Recent Developments for Remediating Acidic Mine Waters Using Sulfidogenic Bacteria

Acetic acid stress response of the acidophilic sulfate reducer Acididesulfobacillus acetoxydans

Acid mine drainage (AMD) waters are a severe environmental threat, due to their high metal content and low pH (pH <3). Current technologies treating AMD utilize neutrophilic sulfate-reducing microorganisms (SRMs), but acidophilic SRM could offer advantages. As AMDs are low in organics these processes require electron donor addition, which is often incompletely oxidized into organic acids (e.g., acetic acid). At low pH, acetic acid is undissociated and toxic to microorganisms. We investigated the stress response of the acetotrophic Acididesulfobacillus acetoxydans to acetic acid. A. acetoxydans was cultivated in bioreactors at pH 5.0 (optimum). For stress experiments, triplicate reactors were spiked until 7.5 mM of acetic acid and compared with (non-spiked) triplicate reactors for physiological, transcriptomic, and membrane lipid changes. After acetic acid spiking, the optical density initially dropped, followed by an adaptation phase during which growth resumed at a lower growth rate. Transcriptome analysis revealed a downregulation of genes involved in glutamate and aspartate synthesis following spiking. Membrane lipid analysis revealed a decrease in iso and anteiso fatty acid relative abundance; and an increase of acetyl-CoA as a fatty acid precursor. These adaptations allow A. acetoxydans to detoxify acetic acid, creating milder conditions for other microorganisms in AMD environments.

Continuous single-stage elemental sulfur reduction and copper sulfide precipitation under thermoacidophilic conditions

Metal sulfide precipitation is a viable technology for high-yield metal recovery from hydrometallurgical streams, with the potential to streamline the process design. A single-stage elemental sulfur (S⁰)-reducing and metal sulfide precipitating process can optimize the operational and capital costs associated with this technology, boosting the competitiveness of this technology for wider industrial application. However, limited research is available on biological sulfur reduction at high temperature and low pH, frequent conditions of hydrometallurgical process waters. Here we assessed the sulfidogenic activity of an industrial granular sludge previously shown to reduce S⁰ under hot (60-80 °C) and acidic conditions (pH 3.6). A 4 L gas-lift reactor was operated for 206 days and fed continuously with culture medium and copper. During the reactor operation, we explored the effect of the hydraulic retention time, copper loading rates, temperature, and H₂ and CO₂ flow rates on the volumetric sulfide production rates (VSPR). A maximum VSPR of 274 ± 6 mg·L^-1·d^-1 was reached, a 3.9-fold increase of the VSPR previously reported with this inoculum in batch operation. Interestingly, the maximum VSPR was achieved at the highest copper loading rates. At the maximum copper loading rate (509 mg·L^-1·d^-1), a 99.96% copper removal efficiency was observed. 16 s rRNA gene amplicon sequencing revealed an increased abundance of reads assigned to Desulfurella and Thermoanaerobacterium in periods of higher sulfidogenic activity.

Alkaline industrial wastes - Characteristics, environmental risks, and potential for mine waste management

The large quantities of alkaline industrial wastes that are generated globally have the potential to be valorized in various applications instead of being landfilled. This study evaluated the potential reuse of green liquor dregs (GLD), wood ashes, coal ash, red mud, mussel, scallop, and oyster shells to control acid and metalliferous drainage (AMD). Low hydraulic conductivities (10^-7 to 10^-9 m/min) suggest that covers constructed from fine-grained GLD, red mud, coal ash and wood fly ash can limit the formation of AMD. Static and kinetic test leachates of pH 5.8 to 10.6 indicate that the tested materials can neutralize acidic drainage and immobilize metal(loid)s by precipitation. The alkalinity is proportional to the amount and reactivity of carbonate and hydroxide fractions with red mud followed by coal ash being the most alkaline over 100 weeks and wood ashes the least. The tested industrial wastes generate leachates with a low metal(loid) risk when screened against the Australian freshwater guidelines. However, oxyanions including Al, Cr, Cu, Se, and V were leached in deleterious concentrations ≤100 times more than the guidelines because of their mobility in alkaline conditions. The outcomes of this study highlighted that alkaline industrial wastes can be potentially used in the long-term remediation of AMD as part of an environmentally sustainable and cost-effective integrated mine waste management strategy.

