AndreaBozzo/ceres-open-data-index huggingface dataset:
Effects of thermal stress on fertilization and early embryogenesis in coral species from the Great Barrier Reef and Japan

Favites chinensis colonies were collected from the reef flat off Sesoko Island, Okinawa and transported to aquaria at Sesoko Station. After spawning, sperm and eggs were separated and then used in fertilization experiments at 7 temperatures (25.5, 26.4, 27.0, 27.8, 28.9, 30.2 and 31.6°C). Early fertilization (first and second cleavage) was assessed after 3 hours using a dissecting microscope.Acropora millepora were collected from Davies Reef on the Great Barrier Reef and transported to aquaria at the Australian Institute of Marine Science. Similar fertilization experiments were carried out at 28.3, 30.4, 31.8, 32.8 and 34.1°C. Embryos were sampled at 2 and 4 hours, fixed in Bouins solution and later assessed for fertilization success and gamete quality.Acropora millepora, Favites abdita and Mycedium elephantotus, were collected from Davies Reef. In this experiment, eggs and sperm were separately pre-exposed to temperatures of 26, 28, 30 and 32°C for 30 minutes prior to fertilization at these tempertures. The embryos were sampled and fixed at 2 and 4 hours and assessed for fertilization success, abnormal embryo development and cell cleavage rates.
 This research was undertaken to examine the influence of seawater temperature on fertilization success and early embryogenesis of reef-building corals, in different families, from the Great Barrier Reef and Japan. Gametes were subjected to temperatures ranging from 2°C below average temperatures during the spawning period at each location to 5-6°C above average, which encompasses the range of increases that might be expected under climate change scenarios.

Organization: Australian Ocean Data Network
Seabed habitats and their biological assemblages: Carnarvon Shelf survey, Western Australia (CERF Marine Biodiversity Hub Survey)

The survey was a collaboration between the Australian Institute of Marine Science (AIMS) and Geoscience Australia (GA) aboard RV Solander, as part of the CERF Marine Biodiversity Hub&#39;s Surrogates Program.

The purpose of the survey was to collect high-quality, accurately co-located data test a range of physical parameters for relationships to the biodiversity and seabed patterns across the offshore Carnarvon shelf, adjacent to Ningaloo. Estimates of relative importance of latitude, distance offshore, water depth, physical setting, exposure and local habitat complexity were explored in relation to biodiversity patterns in the region.

Seabed benthic habitats were examined for distribution and abundance of marine flora and fauna, and for habitat complexity. Towed-video transects, epi-faunal sleds and infaunal grabs were collected across the shelf areas of three sites: Mandu, Point Cloates and Gnaraloo.

Towed-video observations and analysis characterised each site&rsquo;s habitat and macro-organisms, with forward facing video camera and down-facing stills camera towed for approximately 500m from the near shore to shelf break area. Using the AIMS habitat classifications Scheme (Speare et al., 2004) substrata, benthos, and individual organisms are recorded. Total video states at each sites: Mandu (32), Point Cloates (44) and Gnaraloo (46)

Two towed epi-benthic sleds sampled benthic assemblages and distribution of epifauna at seabed stations across the three survey areas. Samples retrieved were weighed for total mass, and specimens were then sorted into taxa-similar groups, photographed and preserved. At some stations, images were recorded during tow deployment. All epi-faunal samples were transported to the Museum of Western Australia for storage, further processing, taxonomic identification. Total of epi-benthic sleds collected: Mandu (30), Point Cloates (38) and Gnaraloo (34)

Sediment samples were collected at stations with a Smith-McIntyre Grab sampler for infaunal distribution and abundance. Two grab attempts were made at each site, and successful grab samples were sieved and retained material was preserved. Samples were transported to GeoScience Australia for sorting and analysis.

Organization: Australian Ocean Data Network
Microbial indicators of coral reef ecosystems

Metagenomic sequencing and 16S rRNA gene sequencing for 381 samples collected over the course of 16 months formed a new comprehensive microbial reference dataset of habitat specific coral reef microbiomes.

