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  • 1
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Science Inc
    The @journal of eukaryotic microbiology 52 (2005), S. 0 
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The genome size of marine phytoplankton is in the order of 106–1011 base pairs. Within the phytoplankton it has often been assumed that dinoflagellates have extraordinarily large genomes that significantly contribute to their nutrient requirements. We test this hypothesis by compiling cell size and genome size data from across many phytoplankton lineages, and apply a simple regression model. Our results suggest that dinoflagellates do not have anomalously large genomes, but instead scale with cell size with the same slope and intercept as many other diverse phytoplankton taxa. Based on the known correlations of genome size and genome content in diverse taxa, we model the approximate expected genome structure in unsequenced lineages of marine phytoplankton. Based on this model, we hypothesize that retrotransposons play a significant role in genome size in marine phytoplankton.
    Type of Medium: Electronic Resource
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  • 2
    Publication Date: 2016-04-07
    Description: Phosphorous is a proximal limiting nutrient in certain oceanic regions. We studied the seasonal dynamics of inorganic and organic phosphorous utilisation over a one-year period (2012) in the NW Mediterranean. 33P-labelled bioassays and flow sorting experiments were combined to address the seasonality in turnover, concentration and uptake rates of phosphate, ATP and DNA by dominant microbial groups. In parallel, 454 pyrosequencing was conducted to link changes in phosphorus substrate utilisation to prokaryotic community composition. Although increases in organic phosphorous utilisation correspond to short phosphate turnover times, phosphate uptake also increases to the extent that the majority of community phosphorous flux is channelled through the inorganic pool, irrespective of the degree of phosphate limitation. Bacteria maintain a fairly uniform pattern phosphorous substrate utilisation throughout the year. In contrast, Synechococcus and Eukaryotic populations rely increasingly on organic phosphorous substrates during times of extreme phosphate limitation. Sequencing data is employed to elucidate whether the observed patterns in substrate utilisation correspond to metabolic flexibility of a dominant ecotype or community dynamics of Synechococcus ecotypes adapted to different phosphorous acquisition strategies.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Conference , notRev
    Format: application/pdf
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  • 3
    Publication Date: 2016-04-07
    Description: A seven-year oceanographic time series in NW Mediterranean surface waters was combined with pyrosequencing of ribosomal RNA (16S rRNA) and ribosomal RNA gene copies (16S rDNA) to examine the environmental controls on SAR11 ecotype dynamics and potential activity. SAR11 diversity exhibited pronounced seasonal cycles remarkably similar to total bacterial diversity. The timing of diversity maxima was similar across narrow and broad phylogenetic clades and strongly associated with deep winter mixing. Diversity minima were associated with periods of stratification that were low in nutrients and phytoplankton biomass and characterised by intense phosphate limitation (turnover time〈5 h). We propose a conceptual framework in which physical mixing of the water column periodically resets SAR11 communities to a high diversity state and the seasonal evolution of phosphate limitation competitively excludes deeper-dwelling ecotypes to promote low diversity states dominated (〉80%) by SAR11 Ia. A partial least squares (PLS) regression model was developed that could reliably predict sequence abundances of SAR11 ecotypes (Q2=0.70) from measured environmental variables, of which mixed layer depth was quantitatively the most important. Comparison of clade-level SAR11 rRNA:rDNA signals with leucine incorporation enabled us to partially validate the use of these ratios as an in-situ activity measure. However, temporal trends in the activity of SAR11 ecotypes and their relationship to environmental variables were unclear. The strong and predictable temporal patterns observed in SAR11 sequence abundance was not linked to metabolic activity of different ecotypes at the phylogenetic and temporal resolution of our study.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 4
    Publication Date: 2022-05-26
    Description: © The Author(s), [year]. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Carvalho, F., Gorbunov, M. Y., Oliver, M. J., Haskins, C., Aragon, D., Kohut, J. T., & Schofield, O. FIReglider: mapping in situ chlorophyll variable fluorescence with autonomous underwater gliders. Limnology and Oceanography: Methods, (2020), doi:10.1002/lom3.10380.
