AndreaBozzo/ceres-open-data-index huggingface dataset:
Fast Repetition Rate Fluorometry (FRRF) data collected on the RV L'Astrolabe from 10/02/2007 to 15/02/2007 (Dumont d'Urville - Hobart)

These data were collected on the RV L'Astrolabe (platform code: FHZI) from 10/02/2007 to 15/02/2007 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
Temperature - Salinity distributions / CTD data at sampling stations on a transect across the mouth of Jervis Bay

This dataset is a component of the 'Jervis Bay Baseline Studies' project conducted by the Department of Defence, CSIRO and the Australian Defence Force Academy. 
Approximately once per month between 1988-1991, temperature-salinity surveys were conducted on various transects within Jervis Bay and out across the continental shelf. This record describes CTD data from the transect running across the mouth of Jervis Bay, running from Point Perpendicular in the north, to Bowen Island in the south. Measurements were made using a Neil Brown 'Smart' CTD. On each day of sampling, ~5 stations were chosen on the transect, with the CTD recorder measuring salinity, temperature and sigma-T through the water column.
For each day of sampling two resources are provided: 1) An excel document providing details of sampling locations and the raw CTD data collected, and 2) A map showing the location of each sampling station. For a number of sampling days a third resource is offered, providing vertically averaged CTD data over 4m depth bins.
This is one of nine child records that relate to the parent, 13391430-2ae8-11dd-a735-00188b4c0af8. A pdf outlining the structure and hierarchy of all metadata records relating to this project is available to download through this record. Also available is a pdf of a published working paper documenting this experiment and the results.

Tags: Oceans | Ocean Circulation | Wind-driven Circulation, Oceans | Ocean Temperature | Water Temperature, Oceans | Salinity/density | Conductivity, Oceans | Salinity/density | Salinity, bearing, date, depth, distance, latitude, longitude, sea_water_density, sea_water_salinity, sea_water_temperature, station_name, time
Organization: Australian Ocean Data Network
Changes in algal, coral and fish assemblages along water quality gradients on the inshore Great Barrier Reef

This research was conducted to understand the relationship between water quality and ecological attributes on coral reef communities, through field surveys on naturally turbid inshore coral reefs that vary in exposure to water bourne sediment, nutrient and chlorophyll concentrations. Reefs in two regions were surveyed for biodiversity of algae, hard corals, octocorals and fish. Region PC: Princess Charlotte Bay (in the Claremont Isles, north of PC Bay) and and Region WT: Wet Tropics (between Tully and Port Douglas). SOme reefs were surveyed for the all four groups of taxa, while others were surveyed for some groups of the biodiversity. 
Four groups of taxa were surveyed using rapid ecological assessments based on standardized scuba-swims by experts:
1 -macroalgae, mostly identified to genus level
2- hard corals , idenified to species level
3- octocorals, identified to genus level
4 -fish, identified to species or species groups
Abundances of the three benthic groups were rated on a 6-point scale as 0 = &lsquo;absent&rsquo;, 1 = &lsquo;rare&rsquo;, 2 = &lsquo;uncommon&rsquo;, 3 = &lsquo;common&rsquo;, 4 = &lsquo;abundant&rsquo;, and 5 = &lsquo;dominant&rsquo;.
Abundances of some of the fish species were estimated on a log (base 5) scale (Williams, 1982), whereas less abundant fish species were fully enumerated.
Water Quality data was collected between December 2000 and April 2002. Surface water samples were taken at each reef for analysis of 12 water quality variables: particulate nitrogen and phosphorus (PN, PP), nitrate, nitrite, ammonium, total dissolved nitrogen and phosphorus (TDN, TDP), silicate (Sil), chlorophyll (Chl), phaeopigments (Phae), salinity (Sal) and suspended solids (SS).
Analysies included: Redundancy analyses, Permutation tests, Log-linear regression models and Model averaging of models based on the Bayesian Information Criterion was used.

