AndreaBozzo/ceres-open-data-index huggingface dataset:
Fast Repetition Rate Fluorometry (FRRF) data collected on the RV L'Astrolabe from 18/02/2005 to 23/02/2005 (Hobart - Dumont d'Urville)

These data were collected on the RV L'Astrolabe (platform code: FHZI) from 18/02/2005 to 23/02/2005 on a trip from Hobart to Dumont D'Urville.
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
ROV exploration of deep-water coral habitats of southwest Australian submarine canyons – water column chemistry data, 2020

Cruise FK200126 was the first ROV exploration of the Bremer canyon systems, Mount Gabi seamount, and nearby continental margins located in the all-important yet poorly studied Southern Ocean offshore SW Australia, and revisited the Perth Canyon in the SE Indian Ocean which represents only the second ROV exploration of that area. The cruise focused on the collection of deep-water corals for post-cruise geochemical studies to reconstruct long-term environmental changes in this region, together with comprehensive characterisation of their present-day environments including physical and chemical oceanography, canyon geomorphology and geology, bathymetric mapping, faunal descriptions, and the first high resolution video imaging of these previously unexplored deep-water habitats.
The NetCDF file contains CTD data and seawater carbonate parameters measured from seawater samples collected on board the SOI Falkor between 2020-01-26T09:18:56 and 2020-02-20T21:32:29, by 12-L Niskin bottles. Temperature and Salinity were measured using a SBE-911plus CTD, Dissolved Oxygen using a SBE-43 DO sensor and Fluorescence by a Wet Labs ECO-FLNTU; Total Alkalinity was measured using a Mettler-Toledo T50 with Rondolino autosampler; DIC was measured using an Apollo SciTech Dissolved Inorganic Carbon analyser; pH, aragonite and calcite saturation states were calculated using version 1.1 of CO2SYS for MATLAB’.

Tags: Aragonite Saturation State, Calcite Saturation State, Sea Water Neutral Density, sea water pH
Organization: Australian Ocean Data Network
Derwent Estuary Recreational Water Quality monitoring program - Taroona

Taroona monitoring site is collected as part of the Derwent Beach Watch program. Derwent Beach Watch is a collaborative program between councils and state government that tests water quality at 18 swimming sites around the estuary during summer months. 
Water samples are collected each Tuesday from the start of December to the end of March and analysed for the faecal indicator bacteria Enterococci (Enteralert method) at the Public health Lab. Because the samples must be cultured, it takes several days to publish the results.

Tags: Derwent Estuary, HydroLab Vertical Profiler, Oceans | Salinity/density | Salinity, Oceans | Water Quality | Contaminants, Oceans | Water Quality | Ph, Oceans | Water Quality | Turbidity, Oceans | Water Quality | Water Temperature, Water Quality Monitoring, sea_water_salinity, sea_water_temperature
Organization: Australian Ocean Data Network
Resilience to periodic disturbances and the long-term genetic stability in Acropora coral

Terracotta settlement tiles were deployed at 18 sites at six of seven reef slope locations monitored through permanent transect sites on the Scott Reef systems. During nine years between 1996 - 2013 settlement tiles were deployed and collected after one month either side of the coral spawning. At each of the sites, groups of six settlement tiles (10 cm x 10 cm) were spaced at 60 m along the permanent transect site, at distances of 30 - 100 cm apart (n-108 tiles total). Density of colony sizes and growth and survival of colonies were recorded. Tissue samples were collected from 982 colonies of a corymbose Acropora (Acropora sp.) at five timepoints (2004, 2009, 2014, 2015, and 2021 for microsatellite genotyping and whole genomes sequencing.

Organization: Australian Ocean Data Network
Biodiversity of marine fauna on the Central West Coast, Western Australia

The WA Museum with funding from Strategic Research Fund for the Marine Environment (SRFME) focused on documenting the fauna of the Central West Coast, Western Australia, specifically  the diversity of fishes, molluscs, crustaceans, echinoderms, scleractinian corals and sponges.   The specific locations were Jurien Bay and Green Head localities with a focus on the Jurien Bay Marine Park, and Cervantes to the South and Dongara to the North.

Tags: Biosphere | Zoology | Corals, Biosphere | Zoology | Crustaceans, Biosphere | Zoology | Echinoderms, Biosphere | Zoology | Fish, Biosphere | Zoology | Mollusks, Biosphere | Zoology | Sponges
Organization: Australian Ocean Data Network
Algal Blooms in the Pearl River Estuary.

The concentration of chlorophyll was analysed from satellite images collected by using the Medium Resolution Imaging Spectrometer (MERIS) sensor on the Envisat satellite, over the period 2004-2006 to understand the spatial and temporal aspects of algal blooms that occurred in the enclosed and semi-enclosed bays of the South China Sea in the Pearl River Estuary region. The ocean colour data obtained by processing the MERIS images in BEAM and the EnviView program was used to derive chlorophyll (Chl.) concentration to elucidate seasonal factors affecting the spatial and temporal distribution and abundance of algal blooms.

