Short Citation:
Pacific Islands Fisheries Science Center, 2019: 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, https://inport.nmfs.noaa.gov/inport/item/46159.

Item Identification

Title: 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
Short Name: Timor: ARMS
Status: Completed
Publication Date: 2017
Abstract:

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 taxanomic 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 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.

Purpose:

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.

Other Citation Details:

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.

Supplemental Information:

As the survey methods described and used herein are also implemented as part of the NOAA Pacific Reef Assessment and Monitoring Program (Pacific RAMP)—an ecosystem-scale interdisciplinary coral reef monitoring program—the data from Timor-Leste are directly comparable to and informed by data collected by NOAA-CREP throughout the U.S. Pacific Islands and Territories. Furthermore, the methods used for establishing ecological baselines for climate change in Timor-Leste (Chapter 4) are being adopted and implemented at 21 sites across eight member states of the Intergovernmental Oceanographic Commission within the Western Pacific (WESTPAC) region. These data provide a foundation for comparing the ecological baselines under current and future stresses associated with climate change in the Coral Triangle region.

Keywords

Theme Keywords

Thesaurus Keyword
CoRIS Discovery Thesaurus Numeric Data Sets > Biology
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Aquatic Habitat > Reef Habitat
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Autonomous Reef Monitoring Structure (ARMS)
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Baseline studies
CoRIS Theme Thesaurus EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > In Situ Biological
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Marine Biology > Brachyura
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Marine Biology > Crytobiota
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Marine Biology > Marine Invertebrates
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Marine Biology > Marine Invertebrates > Biodiversity
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Marine Biology > Marine Invertebrates > Census
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Marine Biology > Marine Invertebrates > Macroinvertebrates
ISO 19115 Topic Category 002
ISO 19115 Topic Category 014
ISO 19115 Topic Category biota
ISO 19115 Topic Category oceans
NODC DATA TYPES THESAURUS IMAGES
NODC DATA TYPES THESAURUS SPECIES IDENTIFICATION
NODC DATA TYPES THESAURUS SPECIES IDENTIFICATION - COUNT
NODC OBSERVATION TYPES THESAURUS biological
NODC OBSERVATION TYPES THESAURUS imagery
NODC OBSERVATION TYPES THESAURUS laboratory analysis
NODC PROJECT NAMES THESAURUS CORAL REEF STUDIES
NODC PROJECT NAMES THESAURUS Coral Triangle Initiative
NODC SUBMITTING INSTITUTION NAMES THESAURUS US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division; Coral Reef Ecosystem Program
None ARMS
None Autonomous Reef Monitoring Structure
None Biodiversity
None Coral Reef Ecosystem Division
None Coral Reef Ecosystem Program
None CRED
None CREP
None Pacific Islands Fisheries Science Center
None PIFSC
None United States Agency for International Development
None USAID

Spatial Keywords

Thesaurus Keyword
CoRIS Place Thesaurus COUNTRY/TERRITORY > Democratic Republic of Timor-Leste (East Timor) (09S126E0001)
CoRIS Place Thesaurus OCEAN BASIN > Indian Ocean > Timor Sea > Democratic Republic of Timor-Leste (East Timor) (09S126E0001)
NODC SEA AREA NAMES THESAURUS Indian Ocean
NODC Sea Area Names Thesaurus Timor Sea
None Atauro
None Baucau
None Bobonaro
None Dili
None Lautem
None Manatuto
None Timor-Leste
None Vila MPA

Physical Location

Organization: Pacific Islands Fisheries Science Center
City: Honolulu
State/Province: HI
Country: USA

Data Set Information

Data Set Scope Code: Data Set
Data Set Type: Mixed
Maintenance Frequency: None Planned
Data Presentation Form: Table (digital), image (digital)
Entity Attribute Overview:

Three types of data are included with this dataset: A) specimen data, B) images, and C) sequences.

A) Specimen retrieval data (CSV file) includes metadata for each ARMS unit (where, deployment / retrieval date) and individual specimens from the 2mm fraction, identified to the lowest taxonomic level possible along with a count. Each column is described in the entities and attributes section.