Eurypsychrophilic acidophiles: From (meta)genomes to low-temperature biotechnologies

Low temperature and acidic environments encompass natural milieus such as acid rock drainage in Antarctica and anthropogenic sites including drained sulfidic sediments in Scandinavia. The microorganisms inhabiting these environments include polyextremophiles that are both extreme acidophiles (defined as having an optimum growth pH &lt; 3), and eurypsychrophiles that grow at low temperatures down to approximately 4°C but have an optimum temperature for growth above 15°C. Eurypsychrophilic acidophiles have important roles in natural biogeochemical cycling on earth and potentially on other planetary bodies and moons along with biotechnological applications in, for instance, low-temperature metal dissolution from metal sulfides. Five low-temperature acidophiles are characterized, namely, Acidithiobacillus ferriphilus, Acidithiobacillus ferrivorans, Acidithiobacillus ferrooxidans, “Ferrovum myxofaciens,” and Alicyclobacillus disulfidooxidans, and their characteristics are reviewed. Our understanding of characterized and environmental eurypsychrophilic acidophiles has been accelerated by the application of “omics” techniques that have aided in revealing adaptations to low pH and temperature that can be synergistic, while other adaptations are potentially antagonistic. The lack of known acidophiles that exclusively grow below 15°C may be due to the antagonistic nature of adaptations in this polyextremophile. In conclusion, this review summarizes the knowledge of eurypsychrophilic acidophiles and places the information in evolutionary, environmental, biotechnological, and exobiology perspectives.

Mining of novel secondary metabolite biosynthetic gene clusters from acid mine drainage

Acid mine drainage (AMD) is usually acidic (pH < 4) and contains high concentrations of dissolved metals and metalloids, making AMD a typical representative of extreme environments. Recent studies have shown that microbes play a key role in AMD bioremediation, and secondary metabolite biosynthetic gene clusters (smBGCs) from AMD microbes are important resources for the synthesis of antibacterial and anticancer drugs. Here, 179 samples from 13 mineral types were used to analyze the putative novel microorganisms and secondary metabolites in AMD environments. Among 7,007 qualified metagenome-assembled genomes (MAGs) mined from these datasets, 6,340 MAGs could not be assigned to any GTDB species representative. Overall, 11,856 smBGCs in eight categories were obtained from 7,007 qualified MAGs, and 10,899 smBGCs were identified as putative novel smBGCs. We anticipate that these datasets will accelerate research in the field of AMD bioremediation, aid in the discovery of novel secondary metabolites, and facilitate investigation into gene functions, metabolic pathways, and CNPS cycles in AMD.

Comparison of two acidophilic sulfidogenic consortia for the treatment of acidic mine water

Sulfate-reducing bioreactors are a biotechnological alternative for the treatment of acid mine drainage (AMD). In this study, two separate bioreactors with pH and temperature-controlled (Bio I and II) were operated with two different acidophilic microbial consortia to determine their efficiencies in sulfate removal from a synthetic acidic mine water. The bioreactors were operated for 302 days in continuous flow mode under the same parameters: fed with a sulfate solution of ∼30 mM with a pH of 2.5, the temperature at 30°C, stirred gently at 40 rpm and using a continuous stream of nitrogen to help remove the H2S produced in the bioreactor. The glycerol consumption, acetate production, and sulfate removal were monitored throughout the course of the experiment. The community composition and potential metabolic functional groups were analyzed via 16S rRNA partial gene sequencing. Bio I consortium reduced the sulfate, achieving a range of sulfate concentration from 4.7 to 19 mM in the effluent liquor. The removal of sulfate in Bio II was between 5.6 and 18 mM. Both bioreactors’ communities showed the presence of the genus Desulfosporosinus as the main sulfate-reducing bacteria (SRB). Despite differences in microbial composition, both bioreactors have similar potential metabolism, with a higher percentage of microorganisms that can use sulfate in respiration. Overall, both bioreactors showed similar performance in treating acidic mine water containing mostly sulfate using two different acidophilic sulfidogenic consortia obtained from different global locations.

