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 layerThis 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 layerSeagrass 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. ovalisCategories: Light (5)Species: C. serrulata, C. rotundata, S. isoetifolium, T. hemprichiiCategories: Light (25)Species: E. acoroides, T. ciliatumCategories: Light (100)Table 3. Mapping precision and methods for seagrass meadows.Mapping precision: Mapping method10-20 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 mapping50-100 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 sitesSeagrass biomass interpolation layerAn 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 & Aquatic Ecosystem Research, CairnsData Dictionary:Site layer1. Temporal survey details:- SITE: unique identifier within the Site Layer representing a single sample site.- DATE2. Spatial survey details- LOCATION- LATITUDE- LONGITUDE3. Substrate information- SUBSTRATE: tags identifying the types of substrates at the sample site. Possible tags are: Sand, Shell, Reef, Mud, Rubble, Rock4. 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 4. 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).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.- 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.6. 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.7. Data custodian and date of update- AUTHOR- UPDATED8. 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 = 100Distribution 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_COMeadow Layer1. 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": 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- "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: 67-73Data Location:This dataset is filed in the eAtlas enduring data repository at: data/TSRA_2018-22/TS_JCU_Orman-Reefs_2017Change 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.本数据集汇总了托雷斯海峡奥曼礁处儒艮（Dugong）与海龟（Turtle）栖息地的海草（seagrass）底栖调查（benthic surveys）数据。样点数据记录了279个潮间带样点的海草覆盖度估算结果；而草甸数据则将样点划分为6个独立的海草草甸。采集的数据涵盖海草物种、底质、生物量、多样性、底栖大型无脊椎动物（benthic macro-invertebrates, BMI）及藻类的盖度目视估算信息。 调查方法：本次潮间带调查遵循TropWATER的规范，针对托雷斯海峡内高航运事故风险区域开展评估（Carter等，2013），调查采用直升机作业。在每个样点，直升机悬停于低空，通过在10平方米圆形区域内随机布设3个0.25平方米的样方，对海草进行分级并估算物种组成。 海草地上生物量采用「生物量目视估算」技术（Mellors，1991），由经过培训的观测人员完成。