Linking soil microbial genomic features to forest-to-pasture conversion in the Amazon

Abstract

The Brazilian Amazon is facing unprecedented threats, including increasing deforestation and degradation, which together impact half of the original forest area. Soil microorganisms are sensitive indicators of land-use change, linked to a rise in microbial methane emissions and antibiotic-resistance genes in the Amazon. However, most Amazonian soil microbes remain unknown, and little attention has been given to their genomes. Using sequencing and bioinformatics, we recovered and characterized 69 soil bacterial and archaeal genomes (metagenome-assembled genomes). These abundant members of the microbial communities diverged across forests and pastures in terms of taxonomic and functional traits. Forest conversion favors organisms with specific genomic features — increased GC content, genome size, and gene number — selecting for microorganisms that can thrive under altered conditions. Our paper helps us understand the intricate relationships between microbes and the environment, which are crucial pieces of information for comprehensive soil health assessments and future policy formulation.