College of Science and Engineering CSE publications Recent publications in Marine Science & Aquaculture

Apply now

Recent publications in Marine Science & Aquaculture

Massault, Cecile, Jeffrey, Cara, Jones, David B., Barnard, Roger, Strugnell, Jan M., Zenger, Kyall R., and Jerry, Dean R. (2022) Non-invasive DNA collection for parentage analysis for bivalves: A case study from the silver-lipped pearl oyster (Pinctada maxima). Aquaculture, 552. 738036.
Due to the high revenues generated by the pearl industry, interest in developing breeding programs is increasing. The traditional approach for collecting DNA for pedigree analyses in breeding programs for the silver-lipped pearl oyster (Pinctada maxima) involves tissue excision from the muscular foot and/or mantle. Tissue excision causes injury and stress to the animal, and can lead to reduced growth efficiency, bacterial infection and subsequent mortality when oysters are returned to the non-sterile marine environment. The approach of swabbing tissue to collect cells for DNA analyses offers a potential non-invasive and rapid method but has not been reported previously for pearl oysters; particularly where DNA is destined for a high-throughput genotype-by-sequencing (GBS) single nucleotide polymorphism (SNP) genotyping platform. To evaluate the potential of swabbing as a method to collect DNA for downstream GBS SNP genotyping under commercial farming conditions, 29 broodstock pearl oysters were swabbed with two different swab brushes (a stiff and soft brush). Concentration of the extracted DNA from swabs was found to meet requirements for genotyping (44 to 59 ng/μL) and 260/280 ratios were in the acceptable range for DNA purity (1.9–2.2). SNP genotype calls derived from swab samples were highly correlated with those derived from tissue excised from the same oyster (mean of 0.97 ± 0.04 for soft bristle – mean of 0.98 ± 0.02 for stiff bristle). Finally, we evaluated the performance of swabbing under a commercial breeding program scenario, whereby 923 spat were genotyped and 18 months later 1927 pearl oysters from the same commercial cohort were swabbed to determine parental contributions for the cohort at the two time periods. Results demonstrated that the swab method is reliable for collecting sufficient quantity and quality of DNA for genome-wide SNP genotyping enabling accurate pedigree reconstruction. This study validated the efficiency of the use of the swab technique to collect DNA for routine parentage assignment, while limiting the adverse effects of destructive tissue sampling for commercial use and/or for the development of breeding programs.

Nankervis, Leo, Cobcroft, Jennifer M., Nguyen, Nguyen V., and Rimmer, Michael A. (2022) Advances in practical feed formulation and adoption for hybrid grouper (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂) aquaculture. Reviews in Aquaculture, 14 (1). pp. 288-307.
Grouper aquaculture is currently trending towards production of hybrids, due to their improved growth and disease resistance. The predominant cross is between tiger grouper (Epinephelus fuscoguttatus) females and giant grouper (Epinephelus lanceolatus) males (TGGG). Sustainable TGGG aquaculture development is limited by reliance on wild-caught ‘trash’ fish as feed rather than commercially formulated feeds. Specific TGGG nutrient requirement values remain limited, especially for larger fish that consume the highest volumes of feed. This limits the effectiveness of formulated feeds to provide optimal growth and feed conversion in an economically efficient manner. This review examines the current knowledge of hybrid grouper nutrient requirements for grow-out feeds and identifies knowledge gaps to inform further research that will enable development of cost-effective feeds that optimize fish growth, feed conversion and health. Current best practice in TGGG feeds specifies a relatively high protein requirement (53.5% crude protein), with higher arginine and lower lysine requirements than previously reported for grouper species. Like other groupers, the hybrid appears to require low lipid levels (10–14%); however, it remains to be elucidated whether this increases significantly with body size. The nutrient requirement data within this review provide a starting point for development of specific hybrid grouper feeds. However, commercialization of such feeds requires better understanding of the socio-economic context of the target industry. While formulated feeds may be more cost-effective, their implementation is limited by inferior growth compared with ‘trash’ fish. Performance gains are expected through increased understanding of size-specific nutrient requirements and specific raw material quality criteria.

