Dataset: Diel multi 'omics data from surface ocean microbial community samples collected during Hawaiʻi Diel Sampling (HaDS) in Kāneʻohe Bay and adjacent offshore waters of Oʻahu, Hawaiʻi from December 2020 to August 2021

Name: Diel multi 'omics data from surface ocean microbial community samples collected during Hawaiʻi Diel Sampling (HaDS) in Kāneʻohe Bay and adjacent offshore waters of Oʻahu, Hawaiʻi from December 2020 to August 2021
Published: 2025-05-30
Keywords: surface ocean microbes, Hawai'i Diel Sampling, multi 'omics, KByT, Kāneʻohe Bay, oceans

ValidatedFinal no updates expectedDOI: 10.26008/1912/bco-dmo.963210.1Version 1 (2025-05-30)Dataset Type:Other Field Results

Scientist: Sarah J. Tucker (University of Hawaiʻi at Mānoa)

Scientist: Jessika Fuessel (University of Chicago)

Scientist: Kelle C. Freel (University of Hawaiʻi at Mānoa)

Scientist: Michael S. Rappé (University of Hawaiʻi at Mānoa)

Principal Investigator: A. Murat Eren (University of Chicago)

BCO-DMO Data Manager: Nancy Copley (Woods Hole Oceanographic Institution)

Program: Center for Chemical Currencies of a Microbial Planet (C-CoMP)

Project: From Signatures of Translational Regulation to Outcomes of Natural Selection: Evolution of Marine Microbes in Changing Environments (C-CoMP Diel Multi 'Omics)

Abstract

This dataset contains biogeochemical data, sampling information, and genetic accession identifiers for the Hawaiʻi Diel Sampling (HaDS) survey in Kāneʻohe Bay and adjacent offshore waters of Oʻahu, Hawaiʻi from December 2020 to August 2021. Study description: Here, we present data from the Hawaiʻi Diel Sampling (HaDS) survey, which represents a high-resolution sampling of surface ocean microbial communities every 1.5 hours for 48 hours across two environments: Kāneʻohe Bay on the windward ...

Cite Dataset

Spatial Extent: N:21.48 E:-157.77 S:21.44 W:-157.80
Temporal Extent: 2020-12-23 - 2021-08-20

Related Data:

NCBI Project ID PRJNA1201851 offers access to all raw data for short-read and long-read metagenomes, as well as metatranscriptomes and transfer RNA (tRNA) transcripts.

doi:10.6084/m9.figshare.28784717 serves anvi’o contigs-db files for the individual co-assemblies of short-read (SR) as well as long-read (LR) sequencing of metagenomes. Please note that an anvi’o contigs-db includes gene calls, functional annotations, HMM hits, and other information about each contig, and you can always use the program anvi-export-contigs to get a FASTA file for sequences.

doi:10.6084/m9.figshare.28784762 serves FASTA files for metagenome-assembled genomes (MAGs) we have reconstructed from short-read and long-read sequencing of the metagenomes. They are the outputs of quite a preliminary effort, thus secondary attempts to recover genomes from the co-assemblies are most welcome (and very much encouraged). Please see the Supplementary Table for taxonomic annotation and completion/redundancy estimates of the MAGs.

doi:10.6084/m9.figshare.28784765. The EcoPhylo output that describes the phylogeography of ribosomal protein L14 (https://anvio.org/help/main/workflows/ecophylo/).

See more about related data and code at https://merenlab.org/data/hads/

Related Datasets

Eren, A. M. (2025). HADS MAGs from Long-read and Short-read Metagenomes [Data set]. figshare. https://doi.org/10.6084/M9.FIGSHARE.28784762

Eren, A. M. (2025). HADS Ribosomal Protein L14 Phylogeography with EcoPhylo [Data set]. figshare. https://doi.org/10.6084/M9.FIGSHARE.28784765

Eren, A. M. (2025). HADS co-assemblies of Long-read and Short-read Metagenomes [Data set]. figshare. https://doi.org/10.6084/M9.FIGSHARE.28784717

IsRelatedTo

Dataset:

Marine Biological Laboratory (2024). Hawaii Diel Sampling for Marine Microbial Multi Omics. 2024/12. In: NCBI:BioProject: PRJNA1201851 [Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; 2011-. Available from: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA1201851

Marine Biological Laboratory (2025). marine metagenome, Hawaii Diel Sampling Metagenome Assembled Genomes. 2025/03. In: NCBI:BioProject: PRJNA1235278. [Internet]. Bethesda, MD: National Library of Medicine (US), National Center for Biotechnology Information; 2011-. Available from: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA1235278.

Related Publications

Results

Tucker SJ, Fuessel J, Freel KC, Kiefl E, Freel EB, Ramfelt O, Sullivan CE, Gajigan AP, Mochimaru H, Souza MR, Quinn M, Ratum C, Tran LL, Miller SE, Trigodet F, Lolans K, Morrison HG, Fallon B, Huettel B, Pan T, Rappé MS, Eren AM. (n.d.) A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA (tRNA) transcripts. In prep for Sci Data.

