Distinct transcriptional signatures of the protistan community at the SPOT and ALOHA ocean time-series stations

Distinct transcriptional signatures of the protistan community at the SPOT and ALOHA ocean time-series stations characterize different depths and locations

Authors: Sarah K. Hu¹, Harriet Alexander², Zhenfeng Liu^3,4, Karla Heidelberg³, Sonya Dyhrman⁵, David A. Caron³

Affilitations: (1) Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States (2) Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, United States (3) Biological Sciences, University of Southern California, Los Angeles, CA 90089, United States (4) Current location: Zymo Research Corporation, Irvine, CA 92614, United States (5) Department of Earth and Environmental Sciences, Columbia University, Palisades, NY 10964, United States

Summary: Understanding how the metabolic potential and taxonomic composition of naturally occurring single-celled microbial eukaryotic communities is necessary if we are to recognize their contribution to marine food web dynamics and biogeochemical cycling. Accessing in situ microbial populations with metatranscriptomics provides details into both the taxonomic and functional profile of a community. In this study, comparisons among samples spanning broad horizontal (oligotrophic North Pacific Subtropical gyre and coastal Southern California) and vertical (surface to 1,000 m depth) scales revealed the degree to which environmental conditions may select for taxonomic groups and how this relates to community metabolic potential. By exploring the taxonomic and transcriptional profiles together, results suggest a degree of functional redundancy among regionally important phototrophs (diatoms, chlorophytes, pelagophytes). Distinct metabolic profiles between euphotic and sub-euphotic depths highlight the roles of protistan heterotrophs, including ciliates, MArine STramenopiles, and rhizaria. Results from the analysis also provide a list of pathways associated with phagotrophy among protists as a way to emphasize the need to highlight heterotrophic modes of nutrition in comparative metatranscriptome studies. Findings link transcriptional profiles and trophic strategies to reveal how individual protistan lineages complete and thrive in oligotrophic and coastal ecosystems.

See related github repo: https://github.com/shu251/CA-ALOHA-metatranscriptome-analysis

1. raw-count-data-metaT-ALOHA-SPOT.txt - raw count data for each unigene, includes taxonomic and Kegg ID assignment
2. raw_count_data_07262018.RData - same as (1), but in R object format
3. Normalized_data_08022018.RData - whole community normalized data (TMM with edgeR) as R objects
4. Normed_avg_annotated_08022018.RData  - normalized data (TMM with edgeR) with complete annotations of pathways and gene names
5. ReNorm_bytax_08022018.RData  - normalized data (TMM with edgeR) by individual taxonomic groups.
6. taxonomic-assign-reference.txt - curated taxonomic assignments, specific to protistan taxonomy
7. Custom_KO_list_30-04-2020.txt - Annotations based on Kegg identities, specifically providing a curated list of key metabolic pathways
8. NormedbyWhole_annotated.RData - Formatted and normalized data (TMM with edgeR) with complete annotations of pathways and gene names
9. Normedbytax_annotated.RData-  Formatted and normalized data (TMM with edgeR) by individual taxonomic groups, includes complete annotations of pathways and gene names