http://lod.bco-dmo.org/id/dataset/965379
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2025-06-17
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Under the ice bacterial cultures and genome sequences from the R/V Kronprins Haakon in the Arctic Ocean from May 18 to 21, 2023
2025-06-18
publication
2025-06-18
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-06-20
publication
https://doi.org/10.26008/1912/bco-dmo.965379.1
Robert Morris
University of Washington
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Morris, R. (2025) Under the ice bacterial cultures and genome sequences from the R/V Kronprins Haakon in the Arctic Ocean from May 18 to 21, 2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-06-18 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.965379.1 [access date]
Arctic Bacterial Genomes Dataset Description: Methods and Sampling: <p>Samples for cultivation were collected at 81.04° N, 10.62° E, from 25 meters (m) below the ice/water interface using a Hydro-Bios 2-liter (L) water sampler. Fifty milliliters (mL) were transferred to a polycarbonate bottle and then 1 mL of seawater was amended to 10% (v/v) glycerol, flash frozen in liquid nitrogen, and stored at -80 degrees Celsius (°C) until used for high-throughput dilution to extinction cultivation. Seawater for culture media (10 L) was collected at 80.96° N, 9.66° E from 1 m below the ice/water interface into acid washed and miliQ rinsed cubitainers. Seawater was then filter-sterilized using a tangential flow filtration (TFF) system equipped with a 30 kDa Pellicon XL Polyethersulfone Biomax filter (MilliporeSigma, Burlington, MA). The resulting media was collected in 1 L acid-washed and autoclaved polycarbonate bottles, incubated for 2 months at 4 °C, and checked for bacterial growth to ensure sterility prior to use.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2201645 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2201645
completed
Robert Morris
University of Washington
206-221-7228
School of Oceanography Box 357940
Seattle
WA
98195-7940
USA
morrisrm@uw.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
isolate
Date
Lat
Lon
id
genome_length
sequencing_covearge
pcnt_gc
coding_ratio
rRNA
genome_accession
bioproject
biosample
sequence_read_archive
Hydro-Bios 2 L water sampler
Oxford Nanopore Technologies (ONT) R10.4.1 Flongle flow cells with the SQK-RAD114 rapid library prep kit
theme
None, User defined
sample identification
date
latitude
longitude
taxon
length
sample description
accession number
NCBI BioProject accession
NCBI BioSample accession
NCBI SRA run accession (SRR)
featureType
BCO-DMO Standard Parameters
Discrete water sampler
Nanopore Sequencer
instrument
BCO-DMO Standard Instruments
2023007008
service
Deployment Activity
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Collaborative Research: Drivers and effects of latent phage activation in marine SAR11
https://osprey.bco-dmo.org/project/874740
Collaborative Research: Drivers and effects of latent phage activation in marine SAR11
<p><em>NSF Award Abstract:</em></p>
<p>Viruses are the most abundant biological entities in the ocean. When they infect plankton, they can alter food webs, induce shifts in nutrient cycles, and enhance genetic exchange. However, the mechanisms that control these important processes are largely unknown, which has limited our ability to predict infection outcomes in nature. The primary goal of this study is to identify key chemical, physical, and biological factors that influence host-virus interactions in cultured bacterioplankton and to use this information to build mathematical models that predict infection dynamics in diverse marine ecosystems. Most of the marine viruses available for detailed study kill bacteria following infection. This novel study focuses on SAR11, the most abundant marine bacteria, which harbor dormant viruses called prophages, to determine what causes prophage activation and host death. Specifically, the research team uses field surveys and laboratory experiments with SAR11-prophage pairs to generate data and mathematical models to predict the outcomes of viral infections in SAR11 and other marine microbes.</p>