Originating from samples derived from three locations:

<code>Geoffrey Bay, Magnetic Island, QLD (monthly samples)

Pioneer Bay, Orpheus Island, QLD (periodic)

Channel, Orpheus Island, QLD (periodic)
</code>

The dataset consists of sequenced bacterial 16S rRNA genes of 381 samples including seawater, sediment, sponge tissue (Coscinoderma matthewsi and Amphimedon queenslandica), coral tissue and mucus (Acropora tenuis and Acropora millepora) and macroalgal surfaces (Sargassum sp.).

Water quality parameters and sea surface temperatures were used to compare environmental sensitivity variation in assembly patterns. Results indicated that seawater microbial community data provide diagnostic value to infer shifts in the surrounding reef environment.

Sample handling, tissue preparation, DNA extraction procedures and methods of analysis, have been described in associated publications listed below.

Accessing the 16S rRNA and metagenome sequences, metadata and protocols are available at the Bioplatforms Australia data portal under the Australian Microbiome project (https://www.bioplatforms.com/australian-microbiome/). Full usage requires free registration. To search for the 16S rRNA sequencing data, navigate to &lsquo;Processed data&rsquo;, select &lsquo;Amplicon is 27f519r_bacteria&rsquo; and &lsquo;Environment is Marine&rsquo;. Add an additional contextual filter, such as select &lsquo;Sampling Site Location Description&rsquo; from the dropdown menu and search for &lsquo;Geoffrey Bay&rsquo;, &#39;Pioneer Bay&#39; and &#39;Channel&#39; or by &lsquo;Sample Type&rsquo; i.e. is &lsquo;Seaweed&rsquo;.

Organization: Australian Ocean Data Network
An assessment workflow to recover microplastics from complex biological matrices

This published study developed a criteria-guided workflow to assess the effectiveness of microplastic separation methods on complex marine biological matrices. More specifically, the use of four microplastic separation methods commonly applied in the literature (nitric acid, HNO3, and potassium hydroxide, KOH, digestions, and sodium chloride, NaCl, and potassium iodide, KI, density flotations) were evaluated on four abundant marine taxa (hard coral, sponge, sea squirt, sea cucumber) using five environmentally relevant microplastics (fragments of polyethylene, polystyrene, polyethylene terephthalate, and polyvinylchloride, as well as rayon fibres). Methods were deemed efficient when (1) rates of sample clarification were appropriate, (2) effects on physical and chemical characteristics of microplastics were negligible, and (3) recovery rates of spiked microplastics into sample matrices were high. Specimens of Acropora millepora (hard coral), Rhopaloeides odorabile (sponge), Polycarpa aurata (sea squirt), and Holothuria atra (sea cucumber) were opportunistically collected from five reefs in the central Great Barrier Reef Marine Park (Rib Reef, Taylor Reef, Feather Reef, John Brewer Reef, Farquharson Reef) in 2017 and 2019. Irregular microplastic fragments and fibres were produced in the laboratory at the Australian Institute of Marine Science (AIMS), in Townsville (Queensland, Australia). This work was primarly conducted through controlled laboratory experiments at AIMS. Microplastic sizes were statistically analysed using general linear model in R. All other parametres assessed were not statistically analysed.

Organization: Australian Ocean Data Network
Nearshore marine habitat mapping of the Norfolk Marine Park

Parks Australia - Our Marine Parks Grants Round 2 Project: Nearshore marine habitat mapping of the Norfolk Marine Park (Grant Activity ID: 4-FIZ391E)

The Norfolk Marine Park is the is the eastern-most Park in the Temperate East Network of Australian Marine Parks, located between the NSW coast and Norfolk Island. The Park encompasses 188,444 km² of ocean and ranges in depth from 0 m at the Norfolk Island high tide mark to more than 5,00 m off the edge of the Norfolk Ridge. The Park includes two key ecological features – the Norfolk Ridge, and the Tasman Front and associated eddy field – both of which are valued for their high productivity, aggregations of marine life, biodiversity, and endemism. Norfolk Marine Park supports a range of species, including those listed as threatened under the Environment Protection and Biodiversity Conservation (EPBC) Act (1999), and contains Biologically Important Areas for breeding, foraging, and migration of seabirds, marine turtles, and humpback whales.

