Soil pore heterogeneity mediates microbial response and recovery following an extreme wetting event across contrasting land uses

Short-term flooding is forecasted to increase in frequency and duration in temperate ecosystems, dramatically altering soil habitats for microbial communities through changes in oxygen concentrations and resource distribution. Microbial sensitivity to flooding may depend on soil pore structure, which influences microbial community composition, dispersal, and resource access. The importance of soil structure in regulating microbial flood responses might be strengthened or weakened by the land-use context that establishes pre-disturbance soil resource concentrations and microbial communities. We conducted laboratory incubations using intact and homogenized soil cores from adjacent agricultural and grassland ecosystems to determine how pore heterogeneity mediates microbial functional and compositional responses to experimental flooding, and assess how this varies by land use. Soils were either maintained at field moisture or flooded for three weeks, followed by drying. Flooding induced substantial microbial and biogeochemical changes across both land uses and soil structures, but fungal community composition remained largely unchanged. The more heterogeneous intact soils were not insensitive to flooding as hypothesized, but instead exhibited altered timing, magnitude, and recovery trajectories of microbial responses. In grassland soils, structural heterogeneity was associated with stimulated enzyme activities during flooding, flood-resistant microbial biomass, enhanced post-flood respiration, and strong shifts in bacterial community composition. In agricultural soils, intact structure supported higher bacterial diversity independent of flooding and was primarily associated with greater microbial biomass post-flood recovery and higher enzyme activity during the flood, relative to unflooded controls. Considering concurrent shifts in soil carbon and nutrient pools and differential abundance patterns, we suggest that preserved structure in grassland soils favors flood-adapted taxa and resource redistribution, whereas higher bacterial alpha diversity in intact agricultural soils may facilitate maintenance and recovery of microbial processes. Our study provides strong evidence that soil pore heterogeneity and land-use context interact to determine microbial response pathways to increasing hydrological extremes.