Matley, Jordan K., Klinard, Natalie V., Barbosa Martins, Ana P., Aarestrup, Kim, Aspillaga, Eneko, Cooke, Steven J., Cowley, Paul D., Heupel, Michelle R., Lowe, Christopher G., Lowerre-Barbieri, Susan K., Mitamura, Hiromichi, Moore, Jean Sébastien, Simpfendorfer, Colin A., Stokesbury, Michael J.W., Taylor, Matthew D., Thorstad, Eva B., Vandergoot, Christopher S., and Fisk, Aaron T. (2022) Global trends in aquatic animal tracking with acoustic telemetry. Trends in Ecology & Evolution, 37 (1). pp. 79-94.
Acoustic telemetry (AT) is a rapidly evolving technique used to track the movements of aquatic animals. As the capacity of AT research expands it is important to optimize its relevance to management while still pursuing key ecological questions. A global review of AT literature revealed region-specific research priorities underscoring the breadth of how AT is applied, but collectively demonstrated a lack of management-driven objectives, particularly relating to fisheries, climate change, and protection of species. In addition to the need for more research with direct pertinence to management, AT research should prioritize ongoing efforts to create collaborative opportunities, establish long-term and ecosystem-based monitoring, and utilize technological advancements to bolster aquatic policy and ecological understanding worldwide.

Bradley, Michael, Nagelkerken, Ivan, Baker, Ronald, Travers, Michael, and Sheaves, Marcus (2022) Local Environmental Context Structures Animal-Habitat Associations Across Biogeographic Regions. Ecosystems, 25. pp. 237-251.
The mechanisms that govern fauna-habitat associations across multiple spatial scales remain largely undefined. Can environmental factors structure fauna-habitat associations over both local and global spatial scales, alongside biogeographical processes and patterns? We compare the extent to which the use of mangroves by fishes is consistent within and between biogeographic locations, and whether any similarities and differences can be attributed to the environmental context of those forests, such as the physical environment, seascape composition and constraints on access by fishes. We focus on three important proxies of these structuring forces for fish—salinity, distance to reefs and tidal amplitude. Using directly comparable remote underwater visual census from a range of diverse environmental contexts in the Central and Eastern Indo-Pacific, we examine similarity in the family-level taxonomic composition of fish assemblages in mangrove forests. Local environmental context appears to explain similarities and differences in mangrove association by fishes at both regional and local scales across the Indo-Pacific. There were strong consistencies in taxonomic composition in similar environmental contexts despite geographic separation. Tidal amplitude was a powerful explanatory factor that interacted with both distance to reef and salinity in partitioning variation in fish assemblage structure. Substantial differences in the use of mangroves between regions appear to be independent of historical biogeography, relating instead to local context. Our findings suggest that the effects of local context on habitat suitability can play out over biogeographical scales, and global similarities in fauna-habitat associations may be partially explained by comparable environmental contexts, with important management implications.

Hobbs, Jean-Paul A., Richards, Zoe T., Popovic, Iva, Lei, Chuan, Staeudle, Timo M., Montanari, Stefano R., and Dibattista, Joseph D. (2022) Hybridisation and the evolution of coral reef biodiversity. Coral Reefs. (In Press)
Hybridisation has traditionally been considered rare and unimportant in generating biodiversity in the marine environment, particularly in coral reefs ecosystems. Here we review the literature for evidence of hybridisation in coral reef organisms and find that hybridisation is prevalent in well-studied groups, namely fish and hermatypic corals. At least 183 fish and 81 scleractinian coral species are reported to hybridise, with the highest prevalence in angelfishes and psammocorid corals (hybridisation in 46–50% of species in each family). Mapping the geographic location of hybrids revealed that hybridisation was positively associated with proximity to biogeographic borders for fish but not corals, and not linked with areas of low species richness in either group. Molecular studies detected admixture, indicative of past hybridisation, in 30 of 53 cases for fish, and in 22 (possibly 39) out of 47 studies for corals. Patterns of introgression described in the fish studies supported a decrease in lineage diversity in nine cases and the formation of hybrid lineages in seven cases. In the other 14 cases, the two parent species remained genetically distinct despite evidence of introgression. For corals, the evidence of hybrid lineages was rare (5 species), rather there was more support indicating that hybridisation leads to a decrease (36 species), or no change (27 species), in lineage diversity. Collectively, these results show that hybridisation can influence the evolution of fishes and corals in multiple ways and suggests the prevalence of hybridisation is likely to be significantly underestimated for coral reef taxa. The application of new genomic tools will advance our knowledge of the prevalence and evolutionary importance of hybridisation in coral reef organisms. Furthermore, these tools will aid in identifying how natural and assisted hybridisation may help coral reef species adapt to increasing environmental changes.

