AndreaBozzo/ceres-open-data-index huggingface dataset:
The relative abundance (%) of planktonic foraminifera over time in core BAR 9403, located off the coast of Sumatra

The advent of deep-sea drilling in the 1950's prompted the use of planktonic foraminifera (unicellular protozans) as palaeoceanographic indicators. They provide a natural archive of past environmental changes due to their global distribution, their prolific productivity and sensitivity to environmental variations. 
The most obvious change in relative abundance in core BAR9403 (off the coast of Sumatra) is shown by sub-polar to transitional 'upwelling' species Ga. bulloides with abundances of 26% at approximately 14,000yrs BP and 22.7% during the Holocene. This is compared to the periods from Marine Isotope Stage (MIS) 3 to the Last Glacial Maximum (LGM) where the relative abundance of Ga. bulloides is generally &lt;10%. Gr. menardii, a tropical 'upwelling' species, also increases its relative abundance during MIS 2 from &lt;8% during MIS 3 to a peak abundance of 16% at ~17,000yrs BP.

Tags: Biosphere | Ecological Dynamics | Population Dynamics, Biosphere | Microbiota | Foraminifers, age_of_core, taxonomic_group_count
Organization: Australian Ocean Data Network
Database of Marine Larval Fish Assemblages in Australian temperate and subtropical waters (1983 - 2016)

Larval fishes are a useful metric of marine ecosystem state and change, as well as species-specific patterns in phenology. The high level of taxonomic expertise required to identify larval fishes to species level, and the considerable effort required to collect them, make these data extremely valuable. Here we collate 3178 samples of larval fishes, from 12 research projects from 1983 to November 2016, from temperate and subtropical Australian waters. This forms a benchmark for the larval fish assemblage for the region, and includes recent monitoring of larval fishes at coastal oceanographic reference stations. Comparing larval fishes among projects can be problematic to due to differences in taxonomic resolution, and identifying all taxa to species can extremely challenging, so this study reports a standard taxonomic resolution (of 221 taxa) for this region to help guide future research. All data reported here has been expertly resolved to this taxonomic resolution. 
The ongoing version of this larval fish database is freely available through the Australian Ocean Data Network Portal (AODN; https://portal.aodn.org.au/search?uuid=8e754b8b-c40f-4a21-ae82-573a67fc3556), and serves as a data repository for surveys of larval fish assemblages in the region.

Organization: Australian Ocean Data Network
IMOS - Satellite Remote Sensing - MODIS - 01 day - Nanoplankton fraction (OC3 model and Brewin et al 2010 algorithm)

The Aqua satellite platform carries a MODIS sensor that observes sunlight reflected from within the ocean surface layer at multiple wavelengths. These multi-spectral measurements are used to infer the concentration of chlorophyll-a (Chl-a), most typically due to phytoplankton, present in the water. An empirical relationship is then used to compute an estimate of the relative abundance of three phytoplankton size classes (micro, nano and picoplankton). 
The methods used to decompose chl_oc3 are described by Brewin et al in two papers in 2010 and 2012. The two methods, denoted Brewin2010at and Brewin2012in, used calibration data from the Atlantic and Indian Oceans respectively.  Users should note that these are unvalidated experimental products and they should familiarise themselves with the underlying algorithms and methodologies described in the published literature before making use of them.
The data are produced from the same data stream as the MODIS Chla_oci data set (https://catalogue-imos.aodn.org.au:443/geonetwork/srv/api/records/d7a14921-8f3f-4522-9a54-e7d1df969c8a). 
Data are provided as two files per day, one with the percentage of nanoplankton, and one for picoplankton. The percentage of microplankton is computed as the balance to 100%, that is %micro = 100 - %nano - %pico.
This collection was removed from the AODN Portal in March 2023, please refer to the Brewin 2012 collection which supersedes this one - https://catalogue-imos.aodn.org.au:443/geonetwork/srv/api/records/9fde091c-9d38-4b2f-ba23-c262c21a41a2