B) Images are organized by IMAGES_SITE and IMAGES_TAXAGROUP.

Photographs in the IMAGES_SITE folder are organized by the original climate survey site name (folders TIM-01 to TIM-10), and within each site folder are three sets of images:

1) PLATES folder. Photographs taken of the 9 ARMS plates (tops and bottoms) as the recovered ARMS units were processed (considered 'data'). Images are organized by ARMS unit (A-D), and named by <SITE>_<YEAR RECOVERED>_<ARMS UNIT>_<SEQUENTIAL 3-DIGIT NUMBER>.jpg Photographs themselves include a label of each plate.

2) SPECIES folder. Specimens that were recovered and identified as part of the 2-mm fraction (considered 'data'), organized by folders that correspond to the SAMPLE_LABEL in the CSV file. Images are named by <SAMPLE_LABEL>_<SEQUENTIAL 3-DIGIT NUMBER>.jpg

3) DEPLOY and RECOVER folders. Photographs taken during the deployment and recovery of ARMS units, which were not consistently captured at each site and are only for reference purposes.

Photographs in the IMAGES_TAXAGROUP folder are specimen photographs (copied from SPECIES folder) that 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. Images are named <TAXAGROUP>_<SCIENTIFIC NAME>_<SAMPLE_LABEL>_<SEQUENCE NUMBER>.jpg

C) Files contained in the SEQUENCES folder include the FASTQ files generated during the DNA metabarcoding process of the 500- and 100-µm fractions and scrapings. Files are named by <SITE><ARMS UNIT>_<FRACTION SIZE>_<SEQUENCE NUMBER>_<L001>_<RUN NUMBER>_<001>.fastq

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.

Data Set Credit: PIFSC Coral Reef Ecosystem Program and funded by the United States Agency for International Development
Instrument (Deprecated): Not applicable
Platform (Deprecated): Not applicable
Physical Collection / Fishing Gear (Deprecated): Autonomous Reef Monitoring Structures (ARMS)

Support Roles

Data Steward

CC ID: 569284
Date Effective From: 2012
Date Effective To:
Contact (Person): Timmers, Molly A
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: molly.timmers@noaa.gov
Phone: (808)725-5449
Contact Instructions:

Email preffered

Distributor

CC ID: 569289
Date Effective From: 2017
Date Effective To:
Contact (Organization): National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD)
Address: NOAA/NESDIS E/OC SSMC3, 4th Floor, 1351 East-West Highway
Silver Spring, MD 20910-3282
Phone: (301) 713-3277

Distributor

CC ID: 569286
Date Effective From: 2012
Date Effective To: 2017
Contact (Person): Kanemura, Troy T
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: troy.kanemura@noaa.gov
Phone: (808)725-5422
Contact Instructions:

Email preferred

Metadata Contact

CC ID: 569287
Date Effective From: 2012
Date Effective To:
Contact (Person): DesRochers, Annette M
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: annette.desrochers@noaa.gov
Phone: (808)725-5461
Business Hours: 8 am - 5 pm
Contact Instructions:

Email preferred

Originator

CC ID: 569282
Date Effective From: 2012
Date Effective To:
Contact (Organization): Pacific Islands Fisheries Science Center (PIFSC)
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Phone: 808-725-5300
URL: http://www.pifsc.noaa.gov
Business Hours: 8:00 a.m. - 4:30 p.m.

Point of Contact

CC ID: 569285
Date Effective From: 2015
Date Effective To:
Contact (Person): Oliver, Thomas
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: thomas.oliver@noaa.gov
Phone: (808)725-5444
Contact Instructions:

Email preferred

Point of Contact

CC ID: 569283
Date Effective From: 2012
Date Effective To: 2014
Contact (Person): Timmers, Molly A
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: molly.timmers@noaa.gov
Phone: (808)725-5449
Contact Instructions:

Email preferred

Extents

Currentness Reference: Ground Condition

Extent Group 1

Extent Description:

Timor-Leste

Extent Group 1 / Geographic Area 1

CC ID: 701381
W° Bound: 125.01319
E° Bound: 127.31222
N° Bound: -8.22438
S° Bound: -8.85321
Description

Extent of climate survey sites in Timor-Leste.

