Seagrass baseline survey for Orman Reef, Torres Strait, 2017 (TropWATER, JCU)

This dataset summarises benthic surveys of seagrass for Dugong and Turtle habitats at Orman Reefs, Torres Strait. The site data describes seagrass coverage estimations at 279 intertidal sites; while the meadow data groups sites into six (6) individual meadows. Data captured includes information on visual estimates for seagrass species, substrate, biomass, diversity, percent cover for benthic macro-invertebrates and algae.

Methods:

A 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 enters a low hover position while 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 (gdw m-2).

Format:

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 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 (3) GIS layers were created to describe spatial features of the region: a site layer, seagrass meadow layer, and seagrass biomass interpolation layer.

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.  

Site layer

This layer contains 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 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, 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 categorise 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 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.

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 Orman Reefs meadows. The interpolation was conducted in ArcMap 10.4. 
Further information can be found in this publication: Carter AB and Rasheed MA (2018), “Torres Strait Seagrass Long-term Monitoring: Dugong Sanctuary, Dungeness Reef and Orman Reefs”, JCU Publication, Report no. 18/17, Centre for Tropical Water &amp; Aquatic Ecosystem Research, Cairns

Data Dictionary:

Site layer



Temporal survey details:

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



DATE




Spatial survey details


LOCATION

LATITUDE



LONGITUDE




Substrate information




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




Seagrass information


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

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.

CS: estimated biomass of "Cymodocea serrulata" 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.

BIOMASS: estimated total biomass for sample site calculated from the mean of the 3 replicate quadrats. 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. For example: site 154 has biomass of 0.69004, estimate 1/3 EA (0.24119), 2/3 TH (0.44885). Unit is gdw m-2.



SE: standard error of biomass at sample site calculated from the 3 replicate quadrats used to estimate biomass at a sample site 




Sample method 


VESSEL: Indicating the type of vessel used to collect the sample

HELICOPTER: Helicopter utilised (1) or not (0) at sample site.

CAMERA: Camera utilised (1) or not (0) at sample site.

GRAB: van Veen grab utilised (1) or not (0) at sample site.

WALKING: Walking access to site utilised (1) or not (0).



DIVER: dive access to site utilised (1) or not (0).




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.

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.




Presence of Dugong feeding trails




DFTS_PRESE: identifies presence (1) or absence (0) of evidence that sample site is part of a Dugong feeding trail.




Data custodian and date of update


AUTHOR



UPDATED




Meadow Survey. 



Distribution of Algae cover (ALGAE_COVE) across the following functional groups:
- TURF (Turf mat)
- ERECT_MACR (Erect macrophyte)
- ENCRUSTING (Erect macrophyte)
- ERECT_CALC (Erect Calcareous)
- FILAMENTOU (Filamentous)

Note: TURF + ERECT_MACR + ENCRUSTING + ERECT_CALC + FILAMENTOU = 100

Distribution of Benthic macro-invertebrates cover across the following broad taxonomic groups:
- OPEN_SUBST: open substrate, no Benthic macro-invertebrates.
- HARD_CORAL
- SOFT_CORAL
- SPONGE
- OTHER_BMI

Note: OPEN_SUBST + HARD_CORAL + SORF_CORAL + SPONGE + OTHER_BMI = BENTHOS_CO

Meadow 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


"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


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

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

"Species": seagrass species found 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.

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


References:

Mellors, J. E. 1991. An evaluation of a rapid visual technique for estimating seagrass biomass. Aquatic Botany, 42: 67-73

Data Location:

This dataset is filed in the eAtlas enduring data repository at: data/TSRA_2018-22/TS_JCU_Orman-Reefs_2017

Change Log:

This section will document changes to the dataset as subsequent versions are released. This section will allow you to tell if you have the latest copy of the dataset.



Version 1 (2018-09-05): Initial release of the dataset. The filenames for this release were: TS_JCU_Orman-Reefs_2017_Seagrass_Site-surveys and TS_JCU_Orman-Reefs-2017_Seagrass_Community-type.


Organization: Australian Ocean Data Network