Microbially mediated sulfur oxidation coupled with arsenate reduction within oligotrophic mining-impacted habitats

Abstract

Arsenate [As(V)] reduction is a major cause of arsenic (As) release from soils, which threatens more than 200 million people worldwide. While heterotrophic As(V) reduction has been investigated extensively, the mechanism of chemolithotrophic As(V) reduction is less studied. Since As is frequently found as a sulfidic mineral in the environment, microbial mediated sulfur oxidation coupled to As(V) reduction (SOAsR), a chemolithotrophic process, may be more favorable in sites impacted by oligotrophic mining (e.g. As-contaminated mine tailings). While SOAsR is thermodynamically favorable, knowledge regarding this biogeochemical process is still limited. The current study suggested that SOAsR was a more prevalent process than heterotrophic As(V) reduction in oligotrophic sites, such as mine tailings. The water-soluble reduced sulfur concentration was predicted to be one of the major geochemical parameters that had a substantial impact on SOAsR potentials. A combination of DNA stable isotope probing and metagenome binning revealed members of the genera Sulfuricella, Ramlibacter, and Sulfuritalea as sulfur oxidizing As(V)-reducing bacteria (SOAsRB) in mine tailings. Genome mining further expanded the list of potential SOAsRB to diverse phylogenetic lineages such as members associated with Burkholderiaceae and Rhodocyclaceae. Metagenome analysis using multiple tailing samples across southern China confirmed that the putative SOAsRB were the dominant As(V) reducers in these sites. Together, the current findings expand our knowledge regarding the chemolithotrophic As(V) reduction process, which may be harnessed to facilitate future remediation practices in mine tailings.

Keywords: arsenate reduction; genome mining; stable isotope probing; sulfur oxidation.

Figure 1

Geochemical analysis of enrichment cultures. (A) Concentration of As species; (B) SO₄²⁻ concentration; and (C) the accumulation of products (As(III) and SO₄²⁻) over the incubation period. Error bars indicate standard deviation of 5 replicates.

Figure 2

Quantification of SSU rRNA (A) and As(V) reductase gene arrA (B) abundances in retrieved SIP fractions. The pink shade denotes the fractions that are considered as ¹³C-incorporated heavy fractions. Error bars indicate standard deviation of triplicate samples. For the fractions that employed for sequencing analysis, please refer to Supplementary Table S2.

Figure 3

Relative abundance of dominant ASVs in SIP fractions. The size of the bubbles represents the average relative abundance of each ASV from triplicate samples, except for the heavy fraction of ¹³C-A + S samples, which was calculated from 6 replicates.

Figure 4

The metabolic potentials of select MAGs. The number of the arrAB gene copies identified in each MAG is indicated in dark red. The green heatmap indicates the completeness (%) of the sulfur metabolism pathways (M00176, assimilatory sulfate reduction; M00596, dissimilatory sulfate reduction; and M00595, thiosulfate oxidation). The yellow heatmap indicates the completeness (%) of the carbon fixation pathways (M00173, reductive citrate cycle; M00375, hydroxypropionate-hydroxybutyrate cycle; M00376, 3-hydroxypropionate bi-cycle; M00374, dicarboxylate-hydroxybutyrate cycle; M00377, reductive acetyl-CoA pathway; M00579, phosphate acetyltransferase-acetate kinase pathway; and M00620, incomplete reductive citrate cycle).

Figure 5

Phylogenetic diversity of putative SOAsRB and their relative abundance in tailing metagenomes. Phylogenetic reconstruction of arrA genes retrieved from assembled MAGs and the GTDB reference genomes (A). The relative abundance of the SOAsRB and non-S-oxidizing As(V) reducers based on the arrA gene (B). The top 10 most abundant SOAsRB genera identified in tailing metagenomes (C).