AndreaBozzo/ceres-open-data-index huggingface dataset:
Recovery of an isolated coral reef system following severe disturbance, Scott Reef and Seringapatam, Timor Sea

Benthic CoverPercentage cover of hard corals, soft corals and other benthic groups on the reef slope at Scott Reef and Seringapatam. During most years from 1994 to 2010, percentage cover was quantified along permanent transects (250 m) at each of 21 sites across seven regions of Scott Reef and Seringapatam.Size-structure and fecunditySize structure and reproductive output of Acropora assemblages on the reef slope at Scott Reef and Seringapatam. The longest linear dimension of Acropora colonies was measured along permanent transects of 200 m² for colonies &gt;10 cm, and 50 m² for colonies Coral recruitmentRecruitment of Acropora corals on the reef slope at Scott Reef and Seringapatam. During most years from 1996 to 2010, terracotta settlement plates (n = 108) were deployed and collected across 18 permanent sites and six regions of Scott Reef and Seringapatam, one month either side of the mass coral spawning in Autumn each year.Coral survivalPost-bleaching survival of corals at Scott Reef and Seringapatam. Colonies (n = 5333) of branching (Acropora spicifera) and massive (Goniastrea retiformis/edwardsi) corals of all sizes were tagged and resurveyed in May each year, at eight sites across four regions of Scott Reef and Seringapatam.
 Coral reef recovery from major disturbance is hypothesised to depend on the arrival of propagules from nearby undisturbed reefs. Therefore, reefs isolated by distance or current patterns are thought to be highly vulnerable to catastrophic disturbance. Here, we show that on an isolated reef system in north Western Australia, coral cover increased from 9% to 44% within 12 years of a coral bleaching event, despite a 94% reduction in larval supply for six years after the bleaching. The initial increase in coral cover was the result of high rates of growth and survival of remnant colonies followed by a significant increase in juvenile recruitment as colonies matured. We show that isolated reefs can recover from major disturbance, and that the benefits of their isolation from chronic anthropogenic pressures can outweigh the costs of limited connectivity.

Organization: Australian Ocean Data Network
Coastal and estuarine resource condition assessment, a baseline survey in the southern NRM region, Tasmania: Moulting Lagoon / Great Swanport

A 12-month program was developed and implemented in order to obtain baseline information on water quality (salinity, water temperature, dissolved oxygen, turbidity, pH, dissolved nutrients, silica), ecological condition as shown by Chlorophyll a, benthic macroinvertebrates, pathogens, and habitat extent determined from habitat mapping. Five key estuaries and coastal waters were assessed in the Southern NRM Region of Tasmania. The data represented by this record was collected in Moulting Lagoon/Great Swanport.

Tags: Abundance - benthic macroinvertebrates, Ammonia, Benthic macroinvertebrates, Chlorophyll a, Degradation, Dissolved oxygen, Human impact, Monitoring program, Nitrate plus Nitrite, Reactive phosphorus, Salinity, Silica, Temperate Reef, Temperature, Turbidity, pH
Organization: Australian Ocean Data Network
MCD43A4: MODIS/Terra and Aqua Nadir BRDF-Adjusted Reflectance Daily L3 Global 500 m SIN Grid V006

The MODIS MCD43A4 Version 6 Nadir Bidirectional reflectance distribution function Adjusted Reflectance (NBAR) data set is a daily 16-day product. The Julian date in the granule ID of each specific file represents the 9th day of the 16 day retrieval period, and consequently the observations are weighted to estimate the Albedo for that day. The MCD43A4 algorithm, as is with all combined products, has the luxury of choosing the best representative pixel from a pool that includes all the acquisitions from both the Terra and Aqua sensors from the retrieval period.

Tags: 0406 - Physical Geography and Environmental Geoscience, Earth Sciences, coastal modelling, marine, model hydrodynamic, scallops
Organization: Australian Ocean Data Network
The hydrodynamic regime at John Brewer Reef, Great Barrier Reef: Mooring CM15: Current Meter

A S4 current meter was attached to mooring CM15, which was deployed in 10m of water. Deployment Details:Date Deployed: 5/5/1987Date Recovered: 7/9/1987Instrument Deployed:S4 #S630; Depth: 5m
 The aim of this project was to collect field data to calibrate a numerical model for the combined tidal and wind-forced circulation at John Brewer Reef, and to apply those circulation patterns to calculate the trajectories, residence times and likelihood of outbreaks of crown-of-thorns starfish on areas of the reef.