Organization: Australian Ocean Data Network
NESP TWQ Project 3.3.3 - Defining the values of the ecological systems that influence the GBR and lie outside the marine park and world heritage area boundaries, 2017-2018 (JCU)

The Great Barrier Reef World Heritage Area (GBRWHA), globally recognised for its outstanding universal value, is an integrated and highly connected part of a larger northeast Australia marine bioregion, which includes Torres Strait, the Coral Sea and the Great Sandy Marine Park (Hervey Bay). Understanding the values (ecological, cultural, social and economic) of these adjacent systems, and especially the connections and interdependencies between systems, is crucial to effective and efficient protection and management of the globally important natural and cultural values within each system. This project will identify and assess the values of these adjacent systems, and characterise the processes and attributes that influence the values and their connectivity at a regional scale, delivering a resource that can inform cross-jurisdictional planning and management.

Tags: National Environmental Science Programme Tropical Water Quality (NESP TWQ) hub, marine
Organization: Australian Ocean Data Network
WAMSI Node 4.2.1b - Development and validation of an estuarine health index for the Swan Estuary

This project (WAMSI Node 4.2.1b) aimed to develop an index for assessing the health of the Swan Estuary, based on fish assemblage characteristics. 
The index incorporates a suite of metrics, each of which measures a different aspect of the fish community, e.g. species diversity and composition, use of the Estuary as a nursery habitat, and the trophic structure (the feeding relationships between species) of the estuarine fish community.The study incorporated and utilized historical data from 1977-2004, plus current sampling (2007-2009), to establish reference conditions for multiple fish community metrics, against which the recent, current and future status of the estuary is assessed.
Data is available as two Excel spreadsheets:
Establishing_reference_and_scoring_seine_Metrics.xls
Establishing_reference_and_scoring_gill_Metrics.xls
The gill net and seine net files contain, respectively, for each offshore and nearshore historical fish sample collected between 1976 and 2009:
(i) the raw values calculated for each of the selected fish metrics comprising the offshore and nearshore health indices;
(ii) the corresponding metric scores (i.e. scored in comparison to the appropriate reference conditions I derived for each metric); and
(iii) the final health index scores for each historical sample.
The historical studies used in the project are all detailed in the final report.

Tags: Biosphere | Aquatic Habitat | Estuarine Habitat, Biosphere | Ecological Dynamics | Community Structure, Marine Features (Australia) | Swan Estuary, WA, Oceans | Marine Biology | Fish, historical_sampling_location, sampling_description, sampling_location, sampling_method, season
Organization: Australian Ocean Data Network
Video surveys of long spined sea urchin (Centrostephanus rodgersii) barrens habitat, Forestier Peninsula, eastern Tasmania

The spatial extent of C. rodgersii "barrens" was estimated by surveying rocky reef habitat with a towed underwater video system. Sampling took place at 13 regions along the east coast of Tasmania, each comprising 3 subsites, this dataset refers to the Forestier Peninsula region, and its 3 subsites: Sisters,  Visscher Island and High Yellow Bluff.

Tags: 25 211001, Algal coverage, Centrostephanus rodgersii, Substratum type, Temperate Reef, Urchin barren coverage
Organization: Australian Ocean Data Network
WAMSI Node 4.2.3 - Fisheries dependent data and climate - Continuous temperature loggers at puerulus collector sites (Western Rock Lobster)

From 1990, continuous (15-minute, 30-minute or hourly) logging of water temperature was conducted at these puerulus (Panulirus cygnus) collector sites: Quobba Pt, Shark Bay South Passage, Port Gregory 
Rat Island, Dongara - 7 Mile Beach, Green Head (offshore), Jurien, Lancelin, Alkimos, Marmion Lagoon,  Warnbro Sound, Cape Mentelle.  Detailed locations are available for download.  
Annual Excel spreadsheets are created containing the hourly data for all the sites, with monthly statistics at the end of the file.

Tags: CAAB Taxon Code 28 820005, Western Rock lobster, Panulirus cygnus
Organization: Australian Ocean Data Network
Determination of water column characteristics in coastal environments using remote sensing

10 separate studies of both the author's own research projects and collaborative projects, in which the author has been the major contributor were used to illustrate the advantages and pitfalls of using spatial data gathered from a remote sensor to simply measure the characteristics of the surface, the column and the features at the bottom of a water body in coastal marine, estuarine and riverine environments.  
This work involved study areas mainly from Perth but also Broome and Geographe Bay ranging from 1986 to 1996.

