This study tested the hypothesis that cocoa monoculture (MS) and cocoa-açai agroforestry systems (AFS) may influence the microbial community structure and populations of plant growth-promoting bacteria (PGPR). Accordingly, the aim was to analyze the microbial community structure and PGPR populations in different agroecosystems in the Brazilian Amazon. To achieve this, the rhizosphere microbial community of cocoa and açai plants in both Amazonian seasons (dry and rainy) was analyzed using culture-dependent (PGPR screening) and -independent methods [PCR-DGGE based on rrs, alp, nifH gene, and intergenic region (ITS) of fungi]. Concerning PGPR screening, out of 48 isolated bacterial strains, 25% were capable of siderophore production, 29% of mineralized organic phosphate, 8% of inorganic phosphate solubilization, and 4% of indole acetic acid production. Moreover, 17% of isolates could inhibit the growth of various phytopathogenic fungi. Statistical analyses of DGGE fingerprints (p < 0.05) showed that bacterial and fungal community structures in the rhizosphere were influenced by the seasons, supporting the results of the physicochemical analysis of the environment. Furthermore, as hypothesized, microbial communities differed statistically when comparing the MS and AFS. These findings provide important insights into the influence of climate and cultivation systems on soil microbial communities to guide the development of sustainable agricultural practices.

The hypothesis that cultivating açaí in agroforestry systems (AFS) can recruit beneficial microorganisms to its rhizosphere was tested in this study. For this purpose, rhizospheric soil samples were collected from an AFS area. The colony-forming unit (CFU) counts of the soil samples were 3.5 × 10⁶ CFU/g, with no statistically significant differences between the plants (p < 0.05). Regarding PGPR characteristics, of the 44 isolated strains, 18% produced siderophores, 9% mineralized organic phosphate, 15% solubilized inorganic phosphate, and 7% produced indole-3-acetic acid (IAA) and antimicrobial substances. Strains AP4-03, AP1-33, and AP2-36 were affiliated with the genus Bacillus sp. and produced IAA at 1.45, 1.35, and 2.02 µg/mL, respectively. Furthermore, these strains were able to inhibit the growth of the fungus Pestalotiopsis by 69%, 67%, and 71%, respectively. Regarding the antifungal activity of bacterial extracts, inhibition zones of 23 mm (AP-03), 20 mm (AP-33), and 18 mm (AP-36), with 96% and 92% inhibition at 50 mg/mL (AP4-03 and AP1-33) and 100% inhibition at 41 mg/mL (AP2-36), were observed. Considering seedling germination, açaí palms inoculated with the strain AP1-33 statistically differed from the controls in terms of root length and hypocotyl length. Furthermore, treatments inoculated with the strain AP2-36 or all strains in the consortium differed when only the hypocotyl length was compared to the control. Thus, the analyzed strains showed potential to improve the initial development of açaí plants.