Cryptobiota metabarcoding using Autonomous Reef Monitoring Structure (ARMS) Deployed in Batangas, Philippines from 2012 to 2015

The data described here includes cytochrome oxidase I (COI) DNA metabarcoding data collected from Autonomous Reef Monitoring Structures (ARMS). ARMS were deployed by the NOAA Pacific Islands Fisheries Science Center (PIFSC), Ecosystem Sciences Division (formerly the Coral Reef Ecosystem Division) in Batangas Philippines within the Verde Island Passage under USAID Philippines. Developed in collaboration with the Census of Marine Life (CoML) Census of Coral Reef Ecosystems (CReefs), ARMS were designed to mimic the structural complexity of a reef and attract/collect colonizing marine invertebrates. The key innovation of the ARMS method is that biodiversity is sampled over precisely the same surface area in the exact same manner.

These data were gathered at specific reef sites within the Verde Island Passage. ARMS units were set-up, deployed and recovered as described in the ARMS record in the related items section below. After ARMS were disassembled, different size fractions of samples and plate scrapings were preserved in ethanol for metabarcoding.

The Coral Reef Ecosystem Program (CREP) at NOAA Fisheries is conducting in-situ climate monitoring across the U.S. Pacific Islands Region. Climate monitoring provides a comprehensive view of climate change impacts on coral reef ecosystems and helps identify areas of resilience and vulnerability. The key indicators used to identify and monitor climate-driven trends include 1) thermal stress caused by changes in sea temperature, 2) ocean acidification resulting from changes in carbonate chemistry, and 3) ecological impacts by collecting data on coral growth rates and community structure to understand the impacts of thermal stress and ocean acidification on the ecosystem.

This particular dataset for the Philippines is part of a 3-year project ("Climate, Biodiversity and Fisheries in the Coral Triangle: Embracing the E in Ecosystem Approaches to Fisheries Management") implemented by CREP. This project was funded by NOAA's Coral Reef Conservation Program (CRCP) and the U.S. Agency for International Development (USAID) Regional Development Mission Asia (RDMA) as part of the U.S. Coral Triangle Initiative, with additional support from the Coral Triangle Support Partnership and USAID Philippines.

The goal of the project was to build on CREP's expertise to provide tools and information about climate change, ocean acidification, and their impacts on biodiversity and fisheries that could inform and be incorporated into an Ecosystem Approach to Fisheries Management (EAFM) for the Philippines. CREP worked with local governments, communities, and NGOs to build science capacity by establishing robust observing capabilities and providing hands-on training to initiate collection of climate science information for the Verde Island Passage in the Philippines that can be used toward adaptive EAFM.

The NOAA Coral Reef Ecosystem Program (CREP) traveled to the Verde Island Passage region of the Philippines in 2012 to deploy moored oceanographic (subsurface temperature recorders [STRs]) and ecological (calcification accretion units [CAUs] and autonomous reef monitoring structures [ARMS]) instrumentation, to collect surface and bottom water samples, and to conduct benthic photo-quadrat surveys, which included the collection of benthic images; in 2013 to collect additional water samples; and again in 2015 to recover the instrumentation and to collect another round of water samples and benthic images. All activities were conducted by SCUBA divers at five locations in the municipalities of Mabini and Tingloy, including Batong Buhay, Koala Reserve Area, Arthur's Reef, Twin Rocks, and Batalang Bato. At each of the five locations, a shallow and deep survey site was established for a total of 10 survey sites.

These data are merged fasta files of the forward and reverse sequencing on a MiSeq platform and have been deposited into Genbank.

Fasta files for each successfully sequenced ARMS fraction that underwent COI DNA metabarcoding. The Sequence Read Archive (SRA) associated with Genbank stores sequences data from next-generation technologies. The SRA access numbers to these data are XXXX-XXXXX 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.

Mabini and Tingloy in Batangas, Philippines

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NOAA Ecosystem Science Division (EDS) 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 Coral Reef Ecosystem Program (CREP), Pacific Islands Fisheries Science Center (PIFSC), National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA), with funding support from the NOAA Coral Reef Conservation Program (CRCP), the United States Agency for International Development, and the National Science Foundation grant #OISE1243541. The analysis and interpretations presented here are solely that of the current authors.”

Data can be accessed online via Genbank.

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Please cite NOAA Coral Reef Ecosystem Program (CREP) when using the data.

Suggested citation:

Ecosystem Sciences Division, Pacific Islands Fisheries Science Center (2020). Cryptobiota metabarcoding using Autonomous Reef Monitoring Structure (ARMS) Deployed in the Batangas in the Philippines from 2012 to 2015. https://www.fisheries.noaa.gov/inport/item/64332.

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Genbank SRA files:

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.

All ARMS units that are recovered are disassembled, photographed, and sorted by size. Genetic analysis of ARMS samples may exist for a subset of fractions and locations. Missing fractions/locations could be a result of: 1) ARMS that were not recovered due to logistical constraints of the mission; 2) ARMS that were not found when divers returned to the site; and 3) ARMS fractions that were unsuccessfully extracted, amplified, or sequenced.

ARMS sample biodiversity over precisely the same surface area in the exact same manner. Thus, the use of ARMS is a systematic, consistent, and comparable method for monitoring the cryptobiota community overtime. Three units are deployed at each site to allow for replicate measurements. Divers typically record ARMS metadata into the master Microsoft Access database within a few days of the field operations and/or ARMS processing. QA/QC procedures are typically completed during the field mission.

Autonomous Reef Monitoring Structures (ARMS) are assembled, deployed, recovered, and processed as described in the ARMS record in the related items section below. The sessile organisms, the 100 um and 500 um motile fractions, as well as plate scrapings, undergo DNA metabarcoding using the COI gene as the amplicon marker.