http://lod.bco-dmo.org/id/dataset/963428
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
2025-06-02
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
SRA accession and collection metadata for sediments samples collected at two Chesapeake Bay stations from Mar 2017 to Aug 2018
2025-06-02
publication
2025-06-02
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-07-08
publication
https://doi.org/10.26008/1912/bco-dmo.963428.1
Sairah Malkin
University of Maryland Center for Environmental Science
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: Malkin, S. (2025) SRA accession and collection metadata for sediments samples collected at two Chesapeake Bay stations from Mar 2017 to Aug 2018. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-06-02 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.963428.1 [access date]
SRA accessions from Chesapeake Bay sediment samples 2017-2018 Dataset Description: Methods and Sampling: <p>From March of 2017 to August of 2018, sediments samples were collected at two Chesapeake Bay stations:&nbsp;CB4.3C (38.55505 N -76.42794 W; 26 m depth) and CB4.3W (38.55728 N&nbsp;-76.49402 W; 9m depth).&nbsp;</p>
<p>Replicate sediment cores were collected using a gravity corer (Uwitec; clear PVC liners, Ø = 8.6 cm), kept in the dark at bottom water temperature in a water bath, and transported back to the laboratory, where they were held in a climate controlled room. From each station, one sediment core was subsampled for nucleic acids, microscopy, and chlorophyll a (Chl a) analyses, two cores were used for microsensor profiling. Sampling was undertaken from small vessels (Parker or Wetsig boats). Surface sediments (0–0.5 cm) were transferred to 5-mL cryovials, rapidly frozen in a liquid nitrogen-charged dry shipper, and stored at -80 degC.&nbsp;</p>
<p>This data set refers to the DNA samples. DNA was extracted from a thawed sediment aliquot. Prior to cell lysis, carbonates were dissolved in an acetate buffer–PBS solution with gentle mixing, and soluble (extracellular) DNA was removed by washing in Tris- EDTA buffer with gentle mixing. Cell lysis was achieved using a combination of bead-beating, repeated heat-thaw cycling, and chemical lysis. Extracted DNA was purified by two washes with a chloroform–isoamyl alcohol solution and then precipitated with a PEG 8000-NaCl solution in the presence of linear polyacrylamide at room temperature. A final wash was made in 70% ethanol, and the resultant DNA pellet was allowed to air dry and then dissolved in water. Extracted DNA quality was checked by agarose gel electrophoresis, and its concentration was measured by fluorometry (Qubit 2.0 fluorometer; Invitrogen) using Qubit dsDNA assay kits. Further purification was found to be unnecessary. The hypervariable region V4-V5 of the 16S rRNA gene was targeted for amplification, using the modified primer pair515F-Y/926R (GTG YCA GCM GCC GCG GTA A)/(CCG YCA ATT YMT TTR AGT TT) (Parada et al. 2015). Amplification,&nbsp; barcoding, and sequencing were performed at the Bioanalytical Services Laboratory (BASLAB, IMET). Amplification proceeded via two steps, first for gene amplification and the second for adding indexes, and clean-up was accomplished using AMPure XP beads (Beckman Coulter). Amplicons were sequenced using an Illumina MiSeq platform (2 x 300 nt paired-end reads).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756877 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756877
