Dungeness Reef Seagrass Baseline Survey, Torres Strait, 2016-2017 (TropWATER, James Cook University)

This dataset summarises benthic surveys in November 2016 and February 2017 into 4 GIS shapefiles. The sites shapefile describes seagrass at 159 intertidal sites and 130 subtidal sites; the meadow shapefile describes seagrass at 8 individual meadows. One interpolation shapefile describes variation in seagrass biomass across sites within meadows.

This project fills an information gap for dugong and turtle habitat management in central Torres Strait. It describes seagrasses at Dungeness Reef. This baseline assessment will form the foundation for ongoing monitoring, and provide essential information to the TSRA, Australian and Queensland governments for dugong and turtle management plans, complimenting dugong and turtle research studies in the region and building skills and capacity of Traditional Owners and Rangers.

Methods:
The sampling methods used to study, describe and monitor 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 and TSRA LSMU ranger vessel. At each site latitude and longitude was recorded by GPS. Depth was recorded when sampling by boat and converted to depth below mean sea level (dbMSL) in metres. 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. Survey methods for helicopter and boat varied slightly:
Helicopter: 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. 



Camera drop and grab from TSRA LSMU Ranger Vessel: Used for the subtidal survey following TropWATER’s methods for port surveys, e.g. Thursday Island (Sozou et al. 2016). Sampling follows the same protocol as helicopter surveys but the three quadrats are assessed by an underwater CCTV camera system attached to a camera frame. At each site an underwater CCTV camera system is lowered from the vessel to the bottom and towed at drift speed (less than one knot) to complete one video transect. The video transect is observed on a TV monitor from the vessel and three “camera drops” are conducted approximately 5m apart. The camera frame serves as a 0.25 m2 quadrat, and seagrass is ranked in real time. A van Veen grab (grab area 0.0625 m2) was used to collect a seagrass sample to identify species present. Species identified from the grab were used to inform species composition assessments of video transects (Kuo and McComb 1989).

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 (gdw 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.

5 Working with the Torres Strait Islander Rangers and Community
The participation of TSRA LSMU Rangers and use of ranger vessels are essential to the success of seagrass research in Torres Strait. TropWATER researchers rely heavily on the Ranger’s local knowledge of the survey areas, logistical support prior to the surveys, and all aspects of sampling including data collection, seagrass identification, and operation of field equipment. Rangers from Poruma, Iama and Warraber Islands were key staff in the Dungeness Reef baseline survey (February 2017).

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 2017), 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. Five seagrass GIS layers were created to describe spatial features of the region: a seagrass site layer, seagrass meadow layer, seagrass biomass interpolation layer, algae site layer, and BMI site layer. 

Site layers
These layers contain data collected at each site, including:
- Temporal details – survey date and time.
- Spatial details – latitude/longitude, dbMSL.
- 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, vessel name, and any relevant comments.

Seagrass meadow layer
Seagrass presence/absence site data was used to construct the meadow (polygon) layer. The meadow layer provides summary information for all sites within the meadow, including:
1.  Habitat information – seagrass species present, intertidal/subtidal, meadow community type, meadow density, mean meadow biomass + standard error (s.e.), meadow area + reliability estimate (R), and number of sites within the meadow. 
2.  Sampling methods and any relevant comments.

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 of the dominant species within the meadow (Table 2).
Mapping precision estimates (in metres) were based on the mapping method used for that meadow (Table 3). Mapping precision estimates ranged from 10-20m for intertidal seagrass meadows and up to 200m for patchy subtidal meadows. Subtidal meadow mapping precision estimates were 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. 

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

100-200 m:
-Site surveyed by boat
-Seagrass meadow boundary determined from distance between sites
-No distinct topographic features from satellite imagery aided in mapping
-Relatively low density of 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 Dungeness Reef meadows. The interpolation was conducted in ArcMap 10.4. 

Further information can be found in this publication:
Carter AB, Wells JN and Rasheed MA (2017), “Torres Strait Seagrass – Dungeness Reef Baseline Survey and Dugong Sanctuary Long-term Monitoring”, JCU Publication, Report no. 17/30, Centre for Tropical Water &amp; Aquatic Ecosystem Research, Cairns, 36 pp.