    Description: Nutrient and light availability regulate phytoplankton physiology and photosynthesis in the ocean. These physiological processes are difficult to sample in time and space over physiologically and ecologically relevant scales using traditional shipboard techniques. Gliders are changing the nature of data collection, by allowing a sustained presence at sea over regional scales, collecting data at resolution not possible using traditional techniques. The integration of a fluorescence induction and relaxation (FIRe) sensor in a Slocum glider allows autonomous high‐resolution and vertically‐resolved measurements of photosynthetic physiological variables together with oceanographic data. In situ measurements of variable fluorescence under ambient light allows a better understanding of the physical controls of primary production (PP). We demonstrate this capability in a laboratory setting and with several glider deployments in the Southern Ocean. Development of these approaches will allow for the in situ evaluation of phytoplankton light stress and photoacclimation mechanisms, as well as the role of vertical mixing in phytoplankton dynamics and the underlying physiology, especially in remote locations and for prolonged duration.
    Description: This work was supported by National Science Foundation (NSF Palmer LTER program, grant 0823101), National Oceanographic Partnership Program (NOPP, grant NA05OAR4601089), and NASA Ocean Biology and Biogeochemistry Program (grants NNX16AT54G and 80NSSC18K1416). Filipa Carvalho was funded by a Portuguese doctoral fellowship from Fundação para a Ciência e Tecnologia (FCT, grant DFRH ‐ SFRH/BD/72705/2010), a Teledyne Marine Graduate Fellowship and a European Research Council Consolidator grant (GOCART, agreement number 724416).
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 5
    Publication Date: 2022-05-26
    Description: © International Council for the Exploration of the Sea, 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ICES Journal of Marine Science 73 (2016): 1839-1850, doi: 10.1093/icesjms/fsw086.
    Description: For terrestrial and marine benthic ecologists, landscape ecology provides a framework to address issues of complexity, patchiness, and scale—providing theory and context for ecosystem based management in a changing climate. Marine pelagic ecosystems are likewise changing in response to warming, changing chemistry, and resource exploitation. However, unlike spatial landscapes that migrate slowly with time, pelagic seascapes are embedded in a turbulent, advective ocean. Adaptations from landscape ecology to marine pelagic ecosystem management must consider the nature and scale of biophysical interactions associated with organisms ranging from microbes to whales, a hierarchical organization shaped by physical processes, and our limited capacity to observe and monitor these phenomena across global oceans. High frequency, multiscale, and synoptic characterization of the 4-D variability of seascapes are now available through improved classification methods, a maturing array of satellite remote sensing products, advances in autonomous sampling of multiple levels of biological complexity, and emergence of observational networks. Merging of oceanographic and ecological paradigms will be necessary to observe, manage, and conserve species embedded in a dynamic seascape mosaic, where the boundaries, extent, and location of features change with time.
    Description: This work was supported by NASA grant NNX14AP62A “National Marine Sanctuaries as Sentinel Sites for a Demonstration Marine Biodiversity Observation Network (MBON)” funded under the National Ocean Partnership Program (NOPP RFP NOAA-NOS-IOOS-2014-2003803 in partnership between NOAA, BOEM, and NASA), the NOAA Integrated Ocean Observing System (IOOS) Program Office, and the LenFest Ocean Program.
    Keywords: Biodiversity ; Conservation ; Landscape ; Ocean observations ; Pelagic ; Phytoplankton ; Seascape
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 6
    Publication Date: 2015-03-05
    Description: Nature Structural & Molecular Biology 22, 272 (2015). doi:10.1038/nsmb0315-272b Author: Jennifer Y Tan, Keith W Vance, Miguel A Varela, Tamara Sirey, Lauren M Watson, Helen J Curtis, Martina Marinello, Sandro Alves, Bruno R Steinkraus, Sarah Cooper, Tatyana Nesterova, Neil Brockdorff, Tudor A Fulga, Alexis Brice, Annie Sittler, Peter L Oliver, Matthew J Wood, Chris P Ponting & Ana C Marques
    Print ISSN: 1545-9993
    Electronic ISSN: 1545-9985
    Topics: Biology , Medicine
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  • 7
    Publication Date: 2014-11-06
    Description: Nature Structural & Molecular Biology 21, 955 (2014). doi:10.1038/nsmb.2902 Authors: Jennifer Y Tan, Keith W Vance, Miguel A Varela, Tamara Sirey, Lauren M Watson, Helen J Curtis, Martina Marinello, Sandro Alves, Bruno R Steinkraus, Sarah Cooper, Tatyana Nesterova, Neil Brockdorff, Tudor A Fulga, Alexis Brice, Annie Sittler, Peter L Oliver, Matthew J Wood, Chris P Ponting & Ana C Marques
    Print ISSN: 1545-9993
    Electronic ISSN: 1545-9985
    Topics: Biology , Medicine
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