Cryptophyte diversity and assembly mechanisms reveal ecological discontinuities in a river-estuary-coast continuum

[Display omitted] •Estuarine cryptophyte diversity peaks, challenging Remane’s Artenminimum hypothesis.•Discontinuities in river-estuary-coast continuum challenge smooth gradient concept.•Estuarine habitats support complex cryptophyte networks, showing high heterogeneity.•Cryptophyte assembly is shaped by both stochastic and deterministic processes.•Mid-salinity zones show specialization in cryptophyte abundance-weighted niches. Cryptophytes, a group of microalgae, play crucial roles in aquatic ecosystems but have been relatively understudied, particularly in terms of their diversity and community assembly along environmental gradients. This study investigated the diversity patterns and assembly mechanisms of cryptophyte communities across a river-estuary-coast continuum in southeast China. Contrary to Remane’s Artenminimum hypothesis, which predicts a minimum in species diversity at intermediate salinities, we observed a peak in cryptophyte richness within the estuarine zone. This finding suggests that cryptophytes may follow different ecological rules compared to macrozoobenthos, perhaps because of the complex habitat heterogeneity and the dynamic mixing of freshwater and marine species in estuaries. Our analyses also revealed significant ecological discontinuities along the continuum, particularly at the estuarine interface, where deterministic processes, such as salinity-driven selection, become more influential in community assembly across habitat boundaries. Co-occurrence network analyses further highlighted the estuary as a hotspot of biological interactions, characterized by a complex network structure that supports high species richness. These results underscore the importance of considering ecological discontinuities and habitat-specific processes in the management and conservation of connected aquatic ecosystems, particularly in transitional environments like estuaries that are subject to rapid environmental changes.