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2022 Publications (links to each paper available at read more)

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Figure 1 from Andrzejaczek et al. (2022) showing deployment and pop-up and/or recapture locations from tracked elasmobranchs.

Diving into the vertical dimension of elasmobranch movement ecology

Andrzejaczek, S, et al. including BM Gillanders. 2022. Science Advances

Knowledge of the three-dimensional movement patterns of elasmobranchs is vital to understand their ecological roles and exposure to anthropogenic pressures. To date, comparative studies among species at global scales have mostly focused on horizontal movements. Our study addresses the knowledge gap of vertical movements by compiling the first global synthesis of vertical habitat use by elasmobranchs from data obtained by deployment of 989 biotelemetry tags on 38 elasmobranch species. Elasmobranchs displayed high intra- and interspecific variability in vertical movement patterns. Substantial vertical overlap was observed for many epipelagic elasmobranchs, indicating an increased likelihood to display spatial overlap, biologically interact, and share similar risk to anthropogenic threats that vary on a vertical gradient. We highlight the critical next steps toward incorporating vertical movement into global management and monitoring strategies for elasmobranchs, emphasizing the need to address geographic and taxonomic biases in deployments and to concurrently consider both horizontal and vertical movements.


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Image: Nicole in the laboratory.

A targeted capture approach to generating reference sequence databases for chloroplast gene regions

Foster, NR, KJ van Dijk, E Biffin, JM Young, VA Thomson, BM Gillanders, AR Jones, and M Waycott. 2022. Ecology and Evolution

Metabarcoding has improved the way we understand plants within our environment, from their ecology and conservation to invasive species management. The notion of identifying plant taxa within environmental samples relies on the ability to match unknown sequences to known reference libraries. Without comprehensive reference databases, species can go undetected or be incorrectly assigned, leading to false-positive and false-negative detections. To improve our ability to generate reference sequence databases, we developed a targeted capture approach using the OZBaits_CP V1.0 set, designed to capture chloroplast gene regions across the entirety of flowering plant diversity. We focused on generating a reference database for coastal temperate plant species given the lack of reference sequences for these taxa. Our approach was successful across all specimens with a target gene recovery rate of 92%, which was achieved in a single assay (i.e., samples were pooled), thus making this approach much faster and more efficient than standard barcoding. Further testing of this database highlighted 80% of all samples could be discriminated to family level across all gene regions with some genes achieving greater resolution than others—which was also dependent on the taxon of interest. Thus, we demonstrate the importance of generating reference sequences across multiple chloroplast gene regions as no single loci are sufficient to discriminate across all plant groups. The targeted capture approach outlined in this study provides a way forward to achieve this.


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Climate Change and Fishes in Estuaries - Chapter 7 in Fish and Fisheries in Estuaries

Gillanders, BM, MN McMillan, P Reis-Santos, LJ Baumgartner, LR Brown, J Conallin, FV Feyrer, S Henriques, NC James, AJ Jaureguizar, ALM Pessanha, RP Vasconcelos, AV Vu, B Walther, and A Wibowo. 2022. Fish and Fisheries in Estuaries, edited by AK Whitfield, KW Able, SJM Blaber, and M Elliott.

This chapter provides an overview of the main drivers of change in estuarine systems, their expected causes and impacts on estuarine fish and fisheries. An analysis of global, regional and local patterns of estuarine fish and how climate induced change may impact estuarine systems and their fish communities is provided. We also examine the main environmental, climatic and biological stressors likely to impact estuarine fish and associated fisheries. A set of case studies is used to illustrate the differences in potential impacts associated with various global regions and types of estuaries. An understanding of climate change in estuaries will support estuarine ecosystem resilience, inform management and facilitate adaptation.


