64540 ARMS Sequencing - Timor Leste Data Set Published / External 63296 ARMS Project In Work 2021-01-01 2021-05-05 2017 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. Theme ISO 19115 Topic Category biota Theme ISO 19115 Topic Category oceans Theme CoRIS Discovery Thesaurus DNA/RNA Sequencing Theme CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Aquatic Habitat > Reef Habitat Theme CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment Theme CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Autonomous Reef Monitoring Structure (ARMS) Theme CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Baseline studies Theme CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > In Situ Biological Theme CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs Theme CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology Theme CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Marine Biology > Cryptobiota Theme CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Marine Biology > Marine Invertebrates Theme CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Marine Biology > Marine Invertebrates > Biodiversity Theme CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Marine Biology > Marine Invertebrates > Census Theme CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Marine Biology > Marine Invertebrates > Macroinvertebrates Theme NODC DATA TYPES THESAURUS IMAGES Theme NODC DATA TYPES THESAURUS SPECIES IDENTIFICATION Theme NODC DATA TYPES THESAURUS SPECIES IDENTIFICATION - COUNT Theme NODC OBSERVATION TYPES THESAURUS biological Theme NODC OBSERVATION TYPES THESAURUS imagery Theme NODC OBSERVATION TYPES THESAURUS laboratory analysis Theme NODC PROJECT NAMES THESAURUS CORAL REEF STUDIES Theme NODC PROJECT NAMES THESAURUS Coral Triangle Initiative Theme NODC SUBMITTING INSTITUTION NAMES THESAURUS US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division; Coral Reef Ecosystem Program Theme ARMS Theme Autonomous Reef Monitoring Structure Theme Biodiversity Theme CRED Theme CREP Theme CReef Theme Census of Marine Life Theme Coral Reef Ecosystem Division Theme Coral Reef Ecosystem Program Theme Ministry of Agriculture and Fisheries of Timor-Leste Theme PIFSC Theme Pacific Islands Fisheries Science Center Theme USAID Theme United States Agency for International Development Theme cytochrome oxidase I Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > Democratic Republic of Timor-Leste (East Timor) (09S126E0001) Spatial CoRIS Place Thesaurus OCEAN BASIN > Indian Ocean > Timor Sea > Democratic Republic of Timor-Leste (East Timor) (09S126E0001) Spatial NODC SEA AREA NAMES THESAURUS Indian Ocean Spatial NODC Sea Area Names Thesaurus Timor Sea Spatial Atauro Spatial Baucau Spatial Bobonaro Spatial Dili Spatial Lautem Spatial Manatuto Spatial Timor-Leste Spatial Vila MPA Instrument NODC INSTRUMENT TYPES THESAURUS ARMS Instrument NODC INSTRUMENT TYPES THESAURUS Autonomous Reef Monitoring Structures Instrument environmental DNA Instrument metabarcoding Pacific Islands Fisheries Science Center Honolulu HI USA Data Set Other None Planned These data are merged fasta files of the forward and reverse sequencing on a MiSeq platform and have been deposited into Genbank. Fasta Files 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/ 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. PIFSC Coral Reef Ecosystem Program and funded by the United States Agency for International Development 64650 Published / External Other This is a text file with sequence data. 1 This file only contains ARMS sequences 1 No No Active A text file with sequence data. Data Steward 2012 Person Timmers, Molly A molly.timmers@noaa.gov 1845 Wasp Blvd. Honolulu HI 96818 USA (808)725-5449 Email preferred Distributor 2017 Organization NOAA National Centers for Environmental Information NCEI ncei.info@noaa.gov https://ror.org/04r0wrp59 https://www.ncei.noaa.gov/contact NCEI Contact Information Information for contacts at NCEI. Online Resource Metadata Contact 2025-11-12 Person Akridge, Michael W michael.akridge@noaa.gov 1845 Wasp Blvd. Honolulu HI 96818 USA (808)725-5483 Metadata Contact 2012 Person DesRochers, Annette M annette.desrochers@noaa.gov 