Rainfall and Substrate Origin Driven Change of Ruminant Manure Microbiomes in Cyprus

Microbial communities drive the stabilisation of organic matter during manure storage; however, the combined influence of substrate origin and sudden rainfall occurrences on these communities remains poorly understood. For the first time in Cyprus, we investigated the effects of manure type (dairy cow vs. goat) and a drying-rainfall simulation pulse on the community composition, diversity, and functional potential during manure storage, using 16S rRNA metabarcoding and shotgun sequencing. Under dry conditions, substrate composition set the baseline, with the more structurally heterogeneous goat manure supporting significantly higher diversity than dairy cow manure. Rainfall simulation then acted as a dominant environmental filter, sharply reducing diversity and driving compositional convergence across manure types. This shift coincided with a rapid rise of fast-responding, stress-tolerant taxa, primarily Bacillota, and an increase in functions linked to sporulation and rapid growth. Ordination and dispersion analyses further showed that substrate origin modulates stability: after rainfall simulation, cow-manure communities exhibited greater compositional displacement and greater variability than those from goat manure. Overall, the efficacy and stability of manure storage systems emerge from the interplay between initial physicochemical template and dynamic moisture stress. Optimising large-scale operations will require management approaches that consider substrate characteristics, microbial community structure, and moisture dynamics.