completed
Sairah Malkin
University of Maryland Center for Environmental Science
410-221-8418
2020 Horns Point Rd.
Cambridge
MD
21613
USA
smalkin@umces.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
sample_name
bioproject_accession
collection_date
Station_Name
Latitude
Longitude
MiSeq platform
water bath
Qubit 2.0 fluorometer
Uwitec gravity corer
theme
None, User defined
sample identification
NCBI BioSample accession
date
station id
latitude
longitude
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
circulating water bath
Fluorometer
Gravity Corer
instrument
BCO-DMO Standard Instruments
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: Probing the Metabolic and Electrical Interactions of Cable Bacteria in Anoxic Sediments
https://osprey.bco-dmo.org/project/773452
Collaborative Research: Probing the Metabolic and Electrical Interactions of Cable Bacteria in Anoxic Sediments
<p><em>NSF Award Abstract:</em><br />
Marine sediments represent the world's largest repository of stored organic carbon, and understanding how microorganisms break down this carbon is an imperative for understanding global carbon cycling. Yet long-standing questions remain regarding how networks of microorganisms work together to accomplish the complete breakdown of organic carbon in marine sediments. Sediment microbes interact in a myriad of ways that couple their metabolism to the break down of organic carbon, including by sharing products of metabolism. Accumulating evidence further suggests that some microorganisms can interact by transferring electrons directly to other unrelated microorganisms. This ability occurs across diverse microorganisms and appears to be widespread in the biosphere, particularly in anaerobic environments such as marine sediments. This project addresses emerging questions about the identity and metabolic linkages between microorganisms that work together in natural anaerobic marine and estuarine sediments to break down organic carbon. The investigators approach these questions by focusing on the influence of a keystone bacterium on its surrounding microbial community. "Cable bacteria" are a recently discovered group of long filamentous bacteria that act as electrical conductors in aquatic sediments providing a conduit for electrons to commute from deeper sulfidic sediments up to the surface oxygen layer by the process of centimeter-scale electron transport. Since their discovery about 6 years ago, these bacteria have been observed in a wide range of depositional sedimentary environments, often at extremely high cell densities. Where these bacteria are abundant, such as in coastal marine muds, they drive intense localized changes in pH and strongly influence the mineral cycling. This research explores the direct and indirect influence of cable bacteria on the metabolic activity of associated microorganisms. This project also advance the education and training of two early-career investigators, two PhD students, and undergraduate students. The skills and expertise gained from these PhD research projects will enable the students to be competitive in academic pursuits and in bioinformatics and technology applications relevant to private industry. The scientific discoveries emerging from this work is being incorporated into undergraduate and graduate level courses in marine microbial ecology. The research team will reach out to the broader community by hosting public lectures promoting a better understanding of environmental microbial ecology.</p>
<p>The proposed work is to investigate the role of cable bacteria in structuring sediment microbial communities. Due to their growth strategy and morphology, cable bacteria are particularly amenable to experimental manipulation, providing an outstanding opportunity to better understand community interactions among microorganisms in a natural and complex anaerobic environment. The investigators will explore the interactions and relationships between cable bacteria and their associated microbial community by manipulating the growth and activity of cable bacteria and quantifying the resultant microbial community response. Specifically, this project aims to (1) identify microorganisms whose growth is enhanced by cable bacteria, (2) identify metabolic processes linked with cable bacteria activity using metatranscriptomics, (3) test specific metabolic links between sediment microorganisms and cable bacteria activity using a DNA-stable isotope probing (SIP) approach, and (4) visually confirm the identity and quantify key microorganisms associated with cable bacteria using microscopy. As more is learned about the identity and the mechanisms by which microorganisms are metabolically linked in anoxic sediments, we will be better able to understand and make predictions about how microorganisms function in their environment and how they can be utilized in bioengineered systems.</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>
Anoxic Sediment Bacteria Interactions
largerWorkCitation
project
eng; USA
biota
oceans
-76.49402
-76.42794
38.55505
38.55728
2017-03-27
2018-08-16
Chesapeake Bay sediments; Mid-Atlantic Coastal sediments
0
BCO-DMO catalogue of parameters from SRA accession and collection metadata for sediments samples collected at two Chesapeake Bay stations from Mar 2017 to Aug 2018
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/963963.rdf
Name: sample_name
Units: unitless
Description: <p>Unique Sample Name</p>
