Orman Reef Seagrass Survey, Torres Strait, September 2019 (TropWATER, James Cook University)

This dataset summarises intertidal benthic surveys of Kai and Gariar Reefs (Orman Reefs, Torres Strait) in September 2019 into 3 GIS shapefiles. (1) The site shapefile describes (a) seagrass presence/absence and (b) species composition at 124 sites. (2) The meadow shapefile describes seagrass communities for the two reef-top meadows. (3) The interpolation shapefile describes variation in seagrass biomass across sites for the two reef-top meadows.

This project is part of ongoing long-term monitoring of intertidal reef-top seagrass in Torres Strait, and follows on from a baseline survey of Orman Reefs in September 2017. It describes seagrasses at two of the largest reefs in the Orman Reef complex – Kai (Koey Maza) and Gariar Reefs. This monitoring provides essential information to the TSRA, Australian and Queensland governments for dugong and turtle management plans, complimenting 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. 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.
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.

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 (g DW 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.

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 Orman Reefs (Source: ESRI, Landsat 2019), 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 GIS layers were created to describe spatial features of the region: a site layer, seagrass meadow layer, and seagrass biomass interpolation layer.
Site layer
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 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. ovalis
Categories: Light (5)
Species: C. serrulata, C. rotundata, S. isoetifolium, T. hemprichii
Categories: Light (25)
Species: E. acoroides, T. ciliatum
Categories: Light (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 Kai and Gariar Reef meadows. The interpolation was conducted in ArcMap 10.4.
An assessment of seagrass condition for Kai and Gariar Reefs, and for all of Torres Strait, can be found in this publication:
Carter AB, Mellors JM, Reason C, & Rasheed MA (2019). ‘Torres Strait Seagrass 2019 Report Card’. Centre for Tropical Water & Aquatic Ecosystem Research Publication 19/16, James Cook University, Cairns

Format:

This dataset consists of 3 shapefiles with a spatial reference of GDA94.

Meadow shapefile

1. Orman Reefs seagrass community type 2018.lpk
Includes 2 individual seagrass meadows at Kai and Gariar Reefs mapped in 2018 with information including individual meadow ID, meadow mean seagrass biomass (g DW m-2) ± SE, number of sites surveyed, seagrass cover, meadow area ± R, seagrass community type, seagrass species present, survey dates, survey method, and data author. ESRI and Landsat satellite image basemaps were used as background source data to check meadow and site boundaries, and re-map where required.

2. Orman Reefs seagrass biomass interpolation 2018.lpk
An inverse distance weighted (IDW) interpolation was applied to seagrass site data to describe spatial variation in biomass across each meadow at Kai and Gariar Reefs.

Site shapefile
Includes information including latitude/longitude, 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 author.

These shapefiles have been presented as 2 layer packages based on symbology from specific columns:

1. Orman Reefs seagrass present absent intertidal 2018.lpk
2. Orman Reefs seagrass species composition 2018.lpk

Data Dictionary:

Survey Site Layer Data Dictionary

1. Temporal survey details:
- FID: feature identifier
- SITE: unique identifier within the Site Layer representing a single sample site.
- DATE: date of survey

2. Spatial survey details
- DEPTH: units in meters (0)
- LOCATION: name of the reef location
- LATITUDE: in decimal degrees
- LONGITUDE: in decimal degrees

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

4. Vessel
- VESSEL: Indicating the type of vessel used to collect the sample (Helicopter)
- HELICOPTER: Indicating the use of Helicoptor to complete the survey

5. 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.
- SEAGRASS_C: Estimated percentage of seagrass cover at sample site. eg: Site 155 has 27% seagrass cover.
- COMMENT: Other noted observations

5. Seagrass information
- PRESENCE: the presence and absence of seagrass, 0 as absence and 1 as presence
- DFTs_Prese: the presence and absence of Dugong Feeding Trails, 0 as absence and 1 as presence

- BIOMASS:estimated 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 above.
- SE: standard error of biomass at sample site calculated from the 3 replicate quadrats 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.

