Facilitation-Dominated Motifs Characterize Cross-Domain Microbial Networks in Co-Occurring Water and Soil Habitats

Microorganisms form complex association networks supporting diverse functions from organic matter decomposition to water quality. However, the prevalence of different network structures (i.e., motifs) and their associations with biodiversity across ecosystems remain poorly understood. We surveyed paired water and soil samples from 20 relatively pristine Tibetan Plateau wetlands, spanning broad climatic and physicochemical gradients. Facilitation-dominated motifs were prevalent in both habitats and positively associated with phylogenetic diversity and species richness across domains; greater positive association prevalence among archaea, bacteria, and eukaryotes likewise correlated with greater biodiversity. These patterns were robust to alternative edge-retention thresholds, abundance table null models, and networks reconstructed from centered log-ratio-transformed or presence/absence data. Facilitation-dominated motifs were most consistently associated with network size- and centralization-related properties, whereas their associations with cohesion- and stability-related properties were more habitat-dependent and were clearer in soil than in water. The cycle facilitation motif, with all three pairwise associations positive, showed the most consistent associations with biodiversity and network properties. Structural equation modeling suggested links between environmental factors and biodiversity through paths involving the motif overrepresentation. Overall, facilitation-dominated co-occurrence structures were consistently associated with biodiversity in water and soil habitats, highlighting the microbial association structure as a useful framework for interpreting wetland biodiversity patterns.