gov.noaa.nmfs.inport:61283
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Pacific Islands Fisheries Science Center
808-725-5300
1845 Wasp Blvd.
Honolulu
HI
96818
USA
http://www.pifsc.noaa.gov
WWW:LINK-1.0-http--link
Website
Website for this organization
information
8:00 a.m. - 4:30 p.m.
resourceProvider
Olenski, Brooke
brooke.olenski@noaa.gov
pointOfContact
2024-02-29T00:00:00
ISO 19115-2 Geographic Information - Metadata Part 2 Extensions for imagery and gridded data
ISO 19115-2:2009(E)
The effects of elevated temperature and acidification on the biodiversity of coral reef cryptobenthic communities that recruited Autonomous Reef Monitoring Structures placed within mesocosms at the Hawaii Institute of Marine Biology between July 2016 and June 2018
Climate change effects on coral reef cryptobenthic communities
2020-12-10
creation
publication
NOAA/NMFS/EDM
61283
https://www.fisheries.noaa.gov/inport/item/61283
WWW:LINK-1.0-http--link
Full Metadata Record
View the complete metadata record on InPort for more information about this dataset.
information
Pacific Islands Fisheries Science Center
808-725-5360
1845 Wasp Blvd.
Honolulu
HI
96818
pifsc.info@noaa.gov
https://www.pifsc.noaa.gov
WWW:LINK-1.0-http--link
Pacific Islands Fisheries Science Center Website
Pacific Island Fisheries Science Center homepage
information
8:00 a.m. - 4:30 p.m.
originator
https://www.fisheries.noaa.gov/region/pacific-islands#science
WWW:LINK-1.0-http--link
NOAA Fisheries Pacific Islands Region - Science Overview
Online Resource
download
Timmers M, Vicente J, Webb M, Jury C, Toonen RJ (2020) Sponging up diversity: evaluating metabarcoding performance for a taxonomically challenging phylum within a complex cryptobenthic community. Environmental DNA. https://doi.org/10.1002/edn3.163.
Timmers M, Jury C, Vicente J, Webb M, and Toonen RJ (In Review) Coral reef biodiversity shuffles but does not decline under the combined stressors of experimental ocean warming and acidification. PNAS.
Jury CP, Bahr K, Barba E, Brainard R, Dobson KL, Graham A, McLachlan R, Nelson C, Price JT, Rocha de Souza M, Shizuru L, Smith C, Sparagon W, Squair C, Timmers M, Tran T, Vicente J, Webb M, Yamase N, Grottoli A, Toonen RJ. (In Review) Experimental reef communities persist under future ocean acidification and warming. Science.
The data described here includes cytochrome oxidase I (COI) DNA metabarcoding data collected from modified Autonomous Reef Monitoring Structures deployed in mesocosms at the Hawaii Institute of Marine Biology as part of an Ocean Acidification Program funded project granted to NOAA's Pacific Islands Fisheries Science Center (PIFSC), Ecosystem Science Division (formerly known as the Coral Reef Ecosystem Division). Treatments in this fully factorial mesocosm experiment included present-day pH and temperature (Ambient treatment), ocean acidification (-0.2 pH units - Acidified treatment), ocean warming (+2°C - Heated treatment), and future ocean combined stressors (-0.2 pH units and +2 °C - Acidified-Heated treatment). ARMS were placed in replicated mesocosms for each treatment on July 2016 and removed June 2018. Upon removal, the ARMS units were individually scraped clean, contents homogenized, and 10 grams were subsampled from each unit for COI DNA metabarcoding.
To examine the long-term responses of biologically diverse coral reef communities to chronic acidification and warming similar to levels projected to occur toward the end of this century. This was the first laboratory study to evaluate the richness and composition of an entire coral reef community that developed over a multi-annual time frame under predicted future ocean conditions.
NOAA Fisheries, Ecosystem Sciences Division and funded by the NOAA Ocean Acidification Program
completed
Timmers, Molly A
(808)725-5449
1845 Wasp Blvd.
Honolulu
HI
96818
molly.timmers@noaa.gov
pointOfContact
Timmers, Molly A
(808)725-5449
1845 Wasp Blvd.
Honolulu
HI
96818
molly.timmers@noaa.gov
custodian
notPlanned
These data are fastq files directly from the MiSeq sequencer and are already deposited into Genbank and thus there is no maintenance.