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

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

7. Data custodian and other location information
- MEDOWID
- UPDATED
- AUTHOR

Data Dictionary - Community Type layer

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

3. Area Cover Seagrass
- "Sites": the number of sample sites within the meadow.
- "Biomass": esimated 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.
- "Method": method in which the survey was conducted ( i.e. Heli = Helicopter)
- "Date": Date of the survey
- "Author": Organisation/Custodian of the data
- "Community": meadow community type, determined according to seagrass species composition within the meadow.
- "Species": seagrass species found within the meadow.
- "Cover": cover type classification of reef

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.

References:

An assessment of seagrass condition for Kai and Gariar Reefs, and for all of Torres Strait, can be found in this publication:

Carter AB, Mellors JM, Reason C, & Rasheed MA (2019). ‘Torres Strait Seagrass 2019 Report Card’. Centre for Tropical Water & Aquatic Ecosystem Research Publication 19/16, James Cook University, Cairns

Data Location:

This dataset is filed in the eAtlas enduring data repository at: data/TSRA_2018-22/TS_JCU_Orman-Reefs_2019

本数据集将2019年9月对托雷斯海峡Orman Reefs的Kai和Gariar Reefs开展的潮间带底栖调查结果汇总为3个地理信息系统（Geographic Information System, GIS）形状文件。（1）站点形状文件描述了124个站点的（a）海草有无情况及（b）物种组成；（2）草甸形状文件描述了两个礁顶海草草甸的群落特征；（3）插值形状文件描述了两个礁顶海草草甸内不同站点间海草生物量的变化。

本项目是托雷斯海峡潮间带礁顶海草长期监测的一部分，承接2017年9月对Orman Reefs的基线调查，记录了Orman Reef群中两个最大礁体——Kai（Koey Maza）和Gariar Reefs的海草情况。该监测为托雷斯海峡区域管理局（TSRA）、澳大利亚及昆士兰州政府制定儒艮和海龟管理计划提供关键信息，补充了该区域儒艮和海龟的研究。

### 方法
1. **位置**
站点调查通过直升机开展。每个站点的经纬度由全球定位系统（Global Positioning System, GPS）记录，同时记录沉积物类型。

2. **海草指标**
每个站点观测员估算海草覆盖百分比，随后对每个站点内的三个样方进行海草生物量分级及物种组成估算。潮间带调查遵循TropWATER方法（Carter et al. 2013），直升机低空悬停，从10㎡圆形区域内随机放置的三个0.25㎡样方中估算海草分级和物种组成。

海草地上生物量通过训练有素的观测员采用‘生物量目视估算’技术（Mellors 1991）测定：参考一系列已预先测定地上生物量的相似海草生境样方照片，对海草生物量进行分级（低生物量、高生物量、Enhalus生物量），同时记录各物种对总地上生物量的百分比贡献。采样结束后，观测员对校准样方分级，计算分级与实际收获值的线性回归关系，用于校准调查期间的生物量估算，最终转换为克干重每平方米（g DW m⁻²）。

3. **底栖大型无脊椎动物**
每个站点记录底栖大型无脊椎动物（benthic macro-invertebrate, BMI）覆盖百分比的目视估算值，分为四大类群：硬珊瑚（所有石珊瑚）、软珊瑚（所有海鸡冠目珊瑚）、海绵、其他BMI（螅形动物、海鞘等，列于GIS站点图层‘comments’列）。

4. **藻类**
每个站点记录藻类覆盖百分比的目视估算值，若存在则分为五个功能群并估算贡献：直立大型藻类（如马尾藻属）、直立钙化藻类（如仙掌藻属）、丝状藻类、壳状藻类（如珊瑚藻）、turf mat藻类。

