Dungeness Reef Seagrass Survey, Torres Strait, February 2019 (TropWATER, James Cook University)

This dataset summarises intertidal benthic surveys of Dungeness Reef, Torres Strait, in February 2019 into 3 GIS shapefiles. The site shapefile describes (1) seagrass presence/absence and (2) species composition at 92 sites. The meadow shapefile describes seagrass community for the reef-top meadow. The interpolation shapefile describes variation in seagrass biomass across sites for the meadow.

This project is part of ongoing long-term monitoring of intertidal reef-top seagrass in Torres Strait. This data describes seagrass at the Dungeness Reef intertidal reef-top meadow in 2019. The reef has been surveyed annually since 2016. This monitoring provides essential information to the TSRA, Australian and Queensland governments for dugong and turtle management plans, complimenting dugong and turtle research studies in the region.

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

1 Location
Sites were surveyed by helicopter. At each site latitude and longitude was recorded by GPS. Sediment type was recorded.

2 Seagrass metrics
At each site observers estimated the percent cover of seagrass, then for three quadrats within each site, ranked seagrass biomass and estimated the percent contribution of each species to that biomass. 
Helicopter was used for the intertidal surveys following TropWATER’s methods to assess areas at high risk from shipping accidents in Torres Strait (Carter et al. 2013). At each site the helicopter comes into a low hover and seagrass was ranked and species composition estimated from three 0.25 m2 quadrats placed randomly within a 10m2 circular area. 

Seagrass above-ground biomass was determined using the “visual estimates of biomass” technique (Mellors 1991) using trained observers. This involves ranking seagrass biomass while referring to a series of quadrat photographs of similar seagrass habitats for which the above-ground biomass has been previously measured. Three separate biomass scales are used: low biomass, high biomass, and Enhalus biomass. The percent contribution of each seagrass species to total above-ground biomass within each quadrat is also recorded. At the completion of sampling each observer ranks a series of calibration quadrats. A linear regression is then calculated for the relationship between the observer ranks and the harvested values. This regression is used to calibrate above-ground biomass estimates for all ranks made by that observer during the survey. Biomass ranks are then converted to above-ground biomass in grams dry weight per square metre (g DW m-2).

3 Benthic macro-invertebrates
At each site a visual estimate of benthic macro-invertebrate (BMI) percent cover was recorded each site according to four broad taxonomic groups:
•   Hard coral – All scleractinian corals including massive, branching, tabular, digitate and mushroom.
•   Soft coral – All alcyonarian corals, i.e. corals lacking a hard limestone skeleton.
•   Sponge.
•   Other BMI – Any other BMI identified, e.g. hydroid, ascidian, barnacle, oyster, mollusc. Other BMI are listed in the “comments” column of the GIS site layer.
4 Algae
A visual estimate of algae percent cover was recorded at each site. When present, algae were categorised into five functional groups and the percent contribution of each functional group was estimated:
•   Erect macrophyte – Macrophytic algae with an erect growth form and high level of cellular differentiation, e.g. Sargassum, Caulerpa and Galaxaura species.
•   Erect calcareous – Algae with erect growth form and high level of cellular differentiation containing calcified segments, e.g. Halimeda species.
•   Filamentous – Thin, thread-like algae with little cellular differentiation.
•   Encrusting – Algae that grows in sheet-like form attached to the substrate or benthos, e.g. coralline algae.
•   Turf mat – Algae that forms a dense mat on the substrate.

Geographic Information System (GIS)
All survey data were entered into a Geographic Information System (GIS) developed for Torres Strait using ArcGIS 10.4. Rectified colour satellite imagery of Dungeness Reef (Source: ESRI, Landsat 2018), 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. 

Site layer
This layer contains data collected at each site, including:
•   Temporal details – survey date.
•   Spatial details – latitude/longitude.
•   Habitat information – sediment type; seagrass information including presence/absence and above-ground biomass (total and for each species); percent cover of seagrass, algae, BMI and open substrate; percent contribution of algae functional groups and BMI categories.
•   Sampling method and any relevant comments.

