Rhizosphere microbiomes are closely linked to seagrass species: a comparative study of three coastal seagrasses

ABSTRACT Seagrass meadows are important marine ecosystems in coastal areas, offering ecological and economic services to the mankind. However, these ecosystems are facing declines due to climate changes and human activities. Rhizosphere-associated microbiomes play critical roles in the survival and adaptation of seagrasses. While prior studies have explored the general microbial communities and their roles in seagrass meadows, there is a gap in understanding the specific rhizosphere microbiomes of different seagrass species and their interdependent relationships. Our study analyzed the microbial community composition and their metabolism in the rhizosphere of Ruppia sinensis (RS), Zostera japonica (ZJ), and Zostera marina (ZM) obtained from the coastal area of Shandong, China, using high throughput and metagenome sequencing. We found that Rhodobacteraceae, Desulfocapsaceae, and Sulfurovaceae were enriched in RS, ZJ, and ZM samples, respectively, compared with the other two seagrass species, and the bacterial connections were decreased from RS to ZM and ZJ samples. The abundances of nirKS and norBC , mediating denitrification, were higher in RS samples with 2.38% ± 0.59% and 2.14% ± 0.24%, respectively. RS samples also showed a higher level of genes in assimilatory sulfate reduction but lower levels in dissimilatory sulfate reduction and oxidation, with a greater ability to convert sulfide into L-cysteine and acetate. Metagenome-assembled genomes from metagenome of RS rhizosphere had a higher diversity and were assigned to eight phyla. Our study could provide a typical project to analyze the bacterial community structures and metabolic functions in the rhizosphere microbiomes of different seagrasses. IMPORTANCE Seagrasses are indispensable in marine ecosystems, offering numerous critical services, with their health significantly influenced by associated rhizosphere microbiomes. Although studies have investigated the microbial communities and their ecological roles in seagrass meadows, the correlations between rhizosphere microbiome and seagrass species from a particular geographic region are limited. Some studies concentrated on the bacterial composition within the rhizosphere of various seagrasses, but the functional aspects of these microbiomes remain unexplored. Our research delves into this void, revealing that Ruppia sinensis , Zostera japonica , and Zostera marina host diverse bacterial community in the composition, connections, functions, and metabolism, such as nitrogen and sulfur metabolism. Our study revealed that seagrass species play an important role in shaping the rhizosphere microbiomes in an equivalent environment, emphasizing the importance of seagrass species in shaping the rhizosphere microbial communities.