Dataset: Sponge-Associated Microbial Communities (via 16S-V4 rRNA amplicon sequencing) Following Storm-Driven Flooding

Name: 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)
Published: 2020-07-23
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.817436.1

Spatial Extent: N:27.9078 E:-93.6002 S:27.8819 W:-93.62829

Temporal Extent: 2016-07-27 - 2018-10-28

Project:

RAPID: Collaborative Research: Impact of freshwater runoff from Hurricane Harvey on coral reef benthic organisms and associated microbial communities (Rapid Reefs Harvey)

Principal Investigator:

Adrienne M.S. Correa (Rice University)

Co-Principal Investigator:

Lory Santiago-Vazquez (University of Houston, UH-Clearlake)

Contact:

Amanda Shore (Rice University)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2020-07-23

Restricted:

Validated:

Yes

Current State:

Final no updates expected

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)

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2020-07-23	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.817436.1	2020-07-24

Description

To document the effects of storm-driven freshwater runoff on sponge-associated microbiomes, we leveraged the heavy rainfall associated with Tax Day Flooding (July 2016) and Hurricane Harvey (August 2017) to characterize sponge-associated bacterial communities at five time points: in July 2016 (at detection of the mortality event), one month after the mortality event (August 2016), immediately after Hurricane Harvey (September 2017), one month after Hurricane Harvey (October 2017), and approximately one year following Hurricane Harvey (October 2018).

These data contain Sequence Read Archive (SRA) and BioSample accession numbers associated with BioProject PRJNA605902 (see https://www.ncbi.nlm.nih.gov/bioproject/605902) at The National Center for Biotechnology Information.

Methods & Sampling

Location:

East and West Banks of the Flower Garden Banks National Marine Sanctuary (FGBNMS)

Sampling Events:

NOAA FGBNMS Cruise July 2016, NOAA FGBNMS Cruise August 2016
Hurricane Harvey FGB October 2017, Hurricane Harvey FGB October 2018

Methodology:

V4-16S bacterial communities libraries were prepared and PE 250bp reads were generated using Illumina MiSeq platform.

Sampling and analytical procedures:

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).

Data Processing Description

Processing description for data in the Sequence Read Archive:
Sequencing processing and statistical analysis were conducted through the QIIME2 2019.10 software package.

BCO-DMO Data Manager Processing notes:
* Made the following changes to the originally submitted file "sponges_ANSedits_7.23.2020.csv"
* converted variable date formatting to ISO8601 format yyyy-mm-dd
* converted lat/lon in degrees decimal minutes with format 27° 52'54.84”,"93° 37'41.84""" to degrees decimal minutes. Made Long negative so it correctly corresponds to the sample location.
* Checked taxonomic names for validity using WoRMS

Identification, lowest taxon match in WoRMS, LSID
Agaricia sp., Agaricia, urn: lsid: marinespecies.org: taxname: 204464
Agelas clathrodes, Agelas clathrodes, urn:lsid:marinespecies.org:taxname:164823, accepted
Xestospongia mute, Xestospongia mute, urn:lsid:marinespecies.org:taxname:166894, accepted

Data Files

File
sponges.csv (Comma Separated Values (.csv), 13.02 KB) MD5:f96a637bbd09cd20e015f7df90eb20bf Primary data file for dataset ID 817436

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1800914

Deployments

None available yet

Instruments

Automated DNA Sequencer

Supplied Name: Illumina MiSeq Platform

Supplied Description:

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Sample_Name	Sample name	unitless	sample
Collection_Date_Start	Sample collection date (start of date range) in ISO 8601 format yyyy-mm-dd	unitless	date
Collection_Date_End	Sample collection date (end of date range) in ISO 8601 format yyyy-mm-dd	unitless	date
Depth_min	Sample collection depth (minimum of depth range)	meters (m)	depth
Depth_max	Sample collection depth (maxiumum of depth range)	meters (m)	depth
Bank	East or west bank of the Flower Garden Banks	unitless	site_descrip
Species	Identification (taxonomic name or organism description)	unitless	taxon
SRA	Sequence Read Archive (SRA) accession number at NCBI	unitless	accession_number
Accession	BioSample accession number at NCBI	unitless	accession_number
Lat	Sample latitude	decimal degrees	lat
Long	Sample longitude	decimal degrees	lon