<p>The conditions that trigger prophage activation and their corresponding contributions to ecosystem processes are largely hypothetical, due primarily to difficulties identifying and culturing host cells with prophages. It is becoming increasingly clear that the impact and importance of these infections are under-characterized and under-estimated. The proposed research revises estimates of prophage activation in globally-important SAR11 by quantifying infection occurrence, identifying prophage activation inducers, and testing the effects of maintaining virus DNA in the host genomes. The frequency of prophage infections is determined by analyzing bacterial metagenomes generated with long-read sequencing technology. Controlled growth experiments under a range of conditions that cause stress (physical, chemical, and biological) and evaluation of shifts in gene expression are employed to identify drivers of prophage activation. The outcomes of prophage infections in culture serve to parameterize key interactions in numerical models that can then predict outcomes in nature. This study fills critical gaps in knowledge about the mechanisms that maintain the large and genetically diverse populations of bacteria and viruses in the ocean and has the potential to change our understanding and capacity to predict host-virus interactions under changing environmental conditions.</p>
SAR11 Prophage
largerWorkCitation
project
eng; USA
oceans
10.62
10.62
81.04
81.04
2023-05-21
2023-05-21
Puget Sound cruises & Laboratory experiments at UW
0
BCO-DMO catalogue of parameters from Under the ice bacterial cultures and genome sequences from the R/V Kronprins Haakon in the Arctic Ocean from May 18 to 21, 2023
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/965539.rdf
Name: isolate
Units: unitless
Description: <p>cultivation number</p>
http://lod.bco-dmo.org/id/dataset-parameter/965540.rdf
Name: Date
Units: unitless
Description: <p>date of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/965541.rdf
Name: Lat
Units: decimal degrees North
Description: <p>latitude of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/965542.rdf
Name: Lon
Units: decimal degrees East
Description: <p>longitude of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/965543.rdf
Name: id
Units: unitless
Description: <p>taxonomic name</p>
http://lod.bco-dmo.org/id/dataset-parameter/965544.rdf
Name: genome_length
Units: number of nucleotides
Description: <p>total length in nucleotides</p>
http://lod.bco-dmo.org/id/dataset-parameter/965545.rdf
Name: sequencing_covearge
Units: unitless
Description: <p>depth of sequence coverage</p>
http://lod.bco-dmo.org/id/dataset-parameter/965546.rdf
Name: pcnt_gc
Units: unitless
Description: <p>percent of guanine and cytosine residues</p>
http://lod.bco-dmo.org/id/dataset-parameter/965547.rdf
Name: coding_ratio
Units: unitless
Description: <p>ratio of protein coding genes</p>
http://lod.bco-dmo.org/id/dataset-parameter/965548.rdf
Name: rRNA
Units: unitless
Description: <p>number of 5S, 16S, and 23S ribosomal RNAs</p>
http://lod.bco-dmo.org/id/dataset-parameter/965549.rdf
Name: genome_accession
Units: unitless
Description: <p>NCBI accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/965550.rdf
Name: bioproject
Units: unitless
Description: <p>NCBI BioProject number</p>
http://lod.bco-dmo.org/id/dataset-parameter/965551.rdf
Name: biosample
Units: unitless
Description: <p>NCBI BioSample number</p>
http://lod.bco-dmo.org/id/dataset-parameter/965552.rdf
Name: sequence_read_archive
Units: unitless
Description: <p>NCBI SRA number</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
4300
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/6a5ec8a9-1885-4080-8b8d-516f4bb472b4/content
download
https://doi.org/10.26008/1912/bco-dmo.965379.1
download
onLine
dataset