Acetotrophic sulfate-reducing consortia develop active biofilms on zeolite and glass beads in batch cultures at initial pH 3

Sulfate-reducing microbial communities remain a suitable option for the remediation of acid mine drainage using several types of carrier materials and appropriate reactor configurations. However, acetate prevails as a product derived from the incomplete oxidation of most organic substrates by sulfate reducers, limiting the efficiency of the whole process. An established sulfate-reducing consortium, able to degrade acetate at initial acidic pH (3.0), was used to develop biofilms over granular activated carbon (GAC), glass beads, and zeolite as carrier materials. In batch assays using glycerol, biofilms successfully formed on zeolite, glass beads, and GAC with sulfide production rates of 0.32, 0.26, and 0.14 mmol H₂S/L·d, respectively, but only with glass beads and zeolite, acetate was degraded completely. The planktonic and biofilm communities were determined by the 16S rRNA gene analysis to evaluate the microbial selectivity of the carrier materials. In total, 46 OTUs (family level) composed the microbial communities. Ruminococcaceae and Clostridiaceae families were present in zeolite and glass beads, whereas Peptococcaceae was mostly enriched on zeolite and Desulfovibrionaceae on glass beads. The most abundant sulfate reducer in the biofilm of zeolite was Desulfotomaculum sp., while Desulfatirhabdium sp. abounded in the planktonic community. With glass beads, Desulfovibrio sp. dominated the biofilm and the planktonic communities. Our results indicate that both materials (glass beads and zeolite) selected different key sulfate-reducing microorganisms able to oxidize glycerol completely at initial acidic pH, which is relevant for a future application of the consortium in continuous bioreactors to treat acidic streams. KEY POINTS: • Complete consumption of glycerol and acetate at acidic pH by sulfate reduction. • Glass beads and zeolite are suitable materials to form sulfate-reducing biofilms. • Acetotrophic sulfate-reducing bacteria attached to zeolite preferably.

A membrane-biofilm system for sulfate conversion to elemental sulfur in mining-influenced waters

A system of two membrane biofilm reactors (MBfRs) was tested for the conversion of sulfate (1.5 g/L) in mining-process water into elemental sulfur (S⁰) particles. Initially, a H₂-based MBfR reduced sulfate to sulfide, and an O₂-based MBfR then oxidized sulfide to S⁰. Later, the two MBfRs were coupled by a recirculation flow. Surface loading, reactor-coupling configuration, and substrate-gas pressure exerted important controls over performance of each MBfR and the coupled system. Continuously recirculating the liquid between the H₂-based MBfR and the O₂-based MBfR, compared to series operation, avoided the buildup of sulfide and gave overall greater sulfate removal (99% vs 62%) and production of S⁰ (61% vs 54%). The trade-off was that recirculation coupling demanded greater delivery of H₂ and O₂ (in air) due to the establishment of a sulfur cycle catalyzed by Sulfurospirillum spp., which had an average abundance of 46% in the H₂-based MBfR fibers and 62% in the O₂-based MBfR fibers at the end of the experiments. Sulfate-reducing bacteria (Desulfovibrio and Desulfomicrobium) and sulfur-oxidizing bacteria (Thiofaba, Thiomonas, Acidithiobacillus and Sulfuricurvum) averaged only 22% and 11% in the H₂-based MBfR and O₂-based MBfR fibers, respectively. Evidence suggests that the undesired Sulfurospirillum species, which reduce S⁰ to sulfide, can be suppressed by increasing sulfate-surface loading and H₂ pressure.