Organization: Australian Ocean Data Network
RAN CTD Profile Data - HMAS LEEUWIN ProjectID: HI454LEE_H From: 2008-06-16 To: 2008-07-02

This dataset contains quality controlled vertical profiles of pressure, temperature and salinity measured by a Conductivity, Temperature and Depth (CTD) probe. The dataset contains 7 CTD profiles (casts) obtained during RAN Hydrographic Survey cruise HI454LEE_H from HMAS LEEUWIN. 
The CTD was manufactured by Falmouth Scientific and is the "2-inch Micro CTD" model. This CTD type is referred to operationally as the HS_CTD. This CTD is fitted within an inductive type conductivity cell, a platinum thermometer and silicon pressure sensor.
The CTD temperature sensor is calibrated on the ITS-90 temperature scale against a master CTD using a controlled temperature bath. The pressure sensor is calibrated using a Druck Pressure Calibrator. The conductivity sensor is calibrated in a temperature controlled bath against seawater samples of known conductivity.
The HS_CTD is lowered and raised by a hand winch sampling at a rate of 1.83 Hz. Data files were recorded in the downcast and upcast direction but most data is from downcasts due to higher quality. Raw CTD pressure data is not always monotonic due to transient up/down motion of winch/ship. Raw pressure data is subsetted to give a monotonic (increasing) sequence and then linearly interpolated to 1 decibar pressure intervals and converted to netCDF format files. Data is then flagged with quality control flags after visual inspection and comparison to average climatology and historical CTD casts.

Tags: Oceans | Ocean Temperature | Water Temperature, Oceans | Salinity/density | Salinity, sea_water_practical_salinity, sea_water_temperature
Organization: Australian Ocean Data Network
IMOS - Deep Water Moorings - Deep Water Arrays (DA) Sub-facility, Indonesian Throughflow array, Timor North (ITFTIN) Mooring Platform

The Timor North deep water mooring was first deployed on 2011-06-14 at (8.86 S, 127.20 E) in the Indonesian Throughflow, , and was decommissioned in April 2014.
Instrumentation includes 150 kHz and 75kHz ADCPs, Seabird SBE39s, discrete current meters and Pressure Inverted Echo Sounders (PIES).
The mooring provides profile velocity data above 500m and point source velocity between 500m and 1200m (depth of controlling sill). Temperature and salinity data are collected for the entire water column.
The aim of IMOS Indonsian Throughflow moorings (Indoflow) is to sustainably and directly measure the leakage of Pacific thermocline and intermediate waters from the western equatorial Pacific into the South Indian Ocean. The Indonesian Passages represent an important 'choke point' of the global ocean overturning circulation and the climate system. The interannual to decadal variability of the size and depth distribution of the flow through this choke point remains a troublesome unknown. In particular, changes in this flow will reflect long term changes in the Pacific and Indian Ocean wind fields, particularly any change in the Walker Circulation, as predicted by coupled climate models forced by increasing Greenhouse Gas scenarios. Changes in the associated heat flux are also anticipated at the global oceans warm. The Indoflow array design is based on the more comprehensive INSTANT process study and is deemed the minimal required mooring array to monitor the Indonesian Throughflow. The Ombai Strait and Timor Passage Throughflow components comprise about 11Sv of the 14 Sv total interbasin exchange. The Indoflow array integrates with the AIMS NAOS shelf line, allowing estimates of the interbasin exchange to include the transport of very warm waters across the Australian North West Shelf. All moorings in the Timor Passage are located along a high precision swath line of the TOPEX/Jason satellite altimeter missions. These data will shed light on how best to exploit altimetric data over our shallow northern shelves, especially in data assimilating models.

