AndreaBozzo/ceres-open-data-index huggingface dataset:
Bramble Cay Automated Marine Weather And Oceanographic Station

This dataset contains meteorological and light data from the weather station located on Bramble Cay in the northern part of the Torres Strait. The station was installed under funding from the National Environmental Science Programme (NESP) Tropical Water Quality Hub under Projects 2.2.1 and Project 5.14 with support from the Torres Strait Regional Authority (TSRA).

These data are collected to support scientific research. Data are made available on request to other researchers and to the public as well as being available from the AIMS web site. This weather station is funded by NESP with support from the Torres Strait Regional Authority (TSRA).

The weather station is an AIMS Mk5 system consisting of a Vaisala WXT520 weather station and a LiCor 192 Light Sensor. The system has seperate underwater sensors that are logged (and so not transmitted in real time). These sensors include a WetLabs NTUS turbidity sensor and a SeaBird SBE37 CDT (Condutivity (salinity), Temperature and Depth) located just off the Cay in 3m of water.

Note that this station is located on land and has NO in-water sensors. 

Data recorded: Barometric Pressure, Air Temperature, Humidity, Solar Radiation (PAR), Wind Direction True (vector averaged), Wind Speed True (30 min average), rain duration and rate, precipitation amount.

The weather stations collect and store data in electronic memory every ten minutes, the station uses the 3G phone network to send the data to AIMS where it is stored in a database and then made available via the web and other systems. 

The data are then checked for accuracy using a number of range and historical checks, longer term summeries are then calculated along with indicies of potential thermal stress.

Organization: Australian Ocean Data Network
Prioritising domestic locations for marine biosecurity management within a regional vessel network

Abstract:

Growing economic development is dramatically increasing international and domestic maritime trade. A network of vessel traffic facilitates this trade, but also the movement and introduction of marine invaders. Each vessel movement can transport organisms beyond their natural range, threatening destination ecosystems and economies. Understanding vessel movements is key to predicting and managing potential incursions and the continued dispersal of non-indigenous species (NIS). Here, we present a powerful, transferable framework for quantifying the relative likelihood of NIS incursion and vessel-mediated dispersal through international and domestic maritime networks. We used two proxies of potential NIS transfer, derived from the movements of commercial and recreational vessels. One for NIS movements via a ship&rsquo;s wetted hull surface area, and a second via ballast water. We demonstrate our framework with a case-study of New Zealand&rsquo;s marine transport system.  Using network analysis, we quantified relative incursion likelihood for each site from 1) international and 2) domestic vessel arrivals. Lastly, we quantified the extent of &lsquo;secondary exposure&rsquo; for sites one more stop downstream of the high-risk sites identified in 1 &amp; 2. Sites with the highest relative incursion likelihood were Auckland, Tauranga, Bluff, and New Plymouth. Several domestic sites were critical stepping-stone sites (e.g. Auckland and Tauranga) or local &lsquo;spatial super-spreaders&rsquo; of NIS (e.g. Wellington, Lyttelton). We identified several locations experiencing elevated secondary exposure (e.g. Whanganui and Ravensbourne) &ndash; sites that may not be flagged by traditional biosecurity prioritisation approaches. This network-based approach is transferable to any jurisdiction with vessel data, to support NIS surveillance and pathway management.

Organization: Australian Ocean Data Network
Benthic hard coral point score estimates for Barracouta shoal, North West Shelf from 2010, 2011, 2013 and 2016

These data consist of 20-point score estimates randomly placed on individual high resolution downward facing benthic digital images taken at Barracouta shoal using the AIMS towed video system.

The AIMS towed video system comprises a towed camera platform sending a live camera feed to a vessel-based, realtime image classification system (see Heyward et al. 2011) and a downward-facing high resolution still camera and strobe system programmed to take sequential still images at fixed time intervals of 10 seconds. The towed platform was deployed over the stern of the vessel, maintained as near as possible within a metre of the seabed and towed at 1-2 knots (1.5 nominal). Transect lengths varied among the years of data collection.

