Margaux Steyaert

Connectivity among coral populations, via larval dispersal, is one of the key mechanisms supporting reef recovery after climate-driven bleaching events. This study examines reef connectivity of remote atolls of the understudied central and western Indian Ocean seascape, focusing on a key reef-building species, Acropora aff. tenuis . Using genomic data from ultra-conserved elements alongside particle- tracking simulations, we investigate patterns of population structure and gene flow, and the influence of ocean currents. Results show asymmetrical connectivity: strong gene flow occurs within the Chagos Archipelago and between Chagos and the Inner Seychelles, highlighting their importance as regional larval sources. In contrast, the Outer Seychelles mainly functions as a larval sink, and Îles Glorieuses appears to be the least connected. Whilst population structure suggests a partially permeable dispersal barrier between the Inner and Outer Seychelles. Differences between genetic patterns and simulated ocean-driven dispersal suggest that ocean currents are not the only important driver of connectivity patterns. Additional factors, such as stepping-stone dispersal among atolls, fine- scale oceanographic processes, and species biology likely play important roles. Overall, we find widespread genomic connectivity across this seascape, which has positive implications for reef resilience, though future resilience will depend on frequency and severity of future bleaching events.

Human‐induced global warming has triggered a persistent decline in the health of marine ecosystems, particularly coral reefs, which are experiencing increasingly frequent and severe bleaching and mortality events. Refining cost‐effective and precise monitoring tools, such as environmental DNA (eDNA) metabarcoding, is essential to supplement future coral reef monitoring programs, with ongoing efforts focused on improving methods, validating results, and understanding limitations. Although eDNA has been widely used in aquatic ecosystem studies, its application to corals (Anthozoa) remains underexplored. Here, we investigate the use of eDNA metabarcoding with molecular markers targeting the ITS2 region of Anthozoa for monitoring coral communities in a remote and relatively undisturbed atoll system. We integrate three mainstream taxonomic assignment approaches (IDTAXA, BLAST Top Hits, and BLAST LCA), retaining only consensus identifications across methods for downstream analyses. This conservative strategy ensures highly robust and reliable taxonomic resolution, with over 90% of the sequences classified within Anthozoa, encompassing 18 genera and 15 genera of hard corals (Scleractinia). A considerable overlap in coral identification is observed between eDNA and traditional benthic transect surveys, giving support to the ability of eDNA to identify the community composition of Anthozoan taxa. Importantly, cryptic genera, such as Cycloseris , Cyphastrea , Merulina , Oxypora , and Turbinaria were identified by the eDNA approach but not the traditional surveys. Conversely, genera such as Alveopora , Astreopora , Caulastrea , Fungia , Galaxea , Halomitra , Herpolitha , Leptastrea , Platygyra , Plerogyra , and Stylophora were identified by the traditional surveys but not the eDNA approach, likely due to primer bias, taxonomic resolution or incomplete reference databases, supporting the complementary use of both methods. We also observe that the eDNA metabarcoding may capture differences in coral community structure between our lagoonal and seaward reef habitat types and point to potential characteristic taxa. This study underscores the utility of eDNA metabarcoding as a noninvasive, cost‐effective tool for coral biodiversity monitoring and provides insights into how to improve eDNA techniques for use as a coral biodiversity monitoring tool.

Amid increasing anthropogenic pressures on ecosystems, standardised biodiversity monitoring is critical for assessing biodiversity change. Marine hard‐bottom habitats, though ubiquitous and biodiverse, present challenges for biodiversity monitoring due to their complex structure and limited accessibility. Autonomous reef monitoring structures (ARMS) have been developed to standardise marine hard‐bottom biodiversity monitoring across sites and research groups. This review analyses the methodological approaches utilised to date, spatial distribution, and temporal coverage of ARMS research across 49 publications. Variation in deployment, retrieval, replication strategy, and processing of ARMS was observed, presenting a barrier to study interoperability. Spatial coverage is biased to coral reef ecosystems and the Northern Hemisphere but is expanding globally. Irregular deployment timing and overall deployment durations constrain temporal coverage across sites and biogeographical regions, with few studies exploring the influence of deployment timing and duration on ARMS' community composition. Genetic methods, namely, DNA barcoding and metabarcoding, dominate community composition analyses but there is significant variation in methods of DNA extraction, PCR protocols, target genes, sequencing platforms, and bioinformatic pipelines. Furthermore, images of ARMS' plates are an underutilised resource for biodiversity investigations and rarely used in conjunction with genetic analyses. This review highlights the need for greater standardisation and reporting consistency in ARMS research to improve study interoperability and reproducibility to enable global biodiversity monitoring in our changing world.

