Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome‐resolved metagenomics

Abstract

Gold ore processing uses cyanide (CN(-) ), which often results in large volumes of thiocyanate- (SCN(-) ) contaminated wastewater requiring treatment. Microbial communities can degrade SCN(-) and CN(-) , but little is known about their membership and metabolic potential. Microbial-based remediation strategies will benefit from an ecological understanding of organisms involved in the breakdown of SCN(-) and CN(-) into sulfur, carbon and nitrogen compounds. We performed metagenomic analysis of samples from two laboratory-scale bioreactors used to study SCN(-) and CN(-) degradation. Community analysis revealed the dominance of Thiobacillus spp., whose genomes harbour a previously unreported operon for SCN(-) degradation. Genome-based metabolic predictions suggest that a large portion of each bioreactor community is autotrophic, relying not on molasses in reactor feed but using energy gained from oxidation of sulfur compounds produced during SCN(-) degradation. Heterotrophs, including a bacterium from a previously uncharacterized phylum, compose a smaller portion of the reactor community. Predation by phage and eukaryotes is predicted to affect community dynamics. Genes for ammonium oxidation and denitrification were detected, indicating the potential for nitrogen removal, as required for complete remediation of wastewater. These findings suggest optimization strategies for reactor design, such as improved aerobic/anaerobic partitioning and elimination of organic carbon from reactor feed.

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

“…() and Kantor et al. (). It was acclimatized to cultivation in the presence of suspended solids as described by van Zyl et al.…”

“…To identify the microorganisms responsible for SCN − degradation, microbial communities in experimental reactors have been characterized by molecular fingerprinting (Felföldi et al., ; Huddy, van Zyl, van Hille, & Harrison, ; Quan et al., ) and genome‐resolved metagenomic analysis (Kantor et al., ; R. S. Kantor, R. J. Huddy, I. Ramsunder, B. C. Thomas, S. Tringe, R. L., Hettich, S. T. L., Harrison, J. F. Banfield, in review). Analysis of the 16S and 18S rRNA in a reactor established with an ASTER ™ consortium revealed that the microbial community was much more diverse than previously expected (Huddy et al., ).…”

“…(), as the inoculum for an ASTER ™ process to treat the effluent from a bioleaching operation exploiting a refractory gold deposit in the Philippines. The aim of the research was to resolve the microbial community associated with an active ASTER ™ solids reactor system and to compare that with previously resolved (Kantor et al., ; R. S. Kantor, R. J. Huddy, I. Ramsunder, B. C. Thomas, S. Tringe, R. L., Hettich, S. T. L., Harrison, J. F. Banfield, in review) ASTER ™ microbial communities. In this study, we used genome‐resolved metagenomics to elucidate the microbial community composition and metabolic potential of the solids‐containing SCN − degradation bioreactor.…”

Long‐term ferrocyanide application via deicing salts promotes the establishment of Actinomycetales assimilating ferrocyanide‐derived carbon in soil

“…However, it has to be taken into account that 13 C incorporation into biomass could only serve as a proxy for ferrocyanide degradation but must not reflect the actual removal rate. Moreover, the diversity of 13 C‐ labelled bacteria differed highly from those of the roadside soils: in soil D and F, ferrocyanide was used as C source mainly by Actinomycetales , while in soil W members of Acidobacteria (Gp3, Gp4, Gp6), Gemmatimonadetes ( Gemmatimonas ) and Gammaproteobacteria ( Thermomonas , unclassified Xanthomonadaceae ) assimilated the 13 C. All those taxa were previously found to be enriched in bioreactors containing mining effluent, indicating their capacity to degrade thiocyanate and cyanide (Kantor et al ., ). Surprisingly, neither Kineosporia nor Mycobacterium assimilated ferrocyanide‐derived C in soil W although their presence at similar abundances when compared with soil D and F. This indicates an adaptation of the microbial community on long‐term ferrocyanide application and consequently its permanent presence as additional C source: in soils first exposed to ferrocyanide, various microorganisms assimilate the new available C but at the end were outcompeted by Actinomycetales , resulting in their increased abundance in roadside soils when compared with soil W. However, it has to be taken into account that ferrocyanide is not applied purely to the road environment but as anticaking agent via deicing salts that itself could impact microbial soil community (Cernohlavkova et al ., ; Hofman et al ., ).…”

Low temperature, autotrophic microbial denitrification using thiosulfate or thiocyanate as electron donor

“…In some microorganisms, SCN − can act as an electron donor as well as providing sulfur and nitrogen to the cell (Ogawa et al 2013). Finally, a novel SCN − degrading pathway has been identified by metagenomics in a Thiobacillus -like strain (Kantor et al 2015). Advantages of ISC fed autotrophic versus heterotrophic denitrification are that less sludge is produced and costs are reduced as an organic electron donor does not need to be added.…”