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The potential for emissions reduction and carbon capture in marine aquaculture

Jones, AR, HK Alleway, D McAfee, P Reis-Santos, SJ Theuerkauf, and RC Jones. 2022. Bioscience

Aquaculture is a critical food source for the world's growing population, producing 52% of the aquatic animal products consumed. Marine aquaculture (mariculture) generates 37.5% of this production and 97% of the world's seaweed harvest. Mariculture products may offer a climate-friendly, high-protein food source, because they often have lower greenhouse gas (GHG) emission footprints than do the equivalent products farmed on land. However, sustainable intensification of low-emissions mariculture is key to maintaining a low GHG footprint as production scales up to meet future demand. We examine the major GHG sources and carbon sinks associated with fed finfish, macroalgae and bivalve mariculture, and the factors influencing variability across sectors. We highlight knowledge gaps and provide recommendations for GHG emissions reductions and carbon storage, including accounting for interactions between mariculture operations and surrounding marine ecosystems. By linking the provision of maricultured products to GHG abatement opportunities, we can advance climate-friendly practices that generate sustainable environmental, social, and economic outcomes.


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Multi-habitat seascape restoration: optimising marine restoration for coastal repair and social benefit

McAfee, D, P Reis-Santos, AR Jones, BM Gillanders, C Mellin, I Nagelkerken, MJ Nursey-Bray, R Baring, GM da Silva, JE Tanner, and SD Connell. 2022. Frontiers in Marine Science

Marine ecosystem restoration is fast becoming the primary tool for repairing the socio-ecological functions and economic benefits of coastal ecosystems. Healthy seascapes are characterized by many interacting species and intermingled habitats (e.g., seagrass, kelp, shellfish, sedimentary) that co-create ecological functions of substantial socio-economic value. These co-created functions not only build stability and resilience at seascape scales, but synergistically combine to enhance ecological productivity that is greater than the sum of the individual habitats. Yet, restoration practice is dominated by single-habitat approaches underpinned by single-species monocultures, potentially limiting the range of benefits that restoration can provide. We propose that for ecosystem restoration to meet its full potential in delivering socio-ecological benefits that are resilient to environmental change, restoration practices should plan beyond single-species and single-habitats to a multi-habitat seascape. Where multiple habitats are co-restored, their positive interactions mutually benefit each other to stabilize and even accelerate ecosystem recovery; such as co-restored shellfish and kelp forests on constructed reefs, which combine to stabilize sediment for seagrass recovery. As fisheries scientists and managers, food and social scientists, and ecologists and oceanographers, we describe multi-habitat marine restoration activities that are readily achievable and provide a vision for the diverse socio-ecological, economic, and culture benefits that may emerge from future seascape-level repair.


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Influence of offshore oil and gas structures on seascape ecological connectivity

McLean, DL, LC Ferreira, JA Benthuysen, KJ Miller, ML Schlappy, MJ Ajemian, O Berry, SNR Birchenough, T Bond, F Boschetti, AS Bull, JT Claisse, SA Condie, P Consoli, JWP Coolen, M Elliott, IS Fortune, AM Fowler, BM Gillanders, HB Harrison, KM Hart, LA Henry, CL Hewitt, N Hicks, K Hock, K Hyder, M Love, PI Macreadie, RJ Miller, WA Montevecchi, MM Nishimoto, HM Page, DM Paterson, CB Pattiaratchi, GT Pecl, JS Porter, DB Reeves, C Riginos, S Rouse, DJF Russell, CDH Sherman, J Teilmann, VLG Todd, EA Treml, DH Williamson, and M Thums. 2022. Global Change Biology