Tebbett, Sterling B., Morais, Juliano, and Bellwood, David R. (2022) Spatial patchiness in change, recruitment, and recovery on coral reefs at Lizard Island following consecutive bleaching events. Marine Environmental Research, 173. 105537.
The world’s coral reef ecosystems are steadily being reconfigured by climate change. Lizard Island, on Australia’s Great Barrier Reef, offers an opportunity to examine coral reef reassembly following disturbance, as this location has been impacted by consecutive tropical cyclones and consecutive coral bleaching events. Based on repeatedly monitoring the same 349 photoquadrats around Lizard Island over a 5-year period (2016-2021) we revealed that bleaching in 2016 drove a ~50% reduction in hard coral cover, and a concomitant increase in algal turf cover. From 2018 to 2021, significant increases (>600%) in coral cover were detected on two semi-exposed reefs and were associated with substantial Acropora recruitment. By contrast, fourteen lagoonal and back reefs exhibited virtually no recovery nor Acropora recruitment. Given that the timeframe between disturbances is set to decrease, our results suggest that some recovery is possible immediately after severe cumulative disturbances, although this recovery may be highly spatially heterogenous.

Aquino, Jon Irish, Elliott, Lisa, Zeng, Chaoshu, and Paris, Damien B.B.P. (2022) Recent developments in male fertility evaluation, sperm cryopreservation and artificial fertilisation, and their potential application to decapod crustacean aquaculture. Reviews in Aquaculture, 14 (2). pp. 848-889.
To maximise productivity, a better understanding of the underlying causes of subfertility that lead to inferior offspring and high mortality is imperative. In decapod crustaceans, most research has focused on female reproductive performance, with little attention given to male fertility. Paternal genetic contribution is critical to both successful embryonic and post-embryonic development. Assessment of sperm quality can be a direct method to determine male subfertility in decapods. Sperm quality parameters such as sperm concentration and morphology have traditionally been used to determine male reproductive performance, but these procedures are time-consuming and can only assess a limited number of sperm cells and males. Alternative diagnostic biomarkers used widely in humans and other mammals could be adapted to decapod crustaceans and may be more indicative of sperm fertilisation competence and male reproductive performance. These predictive biomarkers use fluorescent cellular dyes and high-throughput flow cytometry or computer-assisted sperm microscopic analysis to evaluate sperm viability, mitochondrial function, acrosome reaction and DNA fragmentation. This review examines current and advanced biomarkers to evaluate sperm quality and further explores state-of-the-art procedures of sperm cryopreservation (conventional vs. vitrification techniques) and artificial fertilisation in decapod crustaceans. Sperm freezing coupled with artificial fertilisation in decapods permits the long-term storage, controlled timing and selection of individuals for reproduction. Collectively, these tools can be applied to commercial broodstock management to improve productivity and accelerate selective breeding in the crustacean aquaculture industry.

