http://lod.bco-dmo.org/id/dataset/999321
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
2026-05-22
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Genomic data collected from R/V Atlantis cruise AT50-08 in the Eastern Tropical North Pacific during February-March 2023
2026-05-28
publication
2026-05-28
revision
BCO-DMO Linked Data URI
2026-05-28
creation
http://lod.bco-dmo.org/id/dataset/999321
Maria G. Pachiadaki
Woods Hole Oceanographic Institution
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: Pachiadaki, M. G. (2026) Genomic data collected from R/V Atlantis cruise AT50-08 in the Eastern Tropical North Pacific during February-March 2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2026-05-28 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/999321 [access date]
SAG AT50-08 Data Dataset Description: Methods and Sampling: <p>Water samples (see data file for sampling depths and coordinates) were prepared by cryopreservation according to the protocol recommended by the Bigelow Single Cell Genomics Center (<a href="https://scgc.bigelow.org/wp-content/uploads/2018/06/Sample_cryopreservation_glyTE.pdf" target="_blank">https://scgc.bigelow.org/wp-content/uploads/2018/06/Sample_cryopreservation_glyTE.pdf</a>).</p>
<p>Briefly, small volumes of whole water (1 milliliter (ml)) were aliquoted under Helium (He) atmosphere using a glove box. Redox-Sensor Green (1 microliter (uL)) was added to the aliquots and left to incubate in the dark at in situ temperatures for 30 minutes. At the end of the incubation, glyTE (100 uL) was added and they were subsequently frozen at -80 degrees Celsius.</p>
<p>Sorting was performed on 4 April 2023 (within &lt;2 months from the date the first sample was collected) and SAGs were generated with the modified genomic DNA amplification technique, WGA-Y, which enables a substantially improved average genome recovery from single cells (service S-202).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1924492 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1924492
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1924424 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1924424
onGoing
Maria G. Pachiadaki
Woods Hole Oceanographic Institution
508-289-2943
Redfield Lab
Woods Hole
MA
02543
USA
mpachiadaki@whoi.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
NextSeq 2000 DNA sequencer
BD InFlux Mariner flow cytometer
12L Niskin bottles
theme
None, User defined
Automated DNA Sequencer
Flow Cytometer
Niskin bottle
instrument
BCO-DMO Standard Instruments
AT50-08B
service
Deployment Activity
Eastern Tropical Pacific, Minimum Oxygen Zone (OMZ)
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: Key Microbial Processes in Oxygen Minimum Zones: From In Situ Community Rate Measurements to Single Cells
https://osprey.bco-dmo.org/project/828777
Collaborative Research: Key Microbial Processes in Oxygen Minimum Zones: From In Situ Community Rate Measurements to Single Cells
<p>NSF Award Abstract:</p>
<p>Oxygen availability shapes the distributions and activities of marine organisms. Ongoing human activities and climate change are expected to lead to expansion and intensification of already large oxygen-stressed areas of the coastal and open ocean. Decreases in ocean oxygen have significant ecological consequences, including habitat loss for migratory and bottom-dwelling organisms, modification of the marine food web, and production of trace gases with pronounced feedbacks on climate, such as methane and nitrous oxide. Intense chemical cycling by microorganisms occurs in oxygen-depleted marine habitats. However, a full understanding of the consequences for marine ecosystems is hampered by limited knowledge of actual rates of key microbiological processes and dynamics of the microorganisms mediating them. This study combines novel methods and sampling techniques to understand how these processes are influenced by changes in oxygen concentration to inform predictions of important chemical exchanges within a changing ocean and its production of climate-active gases. This deeply collaborative project trains undergraduates (four of whom participate on the cruise), a graduate student and a postdoctoral fellow. Outreach takes place in middle and high schools and through social media. Data and samples from the cruise are integrated in coursework.</p>
<p>Oxygen depletion alters cycling of major elements (especially carbon, nitrogen, and sulfur) as well as food web functionality. This project addresses major gaps in our knowledge of oxygen minimum zone (OMZ) processes by applying in situ approaches to more accurately measure rates of several key microbial processes (chemoautotrophy, denitrification, anammox, sulfate reduction and sulfide oxidation) central to marine biogeochemical cycling. This work studies the Eastern Tropical North Pacific OMZ, the largest open ocean oxygen-depleted system, to 1) determine the in situ rates of microbial processes involved in carbon, nitrogen, and sulfur cycling, 2) reveal the genomic blueprint of active single cells involved in these processes, and 3) obtain estimates of the relative contributions of the dominant chemoautotrophic and heterotrophic groups to the measured rates. This work include applies cutting-edge equipment for in situ sampling and incubations that minimize artifacts associated with traditional water sampling approaches, allowing more accurate estimates of rates of important biogeochemical processes. Additionally, rate measurements of relatively undisturbed bulk and fractionated water samples make it easier to distinguish the potential role of particle-associated microorganisms in these OMZ processes. Single cell sorting of microorganisms using a fluorescent dye indicative of cell activity together with metatranscriptomics informs on metabolic pathways used for key processes by active microbial community members, as well as the potential coupling of chemoautotrophy and nitrogen or/and sulfur cycling. By combining stable isotope probing, fluorescence in situ hybridization and single cell Raman microspectrometry the relative activity levels of different microbial phylotypes involved in chemoautotrophic and heterotrophic elemental cycling are assessed.</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>