Tags: Radiance Or Imagery | Visible Wavelengths | Visible Imagery, Remote sensing, Water column
Organization: Australian Ocean Data Network
Human fatality in Timor Leste after eating the xanthid crab, Zosimus aeneus

Sodium channel and saxiphilin radioreceptor assays were carried out to determine whether paralytic shellfish toxins were present in the gut contents, liver, blood, bile and urine of a male who died in 2000 after consuming a crab, Zosimus aeneus. A second uneaten specimen from the meal was also tested. HPLC analysis of toxin profiles was also carried out on the gut content and urine of the victim, and the uneaten crab specimen.A dose likely to have been consumed by the victim was calculated (between 1 and 2 µg STX equivalents/kg).
 To use sodium channel and saxiphilin receptor assays, and confirm the results by HPLC analysis, to identify paralytic shellfish toxins in gut contents, various body fluids and tissues obtained post-mortem from the victim.
 Proportions of individual paralytic shellfish toxin profiles (mol% of STX, dcSTX, GTX2, GTX3, NEO) to total toxin content of the samples are given where discernable by HPLC analysis.

Organization: Australian Ocean Data Network
Coastal Lake Assessment and Management Tool (CLAM): Burrill Lake, Shoalhaven City Council

The Coastal Lake Assessment and Management (CLAM) tool allows stakeholders to assess the social, economic and environmental trade-offs associated with development, remediation and use options for coastal lakes and estuaries. Researchers at the Australian National University (ANU) developed CLAM in 2004 when contracted by the NSW State Government to provide sustainability assessments of 8 coastal lakes. Several projects have since been established directly with local government and NRM groups.
To date, 27 CLAMs have been developed in New South Wales, where they generally fit within estuary management or catchment management plans. To develop these CLAMs and build local capacity to maintain them, ANU-Enterprise Pty Ltd - the commercial company of ANU developed an Accreditation Scheme whereby local consultants are trained in the CLAM approach.

Tags: Agriculture | Agricultural Aquatic Sciences | Aquaculture, Agriculture | Agricultural Aquatic Sciences | Fisheries, Agriculture | Agricultural Plant Science | Reclamation/revegetation/restoration, Agriculture | Forest Science | Forest Fire Science, Agriculture | Forest Science | Reforestation, Biosphere | Aquatic Habitat | Coastal Habitat, Biosphere | Aquatic Habitat | Estuarine Habitat, Biosphere | Aquatic Habitat | Lakes, Biosphere | Aquatic Habitat | Rivers/stream Habitat, Biosphere | Aquatic Habitat | Saline Lakes, Biosphere | Terrestrial Ecosystems | Agricultural Lands, Biosphere | Terrestrial Ecosystems | Wetlands, Biosphere | Wetlands | Estuarine Wetlands, Biosphere | Wetlands | Riparian Wetlands, Burrill Lake, Human Dimensions | Economic Resources | Agricultural Economics, Human Dimensions | Environmental Impacts | Eutrophication, Human Dimensions | Environmental Impacts | Reclamation/revegetation/restoration, Human Dimensions | Environmental Impacts | Sewage, Human Dimensions | Environmental Impacts | Urbanization, Human Dimensions | Environmental Impacts | Water Management, Human Dimensions | Land Use/land Cover | Land Management, Hydrosphere | Surface Water | Lakes, Hydrosphere | Surface Water | Rivers/streams, Hydrosphere | Water Quality | Nutrients, Land Surface | Erosion/sedimentation | Suspended Solids, Land Surface | Landscape | Landscape Management, Oceans | Coastal Processes | Estuaries, Oceans | Coastal Processes | Lagoons, Oceans | Coastal Processes | Mangroves, Oceans | Coastal Processes | Sea Level Rise, Oceans | Coastal Processes | Shorelines
Organization: Australian Ocean Data Network
NT Sea Bird Colonies Species

Quantitative ground and aerial surveys of shorebirds, and significant breeding colonies  for the Top End of the Northern Territory (NT), sourced from the Parks and Wildlife Service of the Northern Territory (PWSNT).  At time of collating this report, some gaps were apparent in the data provided. Data exist  from 1990-1999, but records from 2000-2003 are missing.

