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

Area of Science:

• Microbial Genomics
• Ecology
• Environmental Science

Background:

• Amazonian soil microbial communities are sensitive to land-use change.
• Previous studies focused on broad community shifts or specific microbial groups, neglecting genomic insights.
• The genomes of most Amazonian soil microbes remain largely uncharacterized.

Purpose of the Study:

• To characterize soil bacterial and archaeal metagenome-assembled genomes (MAGs) from Amazonian forests and pastures.
• To evaluate the impacts of land conversion on the genomic features and functional traits of soil microbes.
• To expand the genomic data set for Amazonian upland soils and assess novel taxa.

Main Methods:

• Recovery and characterization of 69 soil bacterial and archaeal MAGs from six sites (three forests, three pastures) in the Eastern Brazilian Amazon.
• Comparative analysis of genomic features (GC content, genome size, coding sequences) between forest and pasture MAGs.
• Assessment of taxonomic diversity and functional profiles, particularly genes involved in biogeochemical cycling and carbohydrate metabolism.

Main Results:

• Pasture MAGs exhibited significantly higher GC content (64.9% vs 60.2%), genome size (4.0 vs 3.1 Mbp), and number of coding sequences (4,058 vs 3,306) compared to forest MAGs.
• Ninety percent of the recovered MAGs showed low similarity to known species, indicating a high proportion of potentially novel taxa.
• Land conversion impacted functional profiles, with pasture MAGs showing a higher abundance of genes related to biogeochemical cycling and carbohydrate-active enzymes.

Conclusions:

• Land-use change, specifically forest conversion to pasture, imposes drastic impacts on the genomic characteristics and functional traits of dominant soil microbes in the Brazilian Amazon.
• The study provides the largest single-sourced genomic dataset from upland Amazonian soils to date, increasing known MAG richness by 78%.
• Understanding these microbial genomic shifts is crucial for soil health assessments and informing environmental policy in the face of Amazonian deforestation.