Limited resilience of the soil microbiome to mechanical compaction within three years of agricultural management

Soil compaction affects many soil functions but we have little information about the resilience of microorganisms. In this study, we present data on the response of soil microbial diversity to compaction and its temporal evolution under different agricultural management treatments in the first three years after a compaction event. Crop yield was reduced in the first two growing seasons post compaction (up to 90% reduction), but mostly recovered in the following ones. Soil compaction increased soil bulk density (+15%) and decreased air permeability (-94%) and gas diffusion (-59%), and those properties did not entirely recover after four growing seasons. Compaction induced cropping system dependent shifts in microbial community structures with little resilience over the four growing seasons; however, these compaction effects were much smaller than the spatial and the temporal effects that explained almost 15 and 5 times more of the variance, respectively. Microbial taxa sensitive to soil compaction were broadly distributed across the taxonomic tree and present in all major bacterial and fungal phyla. Compacted soils favored bacterial taxa with known anaerobic metabolisms, whereas taxa with strictly aerobic metabolism were mostly negatively affected. Saprotrophic fungi such as lignin decomposers tended to increase in compacted soils, whereas plant-associated fungi appeared to be more negatively affected. This study demonstrates that soil compaction is a disturbance that can have long-lasting effects on the soil microbiome, but these effects do not necessarily align with differences in crop yield as well as crop yield effects do not necessarily align with soil structural recovery.