Tags: Oceans | Ocean Optics | Ocean Color
Organization: Australian Ocean Data Network
Herbert River Lucinda Jetty Turbidity Data Transect Tuesday 10th 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 suspended sediment concentration (TSS) and turbidity profiles.

Tags: Oceans | Ocean Optics | Turbidity, depth, mass_concentration_of_suspended_matter_in_sea_water, secchi disc depth, secchi_depth_of_sea_water, total suspended sediments, turbidity
Organization: Australian Ocean Data Network
WAMSI Node 3.2.1 - Diversity, abundance and habitat utilisation of sharks and rays - Acoustic data

Elasmobranchs were tagged with acoustic tags and subsequently monitored with acoustic receivers (Vemco VR2, VR2W and VR3) moored on the seabed that constitute the Ningaloo Reef Ecosystem Tracking Array (NRETA). This array is part of the nationwide network of marine acoustic monitoring, the Australian Acoustic Tagging and Monitoring System (AATAMS).
A total of 96 acoustic receivers are deployed at Ningaloo Reef between Coral Bay and Tantabiddi.
A total of 56 acoustic tags were deployed on six species of sharks and three species of rays in the Ningaloo Marine Park in February 2008.
Data is accessible through the IMOS AATAMS website listed below.

Tags: Biosphere | Ecological Dynamics | Range Changes, Blacktip Reef Sharks (Carcharhinus melanopterus), Cowtail Stingrays (Pastinachus atrus), Giant Shovelnose Rays (Glaucostegus typus), Grey Reef Sharks (Carcharhinus amblyrhynchos), Lemon Sharks (Negaprion acutidens), Nervous Sharks (Carcharhinus cautus), Porcupine Rays (Urogymnus asperrimus), Tiger Shark (Galeocerdo cuvier), Whitetip Reef Shark (Triaenodon obesus), sharks, rays, acoustic tagging,
Organization: Australian Ocean Data Network
Distribution and temporal trends in the abundance of nesting sea turtles in the Red Sea

Mobile species often aggregate at predictable places and times to ensure that individuals find mates and breed in suitable habitats. Sea turtles demonstrate this life history trait, which can make these species highly susceptible to population declines if nesting habitats are lost or degraded. Conservation management thus requires knowledge of where and when turtles nest and changes in abundance in these habitats through time. Here, we compiled new and published data and used a novel analysis to describe seasonality, annual abundance and spatial distribution of nesting green (Chelonia mydas) and hawksbill (Eretmochelys imbricata) turtles in data-deficient populations that inhabit the Red Sea. Major new rookeries were identified for green turtles at Jazirat1 Mashabah (113 and 179 nesting females in 2018 and 2019) and for hawksbill turtles at Jazirat Al Waqqadi (79 nesting females in 2018), both of which are located on nearshore islands of the Kingdom of Saudi Arabia in an area subject to industrial, residential and ecotourism developments. An upward trend in annual abundance of nesting sea turtles was estimated at some sites including Ras Al Baridi (Saudi Arabia), a major rookery of green turtles in the Red Sea, where the annual numbers increased from 14&ndash;110 individuals in 1982&ndash;1995 to 178 and 330 individuals in 2018 and 2019. This integrative work provides the most up-to-date, comprehensive information on nesting sea turtles in the Red Sea and documents a critical baseline for sea turtle conservation and future management effort.

Organization: Australian Ocean Data Network
Range expansion of the sea urchin Centrostephanus rodgersii leads to loss of taxonomic diversity in a kelp bed habitat, eastern Tasmania

The long spined sea urchin Centrostephanus rodgersii (Diadematidae) has recently undergone poleward range expansion to eastern Tasmania (southeast Australia). This species is associated with barrens habitat which has been grazed free of macroalgae, and therefore has potentially important consequences for reef structure and biodiversity. 
This study used urchin removal experiments from barrens patches in eastern Tasmania to monitor the subsequent response of the macroalgae relative to unmanipulated barrens patches.
In removal patches, there was a rapid proliferation of canopy-forming macroalgae (Ecklonia radiata and Phyllospora comosa), and within 24 months the algae community structure had converged with that of nearby areas without urchins.
Faunal species richness was comparatively low in barrens habitat, with C. rodgersii grazing activity resulting in an estimated minimum net loss of approximately 150 taxa compared with intact macroalgal habitats.

