Australian Institute Of Marine Science Research Articles

Cross-cultural approach to biobanking of living coral cells on Woppaburra sea Country in the southern inshore Great Barrier Reef

ABSTRACT Biobanking of cryopreserved, living cells is a conservation tool being increasingly integrated into management and recovery efforts for at-risk wildlife. Together with reproductive technologies like in-vitro fertilisation, biobanking can secure biodiversity for decades and beyond to support species’ health and ability to survive and recover in a changing world. An inaugural on-Country coral biobanking project occurred in 2022 on Konomie (North Keppel Island) involving partners from Taronga Conservation Society, the Australian Institute of Marine Science and Woppaburra Traditional Custodians. Biobanking activities were undertaken with free prior and informed consent for the collection, cryopreservation and transfer of living coral material for secure and specialised storage at Taronga’s CryoDiversity Banks on Cammeraygal and Wiradjuri Countries. During this project and a subsequent Biobanking Cultural Safety event in September 2023, we discussed cultural matters related to biobanking and measures that could be taken to ensure that the enduring link to Country of these samples is maintained in perpetuity. These outcomes will form the basis of a best-practice approach to biobanking activities in other regions of the Great Barrier Reef, in partnership with the Traditional Custodians of those sea Countries.

Towards a systems framework for the assurance of maritime autonomous systems

ABSTRACT The burgeoning adoption of Robotic and Autonomous Systems with Artificial Intelligence (RAS-AI) necessitates standardized approaches for Systems Engineering (SE) and assurance of RAS-AI systems. Unlike crewed systems, RAS-AI systems lack real-time human control, posing unique challenges yet to be addressed by existing regulations and SE frameworks. This paper proposes the ”Autonomous Delta” approach for the Assurance of RAS-AI systems (As4AI), focusing on Maritime Autonomous Systems (MAS). It comprises seven parts, contextualizing RAS-AI assurance in an Australian maritime context, providing key definitions, a literature review, and outlining the research methodology. The core of the paper (Part 5) presents an As4AI framework, integrating concepts from SE and high-fidelity flight simulation. A prototype instantiation at the Australian Institute of Marine Science confirmed the framework's utility and identified areas for refinement. The paper concludes with a summary and suggestions for future research enabling operational deployment of MAS specifically and autonomous systems in general.

Environmental benefits of leaving steel-piled jacket platforms in place

With many of the Bass Strait reservoirs having reached the end of their productive life, Esso has been planning and preparing for the decommissioning of facilities including the currently non-producing steel-piled jacket platforms (platforms). Given many of these platforms have been in place for several decades, it is important to understand the ecosystem that has established around them to ensure that the environmental impacts and risks of decommissioning are appropriately assessed. Esso undertook an offshore environmental survey in 2021 using a remotely operated vehicle (ROV) to collect visual imagery of the environment around a representative set of platforms (and pipelines), including reference sites (natural seabed environment), to supplement available literature with site-specific data. The Australian Institute of Marine Science (AIMS) performed detailed analysis of the fish and benthic communities that are associating with the infrastructure to provide insights into understanding the habitat value of the infrastructure. An equal or better environmental outcome assessment undertaken by Esso identified that preserving the marine communities that have established on and around the platforms is a key consideration between complete removal of platforms and the proposed end state of retaining the lower sections (minimum 55 m below mean sea level) of selected platforms in situ.

Broad-scale analysis of fish community data suggests critical need to support regional connectivity of coral reefs.

Connectivity is vital for the biodiversity and functioning of marine ecosystems. It is known to be important for coral reefs, but the scales at which connectivity effects matter-and, correspondingly, the scales at which management responses are needed-are poorly understood in marine systems. We used 23 years of fish monitoring data collected from ~50 different coral reefs by the Australian Institute of Marine Science, together with a range of geographic data layers (including the Allen Coral Atlas) and additional network analysis, to explore the balance of local and regional influence on fish communities. Variance partitioning indicated that 42% of the variance in fish community composition could be explained by regional effects or their interaction with coarse-grained local influences (habitat). The variance explained by regional influences was divided evenly between measures that capture location on environmental gradients (e.g., proximity to coastal shelf, latitude) and cross-scale centrality measures of reef location within a broader reef network. A total of 11% of variance could be directly or indirectly attributed to management. Our results provide clear evidence that management and restoration of reefs across the globe must consider both local and regional influences on reef-associated organisms and highlight the potential benefits of improving connectivity in human-dominated coastal seascapes.