Tags: Countries | Australia, Countries | Fiji, Countries | Indonesia, Countries | Malaysia, Countries | New Caledonia, Countries | New Zealand, Countries | Papua New Guinea, Countries | Philippines, Countries | Singapore, Countries | Thailand, Countries | Timor-Leste, Countries | Vanuatu, Countries | Vietnam, Global / Oceans | Indian Ocean, Global / Oceans | Pacific Ocean, Global / Oceans | Southern Ocean, Marine Features (Australia) | Bass Strait, TAS/VIC, Marine Features (Australia) | Great Australian Bight, SA/WA, Marine Features | Strait of Malacca, Oceans | Ocean Chemistry | Chlorophyll, Oceans | Ocean Optics | Ocean Color, Regional Seas | Andaman Sea, Regional Seas | Arafura Sea, Regional Seas | Banda Sea, Regional Seas | Celebes Sea, Regional Seas | Coral Sea, Regional Seas | Gulf of Thailand, Regional Seas | Java Sea, Regional Seas | Philippine Sea, Regional Seas | Solomon Sea, Regional Seas | South China Sea, Regional Seas | Tasman Sea, Regional Seas | Timor Sea, States, Territories (Australia) | New South Wales, States, Territories (Australia) | Northern Territory, States, Territories (Australia) | Queensland, States, Territories (Australia) | South Australia, States, Territories (Australia) | Tasmania, States, Territories (Australia) | Victoria, States, Territories (Australia) | Western Australia
Organization: Australian Ocean Data Network
Is predation of juvenile crown-of-thorns seastars (Acanthaster cf. solaris) by peppermint shrimp (Lysmata vittata) dependent on age, size, or diet?

Ten predation experiments were carried out examine whether predation of juvenile CoTS by peppermint shrimp (L. vittata) is affected by the age, size, or diet of juvenile CoTS.
Over a span of 9.5 months, ten experiments were carried out with juvenile CoTS ranging from 1 to 9 months of age and 0.34 mm and 21.37 mm in diameter. Juvenile CoTS were reared and fed a diet of either CCA throughout the experiments or corals (introduced at 4 months, and only offered from around 5 months ). Shrimps assessed for health status, measured with callipers to the nearest millimetre (from rostrum to tail) and left to acclimatize unfed in 250 ml jars for two&ndash;three days as suggested for invertebrate gut content analysis experiments, (5&ndash;16 per experimental run, depending on availability).
On the fourth day, a single juvenile CoTS was measured (maximum diameter, with callipers) and introduced into each jar. The jars were monitored daily for the following three days. The condition of the juvenile CoTs was scored as:
None &amp;ndash; if there was not change in appearance

Partial predations &amp;ndash; if they were alive but had missing limbs or injuries

Lethal predation &amp;ndash; if they had been fully consumed by the predator.

Data analysis examined the effects of CoTS size and age on the incidence of partial and lethal predation.

Organization: Australian Ocean Data Network
Determining main carbonate mineralogy, and the primary components of the non carbonate fraction, at two depths in core GC09, collected from the Capricorn Channel

A gravity core (GC09) was collected from a depth of 166m within the Capricorn Channel, southern Great Barrier Reef (GBR). Analysis of other parameters revealed the Last Glacial Maximum (LGM) sitting at a depth of ~60cm's into the core. For this reason two samples were collected for X-ray Diffraction (XRD) analysis, the first at a depth of 5cm (GC09-5) representing interglacial sediment, and the second from a depth of 60cm (GC09-60) representing glacial sediment. Both samples exhibited high Mg calcite and aragonite, compared with calcite, suggesting that the primary carbonate influx to the core is from the surrounding reef platform, rather than pelagic influences. There was also a 10% increase in non carbonate material during the glacial, and this was primarily made up of feldspars and quartz indicating a relative increase in terrestrial sediment during the LGM.