Tags: Buoys | Moored Buoys, CTD (Conductivity-Temperature-Depth Profilers), Current Meters/Profilers | Acoustic Doppler Current Profiler (ADCP), IMOS Facility | Deep Water Moorings, IMOS Platform | ITFTIN | Timor North Mooring, Marine Features (Australia) | Indonesian Throughflow, Oceans | Ocean Circulation | Ocean Currents, Oceans | Ocean Temperature | Water Temperature, Oceans | Salinity/density | Conductivity, Oceans | Salinity/density | Salinity
Organization: Australian Ocean Data Network
Burned Area Monthly L3 Global 500m

MCD45A1 is a monthly Level-3 gridded 500-meter product, which contains burning and quality information on a per-pixel basis. Produced from both the Terra and Aqua MODIS-derived daily surface reflectance inputs, the algorithm analyzes the daily surface reflectance dynamics to locate rapid changes, uses that information to detect the approximate date of burning, and maps only the spatial extent of recent fires. It provides varied quality assessment information and a single summary quality assessment score for each pixel.

Tags: 0406 - Physical Geography and Environmental Geoscience, Earth Sciences, coastal modelling, marine, model hydrodynamic, scallops
Organization: Australian Ocean Data Network
Redmap (Queensland) - Sightings of Invertebrate Species

Redmap is a primarily a website that invites the community to spot, log and map marine species that are uncommon in their region, or along particular parts of their coast. The information collected is mapped and displayed on the site, demonstrating, in time, how species distributions may be changing.
Sightings are divided into two categories – those with a photo that can be ‘verified’ by a marine biologist, and sightings without photos that we call community sightings (anecdotal). All the information collected, with and without photos, is mapped and will be used in the following years to map out a ‘story’ of changes occurring in our marine environment.
The main data collected includes the species sighted (normally selected from a list comprising preselected species of interest), the location, date/time and activity being undertaken.  Other optional information gathered include biological data such as sex, size and weight and environmental data such as water depth and temperature and habitat.
This record is associated with live data (and will subsequently change over time) and spatial elements have reduced accuracy.  It is also subject to a three year embargo (ie. does not contain data less than three years old).  If you wish to discuss obtaining a citable, static dataset, that is current and/or contains accurate spatial elements, please see Point of Contact.

Tags: Hand Sampling, body_length, body_weight, climate change, range shift, species distribution, fishing, latitude, longitude
Organization: Australian Ocean Data Network
Visually mediated neighbour recognition in the fiddler crab Uca capricornis

Mating signals are often directed at numerous senses, and provide information about species identity, gender, receptiveness, individual identity and mate quality. Given the diversity of colourful body patterns in invertebrates, surprisingly few studies have examined the role of these visual signals in mate recognition. This experiment demonstrates that distinct carapace colour patterns in the fiddler crab, Uca capricornis, enable males to discriminate between their female neighbours and unfamiliar females.
The experiment was conducted in the East Point Reserve, Darwin, NT from September to January 2003 and 2004. 
The methodology involved identifying male and female U.capricornis neighbours living 10-30cm apart. The female was caught and randomly assigned to one of seven treatments, including replacement with a similar sized female, and various manipulations to alter her appearance. The female was then tethered close to the males burrow and the interaction monitored. The males behaviour was classified as either 'approach' or 'ignore.' The results show that males tended to approach unfamiliar females tethered nearby, whereas they were more likely to ignore their unaltered neighbours tethered in the same position.

Tags: 28 960036, Behavioural Ecology, Biosphere | Zoology | Crustaceans, Colour Pattern, Fiddler Crab, Mate Recognition, Neighbour Recognition, Ocypodidae, Uca capricornis, experimental_treatment, male_response
Organization: Australian Ocean Data Network
Spatial and structural patterns of benthic communities on reefs of the central Great Barrier Reef

