Neus Garcias-Bonet

Aim: Coral reefs support more than one-third of the global marine biodiversity, but global stressors have negatively impacted their health by disrupting fragile microbial partnerships, leading to widespread mass bleaching events. To address this issue, the use of beneficial microorganisms for coral (BMCs) has been shown to enhance coral resilience. In this study, we evaluated the potential of alginate beads as a delivery method for BMCs underwater. Methods and Results: BMCs were encapsulated in alginate beads and incubated in artificial seawater at 26°C and 32°C. Microbial viability within the beads and bacterial release were monitored over a three-week period. Cell viability and sustained release rate were maintained throughout the experiment, with viable cell release averaging 106 cells h−1 per 50 mL flask by the third week at both temperatures. Co-encapsulation of multiple BMC strains resulted in changes in bacterial dynamics. Conclusions: These findings demonstrate that alginate beads can provide sustained delivery of viable BMCs under marine conditions and represent a promising platform for probiotic-based coral restoration strategies.

Coral reefs face global threats of functional extinction, largely due to anthropogenic impacts, especially climate change. Probiotic treatments using beneficial microorganisms for corals (BMCs) offer a promising solution to alleviate environmental impacts on corals, especially during heatwaves and disease outbreaks. However, the manual administration of these probiotics is not scalable. Here, we present the first automated probiotic delivery device that facilitates in situ delivery of BMCs. The device can deliver 2 L of probiotic solution at a maximum depth of 25 meters for a total duration of approximately 30 days. The device is equipped with a controller, probiotic cartridges with magnetic agitators, pumps, and a battery. The probiotic dosage and rate can be pre-programmed before deployment. The proposed technology contributes to the advancement of the deployment of microbial-based interventions beyond small-scale, manually intensive applications. It represents a step toward more efficient, scalable, and potentially cost-effective approaches for integrating microbial therapies into broader coral reef restoration and management efforts.

Nitrogen (N) plays a critical role in coral growth, but maintaining an N-limited state is essential for coral-algal symbiosis stability. Coral-associated denitrifiers may help regulate excess N, though denitrification in corals remains poorly quantified. To better understand species-specific and environmental effects on the denitrification pathway, we investigated year-long denitrification dynamics in four Red Sea corals, using acetylene inhibition assays alongside physiological and environmental measurements. All species exhibited measurable denitrification activity, ranging from 0 – 0.8 nmol N cm ⁻² h ⁻¹ for Stylophora pistillata and Acropora sp., 0 – 0.4 nmol N cm ⁻² h ⁻¹ for Millepora dichotoma , and 0 – 2.0 nmol N cm ⁻² h ^{− 1} for Dendrophylliidae indet. Denitrification displayed seasonal patterns, with higher rates in the spring/summer compared to autumn/winter, and we identified temperature, dissolved organic carbon (DOC) and nitrate availability as key environmental drivers. Lastly, we observed up to fivefold higher denitrification rates in the fully heterotrophic azooxanthellate coral Dendrophylliidae indet, than among mixotrophic species harbouring Symbiodiniaceae. Our findings indicate that denitrifiers use both photosynthetically derived and environmental carbon (C), with DOC central in maintaining tight coupling of C and N cycling in coral holobionts. Additionally, denitrification is modulated by environmental conditions, highlighting its vulnerability to environmental change.

