High frequency cropping of pulses modifies soil nitrogen level and the rhizosphere bacterial microbiome in 4-year rotation systems of the semiarid prairie

Including pulses in wheat-based cropping systems in semiarid regions may be a strategy for sustainably intensifying crop production. However, the impact of an increase in the frequency of pulse crops on soil bacterial communities is not known. We tested the hypothesis that increasing the frequency of pea, lentil and chickpea in 4-year crop rotation systems would cause corresponding shifts in the soil bacterial community. The first cycle of a field experiment was conducted in 2010-2013 and the second cycle, in 2011-2014. 16S rDNA amplicon pyrosequencing was performed to examine the rhizosphere bacterial communities following the third year (phase-3) of the rotations and root bacterial communities during the fourth year (phase-4), when all rotations were seeded to wheat. We found that three consecutive years of pulse crops modified the structure and increased the diversity of the rhizosphere bacterial community. Changes in community composition led to changes in eleven groups of KEGG pathways, including an increase in nitrogen metabolism and a shift in the production of secondary metabolites towards high production of nitrogenous alkaloids in systems with high pulse frequency. Pulse identity had little influence on bacterial communities; the effect of pulses was related to soil mineral nitrogen level, which increased with pulse frequency. High pulse frequency reduced bacterial diversity in wheat roots in the fourth year of the rotations. The only dominant wheat root-associated operational taxonomic unit (OTU) positively related with wheat yield was identified as Rhizobium. One of the two dominant OTUs negatively related with wheat yield was typical of rotation systems with a pulse frequency of <= 1. Phase-4 grain yield was related with soil mineral nitrogen level. The inclusion of nitrogen in the agroecosystem through biological nitrogen fixation seems to be an important part of the beneficial effect of including pulses in wheat-based rotations. The effect of pulse frequency on the structure and function of rhizobacteria communities and on wheat is mitigated by drought in the semiarid prairie.