AndreaBozzo/ceres-open-data-index huggingface dataset:
Zooplankton community structure in nearshore waters of the Great Barrier Reef

A study of zooplankton from 10 stations located in nearshore waters adjacent to two catchments (one near-pristine - Princess Charlotte Bay, and the other intensely farmed - Innisfail) of the Great Barrier Reef. CTD casts were made through the water column at each station for salinity and temperature data. Water samples for chlorophyll a were made. Environmental variables include day and night, location and date (can allocate season, year).Mesozooplankton community structure and biomass were sampled by triplicate bottom to surface plankton hauls. Half of each sample was analysed for community composition (65 zooplankton taxa found) and the other for DW biomass estimates based on size (73-150µm, 150-350µm, &gt;350µm).Juvenile growth rates of cyclopoid and calanoid copepods, mature female copepod (Paracaluanus aculaeatus, P. aculaeatus minor, P. indicus, Acrocalanus gracilis, Bestiolina similis, Parvocalanus crassirostris) egg production, and secondary production were measured.
 This research was undertaken to examine zooplankton dynamics from two catchments.
 A subset of the data has been provided to the Ocean Biogeographic Information System (OBIS, http://iobis.org/OBISWEB/DisplayMetaData.jsp?content=meta/1464.html).Zooplankton species: Acartia fossae, Acartia pacifica, Acrocalanus gibber, Acrocalanus gracilis, Acrocalanus monachus, Bestiolina similis, Calanopia sp., Calanopia aurivilli, Calanopia elliptica, Calanopia herdmani, Calanus minor, Calanus sp., Calocalanus plumulosus, Calocalanus spp., Candacia catula, Canthocalanus pauper, Centropages elongatus, Centropages furcatus, Centropages orsinii, Clausocalanus arcuicornis, Clausocalanus farrani, Clausocalanus furcatus, Corycaeus agilis, Corycaeus andrewsi, Corycaeus asiaticus, Corycaeus catus, Corycaeus clausi, Corycaeus crassiusculus, Corycaeus dahli, Corycaeus erythraea, Corycaeus pacificus, Corycaeus speciosus, Corycaeus spp., Corycaeus subtilis, Delius sp., Eucalanus crassus, Eucalanus pileatus, Euchaeta concinna, Euchaeta spp., Euterpina acutifrons, Farranula carinata, Farranula concinna, Farranula gibbula, Labidocera farrani, Labidocera spp., Lucicutia spp., Mecynocera clausi, Microsetella sp., Oithona attenuata, Oithona fallax, Oithona nana, Oithona plumifera, Oithona rigida, Oithona simplex, Oithona tenuis, Oncaea spp., Paracalanus aculeatus, Paracalanus aculeatus minor, Paracalanus indicus, Paracalanus sp. 1, Parvocalanus crassirostris, Temora turbinata, Unidentified harpacticoids, Undinula vulgaris.Other generic identifications: Appendicularia, Bivalves, Chaetognaths, Decapod larvae, Euphausiid larvae, Fish larvae, Gastropods, Ostracods, Phyllosoma, Polychaete, Pteropod, Salp, Shrimp, Zoea.

Organization: Australian Ocean Data Network
Patterns in the distribution of the crinoid community at Davies Reef, central Great Barrier Reef

