AndreaBozzo/ceres-open-data-index huggingface dataset:
Interspecific hybridisation provides a low-risk option for increasing genetic diversity of reef-building corals

Interspecific hybridisation increases genetic diversity and has played a significant role in the evolution of corals in the genus Acropora. In vitro fertilisation can be used to increase the frequency of hybridisation among corals, potentially enhancing their ability to adapt to climate change. Here, we assessed the field performance of hybrids derived from the highly cross-fertile coral species Acropora sarmentosa and Acropora florida from the Great Barrier Reef. Following outplanting to an inshore reef environment, the 10-month survivorship of the hybrid offspring groups was intermediate between that of the purebred groups, although not all pairwise comparisons were statistically significant. The A. florida purebreds, which had the lowest survivorship, were significantly larger at 10 months post-deployment compared to the other three groups. The four offspring groups harboured the same intracellular photosymbiont communities (Symbiodiniaceae), indicating that observed performance differences were due to the coral host and not photosymbiont communities. The limited differences in the performance of the groups and the lack of outbreeding depression of the F1 hybrids in the field suggest that interspecific hybridisation may be a useful method to boost the genetic diversity, and as such increase the adaptive capacity, of coral stock for restoration of degraded and potentially genetically eroded populations.

Organization: Australian Ocean Data Network
The last generation: F3 of Echinometra sea urchins under experimental climate change

A &gt;6 years mesocosm experiment was conducted to study the ocean warming and acidification threat to calcifying marine invertebrates such as Echinoderms looking at the cross- or trans-generational plasticity (TGP) as a mechanism for organisms to cope with climate change.

Marine invertebrates were exposed to climate stressors over multiple generations, rearing sea urchins at three climate scenarios (present day, predictions for 2050 and for 2100). Experimental treatments were conducted over 3 generations with Echinometra sp. A adults and larval between April 2016 and January 2022. Parental generation was sourced at Trunk Reef in the central Great Barrier Reef. Treatment conditions included:

Ambient (present day) Temperature based on seasonal profiling average 1991-2012 recorded at Davies Reef;  400 ppm (daily variation = &plusmn;60 ppm pCO2)
2050 (+&thinsp;1&deg;C temperature increase; ~685 ppm pCO2) (daily variation = &plusmn;60 ppm pCO2)
2100 (+&thinsp;2&deg;C temperature increase; ~940 ppm pCO2) (daily variation = &plusmn;60 ppm pCO2)

For full details see Uthicke, et al (2025)- https://doi.org/10.1007/s00227-024-04578-0

Organization: Australian Ocean Data Network
Comparative sensitivity of the early life stages of a coral to heavy fuel oil and UV radiation

This collection consists of a series of data sets assessing the sensitivity of pre-settlement life stages of the coral Acropora millepora to the dissolved fractions of heavy fuel oil under two light conditions: visible light in the absence of ultraviolet radiation and visible light in the presence of ultraviolet radiation. Data was collected on the sensitivity of gametes, developing embryos and planula larvae through laboratory experiments performed at the Australian Institute of Marine Science Townsville site during the mass coral spawning events in November and December of 2017-2019. The data was analysed using Bayesian dose-response modelling using the package jagsNEC in the software R.

For full methodological and analytical details please refer to the full research report, manuscript and supplementary materials.

Organization: Australian Ocean Data Network
Effects of Lobophora chemistry on settlement of coral larvae

The effects of Lobophora allelopathy chemistry on the settlement of larvae of nine species of corals was studied bioassays.

In October 2020, adult colonies of A. muricata, A. hyacinthus, A. intermedia, A. elseyi, Montipora aequituberculata, Goniastrea retiformis, Platygyra daedalea, and Coelastrea aspera were collected from the Keppel Islands. Adult colonies of A.millepora were collected from the Palm Islands and colonies of A. elseyi, were collected in 2019 from Falcon Reef. Spawn from these colonies was collected and cultured and used in settlement assays (in 6 well culture plates) using various extracts and conditioned water of Lobophora (collected from the Keppel Islands) and CCA/Rubble (collected from Palm Island and Davies Reef respectively). All assay were performed at SeaSim.

The cover of Lobophora was measured from photographs of 10 x 10cm quadrats at Mazie Bay, Pumpkin Island and Halfway Island Reefs. All Lobophora within these quadrats was collected, blotted dry and weighted.

