Influence of heterotrophic microbial growth on biological oxidation of pyrite

A novelty strategy for AMD prevention by biogas slurry: Acetate acid inhibition effect on chalcopyrite biooxidation and leachate

With the widespread application of anaerobic digestion technology, biogas slurry become the main source of organic amendments in practice. Comprehensive studies into the inhibitory effects of low molecular weight (LMW) organic acids, essential components in biogas slurry, on the sulfide minerals biooxidation and its bioleaching (AMD) have been lacking. In this study, acetic acid (AA) served as a representative of LMW organic acids in biogas slurry to investigate its impact on the inhibition of chalcopyrite biooxidation by Acidithiobacillus ferrooxidans (A. ferrooxidans). It was shown that AA could slow down the chalcopyrite biooxidation and inhibit the jarosite formation on the mineral surface. Compared with the control group (0 ppm AA), the sulfate increment in the leachate of the 50 ppm, 100 ppm, and 200 ppm AA-treated groups decreased by 36.4%, 66.8%, and 69.0%, respectively. AA treatment (≥50 ppm) could reduce the oxidation of ferrous ions in the leachate by one order of magnitude. At the same time, the bacterial concentration of the leachate in the 50 ppm, 100 ppm, and 200 ppm AA-treated groups decreased by 70%, 93%, and 94%, respectively. These findings provide a scientific basis for new strategies to utilize biogas slurry for mine remediation and contribute to an enhanced comprehension of organic amendments to prevent AMD in situ in mining soil remediation.

AI-driven pan-proteome analyses reveal insights into the biohydrometallurgical properties of Acidithiobacillia

Microorganism-mediated biohydrometallurgy, a sustainable approach for metal recovery from ores, relies on the metabolic activity of acidophilic bacteria. Acidithiobacillia with sulfur/iron-oxidizing capacities are extensively studied and applied in biohydrometallurgy-related processes. However, only 14 distinct proteins from Acidithiobacillia have experimentally determined structures currently available. This significantly hampers in-depth investigations of Acidithiobacillia's structure-based biological mechanisms pertaining to its relevant biohydrometallurgical processes. To address this issue, we employed a state-of-the-art artificial intelligence (AI)-driven approach, with a median model confidence of 0.80, to perform high-quality full-chain structure predictions on the pan-proteome (10,458 proteins) of the type strain Acidithiobacillia. Additionally, we conducted various case studies on de novo protein structural prediction, including sulfate transporter and iron oxidase, to demonstrate how accurate structure predictions and gene co-occurrence networks can contribute to the development of mechanistic insights and hypotheses regarding sulfur and iron utilization proteins. Furthermore, for the unannotated proteins that constitute 35.8% of the Acidithiobacillia proteome, we employed the deep-learning algorithm DeepFRI to make structure-based functional predictions. As a result, we successfully obtained gene ontology (GO) terms for 93.6% of these previously unknown proteins. This study has a significant impact on improving protein structure and function predictions, as well as developing state-of-the-art techniques for high-throughput analysis of large proteomic data.

Prokaryotic communities in the historic silver mine Reiche Zeche

The research and education mine “Reiche Zeche” in Freiberg (Saxony, Germany) represents one of the most famous mining facilities reminiscent to the century-long history of silver production in the Ore Mountains. The mine was set up at the end of the fourteenth century and became part of the “Bergakademie Freiberg” in 1919. Galena, pyrite, sphalerite, arsenopyrite, and chalcopyrite are the most common minerals found in the mine. As acid mine drainage is generated from the dissolution of sulfidic ores, the microbial habitats within the adits and galleries are characterized by low pH and high concentrations of metal(loid)s. The community composition was investigated at locations characterized by biofilm formation and iron-rich bottom pools. Amplicon libraries were sequenced on a MiSeq instrument. The taxonomic survey yielded an unexpected diversity of 25 bacterial phyla including ten genera of iron-oxidizing taxa. The community composition in the snottites and biofilms only slightly differed from the communities found in acidic bottom pools regarding the diversity of iron oxidizers, the key players in most investigated habitats. Sequences of the Candidate Phyla Radiation as, e.g., Dojkabacteria and Eremiobacterota were found in almost all samples. Archaea of the classes Thermoplasmata and Nitrososphaeria were detected in some biofilm communities.

