http://lod.bco-dmo.org/id/dataset/997617
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
2026-04-28
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
NCBI accession metadata for microbial community responses to bacterial extracellular vesicles in the Sargasso Sea, collected on R/V Atlantic Explorer cruises AE2412 and AE2427 in Apr and Nov 2024
2026-04-28
publication
2026-04-28
revision
BCO-DMO Linked Data URI
2026-04-28
creation
http://lod.bco-dmo.org/id/dataset/997617
Steven Biller
Wellesley College
principalInvestigator
Krista Longnecker
Woods Hole Oceanographic Institution
principalInvestigator
Ashley Stein
Wellesley College
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: Biller, S., Longnecker, K., Stein, A., Silvestri, S., Nielsen, C., Jongbloed, C. (2026) NCBI accession metadata for microbial community responses to bacterial extracellular vesicles in the Sargasso Sea, collected on R/V Atlantic Explorer cruises AE2412 and AE2427 in Apr and Nov 2024. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-04-28 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/997617 [access date]
Community changes to vesicle addition Dataset Description: Methods and Sampling: <p>Community samples were collected over a period of four days board the R/V Atlantic Explorer, during cruises AE2412 and AE2427 in April and November 2024.&nbsp;</p>
<p>Replicate 250 mL polycarbonate bottles were filled with 200 mL of surface seawater collected in the Sargasso Sea. Each bottle received either 100 ul of 1x PBS buffer (control), 0.01% glucose (final w/v), or purified extracellular vesicles (approximately 1e9 EVs/mL final concentration). Replicates were placed in a deckboard flow-through incubator and sampled after 0, 24, 48, and 72 hours. The microbial community was sampled by filtering water through a 47mm 0.2 µm Supor filter and frozen at -80 C. &nbsp;DNA was extracted using a phenol-chloroform method utilizing AMPureXP beads (Biller et al 2018). 16S amplicon generation (V4-V5 primers) and sequencing on an Illumina MiSeq was conduced at the Integrated Microbiome Resource, Dalhousie University.&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2049004 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2049004
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2044346 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2044346
onGoing
Steven Biller
Wellesley College
781-283-3294
Department of Biological Sciences 106 Central St.
Wellesley
MA
02481
USA
sbiller@wellesley.edu
pointOfContact
Krista Longnecker
Woods Hole Oceanographic Institution
508-289-2824
266 Woods Hole Road MS# 04
Woods Hole
MA
02543
USA
klongnecker@whoi.edu
pointOfContact
Ashley Stein
Wellesley College
ashleystein06@gmail.com
pointOfContact
asNeeded
Dataset Version: 1
Unknown
study
bioproject_accession
biosample_accession
accession
sample_name
library_ID
library_strategy
library_source
library_selection
library_layout
title
platform
instrument_model
Illumina MiSeq100
Deckboard flow-through incubator
theme
None, User defined
NCBI SRA study accession (SRP)
NCBI BioProject accession
NCBI BioSample accession
NCBI SRA run accession (SRR)
sample identification
seq_descrip
instrument
instrument model
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Incubator
instrument
BCO-DMO Standard Instruments
AE2412
AE2427
service
Deployment Activity
BATS site (31 50 N, 64 10 W)
place
Locations
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: Quantifying the role of microbial extracellular vesicles in marine dissolved organic matter production and consumption
https://osprey.bco-dmo.org/project/853399
Collaborative Research: Quantifying the role of microbial extracellular vesicles in marine dissolved organic matter production and consumption
<p><em>NSF Award Abstract:</em><br />
Microbial production and consumption of organic carbon play critical roles in the marine food web and global carbon cycling. Bacteria release organic matter in a variety of chemical forms and in diverse contexts, ranging from individual molecules to small aggregates and larger biological particles. In recent years we have come to understand that most, if not all, marine microbes release nanoscale structures called extracellular vesicles from their surfaces. These discrete particles, which are abundant in the oceans, are capable of transporting multiple classes of organic molecules between organisms and can serve as a potential nutrient source for other microbes. Extracellular vesicles thus represent a potentially important component of marine microbial food webs, but the magnitude and dynamics of this contribution are unknown. Further, the packaging of material within vesicles may influence the accessibility of this organic material as compared with truly ‘dissolved’ substances to different groups of marine organisms, potentially biasing nutrient exchanges. Broader impacts of this work is providing hands-on research experiences for female undergraduate students - including those from groups historically underrepresented in STEM fields - and training in data analysis tools.</p>
<p>The goal of this project is to advance the understanding of the role that extracellular vesicles play in marine dissolved organic carbon pools and microbial food webs. To determine the contribution of vesicles to organic matter release by marine microbes, the investigators are quantifying the fraction of excreted carbon and nitrogen associated with vesicles released by multiple marine cyanobacteria and heterotrophs. The project is examining how vesicles are ‘consumed’ by heterotrophs to calculate a mass balance of vesicle utilization and produce detailed gene expression data to explore how cells respond to the presence of vesicles. Finally, experiments with coastal and oligotrophic marine communities are providing insights into which organisms utilize vesicles in the field, and whether they are broadly accessible to all microbes or are instead preferentially consumed by a subset of microbes. Collectively, these experiments are opening up a new area of research into the mechanisms underlying the microbial loop and provide foundational insights into the roles of extracellular vesicles in ocean ecosystems.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