Surveys of the diversity and distribution of crinoids were conducted on Davies Reef between 1981 and 1983.A total of 25 fives sites were sampled within 5 habitat types. The habitats sampled were the reef slope, reef crest, moat, lagoon and back reef. The reef slope was further divided into three depth habitats (5m, 10m and 15m). The reef crest was sampled at 0m and the moat, lagoon and back reef were sampled at 5m.A sampling site consisted of 25 adjacent 1m² quadrats along a depth contour on the reef. Four replicate sampling sites were examined in each habitat, except for the 15m reef slope habitat. Within each quadrat, all crinoids on the surface and those occurring within the substrate, to a depth of about 50cm, were recorded. The position of each crinoid within the quadrat was recorded and crinoids collected for later preservation and identification in the laboratory.Habitats were also ranked with respect to the following external factors: current, energy, depth, sediment and coral cover.
 This research was undertaken to determine the structure of the crinoid community at Davies Reef by investigating species diversity and distribution across a variety of reef habitats. This allowed comparisons with other reef communities, such as coral, fish and sponges from the same reef.This survey was also used to establish suitable field and analytical techniques to enable more intensive local distributional studies and more extensive between-reef studies.
 Extensive taxonomic revisions of some of the comasterid genera were published in: "Rowe FWE, Hogget AK, Birtles RA and Vail LL (1986) Revision of some comasterid genera from Australia (Echinodermata: Crinoidea), with descriptions of two new genera and nine new species. Zool J Linn Soc 86:197-277." New species names from this publication are included in the following list of crinoids identified.Crinoid species identified from within quadrats: Comasteridae:Comanthus parvicirrusComanthus samoanus = Comanthus sp. cf. C. wahlbergii (J. Muller)Comanthus sp. AComasterinae n. gen. n. sp. A = Oxycomanthus mirusComasterinae n. gen. n. sp. B = Oxycomanthus exilisComanthina schlegeliComantheria alternansComantheria briareus: to be included with Comantheria alternansComanthus luteofuscum = Clarkcomanthus luteofuscumComanthus timorensis = Clarkcomanthus littoralisComaster multifidusComaster gracilisComatella nigraComatella stelligeraComatella maculataComatula purpureaComissia pectiniferaColobometridae:Cenometra bella Petasometra claraeMariametridae:Stephanometra oxyacantha Tropiometridae:Tropiometra afraAdditional species collected outside quadrats:Comasteridae:Comanthus bennetti = Oxycomanthus bennettiComanthina sp. A = Comanthina nobilisComantheria n. sp. A = Comanthus mirabilisCapillaster multiradiatusColobometridae:Colobometra perspinosaOligimetra serripinna

Organization: Australian Ocean Data Network
Genetic diversity of the sea cucumber, Holothuria scabra in New Caledonia, Australia (Northern Territory) and Bali

Within-region genetic heterogeneity of Holothuria scabra populations in New Caledonia was examined through allozyme electrophoresis. Five locations, each separated by 60-130 km, were selected along the coast of New Caledonia and 2 replicate sites (8-23 km apart) were chosen within 4 of these locations on the west coast of the island. Only one site was selected on the northeast coast. Between 14 and 34 adult Holothuria scabra were collected from each site. A short section of the upper intestine (5-10 cm), without sediments, was dissected from each animal and stored in liquid nitrogen until analysed. Holothuria scabra samples from Bali (n=90) and Knocker Bay, Australia (n=47), and existing data from the western Pacific: Solomon Islands; Torres Strait; and the Queensland Coast (Upstart Bay and Hervey Bay) were compared with the data from New Caledonia to investigate larval connectivity over a wider geographic scale. Seven polymorphic enzyme loci were surveyed using allozyme electrophoresis: GPI, HK, MDH, PEP-1, PEP-2, PEP-3 and PGM. Basic analyses of genetic variability (allele frequencies, number of polymorphic loci, heterozygosity) were carried out. The allelic richness for each population was calculated. F statistics were calculated and genetic distance analyses, cluster analyses and Mantel tests were performed.
 This research was undertaken to improve understanding of the genetic differentiation between stocks of Holothuria scabra at different spatial scales so that the release of cultured juveniles in restocking programs can be planned in a responsible way to preserve the genetic diversity of existing stocks.
 Sampling sites in New Caledonia: A=Baie de Sainte-Marie; B= Ilot Maître; C=Ouano; D=Ilots Kundogi; E=Plateau de Béco; F=Pointe Pindaï; G=Pouangué; H=Ouaco; I=Récif Thaavaam (Ilot Cocotier).

