Cryptobiota metabarcoding using Autonomous Reef Monitoring Structure (ARMS) Deployed at Coral Reef Sites across Timor Leste from 2012 to 2014

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 Timor Leste under USAID Timor Leste. 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 across Timor-Leste. 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 use of ARMS is a systematic, consistent, and comparable method for monitoring the marine cryptobiota community in coral reef ecosystems over time.

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.

In 2011, NOAA and the United States Agency for International Development (USAID) Timor-Leste Mission formed a 5-year bi-lateral partnership agreement from 2012 to 2016, in support of the Government of Timor-Leste—particularly the Ministry of Agriculture and Fisheries (MAF)—by addressing significant information gaps in their nearshore marine ecosystems. Specifically, MAF asked NOAA to address the following questions:

1.Where are the nearshore marine resources?

2.What are the nearshore marine resources?

3.How are they changing over time and what threats are potentially causing these changes?

4.What approaches are needed to manage and conserve the nearshore marine resources?

With financial support from USAID and in-kind support from the NOAA Coral Reef Conservation Program (CRCP), the NOAA Coral Reef Ecosystem Program (CREP) conducted baseline ecosystem assessment surveys to inform ecosystem-based management planning in Timor-Leste. The primary activities conducted by NOAA to answer these questions included:

1.satellite mapping of nearshore habitats,

2.conducting coral reef ecosystem assessments,

3.establishing ecological baselines for climate change, and

4.building management capacity by developing a spatial data framework

The biodiversity data described herein resulted from the third activity to establish ecological baselines for climate change.

Pacific Islands Fisheries Science Center. 2017. Interdisciplinary baseline ecosystem assessment surveys to inform ecosystem-based management planning in Timor-Leste: Final Report. Pacific Islands Fisheries Science Center, PIFSC Special Publication, SP-17-002, 234 p. https://doi.org/10.7289/V5/SP-PIFSC-17-002.

The NOAA Coral Reef Ecosystem Program (CREP) traveled to Timor Leste 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 and again in 2014 to recover the instrumentation and to collect another round of water samples and benthic images. All activities were conducted by SCUBA divers at 8 locations in the municipalities of Dili, Lautem, Baucau, Atauro, Liquica, Manatuto, and Bobonaro.

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.

Timor-Leste

Not applicable

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NOAA Coral Reef Ecosystem Program (CREP) Data Sharing Recommendations, version 9.0 updated August 12, 2015:

CREP welcomes the opportunity to collaborate on research issues contributing to the scientific basis for better management of marine ecosystems. CREP 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 CREP principal investigators.

2) In all presentations, product releases, or publications using data generated by CREP, proper acknowledgement of both CREP 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, CREP requests that you share relevant information on complimentary data collections.

4) Those receiving data are strongly urged to inform the CREP 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 United States Agency for International Development. The analysis and interpretations presented here are solely that of the current authors.”

Data can be accessed online via the NOAA National Centers for Environmental Information (NCEI) Ocean Archive.

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

Suggested citation:

Coral Reef Ecosystem Program; Pacific Islands Fisheries Science Center (2017). Assessing cryptic reef diversity of colonizing marine invertebrates using Autonomous Reef Monitoring Structures (ARMS) deployed at coral reef sites in Timor-Leste from 2012 to 2014. NOAA's National Center for Environmental Information, https://www.fisheries.noaa.gov/inport/item/46159.

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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.