http://lod.bco-dmo.org/id/dataset/885982
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
2022-12-29
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
A characterization of microbes at the San Pedro Ocean Time-series (SPOT) from 2005 to 2018, using SSU rRNA gene sequencing from two size fractions, with a universal primer set that amplifies from prokaryotes and eukaryotes
2022-12-29
publication
2022-12-29
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2023-01-30
publication
https://doi.org/10.26008/1912/bco-dmo.885982.1
Jed A. Fuhrman
University of Southern California
principalInvestigator
Yi-Chun Yeh
University of Southern California
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: Yeh, Y., Fuhrman, J. A. (2023) A characterization of microbes at the San Pedro Ocean Time-series (SPOT) from 2005 to 2018, using SSU rRNA gene sequencing from two size fractions, with a universal primer set that amplifies from prokaryotes and eukaryotes. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-12-29 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.885982.1 [access date]
SSU rRNA Gene Sequencing from SPOT Dataset Description: Methods and Sampling: <p>Monthly San Pedro Ocean Time-series (SPOT) cruises on R/V Yellowfin were conducted in the San Pedro Channel, off the coast of Los Angeles, California,&nbsp;USA (33 N, 118 W). Samples were collected monthly from five depths, including 5 meters (m), deep chlorophyll maximum (DCM), 150m, 500m, and 890 m, between the years 2005 and 2018. Ten to fifteen liters of seawater was sequentially filtered through an 80-micrometer (μm) mesh, a 1-μm A/E filter (Pall, Port Washington, NY), and a 0.2-μm Durapore filter (ED Millipore, Billerica, MA). Filters were stored at -80° Celsius (C) until DNA extraction. Durapore filters (collecting material 0.2 to 1 μm) were used for free-living prokaryotic community analysis, and A/E filters (collecting material between 1 to 80 μm) were used to analyze phytoplankton, microzooplankton, and particle-associated or larger prokaryotic communities. DNA was extracted from the Durapore filters using a hot SDS, phenol/chloroform/isoamyl alcohol, ethanol precipitation extraction protocol as described by Fuhrman et al. (1988). DNA on the A/E filters was extracted using a NaCl/CTAB bead-beating extraction protocol as described by Lie et al. (2013) with slight modification by adding an ethanol precipitation step after lysis to reduce the volume of crude extract, which helps minimize DNA loss during the subsequent purification.</p>
<p>The V4-V5 hyper-variable region of the 16S and 18S rRNA genes were amplified simultaneously using a universal primer set 515Y (GTGYCAGCMGCCGCGGTAA) and 926R (CCGYCAATTYMTTTRAGTTT). All DNA samples were amplified and purified using the same conditions described in Yeh et al. 2021). Purified PCR products were pooled in equal amount and then sequenced on Illumina HiSeq 2500 in PE250 mode or MiSeq PE300.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1737409 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1737409
Funding provided by Gordon and Betty Moore Foundation: Marine Microbiology Initiative (MMI) Award Number: GBMF3779
Funding provided by Simons Foundation (Simons) Award Number: CBIOMES 549943
completed
Jed A. Fuhrman
University of Southern California
213-740-5757
Dept. Biological Sciences, Dornsife College of Letters, Arts, and Sciences 3616 Trousdale Parkway
Los Angeles
CA
90089-0371
USA
fuhrman@usc.edu
pointOfContact
Yi-Chun Yeh
University of Southern California
yichuny@usc.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
study_accession
sample_accession
secondary_sample_accession
run_accession
tax_id
sequence_category
instrument_platform
instrument_model
library_layout
library_strategy
library_source
library_selection
study_title
fastq_ftp
submitted_ftp
submitted_format
sample_title
Illumina HiSeq 2500 sequencer
Illumina MiSeq sequencer
theme
None, User defined
NCBI BioProject accession
NCBI BioSample accession
NCBI SRA run accession (SRR)
taxon
sample type
instrument
instrument model
sampling_method
sample description
sample identification
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
SPOT_Yellowfin_Cruises
service
Deployment Activity
San Pedro Ocean Time Series
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.