Offshore platforms, subsea pipelines, wells and related fixed structures supporting the oil and gas (O&G) industry are prevalent in oceans across the globe, with many approaching the end of their operational life and requiring decommissioning. Although structures can possess high ecological diversity and productivity, information on how they interact with broader ecological processes remains unclear. Here, we review the current state of knowledge on the role of O&G infrastructure in maintaining, altering or enhancing ecological connectivity with natural marine habitats. There is a paucity of studies on the subject with only 33 papers specifically targeting connectivity and O&G structures, although other studies provide important related information. Evidence for O&G structures facilitating vertical and horizontal seascape connectivity exists for larvae and mobile adult invertebrates, fish and megafauna; including threatened and commercially important species. The degree to which these structures represent a beneficial or detrimental net impact remains unclear, is complex and ultimately needs more research to determine the extent to which natural connectivity networks are conserved, enhanced or disrupted. We discuss the potential impacts of different decommissioning approaches on seascape connectivity and identify, through expert elicitation, critical knowledge gaps that, if addressed, may further inform decision making for the life cycle of O&G infrastructure, with relevance for other industries (e.g. renewables). The most highly ranked critical knowledge gap was a need to understand how O&G structures modify and influence the movement patterns of mobile species and dispersal stages of sessile marine species. Understanding how different decommissioning options affect species survival and movement was also highly ranked, as was understanding the extent to which O&G structures contribute to extending species distributions by providing rest stops, foraging habitat, and stepping stones. These questions could be addressed with further dedicated studies of animal movement in relation to structures using telemetry, molecular techniques and movement models. Our review and these priority questions provide a roadmap for advancing research needed to support evidence-based decision making for decommissioning O&G infrastructure.


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Microplastics in decapod crustaceans sourced from Australian seafood markets

Ogunola, SO, P Reis-Santos, N Wootton, and BM Gillanders. 2022. Marine Pollution Bulletin

Microplastic abundance and characteristics were assessed in five decapod crustaceans purchased from seafood markets and collected in coastal waters around Australia (South Australia, New South Wales, Queensland, Northern Territory, and Western Australia). Three species of prawns (king, banana and tiger prawns) and two species of crabs (blue-swimmer and mud crabs) were analysed. Muscle tissues and gastro-intestinal tracts in prawns, and gastro-intestinal tracts in crabs, were chemically digested, with microplastic identification verified using Fourier Transform Infrared spectroscopy. Forty-eight percent of crustaceans contained microplastics. Prawns and crabs had 0.8 ± 0.1 and 1.6 ± 0.1 pieces per individual, respectively, with spatial patterns evident. Microplastics were predominantly fibres (98%) of blue (58%) and black (24%) colours with polyolefin including polyester the most prevalent polymers. Overall, compared to a systematic review we performed of microplastics in decapod crustaceans worldwide, microplastic loads in crustaceans from Australia were in the lower range of plastic contamination.


Image: Prawns at Sydney Fish Market, Maksym Kozlenko, CC-BY-SA-4.0

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Tracing seal predation back to the source colony of their penguin prey: A trace element and stable isotope analysis

Reinhold, SL, SD Goldsworthy, JPY Arnould, BM Gillanders, SD Connell, and RR McIntosh. 2022. Frontiers in Marine Science

Marine predators recovering from historic, commercial, over-harvesting can create conservation challenges when they prey on vulnerable species. Pinniped predation of seabirds presents one such challenge and identifying the source colonies experiencing seal predation are needed to inform conservation management and decision planning. Here, we present a novel application of stable isotope and trace element techniques to identify the source colony of little penguins (Eudyptula minor) predated by long-nosed fur seals (Arctocephalus forsteri). We created baseline biochemical ‘feather-prints’ from feathers for six major breeding colonies across south-east Australia to compare with feathers from predated penguins recovered from seal scats. Feeding trials of captive seals confirmed that digestion of penguin feathers did not compromise stable isotope (δ13C and δ15N) or trace element (Al, Ti, Sr and Mg) signatures. The resulting biochemical ‘feather-prints’ were found to be robust in being correctly classified to local sites (78%) and broader regions (85%). The distinguishing ‘feather-prints’ appeared to be driven by industrial inputs from land, colony-specific foraging patterns and potentially proximity to oceanographic systems (i.e. upwelling). Here, we show that 46-70% of predated feathers were assigned to ‘local’ penguin colonies. We consider that the regional penguin abundances and the proximity of their colonies to seal sites, as well as demographic-specific foraging patterns may shape their contribution to seal diet at local, regional and inter-regional scales. This diagnostic tool is powerful, having broad applications identifying seabird colonies at greatest risk to pinniped predation and informing targeted, site-specific, conservation effort.


