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Microbiome and bacterioplankton rRNA gene sequence data collected from Gulf of Mexico seawater samples, Cruises DP01 and DP02 from May 2015 - August 2015Deep-Pelagic Nekton Dynamics of the Gulf of Mexico (DEEPEND)
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Suggested Citation:
Cole Easson, Jose Lopez. 2017. Microbiome and bacterioplankton rRNA gene sequence data collected from Gulf of Mexico seawater samples, Cruises DP01 and DP02 from May 2015 - August 2015. Distributed by: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/N7P55KWX
Abstract:
Seawater was collected and filtered for microbiome and bacterioplankton sequencing and analyses at various depths during two planned DEEPEND cruise expeditions to the GOM. Filters were stored and then processed for total environmental genomic DNA according to standard methods (see earthmicrobiome.org). 16S rRNA amplicon libraries covering the V4 hypervariable region was generated with universal PCR primers and then sequenced on an Illumina MiSeq DNA sequencing platform. Bioinformatics analyses in QIIME and R was used to quality filter and assess microbial community diversity and taxonomic composition. These baseline characterizations track alpha and beta diversity at different depths ranging from 0 – 1500 m, across the spatial extent of the northern GOM, and over time. Microbiome analyses also considered environmental variables unique to the GOM, including the Mississippi river inputs, mesoscale cyclonic and anticyclonic eddies, and in relation to measured environmental parameters at collection time using the CTD.
Purpose:
The dataset was generated to characterize the composition and dynamics of pelagic microbial communities in the northern Gulf of Mexico.
Theme Keywords:
microbial, sequencing, microbiome, depth, microbial diversity, CTD, seawater
File Format:
csv, docx, fna, biom, word, txt
Filename:
DEEPEND_Year1_microbial_data_GRIIDC.zip (1.03 GB)
Dataset Downloads:
18
Microbiome and bacterioplankton rRNA gene sequence data collected from Gulf of Mexico seawater samples, Cruises DP01 and DP02 from May 2015 - August 2015
Identification Information
Distribution Information
Metadata Maintenance Information
Metadata:
File identifier:
R4.x257.228-0001-metadata.xml
Language:
eng; USA
Character set:
Character set code:
utf8
Hierarchy level:
Scope code:
dataset
Metadata author:
Responsible party:
Individual name:
Jose V. Lopez
Organisation name:
Nova Southeastern University / Halmos College of Natural Sciences and Oceanography
Position name:
Professor
Contact info:
Contact:
Phone:
Telephone:
Voice:
9542623665
Facsimile:
Address:
Address:
Delivery point:
3301 College Ave
City:
Fort Lauderdale
Administrative area:
Florida
Postal code:
33314
Country:
USA
Electronic mail address:
Joslo@Nova.edu
Role:
Role code:
pointOfContact
Date stamp:
2018-08-11T13:28:58+00:00
Metadata standard name:
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
Metadata standard version:
ISO 19115-2:2009(E)
Dataset URI:
https://data.gulfresearchinitiative.org/metadata/R4.x257.228:0001
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Identification info:
Data identification:
Citation:
Citation:
Title:
Microbiome and bacterioplankton rRNA gene sequence data collected from Gulf of Mexico seawater samples,
Cruises DP01 and DP02 from May 2015 - August 2015
Alternate title:
Date:
Date:
Date:
2017-02-20
Date type:
Date type code:
publication
Identifier:
Identifier:
Code:
Anchor: xlink: https://dx.doi.org/10.7266/N7P55KWX title: DOI
doi:10.7266/N7P55KWX
Abstract:
Seawater was collected and filtered for microbiome and bacterioplankton sequencing and analyses at various
depths during two planned DEEPEND cruise expeditions to the GOM. Filters were stored and then processed for
total environmental genomic DNA according to standard methods (see earthmicrobiome.org). 16S rRNA amplicon
libraries covering the V4 hypervariable region was generated with universal PCR primers and then sequenced
on an Illumina MiSeq DNA sequencing platform. Bioinformatics analyses in QIIME and R was used to quality
filter and assess microbial community diversity and taxonomic composition. These baseline characterizations
track alpha and beta diversity at different depths ranging from 0 – 1500 m, across the spatial extent of the
northern GOM, and over time. Microbiome analyses also considered environmental variables unique to the GOM,
including the Mississippi river inputs, mesoscale cyclonic and anticyclonic eddies, and in relation to
measured environmental parameters at collection time using the CTD.
