http://lod.bco-dmo.org/id/dataset/817436
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
2020-06-30
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
SRA accessions and collection information for 16S-V4 rRNA amplicon data from invertebrates sampled at Flower Garden Banks National Marine Sanctuary, Gulf of Mexico following Tax Day Flooding (2016), Hurricane Harvey (2017), and a no flooding year (2018)
2020-07-23
publication
2020-07-23
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-07-24
publication
https://doi.org/10.26008/1912/bco-dmo.817436.1
Adrienne M.S. Correa
Rice University
principalInvestigator
Lory Santiago-Vazquez
University of Houston
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: Correa, A., Santiago-Vazquez, L. (2020) SRA accessions and collection information for 16S-V4 rRNA amplicon data from invertebrates sampled at Flower Garden Banks National Marine Sanctuary, Gulf of Mexico following Tax Day Flooding (2016), Hurricane Harvey (2017), and a no flooding year (2018). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-07-23 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.817436.1 [access date]
Dataset Description: <p>To document the effects of storm-driven freshwater runoff on&nbsp;sponge-associated microbiomes, we leveraged the heavy rainfall&nbsp;associated with Tax Day Flooding (July 2016) and Hurricane Harvey&nbsp;(August 2017) to characterize sponge-associated bacterial communities&nbsp;at five time points: in July 2016 (at detection of the mortality&nbsp;event), one month after the mortality event (August 2016), immediately&nbsp;after Hurricane Harvey (September 2017), one month after Hurricane&nbsp;Harvey (October 2017), and approximately one year following Hurricane&nbsp;Harvey (October 2018).<br />
<br />
These data contain Sequence Read Archive (SRA) and BioSample accession numbers associated with BioProject&nbsp;PRJNA605902 (see&nbsp;https://www.ncbi.nlm.nih.gov/bioproject/605902)&nbsp;at The National Center for Biotechnology Information.</p> Methods and Sampling: <p>Location:<br />
<br />
East and West Banks of the Flower Garden Banks National Marine Sanctuary (FGBNMS)&nbsp;<br />
<br />
Sampling Events:&nbsp;<br />
<br />
NOAA FGBNMS Cruise July 2016, NOAA FGBNMS Cruise August 2016<br />
Hurricane Harvey FGB October 2017, Hurricane Harvey FGB October 2018<br />
<br />
Methodology:<br />
<br />
V4-16S bacterial communities libraries were prepared and PE 250bp reads were generated using Illumina MiSeq platform.&nbsp;<br />
<br />
Sampling and analytical procedures:<br />
<br />
Samples were flash frozen in liquid nitrogen and stored at -20℃ until further processing. DNA was extracted from 250 mg of sponge sample using the Nucleospin Soil DNA extraction kit (Takara Bio) or the DNeasy PowerSoil DNA extraction kit (QIAGEN).&nbsp;&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1800914 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1800914
completed
Adrienne M.S. Correa
Rice University
amsc@berkeley.edu
pointOfContact
Lory Santiago-Vazquez
University of Houston
281-283-3776
Dept. of Biological and Environmental Sciences 2700 Bay Area Blvd.
Houston
TX
77058
USA
santiago@uhcl.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample_Name
Collection_Date_Start
Collection_Date_End
Depth_min
Depth_max
Bank
Species
SRA
Accession
Lat
Long
Illumina MiSeq Platform
theme
None, User defined
sample identification
date
depth
site description
taxon
accession number
latitude
longitude
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
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.
