Torres Strait Seagrass Surveys Collection (TropWATER, JCU)

This data collection describes the common methods and data dictionary of the subtidal and intertidal benthic surveys of Torres Strait conducted by James Cook University. The Centre for Tropical Water & Aquatic Ecosystem Research (TropWATER), in collaboration with the Torres Strait Regional Authority (TSRA) Land and Sea Management Unit (LSMU), have been collecting baseline seagrass data and conducting long-term monitoring in Torres Strait for almost two decades. Each year one or more regions in Torres Strait are surveyed. This dataset collection represents both long-term monitoring regions and baseline surveys. As new surveys are completed and published they will be added and linked to from this record. This record is intended to be a common entry point for these surveys. Note: Not all surveys have yet been published through the eAtlas. When they have been they will be referenced from this record. This record describes the common methods and data formats used for these surveys. This data collection is not a composite of all the surveys, but merely references to them, along with a description of the common methods applied to the survey so this does not need to be repeated in each survey metadata record. Deviations from this common methodology and data formats will be noted in the metadata records for each of the surveys. This metadata record also highlights some of the slight differences in attribute format between these surveys to ensure that those wishing to combine multiple regions or time series are aware of changes that have occurred over time. Each survey is represented by 3 GIS files: 1. A site shapefile that describes (a) seagrass presence/absence, (b) species composition, (c) algae cover and (d) benthic macro-invertebrate cover at each of the sites surveyed (`Seagrass_Site-surveys`). 2. A meadow shapefile that describes seagrass communities for the intertidal meadows (`Seagrass-community-type`). 3. An interpolation raster file that shows the variation in seagrass biomass across sites for the intertidal meadows. (`Seagrass-biomass-interp`) These surveys provide essential information to the TSRA, Australian and Queensland governments for dugong and turtle management plans, complementing 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 (Orman Reefs, Dungeness Reefs, Eastern Torres Strait, Masig) or from boats for subtidal regions (Western Torres Strait). 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. 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. 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). ### 2.1 Intertidal surveys: 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. Three separate biomass scales are used: low biomass, high biomass, and Enhalus biomass. ### 2.2 Subtidal surveys: Subtidal benthic habitats were surveyed following TropWATER’s methods used in previous Torres Strait surveys, e.g. Thursday Island (Wells et al. 2019) and north-west Torres Strait (Carter and Rasheed 2016). At each site latitude and longitude was recorded by GPS. Depth was recorded and converted to depth below mean sea level (dbMSL) in metres. Sediment type was recorded. Benthic habitat was observed using a freediver with a 0.25 m2 quadrat, or a TV monitor connected to an underwater digital camera system with a frame that incorporated a 0.25 m2 quadrat. At each site, the frame and camera were lowered to the sea floor and benthic observations, including seagrass ranks, were conducted in real time. Three replicate freedives or camera “drops” were conducted approximately 5 m apart. A van Veen grab (grab area 0.0625 m2) was used to collect a sample to confirm sediment type and seagrass species identification at each site. Two separate biomass scales were used for this survey: low biomass and high biomass. ## 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 data development All survey data were entered into a Geographic Information System (GIS) developed for Torres Strait using ArcGIS 10.8. 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 (`Seagrass_Site-surveys`): 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-community-type`): 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. uninervis (thin), Categories: Light (<1), Moderate (1 - 4), Dense (>4) - Species: H. ovalis, Categories: Light (<1), Moderate (1 - 5), Dense (>5) - Species: C. serrulata, C. rotundata, T. hemprichii, Categories: Light (<5), Moderate (5 - 25), Dense (>25) - Species: E. acoroides, Categories: Light (<40), Moderate (40 - 100), Dense (>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 (`Seagrass-biomass-interp`): An inverse distance weighted (IDW) interpolation was applied to seagrass site data to describe spatial variation in seagrass biomass within seagrass meadows. 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 et al. (2021) Torres Strait Seagrass 2021 Report Card. TropWATER JCU, Report no. 21/13 # Format: These datasets consist of 3 GIS files with a spatial reference of GDA94. They are available as ESRI layer packages (data and map styling) and in open data format as shapefiles for site data and seagrass meadows and in GeoTiff format for the interpolated seagrass biomass. # Data Dictionary: ## Site layers (`Seagrass_Site-surveys`) 1. Temporal survey details: - `SITE`: unique identifier within the Site Layer representing a single sample site. - `DATE`: sample date 2. Spatial survey details - `LOCATION`: name of location, or blank. - `LATITUDE`: Site location in decimal degrees north - `LONGITUDE`: Site location in decimal degrees east 3. Substrate information - `SUBSTRATE`: tags identifying the types of substrates at the sample site. Possible tags are: Sand, Shell, Reef, Mud, Rubble, Rock and various combinations. 4. Seagrass information Note: Not all regions have all the species attributes. - `Seagrass` or `SEAGRASS`: the presence and absense of seagrass, 0 as absence and (-1 or 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. - `HO`: estimated biomass of "Halophila ovalis" at sample site. Unit is gdw m-2. - `HUW`: estimated biomass of "Halophila uninervis (wide)" at sample site. Unit is gdw m-2. - `HUT`: estimated biomass of "Halophila uninervis (thin)" 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. - `HD`: estimated biomass of "Halophila decipiens" at sample site. Unit is gdw m-2. - `HS`: estimated biomass of "Halophila spinulosa" 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. Unit is gdw m-2 5. Sample method Note: Not all region dataset include all these attributes. Some of the datasets have used (1) to represent true and some have used (-1). (0) Is consistently used to represent false. - `VESSEL`: Indicating the type of vessel used to collect the sample. Examples: ‘Helicopter,’ ‘Sager’, ‘Eclipse Dory’ - `HELICOPTER`: Helicopter utilised (-1 or 1) or not (0) at sample site. - `CAMERA`: Camera utilised (-1 or 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). 6. 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. 7. 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. 8. Data custodian and date of update - `AUTHOR` - `UPDATED` 9. Meadow Survey. Distribution of Algae cover (ALGAE_COVE) across the following functional groups: - `TURF` (Turf mat %) Algae that forms a dense mat on the substrate. - `ERECT_MACR` (Erect macrophyte %) Macrophytic algae with an erect growth form and high level of cellular differentiation, e.g. Sargassum, Caulerpa and Galaxaura species. - `ENCRUSTING` (Encrusting algae %) Algae that grows in sheet-like form attached to the substrate or benthos, e.g. coralline algae. - `ERECT_CALC` (Erect Calcareous) Algae with erect growth form and high level of cellular differentiation containing calcified segments, e.g. Halimeda species. - `FILAMENTOU` (Filamentous) Thin, thread-like algae with little cellular differentiation. 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`: 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, and mollusc. Other BMI are listed in the “comments” attribute. Note: `OPEN_SUBST + HARD_CORAL + SORF_CORAL + SPONGE + OTHER_BMI = BENTHOS_CO` ## Seagrass meadow layer (`Seagrass-community-type`): 1. Layer Identification - `Id`: unique identifier for the seagrass meadow. This value is referenced by the "MEADOW" field of the Site Layer. 2. Spatial survey mapping precision and reliability estimates - `R_m`, (Mapping precision (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 (Ha)): meadow reliability estimate (unit: hectares) expressing the error buffer around each meadow as calculated from the mapping precision estimate. 3. Area Cover Seagrass Note: Some regions record the biomass as a text field containing both the biomass and SE as a single field. In others this is separated into two attributes - `Area__ha_`, `Hectares` (Area (Ha)): estimated meadow size (unit: hectares). - `Type`: meadow community type, determined according to seagrass species composition within the meadow. - `Species` (Seagrass species): seagrass species found within the meadow. Species are recorded as either short codes matching those used in the ‘Site layers’ / ‘Seagrass information’ section or as abbreviated species names such as "E. acoroides, T. hemprichii, C. rotundata, S. isoetifolium, H. ovalis" - `Biomass` ((Biomass (mean) ± Standard Error (gDWm²)): estimated biomass of the meadow (unit: grams dry weight per square metre, 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. Example: "8.89 +/- 0.88" - `Biomass1` (Seagrass biomass (gDW m-2)): Mean biomass calculated from all sites within an individual meadow. - `SE`, `Standard_E` (Standard Error (gDW m-2)): The error is a calculation of standard error of biomass from all sites within an individual meadow. - `Sites`, (Number of survey sites): the number of sample sites within the meadow. ## Seagrass biomass interpolation layer (`Seagrass-biomass-interp`): - `Band 1`: interpolated biomass in gDW m-2. # References: Carter, A., Taylor, H., McKenna, S. and Rasheed, M. 2013. Critical Marine Habitats in High Risk Areas, Torres Strait – Seo Reef to Kai-Wareg Reef. Centre for Tropical Water & Aquatic Ecosystem Research (TropWATER) Publication. James Cook University, Cairns, 67 pp. Carter, A. B. and Rasheed, M. A. 2016. Assessment of Key Dugong and Turtle Seagrass Resources in North-west Torres Strait. Report to the National Environmental Science Programme and Torres Strait Regional Authority. Reef and Rainforest Research Centre Limited, Cairns 40 pp. 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 & Aquatic Ecosystem Research, Cairns, pp.42 Mellors, J. E. 1991. An evaluation of a rapid visual technique for estimating seagrass biomass. Aquatic Botany, 42: 67-73 Wells, J., Rasheed, M. and Coles, R. 2019. Seagrass Habitat in the Port of Thursday Island: Annual Monitoring Report 2019. Centre for Tropical Water & Aquatic Ecosystem Research (TropWATER) Publication 19/27. James Cook University, Cairns, 43 pp.

