1,720,987 research outputs found
Coexistence of dominant groups in marine bacterioplankton community - a combination of experimental and modelling approaches
No full textThe population dynamics in the coastal bacterioplankton community off Plymouth (UK) was studied in samples proportionally diluted (99%, 90%, 66% and 0%) with sterile seawater, incubated in the dark for 2–4 days and monitored by flow cytometry. Nucleic acid content of cells, stained with SYBR Green I DNA specific dye, was used as an index of a genome size. Using flow sorting and fluorescence in situ hybridization (FISH) with a set of ribosomal RNA targeted oligonucleotide probes, the phylogenetic composition of dominant cytometric groups of bacterioplankton was determined to be similar during growth in the dilution series. The proportion of the low nucleic acid (LNA) group decreased and correspondingly the high nucleic acid (HNA) groups increased with dilution. The assimilation rates of free amino acids, a highly labile nutrient pool, were determined by flow sorting the dominant groups after short incubations with 35S-methionine tracer. The relative cellular amino acid assimilation by the LNA cells increased with dilution, while the activity of the HNA cells either decreased or remained unchanged. However, highly metabolically active LNA bacteria were overgrown by the HNA bacteria, presumably because the small genome size—an adaptation to living in an oligotrophic environment—did not allow the LNA group to grow sufficiently fast to compete with the HNA group under experimentally reduced grazing pressure. To examine the experimental results a numerical model of bacterioplankton population dynamics was formulated based on the hypothesis that the LNA cells consume only a labile fraction of organic nutrients (amino acids etc.), while the HNA cells feed on both the labile and more refractory sources of nutrients, and that in the absence of phytoplankton the labile source of nutrients is produced entirely by the bacterivorous flagellates. The model simulations gave credence to the hypothesized primary dependence of the LNA group on labile organic nutrients recycled within the microbial loop
Changes in community composition during dilution cultures of marine bacterioplankton as assessed by flow cytometric and molecular biological techniques
No full textDilution cultures are a common technique for measuring the growth of bacterioplankton communities. In this study, the taxonomic composition of marine bacterioplankton dilution cultures was followed in water samples from Plymouth Sound and the English Channel (UK). Bacterial abundances as well as protein and DNA content were closely monitored by flow cytometry. Denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified 16S rDNA fragments and fluorescence in situ hybridization (FISH) were applied directly to the water samples and to cells sorted from the dilution cultures based on their protein and DNA content. As expected, a rapid activation of bacteria occurred. However, molecular techniques showed that the community developed in the dilution culture within 1 day was significantly different from that in the original water samples. Whereas in the original samples, cells detectable by FISH were dominated by members of the Cytophaga/Flavobacterium (CF) cluster, in dilution cultures, gamma-proteobacteria accounted for the majority of cells detected, followed by alpha-proteobacteria. An actively growing and an apparently non-growing population with average cellular protein contents of 24 and 4.5 fg respectively, were sorted by flow cytometry. FISH indicated mostly gamma- (64%) and alpha-proteobacteria (33%) in the first active fraction and 78% members of the CF cluster in the second fraction. Sequencing of DGGE bands confirmed the FISH assignments of the latter two groups. The data presented clearly show that even relatively short-term dilution experiments do not measure in situ growth, but rather growth patterns of an enrichment. Furthermore, it was demonstrated that the combination of flow cytometric analysis and sorting combined with FISH and DGGE analysis presented a fairly rapid method of analysing the taxonomic composition of marine bacterioplankton. <br/
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Molecular identification of picoplankton populations in contrasting waters of the Arabian Sea
Full text linkThe composition of picoplankton in the southern oligotrophic, northern mesotrophic waters and deep oxygen minimum zone (OMZ) of the Arabian Sea was determined by 16S ribosomal RNA gene cloning and fluorescence in situ hybridisation (FISH). It was hypothesised that the composition of the heterotrophic picoplankton would be different in these contrasting waters. To reduce the total diversity, cells were sorted by flow cytometry according to their scatter and DNA content before PCR amplification. The 16S rRNA clone libraries resulting from flow-sorted populations were different and often dominated by a small number of clades. Libraries from the Prochlorococcus-dominated southerly waters were dominated by sequences related to uncultured clusters of SAR11, SAR86 and Actinobacteria (HGC I). From surface waters of the Synechococcus-dominated northern part of the Arabian Sea, mostly sequences related to the uncultured gammaproteobacterial group ‘Svalbard’ and HGC I were retrieved. The clone libraries from the OMZ were also dominated by sequences falling in the clades SAR11 and SAR406, but included sequences related to those of sulfate-reducing
(Desulfosarcina, Desulfofrigus) and sulfide-oxidising bacteria (endosymbionts of Riftia and Calyptogena). With a recently developed more sensitive FISH protocol approximately 60% of all DAPI stained cells could be identified by general probes as Bacteria, Cren- or Euryarchaeota in both provinces of the Arabian Sea; 40% remained undetected. On this level and on that of the major phylogenetic groups like Alpha- and Gammaproteobacteria only minor differences were detected by FISH. However, the composition of heterotrophic picoplankton clearly differed for the proteobacterial subgroups SAR86, SAR11 and SAR116. These were more abundant in the oligotrophic waters throughout the water column than in the mesotrophic surface waters and the OMZ. This supports our original hypothesis that the contrasting waters in the Arabian Sea harbor different heterotrophic
picoplankton communities. In the future, FISH with a larger set of probes for more narrow phylogenetic groups will enable us to quantify these differences in more detail
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
High rate of uptake of organic nitrogen compounds by Prochlorococcus cyanobacteria as a key to dominance in oligotrophic oceanic waters
Full text linkDirect evidence that marine cyanobacteria take up organic nitrogen compounds in situ at high rates is reported. About 33% of the total bacterioplankton turnover of amino acids, determined with a representative [35S]methionine precursor and flow sorting, can be assigned to Prochlorococcus spp. and 3% can be assigned to Synechococcus spp. in the oligotrophic and mesotrophic parts of the Arabian Sea, respectively. This finding may provide a mechanism for Prochlorococcus' competitive dominance over both strictly autotrophic algae and other bacteria in oligotrophic regions sustained by nutrient remineralization via a microbial loop
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