AndreaBozzo/ceres-open-data-index huggingface dataset:
Scleractinian coral response to microbial biofilms, Great Barrier Reef

Glass microscope slides placed in square polyvinyl chloride frames (112 per grid), exposing the top surface to the seawater, were deployed at Davies Reef, on the Great Barrier Reef at two depths - 4 m (shallow) and 10 m (deep) - within each of 2 sites. To allow biofilm development, slides were maintained at site 1 for 2, 4, and 8 weeks, and at site 2 for 8 weeks prior to the November 2000 mass coral spawning. Slides were used in larval metamorphosis assays, with a minimum of 20 replicate biofilm slides randomly selected for each treatment. To determine biofilm community composition, an additional 30 slides were randomly selected for DNA extraction, 30 slides for fluorescence in situ hybridization (FISH), and 10 slides for scanning electron microscopy (SEM).Coral larvae used in the metamorphosis assays were raised from gametes collected from live colonies of the reef-building coral Acropora microphthalma, from a depth of 6 to 8 m on a fringing reef of Pelorus Island, Great Barrier Reef. Slides were sorted according to whether or not they induced larval metamorphosis, and replicate slides were processed for SEM, FISH, and denaturing gradient gel electrophoresis (DGGE). Sequences of oligonucleotide probes used for FISH. DGGE: the 16S rRNA genes were amplified by PCR with bacterial and eukaryotic primers.Estimates were made of the relative densities of specific probe-targeted bacteria and archaea (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Actinobacteria, Firmicutes, Cytophaga-Flavobacterium, Bacteroidetes, Planctomycetales, Archaea). The importance of three factors (depth, time, and CCA presence) in inducing larval metamorphosis was investigated in an unbalanced repeated-measures analysis of variance (type IV SS; SPSS version 11).Quantitative estimates of biofilm community composition were made using group-specific FISH probes. All densities are expressed as a percentage of total bacterial numbers obtained using dual hybridization reactions with the bacterium-specific probe EUB338. A principal-component analysis (PCA) was used to summarize biofilm community composition using FISH data in which depth of biofilm formation and exposure time of slides were the variables. Cluster analysis was used to identify replicates that generated similar DGGE profiles.
 To examine the community structure of developing coral reef biofilms and their ability to induce the metamorphosis of coral larvae.To examine the role microorganisms not associated with calcareous coralline algae in coral metamorphosis.

Organization: Australian Ocean Data Network
Structure of fish communities on outer slopes of inshore, mid-shelf and outer shelf reefs of the central Great Barrier Reef

The structure of fish communities on the outer slopes of one inshore reef (Pandora), one mid-shelf reef (Rib) and one outer shelf reef (Myrmidon) in the central region of the Great Barrier Reef was examined using small, standardised plastic explosive charges.Ten collections (5 at a depth of 5m and 5 at 9m), were made on each reef in areas of the outer reef slope with the greatest abundance and diversity of fish and coral. Charges were laid on the bottom and after detonation fish were affected over a area of approximately 150 m².Immediately after detonation of the explosive, dead and stunned fish were collected by divers and from a boat using hand nets. Fish were later identified to species, weighed and assigned to trophic categories and feeding guilds within these categories.
 Earlier visual censuses of reef fish across the continental shelf, based on a limited number of species, identified a strong gradient in species composition. In this study, the differences in fish communities among reefs, including biomass measurements and trophic structure were examined for a more comprehensive list of species, by collecting fish using small explosive charges, which is an effective and non-selective collection method.
 A total of 323 species belonging to 45 families and comprising 28,537 individuals were collected.

