Chronic effects of sediment-induced changes in light quality (spectral shifts) and quantity on corals and sponges. (NESP TWQ 2.1.9, AIMS)

This dataset consists of one data file (spreadsheet) from a 28-d experiment examining sediment-induced changes in the spectral quality and quantity of light on three coral species (Acropora millepora, Pocillopora verrucosa and Montipora aequituberculata) and one encrusting sponge species (Cliona orientalis).The aim of the study was to use ecologically relevant turbidity and light profiles obtained from field-based data to test the effects of sediment induced spectral shifts and quantities of light on corals and sponges. Data from this experiment will help to derive more realistic thresholds to be applied during dredging operations.Methods:Three coral species (Acropora millepora, Pocillopora verrucosa and Montipora aequituberculata) and one encrusting sponge species (Cliona orientalis) were used in SeaSim experiments to examine the effects of sediment induced changes in the quality and quantity of light. A. millepora and M. aequituberculata were collected from Falcon Island (18° 45’ 56.4”S; 146° 32’ 02.7”) and P. verrucosa and C. orientalis were collected from Pelorus Island (18° 45’ 36.7”S; 146° 29’18.5” E).Corals were exposed to 5 different nominal suspended sediment concentrations (nominal SSC of 2.5, 5, 7.5, 10 and 15), with corresponding light profiles, for 28 days. Nephelometers used in the experimental tanks to maintain SSCs were calibrated with Formazin and set to measure Formazin Nephelometric Units (FNU), with water samples taken throughout the experiment (n=12) to relate FNU to SSCs (mg L-1). The gravimetric SSC was determined by filtering water samples (250 mL) through pre-weighed 0.4 µm polycarbonate filters, which were then rinsed with deionized water, dried at 60°C for 24 h and re-weighed. Photosynthetic active radiation (PAR) measurements were taken with a Jaz light meter (Jaz-ULM-200, Ocean Optics, the Netherlands) at peak intensity (12:00), with corresponding daily light integral (DLI) measurements obtained from the ramping profiles extracted from the programable logistic controller (PLC).Several response variables were measured at the end of the 28-d experiment: color (mean grey pixel), symbiont density (total Zoox and Zoox/cm2), chlorophyll a content (µg/cm2 and pg/cell), percent total lipids, ratio of storage to structural lipids (Stor:Struct) and lipid classes (WAX, TAG, FFA, ST, AMPL, PE, PSPI, PC, LPC). All species were photographed using a high-resolution digital camera (Nikon D810) with the following settings: ISO-100, F-29 and shutter speed 1/200. Changes in colour were examined using the hitogram function in ImageJ to obain mean pixel intensity values on a black and white scale (range 0-255) of representative live tissue, as previously described (Bessell-Browne et al., 2017). Surface area (cm2) of the corals were calculated using the wax dipping method (Stimson and Kinzie, 1991). This value was used to standardize zooxanthellae density and chlorophyll concentrations. To determine symbiotic zooxanthellae density, a volume of 0.4 mm3 from each blastate aliquot was counted six times using a Neubauer haemocytometer containing 8 µL of homogenised solution.Pigments were extracted using 95% ethanol and analysed on a Power Wave Microplate Scanning Spectrophotometer (BIO-TEK® Instruments, Inc., Vermont USA) as previously described (Pineda et al., 2016).For lipid analyses, total lipids and lipid classes were acquired by extracting freeze-dried samples following the air-spraying method procedures of (Conlan et al. 2017). Response data for all coral species can be found in the ‘coral’ tab, while the data for C. orientalis can be found in the ‘Cliona’ tab. Format:This dataset contains a single Excel file with a size of 96 KB.Data Dictionary:-SampleID: individual ID given to each replicate of the study-Species: Acropora millepora, Pocillopora verrucosa, Montipora aequituberculata-Tank/Ta: holding, 1 -10-Nominal SSC: nominal suspended sediment concentration selected in the spectral model-Gravimetric SSC: actual suspended sediment concentration (mg L-1) corals/sponges were exposed to-PAR: maximum light intensity (photosynthetic active radiation; µmol quanta m-2 s-1) corals/sponges were exposed to-DLI: daily light integral (µmol quanta m-2 s-1) corals/sponges were exposed to-Time: day sampled-SA(cm2): surface area of the coral, calculated using the wax dipping method and used to standardize zooxanthellae density and chlorophyll concentrations. -Density of Zoox/cm2: density of zooxanthellae per cm2 tissue-Total Zoox: total number of zooxanthellae-pg Chl a/cell: picograms of chlorophyll a per zooxanthellae cell-Total Chl a: total amount of chlorophyll a per cm2 tissue-Mean grey pixel: mean grey pixel intensity value from imageJ analysis (0=black, 255=white)-%Lipid: the percent total lipid-WAX: percent wax ester (lipid class)-TAG: percent triacylglycerol (lipid class)-FFA: percent free fatty acid (lipid class)-ST: percent sterol (lipid class)-AMPL: percent acetone mobile polar lipid (lipid class)-PE: percent phosphatidylethanolaimine (lipid class)-PSPI: percent phosphatidylserine-phosphatidylinositol (lipid class)-PC: percent phosphatidylcholine (lipid class)-LPC: percent lyso-phosphatidylcholine (lipid class)Stor:Struct: ratio of storage (WAX, TAG, FFA) to structural lipids (all other classes listed)References:Stimson, J., and Kinzie, R.A. (1991). The temporal pattern and rate of release of zooxanthellae from the reef coral Pocillopora damicornis (Linnaeus) under nitrogen-enrichment and control conditions. Journal of Experimental Marine Biology and Ecology 153, 63-74.Bessell-Browne, P., Negri, A.P., Fisher, R., Clode, P.L., Duckworth, A., and Jones, R. (2017a). Impacts of turbidity on corals: The relative importance of light limitation and suspended sediments. Mar Pollut Bull 117, 161-170.Pineda, M.C., Strehlow, B., Duckworth, A., Doyle, J., Jones, R., and Webster, N.S. (2016). Effects of light attenuation on the sponge holobiont- implications for dredging management. Sci Rep 6, 39038.Conlan, J.A., Rocker, M.M., and Francis, D.S. (2017). A comparison of two common sample preparation techniques for lipid and fatty acid analysis in three different coral morphotypes reveals quantitative and qualitative differences. PeerJ 5, e3645.Data Location:This dataset is filed in the eAtlas enduring data repository at: dataesp2\2.1.9_Dredging-marine-response