The objective of this project was to create the first marine habitat map for the nearshore shallow water surrounding Norfolk, Nepean, and Phillip Islands. This was conducted in collaboration with Norfolk residents to provide local knowledge input and to ground-truth the remotely-sensed habitat mapping. This high-level habitat map will be used for planning purposes, development applications, and EPBC Act referrals within the nearshore waters of the Norfolk Marine Park, where no specific zoning for recreational and commercial activities currently exists. The map provides a basis for any ongoing citizen-science-driven marine habitat impact and condition assessments, ecosystem monitoring, and to provide the Norfolk Island residents with ownership of any future zoning planning. The map can be further refined as more detailed information becomes available from subject matter experts in the future.

Tags: Habitat Mapping, Marine Parks, Satellite Mapping, Seafloor Classification
Organization: Australian Ocean Data Network
IMOS - Ships of Opportunity - Air-Sea Flux: Meteorological and SST Observations collected on the Research Vessel Tangaroa

This dataset contains environmental observations as well as ship parameters (such as speed and direction).

As part of the Ships of Opportunity - Research Vessels Real-Time Air-Sea Flux (ASF) Sub-Facility, R.V. Tangaroa collects underway meteorological and oceanographic observations in Sub-Antarctic. 

Data streams are fed into the existing ship data management system, and broadcast via satellite back to New Zealand daily. The observations are quality controlled at the Bureau of Meteorology and air-sea fluxes calculated using the COARE Bulk Flux algorithm. 

A daily file of 1-minute averages of the observations are generated shortly after 0000UTC and provided to the AODN.

The data is contained in NetCDF format files and consists of environmental observations as well as ship parameters (such as speed and direction).

Tags: Atmosphere | Atmospheric Pressure | Atmospheric Pressure, Atmosphere | Atmospheric Temperature | Surface Air Temperature, Atmosphere | Atmospheric Water Vapor | Humidity, Atmosphere | Precipitation | Precipitation Rate, Atmosphere | Radiation Budget | Longwave Radiation, Atmosphere | Radiation Budget | Shortwave Radiation, Countries | New Zealand, Global / Oceans | Pacific Ocean, Global / Oceans | Southern Ocean, Oceans | Ocean Optics | Photosynthetically Active Radiation, Oceans | Ocean Temperature | Sea Surface Temperature, Oceans | Ocean Winds | Surface Winds, Regional Seas | Coral Sea, Regional Seas | Tasman Sea, air_pressure, air_temperature, relative_humidity, sea_water_temperature, surface_downwelling_longwave_flux_in_air, surface_downwelling_shortwave_flux_in_air, thickness_of_rainfall_amount, wind_from_direction, wind_speed
Organization: Australian Ocean Data Network
The roles of age, parentage and environment on bacterial and algal endosymbiont communities in Acropora corals- OTU tables and metadata

These data are generated for the paper &ldquo;The roles of age, parentage and environment on bacterial and algal endosymbiont communities in Acropora corals&rdquo;. See paper for details on data collection and interpretations. The datasets include the bacterial and Symbiodiniaceae OTU tables, metadata as well as phylogenetic tree generated in Qiime1 for statistical analyses using the R package phyloseq.

Organization: Australian Ocean Data Network
Artificial light disrupts the nearshore dispersal of neonate flatback turtles Natator depressus

We used passive acoustic telemetry to examine the effects of two types of artificial light (metal halide and high pressure sodium) on the movement patterns of flatback turtle (Natator depressus) hatchlings as they disperse through nearshore waters. A total of 91 hatchlings were released, 30 of which were released under ambient conditions, 31 were released when a high pressure sodium light was present on a boat anchored in the nearshore and 30 were released when a metal halide light was present on the boat. Artificial light attracted hatchlings during their dispersal from shore, causing them to become disoriented and thus spend more time in the near shore. The metal halide light was more disruptive than high pressure sodium.  Ocean currents influenced hatchling trajectories under ambient conditions but when light was present, their effect was diminished as attraction to lights caused hatchlings to swim against currents. Under ambient conditions hatchlings moved perpendicular to the shoreline and did not appear to orient towards the peak wave direction. Our study shows that artificial lights at sea can delay the transit of hatchlings through the nearshore and cause them to expend energy lingering around light sources. As such, light mitigation strategies similar to those used on land are needed to minimise impacts on hatchlings in water.