Format:
This dataset was provided as 12 layer packages with a spatial reference of GDA94, showing different symbologies to highlighting aspects of the data.
Site layers
Two site layers that include 159 individual intertidal survey sites and 130 subtidal sites mapped in  2016-2017 with information including latitude/longitude, site depth (depth below mean sea level, m, subtidal sites only), 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 custodian.
These shapefiles have been presented as 8 layer packages based on symbology from specific columns:
1.  Intertidal seagrass presence/absence (Dungeness Reef seagrass present absent intertidal 2016.lpk)
2.  Subtidal seagrass presence/absence (Dungeness Reef seagrass present absent subtidal 2017.lpk)
3.  Intertidal seagrass species composition (Dungeness Reef intertidal seagrass species composition 2016.lpk)
4.  Subtidal seagrass species composition (Dungeness Reef subtidal seagrass species composition 2017.lpk)
5.  Intertidal algae cover (Dungeness Reef intertidal algae cover 2016.lpk)
6.  Subtidal algae cover (Dungeness Reef subtidal algae cover 2017.lpk)
7.  Intertidal benthic macro-invertebrate cover (Dungeness Reef intertidal benthic macro-invertebrate cover 2016.lpk)
8.  Subtidal benthic macro-invertebrate cover (Dungeness Reef subtidal benthic macro-invertebrate cover 2017.lpk)

Meadow layers
1.  Dungeness Reef seagrass meadow community type 2016-2017.lpk
2.  Dungeness Reef seagrass meadow depth 2016-2017.lpk
Includes 8 individual seagrass meadows mapped in 2016-2017 with information including individual meadow ID, meadow depth (intertidal/subtidal), meadow mean seagrass biomass (gdw m-2) + SE, meadow area + R, dominant seagrass species, seagrass species present, survey dates, survey method, and data custodian. ESRI and Landsat satellite image basemaps were used as background source data to check meadow and site boundaries, and re-map where required.

Biomass Interpolation
1.  Dungeness Reef intertidal seagrass biomass (gdw m-2) interpolation 2016.lpk
2.  Dungeness Reef subtidal seagrass biomass (gdw m-2) interpolation 2017.lpk
An inverse distance weighted interpolation (IDW) was applied to seagrass site data to describe spatial variation in biomass across each meadow at Dungeness Reef. 

Data Dictionary:
Site layer data
FID: feature identifier
SITE: unique identifier within the Site Layer representing a single sample site.
DATE: date the survey took place: DD/MM/YYYY
TIME: Time the survey took place where recorded, otherwise 0.
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
HELICOPTER: Helicopter utilised (T/True) or not (F/False) at sample site.
CAMERA: Camera utilised (T/True) or not (F/False) at sample site.
GRAB: van Veen grab utilised (T/True) or not (F/False) at sample site.
WALKING: Walking access to site utilised (T/True) or not (F/False).
DIVER: dive access to site utilised (T/True) or not (F/False).
ALGAE_COVE: Estimated percentage of algae cover at sample site. eg: Site 155 has 10% algae cover.
BENTHOS_CO: Estimated percentage of benthos cover at sample site. eg: Site 155 has 63% benthos 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
DBMSL: Depth was recorded when sampling by boat and converted to depth below mean sea level (dbMSL) in metres. 
 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.
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.
UPDATED - date of last update
AUTHOR - Author of the data (TropWATER)
MEADOW_ID: Identification number of the meadow spatial area
ENCRUSTING: estimated distribution of  ENCRUSTING algae  recorded as percent cover
MACROALGAE: estimated distribution of MACROALGAE (Erect macrophyte) recorded as percent cover
CALCAREOUS: estimated distribution of CALCAREOUS algae (Erect Calcareous) recorded as percent cover
FILAMENTOU: estimated distribution of FILAMENTOU algae (Filamentous) recorded as percent cover
TURF_MAT_A: estimated distribution of TURF algae (Turf mat) recorded as percent cover
OTHER_BMI: estimated distribution of other benthic macro-invertebrate (BMI) 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
SPONGE: estimated distribution of sponges recorded as percent cover
OPEN_SUBST: estimated open substrate, no Benthic macro-invertebrates, recorded as percent cover
latitude: latitude in decimal degrees
longitude: longitude in decimal degrees
BMI_Cover: sum of other biomass category distributions other than seagrass (OTHER_BMI, HARD_CORAL, SOFT_CORAL, SPONGE), recorded as percent cover
Note: ENCRUSTING + MACROALGAE + CALCAREOUS + FILAMENTOU + TURF_MAT_A = 100    
Note: OTHER_BMI + HARD_CORAL + SORF_CORAL + SPONGE + OPEN_SUBST = BENTHOS_CO