DNA/RNA Sequencing
theme
CoRIS Discovery Thesaurus
EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Autonomous Reef Monitoring Structure (ARMS)
EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Molecular Genetic Analysis > DNA/RNA Sequencing
EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs
EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology > BioDiversity
EARTH SCIENCE > Oceans > Marine Biology > Crytobiota
EARTH SCIENCE > Oceans > Marine Biology > Marine Invertebrates > Biodiversity
theme
CoRIS Theme Thesaurus
Biodiversity
theme
NODC DATA TYPES THESAURUS
laboratory analyses
theme
NODC OBSERVATION TYPES THESAURUS
CORAL REEF STUDIES
US DOC; NOAA; Office of Oceanic and Atmospheric Research; Ocean Acidification Program
theme
NODC PROJECT NAMES THESAURUS
US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division
theme
NODC SUBMITTING INSTITUTION NAMES THESAURUS
COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Coconut Island ( Moku o loe ) (21N157W0005)
place
CoRIS Place Thesaurus
Coastal Waters of Hawaii
place
NODC SEA AREA NAMES THESAURUS:
ARMS
instrument
NODC INSTRUMENT TYPES THESAURUS
CRED
CREP
Coral Reef Ecosystem Division
Coral Reef Ecosystem Program
ESD
Ecosystem Sciences Division
PIFSC
Pacific Islands Fisheries Science Center
theme
DOC/NOAA/NMFS/PIFSC > Pacific Islands Fisheries Science Center, National Marine Fisheries Service, NOAA, U.S. Department of Commerce
dataCentre
Global Change Master Directory (GCMD) Data Center Keywords
2017-04-24
publication
8.5
ARMS
project
InPort
otherRestrictions
Cite As: Pacific Islands Fisheries Science Center, [Date of Access]: The effects of elevated temperature and acidification on the biodiversity of coral reef cryptobenthic communities that recruited Autonomous Reef Monitoring Structures placed within mesocosms at the Hawaii Institute of Marine Biology between July 2016 and June 2018 [Data Date Range], https://www.fisheries.noaa.gov/inport/item/61283.
NOAA provides no warranty, nor accepts any liability occurring from any incomplete, incorrect, or misleading data, or from any incorrect, incomplete, or misleading use of the data. It is the responsibility of the user to determine whether or not the data is suitable for the intended purpose.
otherRestrictions
Access Constraints: None
otherRestrictions
Use Constraints: Please cite NOAA Fisheries, Ecosystem Science Division (ESD) when using the data.
Example:
Ecosystem Science Division; COPY INPORT RECORD CITATION HERE (keep ESD).
otherRestrictions
Distribution Liability: While every effort has been made to ensure that these data are accurate and reliable within the limits of the current state of the art, NOAA cannot assume liability for any damages caused by errors or omissions in the data, nor as a result of the failure of the data to function on a particular system. NOAA makes no warranty, expressed or implied, nor does the fact of distribution constitute such a warranty.
unclassified
Not applicable
Not applicable
Cryptobiota metabarcoding using Autonomous Reef Monitoring Structure (ARMS) Deployed at Coral Reef Sites across American Samoa from 2012 to 2015
NOAA/NMFS/EDM
64267
series
Cryptobiota metabarcoding using Autonomous Reef Monitoring Structure (ARMS) Deployed at Coral Reef Sites across Hawaiian Archipelago from 2010 to 2016
NOAA/NMFS/EDM
64268
series
Cryptobiota metabarcoding using Autonomous Reef Monitoring Structure (ARMS) Deployed at Coral Reef Sites across Marianas Archipelago from 2011 to 2014
NOAA/NMFS/EDM
64269
series
Cryptobiota metabarcoding using Autonomous Reef Monitoring Structure (ARMS) Deployed at Coral Reef Sites across PRIA from 2011 to 2015
NOAA/NMFS/EDM
64270
series
Cryptobiota metabarcoding using Autonomous Reef Monitoring Structure (ARMS) Deployed in Batangas, Philippines from 2012 to 2015
NOAA/NMFS/EDM
64332
series
NOAA Data Management Plan (DMP)
NOAA/NMFS/EDM
61283
https://www.fisheries.noaa.gov/inportserve/waf/noaa/nmfs/pifsc/dmp/pdf/61283.pdf
WWW:LINK-1.0-http--link
NOAA Data Management Plan (DMP)
NOAA Data Management Plan for this record on InPort.
information
crossReference
eng; US
biota
climatologyMeteorologyAtmosphere
Genbank SRA files: SRS7105074 ‐ SRS7105095
Go to: https://www.ncbi.nlm.nih.gov/sra/
Coconut Island ( Moku o loe ) (21N157W0005)
-155.06861111111
-155.05861111111
19.72944444444
19.73944444444
Hawaii Institute of Marine Biology on Coconut Island in Kaneohe Bay within the island of Oahu.
