Benthic survey of Dugong and Turtle seagrass habitats in the North-West Torres Strait for November 2015 and January 2016 (NESP TWQ 3.5, TropWATER, JCU)

This dataset summarises benthic surveys of seagrass for Dugong and Turtle habitats in the North-West Torres Strait for November 2015 and January 2016.  The Site data describes seagrass at 853 sites; while the Meadow data describes seagrass at 34 individual meadows.  The data includes information on seagrass species, biomass, diversity, and BMI and algae percent cover.  The dataset is available as shapefiles, GIS layer packages, and/or a CSV file.


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). 

1. Location - Latitude and longitude was recorded by GPS at each site. Depth was recorded when sampling by boat and converted to depth below mean sea level (dbMSL) in metres.

2 Seagrass metrics - Above-ground biomass was determined using a ¿visual estimates of biomass¿ technique (Mellors, 1991) using trained observers. A linear regression was calculated for the relationship between the observer ranks and the harvested values. This regression was used to calculate above-ground biomass for all estimated ranks made from the survey sites. Biomass ranks were then converted into above-ground biomass estimates in grams dry weight per square metre (gdw m-2). Observers ranked seagrass biomass, and the percent contribution of each species to that biomass, using video transects, grabs, free divers, and helicopter:
* Video transect: Commonly used for subtidal meadows sampled from larger boats. At each transect site an underwater CCTV camera system was lowered from the vessel to the bottom. For each transect the camera was towed at drift speed (less than one knot) for approximately 100m. Footage was observed on a TV monitor and digitally recorded. The video was paused at ten random time frames and an observer ranked seagrass biomass and species composition. On completion of the video analysis, the video observer ranked five additional quadrats that had been previously videoed for calibration. These quadrats were videoed in front of a stationary camera, then harvested, dried and weighed. 
* Helicopter: Commonly used for intertidal surveys. At each site seagrass above-ground biomass and species composition were estimated from three 0.25 m2 quadrats placed randomly within a 10m2 circular area. Seagrass percent cover and sediment type were recorded at each site. The ¿visual estimates of biomass¿ technique when applied to helicopter surveys (and free diving/camera drops ¿ see below) involves ranking while referring to a series of quadrat photographs of similar seagrass habitats for which the above-ground biomass has previously been measured. Three separate biomass scales were used: low-biomass, high-biomass, and Enhalus-biomass. The relative proportion (percentage) of the above-ground biomass of each seagrass species within each survey quadrat was also recorded. Field biomass ranks were converted into above-ground biomass estimates in grams dry weight per square metre (gdw m-2). At the completion of sampling each observer ranked a series of calibration quadrats as per video transect surveys.
* Camera drop/free diving: Commonly used for shallow subtidal meadows sampled from a small boat. Sampling follows the same protocol as helicopter surveys but the three quadrats were either assessed by a free diver with quadrat, or by an underwater CCTV camera system camera attached to a frame. Video footage was observed on a TV monitor and seagrass ranked in real time, with the camera frame serving as a quadrat.
* van Veen grab: Commonly used for shallow subtidal meadows sampled from a small boat in conjunction with camera drops, or to record seagrass presence/absence where visibility was too poor for camera drops. A sample of seagrass was collected using a van Veen grab (grab area 0.0625 m2) to identify species present at each site. Species identified from the grab sample were used to inform species composition assessments made from the video drops (Kuo et al., 1989).

3 Benthic macro-invertebrates - A visual estimate of benthic macro-invertebrate (BMI) percent cover was recorded at each shallow subtidal and intertidal site according to four broad taxonomic groups:
* Hard corals ¿ All scleractinian corals including massive, branching, tabular, digitate and mushroom.
* Soft corals ¿ All alcyonarian corals, i.e. corals lacking a hard limestone skeleton.
* Sponges
* Other BMI ¿ Any other BMI identified, e.g. hydroids, ascidians, barnacles, oysters, molluscs. 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 shallow subtidal and intertidal site. When present, algae were categorised into five functional groups and the percent contribution of each functional group was estimated:
* Erect macrophytes ¿ 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.


Format: 

This dataset consists of two (2) GIS layers: a Site layer and a Meadow layer.

