Data Management Plan (Deprecated)

Benthic, urchin, and fish observation data collected utilizing multiple methodologies for coral reef carbonate budget assessments in 2021 in O'ahu, in the Mariana Archipelago in 2022, and in American Samoa in 2023

This data package includes the benthic, urchin, and fish observation data collected for coral reef carbonate budget assessments by the Ecosystem Sciences Division (ESD) of NOAA's Pacific Island Fisheries Science Center (PIFSC) at fixed sites around O'ahu in 2021, across the Marianas Archipelago in 2022, and at two fixed sites in American Samoa in 2023. These data were collected as part of a three-year methods development and pilot project funded by the NOAA Coral Reef Conservation Program (CRCP) in order to establish a standardized carbonate budget methodology for the National Coral Reef Monitoring Program (NCRMP) in the U.S. Pacific Islands. Observational data were collected at the same sites using established Indo-Pacific ReefBudget methodology (Perry et al. 2018), as well as experimental methodologies that leverage existing NCRMP data streams (see lineage section below for additional details on data collection methodologies). Benthic survey data (genus/species, morphology, and surface distance of corals, crustose coralline algae, macroalgae, and other benthic components) and urchin survey data (genus/species, test size, and abundance of bioeroding urchins) were collected using Indo-Pacific Reef Budget-style transects, "chords" transects located within the 12-m diameter circular footprint covered by NCRMP Structure-from-Motion imagery, and virtual transects in fixed site Structure-from-Motion models. Fish survey data (genus/species, count, and size) were collected using Indo-Pacific ReefBudget belt transects, stationary point count surveys conducted at fixed sites, and averaging stationary point count survey data using stratified random survey design around a set distance of the fixed sites.

The raw data in this data package (urchin, benthic cover, parrotfish belt, fish SPC) was utilized with referential databases to calculate coral reef carbonate project estimates for Pacific regions as part to the CRCP Project #31334, titled 'Developing a carbonate budget assessment methodology for the U.S. Pacific Islands'. The referential database used for grazing metrics of herbivorous fishes of the Pacific is already archived with NCEI with its metadata accessible under 'Related Items' of this InPort metadata record. The referential database for calcification rates developed for the Pacific is accessible along with scripts for this project at the github repository: https://github.com/hannahbarkley/reefbudgetR/tree/main

One-time data collection

2021-06-07 to 2021-07-20, 2022-04-12 to 2022-08-10, 2023-07-25 to 2023-08-03

W: -158.271, E: -157.718, N: 21.591, S: 21.242

Extent of carbonate budget assessment survey sites conducted around Oahu, Main Hawaiian Islands in 2021.

W: 144.637741, E: 145.812292, N: 20.036568, S: 13.232681

Extent of carbonate budget assessment survey sites conducted in the Marianas archipelago (Guam, Saipan, Pagan, and Maug) in 2022.

W: -170.763174, E: -168.14581, N: -14.363677, S: -14.53875

Extent of carbonate budget assessment survey sites conducted in American Samoa (Tutuila and Rose Atoll) in 2023.

Table (digital)

No information found

Lori H Luers

Metadata Contact

lori.luers@noaa.gov

No information found

Hannah C Barkley

Data Steward

Yes

Unknown

Lineage Statement:
Benthic, urchin, and fish survey methodology for carbonate budget pilot assessments and methods comparison.

Process Steps:

• Benthic data were collected using three methods: Indo-Pacific ReefBudget (IPRB), chords, and Structure-from-Motion (SfM). Indo-Pacific ReefBudget: Following Indo-Pacific ReefBudget methodology, benthic survey data were collected by divers along six 10-m transects per site. Transects were laid out in two parallel rows of three -- where the middle transects in each row were overlaid on the inshore and offshore 10-m edges of the fixed site box -- with 5-m spacing between adjacent transects. Along each transect, the surface cover (cm) of every benthic component located directly beneath the transect tape was measured with a flexible measuring tape. Data were collected on the following benthic components: hard coral (identified to genus/species and morphology), crustose coralline algae (CCA), macroalgae, turf, sand, carbonate hard substrate, non-carbonate hard substrate, or other (including cyanobacteria, soft coral, seagrass, sponges, zoanthids, corallimorphs, or other invertebrates). The surface cover of coral colonies with open branching morphologies (e.g. Acropora intermedia, Pocillopora grandis) was estimated by multiplying the total number of branches directly beneath the transect tape by the average branch diameter, and empty space between and beneath the live branches was considered to be turf. This approach minimizes potential over-estimation of live coral cover that can occur when draping the tape over an entire branching colony (where void space is included in the surface cover measurement). Surface cover of colonies with closed branching morphologies (e.g. Acropora humilis, Pocillopora damicornis; where void space between branches is minimal and all substrate beneath the transect tape is coral skeleton) was measured by draping the tape over the entire colony. Chords: Divers collected in-water benthic data along the same set of transects that were later surveyed virtually using SfM. To ensure that transects fell within the 12-m SfM circular footprint, a master transect tape was first established along the inshore, 10-m edge of the fixed site box. Six 8-m to 10-m perpendicular transects (2 x 8 m, 2 x 9 m, and 2 x 10 m) were then laid out at predetermined distances along the master transect tape with 1.5-m spacing between transects (shorter transects closer to the edges, longer transects towards the center of the circle). Benthic data were collected along the six perpendicular transects according to the Indo-Pacific ReefBudget methodology outlined above. Yellow dive weights were placed on the benthos at the beginning and end of each diver-completed transect; these weights were included in subsequent SfM imagery collection to mark the locations of diver-collected transects. Structure-from-Motion: Benthic data collection makes use of fixed-site SfM imagery already collected as part of NCRMP monitoring efforts. Imagery was collected at each site following NCRMP standard operating procedures (Rodriguez et al. 2021). The images were processed with Agisoft Metashape photogrammetry software to produce a scaled digital elevation model (DEM) and corresponding orthomosaic for each site. Benthic data were extracted from these two high resolution reef models in ArcGIS Pro 3.0.3 using a customized tool that replicates in-water benthic data collection in the SfM environment. (Citation: Perry CT, Lange I, Januchowski-Hartley FA (2018) ReefBudget Indo Pacific: online resource and methodology. Retrieved from http://geography.exeter.ac.uk/reefbudget/)
• Urchin data were collected using three methods: Indo-Pacific ReefBudget (IPRB), chords, and Structure-from-Motion (SfM). Indo-Pacific ReefBudget: Urchin surveys were conducted over a 1 m-wide belt along the same transects used for Indo-Pacific ReefBudget benthic surveys. Along each transect, divers recorded the number and test size (size of the urchin shell excluding spines) for the following genera/species: Echinostrephus spp., Echinothrix spp., Diadema spp., Echinometra spp. (including Echinometra mathaei), and Parasalenia spp.. Test sizes were measured with a scale bar on the side of the dive slates and binned into 20 mm size classes: 0-20 mm, 21-40 mm, 41-60 mm, 61-80 mm, 81-100 mm, 101-120 mm, 121-140 mm, and 141-160 mm. Chords: urchin surveys (1 m x 8-10 m belt transects) were conducted along the same chords transects surveyed for the benthic methodology following the Indo-Pacific ReefBudget procedure. Structure-from-Motion: Extraction of urchin data from SfM imagery was conducted for Oahu sites using ArcGIS Pro and NOAA Video and Image Analytics for Marine Environments (VIAME) software. In ArcGIS Pro, virtual benthic transects laid in each fixed-site orthomosaic were cropped to the extent of the belt transect survey area (1 m x 8-10 m) and exported as individual jpeg images for each transect. Belt transect images were then uploaded to VIAME, and all visible urchins in were identified to genus/species and sized with a bounding box. The total length of each urchin (length of the test plus spines) was estimated to be the largest dimension of the bounding box. SfM urchin data were not extracted for 2022 Mariana Archipelago or 2023 American Samoa data. (Citation: Perry CT, Lange I, Januchowski-Hartley FA (2018) ReefBudget Indo Pacific: online resource and methodology. Retrieved from http://geography.exeter.ac.uk/reefbudget/)