Protistan, prokaryotic, and viral processes at the San Pedro Ocean Time-series
https://osprey.bco-dmo.org/project/743049
Protistan, prokaryotic, and viral processes at the San Pedro Ocean Time-series
<p>Planktonic marine microbial communities consist of a diverse collection of bacteria, archaea, viruses, protists (phytoplankton and protozoa) and small animals (metazoan). Collectively, these species are responsible for virtually all marine pelagic primary production where they form the basis of food webs and carry out a large fraction of respiratory processes. Microbial interactions include the traditional role of predation, but recent research recognizes the importance of parasitism, symbiosis and viral infection. Characterizing the response of pelagic microbial communities and processes to environmental influences is fundamental to understanding and modeling carbon flow and energy utilization in the ocean, but very few studies have attempted to study all of these assemblages in the same study. This project is comprised of long-term (monthly) and short-term (daily) sampling at the San Pedro Ocean Time-series (SPOT) site. Analysis of the resulting datasets investigates co-occurrence patterns of microbial taxa (e.g. protist-virus and protist-prokaryote interactions, both positive and negative) indicating which species consistently co-occur and potentially interact, followed by examination gene expression to help define the underlying mechanisms. This study augments 20 years of baseline studies of microbial abundance, diversity, rates at the site, and will enable detection of low-frequency changes in composition and potential ecological interactions among microbes, and their responses to changing environmental forcing factors. These responses have important consequences for higher trophic levels and ocean-atmosphere feedbacks. The broader impacts of this project include training graduate and undergraduate students, providing local high school student with summer lab experiences, and PI presentations at local K-12 schools, museums, aquaria and informal learning centers in the region. Additionally, the PIs advise at the local, county and state level regarding coastal marine water quality.</p>
<p>This research project is unique in that it is a holistic study (including all microbes from viruses to small metazoa) of microbial species diversity and ecological activities, carried out at the SPOT site off the coast of southern California. In studying all microbes simultaneously, this work aims to identify important ecological interactions among microbial species, and identify the basis(es) for those interactions. This research involves (1) extensive analyses of prokaryote (archaean and bacterial) and eukaryote (protistan and micro-metazoan) diversity via the sequencing of marker genes, (2) studies of whole-community gene expression by eukaryotes and prokaryotes in order to identify key functional characteristics of microorganismal groups and the detection of active viral infections, and (3) metagenomic analysis of viruses and bacteria to aid interpretation of transcriptomic analyses using genome-encoded information. The project includes exploratory metatranscriptomic analysis of poorly-understood aphotic and hypoxic-zone protists, to examine their stratification, functions and hypothesized prokaryotic symbioses.</p>
SPOT
largerWorkCitation
project
eng; USA
oceans
San Pedro Ocean Time Series
-118.24
-118.24
33.33
33.33
2005-01-19
2018-07-18
San Pedro Channel off the coast of Los Angeles
0
BCO-DMO catalogue of parameters from A characterization of microbes at the San Pedro Ocean Time-series (SPOT) from 2005 to 2018, using SSU rRNA gene sequencing from two size fractions, with a universal primer set that amplifies from prokaryotes and eukaryotes
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/886153.rdf
Name: study_accession
Units: unitless
Description: <p>National Center for Biotechnology Information (NCBI) project identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/886154.rdf
Name: sample_accession
Units: unitless
Description: <p>National Center for Biotechnology Information (NCBI) sample accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/886155.rdf
Name: secondary_sample_accession
Units: unitless
Description: <p>National Center for Biotechnology Information (NCBI) secondary sample accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/886156.rdf
Name: run_accession
Units: unitless
Description: <p>National Center for Biotechnology Information (NCBI) run accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/886157.rdf
Name: tax_id
Units: unitless
Description: <p>National Center for Biotechnology Information (NCBI) taxon ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/886158.rdf
Name: sequence_category