Jerry, Dean R., Jones, David B., Lillehammer, Marie, Massault, Cecile, Loughnan, Shannon, Cate, Holly S., Harrison, Paul J., Strugnell, Jan M., Zenger, Kyall R., and Robinson, Nicholas A. (2022) Predicted strong genetic gains from the application of genomic selection to improve growth related traits in barramundi (Lates calcarifer). Aquaculture, 549. 737761.
Barramundi (Lates calcarifer) is a tropical species of increasing aquaculture interest. In efforts to accumulate genetic gains through selection, the species is now subject to several pedigree-based breeding programs globally; however, these breeding programs would further benefit from the implementation of genomic selection methodologies. Here we make genomic predictions for polygenic growth and body shape traits and compare expected genetic gains from genomic selection across several breeding strategies to those expected from pedigree-based on-farm selective breeding programs. A commercial scale cohort of barramundi (24 half-sib families) was grow-out at two farm locations, a brackishwater pond-based system in Queensland, and a freshwater recirculating aquaculture system (RAS) in Victoria. A total of 2139 fish were genotyped using a custom 70 k AxiomTM myDesignTM SNP array (ThermoFisher ScientificTM) and phenotyped at harvest for whole fish weight (WFW), standard fish length (SL), body depth (BD), Fulton's condition factor (K) and body shape index (BS). Fillet weight (FW) was also recorded on a subset of Victorian fish. Heritabilities based on genomic relationships were estimated across barramundi from both farm sites for WFW (0.33 +/- 0.06 to 0.35 +/- 0.04), SL (0.27 +/- 0.05 to 0.35 +/- 0.04), BD (0.29 +/- 0.06 to 0.30 +/- 0.04), and K (0.14 +/- 0.04 to 0.21 +/- 0.04), and for FW (0.35 +/- 0.16) in the Victorian site only. Genotype-byenvironment interactions were also detected for all traits (GBLUP rg between locations ranging from 0.41 for K to 0.61 for SL). To optomise the design of a breeding program using genomic information, three possible genomic selection strategies were explored: MULTIPLE, separate breeding programs at each farm site; GENERAL, a single breeding program using the general effects from an interaction model; and SINGLE, a single breeding program based on the performance of individuals within one main farm site. The accuracy of GBLUP breeding value prediction for the WFW, SL and BD traits was higher than PBLUP for all scenarios (10-33% and 15-49% improved prediction accuracy in the Victoria and Queensland environments, respectively). Estimates of genetic gain were also consistently higher when GBLUP was applied (19-31% for WFW in VIC) compared to PBLUP (14-23% for WFW in VIC). Under the SINGLE scenario, genetic gains for the target farm site were the same as for MULTIPLE, but only 48-66% of the MULTIPLE gains were predicted for the non-target farm site. In comparison, GENERAL, which operates at half the cost of MULTIPLE, achieved 72-97% of the expected gains of MULTIPLE across farm sites, suggesting that it would be the most appropriate scenario for genomic selection in the production environments evaluated.

D'Alberto, Brooke M., White, William T., Chin, Andrew, Dharmadi, , and Simpfendorfer, Colin A. (2022) Untangling the Indonesian tangle net fishery: Describing a data-poor fishery targeting large, threatened rays (Superorder Batoidea). Aquatic Conservation: marine and freshwater ecosystems, 32 (2). pp. 366-384.
1.Shark-like rays (Order Rhinopristiformes) are among the most threatened families of marine fish, yet little is known about their populations. These rays are normally taken as opportunistic catch in fisheries targeting other species and are thus poorly reported. One exception is the Indonesian tangle net fishery, which targets shark-like rays. 2.Market surveys of Muara Angke landing site in Jakarta, north-western Java were conducted between 2001 and 2005, and the landed catch from the tangle net fishery was recorded (the Muara Angke landing site includes landings from more than one fishery). 3.In total, 1,559 elasmobranchs (sharks and rays) were recorded, comprising 24 species of rays and nine species of sharks. The most abundant species landed were the pink whipray Pateobatis fai and the bottlenose wedgefish Rhynchobatus australiae, the latter being the main target species. 4.Catch composition varied based on differences in species catchability and may also be indicative of localized declines. The fishery was highly selective for larger sized individuals, while smaller size classes of many ray species, including the target species, were also caught in other Indonesian fisheries, resulting in fishing pressure across all age classes. 5.The decline of tangle net vessels in the fishery and the potential shift in catch composition in the Indonesian tangle net fishery increase concerns about the status of shark-like rays and stingrays in Indonesia.

