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CSIRO is working with local partners in the Maldives to develop coral restoration methods to assist with reef recovery.

Coral reefs are under stress throughout the world. To better understand the molecular mechanisms underlying coral biology and their genomic evolution, here we sequenced the genome and transcriptomes of elegance coral Catalaphyllia jardinei (Euphylliidae). This monotypic genus stony coral is widespread but rare, being found across the Indo-West Pacific, from the northern Indian Ocean, Australia, Philippines, to the South China Sea. Due to its popularity among aquarium hobbyists, it is an overexploited species collected in large quantities from the wild for aquarium trade. The assembled genome is ~ 651.3 Mb in total length and of high physical contiguity with a scaffold N50 size of 28.9 Mb. The gene copy numbers of abiotic stress regulator (heat shock protein family genes) and neuropeptides (GLWamide, GRFamide, PRGamide and HIRamide) are similar to other sequenced anthozoans, and we have also identified the first set of sesquiterpenoid biosynthetic pathway genes in coral. Sequencing of small RNAs allows us to identify 35 microRNAs in C. jardinei and update the number of conserved microRNAs in cnidarians. This study established a foundation for further investigation into the roles of sesquiterpenoids and microRNAs in development of coral and understand their responses to climate change. Due to the easiness to culture C. jardinei in reef tanks and the established resources in this study, we propose this species be adopted as a new laboratory model in environmental and ecological experiments aiming to understand coral biology and responses to environmental stressors.

Coral reefs are biodiversity hotspots, places of high endemicity and provide essential services to billions of people globally. With increasing threats to these reefs worldwide, there is a need to implement faster, more efficient ways to monitor spatial and temporal patterns of biodiversity. Environmental DNA (eDNA) metabarcoding offers a promising tool to address this issue, as it has revolutionized our ability to monitor biodiversity from complex environmental samples such as seawater. However, the capacity for eDNA to resolve fine scale shifts in community composition across habitats in seascapes is yet to be fully explored. Here, we applied eDNA metabarcoding using the rRNA 18S Universal eukaryote assay to explore differences in community profiles between samples collected from the lagoon and reef slope habitats across more than 170 km of the Ningaloo Coast World Heritage Area in Western Australia. We recovered 2061 amplicon sequence variants that comprised of 401 taxa spanning 14 different metazoan phyla such as cnidarians, poriferans, molluscs, algae, worms, and echinoderms. Our results revealed strong clustering of samples by habitat type across the length of the reef. Community dissimilarity (beta diversity) between samples collected from the reef slope and lagoon habitats was high and was driven largely by a strong rate of spatial turnover, indicating a distinct set of taxa representing each reef zone community. We also detected a strong pattern of isolation by distance within our slope samples, suggesting that communities are spatially stratified across the length of the reef. Despite high connectivity due to regular flushing of the lagoon environment, our results demonstrate that metabarcoding of seawater eDNA from different habitats can resolve fine scale community structure. By generating multi-trophic biodiversity data, our study also provided baseline data for Ningaloo from which future changes can be assessed.

Analysis of the literature revealed authors from countries with large coral reef systems, such as The Maldives, Papua New Guinea and Indonesia, are underrepresented.

Coral islands support and extend legal maritime jurisdictions.

As seawater temperature rises, repeated thermal bleaching events have negatively affected the reefs of the Andaman Sea for over decades. Studies on the coral-associated microbial diversity of prokaryotes and microbial eukaryotes (microbiome) in healthy and bleached corals are important to better understand the coral holobionts that involved augmented resistance to stresses, and this information remains limited in the Andaman Sea of Thailand. The present study thereby described the microbiomes of healthy (unbleached) and bleached colonies of four prevalent corals, Acropora humilis, Platygyra sp., Pocillopora damicornis, and Porites lutea, along with the surrounding seawater and sediments, that were collected during a 2016 thermal bleaching event, using 16S and 18S rRNA genes next-generation sequencing (NGS). Both prokaryotic and eukaryotic microbes showed isolated community profiles among sample types (corals, sediment, and seawater) [analysis of similarities (ANOSIM): p = 0.038 for prokaryotes, p < 0.001 for microbial eukaryotes] and among coral genera (ANOSIM: p < 0.001 for prokaryotes and microbial eukaryotes). In bleached state corals, we found differences in microbial compositions from the healthy state corals. Prevalent differences shared among bleached coral genera (shared in at least three coral genera) included a loss of reported coral-beneficial microbes, such as Pseudomonadales, Alteromonadales, and Symbiodinium; meanwhile an increase of putative coral-pathogenic Malassezia and Aspergillus. This difference could affect carbon and nitrogen availability for coral growth, reflective of a healthy or bleached state. Our findings in part supported previously microbial dysbiosis knowledge of thermal bleaching coral microbiomes around South East Asia marine geography, and together ongoing efforts are to support the understanding and management of microbial diversity to reduce the negative impacts to corals in massive thermal bleaching events.