Surveys of benthic communities were carried out at Davies Reef, a mid-shelf reef, and Myrmidon Reef, an outer-shelf reef in the central region of the Great Barrier Reef. On each reef, 6 comparable sites were surveyed along contiguous 10 m line transects that followed a depth contour. Sites were located at the reef crest, 5 m, 10 m, 15 m and 20 m depths on the windward slope and one reef flat site running parallel to and about 50 m leeward of the reef edge. The depths were measured using the reef crest lip as datum.At Davies Reef, 12 replicate transects were established per site, except for the reef flat, which had 18 transects (78 transects). At Myrmidon Reef, 10 replicate transects were surveyed per site (60 transects). On each transect the reef substrata were categorized using 19 morphological descriptors, some of which were taxonomically based. A plastic fibre tape marked in centimetres was laid along the depth contour and the intercepts of each substrate category were recorded as a series to the nearest centimetre. Instances of one benthic type visibly influencing its near neighbours on the transect (dead patches visible along the boundaries of one or both the neighbours) were recorded.These data were used for both spatial and structural analyses of the benthos along each transect. The same list of categories was used for each analysis, except that non-living categories such as sand/rubble and water were not included in the structural analyses. Spatial analyses involved calculation of the percent cover of each category averaged over the replicate transects. Coral/coral interactions and interactions between corals and other biota were analysed for Davies Reef only. The lengths of the gaps between hard corals, hard corals and soft corals and hard corals and sponges were measured. Structural analyses were based on the mean number of occurrences of each category per transect and the total length of each category per transect.
 This research was undertaken to:1. collect quantitative data on percentage cover and one dimensional spatial patterns of benthic organisms and non-living substrata at varying depths on the reef slope, which would also allow determination of:- the distribution of non-living substrata on the reef slope- the distribution of space between particular groups of organisms- the distribution of observable interactions between benthic organisms2. investigate the use of physiognomic-structural data, such as morphological descriptions of the coral reef benthos, to characterize some well known reef communities, as a prelude to a world scale analysis of reef community structure

Organization: Australian Ocean Data Network
Historical August Sea-Surface Temperature Estimates Utilising a Diatom Transfer Function with Core MD88-787

The purpose of this study was to estimate past sea-surface temperature in the Southeast Indian Ocean. The accumulation of diatom microplankton assemblages in sediments being the proxy for these records of climatic change. 
A transfer function is a mathematical method that allows quantitative estimations of environmental parameters from past biogenic sedimentation. In this study, a diatom transfer function was established to relate biological species to selected environmental parameter of the ocean (sea-surface temp). These equations were then employed on observed fossil species from core samples to provide quantitative estimates of sea-surface temperature.
Estimates of sea-surface temperature (SST) are given here based on the assemblages of diatoms found in core MD88-787. The information provided gives the extrapolated age-scale through the core, and an estimate of August SST based on a diatom transfer function - DTF 109/24/6.

Tags: Biosphere | Microbiota | Diatoms, Oceans | Ocean Temperature | Sea Surface Temperature, Transfer function, core_depth, diatom_transfer_function_communality, diatom_transfer_function_sea_surface_temperature, extrapolated_age_scale, latitude, longitude, taxonomic_group_count, taxonomic_name
Organization: Australian Ocean Data Network
Herbert River Lucinda Jetty CTD Data Transect 17th February 2004

The objective of the research reported in this thesis was to develop a technique to monitor the dynamics of sediments and nutrients entering the coastal ocean with river plumes associated with high intensity low frequency events (e.g. floods), using ocean colour remote sensing. The data collected included  conductivity-temperature-depth (CTD) profiles as well as Nephelometer and secchi disk measurements.

Tags: Oceans | Salinity/density | Conductivity, depth, salinity, sea_water_salinity, sea_water_temperature, secchi disc depth, secchi_depth_of_sea_water, turbidity
Organization: Australian Ocean Data Network
Antifouling coatings can reduce algal growth in coral aquaculture

The data were collected to test the antifouling efficacy and fouling community composition of recently-developed antifouling coatings on coral plugs. The same plugs were tested for A. tenuis coral larval settlement, to investigate, whether these coatings were a deterrent for coral settlement. The ultimate goal of the research was to investigate whether the coatings reduced algal growth without inhibiting larval settlement adjacent to the coatings. The data were collected from November to December, 2019 at AIMS, by the use of a camera trolley (Nikon D810 with a Nikon AF-S 60 mm f/2.8 G Micro ED Lens outfitted with four Ikelite DS160 strobes). The data (images) were analysed with the Trainable Weka Segmentation (TWS) plugin in the ImageJ software.
This data collection includes:
Images of coral settlement plugs with coral recruits and algal fouling

Model used by the Trainable Weka Segmentation (TWS) plugin for Fiji processing program in ImageJ (version 1.53c) &amp;ndash; this was used to segment images into different classes by the use of machine-learning based image classification models