Organization: Australian Ocean Data Network
Resources for Cyclone Anthony and Cyclone Yasi, north Queensland (January-February 2011)

Cyclone Anthony and Cyclone Yasi impacted the North Queensland coast during January and February 2011. Anthony, a category 2 storm crossed near Bowen on the 30th January. Yasi, a large category 5 system crossed the coast around midnight on 2nd February between Mission Beach and Cardwell.Data summaries from the AIMS weather stations and the FAIMMS sensor network are available for areas affected by both Cyclone Anthony and Cyclone Yasi.BOM cyclone tracks include three colour zones, depicting the current and forecast extent of gale force (62 km/hr), storm force (89km/hr) and hurricane force (117km/hr) winds. A list of reefs predicted to have been impacted within each zone for Cyclone Yasi is available along with a map of the zones.
 To provide data on Cyclone Anthony and Cyclone Yasi for research purposes.

Organization: Australian Ocean Data Network
NSW Drillholes Petroleum

Information about and locations of wells drilled to explore for and assess geology and/or potential petroleum resources. The petroleum drillholes dataset stores information about conventional petroleum wells within NSW. The dataset has been developed to record summary data on petroleum exploration and development drilling for holes drilled in New South Wales. The dataset contains summary information about each drillhole such as location, total depth, azimuth/dip, wireline logs, core availability and library location and DIGS references. This data is part of the New South Wales Geoscientific Data Warehouse (NSW GDW) series.

Tags: Geology, Mining
Organization: Department of Primary Industries and Regional Development (DPIRD)
AIMS Sea Water Temperature Observing System (AIMS Temperature Logger Program)

The data provided here are from a number of sea water temperature monitoring programs conducted in tropical and subtropical coral reefs environments around Australia. Data are available from approximately 80 GBR sites, 16 Coral Sea sites, 7 sites in North West Western Australia (WA), 8 Queensland regional ports, 13 sites in the Solitary Islands, 4 sites in PNG and 10 sites in the Cocos (Keeling) Islands. Data are obtained from in-situ data loggers deployed on the reef. Temperature instruments sample water temperatures every 5-10 minutes (typically) and are exchanged and downloaded approximately every 12 months. Temperature loggers on the reef-flat are generally placed just below Lowest Astronomical Tide level. Reef-slope (or where specified as Upper reef-slope) generally refers to depths 5 - 9 m while Deep reef-slope refers to depths of ~20 m.

Reefs are under threat from climate change. Elevated sea temperature is a major stress to reefs, capable of causing widespread coral bleaching and mortality. Small excursions of temperature outside normal summer levels can cause stress and bleaching in corals, especially sensitive species. Temperature data from this program are used to correlate with bleaching events and derive local bleaching thresholds. Data are also used in a wide variety of other marine research programs, including fisheries, balast water, turtles, sea birds, seagrass, coral disease, oceanography, process studies, validation of proxy climate records etc.

Download via the AODN Portal is currently unavailable, access through programming links below or the AIMS Time Series Explorer - https://apps.aims.gov.au/ts-explorer/

Organization: Australian Ocean Data Network
Myrmidon Reef Sensor Float 1

Sensor network infrastructure was installed at Myrmidon Reef in the central Great Barrier Reef off Townsville, Australia. The infrastructure consists of a base station mounted on the existing reef communications tower and a single buoy which carries the actual sensors.

Myrmidon Reef is on the edge of the continetial shelf and so the station is designed to measure upwelling of water from the slope coming up and onto the continential shelf. The station is linked to stations at Rib Reef (mid-shelf) and Orpheus Island (inshore) to track upwelling water across the shelf.

The project looks to deploy sensor networks at seven sites along the Great Barrier Reef to measure a range of physical parameters at a range of scales. The project will install communications, data and platform infrastructure that will support future sensor work looking at biological and chemical parameters.

Wireless Sensor Networks Facility (formerly known as Facility for The Automated Intelligent Monitoring of Marine Systems (FAIMMS)), part of the Great Barrier Reef Ocean Observing System project (GBROOS) (IMOS)

In February 2011 Cyclone &#39;Yasi&#39; damaged the existing AIMS weather station and so this buoy was deployed with both AIMS weather station sensors and sensors for the IMOS funded GBROOS project. In December 2011, a replacement buoy was deployed with the above water sensors being the existing AIMS weather station units and the in-water sensors being provided under the IMOS funded GBROOS project. This resulted in a data gap between the cyclone in February 2011 and the buoy being deployed in December 2011.