The downward-looking still images were geo-referenced during post-processing then analysed using a point-intercept approach. Information on benthic biota at each shoal was extracted from images using a point intercept approach with the AIMS Reefmon software (Jonker et al., 2008). All images were analysed using the Reefmon database system, with five overlaid points classified per photo and data logged against transect, depth and position.

The data provided here are derived using a machine learning model trained using the original manual annotations. The artificial intelligence engine called BenthoBot was used to re-analyse all seabed images from all years 2010-2016, processing each image using exactly the same approach. BenthoBot is a computer algorithm developed to classify points on an image, based on the spectral properties extracted from each image. It has been developed specifically by the Australian Institute of Marine Science to providean efficient and consistent means of generating the point based broad scale benthic classification data. The benefits of using BenthoBot include standardisation of the number of points sampled per image across all years (20 points per image) and removal of inconsistency in point classification associated with numerous technicians scoring images that may cause spatial and temporal artifacts.

Secondary (textural) datasets correlated with seafloor properties were developed from multibeam bathymetry to provide information on environmental characteristics, and are also provided here extracted for each image location as covariates.

Organization: Australian Ocean Data Network
Badu Island Automated Marine Weather And Oceanographic Station

This dataset contains meteorological and light data from the weather station located on Badu Island in the Central / Western part of the Torres Strait. The station was installed under funding from the Torres Strait Regional Authority (TSRA).

These data are collected to support scientific research.
Data are made available on request to other researchers and to the public. This weather station is funded by the Torres Strait Regional Authority (TSRA).

The weather station is an AIMS Mk5 system consisting of a Vaisala WXT520 weather station and a LiCor 192 Light Sensor.

Note that this station is located on land and has NO in-water sensors. 

Data recorded: Barometric Pressure, Air Temperature, Humidity, Solar Radiation (PAR), Wind Direction True (vector averaged), Wind Speed True (30 min average).

The weather stations collect and store data in electronic memory every ten minutes, the station uses the 3G phone network to send the data to AIMS where it is stored in a database and then made available via the web and other systems. 

The data are then checked for accuracy using a number of range and historical checks, longer term summeries are then calculated along with indicies of potential thermal stress.

Organization: Australian Ocean Data Network
Bleaching in larger benthic foraminifera from the Great Barrier Reef

Experiments were conducted to determine whether larger benthic foraminifera is prone to bleaching caused by increases in temperature and nutrient levels. The experiments aimed to characterise the physiological stress threatening these species, predicted to occur on tropical reef waters in the near future. Nutrient levels were chosen to represent naturally occurring nutrient concentrations during flood-plume events on the GBR, and temperatures were chosen to reflect current and future predictions for the GBR (Lough et al. 2006; Lough 2007).

Specimens of Amphistegina radiata and Heterostegina depressa were collected during dry season 2009 and wet season 2010, from the Whitsundays area nearby sites Double Cone Island, Border Island, Deloraine Island and Edward Island. Calcarina hispida specimens were collected from Heron Island 2009 and Calcarina mayorii from Magnetic Island. Daily average SST was obtained from AIMS AWS stations at Hardy Reef and Heron Island, temperature logger are Nelly Bay. Additional samplesof  A. radiata and H. depressa were collected from Dent Island and Bait Reef. 

A 6 day experiment with temperature manipulation were carried out with five individually set temperatures 23, 28, 30 32 and 33, exposing samples of A.radiata, H. depressa, and C. hispida. These experiments were repeated three times for A. radiata and H. depressa. To avoid thermal shock, the specimens were gradually introduced to the five different temperature treatments. Subsequent experiments used light levels of 11 -15  &micro;mol photos m-2 s-1.

A 30-day flow-through experiment was conducted where the effects of three temperature ranges and three nutrient levels were studied simultaneously:  Temperature: 26, 29 and 31, and nutrient concentrations of 0.5, 1.0 and 1.4 &micro;mol L-1. Specimens of A.radiata and H.depressa contained in six-well plates, and C. mayorii was contained in polypropylene tubes.

Analysis included photosynthetic efficiency, Chl a, motility and growth measurements in A. raditata. Results of these experiments suggested that physiological stress and bleaching are species specific.

