Impact of long-term agricultural management practices on therhizosphere microbiome and plant health

Increasing food and energy demands have resulted in a considerable intensification of farming practices, whichbrought about severe consequences for agricultural soils during last decades. In order to maintain soil quality andhealth for the future, the development of more extensive and sustainable farming strategies is urgently needed.The soil and rhizosphere microbiome play an integral role in virtually all soil processes and are intimately linkedto plant performance. Various studies indicated that agricultural management practices affect soil microbiomes.We therefore hypothesized that this external impact is conveyed by the microbial communities to the currentcrops at the time of their establishment. We used twelve differently managed soils from three long-term fieldtrials established in 1978 (Therwil, Switzerland), 1992 (Bernburg, Germany), and 2006 (Thyrow, Germany) toanalyze the impact of various management strategies (crop rotation, fertilization, tillage) on soil and its associatedrhizosphere microbiomes under consideration of plant productivity, plant health, and the ability of the soils tosuppress soil-borne phytopathogens. The model plant lettuce (Lactuca sativa L.) was cultivated for ten weeks undergrowth-chamber conditions in these soils. High-throughput sequencing of bacterial 16S rRNA genes or fungalITS fragments, respectively, PCR- amplified from total community DNA of rhizosphere and soil samples showedsignificant differences in microbial community compositions between soils that originated from the different fieldsites and long-term farming practices. Moreover, differences depending on long-term agricultural managementin plant productivity and health as measured by RT-qPCR of stress-related plant genes were observed. Localizedanalysis of rhizosphere soil solution was performed using non-invasive sampling techniques with sorption filtersplaced onto the surface of soil-grown roots along the root observation windows with subsequent HPLC-MSprofiling. Ami