http://lod.bco-dmo.org/id/dataset/753343
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
2019-01-22
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Metagenomic, metatranscriptomic, and single cell sequencing data from an Environmental Sample Processor deployment in Monterey Bay, CA in 2016.
2020-03-20
publication
2020-03-20
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-04-01
publication
https://doi.org/10.26008/1912/bco-dmo.753343.2
Mary Ann Moran
University of Georgia
principalInvestigator
Brent Nowinski
University of Georgia
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: Moran, M. A. (2020) Metagenomic, metatranscriptomic, and single cell sequencing data from a Environmental Sample Processor deployment in Monterey Bay, CA from 2016. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2020-03-20 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.753343.2 [access date]
Metagenomic, metatranscriptomic, and single cell sequencing data from the Fall 2016 ESP deployment in Monterey Bay, CA Dataset Description: <p>These metagenomic and metatranscriptomic time-series data cover a 52-day period in the fall of 2016 during an intense bloom of the dinoflagellate Akashiwo sanguinea in Monterey Bay, CA, USA. The dataset comprises 84 metagenomes, 82 metatranscriptomes, and 88 16S rRNA amplicon libraries that capture the functions and taxonomy the bacterial and archaeal community. In addition, 88 18S rRNA amplicon libraries describe the taxonomy of the eukaryotic community during the bloom. Microbial cells were collected at station M0 using the moored autonomous robotic Environmental Sample Processor (ESP) instrument and preserved with RNAlater in the instrument until retrieval.</p> Methods and Sampling: <p>The Environmental Sample Processor (ESP) filtered seawater sequentially through 5.0 um and 0.2 um pore size polyvinylidene fluoride filters. Seawater was evacuated from filters and followed twice with a 2 minute incubation with 1 ml of RNAlater™. RNAlater was evacuated, and filters were stored in the ESP until they were transferred to -80 C upon instrument recovery.&nbsp;</p>
<p>Grab samples for sequencing while the ESP was not deployed were taken using Niskin bottles that collected seawater at the same depth and location of the ESP. Water was transferred to a low-density polyethylene cubitainer and maintained at ambient temperature until return to lab within 30 min. Seawater was filtered as above with vacuum filtration and preserved immediately in liquid nitrogen and transferred to -80 C.</p>
<p>Single-cell sequencing: Seawater was transferred directly from the Niskin bottle to a 50 ml Falcon tube and placed on ice until brought back to lab. Each sampling day, 3 x 1 ml of seawater was preserved in cryovials using 100 ul of glyTe (5 ml glycerol, 3 ml Milli-Q H2O, 1 ml 100 x TE pH 8.0, 0.2 um filter sterilized after mixing the above, and stored in -20 C freezer). Preserved samples were then placed in a -80 C freezer. Samples were processed and sequenced at JGI</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1342694 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1342694
completed
Mary Ann Moran
University of Georgia
706-542-6481
Department of Marine Sciences
Athens
GA
30602
USA
mmoran@uga.edu
pointOfContact
Brent Nowinski
University of Georgia
Department of Marine Science
Athens
GA
30602
nowinksi@uga.edu
pointOfContact
asNeeded
Dataset Version: 2
Unknown
GOLD_Project_ID
Analysis_Project_Name
Type
Assembly_Method
Collection_Date
Instrument
JGI_Contigs_Link
JGI_Project_ID
JGI_Sample_ID
JGI_Sequencing_Project_ID
JGI_Sequencing_Project_Name
Latitude_and_Longitude
NCBI_BioProject_Accession
NCBI_BioSample_Accession
NCBI_Project_ID
NCBI_SRA_Accession_ID
Sample_Name
Sequencing_Run_Mode
Total_Bases
Volume_Seawater_Filtered
env_biome
env_feature
env_material
geo_loc_name
lat
lon
theme
None, User defined
accession number
project
sample description
sampling_method
date
instrument
No BCO-DMO term
sample identification
volume of water filtered
latitude
longitude
featureType
BCO-DMO Standard Parameters
Moran_Monterey_2016
service
Deployment Activity
Monterey Bay, CA, USA; Station M0
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.
Dimensions of Biodiversity
http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503446
Dimensions of Biodiversity
(adapted from the NSF Synopsis of Program)
Dimensions of Biodiversity is a program solicitation from the NSF Directorate for Biological Sciences. FY 2010 was year one of the program. [MORE from NSF]
The NSF Dimensions of Biodiversity program seeks to characterize biodiversity on Earth by using integrative, innovative approaches to fill rapidly the most substantial gaps in our understanding. The program will take a broad view of biodiversity, and in its initial phase will focus on the integration of genetic, taxonomic, and functional dimensions of biodiversity. Project investigators are encouraged to integrate these three dimensions to understand the interactions and feedbacks among them. While this focus complements several core NSF programs, it differs by requiring that multiple dimensions of biodiversity be addressed simultaneously, to understand the roles of biodiversity in critical ecological and evolutionary processes.
