Dungeness Reef Seagrass Survey, Torres Strait, September 2023 (TropWATER, James Cook University)

This dataset summarises intertidal benthic surveys of Dungeness Reef, Torres Strait, in September 2023 into 3 GIS shapefiles. 

(1) The point (site) shapefile describes (a) seagrass presence/absence and (b) species composition across 104 sites.
(2) The meadow shapefile describes the seagrass community for the intertidal meadow. 
(3) The interpolation shapefile describes variation in seagrass biomass across sites for the intertidal meadows.

The full report is: Carter A, Proctor M, David M, Scott A, Rasheed M and Torres Strait Regional Authority Land and Sea Rangers (2024). Torres Strait Seagrass Report Card 2024. Centre for Tropical Water &amp; Aquatic Ecosystem Research Publication 24/15, James Cook University, Cairns

Methods:

The sampling methods used to study, describe and monitor seagrass meadows were developed by TropWATER and tailored to the location and habitat surveyed; these are described in detail in the relevant publications (https://research.jcu.edu.au/tropwater).

Geographic Information System (GIS):
All survey data were entered into a Geographic Information System (GIS) developed for Torres Strait using ArcGIS 10.8. Rectified colour satellite imagery of Eastern Torres (Source: ESRI, Maxar, GeoEye, Earthstar Geographics, CNES/Airbus DS, USDA, USGS, AeroGRID, IGN, and the GIS User Community), field notes and aerial photographs taken from the helicopter during surveys were used to identify geographical features, such as reef tops, channels and deep-water drop-offs, to assist in determining seagrass meadow boundaries. Three GIS layers were created to describe spatial features of the region: a site layer, seagrass meadow layer, and seagrass biomass interpolation layer. 

Seagrass site layer:
This layer contains information on data collected at assessment sites, and includes: 
1.  Temporal survey details – Survey date; 
2.  Spatial position - Latitude/longitude; 
3.  Survey location; 
4.  Seagrass information including presence/absence of seagrass, above-ground biomass (total and for each species), percent cover of seagrass at each site and whether individual species were present/absent at a site; 
5.  Benthic macro-invertebrate information including the percent cover of hard coral, soft coral, sponges and other benthic macro invertebrates (e.g. ascidian, clam) at a site;
6.  Algae information including percent cover of algae at a site and percent contribution of algae functional groups to algae cover at a site;
7.  Open substrate – the percent cover of the site that had no flora or habitat forming benthic invertebrates present;
8.  Dominant sediment type - Sediment type based on grain size visual analysis or deck descriptions.
9.  Survey method
10. Relevant comments and presence/absence of megafauna (dugong, turtle, dolphin, evidence of dugong feeding trails); 
11. Data custodians.

Seagrass meadow layer:
Seagrass presence/absence site data, mapping sites, field notes, and satellite imagery were used to construct meadow boundaries in ArcGIS®. The meadow (polygon) layer provides summary information for all sites within the meadow, including:
1.  Temporal survey details – Survey month and year as individual columns and the survey date (the date range the survey took place);
2.  Spatial survey details – Survey location, meadow identification number that identifies the reef name and the meadow number. This allows individual meadows to be compared among years;
3.  Survey method;
4.  Meadow depth – Intertidal: meadow was mapped on an exposed bank during low tide;
5.  Species presence – a list of the seagrass species in the meadow; 
6.  Meadow density – Seagrass meadows were classified as light, moderate, dense based on the mean biomass of the dominant species within the meadow. For example, a Thalassia hemprichii dominated meadow would be classed as “light” if the mean meadow biomass was &lt;5 grams dry weight m^-2 (g DW m^-2), and “dense” if mean meadow biomass was &gt;25 g DW m^-2.
7.  Meadow community type – Seagrass meadows were classified into community types according to seagrass species composition within each meadow. Species composition was based on the percent each species’ biomass contributed to mean meadow biomass. A standard nomenclature system was used to categorize each meadow.
8.  Mean meadow biomass measured in g DW m^-2 (+ standard error if available);
9.  Meadow area (hectares; ha) (+ mapping precision) of each meadow was calculated in the GDA2020 MGA Zone 54 projection using the ‘calculate geometry’ function in ArcMap. Mapping precision estimates (R; in ha) were based on the mapping method used for that meadow. Mapping precision estimate was used to calculate an error buffer around each meadow; the area of this buffer is expressed as a meadow reliability estimate (R) in hectares;
10. Any relevant comments;
11. Data custodians.