Organization: Australian Ocean Data Network
WAMSI Node 6.2 - Ocean Dynamics at Scott Reef, Western Australia - SUNTANS model

High resolution, three-dimensional numerical modelling of the tidally driven dynamics around Scott Reef. The purpose of the modelling was to capture the fine scale (~100 m) flow structures resulting from the tide interacting with the complex reef topography.
Hourly data of approximately 20 million model grid points were created. 3 tidal cycles during spring-tide conditions were modelled with model output including currents (u, v, w), water level, temperature and density at model grid points. 
Vertical extent is from surface to 3000 metres

Tags: Marine Features (Australia) | North West Shelf, WA, Marine Features (Australia) | Scott Reef, WA, Modelling, Numerical Model, Oceans | Ocean Temperature | Water Temperature, Oceans | Ocean Waves | Internal Waves, Oceans | Salinity/density | Density, Oceans | Sea Surface Height | Sea Surface Height, Oceans | Tides | Tidal Components, Oceans | Tides | Tidal Currents, Oceans | Tides | Tidal Height
Organization: Australian Ocean Data Network
Bacterial community structure in the soft coral, Alcyonium antarcticum from Antarctica

The structure and composition of microbial communities inhabiting the soft coral Alcyonium antarcticum were investigated across 3 differentially contaminated sites within McMurdo Sound, Antarctica - McMurdo Station (MM), Scott Base (SB) and Cape Armitage (CA).Samples from all sites were subjected to culture-based analysis, denaturing gradient gel electrophoresis (DGGE), 16S rRNA gene clone-library analysis, and (FISH).Phylogenetic groups included Gamma-, Alpha- and Beta- proteobacteria; Bacteroidetes; Firmicutes; Actinomycetales; Planctomycetes; and Chlorobi and bacteria from the functional group of sulfate-reducing bacteria.
 To investigate the structure and composition of microbial communities inhabiting the soft coral Alcyonium antarcticum.To examine any variation within and between Alcyonium antarcticum bacterial communities from 3 differentially contaminated sites within McMurdo Sound, Antarctica .
 This was the first investigation of microbial communities associated with Antarctic soft corals.Accession numbers assigned to sequencing products: Culture1-Culture10 (DG312224, DG312225, DG312226, DG312227, DG312228, DG312229, DG312230, DG312231, DG312232, DG312233); OTU1-OTU15 (DG312234, DG312235, DG312236, DG312237, DG312238, DG312239, DG312240, DG312241, DG312242, DG312243, DG312244, DG312245, DG312246, DG312247, DG312248); DGGE Band1-Band11, (DG312249, DG312250, DG312251, DG312252, DG312253, DG312254, DG312255, DG312256, DG312257, DG312258) and Band14-Band16 (DG312259, DG312260, DG312261).

Organization: Australian Ocean Data Network
Temperate Australian quantitative spatial and temporal abundance data for rocky reef biota (biodiversity): long-term Tasmanian MPAs - Tinderbox

The data is quantitative abundance of fish and megafaunal invertebrates and algal % cover derived from transect based counts at a wide range of locations across Temperate Australia. The methods are described in detail in Edgar and Barrett (1997). Primarily the data are derived from transects at 5 m depth and/or 10 m depth at each site surveyed. Methods were initially developed for research on temporal changes following protection in Tasmanian long-term MPAs (Maria Is, Tinderbox, Ninepin Point, Governor Island), and the data represented by this record has been collected at Tinderbox. 
In many cases the dataset involves temporal replication (year scale), particularly for the core Tasmanian MPAs represented by this record.

