Slide Menu
Search Help Show/Hide Menu
Short Citation:
Pacific Islands Fisheries Science Center, 2022: 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, https://www.fisheries.noaa.gov/inport/item/61283.

Item Identification

Title: 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
Short Name: Climate change effects on coral reef cryptobenthic communities
Status: Completed
Creation Date: 2020-12-10
Abstract:

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.

Purpose:

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.

Other Citation Details:

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.

Keywords

Theme Keywords

Thesaurus Keyword
UNCONTROLLED
CoRIS Discovery Thesaurus DNA/RNA Sequencing
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Autonomous Reef Monitoring Structure (ARMS)
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Molecular Genetic Analysis > DNA/RNA Sequencing
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology > BioDiversity
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Marine Biology > Crytobiota
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Marine Biology > Marine Invertebrates > Biodiversity
ISO 19115 Topic Category 002
ISO 19115 Topic Category 004
NODC DATA TYPES THESAURUS Biodiversity
NODC OBSERVATION TYPES THESAURUS laboratory analyses
NODC PROJECT NAMES THESAURUS CORAL REEF STUDIES
NODC PROJECT NAMES THESAURUS US DOC; NOAA; Office of Oceanic and Atmospheric Research; Ocean Acidification Program
NODC SUBMITTING INSTITUTION NAMES THESAURUS US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division
None Coral Reef Ecosystem Division
None Coral Reef Ecosystem Program
None CRED
None CREP
None Ecosystem Sciences Division
None ESD
None Pacific Islands Fisheries Science Center
None PIFSC

Spatial Keywords

Thesaurus Keyword
UNCONTROLLED
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > Hawaii > Honolulu > Coconut Island ( Moku o loe ) (21N157W0005)
NODC SEA AREA NAMES THESAURUS: Coastal Waters of Hawaii

Instrument Keywords

Thesaurus Keyword
UNCONTROLLED
NODC INSTRUMENT TYPES THESAURUS ARMS

Physical Location

Organization: Pacific Islands Fisheries Science Center
City: Honolulu
State/Province: HI
Country: USA

Data Set Information

Data Set Scope Code: Data Set
Data Set Type: Other
Maintenance Frequency: None Planned
Maintenance Note:

These data are fastq files directly from the MiSeq sequencer and are already deposited into Genbank and thus there is no maintenance.

Data Presentation Form: fastq files
Entity Attribute Overview:

Fastq files for both the forward and reverse reads for each ARMS unit that underwent COI DNA metabarcoding. The Sequence Read Archive (SRA) associated with Genbank stores raw sequences data from next-generation technologies. The SRA access numbers to these data are SRS7105074 - SRS7105095 and can be access at: https://www.ncbi.nlm.nih.gov/sra/

Entity Attribute Detail URL: https://www.ncbi.nlm.nih.gov/sra/
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.

Data Set Credit: NOAA Fisheries, Ecosystem Sciences Division and funded by the NOAA Ocean Acidification Program

Support Roles

Data Set Credit

CC ID: 940225
Date Effective From: 2016
Date Effective To:
Contact (Organization): NMFS Office of Science and Technology (OST)
Address: 1315 East West Highway
Silver Spring, MD 20910
USA
Phone: 301-427-8100
URL: http://www.st.nmfs.noaa.gov/
Business Hours: 0700 - 1800 EST/EDT
Contact Instructions:

The Ocean Acidification Program funded this work in conjunction with the National Science Foundation.

Data Steward

CC ID: 940227
Date Effective From: 2016
Date Effective To:
Contact (Person): Timmers, Molly A
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: molly.timmers@noaa.gov
Phone: (808)725-5449

Distributor

CC ID: 940228
Date Effective From: 2020
Date Effective To:
Contact (Organization): Pacific Islands Fisheries Science Center (PIFSC)
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: pifsc.info@noaa.gov
Phone: 808-725-5360
URL: https://www.pifsc.noaa.gov
Business Hours: 8:00 a.m. - 4:30 p.m.

Metadata Contact

CC ID: 940229
Date Effective From: 2019
Date Effective To:
Contact (Person): Olenski, Brooke
Email Address: brooke.olenski@noaa.gov

Originator

CC ID: 940224
Date Effective From: 2019
Date Effective To:
Contact (Organization): Pacific Islands Fisheries Science Center (PIFSC)
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: pifsc.info@noaa.gov
Phone: 808-725-5360
URL: https://www.pifsc.noaa.gov
Business Hours: 8:00 a.m. - 4:30 p.m.

Point of Contact

CC ID: 940226
Date Effective From: 2019
Date Effective To:
Contact (Person): Timmers, Molly A
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: molly.timmers@noaa.gov
Phone: (808)725-5449

Extents

Currentness Reference: UPDATE CURRENTNESS TO REFLECT WHAT TIME FRAME DATES REPRESENT

Extent Group 1

Extent Description:

Coconut Island ( Moku o loe ) (21N157W0005)

Extent Group 1 / Geographic Area 1

CC ID: 998231
W° Bound: -155.06861111111
E° Bound: -155.06861111111
N° Bound: 19.72944444444
S° Bound: 19.72944444444
Description

Hawaii Institute of Marine Biology on Coconut Island in Kaneohe Bay within the island of Oahu.