本数据集包含一份电子表格数据文件，源自一项为期28天的实验，该实验探究了沉积物诱导的光光谱品质与数量变化对3种珊瑚物种（轴孔珊瑚*Acropora millepora*、杯形珊瑚*Pocillopora verrucosa*以及表孔珊瑚*Montipora aequituberculata*）和1种结壳海绵物种（东方粘海绵*Cliona orientalis*）的影响。

本研究旨在利用基于野外数据获取的、符合生态学场景的浊度（turbidity）与光剖面，检验沉积物诱导的光光谱偏移及光量变化对珊瑚与海绵的影响。本实验所得数据将有助于推导疏浚作业期间需采用的更贴合实际的阈值。

### 实验方法
本研究在SeaSim实验系统中开展，选用上述3种珊瑚及1种结壳海绵作为实验材料。轴孔珊瑚和表孔珊瑚采集自Falcon岛（南纬18°45’56.4”；东经146°32’02.7”），杯形珊瑚与东方粘海绵采集自Pelorus岛（南纬18°45’36.7”；东经146°29’18.5”）。
实验中将实验对象暴露于5组不同的名义悬浮沉积物浓度（nominal suspended sediment concentration, 名义SSC分别为2.5、5、7.5、10和15），并配合对应的光剖面，持续暴露28天。实验水箱中使用浊度计（Nephelometers）维持目标SSC，该仪器以福马肼（Formazin）校准，采用福马肼浊度单位（Formazin Nephelometric Units, FNU）进行计量；实验期间共采集12组水样，用于建立FNU与SSC（mg·L⁻¹）的对应关系。
重量法SSC的测定方式为：取250mL水样通过预先称重的0.4μm聚碳酸酯滤膜过滤，随后用去离子水冲洗滤膜，在60℃下烘干24小时后再次称重，以此计算实验对象实际暴露的悬浮沉积物浓度。
光合有效辐射（Photosynthetic Active Radiation, PAR）采用Jaz光度计（Jaz-ULM-200，Ocean Optics，荷兰）在光照峰值时段（12:00）进行测定；每日光积分量（Daily Light Integral, DLI）则通过可编程逻辑控制器（Programmable Logic Controller, PLC）导出的动态光剖面计算得到。
在28天实验结束后，测定多项响应变量：体色（平均灰度像素值）、共生藻密度（总虫黄藻数量及单位面积虫黄藻数量）、叶绿素a含量（µg·cm⁻²及pg·cell⁻¹）、总脂质百分比、储存脂与结构脂的比值（Stor:Struct）以及各类脂质组分（蜡酯WAX、三酰甘油TAG、游离脂肪酸FFA、甾醇ST、丙酮可移动极性脂AMPL、磷脂酰乙醇胺PE、磷脂酰丝氨酸-磷脂酰肌醇PSPI、磷脂酰胆碱PC、溶血磷脂酰胆碱LPC）。
所有实验对象均采用高分辨率数码相机（尼康D810，Nikon D810）拍摄，拍摄参数设置为ISO-100、光圈F-29、快门速度1/200。采用ImageJ软件的直方图功能分析图像，获取活组织区域的灰度像素平均强度值（灰度范围0~255，0为黑色，255为白色），具体方法参照已发表文献（Bessell-Browne等，2017）。
珊瑚的表面积（cm²）采用蜡浸法计算（Stimson和Kinzie，1991），该数值用于校正虫黄藻密度及叶绿素浓度。
为测定共生虫黄藻密度，取0.4mm³的组织匀浆等分样本，使用加有8μL均质液的Neubauer血球计数板（Neubauer haemocytometer）重复计数6次。
色素提取采用95%乙醇，参照已发表方法（Pineda等，2016）在Power Wave微孔板扫描分光光度计（BIO-TEK® Instruments, Inc.，美国佛蒙特州）上进行分析。
脂质分析方面，参照Conlan等（2017）的气喷法流程，从冻干样本中提取总脂质及各类脂质组分。
所有珊瑚物种的响应数据可在Excel表格的"coral"工作表中查看，东方粘海绵的相关数据则位于"Cliona"工作表中。

