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Short Citation:
Pacific Islands Fisheries Science Center, 2022: Cryptobiota metabarcoding using Autonomous Reef Monitoring Structure (ARMS) Deployed at Coral Reef Sites across American Samoa from 2012 to 2015, https://www.fisheries.noaa.gov/inport/item/64267.

Item Identification

Title: Cryptobiota metabarcoding using Autonomous Reef Monitoring Structure (ARMS) Deployed at Coral Reef Sites across American Samoa from 2012 to 2015
Short Name: ARMS Sequencing - American Samoa
Status: In Work
Creation Date: 2021
Revision Date: 2020-01-07
Abstract:

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 American Samoa. 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 American Samoa. 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.

Purpose:

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 diminished through the establishment of molecular operational taxonomic units (MOTU) - species proxies - based on DNA sequence similarities.

Supplemental Information:

The National Coral Reef Monitoring Program (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 will consolidate 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 Science Division (ESD) at NOAA Fisheries is leading biological monitoring in the U.S. Pacific Islands Region.

The biological component of NCRMP in the Pacific provides a triennial ecological characterization at a broad spatial scale of general reef condition for reef fishes, corals and benthic habitat (i.e., fish species composition/density/size, benthic cover, and coral density/size/condition). Each year, ESD scientists work closely with CRCP and local partners to collect biological data on fish populations and coral reef communities from strategically selected sites during Reef Assessment and Monitoring Program (RAMP) missions. Innovative analysis techniques are then 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.

DOI (Digital Object Identifier): 10.7289/v51v5c82
DOI Registration Authority: NOAA

Keywords

Theme Keywords

Thesaurus Keyword
UNCONTROLLED
CoRIS Discovery Thesaurus DNA/RNA Sequencing
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 > In Situ Biological
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology
CoRIS Theme Thesaurus EARTH SCIENCE > Oceans > Marine Biology > Cryptobiota
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
CRCP Project 743
CRCP Project National Coral Reef Monitoring Program
ISO 19115 Topic Category 002
ISO 19115 Topic Category 014
ISO 19115 Topic Category biota
ISO 19115 Topic Category oceans
NODC DATA TYPES THESAURUS Biodiversity
NODC DATA TYPES THESAURUS INVERTEBRATE SPECIES
NODC DATA TYPES THESAURUS laboratory analyses
NODC INSTRUMENT TYPES THESAURUS ARMS
NODC PLATFORM NAMES THESAURUS HI'IALAKAI
NODC PROJECT NAMES THESAURUS Coral Reef Conservation Program
NODC PROJECT NAMES THESAURUS CORAL REEF STUDIES
NODC PROJECT NAMES THESAURUS National Coral Reef Monitoring Program
NODC SUBMITTING INSTITUTION NAMES THESAURUS US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division; Coral Reef Ecosystem Program
None Census of Marine Life
None Coral Reef Ecosystem Program
None CRED
None CReef
None CREP
None cytochrome oxidase I
None Ecosystem Sciences Division
None eDNA
None ESD
None Pacific Islands Fisheries Science Center
None PIFSC

Temporal Keywords

Thesaurus Keyword
UNCONTROLLED
None Triennial

Spatial Keywords

Thesaurus Keyword
UNCONTROLLED
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > American Samoa (14S170W0000)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Ofu Island (14S169W0013)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Olosega Island (14S169W0014)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Rose Atoll (14S168W0001)
CoRIS Place Thesaurus COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Tutuila Island (14S170W0016)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > American Samoa > American Samoa (14S170W0000)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > American Samoa > Rose Atoll (14S168W0001)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > American Samoa > Tutuila Island (14S170W0016)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Manu'a Group > Ofu Island (14S169W0013)
CoRIS Place Thesaurus OCEAN BASIN > Pacific Ocean > Manu'a Group > Olosega Island (14S169W0014)
NODC SEA AREA NAMES THESAURUS Rose Atoll Marine National Monument
NODC SEA AREA NAMES THESAURUS South Pacific Ocean

Instrument Keywords

Thesaurus Keyword
UNCONTROLLED
NODC INSTRUMENT TYPES THESAURUS ARMS
NODC INSTRUMENT TYPES THESAURUS Autonomous Reef Monitoring Structures
None environmental DNA
None metabarcoding

Physical Location

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

NOAA IRC

Data Set Information

Data Set Scope Code: Data Set
Data Set Type: Other
Maintenance Frequency: None Planned
Maintenance Note:

These data are merged fasta files of the forward and reverse sequencing on a MiSeq platform and have been deposited into Genbank.

Data Presentation Form: Fasta Files
Entity Attribute Overview:

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/

Entity Attribute Detail URL: https://www.ncbi.nlm.nih.gov/sra/
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 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

Support Roles

Data Steward

CC ID: 1038159
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 preferred

Distributor

CC ID: 1038164
Date Effective From: 2012
Date Effective To:
Contact (Organization): Pacific Islands Fisheries Science Center (PIFSC)
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: pifsc.info@noaa.gov
Phone: 808-725-5360
URL: https://www.pifsc.noaa.gov
Business Hours: 8:00 a.m. - 4:30 p.m.

