Orman Reefs Seagrass Survey, Torres Strait, October 2020 (TropWATER, James Cook University)

This dataset summarises intertidal benthic surveys of Orman Reefs, Torres Strait in October 2020 into 3 GIS shapefiles. 

(1) The site shapefile describes (a) seagrass presence/absence and (b) species composition at 160 sites. 
(2) The meadow shapefile describes seagrass communities for the reef-top meadow. 
(3) The interpolation shapefile describes variation in seagrass biomass across sites for the two reef-top meadows.

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).

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

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 m^2 quadrats placed randomly within a 10m^2 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).

Benthic macro-invertebrates:
At each site a visual estimate of benthic macro-invertebrate (BMI) percent cover was recorded 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.

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 10.8. Rectified colour satellite imagery of Orman Reefs (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.

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, hard coral, soft coral, sponges, other BMI, and open substrate; percent contribution of algae functional groups to algae cover.
- 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:
- 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. 
- A meadow identification number and reef name; this allows individual meadows to be compared among years.
- 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    Species A is 60-90% of composition
Species A with Species B/Species C  Species A is 50% 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.
(Mean above-ground biomass (gdw m^-2))
Density H. ovalis, H. decipiens, H. uninervis (thin)
Light   &lt; 1
Moderate    1-5
Dense   &gt; 5

Density H. uninervis (wide), C. serrulata, C. rotundata, S. isoetifolium, T. hemprichii
Light   &lt; 5
Moderate    5-25
Dense   &gt; 25

Density H. spinulosa
Light   &lt; 15
Moderate    15-35
Dense   &gt; 35

Density E. acoroides, T. ciliatum
Light   &lt; 40
Moderate    40-100
Dense   &gt; 100

Table 3. Mapping precision and methods for seagrass meadows.
Mapping precision   Mapping methodology
5 m     Meadow boundary mapped in detail by GPS from helicopter,
        Intertidal meadows completely exposed or visible at low tide.

10 m    Meadow boundary determined from helicopter and/or boat surveys,
        Inshore boundaries interpreted from helicopter sites,
        Offshore boundaries interpreted from survey sites and aerial photography,
        Moderately high density of mapping and survey sites.

20 m    Meadow boundaries determined from helicopter and/or boat surveys,
        Inshore boundaries interpreted from helicopter sites,
        Offshore boundaries interpreted from boat survey sites,
        Lower density of survey sites for some sections of boundary.

50 m    Meadow boundaries determined from helicopter and/or boat surveys,
        Meadow boundaries determined from seagrass presence/absence data,
        Low density of survey sites for some sections of boundary.

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

An assessment of seagrass condition for all of Torres Strait, can be found in this publication:
Carter AB, David M, Wilkinson J, Lukac M (2021) Torres Strait Eastern Cluster: Intertidal seagrass baseline survey, JCU Publication, Report no. 21/12, Centre for Tropical Water &amp; Aquatic Ecosystem Research, Cairns, pp.42

Format of the data:

This dataset consists of 3 shapefiles with a spatial reference of GDA94.

Meadow shapefiles
- Orman Reefs meadow community type 2020.lpk
Includes 2 individual seagrass meadows at Orman Reefs mapped in 2020 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 dates, 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.
<ul>
<li>Orman Reefs biomass interpolation 2020.lpk
An inverse distance weighted (IDW) interpolation was applied to seagrass site data to describe spatial variation in biomass across Orman Reefs.</li>
</ul>

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.

These shapefiles have been presented as 2 layer packages based on symbology from specific columns:
- Orman Reefs seagrass presence absence 2020.lpk
- Orman Reefs seagrass species composition 2020.lpk

Data dictionary:

Orman Reefs seagrass survey sites 2020 (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
- Date (numeric) – Survey date/s
- Location (text) – Name of survey location
- Latitude (numeric) – Site location in decimal degrees south
- Longitude (numeric) – Site location in decimal degrees east
- 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
- Biomass (numeric) – Estimated total biomass per square metre for sample site calculated from the mean of three replicate quadrats. Unit is gdw m^-2.
- 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. 
- EA (numeric) – Estimated biomass of Enhalus acoroides at the sample site. Unit is gdw m^-2
- TC (numeric) – Estimated biomass of Thalassodendron ciliatum at the sample site. Unit is gdw  m^-2
- TH (numeric) – Estimated biomass of Thalassia hemprichii at the sample site. Unit is gdw m^-2.
- CR (numeric) – Estimated biomass of Cymodocea rotundata at the sample site. Unit is gdw m^-2
- HO (numeric) – Estimated biomass of Halophila ovalis at the sample site. Unit is gdw m^-2.
- Vessel (text) – Name of vessel used in the survey. If no name then leave blank
- 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
- Algae_cove (numeric) – Estimated % of algae cover at sample site
- turf_mat_a (numeric) – Turf mat algae % cover - forms a dense mat on the substrate
- erect_macr (numeric) – Erect macrophyte algae % cover - erect growth form and high level of cellular differentiation, e.g. Sargassum, Caulerpa and Galaxaura species
- encrusting (numeric) – Encrusting algae % cover - grows in sheet-like form attached to the substrate or benthos, e.g. coralline algae.
- erect_calc (numeric) – Erect calcareous algae % cover - erect growth form and high level of cellular differentiation containing calcified segments, e.g. Halimeda species.
- filamentou (numeric) – Filamentous algae % cover - thin, thread-like algae with little cellular differentiation.
- open_subst (numeric) – Open substrate, no seagrass, algae or benthic macro-invertebrates at site 
- hard_coral (numeric) – Hard coral % cover - all scleractinian corals including massive, branching, tabular, digitate and mushroom
- soft_coral (numeric) – Soft coral % cover - all alcyonarian corals, i.e. corals lacking a hard limestone skeleton
- sponge_cov (numeric) – Sponge % cover
- other_BMI (numeric) – Other benthic macro-invertebrates (BMI) % cover - e.g. ascidians, clams. Other benthic macro-invertebrates are listed in the “comments” attribute
- Comments (text) – Any comments for that site
- Updated (date) – The date the shapefile was last updated
- Author (text) – Creator of the GIS dataset

Orman Reefs seagrass meadows 2020 (polygon data)
- Id (numeric) – Unique identifier representing a single meadow
- Date (text) – Sample date (day/month/year)
- Community (text) – Meadow community type determined according to seagrass species composition within the meadow
- Species (text) – List of seagrass species found within the meadow. Species are recorded as abbreviated species names such as “E. acoroides”
- 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 area of the error buffer around each meadow as calculated from the mapping precision estimate.
- Sites (numeric) – Number of survey sites. The number of sample sites within the meadow
- Biomass (numeric) – Seagrass biomass (gdw m^-2). Mean biomass calculated from all sites (BIO_SITES) within an individual meadow
- Comments (text) – Any relevant comments for that meadow
- Method – method in which the survey was conducted (i.e. Heli = Helicopter)
- Updated (date) – The date the shapefile was last updated
- Author (text) – Creator of the GIS dataset
- Cover – cover type classification of reef
- Reef – Kai or Gariar Reef in the Orman Reef complex

Orman Reefs biomass interpolation 2020 (interpolation layer)
- Band 1: Interpolated biomass in gdw m^-2

References: 

An assessment of seagrass condition for Orman Reefs, and for all of Torres Strait, can be found in this publication:
Carter AB, David M, Whap T, Hoffmann LR, Scott A, and Rasheed MA (2021). ‘Torres Strait Seagrass 2021 Report Card’. Centre for Tropical Water &amp; Aquatic Ecosystem Research Publication 21/13, James Cook University, Cairns, 76 pp.

eAtlas Processing:

The original data were provided as Layer Packages. The lpkg files were imported to ArcGIS and exported as shapefiles and GeoTiff. In the shapefile "TS_JCU_Orman-Reefs_2020_Seagrass_Site-survey.shp" the values indicating seagrass is present (attribute "Seagrass_p") were inverted from -1 to 1. No further 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_Orman-Reefs_2020

Tags: World
Organization: Australian Ocean Data Network