Organization: Australian Ocean Data Network
Response of turtle hatchlings to light emitting diodes at sea

We used passive acoustic telemetry to examine the effects of five different intensities of Light Emitting Diodes (4000K floodlight) on the movement patterns and predation rates of flatback turtle (Natator depressus) hatchlings as they disperse through nearshore waters. A total of 68 hatchlings were released, 36 of which were released when the light sources were present on a boat located to the east of the hatchling release point and 32 were released when the light sources were present on a boat located to the west of the release location. Five or six hatchlings were released in each treatment (Ambient, 10 watt, 30 watt, 50 watt, 70 watt, 120 watt). Attraction of hatchlings to lights increased with light intensity only when lights were located in the direction that hatchlings preferred to disperse under ambient conditions (west). This suggests that the location of the light source in relation to the preferred direction of travel may be important in determining the impact on hatchlings. When the light source was not in the direction of travel, only 25% of hatchlings were attracted to it. Predation of hatchlings was higher when LEDs were illuminated than under ambient light conditions. We found no clear relationship with predation rates or time spent in the nearshore with light intensity, although a combination of high variability in environmental conditions across nights, low sample sizes, and the relatively low intensity of our light treatments might have affected our ability to detect an effect. The hatchling predation rates we recorded and the finding that hatchlings spent 20% longer in predator-rich nearshore areas for all light intensities on one of the nights suggest that the presence of LEDs, regardless of their intensity, is likely to have a negative impact on the survivorship of hatchlings passing through the nearshore.

Organization: Australian Ocean Data Network
Canopy leaf area index and litterfall in stands of the mangrove Rhizophora apiculata in Ca Mau Province, Vietnam (ACIAR Project FIS/94/12)

Sampling was carried out in monocultures of Rhizophora apiculata aged 6, 9, 10, 12, 21 and 36 years in three mixed shrimp farming-mangrove forestry enterprises (Tam Giang 3, SFFE 184 and Kien Vang) in Ca Mau Province, the southern-most province of the Mekong Delta in Vietnam.Three litter traps of 1 m² in cross-sectional area were hung beneath the canopy in each stand. The litter traps were emptied at monthly intervals for 1 year, and the samples sorted into leaves, stipules, flower parts, propagules and a combination of woody material and debris. After counting the number of leaves, stipules and propagules in each sample, all fractions were oven dried to constant weight at 80°C for determination of dry weight (g dry weight/m² ground area/year).Canopy leaf area indices (LAI) were measured in six plots of each age, including those in which litter samples were collected. Measurements were made using a light attenuation method, in which leaf area index is estimated from the ratio of the light flux density beneath the canopy to that above the canopy, assuming that light attenuation within the canopy follows the Beer-Lambert Law. Between 100 and 200 measurements were made of the light flux density beneath the canopy on a clear sunny day between 1100 and 1400 hours, using a handheld quantum sensor. Measurements of the light flux density before and after the readings taken beneath the canopy were made in an open area well outside the canopy. All light readings were corrected for solar angle. This correction was calculated from the length of the shadow cast by a stick of known height thrust vertically into a flat area of ground outside the canopy.
 This research was undertaken to:-quantify the rate of litter fall in mangrove forests of different ages in Ca Mau Peninsula: mangrove derived detritus is a major source of carbon for estuarine food webs-investigate the dynamics of leaf production and leaf loss in relation to the leaf area index of mangrove stands of different ages: these relationships underpin the primary productivity, growth and yield of mangrove forests -investigate reproductive phenology and quantify seed (propagule) production in stands of different ages: this allows prediction of the seed supply for further plantings
 This research was part of a larger study, which aimed to develop better strategies for integrating aquaculture and mangrove forestry in the lower Mekong Delta, Vietnam.

Organization: Australian Ocean Data Network
WAMSI Node 4.2.2b - Establishment of metropolitan fish indicator regions

Vital baseline information on the demersal fish assemblages within the metropolitan area was collected used baited-video stations. The sampling was directed using the knowledge of experienced fishermen, and researchers from the Department of Fisheries and UWA. Recent changes to legislation, banning commercial wetline fishing in the Metropolitan area, have provided an important natural laboratory with which to assess the impacts of fishing on the assemblage of demersal fish.
From 5th October 2008 to 12th October 2008 stereo-baited remote underwater video (stereo BRUV) systems were used to sample these areas shown in green in the thumbnail (around Two Rocks).  It provides a multi-species measure of the state of the fish community, including length measurements of the fish observed. This data will form an important baseline with which to assess any changes in the community and to investigate whether they are due to changes in fishing pressure or other impacts, such as climate change.

