gov.noaa.nmfs.inport:64540
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Pacific Islands Fisheries Science Center
808-725-5300
1845 Wasp Blvd.
Honolulu
HI
96818
USA
http://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
annette.desrochers@noaa.gov
8 am - 5 pm
Email preferred
pointOfContact
2024-02-29T00:00:00
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
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
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
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
National Centers for Environmental Information - Silver Spring, Maryland
(301) 713-3277
NOAA/NESDIS E/OC SSMC3, 4th Floor, 1351 East-West Highway
Silver Spring
MD
20910-3282
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