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

Description

The data described here, including photographs, genetic sequences, and specimen information, were collected by the NOAA Coral Reef Ecosystem Program (CREP) from Autonomous Reef Monitoring Structures, or ARMS, moored for two years at fixed climate survey sites located on hard bottom shallow water (< 15 m) habitats in Timor-Leste. Climate sites were established in Timor-Leste in October 2012 to establish ecological baselines for climate change by measuring multiple features of the coral reef environment (in addition to the data described herein) over time. Three ARMS units were typically deployed by SCUBA divers at each survey site. Each ARMS unit, constructed in-house by CREP, consisted of 23 cm x 23 cm gray, type 1 PVC plates stacked in alternating series of 4 open and 4 obstructed layers and attached to a base plate of 35 cm x 45 cm, which was affixed to the reef. Upon recovery, each ARMS unit was encapsulated, brought to the surface, and disassembled and processed. Disassembled plates were photographed to document recruited sessile organisms, scraped clean and preserved in 95% ethanol for DNA processing. Recruited motile organisms were sieved into 3 size fractions: 2 mm, 500 µm, and 100 µm. The 500 µm and 100 µm fractions were bulked and also preserved in 95% ethanol for DNA processing. The 2 mm fraction was sorted into morphospecies, photographed, and identified to the lowest taxonomic identification possible. The plate photographs, sequences generated from the DNA metabarcoding of the scrapings and the 500- and 100-µm fractions, specimen photographs, and specimen identifications are included in the ARMS dataset. The data can be accessed online via the NOAA National Centers for Environmental Information (NCEI) Ocean Archive. ARMS are used by CREP to assess and monitor cryptic reef diversity across the Pacific. Developed in collaboration with the Census of Marine Life (CoML) Census of Coral Reef Ecosystems (CReefs), ARMS are 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. Thus, the use of ARMS is a systematic, consistent, and comparable method for monitoring the marine cryptobiota community over time.

