Marine microbial eukaryotes are key components of planktonic ecosystems in all ocean biomes. They are, along with cyanobacteria, responsible for nearly half of the global primary production, and play important roles in food-web dynamics as grazers and parasites, carbon export to the deep ocean, and nutrient remineralization. Currently, one of the most common approaches to survey their diversity is sequencing marker genes amplified from genomic DNA extracted from microbial assemblages. However, this approach requires a PCR step, which is known to introduce biases in microbial diversity estimates. One alternative to overcome this issue involves exploiting the taxonomic information contained in metagenomes, which use massive shotgun sequencing of the same DNA extracts with the goal of assessing the putative functions of environmental microbes.

In this study we investigated the potential of metagenomics to provide taxonomic reports of marine microbial eukaryotes. The overall diversity reported by this approach was similar to that obtained by amplicon sequencing, although the latter performed poorly for some taxonomic groups. We then studied the diversity of picoeukaryotes and nanoeukaryotes using 91 metagenomes from surface down to bathypelagic layers in different oceans, unveiling a clear separation of taxonomic groups between size fractions and depth layers.

Overall, this study shows metagenomics as an excellent resource for taxonomic exploration of marine microbial eukaryotes.

This summary was written by the study’s first author, Aleix Obiol.

Full article:
Obiol, A., Giner, C. R., Sánchez, P., Duarte, C. M., Acinas, S. G., & Massana, R. (2020). A metagenomic assessment of microbial eukaryotic diversity in the global ocean. Molecular Ecology Resources. https://doi.org/10.1111/1755-0998.13147