Tags: 25 211001, 54 080001, 54 102001, Canopy coverage, Centrostephanus rodgersii, Ecklonia radiata, Phyllospora comosa, Species coverage, Substrate coverage, Temperate Reef
Organization: Australian Ocean Data Network
Rapid Ecological Assessment (REA) of fringing reefs in the Whitsunday Management Area, Great Barrier Reef

A rapid assessment technique was chosen to survey fringing reefs at 40 locations within the Whitsunday Management Area between August 1994 and May 1995. At each location, surveys were conducted over two depth ranges; 0-3 m below the reef crest and 4-8 m below the reef crest. Data were recorded while swimming down current from haphazardly chosen starting points using SCUBA. Each survey took between 30-60 minutes and covered distances between 100-600m. The start and end points of each survey were recorded with a portable GPS. At the end of each swim, percentage cover categories were assigned to a set of ecological and substrate attributes. Each reef was also classified in terms of reef development.A inventory of benthic taxa was compiled during each survey. Taxa were identified in situ. Hard corals were identified to species where possible, otherwise genus and lifeform. Soft corals and conspicuous macroalage were identified to genus. Other taxa (including sponges, zoanthids, ascidians, bryozoans) were identified to a higher taxonomic level, usually to phylum and growth form. At the end of each survey, the inventory was reviewed and each taxon was categorized in terms of its relative abundance in the community.
 This research was undertaken to collect ecological information on the fringing reefs within the Whitsunday Management Area to enable an assessment to be made of the conservation values of the coral reefs within the area.
 The reefs surveyed were Armit Island, Border Island (2 locations), Champagne Bay, Deloraine Island (2 locations), Dent Island, Double Cone Island (2 locations), Dumbell Island, Eshelby Island (2 locations), Esk Island, Gloucester Island (3 locations), Gumbrell Island, Henning Island, Hideway Bay, Hook Island (2 locations) Little Armit Island, Little Grassy Island, Lupton Island, Middle Island, Olden Island (2 locations), Pelican Island (2 locations), Rattray Island, Teague Island and Whitsunday Island (9 locations).

Organization: Australian Ocean Data Network
Individual haplotyping of whale sharks from seawater environmental DNA

Water samples were collected over two weeks directly behind individual whale sharks at Ningaloo Reef, Australia in May, 2019. A total of 56 seawater samples were collected, filtered immediately through sterile 0.22 &mu;m filters, and stored at -80&deg;C. Tissue biopsy samples were then taken from the same animal using a hand spear with a dart head, totalling 77 individual samples.
Individual whale sharks were identified by their unique spot and stipe patters through photographs analysed by I&sup3;S Classic Software. Re-sightings of the same individual  were removed from the dataset. Following photo-identification, a total of 48 unique individuals were confirmed, of which 42 consisted of both tissue and seawater samples. Additional samples were later discarded from the study, resulting in libraries for 28 seawater samples, and whale shark d-loop haplotypes.
DNA extractions of the tissue samples were carried out and PCR amplification of the mitochondrial control region and reaction protocol verified. Seawater samples were processed and environmental DNA was extracted. Statistical analysis was performed with R Studio.

Organization: Australian Ocean Data Network
Leeuwin Current observations on the Australian North West Shelf, May-June 1993

Observations of the Leeuwin Current, the poleward flow of warm, low salinity water off the west coast of Australia, are described from acoustic Doppler current profiler (ADCP), temperature and salinity (CTD) and moored current meter measurements from the Australian North West Shelf made in May and June 1993. Two cross-shelf and slope transects of ADCP and CTD measurements were completed at latitudes of approximately 17 and 19S.

Tags: Marine Features (Australia) | Leeuwin Current, Oceans | Ocean Circulation | Ocean Currents
Organization: Australian Ocean Data Network
Handline surveys of deep water fish on the outer Great Barrier Reef

