Little is known of how hurricane-induced deposition of canopy material onto tropical forest floors influences the soil microbial communities involved in decomposition of these materials. In this study, to identify how soil bacterial and fungal communities might change after a hurricane, and their possible roles in the C and N cycles, soils were collected from five 2000 m² permanent plots in Lowland, Upland and Riparian primary forests in Costa Rica 3 months before and 7 months after Hurricane Otto damaged the forests. The soil Water, inorganic N and Biomass C increased and total organic C decreased Post-Hurricane, all of which best predicted the changes in the Post-Hurricane soil microbial communities. Post-Hurricane soils from all forest types showed significant changes in community composition of total bacteria, total fungi, and five functional groups of microbes (i.e., degrading/lignin degrading, NH₄⁺-producing, and ammonium oxidizing bacteria, and the complex C degrading/wood rot/lignin degrading and ectomycorrhizal fungi), along with a decrease in richness in genera of all groups. As well, the mean proportion of DNA sequences (MPS) of all five functional groups increased. There were also significant changes in the MPS values of 7 different fungal and 7 different bacterial genera that were part of these functional groups. This is the first evidence that hurricane-induced deposition of canopy material is stimulating changes in the soil microbial communities after the hurricane, involving changes in specific taxonomic and functional group genera, and reduction in the community richness while selecting for dominant genera possibly better suited to process the canopy material. These changes may represent examples of taxonomic switching of functionally redundant microbial genera in response to dramatic changes in resource input. It is possible that differences in these microbial communities and genera may serve as indicators of disturbed and recovering regional soil ecosystems, and should be evaluated in the future.

Inga edulis and Pentaclethra macroloba are dominant N-fixing forest trees in Costa Rica, likely important for recovery of soil N and C after deforestation, yet little is known of their soil microbiomes nor how land use impacts them. Soils from both trees in a primary and secondary forest were assessed for N-cycle metrics and DNA sequence-based composition of total bacterial, potential N-fixing bacterial, and potential ammonium oxidizing bacterial genera. The compositions of the functional groups of bacteria, but not their total relative abundance of DNA, were different across the soils. The P. macroloba soils had greater NO₃⁻ levels and richness of both functional groups, while I. edulis soils had greater NH₄⁺ levels, consistent with its NH₄⁺ preference for root nodule development. The bacterial communities were different by habitat, as secondary forest I. edulis microbiomes were less rich, more dominant, possibly more affected by the disturbance, or reached equilibrium status quicker than the richer, less dominant P. macroloba microbiomes, which may be developing slower along with secondary forest succession, or were less affected by the disturbance. Functional redundancy and switching of 10 N-cycle bacterial genera was evident between the primary and secondary forest soils, likely to maintain stable levels of N-cycle activity following disturbance. In summary, the two tree soil microbiomes are different, land use differentially affects them, and, thus, both tree species should be used during forest regeneration strategies in this region.