1845 Wasp Blvd. Honolulu HI 96818 USA (808)725-5461 8 am - 5 pm Email preferred Originator 2012 Organization Pacific Islands Fisheries Science Center PIFSC pifsc.info@noaa.gov https://ror.org/02apffz65 1845 Wasp Blvd. Honolulu HI 96818 USA 808-725-5360 https://www.pifsc.noaa.gov Pacific Island Fisheries Science Center homepage Online Resource 8:00 a.m. - 4:30 p.m. Point of Contact 2012 2021 Person Timmers, Molly A molly.timmers@noaa.gov 1845 Wasp Blvd. Honolulu HI 96818 USA (808)725-5449 Email preferred Ground Condition Timor-Leste 125.01319 127.31222 -8.22438 -8.85321 Extent of climate survey sites in Timor-Leste. Range 2012-10-15 2014-10-09 Duration that ARMS were deployed (in-water) in Timor-Leste Unclassified Not applicable Not applicable 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. None 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. None None Illumina Sequences Illumina sequences are available in NCBI SRA (Sequence Read Archive) for each successfully sequenced fraction for each ARMS unit. Metabarcoding data was submitted to Genbank via Genome - https://geome-db.org/ which tags and records metadata associated with sequence files. fasta ranges from 17 to 600 MB https://naturalhistory.si.edu/research/global-arms-program Global ARMS program Online Resource Smithsonian partnership - Global ARMS program https://pifscblog.wordpress.com/2012/11/20/final-count-timor-leste/ Online Resource PIFSC blog post, Nov 2012: The final count: summary of mission to Timor-Leste in 2012 https://pifscblog.wordpress.com/2014/09/30/timor-leste-atauro/ Online Resource PIFSC blog post, Sept 2014: Scientists return to Timor-Leste for reef monitoring mission https://www.coris.noaa.gov/activities/projects/timor-leste/ Online Resource Timor-Leste project portal on the NOAA Coral Reef Information Service website where NOAA's final report for Timor-Leste and the datasets generated by NOAA CREP as part of the project can be downloaded. https://www.pifsc.noaa.gov/cred/biodiversity.php Online Resource PHP Information on NOAA CRED's official website https://www.pifsc.noaa.gov/cred/coral_triangle_initiative.php Online Resource PHP Information about the NOAA Coral Reef Ecosystem Program's activities in the Coral Triangle. https://www.pifsc.noaa.gov/cred/survey_methods/arms/index.php Online Resource PHP Pacific Islands Fisheries Science Center, Coral Reef Ecosystem Program official website, ARMS page. 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. Yes Unknown Yes No Unknown Other Unknown 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. PIFSC. 2017. Interdisciplinary baseline ecosystem assessment surveys to inform ecosystem-based management planning in Timor-Leste: Final Report. NOAA Pacific Islands Fisheries Science Center, PIFSC Special Publication, SP-17-02, 234p. Organization Pacific Islands Fisheries Science Center, PIFSC 2017-06-21 https://doi.org/10.7289/V5/SP-PIFSC-17-002 1 ARMS Deployment - ARMS platforms are deployed as described in detail in the ARMS record of the related items section below. Person Timmers, Molly A molly.timmers@noaa.gov 1845 Wasp Blvd. Honolulu HI 96818 USA (808)725-5449 PIFSC. 2017. Interdisciplinary baseline ecosystem assessment surveys to inform ecosystem-based management planning in Timor-Leste: Final Report. NOAA Pacific Islands Fisheries Science Center, PIFSC Special Publication, SP-17-02, 234p. 2 ARMS Recovery and Processing - ARMS units are recovered, initially processed, and documented as described in the ARMS record in the related items section below. When all of the plate layers in the ARMS unit have been photographed and set aside (in seawater), the seawater from the disassembly tub, photo tray, and rinse bucket is sieved through adjoining 2 mm and 500 um sieve pans and an attachable 100 um mesh hand net. Material collected in the 500 um sieve and 100 um net are bulk preserved into two separate jars. Jars are filled with EtOH and labeled accordingly. The preserved 500 and 100 um sample fractions undergo a decantation process at a later date prior to DNA metabarcoding. All plates from an individual ARMS unit are scrapped en masse. Once all plates have been scraped, all the scrapings are transferred