<p>Samples for cultivation were collected at 81.04° N, 10.62° E, from 25 meters (m) below the ice/water interface using a Hydro-Bios 2-liter (L) water sampler. Fifty milliliters (mL) were transferred to a polycarbonate bottle and then 1 mL of seawater was amended to 10% (v/v) glycerol, flash frozen in liquid nitrogen, and stored at -80 degrees Celsius (°C) until used for high-throughput dilution to extinction cultivation. Seawater for culture media (10 L) was collected at 80.96° N, 9.66° E from 1 m below the ice/water interface into acid washed and miliQ rinsed cubitainers. Seawater was then filter-sterilized using a tangential flow filtration (TFF) system equipped with a 30 kDa Pellicon XL Polyethersulfone Biomax filter (MilliporeSigma, Burlington, MA). The resulting media was collected in 1 L acid-washed and autoclaved polycarbonate bottles, incubated for 2 months at 4 °C, and checked for bacterial growth to ensure sterility prior to use.</p>
Specified by the Principal Investigator(s)
<p>Cultures selected for whole genome sequencing were revived from freezer stocks in 1 L acid washed and autoclaved polycarbonate bottles containing TFF sterilized Puget Sound seawater media. Cells were collected on 47-millimeter (mm) 0.2-micrometer (µm) pore size Isopore membrane filters (MilliporeSigma, Burlington, MA) when cultures reached maximum cell densities (between 10^5 and 10^6 cells per mL). High molecular weight DNA was extracted using the Autogen Quickgene DNA Tissue Kit (Autogen, Holliston, MA) following the extraction protocol for animal tissue with minor modifications as noted below.</p>
<p>Filters were cut into small pieces using sterile forceps and scissors and placed in sterile 2 mL DNA LoBind tubes (Eppendorf, Hamburg, Germany) containing 200 microliters (µL) of TE buffer. Filters were then frozen at -80 °C for 20 minutes and heated until thawed at 95 °C. All recommended extraction volumes were doubled, and DNA was eluted in 200 µL of molecular grade water. DNA was cleaned using 1X volume:volume DNA magnetic beads (Sergi Lab Supplies, Seattle WA) with two 80% ethanol washes, then eluted in 20 µL of molecular grade water. DNA was quantified using a Qubit dsDNA Quantitation High Sensitivity kit (Invitrogen, Waltham, MA) and sequenced using the Oxford Nanopore Technologies (ONT) R10.4.1 Flongle flow cells with the SQK-RAD114 rapid library prep kit (Oxford Nanopore Technologies, Oxford, United Kingdom). Bases were called with Dorado (github.com/nanoporetech/dorado), using the dna_r10.4.1_e8.2_400bps_hac@v4.2.0 model.</p>
Specified by the Principal Investigator(s)
- Imported original file "Arctic_genomes_metadata.xlsx" into the BCO-DMO system.
- Converted Date column to YYYY-MM-DD format.
- Removed "° N" and "° E" from the Lat and Lon columns.
- Renamed fields to comply with BCO-DMO naming conventions.
- Saved the final file as "965379_v1_arctic_genomes.csv".
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Hydro-Bios 2 L water sampler
Hydro-Bios 2 L water sampler
PI Supplied Instrument Name: Hydro-Bios 2 L water sampler Instrument Name: Discrete water sampler Instrument Short Name: Instrument Description: A device that collects an in-situ discrete water sample from any depth and returns it to the surface without contamination by the waters through which it passes, such as a water bottle.
Oxford Nanopore Technologies (ONT) R10.4.1 Flongle flow cells with the SQK-RAD114 rapid library prep kit
Oxford Nanopore Technologies (ONT) R10.4.1 Flongle flow cells with the SQK-RAD114 rapid library prep kit
PI Supplied Instrument Name: Oxford Nanopore Technologies (ONT) R10.4.1 Flongle flow cells with the SQK-RAD114 rapid library prep kit Instrument Name: Nanopore Sequencer Instrument Short Name: Instrument Description: A proprietary high-throughput DNA sequencing technology from Oxford Nanopore Technologies that can directly identify and sequence DNA molecules as they pass through nanopores, driven by electrophoresis.
Cruise: 2023007008
2023007008
Community Standard Description
International Council for the Exploration of the Sea
R/V Kronprins Haakon
vessel
Community Standard Description
International Council for the Exploration of the Sea
R/V Kronprins Haakon
vessel