Marine microeukaryotem metatranscriptomics: sample processing and bioinformatic workflow recommendations for ecological applications

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Cohen, N., Alexander, H., Krinos, A., Hu, S., & Lampe, R. Marine microeukaryotem metatranscriptomics: sample processing and bioinformatic workflow recommendations for ecological applications. Frontiers in Marine Science, 9, (2022): 867007, https://doi.org/10.3389/fmars.2022.867007.
Microeukaryotes (protists) serve fundamental roles in the marine environment as contributors to biogeochemical nutrient cycling and ecosystem function. Their activities can be inferred through metatranscriptomic investigations, which provide a detailed view into cellular processes, chemical-biological interactions in the environment, and ecological relationships among taxonomic groups. Established workflows have been individually put forth describing biomass collection at sea, laboratory RNA extraction protocols, and bioinformatic processing and computational approaches. Here, we present a compilation of current practices and lessons learned in carrying out metatranscriptomics of marine pelagic protistan communities, highlighting effective strategies and tools used by practitioners over the past decade. We anticipate that these guidelines will serve as a roadmap for new marine scientists beginning in the realms of molecular biology and/or bioinformatics, and will equip readers with foundational principles needed to delve into protistan metatranscriptomics.
We acknowledge funding support from the University of Georgia Skidaway Institute of Oceanography (to NRC), National Science Foundation (NSF) (OCE-1948025 to HA), and Department of Energy Computational Science Graduate Fellowship (DE-SC0020347 to AIK). SKH participation was supported through NSF OCE-1947776.