The democratisation of next‐generation sequencing has vastly increased the availability of sequencing data from metabarcoding. However, to effectively prepare these metabarcoding data for subsequent analysis, researchers must consistently apply several different bioinformatic tools—including those which denoise reads, cluster sequences and assign taxonomic identities. This often creates a bioinformatics bottleneck in workflows for non‐specialists due to obstacles around: (a) integrating different tools, (b) the inability to easily modify and rerun bioinformatic pipelines involving non‐scripted (‘point‐and‐click’) elements and (c) the multiple outputs that may be required of a single dataset (e.g. amplicon sequence variants [ASVs] and operational taxonomic units [OTUs]), which often results in users running pipelines multiple times. Here, we introduce SimpleMetaPipeline, an open‐source bioinformatics pipeline implemented in R, which addresses these obstacles. SimpleMetaPipeline integrates the most robust and commonly used existing bioinformatic tools in a single reproducible pipeline, with a streamlined choice of parameters, to generate a sequence data table containing alternative clustering and assignment options. SimpleMetaPipeline accepts demultiplexed paired‐end and single reads from multiple sequencing runs. We describe the pipeline and demonstrate how alternative annotations enable the easy implementation of multi‐algorithm agreement tests to strengthen inferences. SimpleMetaPipeline represents a valuable addition to the existing library of pipelines, providing easy and reproducible bioinformatics, including a range of commonly desired clustering and assignment options, such as OTUs and ASVs.

Fluorescence imaging of benthic communities is a widely used tool for determining the rate of hard coral recruitment in tropical reefs. Whilst fluorescent proteins are well-studied in scleractinian corals, less is understood about their distribution and function in other sessile reef invertebrates. This short study examines fluorescence images of benthic communities on Autonomous Reef Monitoring Structures (ARMS) from a remote and protected Indian Ocean reef system. We compare the abundance of adult and juvenile hard corals across three sites and between the topside and underside of ARMS recruitment plates. We also discuss observations of skeletal fluorescence in sponges, as well as uneven green fluorescent protein (GFP) concentrations across adult coral colonies. Our findings provide an insight into the recovery of shallow reefs previously hit by severe bleaching events and highlight the potential of ARMS fluorescence imaging for the analysis of cryptobenthic communities.

In a time of unprecedented ecological change, understanding natural biophysical relationships between reef resilience and physical drivers is of increasing importance. This study evaluates how wave forcing structures coral reef benthic community composition and recovery trajectories after the major 2015/2016 bleaching event in the remote Chagos Archipelago, Indian Ocean. Benthic cover and substrate rugosity were quantified from digital imagery at 23 fore reef sites around a small coral atoll (Salomon) in 2020 and compared to data from a similar survey in 2006 and opportunistic surveys in intermediate years. Cluster analysis and principal component analysis show strong separation of community composition between exposed (modelled wave exposure > 1000 J m⁻³) and sheltered sites (< 1000 J m⁻³) in 2020. This difference is driven by relatively high cover of Porites sp., other massive corals, encrusting corals, soft corals, rubble and dead table corals at sheltered sites versus high cover of pavement and sponges at exposed sites. Total coral cover and rugosity were also higher at sheltered sites. Adding data from previous years shows benthic community shifts from distinct exposure-driven assemblages and high live coral cover in 2006 towards bare pavement, dead Acropora tables and rubble after the 2015/2016 bleaching event. The subsequent recovery trajectories at sheltered and exposed sites are surprisingly parallel and lead communities towards their respective pre-bleaching communities. These results demonstrate that in the absence of human stressors, community patterns on fore reefs are strongly controlled by wave exposure, even during and after widespread coral loss from bleaching events.

Reliable and accurate biodiversity census methods are essential for monitoring ecosystem health and assessing potential ecological impacts of future development projects. Although metabarcoding is increasingly used to study biodiversity across ecological research, morphology‐based identification remains the preferred approach for marine ecological impact assessments. Comparing metabarcoding to morphology‐based protocols currently used by ecological surveyors is essential to determine whether this DNA‐based approach is suitable for long‐term monitoring of the marine ecosystems. We compared metabarcoding and morphology‐based approaches for the analysis of invertebrates in low diversity intertidal marine sediment samples. We used a recently developed bioinformatics pipeline and two taxonomic assignment methods to resolve and assign amplicon sequence variants (ASVs) from Illumina amplicon data. We analysed the community composition recovered by both methods and tested the effects, on the levels of diversity detected by the metabarcoding method, of sieving samples prior to DNA extraction. Metabarcoding of the mitochondrial marker cytochrome c oxidase I (COI) gene recovers the presence of more taxonomic groups than the morphological approach. We found that sieving samples results in lower alpha diversity detected and suggests a community composition that differs significantly from that suggested by un‐sieved samples in our metabarcoding analysis. We found that while metabarcoding and morphological approaches detected similar numbers of species, they are unable to identify the same set of species across samples. Synthesis and applications. We show that metabarcoding using the cytochrome c oxidase I (COI) marker provides a more holistic, community‐based, analysis of benthic invertebrate diversity than a traditional morphological approach. We also highlight current gaps in reference databases and bioinformatic pipelines for the identification of intertidal benthic invertebrates that need to be addressed before metabarcoding can replace traditional methods. Ultimately, with these limitations taken into consideration, resolving community‐wide diversity patterns with metabarcoding could improve the management of non‐protected marine habitats in the United Kingdom.