Tags: Oceans | Marine Biology | Fish, Oceans | Marine Biology | Marine Habitat, bait_sampled, depth, file_name, frame_number, sampling_code, tape_reader, taxonomic_family_name, taxonomic_genus_name, taxonomic_group_count, taxonomic_name
Organization: Australian Ocean Data Network
A preliminary assessment of fish and coral communities on reefs in Ningaloo Marine Park, Western Australia

Ningaloo Marine Park extends southward from North West Cape along 230 km of coastline. In most places, the seaward margin of the reef is generally less than 3 km from the shoreline, with a sandy lagoon between the reef edge and the shoreline.During this first AIMS survey of fish and coral communities within the Ningaloo Reef system, 26 sites were visited. Systematic surveys of coral and fish community structure were carried out at five locations along the length of the Ningaloo Reef (separated by 10s of km). Within each region, surveys were made at two sites on both the outer reef slope and within the shallow lagoon. In response to a request from the Western Australian Department of Conservation and Land Management (CALM), surveys were also carried out at six sites within the Ningaloo Dugong Sanctuary.
 There was scant biological information available regarding coral and fish populations within the Ningaloo Marine Park. Veron (1993) recorded 214 species of corals in Ningaloo Reef. Hutchins (1994) recorded 482 fish species, making it the most diverse mainland reef habitat along the Australian coast. The first quantitative assessments of coral and fish populations were carried out in the late 1980s (Ayling and Ayling, 1987).Prior to the AIMS surveys, no baseline ecological data had been collected on benthic and fish communities within the Ningaloo Dugong sanctuary zone.
 Fish were surveyed using actual counts on 20 minute timed transects (three transects per site). Video surveys were carried out on 20 metre transects (5 transects per site). The starting point for fish and video transects were the same, but observers moved in different directions from that point.Lists were made of fish and coral species observed at each site and specimens of coral and algae were taken for taxonomic reference collections.

Organization: Australian Ocean Data Network
Evaluation of Value-Added Grains Protein Products for Atlantic Salmon and Black Tiger Prawns

This project coordinates and manages the implementation of research that addresses the development of the potential of key Western Australian produced commodities, such as lupin meals and isolates, for inclusion the in aquaculture feeds. This specific project addresses the extension of work from an accessory and larger grains project to other key species, notably Atlantic salmon and prawns. This work involves substantial liaison with the grain production and processing industries, the aquaculture feed production industries and additional research contractors to deliver the outcomes. Present activities include the assessment of value-added protein meals from lupins in both animal species using both growth and digestibility studies.
This project involves:
* Improving our understanding of the limitations to use of lupin meals in the diets of Atlantic salmon and black tiger prawns, through the assessment of new value-added grain products intended for the aquaculture feeds sector.
* Facilitation of the transfer of processing and nutritional technology to the commercial sector by close liaison with the feed manufacturing industries for Atlantic salmon and prawns.
* Coordinating national research on grain application in aquaculture feeds.

The coordination of this project is managed in WA through UWA's Centre for Legumes in Mediterranean Agriculture (CLIMA), but the Atlantic salmon work is done in Tasmania by the University of Tasmania's School and Aquaculture and the prawn work is done by CSIRO Marine and Atmospheric Research in Queensland.
Time : ends June 2006

Organization: Australian Ocean Data Network
Grainsize of surface samples collected from the leeward, off-reef physiographic zone of Wistari Reef

Wistari Reef is a lagoonal platform reef, situated on the Tropic of Capricorn, within the Capricorn and Bunker region of the southern Great Barrier Reef. Six surface samples were taken from the leeward, off-reef area and analysed to determine grainsize and the sorting coefficient (expressed as the standard deviation of grainsize) within each sample. The sediments of the leeward off-reef floor are relatively mature. Most samples are moderately well-sorted medium sand, and are moderately well-rounded. Patch reefs, and small individual colonial and solitary corals contribute a small amount of coarser material to the sediment.