Smith, Hillary A., Brown, Dylan A., Arjunwadkar, Chaitanya V., Fulton, Stella E., Whitman, Taylor, Hermanto, Bambang, Mastroianni, Elissa, Mattocks, Neil, Smith, Adam K., Harrison, Peter L., Boström-Einarsson, Lisa, McLeod, Ian M., and Bourne, David G. (2022) Removal of macroalgae from degraded reefs enhances coral recruitment. Restoration Ecology. (In Press)
Declining coral cover on tropical coral reefs often results in a concomitant increase in macroalgae. When proliferation of macroalgae persists outside regular seasonal growth, it can shift the ecosystem dominance away from corals into a permanently altered system. Such an altered system is unlikely to recover naturally, despite ample supply of coral larvae, as coral settlement and survival is reduced by the presence of macroalgae. Physical removal of macroalgae has been proposed to overcome this biotic barrier to recovery, although empirical evidence demonstrating the effects of removal on phase-shifted reefs is lacking. Here, we manually removed macroalgae from twelve 25 m(2) experimental plots (88.5 +/- 6.2 kg wet weight per plot; 90% benthic cover decrease) on a degraded reef prior to coral mass spawning across 2 years and recorded the number of coral recruits to settlement tiles and natural substrata. Four months after each spawning event, we found a threefold increase in coral recruits to tiles in plots where macroalgae had been removed (n = 12 plots; February 2019: mean 45.9 +/- 12.7 recruits per tile; February 2020: mean 53.9 +/- 5.9 recruits per tile) compared to control plots where macroalgae remained (n = 12 plots; February 2019 mean: 13.6 +/- 2.8 recruits per tile; February 2020 mean: 17.5 +/- 3.5 recruits per tile). These results suggest that, at small scales, macroalgae removal may be a useful intervention to boost recruitment on degraded reefs. Longer-term monitoring is needed to document if coral survivorship, growth, and subsequent reef recovery occurs.

Borland, Hayden P., Gilby, Ben L., Henderson, Christopher J., Connolly, Rod M., Gorissen, Bob, Ortodossi, Nicholas L., Rummell, Ashley J., Pittman, Simon J., Sheaves, Marcus, and Olds, Andrew D. (2022) Dredging fundamentally reshapes the ecological significance of 3D terrain features for fish in estuarine seascapes. Landscape Ecology, 37. pp. 1385-1400.
Context: Landscape modification alters the condition of ecosystems and the structure of terrain, with widespread impacts on biodiversity and ecosystem functioning. Seafloor dredging impacts a diversity of flora and fauna in many coastal landscapes, and these processes also transform three-dimensional terrain features. The potential ecological significance of these terrain changes in urban seascapes has, however, not been investigated. Objectives: We examined the effects of terrain variation on fish assemblages in 29 estuaries in eastern Australia, and tested whether dredging changes how fish associate with terrain features. Methods: We surveyed fish assemblages with baited remote underwater video stations and quantified terrain variation with nine complementary metrics (e.g. depth, aspect, curvature, slope, roughness), extracted from bathymetry maps created with multi-beam sonar. Results: Fish diversity and abundance were strongly linked to seafloor terrain in both natural and dredged estuaries, and were highest in shallow waters and near features with high curvature. Dredging, however, significantly altered the terrain of dredged estuaries and transformed the significance of terrain features for fish assemblages. Abundance and diversity switched from being correlated with lower roughness and steeper slopes in natural estuaries to being linked to features with higher roughness and gentler slopes in dredged estuaries. Conclusions: Contrasting fish-terrain relationships highlight previously unrecognised ecological impacts of dredging, but indicate that plasticity in terrain use might be characteristic of assemblages in urban landscapes. Incorporating terrain features into spatial conservation planning might help to improve management outcomes, but we suggest that different approaches would be needed in natural and modified landscapes.

Buddle, Alice L., Van Dyke, James U., Thompson, Michael B., Simpfendorfer, Colin A., Murphy, Christopher R., Day, Margot L., and Whittington, Camilla M. (2022) Structure and permeability of the egg capsule of the placental Australian sharpnose shark, Rhizoprionodon taylori. Journal of Comparative Physiology B: Biochemical Systemic and Environmental Physiology, 192. pp. 263-273.
Shark placentae are derived from modifications to the fetal yolk sac and the maternal uterine mucosa. In almost all placental sharks, embryonic development occurs in an egg capsule that remains intact for the entire pregnancy, separating the fetal tissues from the maternal tissues at the placental interface. Here, we investigate the structure and permeability of the egg capsules that surround developing embryos of the placental Australian sharpnose shark (Rhizoprionodon taylori) during late pregnancy. The egg capsule is an acellular fibrous structure that is 0.42 ± 0.04 μm thick at the placental interface between the yolk sac and uterine tissues, and 0.67 ± 0.08 μm thick in the paraplacental regions. This is the thinnest egg capsule of any placental shark measured so far, which may increase the diffusion rate of respiratory gases, fetal wastes, water and nutrients between maternal and fetal tissues. Molecules smaller than or equal to ~ 1000 Da can diffuse through the egg capsule, but larger proteins (~ 3000–26,000 Da) cannot. Similar permeability characteristics between the egg capsule of R. taylori and other placental sharks suggest that molecular size is an important determinant of the molecules that can be exchanged between the mother and her embryos during pregnancy.