Three surveys were conducted off the Great Barrier Reef (GBR) in 1992. The first and third surveys (16-21 April and 26-31 December) were in the vicinity of Myrmidon Reef in the central section of the GBR. The second survey (19-29 June) was conducted at No.9 and No.10 Ribbon Reefs in the northern section of the GBR.Hawaiian-style deep-water handlines were used to survey fish at depths ranging from 40 to 340 m. Fishing operations were conducted during the day over the outer slope of the continental shelf. The vessel drifted over bottom features such as ledges, pinnacles, and drop-offs, which were located using a depth sounder. The rate of drift was controlled by using the engines to keep the bow of the vessel at a quartering angle into the dominant wind, sea, or current. At capture, fish were photographed next to a 30-cm rule, measured for standard length (SL) in cm and weighed. Otoliths were removed for age and growth studies and tissues were removed for genetic studies. One specimen of each species was frozen and deposited in the Western Australian Museum (WAM) for identification and cataloguing. Catch per unit effort was also calculated (number of fish/handline hour and kg/handline hour).
 Surveys were undertaken to assess the potential for establishing a deep reef slope fishery off the Great Barrier Reef.
 Eighteen new fish records for the Great Barrier Reef, including seven new records for Australia, were reported from the line fishing surveys. The following 18 species represent new records for the Great Barrier Reef region, with the seven for Australia noted with an asterisk ().Serranidae:Epinephelus magniscuttis Postel et al. Epinephelus morrhua (Valenciennes) Epinephelus octofasciatus Griffin Epinephelus radiatus (Day) Saloptia powelli Smith Branchiostegidae: Branchiostegus wardi Whitley Lutjanidae:Etelis carbunculus CuvierEtelis coruscans ValenciennesEtelis radiosus AndersonParacaesio kusakarii Abe Paracaesio stonei Raj and Seeto Pristipomoides argyrogrammicus (Valenciennes) Pristipomoides auricilla (Jordon et al.) Pristipomoides filamentosus (Valenciennes)Pristipomoides flavipinnis Shinohara Pristipomoides multidens (Day)Pristipomoides zonatus (Valenciennes) Lethrinidae:Wattsia mossambica (Smith)Additional species captured during the surveys:Aphareus rutilansAprion virescensCarangoides chrysophrysEpinephelus cyanopodusEpinephelus maculatusEpinephelus tukulaGymnocranius euanusGymnocranius granoculusLethrinus miniatusLutjanus boharPlectropomus leopardusSeriola dumerili

Organization: Australian Ocean Data Network
Redmap (Victoria) - Sightings of Bony Fish 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
Deeper water fish and benthic surveys in the Lord Howe Island Marine Park (Commonwealth Waters)

In February/March 2004, surveys of benthic habitats and fish faunas were undertaken in deeper waters of the Commonwealth waters surrounding Lord Howe and Balls Pyramid rises. With limited time available to undertake the work, local knowledge from resident fishermen was employed to target areas of bathymetric and piscatorial interest across both rises.A towed underwater video camera, with a still camera attached was used to obtain video and still images of habitats and epibenthos. Baited remote underwater video stations (BRUVS (TM)) were used as a non-extractive method to sample the fish and shark fauna.Plans to use a remotely operated vehicle (ROV) for further surveys were abandoned due to adverse weather conditions.
 This preliminary, rapid ecological assessment aimed to describe habitats and fish-habitat associations in deeper waters, below the depth limits of SCUBA observations, where little information was previously available.
 The Lord Howe Island and Balls Pyramid rises, 770 km ENE of Sydney, are the most southerly of a chain of volcanic seamounts and are remarkable for supporting the highest latitude coral reefs in the world. The World Heritage listing, encompassing Lord Howe Island, the Admiralty group and Balls Pyramid, overlaps sections of the NSW State Marine Park to 3nm offshore and the Commonwealth Marine Park to 12nm offshore. The Commonwealth Marine Park has two sanctuary zones, one to the east of the island and the other across the rise south of Balls Pyramid. The primary objective of the Parks is to protect the conservation values of the seamount system associated with marine biodiversity, seafloor habitats and ecological processes.

Organization: Australian Ocean Data Network
Influence of life history variation and habitat on mercury bioaccumulation in a high-order predatory fish in tropical Australia

A study of mercury distribution and bioaccumulation in aquatic ecosystems was conducted in the Mary River System, Northern Territory. Barramundi (Lates calcarifer) was gathered over four years (2013&ndash;2017, across both wet and dry seasons).
A total of 310 barramundi tissue samples were collected over the three river environs over four years
Billabongs n = 114;

Barrage/Upper Estuary n = 106;

Estuary Mouth n = 90

Methods of sample analysis included:
direct combustion&amp;ndash;atomic absorption spectrometry to determine total mercury

stable isotope mass spectrometry to determine carbon and nitrogen isotopes in tissues samples (source of nutrition and trophic position of barramundi in the food web)

laser ablation&amp;ndash;ICPMS to determine strontium isotopes in otoliths (informing freshwater and saltwater habitat residence)

For full sampling procedures and results, see Butler et al (2022)

Organization: Australian Ocean Data Network
Biodiversity and degradation of estuaries in North-Western Tasmania: Black River

Water quality and biological data was collected from four tide-dominated river estuaries indicative of catchments with varying levels of human impacts to: 1) assess draft indicator levels for water quality, and 2) investigate biological indicators of estuarine health in NW Tasmania. The data represented by this record was collected in the Black River.

Tags: Abundance - macroinvertebrates, Ammonia, Benthic macroinvertebrates, Degradation, Dissolved oxygen, Human impact, Nitrate, Nitrates and Nitrites, Number of individuals caught - fish, Number of species - macroinvertebrates, Reactive phosphorus, Salinity, Sediment organic carbon, Sediment particle size, Temperate Reef, Turbidity
Organization: Australian Ocean Data Network