Principal Investigator
Carter, Alex, Dr Centre for Tropical Water & Aquatic Ecosystem Research (TropWATER), James Cook University
Co Investigator
Wilkinson, Juliette, Ms Centre for Tropical Water & Aquatic Ecosystem Research (TropWATER), James Cook University
Point Of Contact
Carter, Alex, Dr Centre for Tropical Water & Aquatic Ecosystem Research (TropWATER), James Cook University alexandra.carter@jcu.edu.au

Data collected from 15 Sep 2020 until 18 Sep 2020 | Data collected from 16 Sep 2020 until 17 Sep 2020 | Data collected from 14 Nov 2016 until 11 Feb 2020 | Data collected from 16 Sep 2017 until 16 Oct 2020 | Data collected from 15 Sep 2020 until 18 Sep 2020 |


Data Usage Constraints
  • Attribution 3.0 Australia
  • TropWATER gives no warranty in relation to the data (including accuracy, reliability, completeness, currency or suitability) and accepts no liability (including without limitation, liability in negligence) for any loss, damage or costs (including consequential damage) relating to any use of the data. TropWATER reserves the right to update, modify or correct the data at any time. The TropWATER Seagrass Group would appreciate the opportunity to review documents providing research, management, legislative or compliance advice based on this data.

Tags: marine