该方法通过参照一系列已实测地上生物量的同类海草生境样方照片，对海草生物量进行分级。本次采用三套独立的生物量分级标准：低生物量、高生物量及海神草（Enhalus）生物量。同时记录每个样方内各海草物种对总地上生物量的百分比贡献。采样结束后，每位观测人员需对一系列校准样方进行分级，随后计算观测分级与实测收获值之间的线性回归模型，以此校准该观测人员在本次调查中所有分级结果的地上生物量估算值。最终将生物量分级转换为单位为克干重/平方米（gdw m⁻²）的地上生物量。 数据格式：所有调查数据均录入专为托雷斯海峡开发的地理信息系统（Geographic Information System, GIS），该系统基于ArcGIS 10.4构建。奥曼礁的校正彩色卫星影像（来源：ESRI，Landsat 2018）、野外记录及调查期间直升机拍摄的航空照片，被用于识别礁顶、水道、深水陡坡等地理特征，辅助划定海草草甸边界。共创建3个GIS图层以描述该区域的空间特征：样点图层、海草草甸图层及海草生物量插值图层。 eAtlas数据处理：原始数据以ArcMap图层包形式提供，现已转换为开放格式（Shapefile、CSV及GeoTIFF），以供eAtlas制图系统使用并作为数据集下载资源。转换过程未对原始数据进行任何修改。 样点图层：该图层包含每个样点的采集数据，具体包括： - 时间细节：调查日期与时间。 - 空间细节：纬度/经度、相对于平均海平面的深度（depth below mean sea level, dbMSL）。 - 生境信息：沉积物类型；海草信息，包括有无情况及地上生物量（总量及各物种分量）；海草、藻类、底栖大型无脊椎动物及裸露底质的盖度百分比；藻类功能群与底栖大型无脊椎动物类别的百分比贡献。 - 采样方法及相关备注。 海草草甸图层：利用海草有无的样点数据构建草甸（多边形）图层。该图层提供草甸内所有样点的汇总信息，包括： 1. 生境信息：海草物种组成、草甸群落类型、草甸密度、平均草甸生物量±标准误（standard error, s.e.）、草甸面积±可靠性估计值（R）及草甸内样点数量。 2. 采样方法及相关备注。 草甸群落类型根据每个草甸内的海草物种组成确定，物种组成基于各物种生物量对草甸平均生物量的百分比贡献。采用标准命名系统对每个草甸进行分类（表1），该命名系统还包含基于草甸内优势物种平均生物量确定的草甸密度分级（低密度、中等密度、高密度）（表2）。 制图精度估计值（单位：米）基于该草甸所采用的制图方法确定（表3）。潮间带海草草甸的制图精度范围为10-20米，而基于有无海草样点间距计算的草甸制图精度最高可达100米。制图精度估计值被用于计算每个草甸周边的误差缓冲区，该缓冲区的面积以草甸可靠性估计值（R）表示，单位为公顷。 表1 海草群落类型命名规则 | 群落类型（物种组成） | 占比说明 | | ---- | ---- | | 物种A | 物种A占比90%-100% | | 物种A伴生物种B | 物种A占比60%-90% | | 物种A伴生物种B/物种C | 物种A占比50% | | 物种A/物种B | 物种A占比40%-60% | 表2 用于确定海草草甸密度的物种密度分级及平均地上生物量范围 | 物种 | 密度分级 | 平均生物量阈值 | | ---- | ---- | ---- | | H. ovalis | 低密度 | 5 gdw m⁻² | | C. serrulata、C. rotundata、S. isoetifolium、T. hemprichii | 低密度 | 25 gdw m⁻² | | E. acoroides、T. ciliatum | 低密度 | 100 gdw m⁻² | 表3 海草草甸的制图精度与方法 | 制图精度 | 制图方法 | | ---- | ---- | | 10-20米 | 1. 通过直升机搭载GPS详细绘制草甸边界；2. 潮间带草甸在低潮时完全裸露或可见；3. 制图与调查样点密度相对较高；4. 近期航空照片与卫星影像辅助制图 | | 50-100米 | 1. 通过直升机与相机确定草甸边界；2. 近岸边界由直升机绘制；3. 远岸边界通过调查样点与卫星影像解译；4. 制图与调查样点密度相对较高 | 海草生物量插值图层：对海草样点数据采用反距离加权（inverse distance weighted, IDW）插值法，以描述奥曼礁海草草甸的生物量空间变异。插值操作在ArcMap 10.4中完成。更多详细信息可参考以下出版物：Carter AB与Rasheed MA（2018），《托雷斯海峡海草长期监测：儒艮保护区、邓杰内斯礁与奥曼礁》，詹姆斯库克大学（James Cook University, JCU）出版物，报告编号18/17，热带水与水生生态系统研究中心，凯恩斯。 数据字典： ### 样点图层 1. 时间调查细节： - "SITE"：样点图层内的唯一标识符，代表单个采样样点。 - "DATE"：调查日期 2. 空间调查细节： - "LOCATION"：位置 - "LATITUDE"：纬度 - "LONGITUDE"：经度 3. 底质信息： - "SUBSTRATE"：采样点底质类型标签，可选值包括：Sand（沙质）、Shell（贝壳）、Reef（礁岩）、Mud（泥质）、Rubble（碎石）、Rock（岩石） 4. 