Reef Havens Research Project (Temperature, Current, CTD casts at Moore Reef) 2018 - 2021

The dataset consists of multiple data files from four types of instruments to visualize current, temperature flow patterns and coral stress responses around the north west section of Moore Reef including a reef pass, taken during 2018-2021. These include 19 temperature and 12 current loggers and 69 CTD casts, along with fluorometry measurements of 33 tagged coral colonies. This dataset also includes photos of the tagged corals along with CoralWatch colour cards during a 5-week period from Nov-Dec 2020.The three-year Reef Havens Research Project commenced in December 2017 in response to the unprecedented back-to-back coral bleaching events on the Great Barrier Reef in 2016 and 2017. The proposal was based on anecdotal observations during those bleaching events that local environmental conditions were a significant factor affecting bleaching severity and recovery after bleaching: reefs that were near upwellings, or experienced cooler currents or wind mixing, tended to experience less severe bleaching, and those with few other pressures tended to recover better. Could science-based localised interventions that mimic these natural stress-reducing phenomena (for example by incrementally increasing water movement, reducing water temperature by 1-2°C, or disrupting the water’s surface) reduce coral stress, bleaching severity and/or promote recovery on key reef sites, potentially providing time and space for natural acclimatization and adaptation processes to occur?The Reef Havens Research Project is a foundational investment in an in?situ research platform that was intended to closely observe the impacts of changes in flow and temperature on coral stress, bleaching and recovery outcomes at the very small scale of a tourism site. Once small-scale water movements associated with bleaching events were understood, the project also tested whether an engineering intervention could restore “normal” water movement and mixing during doldrum coral bleaching conditions at a very small area of Moore Reef, one of the key tourism industry sites on the GBR near Cairns. It is hoped that the data generated through this research project will be used by others to build further understanding of the connection between environmental conditions and coral stress, and the potential for interventions to improve bleaching outcomes at small scales. Methods:To quantify current and temperature flow patterns and their impacts through the Moore Reef Pass and adjacent tourism site areas, an array of instruments was deployed. The instruments used were a Marotte HS current meter, HOBO TidbiT MX Temp 400 logger, a Walz DIVING-PAM-II underwater fluorometer and a SonTek Castaway conductivity, temperature and depth recorder (CTD).The Marotte HS current meter is a drag-tilt current meter, developed and manufactured by the Marine Geophysics laboratory at James Cook University. The instrument consists of a buoyant enclosure containing an electronic logger, which is then fixed to a stationary point. The buoyancy force causes the instrument to float directly upwards in the absence of current. Movement of the water exerts a drag force on the instrument, tilting it over until the buoyancy, drag and tether forces are balanced. The amount of tilt is proportional to the speed of the water. The logger records the tilt angle using an accelerometer, and the tilt direction using a magnetometer. Both tilt and tilt angle were converted to current speed and direction in post-processing using a pre-defined tilt-to-speed calibration curve. The instrument also contained a temperature sensor (thermistor type with ±0.2C repeatability) that was fixed to the bottom of the logger (JCU and Marine-Geophysics-Laboratory, 2017).An array of 12 current meters were fixed to star pickets 0.5 m above the substrate (see Marotte deployment picture) at selected locations, substrate types and depths through the reef pass and tourism pontoon areas for 5 deployments between 2018 and 2021 (see downloadable documents for details of deployments). The loggers were set to record current speed and direction (in m/s and degrees) at one second intervals, along with temperature in Celsius at one-minute intervals. The data were recorded on a micro SD card and the instrument was powered by 2 AA batteries. The raw data were converted into current speed and direction and temperature to one minute intervals with the Marotte HS config program (JCU and Marine-Geophysics-Laboratory, 2017). Along with each csv file per instrument per deployment there is a metadata text file containing the calibration and processing information. All 12 current meters were removed and data downloaded on the 13-Sept-2018.Nineteen HOBO TidbiT MX Temp 400 loggers were installed at various depths at the northern section of Moore Reef (see Moore Reef Hobo Map) for 4 deployments between 2018 and 2021 (see downloadable document for details of deployments). Some loggers were fixed to star pickets at ~ 50cm above the substrate and others were fixed to mooring lines. The loggers recorded temperature in Celsius at five-minute intervals and at this ratio had nominal battery life of 340 