Se-rich riverine ecosystem Raw sequence reads

Microorganisms govern the mobility and bioavailability of selenium (Se) in aqueous environment by mediating the reductive transformation of Se. However, the genetic mechanisms for microbial Se(IV) reduction are currently unresolved. In this study, DNA-stable isotope probing (DNA-SIP) and metagenomics analysis were combined to identify putative Se(IV)-reducing bacteria (SeIVRBs) and predict the metabolic pathways involved in Se(IV) reduction. Se(IV)-reducing cultures inoculated with Se-contaminated sediment demonstrated that the indigenous microbiome was able to reduce Se(IV) heterotrophically. DNA-SIP identified bacteria associated with Pseudomonas, Geobacter, Comamonas, and Anaeromyxobacter as putative SeIVRBs. In addition, four high-quality metagenome-assembled genomes (MAGs) of these putative SeIVRBs were obtained by metagenomic binning. MAGs associated with four SeIVRBs contained putative Se(IV)-reducing genes encoding the dimethyl sulfoxide (DMSO) reductase family, fumarate reductase, sulfite reductase, periplasmic nitrate/nitrite reductase, thioredoxin reductase, glutathione reductase, and hydrogenase I. Furthermore, metatranscriptomic analysis was performed to investigate genes highly expressed in Se(IV)-reducing cultures. Genes associated with DMSO reductase (serA/PHGDH), fumarate reductase (sdhCD/frdCD), and sulfite reductase (cysDIH) were upregulated in the metatranscriptomes of Se(IV)-reducing cultures compared to their control counterpart, suggesting that these genes may be responsible for Se(IV) reduction. The metabolic versatility of these putative SeIVRBs may be central to their ability to flourish in Se-contaminated sediment.