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

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.

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.

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

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/

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.

Coconut Island ( Moku o loe ) (21N157W0005)

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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 can be accessed online via Genebank.

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Please cite NOAA Fisheries, Ecosystem Science Division (ESD) when using the data.

Example:

Ecosystem Science Division; COPY INPORT RECORD CITATION HERE (keep ESD).

None

None

Genbank SRA files: SRS7105074 ‐ SRS7105095

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

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 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.

As stated in the Analytical Accuracy section, bias in the data may result in one's choice of tools to bioinformatically process sequencing data.

If the reader follows the direct bioinformatic processing steps as outlined in Timmers et al. XXX, the data will be comparable.

See Timmers et al. XXX

See Timmers et al. XXX

See Timmers et al. XXX

NOAA IRC and NOAA Fisheries ITS resources and assets.

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.