Resources

Name Format Description Link
0 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.coris.noaa.gov/activities/projects/timor-leste/
33 NOAA Data Management Plan for this record on InPort. https://www.fisheries.noaa.gov/inportserve/waf/noaa/nmfs/pifsc/dmp/pdf/46159.pdf
0 ARMS 2-mm fraction specimens recovered by the NOAA Coral Reef Ecosystem Program (CREP) from Timor-Leste in 2014. https://accession.nodc.noaa.gov/0169338
0 Information on NOAA CRED's official website https://origin-apps-pifsc.fisheries.noaa.gov/cred/index.php
0 NOAA's official page for ARMS https://origin-apps-pifsc.fisheries.noaa.gov/cred/survey_methods/arms/overview.php
0 PIFSC blog post, Sept 2014: Scientists return to Timor-Leste for reef monitoring mission https://pifscblog.wordpress.com/2014/09/30/timor-leste-atauro/
0 Pacific Islands Fisheries Science Center, Coral Reef Ecosystems survey methods. https://www.fisheries.noaa.gov/pacific-islands/ecosystems/coral-reefs-pacific#survey-methods
0 FASTQ files generated during the DNA metabarcoding process of the 500- and 100-µm fractions and scrapings from ARMS units deployed in Timor-Leste in 2012 and recovered in 2014 by the NOAA Coral Reef Ecosystem Program (CREP). FASTQ files are zipped (*.gz) https://accession.nodc.noaa.gov/0169338
0 View the complete metadata record on InPort for more information about this dataset. https://www.fisheries.noaa.gov/inport/item/46159
0 Pacific Island Fisheries Science Center homepage https://www.pifsc.noaa.gov
0 PIFSC blog post, Nov 2012: The final count: summary of mission to Timor-Leste in 2012 https://pifscblog.wordpress.com/2012/11/20/final-count-timor-leste/
0 Images organized by climate survey site (TIM-01 to TIM-10) from ARMS deployed in Timor-Leste in 2012 and recovered in 2014 by the NOAA Coral Reef Ecosystem Program (CREP). Images are organized by 1) photographs taken of the PLATES (tops and bottoms) as the recovered ARMS units were processed, 2) specimens that were recovered and identified as part of the 2-mm fraction (SPECIES folder, which corresponds to SAMPLE_LABEL in the CSV), and 3) photographs taken during the deployment and recovery of ARMS units (DEPLOY and RECOVER folders). https://accession.nodc.noaa.gov/0169338
0 Photographs (copied from the SPECIES folder in IMAGES_SITE) of the 2-mm fraction specimens recovered from ARMS units deployed in Timor-Leste in 2012 (and recovered in 2014) by the NOAA Coral Reef Ecosystem Program (CREP). Images are organized by taxa group. These specimen photographs have been cross-indexed and organized by the TAXA GROUP (e.g., anemone, crab, flatworm, isopod), which corresponds to the Taxa Group in the CSV file. https://accession.nodc.noaa.gov/0169338
0 Information about the NOAA Coral Reef Ecosystem Program's activities in the Coral Triangle. https://origin-apps-pifsc.fisheries.noaa.gov/cred/coral_triangle_initiative.php
0 Global Change Master Directory (GCMD). 2024. GCMD Keywords, Version 19. 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 https://forum.earthdata.nasa.gov/app.php/tag/GCMD%2BKeywords
0 ARMS 2-mm fraction specimens recovered by the NOAA Coral Reef Ecosystem Program (CREP) from Timor-Leste in 2014. https://accession.nodc.noaa.gov/0169338
0 Images organized by climate survey site (TIM-01 to TIM-10) from ARMS deployed in Timor-Leste in 2012 and recovered in 2014 by the NOAA Coral Reef Ecosystem Program (CREP). Images are organized by 1) photographs taken of the PLATES (tops and bottoms) as the recovered ARMS units were processed, 2) specimens that were recovered and identified as part of the 2-mm fraction (SPECIES folder, which corresponds to SAMPLE_LABEL in the CSV), and 3) photographs taken during the deployment and recovery of ARMS units (DEPLOY and RECOVER folders). https://accession.nodc.noaa.gov/0169338
0 Photographs (copied from the SPECIES folder in IMAGES_SITE) of the 2-mm fraction specimens recovered from ARMS units deployed in Timor-Leste in 2012 (and recovered in 2014) by the NOAA Coral Reef Ecosystem Program (CREP). Images are organized by taxa group. These specimen photographs have been cross-indexed and organized by the TAXA GROUP (e.g., anemone, crab, flatworm, isopod), which corresponds to the Taxa Group in the CSV file. https://accession.nodc.noaa.gov/0169338
0 FASTQ files generated during the DNA metabarcoding process of the 500- and 100-µm fractions and scrapings from ARMS units deployed in Timor-Leste in 2012 and recovered in 2014 by the NOAA Coral Reef Ecosystem Program (CREP). FASTQ files are zipped (*.gz) https://accession.nodc.noaa.gov/0169338
0 Pacific Island Fisheries Science Center homepage https://www.pifsc.noaa.gov
0 Information about the NOAA Coral Reef Ecosystem Program's activities in the Coral Triangle. https://origin-apps-pifsc.fisheries.noaa.gov/cred/coral_triangle_initiative.php
0 Information on NOAA CRED's official website https://origin-apps-pifsc.fisheries.noaa.gov/cred/index.php
0 NOAA's official page for ARMS https://origin-apps-pifsc.fisheries.noaa.gov/cred/survey_methods/arms/overview.php
0 PIFSC blog post, Nov 2012: The final count: summary of mission to Timor-Leste in 2012 https://pifscblog.wordpress.com/2012/11/20/final-count-timor-leste/
0 PIFSC blog post, Sept 2014: Scientists return to Timor-Leste for reef monitoring mission https://pifscblog.wordpress.com/2014/09/30/timor-leste-atauro/
0 Pacific Islands Fisheries Science Center, Coral Reef Ecosystems survey methods. https://www.fisheries.noaa.gov/pacific-islands/ecosystems/coral-reefs-pacific#survey-methods
0 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.coris.noaa.gov/activities/projects/timor-leste/
33 NOAA Data Management Plan for this record on InPort. https://www.fisheries.noaa.gov/inportserve/waf/noaa/nmfs/pifsc/dmp/pdf/46159.pdf
0 View the complete metadata record on InPort for more information about this dataset. https://www.fisheries.noaa.gov/inport/item/46159
0 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 https://forum.earthdata.nasa.gov/app.php/tag/GCMD%2BKeywords
0 Information on NOAA CRED's official website https://origin-apps-pifsc.fisheries.noaa.gov/cred/index.php
0 Images organized by climate survey site (TIM-01 to TIM-10) from ARMS deployed in Timor-Leste in 2012 and recovered in 2014 by the NOAA Coral Reef Ecosystem Program (CREP). Images are organized by 1) photographs taken of the PLATES (tops and bottoms) as the recovered ARMS units were processed, 2) specimens that were recovered and identified as part of the 2-mm fraction (SPECIES folder, which corresponds to SAMPLE_LABEL in the CSV), and 3) photographs taken during the deployment and recovery of ARMS units (DEPLOY and RECOVER folders). https://accession.nodc.noaa.gov/0169338
0 ARMS 2-mm fraction specimens recovered by the NOAA Coral Reef Ecosystem Program (CREP) from Timor-Leste in 2014. https://accession.nodc.noaa.gov/0169338
0 Photographs (copied from the SPECIES folder in IMAGES_SITE) of the 2-mm fraction specimens recovered from ARMS units deployed in Timor-Leste in 2012 (and recovered in 2014) by the NOAA Coral Reef Ecosystem Program (CREP). Images are organized by taxa group. These specimen photographs have been cross-indexed and organized by the TAXA GROUP (e.g., anemone, crab, flatworm, isopod), which corresponds to the Taxa Group in the CSV file. https://accession.nodc.noaa.gov/0169338
0 FASTQ files generated during the DNA metabarcoding process of the 500- and 100-µm fractions and scrapings from ARMS units deployed in Timor-Leste in 2012 and recovered in 2014 by the NOAA Coral Reef Ecosystem Program (CREP). FASTQ files are zipped (*.gz) https://accession.nodc.noaa.gov/0169338
0 View the complete metadata record on InPort for more information about this dataset. https://www.fisheries.noaa.gov/inport/item/46159
0 Pacific Island Fisheries Science Center homepage https://www.pifsc.noaa.gov
0 Information about the NOAA Coral Reef Ecosystem Program's activities in the Coral Triangle. https://origin-apps-pifsc.fisheries.noaa.gov/cred/coral_triangle_initiative.php
0 NOAA's official page for ARMS https://origin-apps-pifsc.fisheries.noaa.gov/cred/survey_methods/arms/overview.php
0 PIFSC blog post, Nov 2012: The final count: summary of mission to Timor-Leste in 2012 https://pifscblog.wordpress.com/2012/11/20/final-count-timor-leste/
0 PIFSC blog post, Sept 2014: Scientists return to Timor-Leste for reef monitoring mission https://pifscblog.wordpress.com/2014/09/30/timor-leste-atauro/
0 Pacific Islands Fisheries Science Center, Coral Reef Ecosystems survey methods. https://www.fisheries.noaa.gov/pacific-islands/ecosystems/coral-reefs-pacific#survey-methods
0 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.coris.noaa.gov/activities/projects/timor-leste/
0 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 https://forum.earthdata.nasa.gov/app.php/tag/GCMD%2BKeywords
33 NOAA Data Management Plan for this record on InPort. https://www.fisheries.noaa.gov/inportserve/waf/noaa/nmfs/pifsc/dmp/pdf/46159.pdf

