Orman Reef Seagrass Survey, Torres Strait, September 2019 (TropWATER, James Cook University)

This dataset summarises intertidal benthic surveys of Kai and Gariar Reefs (Orman Reefs, Torres Strait) in September 2019 into 3 GIS shapefiles. (1) The site shapefile describes (a) seagrass presence/absence and (b) species composition at 124 sites. (2) The meadow shapefile describes seagrass communities for the two reef-top meadows. (3) The interpolation shapefile describes variation in seagrass biomass across sites for the two reef-top meadows.

This project is part of ongoing long-term monitoring of intertidal reef-top seagrass in Torres Strait, and follows on from a baseline survey of Orman Reefs in September 2017. It describes seagrasses at two of the largest reefs in the Orman Reef complex – Kai (Koey Maza) and Gariar Reefs. 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 Orman Reefs (Source: ESRI, Landsat 2019), 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:
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 (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.

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 Kai and Gariar Reef meadows. The interpolation was conducted in ArcMap 10.4. 
An assessment of seagrass condition for Kai and Gariar Reefs, 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:

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

Meadow shapefile





Orman Reefs seagrass community type 2018.lpk
Includes 2 individual seagrass meadows at Kai and Gariar Reefs mapped in 2018 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.




Orman Reefs seagrass biomass interpolation 2018.lpk
An inverse distance weighted (IDW) interpolation was applied to seagrass site data to describe spatial variation in biomass across each meadow at Kai and Gariar Reefs.



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 present absent intertidal 2018.lpk

Orman Reefs seagrass species composition 2018.lpk


Data Dictionary:

Survey Site Layer Data Dictionary



Temporal survey details:

FID: feature identifier

SITE: unique identifier within the Site Layer representing a single sample site.



DATE: date of survey




Spatial survey details


DEPTH: units in meters (0)

LOCATION: name of the reef location

LATITUDE: in decimal degrees



LONGITUDE: in decimal degrees




Substrate information




SUBSTRATE: tags identifying the types of substrates at the sample site. Possible tags are: Sand, Shell, Reef, Mud, Rubble, Rock




Vessel


VESSEL: Indicating the type of vessel used to collect the sample (Helicopter)



HELICOPTER: Indicating the use of Helicoptor to complete the survey




Percentage of substrate coverage. Note: ALGAE_COVE + BENTHOS_CO + SEAGRASS_C = 100%


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.



COMMENT: Other noted observations




Seagrass information


PRESENCE: the presence and absence of seagrass, 0 as absence and 1 as presence 



DFTs_Prese: the presence and absence of Dugong Feeding Trails, 0 as absence and 1 as presence 




BIOMASS:estimated 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 above. 




SE: standard error of biomass at sample site calculated from the 3 replicate quadrats 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.

SI: estimated biomass of "Syringodium isoetifolium" at sample site. Unit is gdw m-2.



HO: estimated biomass of "Halophila ovalis" at sample site. Unit is gdw m-2.




Meadow Survey. 




Distribution of Benthic cover





Distribution of Benthic macro-invertebrates across the following broad taxonomic groups:



OPEN_SUBST: open substrate, no Benthic macro-invertebrates.

HARD_CORAL

SOFT_CORAL

SPONGE_COV

OTHER_BMI





Distribution of Algae cover (ALGAE_COVE) across the following functional groups:



ERECT_MACRO - (Erect macrophyte)

FILAMENTOU - (Filamentous)

TURF_ALGAE - (Turf mat)

ERECT_CALC - (Erect Calcareous)

ENCRUSTING - (Erect macrophyteErect macrophyte)







Data custodian and other location information


MEDOWID

UPDATED

AUTHOR


Data Dictionary - Community Type layer



Layer Identification



"Id": unique identifier for the seagrass meadow. This value is referenced by the "MEADOW" field of the Site Layer.




Spatial survey mapping precision and reliability estimates


"Area__ha_": estimated meadow size (unit: hectares).

"R_m": estimated mapping precision based on mapping method. All meadows of this dataset have been mapped via helicopter and therefore have a corresponding mapping precision of "50-100m".



"R_Ha": meadow reliability estimate (unit: hectares) expressing the error buffer around each meadow as calculated from the mapping precision estimate.




Area Cover Seagrass


"Sites": the number of sample sites within the meadow.

"Biomass": esimated biomass of the meadow (unit: gdw m-2) along with estimated error. The error is a calculation of standard error of biomass. Mean biomass and SE calculated from all sites within an individual meadow.

"Method": method in which the survey was conducted ( i.e. Heli = Helicopter)

"Date": Date of the survey

"Author": Organisation/Custodian of the data

"Community": meadow community type, determined according to seagrass species composition within the meadow. 

"Species": seagrass species found within the meadow.

"Cover": cover type classification of reef


eAtlas Processing:

The original data was provided as ArcMap Layer Packages which were converted to open formats (Shapefile, CSV and GeoTiff) for use in the eAtlas mapping system and as part of the dataset download. These conversion were performed with no modifications to the underlying data.

References:

An assessment of seagrass condition for Kai and Gariar Reefs, 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

Data Location:

This dataset is filed in the eAtlas enduring data repository at: data/TSRA_2018-22/TS_JCU_Orman-Reefs_2019

Organization: Australian Ocean Data Network