Organization: Australian Ocean Data Network
Depletion Based Population Estimates for Western Rock Lobster

Depletion methods examine the decline in catch rate as catch is removed from a closed population. These methods provide a way to estimate original population size before fishing and the residual biomass after fishing and hence exploitation rate. This approach allows long-term changes in catchability and hence fishing efficiency to be assessed in the estimate of exploitation rate. The technique is applied to the western rock lobster fishery in Western Australia for the non-migrating part of the season, March to June. The trends in catchability, residual biomass and exploitation for three zones of the fishery since the 1984/85 season are examined.
Time: completion June 2004

Organization: Australian Ocean Data Network
Environmental pollution around the South China Sea: developing a regional response to a regional problem: WORKING PAPER

This record describes, and links to a working paper produced through the Resource Management in Asia-Pacific (RMAP) Program based at The Australian National University in Canberra.

This study focuses on the South China Sea because it is an integral ecosystem and a vital international shipping lane. It is also an arena for competing security interests. Countries bordering the South China Sea have been more concerned with maximizing economic growth and ensuring adequate energy supplies than in preserving their common natural resources. They have staked territorial claims to areas with potential oil and natural gas reserves; however, these claims are overlapping and conflicting. While a territorial settlement is unlikely in the short term, other avenues of regional cooperation have emerged, in particular, the Association of Southeast Asian Nations (ASEAN) effort to curb smoke haze.

Tags: Human Dimensions | Economic Resources, Human Dimensions | Environmental Impacts | Biomass Burning, Human Dimensions | Environmental Impacts | Fossil Fuel Burning
Organization: Australian Ocean Data Network
Changes in coral-associated microbial communities during a bleaching event in 2002, Great Barrier Reef

34 colonies of Acropora millepora were tagged on the reef flat of Nelly Bay, Magnetic Island in October 2000, and monitored for coral condition (visual signs of colour loss due to bleaching) and subsampled for molecular microbial analysis and zooxanthellae counts.Surface water temperatures on the Nelly Bay reef flat were obtained from October 2000 through to March 2003 using a temperature logger located approximately 50-100m from tagged colonies, which recorded half-hourly sea water temperatures. Daily mean temperatures were calculated for the duration of the monitoring period. In addition, the daily average sea water temperatures were calculated and averaged for the 10-year period 1990 to 2000 for the Nelly Bay site, using data from the Great Barrier Reef Marine Park Authority water-temperature monitoring program (supplied by R Berkelmans, Australian Institute of Marine Science).The spatial extent of bleaching (white coloration) was estimated as a percentage of colony surface area on each sampling occasion. Categories were based on visual estimates of bleaching: normally pigmented, lightly bleached (50% white) and dead (&gt;90% dead).15 colonies were randomly selected for quantification of bleaching parameters: zooxanthellae density (cells cm-2); percentage of zooxanthellae degenerate in appearance; and µg of total protein.Clone libraries were constructed from each time period [?monthly or daily] and hybridized with digoxigenin (DIG)-labelled Vibrio-specific oligonucleotide probes. Percentages of Vibrio-affiliated clones were calculated.
 To better understand the effect of increased temperatures and subsequent bleaching on coral-associated microbial communities.
 Affiliation of DGGE bacterial sequences retrieved from coral colonies to closest relative (and accession number):Delftia acidovorans strain LMG 1226 (EU024145); Achromobacter sp PW-1 (DQ869036); Achromobacter sp PW-1 (DQ869036); Vibrio alginolyticus strain YJ06167B (EF542800); Acidovorax sp B-206 (EF596912); Marine bacterium ATAM173a_51 (AF359538); Marinobacter sp P11-B-10 (EU016152); Spongiobacter nickelotolerans (AB205011).Affiliation of cloned bacterial sequences closest relative and database accession number:OTU1 Uncultured Spongiobacter sp clone ME82 (DQ917877); OTU2 S. nickelotolerans (AB205011); OTU3 Brevundimonas mediterranea (AJ244706); OTU4 Vibrio costicola (ATCC 35508T) (X74699); OTU5 Stenotrophomonas maltophilia (AB255384); OTU6 Uncultured a-proteobacterium clone FB-1_C11 (EF220223.1); OTU7 Brevundimonas vesicularis (AJ007801); OTU8 Methylarcula sp BIO-204 (AJ534208); OTU9 Vibrio chagasii (AJ490157); OTU10 Uncultured Spongiobacter sp clone EF0305 (EF657844); OTU11 Serratia marcescens (AB117954) 654 99 3 g-Proteobacteria; OTU12 Spongiobacter nickelotolerans (AB205011); OTU13 Bacterium Ellin5130 (AY234547); OTU14 Aranicola sp EP18 (AM398227).