days. The data were downloaded using HOBO’s mobile phone app and are provided as CSV files.To investigate changes in coral stress associated with water movement, 33 corals from 11 species located along pre-existing monitoring sites were selected and tagged with labelled cattle tags (see downloadable document for details). These individual colonies were underwater photographed with a CoralWatch card in which a finger was visible pointing to the colour on the card that matched the colour of the colony. Sampling was conducted once a week over 5 weeks Nov-19 to Dec-20. The intent was to compare coral stress levels in early summer, during well-mixed conditions, with late-summer, stratified, potentially bleaching conditions. Baseline early-summer stress measurements of these colonies were made with the Walz DIVING-PAM-II underwater fluorometer in 2019 but unfortunately we were prevented from accessing the tagged corals during late summer (March 2020), even though some bleaching was reported, when coronavirus restrictions shut down the GBR tourism industry. Instead we repeated the late-summer fluorometer measurements in April 2021, even though conditions were not stratified. Data were downloaded using Walz’s fluorometry software. The CastAway CTD enabled near-instantaneous vertical profiles of temperature and salinity to be obtained at and around our field site at Moore Reef. The CastAway CTD was deployed using a modified fishing rod and 200 lb breaking strain braid Dyneema fishing line either directly from the back of the Reef Magic Marine World Pontoon or via a small tender. The instrument was allowed to sink to the bottom and then rapidly retrieved, making measurements both on the way down and on the way up. The CastAway recorded the GPS location before and after each cast. Plots of conductivity, temperature, salinity and sound speed versus depth could be viewed immediately on the CastAway's integrated color LCD screen in the field. A total of 69 casts were performed, with each cast collecting ~100 data points. Raw data were downloaded via Bluetooth to a Windows computer for detailed analysis and/or export.Limitations of the data:The first and last 24 hours of the Marotte and HOBO logger datasets should be treated with caution as this may include transportation time to and from deployment site. Current Meter 12 stopped recording on the 21-Jun-2018.The CastAway CTD was deployed on an event-based basis, enabling comparison of patterns during normal well-mixed conditions and also during calm, sunny doldrum conditions when normal mixing had failed. Two different instruments were used during the 2019-2020 sampling period, with differing calibration history. While the conductivity measurements should therefore be treated with caution, the temperature data are considered reliable.Format:The data set contains multiple parts which are the Marotte current meters, Hobo Temperature meters, CTD casts and fluorometry/coral watch data. The Marotte current meter dataset consists of individual csv files for 12 instruments for 5 deployments (see downloadable documents for details of deployments).The HOBO temperature meters datasets consist of individual csv files for an array of HOBO loggers for 4 deployments (see downloadable documents for deployment details).The CTD datasets consist of CSV files for deployments on each of three dates. Please note that these deployments were deliberately performed on particular dates to measure extreme conditions of stratification, and their deviation from normality, rather than an attempt to rigorously document conditions over time. The coral watch data consist of two photos for each colony, the first with a close up of the labelled cattle tag and the second showing the coral watch card colour reference matched to coral colony colour. There are 5 folders labelled according to sampling date. This also includes a CSV file with the PAM data.Data Dictionary:- This dataset consists of data files compiled from 12 Marotte HS current meters over 5 deployments at Moore Reef Pass (see Moore Reef Marotte Map) between May-18 and Aug-20. The spreadsheet for each Marotte contains the processed data of: Timestamp (one minute intervals), Current Speed (m/s), Direction (degrees), Speed Upper (m/s), Speed lower (m/s), Tilt (radians), Direction (radians), Battery (Volts) and Temperature (Celsius). - This dataset also consist of HOBO temperature logger data, that recorded water temperature (Celsius) and Timestamp (5 minute intervals) for 4 deployments between Jun-20 and Aug-20. - The dataset contains 5 folders under coral watch colonies, with each folder containing jpeg photos of tagged coral colonies.- PAM data:Type = F (fluorometer) or SPEC (Spectrophotometer)No. = measurement number by this fluorometer (for its own internal record-keeping)1:Mark = coral colony tag as referred to in the “Pam transect species list” that I’ve just uploaded1:F = Light adapted minimum fluorescence1:Fm1 = maximum fluorescence1:PAR = photosynthetically active radiation1:Y (II) = effective quantum yield of Photosystem II1:ETR = electron transport rateData Location:This dataset is filed in the eAtlas enduring data repository at: data\custodian\2020-2029-other\Reef-Havens

