ena-STUDY-Alfred-Wegener-Institut Helmholtz-Zentrum fuer Polar- und Meeresforschung-06-03-2018-08:40:08:828-623
Marine Oomycetes: community barcoding results from an early winter plankton bloom (2012) in the Brudenell River (Prince Edward Island)
Marine Oomycetes are highly diverse, globally distributed and play key roles in marine food webs (decomposer, food source, parasites). As species identification based on morphological characteristics and/or molecular genetic analyses of isolated single species are very labour-intensive, most of our knowledge about Oomycetes remains limited to pathogenic species of economically important crops. Despite their potential importance in the world's ocean ecosystems, marine Oomycetes are comparatively little studied. In this study we tested if the primer pair cox2F_Hud and cox2-RC4, which is already well established for phylogenetic investigations of Oomycetes, can also be used on a high throughput sequencing platform in a community barcoding approach. The Illumina sequencing of the investigated plankton sample, taken in the Brudenell River, revealed six distinct phylotypes, reflecting mean Oomycete diversity in a marine plankton sample. Nonetheless, the fact that the identified phylotypes were not unambiguously assigned to sequences from existing databases again reflects how unexplored marine Oomycetes are and that databases must be further expanded. The here implemented community barcoding pipeline provides a fast and accurate tool for the identification of marine Oomycetes and would also be suitable for future barcoding programs.
Marine Oomycetes are highly diverse, globally distributed and play key roles in marine food webs (decomposer, food source, parasites). As species identification based on morphological characteristics and/or molecular genetic analyses of isolated single species are very labour-intensive, most of our knowledge about Oomycetes remains limited to pathogenic species of economically important crops. Despite their potential importance in the world's ocean ecosystems, marine Oomycetes are comparatively little studied. In this study we tested if the primer pair cox2F_Hud and cox2-RC4, which is already well established for phylogenetic investigations of Oomycetes, can also be used on a high throughput sequencing platform in a community barcoding approach. The Illumina sequencing of the investigated plankton sample, taken in the Brudenell River, revealed six distinct phylotypes, reflecting mean Oomycete diversity in a marine plankton sample. Nonetheless, the fact that the identified phylotypes were not unambiguously assigned to sequences from existing databases again reflects how unexplored marine Oomycetes are and that databases must be further expanded. The here implemented community barcoding pipeline provides a fast and accurate tool for the identification of marine Oomycetes and would also be suitable for future barcoding programs.