Units: unitless
Description: <p>Sample category type</p>
http://lod.bco-dmo.org/id/dataset-parameter/886159.rdf
Name: instrument_platform
Units: unitless
Description: <p>Sequencing platform ("ILLUMINA")</p>
http://lod.bco-dmo.org/id/dataset-parameter/886160.rdf
Name: instrument_model
Units: unitless
Description: <p>Sequencing instrument model</p>
http://lod.bco-dmo.org/id/dataset-parameter/886161.rdf
Name: library_layout
Units: unitless
Description: <p>Library layout ("PAIRED")</p>
http://lod.bco-dmo.org/id/dataset-parameter/886162.rdf
Name: library_strategy
Units: unitless
Description: <p>Library strategy ("AMPLICON")</p>
http://lod.bco-dmo.org/id/dataset-parameter/886163.rdf
Name: library_source
Units: unitless
Description: <p>Library source ("METAGENOMIC")</p>
http://lod.bco-dmo.org/id/dataset-parameter/886164.rdf
Name: library_selection
Units: unitless
Description: <p>Library selection ("PCR")</p>
http://lod.bco-dmo.org/id/dataset-parameter/886165.rdf
Name: study_title
Units: unitless
Description: <p>Study title</p>
http://lod.bco-dmo.org/id/dataset-parameter/886166.rdf
Name: fastq_ftp
Units: unitless
Description: <p>Generated FASTQ files: FTP</p>
http://lod.bco-dmo.org/id/dataset-parameter/886167.rdf
Name: submitted_ftp
Units: unitless
Description: <p>Submitted files: FTP</p>
http://lod.bco-dmo.org/id/dataset-parameter/886168.rdf
Name: submitted_format
Units: unitless
Description: <p>File format ("FASTQ")</p>
http://lod.bco-dmo.org/id/dataset-parameter/886169.rdf
Name: sample_title
Units: unitless
Description: <p>Sample name</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
783985
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/4d5adb54-c738-5d48-8bf8-ea0f1f6d9edb/content
download
https://doi.org/10.26008/1912/bco-dmo.885982.1
download
onLine
dataset
<p>Monthly San Pedro Ocean Time-series (SPOT) cruises on R/V Yellowfin were conducted in the San Pedro Channel, off the coast of Los Angeles, California,&nbsp;USA (33 N, 118 W). Samples were collected monthly from five depths, including 5 meters (m), deep chlorophyll maximum (DCM), 150m, 500m, and 890 m, between the years 2005 and 2018. Ten to fifteen liters of seawater was sequentially filtered through an 80-micrometer (μm) mesh, a 1-μm A/E filter (Pall, Port Washington, NY), and a 0.2-μm Durapore filter (ED Millipore, Billerica, MA). Filters were stored at -80° Celsius (C) until DNA extraction. Durapore filters (collecting material 0.2 to 1 μm) were used for free-living prokaryotic community analysis, and A/E filters (collecting material between 1 to 80 μm) were used to analyze phytoplankton, microzooplankton, and particle-associated or larger prokaryotic communities. DNA was extracted from the Durapore filters using a hot SDS, phenol/chloroform/isoamyl alcohol, ethanol precipitation extraction protocol as described by Fuhrman et al. (1988). DNA on the A/E filters was extracted using a NaCl/CTAB bead-beating extraction protocol as described by Lie et al. (2013) with slight modification by adding an ethanol precipitation step after lysis to reduce the volume of crude extract, which helps minimize DNA loss during the subsequent purification.</p>
<p>The V4-V5 hyper-variable region of the 16S and 18S rRNA genes were amplified simultaneously using a universal primer set 515Y (GTGYCAGCMGCCGCGGTAA) and 926R (CCGYCAATTYMTTTRAGTTT). All DNA samples were amplified and purified using the same conditions described in Yeh et al. 2021). Purified PCR products were pooled in equal amount and then sequenced on Illumina HiSeq 2500 in PE250 mode or MiSeq PE300.</p>
Specified by the Principal Investigator(s)
<p>The code used for processing the raw sequence data and getting the reads into ASVs that can be used for downstream community composition analyses has been saved in Zenodo with DOI <a href="http://dx.doi.org/10.5281/zenodo.7340378" target="_blank">10.5281/zenodo.7340378</a>.</p>
<p><strong>BCO-DMO Processing:</strong><br />
- concatenated two separate .csv files (one per BioProject) into one dataset.</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
Illumina HiSeq 2500 sequencer
Illumina HiSeq 2500 sequencer
PI Supplied Instrument Name: Illumina HiSeq 2500 sequencer PI Supplied Instrument Description:Purified PCR products were sequenced on an Illumina HiSeq 2500 in PE250 mode or MiSeq PE300. 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.
Illumina MiSeq sequencer
Illumina MiSeq sequencer
PI Supplied Instrument Name: Illumina MiSeq sequencer PI Supplied Instrument Description:Purified PCR products were sequenced on an Illumina HiSeq 2500 in PE250 mode or MiSeq PE300. 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.
Cruise: SPOT_Yellowfin_Cruises
SPOT_Yellowfin_Cruises
R/V Yellowfin
R/V Yellowfin
vessel
R/V Yellowfin
R/V Yellowfin
vessel