Environmental filtering shapes patch dynamics across isolated mesophotic reefs

Mesophotic coral ecosystems (MCEs; ∼30–150 m) encompass vast but poorly characterized reef habitats. Using Autonomous Reef Monitoring Structures (ARMS), environmental DNA (eDNA), metabarcoding (COI, 18S), image analysis, and 1-km hydrodynamic models, we investigated the mechanisms structuring cryptobenthic metazoan communities across six mesophotic banks on the northwestern Texas–Louisiana continental shelf. Community composition was governed primarily by environmental filtering: depth and turbidity jointly explained nearly twice as much variance than geographic effects in ARMS metabarcoding datasets. Environmental distance predicted community dissimilarity up to tenfold better than geographic distance, and environmental coefficients were 5–15× larger than geographic ones in multiple regression models. Turbidity, shaped by the benthic nepheloid layer, was the dominant filter, influencing 57 % of COI phyla and 115 families in 18S data, favoring sediment-tolerant suspension feeders and excluding photoautotrophs. Depth effects, although significant, were weaker and taxon-specific. Hydrodynamic simulations revealed episodic, bidirectional connectivity among banks with low connection strengths, indicating variable but non-limiting dispersal. Residual spatial structure likely reflects stochastic dispersal and spatially structured habitat heterogeneity. Collectively, these results demonstrate that environmental filtering, dominated by turbidity, overrides dispersal limitation in shaping mesophotic cryptobenthic communities, identifying the nepheloid layer as a key physical driver linking shelf oceanography, biodiversity, and ecosystem function. Suspended particle dynamics associated with bottom nepheloid layers merit integration into conservation planning as important mediators of ecological connectivity in mesophotic and other patchy reef systems globally.