Evaluation of DNA Extraction Methods and Bioinformatic Pipelines for Marine Nano- and Pico-Eukaryotic Plankton Analysis

The smallest size fractions of plankton, nano- and pico-plankton, have been highlighted due to they accomplish key functions in marine ecosystems. However, the knowledge about some them is scarce because are difficult or impossible be detected identified with non-DNA-based methodologies. Here we evaluated five DNA extraction protocols (MT1–MT5) seven bioinformatic pipelines (P1–P7) find best protocol for detecting most eukaryotic species pico-plankton present an environmental sample using Ion Torrent technology. MT3 was reproducible methodology, showing less variation among samples, good quality sufficient quantity amplify sequence eukaryote species, offering results after sequencing. For analyses, P1 P7 resulted highest percentage detection difficult-to-detect mock communities. only avoided confusion other closed during taxonomic assignment. final protocols, MT3-P1 (free) MT3-P7 (private), showed consistent when were applied sample, being a valuable tool study eukaryotes samples even genera that by techniques.