Revealing the Bacteriome in Crop–Livestock–Forest Integration Systems in the Cerrado of MATOPIBA, Brazil

Sustainable agriculture relies on effective soil management, making it crucial to assess soil health, especially in areas of agricultural expansion, such as the Cerrado in the MATOPIBA region. Sustainable strategies, such as integrated production systems (crop–livestock–forestry), are essential to mitigate these impacts. However, little is known about the effects of these systems on soil microbial communities. The objective of this study was to evaluate bacterial communities associated with soils under different integrated production systems in the MATOPIBA region. Soil samples from the 0–10 cm depth layer were collected from the following land use systems: (i) native Cerrado vegetation (NCV), (ii) native Babassu forest (NPV), (iii) no-tillage soybean—regional standard system (NT-S), (iv) crop–forest integration (CFI), (v) crop–livestock integration (CLI), and (vi) livestock–forest integration (LFI). We measured chemical properties and bacterial communities using next-generation sequencing (NGS) of the V3-V4 hypervariable region of the 16S rRNA gene. The results revealed that the integration systems (CFI, CLI, and LFI) resulted in changes in soil chemical properties, which contributed to the modulation of the bacterial communities. The most abundant taxa in integrated production systems shows a positive correlation with soil pH and phosphorus content. Members of the Nitrosomonadaceae and Sphingomonadaceae families are more related to integrated production systems containing a forestry component (CFI and LFI), while Bacillaceae are more evident in crop–livestock integration systems (CLI).