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  • 1
    Online Resource
    Online Resource
    Picoeukaryote Plankton Composition off West Spitsbergen at the Entrance to the Arctic Ocean
    Wiley ; 2014
    In:  Journal of Eukaryotic Microbiology Vol. 61, No. 6 ( 2014-11), p. 569-579
    Details
    In: Journal of Eukaryotic Microbiology, Wiley, Vol. 61, No. 6 ( 2014-11), p. 569-579
    Abstract: Investigation of marine eukaryotic picoplankton composition is limited by missing morphological features for appropriate identification. Consequently, molecular methods are required. In this study, we used 454‐pyrosequencing to study picoplankton communities at four stations in the West Spitsbergen Current ( WSC ; Fram Strait). High abundances of Micromonas pusilla were detected in the station situated closest to Spitsbergen, as seen in surveys of picoplankton assemblages in the Beaufort Sea. At the other three stations, other phylotypes, affiliating with Phaeocystis pouchetii and Syndiniales in the phylogenetic tree, were present in high numbers, dominating most of them. The picoplankton community structures at three of the stations, all with similar salinity and temperature, were alike. At the fourth station, the influence of the East Spitsbergen Current, transporting cold water from the Barents Sea around Spitsbergen, causes different abiotic parameters that result in a significantly different picoeukaryote community composition, which is dominated by M. pusilla . This observation is particularly interesting with regard to ongoing environmental changes in the Arctic. Ongoing warming of the WSC could convey a new picoplankton assemblage into the Arctic Ocean, which may come to affect the dominance of M. pusilla .
    Type of Medium: Online Resource
    ISSN: 1066-5234 , 1550-7408
    URL: Issue
    URL: Article
    DOI: 10.1111/jeu.2014.61.issue-6
    DOI: 10.1111/jeu.12134
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2014
    detail.hit.zdb_id: 2126326-7
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Feasibility of Transferring Fluorescent In Situ Hybridization Probes to an 18S rRNA Gene Phylochip and Mapping of Signal Intensities
    American Society for Microbiology ; 2008
    In:  Applied and Environmental Microbiology Vol. 74, No. 9 ( 2008-05), p. 2814-2821
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 74, No. 9 ( 2008-05), p. 2814-2821
    Abstract: DNA microarray technology offers the possibility to analyze microbial communities without cultivation, thus benefiting biodiversity studies. We developed a DNA phylochip to assess phytoplankton diversity and transferred 18S rRNA probes from dot blot or fluorescent in situ hybridization (FISH) analyses to a microarray format. Similar studies with 16S rRNA probes have been done determined that in order to achieve a signal on the microarray, the 16S rRNA molecule had to be fragmented, or PCR amplicons had to be 〈 150 bp in length to minimize the formation of a secondary structure in the molecule so that the probe could bind to the target site. We found different results with the 18S rRNA molecule. Four out of 12 FISH probes exhibited false-negative signals on the microarray; eight exhibited strong but variable signals using full-length 18S RNA molecules. A systematic investigation of the probe's accessibility to the 18S rRNA gene was made using Prymenisum parvum as the target. Fourteen additional probes identical to this target covered the regions not tested with existing FISH probes. Probes with a binding site in the first 900 bp of the gene generated positive signals. Six out of nine probes binding in the last 900 bp of the gene produced no signal. Our results suggest that although secondary structure affected probe binding, the effect is not the same for the 18S rRNA gene and the 16S rRNA gene. For the 16S rRNA gene, the secondary structure is stronger in the first half of the molecule, whereas in the 18S rRNA gene, the last half of the molecule is critical. Probe-binding sites within 18S rRNA gene molecules are important for the probe design for DNA phylochips because signal intensity appears to be correlated with the secondary structure at the binding site in this molecule. If probes are designed from the first half of the 18S rRNA molecule, then full-length 18S rRNA molecules can be used in the hybridization on the chip, avoiding the fragmentation and the necessity for the short PCR amplicons that are associated with using the 16S rRNA molecule. Thus, the 18S rRNA molecule is a more attractive molecule for use in environmental studies where some level of quantification is desired. Target size was a minor problem, whereas for 16S rRNA molecules target size rather than probe site was important.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.02122-07