Purpose:
The dataset was generated to characterize the composition and dynamics of pelagic microbial communities in the
northern Gulf of Mexico.
Status:
Progress code:
completed
Point of contact:
Responsible party:
Individual name:
Jose V. Lopez
Organisation name:
Nova Southeastern University / Halmos College of Natural Sciences and Oceanography
Position name:
Professor
Contact info:
Contact:
Phone:
Telephone:
Voice:
9542623665
Facsimile:
Address:
Address:
Delivery point:
3301 College Ave
City:
Fort Lauderdale
Administrative area:
Florida
Postal code:
33314
Country:
USA
Electronic mail address:
Joslo@Nova.edu
Role:
Role code:
pointOfContact
Descriptive keywords:
Keywords:
Keyword:
microbial
Keyword:
sequencing
Keyword:
microbiome
Keyword:
depth
Keyword:
microbial diversity
Keyword:
CTD
Keyword:
seawater
Type:
Keyword type code:
theme
Descriptive keywords:
Keywords:
Keyword:
Gulf of Mexico
Type:
Keyword type code:
place
Resource constraints: title: Cite As
Constraints:
Use limitation:
Cole Easson, Jose Lopez. 2017. Microbiome and bacterioplankton rRNA gene sequence data collected from Gulf
of Mexico seawater samples, Cruises DP01 and DP02 from May 2015 - August 2015. Distributed by: Gulf of
Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas
A&M University–Corpus Christi. doi:10.7266/N7P55KWX
Resource constraints: title: CC0 License
Legal constraints:
Use constraints:
Restriction code:
licenceUnrestricted
Other constraints:
This information is released under the Creative Commons license - No Rights Reserved - CC0 1.0 Universal
(https://creativecommons.org/publicdomain/zero/1.0/). The person who associated a work with this deed
has dedicated the work to the public domain by waiving all of his or her rights to the work worldwide
under copyright law, including all related and neighboring rights, to the extent allowed by law. You can
copy, modify, distribute and perform the work, even for commercial purposes, all without asking
permission.
Resource constraints: title: Liability and Warranty
Legal constraints:
Other constraints:
All materials on this website are made available to GRIIDC and in turn to you "as-is." Content may only be
submitted by an individual who represents and warrants that s/he has sufficient rights to be able to
make the content available under a CC0 waiver. There is no warranty (expressed or implied) to these
materials, their title, accuracy, non-infringement of third party rights, or fitness for any particular
purpose, including the performance or results you may obtain from their use. Use these materials at your
own risk. Under no circumstances shall GRIIDC be liable for any direct, incidental, special,
consequential, indirect, or punitive damages that result from the use or the inability to use either
this website or the materials available via this website. If you are dissatisfied with any website
feature, content, or terms of use, your sole and exclusive remedy is to discontinue use.
Aggregation Info:
AggregateInformation:
Aggregate Data Set Name: title: Related Publication Citation
Citation:
Title:
Easson, C. G., & Lopez, J. V. (2019). Depth-Dependent Environmental Drivers of Microbial Plankton
Community Structure in the Northern Gulf of Mexico. Frontiers in Microbiology, 9.
doi:10.3389/fmicb.2018.03175
Date:
inapplicable
Aggregate Data Set Identifier: title: Related Publication DOI
Identifier:
Code:
Anchor: xlink: https://dx.doi.org/10.3389/fmicb.2018.03175 title: DOI
doi:10.3389/fmicb.2018.03175
Association Type:
Association type code:
crossReference
Aggregation Info:
AggregateInformation:
Aggregate Data Set Name: title: Related Publication Citation
Citation:
Title:
Freed, L. L., Easson, C., Baker, L. J., Fenolio, D., Sutton, T. T., Khan, Y., … Lopez, J. V. (2019).
