Dataset: Amplicon sequence variants (ASVs) and taxonomy of Pseudo-nitzschia spp. from Narragansett Bay in Rhode Island, USA and the Northeast U.S. Shelf (NES-LTER transect) from 2018-2023

Name: Amplicon sequence variants (ASVs) and taxonomy of Pseudo-nitzschia spp. from Narragansett Bay in Rhode Island, USA and the Northeast U.S. Shelf (NES-LTER transect) from 2018-2023
Published: 2024-10-11
Keywords: harmful algal blooms, domoic acid, Pseudo-nitzschia, time series, diatoms, oceans

Release Date:2025-02-28Final no updates expectedDOI: 10.26008/1912/bco-dmo.936849.1Version 1 (2024-10-11)Dataset Type:experimentalDataset Type:Other Field Results

Principal Investigator: Bethany D. Jenkins (University of Rhode Island)

Co-Principal Investigator: Matthew Bertin (University of Rhode Island)

Scientist: Riley Kirk (University of Rhode Island)

Scientist: Tatiana A. Rynearson (University of Rhode Island)

Scientist: Alexa Sterling (University of Rhode Island)

Student: Isabella Church (University of Rhode Island)

Student: Andrew Kim (University of Rhode Island)

Student, Contact: Katherine M. Roche (University of Rhode Island)

BCO-DMO Data Manager: Lynne M. Merchant (Woods Hole Oceanographic Institution)

Program: Long Term Ecological Research network (LTER)

Project: Northeast U.S. Shelf Long Term Ecological Research site (NES LTER)

Project: RII Track-1: Rhode Island Consortium for Coastal Ecology Assessment, Innovation, and Modeling (C-AIM)

Project: Narragansett Bay Long-Term Plankton Time Series (NBPTS)

Abstract

This dataset includes amplicon sequence variants (ASVs) representing species of the harmful algal bloom diatom genus Pseudo-nitzschia that were sampled from various sites in Narragansett Bay, Rhode Island, including the Narragansett Bay Long Term Plankton Time Series site, and various stations along the Northeast U.S. Shelf Long Term Ecological Research program transect. These data correspond to an analysis of Pseudo-nitzschia species composition and domoic acid toxin production during winters a...

Cite Dataset

Spatial Extent: N:41.57 E:-70.77 S:39.93 W:-71.42
Temporal Extent: 2018-01-31 - 2023-01-16

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Acknowledgement:

We acknowledge the NSF RI C-AIM EPSCoR Cooperative Agreement (OIA-1004057) for research support. Sequencing was performed at the University of Rhode Island Molecular Informatics Core supported by the Institutional Development Award (IDeA) Network for Biomedical Research Excellence from the National Institute of General Medical Sciences of the National Institutes of Health (P20GM103430).

Related Datasets

Roche, K. M., Church, I., Sterling, A., Rynearson, T. A., Bertin, M., Kim, A., Kirk, R., Jenkins, B. D. (2024) Pseudo-nitzschia spp. presence-absence and environmental data in Narragansett Bay in Rhode Island, USA and the Northeast U.S. Shelf (NES-LTER transect) from 2018-2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-10-14 doi:10.26008/1912/bco-dmo.936856.1

Related Publications

Results

Roche, K.M., Church, I.N., Sterling, A.R., Rynearson, T.A., Bertin, M.J., Kim, A.M., Kirk, R.D., Jenkins, B.D. (2024). Connectivity of toxigenic Pseudo-nitzschia species assemblages between the Northeast U.S. continental shelf and an adjacent estuary. Manuscript submitted for publication.

Methods

Roche, K. M., Sterling, A. R., Rynearson, T. A., Bertin, M. J., & Jenkins, B. D. (2022). A Decade of Time Series Sampling Reveals Thermal Variation and Shifts in Pseudo-nitzschia Species Composition That Contribute to Harmful Algal Blooms in an Eastern US Estuary. Frontiers in Marine Science, 9. https://doi.org/10.3389/fmars.2022.889840

Methods

Sterling, A. R., Kirk, R. D., Bertin, M. J., Rynearson, T. A., Borkman, D. G., Caponi, M. C., Carney, J., Hubbard, K. A., King, M. A., Maranda, L., McDermith, E. J., Santos, N. R., Strock, J. P., Tully, E. M., Vaverka, S. B., Wilson, P. D., & Jenkins, B. D. (2022). Emerging harmful algal blooms caused by distinct seasonal assemblages of a toxic diatom. Limnology and Oceanography, 67(11), 2341–2359. Portico. https://doi.org/10.1002/lno.12189

Methods

White, T. J., Bruns, T., Lee, S., & Taylor, J. (1990). AMPLIFICATION AND DIRECT SEQUENCING OF FUNGAL RIBOSOMAL RNA GENES FOR PHYLOGENETICS. PCR Protocols, 315–322. https://doi.org/10.1016/b978-0-12-372180-8.50042-1

Software

Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc

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Dataset: Amplicon sequence variants (ASVs) and taxonomy of Pseudo-nitzschia spp. from Narragansett Bay in Rhode Island, USA and the Northeast U.S. Shelf (NES-LTER transect) from 2018-2023