RAPID: Collaborative Research: Impact of freshwater runoff from Hurricane Harvey on coral reef benthic organisms and associated microbial communities
https://osprey.bco-dmo.org/project/746814
RAPID: Collaborative Research: Impact of freshwater runoff from Hurricane Harvey on coral reef benthic organisms and associated microbial communities
<p><em>NSF Award Abstract:</em><br />
Coral reefs are ecologically and economically important ecosystems, and are threatened by a variety of global (climate change) and local (overfishing, pollution) stressors. Anthropogenic climate change is increasing the frequency and severity of storms, which can physically damage reef structures and reduce reef health through changes in seawater quality. In August of 2017, Hurricane Harvey caused widespread flooding in southeast Texas when it released more than 50 trillion liters of rain, which then accumulated along the Texas Shelf. This runoff is expected to impact nearby coral reefs in the Flower Garden Banks National Marine Sanctuary (FGBNMS, northwest Gulf of Mexico) via eddies and jets that transport coastal waters offshore. Findings from this project will allow managers to quickly predict whether extreme storm events are likely to induce reef mortality and ecosystem decline due to freshwater accumulation, by tracking of low salinity water masses coupled with microbial community characterization and metrics of coral health. These data are critical to managing coastal ecosystems, including the high coral cover reefs in the FGBNMS, and will help stakeholders (e.g., diving and fishing communities) plan for and minimize disruption to their livelihoods following these storms. Results will be communicated broadly across scientific arenas, in graduate and undergraduate education and training programs, and to the general public through outreach. The investigators have seven 7 square meter 2-D Reef Replicas from 2014 depicting representative FGBNMS reef bottoms, and will construct additional 2-D Reef Replicas from both banks following the arrival of Harvey runoff, allowing the public to directly experience and quantify the effects of Hurricane Harvey on local reefs using quadrats and identification guides. This project will also synergize with NSF REU programs at Boston University and Texas A&M University, providing transformative research experiences for undergraduates. One post-doctoral scholar, four graduate students, a technician and more than 5 undergraduates will be involved in all aspects of the research. All datasets will be made freely available to the public, and will serve as an important set of baselines for future lines of inquiry into the processes by which hurricanes and other extreme storms impact reef health.</p>
<p>Hurricanes and other extreme storm events can decimate coral reefs through wave-driven physical damage. Freshwater runoff from extreme storms is also potentially detrimental to reefs but has received comparatively less attention. This research will provide unprecedented resolution on how hurricanes and other extreme storm events may trigger cascading interactions among water chemistry, declines in metazoan health and shifts in their associated microbial communities, ultimately resulting in coral reef decline. The freshwater runoff initiated by Hurricane Harvey is likely to impact reefs within the FGBNMS, one of the few remaining coral-dominated reefs in the greater Caribbean. The effects of Harvey runoff will be compared to a previously documented storm-driven runoff event that was associated with invertebrate mortality on the same reef system. Sampling seawater chemistry, microbial communities (water column and benthic), and host gene expression and proteomics before, immediately after, and six months after Harvey runoff enters the FGBNMS will allow us to identify commonalities among large-scale freshwater runoff events and track the response of benthic invertebrate health, microbial community diversity, and the trajectory of reef community recovery or decline. The investigators will determine if changes in water chemistry induce pelagic microbial shifts, if microbial communities typically associated with corals and sponges are altered, and whether feedbacks occur between these potential drivers of benthic invertebrate mortality.</p>
Rapid Reefs Harvey
largerWorkCitation
project
eng; USA
oceans
-93.62829
-93.6002
27.8819
27.9078