1. Site layer
This layer contains data collected at 853 individual survey sites mapped in 2015-2016, and includes:
* Temporal details - survey date and time.
* Spatial details ¿ latitude/longitude, dbMSL, sediment type, NRM region, site depth (depth below mean sea level, m).
* Habitat information ¿ seagrass presence absence, dominant seagrass species, presence/absence of individual species, seagrass above-ground biomass (for each species), Shannon-Weaver seagrass diversity values, dugong feeding trail presence/absence (intertidal sites only), and percent cover for seagrass, algae groups and benthic macro-invertebrates.
* Sampling methods, any relevant comments, and data custodian.

This layer is presented as five (5) alternate layer packages based on symbology from specific columns:
* Seagrass presence/absence (Torres Strait seagrass present absent NESP 2015.lpk)
* Seagrass species composition (Torres Strait seagrass species composition NESP 2015.lpk)
* Dugong feeding trail presence absence (Torres Strait dugong feeding trail presence absence NESP 2015.lpk) (Note: this layer only includes site information for intertidal helicopter surveys)
* Algae cover (Torres Strait algae cover NESP 2015.lpk)
* Benthic macro-invertebrate cover (Torres Strait benthic macro-invertebrate cover NESP 2015.lpk)


2. Meadow layer
Seagrass presence/absence site data was used to construct the polygon (meadow) layer. The meadow layer provides summary information for all sites within the meadow, and includes:
* Spatial details ¿ depth range of sites and meadow location.
* Habitat information ¿ seagrass species present, meadow community type and density, mean meadow biomass + standard error (s.e.), meadow area + reliability estimate (R) and number of sites within the meadow. 
* Sampling methods and any relevant comments.

This layer is presented as three (3) alternate layer packages, including interpolation layers which were created using site data and meadow boundaries to describe spatial variation in biomass, species diversity and depth gradients.  The layers are:
* "Torres Strait meadow community type NESP 2015.lpk" - Includes 34 individual seagrass meadows mapped in  2015-2016 with information including individual meadow ID, meadow location (intertidal/shallow subtidal/subtidal), meadow density based on mean biomass, meadow area, 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.
* "Torres Strait biomass (g dw m-2) interpolation NESP 2015.lpk" - An inverse distance weighted interpolation (IDW) was applied to seagrass site data to describe spatial variation in biomass across each meadow and throughout the north-west Torres Strait region. 
* "Torres Strait Shannon Weaver diversity interpolation NESP 2015.lpk" - An inverse distance weighted interpolation (IDW) was applied to seagrass site data to describe spatial variation in seagrass species diversity across each meadow and throughout the north-west Torres Strait region. The Shannon-Weaver index is a mathematical measure of species diversity that uses species richness (the number of species present, where a score of 0 = one species present) and the relative abundance of different species (Spellerberg et al., 2003).


Data Dictionary:
* Meadow location was classed according to whether meadows were intertidal (all sites surveyed by helicopter), shallow subtidal (generally an extension of an intertidal meadow into shallow waters <5m deep), or subtidal (no intertidal sites adjoining the meadow).
* Seagrass community types were determined according to species composition within a 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 (see Table 1 "Nomenclature for seagrass community types" in final report). This nomenclature also included a measure of meadow density categories (light, moderate, dense) determined by mean biomass of the dominant species within the meadow (see Table 2 "Density categories and mean above-ground biomass ranges for each species used in determining seagrass community density" in final report).
* Mapping precision estimates (in metres) were based on the mapping method used for that meadow (Table 3 "Mapping precision and methods for seagrass meadows" in final report). Mapping precision estimates ranged from 1-10m for intertidal seagrass meadows to >100m for patchy subtidal meadows. Subtidal meadow mapping precision estimates were based on the distance between sites with and without seagrass. The 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. 

Further information can be found in this publication:
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).


References:

Kuo, J., & McComb, A. J. (1989). Seagrass taxonomy, structure and development. In A. W. D. Larkum, A. J. McComb, & S. A. Shepherd (Eds.), Biology of seagrasses: a treatise on the biology of seagrasses with special reference to the Australian Region (pp. 6-73). New York: Elsevier.

Mellors, J. E. (1991). An evaluation of a rapid visual technique for estimating seagrass biomass. Aquatic Botany, 42(1), 67-73. 

Spellerberg, I. F., & Fedor, P. J. (2003). A tribute to Claude Shannon (1916¿2001) and a plea for more rigorous use of species richness, species diversity and the ¿Shannon¿Wiener¿ Index. Global Ecology and Biogeography, 12(3), 177-179. 


Data Location:

This dataset is saved in the eAtlas enduring data repository at: data\NESP1\3.5_North-West-TS_Seagrass

Tags: marine
Organization: TropWATER, James Cook University (JCU)