Ferreira, P., Kwan, G.T., Haldorson, S., Rummer, J.L., Tashiro, F., Castro, L.F.C., Tresguerres, M., and Wilson, J.M. (2022) A multi-tasking stomach: functional coexistence of acid-peptic digestion and defensive body inflation in three distantly related vertebrate lineages. Biology Letters, 18 (2). 20210583.
Puffer and porcupine fishes (families Diodontidae and Tetraodontidae, order Tetradontiformes) are known for their extraordinary ability to triple their body size by swallowing and retaining large amounts of seawater in their accommodating stomachs. This inflation mechanism provides a defence to predation; however, it is associated with the secondary loss of the stomach's digestive function. Ingestion of alkaline seawater during inflation would make acidification inefficient (a potential driver for the loss of gastric digestion), paralleled by the loss of acid–peptic genes. We tested the hypothesis of stomach inflation as a driver for the convergent evolution of stomach loss by investigating the gastric phenotype and genotype of four distantly related stomach inflating gnathostomes: sargassum fish, swellshark, bearded goby and the pygmy leatherjacket. Strikingly, unlike in the puffer/porcupine fishes, we found no evidence for the loss of stomach function in sargassum fish, swellshark and bearded goby. Only the pygmy leatherjacket (Monochanthidae, Tetraodontiformes) lacked the gastric phenotype and genotype. In conclusion, ingestion of seawater for inflation, associated with loss of gastric acid secretion, is restricted to the Tetraodontiformes and is not a selective pressure for gastric loss in other reported gastric inflating fishes.

Bouyoucos, Ian A., Simpfendorfer, Colin A., Planes, Serge, Schwieterman, Gail D., Weideli, Ornella C., and Rummer, Jodie L. (2022) Thermally insensitive physiological performance allows neonatal sharks to use coastal habitats as nursery areas. Marine Ecology Progress Series, 682. pp. 137-152.
Coastal sharks can use shallow, nearshore habitats as nursery areas, which is a behaviour that may increase fitness. The ecological benefits of shark nursery areas are well studied; yet the physiological mechanisms that enable sharks to exploit coastal habitats, especially those that experience extreme and dynamic temperatures, remain understudied. We hypothesised that neonatal sharks are able to use thermally dynamic coastal habitats as nursery areas because temperature does not strongly affect their physiology. To test this hypothesis, we defined patterns of nursery area use and temperature-dependent physiological performance in 2 reef shark species. First, we determined whether 10 sites around the island of Moorea, French Polynesia, satisfied nursery area criteria for neonate populations of blacktip reef sharks Carcharhinus melanopterus and sicklefin lemon sharks Negaprion acutidens using 5 consecutive years of abundance surveys. We then quantified effects of thermal exposure in situ on growth in recaptured individuals and quantified the temperature dependence of metabolic rate ex situ using respirometry. We found several potential C. melanopterus nursery areas, but during different sampling years, and identified 1 N. acutidens nursery area that remained consistent during the entire 5 yr study. In support of our hypothesis, growth and metabolic performance were not strongly affected by temperature in either species. Thus, thermally insensitive physiological performance may be a trait that elasmobranchs exhibit in thermally variable coastal habitats, including shark nursery areas. Together, this approach demonstrates how physiological and ecological concepts complement each other to improve our understanding of nursery area use in coastal shark populations.

