Nitrogen-dependent bacterial community shifts in root, rhizome and rhizosphere of nutrient-efficient Miscanthus x giganteus from long-term field trials

Abstract

The perennial energy crop Miscanthus × giganteus is recognized for its extraordinary nitrogen-use efficiency. While the remobilization of nitrogen (N) to the rhizome after the growth phase contributes to this efficiency, the plant-associated microbiome might also contribute, as N-fixing bacterial species had been isolated from this grass. Here, we studied established Miscanthus × giganteus plots in southern Germany that either received 80 kg N ha−1 a−1 or that were not N-fertilized for 14 years. The bacterial communities of the bulk soil, rhizosphere, roots and rhizomes were analysed. Major differences were encountered between plant-associated fractions. Nitrogen had little effect on soil communities. The roots and rhizomes showed less microbial diversity than soil fractions. In these compartments, Actinobacteria and N-fixing symbiosis-associated Proteobacteria depended on N. Intriguingly, N2-fixing-related bacterial families were enriched in the rhizomes in long-term zero N plots, while denitrifier-related families were depleted. These findings point to the rhizome as a potentially interesting plant organ for N fixation and demonstrate long-term differences in the organ-specific bacterial communities associated with different N supply, which are mainly shaped by the plant.