Urea fertilization can reduce soil bacterial and archaeal diversity in agroforestry systems

Agroforestry systems can be beneficial to soil microbial diversity, however, it might be affected by inorganic fertilizer use. This study evaluated the effects of urea (0, 100, 200, and 400 kg N ha⁻¹ year⁻¹) on soil bacterial and archaeal diversity in an agroforestry system in the Amazon region (Brazil). The system was composed of grass, native palms, and N-fixing legume trees. The experimental design was a randomized complete block with four treatments and three replications, each experimental unit had 0.25 ha⁻¹. Bacterial and archaeal diversity were investigated by next-generation sequencing (MiSeq sequencing platform). Bacterial quantities were assessed by colony-forming units; and 16 rRNA gene copy numbers (GCN) via Real-time PCR. Soil colony-forming units (CFU) did not differ across the levels of N inputs (p = 0.458) ranging 10⁵–10⁶ CFU per g⁻¹ soil, bacterial 16 rRNA GCN was lower at 400 kg N ha⁻¹ year⁻¹ compared to the control without urea application (p < 0.05); 16 rRNA GCN ranged at 10⁹ g⁻¹ soil. The highest urea level (400 kg N ha⁻¹ year⁻¹) reduced bacterial and archaeal diversity and increased ammonia-oxidizing archaea over methanogens. Nitrososphaera was a predominant archaeal genus (47%) in this agroforestry soil. Bacillus was the most abundant bacterial genus (18%) regardless of urea application. The bacterial community was less affected by the inputs of N than the archaea. The findings of this study suggest that the expected benefits of adopting agroforestry systems on soil microbial diversity can be reduced or neutralized by excessive and long-term N inputs using urea.