Organization: Australian Ocean Data Network
IMOS - Satellite Remote Sensing - Ocean colour Sub-Facility

The Aqua satellite platform carries a MODIS sensor that observes sunlight reflected from within the ocean surface layer at multiple wavelengths.  These multi-spectral measurements are used to infer the concentration of chlorophyll-a (Chl-a), most typically due to phytoplankton, present in the water.  
The data are produced from the near real time (nrt) data stream formed by combining data from all the available direct broadcast reception stations in Australia (Alice Springs, Melbourne, Townsville, Perth, Hobart). The data are presented as a sequence of granules, each with a maximum size corresponding to 5 minutes of data, and beginning on UTC-5 minute boundary (eg. 04:05, 04:10, 04:15). The granules have been remapped from satellite projection into a geographic (Latitude/Longitude axes) projection and are formatted as CF-compliant netCDF files. It should be noted that the data are not processed until the definitive spacecraft ephemeris becomes available, usually 12-24 hours after the overpass. This means that the geolocation should be of a uniformly high standard.
There are multiple retrieval algorithms for estimating Chl-a. These data use the OC3 method recommended by the NASA Ocean Biology Processing Group and implemented in the SeaDAS processing software l2gen.  The radiometric sensitivity of the MODIS sensor is evolving continuously during its mission and is being monitored regularly.  The SeaDAS software uses tables of calibration coefficients that are updated periodically.  From time to time upgrades to the algorithms and thand/or the format of the calibration tables are required, in which case a new version of SeaDAS is released. These data are initially being produced using SeaDAS 6.1, then SeaDAS 6.4 and eventually with SeaDAS 7.x.  The data processed with each different version can be distinguished by the digits at the end of the root URL for the data; for example l2oc.nrt.61 is level-2 ocean colour (l2oc), using the near real time (nrt) data stream, produced using SeaDAS 6.1.

Tags: IMOS Sub-Facility | SRS-MODIS | Aqua OC3 Chlorophyll-a Ocean Colour, Oceans | Ocean Chemistry | Chlorophyll, Oceans | Ocean Optics | Ocean Color, latitude, longitude, mass_concentration_of_chlorophyll_a_in_sea_water, time
Organization: Australian Ocean Data Network
Marine and estuarine studies of the Dickson Inlet area, Port Douglas, north Queensland

This research was undertaken to describe the marine and estuarine environment of Dickson Inlet, Port Douglas and consisted of the following projects: 1. Studies of the hydrology of Dickson Inlet, including the use of a water exchange model to predict the effect of the removal of mangroves on sedimentation rates in the Inlet.2. Studies of the soil and water chemistry and mangrove forest structure and productivity in Dickson Inlet, with a brief survey of forest types in the nearby Mowbray River.3. Studies of the fish and zooplankton communities inhabiting the waterways of the Inlet. These, like the hydrodynamics studies, were again carried out in both the wet and dry seasons as the hydrological conditions leading to greater stresses are likely to primarily affect these faunal communities.4. A summary of the likely key ecological relationships in the mangrove/waterway complex of Dickson Inlet, and their sensitivity to past, present and projected disturbances.The initial brief was expanded in August 1989 to include:5. A report on the status and significance of the near-shore Alexandra Reef system.
 The study was instigated because of proposed developments for the Dickson Inlet area, including expansions to the Mirage Resort at Port Douglas. Research was concentrated primarily on the role of mangroves in the Dickson Inlet area, because these were the forest and faunal communities, which would be directly affected by most proposed developments.

Organization: Australian Ocean Data Network
Spencer Gulf Abalone biological sampling

Measures of abalone biology - length, weight, growth rate in the Spencer Gulf, South Australia.

Tags: Biosphere | Zoology | Mollusks, Field surveys, Global/Oceans | Southern Ocean/ Australia extension, Greenlip abalone, Haliotis laevigata, Marine Features (Australia) | Spencer Gulf, SA, Marine Features (Australia) | Tiparra Reef, SA, Oceans | Marine Biology | Marine Invertebrates, SCUBA (observations and/or sampling), Visual Counts/Observations, growth_rate, length, weight
Organization: Australian Ocean Data Network