Update on Australia's National Reference Stations

The Integrated Marine Observing System National Reference Station network provides unprecedented open access to species-level phytoplankton and zooplankton data for researchers, managers and policy makers interested in resource condition, and detecting and understanding the magnitude and time-scales of change in our marine environment. We describe how to access spatial and temporal plankton data collected from the seven reference stations located around the Australian coastline, and a summary of the associated physical and chemical parameters measured that help in the interpretation of plankton data. Details on the rationale for site locations, sampling methodologies and laboratory analysis protocols are provided to assist with use of the data, and design of complimentary investigations. Information on taxonomic entities reported in the plankton database, and changes in taxonomic nomenclature and other issues that may affect data interpretation, are included. Data from more than 1250 plankton samples are freely available via the Australian Ocean Data Network portal and we encourage uptake and use of this continental-scale dataset, giving summaries of data currently available and some practical applications. The full methods manual that includes sampling and analysis protocols for the Integrated Marine Observing System Biogeochemical Operations can be found on-line.

The Ocean Biogeographic Information System (OBIS) began in 2000 as the repository for data from the Census of Marine Life. Since that time, OBIS has expanded its goals beyond simply hosting data to supporting more aspects of marine conservation (Pooter et al. 2017). In order to accomplish those goals, the OBIS secretariat in partnership with its European node (EurOBIS) hosted at the Flanders Marine Institute (VLIZ, Belgium), and the Intergovernmental Oceanographic Commission (IOC) Committee on International Oceanographic Data and Information Exchange (IODE, 23rd session, March 2015, Brugge) established a 2-year pilot project to address a particularly problematic issue that environmental data collected as part of marine biological research were being disassociated from the biological data. OBIS-Event-Data is the solution that was developed from that pilot project, which devised a method for keeping environmental data together with the biological data (Pooter et al. 2017). OBIS is seeking early adopters of the new data standard OBIS-Event-Data from among the marine biodiversity monitoring communities, to further validate the data standard, and develop data products and scientific applications to support the enhancement of Biological and Ecosystem Essential Ocean Variables (EOVs) in the framework of the Global Ocean Observing System (GOOS) and the Marine Biodiversity Observation Network of the Group on Earth Observations (GEO BON MBON). After the successful 2-year IODE pilot project OBIS-ENV-DATA, the IOC established a new 2-year IODE pilot project OBIS-Event-Data for Scientific Applications (2017-2019). The OBIS-Event-Data data standard, building on Darwin Core, provides a technical solution for combined biological and environmental data, and incorporates details about sampling methods and effort, including event hierarchy. It also implements standardization of parameters involved in biological, environmental, and sampling details using an international standard controlled vocabulary (British Oceanographic Data Centre Natural Environment Research Council). A workshop organized by IODE/OBIS in April brought together major animal tagging and tracking networks such as the Ocean Tracking Network (OTN), the Animal Telemetry Network (ATN), the Integrated Marine Observing System (IMOS), the European Tracking Network (ETN) and the Acoustic Tracking Array Platform (ATAP) to test the OBIS-Event-Data standard through the development of some data products and science applications. Additionally, this workshop contributes to the further maturation of the GOOS EOV on fish as well as the EOV on birds, mammals and turtles. We will present the outcomes as well as any lessons learned from this workshop on problems, solutions, and applications of using Darwin Core/OBIS-Event-Data for bio-logging data.

The Australian Integrated Marine Observing System (IMOS) is funded by the Australian Government, and designed to be a fully-integrated national array of observing equipment to monitor the open oceans and coastal marine environment around Australia. IMOS delivers physical, chemical and biological data comprising of observations from a wide spectrum of platforms including weather stations, oceanographic moorings, underway ship observations, seagliders, ocean surface radar, satellite image reception and reef based sensor networks. When data from ocean observing systems can be provided in near real-time, the operational aspects are further enhanced and provide potential for a range of value added products to be developed. Here we provide three examples of co-invested partnerships that have facilitated the development of real-time moored ocean observing systems in the coastal zone, operated by the Queensland IMOS node. For each of these examples, the project is introduced, a detailed technical description of the system is provided, operational aspects are summarised, and the uptake of data from stakeholders is discussed. These examples demonstrate the benefits of having a national collaborative approach to marine observing with a clear focus on open access to data. It is also demonstrated that the benefits and opportunities offered by real-time ocean observing can outweigh the technical challenges of developing and maintaining these complex systems.