VesicleDOM
largerWorkCitation
project
eng; USA
biota
oceans
BATS site (31 50 N, 64 10 W)
2024-04-25
2024-11-20
Laboratory; Vineyard Sound, MA, USA; Bermuda Atlantic Time Series Station
0
BCO-DMO catalogue of parameters from NCBI accession metadata for microbial community responses to bacterial extracellular vesicles in the Sargasso Sea, collected on R/V Atlantic Explorer cruises AE2412 and AE2427 in Apr and Nov 2024
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/997652.rdf
Name: study
Units: unitless
Description: <p>The overall research project identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/997653.rdf
Name: bioproject_accession
Units: unitless
Description: <p>Links to the BioProject database, which provides a central location for related projects</p>
http://lod.bco-dmo.org/id/dataset-parameter/997654.rdf
Name: biosample_accession
Units: unitless
Description: <p>Accession number for the sample, in the format of SAMN#, identifies the biological sample being studied</p>
http://lod.bco-dmo.org/id/dataset-parameter/997655.rdf
Name: accession
Units: unitless
Description: <p>The unique identifer for data files and associated metadata in the Sequence Read Archive (SRA)</p>
http://lod.bco-dmo.org/id/dataset-parameter/997656.rdf
Name: sample_name
Units: unitless
Description: <p>Unique name for each sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/997657.rdf
Name: library_ID
Units: unitless
Description: <p>Short unique ID for each sample library</p>
http://lod.bco-dmo.org/id/dataset-parameter/997658.rdf
Name: library_strategy
Units: unitless
Description: <p>Describes the sequencing protocol; amplicon (primer targeted) or genomic/metagenomic</p>
http://lod.bco-dmo.org/id/dataset-parameter/997659.rdf
Name: library_source
Units: unitless
Description: <p>Source for library material (genomic DNA, PCR product, etc)</p>
http://lod.bco-dmo.org/id/dataset-parameter/997660.rdf
Name: library_selection
Units: unitless
Description: <p>Library selection method (PCR based or not)</p>
http://lod.bco-dmo.org/id/dataset-parameter/997661.rdf
Name: library_layout
Units: unitless
Description: <p>Layout of library (single or paired end reads)</p>
http://lod.bco-dmo.org/id/dataset-parameter/997662.rdf
Name: title
Units: unitless
Description: <p>Short project title</p>
http://lod.bco-dmo.org/id/dataset-parameter/997663.rdf
Name: platform
Units: unitless
Description: <p>Sequencing platform used</p>
http://lod.bco-dmo.org/id/dataset-parameter/997664.rdf
Name: instrument_model
Units: unitless
Description: <p>Model of sequencing instrument used</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
https://osprey.bco-dmo.org/dataset/997617/data/download
download
onLine
dataset
<p>Community samples were collected over a period of four days board the R/V Atlantic Explorer, during cruises AE2412 and AE2427 in April and November 2024.&nbsp;</p>
<p>Replicate 250 mL polycarbonate bottles were filled with 200 mL of surface seawater collected in the Sargasso Sea. Each bottle received either 100 ul of 1x PBS buffer (control), 0.01% glucose (final w/v), or purified extracellular vesicles (approximately 1e9 EVs/mL final concentration). Replicates were placed in a deckboard flow-through incubator and sampled after 0, 24, 48, and 72 hours. The microbial community was sampled by filtering water through a 47mm 0.2 µm Supor filter and frozen at -80 C. &nbsp;DNA was extracted using a phenol-chloroform method utilizing AMPureXP beads (Biller et al 2018). 16S amplicon generation (V4-V5 primers) and sequencing on an Illumina MiSeq was conduced at the Integrated Microbiome Resource, Dalhousie University.&nbsp;</p>
Specified by the Principal Investigator(s)
- Loaded TSV file "SRA_metadata_012628.tsv" using filename as resource name; treated empty strings and "nd" as missing values; headers from row 1
- Removed quotation marks from the title field using find/replace
- Reordered fields to: study, bioproject_accession, biosample_accession, accession, sample_name, library_ID, library_strategy, library_source, library_selection, library_layout, title, platform, instrument_model
- Output written to "997617_v1_sra_microbial_community_composition.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
Illumina MiSeq100
Illumina MiSeq100
PI Supplied Instrument Name: Illumina MiSeq100 PI Supplied Instrument Description:16S amplicon generation (V4-V5 primers) and sequencing on an Illumina MiSeq was conduced at the Integrated Microbiome Resource, Dalhousie University. Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
Deckboard flow-through incubator
Deckboard flow-through incubator
PI Supplied Instrument Name: Deckboard flow-through incubator PI Supplied Instrument Description:Replicates were placed in a deckboard flow-through incubator and sampled after 0, 24, 48, and 72 hours. Instrument Name: Incubator Instrument Short Name:incubator (general) Instrument Description: A device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled.
Note: we have more specific terms for shipboard incubators (https://www.bco-dmo.org/instrument/629001) and in-situ incubators (https://www.bco-dmo.org/instrument/494).
Cruise: AE2412
AE2412
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE2412
Claire Medley
Bermuda Institute of Ocean Sciences
Cruise: AE2427
AE2427
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE2427
Claire Medley
Bermuda Institute of Ocean Sciences
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel