Culturing bias in the study of marine heterotrophic flagellates diversity

Abstract

Our main goal in this study was to overcome the culture bias in marine heterotrophic flagellates. This main aim could be structured in three general aspects. The first was to determine the importance and representativity of cultured flagellates in environmental molecular studies. The second was the study of the culture bias from an experimental point of view. Finally, we aimed at obtaining new cultures of heterotrophic flagellates. To achieve this we defined more specific objectives: 1. Determine the clonal contribution of 18S rDNA sequences of chrysophytes, choanoflagellates and bicosoecids in marine and freshwater systems, improve the phylogeny of these groups and analyze their sequence novelty. 2. Determine the effect of PCR induced biases by comparing 18S rDNA sequences obtained from the Global Ocean Survey (GOS) metagenomic database (Rusch et al. 2007) and from standard clone libraries (Massana and Pedrós-Alió 2008). 3. Compare the protist diversity inferred from clone libraries both from extracted DNA and extracted RNA from the same sample, in order to delineate the biases introduced in environmental diversity studies generally based on DNA. 4. Report the effects of different organic matter enrichments to heterotrophic flagellates community structure and put together ideas and concepts related to the culturing bias that had been generally assumed or refused but never specifically addressed. 5. Develop a new culturing approach to isolate previously uncultured heterotrophic flagellates species that might be abundant in the marine plankton