Australia’s Integrated Marine Observing System (IMOS, imos.org.au) is research infrastructure to establish an enduring observing program for Australian oceanic waters and shelf seas. The observations cover physical, biological, and chemical variables to address themes of multi-decadal ocean change, climate variability and weather extremes, boundary currents and inter-basin flows, continental shelf processes and ecosystem responses. IMOS observations are collected by national facilities based on various platform types and operated by partner institutions around the country. In this paper we describe the infrastructure and workflows developed to manage and distribute the data to the public. We highlight the existing standards and open-source software we have adopted, and the contributions we have made. To demonstrate the value of this infrastructure we provide some illustrations of use and uptake. All IMOS data are freely and openly available to the public via the Ocean Portal ( https://imos.aodn.org.au ). All IMOS-developed software is open-source and accessible at https://github.com/aodn .

Shedding light on the distribution and ecosystem function of mesopelagic communities in the twilight zone (~200–1000 m depth) of global oceans can bridge the gap in estimates of species biomass, trophic linkages, and carbon sequestration role. Ocean basin-scale bioacoustic data from ships of opportunity programs are increasingly improving this situation by providing spatio-temporal calibrated acoustic snapshots of mesopelagic communities that can mutually complement established global ecosystem, carbon, and biogeochemical models. This data descriptor provides an overview of such bioacoustic data from Australia’s Integrated Marine Observing System (IMOS) Ships of Opportunity (SOOP) Bioacoustics sub-Facility. Until 30 September 2020, more than 600,000 km of data from 22 platforms were processed and made available to a publicly accessible Australian Ocean Data Network (AODN) Portal. Approximately 67% of total data holdings were collected by 13 commercial fishing vessels, fostering collaborations between researchers and ocean industry. IMOS Bioacoustics sub-Facility offers the prospect of acquiring new data, improved insights, and delving into new research challenges for investigating status and trend of mesopelagic ecosystems.

AimTo use a long‐term collection of bulk plankton samples to test the capacity of DNA metabarcoding to characterize the spatial and seasonal patterns found within a range of zooplankton communities, and investigate links with concurrent abiotic data collected as part of Australia's Integrated Marine Observing System (IMOS) programme.LocationSamples were sourced seasonally for 3 years from nine Pan‐Australian marine sites (n = 90).MethodsHere, we apply a multi‐assay metabarcoding approach to environmental DNA extracted from bulk plankton samples. Six assays (targeting 16SrRNA and COI genes) were used to target, amplify and sequence the zooplankton diversity found within each sample. The data generated from each assay were filtered and clustered into OTUs prior to analysis. Abiotic IMOS data collected contemporaneously enabled us to explore the physical and chemical drivers of community composition.ResultsFrom over 25 million sequences, we identified in excess of 500 distinct taxa and detected clear spatial differences. We found that site and sea surface temperature are the most consistent predictors of differences between zooplankton communities. We detected endangered and invasive species such as the bryozoan Membranipora membranacea and the mollusc Maoricolpus roseus, and seasonal occurrences of species such as humpback whales (Megaptera novaeangliae). We also estimated the number of samples required to detect any significant seasonal changes. For OTU richness, this was found to be assay dependent and for OTU assemblage, a minimum of nine samples per season would be required.Main ConclusionOur results demonstrate the ability of DNA to capture and map zooplankton community changes in response to seasonal and spatial stressors and provide vital evidence to environmental stakeholders. We confirm that a metabarcoding method offers a practical opportunity for an ecosystem‐wide approach to long‐term biomonitoring and understanding marine biomes where morphological analysis is not feasible.

We assess the performance of the ACOLITE (version 20231023.0) atmospheric correction algorithm using in situ radiometric instruments at a tropical coastal site. Specifically, we evaluate the ACOLITE remote sensing reflectance (Rrs) derived from Landsat-8, -9, Sentinel-2A, and -2B observations at the Integrated Marine Observing System (IMOS) Lucinda Jetty Coastal Observatory (LJCO), Queensland, Australia. The ground-based data used in our evaluation include both multi-spectral (AERONET-OC) and hyperspectral (Sea-Bird Scientific HyperOCR) measurements. Generally, we find excellent agreement (r2 > 0.8), low root-mean-squared-error (RMSE; ∼2.4 × 10 -3 sr-1), low mean bias error (MBE; ∼1.1 × 10 -3 sr-1) and low mean absolute percentage error (MAPE; ∼25 %) between the ground and satellite measurements; however, performance varies when broken down by sensor channel, satellite platform and validation dataset used. Considering individual channels, across all sensors, we find that ACOLITE performs best for the green band (560 nm; r2 = 0.91; RMSE = 1.68 × 10 -3 sr-1, MBE = 3.88 × 10 -4 sr-1, MAPE = 11 %) whereas the poorest performance was found for the coastal aerosol band (443 nm; r2 = 0.65; RMSE = 3.36 × 10 -3 sr-1, MBE = 2.73 × 10 -3 sr-1, MAPE = 40 %). We also find that better agreement is found when the satellite retrievals are compared against HyperOCR rather than AERONET-OC. Overall, the results show that ACOLITE provides reliable and accurate Rrs for the coastal waters encountered at LJCO.

