Benthic habitats of Marra Sea Country - Gulf of Carpentaria - 2021 (JCU, Mabunji, CDU)

This dataset summarises benthic surveys in Marra Sea Country, including the Limmen Marine Park (Commonwealth) and Limmen Bight Marine Park (Northern Territory) into 4 GIS shapefiles. 

(1) A point (site) shapefile describes (a) seagrass presence/absence, (b) seagrass species composition, (c) algae cover and (d) benthic macro-invertebrate cover at n=2018 sites surveyed by small vessel and helicopter. 
(2) A point (site) shapefile describes deep-water (a) seagrass presence/absence, (b) seagrass species composition, (c) algae cover and (d) benthic macro-invertebrate cover at 54 sites surveyed by benthic towed camera and sled net. 
(3) The meadow shapefile describes attributes of 69 seagrass meadows. 
(4) The interpolation shapefile describes variation in seagrass biomass across the seagrass meadows.

The full report is: Collier C.J., Carter A., Shepherd L., van de Wetering C., Coles R., Evans S., Barrett D., Willan R.C., Groom R. (2022) Benthic habitats of Marra Sea Country - Gulf of Carpentaria. Centre for Tropical Water &amp; Aquatic 

Marra land and sea country includes coastal waters in the southern Gulf of Carpentaria in the Northern Territory (NT). The Limmen Marine Park (Commonwealth Government) and the Limmen Bight Marine Park (NT Government) are in Marra country. The co-management aspirations identified within the two Marine Park Plans of Management and the Marra Healthy Country Plan include a need to improve information on habitats and key species because they have not been previously mapped.

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). 
Geographic Information System (GIS)
All survey data were entered into a Geographic Information System (GIS) developed for Torres Strait using ArcGIS 10.8. Rectified colour satellite imagery of Limmen Bight (Source: Allen Coral Atlas and ESRI), 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. Four GIS layers were created to describe spatial features of the region: a site layer, seagrass meadow layer, and seagrass biomass interpolation layer. 

Seagrass site layers
Two layers were produced because of additional columns/details on benthic invertebrates that are included in the deep-water shapefile. These layers contains information on data collected at assessment sites and includes: 
1.  Temporal survey details – Survey date; 
2.  Spatial position - Latitude/longitude; 
3.  Survey location; 
4.  Seagrass information including presence/absence of seagrass, above-ground biomass (total and for each species), percent cover of seagrass at each site and whether individual species were present/absent at a site; 
5.  Benthic macro-invertebrate information including the percent cover of hard coral, soft coral, sponges and other benthic macro invertebrates (e.g. ascidian, clam) at a site;
6.  Algae information including percent cover of algae at a site and percent contribution of algae functional groups to algae cover at a site;
7.  Open substrate – the percent cover of the site that had no flora or habitat forming benthic invertebrates present;
8.  Dominant sediment type - Sediment type based on grain size visual assessment or deck descriptions.
9.  Survey method and vessel
10. Relevant comments and presence/absence of megafauna and animals of interest (sea cucumber, dugong, turtle, dolphin, evidence of dugong feeding trails); 
11. Data custodians. 

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 each seagrass meadow, including:
1.  Temporal survey details – Survey month and year as individual columns and the survey date (the date range the survey took place);
2.  Spatial survey details – Survey location, meadow identification number that identifies the reef name and the meadow number. This allows individual meadows to be compared among years;
3.  Survey method;
4.  Meadow depth for subtidal meadows. Intertidal: meadow was mapped on an exposed bank during low tide;
5.  Species presence – a list of the seagrass species in the meadow; 
6.  Meadow density – Seagrass meadows were classified as light, moderate, dense based on the mean biomass of the dominant species within the meadow (see Table 3 in Reason et al. 2022). For example, a Thalassia hemprichii dominated meadow would be classed as “light” if the mean meadow biomass was &lt;5 grams dry weight m-2 (g DW m-2), and “dense” if mean meadow biomass was &gt;25 g DW m-2 .
7.  Meadow community type – Seagrass meadows were classified into community types 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 (see Collier et al 2022). 
8.  Mean meadow biomass measured in g DW m-2 (+ standard error if available);
9.  Meadow area (hectares; ha) (+ mapping precision) of each meadow was calculated in the GDA 1994 Geoscience Australia MGA Zone 54 projection using the ‘calculate geometry’ function in ArcMap. Mapping precision estimates (R; in ha) were based on the mapping method used for that meadow (see Collier et al. 2022). 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;
10. Any relevant comments;
11. Data custodians.