Microbes or microbial consortia support coral health and resilience, ultimately enabling the development of microbiome-based interventions to protect and restore coral reef ecosystems.Fundamentally, Peixoto and Voolstra highlight that many marine microbiomes have already been altered from their presumed "pristine" states due to human impacts, challenging the objective of restoring ecosystems to a historical baseline. Instead, restoring healthy microbiomes should become a central component in conservation strategies. In this perspective, the authors emphasize that microbiome-based interventions aimed at helping to mitigate ecosystem decline should be referred as "microbiome restoration" or "microbiome rehabilitation", rather than "microbiome manipulation", to appropriately convey the need to reverse impacted microbiomes, towards healthier or less pathogenic assemblages.Coral reefs illustrate this particularly clearly, as anthropogenic impacts on coral reefs have been linked to dysbiosis and microbiome shifts toward pathogenic assemblages associated with coral diseases (Voolstra et al., 2024). One key question remains: how do pathogenic microbes reach and colonize corals in the first place? Consumer-mediated microbial dispersal through trophic transmission may play an important role in shaping coral microbiota. For example, fish feces can act as a source of naturally occurring coral-associated microorganisms, including both beneficial microbes and potential pathogens. Grupstra et al. experimentally demonstrated that feces from grazer/detritivorous fishes caused larger microbial-mediated lesions and contained higher abundances of the coral pathogen Vibrio coralliilyticus than feces from corallivorous fishes, which were enriched in native coral-associated bacteria such as Endozoicomonadaceae. These findings demonstrate that fish trophic guilds can differentially influence coral microbial communities and, ultimately, coral health. probiotic application methods were tested, with contrasting outcomes: i) whole-colony bagging with the probiotic suspension resulted in treated corals retaining 79.0% of their tissue area over 2.5 years, compared with 53.3 % tissue loss in bagged controls; whereas ii) application of probiotic paste over visible lesions was ineffective, with treated corals retaining only 27.8% of their tissue area compared with 59.2% in controls. Overall, while these findings highlight the potential of probiotic inoculation as an effective treatment for SCTLD, they demonstrate that treatment efficacy depends strongly on the delivery method, providing important insights for the management of coral disease interventions.Together these studies highlight recent progress in the emerging field of marine microbiome manipulations, yet they also reveal how far this field must still travel. Most of the contributions to this Research Topic are framed around pathogens and disease, aiming at identifying and suppressing causative agents and sources, or enhancing host defenses. This experimental focus is Deleted:very much driven by the urgency of coral loss due to the rise of marine infectious diseases in the face of global climate change, with several field trials addressing real-world challenges in the Caribbean (Neely et al., 2020;Johnston et al., 2023). However, disease-centric experiments capture only one facet of global environmental change. It is therefore imperative to broaden microbiome-based strategies from a disease-mitigation tactic into a general method of functional inquiry (Garcias-Bonet et al., 2024). Well-designed and thoughtful manipulative experiments can serve a dual purpose: an intervention that enhances coral stress tolerance or preserves health may simultaneously serve as a controlled approach to elucidate functional roles of a given microbe, consortium, or interaction. Medicine and agriculture reached their advanced engineering capabilities precisely in this manner: by pairing intervention with mechanism. Marine research in general, and coral reef research in particular, are now following the same path by having invested substantially in research related to disease control (as highlighted by the studies in this Research Topic), while also recently piloting the first microbiome-based intervention field trials (Doering et al., 2021;Delgadillo-Ordoñez et al., 2024;Santoro et al., 2025), or developing gnotobiotic models for reef-building corals (Puntin et al., 2022). The papers gathered here are hence best read not as endpoints but as a foundation for functional experimental work that aims to establish what coral-associated microbes do, while deepening our mechanistic understanding and delivering the deployable interventions that reef conservation urgently needs.

Corals are increasingly threatened by climate change, yet the interplay between ocean warming and fungal infection remains experimentally underexplored. Here, we demonstrate that thermal stress exacerbates the pathogenicity of the fungus Aspergillus sydowii , driving physiological collapse and functional reorganization in the octocoral Sclerophytum sp. We deployed a 34-day mesocosm heat-stress experiment and quantified performance, mortality, and taxonomic and functional microbiome shifts. Combined heat and fungal exposure proved highly lethal, causing 45% mortality compared to 7% under heat exposure alone. Re-isolation from diseased nubbins implicates A. sydowii as the causal agent. Metagenomic profiling indicated that physiological collapse was underpinned by a functional transition from mutualism to antagonism in the microbiome. Specifically, combined heat and fungal stress triggered a depletion of ankyrin- and WD40-repeat proteins - hallmarks of symbiotic stability - concurrent with a surge in genes involved in fungal cell wall degradation and secondary metabolite biosynthesis. While surviving holobionts recovered full photosynthetic efficiency after combined stress, their microbiomes did not revert to baseline. Instead, they assembled into a taxonomically distinct configuration characterized by enrichments of sulfate-reducers ( Thermodesulfobacteriota ) and thermotolerant phototrophs ( Thermosynechococcales ). This suggests that despite the rapid photosystem recovery, the holobiont retained a complex legacy of thermal and biotic stress across both its internal chemical microenvironment and its microbiome. These findings highlight the decoupled recovery processes of different holobiont components, demonstrating that even though some corals may survive severe climate-driven disease, they emerge as ecologically reorganized entities.

