GLORIA

GEOMAR Library Ocean Research Information Access

X

Your email was sent successfully. Check your inbox.

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

Proceed reservation?

Export
  • 1
    Online Resource
    Online Resource
    Cyanorak v2.1: a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes
    Oxford University Press (OUP) ; 2021
    In:  Nucleic Acids Research Vol. 49, No. D1 ( 2021-01-08), p. D667-D676
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 49, No. D1 ( 2021-01-08), p. D667-D676
    Abstract: Cyanorak v2.1 (http://www.sb-roscoff.fr/cyanorak) is an information system dedicated to visualizing, comparing and curating the genomes of Prochlorococcus, Synechococcus and Cyanobium, the most abundant photosynthetic microorganisms on Earth. The database encompasses sequences from 97 genomes, covering most of the wide genetic diversity known so far within these groups, and which were split into 25,834 clusters of likely orthologous groups (CLOGs). The user interface gives access to genomic characteristics, accession numbers as well as an interactive map showing strain isolation sites. The main entry to the database is through search for a term (gene name, product, etc.), resulting in a list of CLOGs and individual genes. Each CLOG benefits from a rich functional annotation including EggNOG, EC/K numbers, GO terms, TIGR Roles, custom-designed Cyanorak Roles as well as several protein motif predictions. Cyanorak also displays a phyletic profile, indicating the genotype and pigment type for each CLOG, and a genome viewer (Jbrowse) to visualize additional data on each genome such as predicted operons, genomic islands or transcriptomic data, when available. This information system also includes a BLAST search tool, comparative genomic context as well as various data export options. Altogether, Cyanorak v2.1 constitutes an invaluable, scalable tool for comparative genomics of ecologically relevant marine microorganisms.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkaa958
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 1472175-2
    SSG: 12
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 2
    Online Resource
    Online Resource
    From egg to maturity: a closed system for complete life cycle studies of the holopelagic jellyfish Pelagia noctiluca
    Oxford University Press (OUP) ; 2019
    In:  Journal of Plankton Research Vol. 41, No. 3 ( 2019-05-31), p. 207-217
    Details
    In: Journal of Plankton Research, Oxford University Press (OUP), Vol. 41, No. 3 ( 2019-05-31), p. 207-217
    Abstract: Despite its wide spatial distribution and its high abundance in the Mediterranean Sea, the biology and the ecology of the scyphozoan species Pelagia noctiluca remain poorly understood. This is mainly due to difficulties related to sampling and its maintenance in laboratory conditions. Thus, only a few studies exist on the ecophysiology of this jellyfish species under laboratory conditions. As an example, the maximum sizes of individuals obtained in previous culturing systems were not comparable to the ones found in the environment and the authors could not obtain a second generation. Here we present an improved rearing system for P. noctiluca employing a new enclosed system running with artificial seawater. The monitoring of the jellyfish in this new system highlights the importance of the quality of the food sources provided to the cultures, as well as the volume available for jellyfish growth. We obtain adults similar in size to the ones found in the open ocean ( 〉 11 cm), and we were able to obtain a second generation, 140 days after the first one. Our system is both less time-consuming and less stressful for the jellyfish.
    Type of Medium: Online Resource
    ISSN: 0142-7873 , 1464-3774
    URL: Article
    DOI: 10.1093/plankt/fbz013
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 756271-8
    detail.hit.zdb_id: 1474909-9
    SSG: 12
    SSG: 21,3
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 3
    Online Resource
    Online Resource
    Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies
    Springer Science and Business Media LLC ; 2023
    In:  The ISME Journal Vol. 17, No. 5 ( 2023-05), p. 720-732
    Details
    In: The ISME Journal, Springer Science and Business Media LLC, Vol. 17, No. 5 ( 2023-05), p. 720-732
