Editorial: Using direct microbiome manipulation to understand causal roles of microbes in the health and stress resistance of corals
Abstract
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.
Related
- Does host diversity beget microbiome diversity? Effects of zooplankton diversity and composition on environmental and host-associated microbes
- Editorial: Microbiome-driven strategies for alleviation of biotic and abiotic stresses in agriculture
- Editorial: Advancing plant histopathology: unraveling plant-pathogen interactions and disease resistance mechanisms
- Editorial: Evolution of antimicrobial resistance in intracellular bacterial pathogens: a genomic and historical perspective
- Editorial: Preclinical models and emerging technologies to study the effects of the tumor microenvironment on cancer heterogeneity and drug resistance
BibTeX
@article{garciasbonet2026editorial,
title = {{Editorial: Using direct microbiome manipulation to understand causal roles of microbes in the health and stress resistance of corals}},
author = {Neus Garcias-Bonet and Anna Roik and Helena Villela and Claudia Pogoreutz and Kshitij Tandon},
journal = {Frontiers in Marine Science},
year = {2026},
month = aug,
doi = {10.3389/fmars.2026.1951962},
url = {https://univ-perp.hal.science/hal-05764507v1},
note = {CC BY},
}
RIS
TY - JOUR
TI - Editorial: Using direct microbiome manipulation to understand causal roles of microbes in the health and stress resistance of corals
AU - Neus Garcias-Bonet
AU - Anna Roik
AU - Helena Villela
AU - Claudia Pogoreutz
AU - Kshitij Tandon
PY - 2026
DA - 2026/08/27
JO - Frontiers in Marine Science
DO - 10.3389/fmars.2026.1951962
UR - https://univ-perp.hal.science/hal-05764507v1
AB - 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.
SN - 2296-7745
ER -