It is antcipated that the AIMS weather station will be restored in late 2012 in which case the above water sensors will transition back to the AIMS tower with the in-water sensors remaining as part of the IMOS funded work.

Organization: Australian Ocean Data Network
Maternal effects in gene expression of interspecific coral hybrids

Parental coral colonies of A. tenuis and A. loripes were collected from Trunk Reef on the central Great Barrier Reef in November 2015. During spawning, four offspring groups (i.e., reciprocal F1 hybrids and two parental purebreds: TT (purebred A. tenuis), TL (hybrid), LT (hybrid) and LL (purebred A. loripes), were recruited and settled onto ceramic plugs. Detailed crossing protocol and experimental design is described in Chan et al. (2018).

Coral recruits were reared under treatment conditions in filtered seawater for seven months at the National Sea Simulator of the Australian Institute of Marine Science. Treatment conditions included exposure to ambient or elevated temperature and pCO2 conditions:

<code>ambient conditions (27&amp;ordm;C and 415 ppm pCO2)

elevated conditions (ambient +1 &amp;deg;C and 685 ppm pCO2)
</code>

RNA-sequencing was conducted and the analysis showed that gene expression of the hybrid Acropora also showed clear maternal effects. Further details are presented in the paper Chan, WY, Chung, J, Peplow, LM, Hoffmann, AA, van Oppen, MJH. Maternal effects in gene expression of interspecific coral hybrids. Mol Ecol. 2021; 30: 517&ndash; 527. https://doi.org/10.1111/mec.15727

Organization: Australian Ocean Data Network
The role of gene expression and symbiosis in reef-building coral acquired heat tolerance

Wild coral colonies of Acropora tenuis were collected throughout the Great Barrier Reef and transferred to the Australian Sea Simulater (SeaSim). Corals were spawned, and produced purebred and hybris crosses, see Quigley &amp; van Oppen (2022) and Dixon &amp; Kenkel (2019) for full details of spawning and reproductive crossing.

Larvae produced from these crosses were sampled for gene expression and assayed using RNAseq before being exposed to control and heat stress for 36 hours (27 and 35.5 &deg;C) in replicates of n=6 (&ldquo;post&rdquo; exposure samples).

Separate cohorts of each larval cross not used in the heat trials were then induced to settle and exposed to four symbiont treatments. These replicates were sampled for RNAseq for each of the crosses prior to the heat stress at time 0 and 56 hours at 27&deg;C and 35.5&deg;C treatments.

For survival measurements, individual larvae were counted within net-wells in replicate plates within each temperature treatment. Each larval survival measurement represents a discrete sample measurement. The unit of measure is the number of individual replicate wells containing larvae.

Juvenile replicates RNAseq samples were taken in each of the crosses after 58 days at 27 and 32&deg;C. Survival measurements represent individual juvenile survival. Each represents a discrete sample measurement. The unit of measure is the number of individual replicate juveniles per replicate well, per replicate plate, per replicate tank for each temperature and symbiont treatment.

Larval survival was counted from 0 to 56 hours at 27&deg;C and 35.5&deg;C. Juvenile survival was counted at 0 and after 58 days at 27 and 32&deg;C treatments. Larvae were assayed for RNAseq at 0 and 56 hours, and juveniles only at 58 days. 

Experimental metadata of detailed replicates for larval treatments are found on the github repository in file J19188meta.csv. For&ldquo;pre&rdquo;, and &ldquo;post-ambient&rdquo; there were 33 larval replicates. For &ldquo;post-hot&rdquo; there were 30 replicates. Each replicate represented 10 pooled larvae. Each of the 11 crosses was replicated 3 times within each of those 3 treatment groups. There was a total of 96 larval samples.

Experimental metadata for juvenile data is found on the github repository in file J19234meta.csv. Of the juvenile samples, 119 werein ambient conditions with 27 in the heat treatment. Each of the 10 crosses was represented in the juvenile dataset 12-18 times. Thesymbiont treatments had 29 samples in C1, 38 samples in D1, 43 samples in SED, and 36 in SS1. There was a total of 146 juvenile samples.

Derived statistics presented are defined as independent observations of n= independent larval or juvenile survival based on the number

Organization: Australian Ocean Data Network