Release Date:2025-02-28Final no updates expectedDOI: 10.26008/1912/bco-dmo.936849.1Version 1 (2024-10-11)Dataset Type:experimentalDataset Type:Other Field Results

Principal Investigator: Bethany D. Jenkins (University of Rhode Island)

Co-Principal Investigator: Matthew Bertin (University of Rhode Island)

Scientist: Riley Kirk (University of Rhode Island)

Scientist: Tatiana A. Rynearson (University of Rhode Island)

Scientist: Alexa Sterling (University of Rhode Island)

Student: Isabella Church (University of Rhode Island)

Student: Andrew Kim (University of Rhode Island)

Student, Contact: Katherine M. Roche (University of Rhode Island)

BCO-DMO Data Manager: Lynne M. Merchant (Woods Hole Oceanographic Institution)

Program: Long Term Ecological Research network (LTER)

Project: Northeast U.S. Shelf Long Term Ecological Research site (NES LTER)

Project: RII Track-1: Rhode Island Consortium for Coastal Ecology Assessment, Innovation, and Modeling (C-AIM)

Project: Narragansett Bay Long-Term Plankton Time Series (NBPTS)

Abstract

Cite Dataset

Spatial Extent: N:41.57 E:-70.77 S:39.93 W:-71.42
Temporal Extent: 2018-01-31 - 2023-01-16

XXX

Views

XX

Downloads

X

Citations

Acknowledgement:

Related Datasets

Related Publications

Results

Methods

Software

Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc

File(s)	Type	Description	Action
936849_v1_pseudo_nitzschia_amplicon_seq_variant.csv (64.46 KB)	Comma Separated Values (.csv)	Primary data file for dataset ID 936849, version 1

Supplemental File(s)	Type	Description	Action
species_taxonomy.csv (4.61 KB)	Comma Separated Values (.csv)	Species taxonomy from WoRMS with columns: ScientificName, AphiaID, LSID, Kingdom, Phylum, Class, Order, Family, Genus, Species

File(s)	Type	Description	Action
936849_v1_pseudo_nitzschia_amplicon_seq_variant.csv (64.46 KB)	Comma Separated Values (.csv)	Primary data file for dataset ID 936849, version 1

Supplemental File(s)	Type	Description	Action
species_taxonomy.csv (4.61 KB)	Comma Separated Values (.csv)	Species taxonomy from WoRMS with columns: ScientificName, AphiaID, LSID, Kingdom, Phylum, Class, Order, Family, Genus, Species

Dataset: Amplicon sequence variants (ASVs) and taxonomy of Pseudo-nitzschia spp. from Narragansett Bay in Rhode Island, USA and the Northeast U.S. Shelf (NES-LTER transect) from 2018-2023

Principal Investigator: Bethany D. Jenkins (University of Rhode Island)

Co-Principal Investigator: Matthew Bertin (University of Rhode Island)

Scientist: Riley Kirk (University of Rhode Island)

Scientist: Tatiana A. Rynearson (University of Rhode Island)

Scientist: Alexa Sterling (University of Rhode Island)

Student: Isabella Church (University of Rhode Island)

Student: Andrew Kim (University of Rhode Island)

Student, Contact: Katherine M. Roche (University of Rhode Island)

BCO-DMO Data Manager: Lynne M. Merchant (Woods Hole Oceanographic Institution)

Program: Long Term Ecological Research network (LTER)

Project: Northeast U.S. Shelf Long Term Ecological Research site (NES LTER)

Project: RII Track-1: Rhode Island Consortium for Coastal Ecology Assessment, Innovation, and Modeling (C-AIM)

Project: Narragansett Bay Long-Term Plankton Time Series (NBPTS)

Abstract

Metadata

XXX

XX

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Related Datasets

Related Publications

Dataset: Amplicon sequence variants (ASVs) and taxonomy of Pseudo-nitzschia spp. from Narragansett Bay in Rhode Island, USA and the Northeast U.S. Shelf (NES-LTER transect) from 2018-2023

Principal Investigator: Bethany D. Jenkins (University of Rhode Island)

Co-Principal Investigator: Matthew Bertin (University of Rhode Island)

Scientist: Riley Kirk (University of Rhode Island)

Scientist: Tatiana A. Rynearson (University of Rhode Island)

Scientist: Alexa Sterling (University of Rhode Island)

Student: Isabella Church (University of Rhode Island)

Student: Andrew Kim (University of Rhode Island)

Student, Contact: Katherine M. Roche (University of Rhode Island)

BCO-DMO Data Manager: Lynne M. Merchant (Woods Hole Oceanographic Institution)

Program: Long Term Ecological Research network (LTER)

Project: Northeast U.S. Shelf Long Term Ecological Research site (NES LTER)

Project: RII Track-1: Rhode Island Consortium for Coastal Ecology Assessment, Innovation, and Modeling (C-AIM)

Project: Narragansett Bay Long-Term Plankton Time Series (NBPTS)

Abstract

Metadata

XXX

XX

X

Related Datasets

Related Publications