Genome‐resolved metagenomics of a bioremediation system for degradation of thiocyanate in mine water containing suspended solid tailings

Abstract

Thiocyanate (SCN−) is a toxic compound that forms when cyanide (CN−), used to recover gold, reacts with sulfur species. SCN−‐degrading microbial communities have been studied, using bioreactors fed synthetic wastewater. The inclusion of suspended solids in the form of mineral tailings, during the development of the acclimatized microbial consortium, led to the selection of an active planktonic microbial community. Preliminary analysis of the community composition revealed reduced microbial diversity relative to the laboratory‐based reactors operated without suspended solids. Despite minor upsets during the acclimation period, the SCN− degradation performance was largely unchanged under stable operating conditions. Here, we characterized the microbial community in the SCN− degrading bioreactor that included solid particulate tailings and determined how it differed from the biofilm‐based communities in solids‐free reactor systems inoculated from the same source. Genome‐based analysis revealed that the presence of solids decreased microbial diversity, selected for different strains, suppressed growth of thiobacilli inferred to be primarily responsible for SCN− degradation, and promoted growth of Trupera, an organism not detected in the reactors without solids. In the solids reactor community, heterotrophy and aerobic respiration represent the dominant metabolisms. Many organisms have genes for denitrification and sulfur oxidation, but only one Thiobacillus sp. in the solids reactor has SCN− degradation genes. The presence of the solids prevented floc and biofilm formation, leading to the observed reduced microbial diversity. Collectively the presence of the solids and lack of biofilm community may result in a process with reduced resilience to process perturbations, including fluctuations in the influent composition and pH. The results from this investigation have provided novel insights into the community composition of this industrially relevant community, giving potential for improved process control and operation through ongoing process monitoring.

Thiocyanate and organic carbon inputs drive convergent selection for specific autotrophicAfipiaandThiobacillusstrains within complex microbiomes

“…As expected based on prior work [6][7][8]10], various thiobacilli were prominent in the reactors. However, Thiobacillus_63_590, which was highly abundant especially in the molasses reactors and in the molasses-free reactor at the highest SCNinput concentrations (Thiobacillus-i in Table 2A) is distinct from strains/species abundant in prior studies.…”

“…The series coverage information was used to create bins using ABAWACA [20], CONCOCT [21], MaxBin2 [22], and MetaBAT2 [23]. Bins were also manually generated by leveraging information derived from matching against a dereplicated set of genomes from prior research SCN --degrading communities [6][7][8] and UniProt [24]. The resulting taxonomic profile and other "manual binning" signals (GC content, coverage, and single copy gene inventory were integrated for human-guided binning.…”

“…Some field reactors are inoculated with active laboratory-maintained consortia and continuously cultured with input of organic carbon, often in the form of molasses, and phosphate [3,5]. Previously, we characterized microbial communities derived from laboratory-maintained Activated Sludge Tailings Effluent Remediation (ASTER™, Outotec, South Africa) systems using a shotgun sequencing-based method that enabled recovery of genomes from many consortia members [6][7][8]. Different strain combinations proliferated under distinct operating conditions in these molasses-amended reactors, and the communities were very complex, with a reservoir of over 150 genotypes.…”

Analysis of Microbial Communities Associated with Bioremediation Systems for Thiocyanate-Laden Mine Water Effluents

“…A comparative reactor system was acclimatized to and then operated in the presence of 5.5% (w/v) solids, in the form of mineral tailings, as described by van Zyl et al [2] ahead of implementation at a site where complete tailings removal was not possible. This SCNdegrading culture was maintained as a "draw-and-fill" system with 10% volume removal and replacement by fresh feed solution containing 450 mg/L SCN − per week, as described by Rahman et al [7]. Two samples of planktonic cells were aseptically removed from the solids reactor, separated by an interval of 25 days for community analysis.…”

“…The microbial ecology of laboratory-scale SCNbioremediation processes, based upon the industrial ASTER™ process, has been investigated using 16S rRNA gene surveys [2,5] and genome-resolved metagenomics [6][7][8]. The use of these culture-independent techniques facilitates access to the microbial community composition and functional potential of key microbial species within these mixed bioremediation systems.…”