This research was supported by the Australian government&rsquo;s Marine and Tropical Sciences Research Facility, implemented by the Reef and Rainforest Research Centre in northern Queensland, Australia.

Organization: Australian Ocean Data Network
Seeded Acropora digitifera corals survive best on wave-exposed reefs with grazing from small fishes

In a 16-month field study, we deployed aquaria-reared Acropora digitifera spat on engineered coral seeding devices across 10 sites spanning a wave-energy gradient at Moore Reef (Great Barrier Reef, Australia). Two devices were used to investigate the role of grazing: a fish-exclusion device and a featureless control.

Mature gravid Acorpora digitifera (Dana 1846) colonies were collected from Moore Reef ahead of coral spawning in February 2022.  The corals were transported back to the Australian Institute of Marine Science National Sea Simulator (SeaSim) facility and kept in temperature controlled outdoor aquaria. Gamete bundles were collected, separated, washed and fertilized, then the embryos were transferred to indoor larval rearing tanks where they remained until they reached settlement competency after 5-6 days.  Conditioned concrete tabs (14 &times; 14 mm2; developed under the Reef Restoration and Adaptation Program) were used as settlement substrates. The plugs contained a mixed community of crustose coralline algae and bacteria biofilms that are known to induce settlement of Acorpora corals; these were conditioned in aquaria for 2-months prior to settlement and the corals were held in aquaria (temperature control, flow through, no light, mixed feed of microalage and enriched rotifers) for 2-months after settlement. 

Corals were seeded to 10 sites on Moore Reef in May 2022. The field deployment followed a hierarchical design including location (n=1), sites (n=10), experimental plots (n=25, 2 devices per plot), device type (n=2, featureless control and a fish exclusion device), contrete settlement tabs (n=3 per device), and coral spat (n=&gt; 5 per tab) . Devices were deployed to the reef crest (3-5 m depth, high tide) and fixed in experimental plots with a cable tie in an upright, horizontal position. Devices and their fixings were removed after 16 months.

Data were collected at six timepoints and included quantitative and qualitative assessments to determine the influence of biological (fish abundance and grazing, benthic composition) and environmental (wave energy) drivers on coral growth and survival. Assessments were categorised and analysed by spatial scale. Bayesian hierarchical logistic mixed-effects regression models, principal component and redundancy analyses were used to interogate the data.

Organization: Australian Ocean Data Network
Bayesian concentration-response modelling using jagsNEC

This project used a suite of modern statistical methods to build robust tools for deriving probabilistic management thresholds from ecotoxicological data for use in water quality assessment and environmental risk assessment. 

This record documents the R packages developed under the project which proposed statistical solutions to account for uncertainty and appropriate methods for dealing with small samples:
<ul>
<li>

bayesnec is a No-Effect-Concentration estimation package that uses brms to fit concentration(dose)-response data using Bayesian methods for the purpose of estimating both ECX values, but more particularly NEC. 
</li>
<li>

the jagsNEC is an R package to fit concentration(dose) - response curves to toxicity data, and derive No-Effect-Concentration (NEC), No-Significant-Effect-Concentration (NSEC), and Effect-Concentration (of specified percentage &lsquo;x&rsquo;, ECx) thresholds from non-linear models fitted using Bayesian MCMC fitting methods via the R2jags package and jags.
</li>
</ul>

Organization: Australian Ocean Data Network
Associated invertebrate diversity from 11 sponge species in shallow tropical and temperate reefs

Samples of sponges were collected to assess the differences in abundance and diversity of invetebrate taxa from Ningaloo Reef (tropical) and Rottnest Island (temperate), Western Australia. The immediate habitat and substrate were sampled to assess any differences in faunal communities from surrounding habitats to sponge-associated fauna. Invertebrate communities were quantified from 11 sponge species across eight functional morphologies, and a total of 3966 individuals from 125 taxa were extracted. Four out of the 11 sponges supported higher fauna abundance compared to their surrounding substrate.