Results

Tucker, S. J., Freel, K. C., Monaghan, E. A., Sullivan, C. E. S., Ramfelt, O., Rii, Y. M., & Rappé, M. S. (2021). Spatial and temporal dynamics of SAR11 marine bacteria across a nearshore to offshore transect in the tropical Pacific Ocean. PeerJ, 9, e12274. Portico. https://doi.org/10.7717/peerj.12274

Results

Tucker, S. J., Rii, Y. M., Freel, K. C., Kotubetey, K., Kawelo, A. H., Winter, K. B., & Rappé, M. S. (2025). Seasonal and spatial transitions in phytoplankton assemblages spanning estuarine to open ocean waters of the tropical Pacific. Limnology and Oceanography. Portico. https://doi.org/10.1002/lno.70075

Methods

Becker, J. W., Brandon, M. L., & Rappe, M. S. (2007). Cultivating Microorganisms from Dilute Aquatic Environments: Melding Traditional Methodology with New Cultivation Techniques and Molecular Methods. Manual of Environmental Microbiology, 399–406. Portico. https://doi.org/10.1128/9781555815882.ch32

Methods

Donaldson, G. P., Chou, W.-C., Manson, A. L., Rogov, P., Abeel, T., Bochicchio, J., Ciulla, D., Melnikov, A., Ernst, P. B., Chu, H., Giannoukos, G., Earl, A. M., & Mazmanian, S. K. (2020). Spatially distinct physiology of Bacteroides fragilis within the proximal colon of gnotobiotic mice. Nature Microbiology, 5(5), 746–756. https://doi.org/10.1038/s41564-020-0683-3

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Dataset: Diel multi 'omics data from surface ocean microbial community samples collected during Hawaiʻi Diel Sampling (HaDS) in Kāneʻohe Bay and adjacent offshore waters of Oʻahu, Hawaiʻi from December 2020 to August 2021

ValidatedFinal no updates expectedDOI: 10.26008/1912/bco-dmo.963210.1Version 1 (2025-05-30)Dataset Type:Other Field Results

Scientist: Sarah J. Tucker (University of Hawaiʻi at Mānoa)

Scientist: Jessika Fuessel (University of Chicago)

Scientist: Kelle C. Freel (University of Hawaiʻi at Mānoa)

Scientist: Michael S. Rappé (University of Hawaiʻi at Mānoa)

Principal Investigator: A. Murat Eren (University of Chicago)

BCO-DMO Data Manager: Nancy Copley (Woods Hole Oceanographic Institution)

Program: Center for Chemical Currencies of a Microbial Planet (C-CoMP)

Project: From Signatures of Translational Regulation to Outcomes of Natural Selection: Evolution of Marine Microbes in Changing Environments (C-CoMP Diel Multi 'Omics)

Abstract

Cite Dataset

Spatial Extent: N:21.48 E:-157.77 S:21.44 W:-157.80
Temporal Extent: 2020-12-23 - 2021-08-20

Related Data:

NCBI Project ID PRJNA1201851 offers access to all raw data for short-read and long-read metagenomes, as well as metatranscriptomes and transfer RNA (tRNA) transcripts.

doi:10.6084/m9.figshare.28784765. The EcoPhylo output that describes the phylogeography of ribosomal protein L14 (https://anvio.org/help/main/workflows/ecophylo/).

See more about related data and code at https://merenlab.org/data/hads/

Related Datasets

Eren, A. M. (2025). HADS MAGs from Long-read and Short-read Metagenomes [Data set]. figshare. https://doi.org/10.6084/M9.FIGSHARE.28784762

Eren, A. M. (2025). HADS Ribosomal Protein L14 Phylogeography with EcoPhylo [Data set]. figshare. https://doi.org/10.6084/M9.FIGSHARE.28784765

Eren, A. M. (2025). HADS co-assemblies of Long-read and Short-read Metagenomes [Data set]. figshare. https://doi.org/10.6084/M9.FIGSHARE.28784717

IsRelatedTo

Dataset:

Related Publications

Results

Methods

Data File(s)	Type	Description	Action
963210_v1_biogeochem-and-sampling-info-hads.csv (40.57 KB)	Comma Separated Values (.csv)	Primary data file for dataset ID 963210, version 1	Add to Cart Download View Table What is ERDDAP? SUBSET DATA VIEW TABLE CSV TSV GeoJSON MATLAB netCDF ODV

Supplemental File(s)	Type	Description	Action
Meren_Lab_HaDS_Website_20250604.pdf (4.73 MB)	Portable Document Format (.pdf)	PDF containing the contents of Meren Lab website page "Hawaiʻi Diel Sampling (HaDS)" https://merenlab.org/data/hads/ on 2025-06-04 (© 2025 Meren Lab) which includes further explanation of related datasets and code.	Add to Cart Download