Seagrass biomass interpolation layer:
An inverse distance weighted (IDW) interpolation was applied to seagrass site data to describe spatial variation in seagrass biomass within seagrass meadows. The interpolation was conducted in ArcMap 10.8. 

Base map:
The base map used is courtesy ESRI 2023.

Format of the data:

This dataset consists of 3 shapefiles with a spatial reference of GDA2020 MGA Zone 54. 

Meadow shapefile
- Dungeness Reef seagrass community type Sept 2023.lpk
Includes 1 seagrass meadow at Dungeness Reef mapped in September 2023 with information including meadow ID, meadow mean seagrass biomass (g DW m^-2) + standard error (SE), number of sites surveyed, seagrass cover, meadow area + reliability index (R), seagrass community type, seagrass species present, survey dates, survey method, and data author. ESRI and eAtlas satellite image basemaps were used as background source data to check meadow and site boundaries.



Dungeness Reef biomass interpolation Sept 2023.lpk
An inverse distance weighted (IDW) interpolation was applied to seagrass site data to describe spatial variation in biomass across Dungeness Reef. 


Site shapefile
Includes information including latitude/longitude, seagrass presence/absence, algae and benthic macro-invertebrate percent cover, percent cover of algae functional groups, individual seagrass species biomass, survey date, survey method, and data author.

This shapefile has been presented as 2 layer packages based on symbology from specific columns:
- Dungeness Reef seagrass presence absence Sept 2023.lpk
- Dungeness Reef seagrass species composition Sept 2023.lpk

Data dictionary:

Dungeness Reef seagrass survey sites September 2023 (point data)
- SITE (numeric) - Unique identifier representing a single sample site
- MEADOW_ID (numeric) - Unique identifier representing what meadow the sample site is located in. Blank if sample site is not located within a meadow 
- MONTH - (text) Survey month
- YEAR – (numeric) Survey year 
- DATE (numeric) – Survey date/s
- TIME (numeric) - sample time (24 hours; AEST GMT +10)
- SURVEY_NAM (text) – Name of survey location
- LATITUDE (numeric) – Site location in decimal degrees south
- LONGITUDE (numeric) – Site location in decimal degrees east
- DEPTH (numeric) – Depth of site below mean sea level (dbmsl) unit is in metres
- TIDAL (text) – Sample site is intertidal, intertidal-subtidal, subtidal
- SUBSTRATE (text) – Tags identifying the types of substrates at the sample site. Possible tags are Sand, Shell, Rock, Reef, Rubble and various combinations
- SEAGRASS_P (numeric) – Absence (0) or Presence (1) of seagrass
- SEAGRASS_C (numeric) - Estimated % of seagrass cover at sample site
- SEAGRASS_B (numeric) - Estimated total biomass per square metre for sample site calculated from the mean of three replicate quadrats. Unit is gdw m^-2
- BIO_SE (numeric) – standard error of biomass at sample site calculated from the three replicate quadrats used to estimate biomass at a sample site. Unit is gdw m^-2
- EXCLUDE_FR (numeric) – Any site identified that needs to be excluded from contributing to the calculation of mean meadow biomass, e.g. where a visual estimate of biomass could not be optioned (i.e. no visibility at the site, only a van Veen sediment grab was used at the site)
- EA_BIO (numeric) – Estimated biomass of Enhalus acoroides at the sample site. Unit is gdw m^-2
- TC_BIO (numeric) – Estimated biomass of Thalassodendron ciliatum at the sample site. Unit is gdw m^-2
- TH_BIO (numeric) – Estimated biomass of Thalassia hemprichii at the sample site. Unit is gdw m^-2
- CS_BIO (numeric) – Estimated biomass of Cymodocea serrulata at the sample site. Unit is gdw m^-2
- CR_BIO (numeric) – Estimated biomass of Cymodocea rotundata at the sample site. Unit is gdw m^-2
- ZM_BIO (numeric) – Estimated biomass of Zostera muelleri at the sample site. Unit is gdw m^-2
- HUW_BIO (numeric) – Estimated biomass of Halodule uninervis (wide morphology) at the sample site. Unit is gdw m^-2
- HUT_BIO (numeric) – Estimated biomass of Halodule uninervis (thin morphology) at the sample site. Unit is gdw m^-2
- SI_BIO (numeric) – Estimated biomass of Syringodium isoetifolium at the sample site. Unit is gdw m^-2        
- HS_BIO (numeric) – Estimated biomass of Halophila spinulosa at the sample site. Unit is gdw m^-2        
- HT_BIO (numeric) – Estimated biomass of Halophila tricostata at the sample site. Unit is gdw m^-2     
- HO_BIO (numeric) – Estimated biomass of Halophila ovalis at the sample site. Unit is gdw m^-2
- HD_BIO (numeric) – Estimated biomass of Halophila decipiens at the sample site. Unit is gdw m^-2        
- VESSEL (text) - Name of vessel used in the survey. If no name then leave blank
- CAMERA (numeric) – Drop camera utilised (1) or not (0) at sample site
- SLED (numeric) - Sled utilised (1) or not (0) at sample site
- GRAB (numeric) - Grab utilised (1) or not (0) at sample site
- FREE_DIVIN (numeric) – Free diving utilised (1) or not (0) at sample site
- DIVER (numeric) – SCUBA utilised (1) or not (0) at sample site
- WALKING (numeric) – Walking access utilised (1) or not (0) at sample site
- HELICOPTER (numeric) – Helicopter utilised (1) or not (0) at sample site
- DFTS_PRESE (numeric) - Absence (0) or Presence (1) of dugong feeding trails at site
- CUSTODIAN (text) – Data owner
- AUTHOR (text) – Author of this dataset
- COMMENTS (text) – Any comments for that site
- UPDATED (date) – The date the shapefile was last updated
- ALGAE_COVE (numeric) - Estimated % of algae cover at sample site
- TURF_MAT (numeric) – (Turf mat %) Algae that forms a dense mat on the substrate
- ERECT_MACR (numeric) – (Erect macrophyte %) Macrophytic algae with an erect growth form and high level of cellular differentiation, e.g. Sargassum, Caulerpa and Galaxaura species
- ENCRUSTING (numeric) – (Encrusting algae %) Algae that grows in sheet-like form attached to the substrate or benthos, e.g. coralline algae.
- ERECT_CALC (numeric) – (Erect calcareous %) Algae with erect growth form and high level of cellular differentiation containing calcified segments, e.g. Halimeda species.
- FILAMENTOU (numeric) – (Filamentous %) Thin, thread-like algae with little cellular differentiation.
Note: TURF_MAT + ERECT_MACR + ENCRUSTING + ERECT_CALC = 100%
- OPEN_SUBST (numeric) – Open substrate, no benthic macro-invertebrates at site 
- HARD_CORAL (numeric) – (Hard coral %) All scleractinian corals including massive, branching, tabular, digitate and mushroom
- SOFT_CORAL (numeric) – (Soft coral %) All alcyonarian corals, i.e. corals lacking a hard limestone skeleton
- SPONGE (numeric) – (Sponge %)
- OTHER_BMI (numeric) – Any other benthic macro-invertebrates identified, e.g. ascidians, clams. Other benthic macro-invertebrates are listed in the “comments” attribute
Note: SEAGRASS_C + ALGAE_COVE + OPEN_SUBST + HARD_CORAL + SOFT_CORAL + SPONGE + OTHER_BMI = 100%