Tags: Abundance - fish, Abundance - invertebrates, Carapace length - rock lobster, Fish size class, Percentage cover algal species, Shell length - abalone
Organization: Australian Ocean Data Network
Spencer Gulf fisheries, Prawn Fisheries Catch and Effort Logbook Data

The Western King Prawn species (Penaeus latisculcatus) is landed from South Australian (SA) waters. The prawn industry in SA is divided into the Gulf St Vincent, Spencer Gulf, and West Coast fisheries. A separate fishery in Investigator Strait operated until 1986/87 when it was amalgamated into the Gulf St Vincent fishery. The Gulf St Vincent fishery was closed in 1991/92 and 1992/93. The West Coast fishery was voluntarily closed in 1992/93. This system monitors catch and effort fluctuations in the state's prawn industry. The quantity of prawns (kg) and effort (hours trawled) to catch the prawns are recorded for each fishing period from records submitted by the trawler operators.

Tags: Agriculture | Agricultural Aquatic Sciences | Fisheries, Biosphere | Zoology | Crustaceans, Boats and Small Vessels, Global/Oceans | Southern Ocean/ Australia extension, Logbook/Catch Data, Marine Features (Australia) | Spencer Gulf, SA, Oceans | Marine Biology | Marine Invertebrates, Penaeus latisculcatus, Trawls | Prawn Trawls, Visual Counts/Observations, Western King Prawn, catch
Organization: Australian Ocean Data Network
'Seabase' - Marine environmental monitoring data

'Seabase' is a fully relational on-line database which holds all the PLOOM (Perth Long-Term Ocean Outlet Monitoring), SDOOL (Sepia Depression Ocean Landline) and Bunbury Ocean Outfall water quality monitoring data, as well as data from the Perth Coastal Waters Study, the Alkimos Marine Studies Programme and the Metropolitan Desalination Plant Monitoring Programme.  Secure, read-only access is provided to authorised users

Tags: Agriculture | Agricultural Chemicals | Pesticides, Alkimos, Biosphere | Microbiota | Bacteria, Biosphere | Vegetation | Phytoplankton, Bunbury, Cockburn Sound, Hydrosphere | Water Quality, Hydrosphere | Water Quality | Chlorophyll, Hydrosphere | Water Quality | Light Transmission, Hydrosphere | Water Quality | Nutrients, Hydrosphere | Water Quality | Oxygen, Hydrosphere | Water Quality | Trace Metals, Mandurah Waters, Ocean Reef, Oceans | Coastal Processes | Sedimentation, Oceans | Marine Biology | Marine Habitat, Oceans | Marine Environment Monitoring, Oceans | Ocean Temperature | Water Temperature, Owen Anchorage, Periphyton, Perth, Rottnest, Seagrass, Sepia Depression, Swanbourne, Warnbro Sound, herbicides, light attenuation, outfall, particle size
Organization: Australian Ocean Data Network
Using scales and otoliths to trace life histories of barramundi (Lates calcarifer) from north Queensland

Fish scales and sagittal otoliths from barramundi were analysed to determine whether types of habitats - freshwater lagoons, rivers and weirs; estuarine; marine - could be identified from the known lifecycle history of individual fish. The experiments ran between July 2000 and February 2003. Elemental abundances (Ba, Ca, Fe, K, Mg, Mn, Na, P, S, Sr) and Sr isotopic compositions were analysed using in situ laser ablation (UV) multi-collector inductively coupled plasma mass spectrometry (MC-ICP-MS) measurements. Multiple additive regression tree (MART) and linear discriminant analysis (LDA) were used to classify otolith scales as estuarine or freshwater and validated against the known history of caged fish subjected to repeated scale sampling at capture, after 82 and 240 days, and at death (between 99 and 310 days). An Sr fingerprint was created which was able to group otoliths to the fish's source locatuion.Sample fish were captured from Cape Cleveland, Magnetic Island, Gordon Creek, Upper Alligator Creek, Inkerman Station, Black's Weir; and from dry tropic (Burdekin, Barrattas, Haughton, Ross) and wet tropic (Herbert, Johnstone) rivers.Note was also made of fish size (total length; small,  625mm).
 To determine whether types of habitats (e.g. freshwater or estuarine) could be identified from scales and otoliths and verified against the known lifecycle history of individual fish in the sample.

