Metagenomics of soil microbiome uncovers community homogenization in agricultural landscapes in Cerrado

Deforestation and land use intensification have been affecting the soil microbiota community, decreasing taxonomic and functional diversity of soil Archaea and Bacteria, and thus affecting key ecosystem functions. Here, we assess the influence of landscape structure and soil physico-chemical properties on microbiota community (Archaea and Bacteria) in agricultural landscapes in the Cerrado ecoregion. We used a metagenomics approach to obtain the soil microbiome community composition in 32 agricultural landscapes, and piecewise structural equation models to conjointly analyze the effects of landscape structure and soil on taxonomic, phylogenetic, and functional alpha diversity. We also analyzed the effects of landscape structure and soil properties on community taxonomic and phylogenetic beta diversity, using multiple matrix regression with randomization. We found that the number and shape of natural vegetation (NV) areas positively affected taxonomic, phylogenetic, and functional soil microbiota alpha diversity. Percentage of pasture and shape of NV had a positive influence on phosphorus content. Percentage of savanna and landscape compositional heterogeneity negatively affected soil organic matter content. However, soil properties had only an indirect effect on the microbiota alpha diversity. Taxonomic and phylogenetic beta diversity and their components, nestedness and turnover, were very low between soil sites, and positively related to the amount of NV in the landscape and soil chromium concentration. Our results show that rather than decreasing Archaea and Bacteria species richness, intensive agriculture is modifying the community’s structure homogenizing species composition between landscapes, leading to a dominance of groups more adapted to intensive agriculture production systems. • Intensive agriculture is modifying community’s structure homogenizing Archaea and Bacteria species composition between landscapes • Habitat fragmentation had a positive effect on taxonomic, phylogenetic, and functional soil microbiota diversity • Taxonomic and phylogenetic beta diversity, including nestedness and turnover were very low between all pairs of sites. • Soil properties had only indirect effects on microbiota alpha diversity • The amount of natural vegetation and soil chromium concentration affected positively beta diversity