Cook, Nathan, Smith, Adam, Songcuan, Al, Cassidy, Daniel, Sartori, Greta, and McLeod, Ian (2022) Lessons learned from small-scale coral outplanting intervention at a restoration site on the Great Barrier Reef. Ecological Management and Restoration, 23 (1). pp. 89-93.
Scientific, tourism and non-government organisations collaborated to design and undertake a small-scale coral outplanting intervention at Fitzroy Island, the Great Barrier Reef (GBR), Cairns, Australia. Activities were implemented to assist recovery of a reef showing signs of reduced coral cover after recent coral bleaching and to trial potential for implementation of work of this kind by community members. In December 2017, 240 coral fragments were collected and deployed on mid-water coral nursery infrastructure. Ten months later, 96 corals (˜15 cm) were outplanted onto bare sections of the surrounding reef rock at depths of 2–8 m. Monitoring was undertaken to measure changes in coral cover at treatment and control locations to determine the potential of using coral outplanting intervention to assist the recovery of degraded reefs. We found no significant difference in live coral cover between controls and treatment over a 12-month period. Although statistically insignificant, we observed an increase in live coral cover in treatment plots (9.8%) and control plots (2.2%), indicating natural recovery processes occurring across the reef. Total number of fish species and abundance increased significantly over time. Although the outplanting may not have been needed in this case, as a pilot project and the first coral nursery and active reef restoration project in the GBR Marine Park, the research provided valuable lessons associated with project collaboration and planning, site selection, monitoring and natural recovery vs restoration.

Cooper, Madalyn K., Villacorta-Rath, Cecilia, Burrows, Damien, Jerry, Dean R., Carr, Leah, Barnett, Adam, Huveneers, Charlie, and Simpfendorfer, Colin A. (2022) Practical eDNA sampling methods inferred from particle size distribution and comparison of capture techniques for a Critically Endangered elasmobranch. Environmental DNA. (In Press)
Environmental DNA (eDNA) methods are increasingly applied in the marine environment to identify species and community structure. To establish widely applicable eDNA techniques for elasmobranchs, we used the Critically Endangered largetooth sawfish (Pristis pristis Linnaeus, 1758) as a model species for: (1) assessing eDNA particle size distribution; (2) assessing the efficiency of long-term preservation of water samples; and (3) comparing the efficiency and detection sensitivity of filtration and precipitation methods. Water samples (1 L) collected from a tank containing one largetooth sawfish specimen were sequentially filtered through five filter membranes of decreasing pore size (20, 10, 5, 1.2, and 0.45 μm). The proportion of sawfish eDNA retained within each size class was determined through quantitative real-time PCR (qPCR) using a species-specific TaqMan probe assay. A linear mixed-effects model (lme) showed that the 1.2 and 20 μm filters captured most of the eDNA particles present in the sampled water. Additionally, whole water samples (0.375 L) were preserved in Longmire's buffer, stored at tropical ambient temperatures (26.3°C ± 3.0 SD) and extracted at five time points: immediately, one, two, and three months after collection, as well as frozen and extracted three months later, to assess the preservation efficiency of Longmire's buffer via qPCR analysis. A linear mixed-effects model showed that samples maintained maximal eDNA yield for at least three months after collection at ambient storage. Lastly, when comparing the filtration and precipitation methods, filtration using 0.45 μm pore size was more sensitive to capture of large-tooth sawfish eDNA than filtration with 20 μm filter or water precipitation. However, water precipitation was more efficient when accounting for volume of water processed. These results provide options for best capture and preservation of elasmobranch eDNA.

Xu, Tian, and Zeng, Chaoshu (2022) Establishing larval feeding regimens for the decorator crab Camposcia retusa: effects of live prey types and density on larval survival and development. Aquaculture Research, 53 (7). pp. 2772-2784.
Decorator crab Camposcia retusa is a popular marine ornamental species; however, it has never been bred previously. To establish a feeding regime for C. retusa larvae, which include two zoeal and a megalopal stage, three experiments were conducted. In all experiments, >= 60% of unfed 1st zoeal (Z(1)) larvae survived to the next stage, combined with the orange guts observed in larvae fed Artemia, suggesting Z(1) larvae are facultative lecithotrophic. Experiment 1 evaluated the suitability of ss-type rotifer Brachionus rotundiformis as prey. Z(1) larvae were fed rotifer at a density from 0 to 90 ind./ml. There was no significant difference in Z(1) survival among treatments (56.7-68.3%, p > 0.05); therefore, ss-type rotifer is considered an unsuitable prey for the larvae. Experiment 2 examined the suitability and optimal density of Artemia nauplii, and co-feeding copepod Pavocalanus crassirostris with Artemia, for larval rearing. The larvae fed 10 Artemia/ml had the highest survival to megalopae (91.3 +/- 3.1%, p < 0.05). However, high mortality occurred in megalopae, resulting in poor survival to the 1st crab stage (1.3%-12.5%) in all treatments (p > 0.05). Meanwhile, co-feeding copepods with Artemia showed significantly inferior survival and development to megalopae when compared to that of 10 Artemia/ml treatment. Experiment 3 evaluated the effects of Artemia enrichment on larval performance. The results suggested that Artemia enrichment did not improve larval survival or development. Based on our results, Artemia nauplii fed at 10 ind./ml throughout larval development appears to be appropriate for C. retusa.