本数据集包含四类仪器采集的多份数据文件，用于可视化2018-2021年间摩尔礁（Moore Reef）西北段（含礁通道）周边的流场、温度场分布及珊瑚应激响应情况。数据集涵盖19台温度记录仪、12台海流计、69次温盐深（Conductivity, Temperature and Depth, CTD）剖面测量，以及对33个标记珊瑚群落的荧光法测量数据。此外还包含2020年11-12月共5周内拍摄的标记珊瑚与CoralWatch比色卡的实拍照片。

为期三年的“珊瑚礁庇护所”研究项目（Reef Havens Research Project）于2017年12月启动，旨在应对2016、2017年大堡礁（Great Barrier Reef, GBR）接连发生的史无前例的珊瑚白化事件。该项目的立项依据来自上述白化事件中的轶事观察：局部环境条件是影响白化严重程度及白化后恢复情况的关键因素——靠近上升流、经历低温海流或风力混合的礁体，白化严重程度更低；而受其他胁迫较少的礁体恢复情况更佳。项目旨在探究：模仿这些自然减胁迫现象的科学本地化干预措施（例如逐步增强水体流动、将水温降低1-2℃，或扰动水体表面），是否能够在关键礁区减轻珊瑚应激、降低白化严重程度并/或促进恢复，从而为自然驯化与适应过程争取时间与空间？

“珊瑚礁庇护所”研究项目是对原位（in situ）研究平台的基础性投入，该平台旨在以旅游景点的极小尺度，精准观测流场与温度变化对珊瑚应激、白化及恢复结果的影响。在明确与白化事件相关的小尺度水体流动规律后，项目还测试了工程干预手段能否在摩尔礁——大堡礁靠近凯恩斯的核心旅游景点之一——的极小区域内，在静稳珊瑚白化条件下恢复“正常”的水体流动与混合状态。本研究产生的数据，期望能为其他研究者进一步理解环境条件与珊瑚应激之间的关联，以及小尺度干预措施改善白化结果的潜力提供支撑。

### 研究方法
为量化摩尔礁通道及邻近旅游区域的流场、温度场分布及其影响，研究团队部署了一系列仪器。所用仪器包括：Marotte HS海流计（Marotte HS current meter）、HOBO TidbiT MX Temp 400温度记录仪（HOBO TidbiT MX Temp 400 logger）、Walz DIVING-PAM-II水下荧光计（Walz DIVING-PAM-II underwater fluorometer），以及SonTek Castaway温盐深仪（SonTek Castaway conductivity, temperature and depth recorder, CTD）。

#### Marotte HS海流计
该仪器为拖曳倾斜式海流计，由詹姆斯·库克大学（James Cook University, JCU）海洋地球物理实验室研发制造。仪器由搭载电子记录仪的浮力外壳组成，固定于静止点位。无水流时，浮力使仪器垂直向上漂浮；水流产生的拖曳力会使仪器倾斜，直至浮力、拖曳力与系绳拉力达到平衡，倾斜角度与水流速度成正比。记录仪通过加速度计记录倾斜角度，通过磁强计记录倾斜方向。后续处理阶段，研究团队通过预设的倾斜-流速校准曲线，将倾斜量与倾斜方向转换为海流流速与流向。该仪器还搭载了一款热敏电阻式温度传感器（重复性±0.2℃），固定于记录仪底部（JCU与Marine-Geophysics-Laboratory, 2017）。

研究团队在礁通道与旅游浮筒区域的选定点位、底质类型与水深下，将12台海流计固定于距离底质0.5米的尖桩上（详见Marotte部署照片），分别于2018-2021年间开展5次部署（部署细节见可下载文档）。记录仪设置为每秒记录一次流速与流向（单位：m/s与角度），并每分钟记录一次水温（摄氏度）。数据存储于微型SD卡中，仪器由2节AA电池供电。原始数据通过Marotte HS配置程序（JCU与Marine-Geophysics-Laboratory, 2017）转换为1分钟间隔的流速、流向与水温数据。每份仪器每次部署对应一个CSV文件，同时附带一份元数据文本文件，包含校准与处理信息。所有12台海流计均于2018年9月13日回收并下载数据。

#### HOBO TidbiT MX Temp 400温度记录仪
19台该型号记录仪被部署于摩尔礁北段的不同水深点位（详见摩尔礁HOBO分布图），于2018-2021年间开展4次部署（部署细节见可下载文档）。部分记录仪固定于距离底质约50厘米的尖桩上，其余则固定于系泊缆绳上。记录仪以5分钟间隔记录水温（摄氏度），该配置下标称电池续航时长为340天。数据通过HOBO手机应用下载，以CSV文件格式提供。