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2008
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    CONTRIBUTION OF THE CLASS CRYPTOPHYCEAE TO PHYTOPLANKTON STRUCTURE IN THE GERMAN BIGHT1 : CRYPTOPHYTE SEASONALITY IN THE NORTH SEA
    Wiley ; 2010
    In:  Journal of Phycology Vol. 46, No. 6 ( 2010-12), p. 1152-1160
    Details
    In: Journal of Phycology, Wiley, Vol. 46, No. 6 ( 2010-12), p. 1152-1160
    Type of Medium: Online Resource
    ISSN: 0022-3646
    URL: Article
    DOI: 10.1111/j.1529-8817.2010.00902.x
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2010
    detail.hit.zdb_id: 281226-5
    detail.hit.zdb_id: 1478748-9
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Pilot study of an EST approach of the coccolithophorid Emiliania huxleyi during a virus infection
    Elsevier BV ; 2007
    In:  Gene Vol. 406, No. 1-2 ( 2007-12), p. 209-216
    Details
    In: Gene, Elsevier BV, Vol. 406, No. 1-2 ( 2007-12), p. 209-216
    Type of Medium: Online Resource
    ISSN: 0378-1119
    URL: Article
    DOI: 10.1016/j.gene.2007.10.007
    RVK:
    WA 15000
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2007
    detail.hit.zdb_id: 1491012-3
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    Feasibility of Assessing the Community Composition of Prasinophytes at the Helgoland Roads Sampling Site with a DNA Microarray
    American Society for Microbiology ; 2008
    In:  Applied and Environmental Microbiology Vol. 74, No. 17 ( 2008-09), p. 5305-5316
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 74, No. 17 ( 2008-09), p. 5305-5316
    Abstract: The microalgal class Prasinophyceae (Chlorophyta) contains several picoeukaryotic species, which are known to be common in temperate and cold waters and have been observed to constitute major fractions of marine picoplankton. However, reliable detection and classification of prasinophytes are mainly hampered by their small size and few morphological markers. Consequently, very little is known about the abundance and ecology of the members of this class. In order to facilitate the assessment of the abundance of the Prasinophyceae, we have designed and evaluated an 18S rRNA gene-targeted oligonucleotide microarray consisting of 21 probes targeting different taxonomic levels of prasinophytes. The microarray contains both previously published probes from other hybridization methods and new probes, which were designed for novel prasinophyte groups. The evaluation of the probe set was done under stringent conditions with 18S PCR fragments from 20 unialgal reference cultures used as positive targets. This microarray has been applied to assess the community composition of prasinophytes at Helgoland, an island in the North Sea where time series data are collected and analyzed daily but only for the nano- and microplankton-size fractions. There is no identification of prasinophytes other than to record them numerically in the flagellate fraction. The samples were collected every 2 weeks between February 2004 and December 2006. The study here demonstrates the potential of DNA microarrays to be applied as a tool for quick general monitoring of this important picoplanktonic algal group.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.01271-08
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2008
    detail.hit.zdb_id: 223011-2
    detail.hit.zdb_id: 1478346-0
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    Protist distribution in the Western Fram Strait in summer 2010 based on 454‐pyrosequencing of 18S rDNA
    Wiley ; 2013
    In:  Journal of Phycology Vol. 49, No. 5 ( 2013-10), p. 996-1010
    Details
    In: Journal of Phycology, Wiley, Vol. 49, No. 5 ( 2013-10), p. 996-1010
