http://lod.bco-dmo.org/id/dataset/922101
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
2024-03-13
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Results of 18S sequencing of full-length 18S rDNA for metabarcoding samples collected during R/V Point Sur cruise PS18-09 in the Western Gulf of Mexico in September 2017
2024-03-14
publication
2024-03-14
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-03-15
publication
https://doi.org/10.26008/1912/bco-dmo.922101.1
Lisa Campbell
Texas A&M University
principalInvestigator
Darren W. Henrichs
Texas A&M University
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: Campbell, L., Henrichs, D. W., Gaonkar, C. (2024) Results of 18S sequencing of full-length 18S rDNA for metabarcoding samples collected during R/V Point Sur cruise PS18-09 in the Western Gulf of Mexico in September 2017. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-03-14 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.922101.1 [access date]
HRR 18S full-length sequence BLAST results Dataset Description: Methods and Sampling: <p>On September 23, 2017, on HRR cruise Leg 1 (R/V Point Sur PS18-09), samples were collected at 6 stations (S06, S11, S16, S21, SS, and GI) from the surface depth bottle in a CTD rosette. Triplicate 500-1000 milliliter (mL) samples were filtered and immediately fixed in RNALater. Triplicate samples from each station/depth were extracted with AllPrep DNA/RNA MiniKit (Qiagen, USA) following the manufacturer's instructions. DNA concentration and quality were evaluated using a Nanodrop spectrophotometer (Thermo Fisher Scientific Inc, USA). All the samples extracted for DNA were normalized to 5 nanograms per microliter (ng/µL) concentration for the amplicon library construction.</p>
<p>The full-length 18S rDNA region was amplified using 18S primers (Medlin et al. 1988; Edgar &amp; Theriot 2004). Library construction and amplicon sequencing were performed at the Campbell Lab, Texas A&amp;M University using Oxford Nanopore minION. The output sequencing results as fasta files were deposited in NCBI's GenBank under the project number PRJNA592369.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1760620 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1760620
completed
Lisa Campbell
Texas A&M University
979-845-5706
3146 TAMU, Department of Oceanography Texas A&M University
College Station
Texas
77843
USA
lisacampbell@tamu.edu
pointOfContact
Darren W. Henrichs
Texas A&M University
979-845-5738
3146 TAMU, Department of Oceanography Texas A&M University
College Station
Texas
77843
USA
dhenrichs@tamu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Station
Leg
Latitude
Longitude
Sequence_ID
Taxonomy
Similarity
length
mismatches
gaps
Q_start
Q_end
R_start
R_end
e_value
score
file_name_orig
Oxford Nanopore minION Mk1C
CTD rosette bottle
Nanodrop spectrophotometer
theme
None, User defined
station
leg of cruise
latitude
longitude
sequence
taxon
sample description
length
file_name
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
CTD - profiler
Spectrophotometer
instrument
BCO-DMO Standard Instruments
PS1809
service
Deployment Activity
Western Gulf of Mexico, Continental Shelf, Louisiana and Texas coasts
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.
RAPID: Hurricane Impact on Phytoplankton Community Dynamics and Metabolic Response
https://osprey.bco-dmo.org/project/715170
RAPID: Hurricane Impact on Phytoplankton Community Dynamics and Metabolic Response
<p><em>NSF Award Abstract:</em><br />
Hurricane Harvey is the strongest hurricane to hit the Texas coast in decades and the resulting tidal surges, flooding and terrestrial runoff have had a severe impact on the coastal ocean. The effects on the phytoplankton, the first link in the food chain, may be unprecedented. To determine how the phytoplankton community will respond to such drastic changes in salinity, nutrient inputs, and potential toxins, immediate and continuous sampling is the only way to fully capture the effects and to identify when conditions return to "normal". An automated, continuous phytoplankton imaging instrument that is deployed on the Texas coast records images of the phytoplankton and permits calculation of the abundance of different species. Together with molecular information on the genes that have been "turned on", or expressed, outcomes of this project will help determine the responses of individual types of phytoplankton. Extreme storms are expected to increase in frequency with future climate change, so the responses identified now will be valuable in predicting how such events will affect these primary producers, which in turn support most of the food webs in marine ecosystems, in the future.</p>