Extent Group 1 / Time Frame 1

CC ID: 701382
Time Frame Type: Range
Start: 2012-10-15
End: 2014-10-09
Description:

Duration that ARMS were deployed (in-water) in Timor-Leste

Access Information

Security Class: Unclassified
Security Classification System:

Not applicable

Security Handling Description:

Not applicable

Data Access Policy:

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 Access Procedure:

Data can be accessed online via the NOAA National Centers for Environmental Information (NCEI) Ocean Archive.

Data Access Constraints:

None

Data 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://inport.nmfs.noaa.gov/inport/item/46159.

Metadata Access Constraints:

None

Metadata Use Constraints:

None

Distribution Information

Distribution 1

CC ID: 701390
Download URL: http://accession.nodc.noaa.gov/0169338
Distributor: National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD) (2017 - Present)
File Name: IMAGES_SITE
Description:

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).

File Type: JPEG

Distribution 2

CC ID: 701392
Download URL: http://accession.nodc.noaa.gov/0169338
Distributor: National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD) (2017 - Present)
File Name: IMAGES_TAXAGROUP
Description:

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.

File Type: JPEG
File Size: 8.5 GB

Distribution 3

CC ID: 701395
Download URL: http://accession.nodc.noaa.gov/0169338
Distributor: National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD) (2017 - Present)
File Name: SEQUENCES
Description:

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)

File Type: FASTQ
File Size: 6 GB
Compression: GZIP

Distribution 4

CC ID: 569290
Start Date: 2012-10-15
End Date: 2014-10-09
Download URL: http://accession.nodc.noaa.gov/0169338
Distributor: National Centers for Environmental Information - Silver Spring, Maryland (NCEI-MD) (2017 - Present)
File Name: ARMS_2mmSpecimenRetrieval_Timor_2014.csv
Description:

ARMS 2-mm fraction specimens recovered by the NOAA Coral Reef Ecosystem Program (CREP) from Timor-Leste in 2014.

File Date/Time: 2017-06-01 00:00:00
File Type: csv (comma-separated values)

URLs

URL 1

CC ID: 569291
URL: https://www.pifsc.noaa.gov/cred/survey_methods/arms/index.php
URL Type:
Online Resource
File Resource Format: PHP
Description:

Pacific Islands Fisheries Science Center, Coral Reef Ecosystem Program official website, ARMS page.

URL 2

CC ID: 569292
URL: https://www.pifsc.noaa.gov/cred/coral_triangle_initiative.php
URL Type:
Online Resource
File Resource Format: PHP
Description:

Information about the NOAA Coral Reef Ecosystem Program's activities in the Coral Triangle.

URL 3

CC ID: 569293
URL: https://www.coris.noaa.gov/activities/projects/timor-leste/
URL Type:
Online Resource
Description:

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.

URL 4

CC ID: 569294
URL: http://www.pifsc.noaa.gov/cred/biodiversity.php
URL Type:
Online Resource
File Resource Format: PHP
Description:

Information on NOAA CRED's official website

URL 5

CC ID: 569295
URL: http://www.pifsc.noaa.gov/cred/images/arms_install_sm.jpg
URL Type:
Browse Graphic
File Resource Format: JPEG
Description:

A NOAA diver installing an ARMS unit.

URL 6

CC ID: 569296
URL: http://www.pifsc.noaa.gov/cred/images/arms_deployed4_sm.jpg
URL Type:
Browse Graphic
File Resource Format: JPEG
Description:

ARMS recruitment after 2 years

URL 7

CC ID: 701396
URL: https://pifscblog.wordpress.com/2012/11/20/final-count-timor-leste/
URL Type:
Online Resource
Description:

PIFSC blog post, Nov 2012: The final count: summary of mission to Timor-Leste in 2012

URL 8

CC ID: 701397
URL: https://pifscblog.wordpress.com/2014/09/30/timor-leste-atauro/
URL Type:
Online Resource
Description:

PIFSC blog post, Sept 2014: Scientists return to Timor-Leste for reef monitoring mission

Technical Environment

Description:

CSV: Microsoft Access, query: TTK: QRY_ARMS Specimens, ISLAND=Timor-Leste.