### 地理信息系统（GIS）
所有调查数据录入基于ArcGIS 10.4开发的托雷斯海峡GIS系统，结合校正卫星影像（ESRI, Landsat 2019）、野外记录及直升机航拍照片识别地理特征，辅助确定草甸边界。创建三个GIS图层：

- **站点图层**：包含每个站点的时间（调查日期）、空间（经纬度）、生境（沉积物类型、海草有无及生物量）、覆盖百分比（海草、藻类、BMI等）及采样方法信息。

- **海草草甸图层**：基于海草有无数据、映射站点、野外记录及卫星影像构建草甸边界，提供群落类型（按物种组成分类）、平均生物量±标准误差（SE）、面积±可靠性估算（R）、站点数量等信息。群落密度依据平均生物量范围（表2）划分，映射精度（表3）用于计算草甸误差缓冲区（单位：公顷）。

- **海草生物量插值图层**：采用反距离加权（Inverse Distance Weighted, IDW）插值法（ArcMap 10.4）描述Kai和Gariar Reef草甸的海草生物量空间变化。

### 格式
本数据集包含3个采用GDA94空间参考的形状文件：
1. Orman Reefs seagrass community type 2018.lpk：2018年映射的两个礁顶海草草甸群落类型，含草甸ID、平均生物量±SE、站点数、覆盖度、面积±R、群落类型等信息。
2. Orman Reefs seagrass biomass interpolation 2018.lpk：海草生物量IDW插值结果。
3. 站点形状文件：含经纬度、海草有无、藻类及BMI覆盖百分比、物种生物量等信息。

### 数据字典
#### 站点图层数据字典
1. **时间信息**：FID（特征标识符）、SITE（站点唯一ID）、DATE（调查日期）
2. **空间信息**：DEPTH（深度，单位：米）、LOCATION（礁体名称）、LATITUDE（纬度，十进制度）、LONGITUDE（经度，十进制度）
3. **基质信息**：SUBSTRATE（基质类型标签：Sand、Shell、Reef、Mud、Rubble、Rock）
4. **采样工具**：VESSEL（直升机）、HELICOPTER（直升机使用标识）
5. **覆盖百分比**：ALGAE_COVE（藻类覆盖百分比）、SEAGRASS_C（海草覆盖百分比）、COMMENT（其他观测）
6. **海草信息**：PRESENCE（海草有无：0=无，1=有）、DFTs_Prese（儒艮摄食痕迹有无：0=无，1=有）、BIOMASS（总生物量估算值）、SE（生物量标准误差）、EA/TH/CR等（各物种生物量，单位：g DW m⁻²）
7. **底栖与藻类分布**：OPEN_SUBST（开放基质）、HARD_CORAL（硬珊瑚）、SOFT_CORAL（软珊瑚）、SPONGE_COV（海绵）、OTHER_BMI（其他BMI）；ERECT_MACRO（直立大型藻类）、FILAMENTOU（丝状藻类）等
8. **数据管理**：MEDOWID（草甸ID）、UPDATED（更新时间）、AUTHOR（作者）

#### 群落类型图层数据字典
1. **图层标识**：Id（草甸唯一ID，关联站点图层MEADOW字段）
2. **空间精度**：Area__ha_（草甸面积，单位：公顷）、R_m（映射精度：50-100m）、R_Ha（可靠性估算，单位：公顷）
3. **草甸信息**：Sites（站点数）、Biomass（平均生物量±SE）、Method（采样方法：直升机）、Date（调查日期）、Author（数据 custodian）、Community（群落类型）、Species（海草物种）

### 表格
表1：海草群落类型命名规则
表2：各物种密度类别及平均地上生物量范围
表3：海草草甸映射精度与方法

### eAtlas处理
原始数据以ArcMap图层包形式提供，已转换为开放格式（Shapefile、CSV、GeoTiff）供eAtlas系统使用，转换未修改底层数据。

### 参考文献
Carter AB, Mellors JM, Reason C, & Rasheed MA (2019). 《Torres Strait Seagrass 2019 Report Card》. 詹姆斯库克大学热带水与水生生态系统研究中心出版物19/16，凯恩斯.

### 数据位置
本数据集存储于eAtlas持久数据仓库：data/TSRA_2018-22/TS_JCU_Orman-Reefs_2019