An Immersive Digital Commemoration of the Japanese Submarine I-124 Sunk in 1942 outside Darwin Harbor, Australia

The Japanese submarine I-124 was sunk in a military engagement with Allied forces outside Darwin Harbor, Australia, with 80 submariners aboard on 20 January 1942. To mark the 80th anniversary of this historic event and complement more traditional commemorative activities, a virtual-reality experience was created for general public engagement. The experience was based on a high-resolution multi-beam sonar survey completed in October 2021 by the Australian Institute of Marine Science, and used an animation-based workflow to illustrate the survey of the submarine, the events of its sinking and the historical data used to digitally reconstruct it. The animation culminates in a virtual dive across its decks as they may have appeared in the years after the sinking. Future plans for the site include diver-based surveys for photogrammetric survey and management-based monitoring. The creation of the experience required an in-depth consideration of a wide range of stakeholder needs and Australian and Japanese cultural attitudes to commemoration of World War II casualties. We describe the technical and cultural challenges encountered throughout the project.

A fast, precise, in‐vivo method for micron‐level 3D models of corals using dental scanners

Abstract Several sampling and measurement strategies have been developed to assess biological forms in three dimensions, including corals. However, the effectiveness (in speed and precision) of current three‐dimensional (3D) methods in scanning and model construction are challenging at small scales (μm–mm). In this paper, a practical 3D scanning and model construction tool using an intra‐oral dental scanner was assessed to measure the surface area and volume of coral juveniles across multiple species. Intra‐oral scanners using confocal imaging are fast, precise to the μm scale and safe to use with live tissue, thereby eliminating the need to harm or kill the animals. The trial was conducted at the National Sea Simulator at the Australian Institute of Marine Science. High‐quality 3D scans of individual coral juveniles were successfully generated and integrated automatically into high‐resolution (μm) mesh from point clouds. The attained average scanning efficiency was <2 min/individual, without a significant difference in speed given coral complexity or between live colonies or dead coral skeletons. Overall, this fast and precise system could become a promising tool for marine environmental surveys and restoration initiatives. This tool also removes the need to sacrifice animals for measurement analysis, thereby increasing conservation and animal welfare.

Chelarctus and Crenarctus (Crustacea: Scyllaridae) from Coral Sea waters, with molecular identification of their larvae

Chelarctus Holthuis, 2002 is widely distributed throughout the Indo-West Pacific, but its biogeographic patterns are unknown because Southern Hemisphere areas, such as the Coral Sea, remained poorly explored. Recent cruises organized by the Muséum national d'Histoire naturelle of Paris and the Australian Institute of Marine Science allowed the molecular identification of Crenarctus crenatus (Whitelegge, 1900), Chelarctus aureus (Holthuis, 1963) and Chelarctus crosnieri Holthuis, 2002 phyllosomae. The Coral Sea C. crenatus larvae are identical to stages IX and X of Scyllarus sp. Z, described in detail by Webber and Booth (2001). Descriptions of phyllosoma stages VI, IX and X of Ch. aureus and stages IX and X of Ch. crosnieri are also presented here. Morphological differences between Crenarctus and Chelarctus larvae are established for the first time and previous misidentifications in the literature are re-assessed.