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.  Habitat information – seagrass species present, meadow community type, meadow cover, mean meadow biomass + standard error (SE), meadow area + reliability estimate (R), and number of sites within the meadow. 
2.  A meadow identification number and reef name; this allows individual meadows to be compared among years.
3.  Sampling methods.

Meadow community type was determined 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 (Table 1). This nomenclature also included a measure of meadow density categories (light, moderate, dense) determined by mean biomass and the dominant species within the meadow (Table 2).
Mapping precision estimates (R; in metres) were based on the mapping method used for that meadow (Table 3). Mapping precision estimates ranged from 10-50m for intertidal seagrass meadows and up to 100m for meadow mapping precision estimates based on the distance between sites with and without seagrass. 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. Meadow area and error buffers were determined in hectares using the calculate geometry function in ArcGIS. 

Table 1. Nomenclature for seagrass community types.

Community type (Species composition)
Species A - (Species A is 90-100% of composition)

Species A with Species B (2 species present) / Species A with mixed species - (Species A is 60-90% of composition)

Species A/Species B - (Species A is 40-60% of composition)

Table 2. Density categories and mean above-ground biomass ranges for each species used in determining seagrass community density.

Species: H. ovalis
Categories: Light (&lt;1), Moderate (1 - 5), Dense (&gt;5)

Species: C. serrulata, C. rotundata, S. isoetifolium, T. hemprichii
Categories: Light (&lt;5), Moderate (5 - 25), Dense (&gt;25)

Species: E. acoroides, T. ciliatum
Categories: Light (&lt;40), Moderate (40 - 100), Dense (&gt;100)

Table 3. Mapping precision and methods for seagrass meadows.
Mapping precision: Mapping method

10-20 m:
- Meadow boundaries mapped in detail by GPS from helicopter
- Intertidal meadows completely exposed or visible at low tide
- Relatively high density of mapping and survey sites
- Recent aerial photography and satellite imagery aided in mapping

50-100 m:
- Meadow boundaries determined from helicopter and camera
- Inshore boundaries mapped from helicopter
- Offshore boundaries interpreted from survey sites and satellite imagery
- Relatively high density of mapping and survey sites

Seagrass biomass interpolation layer
An inverse distance weighted (IDW) interpolation was applied to seagrass site data to describe spatial variation in seagrass biomass across the Dungeness Reef meadow. The interpolation was conducted in ArcMap 10.4. 

An assessment of seagrass condition for Dungeness Reef, and for all of Torres Strait, can be found in this publication:

Carter AB, Mellors JM, Reason C, &amp; Rasheed MA (2019). ‘Torres Strait Seagrass 2019 Report Card’. Centre for Tropical Water &amp; Aquatic Ecosystem Research Publication 19/16, James Cook University, Cairns

Format of the data:
This dataset consists of 3 shapefiles with a spatial reference of GDA94. 
Meadow shapefile
1.  Dungeness Reef seagrass community type 2019.lpk
Includes one seagrass meadow at Dungeness Reef mapped in 2019 with information including individual meadow ID, meadow mean seagrass biomass (g DW m-2) + SE, number of sites surveyed, seagrass cover, meadow area + R, seagrass community type, seagrass species present, survey date, survey method, and data author. ESRI and Landsat satellite image basemaps were used as background source data to check meadow and site boundaries, and re-map where required.
<ol>
<li>Dungeness Reef seagrass biomass interpolation 2019.lpk
An inverse distance weighted (IDW) interpolation was applied to seagrass site data to describe spatial variation in biomass across the Dungeness Reef meadow. 
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.</li>
</ol>

These shapefiles have been presented as 2 layer packages based on symbology from specific columns:
1.  Dungeness Reef seagrass presence absence 2019.lpk
2.  Dungeness Reef seagrass species composition 2019.lpk

Data dictionary:

Seagrass Site Layer Data Dictionary
Site: unique identifier within the Site Layer representing a single sample site.
Date: date the survey took place: DD/MM/YYYY
Depth: in meters (0) as surface survey
Location: Location of survey (Dungeness Reef)
Substrate: types of substrate identified at the sample site (Sand, Shell, Reef, Mud, Rubble, Rock)
Vessel: Indicating the type of vessel used to collect the sample
Algae_cove: Estimated percentage of algae cover at sample site. eg: Site 155 has 10% algae cover.
Seagrass_c: Estimated percentage of seagrass cover at sample site. eg: Site 155 has 27% seagrass cover.
Comments: other observations made at survey site
Seagrass: the presence and absence of seagrass, F/False as absence and T/True as presence
Latitude: latitude in decimal degrees
Longitude: longitude in decimal degrees
Biomass: total biomass for sample site. Process is to estimate total biomass for the site, then estimate percentage of each seagrass species at the site, then attribute the biomass to each species, which is then recorded in the corresponding species column.
Standard_E: standard error of biomass at sample site calculated from the 3 replicate quadrants used to estimate biomass at a sample site
EA: estimated biomass of "Enhalus acoroides" at sample site. Unit is gdw m-2.
TH: estimated biomass of "Thalassia hemprichii" at sample site. Unit is gdw m-2.
CR: estimated biomass of "Cymodocea rotundata" at sample site. Unit is gdw m-2.
TC: estimated biomass of "Thalassodendron ciliatum" at sample site. Unit is gdw m-2.
HO: estimated biomass of "Halophila ovalis" at sample site. Unit is gdw m-2.
Author - Author of the data (TropWATER)
Meadow_ID: Identification number of the meadow spatial area
Open_subst: estimated open substrate, no Benthic macro-invertebrates, recorded as percent cover
Hard_coral: estimated distribution of hard coral recorded as percent cover
Soft_coral: estimated distribution of soft coral recorded as percent cover
Other_BMI: estimated distribution of other benthic macro-invertebrate (BMI) recorded as percent cover
Sponge_cov: estimated distribution of sponges recorded as percent cover
F_Filamen: estimated distribution of FILAMENTOU algae (Filamentous) recorded as percent cover
F_erect_m: estimated distribution of MACROALGAE (Erect macrophyte) recorded as percent cover
F_erect_c: estimated distribution of CALCAREOUS algae (Erect Calcareous) recorded as percent cover
F_encrust: estimated distribution of ENCRUSTING algae recorded as percent cover
F_turf_ma: estimated distribution of TURF algae (Turf mat) recorded as percent cover

Seagrass Meadow Layer Data Dictionary
Id - Unique identifier representing a single meadow
Area - (Meadow area (Ha)): Estimated meadow size (unit: hectares)
R_m - - (Meadow reliability estimate (Ha)): Meadow reliability estimate (unit: hectares). Expressing the error buffer around each meadow as calculated from the mapping precision estimate
R_ha - Meadow reliability estimate (unit: hectares). Expressing the error buffer around each meadow as calculated from the mapping precision estimate
Meadow - Estimated meadow size (unit: hectares)
Reef - Name of survey Reef location
Cover - Meadow density categories - Continuous cover
Biomass_m - – (Seagrass biomass (gdw m-2)): Mean biomass calculated from all sites (BIO_SITES) within an individual meadow
sites - the number of sample sites within the meadow that contributed to calculating the mean meadow biomass
Methods - Survey method (Helicopter, Scuba, Freediving, Walking, Camera, Sled, Grab)
Date - The date the shapefile was last updated
Author - Custodian/owner of the data set
Species - seagrass species composition within the meadow
Community - Meadow community type determined according to seagrass species composition within the meadow

Dungeness Reef biomass interpolation
Band 1: Interpolated biomass in gdw m-2

References:
An assessment of seagrass condition Dungeness Reef, and for all of Torres Strait, can be found in this publication:
Carter AB, Mellors JM, Reason C, &amp; Rasheed MA (2019). ‘Torres Strait Seagrass 2019 Report Card’. Centre for Tropical Water &amp; Aquatic Ecosystem Research Publication 19/16, 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.  No modifications 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\2018-2022-TSRA\TS_JCU_Dungeness_2019

Tags: World
Organization: Australian Ocean Data Network