into a blender (Brevill; BBL600XL). The scrapings are blended for 45-60 seconds on maximum power until the sample is homogenized. The sample is then transferred from the blender to a 40 um net. The sample in the net is rinsed with filtered (< 40 um) seawater until all discharge from net is clear (takes ~2 gal). Four ~10 ml samples are preserved in 50 ml falcon tubes with DMSO and 4 ~10 ml samples are preserved in 95% EtOH. These blended preserved samples undergo DNA metabarcoding. The remaining sample is stored in a sterile whirlpak at -20C. Between the processing of each ARMS unit the blender is rinsed in fresh water to remove any remaining homogenate. The blender is then placed in a 10% bleach solution for 15 minutes. Finally all parts thoroughly rinsed with DI water if available or fresh water. Person Timmers, Molly A molly.timmers@noaa.gov 1845 Wasp Blvd. Honolulu HI 96818 USA (808)725-5449 3 Decantation of the 100 and 500 um fractions: NOTE: All equipment used in this step that is not already sterile need to be rinsed with fresh water, placed in 10% bleach solution for 20 minutes (new every day), transferred to Milliq water for 20 minutes (bleach bucket that the milliq water will go in first, and rinse) and then place under a UV light for 20 minutes. Wear gloves. Take sample out the freezer and let sit to defrost before decantation. Empty container(s) into a 1 L conical flask (that has been bleached, rinsed and UV sterilized). Fill the conical flask with ~300 ml of Milli-Q water. Seal neck of flask with parafilm and shake vigorously for 30 seconds. Make sure to hold the parafilm tightly in place with one hand and place the other hand on the base of the flask. When finished, immediately carefully pour the liquid through the correct sieve (45 μm for 100- 500 μm fraction; 106 μm for 500 μm – 2 mm fraction) trying not to pour the more dense sediment into the sieve. Fill flask with another 300 ml of Milli-Q and repeat process. Do this 7 times. The aim is to remove all the less dense biological material from the flask through decantation, while keeping the more dense sediment in the flask. Collect the material in the sieve and weigh it using a sterile spatula and falcon tube. Put exactly half of the material in a 50 ml falcon tube, fill the tube with ethanol and freeze as a back-up. Place the other half in a sterile mortar and use a pestle to crush the sample for 1 minute. Collect the sample in a 50 ml falcon tube, using a little ethanol to re-suspend it and fill the tube with 95 % ethanol. This sample is now ready for DNA extraction. Store samples at -20C until extraction. Finally, collect the sediment left in the conical flask, using a little Milliq water and pour into the same sieve used in the previous step. Collect the material, weigh it and place in a 50ml falcon tube. Fill with ethanol and freeze at -20C. Person Timmers, Molly A molly.timmers@noaa.gov 1845 Wasp Blvd. Honolulu HI 96818 USA (808)725-5449 4 For DNA extraction, amplification, and sequencing methods see- 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 Person Timmers, Molly A molly.timmers@noaa.gov 1845 Wasp Blvd. Honolulu HI 96818 USA (808)725-5449 5 To obtain the sequencing data, go to XXXXXXX which takes you to the National Center for Biotechnology Information (NCBI) which hosts Genbank, 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. Person Timmers, Molly A molly.timmers@noaa.gov 1845 Wasp Blvd. Honolulu HI 96818 USA (808)725-5449 6 Once sequences are downloaded, you may choose to conduct the bioinformatics in a numbers of ways based on your preference. Person Timmers, Molly A molly.timmers@noaa.gov 1845 Wasp Blvd. Honolulu HI 96818 USA (808)725-5449 Not Applicable Not Applicable 64650 Entity 46159 Data Set Series 64267 Data Set Series 64268 Data Set Series 64269 Data Set Series 64270 Data Set Series 64332 Data Set Series 61283 Data Set Cross Reference gov.noaa.nmfs.inport:64540 Brooke Olenski 2021-04-15T00:41:31 SysAdmin InPortAdmin 2026-03-04T19:17:17 2022-02-04 Pacific Islands Fisheries Science Center PIFSC 1845 Wasp Blvd. Honolulu HI 96818 USA 808-725-5300 https://www.pifsc.noaa.gov 8:00 a.m. - 4:30 p.m. 1001 Public No No 2022-02-04 1 Year 2023-02-04