Seagrass biomass interpolation layer
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. 

Base map
The base map used is courtesy ESRI 2022. 

Format of the data:
This dataset consists of a 2 point layer packages, 1 polygon layer package and 1 raster file with a geographic coordinate system of GDA2020:
1.  Marra Sea Country sites 2021.lpk
    Symbology representing seagrass presence/absence at each survey site
2.  Marra Sea Country deepwater sites 2021.lpk
    Symbology representing seagrass presence/absence at each survey site
3.  Marra Sea Country seagrass meadows 2021.lpk
4.  Marra Sea Country seagrass biomass interpolation 2021.lpk
    Symbology representing the spatial variation in seagrass biomass within each seagrass meadow

Data dictionary:
1. Marra Sea Country sites 2021 (point data)
SITE (numeric) - Unique identifier representing a single sample site
MEADOW (text) - Unique identifier representing what meadow the sample site is located in. Blank if sample site is not located within a meadow 
DATE (numeric) – survey date (day/month/year)
MONTH (numeric) – survey month
YEAR (numeric) – survey year
SURVEY NAME (text) – Name of survey location
LOCATION (text) – Name of survey location
LATITUDE (numeric) – Site location in decimal degrees south
LONGITUDE (numeric) – Site location in decimal degrees east
TIME (numeric) – sample time (24 hours; GMT +9:30) (NT time - subtidal sites only)
DEPTH (numeric) – depth recorded from vessel depth sounder (metres) for subtidal sites. Intertidal sites depth recorded as 0.
DBMSL (numeric) – depth below mean sea level (metres) for subtidal sites. Intertidal sites depth recorded as 0.
SUBSTRATE (text) – tags identifying the types of substrates at the sample site. Possible tags are Mud, Sand, Coarse Sand, Silt, Shell, Rock, Reef, Rubble and various combinations. Listed in order from most dominant substrate to least dominant.
SEAGRASS_P (numeric) – Absence (0) or Presence (1) of seagrass
SEAGRASS_C (numeric) - Estimated % of seagrass cover at sample site
SEAGRASS_B (numeric) - Estimated total biomass per square metre for sample site calculated from the mean of three replicate quadrats. Unit is gdw m-2.
SEAGRASS_SE (numeric) – standard error of biomass at sample site calculated from the three replicate quadrats used to estimate biomass at a sample site. Unit is gdw m-2. 
EXCLUDE_FR (numeric) – Include (0) or Exclude (1). Any site identified that needs to be excluded from contributing to the calculation of mean meadow biomass, e.g. where a visual estimate of biomass could not be optioned (i.e. no visibility at the site, only a van Veen sediment grab was used at the site)
CR - C. rotundata (numeric). Estimated biomass of Cymodocea rotundata at the sample site. Unit is gdw m-2.
CS - C. serrulata (numeric). Estimated biomass of Cymodocea serrulata at the sample site. Unit is gdw m-2.
EA - E. acoroides (numeric). Estimated biomass of Enhalus acoroides at the sample site. Unit is gdw m-2. 
HUT - H. uninervis (narrow) biomass (numeric). Estimated biomass of Halodule uninervis (narrow leaf morphology) at the sample site. Unit is gdw m-2.
HUW - H. uninervis (wide) (numeric). Estimated biomass of Halodule uninervis (wide leaf morphology) at the sample site. Unit is gdw m-2.
HD - H. decipiens (numeric). Estimated biomass of Halophila decipiens at the sample site. Unit is gdw m-2.
