A Pan-Biome Metagenomic Atlas of the Brazilian Rhizosphere, Root, and Soil Microbiomes

Brazil encompasses some of the world’s most critical reservoirs of biodiversity, yet the microbial dimension of these ecosystems remains fragmented and poorly mapped. Understanding the soil microbiome is essential for predicting ecosystem responses to climate change and discovering novel biotechnological resources. Here, we present a comprehensive metagenomic atlas characterizing the soil, rhizosphere, and root microbiomes across all six Brazilian biomes: Amazon, Atlantic Forest, Cerrado, Caatinga, Pampa, and Pantanal. We employed a dual-sequencing approach, combining 16S/18S/ITS amplicon profiling with shotgun metagenomics, to catalogue microbial diversity in 79 samples representing a gradient from humid rainforests to semi-arid drylands. Our analysis reveals that while Proteobacteria are ubiquitous, their dominance is significantly reshaped by environmental stress. Humid biomes (Amazon, Pantanal) supported complex networks of fast-growing nutrient cyclers, whereas the semi-arid Caatinga was defined by a distinct "dry-adapted" core microbiome dominated by Actinobacteria . Fungal diversity was driven by moisture availability, with Ascomycota maintaining ubiquity across all ecosystems while Basidiomycota abundance declined in drier soils. This study provides the first unified baseline database of Brazilian soil microbiology, offering unprecedented insights into the "below-ground" biodiversity that sustains these globally vital ecosystems and establishing a reference for future research in synthetic biology, sustainable agriculture, and conservation.