soil metagenome Raw sequence reads

Arsenite (As(III)) oxidation has important environmental implications by decreasing both the mobility and toxicity of As in the environment. Microorganisms play important roles in accelerating this biogeochemical process. Nitrate-dependent As(III) oxidation (NDAO) may be an important process for As(III) oxidation in anoxic environments, such as water logged paddy fields or wetlands, and it has been proposed that many bacteria can oxidize As(III) under denitrifying conditions. Our current knowledge of nitrate-dependent As(III)-oxidizing bacteria (NDAB), however, is largely based on isolates and thus the diversity of NDAB may be underestimated. In this study, stable isotope probing (SIP) with 13C-labelled NaHCO3 as the sole carbon source, amplicon sequencing, and shotgun metagenomics were combined to identify NDAB and investigate their metabolism. As(III) oxidation was observed in the treatment amended with nitrate while no obvious As(III) oxidation was observed without nitrate addition. The increase in the gene copies of aioA, which encodes for arsenite oxidase, in the nitrate amended treatment suggested that As(III) oxidation was mediated by microorganisms containing the aioA gene. Furthermore, DNA-SIP identified diverse putative NDAB in the As contaminated soils, such as Azoarcus, Rhodanobacter, Pseudomonas, and Burkholderials-related bacteria. Metagenomic analysis further indicated that most of these putative NDAB contained genes for As(III) oxidation and nitrate reduction, confirming their roles in NDAO. The identification of diverse and novel putative NDAB expands current knowledge regarding the diversity of NDAB in As contaminated environments.