Organization: Australian Ocean Data Network
Flatback turtle tagging and hatching success studies at Cape Domett

PART 1. BIOLOGY
Cape Domett, located in tropical Western Australia, has been known as a flatback turtle, Natator depressus, nesting site but its magnitude was previously underestimated. We assessed temporal abundance within a year (by visiting the beach every seven weeks between April 2006 and March 2007) to find turtles nested throughout the year with peak nesting occurring between August and September. Annual nesting abundance was estimated in the order of several thousand individuals (2582  3250) equating to one of the largest populations of flatback turtles globally. As Cape Domett is currently unassigned to a genetic management unit, we used size and scale morphology to group the Cape Domett population within the Northern Territory genetic management unit. Threats to eggs, hatchlings and adults were examined using observations of predation and measures of incubation success. We re-evaluated the importance of this major flatback turtle nesting site and give a detailed examination of flatback turtle nesting biology in north-western Australia. 
PART 2. MONITORING METHODOLOGY
We used mathematical modelling of the available data and biology of the species to developed costeffective monitoring protocols for future monitoring of flatback turtles at Cape Domett.

Tags: Field Surveys | Shore Surveys, Flatback Turtles, Hatching Success, Marine Features (Australia) | Kimberley Coast, WA, Modelling, Monitoring, Nesting, Tags and Tracking Devices
Organization: Australian Ocean Data Network
IMOS - National Mooring Network - Passive Acoustic Observatory at Portland, VIC (PAPOR)

The Portland Passive Acoustic Observatory consists of two to four moorings fitted with hydrophones set on the seabed at ~170 m depth that record noise in the ocean. This system can be used to monitor whale and fish migrations, seismic activity and other natural and man-made noise sources. If four moorings are set they are configured with a mooring at each apex of an approximate equilateral triangle of 5 km side with the fourth mooring in the triangle centre. Temperature loggers are set on each mooring at the seabed.
Each logger records at a sampling rate of 6 kHz for between 3-8 min of every 15 min. If four loggers are set a 22 kHz recording is also made once a day to allow accurate synchronisation of the instrument clocks. This is required for locating the source of a sound based on its time of arrival at each hydrophone in the array. A 7 kHz pinger set on the central mooring pings for 35 minutes at a 20 s interval once per day to overlap the 22 kHz sample.
Raw data from each logger is in the form of mixed binary/text files comprised of:
1) text header and footer containing recording start and end date/time, quality control and sampling configuration; and
2) sea noise data of 16 bit unsigned integer, binary values (IEEE, little endian).
Instruments are calibrated for system gain with white noise of known level input with the hydrophone in series, before and after deployments. System calibrations are made over 2 Hz to the Nyquist frequency. The instrument clock drift is checked against GPS transmitted UTC time before and after deployment.
The raw data can be obtained on portable disk from the Australian Ocean Data Network (AODN).
The Centre for Marine Science and Technology (CMST) at Curtin University has developed Matlab software to process and analyse these data.
This observatory was decommissioned early in 2018.

Tags: Coastal Cities / Towns (Australia) | Portland, VIC, IMOS Site | PAPOR | Portland, VIC Passive Acoustic Observatory, Passive Acoustic Listening Stations, Passive Acoustic Observing System
Organization: Australian Ocean Data Network
NERP Marine Biodiversity Hub, Theme 1 - Flinders Commonwealth Marine Reserve Pilot Survey- Shelf Baited Underwater Video (BRUV) component