Dimensions of Biodiversity
largerWorkCitation
program
Bacterial Taxa that Control Sulfur Flux from the Ocean to the Atmosphere
https://osprey.bco-dmo.org/project/541255
Bacterial Taxa that Control Sulfur Flux from the Ocean to the Atmosphere
<p>Surface ocean bacterioplankton preside over a divergence point in the marine sulfur cycle where the fate of dimethylsulfoniopropionate (DMSP) is determined. While it is well recognized that this juncture influences the fate of sulfur in the ocean and atmosphere, its regulation by bacterioplankton is not yet understood. Based on recent findings in biogeochemistry, bacterial physiology, bacterial genetics, and ocean instrumentation, the microbial oceanography community is poised to make major advances in knowledge of this control point. This research project is ascertaining how the major taxa of bacterial DMSP degraders in seawater regulate DMSP transformations, and addresses the implications of bacterial functional, genetic, and taxonomic diversity for global sulfur cycling.</p>
<p>The project is founded on the globally important function of bacterial transformation of the ubiquitous organic sulfur compound DMSP in ocean surface waters. Recent genetic discoveries have identified key genes in the two major DMSP degradation pathways, and the stage is now set to identify the factors that regulate gene expression to favor one or the other pathway during DMSP processing. The taxonomy of the bacteria mediating DMSP cycling has been deduced from genomic and metagenomic sequencing surveys to include four major groups of surface ocean bacterioplankton. How regulation of DMSP degradation differs among these groups and maps to phylogeny in co-occurring members is key information for understanding the marine sulfur cycle and predicting its function in a changing ocean. Using model organism studies, microcosm experiments (at Dauphin Island Sea Lab, AL), and time-series field studies with an autonomous sample collection instrument (at Monterey Bay, CA), this project is taking a taxon-specific approach to decipher the regulation of bacterial DMSP degradation.</p>
<p>This research addresses fundamental questions of how the diversity of microbial life influences the geochemical environment of the oceans and atmosphere, linking the genetic basis of metabolic potential to taxonomic diversity. The project is training graduate students and post-doctoral scholars in microbial biodiversity and providing research opportunities and mentoring for undergraduate students. An outreach program is enhance understanding of the role and diversity of marine microorganisms in global elemental cycles among high school students. Advanced Placement Biology students are participating in marine microbial research that covers key learning goals in the AP Biology curriculum. Two high school students are selected each year for summer research internships in PI laboratories.</p>
OceanSulfurFluxBact
largerWorkCitation
project
eng; USA
oceans
Monterey Bay, CA, USA; Station M0
-121.901
-121.901
36.835
36.835
2016-09-26
2016-11-16
0
BCO-DMO catalogue of parameters from Metagenomic, metatranscriptomic, and single cell sequencing data from an Environmental Sample Processor deployment in Monterey Bay, CA in 2016.
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/806713.rdf
Name: GOLD_Project_ID
Units: unitless
Description: <p>Accession number at DOE JGI IMG database: <a href="https://img.jgi.doe.gov">https://img.jgi.doe.gov</a></p>
http://lod.bco-dmo.org/id/dataset-parameter/806714.rdf
Name: Analysis_Project_Name
Units: unitless
Description: <p>Name of sequencing project</p>
http://lod.bco-dmo.org/id/dataset-parameter/806715.rdf
Name: Type
Units: unitless
Description: <p>Material type sequenced</p>
http://lod.bco-dmo.org/id/dataset-parameter/806716.rdf
Name: Assembly_Method
Units: unitless
Description: <p>assembly method</p>
http://lod.bco-dmo.org/id/dataset-parameter/806717.rdf
Name: Collection_Date
Units: unitless
Description: <p>collection date of samples</p>
http://lod.bco-dmo.org/id/dataset-parameter/806718.rdf
Name: Instrument
Units: unitless
Description: <p>instrument</p>
http://lod.bco-dmo.org/id/dataset-parameter/806719.rdf
Name: JGI_Contigs_Link
Units: unitless
Description: <p>JGI Contigs Link</p>
http://lod.bco-dmo.org/id/dataset-parameter/806720.rdf
Name: JGI_Project_ID
Units: unitless
Description: <p>JGI Project ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/806721.rdf
Name: JGI_Sample_ID
Units: unitless
Description: <p>JGI Sample ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/806722.rdf
Name: JGI_Sequencing_Project_ID
Units: unitless
Description: <p>JGI Sequencing Project ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/806723.rdf
Name: JGI_Sequencing_Project_Name
Units: unitless
Description: <p>JGI Sequencing Project Name</p>
