Microbial community composition in agricultural soils during freeze-thaw and fertilizer stress

Microbial activity persists in agricultural soils throughout the non-growing season (NGS; winter plus portions of the shoulder seasons) and related freeze-thaw cycles (FTCs), with peak activity during thaw events. Climate change is expected to increase the frequency of FTCs in temperate cold regions, which may hasten microbial consumption of fall-amended fertilizers, decreasing potency come the growing season. We conducted a high-resolution examination of the impacts of freeze-thaw and nutrient stress on microbial communities in agricultural soils across both soil depth and time. Four soil columns were incubated under a climate model of a NGS including precipitation, temperature, and thermal gradient with depth over 60 days. Two columns were amended with fertilizer, and two incubated as unamended soil. The impacts of repeated FTCs and nutrient stress on bacterial, archaeal, and fungal soil community members were determined, providing a deeply sampled longitudinal view of soil microbial response to NGS conditions. Geochemical changes from flow-through leachate and amplicon sequencing of 16S and ITS rRNA genes were used to assess community response to fertilizer and FTCs over time. Despite significant nitrification observed in fertilized columns, there were no significant microbial diversity, core community, or nitrogen cycling population trends in response to nutrient stress. The impact of FTCs was observable as an increase in community alpha diversity during FTCs. Community compositions shifted across a longer time frame than individual FTCs, with bulk changes to the community in each phase of the experiment (pre-FTC, during FTC, and post-FTC). Our results demonstrate microbial community composition remains relatively stable for archaea, bacteria, and fungi through a NGS, independent of nutrient availability. This observation contrasts canonical thinking that FTCs have significant and prolonged effects on microbial communities. In contrast to permafrost and other soils experiencing rare FTCs, in temperate agricultural soils regularly experiencing such perturbations, the response to freeze-thaw and fertilizer stress may be muted by a more resilient community or be controlled at the level of gene expression rather than population turn-over. These results clarify the impacts of winter FTCs on fertilizer consumption, with implications for agricultural best practices and modeling of biogeochemical cycling in agroecosystems.