Abstract
Soil microbes are an essential component of terrestrial ecosystems and drive many biogeochemical processes throughout the soil profile. Prior field studies mainly focused on the vertical patterns of soil microbial communities, meaning their temporal dynamics have been largely neglected. In the present study, we investigated the vertical and temporal patterns of soil bacterial and archaeal communities in a wheat-soybean rotation agroecosystem at a depth of millions of sequences per sample. Our results revealed different vertical bacterial and archaeal richness patterns: bacterial richness was lowest in the deep soil layer and peaked in the surface or middle soil layer. In contrast, archaeal richness did not differ among soil layers. PERMANOVA analysis indicated that both bacterial and archaeal community compositions were significantly impacted by soil depth but unaffected by sampling time. Notably, the proportion of rare bacteria gradually decreased along with the soil profile. The rare bacterial community composition was the most important indicator for soil nutrient fertility index, as determined by random forest analysis. The soil prokaryotic co-occurrence networks of the surface and middle soil layers are more connected and harbored fewer negative links than that of the deep soil layer. Overall, our results highlighted soil depth as a more important determinant than temporal variation in shaping the soil prokaryotic community and interspecific interactions and revealed a potential role of rare taxa in soil biogeochemical function.