Organization: Australian Ocean Data Network
Assessing the potential for “assisted gene flow” to enhance heat tolerance of multiple coral genera over three key phenotypic traits

Mass coral bleaching and mortality events have increased in frequency over the last 30 years, with ocean temperatures projected to reach bleaching thresholds annually by 2050. Genetic interventions like assisted gene flow may speed up adaptation in reefs with less heat-tolerant corals by increasing the frequency of heat tolerance-associated genetic variants, but the effectiveness of the intervention across species and life stages remains uncertain. To investigate, we generated reproductive crosses of corals from reefs along a thermal gradient on the Great Barrier Reef, comparing fitness traits in intra-region (same region) and inter-region (different region) offspring from three species (Acropora kenti, A. hyacinthus, and Goniastrea retiformis). Juveniles were inoculated with three heat-tolerant symbionts: Durusdinium trenchii, a heat-evolved Cladocopium goreaui strain, and &ldquo;wild&rdquo; symbionts from northern reef sediments, to assess symbiosis impacts on heat tolerance. Survival, growth, colour change (proxy for bleaching), and effective quantum yield of photosystem II (YII) were measured across larvae, juveniles, and adults at elevated (32 &deg;C, 35.5 &deg;C) and ambient (27.5 &deg;C) temperatures. Results showed higher survival in some inter-region crosses compared to intra-region crosses from central reefs in larvae and juvenile corals, though enhancement varied by species. Furthermore, heat-tolerant parents did not always produce heat-tolerant offspring, and larval heat tolerance did not always persist to the juvenile stage. Parent genetic background influenced survival more than symbiont treatment. These findings underscore the complexity of heat tolerance acquisition in early coral life stages.

See Macadam et al (2025) for full details - https://doi.org/10.1016/j.biocon.2025.111155

Organization: Australian Ocean Data Network
Establishing Guideline Values for Copper Toxicity to Marine Microbiomes

This data collection consists of water quality measurements, nutrient data and measured copper concentrations associated with an experiment exploring the effects of copper on seawater microbial communities to establish guideline values for copper toxicity to seawater microbiomes. Seawater for the experiment was collected from the AIMS jetty (19&deg;16&#39;38.4&quot;S 147&deg;03&#39;32.1&quot;E) in December 2020 and subsequently used in a 48-h exposure experiment. Water quality measurements (dissolved oxygen, pH and salinity) and water samples for nutrients (dissolved organic / inorganic carbon and nitrogen) were taken at 0-h and 48-h, following standard AIMS procedures. Representative water samples from the nominal experimental treatments (0, 0.1, 0.3, 1, 3, 10, 30, 100, 300 and 1000 &micro;g L-1) were sent to Townsville Laboratory Services for dissolved copper quantification. Data was entered into excel.

For full methodological and analytical details please refer to the full research publication, Thomas et al. (in press) its supplementary materials and the associated GitHub repository (GitHub - MarieCThomas/Copper.microbiome: Establishing guideline values for copper toxicity to marine microbiomes). Additionally, raw sequencing data can be found in the NCBI Sequence Read Archives under BioProject number PRJNA983933.

Organization: Australian Ocean Data Network
Coastal and estuarine resource condition assessment, a baseline survey in the southern NRM region, Tasmania: Little Swanport

A 12-month program was developed and implemented in order to obtain baseline information on water quality (salinity, water temperature, dissolved oxygen, turbidity, pH, dissolved nutrients, silica), ecological condition as shown by Chlorophyll a, benthic macroinvertebrates, pathogens, and habitat extent determined from habitat mapping. Five key estuaries and coastal waters were assessed in the Southern NRM Region of Tasmania. The data represented by this record was collected in Little Swanport.

Tags: Benthic macroinvertebrates, Degradation, Human impact, Monitoring program, Temperate Reef
Organization: Australian Ocean Data Network
Interactive effects of climate change and eutrophication on the dinoflagellate bearing benthic foraminifera Marginopora vertebralis

This study investigated the effects of increased temperature and nutrients on dinoflagellate-bearing foraminifera Marginopora vertebralis. The experiments manipulating temperature, and temperature combined with increased nitrate concentration, demonstrate that growth rates and mortality in M. vertebralis were significantly affected by temperature increase and nitrate addition. 