Biosulfidogenesis Mediates Natural Attenuation in Acidic Mine Pit Lakes

Acidic pit lakes are abandoned open pit mines filled with acid mine drainage (AMD)-highly acidic, metalliferous waters that pose a severe threat to the environment and are rarely properly remediated. Here, we investigated two meromictic, oligotrophic acidic mine pit lakes in the Iberian Pyrite Belt (IPB), Filón Centro (Tharsis) (FC) and La Zarza (LZ). We observed a natural attenuation of acidity and toxic metal concentrations towards the lake bottom, which was more pronounced in FC. The detection of Cu and Zn sulfides in the monimolimnion of FC suggests precipitation of dissolved metals as metal sulfides, pointing to biogenic sulfide formation. This was supported by microbial diversity analysis via 16S rRNA gene amplicon sequencing of samples from the water column, which showed the presence of sulfidogenic microbial taxa in FC and LZ. In the monimolimnion of FC, sequences affiliated with the putative sulfate-reducing genus Desulfomonile were dominant (58%), whereas in the more acidic and metal-enriched LZ, elemental sulfur-reducing Acidianus and Thermoplasma spp., and disproportionating Desulfocapsa spp. were more abundant. Furthermore, the detection of reads classified as methanogens and Desulfosporosinus spp., although at low relative abundance, represents one of the lowest pH values (2.9 in LZ) at which these taxa have been reported, to our knowledge. Analysis of potential biomarker lipids provided evidence that high levels of phosphocholine lipids with mixed acyl/ether glycerol core structures were associated with Desulfomonile, while ceramide lipids were characteristic of Microbacter in these environments. We propose that FC and LZ function as natural bioremediation reactors where metal sulfide precipitation is mediated by biosulfidogenesis starting from elemental sulfur reduction and disproportionation at an early stage (LZ), followed by sulfate reduction at a later stage (FC).

Characteristics of an Iron-Reducing, Moderately Acidophilic Actinobacterium Isolated from Pyritic Mine Waste, and Its Potential Role in Mitigating Mineral Dissolution in Mineral Tailings Deposits

Reactive pyritic mine tailings can be populated by chemolithotrophic prokaryotes that enhance the solubilities of many metals, though iron-reducing heterotrophic microorganisms can inhibit the environmental risk posed by tailings by promoting processes that are the reverse of those carried out by pyrite-oxidising autotrophic bacteria. A strain (IT2) of Curtobacterium ammoniigenes, a bacterium not previously identified as being associated with acidic mine wastes, was isolated from pyritic mine tailings and partially characterized. Strain IT2 was able to reduce ferric iron under anaerobic conditions, but was not found to catalyse the oxidation of ferrous iron or elemental (zero-valent) sulfur, and was an obligate heterotrophic. It metabolized monosaccharides and required small amounts of yeast extract for growth. Isolate IT2 is a mesophilic bacterium, with a temperature growth optimum of 30 °C and is moderately acidophilic, growing optimally at pH 4.0 and between pH 2.7 and 5.0. The isolate tolerated elevated concentrations of many transition metals, and was able to grow in the cell-free spent medium of the acidophilic autotroph Acidithiobacillus ferrooxidans, supporting the hypothesis that it can proliferate in acidic mine tailings. Its potential role in mitigating the production of acidic, metal-rich drainage waters from mine wastes is discussed.

Ex-situ treatment of sediment from a black-odor water body using activated sludge

Sediment containing numerous nutrients and pollutants has become an important consideration when treating black-odor water. Excessive activated sludge produced in wastewater treatment plants contains a large number of microorganisms, which is beneficial for removing organics and nutrients from the black-odor sediment. In this study, three types of sludge from a secondary sedimentation tank (SST), a digestion tank (DT), and an aerobic tank treating landfill leachate (AT_leachate) were used to treat black-odor sediment, respectively. All the three types of activated sludge enhanced the treatment performance of sediment. The SST sludge worked the best with the optimal dosage of 2.56 g/(kg sediment), and the removal of nitrogen and organics reached 57.03 and 28.14%, respectively. Illumina MiSeq sequencing revealed that the activated sludge significantly affected the microbial community of the sediment. In particular, SST sludge resulted in significant increase in the number of microorganisms related to nitrification and sulfur metabolism to 10.68 and 10.97%, respectively. This was found to be important for degrading organics and promoting nitrogen removal. This study provides an efficient strategy for the treatment of black-odor sediment, and also realizes the complete utilization of waste activated sludge.