2016-07-27
2018-10-28
Flower Garden Banks National Marine Sanctuary, Northwest Gulf of Mexico
0
BCO-DMO catalogue of parameters from SRA accessions and collection information for 16S-V4 rRNA amplicon data from invertebrates sampled at Flower Garden Banks National Marine Sanctuary, Gulf of Mexico following Tax Day Flooding (2016), Hurricane Harvey (2017), and a no flooding year (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/818908.rdf
Name: Sample_Name
Units: unitless
Description: <p>Sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/818909.rdf
Name: Collection_Date_Start
Units: unitless
Description: <p>Sample collection date (start of date range) in ISO 8601 format yyyy-mm-dd</p>
http://lod.bco-dmo.org/id/dataset-parameter/818910.rdf
Name: Collection_Date_End
Units: unitless
Description: <p>Sample collection date (end of date range) in ISO 8601 format yyyy-mm-dd</p>
http://lod.bco-dmo.org/id/dataset-parameter/818911.rdf
Name: Depth_min
Units: meters (m)
Description: <p>Sample collection depth (minimum of depth range)</p>
http://lod.bco-dmo.org/id/dataset-parameter/818912.rdf
Name: Depth_max
Units: meters (m)
Description: <p>Sample collection depth (maxiumum of depth range)</p>
http://lod.bco-dmo.org/id/dataset-parameter/818913.rdf
Name: Bank
Units: unitless
Description: <p>East or west bank of the Flower Garden Banks</p>
http://lod.bco-dmo.org/id/dataset-parameter/818914.rdf
Name: Species
Units: unitless
Description: <p>Identification (taxonomic name or organism description)</p>
http://lod.bco-dmo.org/id/dataset-parameter/818915.rdf
Name: SRA
Units: unitless
Description: <p>Sequence Read Archive (SRA) accession number at NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/818916.rdf
Name: Accession
Units: unitless
Description: <p>BioSample accession number at NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/819303.rdf
Name: Lat
Units: decimal degrees
Description: <p>Sample latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/819304.rdf
Name: Long
Units: decimal degrees
Description: <p>Sample longitude</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
13333
https://darchive.mblwhoilibrary.org/bitstream/1912/25988/1/dataset-817436_sponge-associated-microbial-communities-16s-v4-rrna-amplicon-sequencing-following-storm-driven__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.817436.1
download
onLine
dataset
<p>Location:<br />
<br />
East and West Banks of the Flower Garden Banks National Marine Sanctuary (FGBNMS)&nbsp;<br />
<br />
Sampling Events:&nbsp;<br />
<br />
NOAA FGBNMS Cruise July 2016, NOAA FGBNMS Cruise August 2016<br />
Hurricane Harvey FGB October 2017, Hurricane Harvey FGB October 2018<br />
<br />
Methodology:<br />
<br />
V4-16S bacterial communities libraries were prepared and PE 250bp reads were generated using Illumina MiSeq platform.&nbsp;<br />
<br />
Sampling and analytical procedures:<br />
<br />
Samples were flash frozen in liquid nitrogen and stored at -20℃ until further processing. DNA was extracted from 250 mg of sponge sample using the Nucleospin Soil DNA extraction kit (Takara Bio) or the DNeasy PowerSoil DNA extraction kit (QIAGEN).&nbsp;&nbsp;</p>
Specified by the Principal Investigator(s)
<p>Processing description for data in the Sequence Read Archive:<br />
Sequencing processing and statistical analysis were conducted through&nbsp;the QIIME2 2019.10 software package.<br />
<br />
BCO-DMO Data Manager Processing notes:<br />
* Made the following changes to the originally submitted file "sponges_ANSedits_7.23.2020.csv"<br />
* converted variable date formatting to ISO8601 format yyyy-mm-dd<br />
* converted lat/lon in degrees decimal minutes with format&nbsp;27° 52'54.84”,"93° 37'41.84""" to degrees decimal minutes.&nbsp; Made Long negative so it correctly corresponds to the sample location.<br />
* Checked taxonomic names for validity using WoRMS<br />
<br />
Identification, lowest taxon match in WoRMS, LSID<br />
Agaricia sp., Agaricia,&nbsp;urn: lsid: marinespecies.org: taxname: 204464<br />
Agelas clathrodes,&nbsp;Agelas clathrodes, urn:lsid:marinespecies.org:taxname:164823, accepted<br />
Xestospongia mute,&nbsp;Xestospongia mute, urn:lsid:marinespecies.org:taxname:166894, accepted</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 MiSeq Platform
Illumina MiSeq Platform
PI Supplied Instrument Name: 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.