Specimens were collected from Shaw Island in the Whitsunday Region of the Great Barrier Reef at depths of 3 - 5 meters. 

Experiments tested a range of parameters including photosynthesis and respiration, composition of photosynthetic and photoprotective pigments, growth and mortality; measuring the response of the host-symbiont system.

This study included:

-a static incubator temperature range-finding experiment ran for 37 days. Five individual incubators were temperature controlled at 28, 30, 31, 32, and 34&deg;C. Each incubator held 4 containers holding 16 specimens of M. vertebralis.  

-a flow-through experiment where three temperature levels of 26, 29 and 31&deg;C and three nitrate concentrations were studied over a 30 day period. Three replicas of each variation were used, resulting in 27 aquaria each holding 12 specimens of M. vertebralis.

Organization: Australian Ocean Data Network
Changes in the metabolic potential of the sponge microbiome under ocean acidification

This study investigated the changes occurring in the functional potential of the microbiome of two marine sponge species living in low pH, &quot;acidified&quot; waters and adjacent (~ 500m away) ,&quot;control&quot; waters, at shallow coral reefs CO2 seep sites in Papua New Guinea.

Field work was carried out in the Milne Bay Province in the d&#39;Entrecasteaux Channel in Papua New Guinea at a depth of 5m. Control site GPS coordinates: 9.828217 S 150.820517 E, Seep site GPS coordinates: 9.8241 S 150.825833 E.

Three samples of each of two sponge species were collected. The species were Coelocarteria singaporensis and Stylissa flabelliformis. These particular species were chosen based on a previous study (Morrow et al., 2015) characterizeing the microbial communities of the 2 species at these particular field sites.

Sample size of three samples per species was chosen based on the following criteria:

1) minimizing impact on the field site
2) accounting for statistical testing sample size requirements
3) space availability for storage in the field and during transport
4) cost (temporal and financial) of sample processing and sequencing

Environmental data were collected over multiple expeditions as well as via remote loggers. Data was collected in August-2010, January 2013 and betweek December 2011-April 2014. For more information on environmental data for this study, please see Supplementary tables 3, 3 and 4.

Microbial functions of the two sponge species of the seep and control sites were compared, including transport of carbon and host derived compounds, carbon fixation and carbonic anhydrase, nitrogen and sulfur metabolism.

Organization: Australian Ocean Data Network
Biological Oceanographic Reconnaissance of the Arafura Sea

24 sampling stations in Arafura Sea were occupied during Cruise 5451 to study pelagic metabolism and primary production.

Observations included:

<code>Six 14C production experiments;

Five oxygen based P:R experiments;

Sixteen replicated (3) zooplankton stations with 100 and 330um nets, including two 24h time series (WES002-007 and WES015-018);

Continuous thermosalinograph measurements along the ship&amp;#39;s track;

Continuous measurement of remote sensing reflectance using the DALEC;

Four cross calibrations of DALEC data with Tricho-Cam imagery.
</code>

CTD transects recorded depth, pressure, temperature, salinity, density fluorescence, PAR, surface light, beam transfer, oxygen measurements.

Plankton and larval fish sampling was conducted using a conducted using the bongo net fitted with a Laser Optical Plankton Counter (LOPC) which counted particles in size bins between 100&micro;m and 2mm in equivalent spherical diameter (ESD). Depth-integrated bongo net sampling allowed the characterisation of fish larvae assembles and distribution. 

Water column structure, relative fluorescence and respiration rate and net community productions were analysed for hydrographic, chlorophyll and nutrient profiles for several locations.

59 species of copepods were identified in the region. 