<p>High temporal resolution observations from the Imaging FlowCytobot (IFCB) have revealed that hurricanes in the Gulf of Mexico cause drastic changes in the phytoplankton community structure. The objectives of this RAPID project are: 1) to characterize the dynamics of the phytoplankton species in relation to the environmental variables along the Texas coast; 2) to assess the short and long-term changes in the phytoplankton community; and 3) to identify the strategies of the phytoplankton community for resource acquisition. To accomplish these objectives, this project will utilize IFCB time series to follow phytoplankton community structure during the recovery period from Hurricane Harvey. In addition, two RAPID response cruises (in late September and early October) to sample at 5 sites along a transect from Galveston to Port Aransas, TX. At each station, CTD profiles and water samples from surface and the chlorophyll maximum will be collected for nutrients, carbonate chemistry, and RNA sequencing for metatranscriptomic analysis. Metatranscriptomics can provide an indication of the metabolic strategies employed and functional relationships within the plankton community in response to changes in the environment. The advantage of a metatranscriptomic approach is that the entire molecular response to the environment is captured. So, while the response of phytoplankton to increased nutrient inputs from floodwater runoff is targeted, the responses to other environmental stresses (toxics, hypoxia, acidification) are also captured. Analyses of this time series using multivariate statistical techniques, such as principal component analysis (PCA), and network analysis, a powerful technique for identifying potential interactions among taxa, will provide insights on the environmental factors and metabolic responses structuring the community during the aftermath of the hurricane.</p>
<p><strong>Related data from the The Texas Observatory for Algal Succession Time-Series (TOAST) can be found at the following: </strong><a href="https://toast.tamu.edu/timeline?dataset=HRR_Cruise" target="_blank">https://toast.tamu.edu/timeline?dataset=HRR_Cruise</a></p>
HRR
largerWorkCitation
project
eng; USA
oceans
Western Gulf of Mexico, Continental Shelf, Louisiana and Texas coasts
-96.9874
-94.9
27.8358
29.0649
2017-09-23
2017-09-23
Texas coast
0
BCO-DMO catalogue of parameters from Results of 18S sequencing of full-length 18S rDNA for metabarcoding samples collected during R/V Point Sur cruise PS18-09 in the Western Gulf of Mexico in September 2017
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/922206.rdf
Name: Station
Units: unitless
Description: <p>sampling station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/922207.rdf
Name: Leg
Units: unitless
Description: <p>cruise leg</p>
http://lod.bco-dmo.org/id/dataset-parameter/922208.rdf
Name: Latitude
Units: decimal degrees
Description: <p>latitude of sampling station; positive values = North</p>
http://lod.bco-dmo.org/id/dataset-parameter/922209.rdf
Name: Longitude
Units: decimal degrees
Description: <p>longitude of sampling station; negative values = West</p>
http://lod.bco-dmo.org/id/dataset-parameter/922210.rdf
Name: Sequence_ID
Units: unitless
Description: <p>OTU sequence generated from the HRR data</p>
http://lod.bco-dmo.org/id/dataset-parameter/922211.rdf
Name: Taxonomy
Units: unitless
Description: <p>taxonomic annotation of the O.T.U.</p>
http://lod.bco-dmo.org/id/dataset-parameter/922212.rdf
Name: Similarity
Units: percent
Description: <p>percentage of identical matches</p>
http://lod.bco-dmo.org/id/dataset-parameter/922213.rdf
Name: length
Units: base pairs (bp)
Description: <p>alignment length (sequence overlap)</p>
http://lod.bco-dmo.org/id/dataset-parameter/922214.rdf
Name: mismatches
Units: base pairs (bp)
Description: <p>number of mismatches</p>
http://lod.bco-dmo.org/id/dataset-parameter/922215.rdf
Name: gaps
Units: unitless
Description: <p>number of gap openings</p>
http://lod.bco-dmo.org/id/dataset-parameter/922216.rdf
Name: Q_start
Units: base pairs (bp)
Description: <p>start of alignment in query</p>
http://lod.bco-dmo.org/id/dataset-parameter/922217.rdf
Name: Q_end
Units: base pairs (bp)
Description: <p>end of alignment in query</p>
http://lod.bco-dmo.org/id/dataset-parameter/922218.rdf
Name: R_start
Units: base pairs (bp)
Description: <p>start of alignment in reference sequence</p>
http://lod.bco-dmo.org/id/dataset-parameter/922219.rdf
Name: R_end
Units: base pairs (bp)
Description: <p>end of alignment in reference sequence</p>
http://lod.bco-dmo.org/id/dataset-parameter/922220.rdf
Name: e_value
Units: unitless
Description: <p>number of expected hits of similar quality</p>
http://lod.bco-dmo.org/id/dataset-parameter/922221.rdf
Name: score
Units: unitless
Description: <p>Bit-score</p>
http://lod.bco-dmo.org/id/dataset-parameter/922222.rdf
Name: file_name_orig