    Abstract: The ever-increasing number of available microbial genomes and metagenomes provides new opportunities to investigate the links between niche partitioning and genome evolution in the ocean, especially for the abundant and ubiquitous marine picocyanobacteria Prochlorococcus and Synechococcus . Here, by combining metagenome analyses of the Tara Oceans dataset with comparative genomics, including phyletic patterns and genomic context of individual genes from 256 reference genomes, we show that picocyanobacterial communities thriving in different niches possess distinct gene repertoires. We also identify clusters of adjacent genes that display specific distribution patterns in the field (eCAGs) and are thus potentially involved in the same metabolic pathway and may have a key role in niche adaptation. Several eCAGs are likely involved in the uptake or incorporation of complex organic forms of nutrients, such as guanidine, cyanate, cyanide, pyrimidine, or phosphonates, which might be either directly used by cells, for example for the biosynthesis of proteins or DNA, or degraded to inorganic nitrogen and/or phosphorus forms. We also highlight the enrichment of eCAGs involved in polysaccharide capsule biosynthesis in Synechococcus populations thriving in both nitrogen- and phosphorus-depleted areas vs. low-iron (Fe) regions, suggesting that the complexes they encode may be too energy-consuming for picocyanobacteria thriving in the latter areas. In contrast, Prochlorococcus populations thriving in Fe-depleted areas specifically possess an alternative respiratory terminal oxidase, potentially involved in the reduction of Fe(III) to Fe(II). Altogether, this study provides insights into how phytoplankton communities populate oceanic ecosystems, which is relevant to understanding their capacity to respond to ongoing climate change.
    Type of Medium: Online Resource
    ISSN: 1751-7362 , 1751-7370
    URL: Article
    DOI: 10.1038/s41396-023-01386-0
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
    detail.hit.zdb_id: 2299378-2
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
  • 4
    Online Resource
    Online Resource
    Table_2.XLSX
    Frontiers Media SA ; 2022
    In:  Frontiers in Microbiology Vol. 13 ( 2022-5-9)
    Details
    In: Frontiers in Microbiology, Frontiers Media SA, Vol. 13 ( 2022-5-9)
    Abstract: Marine Synechococcus cyanobacteria are ubiquitous in the ocean, a feature likely related to their extensive genetic diversity. Amongst the major lineages, clades I and IV preferentially thrive in temperate and cold, nutrient-rich waters, whilst clades II and III prefer warm, nitrogen or phosphorus-depleted waters. The existence of such cold (I/IV) and warm (II/III) thermotypes is corroborated by physiological characterization of representative strains. A fifth clade, CRD1, was recently shown to dominate the Synechococcus community in iron-depleted areas of the world ocean and to encompass three distinct ecologically significant taxonomic units (ESTUs CRD1A-C) occupying different thermal niches, suggesting that distinct thermotypes could also occur within this clade. Here, using comparative thermophysiology of strains representative of these three CRD1 ESTUs we show that the CRD1A strain MITS9220 is a warm thermotype, the CRD1B strain BIOS-U3-1 a cold temperate thermotype, and the CRD1C strain BIOS-E4-1 a warm temperate stenotherm. Curiously, the CRD1B thermotype lacks traits and/or genomic features typical of cold thermotypes. In contrast, we found specific physiological traits of the CRD1 strains compared to their clade I, II, III, and IV counterparts, including a lower growth rate and photosystem II maximal quantum yield at most temperatures and a higher turnover rate of the D1 protein. Together, our data suggests that the CRD1 clade prioritizes adaptation to low-iron conditions over temperature adaptation, even though the occurrence of several CRD1 thermotypes likely explains why the CRD1 clade as a whole occupies most iron-limited waters.
    Type of Medium: Online Resource
    ISSN: 1664-302X
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fmicb.2022.893413
    DOI: 10.3389/fmicb.2022.893413.s001
    DOI: 10.3389/fmicb.2022.893413.s002
    DOI: 10.3389/fmicb.2022.893413.s003
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2022
    detail.hit.zdb_id: 2587354-4
    Location Call Number Limitation Availability
    BibTip Others were also interested in ...
    Online Resource
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...