64270 ARMS Sequencing - PRIA Data Set Published / External 63296 ARMS Project In Work 2017 2020-01-07 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) under the National Coral Reef Monitoring Program (NCRMP) at stationary climate monitoring sites and used to assess and monitor cryptic reef diversity in the Pacific Remote Island Areas (PRIA). 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 the PRIAs. 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. Coral reefs are among the most biologically diverse, complex, and productive of ecosystems. The vast majority of coral reef biodiversity is made up of the small and cryptic organisms living unseen by most within the reef matrix. This hidden community, the cryptobiota, are a critical component of coral reef trophic dynamics and play an essential role in nutrient recycling that enable reefs to thrive in oligotrophic environments. Despite their ecological importance, the cryptobiota are often ignored because they live deep within the reef matrix and require significant taxonomic expertise and time to collect and identify. By leaving ARMS units on the benthos for over two-years to attract the colonization and establishment of the cryptobiota ARMS overcome extraction constraints and by integrating next-generation DNA sequencing into ARMS unit processing, taxonomic limitations are diminshed through the establishment of molecular operational taxonomic units (MOTU) - species proxies - based on DNA sequence similarities. NCRMP is a framework for conducting sustained observations of biological, climate, and socioeconomic indicators at 10 priority coral reefs across the U.S. and its territories. This integrated approach consolidates monitoring of coral reefs under a uniform method in the Pacific, Atlantic, Caribbean, and the Gulf of Mexico for the first time. NCRMP is funded by the CRCP and supported by NOAA Fisheries, NOAA National Centers for Coastal Ocean Science (NCCOS), and many other partners. The Ecosystem Sciences Division at NOAA Fisheries is leading climate monitoring in the U.S. Pacific Islands Region. The climate component of NCRMP in the Pacific 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, erosion, and community structure to understand the impacts of thermal stress and ocean acidification on the ecosystem. Each year, ESD scientists work closely with CRCP and partners during Pacific RAMP missions to collect data using moored oceanographic (subsurface temperature recorders) and ecological (calcification accretion units [CAUs] and autonomous reef monitoring structures [ARMS]) instruments stationed at fixed sites in the Pacific Ocean, and water samples collected by divers. The in-situ data (along with satellite-based observations) are also used in modeling efforts. Innovative analysis techniques are used to develop products that give fellow scientists, managers, decision makers and the public a better understanding of a region's resources and how they are changing over time. 10.7289/v54x563c NOAA Theme ISO 19115 Topic Category biota Theme ISO 19115 Topic Category oceans Theme CRCP Project 743 Theme CRCP Project National Coral Reef Monitoring Program Theme CoRIS Discovery Thesaurus DNA/RNA Sequencing Theme CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Aquatic Habitat > Benthic Habitat 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 > 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 INVERTEBRATE SPECIES 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 in situ Theme NODC PLATFORM NAMES THESAURUS HI'IALAKAI Theme NODC PROJECT NAMES THESAURUS CORAL REEF STUDIES Theme NODC PROJECT NAMES THESAURUS Coral Reef Conservation Program Theme NODC PROJECT NAMES THESAURUS National Coral Reef Monitoring Program Theme NODC SUBMITTING INSTITUTION NAMES THESAURUS US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division Theme ARMS Theme Autonomous Reef Monitoring Structure Theme CRED Theme CREP Theme CReef Theme Census of Marine Life Theme Coral Reef Ecosystem Division Theme Coral Reef Ecosystem Program Theme ESD Theme Ecosystem Sciences Division Theme PIFSC Theme Pacific Islands Fisheries Science Center Theme RAMP Theme Reef Assessment and Monitoring Program Theme cytochrome oxidase I Temporal Triennial Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Jarvis Island (00S160W0001) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Kingman Reef (06N162W0001) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Palmyra Atoll (05N162W0001) Spatial CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Wake Atoll (19N167E0001) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Line Islands > Jarvis Island (00S160W0001) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Line Islands > Kingman Reef (06N162W0001) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Line Islands > Palmyra Atoll (05N162W0001) Spatial CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Wake Atoll > Wake Atoll (19N167E0001) Spatial NODC Sea Area Names Thesaurus Equatorial Pacific Ocean Spatial NODC Sea Area Names Thesaurus Pacific Remote Islands Marine National Monument Spatial PRIA Spatial PRIMNM Spatial Pacific Remote Island Areas 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 NOAA IRC 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 Ecosystem Sciences Division and partners, with support from the Census of Marine Life (2008-2010), NOAA's Ocean Acidification Program (2010-2012), the Coral Reef Conservation Program (2012-2018), and the National Science Foundation grant # OISE12343541 Data Steward 2011 Person Timmers, Molly A molly.timmers@noaa.gov 1845 Wasp Blvd. Honolulu HI 96818 USA (808)725-5449 Email preferred Distributor 2011 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. 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 2011 Person Olenski, Brooke brooke.olenski@noaa.gov Email preferred Originator 2011 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 2011 2021 Person Timmers, Molly A molly.timmers@noaa.gov 1845 Wasp Blvd. Honolulu HI 96818 USA (808)725-5449 Email preferred Ground Condition Pacific Remote Island Areas (PRIA) including Baker, Howland, and Jarvis islands, Kingman Reef, and Johnston, Palmyra, and Wake atolls. 166.59824 166.65155 19.31654 19.27116 Wake Atoll, one of the seven PRIA, is routinely surveyed as part of the Mariana Archipelago RAMP (MARAMP) missions. -162.3843 -159.99086 6.3947 -0.3818 Phoenix (Baker and Howland) and Line Islands (Jarvis, Kingman, and Palmyra), and Johnston Atoll. These six of the seven PRIA are routinely surveyed as part of the American Samoa RAMP (ASRAMP) missions (Johnston, Baker and Howland during the first leg of ASRAMP, and Jarvis, Kingman, and Palmyra during the last leg of ASRAMP). Range 2011-03-23 2014-03-19 HA1101 HA1401 ARMS across Wake Atoll, deployed in 2011 and recovered in 2014 Range 2012-05-03 2015-04-28 HA1201 HA1501 ARMS across the Pacific Remote Island Areas (excluding Wake Atoll) deployed in 2012 and recovered in 2015 Range 2014-03-16 2017-04-23 HA1401 HA1701 ARMS across Wake Atoll, deployed in 2014 and recovered in 2017 Range 2015-04-08 2018-08-05 HA_1501 HA_1801 ARMS across the Pacific Remote Island Areas Geographic 2D EPSG:4326 WGS 84 World Geodetic System 1984 WGS 84 6378137 298.257223563 1 Geodetic Lattitude Lat degree north 2 Geodetic Longitude Lon degree east Unclassified Not applicable Not applicable 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 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 Coral Reef Conservation Program (CRCP) 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. None Please cite PIFSC Ecosystem Sciences Division when using the data. Suggested citation: Ecosystem Sciences Division, Pacific Islands Fisheries Science Center, 2020: Cryptobiota metabarcoding using Autonomous Reef Monitoring Structure (ARMS) Deployed at Coral Reef Sites across PRIA from 2011 to 2015, https://www.fisheries.noaa.gov/inport/item/64267. 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. 2017-04-24T00:00:00 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://www.coris.noaa.gov/monitoring/ NOAA's National Coral Reef Monitoring Program Online Resource https://www.fisheries.noaa.gov/region/pacific-islands#science Information on NOAA PIFSC's official website Online Resource 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 by the ARMS team and the Cruise Data Manager 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. Autonomous Reef Monitoring Structures (ARMS) Overview Person Molly Timmers Originator https://origin-apps-pifsc.fisheries.noaa.gov/cred/survey_methods.php#arms Pacific Islands Fisheries Science Center Protocol 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 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 64268 Data Set Series 64269 Data Set Series 64332 Data Set Series 22465 Data Set Series 61283 Data Set Cross Reference gov.noaa.nmfs.inport:64270 Brooke Olenski 2021-02-09T08:31:25 SysAdmin InPortAdmin 2025-12-03T01:00:28 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