A triple-chamber microbial fuel cell enabled to synchronously recover iron and sulfur elements from sulfide tailings

Bioleaching by coupling iron oxidization with microbial growth is a process frequently used to extract target metals from sulfide tailing piles. However, the slower leaching, longer operational times, and lower efficiency compared to those of other extracting processes are the most important reasons that make this approach unattractive for the recovery of target elements. A triple-chamber microbial fuel cell (MFC) was explored to elevate the dissolution of sulfide tailings via in-situ removal of bioleached Fe³⁺/Fe²⁺ and SO₄^2-, during which iron and SO₄^2- ions were synchronously recovered as Fe(OH)₃ and S° in the first and second cathode chambers, respectively. 107.9 % of iron and 99.8 % of sulfur contained in the sulfide tailings was bioleached over 50 h, with 80.0 % iron and 22.1 % sulfur elements synchronously recovered. The purities of the Fe(OH)₃ and S° precipitates with high metallurgical values were up to 93.1 % and 90.2 %, respectively. The excellent leaching performance of the explored triple-chamber MFC was attributed to the synergistic effect of Acidithiobacillia catalysis and electrochemical oxidation. The explored approach, by virtue of having the higher bioleaching efficiency, less aggressive conditions and shorter operating times than the conventional bioleaching, is of potential commercial value.

Soil Microbiome Dynamics During Pyritic Mine Tailing Phytostabilization: Understanding Microbial Bioindicators of Soil Acidification

Challenges to the reclamation of pyritic mine tailings arise from in situ acid generation that severely constrains the growth of natural revegetation. While acid mine drainage (AMD) microbial communities are well-studied under highly acidic conditions, fewer studies document the dynamics of microbial communities that generate acid from pyritic material under less acidic conditions that can allow establishment and support of plant growth. This research characterizes the taxonomic composition dynamics of microbial communities present during a 6-year compost-assisted phytostabilization field study in extremely acidic pyritic mine tailings. A complementary microcosm experiment was performed to identify successional community populations that enable the acidification process across a pH gradient. Taxonomic profiles of the microbial populations in both the field study and microcosms reveal shifts in microbial communities that play pivotal roles in facilitating acidification during the transition between moderately and highly acidic conditions. The potential co-occurrence of organoheterotrophic and lithoautotrophic energy metabolisms during acid generation suggests the importance of both groups in facilitating acidification. Taken together, this research suggests that key microbial populations associated with pH transitions could be used as bioindicators for either sustained future plant growth or for acid generation conditions that inhibit further plant growth.

Microbial Diversity and Community Assembly across Environmental Gradients in Acid Mine Drainage

Microorganisms play an important role in weathering sulfide minerals worldwide and thrive in metal-rich and extremely acidic environments in acid mine drainage (AMD). Advanced molecular methods provide in-depth information on the microbial diversity and community dynamics in the AMD-generating environment. Although the diversity is relatively low and in general inversely correlated with the acidity, a considerable number of microbial species have been detected and described in AMD ecosystems. The acidophilic microbial communities dominated by iron/sulfur-oxidizing microbes vary widely in their composition and structure across diverse environmental gradients. Environmental conditions affect the microbial community assembly via direct and indirect interactions with microbes, resulting in an environmentally dependent biogeographic pattern. This article summarizes the latest studies to provide a better understanding of the microbial biodiversity and community assembly in AMD environments.

Soluble microbial products decrease pyrite oxidation by ferric iron at pH < 2

Research on microbial activity in acid mine drainage (AMD) has focused on transformations of iron and sulfur. However, carbon cycling, including formation of soluble microbial products (SMP) from cell growth and decay, is an important biogeochemical component of the AMD environment. Experiments were conducted to study the interaction of SMP with soluble ferric iron in acidic conditions, particularly the formation of complexes that inhibit its effectiveness as the primary oxidant of pyrite during AMD generation. The rate of pyrite oxidation by ferric iron in sterile suspensions at pH 1.8 was reduced by 87% in the presence of SMP produced from autoclaved cells at a ratio of 0.3 mg DOC per mg total soluble ferric iron. Inhibition of pyrite oxidation by SMP was shown to be comparable to, but weaker than, the effect of a chelating synthetic siderophore, DFAM. Two computational models incorporating SMP complexation were fitted to experimental results. Results suggest that bacterially produced organic matter can play a role in slowing pyrite oxidation.

