoms ; Bacteria ; DHPS ; Sulfonates ; Vitamin B12 ; RNA-Seq
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
    Format: application/pdf
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 8
    facet.materialart.
    Unknown
    The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) : illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing (2014)
    Public Library of Science
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS Biology 12 (2014): e1001889, doi:10.1371/journal.pbio.1001889.
    Description: Microbial ecology is plagued by problems of an abstract nature. Cell sizes are so small and population sizes so large that both are virtually incomprehensible. Niches are so far from our everyday experience as to make their very definition elusive. Organisms that may be abundant and critical to our survival are little understood, seldom described and/or cultured, and sometimes yet to be even seen. One way to confront these problems is to use data of an even more abstract nature: molecular sequence data. Massive environmental nucleic acid sequencing, such as metagenomics or metatranscriptomics, promises functional analysis of microbial communities as a whole, without prior knowledge of which organisms are in the environment or exactly how they are interacting. But sequence-based ecological studies nearly always use a comparative approach, and that requires relevant reference sequences, which are an extremely limited resource when it comes to microbial eukaryotes. In practice, this means sequence databases need to be populated with enormous quantities of data for which we have some certainties about the source. Most important is the taxonomic identity of the organism from which a sequence is derived and as much functional identification of the encoded proteins as possible. In an ideal world, such information would be available as a large set of complete, well-curated, and annotated genomes for all the major organisms from the environment in question. Reality substantially diverges from this ideal, but at least for bacterial molecular ecology, there is a database consisting of thousands of complete genomes from a wide range of taxa, supplemented by a phylogeny-driven approach to diversifying genomics. For eukaryotes, the number of available genomes is far, far fewer, and we have relied much more heavily on random growth of sequence databases, raising the question as to whether this is fit for purpose.
    Description: This project was funded by the Gordon and Betty Moore Foundation (GBMF; Grants GBMF2637 and GBMF3111) to the National Center for Genome Resources (NCGR) and the National Center for Marine Algae and Microbiota (NCMA).
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/msword
    Format: application/pdf
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    PAPER (OA)
  • 9
    facet.materialart.
    Unknown
    Digital expression profiling of novel diatom transcripts provides insight into their biological functions (2010)
    BioMed Central
    In:  Genome Biology, 11 (8). R85.
    Details
    Publication Date: 2019-01-22
    Description: Background: Diatoms represent the predominant group of eukaryotic phytoplankton in the oceans and are responsible for around 20% of global photosynthesis. Two whole genome sequences are now available. Notwithstanding, our knowledge of diatom biology remains limited because only around half of their genes can be ascribed a function based onhomology-based methods. High throughput tools are needed, therefore, to associate functions with diatom-specific genes. Results: We have performed a systematic analysis of 130,000 ESTs derived from Phaeodactylum tricornutum cells grown in 16 different conditions. These include different sources of nitrogen, different concentrations of carbon dioxide, silicate and iron, and abiotic stresses such as low temperature and low salinity. Based on unbiased statistical methods, we have catalogued transcripts with similar expression profiles and identified transcripts differentially expressed in response to specific treatments. Functional annotation of these transcripts provides insights into expression patterns of genes involved in various metabolic and regulatory pathways and into the roles of novel genes with unknown functions. Specific growth conditions could be associated with enhanced gene diversity, known gene product functions, and over-representation of novel transcripts. Comparative analysis of data from the other sequenced diatom, Thalassiosira pseudonana, helped identify several unique diatom genes that are specifically regulated under particular conditions, thus facilitating studies of gene function, genome annotation and the molecular basis of species diversity. Conclusions: The digital gene expression database represents a new resource for identifying candidate diatom-specific genes involved in processes of major ecological relevance.
    Type: Article , PeerReviewed
    Format: text
    Format: other
    Format: text
    Format: other
    Format: other
    Format: text
    Format: other
    Format: other
    Format: image
    Format: other
    Format: text
    Format: text
    Format: text
    Format: other
    DOI: 10.1186/gb-2010-11-8-r85
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 10
    facet.materialart.
    Unknown
    SeaFlow data v1, high-resolution abundance, size and biomass of small phytoplankton in the North Pacific (2019)
    Nature Research
    In:  Scientific Data, 6 (1). Art.Nr. 277.
    Details
    Publication Date: 2022-01-31
    Description: SeaFlow is an underway flow cytometer that provides continuous shipboard observations of the abundance and optical properties of small phytoplankton (〈5 mu m in equivalent spherical diameter, ESD). Here we present data sets consisting of SeaFlow-based cell abundance, forward light scatter, and pigment fluorescence of individual cells, as well as derived estimates of ESD and cellular carbon content of picophytoplankton, which includes the cyanobacteria Prochlorococcus, Synechococcus and small-sized Crocosphaera (〈5 mu m ESD), and picophytoplankton and nanophytoplankton (2-5 mu m ESD). Data were collected in surface waters (approximate to 5 m depth) from 27 oceanographic cruises carried out in the Northeast Pacific Ocean between 2010 and 2018. Thirteen cruises provide high spatial resolution (approximate to 1 km) measurements across 32,500 km of the Northeast Pacific Ocean and 14 near-monthly cruises beginning in 2015 provide seasonal distributions at the long-term sampling site (Station ALOHA) of the Hawaii Ocean Time-Series. These data sets expand our knowledge of the current spatial and temporal distributions of picophytoplankton in the surface ocean.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1038/s41597-019-0292-2
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    OceanRep: Article in a Scientific Journal - peer-reviewed
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...