The Flinders CMR survey was a pilot study undertaken in August 2012 as part of the National Marine Biodiversity Hub's National monitoring, evaluation and reporting theme. The aim of this theme is to develop a bluepint for the sustained monitoring of the South-east Commonwealth Marine Reserve Network. The particular aims of the survey were twofold; 1) to contribute to an inventory of demersal and epibenthic conservation values in the reserve and 2) to test methodologies and deployment strategies in order to inform future survey design efforts. Several gear types were deployed; including multibeam sonar, shallow-water (less than 150m) Baited Remote Underwater Video (BRUVs), deep- water BRUVs, towed video and digital stereo stills. This resource contains the shallow-water BRUV footage captured on the FLinders CMR shelf (less than 150 m).
Stereo BRUV's were deployed using a probabalistic and spatially-balanced survey design called Generalized Random Tessellation Stratified (GRTS). Habitats were identified in a previous multibeam survey and consisted of 'mixed reef' (containing patchy reef) and sand. Mixed reef habitat was targeted in this survey (9 GRTS mixed reef sites versus 3 sand sites). A total of 60 stereo BRUVs were deployed.
Data contained here represents footage collected using these drops and the associated scored data (abundance (MaxN) and lengths).

Tags: NERP Marine Biodiversity Hub Theme 1, Temperate Reef, fish
Organization: Australian Ocean Data Network
Comparing the effects of an introduced and native species of bryozoan

An experiment was conducted to compare the effects of the introduced bryozoan, Bugula neritina, and the native bryozoan, Bugula dentata, on sessile invertebrate assemblages. Individuals of both species were collected from Workshops Jetty and Altona Pier prior to the experiment and transported back to the laboratory. Two colonies of either B. neritina or B. dentata were attached to each plate using sponges that expanded when wet. The plates were then transported to Workshops Jetty and attached to plates and left for 12 days. At the conclusion of the experiment plates were collected and abundances of species on the plates were counted and identified.

Tags: 20 331002, 20 331013, 35 033006, Biosphere | Aquatic Habitat | Benthic Habitat, Biosphere | Ecological Dynamics | Community Structure, Biosphere | Ecological Dynamics | Species Recruitment, Biosphere | Zoology | Invertebrates, Botryllus schlosseri, Bugula dentata, Bugula neritina, Human Dimensions | Environmental Impacts, Oceans | Marine Biology | Marine Invertebrates, Port Phillip Bay, Williamstown, Workshops Jetty
Organization: Australian Ocean Data Network
Holocene Sea Level transgression in carbonate sediments, Torres Strait

Torres Strait, a shallow continental shelf seaway, with a number of reef and island fringed passages, separates Australia from Papua New Guinea. The Strait offers challenging opportunities for geological research into variation in depositional environments, and at the same time, it has been a biogeographical boundary and cultural filter. 
The collection and analysis of vibrocoring and shallow seismic profiling was undertaken to better understand the Quaternary development of the region. The distinct morphologic features that have been recognised in the shallow seismic sections, provided evidence of repeated history of emergence, subaerial exposure, and fluvial and marine sedimentation. On the basis of grain composition and geomorphic relations, four facies associations are recognisable in the area: (1) Late Pleistocene Terrigenous Clay (A); (2) Transgressive Marine Units (8); (3) Holocene Marine Sediments (C); and (4) Holocene Terrigenous Facies (D). Radiocarbon dates have been derived from Holocene Marine (C) and Transgressive (8) units to obtain a time frame for the late Quaternary geological history. SEM results, pollen analysis and petrographic observations led to several ideas regarding depositional environment, provenance and transport processes. The sedimentary environments within the Torres Strait shelf have been influenced by a number of factors, among which are: subaerial exposure, rapid transgression, climate, prevailing oceanographic factors, shelf bathymetry, carbonate production and the quantity of terrigenous sediment being transported to the shelf. The diversity of sedimentary conditions, together with the extent of inter-reef sediments (Great North East Channel) and estuarine/deltaic deposits (Fly River Delta/Estuary), have caused an evolution of a mixed carbonate siliciclastic shelf system.

Tags: Oceans | Marine Sediments | Sedimentation
Organization: Australian Ocean Data Network