Electrotrophic perchlorate reduction by a psychrotolerant acidophile isolated from an acid rock drainage in Antarctica

A new extremophilic isolate (USS-CCA7) was obtained from an acidic environment (pH ∼ 3.2) in Antarctica phylogenetically related to Acidithiobacillus ferrivorans; its electrotrophic capacities were evaluated in a three-electrode electrochemical cell. Cyclic voltammetry showed cathodic peaks of -428 mV, -536 mV, and -634 mV (vs. Ag/AgCl; pH = 1.7; 3 M KCl) for nitrate, oxygen, and perchlorate, respectively. The catalytic role of this microorganism was also observed by a decrease in the charge transfer resistance registered via electrochemical impedance spectroscopy. Five-day chronoamperometry of culture at pH = 1.7, USS-CCA7 showed a perchlorate removal rate of 19.106 ± 1.689 mgL^-1 day^-1 and a cathodic efficiency of 112 ± 5.2  %. Growth on electrodes was observed by epifluorescence and scanning electron microscopy. Interestingly, the results showed that toward higher pH, the cathodic peak of perchlorate is reduced in the voltammetric profiles. This study highlights the use of this psychrotolerant acidophile for the bioremediation of harsh perchlorate-pressured terrestrial under acidic conditions.

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.

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.

Enrichment and isolation of acid-tolerant sulfate-reducing microorganisms in the anoxic, acidic hot spring sediments from Copahue volcano, Argentina

The geothermal Copahue-Caviahue (GCC) system (Argentina) is an extreme acidic environment, dominated by the activity of Copahue volcano. Environments characterised by low pH values, such as volcanic areas, are of particular interest for the search of acidophilic microorganisms with application in biotechnological processes. In this work, sulfate-reducing microorganisms were investigated in geothermal acidic, anaerobic zones from GCC system. Sediment samples from Agua del Limón (AL1), Las Máquinas (LMa2), Las Maquinitas (LMi) and Baño 9 (B9-2, B9-3) were found to be acidic (pH values 2.1-3.0) to moderate acidic (5.1-5.2), containing small total organic carbon values, and ferric iron precipitates. The organic electron donor added to the enrichment was completely oxidised to CO2. Bacteria related to 'Desulfobacillus acidavidus' strain CL4 were found to be dominant (67-83% of the total number of clones) in the enrichment cultures, and their presence was confirmed by their isolation on overlay plates. Other bacteria were also detected with lower abundance (6-20% of the total number of clones), with representatives of the genera Acidithiobacillus, Sulfobacillus, Alicyclobacillus and Athalassotoga/Mesoaciditoga. These enrichment and isolates found at low pH confirm the presence of anaerobic activities in the acidic sediments from the geothermal Copahue-Caviahue system.

Acidiferrimicrobium australe gen. nov., sp. nov., an acidophilic and obligately heterotrophic, member of the Actinobacteria that catalyses dissimilatory oxido-reduction of iron isolated from metal-rich acidic water in Chile

A novel acidophilic member of the phylum Actinobacteria was isolated from an acidic, metal-contaminated stream draining from an abandoned underground coal mine (Trongol mine), situated close to Curanilahue, Biobío Region, Chile. The isolate (USS-CCA1^T) was demonstrated to be a heterotroph that catalysed under aerobic conditions the oxidation of ferrous iron and the reduction of ferric iron under anaerobic conditions, but not the oxidation of sulfur nor hydrogen. USS-CCA1^T is a Gram-positive, motile, short rod-shaped, mesophilic bacterium with a temperature growth optimum at 30 °C (range 20-39 °C). It was categorized as an extreme acidophile growing between 1.7 and 4.5 and optimally at pH 3.0. The G+C content of the chromosomal DNA of the isolate was 74.1 mol%, which is highly related to Aciditerrimonas ferrireducens IC-180^T , (the most closely related genus; 94.4 % 16S rRNA gene identity), and higher than other acidophilic actinobacteria. The isolate (USS-CCA1^T) was shown to form a distinct 16S rRNA clade from characterized acidophilic actinobacteria, well separated from the genera Acidimicrobium, Ferrimicrobium, Ferrithrix, 'Acidithrix' and Aciditerrimonas. Genomic indexes (ANIb, DDH, AAI, POCP) derived from the USS-CCA1^T draft genome sequence (deposited at DDBJ/ENA/GenBank under the accession WJHE00000000) support assignment of the isolate to a new species and a new genus within the Acidimicrobiaceae family. Isolate USS-CCA1^T is the designated type strain of the novel species Acidiferrimicrobium australe (=DSM 106828^T,=RGM 2506^T).

