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Culturing Bias in Marine Heterotrophic Flagellates Analyzed Through Seawater Enrichment Incubations

  • Microbiology of Aquatic Systems
  • Published:
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Abstract

The diversity of heterotrophic flagellates is generally based on cultivated strains, on which ultrastructural, physiological, and molecular studies have been performed. However, the relevance of these cultured strains as models of the dominant heterotrophic flagellates in the marine planktonic environment is unclear. In fact, molecular surveys typically recover novel eukaryotic lineages that have refused cultivation so far. This study was designed to directly address the culturing bias in planktonic marine heterotrophic flagellates. Several microcosms were established adding increasing amounts and sources of organic matter to a confined natural microbial community pre-filtered by 3 μm. Growth dynamics were followed by epifluorescence microscopy and showed the expected higher yield of bacteria and heterotrophic flagellates at increased organic matter additions. Moreover, protist diversity analyzed by molecular tools showed a clear substitution in the community, which differed more and more from the initial sample as the organic matter increased. Within this gradient, there was also an increase of sequences related to cultured organisms as well as a decrease in diversity. Culturing bias is partly explained by the use of organic matter in the isolation process, which drives a shift in the community to conditions closer to laboratory cultures. An intensive culturing effort using alternative isolation methods is necessary to allow the access to the missing heterotrophic flagellates that constitute the abundant and active taxa in marine systems.

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Acknowledgments

This study was supported by projects MICROVIS (CTM2007-62140/MAR, MEC), FLAME (CGL2010-16304, MICINN) and the European Funding Agencies from the ERA-net program BiodivERsA under the BioMarKs project. Javier del Campo was funded by I3P program (I3PPRE-06-00676, CSIC).

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  1. Javier del Campo

    Present address: Institut de Biologia Evolutiva, CSIC-UPF, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Catalonia, Spain

Authors and Affiliations

  1. Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta, 37-49, 08003, Barcelona, Catalonia, Spain

    Javier del Campo, Vanessa Balagué, Irene Forn, Itziar Lekunberri & Ramon Massana

  2. Department of Marine Biology, Faculty Center of Ecology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria

    Itziar Lekunberri

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Correspondence to Javier del Campo.

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Supplementary Fig. 1

UniFrac Cluster Sample analysis. The scale bar shows the distance between clusters in UniFrac units: a distance of 0 means that two samples are identical, and a distance of 0.5 means that two samples contain mutually exclusive lineages. (PDF 250 kb)

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del Campo, J., Balagué, V., Forn, I. et al. Culturing Bias in Marine Heterotrophic Flagellates Analyzed Through Seawater Enrichment Incubations. Microb Ecol 66, 489–499 (2013). https://doi.org/10.1007/s00248-013-0251-y

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