海草信息： - "PRESENCE"：海草存在与否，0代表不存在，1代表存在 - "EA"：采样点「海神草（Enhalus acoroides）」的估算生物量，单位为gdw m⁻² - "TH"：采样点「泰莱草（Thalassia hemprichii）」的估算生物量，单位为gdw m⁻² - "CR"：采样点「圆叶丝粉藻（Cymodocea rotundata）」的估算生物量，单位为gdw m⁻² - "CS"：采样点「齿叶丝粉藻（Cymodocea serrulata）」的估算生物量，单位为gdw m⁻² - "TC"：采样点「毛叶盐藻（Thalassodendron ciliatum）」的估算生物量，单位为gdw m⁻² - "SI"：采样点「异叶藻（Syringodium isoetifolium）」的估算生物量，单位为gdw m⁻² - "HO"：采样点「卵形海韭菜（Halophila ovalis）」的估算生物量，单位为gdw m⁻² - "BIOMASS"：采样点总估算生物量，由3个重复样方的均值计算得到。计算流程为：先估算样点总生物量，再估算样点内各海草物种的占比，随后将生物量分配至各物种，最终记录于上方对应的物种列中。例如：样点154的生物量为0.69004 gdw m⁻²，其中EA占比1/3（0.24119），TH占比2/3（0.44885）。单位为gdw m⁻² - "SE"：采样点生物量的标准误，由用于估算样点生物量的3个重复样方计算得到 5. 采样方法： - "VESSEL"：采样所用船只类型 - "HELICOPTER"：采样点是否使用直升机，1代表使用，0代表未使用 - "CAMERA"：采样点是否使用相机，1代表使用，0代表未使用 - "GRAB"：采样点是否使用范·维恩采泥器，1代表使用，0代表未使用 - "WALKING"：采样点是否可步行抵达，1代表是，0代表否 - "DIVER"：采样点是否通过潜水方式抵达，1代表是，0代表否 6. 底质盖度百分比。注：ALGAE_COVE + BENTHOS_CO + SEAGRASS_C = 100% - "ALGAE_COVE"：采样点藻类盖度估算百分比，例如：样点155的藻类盖度为10% - "BENTHOS_CO"：采样点底栖生物盖度估算百分比，例如：样点155的底栖生物盖度为63% - "SEAGRASS_C"：采样点海草盖度估算百分比，例如：样点155的海草盖度为27% 7. 儒艮觅食痕迹： - "DFTS_PRESE"：标识采样点是否存在儒艮觅食痕迹，1代表存在，0代表不存在 8. 数据管理者与更新日期： - "AUTHOR"：数据作者 - "UPDATED"：更新日期 9. 草甸调查：藻类盖度（ALGAE_COVE）在以下功能群中的分布： - "TURF"（藻席） - "ERECT_MACR"（直立大型藻类） - "ENCRUSTING"（结壳藻类） - "ERECT_CALC"（钙化直立藻类） - "FILAMENTOU"（丝状藻类） 注：TURF + ERECT_MACR + ENCRUSTING + ERECT_CALC + FILAMENTOU = 100% 底栖大型无脊椎动物盖度在以下宽泛分类群中的分布： - "OPEN_SUBST"：裸露底质，无大型无脊椎动物 - "HARD_CORAL"：硬珊瑚 - "SOFT_CORAL"：软珊瑚 - "SPONGE"：海绵 - "OTHER_BMI"：其他底栖大型无脊椎动物 注：OPEN_SUBST + HARD_CORAL + SOFT_CORAL + SPONGE + OTHER_BMI = BENTHOS_CO ### 草甸图层 1. 图层标识： - "Id"：海草草甸的唯一标识符，该值将被样点图层的"MEADOW"字段引用。 2. 空间调查制图精度与可靠性估计值： - "R_m"：基于制图方法的估算制图精度。本数据集所有草甸均通过直升机制图，因此对应的制图精度为"50-100米"。 - "R_Ha"：草甸可靠性估计值（单位：公顷），表示由制图精度计算得到的每个草甸周边误差缓冲区的面积。 3. 海草覆盖面积： - "Area__ha_"：估算草甸面积（单位：公顷）。 - "Type"：草甸群落类型，根据草甸内的海草物种组成确定。 - "Species"：草甸内发现的海草物种。 - "Biomass"：草甸的估算生物量（单位：gdw m⁻²）及估算误差，误差为生物量标准误。平均生物量与标准误由单个草甸内的所有样点计算得到。 - "Sites"：草甸内的采样样点数量。 参考文献： Mellors, J. E. 1991. 海草生物量快速目视估算技术的评估. 水生植物学, 42: 67-73 数据存储位置：本数据集存储于eAtlas永久数据仓库中，路径为：data/TSRA_2018-22/TS_JCU_Orman-Reefs_2017 变更日志：本章节将记录数据集后续版本的更新内容，以便用户确认所获取的为最新版本。 - 版本1（2018-09-05）：数据集首次发布，本次发布的文件名为：TS_JCU_Orman-Reefs_2017_Seagrass_Site-surveys 与 TS_JCU_Orman-Reefs-2017_Seagrass_Community-type。