bacteria associated with the class Acidobacteriia in metal-contaminated soil revealed by metagenomic-binning Raw sequence reads

Bacteria associated with the phylum Acidobacteria represent one of the most abundant bacterial groups detected in a wide range of habitats. Low pH may facilitate the abundance of Acidobacteria probably because members of the Acidobacteriia, which is the most commonly detected class within Acidobacteria, prefer acidic environments. It is also observed that Acidobacteria was one of the dominant groups in various metal-contaminated sites located in Southwest China. Our understanding regarding the metabolisms of Acidobacteriia in metal contaminated soils, however, has been scarce. In this study, a naturally acidic site with high metal contents and multiple acidic low metal sites in Southwest China, where the Acidobacteriia accounted for a major proportion of the microbial communities, was selected to investigate the microbial adaptation by this group of microorganisms. The abundances of Acidobacteriia were positively correlated with the concentrations of arsenic (As), mercury (Hg), chromium (Cr), copper (Cu), and other metals, suggesting their tolerance to the metal-rich environments. Further, metagenomic-binning reconstructed 29 high-quality metagenome-assembled genomes (MAGs) associated with Acidobacteriia, providing an opportunity to study the metabolic potentials of Acidobacteriia. It was observed that Acidobacteriia-associated MAGs contained genes to transform As, Hg, and Cr through oxidation, reduction, efflux, and demethylation processes, suggesting the potential of Acidobacteriia to transform such metal(loid)s. In addition, the genes associated with alleviation of acid and metal stress were also detected in Acidobacteriia-associated MAGs. Notably, the Acidobacteriia-associated MAGs retrieved from five additional metal-contaminated sites across Southwest China further validated the possession of genes responsible for various metal resistance and cycling. The detection of genes associated with metal transformation and stress alleviation suggested the adaptation of Acidobacteriia to acidic metal-rich environments. This study revealed the potential ecological roles of Acidobacteriia and expands our understanding of its genomic potentials in terrestrial habitats.