HF ocean radar is a leading technology for measuring parameters of the ocean's surface in coastal waters. The technical and logistical advantage of shore-based measurements of the coastal ocean is a significant improvement over in situ measurements, and the cost per data point is low. The ability of HF radars to make 2D maps of surface currents and other parameters over quite large coastal areas is powerful and when establishment decisions were being made for the Integrated Marine Observing System (IMOS) in Australia a plan was adopted to establish the Australian Coastal Ocean Radar Network (ACORN). At the time of establishment we knew that HF coastal ocean radar was dominated by two genres of technology, and a planning decision was made to include elements of each of the phased array and crossed-loop genres into the new network. Because these are new technologies some of the applications and issues around quality control are still being developed and the inclusion of both genres allows ACORN staff and users of the archived data to fairly compare the genres. This paper addresses issues of process in setting up radar stations and establishing a data archive of good quality and easy access.

Surface velocity data from two WERA high-frequency (HF) ocean radar systems, deployed as part of the Australian Integrated Marine Observing System (IMOS), are compared with near-surface currents obtained from drifters and acoustic Doppler current profilers (ADCPs). We evaluate data from two contrasting locations in the first detailed evaluation of the IMOS HF radar surface velocities. HF radar measurements are generally robust but demand quality-control procedures to eliminate obvious errors and outliers that appear temporarily or systematically in the data. A number of different quality control procedures and filters are applied and assessed including Taylor diagrams and Hampel and Savitzky–Golay filters. In addition, the need for and effect of averaging are discussed. The radar measurements of surface current agreed better with the near-surface drifter currents than with the subsurface ADCP currents. Nonetheless, the ADCP comparisons are consistent with those previously reported in other regions. The value of the Taylor diagram for comparing different surface current data sets and processing approaches is demonstrated. Noise levels in the radar current spectra are used to estimate the error in the measurements and in some cases, these errors were found to approach the precision of the radar estimates. Our results give guidance on the most useful temporal sampling resolution. In particular we show that at these sites and these operating frequencies, using 10-min sampling without further averaging does not provide additional information because the higher frequencies are dominated by noise. Averaging the radials over 30 min may be sufficient for many applications.

Here, we describe a new national tide gauge‐based sea level dataset for monitoring sea level changes around Australia, and the novel homogenization methodology used to develop it. Homogenization is a two‐step process that involves the detection of jumps or steps in the data (inhomogeneities) followed by a correction applied to remove the change. This new dataset is called the Australian National Collection of Homogenized Observations of Relative Sea Level (ANCHORS). ANCHORS provides coastal sea levels at hourly resolution with homogenization performed on annual means. ANCHORS is intended to be a national tide gauge‐based sea level dataset to monitor changes in mean sea level and resultant coastal flood frequency changes around Australia. Whilst sea levels are rising around Australia in response to global mean sea level changes, coastal water levels represent a notable gap in the suite of in situ high‐quality datasets available for researchers, governments and industry. Tide gauge datasets are well suited to impact‐based assessments of changes in flood frequency, duration and risk. In this regard, ANCHORS will sit alongside existing satellite‐ and numerical modelling‐based sea level datasets to provide enhanced insights into the physical impacts of sea level rise on Australian coastlines. We have adapted established homogenization techniques to develop a national collection of homogenous long tide gauge records. The dataset comprises 38 tide gauge records from around Australia, varying in length from 34 to 123 years, with an average of 57 years. Finally, we discuss limitations and potential applications for ANCHORS and how these have informed the design of this coastal sea level dataset.

Malaysia has more than 630 culturists who are involved in the ornamental fish industry and culture 250 species, including local and exotic species. Among these viruses, megalocytiviruses have been associated with severe systemic diseases and economic losses in ornamental fish. The intensity of Megalocytivirus infection in Pterophyllum scalare in Malaysia remains unknown. Thus, this study aimed to investigate the occurrence of Megalocytivirus while discovering its associated risk factors and the genotypes of its causative agents in an ornamental fish farm in Malaysia. Seven broodstock pairs of P. scalare were used in this study to follow the life stages of fish, from egg to market size. Water samples and other samples, such as mucus swabs, gill swabs, P. scalare eggs, fries, juveniles, snails, snail eggs, live feed (Tubifex worms and Moina spp.), sediment samples, and wild fish, were collected periodically for initial environmental sampling from day 0 to day 60. Nested polymerase chain reaction amplifications were performed for megalocytivirus-related sequences. The phylogenetic tree, including the sampled causative agents of megalocytiviruses, was inferred from the major capsid protein genes of all known Iridoviridae species. Pearson's correlation coefficients were calculated to determine the strength of the correlation between the presence of megalocytiviruses in P. scalare samples and the associated risk factors. A total of 312 out of 935 pooled and individual samples tested positive for the presence of Megalocytivirus-related sequences, except snail eggs and wild fish (Poecilia reticulata). No clinical symptoms were observed in any fish samples. Megalocytivirus-associated viruses detected in water samples indicate horizontal transmission of the virus. All the nucleotide sequences found in this study had high nucleotide identities of 95%-99 % and were closely related to Megalocytivirus genotype I infectious spleen and kidney necrosis virus. Risk factors associated with Megalocytivirus include water temperature, dissolved oxygen (DO), pH, ammonia, nitrate, nitrite, and the life stages of P. scalare. High Megalocytivirus infection was detected when the water temperature, DO, and pH were high in P. scalare, high water temperature and nitrate in the water samples, and the same rate of Megalocytivirus infection in P. scalare fry and juveniles. This is the first study to confirm the existence of different possible routes of megalocytivirus distribution in ornamental fish farms in Malaysia. Nevertheless, the connection between the mode of transmission and the risk factors for this virus needs to be explored further to recognize the evolution and potential new host species.

