gov.noaa.nmfs.inport:64540 eng UTF8 dataset Other Pacific Islands Fisheries Science Center 808-725-5300 1845 Wasp Blvd. Honolulu HI 96818 USA https://www.pifsc.noaa.gov WWW:LINK-1.0-http--link Website Website for this organization information 8:00 a.m. - 4:30 p.m. resourceProvider DesRochers, Annette M (808)725-5461 1845 Wasp Blvd. Honolulu HI 96818 USA annette.desrochers@noaa.gov 8 am - 5 pm Email preferred pointOfContact Akridge, Michael W (808)725-5483 1845 Wasp Blvd. Honolulu HI 96818 USA michael.akridge@noaa.gov pointOfContact 2026-03-04T19:17:17 ISO 19115-2 Geographic Information - Metadata Part 2 Extensions for imagery and gridded data ISO 19115-2:2009(E) Cryptobiota metabarcoding using Autonomous Reef Monitoring Structure (ARMS) Deployed at Coral Reef Sites across Timor Leste from 2012 to 2014 ARMS Sequencing - Timor Leste 2021-01-01 creation 2021-05-05 revision 2017 publication NOAA/NMFS/EDM 64540 https://www.fisheries.noaa.gov/inport/item/64540 WWW:LINK-1.0-http--link Full Metadata Record View the complete metadata record on InPort for more information about this dataset. information Pacific Islands Fisheries Science Center 808-725-5360 1845 Wasp Blvd. Honolulu HI 96818 USA pifsc.info@noaa.gov https://www.pifsc.noaa.gov WWW:LINK-1.0-http--link Pacific Islands Fisheries Science Center Website Pacific Island Fisheries Science Center homepage information 8:00 a.m. - 4:30 p.m. originator https://naturalhistory.si.edu/research/global-arms-program WWW:LINK-1.0-http--link Global ARMS program Smithsonian partnership - Global ARMS program download https://www.pifsc.noaa.gov/cred/coral_triangle_initiative.php WWW:LINK-1.0-http--link Citation URL Information about the NOAA Coral Reef Ecosystem Program's activities in the Coral Triangle. download https://www.pifsc.noaa.gov/cred/biodiversity.php WWW:LINK-1.0-http--link Citation URL Information on NOAA CRED's official website download https://pifscblog.wordpress.com/2012/11/20/final-count-timor-leste/ WWW:LINK-1.0-http--link Citation URL PIFSC blog post, Nov 2012: The final count: summary of mission to Timor-Leste in 2012 download https://pifscblog.wordpress.com/2014/09/30/timor-leste-atauro/ WWW:LINK-1.0-http--link Citation URL PIFSC blog post, Sept 2014: Scientists return to Timor-Leste for reef monitoring mission download https://www.pifsc.noaa.gov/cred/survey_methods/arms/index.php WWW:LINK-1.0-http--link Citation URL Pacific Islands Fisheries Science Center, Coral Reef Ecosystem Program official website, ARMS page. download https://www.coris.noaa.gov/activities/projects/timor-leste/ WWW:LINK-1.0-http--link Citation URL 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. download 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 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. PIFSC Coral Reef Ecosystem Program and funded by the United States Agency for International Development underDevelopment Timmers, Molly A (808)725-5449 1845 Wasp Blvd. Honolulu HI 96818 USA molly.timmers@noaa.gov Email preferred custodian notPlanned These data are merged fasta files of the forward and reverse sequencing on a MiSeq platform and have been deposited into Genbank. DNA/RNA Sequencing theme CoRIS Discovery Thesaurus EARTH SCIENCE > Biosphere > Aquatic Habitat > Reef Habitat EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Autonomous Reef Monitoring Structure (ARMS) EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Baseline studies EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > In Situ Biological EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology EARTH SCIENCE > Oceans > Marine Biology > Cryptobiota EARTH SCIENCE > Oceans > Marine Biology > Marine Invertebrates EARTH SCIENCE > Oceans > Marine Biology > Marine Invertebrates > Biodiversity EARTH SCIENCE > Oceans > Marine Biology > Marine Invertebrates > Census EARTH SCIENCE > Oceans > Marine Biology > Marine Invertebrates > Macroinvertebrates theme CoRIS Theme Thesaurus IMAGES SPECIES IDENTIFICATION SPECIES IDENTIFICATION - COUNT theme NODC DATA TYPES THESAURUS biological imagery laboratory analysis theme NODC OBSERVATION TYPES THESAURUS CORAL REEF STUDIES Coral Triangle Initiative theme NODC PROJECT NAMES THESAURUS US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division; Coral Reef Ecosystem Program theme NODC SUBMITTING INSTITUTION NAMES THESAURUS COUNTRY/TERRITORY > Democratic Republic of Timor-Leste (East Timor) (09S126E0001) OCEAN BASIN > Indian Ocean > Timor Sea > Democratic Republic of Timor-Leste (East Timor) (09S126E0001) place CoRIS Place Thesaurus Indian Ocean place NODC SEA AREA NAMES THESAURUS Timor Sea place NODC Sea Area Names Thesaurus ARMS Autonomous Reef Monitoring Structures instrument NODC INSTRUMENT TYPES THESAURUS ARMS Autonomous Reef Monitoring Structure Biodiversity CRED CREP CReef Census of Marine Life Coral Reef Ecosystem Division Coral Reef Ecosystem Program Ministry of Agriculture and Fisheries of Timor-Leste PIFSC Pacific Islands Fisheries Science Center USAID United States Agency for International Development cytochrome oxidase I theme Atauro Baucau Bobonaro Dili Lautem Manatuto Timor-Leste Vila MPA place environmental DNA metabarcoding instrument DOC/NOAA/NMFS/PIFSC > Pacific Islands Fisheries Science Center, National Marine Fisheries Service, NOAA, U.S. Department of Commerce dataCentre Global Change Master Directory (GCMD) Data Center Keywords 2017-04-24 publication 8.5 Earth Science Data and Information System, Earth Science Projects Division, Goddard Space Flight Center (GSFC), National Aeronautics and Space Administration (NASA) https://forum.earthdata.nasa.gov/app.php/tag/GCMD%2BKeywords GCMD Keyword Forum Page Global Change Master Directory (GCMD). 2025. GCMD Keywords, Version 22. Greenbelt, MD: Earth Science Data and Information System, Earth Science Projects Division, Goddard Space Flight Center (GSFC), National Aeronautics and Space Administration (NASA). URL (GCMD Keyword Forum Page): https://forum.earthdata.nasa.gov/app.php/tag/GCMD+Keywords information custodian ARMS project InPort otherRestrictions Cite As: Pacific Islands Fisheries Science Center, [Date of Access]: Cryptobiota metabarcoding using Autonomous Reef Monitoring Structure (ARMS) Deployed at Coral Reef Sites across Timor Leste from 2012 to 2014 [Data Date Range], https://www.fisheries.noaa.gov/inport/item/64540. NOAA provides no warranty, nor accepts any liability occurring from any incomplete, incorrect, or misleading data, or from any incorrect, incomplete, or misleading use of the data. It is the responsibility of the user to determine whether or not the data is suitable for the intended purpose. otherRestrictions Access Constraints: None otherRestrictions Use Constraints: 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. otherRestrictions 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. unclassified Not applicable Not applicable 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/NMFS/EDM 46159 series Cryptobiota metabarcoding using Autonomous Reef Monitoring Structure (ARMS) Deployed at Coral Reef Sites across American Samoa from 2012 to 2015 NOAA/NMFS/EDM 64267 series Cryptobiota metabarcoding using Autonomous Reef Monitoring Structure (ARMS) Deployed at Coral Reef Sites across Hawaiian Archipelago from 2010 to 2016 NOAA/NMFS/EDM 64268 series Cryptobiota metabarcoding using Autonomous Reef Monitoring Structure (ARMS) Deployed at Coral Reef Sites across Marianas Archipelago from 2011 to 2014 NOAA/NMFS/EDM 64269 series Cryptobiota metabarcoding using Autonomous Reef Monitoring Structure (ARMS) Deployed at Coral Reef Sites across PRIA from 2011 to 2015 NOAA/NMFS/EDM 64270 series Cryptobiota metabarcoding using Autonomous Reef Monitoring Structure (ARMS) Deployed in Batangas, Philippines from 2012 to 2015 NOAA/NMFS/EDM 64332 series 