Publication Performance and Trends in Mangrove Forests: A Bibliometric Analysis

Mangroves are one the most productive ecosystems on Earth, and they are geographically located in the tropics and sub-tropics. Notwithstanding their critical role in providing a large number of environmental services and benefits as well as livelihood provisions, mangrove forests are being lost globally at an alarming rate. At the same time, they are increasingly recognized as a cost-effective nature-based climate solution for their carbon sequestration and storage capacity. Despite their enormous importance to people’s lives and the ecosystem, no bibliometric study on this topic has been published to our knowledge. Here, we provide a bibliometric analysis of the research on mangroves with research trends, most influential research based on citation count, and the origins (country and institution) of major research. Using the Science Citation Index Expanded (SCI-EXPANDED) database of the Web of Science Core Collection (Clarivate Analytics), we identified 13,918 documents published between 1990 and 2019. Nevertheless, 12,955 articles met our final criteria and were analyzed in detail. Six publications and their citations per publication (CPP2019) were applied to evaluate the publication performance of countries and institutes. When considering the top ten Web of Science subject categories, articles published on the ecology of mangroves had the highest CPP2019 of 28. Environmental sciences have been the major category since 2013. The USA dominated the total articles and single-author articles. The USA was also the most frequent partner of international collaborative publications. China published the most single-country articles, first-author articles, and corresponding-author articles. However, articles by the USA and Australia had a higher CPP2019. Sun Yat Sen University in China was the most active university. The Australian Institute of Marine Science dominated all kinds of publications with the top CPP2019. Together with the USA, Australia, China, India, Brazil, and Japan ranked both the top six on total publications and total publications in 2019. Our bibliometric study provides useful visualization of the past and current landscape of research on mangroves and emerging fields, to facilitate future research collaboration and knowledge exchange.

Great Barrier Reef degradation, sea surface temperatures, and atmospheric CO2 levels collectively exhibit a stochastic process with memory

Quantifying ecological memory could be done at several levels from the rate of physiological changes in an ecosystem all the way down to responses at the genetic level. One way of unlocking the information encoded in a collective environmental memory is to examine the recorded time-series data generated by different components of an ecosystem. In this paper, we probe into the case of the Great Barrier Reef (GBR) which is threatened by elevated sea surface temperatures (SST) and ocean acidification attributed to rising atmospheric CO2 levels. Specifically, we investigate the interrelated dynamics between the degradation of the GBR, SST, and rising atmospheric CO2 levels, by considering three datasets: (a) the mean percentage hard coral cover of the GBR from the archives of the Australian Institute of Marine Science; (b) SST close to the GBR from the National Oceanic and Atmospheric Administration; and (c) the Keeling curve for atmospheric CO2 levels measured by the Mauna Loa Observatory. We show that fluctuating observables in these datasets have the same memory behavior described by a non-Markovian stochastic process. All three datasets show a good match between empirical and analytical mean square deviation. An explicit analytical form for the corresponding probability density function is obtained which obeys a modified diffusion equation with a time dependent diffusion coefficient. This study provides a new perspective on the similarities of and interaction between the GBR’s declining hard coral cover, SST, and rising atmospheric CO2 levels by putting all three systems into one unified framework indexed by a memory parameter \(\mu \) and a characteristic frequency \(\nu \). The short-time dynamics of CO2 levels and SST fall in the superdiffusive regime, while the GBR exhibits hyperballistic fluctuation in percent coral cover with the highest values for \(\mu \) and \(\nu \).

Cross-generational effects of climate change on the microbiome of a photosynthetic sponge.

Coral reefs are facing increasing pressure from rising seawater temperatures and ocean acidification. Sponges have been proposed as possible winners in the face of climate change; however, little is known about the mechanisms underpinning their predicted tolerance. Here we assessed whether microbiome-mediated cross-generational acclimatization could enable the photosynthetic sponge Carteriospongia foliascens to survive under future climate scenarios. To achieve this, we first established the potential for vertical (cross-generational) transmission of symbionts. Sixty-four amplicon sequence variants accounting for >90% of the total C. foliascens microbial community were present across adult, larval and juvenile life stages, showing that a large proportion of the microbiome is vertically acquired and maintained. When C. foliascens were exposed to climate scenarios projected for 2050 and 2100, the host remained visibly unaffected (i.e. no necrosis/bleaching) and the overall microbiome was not significantly different amongst treatments in adult tissue, the respective larvae or recruits transplanted amongst climate treatments. However, indicator species analysis revealed that parental exposure to future climate scenarios altered the presence and abundance of a small suite of microbial taxa in the recruits, thereby revealing the potential for microbiome-mediated cross-generational acclimatization through both symbiont shuffling and symbiont switching within a vertically acquired microbiome.

Regional Movements of Reef Manta Rays (Mobula alfredi) in Seychelles Waters

This study was funded by the Save Our Seas Foundation (SOSF) and supported by The Manta Trust, The University of Western Australia, and the Australian Institute of Marine Science. Field work was supported by the SOSF-D'Arros Research Centre, Island Conservation Society (ICS), Alphonse Foundation, Islands Development Company, Blue Safari, the Alphonse Island Lodge, and the UWA Postgraduate Student's Association.