HO - H. ovalis (numeric). Estimated biomass of Halophila ovalis at the sample site. Unit is gdw m-2.
HS - H. spinulosa (numeric). Estimated biomass of Halophila spinulosa at the sample site. Unit is gdw m-2.
HTricost_B - H. tricostata (numeric). Estimated biomass of Halophila tricostata at the sample site. Unit is gdw m-2.
SI - S. isoetifolium (numeric). Estimated biomass of Syringodium isoetifolium at the sample site. Unit is gdw m-2.
TCilatu_B - T. ciliatum biomass (numeric). Estimated biomass of Thalassodendron ciliatum at the sample site. Unit is gdw m-2.
THempric_B - T. hemprichii (numeric). Estimated biomass of Thalassia hemprichii at the sample site. Unit is gdw m-2.
ZMueller_B - Z. muelleri biomass (numeric). Estimated biomass of Zostera muelleri at the sample site. Unit is gdw m-2.
ALGAE_COVER (numeric) - Estimated % of algae cover at sample site (all algae types grouped)
TURF_MAT_A (numeric) – (Turf mat algae % contribution to algae cover). Algae that forms a dense mat on the substrate
ERECT_MACROPHYTE (numeric) – (Erect macrophyte algae % contribution to algae cover). Macrophytic algae with an erect growth form and high level of cellular differentiation, e.g. Sargassum, Caulerpa and Galaxaura species
ENCRUSTING (numeric) – (Encrusting algae % contribution to algae cover). Algae that grows in sheet-like form attached to the substrate or benthos, e.g. coralline algae.
ERECT_CALCAREOUS (numeric) – (Erect calcareous algae % contribution to algae cover). Algae with erect growth form and high level of cellular differentiation containing calcified segments, e.g. Halimeda species.
FILAMENTOUS (numeric) – (Filamentous algae % contribution to algae cover). Thin, thread-like algae with little cellular differentiation.
        Note: TURF_MAT + ERECT_MACROPHYTE + ENCRUSTING + ERECT_CALCAREOUS + FILAMENTOUS = 100% of algae cover
HARD_CORAL (numeric) – (Hard coral %). All scleractinian corals including massive, branching, tabular, digitate and mushroom
SOFT_CORAL (numeric) – (Soft coral %). All alcyonarian corals, i.e. corals lacking a hard limestone skeleton
SPONGE (numeric) – (Sponge %)
OTHER_BMI (numeric) – Any other benthic macro-invertebrates identified, e.g. oysters, ascidians, clams. Other benthic macro-invertebrates are listed in the “comments” attribute for intertidal and shallow subtidal camera drops, and listed as percent cover in the deepwater GIS.
OPEN_SUBSTRATE (numeric) – Open substrate, no seagrass, algae or benthic macro-invertebrates at site 
DUGONG (numeric) - Absence (0) or Presence (1) of dugong/s at site
TURTLE (numeric) - Absence (0) or Presence (1) of turtle/s at site
DOLPHIN (numeric) - Absence (0) or Presence (1) of dolphin/s at site
SEA CUCUMBER (numeric) - Absence (0) or Count (&gt;1) of sea cucumbers at site
DFT PRESENT (numeric) - Absence (0) or Presence (1) of dugong feeding trails at site. Only clearly visible and therefore assessed at intertidal sites. Subtidal sites not assessed for DFTs coded as -999
METHOD (text) – e.g. helicopter, walking, hovercraft, boat-based including camera, free diving, scuba diving, van Veen grab, sled net
VESSEL (text) – Vessel name (if known)
COMMENTS (text) – Any comments for that site
AUTHOR (text) – Creator of GIS from the data set
CUSTODIAN (text) – Custodian/owner of the data set
        Note: SEAGRASS_C + ALGAE_COVER + HARD_CORAL + SOFT_CORAL + SPONGE + OTHER_BMI + OPEN_SUBSTRATE = 100% of benthic cover





