Bacteria Responsible for Nitrate-dependent Antimonite Oxidation in Antimony-contaminated Paddy Soil Revealed by the Combination of DNA-SIP and Metagenomics

Abstract

Background: Antimonite (Sb(III)) oxidation (SbO) can decrease the toxicity of antimony (Sb) and its uptake into plants (e.g., rice), thus serving an ecological role in bioremediation of Sb contamination. In some anoxic environments, Sb(III) can be oxidized coupled with nitrate as the electron acceptor. Here we investigate the potential for nitrate-dependent SbO in Sb contaminated rice paddies and identify nitrate-dependent Sb(III)-oxidizing bacteria (SbOB) using stable isotope probing (SIP) coupled with amplicon and shotgun metagenomic sequencing.Results: Anaerobic SbO was exclusively observed in the paddy soil amended with both Sb(III) and NO3-, whereas no apparent SbO was detected in the soil amended with Sb(III) only. The increasing abundance of the arsenite oxidase (aioA) gene suggests that nitrate-dependent SbO was catalysed by microorganisms harbouring the aioA gene. After 60-day DNA-SIP incubation, obvious shift in the aioA gene to heavy DNA fractions only in the treatment amended with 13C-NaHCO3, Sb(III) and NO3- suggested the incorporation of 13C by nitrate-dependent SbOB. Accordingly, DNA-SIP identified a number of putative nitrate-dependent SbOB in the paddy soil, including Azoarcus, Azospira and Chelativorans. Metagenomic analysis further revealed that they contained aioA gene and genes involved in denitrification and carbon fixation, supporting their capability for nitrate-dependent SbO.Conclusions: These observations in this study suggested the occurrence of nitrate-dependent SbO in paddy soils. A number of putative nitrate-dependent SbOB (i.e., Azoarcus, Azospira and Chelativorans) were reported here, which expands our current knowledge regarding the diversity of nitrate-dependent SbOB. In addition, this study provides a proof of concept using DNA-SIP to identify nitrate-dependent SbOB.

Unveiling metabolic characteristics of an uncultured Gammaproteobacterium responsible for in situ PAH biodegradation in petroleum polluted soil

“…Metagenomics, another cultivation-independent technique, is commonly used to recreate the genomes of environmental microbes, permitting the exploration of their metabolic functions (Chen and Murrell, 2010;Castaneda and Barbosa, 2017). Thus, the combination of SIP and metagenomics (SIP-metagenomics) (Zhang et al, 2020(Zhang et al, , 2021a(Zhang et al, , 2021b) not only allows the identification of PAH degraders, but also facilitates the detection of the catabolic pathways and novel enzymes involved in PAHs degradation from metagenomic libraries. To date, only one study has successfully used SIP-metagenomics to obtain relatively complete genomes from PAH degraders to explore their PAH metabolism in oil polluted waters (Dombrowski et al, 2016).…”