Antimony-reducing bacteria identified by DNA-stable isotope probing and their potential metabolic traits revealed by metagenomic-binning Raw sequence reads

Anaerobic Sb(V) reduction is a promising bioremediation strategy because it can remove Sb from wastewater and prevent plants (e.g., rice) from adsorbing Sb from the soil. However, our understanding of Sb(V)-reducing microorganisms is limited and the molecular mechanisms for Sb(V) reduction are largely unknown. In this study, DNA-stable isotope probing (DNA-SIP) and metagenomic-binning were combined to identify potential Sb(V)-reducing bacteria (SbRB) and predict their possible metabolic pathways for Sb(V) reduction. Cultures inoculated from Sb-contaminated paddy and cornfield soils demonstrated a capability to reduce Sb(V) by innate microbial communities. DNA-SIP identified that bacteria affiliated with the genera Pseudomonas, Lysinibacillus, and Geobacter and the family Enterobacteriaceae were putative SbRB. Metagenomic-binning was performed to investigate the metabolic potentials of the Sb(V)-reducing cultures with a focus on those identified as putative SbRB by DNA-SIP. Near complete draft genomes (>90% completeness) of bins affiliated with putative SbRB were obtained by metagenomic-binning. Given the similar chemical structure of As and Sb and the lack of known Sb-related genes in the existing databases, we focused our search on As-related genes, especially for genes encoding As(V) reduction. Notably, bins affiliated with Pseudomonas, Geobacter, and Enterobacteriaceae contained the respiratory arsenate reductase (arr) gene. In contrast, arrA was not detected in bins affiliated with Lysinibacillus. In addition, other genes related to As resistance and transformation were also detected in the metagenomes of Sb(V)-reducing cultures. This current work represents the first attempts of using DNA-SIP and metagenomic-binning to identify anaerobic SbRB and their metabolic potential and provided valuable datasets to link bacterial identities with Sb(V) reduction.