Saving coral reefs

When ecologist Carly Randall first dove into the waters of the Great Barrier Reef in 2017, she was bracing herself for the worst. During the prior year or so, the reef had been ravaged by back-to-back heat waves and an invasion of crown-of-thorns starfish. When corals get too hot, they release the algae that live in their cells and provide them with nutrients, turning the corals white and sometimes causing them to starve. And crown-of-thorns starfish, which look like hostile creatures from a B movie, feast on reef-building corals, leaving behind skeletons. But rather than a disintegrating ecosystem reminiscent of a horror flick, Randall saw a reef full of vibrant corals, teeming with fish and other aquatic life. “What did they even hire me to do restoration for? This reef looks amazing,” she remembers wondering. Randall had just moved from the US to the Australian Institute of Marine Science to

First person – Kate Quigley

ABSTRACTFirst Person is a series of interviews with the first authors of a selection of papers published in Biology Open, helping early-career researchers promote themselves alongside their papers. Kate Quigley is first author on ‘Assessing the role of historical temperature regime and algal symbionts on the heat tolerance of coral juveniles’, published in BIO. Kate is a postdoc in the lab of Madeleine van Oppen and Line Bay at Australian Institute of Marine Science, Australia, investigating the genomic mechanisms associated with population connectivity, thermal tolerance and adaptation, and resiliency of coral reef organisms.

The effect of marine seismic surveys on the movement, abundance and community structure of demersal fish assemblages on the North West Shelf

In 2018, the Australian Institute of Marine Science (AIMS) and its partners, conducted an experiment to investigate the effect of exposure to a 3D seismic survey on demersal fishes. The experiment involved the use of a commercial seismic vessel equipped with a 2600 cubic inch air-gun array, sailing a racetrack pattern with eight operational (high exposure zone) and eight inactive (vessel control zone) sail lines, with a 500 m sequential line separation and ≈18 m shot point spacing. The high exposure and vessel control lines were separated by 35 km. Demersal fishes were observed in five sampling surveys over a 6-month period (three surveys before and two after exposure), using acoustic telemetry and stereo baited remote underwater videos systems (BRUVS). The telemetry component included the capture, tagging with acoustic transmitters and release of 387 red emperor (Lutjanus sebae) within two telemetry receiver arrays. These arrays, one in each zone, comprised 37 and 39 acoustic receivers over ≈32 km2, to record movements of tagged fish. The receivers provided near-continuous data on tag locations, and, hence, movement of fish in the area, until removal in December 2018. During each sampling survey, BRUVS were deployed at various distances from the area of the seismic survey. Study results are currently being finalised for presentation.

First person – Camilla Elinor Korsvig-Nielsen

ABSTRACTFirst Person is a series of interviews with the first authors of a selection of papers published in Biology Open, helping early-career researchers promote themselves alongside their papers. Camilla Elinor Korsvig-Nielsen is first author on ‘Eyes and negative phototaxis in juvenile crown-of-thorns starfish, Acanthaster species complex‘, published in BiO. Camilla Elinor conducted the research described in this article while a bachelor's student in Anders Garm's lab at University of Copenhagen and Mike Hall and Cherie Motti's lab at Australian Institute of Marine Science after a semester at The University of Queensland. She is now a master's student in the lab of Anders Garm at University of Copenhagen, investigating marine invertebrate sensory behaviour and ecology with emphasis on vision and olfaction.

Good, bad or ugly: all a matter of perspective?

Seafood Industry Australia (SIA) is the national peak body that represents the Australian seafood industry as a whole, including members from wild catch, aquaculture and post-harvest sectors. According to the Australian Institute of Marine Science (AIMS), the fishing and petroleum industries represent a combined contribution to the Australian economy of ~AU$28.5 billion (in 2015–2016) and employ (directly and indirectly) over 55000 Australians.1 At times, our industries’ interests have competed. However, we recognise that we can unlock value for the economy, and those who work in our industries, by finding effective ways to work together. In 2014, a Memorandum of Understanding (MOU) was signed between five commercial fishing and seafood industry associations and APPEA. This MOU committed to the core principles of improved cooperation, open communication and stronger consultation. There is significant benefit for both industries in learning how to improve shared access to marine resources, whether at the early stages of petroleum activities (e.g. seismic) or at the end of an asset’s life (e.g. decommissioning). This presentation will look at efforts to improve relationships between our two industries and make observations about potential ways forward.