Influence of operating conditions on sulfate reduction from real mining process water by membrane biofilm reactors

Two H₂-based membrane biofilm reactor (H₂-MBfR) systems, differing in membrane type, were tested for sulfate reduction from a real mining-process water having low alkalinity and high concentrations of dissolved sulfate and calcium. Maximum sulfate reductions were 99%, with an optimum pH range between 8 and 8.5, which minimized any toxic effect of unionized hydrogen sulfide (H₂S) on sulfate-reducing bacteria (SRB) and calcite scaling on the fibers and in the biofilm. Although several strategies for control of pH and gas back-diffusion were applied, it was not possible to sustain a high degree of sulfate reduction over the long-term. The most likely cause was precipitation of calcite inside the biofilm and on the surface of fibers, which was shown by scanning electron microscopy coupled with energy dispersive spectroscopy (SEM-EDS) analysis. Another possible cause was a decline in pH, leading to inhibition by H₂S. A H₂/CO₂ mixture in the gas supply was able to temporarily recover the effectiveness of the reactors and stabilize the pH. Biomolecular analysis showed that the biofilm was comprised of 15-20% SRB, but a great variety of autotrophic and heterotrophic genera, including sulfur-oxidizing bacteria, were present. Results also suggest that the MBfR system can be optimized by improving H₂ mass transfer using fibers of higher gas permeability and by feeding a H₂/CO₂ mixture that is automatically adjusted for pH control.

Biological remediation of acid mine drainage: Review of past trends and current outlook

Formation of acid mine drainage (AMD) is a widespread environmental issue that has not subsided throughout decades of continuing research. Highly acidic and highly concentrated metallic streams are characteristics of such streams. Humans, plants and surrounding ecosystems that are in proximity to AMD producing sites face immediate threats. Remediation options include active and passive biological treatments which are markedly different in many aspects. Sulfate reducing bacteria (SRB) remove sulfate and heavy metals to generate non-toxic streams. Passive systems are inexpensive to operate but entail fundamental drawbacks such as large land requirements and prolonged treatment period. Active bioreactors offer greater operational predictability and quicker treatment time but require higher investment costs and wide scale usage is limited by lack of expertise. Recent advancements include the use of renewable raw materials for AMD clean up purposes, which will likely achieve much greener mitigation solutions.

Changes in microbial communities of a passive coal mine drainage bioremediation system

Drainage from abandoned mines is one factor greatly affecting the streams and vegetation in and around Pittsburgh and the Appalachian Mountains where coal mining occurred. This drainage may be more acidic, alkaline, or metal based. Different methods for remediation exist. Passive remediation is one method used to naturally allow the metals to precipitate out and aid in cleaning up the water. The goal of this study is to sample different holding ponds in a sequential passive remediation system and determine microbial communities present at each site of an abandoned coal mine drainage site. Sequencing of the 16S rRNA gene of the sediment indicated the most abundant phyla at each of the 5 ponds and wetland area included Proteobacteria (36%–43%), Bacteroidetes (12%–37%), Firmicutes (3%–11%), and Verrucomicrobia (6%–11%). Analysis of genera between the first, and most polluted, pond included Solitalea, Pedosphaera, and Rhodocyclus, whereas the microbial community from the wetland site at the end of the remediation system included Ignavibacterium, Pelotomaculum, and Petrimonas. The results of our microbial community composition study of sediment from a passive treatment system are in line with organisms commonly found in sediment regardless of iron oxide precipitation, while others are preferentially found in the less polluted wetland site.