Images: PIFSC network/file system \\picmakai\optical\OPTICAL\

Sequences: Sample libraries were pooled and sequenced on an Illumina MiSeq platform, and the Illumina reads were parsed into FASTQ files sorted by index.

Data Quality

Accuracy:

All species identifications are made visually by a trained analyst and subsequently reviewed by a taxonomic expert or through molecular processing for accuracy.

Images are taken of the plates and specimens first with a label in the photograph, and then without.

Sample libraries were validated by visualization on an Agilent 2100 BioAnalyzer.

Completeness Report:

All ARMS units that are recovered are disassembled, photographed, and sorted by size. Taxonomic classification occurs for materials greater than 2 mm. The research and development of the genetic analysis of ARMS samples is being done in collaboration with partners and data currently exists for a subset of the dataset. ARMS that were deployed were not recovered due to logistical constraints at 2 of the 10 original climate sruvey sites, or could not be found when divers returned to the site.

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.

Quality Control Procedures Employed:

The data entered in the MS Access database is quality controlled following data entry.

Data Management

Have Resources for Management of these Data Been Identified?: Yes
Approximate Percentage of Budget for these Data Devoted to Data Management: Unknown
Do these Data Comply with the Data Access Directive?: Yes
Is Access to the Data Limited Based on an Approved Waiver?: No
Approximate Delay Between Data Collection and Dissemination: Unknown
Actual or Planned Long-Term Data Archive Location: NCEI-MD
Approximate Delay Between Data Collection and Archiving: Unknown
How Will the Data Be Protected from Accidental or Malicious Modification or Deletion Prior to Receipt by the Archive?:

NOAA IRC and NOAA Fisheries ITS resources and assets. The MS Access database is stored on the PIFSC network and regularly backed up by ITS.

Lineage

Lineage Statement:

Autonomous Reef Monitoring Structures (ARMS) field, laboratory, and analysis methods used for ARMS in Timor-Leste

Sources

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.

CC ID: 569300
Contact Type: Organization
Contact Name: Pacific Islands Fisheries Science Center, PIFSC
Publish Date: 2017-06-21
Citation URL: https://doi.org/10.7289/V5/SP-PIFSC-17-002

Process Steps

Process Step 1

CC ID: 569301
Description:

FIELD METHOD: ARMS, composed of nine PVC plates (23 cm x 23 cm) stacked in alternating series of open and semi-enclosed layers, were affixed to the seafloor between 12–15 m in replicate sets of three. They remained on the benthos for two years during which time they were naturally colonized with marine organisms. After the 2-year deployment period, the ARMS units were encapsulated within a 106-µm nitex-lined crate, brought to the surface, placed within a large seawater holding bin and transported to shore. On shore, they were disassembled plate by plate, with both sides photo-documented. The plates were then scraped clear of all the accumulated sessile biomass and immediately homogenized in a blender, filtered with a 40-µm net, subsampled, and preserved for metabarcoding.

The seawater used during processing was sieved using 2-mm, 500-µm and 106-µm geologic sieves to create three size fractions. The >2 mm fraction was sorted to morphospecies, photographed, and brachyuran crabs were preserved for DNA barcoding. The two smaller motile fractions were preserved for additional lab and molecular processing.

Source: 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.

Process Step 2

CC ID: 701398
Description:

LAB METHOD:

Decantation—Due to sediment within the 500-µm and 106-µm fractions that can inhibit metabarcoding laboratory processing, a decantation procedure was conducted on these fractions from each ARMS unit to separate the sediment from the organic matter. Upon the completion of the decantation process, half of the sample was crushed with a mortar and pestle for DNA extraction and metabarcoding while the other half was preserved as a backup.

DNA barcoding—Legs from brachyuran crabs were subsampled, and genomic DNA was extracted using standard proteinase-k digestion followed by phenol-chloroform extraction on the AutoGenprep 965 (Autogen). Primers were used to target approximately 658 base pairs of the COI gene and automated sequencing techniques were used to sequence in both directions.