Tags: Oceans | Coastal Processes | Coral Reefs, Oceans | Marine Sediments | Sediment Grain Size, grainsize_size_category, latitude, longitude
Organization: Australian Ocean Data Network
IMOS - Ocean Gliders - Seaglider deployment in New South Wales off Crowdy Head (August 2010 - December 2010)

The dataset contains temperature, salinity and biological parameters like for example dissolved oxygen and turbidity data measured by a Seaglider in the region of Crowdy Head (New South Wales).
The Ocean Gliders Facility (formerly known as the Australian National Facility for Ocean Gliders (ANFOG)), located at the University of Western Australia manages Seagliders to monitor the boundary currents surroundings Australia.
The variables available in this dataset are:
Temperature, salinity, conductivity, density, pressure, chromophoric dissolved oxygen matter, dissolved oxygen, fluorescence and backscatter coefficient at 660nm.

Tags: CTD (Conductivity-Temperature-Depth Profilers), Coloured Dissolved Organic Matter (CDOM), Countries | Australia, Fluorometers, Glider, IMOS Node | Bluewater and Climate, Oceans | Ocean Chemistry | Chlorophyll, Oceans | Ocean Chemistry | Oxygen, Oceans | Ocean Chemistry | Suspended Solids, Oceans | Ocean Circulation | Ocean Currents, Oceans | Ocean Optics | Fluorescence, Oceans | Ocean Optics | Turbidity, Oceans | Ocean Temperature | Water Temperature, Oceans | Salinity/density | Conductivity, Seaglider, States, Territories (Australia) | New South Wales, concentration_of_coloured_dissolved_organic_matter, fluorescence_in_sea_water, mass_concentration_of_oxygen_in_sea_water, sea_water_electrical_conductivity, sea_water_pressure, sea_water_salinity, sea_water_temperature, volumetric_backscatter_coefficient
Organization: Australian Ocean Data Network
Fast Repetition Rate Fluorometry (FRRF) data collected on the RV L'Astrolabe from 22/01/2008 to 27/01/2008 (Dumont d'Urville - Hobart)

These data were collected on the RV L'Astrolabe (platform code: FHZI) from 22/01/2008 to 27/01/2008 on a trip from Dumont D'Urville to Hobart.
Maximum photochemical efficiency of photosystem II (PSII), also called maximum quantum yield of PSII (Fv/Fm), has become one of the most widely utilized fluorescence parameters in phytoplankton research. It represents the potential photochemical efficiency, which is the probability that the light energy captured by the photosynthetic apparatus is being utilized as photochemistry. Fv/Fm has been shown to have an instant response to variations in physical and chemical properties and is interpreted as a diagnostic of the overall health or competence of phytoplankton. Together with the absorption cross section area of PSII and chlorophyll concentration, it can be used to measure primary production (Cheah et al. 2011, Deep Sea Research).
Seawater from 3 m depth was supplied continuously from the ship’s clean seawater line. FRR fluorescence yields were measured continuously at 1 minute intervals in dark-adapted state (! 15 minutes dark-adaptation) using a flash sequence consisting of a series of 100 subsaturation flashlets (1.1 μs flash duration and 2.8 μs interflash period) and a series of 20 relaxation flashlets (1.1 μs flash duration and 51.6 μs interflash period).

