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  • Benthic  (1)
  • Bromodeoxyuridine  (1)
  • Inter-Research  (2)
  • BioMed Central
  • IEEE
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  • Inter-Research  (2)
  • BioMed Central
  • IEEE
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  • 1
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    Linking bacterivory and phyletic diversity of protists with a marker gene survey and experimental feeding with BrdU-labeled bacteria (2014)
    Inter-Research
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © Inter-Research, 2013. This article is posted here by permission of Inter-Research for personal use, not for redistribution. The definitive version was published in Aquatic Microbial Ecology 71 (2013):141-153, doi:10.3354/ame01674.
    Description: Over the last few decades, molecular methods have vastly improved our ability to study the diversity of microbial communities. In molecular diversity surveys, the function of protists is often inferred from phylogeny. Yet these surveys are unable to distinguish between different trophic modes among closely related taxa. Here we present results from a culture-independent study linking bacterivory to the diversity of pelagic protists from 3 depths of a stratified mesotrophic lake. Bacteria were labeled with bromodeoxyuridine (BrdU) and added to lakewater samples; after incubation, total DNA was extracted from filtered samples. Part of the DNA extract was subjected to immunoprecipitation with anti-BrdU antibodies, and then both whole DNA and BrdU-labeled samples were analyzed using 454-pyrosequencing of the v9 region of 18S small subunit rRNA gene amplicons. The results show that a different community of protists exists at each depth, with limited overlap of taxonomic composition between depths. The community of BrdU-labeled protists, deemed putative bacterivores, is largely a subset of the community found in the whole DNA samples. Many of these BrdU-labeled taxa are poorly represented in GenBank and thus are probably rarely isolated and/or uncultured species. Several of the taxa identified as bacterivores are also phototrophs, highlighting the important role of mixotrophy among eukaryotic microbes. Definitive identity of functional traits among taxa requires careful experimentation, yet this method allows a first-pass assay of the trophic role of microbial eukaryotes from environmental samples.
    Description: This work was funded in part by NSF grants OPP-0838847 and OPP-0838955.
    Keywords: Molecular methods ; Microbial community ; Mixotrophy ; Bromodeoxyuridine ; Culture-independent ; Eukaryotic microbes ; Pyrosequencing ; Lake microbes
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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  • 2
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    Community structure of marine sedimentary protists in relation to flow and grain size (2011)
    Inter-Research
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © Inter-Research, 2007. This article is posted here by permission of Inter-Research for personal use, not for redistribution. The definitive version was published in Aquatic Microbial Ecology 48 (2007): 91-104, doi:10.3354/ame048091.
    Description: Populations of unicellular, marine sedimentary protists are constrained by a variety of physical environmental factors, but influences of flow regime have rarely been studied. We compared community structure among 3 subtidal sites differing in flow strength and grain size in a coastal bay. We used denaturing gradient gel electrophoresis (DGGE) to assess eukaryotic diversity based on 18S rDNA, and quantitative Protargol staining (QPS) to examine ciliate communities by microscopy. Sedimentary 18S rDNA in mid-summer was dominated by diatoms. Analyses of gel bands by presence/ absence among sites, dendogram, and multidimensional scaling showed that eukaryotic community structure was related to grain size more strongly than to flow regime. Among bands identified as diatoms by recovery and sequence analysis, 4 taxa (40%) differed among sites in relation to flow strength, and 2 taxa (29%) differed in relation to grain size. No bands had sequences matching ciliates, but QPS showed that 6 ciliate species (20%) were distributed in relation to flow, and 10 species (33%), in relation to grain size. Ciliate species richness and community similarity were greatest for the 2 strong-flow sites, despite differences in mean grain size. The strong-flow, silty site had the highest concentrations of chlorophyll a, total ciliates, karyorelictids, and scuticociliates, and the lowest ciliate species diversity. DGGE was run again for this site 1 mo later and revealed a shift in the rDNA pool to dominance by metazoans. Flow regime and grain size may be important factors structuring subtidal communities of sedimentary protists.
    Description: This work was supported by Franklin & Marshall College and the Woods Hole Center for Oceans and Human Health (NIEHS P50 ES012742 & NSF OCE0430724).
    Keywords: Ciliates ; Diatoms ; Benthic ; Community structure ; Flow ; Grain size ; DGGE
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
    Location Call Number Limitation Availability
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