Cryptobiota metabarcoding using Autonomous Reef Monitoring Structure (ARMS) Deployed at Coral Reef Sites across PRIA from 2011 to 2015
Data Set (DS) | Pacific Islands Fisheries Science Center (PIFSC)GUID: gov.noaa.nmfs.inport:64270 | Updated: May 30, 2023 | Published / External
Summary
Short Citation
Pacific Islands Fisheries Science Center, 2024: Cryptobiota metabarcoding using Autonomous Reef Monitoring Structure (ARMS) Deployed at Coral Reef Sites across PRIA from 2011 to 2015, https://www.fisheries.noaa.gov/inport/item/64270.
Full Citation Examples
DOI: 10.7289/v54x563c
AbstractThe data described here includes cytochrome oxidase I (COI) DNA metabarcoding data collected from Autonomous Reef Monitoring Structures (ARMS). ARMS were deployed by the NOAA Pacific Islands Fisheries Science Center (PIFSC), Ecosystem Sciences Division (formerly the Coral Reef Ecosystem Division) under the National Coral Reef Monitoring Program (NCRMP) at stationary climate monitoring sites and used to assess and monitor cryptic reef diversity in the Pacific Remote Island Areas (PRIA). Developed in collaboration with the Census of Marine Life (CoML) Census of Coral Reef Ecosystems (CReefs), ARMS were designed to mimic the structural complexity of a reef and attract/collect colonizing marine invertebrates. The key innovation of the ARMS method is that biodiversity is sampled over precisely the same surface area in the exact same manner.
These data were gathered at specific reef sites across the PRIAs. ARMS units were set-up, deployed and recovered as described in the ARMS record in the related items section below. After ARMS were disassembled, different size fractions of samples and plate scrapings were preserved in ethanol for metabarcoding.
Distribution Information
-
Illumina Sequencesranges from 17 to 600 MB
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.
None
Please cite PIFSC Ecosystem Sciences Division when using the data.
Suggested citation:
Ecosystem Sciences Division, Pacific Islands Fisheries Science Center, 2020: Cryptobiota metabarcoding using Autonomous Reef Monitoring Structure (ARMS) Deployed at Coral Reef Sites across PRIA from 2011 to 2015, https://www.fisheries.noaa.gov/inport/item/64267.
Controlled Theme Keywords
biota, oceans
Child Items
No Child Items for this record.
Contact Information
Metadata Contact
Brooke Olenski
brooke.olenski@noaa.gov
Extents
166.59824° W,
166.65155° E,
19.31654° N,
19.27116° S
Wake Atoll, one of the seven PRIA, is routinely surveyed as part of the Mariana Archipelago RAMP (MARAMP) missions.
-162.3843° W,
-159.99086° E,
6.3947° N,
-0.3818° S
Phoenix (Baker and Howland) and Line Islands (Jarvis, Kingman, and Palmyra), and Johnston Atoll. These six of the seven PRIA are routinely surveyed as part of the American Samoa RAMP (ASRAMP) missions (Johnston, Baker and Howland during the first leg of ASRAMP, and Jarvis, Kingman, and Palmyra during the last leg of ASRAMP).
2012-05-03 - 2015-04-28
ARMS across the Pacific Remote Island Areas (excluding Wake Atoll) deployed in 2012 and recovered in 2015
2014-03-16 - 2017-04-23
ARMS across Wake Atoll, deployed in 2014 and recovered in 2017
2015-04-08 - 2018-08-05
ARMS across the Pacific Remote Island Areas
2011-03-23 - 2014-03-19
ARMS across Wake Atoll, deployed in 2011 and recovered in 2014
Item Identification
Title: | Cryptobiota metabarcoding using Autonomous Reef Monitoring Structure (ARMS) Deployed at Coral Reef Sites across PRIA from 2011 to 2015 |
---|---|
Short Name: | ARMS Sequencing - PRIA |
Status: | In Work |
Creation Date: | 2017 |
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 the Pacific Remote Island Areas (PRIA). Developed in collaboration with the Census of Marine Life (CoML) Census of Coral Reef Ecosystems (CReefs), ARMS were designed to mimic the structural complexity of a reef and attract/collect colonizing marine invertebrates. The key innovation of the ARMS method is that biodiversity is sampled over precisely the same surface area in the exact same manner. These data were gathered at specific reef sites across the PRIAs. ARMS units were set-up, deployed and recovered as described in the ARMS record in the related items section below. After ARMS were disassembled, different size fractions of samples and plate scrapings were preserved in ethanol for metabarcoding. |
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 diminshed through the establishment of molecular operational taxonomic units (MOTU) - species proxies - based on DNA sequence similarities. |
Supplemental Information: |
