Wayne Andrew O'COnnor

Context: Oysters have ecological and economic importance worldwide because they provide ecosystem services and sustain profitable aquaculture industries. Calcifying bivalves including oysters have been found to be sensitive to ocean warming and acidification caused by anthropogenic climate change. Aims: This study tested whether adult wild Sydney rock oysters, Saccostrea glomerata, have resilience and can maintain sufficient scope for growth or are pushed into a suboptimal state. Methods: Oysters were exposed to elevated pCO2 (335 and 857 μatm) and temperature (24 and 28°C) in an orthogonal design for 5 weeks. At the end of the exposure, growth, condition index, clearance, ingestion and absorption efficiency and rates were measured and scope for growth calculated. Key results: Sydney rock oysters responded to elevated pCO2 and temperature with no change in overall growth or condition index, but with significantly increased metabolic, clearance, ingestion, and absorption rates and positive scope for growth. Conclusions: Our results indicated that adult S. glomerata can cope with the moderate level of climate-change stress predicted for 2100, through increased standard metabolic rate and increased energetic processes. Implications: If food availability becomes limiting, and other environmental stressors interact with climate change stressors, then resilience thresholds maybe breached for this economically, ecologically and indigenous significant and iconic oyster species.

True oysters, molluscs in the family Ostreidae, are important species in fisheries and aquaculture. As such, genome-enabled research can improve these industries and the conservation of these species. The tropical rock oyster Magallana bilineata (known as the black scar oyster or Indian backwater oyster) is naturally distributed in the tropical Indo-Pacific Ocean excluding Australia and is intensively cultured in India and the Philippines. It is also an aquaculture species in Sri Lanka with potential for much greater cultivation. We present the first reference genome for M. bilineata sourced from a Sri Lankan individual along with genetic variants that can be used in tool development for questions of molecular ecology and evolution as well as in breeding and commercial applications. Long-read PacBio data from a single M. bilineata were assembled following the Vertebrate Genomes Project workflow on the Galaxy Australia platform. A primary assembly composed of 105 contigs that is 551.94 Mbp in size was produced. The assembly N50 is 13.42 Mb and has a BUSCO completeness score of 98.1%. As collection and transport conditions challenged transcriptomic as well as scaffolding data generation, these approaches were undertaken computationally. Genetic variants in the form of SNPs from 90 individuals representing three naturally occurring populations in Sri Lanka and a fourth introduced population in Fiji was generated through DArTseq and a set of 3,115 SNPs produced after filtering. Combined, we present the first known genome assembly and the first genome-wide SNP data from M. bilineata, both of which have diverse applications for conservation and aquaculture.

Context The Sydney rock oyster (Saccostrea glomerata) is an iconic Australian native species of great commercial and ecological significance, that has been farmed in New South Wales for over 150 years. Aim To highlight the role of S. glomerata industry in safeguarding Australia’s estuaries. Method Literature review. Key results S. glomerata, more than any other species, has served to highlight emerging threats to estuaries, ranging from viral and bacterial contamination to chemical pollution, and climate change. Their use as biomonitors and in bioassays for pollutants (metals, PAHs, PFAS and pesticides) has been instrumental in identifying and quantifying potential threats. The oyster industry provides one of NSW’s largest and longest-running monitoring programs for estuarine environmental conditions. Currently, S. glomerata is at the forefront of remediation efforts, leading legislative change in environmental protection, and using ecoengineering, reef restoration and selective breeding programs to bolster oyster resilience. Conclusions Even though the community has long recognised the intrinsic link between oyster health and estuarine well-being and works with industry to advocate for estuarine ecosystem conservation and the species present, the contribution the industry makes is underestimated. Implications Amid debate over aquaculture expansion, greater consideration of the positives arising from culture activities is warranted.