    Abstract: In this study, we present the first comprehensive analyses of the diversity and distribution of marine protist (micro‐, nano‐, and picoeukaryotes) in the Western Fram Strait, using 454‐pyrosequencing and high‐pressure liquid chromatography ( HPLC ) at five stations in summer 2010. Three stations (T1; T5; T7) were influenced by Polar Water, characterized by cold water with lower salinity ( 〈 33) and different extents of ice concentrations. Atlantic Water influenced the other two stations (T6; T9). While T6 was located in the mixed water zone characterized by cold water with intermediate salinity (~33) and high ice concentrations, T9 was located in warm water with high salinity (~35) and no ice‐coverage at all. General trends in community structure according to prevailing environmental settings, observed with both methods, coincided well. At two stations, T1 and T7, characterized by lower ice concentrations, diatoms ( F ragilariopsis sp. , P orosira sp., T halassiosira spp.) dominated the protist community. The third station (T5) was ice‐covered, but has been ice‐free for ~4 weeks prior to sampling. At this station, dinoflagellates ( D inophyceae 1, W oloszynskia sp. and G yrodinium sp.) were dominant, reflecting a post‐bloom situation. At station T6 and T9, the protist communities consisted mainly of picoeukaryotes, e.g., M icromonas spp. Based on our results, 454‐pyrosequencing has proven to be an adequate tool to provide comprehensive information on the composition of protist communities. Furthermore, this study suggests that a snap‐shot of a few, but well‐chosen samples can provide an overview of community structure patterns and succession in a dynamic marine environment.
    Type of Medium: Online Resource
    ISSN: 0022-3646 , 1529-8817
    URL: Issue
    URL: Article
    DOI: 10.1111/jpy.2013.49.issue-5
    DOI: 10.1111/jpy.12109
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2013
    detail.hit.zdb_id: 281226-5
    detail.hit.zdb_id: 1478748-9
    SSG: 12
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  • 7
    Online Resource
    Online Resource
    DNA microchips for phytoplankton: The fluorescent wave of the future
    Schweizerbart ; 2004
    In:  Nova Hedwigia Vol. 79, No. 1-2 ( 2004-08-01), p. 321-327
    Details
    In: Nova Hedwigia, Schweizerbart, Vol. 79, No. 1-2 ( 2004-08-01), p. 321-327
    Type of Medium: Online Resource
    ISSN: 0029-5035
    Uniform Title: DNA microchips for phytoplankton: The fluorescent wave of the future
    URL: Article
    DOI: 10.1127/0029-5035/2004/0079-0321
    RVK:
    WA 15000
    Language: English , English
    Publisher: Schweizerbart
    Publication Date: 2004
    detail.hit.zdb_id: 2075554-5
    detail.hit.zdb_id: 2408-9
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    Limited sinking of Phaeocystis during a 12 days sediment trap study
    Wiley ; 2016
    In:  Molecular Ecology Vol. 25, No. 14 ( 2016-07), p. 3428-3435
    Details
    In: Molecular Ecology, Wiley, Vol. 25, No. 14 ( 2016-07), p. 3428-3435
    Abstract: There is a controversy discussion about the contribution of the genus Phaeocystis to the vertical carbon export with evidence for and against sedimentation of Phaeocystis . So far, the presence of Phaeocystis in sinking matter was investigated with methods depending on morphological features (microscopy) and fast degradable substances (biochemical analyses). In this study, we determine the occurrence and abundance of Phaeocystis antarctica in short‐term sediment traps and the overlying water column during a 12‐day time period in the Atlantic sector of the Southern Ocean with 454‐pyrosequencing and microscopy counting. In the sediment trap samples, we only found few sequences belonging to Phaeocystis , which was not reflecting the situation in the water column above. The cell counts showed the same results. We conclude that Phaeocystis cells are not generally transported downwards by active sinking or other sinking processes.
    Type of Medium: Online Resource
    ISSN: 0962-1083 , 1365-294X
    URL: Issue
    URL: Article
    DOI: 10.1111/mec.2016.25.issue-14
    DOI: 10.1111/mec.13697
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2016
    detail.hit.zdb_id: 2020749-9
    detail.hit.zdb_id: 1126687-9
    SSG: 12
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