Whole-genome resequencing highlights the phycosphere microbial network in global populations of the edible kelp Undaria pinnatifida

Abstract

The interplay between the host and microbiome has emerged as a central issue in biological science. This concept considers both host and microbiome sides to investigate their physiological and metabolic mechanisms, often referred to as a holobiont. Macroalgae, which can provide tremendous habitats to associated microorganisms in coastlines by constituting the marine forest, are promising targets to explore the interaction. Undaria pinnatifida is one of the edible brown macroalgae that is intensively cultured in Northeast Asia. Despite its ecological and economical importance, the microbiome of its phycosphere is largely unknown. In this study, we explored the microbial communities from 41 whole-genome resequencing data collected from South Korea (KR), New Zealand (NZ), and France (FR). We investigated the microbiome profiles and microbial ecological network to identify ecological and functional central taxa. We demonstrated that the microbiome profiles of KR cultivars are more similar to those of overseas introduced populations (i.e., NZ, and FR) than to those of the KR natural populations. We also identified two groups of central genera of the algal species' microbiome, the algal polysaccharide depolymerizing group (e.g., Lacinutrix and Winogradskiella) and the algal growth-promoting group (e.g., Sulfitobacter). This study supports the idea that the microbiome can be secured from unmapped reads of the host sequencing data. Furthermore, our data provide the first study on the U. pinnatifida microbiome, which probably will be used to develop new aquaculture strategies for this important seaweed.