Recent advances in dissimilatory sulfate reduction: From metabolic study to application

Sulfate-reducing bacteria (SRB) are a group of diverse anaerobic microorganisms omnipresent in natural habitats and engineered environments that use sulfur compounds as the electron acceptor for energy metabolism. Dissimilatory sulfate reduction (DSR)-based techniques mediated by SRB have been utilized in many sulfate-containing wastewater treatment systems worldwide, particularly for acid mine drainage, groundwater, sewage and industrial wastewater remediation. However, DSR processes are often operated suboptimally and disturbances are common in practical application. To improve the efficiency and robustness of SRB-based processes, it is necessary to study SRB metabolism and operational conditions. In this review, the mechanisms of DSR processes are reviewed and discussed focusing on intracellular and extracellular electron transfer with different electron donors (hydrogen, organics, methane and electrodes). Based on the understanding of the metabolism of SRB, responses of SRB to environmental stress (pH-, temperature-, and salinity-related stress) are summarized at the species and community levels. Application in these stressed conditions is discussed and future research is proposed. The feasibility of recovering energy and resources such as biohydrogen, hydrocarbons, polyhydroxyalkanoates, magnetite and metal sulfides through the use of SRB were investigated but some long-standing questions remain unanswered. Linking the existing scientific understanding and observations to practical application is the challenge as always for promotion of SRB-based techniques.

Bioleaching for Copper Extraction of Marginal Ores from the Brazilian Amazon Region

The use of biotechnology to explore low-grade ore deposits and mining tailings is one of the most promising alternatives to reduce environmental impacts and costs of copper extraction. However, such technology still depends on improvements to be fully applied in Brazil under industrial scale. In this way, the bioleaching, by Acidithiobacillus ferrooxidans, in columns and stirred reactors were evaluated regarding to copper extraction of a mineral sulfide and a weathered ore from the Brazilian Amazon region. Samples (granulometry of 2.0/4.75 mm) were characterized by X-ray diffraction (XRD), energy dispersive X-ray fluorescence (EDXRF) spectrometry and scanning electrons microscopy (SEM). The pH and Oxidation-reduction potential (Eh) were daily monitored and leachate samples were collected for copper extraction determination by EDXRF. After 47 days, the columns bioleaching efficiency was 1% (1298 mg Cu·L−1) and 0.95% (985 mg Cu·L−1) for 2.00/4.75 mm sulfide ore, respectively, whereas the stirred reactors bioleaching resulted in 4% (348 mg Cu·L−1) for the mineral sulfide and 47% (295.5 mg Cu·L−1) for the weathered ore.

Design and Application of a Low pH Upflow Biofilm Sulfidogenic Bioreactor for Recovering Transition Metals From Synthetic Waste Water at a Brazilian Copper Mine

A sulfidogenic bioreactor, operated at low pH (4–5), was set up and used to remove transition metals (copper, nickel, cobalt, and zinc) from a synthetic mine water, based on the chemistry of a moderately acidic (pH 5) drainage stream at an operating copper mine in Brazil. The module was constructed as an upflow biofilm reactor, with microorganisms immobilized on porous glass beads, and was operated continuously for 462 days, during which time the 2 L bioreactor processed >2,000 L of synthetic mine water. The initial treatment involved removing copper (the most abundant metal present) off-line in a stream of H₂S-containing gas generated by the bioreactor, which caused the synthetic mine water pH to fall to 2.1. The copper-free water was then amended with glycerol (the principal electron donor), yeast extract and basal salts, and pumped directly into the bioreactor where the other three transition metals were precipitated (also as sulfides), concurrent with increased solution pH. Although some acetate was generated, most of the glycerol fed to the bioreactor was oxidized to carbon dioxide, and was coupled to the reduction of sulfate to hydrogen sulfide. No archaea or eukaryotes were detected in the bioreactor microbial community, which was dominated by acidophilic sulfate-reducing Firmicutes (Peptococcaceae strain CEB3 and Desulfosporosinus acididurans); facultatively anaerobic non-sulfidogens (Acidithiobacillus ferrooxidans and Actinobacterium strain AR3) were also found in small relative abundance. This work demonstrated how a single low pH sulfidogenic bioreactor can be used to remediate a metal-rich mine water, and to facilitate the recovery (and therefore recycling) of target metals. The system was robust, and was operated empirically by means of pH control. Comparison of costs of the main consumables (glycerol and yeast extract) and the values of the metals recovered showed a major excess of the latter, supporting the view that sulfidogenic biotechnology can have significant economic as well as environmental advantages over current approaches used to remediate mine waters which produce secondary toxic wastes and fail to recover valuable metals.