Tags: Oceans | Marine Sediments | Sediment Composition, Paleoclimate | Ocean/lake Records | Sediments, amount_of_sample_components, error
Organization: Australian Ocean Data Network
RAN CTD Profile Data - HMAS MELVILLE ProjectID: HI470MEL_H From: 2009-11-16 To: 2009-11-16

This dataset contains quality controlled vertical profiles of pressure, temperature and salinity measured by a Conductivity, Temperature and Depth (CTD) probe. The dataset contains 1 CTD profiles (casts) obtained during RAN Hydrographic Survey cruise HI470MEL_H from HMAS MELVILLE. 
The CTD was manufactured by Falmouth Scientific and is the "2-inch Micro CTD" model. This CTD type is referred to operationally as the HS_CTD. This CTD is fitted within an inductive type conductivity cell, a platinum thermometer and silicon pressure sensor.
The CTD temperature sensor is calibrated on the ITS-90 temperature scale against a master CTD using a controlled temperature bath. The pressure sensor is calibrated using a Druck Pressure Calibrator. The conductivity sensor is calibrated in a temperature controlled bath against seawater samples of known conductivity.
The HS_CTD is lowered and raised by a hand winch sampling at a rate of 1.83 Hz. Data files were recorded in the downcast and upcast direction but most data is from downcasts due to higher quality. Raw CTD pressure data is not always monotonic due to transient up/down motion of winch/ship. Raw pressure data is subsetted to give a monotonic (increasing) sequence and then linearly interpolated to 1 decibar pressure intervals and converted to netCDF format files. Data is then flagged with quality control flags after visual inspection and comparison to average climatology and historical CTD casts.

Tags: Oceans | Ocean Temperature | Water Temperature, Oceans | Salinity/density | Salinity, sea_water_practical_salinity, sea_water_temperature
Organization: Australian Ocean Data Network
CARS 2009 - CSIRO Atlas of Regional Seas - Australian weekly

CARS (CSIRO Atlas of Regional Seas) is a digital climatology, or atlas of seasonal ocean water properties: temperature, salinity, dissolved oxygen, nitrate, phosphate and silicate. It comprises gridded fields of mean ocean properties over the period of modern ocean measurement, and average seasonal cycles for that period. It is derived from a quality-controlled archive of all available historical subsurface ocean property measurements - primarily research vessel instrument profiles and autonomous profiling buoys. As data availability has enormously increased in recent years, the CARS mean values are inevitably biased towards the recent ocean state.
CARS2009 covers the full global oceans on a 1/2 degree grid, but until June 2011 only included temperature and salinity fields. The T and S fields were created in July 2009 and were was based on World Ocean Database 2005 (WOD05) [July 2008 Update], surface-pressure-corrected Argo global archives to May 2009, WOCE Global Hydrographic Program (v3.0), and many other datasets available up to 2008. The data was collated from many sources and rigorously screened to form BLUElink Ocean Archive (BOA).
This metadata record describes all CARS parameters, which can then be visualised as a single collection through the portal interface.

Tags: Argo float, Atmosphere, CTD (Conductivity-Temperature-Depth Profilers), Chemical Oceanography, Climatology, Countries | Australia, Countries | Indonesia, Countries | Papua New Guinea, Countries | Timor-Leste, Global / Oceans | Indian Ocean, Global / Oceans | Pacific Ocean, Global / Oceans | Southern Ocean, Marine Features (Australia) | Bass Strait, TAS/VIC, Marine Features (Australia) | Great Australian Bight, SA/WA, Meteorology, Nansen Bottles, Niskin Bottles, Oceans | Ocean Chemistry | Nitrate, Oceans | Ocean Chemistry | Oxygen, Oceans | Ocean Chemistry | Phosphate, Oceans | Ocean Chemistry | Silicate, Oceans | Ocean Temperature | Water Temperature, Oceans | Salinity/density | Salinity, Physical Oceanography, Regional Seas | Arafura Sea, Regional Seas | Banda Sea, Regional Seas | Coral Sea, Regional Seas | Java Sea, Regional Seas | Solomon Sea, Regional Seas | Tasman Sea, Regional Seas | Timor Sea, Seasonal cycles in ocean properties, States, Territories (Australia) | New South Wales, States, Territories (Australia) | Northern Territory, States, Territories (Australia) | Queensland, States, Territories (Australia) | South Australia, States, Territories (Australia) | Tasmania, States, Territories (Australia) | Victoria, States, Territories (Australia) | Western Australia, Water masses
Organization: Australian Ocean Data Network
Experimental Evolution Of The Coral Algal Endosymbiont, Cladocopium Goreaui, For Coral Heat Tolerance

