Brazilian Cerrado soil microbiota captures the impacts of agricultural practices and unveils a promising ecosystem for antimicrobial peptide discovery

Abstract

The concept that agricultural practices promote impacts on physicochemical and biological soil properties is well established. However, their influence on soil-associated microbiome is still poorly understood. This work aimed to investigate the bacterial communities settled in cultivated Brazilian Cerrado soils. For this purpose, soil samples were collected from corn (Zea mays L.) or soybean (Glycine max (L.) Merr.) crop fields cultivated in a Red Latosol (Rhodic Haplustox) soil type under no-tillage (NT, i.e., without agricultural land preparation) and under conventional tillage (CT). The Cerrado native vegetation adjacent to the experimental areas was used as a reference for original (undisturbed) soil condition. Firstly, the genetic structure of the most representative bacteria found in the given conditions was characterized. The 16S ribosomal DNA (rDNA) sequence analysis showed that Actinobacteria was the dominant phylum in both corn and soybean cropped soils under the NT system, with Arthrobacter being the most representative genus. On the other hand, β-proteobacteria was the most abundant phylum in soils under the CT system, as well as in the native Cerrado reference condition, with a prevalence of organisms from Burkholderia genus. In order to further profile the complex soil ecosystem, a functional metaproteomic analysis comparing soil samples between native Cerrado and NT soybean fields was performed and revealed a total of 305 proteins, of which 25 were differentially abundant and whose major functional categories were associated with transmembrane transport and proteolysis. Furthermore, bioprospecting antimicrobial peptides (AMPs) from the proteome data of native Cerrado soil samples, using predictive algorithms, identified promising candidates with potential antibacterial activity. Our results capture the influences of agricultural practices on the diversity of soil microbiota, provide the scientific community with a framework of the genetic structure of microorganisms settled in native and cultivated Cerrado soils, and underline the biotechnological potential of this important Brazilian biome.