Image: New Zealand fur seal Arctocephalus forsteri at the east side of Pearson Island, South Australia, Peter Southward, CC-BY-SA-3.0

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Reading the biomineralized book of life: expanding otolith biogeochemical research and applications for fisheries and ecosystem-based management

Reis-Santos, P, BM Gillanders, AM Sturrock, C Izzo, DS Oxman, JA Lueders-Dumont, K Hussy, SE Tanner, T Rogers, ZA Doubleday, AH Andrews, C Trueman, D Brophy, JD Thiem, LJ Baumgartner, M Willmes, MT Chung, P Charapata, RC Johnson, S Trumble, Y Heimbrand, KE Limburg, and BD Walther. 2022. Reviews in Fish Biology and Fisheries

Chemical analysis of calcified structures continues to flourish, as analytical and technological advances enable researchers to tap into trace elements and isotopes taken up in otoliths and other archival tissues at ever greater resolution. Increasingly, these tracers are applied to refine age estimation and interpretation, and to chronicle responses to environmental stressors, linking these to ecological, physiological, and life-history processes. Here, we review emerging approaches and innovative research directions in otolith chemistry, as well as in the chemistry of other archival tissues, outlining their value for fisheries and ecosystem-based management, turning the spotlight on areas where such biomarkers can support decision making. We summarise recent milestones and the challenges that lie ahead to using otoliths and archival tissues as biomarkers, grouped into seven, rapidly expanding and application-oriented research areas that apply chemical analysis in a variety of contexts, namely: (1) supporting fish age estimation; (2) evaluating environmental stress, ecophysiology and individual performance; (3) confirming seafood provenance; (4) resolving connectivity and movement pathways; (5) characterising food webs and trophic interactions; (6) reconstructing reproductive life histories; and (7) tracing stock enhancement efforts. Emerging research directions that apply hard part chemistry to combat seafood fraud, quantify past food webs, as well as to reconcile growth, movement, thermal, metabolic, stress and reproductive life-histories provide opportunities to examine how harvesting and global change impact fish health and fisheries productivity. Ultimately, improved appreciation of the many practical benefits of archival tissue chemistry to fisheries and ecosystem-based management will support their increased implementation into routine monitoring.


Graphical abstract: Nina Wootton

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Habitat transitions by a large coastal sciaenid across life history stages, resolved using otolith chemistry

Russell, A, MD Taylor, TC Barnes, DD Johnson, and BM Gillanders. 2022. Marine Environmental Research

Many coastal species move between estuarine and coastal environments throughout their life. Migration patterns develop as a result of ecology and evolution and must be understood to effectively manage harvested stocks. This study examined movements across estuarine and coastal marine habitats in adult Mulloway (Argyrosomus japonicus); a commercially, indigenous and recreationally harvested sciaenid of south-eastern Australia. Chemical profiles across the otolith (ear bone) were used to examine transitions between estuary and marine habitats over life history. Patterns in otolith Ba:Ca concentrations indicated that the majority of fish migrated between estuary and marine habitats, but a small proportion of fish appeared to remain in either the estuary or the marine habitat. Such movements may potentially be driven by a range of biological and environmental factors. This approach allows questions about the life history and habitat use of Mulloway to be addressed, which will aid management and provide a platform for future research on Mulloway, other sciaenid’s and coastal migratory species.