NCRMP is a framework for conducting sustained observations of biological, climate, and socioeconomic indicators at 10 priority coral reefs across the U.S. and its territories. This integrated approach consolidates monitoring of coral reefs under a uniform method in the Pacific, Atlantic, Caribbean, and the Gulf of Mexico for the first time. NCRMP is funded by the CRCP and supported by NOAA Fisheries, NOAA National Centers for Coastal Ocean Science (NCCOS), and many other partners. The Ecosystem Sciences Division at NOAA Fisheries is leading climate monitoring in the U.S. Pacific Islands Region. The climate component of NCRMP in the Pacific provides a comprehensive view of climate change impacts on coral reef ecosystems and helps identify areas of resilience and vulnerability. The key indicators used to identify and monitor climate-driven trends include 1) thermal stress caused by changes in sea temperature, 2) ocean acidification resulting from changes in carbonate chemistry, and 3) ecological impacts by collecting data on coral growth rates, erosion, and community structure to understand the impacts of thermal stress and ocean acidification on the ecosystem. Each year, ESD scientists work closely with CRCP and partners during Pacific RAMP missions to collect data using moored oceanographic (subsurface temperature recorders) and ecological (calcification accretion units [CAUs] and autonomous reef monitoring structures [ARMS]) instruments stationed at fixed sites in the Pacific Ocean, and water samples collected by divers. The in-situ data (along with satellite-based observations) are also used in modeling efforts. Innovative analysis techniques are used to develop products that give fellow scientists, managers, decision makers and the public a better understanding of a region's resources and how they are changing over time. |
DOI (Digital Object Identifier): | 10.7289/v54x563c |
DOI Registration Authority: | NOAA |
Keywords
Theme Keywords
Thesaurus | Keyword |
---|---|
ISO 19115 Topic Category |
biota
|
ISO 19115 Topic Category |
oceans
|
UNCONTROLLED | |
CoRIS Discovery Thesaurus | DNA/RNA Sequencing |
CoRIS Theme Thesaurus | EARTH SCIENCE > Biosphere > Aquatic Habitat > Benthic Habitat |
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 > 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 > 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 |
NODC DATA TYPES THESAURUS | INVERTEBRATE SPECIES |
NODC DATA TYPES THESAURUS | SPECIES IDENTIFICATION |
NODC DATA TYPES THESAURUS | SPECIES IDENTIFICATION - COUNT |
NODC OBSERVATION TYPES THESAURUS | biological |
NODC OBSERVATION TYPES THESAURUS | in situ |
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 |
None | ARMS |
None | Autonomous Reef Monitoring Structure |
None | Census of Marine Life |
None | Coral Reef Ecosystem Division |
None | Coral Reef Ecosystem Program |
None | CRED |
None | CReef |
None | CREP |
None | cytochrome oxidase I |
None | Ecosystem Sciences Division |
None | ESD |
None | Pacific Islands Fisheries Science Center |
None | PIFSC |
None | RAMP |
None | Reef Assessment and Monitoring Program |
Temporal Keywords
Thesaurus | Keyword |
---|---|
UNCONTROLLED | |
None | Triennial |
Spatial Keywords
Thesaurus | Keyword |
---|---|
UNCONTROLLED | |
CoRIS Place Thesaurus | COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Jarvis Island (00S160W0001) |
CoRIS Place Thesaurus | COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Kingman Reef (06N162W0001) |
CoRIS Place Thesaurus | COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Palmyra Atoll (05N162W0001) |
CoRIS Place Thesaurus | COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Wake Atoll (19N167E0001) |
CoRIS Place Thesaurus | OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Line Islands > Jarvis Island (00S160W0001) |
CoRIS Place Thesaurus | OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Line Islands > Kingman Reef (06N162W0001) |
CoRIS Place Thesaurus | OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Line Islands > Palmyra Atoll (05N162W0001) |
CoRIS Place Thesaurus | OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Wake Atoll > Wake Atoll (19N167E0001) |
NODC Sea Area Names Thesaurus | Equatorial Pacific Ocean |
NODC Sea Area Names Thesaurus | Pacific Remote Islands Marine National Monument |
None | Pacific Remote Island Areas |
None | PRIA |
None | PRIMNM |
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
Date Effective From: | 2011 |
---|---|
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
Date Effective From: | 2011 |
---|---|
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
Date Effective From: | 2011 |
---|---|
Date Effective To: | |
Contact (Person): | Olenski, Brooke |
Email Address: | brooke.olenski@noaa.gov |
Contact Instructions: |
Email preferred |
Originator
Date Effective From: | 2011 |
---|---|
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. |
Extents
Currentness Reference: | Ground Condition |
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Extent Group 1
Extent Description: |
Pacific Remote Island Areas (PRIA) including Baker, Howland, and Jarvis islands, Kingman Reef, and Johnston, Palmyra, and Wake atolls. |
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Extent Group 1 / Geographic Area 1
W° Bound: | 166.59824 | |
---|---|---|
E° Bound: | 166.65155 | |
N° Bound: | 19.31654 | |
S° Bound: | 19.27116 | |
Description |
Wake Atoll, one of the seven PRIA, is routinely surveyed as part of the Mariana Archipelago RAMP (MARAMP) missions. |
Extent Group 1 / Geographic Area 2
W° Bound: | -162.3843 | |
---|---|---|
E° Bound: | -159.99086 | |
N° Bound: | 6.3947 | |
S° Bound: | -0.3818 | |
Description |
Phoenix (Baker and Howland) and Line Islands (Jarvis, Kingman, and Palmyra), and Johnston Atoll. These six of the seven PRIA are routinely surveyed as part of the American Samoa RAMP (ASRAMP) missions (Johnston, Baker and Howland during the first leg of ASRAMP, and Jarvis, Kingman, and Palmyra during the last leg of ASRAMP). |
