Harnessing native microbiomes for coastal ecosystem restoration: Theory, evidence, and practice

Coastal systems are significant sites of ecosystem services, yet they are experiencing unparalleled levels of degradation as a result of anthropogenic stressors and global change. Conventional restoration efforts which target physical habitat restoration and transplantation of foundation species often result in variable success, as many sites still have not realized reference conditions despite decades since the intervention. This review consolidates the knowledge on utilizing indigenous microbiomes like complex bacterial, archaea, fungal and viral within mangroves, salt marshes, seagrasses and corals. The conceptual bases were reviewed to range from the functional roles of the microbiome in nutrient cycling, biogeochemical processes, host-microbe interactions and disease suppression to ecological principles that control community assembly, succession and resistance. Empirically, disturbances lead to a fundamental shift of microbial communities with lasting functional impacts from which natural recovery frequently lags or is incomplete, arguing for actively managing the microbiome. Practical implications include the use of diagnosis to identify potential microbial bottlenecks and define interventions or manipulations such as bioaugmentation, probiotic applications or environmental changes that support beneficial taxa. The coral probiotics and seagrass rhizosphere manipulation case studies can illustrate the feasibility and lessons for implementation. At the same time, there are still major challenges of scaling interventions, predicting ecological outcomes and navigating regulatory frameworks-but these are opportunities for innovation rather than intractable barriers. New research directions should focus on elucidating the causative pathways by which microbial interventions drive ecosystem outcomes, and creating predictive frameworks to meet future challenges related to climate change. Microbiome-guided restoration holds the promise of transforming our ability to ameliorate biological constraints that confound traditional approaches, equipping practitioners with an expanded toolkit for ecosystem resurgence in a time of rapid environmental change.