Organic matter in sediments of an acidic mining lake as assessed by lipid analysis. Part I: fatty acids

Fatty acid (FA) patterns of sediments collected from the bottom of an acidic mine pit lake (AML) at different depths (surface sediment: 0 to 1cm; deep sediment: 4 to 5 cm) were studied to characterize microbial communities and the sources of sedimentary organic matter (SOM). Studies were performed on the molecular level utilizing source-specific, diagnostic FA biomarkers. The biomarker-based approach has been used widely in marine sediment studies, but has not been applied for sediments from AMLs so far. Combined FA concentrations in the surface sediment were higher compared to those in the deep sediment (497 vs. 127 μg g(-1)d.w., respectively). This was related to deposition of autochthonous biomass and higher terrestrial plants onto the surface sediment, as well as--to lesser extent--with higher bacterial activity on the sediment-water interface. The FA distribution in both sediments was characterized by a strong even-over-odd preference and was bimodal in nature: there was a cluster at nC(14)-nC(18) characteristic of chiefly autochthonous (algal and bacterial) SOM production, and another cluster at nC(22-28) related to input from higher plants. The FA distribution in the surface sediment pointed to higher terrestrial input compared to autochthonous contribution to SOM (67%:33%) as an estimate. Fingerprinting of viable bacteria was accomplished through signature FA markers including branched C(15) and C(17) surrogates, cyclopropanoic acids, 3-hydroxy (OH) acids and monounsaturated surrogates with unusual double bond localization. The abundance of Gram-negative bacteria was higher in the surface sediment as evidenced by total diagnostic 3-OH-fatty acids (37 μg g(-1) versus 25 μg g(-1)). Potential source taxa in both sediment layers included acidophilic iron- and sulfur-oxidizing bacteria including Acidithiobacillus ferrooxidans. High abundances of terminally branched C(15) and C(17) surrogates in both sediments pointed to sulfate- and iron-reducing bacteria. Signature FAs characteristic of methanotrophs were virtually lacking in both sediments.

The co-culture of Acidithiobacillus ferrooxidans and Acidiphilium acidophilum enhances the growth, iron oxidation, and CO2 fixation

Although the synergetic interactions between chemolithoautotroph Acidithiobacillus ferrooxidans and heterotroph Acidiphilium acidophilum have drawn a share of attention, the influence of Aph. acidophilum on growth and metabolic functions of At. ferrooxidans is still unknown on transcriptional level. To assess this influence, a co-culture composed by At. ferrooxidans and Aph. acidophilum was successfully acclimated in this study. Depending on the growth dynamics, At. ferrooxidans in co-culture had 2 days longer exponential phase and 5 times more cell number than that in pure culture. The ferrous iron concentration in culture medium and the expression of iron oxidation-related genes revealed that the energy acquisition of At. ferrooxidans in co-culture was more efficient than that in pure culture. Besides, the analysis of CO2 fixation-related genes in At. ferrooxidans indicated that the second copy of RuBisCO-encoding genes cbbLS-2 and the positive regulator-encoding gene cbbR were up-regulated in co-culture system. All of these results verified that Aph. acidophilum could heterotrophically grow with At. ferrooxidans and promote the growth of it. By means of activating iron oxidation-related genes and the second set of cbbLS genes in At. ferrooxidans, the Aph. acidophilum facilitated the iron oxidation and CO2 fixation by At. ferrooxidans.