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Determining population structure and connectivity through otolith chemistry of stout whiting, Sillago robusta

Sarakinis, KG, MD Taylor, DD Johnson, and BM Gillanders. 2022. Fisheries Management and Ecology

Fish otoliths encode information on surrounding environmental conditions. This study used otolith chemistry to investigate population structure and potential connectivity in stout whiting (Sillago robusta) along the east coast of Australia. Otoliths were analysed for both minor and trace elements, targeting the otolith core (location of birth) and otolith edge (location of capture), along with Ba:Ca transects to investigate life histories. Significant differences were found between core and edge signatures as well as among sample zones for select trace and minor elements. Otolith edge signatures showed evidence of some heterogeneity among zones, likely influenced by both environmental and physiological factors. This combination of factors is reflected in poor separation of sample zones from the multielement analysis, suggesting that future research may benefit from incorporating additional natural markers. Transects reflected some degree of individuality in Ba:Ca profiles, with evidence for potential exposure to upwelling events, or movement from shallow, inshore habitats into deeper waters. The variation in Ba:Ca profiles among fish suggests that populations are comprised of both resident and migratory individuals. While analysis of otolith chemistry could not reliably separate capture locations, patterns in the data suggest that inshore juvenile habitats are likely to be important in supporting exploited populations.


Image: Stereo microscope image of a sectioned otolith from a seven-year-old adult, male Sillago robusta

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Life history strategies of Mekong pangasiid catfishes revealed by otolith microchemistry

Vu, AV, L.J. Baumgartner, K.E. Limburg, G.S. Doran, M. Mallen-Cooper, B.M. Gillanders, J.D. Thiem, J.A. Howitt, C.M. Kewish, J. Reinhardt, and I.G. Cowx. 2022. Fisheries Research

Fourteen species of pangasiid catfish are found in the Mekong River. They are key components of both capture fisheries and aquaculture, although little is known about their migratory ecology, which is particularly important as some species are in decline. In order to examine the life-history strategies of key pangasiid catfishes in the Mekong River, we collected otoliths from 126 specimens belonging to four species in the Lower Mekong Basin. We analysed the otolith microchemical structure using two methods (Laser Ablation – Inductively Coupled Plasma Mass Spectrometry and Scanning X-ray Fluorescence Microscopy) to identify evidence of diadromy (movements between the ocean and upstream waters). We followed an established method of examining patterns of strontium to calcium (Sr:Ca) and barium to calcium (Ba:Ca) ratios along otolith transect profiles to interpret whether fish were in fresh or salt water at various stages of their life. We confirmed anadromy in two species (Pangasius krempfi and P. mekongensis; spawning in river but growing in marine waters) with at least three migratory tactics identified for each species, thus highlighting more diverse life history strategies than previously thought. Based on locations where we collected fish, we can infer these species migrate up to 700 km (P. mekongensis) and 1400 km (P. krempfi) from the sea into the Mekong River for spawning. The other two catfishes (P. elongatus and P. bocourti) appeared to be freshwater species that occasionally strayed into the estuary. Long-distance migratory species require free flowing rivers to connect critical habitats used at different life stages. Any activity disrupting these migratory pathways and disconnecting these habitats must be carefully considered. Conservation and management of transboundary species require international agreements to protect them from the impacts of river development, and the evidence presented here is pertinent for catfish in the Mekong River.


Image: Variations in Sr:Ca and Ba:Ca ratios along the laser transect (core-to-edge or birth-to-capture) from two typical individuals of P. krempfi captured in fresh water (Khone Falls, ~700 km from the sea), overlain onto images of otolith sections (Fig. 10 of paper)

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Diverse migration tactics of fishes within the large tropical Mekong River system

Vu, A.V., L.J. Baumgartner, M. Mallen-Cooper, G.S. Doran, K.E. Limburg, B.M. Gillanders, J.D. Thiem, J.A. Howitt, C.M. Kewish, J. Reinhardt, and I.G. Cowx. 2022. Fisheries Research