Anthropogenic climate change has caused widespread loss of species biodiversity and ecosystem productivity across the globe, particularly on tropical coral reefs. Predicting the future vulnerability of reef-building corals, the foundation species of coral reef ecosystems, is crucial for cost-effective conservation planning in the Anthropocene. In this study, we combine regional population genetic connectivity and seascape analyses to explore patterns of genetic offset (the mismatch of gene-environmental associations under future climate conditions) in Acropora digitifera across 12 degrees of latitude in Western Australia. Our data revealed a pattern of restricted gene flow and limited genetic connectivity among geographically distant reef systems. Environmental association analyses identified a suite of loci strongly associated with the regional temperature variation. These loci helped forecast future genetic offset in gradient forest and generalized dissimilarity models. These analyses predicted pronounced differences in the response of different reef systems in Western Australia to rising temperatures. Under the most optimistic future warming scenario (RCP 2.6), we predicted a general pattern of increasing genetic offset with latitude. Under the extreme climate scenario (RCP 8.5 in 2090-2100), coral populations at the Ningaloo World Heritage Area were predicted to experience a higher mismatch between current allele frequencies and those required to cope with local environmental change, compared to populations in the inshore Kimberley region. The study suggests complex and spatially heterogeneous patterns of climate-change vulnerability in coral populations across Western Australia, reinforcing the notion that regionally tailored conservation efforts will be most effective at managing coral reef resilience into the future.

The relatively pristine coral populations of WA's inshore Kimberley region are better equipped to survive ocean warming than the World Heritage-listed Ningaloo Marine Park, according to a new CURTIN University study.

In southeast Kenya, near the border with Tanzania, lies a coral reef in the Indian ocean. The coral reef has degraded due to unsustainable fishing and climate change. WUR PhD student Joshua Wambugu is investigating how the local community and other stakeholders can contribute to restoring the reef and finding a sustainable livelihood.

The Indo-West Pacific is the largest, most biodiverse marine ecosystem on Earth, and many of the species it supports have comparably wide ranges. Writing in "The Origin of Species," Charles DARWIN noted that "… many fish range from the Pacific into the Indian Ocean, and many shells are common to the eastern islands of the Pacific and the eastern shores of Africa, on almost exactly opposite meridians of latitude."

Monitoring of reef restoration efforts and artificial reefs (ARs) has typically been limited to coral fragment survival, hampering evaluation of broader objectives such as ecosystem recovery. This study aimed to determine to what extent AR design influences the ecological recovery of restored reefs by monitoring outplanted coral fragments, benthic cover, coral recruitment and fish and invertebrate communities for two years. Four AR designs (16 m2), unrestored controls and natural reef patches as reference (n = 10) were established in Mkwiro, Kenya. ARs consisted either of concrete disks with bottles, layered concrete disks, metal cages or a combination thereof. A mixture of 18 branching coral species (mainly Acropora spp.) was outplanted on ARs at a density of 7 corals m-2. After two years, 60% of all outplanted fragments had survived, already resulting in coral cover on most ARs comparable (though Acropora-dominated) to reference patches. Coral survival differed between ARs, with highest survival on cages due to the absence of crown-of-thorns sea star predation on this design. In total, 32 coral genera recruited on ARs and recruit densities were highest on reference patches, moderate on concrete ARs and low on cages. ARs and reference patches featured nearly twice the fish species richness and around an order of magnitude higher fish abundance and biomass compared to control patches. Fish abundance and biomass strongly correlated with coral cover on ARs. AR, reference and control patches all had distinct fish species compositions, but AR and reference patches were similar in terms of trophic structure of their fish communities. Motile invertebrates including gastropods, sea urchins, sea cucumbers and sea stars were present at ARs, but generally more abundant and diverse at natural reference patches. Taken together, all studied ecological parameters progressed towards reef ecosystem recovery, with varying influences of AR design and material. We recommend a combinat

Deep reefs below 30 m provide essential ecosystem services for ocean health and human well-being such as food security and climate change resilience. Yet, deep reefs remain poorly researched and largely unprotected, including in the Western Indian Ocean (WIO). Here, we assessed current conservation approaches in the WIO focusing on deep reefs, using a combination of online surveys and semi-structured interviews. Results indicated that deep-reef data are sparse and commonly stemming from non-peer-reviewed or non-publicly available sources, and are often not used to inform conservation of WIO marine protected areas. Based on those findings, we co-developed a framework with WIO stakeholders comprising recommendations linked to specific actions to be undertaken by regional actors to improve the capacity of the region to collect and share deep-reef information. We hope this framework will enhance deep-reef stewardship and management throughout the WIO and thus aid sustainable blue economic growth in the region.

Mass coral bleaching events are making it harder for some species of reef fish to identify competitors, new research reveals.