Community Type layer
FID: Identification of site via number. 
ID: (0= not recorded)
NAME: Name of meadow area (numberical)
SITES: Number of sites within the meadow boundary.
HECTARES: Estimated meadow size (unit: hectares).
R_M: Estimated mapping precision based on mapping method. Meadows in this dataset have been mapped via helicopter or boat and have a corresponding mapping precision of "10-200m".
UPDATED: Last updates to the dataset
AUTHOR: Author of the dataset
TYPE: Meadow community type, determined according to seagrass species composition within the meadow. 
BIOMASS: Estimated 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.
METHODS: Method by which the survey was undertakes (Boat - camera and grab or Helicopter)
SURVEY: Indicates the dates the survey was completed
DEPTH: Intertidal or sub tidal sites
SPECIES: Seagrass species found within the meadow.
COMMENT: Additional information about the survey location
R_HA: Meadow reliability estimate (unit: hectares) expressing the error buffer around each meadow as calculated from the mapping precision estimate.

References:
A detailed report describing this project is available:
Carter AB, Wells JN and Rasheed MA (2017), “Torres Strait Seagrass – Dungeness Reef Baseline Survey and Dugong Sanctuary Long-term Monitoring”, JCU Publication, Report no. 17/30, Centre for Tropical Water &amp; Aquatic Ecosystem Research, Cairns, 36 pp.

eAtlas Processing:
12 Layer packages were provided. The ESRI Layer Packages were opened using ArcMap then exported as shapefiles. The underlying data for several of the layer visualisations is the same:
Dungeness Reef intertidal algae cover 2016.lpk, 
Dungeness Reef seagrass present absent intertidal 2016.lpk.  These layer packages simply visualise different attributes of the same dataset. This common dataset was exported as `TS_JCU_Dungeness-Reef_2016_Seagrass_Intertidal-Site-Survey.shp. The following layers are expected to have the same underlying data (layers did not open), Dungeness Reef intertidal benthic macro-invertebrate cover 2016.lpk' and 'Dungeness Reef intertidal seagrass species composition 2016.lpk' based on images provided by the research team. 

The data from  'Dungeness Reef seagrass meadow community type 2016-2017.lpkand 'Dungeness Reef seagrass meadow depth 2016-2017.lpk' is the same, and was exported as a ShapefileTS_JCU_Dungeness-Reef_2017_Seagrass_Community-type.shp. The layer 'Dungeness Reef subtidal benthic macro-invertebrate cover 2017.lpk' (layer did not open) is expected to have the same underlying data based on imagery provided by the project team. 

The data from Dungeness Reef subtidal algae cover 2017.lpk and Dungeness Reef subtidal seagrass species composition 2017.lpk is the same and was exported as 'TS_JCU_Dungeness-Reef_2017_Seagrass_Subtidal-Site-Surveys.shp'

The following layers will be added (did not open):
Dungeness Reef intertidal seagrass biomass (gdw m-2) interpolation 2016.lpk
Dungeness Reef subtidal seagrass biomass (gdw m-2) interpolation 2017.lpk

Data Location:
This dataset is filed in the eAtlas enduring data repository at: data/TSRA_2018_22/TS_JCU_Dungeness-Reefs_2016-2017

Organization: Australian Ocean Data Network