Metadata Contact

CC ID: 1038162
Date Effective From: 2012
Date Effective To:
Contact (Person): Olenski, Brooke
Email Address: brooke.olenski@noaa.gov
Contact Instructions:

Email preferred

Originator

CC ID: 1038157
Date Effective From: 2012
Date Effective To:
Contact (Organization): Pacific Islands Fisheries Science Center (PIFSC)
Address: 1845 Wasp Blvd.
Honolulu, HI 96818
USA
Email Address: pifsc.info@noaa.gov
Phone: 808-725-5360
URL: https://www.pifsc.noaa.gov
Business Hours: 8:00 a.m. - 4:30 p.m.
View Historical Support Roles

Extents

Currentness Reference: Ground Condition

Extent Group 1

Extent Description:

American Samoa including Tutuila, Manu'a (Ofo and Olosega), Rose Atoll, and Swains.

Extent Group 1 / Geographic Area 1

CC ID: 1038180
W° Bound: -170.76336
E° Bound: -168.13792
N° Bound: -14.17737
S° Bound: -14.559317

Extent Group 1 / Time Frame 1

CC ID: 1038179
Time Frame Type: Range
Start: 2012-04-03
End: 2015-03-26
Alternate Start As Of Info: HA1201
Alternate End As Of Info: HA1501
Description:

ARMS across American Samoa, deployed in 2012 and recovered in 2015

Spatial Information

Reference Systems

Reference System 1

CC ID: 1038174

Coordinate Reference System

CRS Type: Geographic 2D
EPSG Code: EPSG:4326
EPSG Name: WGS 84
See Full Coordinate Reference System Information

Access Information

Security Class: Unclassified
Security Classification System:

Not applicable

Security Handling Description:

Not applicable

Data Access Policy:

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 Access Procedure:

Data can be accessed online via Genbank.

Data Access Constraints:

None

Data Use Constraints:

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 American Samoa from 2012 to 2015, https://www.fisheries.noaa.gov/inport/item/64267.

Metadata Access Constraints:

None

Metadata Use Constraints:

None

Distribution Information

Distribution 1

CC ID: 1038165
Start Date: 2021-01-01
End Date: Present
Distributor:
File Name: Illumina Sequences
Description:

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.

File Date/Time: 2017-04-24 00:00:00
File Type: fasta
File Size: ranges from 17 to 600 MB

URLs

URL 1

CC ID: 1038166
URL: https://www.fisheries.noaa.gov/region/pacific-islands#science
Name: NOAA Fisheries: Pacific Islands
URL Type:
Online Resource

URL 2

CC ID: 1038169
URL: https://naturalhistory.si.edu/research/global-arms-program
Name: Global ARMS program
URL Type:
Online Resource
Description:

Smithsonian partnership - Global ARMS program

URL 3

CC ID: 1057269
URL: https://www.coris.noaa.gov/monitoring/
Name: NOAA's National Coral Reef Monitoring Program
URL Type:
Online Resource

Technical Environment

Description:

Genbank SRA files:

Go to: https://www.ncbi.nlm.nih.gov/sra/

Data Quality

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 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.

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: Other
If World Data Center or Other, Specify: Genbank
Approximate Delay Between Data Collection and Archiving: Unknown

Lineage

Lineage Statement:

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.

Sources

Autonomous Reef Monitoring Structures (ARMS) Overview

CC ID: 1038175
Contact Role Type: Originator
Contact Type: Person
Contact Name: Molly Timmers
Citation URL: https://origin-apps-pifsc.fisheries.noaa.gov/cred/survey_methods.php#arms
Citation URL Name: Pacific Islands Fisheries Science Center website
Source Contribution:

Protocol

Process Steps

Process Step 1

CC ID: 1057261
Description:

ARMS Deployment -

The platforms were deployed as described in the ARMS record of the related items section below.

Process Contact: Timmers, Molly A
Phone (Voice): (808)725-5449
Email Address: molly.timmers@noaa.gov

Process Step 2

CC ID: 1057262
Description:

ARMS Recovery and Processing -

ARMS units are recovered, initially processed, and documented as described in related items 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.

Process Step 3

CC ID: 1057263
Description:

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.

Process Contact: Timmers, Molly A
Phone (Voice): (808)725-5449
Email Address: molly.timmers@noaa.gov

Process Step 4

CC ID: 1057264
Description:

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

Process Contact: Timmers, Molly A
Phone (Voice): (808)725-5449
Email Address: molly.timmers@noaa.gov

Process Step 5

CC ID: 1038176
Description:

To obtain the sequencing data, go to XXXXXXX which takes you to the National Center for Biotechnology Information (NCBI) which hosts Genebank, 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.

Process Contact: Timmers, Molly A
Phone (Voice): (808)725-5449
Email Address: molly.timmers@noaa.gov

Process Step 6

CC ID: 1038177
Description:

Once sequences are downloaded, you may choose to conduct the bioinformatics in a number of ways based on your preference.

Process Contact: Timmers, Molly A
Phone (Voice): (808)725-5449
Email Address: molly.timmers@noaa.gov

Acquisition Information

Instruments

Instrument Unavailable Reason: Not Applicable

Platforms

Platform Unavailable Reason: Not Applicable

Child Items

Rubric scores updated every 15m

Rubric Score Type Title
Entity ARMS Metabarcoding

Catalog Details

Catalog Item ID: 64267
GUID: gov.noaa.nmfs.inport:64267
Metadata Record Created By: Brooke Olenski
Metadata Record Created: 2021-02-09 08:28+0000
Metadata Record Last Modified By: Sarah Kunkel
Metadata Record Last Modified: 2022-10-30 02:41+0000
Metadata Record Published: 2022-02-04
Owner Org: PIFSC
Metadata Publication Status: Published Externally
Do Not Publish?: N
Metadata Last Review Date: 2022-02-04
Metadata Review Frequency: 1 Year
Metadata Next Review Date: 2023-02-04