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  • 1
    Electronic Resource
    Electronic Resource
    Molecular Identification of Nanoplanktonic Protists Based on Small Subunit Ribosomal RNA Gene Sequences for Ecological Studies (1996)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 43 (1996), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Nanoplanktonic protists are comprised of a diverse assemblage of species which are responsible for a variety of trophic processes in marine and freshwater ecosystems. Current methods for identifying small protists by electron microscopy do not readily permit both identification and enumeration of nanoplanktonic protists in field samples. Thus, one major goal in the application of molecular approaches in protistan ecology has been the detection and quantification of individual species in natural water samples. Sequences of small subunit ribosomal RNA (SSU rRNA) genes have proven to be useful towards achieving this goal. Comparison of sequences from clone libraries of protistan SSU rRNA genes amplified from natural assemblages of protists by the polymerase chain reaction (PCR) can be used to examine protistan diversity. Furthermore, oligonucleotide probes complementary to short sequence regions unique to species of small protists can be designed by comparative analysis of rRNA gene sequences. These probes may be used to either detect the RNA of particular species of protists in total nucleic acid extracts immobilized on membranes, or the presence of target species in water samples via in situ hybridization of whole cells. Oligonucleotide probes may also serve as primers for the selective amplification of target sequences from total population DNA by PCR. Thus, molecular sequence information is becoming increasingly useful for identifying and enumerating protists, and for studying their spatial and temporal distribution in nature. Knowledge of protistan species composition, abundance and variability in an environment can ultimately be used to relate community structure to various aspects of community function and biogeochemical activity.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.1996.tb04488.x
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    Paper (German National Licenses)
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  • 2
    Electronic Resource
    Electronic Resource
    Identification of Heterotrophic Nanoflagellates by Restriction Fragment Length Polymorphism Analysis of Small Subunit Ribosomal DNA (2001)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 48 (2001), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: . Thirty clones derived from twenty isolates of heterotrophic nanoflagellates originating from a variety of marine and freshwater environments were examined by restriction fragment length polymorphism analysis of small subunit ribosomal RNA genes amplified by the polymerase chain reaction (riboprinting). The data were compared with light and electron microscopical identification of the isolates. On morphological criteria, sixteen of the thirty clones belonged to the genus Paraphysomonas De Saedeleer, seven to the genus Spumella Cienkowski, four to the genus Pteridomonas Penard and three to the genus Cafeteria Fenchel and Patterson. Among these taxa, eleven ribotypes were detected by analysis with the restriction enzymes Hinf I, Hae III, Sau 3A I, and Msp I. Differentiation of nanoflagellate taxa by the riboprinting method supported taxonomic classification based on morphology at the generic and species level. The utility of the method for discriminating the ‘naked’ flagellates and for confirming the identity of polymorphic forms among species of Paraphysomonas is demonstrated.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2001.tb00312.x
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  • 3
    Electronic Resource
    Electronic Resource
    Light-dependent phagotrophy in the freshwater mixotrophic chrysophyte Dinobryon cylindricum (1993)
    Springer
    Microbial ecology 25 (1993), S. 93-111 
    Details
    ISSN: 1432-184X
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The mixotrophic (bacterivorous), freshwater chrysophyte Dinobryon cylindricum was cultured under a variety of light regimes and in bacterized and axenic cultures to investigate the role of phototrophy and phagotrophy for the growth of this alga. D. cylindricum was found to be an obligate phototroph. The alga was unable to survive in continuous darkness even when cultures were supplemented with high concentrations of bacteria, and bacterivory ceased in cultures placed in the dark for a period longer than one day. Axenic growth of the alga was poor even in an optimal light regime. Live bacteria were required for sustained, vigorous growth of the alga in the light. Carbon (C), nitrogen (N), and phosphorus (P) budgets determined for the alga during growth in bacterized cultures indicated that bacterial biomass ingested by the alga may have contributed up to 25% of the organic carbon budget of the alga. Photosynthesis was the source of most (⩾75%) of the organic carbon of the alga. D. cylindricum populations survived but did not grow when cultured in a continuous low light intensity (30 μE m−2 sec−1), or in a light intensity of 150 μE m−2 sec−1 for only two hours each day. Net efficiency of incorporation of bacterial C, N, and P into algal biomass under these two conditions was zero (i.e., no net algal population growth). We conclude that the primary function of bacterivorous behavior in D. cylindricum may be to provide essential growth factor(s) or major nutrients for photosynthetic growth, or to allow for the survival of individuals during periods of very low light intensity or short photoperiod.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00182132
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  • 4
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    Diversity and dynamics of a North Atlantic coastal Vibrio community (2005)
    American Society for Microbiology
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Society for Microbiology, 2004. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 70 (2004): 4103-4110, doi:10.1128/AEM.70.7.4103-4110.2004.
    Description: Vibrios are ubiquitous marine bacteria that have long served as models for heterotrophic processes and have received renewed attention because of the discovery of increasing numbers of facultatively pathogenic strains. Because the occurrence of specific vibrios has frequently been linked to the temperature, salinity, and nutrient status of water, we hypothesized that seasonal changes in coastal water bodies lead to distinct vibrio communities and sought to characterize their level of differentiation. A novel technique was used to quantify shifts in 16S rRNA gene abundance in samples from Barnegat Bay, N.J., collected over a 15-month period. Quantitative PCR (QPCR) with primers specific for the genus Vibrio was combined with separation and quantification of amplicons by constant denaturant capillary electrophoresis (CDCE). Vibrio populations identified by QPCR-CDCE varied between summer and winter samples, suggesting distinct warm-water and year-round populations. Identification of the CDCE populations by cloning and sequencing of 16S rRNA genes from two summer and two winter samples confirmed this distinction. It further showed that CDCE populations corresponded in most cases to ~98% rRNA similarity groups and suggested that the abundance of these follows temperature trends. Phylogenetic comparison yielded closely related cultured and often pathogenic representatives for most sequences, and the temperature ranges of these isolates confirmed the trends seen in the environmental samples. Overall, this suggests that temperature is a good predictor of the occurrence of closely related vibrios but that considerable microdiversity of unknown significance coexists within this trend.