Extent Group 1 / Time Frame 1
Time Frame Type: | Range |
---|---|
Start: | 2012-05-03 |
End: | 2015-04-28 |
Alternate Start As Of Info: | HA1201 |
Alternate End As Of Info: | HA1501 |
Description: |
ARMS across the Pacific Remote Island Areas (excluding Wake Atoll) deployed in 2012 and recovered in 2015 |
Extent Group 1 / Time Frame 2
Time Frame Type: | Range |
---|---|
Start: | 2014-03-16 |
End: | 2017-04-23 |
Alternate Start As Of Info: | HA1401 |
Alternate End As Of Info: | HA1701 |
Description: |
ARMS across Wake Atoll, deployed in 2014 and recovered in 2017 |
Extent Group 1 / Time Frame 3
Time Frame Type: | Range |
---|---|
Start: | 2015-04-08 |
End: | 2018-08-05 |
Alternate Start As Of Info: | HA_1501 |
Alternate End As Of Info: | HA_1801 |
Description: |
ARMS across the Pacific Remote Island Areas |
Extent Group 1 / Time Frame 4
Time Frame Type: | Range |
---|---|
Start: | 2011-03-23 |
End: | 2014-03-19 |
Alternate Start As Of Info: | HA1101 |
Alternate End As Of Info: | HA1401 |
Description: |
ARMS across Wake Atoll, deployed in 2011 and recovered in 2014 |
Spatial Information
Reference Systems
Reference System 1
Coordinate Reference System |
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|
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 PRIA from 2011 to 2015, https://www.fisheries.noaa.gov/inport/item/64267. |
Metadata Access Constraints: |
None |
Metadata Use Constraints: |
None |
Distribution Information
Distribution 1
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 (Deprecated): | fasta |
File Size: | ranges from 17 to 600 MB |
URLs
URL 1
URL: | https://www.fisheries.noaa.gov/region/pacific-islands#science |
---|---|
Name: | Information on NOAA PIFSC's official website |
URL Type: |
Online Resource
|
URL 2
URL: | https://naturalhistory.si.edu/research/global-arms-program |
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Name: | Global ARMS program |
URL Type: |
Online Resource
|
Description: |
Smithsonian partnership - Global ARMS program |
URL 3
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/ |
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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 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. |
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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 by the ARMS team and the Cruise Data Manager are typically completed during the field mission. |
Data Management
Have Resources for Management of these Data Been Identified?: | Yes |
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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. |
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Sources
Autonomous Reef Monitoring Structures (ARMS) Overview
Contact Role Type: | Originator |
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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 |
Source Contribution: |
Protocol |
Process Steps
Process Step 1
Description: |
ARMS Deployment - ARMS platforms are deployed as described in detail in the ARMS record of the related items section below. |
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Process Contact: | Timmers, Molly A |
Phone (Voice): | (808)725-5449 |
Email Address: | molly.timmers@noaa.gov |
Process Step 2
Description: |
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. |
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Process Contact: | Timmers, Molly A |
Phone (Voice): | (808)725-5449 |
Email Address: | molly.timmers@noaa.gov |
Process Step 3
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. |
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Process Contact: | Timmers, Molly A |
Phone (Voice): | (808)725-5449 |
Email Address: | molly.timmers@noaa.gov |
Process Step 4
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 |
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Process Contact: | Timmers, Molly A |
Phone (Voice): | (808)725-5449 |
Email Address: | molly.timmers@noaa.gov |
Process Step 5
Description: |
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. |
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Process Contact: | Timmers, Molly A |
Phone (Voice): | (808)725-5449 |
Email Address: | molly.timmers@noaa.gov |
Process Step 6
Description: |
Once sequences are downloaded, you may choose to conduct the bioinformatics in a numbers of ways based on your preference. |
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Process Contact: | Timmers, Molly A |
Phone (Voice): | (808)725-5449 |
Email Address: | molly.timmers@noaa.gov |
Acquisition Information
Instruments
Instrument Unavailable Reason: | Not Applicable |
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Platforms
Platform Unavailable Reason: | Not Applicable |
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Related Items
Catalog Details
Catalog Item ID: | 64270 |
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GUID: | gov.noaa.nmfs.inport:64270 |
Metadata Record Created By: | Brooke Olenski |
Metadata Record Created: | 2021-02-09 08:31+0000 |
Metadata Record Last Modified By: | SysAdmin InPortAdmin |
Metadata Record Last Modified: | 2023-05-30 18:10+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 |