An experimental and theoretical approach to determining linkages between geochemical variability and microbial biodiversity in seafloor hydrothermal chimneys

New experimental results of fluid-mineral reactions at hydrothermal conditions relevant to life demonstrate that key redox reactions involving iron, sulfur, and hydrogen remain at disequilibrium at 100 °C, even in a heterogeneous system and thus are energetically favorable for microbial metabolism. Predictions from geochemical models utilizing the experimental results and specific to two contrasting case studies from the East Pacific Rise were statistically characterized and correlated to the energetics of redox reactions available for intra-chimney microbial populations. In general, predictions of available energy for autotrophic metabolism are largely similar between the mature and the nascent chimneys, although important differences still exist. Metabolic processes predicted by energetics exhibit the same trends observed in the field data for the mature chimney, but overestimate the diversity observed in the nascent chimney. Several combinations of redox reaction pairs are predicted to support mixed consortia, while some combinations appear to favor more versatile microbes capable of utilizing several reactions under rapidly changing environmental conditions within chimney walls. In addition, conditions favorable to elemental sulfur reduction and methanogenesis exhibit a negative control on the diversity of microbial populations within these chimney walls, whereas H₂S oxidation, elemental sulfur oxidation and the knallgas reaction are positively correlated with both abundance and diversity of micro-organisms. Coupling field observations of both microbial diversity and geochemical heterogeneity with lab-based experimental and theoretical modeling can facilitate translation of the observed genetic diversity into physiological diversity, thus enhancing understanding of linked phenomena of microbially induced biogeochemical transformations in complex heterogeneous systems.

Microbial architecture of environmental sulfur processes: a novel syntrophic sulfur-metabolizing consortia

Microbial oxidation of sulfur-rich mining waste materials drives acid mine drainage (AMD) and affects the global sulfur biogeochemical cycle. The generation of AMD is a complex, dynamic process that proceeds via multiple reaction pathways. The role of natural consortia of microbes in AMD generation, however, has received very little attention despite their widespread occurrence in mining environments. Through a combination of geochemical experimentation and modeling, scanning transmission X-ray microscopy, and fluorescent in situ hybridization, we show a novel interdependent metabolic arrangement of two ubiquitous and abundant AMD bacteria: chemoautotrophic sulfur-oxidizing Acidithiobacillus sp. and heterotrophic Acidiphilium sp. Highly reminiscent of anaerobic methane oxidation (AOM) consortia, these bacteria are spatially segregated within a planktonic macrostructure of extracellular polymeric substance in which they syntrophically couple sulfur oxidation and reduction reactions in a mutually beneficial arrangement that regenerates their respective sulfur substrates. As discussed here, the geochemical impacts of microbial metabolism are linked to the consortial organization and development of the pod structure, which affects cell-cell interactions and interactions with the surrounding geochemical microenvironment. If these pods are widespread in mine waters, echoing the now widespread discovery of AOM consortia, then AMD-driven CO(2) atmospheric fluxes from H(2)SO(4) carbonate weathering could be reduced by as much as 26 TgC/yr. This novel sulfur consortial discovery indicates that organized metabolically linked microbial partnerships are likely widespread and more significant in global elemental cycling than previously considered.

Reductive dechlorination of trichloroethylene by combining autotrophic hydrogen-bacteria and zero-valent iron particles

The objective of this study was to evaluate the dechlorination rate (from an initial concentration of 180 micromol l(-1)) and synergistic effect of combining commercial Fe(0) and autotrophic hydrogen-bacteria in the presence of hydrogen, during TCE degradation process. In the batch test, the treatment using Fe(0) in the presence of hydrogen (Fe(0)/H(2)), showed more effective dechlorination and less iron consumption than Fe(0) utilized only (Fe(0)/N(2)), meaning that catalytic degradation had promoted transformation of TCE, and the iron was protected by cathodic hydrogen. The combined use of Fe(0) and autotrophic hydrogen-bacteria was found to be more effective than did the individual exercise even though the hydrogen was insufficient during the batch test. By the analysis of XRPD, the crystal of FeS transformed by sulfate reducing bacteria (SRB) was detected on the surface of iron after the combined treatment. The synergistic impact was caused by FeS precipitates, which enhanced TCE degradation through catalytic dechlorination. Additionally, the dechlorination rate coefficient of the combined method in MFSB was 3.2-fold higher than that of iron particles individual use. Results from batch and MFSB experiments revealed that, the proposed combined method has the potential to become a cost-effective remediation technology for chlorinated-solvent contaminated site.

