title: Protistan diversity and activity inferred from RNA and DNA at a coastal ocean site in the eastern North Pacific.
abstract: Microbial eukaryotes fulfill key ecological positions in marine food webs. Molecular approaches that connect protistan diversity and biogeography to their diverse metabolisms will greatly improve our understanding of marine ecosystem function. The majority of molecular-based studies to date use 18S rRNA gene sequencing to characterize natural microbial assemblages, but this approach does not necessarily discriminate between active and non-active cells. We incorporated RNA sequencing into standard 18S rRNA gene sequence surveys with the purpose of assessing those members of the protistan community contributing to biogeochemical cycling (active organisms), using the ratio of cDNA (reverse transcribed from total RNA) to 18S rRNA gene sequences within major protistan taxonomic groups. Trophically important phytoplankton, such as diatoms and chlorophytes exhibited seasonal trends in relative activity. Additionally, both radiolaria and ciliates displayed previously unreported high relative activities below the euphotic zone. This study sheds new light on the relative metabolic activity of specific protistan groups and how microbial communities respond to changing environmental conditions.
authors.affiliation: Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089-0371, USA sarah.hu@usc.edu.
authors.forename: Sarah K
authors.initials: SK
authors.lastname: Hu
authors.affiliation: Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089-0371, USA UW Medicine, Division Allergy and Infectious Diseases, 750 Republican St., Seattle, WA 98109, USA.
authors.forename: Victoria
authors.initials: V
authors.lastname: Campbell
authors.affiliation: Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089-0371, USA.
authors.forename: Paige
authors.initials: P
authors.lastname: Connell
authors.affiliation: Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089-0371, USA.
authors.forename: Alyssa G
authors.initials: AG
authors.lastname: Gellene
authors.affiliation: Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089-0371, USA.
authors.forename: Zhenfeng
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089-0371, USA.
authors.forename: Ramon
authors.initials: R
authors.lastname: Terrado
authors.affiliation: Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA 90089-0371, USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Caron
mesh_terms: D016798:Ciliophora / Q000145:classification* / Q000235:genetics*; D004247:DNA / Q000235:genetics*; D017753:Ecosystem; D010140:Pacific Ocean; D010839:Phytoplankton / Q000235:genetics*; D012313:RNA; D012337:RNA, Ribosomal, 18S / Q000235:genetics*; D012623:Seawater; D017422:Sequence Analysis, DNA
chemical_list: D012337:RNA, Ribosomal, 18S; D012313:RNA; D004247:DNA
keywords: 18S rRNA gene sequencing; DNA/RNA comparison; cDNA sequencing; microbial ecology; microbial eukaryotes; protistan diversity