Seagrass-microbe interactions: a systematic review of current research trends and mapping of the core microbiome

Seagrass-microbe interactions are crucial for seagrass performance and the coastal ecosystem services they support. However, significant variation in experimental and analytical approaches has hindered our broader understanding of seagrass-microbe interactions and the potential existence of a functional core microbiome, i.e. microbial taxa that are consistently present on hosts and likely exert a disproportionate impact on host function. Through a systematic review, we aimed first to understand current trends and knowledge gaps in seagrass-microbe research. Additionally, we conducted a systematic mapping of global 16S ribosomal RNA (rRNA) gene sequencing data to characterise core bacterial taxa in three plant microenvironments (leaves, roots and rhizosphere) across multiple species and within a highly studied seagrass species, Zostera marina. The results revealed a growing number of studies since the 2010s manipulating environmental variables and/or seagrass microbes to investigate their roles in seagrass performance and responses to stressors. Most studies have primarily focused on seagrass leaves, examined a limited number of species, and investigated only bacteria via 16S rRNA gene amplicon sequencing. A few studies attempted to characterise seagrass core microbiomes, often using highly variable approaches to define core taxa. Our systematic mapping based on global sequencing data allowed the identification of prevalent bacterial taxa belonging to the families Desulfocapsaceae and Sulfurovaceae in the seagrass rhizosphere, which may play an important role in the performance of Z. marina and other seagrass species. The results also showed that many other bacterial families were prevalent across different seagrass microenvironments, such as Rhodobacteraceae and Flavobacteriaceae, with substantial taxonomic variability and functional metabolic redundancy. We identified key challenges stemming from available data and variable methodologies and provided insights to guide future experimental work and deepen our understanding of seagrass-microbe interactions. We argue that such knowledge may improve seagrass management outcomes, especially by informing restoration strategies based on core microbial taxa.