In several species, vaccine-like approaches, where hosts are primed through controlled pathogen exposure, have proven effective in enhancing responses to subsequent infections. This principle remains unexplored in corals. Here, we demonstrate that chronic exposure to non-lethal concentrations of live or inactivated Vibrio coralliilyticus primes the coral holobiont to counter subsequent infections under heat stress. Non-primed corals experienced greater heat stress pathogen-driven bleaching and a significant decline in their photosynthetic efficiency compared to primed samples. These results were linked to microbiome conditioning and the host gene expression modulation, including a layered, fine-tuned immune and cellular response to microbial invasion. This proof-of-concept challenges the view that coral immune responses are strictly innate, fixed, and positions immune priming and microbiome conditioning as integrated mechanisms of coral holobiont resilience. Together, these findings can contribute to redefining coral immunity concepts and lay the groundwork for developing new microbiome-based strategies to enhance coral health for reef conservation under climate change.

Coral holobionts acquire energy and nutrients from heterotrophic feeding, Symbiodiniaceae symbiosis, and additional metabolic functions (e.g. nitrogen (N) fixation) from associated bacterial communities. Since symbioses often require stable environmental conditions, corals in environments with seasonal variability have likely evolved adaptation strategies by either maintaining (i.e. regulating) or shifting (i.e. conforming) key functional traits, but empirical data is needed. We investigated carbon (C) and N elemental and stable isotope ratios alongside bacterial community composition in the hydrocoral Millepora dichotoma and the scleractinian coral Stylophora pistillata every two months over one year. These data were integrated with environmental parameters to investigate potential adaptation strategies of the coral holobionts over a seasonal cycle. S. pistillata showed temporal changes in δ13C, δ15N and C:N ratios in both host and Symbiodiniaceae tissues (indicating stable host-Symbiodiniaceae C/N cycling), in combination with stable bacterial communities. M. dichotoma, did not exhibit temporal changes in elemental and stable isotope ratios, but higher δ15N and C:N variability, and 61% higher C:N ratios in Symbiodiniaceae compared to host tissue. Temporal shifts in bacterial communities resulted in significantly enriched predicted metabolic functions for C, N, and sulfur cycling in winter. Stable C/N cycling and bacterial community composition suggest a regulator-like life history strategy of S. pistillata, whereas variable C/N cycling and flexible bacterial communities indicate a conformer-like life history strategy for M. dichotoma. Both contrasting adaptation strategies enable these organisms to succeed amid current environmental change, yet to what extent this can be maintained under future climate scenarios remains to be investigated.

Coral bleaching is most commonly associated with heat stress, while cold-water bleaching remains an underrecognized threat. Building upon the widely used ED50 metric for standardized heat tolerance, we introduce a new metric, cold ED50, to quantify cold bleaching thresholds. By comparing cold and heat ED50s, we define the temperature variability range of coral species. To achieve this, we used Coral Bleaching Automated Stress System (CBASS) assays to assess heat and cold temperature tolerance across three Red Sea scleractinian corals ( Acropora sp., Pocillopora favosa , Stylophora pistillata ) during peak summer and winter along with microbial profiling. Acropora sp. exhibited the highest heat ED50 (38.68 ± 0.39 °C) in summer, while S. pistillata had the lowest cold ED50 (15.63 ± 0.26 °C) in winter. Our results revealed species-specific bacterial communities, with Endozoicomonadaceae dominating across seasons. We show that bleaching thresholds are negatively correlated with the abundance of Endozoicomonadaceae in Acropora sp. during summer. Notably, coral recovery capabilities after extreme temperatures also vary between species. This dual temperature tolerance framework offers a more comprehensive assessment of coral resilience and vulnerability in a rapidly changing climate.

Microbial therapies are emerging as promising tools for coral protection against heat stress, yet such application was not tested in situ . We tested two coral-derived probiotic consortia and their heat-killed counterparts (postbiotics) on bleaching Acropora cf. valida in the Red Sea during a marine heatwave. Over 15 days, both live and one of the heat-killed treatments maintained photosynthetic efficiency ( Fv/Fm ), whereas placebo-treated corals exhibited significant thermal stress-induced decline. 16S rRNA gene sequencing profiling showed enrichment of putatively beneficial genera (e.g., Terasakiispira spp. , Pseudoalteromonas spp. ), and untargeted metabolomics resolved treatment-specific metabolic signatures that differed among consortia and between live and inactivated formulations. These molecular fingerprints illuminate specific underlying protective mechanisms and host–microbiome interactions under heat stress. Together, our results position microbial therapies (probiotics and specific postbiotics) as field-validated, mechanism-informed interventions capable of minimizing impacts on corals during real-world thermal extremes and provide design cues for scalable deployment.