16S and ITS amplicons from soil samples Raw sequence reads

Soil microbiome responses to short-term nitrogen (N) inputs within the context of existing spatio-temporal variability remain uncertain. Here, we examined soil bacterial and fungal communities pre/post-N fertilization in an 8 year-old switchgrass field, in which twenty-four plots received N fertilization at three levels (0, 100, and 200 kg N ha-1 as NH4NO3) for the first time since planting. Soils were collected at two depths, 0-5 and 5-15 cm, for DNA extraction and amplicon sequencing of 16S rRNA genes and ITS regions, and soil metagenomic analysis. Baseline assessment prior to fertilization revealed no pre-existing differences in either bacterial or fungal communities across plots. The one-time N fertilization increased switchgrass yields and tissue N content, and the added N was nearly completely removed from the soil of fertilized plots by the end of the growing season. Both bacterial/archaeal and fungal communities showed large spatial (by depth) and temporal variation (by season) within each plot, accounting for 17 and 12-22 % of the variation in bacterial/archaeal and fungal community composition, respectively. While N fertilization effects accounted for only ~4% of overall variation, some specific microbial groups, including the bacterial genus Pseudonocardia and the fungal genus Archaeorhizomyces, were notably repressed by fertilization at 200 kg N ha-1. Bacterial groups varied with both depth in the soil profile and time of sampling, while temporal variability shaped the fungal community more significantly than vertical heterogeneity in the soil. Thus, variability within the field might override the changes induced by N addition. Continued analyses of these trends over time with annual fertilization and management will be needed to understand whether these transient effects change over time.