    Description: Funding was for this study was provided by grants from Seagrant and NOAA to M.F.P. and graduate fellowships from the National Science Foundation, the Switzer Environmental Science Foundation, and the Whittaker Health Sciences Foundation to J.R.T.
    Keywords: Vibrios ; Marine bacteria
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: 601108 bytes
    Format: application/pdf
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  • 5
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    New insights on the ecology of free-living heterotrophic nanoflagellates based on the use of molecular biological approaches (2013)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-05-25
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution March 1997
    Description: Nanoplanktonic protists comprise a diverse assemblage of flagellate species responsible for various trophic processes in marine and freshwater ecosystems. Current methods for identifying small protists do not readily permit identification and enumeration of nanoplanktonic flagellates in cultures or field samples. The aim of this study was to apply molecular biological techniques for identification and enumeration of nanoflagellate taxa in water samples. Restriction fragment length polymorphism (RFLP) analysis of small subunit ribosomal DNA (SSU rONA) amplified by the polymerase chain reaction (PCR) differentiated pure cultures of heterotrophic nanoflagellates according to established taxonomic classification at the generic and species level. In addition, RFLP analysis of amplified SSU rONA permitted discrimination of polymorphic forms among species of flagellates from the genus Paraphysomonas. A fluorescent in situ hybridization method that uses rRNA-targeted oligonucleotide probes for counting protists from cultures and environmental water samples was developed. Preserved cells were intensely labeled with multiple eukaryote-specific oligonucleotide probes end-labeled with biotin and detected by fluorescein (FITC)-avidin. This probe hybridization method gave estimates of nanoplankton abundances that were often more representative of natural abundances than estimates obtained by commonly employed fluorochrome stains. The geographical distribution and seasonal abundance of the cosmopolitan heterotrophic flagellate, Paraphysomonas imperforata was examined in coastal waters using species-specific oligonucleotide probes. P. imperforata was found to occur at extremely low abundances in coastal environments, constituting ≤1% of the TNAN. However, P. imperforata often dominated the nanoplankton (up to 98% of TNAN) when water samples were enriched with bacteria. P. imperforata appears to be an opportunistic species capable of growing rapidly to high abundances when prey are abundant. Water temperature, small differences in the absolute abundance of P. imperforata, and nanoplankton grazers appeared to play a role in determining P. imperforata dominance. Results from this study also suggest that enrichment cultivation or perhaps incubations in general can select for nanoflagellates such as P. imperforata that may not be representative of abundant oceanic species.
    Keywords: Protista ; RNA
    Repository Name: Woods Hole Open Access Server
    Type: Thesis
    Format: application/pdf
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  • 6
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    Heterotrophic and mixotrophic nanoplankton predation on picoplankton in the Saragasso Sea and on Georges Bank. (2000)
    Inter Research
    In:  Marine Ecology Progress Series, 192 . pp. 103-118.
    Details
    Publication Date: 2018-05-08
    Description: Nanoplankton and picoplankton abundance and community grazing on picoplankton were determined in summer and autumn at several stations in a productive coastal environment (Georges Bank, NW Atlantic Ocean) and in an oligotrophic oceanic ecosystem (Sargasso Sea). Ranges of heterotrophic nanoplankton (HNAN) abundance were 1.2 to 3.6 x 103 cells ml-1 on Georges Bank, and 2.2 to 6.8 x 102 cells ml-1 in the Sargasso Sea. Ranges of phototrophic nanoplankton (PNAN) abundance in these ecosystems were 1.9 to 6.0 x 103 and 1.3 to 4.7 x 102, respectively. Mixotrophic nanoplankton (MNAN), operationally defined here as chloroplast-bearing nanoplankton that ingested fluorescent tracers, comprised an average of 12 to 17% of PNAN in surface waters in both environments during August and October. Mixotrophs at specific stations constituted as much as 38% of total PNAN abundance on Georges Bank and 30% in the Sargasso Sea. Mixotrophs represented up to 39% of the total phagotrophic nanoplankton abundance (MNAN/[MNAN + HNAN]). Community grazing impact was estimated from the disappearance of fluorescent prey surrogates (fluorescently labeled bacteria, FLB; cyanobacteria, FLC; and 〈\3 µm algae, FLA). Absolute grazing rates (total picoplankton cells removed d-1) on Georges Bank exceeded those in the Sargasso Sea due to the greater abundances of predators and prey. However, there was overlap in the specific grazing losses at the 2 sites (ranges = 0.08 to 0.38 d-1 in the coastal ocean and 0.05 to 0.24 d-1 in the oligotrophic ocean). Rates of bacterivory were in approximate balance with rates of bacterial production (3H-thymidine uptake), but production exceeded bacterivory on Georges Bank during the summer cruise. These data are among the first documenting the impact of grazing on picoplankton in these environments, and they are consistent with the prediction that nanoplanktonic protists are major predators of picoplankton. While the proportion of phototrophs that are phagotrophic was highly variable, our study indicates that algal mixotrophy is widespread in the marine environment, occurring in both coastal and oligotrophic sites, and should be considered quantitatively in microbial food web investigations.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.3354/meps192103
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    OceanRep: Article in a Scientific Journal - peer-reviewed
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