Tags

  • autonomous reef monitoring structure
  • crep
  • doc/noaa/nmfs/pifsc
  • reef monitoring and assessment
  • aquatic habitat
  • corals
  • benthic habitat
  • coral reef ecosystem division
  • pifsc
  • in situ biological
  • biosphere
  • biodiversity
  • species identification
  • creefs
  • oceans
  • atauro
  • marine invertebrates
  • noaa
  • numeric data sets
  • brachyura
  • images
  • nmfs
  • baseline studies
  • dili
  • imagery
  • macroinvertebrates
  • biology
  • us doc
  • timor-leste
  • pacific islands fisheries science center
  • u.s. department of commerce
  • earth science
  • bobonaro
  • census of marine life
  • national marine fisheries service
  • indian ocean
  • lautem
  • autonomous reef monitoring structure (arms)
  • coral triangle initiative
  • marine biology
  • cred
  • biological
  • arms
  • united states agency for international development
  • autonomous reef monitoring structures
  • pacific reef assessment and monitoring program: monitoring coral reef ecosystems of the us pacific i
  • reef habitat
  • baucau
  • timor sea
  • coral reef ecology
  • ocean basin
  • ecosystem sciences division
  • manatuto
  • laboratory analysis
  • coastal processes
  • timor leste
  • census
  • zoology
  • coral reefs
  • cryptobiota
  • usaid
  • species identification - count
  • country/territory
  • vila mpa
  • democratic republic of timor-leste (east timor) (09s126e0001)
  • 587
  • coral reef studies
  • coral reef ecosystem program

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