Coupling sulfur oxidation to antimonate reduction – a novel biogeochemical process mediated by Desulfurivibrio spp.

        Extreme environments are widely distibuted on earth, such as deserts, glaciers, permafrosts, acid mine drainages, and deepsea sediments. The life residing in extreme environments are facing various environmental stresses, such as aridity, cold, nutrient deficient, high metal toxicity, and hydrostatic pressure. Microorganism residing in these extreme environments can adopt different life styles to cope with the harsh environmental conditions. Thus, investigation of the microorganisms is of interest to identify novel metabolisms or to understand the microbial ecology, evolution, and environmental adaptation [1] [2].

        Tailings are fine-grained particles generated during mining production, which is considered as the largest waste-producing industry. The annual production of mine tailings is one of the major causes of anthropogenic land erosion with an estimated annual production at 14 billion tons globally [3]. Thus, the reclamation of mine tailings is of significant importance. The reclamation of mine tailings, however, are often impeded by its extreme environmental conditions. As a byproduct generated during mineral ore processing, mine tailings contain extremely high metal concentrations and low availability of TOC [4]. Therefore, it occurred to us that successful reclamation of mine tailings should start from understanding the life style of in situ microbes.

        In the current study, we chose the samples collected from stibnite (Sb₂S₃) mine tailing dam from the world largest Sb mining area (i.e., Xikuangshan) as an example. The tailing dam has been a major source of Sb contamination since it came into use in 1983 [5]. As the dam was going to cease by the end of 2021, its remediation is critical to the safety of surrounding environments and residents. Microbial mediated Sb reduction can transform Sb(V) to Sb(III), which decrease the solubility of Sb and restrain it from releasing to the surrounding area. Due to the low TOC availability, the reduced S compounds are preferred electron donor for microbial activity in mine tailings [4, 6]. Giving the abundance of S and Sb in stibnite mine tailings, we hypothesize that S-oxidation coupling to Sb reduction, which is an energy metabolism pathway has not been reported previously, may be critical for indigenous microorganisms.

Figure 1. Microbial mediated S oxidation coupled to Sb reduction

        We used a workflow combining geochemical analysis, culture-independent incubation, and bioinformatics to comprehensively elucidate: 1) the feasibility, 2) the environmental controls, and 3) the geochemical distribution of S oxidation Sb reduction. Stable isotope probing (SIP) technique is employed to identify the functional microorganisms that capable of S oxidation Sb reduction. SIP has been widely recognized as a reliable tool for identifying specific taxa mediating a biogeochemical process in the absence of a pure culture [7–11]. When combined with metagenomics, DNA-SIP has now become even more powerful, with the ability to examine the putative metabolic pathways by which certain taxa catalyze the targeted process, providing further evidence to link specific genes with a function [12, 13]. Accordingly, we have identified members associated with the genus Desulfurivibrio as the S-oxidizing Sb reducer residing in stibnite mine tailings. This population contains a non-concanical sulfate-reducing dsr system that could catalyze reverse recation to oxidize reduced S. Also, it encoded both antimonate reductase and arsenate reductase genes (anrA and arrA, respectively), both of which are capable of reuding Sb(V) to Sb(III).  Taken together, the presence of these functional genes guarntee the metabolic potential of coupling S oxidiation to Sb reduction by indigenous Desulfurivibrio population in the Xikuangshan stibnite mine tailing.

        Additional analyses were performed to characterize the distribution of Desulfurivibrio spp. and investigate its metabolic potential in Xikuangshan Sb mining impacted areas as well as other As- and Sb-contaminated sites. The Desulfurivibrio spp. is identified as a dominant microbial taxon in the Xikuangshan tailings, while its abundances are significantly lower in surrounding environments (adjacent soils, nearby river sediments and rice paddy sediments), which are also impacted by mining activities. As revealed by Random Forest predictions, the unique geochemical conditions present in tailing environments, which are depleted in organic carbon but replete in Sb and S, facilitate the dominance of Desulfurivibrio spp. compared to surrounding environments. This observation is supported by the previous literatures, which often found Desulfurivibrio spp. in environments with active S [14–16] and Sb [17, 18] cycles. 

Figure 2. Environmental controls of Desulfurivibrio spp.

        Further, pangenomic analysis was conducted to investigate relevant metabolic potentials of known Desulfurivibrio gnomes and metagenome assembled genomes (MAGs). Four environmental MAGs were retrieved from As and Sb contaminate sites in southern China. Additional genomes/MAGs were downloaded from NCBI database. The non-canonical oxidative-type dsr cluster is part of the core genes encoded by all Desulfurivibrio genomes/MAGs. On the other hand, the presence of anrA and arrA genes were only found in the genomes/MAGs retrieved from sites with active Sb/As cycles, including mine tailings, soda lakes, and high-As groundwaters. 

Figure 3. Pangenomic analysis of Desulfurivibrio populations

        In summary, a new biogeochemical cycle – S oxidation coupled to Sb reduction is demonstrated to be important for Desulfurivibrio populations residing in stibnite mine tailings – an extreme environment with elevated metal contamination and low TOC availability. We suggest that Desulfurivibrio should be further investigated as model organisms for harnessing S-oxidizing SbRB to facilitate future remediation of Sb mine tailings. 

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