### 数据集格式
本数据集为单份Excel文件，文件大小为96KB。

### 数据字典
- SampleID：本研究每个重复样本的唯一标识符
- Species：实验所用物种，包括轴孔珊瑚*Acropora millepora*、杯形珊瑚*Pocillopora verrucosa*、表孔珊瑚*Montipora aequituberculata*
- Tank/Ta：培养容器编号，范围为1~10
- Nominal SSC：光谱模型中设置的名义悬浮沉积物浓度
- Gravimetric SSC：实验对象实际暴露的悬浮沉积物浓度（mg·L⁻¹）
- PAR：实验对象实际暴露的最大光合有效辐射强度（µmol quanta·m⁻²·s⁻¹）
- DLI：实验对象实际暴露的每日光积分量（µmol quanta·m⁻²·s⁻¹）
- Time：采样天数
- SA(cm2)：采用蜡浸法计算的珊瑚表面积，用于校正虫黄藻密度及叶绿素浓度
- Density of Zoox/cm2：每平方厘米组织的虫黄藻密度
- Total Zoox：总虫黄藻数量
- pg Chl a/cell：每个虫黄藻细胞的叶绿素a含量（皮克）
- Total Chl a：每平方厘米组织的总叶绿素a含量
- Mean grey pixel：ImageJ分析得到的平均灰度像素强度值（0=黑色，255=白色）
- %Lipid：总脂质百分比
- WAX：蜡酯（脂质组分）百分比
- TAG：三酰甘油（脂质组分）百分比
- FFA：游离脂肪酸（脂质组分）百分比
- ST：甾醇（脂质组分）百分比
- AMPL：丙酮可移动极性脂（脂质组分）百分比
- PE：磷脂酰乙醇胺（脂质组分）百分比
- PSPI：磷脂酰丝氨酸-磷脂酰肌醇（脂质组分）百分比
- PC：磷脂酰胆碱（脂质组分）百分比
- LPC：溶血磷脂酰胆碱（脂质组分）百分比
- Stor:Struct：储存脂（WAX、TAG、FFA）与结构脂（其余所列脂质组分）的比值

### 参考文献
1. Stimson J, Kinzie RA. 1991. The temporal pattern and rate of release of zooxanthellae from the reef coral *Pocillopora damicornis* (Linnaeus) under nitrogen-enrichment and control conditions. *Journal of Experimental Marine Biology and Ecology*, 153:63-74.
2. Bessell-Browne P, Negri AP, Fisher R, Clode PL, Duckworth A, Jones R. 2017a. Impacts of turbidity on corals: The relative importance of light limitation and suspended sediments. *Mar Pollut Bull*, 117:161-170.
3. Pineda MC, Strehlow B, Duckworth A, Doyle J, Jones R, Webster NS. 2016. Effects of light attenuation on the sponge holobiont- implications for dredging management. *Sci Rep*, 6:39038.
4. Conlan JA, Rocker MM, Francis DS. 2017. A comparison of two common sample preparation techniques for lipid and fatty acid analysis in three different coral morphotypes reveals quantitative and qualitative differences. *PeerJ*, 5:e3645.

### 数据存储位置
本数据集存储于eAtlas持久化数据仓库，路径为：dataesp22.1.9_Dredging-marine-response