DNA metabarcoding—DNA was extracted from 10 grams of the homogenized sessile scrapings and from the decanted 500-µm and 100-µm motile fractions using the MO-Bio PowerMax Soil extraction kits. Using the reverse primer, jgHCO2198, and the forward primer, mlCOIintF, a 313 base pair fragment of COI was amplified using a PCR (polymerase chain reaction) touchdown protocol with 16 initial cycles: denaturation for 10 seconds at 95°C, annealing for 30 seconds at 62°C (–1°C per cycle), and extension for 60 seconds at 72°C, followed by 25 cycles at 46°C annealing temperature. PCRs were performed in triplicates and inspected on agarose gels. Triplicate PCR products were pooled, cleaned using Agencourt AMPure beads, and quantified using Biotum AccuClear Ultra High Sensitivity Quantification Kit. PCR products were then inserted directly into the Kappa Systems Hyper-Prep sample kit using dual-end Illumina adapters for ligation. Sample libraries were validated by visualization on an Agilent 2100 BioAnalyzer, quantified using qPCR, pooled, and sequenced on an Illumina MiSeq platform. Each library yielded approximately 250,000 reads per sample, and a standard quality control filter was run to parse the Illumina reads into FASTQ files sorted by index.

Source: 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.

Process Step 3

CC ID: 701399
Description:

ANALYSIS:

Morphospecies (2-mm size fraction)—Overall abundance of >2 mm organisms was averaged between ARMS units recovered at each site to give a site-level metric. Organisms were additionally averaged by ARMS unit at the island scale for comparison with other ARMS recovery locations across the Pacific. Dominant phyla and taxa groups within phyla were averaged between ARMS units and compared across sites.

Crab DNA barcoding—Resulting sequences of crabs were clustered into Operational Taxonomic Units (OTUs) and blasted (cross checked) against existing DNA-barcoding libraries (Barcode of Life Data Systems [BOLD] and Moorea Biocode). Matched sequences with >97% identity and >85% coverage were identified to an existing record of the species within the databases. Those crab sequences with <97% identity and >85% coverage underwent a phylogenetic Bayesian approach using the Statistical Assignment Package (SAP) to assign OTUs to higher taxonomic levels in the absence of a direct match. Species richness was averaged by ARMS unit at each site and examined on the island scale in relation to the richness of brachyuran crabs from other ARMS units collected by NOAA-CREP in the Pacific Ocean. Broad scale richness values were calculated per ARMS unit richness rather than by island due to the variability in the number of ARMS units deployed across islands.

Metabarcoding bioinformatics—Sequences were assembled, trimmed, cleaned, and dereplicated following standard bioinformatics techniques using available software programs. Dereplicated sequences were then aligned to COI barcodes from the BOLD database. Matched sequences =97% identity and =85% coverage are presented herein. Sequences that did not have a direct match have not been directly DNA barcoded and thus species resolution is not available. Once the phylogenetic approaches and bioinformatic software have been refined, the remaining unknown sequences can be determined. Currently available software is not capable of working through 10 million plus sequence reads that span across multiple phyla. However, through the efforts of a third-party bioinformation specialist working on these data sets for Timor-Leste, a solution will be found in the near future to provide phyla-based resolution of the remaining sequences that will indicate percent cover of the phyla communities that have recruited to the ARMS units.

Source: 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.

Child Items

Rubric scores updated every 15m

Type Title
Entity (ENT) ARMS 2mm Specimens - Attributes

Catalog Details

Catalog Item ID: 46159
Metadata Record Created By: Annette M DesRochers
Metadata Record Created: 2017-06-02 03:15+0000
Metadata Record Last Modified By: SysAdmin InPortAdmin
Metadata Record Last Modified: 2019-06-04 13:14+0000
Metadata Record Published: 2017-12-15
Owner Org: PIFSC
Metadata Publication Status: Published Externally
Do Not Publish?: N
Metadata Next Review Date: 2018-12-16