Tags: Continents | Antarctica, Countries | Australia, Fast Repetition Rate Fluorometer (FRRF), Global/Oceans | Southern Ocean, Instrument's photomultiplier electronic sensitivity (1-256), Latitude, Longitude, Maximum quantum yield (Fv/Fm), Minimum fluorescence in the light chamber of the FRRF (also used as a proxy for biomass), Oceans | Ocean Temperature | Sea Surface Temperature, Oceans | Salinity/density | Salinity, Photosynthesis, connectivity between PSII reaction centres under actinic light, functional absorption cross section of PSII (measure of the proportion of light harvested for photoc, maximum fluorescence in the light chamber of the FRRF, maximum quantum yield of photosystem II ( (FmL - FoL) / FmL), primary production, time constant of electron transport from PSII to PSI, variable fluorescence (FmL - FoL)
Organization: Australian Ocean Data Network
RAN CTD Profile Data - HMAS PALUMA ProjectID: HI580PAL_M From: 2015-09-05 To: 2015-10-15

This dataset contains quality controlled vertical profiles of pressure, temperature and salinity measured by a Conductivity, Temperature and Depth (CTD) probe. The dataset contains 45 CTD profiles (casts) obtained during RAN Hydrographic Survey cruise HI580PAL_M from HMAS PALUMA.
The CTD was manufactured by Applied Microsystems Limited and is the "Micro CTD" model. This CTD type is referred to operationally as the MVP200_CTD. This CTD is fitted with a 4 electrode platinized conductivity cell, thermistor temperature sensor and a semiconductor strain gauge pressure sensor.
The CTD sensors are calibrated at the manufacturer Applied Microsystems Limited on a 12-18 month schedule. The CTD temperature sensor is calibrated against 'Hart' temperature standards. The pressure sensor is calibrated using 'Budenburg Deadweight' standards. The conductivity sensor is calibrated using 'Hart' temperature standards and seawater samples of known conductivity.
The CTD sensors are mounted to a fish-shape probe. The probe is controlled by an electric winch (MVP200 type). For downcasts the fish is allowed to free-fall (winch is in 'free-wheel' mode) under its own weight at about 2-3 ms-1 and then is winched back. Data is recorded in downcast and usually in upcast direction at a sampling rate of 25 Hz. The downcast data is of higher quality because sensors encounter undisturbed seawater that flows through the nose of the fish. On the upcast the fish is flipped around (tail first) and the sensors in the nose encounter disturbed flow from the fish tail.
This type of CTD is prone to a phenomenon called 'salinity spiking' caused by a mismatch between the response times of the temperature and conductivity sensor. Data undergoes a salinity de-spiking routine to correct for this. See the history metadata for further details on the salinity de-spiking process.
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. 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
Gulf St Vincent marine ecology: seagrass cover survey

Data on seagrass cover along the Adelaide coast, Gulf St Vincent, South Australia from 2006-2007.

Tags: Biosphere | Aquatic Habitat | Benthic Habitat, Cameras | Video Cameras - underwater, Global/Oceans | Southern Ocean/ Australia extension, Marine Features (Australia) | Gulf St. Vincent, SA, Oceans | Marine Biology | Marine Plants, coverage
Organization: Australian Ocean Data Network
Redmap (South Australia) - Sightings of Mammal 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
IMOS Argo - Aggregation (yearly composite) of Argo profiles for the Atlantic, North Pacific, South Pacific and Indian ocean from 1998 to now

This dataset contains aggregated Argo profiles collected around the world since 1998.
Yearly composites for 4 different oceans have been created:
 - Atlantic Ocean,
 - North Pacific Ocean,
 - South Pacific Ocean,
 - Indian Ocean.

Tags: Global / Oceans | Atlantic Ocean, Global / Oceans | Indian Ocean, Global / Oceans | Pacific Ocean, Oceans | Ocean Pressure | Water Pressure, Oceans | Ocean Temperature | Water Temperature, Oceans | Salinity/density | Salinity, sea_water_pressure, sea_water_salinity, sea_water_temperature
Organization: Australian Ocean Data Network