Photographs of the sponges were taken in situ prior to collection with a numbered calico bag being placed over the entire sponge. A flat blade scraper was used to remove the sponge from the substrate and then sealed underwater.  Sponge size (volume), % of internal space, minimum diameter of internal space, and gross morphological complexity were determined. 

Substrate type included sand, rubble, consolidated reef and macroalgae. See Chin etal (2020) for further descriptions of the methods and materials.

Organization: Australian Ocean Data Network
Coastal and estuarine resource condition assessment, a baseline survey in the southern NRM region, Tasmania: Moulting Lagoon / Great 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 Moulting Lagoon/Great Swanport.

Tags: Benthic macroinvertebrates, Degradation, Human impact, Monitoring program, Temperate Reef
Organization: Australian Ocean Data Network
Research vessel Tangaroa: a platform of the IMOS Ships of Opportunity - Research Vessels Real-Time Air-Sea Flux Sub-Facility

As part of the Ships of Opportunity - Research Vessels Real-Time Air-Sea Flux (ASF) Sub-Facility - research vessel Tangaroa collects underway meteorological and oceanographic observations (including SST) during its voyages in Sub-Antarctic. Data products are quality controlled meteorological and SST observations, and bulk air-sea fluxes. 

Tangaroa is a New Zealand multi purpose vessel which is configured for a wide range of environmental survey and ocean science work. 

Tangaroa is a 70m, 2291t vessel and operates under the call sign ZMFR.

Real-time, Sea Surface Temperature (SST) is processed from the vessel's SBE 38 calibrated temperature sensor located in the water intake pipe at 3 m depth.

Research Vessel Real Time Air-Sea Fluxes, aims to provide with "climate quality" meteorological measurement systems, capable of providing high quality air-sea flux measurements and delivered to researchers on a near real-time basis. Observations are obtained from NZ MetService AWS (wind speed and direction, air temperature, relative humidity, air pressure) and long-wave and short-wave radiation sensors (Eppley PIR and PSP) and precipitation sensor (RM Young siphon gauge).

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 and a daily file of 5-minute average calculated bulk fluxes are generated shortly after 0000UTC and provided to the AODN.

Tags: Atmosphere | Atmospheric Pressure | Atmospheric Pressure, Atmosphere | Atmospheric Temperature | Skin Temperature, Atmosphere | Atmospheric Temperature | Surface Air Temperature, Atmosphere | Atmospheric Water Vapor | Humidity, Atmosphere | Precipitation | Precipitation Rate, Atmosphere | Radiation Budget | Heat Flux, Atmosphere | Radiation Budget | Longwave Radiation, Atmosphere | Radiation Budget | Shortwave Radiation, Countries | New Zealand, Global / Oceans | Pacific Ocean, Global / Oceans | Southern Ocean, IMOS Platform | ZMFR | Tangaroa, Oceans | Ocean Temperature | Sea Surface Temperature, Regional Seas | Coral Sea, Regional Seas | Tasman Sea
Organization: Australian Ocean Data Network
A fast, precise, in-vivo method for micron-level 3D models of corals using dental scanners

The use of intra-oral dental scanning technology for the 3D scanning and model building of juvenile coral colonies was investigated.

Individual corals were scanned and measurements of volume and surface area were calculated, as well as the time it took to scan and build the models.

This collection includes a standard operating procedure workflow, 3D Objects, and csv + code.

Organization: Australian Ocean Data Network
Rapid Egestion of Microplastics in Juvenile Barramundi: No Evidence of Gut Retention or Tissue Translocation

This collection presents experimental data and a literature meta-analysis to understand microplastic translocation to fish tissue and egestion rates. Juvenile barramundi (Lates calcifer) were exposed through their diet to polyamide (PA) fibres and polyethylene terephthalate (PET) fibres and fragments (8&ndash;547 &mu;m in length) to determine if shape, size, and polymer type influence microplastic translocation and egestion rates.