Evaluation of the bio-protection mechanism in diffusive exchange permeable reactive barriers for the treatment of acid mine drainage

This research studied the bio-protection mechanism based on chemical gradients in diffusive exchange permeable reactive barriers, evaluating the thickness of the reactive layers in the treatment of concentrated acid mine drainage (AMD). Six bench-scale reactors were constructed with reactive layer thicknesses of 2.5, 5, and 7.5 cm in duplicate. The reactors were first fed a sulfated solution for 55 days, followed by concentrated AMD for 166 days. The change of feed to AMD mainly affected the reactors with thinner 2.5 cm layers in comparison to the reactors with 5 and 7.5 cm layers. Cu and Zn removal efficiency was practically 100% in all the reactors; however, in the thinner layer reactors, metal breakthrough occurred towards the end of the experiment concurrently with inhibitory metal concentrations in the reactive layers. On the contrary, the reactors with layer thicknesses of 5 and 7.5 cm evaluated did not present toxic concentrations of these metals at any of the monitoring points. The bio-protection criterion q_D correctly predicted that the thin-layer reactor would be the most affected by the toxicity of AMD. The criterion also indicated that all the reactors should fail. Nevertheless, the fault in the thinner layer reactor registered in the effluent after >150 days; therefore, the possibility of failure in the 5 and 7.5 cm thickness reactors is not rejected, as it could have occurred if the experiment had continued.

Recent Developments for Remediating Acidic Mine Waters Using Sulfidogenic Bacteria

Acidic mine drainage (AMD) is regarded as a pollutant and considered as potential source of valuable metals. With diminishing metal resources and ever-increasing demand on industry, recovering AMD metals is a sustainable initiative, despite facing major challenges. AMD refers to effluents draining from abandoned mines and mine wastes usually highly acidic that contain a variety of dissolved metals (Fe, Mn, Cu, Ni, and Zn) in much greater concentration than what is found in natural water bodies. There are numerous remediation treatments including chemical (lime treatment) or biological methods (aerobic wetlands and compost bioreactors) used for metal precipitation and removal from AMD. However, controlled biomineralization and selective recovering of metals using sulfidogenic bacteria are advantageous, reducing costs and environmental risks of sludge disposal. The increased understanding of the microbiology of acid-tolerant sulfidogenic bacteria will lead to the development of novel approaches to AMD treatment. We present and discuss several important recent approaches using low sulfidogenic bioreactors to both remediate and selectively recover metal sulfides from AMD. This work also highlights the efficiency and drawbacks of these types of treatments for metal recovery and points to future research for enhancing the use of novel acidophilic and acid-tolerant sulfidogenic microorganisms in AMD treatment.

Interaction networks for identifying coupled molecular processes in microbial communities

BACKGROUND

Microbial communities adapt to environmental conditions for optimizing metabolic flux. Such adaption may include cooperative mechanisms eventually resulting in phenotypic observables as emergent properties that cannot be attributed to an individual species alone. Understanding the molecular basis of cross-species cooperation adds to utilization of microbial communities in industrial applications including metal bioleaching and bioremediation processes. With significant advancements in metagenomics the composition of microbial communities became amenable for integrative analysis on the level of entangled molecular processes involving more than one species, in turn offering a data matrix for analyzing the molecular basis of cooperative phenomena.

METHODS

We present an analysis framework aligned with a dynamical hierarchies concept for unraveling emergent properties in microbial communities, and exemplify this approach for a co-culture setting of At. ferrooxidans and At. thiooxidans. This minimum microbial community demonstrates a significant increase in bioleaching efficiency compared to the activity of individual species, involving mechanisms of the thiosulfate, the polysulfide and the iron oxidation pathway.

RESULTS

Populating gene-centric data structures holding rich functional annotation and interaction information allows deriving network models at the functional level coupling energy production and transport processes of both microbial species. Applying a network segmentation approach on the interaction network of ortholog genes covering energy production and transport proposes a set of specific molecular processes of relevance in bioleaching. The resulting molecular process model essentially involves functionalities such as iron oxidation, nitrogen metabolism and proton transport, complemented by sulfur oxidation and nitrogen metabolism, as well as a set of ion transporter functionalities. At. ferrooxidans-specific genes embedded in the molecular model representation hold gene functions supportive for ammonia utilization as well as for biofilm formation, resembling key elements for effective chalcopyrite bioleaching as emergent property in the co-culture situation.

CONCLUSIONS

Analyzing the entangled molecular processes of a microbial community on the level of segmented, gene-centric interaction networks allows identification of core molecular processes and functionalities adding to our mechanistic understanding of emergent properties of microbial consortia.

Selective removal of transition metals from acidic mine waters by novel consortia of acidophilic sulfidogenic bacteria

Two continuous‐flow bench‐scale bioreactor systems populated by mixed communities of acidophilic sulfate‐reducing bacteria were constructed and tested for their abilities to promote the selective precipitation of transition metals (as sulfides) present in synthetic mine waters, using glycerol as electron donor. The objective with the first system (selective precipitation of copper from acidic mine water containing a variety of soluble metals) was achieved by maintaining a bioreactor pH of ∼2.2–2.5. The second system was fed with acidic (pH 2.5) synthetic mine water containing 3 mM of both zinc and ferrous iron, and varying concentrations (0.5–30 mM) of aluminium. Selective precipitation of zinc sulfide was possible by operating the bioreactor at pH 4.0 and supplementing the synthetic mine water with 4 mM glycerol. Analysis of the microbial populations in the bioreactors showed that they changed with varying operational parameters, and novel acidophilic bacteria (including one sulfidogen) were isolated from the bioreactors. The acidophilic sulfidogenic bioreactors provided ‘proof of principle’ that segregation of metals present in mine waters is possible using simple online systems within which controlled pH conditions are maintained. The modular units are versatile and robust, and involve minimum engineering complexity.