Long-term fertilization rather than plant species shapes rhizosphere and bulk soil prokaryotic communities in agroecosystems

Abstract

The rhizosphere microbiome plays an important role in disease-suppressive soils and is closely related to plant health. While a key role of plant-related factors in shaping the rhizosphere microbiome is well known for natural ecosystems and similarly fertilized agricultural systems, the interaction between fertilization and plant species effects on rhizosphere microbial communities has less been determined. Here, we assessed the influence of plant- and fertilization-related factors on the abundance, biomass and composition of rhizosphere and bulk soil prokaryotic communities. Soil samples were collected from the bulk soil and the rhizosphere of maize, potato, and white mustard under mineral (N180P150K150 per year) and organic (50 t ha−1 of fresh cattle manure) fertilization treatments within a long-term microplot experiment. Total (DNA) and potentially active (RNA) prokaryotic communities were analyzed using RT-PCR and Illumina MiSeq amplicon sequencing. Both NPK and manure fertilization systems led to the similarity of the prokaryotic community structures in rhizosphere and bulk soil. Long-term application of manure increased significantly prokaryotic abundance and diversity due to development of many underrepresented taxa. NPK significantly reduced prokaryotic diversity and the total number of species. Our findings suggest that fertilization is a more important factor in determining the abundance and diversity of prokaryotic communities in the rhizosphere than plant species. Thus, the traditional concept of the key role of plant species in shaping prokaryotic communities in the rhizosphere which is valid for non-cultivated plant species was not confirmed for the agricultural ecosystems and crops investigated here.