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 NOAA/NMFS/EDM 61283 crossReference NOAA Data Management Plan (DMP) NOAA/NMFS/EDM 64540 https://www.fisheries.noaa.gov/inportserve/waf/noaa/nmfs/pifsc/dmp/pdf/64540.pdf WWW:LINK-1.0-http--link NOAA Data Management Plan (DMP) NOAA Data Management Plan for this record on InPort. information crossReference eng; US biota oceans Genbank SRA files: Go to: https://www.ncbi.nlm.nih.gov/sra/ Timor-Leste 125.01319 127.31222 -8.85321 -8.22438 Extent of climate survey sites in Timor-Leste. Duration that ARMS were deployed (in-water) in Timor-Leste | Currentness: Ground Condition 2012-10-15 2014-10-09 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. false eng false Other ARMS Metabarcoding 2022-02-04 publication NOAA National Centers for Environmental Information ncei.info@noaa.gov https://www.ncei.noaa.gov/contact WWW:LINK-1.0-http--link NCEI Contact Information Information for contacts at NCEI. information distributor https://naturalhistory.si.edu/research/global-arms-program WWW:LINK-1.0-http--link Global ARMS program Smithsonian partnership - Global ARMS program download https://www.pifsc.noaa.gov/cred/coral_triangle_initiative.php WWW:LINK-1.0-http--link https://www.pifsc.noaa.gov/cred/coral_triangle_initiative.php Information about the NOAA Coral Reef Ecosystem Program's activities in the Coral Triangle. download https://www.pifsc.noaa.gov/cred/biodiversity.php WWW:LINK-1.0-http--link https://www.pifsc.noaa.gov/cred/biodiversity.php Information on NOAA CRED's official website download https://pifscblog.wordpress.com/2012/11/20/final-count-timor-leste/ WWW:LINK-1.0-http--link https://pifscblog.wordpress.com/2012/11/20/final-count-timor-leste/ PIFSC blog post, Nov 2012: The final count: summary of mission to Timor-Leste in 2012 download https://pifscblog.wordpress.com/2014/09/30/timor-leste-atauro/ WWW:LINK-1.0-http--link https://pifscblog.wordpress.com/2014/09/30/timor-leste-atauro/ PIFSC blog post, Sept 2014: Scientists return to Timor-Leste for reef monitoring mission download https://www.pifsc.noaa.gov/cred/survey_methods/arms/index.php WWW:LINK-1.0-http--link https://www.pifsc.noaa.gov/cred/survey_methods/arms/index.php Pacific Islands Fisheries Science Center, Coral Reef Ecosystem Program official website, ARMS page. download https://www.coris.noaa.gov/activities/projects/timor-leste/ WWW:LINK-1.0-http--link https://www.coris.noaa.gov/activities/projects/timor-leste/ 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. download dataset 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. Completeness Report 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. Conceptual Consistency 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. ARMS Deployment - ARMS platforms are deployed as described in detail in the ARMS record of the related items section below. Timmers, Molly A (808)725-5449 molly.timmers@noaa.gov processor 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. Timmers, Molly A (808)725-5449 molly.timmers@noaa.gov processor 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. Timmers, Molly A (808)725-5449 molly.timmers@noaa.gov processor 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 Timmers, Molly A (808)725-5449 molly.timmers@noaa.gov processor 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. Timmers, Molly A (808)725-5449 molly.timmers@noaa.gov processor Once sequences are downloaded, you may choose to conduct the bioinformatics in a numbers of ways based on your preference. Timmers, Molly A (808)725-5449 molly.timmers@noaa.gov processor 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. 2017-06-21 publication Pacific Islands Fisheries Science Center, PIFSC https://doi.org/10.7289/V5/SP-PIFSC-17-002 WWW:LINK-1.0-http--link Source Citation URL Source Citation URL information otherRestrictions otherRestrictions Access Constraints: None | Use Constraints: None