Many important ecosystem functions are underpinned by below‐ground biodiversity and processes. Marine sediments, one of the most abundant habitats on earth, are essential to the mineralisation of organic matter. However, they are increasingly polluted by urban activities leading to the loss of biodiversity and the functions they provide. While traditional sediment remediation strategies are focussed on microbial and engineering solutions, we propose that the reintroduction of below‐ground ecosystem engineers (bioturbators) is important to rehabilitate polluted sediments and drive recovery of their functions in urban coastal ecosystems. We tested this notion by introducing bioturbators to nutrient polluted sediments to assess their survival, as well as their capacity to drive biodiversity and oxygenation and their potential to remediate nutrient pollution. Polychaete wormsDiopatra aciculataand clamsKatelysiasp. were added to mesocosms (ex‐situ), and the worms also added to experimental plots in‐situ. Potential for remediation was assessed with measures of nutrient content. All animals survived when introduced to polluted sediments and showed no evidence of sub‐lethal effects. Worms oxygenated sediments and reduced organic matter content by up to 50% in‐situ. The worms also drove shifts in the receiving communities at all locations and increased the number of taxa at one location. On the other hand, the effects of clams were variable, showing opposite effects in organic matter content at different sites and levels of pollution. Synthesis and applications. Global seafloor habitats are becoming increasingly degraded and novel strategies that combine biodiversity restoration with remediation are urgently needed to return function. Tube‐building bioturbators can stimulate nutrient processing in sediments proving multiple functional outcomes, but these effects are dependent on the receiving environment. In areas with medium levels of pollution, they can kick‐start recovery in a feedback loop whereby bioturbation increases oxygenation and nutrient remediation, shifting sediment biodiversity and contributing to further recovery. This can drive long‐term changes in sediment communities, particularly in urban areas where unvegetated sediments are conspicuous.

Commercial shellfish aquaculture is vulnerable to the impacts of ocean acidification driven by increasing carbon dioxide (CO₂) absorption by the ocean as well as to coastal acidification driven by land run off and rising sea level. These drivers of environmental acidification have deleterious effects on biomineralization. We investigated shell biomineralization of selectively bred and wild‐type families of the Sydney rock oyster Saccostrea glomerata in a study of oysters being farmed in estuaries at aquaculture leases differing in environmental acidification. The contrasting estuarine pH regimes enabled us to determine the mechanisms of shell growth and the vulnerability of this species to contemporary environmental acidification. Determination of the source of carbon, the mechanism of carbon uptake and use of carbon in biomineral formation are key to understanding the vulnerability of shellfish aquaculture to contemporary and future environmental acidification. We, therefore, characterized the crystallography and carbon uptake in the shells of S. glomerata, resident in habitats subjected to coastal acidification, using high‐resolution electron backscatter diffraction and carbon isotope analyses (as δ¹³C). We show that oyster families selectively bred for fast growth and families selected for disease resistance can alter their mechanisms of calcite crystal biomineralization, promoting resilience to acidification. The responses of S. glomerata to acidification in their estuarine habitat provide key insights into mechanisms of mollusc shell growth under future climate change conditions. Importantly, we show that selective breeding in oysters is likely to be an important global mitigation strategy for sustainable shellfish aquaculture to withstand future climate‐driven change to habitat acidification.

Oyster diseases are a major impediment to the profitability and growth of the oyster aquaculture industry. In recent years, geographically widespread outbreaks of disease caused by ostreid herpesvirus-1 microvariant (OsHV-1 μvar) have led to mass mortalities among Crassostrea gigas, the Pacific Oyster. Attempts to minimize the impact of this disease have been largely focused on breeding programs, and although these have shown some success in producing oyster families with reduced mortality, the mechanism(s) behind this protection is poorly understood. One possible factor is modification of the C. gigas microbiome. To explore how breeding for resistance to OsHV-1 μvar affects the oyster microbiome, we used 16S rRNA amplicon sequencing to characterize the bacterial communities associated with 35 C. gigas families, incorporating oysters with different levels of susceptibility to OsHV-1 μvar disease. The microbiomes of disease-susceptible families were significantly different to the microbiomes of disease-resistant families. OTUs assigned to the Photobacterium, Vibrio, Aliivibrio, Streptococcus, and Roseovarius genera were associated with low disease resistance. In partial support of this finding, qPCR identified a statistically significant increase of Vibrio-specific 16S rRNA gene copies in the low disease resistance families, possibly indicative of a reduced host immune response to these pathogens. In addition to these results, examination of the core microbiome revealed that each family possessed a small core community, with OTUs assigned to the Winogradskyella genus and the Bradyrhizobiaceae family consistent members across most disease-resistant families. This study examines patterns in the microbiome of oyster families exhibiting differing levels of OsHV-1 μvar disease resistance and reveals some key bacterial taxa that may provide a protective or detrimental role in OsHV-1 μvar disease outbreaks.