DOI: 10.5281/zenodo.11490399
title: Database Darkly files

description: Database Darkly website

File description



deepsea-18s-merged-asv-table-05022025.qza - QIIME2 output of merged ASV table



deepsea-18s-merged-asv-table-05022025.tsv - tab separated version of merged ASV table




ref-seqs-deepsea-DB_052025.fasta - reference sequences for all ASVs - matches Feature ID




deepsea-18s-merged-seqs-05022025.qza - QIIME2 output of merged reference sequences




taxonomy-05022025.tsv - tab seaprated PR2 (version 5.0.0) assigned taxonomy for ASV table above (matcheds Feature ID). Qiime2 code used 0.9 identity with 0.8 consensus


axial-2023-metadata.csv - metadata for Axial 2023 and 2022 data

metadata-deepsea_GR_MCR_Axial-18S.csv - metadata for Gorda Ridge, Mid-Cayman Rise, and archived Axial data. This metadata is also associated with this publication: S. K. Hu, A. R. Smith, R. E. Anderson, S. P. Sylva, M. Setzer, M. Steadmon, K. L. Frank, E. W. Chan, D. S. S. Lim, C. R. German, J. A. Breier, S. Q. Lang, D. A. Butterfield, C. S. Fortunato, J. S. Seewald, J. A. Huber, Globally-distributed microbial eukaryotes exhibit endemism at deep-sea hydrothermal vents. Mol. Ecol. 32, 6580–6598 (2023).


Project goals:

Curate and annotate what we know about deep-sea marine microbial eukaryotes. Much of what we know about deep-sea microorganisms comes from the biogeography and inferred ecology of environmental species or strains. This database originates from deep-sea marine habitats, specifically hydrothermal vents. Species and strains capture are assumed to be present in these environments; however what we know about their ecological roles remains understudied. This database project involves extensive literature searches, comparative analyses, and inventories of these species, so we can get closer to having a more complete understanding of the roles protists play in the deep ocean.

There are three primary goals of this project: (1) Complement our comprehensive sequence database of deep-sea microbial eukaryotic diversity with metadata on taxonomic nomenclature (Costello et al. 2013; Horton et al. 2017), tree of life placement (e.g., iTOL and Open Tree of Life Letunic and Bork 2021; Michonneau et al. 2016; OpenTreeOfLife et al. 2019), a functional trait database (e.g., cell morphology, motility, ploidy, etc.; Ramond et al. 2019), and accounts of planktonic protist interactions (Bjorbækmo et al. 2020), (2) to highlight the number of taxonomic lineages that are severely lacking representation in the sequence reference database (Guillou et al. 2012), and (3) to look for patterns in the assignment of the phylogenetically elusive protists that may be related to fluid geochemistry or biogeography.

 

Contributors to curation effort:



Sarah Hu (PI, TAMU)

Abby Day (Undergrad, TAMU)

Madeleine Lerma (Undergrad, TAMU)

Meagan Sonsel (Undergrad, TAMU)

Siddarth Seshampally (Undergrad, TAMU)

Alexis Adams (PhD student, TAMU)

Kayla Nedd (PhD student, TAMU)


 

Project updates:

Version 2 updates - May 2025

- New dataset added from Axial Seamount. All sequences re-merged and re-assigned taxonomy with updated PR2 version 5.0.0

 

Version 1 files: (published June 2024)



DatabaseDarkly_taxa_06052024.csv - version 1 of a curated database. Taxonomic assignments from all deep-sea hydrothermal vent ASVs were compiled with exisiting knowledge

reference-seqs-databasedarkly.fasta - reference sequences for all ASVs and taxonomic assignments

reference-taxIDs-databasedarkly.tsv - Table with taxonomic assignments and sequence IDs (Feature ID)

QIIME2 files - Use the below .qza files in your qiime2 pipeline to compare ASVs.



microeuk-merged-asv-table.qza

microeuk-merged-ref-seqs.qza

microeuk-merged-taxa.qza