Darwin Harbour – a partnership approach to understanding and evaluating environmental challenges

Darwin Port plays a critical role in the Northern Territory’s export-oriented economy and in supporting the economy of northern Australia more generally. Darwin Port is the only true multi-modal port in northern Australia, with direct connectivity to southern Australia and beyond via the southern rail link. The port has developed rapidly over the past decades, with redevelopment of the Waterfront Precinct, development of numerous residential marinas, construction of the East Arm Wharf and marine supply base, and construction and operation of liquefied gas processing and export facilities. Future development plans include Middle Arm Industrial Precinct and Marine Industry Park. These developments have resulted in an order of magnitude increase in dredging requirements, an increase in vessel traffic and an increase in public focus on environmental quality within the harbour. A coordinated, multi-agency approach to understand the complex marine environment of Darwin Harbour has underpinned much of the development activity and provided a sound scientific basis to evaluate potential environmental impacts associate with past and future developments. Through a hierarchical process of environmental assessment and identification and mitigation potential risks, the Australian Institute of Marine Science has partnered with industry, government and other research providers to deliver projects to map and assess habitats, monitor environmental attributes and evaluate potential impacts, and provide environmental information in novel and accessible ways to support harbour operations and inform strategic planning. The partnership approach adopted for Darwin Harbour serves as a model for leveraging resources to understand and manage environmental and operational risks in northern ports.

Innovation and technology in marine science: AIMS' North West Shoals to Shore Research Program – an update

In 2017, the Australian Institute of Marine Science and its partners commenced the North West Shoals to Shore Research Program. The program is designed to address significant scientific and environmental knowledge gaps pertinent to the management of the offshore petroleum industry, a key stakeholder in this ecologically and commercially important region of Australia. The program comprises four themes. 1. Marine noise monitoring and impacts: includes two seismic source (2600 cubic inch air-gun array) exposure experiments have been conducted to investigate selected responses by demersal fishes and pearl oysters across different spatial and temporal scales. 2. Seabed habitats and demersal biodiversity: seeks to understand the physical and biological characteristics of the ancient coastline key ecological feature around the 125 m depth contour and pearl oyster habitats offshore from Eighty Mile Beach. The work examines the ecological processes that maintain benthic communities on both ancient and contemporary coastlines 3. Protected and iconic species movement, distribution and threats: uses innovative sampling techniques to confirm biologically important areas for pygmy blue whales, hawksbill and green turtles. This will assist the quantification and mitigation of the risks vessel movements, industrial infrastructure and activities pose to marine megafauna on the Northwest Shelf. 4. Spatial dynamics of isolated coral reef atolls: develops a habitat model and adaptive monitoring program that informs the future condition of these remote coral reef atolls. Significant progress has been made by the program in 2018, including the development of innovative and technical approaches to sampling.

Never Off the Hook—How Fishing Subverts Predator-Prey Relationships in Marine Teleosts

We acknowledge financial support of the Australian Institute of Marine Science, James Cook University and the University of Saskatchewan.

Rarity of the “common” coral Pocillopora damicornis in the western Philippine archipelago

Extensive phenotypic plasticity generally confounds identification of the common reef-building coral Pocillopora damicornis. With the recognition of P. damicornis genetic lineages as taxonomic species, this study surveyed genetic lineages within P. damicornis sensu lato (Veron and Pichon in Scleractinia of Eastern Australia, Australian Institute of Marine Science, Australia, 1976) in the Philippines. Employing a PCR–RFLP assay of the mitochondrial control region and sequencing of the mitochondrial open reading frame for lineage identification, we examined 694 P. damicornis s.l. colonies from 16 locations across the Philippine archipelago to characterize Pocillopora species distribution in the region. Genetic identification reveals the occurrence of P. acuta and the absence of P. damicornis in the Philippines. This study highlights the need to revisit the distributional limits of this extensively studied species complex and the necessity of using genetic information for taxonomic identification where morphological identification is unreliable.