Data is aggregated in a Microsoft Access Database

Organization: Australian Ocean Data Network
Modelled flood plumes - central and northern Great Barrier Reef

MECCA - a verified 3-dimensional hydrodynamic model was used to simulate river plume dynamics.Model simulations were compiled to examine the intensity, duration and frequency of different lower salinity events. Return periods were then calculated from the annual frequency of such events.The model was forced using daily river discharge data and time-series wind observation data. A mixing parameter was used to simulate tidal forcings.
 Use of computer simulation to understand the fate of riverine water as it mixes and moves around with the currents and winds.Used to quantify the connectivity between coastal runoff and the central and northern GBR.The simulations demonstrate a range of common spatial patterns and unusual events that can be expected from a dynamic process. Using this information a risk assessment using return period analysis of the frequency of different impact events can be undertaken to identify 'high-risk' regions or reefs.Environmental managers can use analyses based on the model for risk assessment on implications for dilutions and residence times of dissolved and suspended material carried within catchment runoff, as well as identifying potential plume pathways and travel times for the runoff and its contents to reach reefs.
 The model has been used for flood plume analyses on the Burdekin River (1966 - 1995); the Burdekin, Herbert, Tully, Johnstone, Russell, Barron, Daintree, Endeavour, Jeannie and Normanby Rivers (1969 - 1998); and the GBR lagoon.The database for analysis by the model created includes information on the duration of exposure to fresh water (exceedance), the minimum salinity and the return periods for the modelled domain.Wind data (recorded every 3 hours) was obtained from the Mackay weather station (just south of model domain) for the period 1966-1991, and from the AIMS weather stations for the period 1992-1998. Daily discharge data from the rivers was obtained from the Queensland Water Resources Commission. Tidal influences were included implicitly via the mixing parameters based on the work of King and Wolanski (1996). Thus these data can be applied to the model to simulate any of the major flood events of the rivers in this region over the last 30 years. The model has subsequently been run for the 2008 flood period.

Organization: Australian Ocean Data Network
Periodic and continuous thermal selection of Durusdinium trenchii

We investigated how 1) the selection of a coral photoymbiont under fluctuating temperatures compared to continuous selection under elevated temperatures and 2) the frequency of temperature oscillations influenced adaptation.

To this end, we exposed a Durususdinium trenchii culture (SCF086.01) to five temperatures profiles: diurnal fluctuations between an ambient and elevated temperature, fluctuations every 2-3 generations, fluctuations every 4-5 generations, continuous exposure to elevated temperatures and continuous exposure to an ambient temperature. We measured the growth performances of D. trenchii lineages to their respective selection strategies for 2.1 years. After 2.1 years of experimental evolution, we characterised the adaptive responses of the heat-evolved lineages at a range of temperatures (21-31&deg;C) and contrasted these to wild-types. We measured growth rates, oxidative stress, photochemical efficiency, photosynthesis and respiration rates.

This dataset contains the data collected during the experimental evolution and thermal performance assay. The experiments and measurements were carried out at the Symbiont Culture Facility at AIMS between 11.11.2020 and 20.04.2023.

Organization: Australian Ocean Data Network
A bioluminescent bacterial toxicity assay for tropical marine environments

This data collection consists of raw luminescence data, measured as relative luminesence units (RLUs), from the tropical bioluminsencent bacterium Vibrio azureus exposed to the reference toxicants, copper and zinc. V. azureus cells were exposed to various different concentrations of both toxicants over acute (15, 30 min) and chronic (&gt;24 h) exposure periods. In addition, luminescence data from the industry standard bacterial species, Aliivibrio fischeri, is included to benchmark the new bacterial toxicity assay.

For full methodological and analytical details please refer to the full research publication, Luter et al. (in review) its supplementary materials and the associated GitHub repository (https://github.com/open-AIMS/Lum31-tox-assays.git).

Organization: Australian Ocean Data Network
Browse Island Environmental Survey April 2017, Western Australia (ARP7 Reefs)

Towed Video transects + Digital StillsSloVid Digital StillsCTDBRUVSSBRUVSEcho SounderDrone ImagerySediment Samples (CSIRO)
 ARP7 Reefs Trip 6684To characterise the status of and natural temporal variability in sessile benthic biota and associated fish communities, across the plateau areas around Browse Island and its deeper waters. The project will provide a reference dataset, updated seasonally for two years, for the status of key biodiversity indicator habitats around Browse Island.

Organization: Australian Ocean Data Network
Coastal and estuarine resource condition assessment, a baseline survey in the southern NRM region, Tasmania: Port Cygnet

A 12-month program was developed and implemented in order to obtain baseline information on water quality (salinity, water temperature, dissolved oxygen, turbidity, pH, dissolved nutrients, silica), ecological condition as shown by Chlorophyll a, benthic macroinvertebrates, pathogens, and habitat extent determined from habitat mapping. Five key estuaries and coastal waters were assessed in the Southern NRM Region of Tasmania. The data represented by this record was collected in Port Cygnet.