Organization: Australian Ocean Data Network
Population genetics of the mangrove Rhizophora stylosa in northern Australia

Starch gel electrophoresis was used to examine genetic variation in five widely separated populations of the mangrove Rhizophora stylosa Griff. Shoots containing leaves and well developed apical buds were collected between March and August 1987 from Darwin, the Daintree River, 2 sites at Missionary Bay (Hinchinbrook Island), Chunda Bay (Cape Ferguson) and Lardelli Creek (Ayr). No two trees at each sampling site were separated by more than 1km, except for the Daintree River site, which was sampled over 2km.A suitable extraction buffer was developed by modifying a buffer developed by Dr Gavin Moran (CSIRO) for eucalypts and acacias.Twenty eight enzymes were investigated for the Rhizophora stylosa samples (ACP, ACON, AK, ADH, ALD, AAT, EST(FL), FH, BetaGAL, G6PD, GPI, GDH, GSR, GAPDH, HK, IDH, LAP, LGGP, LTP, LPP, MDH, ME, MDR, PER, PGM, 6PGD, SKDH, TPI). Fourteen enzymes were resolved adequately for these samples (ACON, AAT, GPI, GDH, GSR, HK, IDH, LAP, LTP, MDH, ME, PER, 6PGD, TPI).Other Rhizophoraceae successfully tested for enzyme activity in leaf and apical bud tissue, using the same methods were Rhizophora apiculata Blume, R. lamarckii Montr., R. mucronata Lamarck, Bruguiera gymnorhiza Lamarck, Ceriops decandra (Griff.) Ding Hou, C. tagal (Perr.) C.B. Rob. var. tagal and C. tagal var. australis C.T. White. Other mangrove species producing clear repeatable results included Lumnitzera racemosa Willdenow, Xylocarpus australasicus Ridley, Sonneratia alba J.E. Smith, Acrostichum speciosum Willdenow, Avicennia marina (Forssk.) Vierh. and A. officinalis Linnaeus.While leaves and buds were chosen initially, due to their year round availability, whole anthers and the plumule of the progagule of Rhizophora stylosa were also successfully tested for enzyme activity.
 This research was undertaken to:1. develop an effective extraction buffer to counteract the effect of complex secondary metabolites in mangroves, which denature proteins during enzyme extraction.2. develop techniques for the electrophoresis of mangrove tissue and to use these to investigate genetic variability in Rhizophora stylosa and other Rhizophoraceae.

Organization: Australian Ocean Data Network
Benthic Surveys & seafloor mapping of Wessel MP and Dhimurru IPA

This project is a partnership project between Dhimurru Aboriginal Corporation, AIMS and Deakin University to provide benthic habitat and bathymetry mapping and assessment.

This project will conduct seafloor mapping, and surveys of benthic and fish communities to obtain the baseline data required to understand the similarities between the Bremer Island Region and a Shoal in Wessel Marine Park, particulartly the areas which may support a reef system: Truant Bank, Pugh Shoal and Barbette Shoal. This project will collect baseline community data for these shoals as well as oceanographic data and compare to Bremer Island and in particular, Sykes shoal. The baseline data collected within the Wessel Marine Park will not only provide an understanding of the how the species in the Wessel Marine Park compared to other regionally important areas but also develop an understanding about connectivity between these areas and improve current scientific knowledge of the Marine Park.

&bull; The project will survey the bathymetry at Truant Bank, Pugh Shoal and Barbette Shoal using the R2Sonic multibeam echo sounder on AIMS&rsquo;s vessel Solander. At Bremer Island Kongsberg 2040C multibeam echo sounder surveys will be conducted on the Deakin University vessel MV Yolla. The MBES will be used to survey in the marine park. At Bremer Island 2400 kilometres will be surveyed with the MBES on the Yolla linking coverage to the Wessel marine park.

&bull; The benthic communities at the sites in the Wessel Marine Park will be surveyed using the towed video system on the Solander. In the marine park 20 towed video lines of 1.5 kilometres will be surveyed. At Bremer Island, ~25 sites will be surveyed with the drop camera system.

&bull; Baited remote underwater videos (BRUVs) will be used to survey fish populations at all sites. In the marine park, BRUVs will be deployed at 48 sites from the Solander. At Bremer Island BRUVs will be deployed at ~25-30 sites from the Ranger boat.

Organization: Australian Ocean Data Network