Amazon forest-to-agriculture conversion alters rhizosphere microbiome composition while functions are kept

Abstract

The conversion of native forest to agriculture is the main cause of microbial biodiversity loss in Amazon soils. In order to better understand this effect, we used metagenomics to investigate microbial patterns and functions in bulk soil and rhizosphere of soybean, in a long-term forest-to-agriculture conversion. Long-term forest-to-agriculture led to microbial homogenization and loss of diversity in both bulk soil and rhizosphere, mainly driven by decreasing aluminum concentration and increased cations saturation in soil, due liming and fertilization in long-term no-till cropping. Data revealed that long-term no-till culminated with decrease in Acidobacteria, Actinobacteria and Proteobacteria abundances. However, α- and β-Proteobacteria abundances were higher in rhizosphere than in bulk soil, regardless time after forest-to-agriculture conversion. Changes in functional potential occurred predominantly in bulk soil, with decreases in functions related to potassium metabolism and virulence, disease and defense while functions related to nucleic acids metabolism increased. Functions in soybean rhizosphere remained stable, except for those related to potassium metabolism, which decreased after 20-year no-till cropping. Together, our results show that soybean root system selects microbial taxa via trade-offs, to keep functional resilience in the rhizosphere microbiome along time.

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