Tags: Benthic macroinvertebrates, Degradation, Human impact, Monitoring program, Temperate Reef
Organization: Australian Ocean Data Network
Limited genetic signal from potential cloning and selfing within wild populations of coral-eating crown-of-thorns seastars (Acanthaster cf. solaris)

Population outbreaks of crown-of-thorns seastars (CoTS; Acanthaster spp.) are contributing to extensive coral loss and reef degradation throughout the Indo west-Pacific, but the causes and underlying mechanisms of population maintenance and outbreaks are equivocal. Two recent publications suggest that, in addition to outbreeding sexual reproduction, asexual reproduction through larval fission and selfing may contribute to rapid increases in the local abundance of Acanthaster spp. We re-analysed two large microsatellite datasets (collectively representing 3,714 individuals) that investigated connectivity in the Great Barrier Reef and Pacific region to investigate if potential cloning or selfing can be evidenced in the population genetic structure. Within this dataset we identified only a small number (18, &lt; 0.5%) of putative clones (repeated multi locus genotypes). We argue that several of these are due to sampling and processing errors rather than direct evidence of cloning. Analysis of the population genetic structure (i.e., pairwise genetic differences between individuals, deviations from Hardy-Weinberg-Equilibrium, and linkage disequilibrium) also yielded no genetic evidence for asexual reproduction. There was a tendency towards slight heterozygote deficits, so we cannot refute that selfing does occur, but this is mostly likely attributable to sampling artefacts. Although we cannot exclude that asexual reproduction occurs to some extent in Acanthaster populations, we find no evidence that these processes make a contribution to population structure or directly enhance larval supply.

This study was carried out during 2019.

Record Point of Truth: Uthicke, Sven; Pratchett, Morgan; Messmer, Vanessa; Harrison, Hugo (2020), Limited evidence of cloning and selfing within wild populations of coral-eating crown-of thorns seastar (Acanthaster cf. solaris), Dryad, Dataset, https://doi.org/10.5061/dryad.b5mkkwh93

Organization: Australian Ocean Data Network
Baseline coastal and estuarine condition assessment of the southern NRM region, Tasmania

A 12-month program was developed and implemented in order to obtain baseline information on water quality (salinity, water temperature, dissolved oxygen, turbidity, pH, dissolved nutrients, silica), ecological condition as shown by Chlorophyll a, benthic macroinvertebrates, pathogens, and habitat extent determined from habitat mapping. Five key estuaries and coastal waters were assessed in the Southern NRM Region of Tasmania. This data includes sampling from Pitt Water / Orielton Lagoon, North West Bay, Port Cygnet, Little Swanport, Moulting Lagoon / Great Swanport.

Tags: Benthic macroinvertebrates, Degradation, Human impact, Monitoring program, Temperate Reef
Organization: Australian Ocean Data Network
Tracing blue carbon flows across diverse seascapes

Abstract: 

Plants occupying coastal ecosystems draw in carbon dioxide (CO2) from the air and water around them during photosynthesis. A fraction of this CO2 becomes fixed into plant biomass and can eventually contribute to the blue carbon pool&mdash;organic carbon (Corg) sequestered in slow-turnover sinks. An important step in protecting and enhancing this natural carbon sequestration pathway is determining the relative contributions of different coastal plants to this blue carbon pool in durable sinks. We compiled a global dataset of coastal soil carbon measurements and used  a Bayesian hierarchical meta-regression model to explore the relative contribution of local (autochthonous) versus external (allochthonous) sources of Corg in the soils beneath tidal saltmarsh, mangrove, and seagrass wetlands. We found most soil Corg in coastal wetlands came from allochthonous sources, rather than the habitat-forming plants. Managing climate-resilient blue carbon seascapes, therefore, requires an awareness of this portfolio of contributors to soil carbon sequestration.  However, study design aspects such as soil sampling depth, levels of sample replication, and the modelling approach used to trace Corg can  have pronounced effects on the estimated contributions of different carbon sources. We outline a roadmap for improving how we track the various drivers of soil carbon sequestration in diverse mosaics of coastal  vegetation.

Organization: Australian Ocean Data Network