Organization: Australian Ocean Data Network
Turtle Track Monitoring by the West Pilbara Community Turtle Program (WPCTP)

The WPCTP is a local community group that monitors turtle nesting activity and identifies threats/disturbances to nesting turtles and hatchlings on Bells Beach near Wickham.  The program is part of a coordinated and concerted effort in the conservation and recovery of marine turtles and their habitats along the Pilbara coast.  The WPCTP is supported by the Department of Environment and Conservation (DEC) and the Ningaloo Turtle Program (including Cape Conservation Group and WWF Australia) and is funded by Rio Tinto Iron Ore (RTIO)

Tags: Community Monitoring, Conservation, Marine Features (Australia) | Pilbara Coast, WA, Nesting, Turtle
Organization: Australian Ocean Data Network
Fish and Invertebrate Assemblages in Seagrass, Mangrove, Saltmarsh, and Nonvegetated Habitats

Many studies compare utilization of different marine habitats by fish and decapod crustaceans; few compare multiple vegetated habitats, especially using the same sampling equipment. Fish and invertebrates in seagrass, mangrove, saltmarsh, and nonvegetated habitats were sampled during May–August (Austral winter) and December–January (Austral summer) in the Barker Inlet-Port River estuary, South Australia. Sampling was undertaken using pop nets in all habitats and seine nets in seagrass and nonvegetated areas. A total of 7,895 fish and invertebrates spanning 3 classes, 9 orders, and at least 23 families were collected. Only one fish species, Atherinosoma microstoma, was collected in all 4 habitats, 11 species were found in 3 habitats (mangroves, seagrass, and nonvegetated), and 13 species were only caught in seagrass and nonvegetated habitats. Seagrass generally supported the highest numbers of fish and invertebrates and had the greatest species richness. Saltmarsh was at the other extreme with 29 individuals caught from two species. Mangroves and nonvegetated habitats generally had more fish, invertebrates, and species than saltmarsh, but less than seagrass. Analyses of abundances of individual species generally showed an interaction between habitat and month indicating that the same patterns were not found through time in all habitats. All habitats supported distinct assemblages although seagrass and nonvegetated assemblages were similar in some months. The generality of these patterns requires further investigation at other estuaries. Loss of vegetated habitats, particularly seagrass, could result in loss of species richness and abundance, especially for organisms that were not found in other habitats. Although low abundances were found in saltmarsh and mangroves, species may use these habitats for varying reasons, such as spawning, and such use should not be ignored.

Tags: Atherinosoma microstoma, Biosphere | Aquatic Habitat | Coastal Habitat, Biosphere | Aquatic Habitat | Estuarine Habitat, Biosphere | Zoology | Crustaceans, Favonigobius lateralis, Global/Oceans | Southern Ocean/ Australia extension, Marine Features (Australia) | Barker Inlet-Port River estuary, SA, Marine Features (Australia) | Gulf St. Vincent, SA, Nets | Pop Nets, Nets | Seine Nets, Oceans | Coastal Processes | Estuaries, Oceans | Coastal Processes | Mangroves, Oceans | Coastal Processes | Marshes, Oceans | Marine Biology | Fish, Oceans | Marine Biology | Marine Habitat, Oceans | Marine Biology | Marine Invertebrates, Palaemonid spp., Pseudogobius olorum, Saltmarsh, Seagrass, Sillaginodes punctata, taxonomic_group_count, taxonomic_name
Organization: Australian Ocean Data Network