Analysis of the soil bacteria microbiota in the long-term fertilization experiment (LTFE) of the Weilburgergrenze experimental field (Uni-Giessen).

Long-Term Field Experiments (LTFE) are ideal experimental platforms to test the effects of different agronomic practices on the soil microbiome. In this work, we analyzed the prokaryotic soil microbiota of the long-term field experiment of Giessen (Germany), with the aim to understand the effect of different nitrogen fertilization regimes in three soil habitats: post-harvest-, rhizospheric- and bulk soil. The fertilization treatments were: mineral-N, manure, mineral-N + manure and no N-amendment. High-throughput sequencing of 16S rRNA genes, qPCR of nitrogen cycle-related genes (bacterial and archaeal amoA, nirK, nirS, nosZ and nosZ-atypical) and soil physico-chemical analyses were performed. A co-occurrence correlation analysis was finally performed between all data. The response of the microbiota to the fertilization treatments was different in the three soil habitats, being highest in the bulk soil (~25% of the total microbiota) and lowest in the post-harvest soil. The functional genes tested were affected by the fertilization treatments in opposite ways in the different soil habitats, suggesting functional segregation. The co-occurrence correlation analysis performed on bulk and post-harvest soils showed a microbial organization in two clusters: one cluster (enriched in the post-harvest soil) associated to both nitrification and denitrification, and was characterized by Beta- and Gammaproteobacteria; the second cluster (enriched in the bulk soil) associated to denitrification, and was characterized by Acidobacteria. This work highlighted the different response of the soil microbiome to long-term nitrogen fertilization in three different soil habitats, and unraveled the taxonomical-functional interactions that shaped the microbial correlation network.