Units: unitless
Description: <p>original name of the csv file for this station+leg</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
122847594
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/6239ab6e-e5d8-4254-98fd-4475685b51e9/content
download
https://doi.org/10.26008/1912/bco-dmo.922101.1
download
onLine
dataset
<p>On September 23, 2017, on HRR cruise Leg 1 (R/V Point Sur PS18-09), samples were collected at 6 stations (S06, S11, S16, S21, SS, and GI) from the surface depth bottle in a CTD rosette. Triplicate 500-1000 milliliter (mL) samples were filtered and immediately fixed in RNALater. Triplicate samples from each station/depth were extracted with AllPrep DNA/RNA MiniKit (Qiagen, USA) following the manufacturer's instructions. DNA concentration and quality were evaluated using a Nanodrop spectrophotometer (Thermo Fisher Scientific Inc, USA). All the samples extracted for DNA were normalized to 5 nanograms per microliter (ng/µL) concentration for the amplicon library construction.</p>
<p>The full-length 18S rDNA region was amplified using 18S primers (Medlin et al. 1988; Edgar &amp; Theriot 2004). Library construction and amplicon sequencing were performed at the Campbell Lab, Texas A&amp;M University using Oxford Nanopore minION. The output sequencing results as fasta files were deposited in NCBI's GenBank under the project number PRJNA592369.</p>
Specified by the Principal Investigator(s)
<p>Fastq files for all six station samples were quality checked using FastQC. Resulting sequences were taxonomically annotated using BLAST search against PR2 database v5.0.0. The BLAST analysis used an assignment approach with similarity was ≥ 90% and query coverage was ≥ 1000 bp against the reference sequence. Any sequence that did not compile with this criterion was not used in this study. The following thresholds for identity with BLAST results were used for taxonomic assignment clustering: genus (95%), family (93%), class (92%), and order (90%). Archaeal and Bacterial sequences were removed from these results.</p>
<p><em>Additional tools used are:</em><br />
Oxford Nanopore Technologies. Guppy protocol. Available at: <a href="https://community.nanoporetech.com/docs/prepare/library_prep_protocols/Guppy-protocol/v/gpb_2003_v1_revax_14dec2018/guppy-software-overview" target="_blank">https://community.nanoporetech.com/docs/prepare/library_prep_protocols/Guppy-protocol/v/gpb_2003_v1_revax_14dec2018/guppy-software-overview</a> [Accessed 21 Aug 2023].</p>
Specified by the Principal Investigator(s)
- Saved the location table (station number, lat, lon, etc.) submitted as part of the dataset metadata in a separate spreadsheet.
- Imported the 6 original CSV files (provided in zip "HRR_18S_BLAST_results.zip") into the BCO-DMO system.
- Concatenated the 6 CSV files into a single data table.
- Joined the columns from the location table to the primary data table by matching on Station number.
- Saved final file as "922101_v1_hrr_18s_blast_results.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
Oxford Nanopore minION Mk1C
Oxford Nanopore minION Mk1C
PI Supplied Instrument Name: Oxford Nanopore minION Mk1C PI Supplied Instrument Description:Library construction and amplicon sequencing was performed at Campbell Lab, Texas A&M University using Oxford Nanopore minION. 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.
CTD rosette bottle
CTD rosette bottle
PI Supplied Instrument Name: CTD rosette bottle PI Supplied Instrument Description:Samples were collected from the surface depth bottle in a CTD rosette. Instrument Name: CTD - profiler Instrument Short Name: Instrument Description: The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column. It permits scientists to observe the physical properties in real-time via a conducting cable, which is typically connected to a CTD to a deck unit and computer on a ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast.
This term applies to profiling CTDs. For fixed CTDs, see https://www.bco-dmo.org/instrument/869934. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
Nanodrop spectrophotometer
Nanodrop spectrophotometer
PI Supplied Instrument Name: Nanodrop spectrophotometer PI Supplied Instrument Description:DNA concentration and quality were evaluated using a Nanodrop spectrophotometer (Thermo Fisher Scientific Inc, USA). Instrument Name: Spectrophotometer Instrument Short Name:Spectrophotometer Instrument Description: An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/
Cruise: PS1809
PS1809
R/V Point Sur
Community Standard Description
International Council for the Exploration of the Sea
R/V Point Sur
vessel
PS1809
Lisa Campbell
Texas A&M University
R/V Point Sur
Community Standard Description
International Council for the Exploration of the Sea
R/V Point Sur
vessel