Investigating waves in the nearshore zone is of key importance for coastal management, marine spatial planning, coastal risk mitigation and also for the understanding of coastal geomorphology. Among the existing systems to measure wave parameters in the nearhsore, the deployment of pressure sensors in the intertidal zone is an easy, low cost and energy-efficient solution. This solution extensively used to investigate the hydrodynamics of sandy beaches, has been less used in the case of steep rocky cliffs where the breaking process can be extremely energetic. Hence, the instruments deployed in such environments need to be able to resist extreme conditions. In this study, we present the pressure-sensor based measurement of wave parameters deployed on Banneg Isalnd, in the Molène archipelago, during four consecutive winters. This system is adequate for extreme wave conditions and can be used for long-term monitoring.

Box Model of Freshwater, Salinity and Nutrient in the Delta Mahakam East Kalimantan. Research has been conducted in the southern part of the Mahakam Delta, East Kalimantan. Method of measuring temperature, salinity, light transmission and turbidity by using CTD model 603 SBE and current measurement and bathymetry by using ADCP model RDI. Measurement parameters on the nutrient chemistry are based of water samples taken using Nansen bottles from two depths. The purpose of this study to determine the mechanism of freshwater, salinity and nutrient transport from the land of the Mahakam River which interact with seawater by using box models. The results illustrate that the vertical distribution of salinity in the Mahakam Delta has obtained a high stratification, where the freshwater salinity 12.30 psu at the surface of a river flowing toward the sea, and seawater of high salinity 30.07 psu flowing in the direction river under the surface that are separated by a layer of mixture. Freshwater budget of the sea (VSurf) obtained for 0,0306 x 109 m3 day-1, and the sea water salinity budget is going into the bottom layer system (VDeep.SOcn-d) obtained for 20,727 x 109 psu day-1. While time dilution (τSyst) obtained for 0.245 day-1 or 5.87 hours. Nutrient budget in the surface layer obtained by the system is autotrophic while in layers near the bottom tend to be heterotrophic. Keywords: box model, freshwater, Mahakam Delta, nutrient, salinity

Rogowski coil is used for measuring the alternating current (AC) and high-speed current pulses. However, the technology makes the Rogowski coil (RC) come out with more improvement, modification and until today it’s still being studied for the new application. The Rogowski coil has a few advantages compared to the high frequency current transformer (HFCT). A brief review on the basic theory and the application of Rogowski coil as a current sensor measurement that been done by previous researchers are presented and discussed in this paper. Additionally, the review also focused on the capability of Rogowski coil for high current sensor measurement and their application for fault detection, over voltage current sensor, lightning current sensor and high impulse current detection. The experimental set up, techniques and measurement parameters in models also been discussed. Finally, a brief review on the performance analysis of current sensor measurement of Rogowski coil likes sensitivity, the maximum and current detection which could be used as a guideline to another researcher in order to develop an advanced RC as high current sensor in future is presented. This review reveal that the RC has a very good performance in high current sensor detection in term of sensitivity which is up to a few nanosecond, higher bandwidth, excellent in detection of high fault and also could measuring lightning current up to 400kA and has many advantages compare to conventional current transformer(CT).

This paper presents a comparison of radial currents measured using a SeaSonde and a WERA HF radar on the West Coast of Australia. These radars are part of the Australian Coastal Ocean Radar Network which is a facility of the Australian Integrated Marine Observing system. Radial currents are the component of current along the radar look direction which is the measurement obtainable from an individual radar system. The two radars are sited 7km apart and the assumption is made that the radial currents from the two radars should be similar far enough away from these sites. The results, although preliminary, show that there is reasonable agreement at these distances. In addition the radial currents from both radars agree well with ADCP measurements at one of the ADCP sites. There is less agreement at the second ADCP site which is attributed to the more complex topography at that site.