Extent Group 1 / Time Frame 1

CC ID: 998230
Time Frame Type: Range
Start: 2016-07-06
End: 2018-06-14
Description:

This represents the time frame in which the ARMS remained within the mesocosm treatments.

Access Information

Security Class: Unclassified
Security Classification System:

Not applicable

Security Handling Description:

Not applicable

Data Access Policy:

NOAA Ecosystem Science Division (ESD) Data Sharing Recommendations, version 9.0 updated August 12, 2015:

ESD welcomes the opportunity to collaborate on research issues contributing to the scientific basis for better management of marine ecosystems. ESD has a very diverse set of field activities that generates large volumes of data using an array of data collection protocols.

The following recommendations are for your consideration as you use this data:

1) Data analyses should take all field exigencies into account. The most effective way to do this would be active collaboration with ESD principal investigators.

2) In all presentations, product releases, or publications using data generated by ESD, proper acknowledgement of both ESD and the individuals responsible for data collection is expected. Citing the DOI (if available) is preferred, a non-DOI example is listed below.

3) If you collect or generate data for the same study areas, ESD requests that you share relevant information on complimentary data collections.

4) Those receiving data are strongly urged to inform the ESD Data Management Team of any errors and discrepancies that are discovered during the course of using these data. They are further urged to bring to the attention of the Team all problems and difficulties encountered in using these data. This information is necessary in order to improve the collections and to facilitate more efficient and economical data processing and retrieval. The users are asked to supply copies of any missing data that may be located, and to provide information as to significant subsets and special aggregations of data that are developed in using the material provided.

Example citation:

"This publication makes use of data products provided by the Ecosystem Science Division (ESD), Pacific Islands Fisheries Science Center (PIFSC), National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA), with funding support from the NOAA Ocean Acidification Program (OAP). The analysis and interpretations presented here are solely that of the current authors.”

Data Access Procedure:

Data can be accessed online via Genebank.

Data Access Constraints:

None

Data 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).

Metadata Access Constraints:

None

Metadata Use Constraints:

None

Distribution Information

Distribution 1

CC ID: 940230
Start Date: 2021-02-08
End Date: Present
Download URL: https://www.ncbi.nlm.nih.gov/biosample?LinkName=bioproject_biosample_all&from_uid=649058
Distributor: Pacific Islands Fisheries Science Center (PIFSC) (2020 - Present)
File Name: Illumina Sequences
Description:

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.

File Type: FASTQ
File Size: ranges from 17 to 400 MB

URLs

URL 1

CC ID: 940231
URL: https://www.fisheries.noaa.gov/region/pacific-islands#science
Name: NOAA Fisheries Pacific Islands Region - Science Overview
URL Type:
Online Resource

Technical Environment

Description:

Genbank SRA files: SRS7105074 ‐ SRS7105095

Go to: https://www.ncbi.nlm.nih.gov/sra/

Data Quality

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

Quality Control Procedures Employed:

See Timmers et al. XXX

Data Management

Have Resources for Management of these Data Been Identified?: Yes
Approximate Percentage of Budget for these Data Devoted to Data Management: Unknown
Do these Data Comply with the Data Access Directive?: Yes
Is Access to the Data Limited Based on an Approved Waiver?: No
Approximate Delay Between Data Collection and Dissemination: Unknown
Actual or Planned Long-Term Data Archive Location: Other
Approximate Delay Between Data Collection and Archiving: Unknown
How Will the Data Be Protected from Accidental or Malicious Modification or Deletion Prior to Receipt by the Archive?:

NOAA IRC and NOAA Fisheries ITS resources and assets.

Lineage

Lineage Statement:

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.

Sources

Biodiversity of coral reef cryptobiota shuffles but does not decline under the combined stressors of ocean warming and acidification

CC ID: 1125027
Contact Role Type: Originator
Contact Type: Person
Contact Name: Molly Timmers
Publish Date: 2021-09-28
Citation URL: https://www.pnas.org/content/118/39/e2103275118

Process Steps

Process Step 1

CC ID: 1057265
Description:

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.

Process Contact: Timmers, Molly A
Phone (Voice): (808)725-5449
Email Address: molly.timmers@noaa.gov

Process Step 2

CC ID: 998232
Description:

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.

Process Contact: Timmers, Molly A
Phone (Voice): (808)725-5449
Email Address: molly.timmers@noaa.gov

Process Step 3

CC ID: 1038113
Description:

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.

Process Contact: Timmers, Molly A
Phone (Voice): (808)725-5449
Email Address: molly.timmers@noaa.gov

Acquisition Information

Instruments

Instrument Unavailable Reason: Not Applicable

Platforms

Platform Unavailable Reason: Not Applicable

Catalog Details

Catalog Item ID: 61283
GUID: gov.noaa.nmfs.inport:61283
Metadata Record Created By: Annette M DesRochers
Metadata Record Created: 2020-07-28 19:13+0000
Metadata Record Last Modified By: SysAdmin InPortAdmin
Metadata Record Last Modified: 2022-10-20 02:17+0000
Metadata Record Published: 2022-02-04
Owner Org: PIFSC
Metadata Publication Status: Published Externally
Do Not Publish?: N
Metadata Last Review Date: 2022-02-04
Metadata Review Frequency: 1 Year
Metadata Next Review Date: 2023-02-04