Abstract
Background Excessive fertilization and tillage erosion pose threats to food security and crop yields. A transition towards more sustainable agricultural practices may be advanced by harnessing ecosystem services provided by plant microbiomes. However, targeting microbiota at the agroecosystem scale necessitates bridging the gap to micro-scale structures of microbiomes. We hypothesized, that relevant changes of microbial N cycle guilds in the rhizosphere of rye align with a soil catena determined by tillage erosion. Aboveground patterns of crop biomass along such a catena persist in hummocky landscapes and are of practical relevance to farmers.
Results The rhizosphere of the topsoil at four typical soils in an arable field grown with rye within the Quillow catchment (NE Germany) was sampled. The soils represent a complete tillage erosion gradient from an extremely eroded Calcaric Regosol over a strongly eroded Nudiargic Luvisol to a non-eroded Calcic Luvisol and colluvial Gleyic-Colluvic Regosols. Gene abundances characteristic of microbial N cycle guilds were analysed using shotgun metagenomic sequencing. Distinct growth of rye plants along the catena was correlated with the nitrogen cycle functions of the rhizosphere microbiome based on multivariate analyses. Gene ratios describing differential denitrification potential of the microbiome differed significantly between soils. The norBC gene abundance was most strongly coupled to plant productivity, which is likely due to its involvement into multiple plant microbiome interactions besides denitrification. Genes associated with DNRA and diazotrophy prevailed at eroded soils. The eroded sites showed the lowest plant productivity and soil mineral N availability. Additionally, N limitation at the eroded sites was implied by the lowered gdh to glnA ratio and its association to plant productivity compared to the depositional site.
Conclusions Thus, gradients in legacy of agricultural management such as tillage erosion capture substantial changes in rhizosphere microbiome functionality. These specific microbiome assembly patterns are a function of above ground in field-plant productivity patterns accessible by remote sensing. Thus, the interrelation of in-field crop biomass patterns and the rhizosphere microbiome opens up the opportunity to assess distribution patterns of plant microbiota functional distribution at scales relevant to agricultural production and agroecosystems functioning.