Thatcher, Callaway, Hoj, Lone, and Bourne, David G. (2022) Probiotics for coral aquaculture: challenges and considerations. Current Opinion in Biotechnology, 73. pp. 380-386.
Globally, coral reefs are under pressure from climate change, with concerning declines in coral abundance observed due to increasing cumulative impacts. Active intervention measures that mitigate the declines are increasingly being applied to buy time for coral reefs as the world transitions to a low-carbon economy. One such mitigation strategy is coral restoration based on large-scale coral aquaculture to provide stock for reseeding reefs, with the added potential of selecting corals that better tolerate environmental stress. Application of probiotics during production and deployment, to modulate the naturally occurring bacteria associated with corals, may confer health benefits such as disease resistance, increased environmental tolerance or improved coral nutrition. Here, we briefly describe coral associated bacteria and their role in the coral holobiont, identify probiotics traits potentially beneficial to coral, and discuss current research directions required to develop, test and verify the feasibility for probiotics to improve coral aquaculture at industrial scales.

Nankervis, Leo, and Jones, Clive (2022) Recent advances and future directions in practical diet formulation and adoption in tropical Palinurid lobster aquaculture. Reviews in Aquaculture. (In Press)
The spiny lobsters Panulirus ornatus and Panulirus homarus are important developing tropical aquaculture species, with high demand and limited supply. The established industry in Vietnam relies on wild-caught mixed seafood bycatch as feed, a practice linked to water quality degradation and potentially disease proliferation in lobster aquaculture, necessitating formulated feed development. The emerging Indonesian and Australian industries lack the crustacean and mollusc component of the seafood bycatch used in Vietnam, increasing the need for manufactured feeds. Development of such feeds is reliant on knowledge of nutrient requirements, ingredient quality, physical feed requirements, and the link between feeding behaviour and feeding methods. This review will elaborate on the development of these knowledge areas to date and outline the two main reference diet recipes that are available as the basis for future research. Research to date has focused on developing a feed recipe that will be consumed and supports adequate growth rather than steering commercial least-cost formulation practices. Future research is clearly needed to inform formulation, but equally an understanding of the disparate emerging lobster farming industries and their drivers for adoption of formulated feeds is required to ensure that such research is applied. This will require engagement throughout the supply chain to ensure that research is implementable and to address farmer perception toward formulated feeds. Technical aspects of feed manufacture and scale-up of feed developments will be critical to adoption of research results, while validation though semi-commercial benchmarks and demonstration farm models are expected to increase commercial uptake of developed feeds.

Saleh, Alzayat, Sheaves, Marcus, and Rahimi Azghadi, Mostafa (2022) Computer vision and deep learning for fish classification in underwater habitats: A survey. Fish and Fisheries. (In Press)
Marine scientists use remote underwater image and video recording to survey fish species in their natural habitats. This helps them get a step closer towards understanding and predicting how fish respond to climate change, habitat degradation and fishing pressure. This information is essential for developing sustainable fisheries for human consumption, and for preserving the environment. However, the enormous volume of collected videos makes extracting useful information a daunting and time-consuming task for a human being. A promising method to address this problem is the cutting-edge deep learning (DL) technology. DL can help marine scientists parse large volumes of video promptly and efficiently, unlocking niche information that cannot be obtained using conventional manual monitoring methods. In this paper, we first provide a survey of computer visions (CVs) and DL studies conducted between 2003 and 2021 on fish classification in underwater habitats. We then give an overview of the key concepts of DL, while analysing and synthesizing DL studies. We also discuss the main challenges faced when developing DL for underwater image processing and propose approaches to address them. Finally, we provide insights into the marine habitat monitoring research domain and shed light on what the future of DL for underwater image processing may hold. This paper aims to inform marine scientists who would like to gain a high-level understanding of essential DL concepts and survey state-of-the-art DL-based fish classification in their underwater habitat.

 Find more publications @ JCU Research Online