Dungeness Reef seagrass meadows September 2023 (polygon data)
- MEAD_ID (numeric) - Unique identifier representing a single meadow
- MONTH (numeric) – Sample month 
- YEAR (numeric) – Sample year
- Survey_Dat (numeric) – Sample date (day/month/year)
- LOCATION (text) – Name of survey location
- TIDAL (text) – Classified into three categories (intertidal, subtidal, intertidal-subtidal)
- DENSITY (text) – Meadow density categories (light, moderate, dense)
- Community (text) - Meadow community type determined according to seagrass species composition within the meadow
- Landscape (text) – seagrass meadow landscape categories: isolated patches, aggregated patches, continuous seagrass cover
- Species (text) - List of seagrass species found within the meadow. Species are recorded as abbreviated species names such as “E. acoroides”
- PERSISTENC (text) - meadow form on three categories: enduring, transitory, unknown: enduring meadows are persistent over time (seagrass is present in the meadow ≥90% of the surveys), transitory meadows are not persistent over time (seagrass is present in the meadow &lt;90% of the surveys), unknown (the meadow was surveyed less than five times)
- Area_ha (numeric) – (Meadow area (Ha)): Estimated meadow size (unit: hectares)
- R_m (numeric) – (Meadow mapping precision (m)): Estimated mapping precision based on mapping method. 
- R_ha (numeric) - (Meadow reliability estimate (Ha)): Meadow reliability estimate (unit: hectares). Expressing the error buffer around each meadow as calculated from the mapping precision estimate
- Tot_Sites (numeric) – (Number of survey sites): the number of sample sites within the meadow
- Bio_Sites (numeric) - (Number of survey sites): the number of sample sites within the meadow that contributed to calculating the mean meadow biomass
- Biomass (numeric) – (Seagrass biomass (gdw m^-2)): Mean biomass calculated from all sites (Bio_Sites) within an individual meadow
- SE (numeric) – (Standard Error (gdw m^-2)): The error is a calculation of standard error of biomass from all (Bio_Sites) sites within an individual meadow
- EA_PA (numeric) - Absence (0) or Presence (1) of Enhalus acoroides  in the meadow - All species listed out in your database regardless of whether they are present or not
- TC_PA (numeric) - Absence (0) or Presence (1) of Thallasodendron ciliatum  in the meadow
- TH_PA (numeric) - Absence (0) or Presence (1) of Thalassia hemprichii  in the meadow
- CS_PA (numeric) - Absence (0) or Presence (1) of Cymodocea serrulata in the meadow
- CR_PA (numeric) - Absence (0) or Presence (1) of Cymodocea rotundata in the meadow
- ZM_PA (numeric) - Absence (0) or Presence (1) of Zostera muelleri in the meadow
- HUW_PA (numeric) - Absence (0) or Presence (1) of Halodule uninervis (wide morphology) in the meadow
- HUT_PA (numeric) - Absence (0) or Presence (1) of Halodule uninervis (thin morphology) in the meadow 
- SI_PA (numeric) - Absence (0) or Presence (1) of Syringodium isoetifolium in the meadow
- HS_PA (numeric) - Absence (0) or Presence (1) of Halophila spinulosa in the meadow
- HT_PA (numeric) - Absence (0) or Presence (1) of Halophila tricostata in the meadow
- HO_PA (numeric) - Absence (0) or Presence (1) of Halophila ovalis in the meadow
- HD_PA (numeric) - Absence (0) or Presence (1) of Halophila decipiens in the meadow
- CAMERA (numeric) - Camera utilised (1) or not (0) in meadow
- SLED (numeric) - Sled utilised (1) or not (0) in meadow
- GRAB (numeric) – Van Veen grab utilised (1) or not (0) in meadow 
- FREE_DIVIN (numeric) Free diving utilised (1) or not (0) in meadow
- SCUBA (numeric) - SCUBA utilised (1) or not (0) in meadow
- HELICOPTER (numeric) - Helicopter utilised (1) or not (0) in meadow
- WALKING (numeric) - Walking utilised (1) or not (0) in meadow
- DFTS (numeric) - Identifies presence (1 ) or absence (0) of evidence that the meadow has dugong feeding trails in it
- Comments (text) – Any relevant comments for that meadow
- Updated (date) – The date the shapefile was last updated
- CUSTODIAN (text) – Custodian/owner of the dataset
- Author (text) – Author of this dataset

Dungeness Reef biomass interpolation September 2023 (interpolation layer)
- Band 1: Interpolated biomass in gdw m^-2

References: 

Carter A, Proctor M, David M, Scott A, Rasheed M and Torres Strait Regional Authority Land and Sea Rangers (2024). Torres Strait Seagrass Report Card 2024. Centre for Tropical Water &amp; Aquatic Ecosystem Research Publication 24/15, James Cook University, Cairns

eAtlas Processing:

The original data were provided as Layer Packages. The lpkg files were imported to ArcGIS and exported as shapefiles and GeoTiff. The attribute "ZC_BIO" in TS_JCU_Dungeness-Reef_2023-Sep_Seagrass-Site-Surveys.shp was renamed to "ZM_BIO" as according to the data dictionary and previous datasets, and the attribute "BENTHOS_CO" was removed (redundant column as advised by the author). No modifications to the underlying data were performed and the data package are provided as submitted.

Location of the data:

This dataset is filed in the eAtlas enduring data repository at: data\custodian\2018-2025-TSRA\TS_JCU_Dungeness_2023-Sep

Tags: World
Organization: Australian Ocean Data Network