Coral reef is one of the most productive, biodiverse, and complex marine ecosystems. The individual characteristics of coral-endosymbiotic Symbiodiniaceae will affect the sensitivity and adaption of their hosts to the marine environment. Environmental Symbiodiniaceae are essential for 80-85% of coral species, and the acquisition of new symbionts from the surrounding environment is widely recognized as a defense mechanism for corals to cope with environmental stress. Knowledge on the diversity and dynamics of coral-endosymbiotic and environmental Symbiodiniaceae community is the key to understanding coral-symbiosis interaction, evolution, development, and resilience. However, few studies have been conducted in environmental Symbiodiniaceae community.

Endosymbiotic Symbiodiniaceae were collected from Pocillopora damicornis and Galaxea fascicularis, and environmental Symbiodiniaceae were collected from seawater surrounding coral colonies, aiming to investigate the diversity distribution, driving factors and assembly mechanisms of coral-endosymbiotic and environmental Symbiodiniaceae communities in the northern South China Sea by using high-throughput sequencing of the nuclear ribosomal RNA gene ITS2.

The results showed that the alpha diversity indices values were significantly higher in environmental Symbiodiniaceae community than in coral-endosymbiotic Symbiodiniaceae communities. Among all samples, Cladocopium and Durusdinium were the absolute dominant genera. From north to south, it was found that the Symbiodiniaceae community dominated by Cladocopium changed to that dominated by Durusdinium. The main environmental factors driving the variation of Symbiodiniaceae community were temperature and salinity. The deterministic process played a leading role in the coral-endosymbiotic Symbiodiniaceae Communities assembly, while the stochastic process played a decisive role in the community assembly of environmental Symbiodiniaceae.