Fish often migrate to feed, reproduce and seek refuge from predators and prevailing

environmental conditions. As a result, migration tactics often vary among species

based on a diversity of life history needs, although variation within species is increasingly being recognised as important to population resilience. In this study, within-and among-species diversity in life history migratory tactics of six Mekong fish genera was examined using otolith microchemistry to explore diadromous and potamodromous traits. Two species were catadromous and one species was an estuarine resident, while the remaining three species were facultative in their migration strategies, with up to four tactics within a single species. Migrant and resident contingents co-existed within the same species. Management, conservation and mitigation strategies that maintain connectivity in large tropical rivers, such as effective fishway design, should consider a diversity of migration tactics at the individual level for improved outcomes.


Image: Hypothetical diagram of life histories in relation to Sr:Ca ratios in fish otoliths (Fig. 2 from paper)


Perceptions of plastic pollution in a prominent fishery: Building strategies to inform management

Wootton, N, M Nursey-Bray, P Reis-Santos, BM Gillanders. 2022. Marine Policy

Plastic ingestion in seafood species, and human consumers, are thought to have potential harmful impacts. However, there is limited information from seafood industry stakeholder groups, including processors, traders and fishers, about how they perceive plastic pollution, its impacts and potential management. Using the South Australian Marine Scalefish Fishery as a case study, we uncover levels of awareness, knowledge and concern, as well as impacts and potential solutions of marine plastic pollution from commercial and recreational fishers and fishmongers. Stakeholders highlight key areas of concern and motivations to champion the mitigation of plastic pollution, and promote management pathways with increased stakeholder support, including the implementation of education resources, improvement of waste disposal facilities and exploration of plastic-free fishing equipment. Understanding the perceptions of stakeholder groups will inform policy makers and empower managers to build awareness strategies, shift opinions through communication and reduce plastic pollution.


Graphical abstract: Nina Wootton

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Microplastic in oysters: A review of global trends and comparison to southern Australia

Wootton, N., K. Sarakinis, R. Varea, P. Reis-Santos, and B.M. Gillanders. 2022. Chemosphere

Microplastics have been documented in a plethora of marine environments and organisms. These small plastics threaten ecosystem health, with implications for seafood species’ health. Oysters are an important cultural and economic aquaculture species globally. Due to their filter feeding mechanisms, they can act as an indicator species and proxy for environmental contamination. This makes them an ideal organism for investigating microplastic pollution. Here, we first systematically reviewed the global literature investigating microplastic in oysters. Globally, 94.4% of all oysters had microplastics, with an average of 1.41 ± 0.33 per gram of soft tissue wet weight (gww). The review showed that wild-caught oysters contained more than double the amount of microplastic than aquaculture raised specimens, likely reflecting the clean and productive waters in which oyster aquaculture systems are commonly located. Second, we quantified microplastic presence and polymer type in commercially farmed oysters (Crassostrea gigas and Saccostrea glomerata) across a broad spatial scale, covering eight sites in southern Australia. Microplastics were present in 49.4% of all sampled oysters, with specimens from all locations containing microplastics. On average, whole oysters contained 0.83 ± 0.08 microplastics per individual or 0.09 ± 0.01 microplastics gww. Using Fourier-Transform Infrared Spectroscopy, we identified that 62% of the verified microplastics were vexar plastic netting, a low-density polyethylene commonly used in aquaculture production. Understanding the abundance and source of microplastic in these key seafood species is essential to determine if oysters are vulnerable to these contaminants and pose a risk to the oyster aquaculture industry as an important food resource.


Graphical abstract: Nina Wootton

Near Calperun Station, SA

Near Calperun Station, SA

Giant Australian cuttlefish

Giant Australian cuttlefish

Flinders Chase

Flinders Chase

Tourville Bay

Tourville Bay

Streaky Bay

Streaky Bay

Kangaroo Island

Kangaroo Island

Routeburn Track

Routeburn Track

White Island

White Island

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