An experiment was carried out to compare the performance of coral juveniles using cultured symbionts selected for enhanced tolerance in Cladocopium goreaui (C1) over multiple time scales.
Symbiotic cells were extracted from colonies of Acropora tenuis from Nelly Bay, Magnetic Island in 2010. The cells were isolated, cultured and maintained, then split into 16 independent replicates under an experiment to select for thermally tolerant Symbiodiniacae.
Colonies of A. tenuis were collected from Geoffery Bay, Magnetic Island In November, 2014 and transported to the National Sea Simulator facility (SeaSim) at the Australian Institute of Marine Science (AIMS). Larvae raised from A. tenuis were infected with symbionts at 22 and 28 days post spawning.
A mix of wild type (WT) strains (10 strains) and a separate mix of thermally tolerant Symbiodiniaceae (SS) with 21 generations of selection (10 strains) were used to infect coral juveniles.
The performance of SS- and WT-juveniles was compared with survival and growth rate, cell density and photosynthetic function of symbionts at three temperatures (27, 31, and 32.5&deg;C) over short (28 days) and longer (72 days) periods of heat stress. The results of this experiment using symbionts selected after 21 generations were then compared with the results of later studies that used symbionts after 73 (Chakravarti et al. 2017) or 130 (Buergeret al. 2020) generations of selection, to test host costs or bene¿ts over varying periods of time.
Further details are presented in the paper and supplementary methods: Quigley, K.M., Alvarez Roa, C., Beltran, V.H., Leggat, B. and Willis, B.L. (2021), Experimental evolution of the coral algal endosymbiont, Cladocopium goreaui: lessons learnt across a decade of stress experiments to enhance coral heat tolerance. Restor Ecol, 29: e13342. https://doi.org/10.1111/rec.13342

Organization: Australian Ocean Data Network
WAMSI 2 - Dredging Node 3.2.1 - Plume Characteristics (Field) - Field Trip 3

Plume Characterization:
The key objectives of Project 3.2:
(1) Characterize the physical/optical properties of sediment suspensions;
(2) Map the dredge-generated plume;
(3) Provide data to optimize and validate plume modelling;
(5) Assess the spatial and temporal variability (~10 years) of background suspended sediment loads using archived remote sensing data;
(6) To estimate the benthic light field with respect to TSS;
A voyage of opportunity as part of an AIMS field trip in Jun 2015, collected data from 3rd - 13th July 2015 using RV Solander (AIMS).

Tags: ADCP, Biosphere | Aquatic Habitat | Benthic Habitat, CDT, Chevron, Hydrorad, Hydroscat, LISST, Oceans | Coastal Processes | Sediment Transport, Oceans | Marine Biology | Marine Plants, Oceans | Marine Sediments | Turbidity, Oceans | Water Quality | Light Transmission, Wheatstone, dredge plume mapping, dredging
Organization: Australian Ocean Data Network
Population genetics and taxonomy of the green alga, Caulerpa from the central Great Barrier Reef

Allozyme variation was examined in 7 species and 4 varieties of Caulerpa sampled from the central Great Barrier Reef region. The species examined were: Caulerpa racemosa, (vars imbricata, laetevirens, and racemosa, and a peltate morph of C. racemosa), C. cupressoides, C. lentillifera, C. peltata, C. serrulata, C. sertularioides, and C. taxifolia.Differences were examined between species and between populations of the same taxon sampled from different geographical locations, and typically included fixed gene differences (no alleles found in one taxon shared by the other taxon) at two or more loci.Cluster and cladistic analyses were carried out. Eight of 13 plants identified initially as C. serrulata were distinguished at several loci, indicating the presence of an undetermined cryptic taxon. Population genetic analysis of polymorphisms, which occurred in some taxa, demonstrated strong spatial differentiation among some populations and significant but variable degrees of clonality and/or inbreeding within these populations.Allozymes proved to be a useful tool for defining species boundaries and investigating population structure in Caulerpa, but not for determining phylogenetic relationships within the genus.Collection locations: Shelly Beach (SB), Cape Pallarenda (CP), Kissing Point (KP), The Strand (ST), The Breakwater at Townsville Harbour (EB), Horseshoe Bay on Magnetic Island (HB), Lodestone Reef (LR).
 To examine differences between species and between populations of the same taxon sampled from different geographical locations.