Marra Sea Country deepwater survey sites 2021 (point data)
In addition to the above columns, the additional columns are included in the deepwater site data:
CORAL BLEACHING (numeric) - Absence (0), Presence (1) of coral bleaching at site. Sites without coral coded as -999
pc_Anemone (numeric) – Anemone % benthic cover. Soft coral category.
pc_Ascidian (numeric) – Ascidian % benthic cover. Other BMI category.
pc_Bryozoan (numeric) – Bryozoan % benthic cover. Other BMI category.
pc_Crinoids (numeric) – Crinoid % benthic cover. Other BMI category.
pc_Gorgonian (numeric) – Gorgonian % benthic cover. Soft coral category.
pc_Hydroid (numeric) – Hydroid % benthic cover. Other BMI category.
pc_SeaWhip (numeric) – Sea whip % benthic cover. Soft coral category.
pc_SCOther (numeric) – Other soft corals % benthic cover. Soft coral category.
        Note: pc_Anemone + pc_Gorgonia + pc_SeaWhip + pc_SCOther = SOFT_CORAL % cover
        Note: pc_ Ascidian + pc_ Bryozoan + pc_ Crinoids + pc_ Hydroid = OTHER_BMI % cover




Marra Sea Country seagrass meadows 2021 (polygon data)
ID (numeric) - Unique identifier representing a single meadow
SURVEY_NAME (text) – Name of survey location
LOCATION (text) – Name of survey location
SURVEY_DATE (numeric) – Sample date (day/month/year)
MONTH (numeric) – Sample month 
YEAR (numeric) – Sample year
MEADOW_DEPTH (text) – Classified into three categories (intertidal, subtidal, intertidal-subtidal)
PERSISTENCE (text) – Meadow form on three categories: enduring, transitory, unknown
DENSITY (text) – Meadow density categories (light, moderate, dense)
TYPE (text) - Meadow community type determined according to seagrass species composition within the meadow
SPECIES (text) – (Seagrass species): seagrass species found within the meadow. Species are recorded as abbreviated species names such as “E. acoroides”
TOT_SITES (numeric) – (Number of survey sites): the number of sample sites within the meadow
BIOMASS (numeric) – (Seagrass biomass (gdw m-2)): Mean biomass calculated from all sites (BIO_SITES) within an individual meadow
SE (numeric) – (Standard Error (gdw m-2)): The error is a calculation of standard error of biomass from all (BIO_SITES) sites within an individual meadow
AREA_HA (numeric) – (Meadow area (Ha)): Estimated meadow size (unit: hectares)
R_M (numeric) – (Meadow mapping precision (m)): Estimated mapping precision based on mapping method. 
R_HA (numeric) - (Meadow reliability estimate (Ha)): Meadow reliability estimate (unit: hectares). Expressing the error buffer around each meadow as calculated from the mapping precision estimate
SURVEY METHOD (text) – e.g. helicopter, walking, hovercraft, boat-based including camera, free diving, scuba diving, van Veen grab, sled net
VESSEL (text) – Vessel name (if known)
COMMENTS (text) – Any relevant comments for that meadow
UPDATED (date) – The date the shapefile was last updated
CUSTODIAN (text) – Custodian/owner of the data set




Marra Sea Country biomass interpolation 2021 (interpolation layer)
Inverse Distance Weighted interpolation.
Band 1: Interpolated biomass in gdw m-2



eAtlas processing:
The original data were provided as layer packages which were converted into Shapefiles and Tiff. Minor modifications to the underlying atrribute table on the meadows layer was performed to align the exported shapefile to the data dictionary order. The projection was changed on both the Meadows and Biomass Interpolation layers to allow visualisation on the eAtlas. 

Location of the data:
This dataset is filed in the eAtlas enduring data repository at: data\custodian\2020-2029-other\GoC_JCU_Murra-Sea-Country-Seagrass_2021

Tags: World, marine
Organization: Australian Ocean Data Network