• Fish data were collected using belt and stationary point count methods. Belt surveys: The belt method is used to conduct reef fish surveys around the Hawaiian Archipelago and the Marianas Archipelago as part of the carbonate budget pilot study. Fish are counted and sized (total length in centimeters, binned into 10cm size classes) along a 5 x 30 m transect area at ten different locations within 30m of a fixed site previously established by ESD's Ocean and Climate Change team. The belt method catalogs the density (abundance per hectare), biomass (kg per hectare), and bioerosion (kilograms per meters squared per year) of diurnally active reef fish assemblages in shallow-water (average 15m) hard-bottom habitats. Bioerosion metrics are calculated using foraging metrics that have been derived from literature where Pacific fish species were prioritized. These three values include: 1) proportion of bites leaving scars, 2) bite rates (bites per minute), and 3) volume removed per bite (centimeters cubed). Stationary Point Count surveys: The stationary point count (SPC) method is used to conduct reef fish surveys as part of the NOAA National Coral Reef Monitoring Program (NCRMP). The SPC method catalogs the diversity (species richness), abundance (numeric density) and biomass (fish mass per unit area) of diurnally active reef fish assemblages in shallow-water (less than 30 m) hard-bottom habitats. This study uses two complimentary sampling designs to survey the coral reef ecosystems at and around selected fixed-sites: 1) A stratified random sampling (StRS) design and 2) a fixed-site (fixed SPC) sampling design. The StRS survey domain encompasses the majority of the mapped area of reef and hard bottom habitats within 12.5 km of permanent fixed-sites previously established by ESD's Ocean and Climate Change team. The stratification includes island, reef zone, depth, and habitat structure type. Sampling effort is anywhere between 16 to 55 StRS SPC sites within 12.5 kilometers of each fixed-site, excluding the fixed SPC data. These data implement a different site selection method from all previous NCRMP missions around the Hawaiian Archipelago including the Main Hawaiian Islands in 2013, 2016, and 2019, and the Northwestern Hawaiian Islands in 2016 as well as data collected as part of Papahanaumokuakea Marine National Monument funded research cruises in the Northwestern Hawaiian Islands in 2014, 2015, and 2017 and a PIFSC-funded Reef Fish Survey cruise in the Main Hawaiian Islands in 2015. These data also implement a different site selection method from all previous NCRMP missions around the Marianas Archipelago as well as a concurrent 2022 nSPC dataset (National Coral Reef Monitoring Program: Stratified Random Surveys (StRS) of Reef Fish, including Benthic Estimate Data of the Mariana Archipelago since 2014). (Citation: Ayotte, P., K. McCoy, A. Heenan, I. Williams, and J. Zamzow. 2015. Coral Reef Ecosystem Division standard operating procedures: data collection for Rapid Ecological Assessment fish surveys. Pacific Islands Fish. Sci. Cent., Natl. Mar. Fish. Serv., NOAA, Honolulu, HI 96818-5007. Pacific Islands Fish. Sci. Cent. Admin. Rep. H-15-07, 33 p. doi: 10.7289/V5SN06ZT.)
• A customized calcification rates database was developed for the U.S. Pacific Islands based on the existing Indo-Pacific ReefBudget calcification database (v 1.3) . Where possible, the spatial extent of the database of published coral extension rates and densities was limited to studies from the western, central, or south Pacific Ocean. Genus and/or species average calcification rates and densities were then calculated at the taxonomic levels used by the NCRMP benthic team. This database improves regional estimates of coral calcification rates and increases integration with existing NCRMP benthic data collection. When Pacific growth rate data were not available for a particular genus/species, Indo-Pacific rates were substituted for the closest genus and morphology pair in the Indo-Pacific ReefBudget database. CCA growth rates were estimated using a Pacific-wide average of CAU accretion data. The calcification rates database, summary of supporting studies contributing to the database, and data dictionaries are publicly available at: https://github.com/hannahbarkley/reefbudgetR/tree/main/Calcification%20Rates%20Database Urchin erosion rates are calculated using Indo-Pacific ReefBudget methodology and equations (v 1.3). Parrotfish erosion rates can be calculated using Indo-Pacific ReefBudget methodology and equations (v 1.4) or using a new database consisting of allometric foraging equations for herbivorous fishes in the Pacific synthesized by Kindinger et al. (https://www.fisheries.noaa.gov/inport/item/65072). R package reefbudgetR (which includes processing scripts for benthic, urchin, and fish data and calcification and erosion databases) is available at: https://github.com/hannahbarkley/reefbudgetR (Citation: Perry CT, Lange I, Januchowski-Hartley FA (2018) ReefBudget Indo Pacific: online resource and methodology. Retrieved from http://geography.exeter.ac.uk/reefbudget/)

Data entry is usually conducted on the same day as the surveys using a data entry interface with several data controls employed, and are quality controlled by the divers using a two-person system. Observations, including species identification and sizing, are periodically checked during expeditions for consistency between divers. Following a mission, the data is then run through rigorous quality control checks. Given the size of the data set, there remains some possibility of typographical or other errors.

No

NMFS Office of Science and Technology

https://www.fisheries.noaa.gov/inport/item/67804

Metadata produced and maintained in accordance with the NOAA Data Documentation Procedural Directive: https://nosc.noaa.gov/EDMC/DAARWG/docs/EDMC_PD-Data_Documentation_v1.pdf

Yes

NOAA National Centers for Environmental Information (NCEI)

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

Unknown

NCEI_MD

Pacific Islands Fisheries Science Center - Honolulu, HI

Unknown

NOAA IRC and NOAA Fisheries ITS resources and assets.