#### 珊瑚应激测量与荧光法数据
为探究与水体流动相关的珊瑚应激变化，研究团队从现有监测点位的11个物种中选取33个珊瑚群落，使用带标识的牛耳标进行标记（详情见可下载文档）。对每个群落，研究团队均拍摄水下照片，照片中包含CoralWatch比色卡，且有手指指向与珊瑚群落颜色匹配的比色卡色块。采样于2019年11月至2020年12月的5周内每周开展一次，旨在对比早夏季（水体充分混合条件下）与晚夏季（水体分层、潜在白化条件下）的珊瑚应激水平。2019年，研究团队使用Walz DIVING-PAM-II水下荧光计完成了这些群落的基线早夏季应激测量，但由于新冠疫情限制措施关停了大堡礁旅游业，即便当时已有白化现象报告，研究团队仍无法在2020年3月晚夏季时段访问标记珊瑚。因此，研究团队于2021年4月补测了晚夏季的荧光数据，尽管当时水体并未分层。数据通过Walz荧光计软件下载。

#### SonTek Castaway温盐深仪
该仪器可在摩尔礁研究点位及周边获取近乎瞬时的温度与盐度垂直剖面。研究团队使用改装的钓鱼竿与200磅断裂强度的Dyneema编织钓鱼线，从Reef Magic Marine World浮筒后方或通过小型接驳艇投放该仪器。仪器下沉至海底后快速回收，在下沉与上浮过程中均完成测量。每次投放前与投放后，CTD均记录GPS位置。现场可通过Castaway集成的彩色LCD屏幕，实时查看电导率、温度、盐度与声速随深度变化的曲线。本次研究共完成69次剖面投放，每次投放采集约100个数据点。原始数据通过蓝牙传输至Windows电脑，用于详细分析或导出。

### 数据局限性
1. Marotte与HOBO记录仪数据集的首尾24小时数据需谨慎使用，因为可能包含仪器往返部署点位的运输时段数据。
2. 编号为12的海流计于2018年6月21日停止记录。
3. Castaway CTD基于事件触发部署，可对比正常充分混合条件与静稳晴朗、水体混合失效的静稳条件下的流场模式。
4. 2019-2020年采样期间使用了两台不同校准历史的仪器，因此电导率测量数据需谨慎处理，但温度数据被认为可靠。

### 数据格式
本数据集包含多个组成部分：Marotte海流计数据、HOBO温度记录仪数据、CTD剖面数据及荧光法/CoralWatch数据。
1. Marotte海流计数据集：包含12台仪器在5次部署中的单独CSV文件（部署细节见可下载文档）。
2. HOBO温度记录仪数据集：包含19台记录仪在4次部署中的单独CSV文件（部署细节见可下载文档）。
3. CTD数据集：包含3个日期部署的CSV文件。需注意，本次部署刻意选择特定日期以测量分层极端条件及其与常态的偏差，而非旨在严格记录随时间变化的环境条件。
4. CoralWatch数据：包含每个珊瑚群落的两张照片，第一张为带标识牛耳标的特写，第二张为匹配珊瑚群落颜色的CoralWatch比色卡。数据集包含5个按采样日期命名的文件夹，同时附带一份包含PAM数据的CSV文件。

### 数据字典
1. Marotte海流计数据：本数据集包含2018年5月至2020年8月间，在摩尔礁通道（详见摩尔礁Marotte分布图）开展的5次部署中12台Marotte HS海流计的汇总数据文件。每份Marotte数据表格包含以下处理后数据：时间戳（1分钟间隔）、流速（m/s）、流向（角度）、上限流速（m/s）、下限流速（m/s）、倾斜量（弧度）、流向（弧度）、电池电压（Volts）与水温（摄氏度）。
2. HOBO温度记录仪数据：本数据集包含2020年6月至2020年8月间4次部署中，记录仪记录的水温（摄氏度）与时间戳（5分钟间隔）数据。
3. CoralWatch珊瑚群落数据：包含5个文件夹，每个文件夹内为标记珊瑚群落的JPEG照片。
4. PAM数据：
- 类型（Type）= F（荧光计）或SPEC（分光光度计）
- 编号（No.）= 该荧光计的测量序号（用于其内部记录）
- 1:Mark = 珊瑚群落标签，对应已上传的“PAM样线物种列表”
- 1:F = 光适应最小荧光值
- 1:Fm1 = 最大荧光值
- 1:PAR = 光合有效辐射
- 1:Y (II) = 光系统II的有效量子产率
- 1:ETR = 电子传递速率

### 数据存储位置
本数据集存储于eAtlas永久数据仓库中，路径为：datacustodian2020-2029-otherReef-Havens