This represents the time frame in which the ARMS remained within the mesocosm treatments. | Currentness: UPDATE CURRENTNESS TO REFLECT WHAT TIME FRAME DATES REPRESENT
2016-07-06
2018-06-14
false
eng
false
Entity Attribute Detail Citation
https://www.ncbi.nlm.nih.gov/sra/
WWW:LINK-1.0-http--link
Entity Attribute Detail URL
Entity Attribute Detail URL
information
FASTQ
Pacific Islands Fisheries Science Center
808-725-5360
1845 Wasp Blvd.
Honolulu
HI
96818
pifsc.info@noaa.gov
https://www.pifsc.noaa.gov
WWW:LINK-1.0-http--link
Pacific Islands Fisheries Science Center Website
Pacific Island Fisheries Science Center homepage
information
8:00 a.m. - 4:30 p.m.
distributor
https://www.ncbi.nlm.nih.gov/biosample?LinkName=bioproject_biosample_all&from_uid=649058
WWW:LINK-1.0-http--link
Illumina Sequences
Raw illumina sequences are available in NCBI SRA (Sequence Read Archive, Accession: SRS7105074‐SRS7105095. These accession numbers represent 22 samples and includes the forward and reverse fastq file for each sample. Metabarcoding data was submitted to Genebank via Genome - https://geome-db.org/ which tags and records metadata associated with sequence files.
download
dataset
Accuracy
DNA metabarcoding has inevitable PCR amplification and sequencing biases associated with using universal primers that amplify widely divergent taxa, and the variable rates of evolution within and among phyla that affect sequence clustering with a fixed divergence thresholds. Thus, some organisms may not be represented in the DNA metabarcoding data even though they were present on the plates. See https://onlinelibrary.wiley.com/doi/10.1002/edn3.163 for more details.
Analytical Accuracy
Analytical results could be different depending on the bioinformatics used to process the raw sequencing data, however, the overall picture will most likely remain the same.
Bias
As stated in the Analytical Accuracy section, bias in the data may result in one's choice of tools to bioinformatically process sequencing data.
Comparability
If the reader follows the direct bioinformatic processing steps as outlined in Timmers et al. XXX, the data will be comparable.
Completeness Report
See Timmers et al. XXX
Conceptual Consistency
See Timmers et al. XXX
These data represent the first laboratory study to evaluate the richness and composition of an entire coral reef community that developed over a multi-annual time frame under predicted future ocean conditions.
For mesocosm set-up, ARMS processing, DNA extraction, amplification, and sequencing see Timmers M, Jury C, Vicente J, Webb M, and Toonen RJ (In Review) Coral reef biodiversity shuffles but does not decline under the combined stressors of experimental ocean warming and acidification. PNAS.
Timmers, Molly A
(808)725-5449
molly.timmers@noaa.gov
processor
To obtain the sequencing data from this study, go to https://www.ncbi.nlm.nih.gov/biosample?LinkName=bioproject_biosample_all&from_uid=649058 which takes you to the National Center for Biotechnology Information (NCBI) which hosts Genebank, a genetic sequence database collection of all publicly available DNA sequences. To download a sequence file, click on the SRA link associated with each entry. Click on the data access tab in the new link and select the highlighted name to download the sequence file.
Timmers, Molly A
(808)725-5449
molly.timmers@noaa.gov
processor
Once sequences are downloaded, you may choose to conduct the bioinformatics in a numbers of ways based on your preference. To process the samples in the same way as was conducted by NOAA, please refer to the supplementary information in the paper, Coral reef biodiversity shuffles but does not decline under the combined stressors of experimental ocean warming and acidification.
Timmers, Molly A
(808)725-5449
molly.timmers@noaa.gov
processor
Biodiversity of coral reef cryptobiota shuffles but does not decline under the combined stressors of ocean warming and acidification
2021-09-28
publication
Molly Timmers
https://www.pnas.org/content/118/39/e2103275118
WWW:LINK-1.0-http--link
Source Citation URL
Source Citation URL
information
originator
otherRestrictions
otherRestrictions
Access Constraints: None | Use Constraints: None