Organization: Australian Ocean Data Network
Management strategy evaluations for multiple use management of Australias North West Shelf - Visualisation software and user guide.

As its name suggests, management strategy evaluation (MSE) provides the opportunity for managers to evaluate the performance of alternative natural resource management strategies by comparison among indicators of social, economic and environmental performance. One of the primary difficulties faced when comparing these indicators is the sheer volume of data which needs to be assimilated. In the case of the North West Shelf Joint Environmental Management Study (NWSJEMS) the combination of three operating models, three development scenarios and three management strategies offers a total of twenty seven possible alternatives for evaluation. For the NWSJEMS an agent based computer program, InVitro, was used to model the impact of future development in the North West Shelf. As InVitro has stochastic components it was necessary to have multiple instances of model runs using the same initial model parameters, a process which creates enormous quantities of data. Two software packages were developed for dealing with NWSJEMS data. The first, ViewNWS, is specifically tailored for use by environmental managers needing to have an overall comparison of alternative management outcomes. It uses pre-packaged, processed data produced by InVitro and has a straightforward graphical user interface (GUI). The second software package, the NWS Technical User Interface, is targeted at modellers and programmers. It allows the user to visualise raw model output to allow rapid model and parameter changes.

Organization: Australian Ocean Data Network
Comparative foraging ecology of five sympatric terns at a sub-tropical island in the eastern Indian Ocean

Dietary samples (regurgitates) were collected from the five most numerous tern species from 1993 to 1999 on Pelsaert Island, Houtman Abrolhos island group, off the mid-western coast of Australia. Items identified were related to observations of foraging seabirds around the island.

Tags: 40 128002, 40 128003, 40 128025, 40 128027, 40 128028, Anous stolidus, Anous tenuirostris, Oceans | Marine Biology | Marine Birds, Sterna bergii, Sterna dougallii, Sterna fuscata
Organization: Australian Ocean Data Network
Surface scars on massive corals as evidence of previous crown-of-thorns starfish (Acanthaster planci) outbreaks on the Great Barrier Reef

In April 1985, massive corals on 5 mid-shelf reefs (Green Island, Feather Reef, John Brewer Reef, Rib Reef and Wheeler Reef) and 1 outer-shelf reef (Potter Reef) were surveyed for feeding scars caused by the crown-of thorns starfish (Acanthaster planci). Each reef, with the exception of Wheeler Reef, had experienced crown-of-thorns starfish outbreaks between 1962 and 1985.The survey involved 2 divers using SCUBA equipment swimming along randomly placed 200 m (approximately) sections of the reef perimeter. These swims were carried out in a slow meandering pattern covering as much of the reef slope as possible to a depth of approximately 12m. Various size classes of Diploastrea heliopora and a number of species of Porites were surveyed. Each individual colony encountered was recorded in 1 of 4 diameter categories and 1 of 4 proportional damage categories. The height difference between the scarred surface and the living surface was measured using a specially built PVC height gauge.Shallow cores (to 20 cm) were taken in the dead surfaces of some Porites colonies for the purpose of dating the dead surface. For each colony, measurements were made of total height, maximum diameter, the diameter perpendicular to the maximum diameter, and 5 independent measurements of the heights between adjacent 'steps', where a 'step' is the distance between adjacent dead or living and dead surfaces normal to the lower surface. The cores were bleached, sun dried and logged. The dead surfaces were then dated using a fluorescent banding technique.
 This study set out to examine the feasibility of eliciting reliable data on previous crown-of-thorns (Acanthaster planci) aggregations by dating surface scars on massive corals. The objectives of the surveys were to assess the level of damage caused by the most recent Acanthaster planci outbreaks on various size classes of Porites and Diploastrea, and to locate suitable specimens for detailed measurement and dating of scars.
 This research was a component of 'The Crown-of thorns Study', which was supported by the Commonwealth Community Employment Program'

Organization: Australian Ocean Data Network