http://lod.bco-dmo.org/id/dataset-parameter/963964.rdf
Name: bioproject_accession
Units: unitless
Description: <p>Accession number in NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/963965.rdf
Name: collection_date
Units: unitless
Description: <p>Date of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/963966.rdf
Name: Station_Name
Units: unitless
Description: <p>Name of station (CB4.3C or CB4.3W)</p>
http://lod.bco-dmo.org/id/dataset-parameter/963967.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude of sample collection, postive is North</p>
http://lod.bco-dmo.org/id/dataset-parameter/963968.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude of sample collection, negative is West</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
1110
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/e01168bd-d5bb-4fce-bd36-01e76e7de4dd/content
download
https://doi.org/10.26008/1912/bco-dmo.963428.1
download
onLine
dataset
<p>From March of 2017 to August of 2018, sediments samples were collected at two Chesapeake Bay stations:&nbsp;CB4.3C (38.55505 N -76.42794 W; 26 m depth) and CB4.3W (38.55728 N&nbsp;-76.49402 W; 9m depth).&nbsp;</p>
<p>Replicate sediment cores were collected using a gravity corer (Uwitec; clear PVC liners, Ø = 8.6 cm), kept in the dark at bottom water temperature in a water bath, and transported back to the laboratory, where they were held in a climate controlled room. From each station, one sediment core was subsampled for nucleic acids, microscopy, and chlorophyll a (Chl a) analyses, two cores were used for microsensor profiling. Sampling was undertaken from small vessels (Parker or Wetsig boats). Surface sediments (0–0.5 cm) were transferred to 5-mL cryovials, rapidly frozen in a liquid nitrogen-charged dry shipper, and stored at -80 degC.&nbsp;</p>
<p>This data set refers to the DNA samples. DNA was extracted from a thawed sediment aliquot. Prior to cell lysis, carbonates were dissolved in an acetate buffer–PBS solution with gentle mixing, and soluble (extracellular) DNA was removed by washing in Tris- EDTA buffer with gentle mixing. Cell lysis was achieved using a combination of bead-beating, repeated heat-thaw cycling, and chemical lysis. Extracted DNA was purified by two washes with a chloroform–isoamyl alcohol solution and then precipitated with a PEG 8000-NaCl solution in the presence of linear polyacrylamide at room temperature. A final wash was made in 70% ethanol, and the resultant DNA pellet was allowed to air dry and then dissolved in water. Extracted DNA quality was checked by agarose gel electrophoresis, and its concentration was measured by fluorometry (Qubit 2.0 fluorometer; Invitrogen) using Qubit dsDNA assay kits. Further purification was found to be unnecessary. The hypervariable region V4-V5 of the 16S rRNA gene was targeted for amplification, using the modified primer pair515F-Y/926R (GTG YCA GCM GCC GCG GTA A)/(CCG YCA ATT YMT TTR AGT TT) (Parada et al. 2015). Amplification,&nbsp; barcoding, and sequencing were performed at the Bioanalytical Services Laboratory (BASLAB, IMET). Amplification proceeded via two steps, first for gene amplification and the second for adding indexes, and clean-up was accomplished using AMPure XP beads (Beckman Coulter). Amplicons were sequenced using an Illumina MiSeq platform (2 x 300 nt paired-end reads).</p>
Specified by the Principal Investigator(s)
- Imported "SRA_samples_ChesapeakeBay_sediments_2017-2018.xlsx" into BCO-DMO system
- Added "Latitude" and "Longitude" for stations as described in the metadata
- Exported file as "963428_v1_sra_samples_cb_sediments.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
MiSeq platform
MiSeq platform
PI Supplied Instrument Name: MiSeq platform PI Supplied Instrument Description: Amplification, barcoding, and sequencing were performed at the Bioanalytical Services Laboratory (BASLAB, IMET), where amplicons were sequenced using an Illumina MiSeq platform. 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.
water bath
water bath
PI Supplied Instrument Name: water bath PI Supplied Instrument Description:Replicate sediment cores were collected using a gravity corer (Uwitec; clear PVC liners, Ø = 8.6 cm), kept in the dark at bottom water temperature in a water bath, and transported back to the laboratory, where they were held in a climate controlled room. Instrument Name: circulating water bath Instrument Short Name: Instrument Description: A device designed to regulate the temperature of a vessel by bathing it in water held at the desired temperature. [Definition Source: NCI]
Qubit 2.0 fluorometer
Qubit 2.0 fluorometer
PI Supplied Instrument Name: Qubit 2.0 fluorometer PI Supplied Instrument Description:Extracted DNA was quantified using a Qubit 2.0 fluorometer (Invitrogen). Instrument Name: Fluorometer Instrument Short Name:Fluorometer Instrument Description: A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/113/
Uwitec gravity corer
Uwitec gravity corer
PI Supplied Instrument Name: Uwitec gravity corer PI Supplied Instrument Description:Coring was undertaken using a Uwitec gravity corer. Instrument Name: Gravity Corer Instrument Short Name:Gravity Corer Instrument Description: The gravity corer allows researchers to sample sediment layers at the bottom of lakes or oceans. The coring device is deployed from the ship and gravity carries it to the seafloor. (http://www.whoi.edu/instruments/viewInstrument.do?id=1079). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/51/