Effects of soil management practices on the microbiome of the agricultural Long-Term-Experiment (LTE-1) at Bernburg (Saxony-Anhalt, Germany).

Effects of soil management practices on the structure and function of the indigenous microbiome were followed by high-throughput (HT) metagenome sequencing of soil samples from a long-term field experiment designated LTE-1 carried out at Bernburg-Strenzfeld (Saxony-Anhalt, Germany). Total community DNA was obtained from soil samples treated as follows: i) ploughed with standard nitrogen fertilization and use of pesticides, ii) ploughed with reduced (50%) nitrogen fertilization, iii) cultivator treatment with standard nitrogen fertilization and use of pesticides, and iv) cultivator treatment with reduced (50%) nitrogen fertilization. Bulk soil, as well as soil influenced by plant roots were processed for all treatments in replicates. The indigenous soil microbiome was characterized at the taxonomic and functional level focusing on the identification of potential plant-beneficial, plant-growth-promoting and biocontrol determinants. Moreover, soil metagenome sequences were assembled and taxonomically binned to yield Metagenomically Assembled Genomes (MAGs) representing abundant soil microbiome members. MAGs were functionally profiled by genome-based metabolic reconstruction to identify putative new plant-growth-promoting or plant-beneficial bacteria. Soil management practices affect the abundance of particular MAGs. Hence, management regimes promoting beneficial soil microbiome members may be advantageous for the whole agrosystem, its health, carbon sequestration and plant productivity.