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Temporal dynamics of eukaryotic microbial diversity at a coastal Pacific site

Dataset homepage

Citation

MGnify (2019). Temporal dynamics of eukaryotic microbial diversity at a coastal Pacific site. Sampling event dataset https://doi.org/10.15468/obfeym accessed via GBIF.org on 2023-02-07.

Description

High-throughput sequencing of ocean biomes has revealed vast eukaryotic microbial diversity, asignificant proportion of which remains uncharacterized. Here we use a temporal approach tounderstanding eukaryotic diversity at the Scripps Pier, La Jolla, California, USA, via high-throughput amplicon sequencing of the 18S rRNA gene, the abundances of both Synechococcusand Synechococcus grazers, and traditional oceanographic parameters. We also exploit ourability to track OTUs temporally to evaluate the ability of 18S sequence-based OTU assignmentsto meaningfully reflect ecological dynamics. The eukaryotic community is highly dynamic interms of both species richness and composition, though proportional representation of higher-order taxa remains fairly consistent over time. Synechococcus abundance fluctuates throughoutthe year. This study has resulted in a temporal dataset of eukaryotic 18S sequences that cover a wide range of taxa and offers insights into the pier microbial community and how it changes with time.

Sampling Description

Sampling

High-throughput sequencing of ocean biomes has revealed vast eukaryotic microbial diversity, asignificant proportion of which remains uncharacterized. Here we use a temporal approach tounderstanding eukaryotic diversity at the Scripps Pier, La Jolla, California, USA, via high-throughput amplicon sequencing of the 18S rRNA gene, the abundances of both Synechococcusand Synechococcus grazers, and traditional oceanographic parameters. We also exploit ourability to track OTUs temporally to evaluate the ability of 18S sequence-based OTU assignmentsto meaningfully reflect ecological dynamics. The eukaryotic community is highly dynamic interms of both species richness and composition, though proportional representation of higher-order taxa remains fairly consistent over time. Synechococcus abundance fluctuates throughoutthe year. This study has resulted in a temporal dataset of eukaryotic 18S sequences that cover a wide range of taxa and offers insights into the pier microbial community and how it changes with time.

Method steps

  1. Pipeline used: https://www.ebi.ac.uk/metagenomics/pipelines/4.1

Taxonomic Coverages

Geographic Coverages

Bibliographic Citations

  1. Nagarkar M, Countway PD, Du Yoo Y, Daniels E, Poulton NJ, Palenik B. 2018. Temporal dynamics of eukaryotic microbial diversity at a coastal Pacific site. ISME J vol. 12 - DOI:10.1038/s41396-018-0172-3

Contacts

originator
Scripps Institution of Oceanography
metadata author
Scripps Institution of Oceanography
administrative point of contact
Scripps Institution of Oceanography
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