Data File(s)	Type	Description	Action
963210_v1_biogeochem-and-sampling-info-hads.csv (40.57 KB)	Comma Separated Values (.csv)	Primary data file for dataset ID 963210, version 1	Add to Cart Download View Table What is ERDDAP? SUBSET DATA VIEW TABLE CSV TSV GeoJSON MATLAB netCDF ODV

Supplemental File(s)	Type	Description	Action
Meren_Lab_HaDS_Website_20250604.pdf (4.73 MB)	Portable Document Format (.pdf)	PDF containing the contents of Meren Lab website page "Hawaiʻi Diel Sampling (HaDS)" https://merenlab.org/data/hads/ on 2025-06-04 (© 2025 Meren Lab) which includes further explanation of related datasets and code.	Add to Cart Download

Dataset: Diel multi 'omics data from surface ocean microbial community samples collected during Hawaiʻi Diel Sampling (HaDS) in Kāneʻohe Bay and adjacent offshore waters of Oʻahu, Hawaiʻi from December 2020 to August 2021

Scientist: Sarah J. Tucker (University of Hawaiʻi at Mānoa)

Scientist: Jessika Fuessel (University of Chicago)

Scientist: Kelle C. Freel (University of Hawaiʻi at Mānoa)

Scientist: Michael S. Rappé (University of Hawaiʻi at Mānoa)

Principal Investigator: A. Murat Eren (University of Chicago)

BCO-DMO Data Manager: Nancy Copley (Woods Hole Oceanographic Institution)

Program: Center for Chemical Currencies of a Microbial Planet (C-CoMP)

Project: From Signatures of Translational Regulation to Outcomes of Natural Selection: Evolution of Marine Microbes in Changing Environments (C-CoMP Diel Multi 'Omics)

Abstract

Files

Supplemental Files

Related Datasets

Related Publications

Dataset: Diel multi 'omics data from surface ocean microbial community samples collected during Hawaiʻi Diel Sampling (HaDS) in Kāneʻohe Bay and adjacent offshore waters of Oʻahu, Hawaiʻi from December 2020 to August 2021

Scientist: Sarah J. Tucker (University of Hawaiʻi at Mānoa)

Scientist: Jessika Fuessel (University of Chicago)

Scientist: Kelle C. Freel (University of Hawaiʻi at Mānoa)

Scientist: Michael S. Rappé (University of Hawaiʻi at Mānoa)

Principal Investigator: A. Murat Eren (University of Chicago)

BCO-DMO Data Manager: Nancy Copley (Woods Hole Oceanographic Institution)

Program: Center for Chemical Currencies of a Microbial Planet (C-CoMP)

Project: From Signatures of Translational Regulation to Outcomes of Natural Selection: Evolution of Marine Microbes in Changing Environments (C-CoMP Diel Multi 'Omics)

Abstract

Files

Supplemental Files

Related Datasets

Related Publications

Dataset: Diel multi 'omics data from surface ocean microbial community samples collected during Hawaiʻi Diel Sampling (HaDS) in Kāneʻohe Bay and adjacent offshore waters of Oʻahu, Hawaiʻi from December 2020 to August 2021

Scientist: Sarah J. Tucker (University of Hawaiʻi at Mānoa)

Scientist: Jessika Fuessel (University of Chicago)

Scientist: Kelle C. Freel (University of Hawaiʻi at Mānoa)

Scientist: Michael S. Rappé (University of Hawaiʻi at Mānoa)

Principal Investigator: A. Murat Eren (University of Chicago)

BCO-DMO Data Manager: Nancy Copley (Woods Hole Oceanographic Institution)

Program: Center for Chemical Currencies of a Microbial Planet (C-CoMP)

Project: From Signatures of Translational Regulation to Outcomes of Natural Selection: Evolution of Marine Microbes in Changing Environments (C-CoMP Diel Multi 'Omics)

Abstract

Metadata

Files

Supplemental Files

Related Datasets

Related Publications

Dataset: Diel multi 'omics data from surface ocean microbial community samples collected during Hawaiʻi Diel Sampling (HaDS) in Kāneʻohe Bay and adjacent offshore waters of Oʻahu, Hawaiʻi from December 2020 to August 2021

Scientist: Sarah J. Tucker (University of Hawaiʻi at Mānoa)

Scientist: Jessika Fuessel (University of Chicago)

Scientist: Kelle C. Freel (University of Hawaiʻi at Mānoa)

Scientist: Michael S. Rappé (University of Hawaiʻi at Mānoa)

Principal Investigator: A. Murat Eren (University of Chicago)

BCO-DMO Data Manager: Nancy Copley (Woods Hole Oceanographic Institution)

Program: Center for Chemical Currencies of a Microbial Planet (C-CoMP)

Project: From Signatures of Translational Regulation to Outcomes of Natural Selection: Evolution of Marine Microbes in Changing Environments (C-CoMP Diel Multi 'Omics)

Abstract

Metadata

Files

Supplemental Files

Related Datasets

Related Publications