MicroPro
largerWorkCitation
project
eng; USA
oceans
Eastern Tropical Pacific, Minimum Oxygen Zone (OMZ)
2026-05-28
East Tropical North Pacific Ocean
0
BCO-DMO catalogue of parameters from Genomic data collected from R/V Atlantis cruise AT50-08 in the Eastern Tropical North Pacific during February-March 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
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/999321/data/download
download
onLine
dataset
<p>Water samples (see data file for sampling depths and coordinates) were prepared by cryopreservation according to the protocol recommended by the Bigelow Single Cell Genomics Center (<a href="https://scgc.bigelow.org/wp-content/uploads/2018/06/Sample_cryopreservation_glyTE.pdf" target="_blank">https://scgc.bigelow.org/wp-content/uploads/2018/06/Sample_cryopreservation_glyTE.pdf</a>).</p>
<p>Briefly, small volumes of whole water (1 milliliter (ml)) were aliquoted under Helium (He) atmosphere using a glove box. Redox-Sensor Green (1 microliter (uL)) was added to the aliquots and left to incubate in the dark at in situ temperatures for 30 minutes. At the end of the incubation, glyTE (100 uL) was added and they were subsequently frozen at -80 degrees Celsius.</p>
<p>Sorting was performed on 4 April 2023 (within &lt;2 months from the date the first sample was collected) and SAGs were generated with the modified genomic DNA amplification technique, WGA-Y, which enables a substantially improved average genome recovery from single cells (service S-202).</p>
Specified by the Principal Investigator(s)
<p>The obtained sequence reads were quality-trimmed with Trimmomatic v0.32 using the following settings: -phred33 LEADING:0 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36. Reads matching the <em>H. sapiens </em>reference assembly GRCh38 and a local database of WGA-X reagent contaminants (≥95% identity of ≥100 bp alignments), as well as low complexity reads (containing &lt;5% of any nucleotide) were removed. The remaining reads were digitally normalized with kmernorm 1.05 (<a href="http://sourceforge.net/projects/kmernorm" target="_blank">http://sourceforge.net/projects/kmernorm</a>) using settings -k 21 -t 30 -c 3 and then assembled with SPAdes v.3.15.2 &nbsp;using the following settings: --careful --sc --phred-offset 33. Each end of the obtained contigs was trimmed by 100 bp, and then only contigs longer than 2,000 bp were retained. Contigs matching the <em>H. sapiens </em>reference assembly GRCh38 and a local database of WGA-X reagent contaminants (≥95% identity of ≥100 bp alignments) were removed. This workflow was evaluated for assembly errors using three bacterial benchmark cultures with diverse genome complexity and %GC, indicating no non-target and undefined bases in the assemblies and average frequencies of mis-assemblies, indels, and mismatches per 100 kbp: 1.5, 3.0 and 5.0.</p>
<p>SAG taxonomic assignments were obtained with GTDB-Tk v2.2.6. In addition, 16S rRNA gene regions longer than 500 bp were identified using local alignments provided by BLAST against CREST's curated SILVA reference database SILVAMod v128 and classified using a reimplementation of CREST's last common ancestor algorithm. Genome functional annotation was first performed using Prokka with default Swiss-Prot databases supplied by the software. Prokka was run a second time with a custom protein annotation database built from compiling Swiss-Prot entries for Archaea and Bacteria.&nbsp;</p>
Specified by the Principal Investigator(s)
currently being processed
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
NextSeq 2000 DNA sequencer
NextSeq 2000 DNA sequencer
PI Supplied Instrument Name: NextSeq 2000 DNA sequencer PI Supplied Instrument Description:The genomic material was sequenced using NextSeq 2000 DNA sequencer. 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.
BD InFlux Mariner flow cytometer
BD InFlux Mariner flow cytometer
PI Supplied Instrument Name: BD InFlux Mariner flow cytometer PI Supplied Instrument Description:Cells were sorted using an BD InFlux Mariner flow cytometer Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer Instrument Description: Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/
12L Niskin bottles
12L Niskin bottles
PI Supplied Instrument Name: 12L Niskin bottles PI Supplied Instrument Description:Seawater samples were collected using a 24-bottle rosette equipped with 12 L Niskin bottles. Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
Cruise: AT50-08B
AT50-08B
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel
AT50-08B
Maria G. Pachiadaki
Woods Hole Oceanographic Institution
R/V Atlantis
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantis
vessel