http://lod.bco-dmo.org/id/dataset-parameter/806724.rdf
Name: Latitude_and_Longitude
Units: unitless
Description: <p>Latitude and Longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/806725.rdf
Name: NCBI_BioProject_Accession
Units: unitless
Description: <p>NCBI BioProject Accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/806726.rdf
Name: NCBI_BioSample_Accession
Units: unitless
Description: <p>NCBI BioSample Accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/806727.rdf
Name: NCBI_Project_ID
Units: unitless
Description: <p>NCBI Project ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/806728.rdf
Name: NCBI_SRA_Accession_ID
Units: unitless
Description: <p>NCBI SRA Accession ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/806729.rdf
Name: Sample_Name
Units: unitless
Description: <p>sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/806730.rdf
Name: Sequencing_Run_Mode
Units: unitless
Description: <p>sequencing run mode</p>
http://lod.bco-dmo.org/id/dataset-parameter/806731.rdf
Name: Total_Bases
Units: unitless
Description: <p>total bases</p>
http://lod.bco-dmo.org/id/dataset-parameter/806732.rdf
Name: Volume_Seawater_Filtered
Units: milliliters (mL)
Description: <p>Volume Seawater Filtered</p>
http://lod.bco-dmo.org/id/dataset-parameter/806733.rdf
Name: env_biome
Units: unitless
Description: <p>environmental biome</p>
http://lod.bco-dmo.org/id/dataset-parameter/806734.rdf
Name: env_feature
Units: unitless
Description: <p>environmental feature</p>
http://lod.bco-dmo.org/id/dataset-parameter/806735.rdf
Name: env_material
Units: unitless
Description: <p>environmental material</p>
http://lod.bco-dmo.org/id/dataset-parameter/806736.rdf
Name: geo_loc_name
Units: unitless
Description: <p>location name</p>
http://lod.bco-dmo.org/id/dataset-parameter/806737.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude with positive values indicating North</p>
http://lod.bco-dmo.org/id/dataset-parameter/806738.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude with negative values indicating 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
148389
https://darchive.mblwhoilibrary.org/bitstream/1912/25603/1/dataset-753343_esp-2016-seq__v2.tsv
download
https://doi.org/10.26008/1912/bco-dmo.753343.2
download
onLine
dataset
<p>The Environmental Sample Processor (ESP) filtered seawater sequentially through 5.0 um and 0.2 um pore size polyvinylidene fluoride filters. Seawater was evacuated from filters and followed twice with a 2 minute incubation with 1 ml of RNAlater™. RNAlater was evacuated, and filters were stored in the ESP until they were transferred to -80 C upon instrument recovery.&nbsp;</p>
<p>Grab samples for sequencing while the ESP was not deployed were taken using Niskin bottles that collected seawater at the same depth and location of the ESP. Water was transferred to a low-density polyethylene cubitainer and maintained at ambient temperature until return to lab within 30 min. Seawater was filtered as above with vacuum filtration and preserved immediately in liquid nitrogen and transferred to -80 C.</p>
<p>Single-cell sequencing: Seawater was transferred directly from the Niskin bottle to a 50 ml Falcon tube and placed on ice until brought back to lab. Each sampling day, 3 x 1 ml of seawater was preserved in cryovials using 100 ul of glyTe (5 ml glycerol, 3 ml Milli-Q H2O, 1 ml 100 x TE pH 8.0, 0.2 um filter sterilized after mixing the above, and stored in -20 C freezer). Preserved samples were then placed in a -80 C freezer. Samples were processed and sequenced at JGI</p>
Specified by the Principal Investigator(s)
<p>ESP and grab sample filters were processed for DNA and RNA using the Zymobiomics DNA/RNA Mini Kit. Turbo DNase and RiboZero were performed on RNA samples. Illumina HiSeq-2500 1TB 2 x 151 bp sequencing was performed at the Joint Genome Institute (JGI).&nbsp;</p>
<p>BBtools was used to trim and screen reads, followed by read correction using bfc (version r181). Reads with no mate pair were removed. Metagenomes were assembled using SPAdes assembler 3.11.1. The entire filtered read set was mapped to the final assembly and coverage information generated using bbmap (version 37.78). Metatranscriptomes were assembled using MEGAHIT v1.1.2 and reads were mapped to the assembly using BBMap. The JGI Integrated Microbial Genomes System (IMG) was used for annotation of the metagenomes and metatranscriptomes.</p>
<p><strong>BCO-DMO Processing notes:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- reformatted date from Mon-DD (Oct-04) to YYYYMMDD (20141004)</p>
Specified by the Principal Investigator(s)
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
Deployment: Moran_Monterey_2016
Moran_Monterey_2016
Environmental Sample Processor
float
Moran_Monterey_2016
Brent Nowinski
University of Georgia
Environmental Sample Processor
float