Characterization of the microbiome and bioluminescent symbionts across life stages of ceratioid
anglerfishes of the gulf of mexico. FEMS Microbiology Ecology. doi:10.1093/femsec/fiz146
Date:
inapplicable
Aggregate Data Set Identifier: title: Related Publication DOI
Identifier:
Code:
Anchor: xlink: https://dx.doi.org/10.1093/femsec/fiz146 title: DOI
doi:10.1093/femsec/fiz146
Association Type:
Association type code:
crossReference
Aggregation Info:
AggregateInformation:
Aggregate Data Set Name: title: Related Publication Citation
Citation:
Title:
Baker, L. J., Freed, L. L., Easson, C. G., Lopez, J. V., Fenolio, D., Sutton, T. T., … Hendry, T. A.
(2019). Diverse deep-sea anglerfishes share a genetically reduced luminous symbiont that is acquired
from the environment. eLife, 8. doi:10.7554/elife.47606
Date:
inapplicable
Aggregate Data Set Identifier: title: Related Publication DOI
Identifier:
Code:
Anchor: xlink: https://dx.doi.org/10.7554/eLife.47606 title: DOI
doi:10.7554/eLife.47606
Association Type:
Association type code:
crossReference
Language:
eng; USA
Topic category:
Topic category code:
environment
Topic category:
Topic category code:
oceans
Extent:
Extent:
Geographic element:
Geographic bounding box:
West bound longitude:
-89
East bound longitude:
-86.50765
South bound latitude:
26.88267
North bound latitude:
29.065
Geographic element:
BoundingPolygon:
Polygon:
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Temporal element:
Temporal extent:
Extent:
Time period:
Description:
ground condition
Begin date:
2015-05-01
End date:
2015-08-31
Supplemental Information:
SampleID_in_OTU_table – sample label corresponding to OTU table columns and Sequence labels Original Tube
label – Label on original sample New Tube label - sample label corresponding to OTU table columns and
Sequence labels Cruise number – Sequential cruise number Sample_depth – depth in meters from which sample
was collected Site - Site name from which the sample was collected. LAT – Latitude of collection site in
decimal degrees LONG – Longitude of collection site in decimal degrees Pelagic_zone – Pelagic depth zone in
which the sample was collected Identifier – Unique sample identifier SampleID-Long – Complete SampleID
Feature – Depth feature from which sample was taken|||||
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Distribution info:
Distribution:
Distributor:
Distributor:
Distributor contact:
Responsible party:
Organisation name:
Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC)
Contact info:
Contact:
Phone:
Telephone:
Voice:
3618253604
Address:
Address:
Delivery point:
6300 Ocean Drive
City:
Corpus Christi
Administrative area:
TX
Postal code:
78412
Country:
USA
Electronic mail address:
griidc@gomri.org
Online Resource:
Online Resource:
Linkage:
URL:
https://data.gulfresearchinitiative.org
Role:
Role code:
distributor
Distributor format:
Format:
Name:
csv, docx, fna, biom, word, txt
Version:
inapplicable
File decompression technique:
zip
Distributor transfer options:
Digital transfer options:
Transfer size:
1026.8291
Online:
Online Resource:
Linkage:
URL:
https://data.gulfresearchinitiative.org/data/R4.x257.228:0001
Protocol:
https
Name:
Data Landing Page
Description:
GRIIDC dataset landing page
Function:
Online function code:
information
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Metadata maintenance:
Maintenance information:
Maintenance and update frequency:
unknown
Maintenance note:
This ISO metadata record was automatically generated from information provided to GRIIDC for dataset:
R4.x257.228:0001 on 2020-09-27T03:33:56-05:00
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