Acidophilic microbial communities associated with a natural, biodegraded hydrocarbon seepage

Characterization of microbial communities present in a surface petroleum seep in which hydrocarbons have been biodegraded for thousands of years in order to improve the understanding on natural petroleum biodegradation. DNA was extracted from a natural, surface petroleum seep and subjected to culture independent analysis (rRNA gene-based denaturing gradient gel electrophoresis and phylogenetic analysis of clone libraries). Molecular analysis suggested dominance by acidophilic bacteria, especially Alphaproteobacteria (mainly bacteria related to Acidiphilium and Acidocella). Archaea were not detected, but fungi were present. pH of the samples was around 3.5. Acidophilic microbial communities are associated with an acidic petroleum seep. Microbial community structure analysis gives information on the environmental conditions under which petroleum biodegradation occurs. This knowledge could be applied to define conditions for specific cultivation or activity measurements. The activity of acidophilic micro-organisms deserves more attention with respect to their involvement in natural petroleum degradation. This knowledge will contribute to the design of oil bioremediation strategies for polluted acidic settings.

Effects of soluble ferri-hydroxide complexes on microbial neutralization of acid mine drainage

Heterotrophic respiration of ferric iron by Acidiphilium cryptum was investigated in anoxic microcosms with initial media pH values from 1.5 to 3.5. No organic carbon consumption or iron reduction was observed with an initial pH of 1.5, indicating that A. cryptum may not be capable of iron respiration at this pH. Significant iron reduction was observed at pH 2.5 and 3.5, with different effects. When the initial pH was 3.5, pH increased to 4.7-5.5 over 60 days of incubation with simultaneous production of 0.4 g L(-1) Fe2+. However, at an initial pH of 2.5, no significant change in pH was observed during iron respiration, although the accumulation of soluble ferrous iron was significantly higher, averaging 1.1 g L(-1) Fe2+. The speciation of the ferric iron electron acceptor may explain these results. At pH values of 3.5 and higher, precipitated ferric hydroxide Fe- (OH)3 would have been the primary source of ferric iron, with reduction resulting in net production of OH- ions and the significant increases in media pH observed. However at pH 2.5, soluble complexes, FeOH2+ and Fe(OH)2+, may have been the more prevalent electron acceptors, and the alkalinity generated by reduction of complexed iron was low. The existence of charged ferri-hydroxide complexes at pH 2.5 was verified by voltammetry. Results suggest that initiation of bacterial iron reduction may result in neutralization of acid mine drainage. However, this effect is extremely sensitive to iron speciation within a relatively small and critical pH range.

Metal bioremediation through growing cells

Heavy-metal pollution represents an important environmental problem due to the toxic effects of metals, and their accumulation throughout the food chain leads to serious ecological and health problems. Metal remediation through common physico-chemical techniques is expensive and unsuitable in case of voluminous effluents containing complexing organic matter and low metal contamination. Biotechnological approaches that are designed to cover such niches have, therefore, received great deal of attention in the recent years. Biosorption studies involving low-cost and often dead/pretreated biomass have dominated the literature and, subsequently, extensive reviews focusing on equilibrium and kinetics of metal biosorption have also come up. However, the low binding capacity of biomass for certain recalcitrant metals such as Ni and failure to effectively remove metals from real industrial effluents due to presence of organic or inorganic ligands limit this approach. At times, when pure biosorptive metal removal is not feasible, application of a judicious consortium of growing metal-resistant cells can ensure better removal through a combination of bioprecipitation, biosorption and continuous metabolic uptake of metals after physical adsorption. Such approach may lead to simultaneous removal of toxic metals, organic loads and other inorganic impurities, as well as allow optimization through development of resistant species. However, sensitivity of living cells to extremes of pH or high metal concentration and need to furnish metabolic energy are some of the major constraints of employing growing cells for bioremediation. The efforts to meet such challenges via isolation of metal-resistant bacterial/fungal strains and exploitation of organic wastes as carbon substrates have began. Recent studies show that the strains (bacteria, yeast and fungi) isolated from contaminated sites possess excellent capability of metal scavenging. Some bacterial strains possess high tolerance to various metals and may be potential candidates for their simultaneous removal from wastes. Evidently, the stage has already been set for the application of metal-resistant growing microbial cells for metal harvesting. This review focuses on the applicability of growing bacterial/fungal/algal cells for metal removal and the efforts directed towards cell/process development to make this option technically/economically viable for the comprehensive treatment of metal-rich effluents.