RedoxRRI: a compositional framework for modelling holobiont redox resilience across the soil-plant-microbiome continuum

Redox dynamics structure the soil-plant-microbiome continuum through coupled electron-transfer processes that integrate geochemistry, plant physiology, and microbial metabolism. Yet resilience in such systems is typically quantified within domains rather than as an emergent, cross-domain property. We propose a holobiont-scale Redox Resilience Index (RRI) grounded in the hypothesis that electron-processing capacity is bounded and redistributed among plant, soil, and microbial compartments under disturbance. By formalising resilience as coordinated buffering within a closed compositional state space, the framework yields both domain-specific capacities and their relative allocation on the simplex. We introduce direction-identifiable latent scoring, robust scaling within ecological strata, optional cross-domain coherence terms, and spatio-temporal modes capturing resistance and recovery. A generative simulation engine embeds hierarchical spatial structure, redox oscillations, sparse microbiome features, and non-random measurement dropout to benchmark performance under controlled ground truth. Embedding redox ecology within compositional geometry provides a unifying, mechanistically interpretable basis for analysing resilience as a multi-domain property of holobiont systems.https://github.com/mghotbi/RedoxRRI