Seaweeds are ecologically important primary producers, forming unique habitats. Microeukaryotes are pivotal in ecological functioning of seaweeds, but their ecological role and processes in seaweed habitats remain poorly understood due to a lack of field data. Here we presented an innovative insights into the microeukaryotic communities along the seaweed habitat gradients using 18S rDNA sequencing around a typical reef island, Gouqi Island. We set and verified habitat gradients of brown (HB, mainly Sargassum) and green algae (HG, mainly Ulva), and the control site between them (M), with detritus samples collected from collectors by SCUBA (Self-Contained Underwater Breathing Apparatus). Along the seaweed habitats, microeukaryotic biodiversity decreased from the detritus close to the seaweed habitats to surface water with increasing distance from detritus. For the dominant ecological function, clear distinction was also found in detritus and water samples along the seaweed habitat gradient, where phototrophs, mixotrophs and phagotrophs dominated in the detritus of brown algae dominated site, medium site, and green algae dominated site, respectively, responding differently to the environmental factors and seaweeds by Mantel analysis. Furthermore, we found that stochastic processes dominated in microeukaryotic community assembly in the brown seaweed habitat whereas deterministic processes dominated in green algae habitat. Highly varied occupancy was revealed in the green algae habitat by Specificity-Occupancy (SPEC-OCCU) analysis. Our result contributed to a better understanding of the ecological functioning of microeukaryotic communities in seaweed habitats, and further provided data for the bioassessment and conservation of seaweed habitats within marine ecosystems.
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