Microbial reduction of Fe(III) in the presence of oxygen under low pH conditions

Goethite dissolution by acidophilic bacteria

Previous studies have reported the role of some species of acidophilic bacteria in accelerating the dissolution of goethite under aerobic and anaerobic conditions. This has relevance for environments impacted by acid mine drainage and for the potential bioleaching of limonitic laterite ores. In this study, natural well-characterized goethite mineral samples and synthetic goethite were used in aerobic and anaerobic laboratory batch culture incubation experiments with ferric iron-reducing, acidophilic bacteria, including the lithoautotrophic species Acidithiobacillus (At.) thiooxidans, At. ferrooxidans, and At. caldus, as well as two strains of the organoheterotrophic species Acidiphilium cryptum. All bacteria remained alive throughout the experiments and efficiently reduced soluble ferric iron in solution in positive control assays. However, goethite dissolution was low to negligible in all experimental assays with natural goethite, while some dissolution occurred with synthetic goethite in agreement with previous publications. The results indicate that ferric iron-reducing microbial activity at low pH is less relevant for goethite dissolution than the oxidation of elemental sulfur to sulfuric acid. Microbial ferric iron reduction enhances but does not initiate goethite dissolution in very acidic liquors.

Coupled Fe(III) reduction and phenanthrene degradation by marine-derived Kocuria oceani FXJ8.057 under aerobic condition

Diverse aerobic actinobacteria possess the capacity to degrade polycyclic aromatic hydrocarbons (PAHs) and have recently been shown to reduce Fe(III). However, the coupling of the two processes under oxic conditions remains unclear. Here, the co-metabolism of phenanthrene (PHE) and Fe(III) by marine-derived Kocuria oceani FXJ8.057 was realized under aerobic condition. In the presence of both PHE and Fe(III), the rates of PHE degradation (83.91 %) and Fe(III) reduction (50.00 %) were synchronously enhanced, compared to those with PHE (67.34 %) or Fe(III) (38.00 %) alone. Transcriptome analysis detected upregulation of PHE biodegradation and riboflavin biosynthesis in the strain cultured with both PHE and Fe(III) compared to that with PHE alone. Metabolite analysis indicated that, with the addition of Fe(III), the strain could efficiently degrade PHE via three pathways. Moreover, the strain secreted riboflavin, which acted as a shuttle to promote electron transfer from PHE to Fe(III). It also secreted organic acids that could delay Fe(II) reoxidation. Finally, H2O2 secreted by the strain caused extracellular Fenton reaction to generate •OH, which also played a minor role in the PHE degradation. These findings provide the first example of an aerobic bacterium that couples PAH degradation to Fe(III) reduction and extend our understanding of Fe(III)-reducing microorganisms.

Acidophilic microorganisms in remediation of contaminants present in extremely acidic conditions

Acidophiles are a group of microorganisms that thrive in acidic environments where pH level is far below the neutral value 7.0. They belong to a larger family called extremophiles, which is a group that thrives in various extreme environmental conditions which are normally inhospitable to other organisms. Several human activities such as mining, construction and other industrial processes release highly acidic effluents and wastes into the environment. Those acidic wastes and wastewaters contain different types of pollutants such as heavy metals, radioactive, and organic, whose have adverse effects on human being as well as on other living organisms. To protect the whole ecosystem, those pollutants containing effluents or wastes must be clean properly before releasing into environment. Physicochemical cleanup processes under extremely acidic conditions are not always successful due to high cost and release of toxic byproducts. While in case of biological methods, except acidophiles, no other microorganisms cannot survive in highly acidic conditions. Therefore, acidophiles can be a good choice for remediation of different types of contaminants present in acidic conditions. In this review article, various roles of acidophilic microorganisms responsible for removing heavy metals and radioactive pollutants from acidic environments were discussed. Bioremediation of various acidic organic pollutants by using acidophiles was also studied. Overall, this review could be helpful to extend our knowledge as well as to do further relevant novel studies in the field of acidic pollutants remediation by applying acidophilic microorganisms.

Biogeochemical Niches of Fe-Cycling Communities Influencing Heavy Metal Transport along the Rio Tinto, Spain

In the mining-impacted Rio Tinto, Spain, Fe-cycling microorganisms influence the transport of heavy metals (HMs) into the Atlantic Ocean. However, it remains largely unknown how spatial and temporal hydrogeochemical gradients along the Rio Tinto shape the composition of Fe-cycling microbial communities and how this in turn affects HM mobility. Using a combination of DNA- and RNA-based 16S rRNA (gene) amplicon sequencing and hydrogeochemical analyses, we explored the impact of pH, Fe(III), Fe(II), and Cl- on Fe-cycling microorganisms. We showed that the water column at the acidic (pH 2.2) middle course of the river was colonized by Fe(II) oxidizers affiliated with Acidithiobacillus and Leptospirillum. At the upper estuary, daily fluctuations of pH (2.7 to 3.7) and Cl- (6.9 to 16.6 g/L) contributed to the establishment of a unique microbial community, including Fe(II) oxidizers belonging to Acidihalobacter, Marinobacter, and Mariprofundus, identified at this site. Furthermore, DNA- and RNA-based profiles of the benthic community suggested that acidophilic and neutrophilic Fe(II) oxidizers (e.g., Acidihalobacter, Marinobacter, and Mariprofundus), Fe(III) reducers (e.g., Thermoanaerobaculum), and sulfate-reducing bacteria drive the Fe cycle in the estuarine sediments. RNA-based relative abundances of Leptospirillum at the middle course as well as abundances of Acidihalobacter and Mariprofundus at the upper estuary were higher than DNA-based results, suggesting a potentially higher level of activity of these taxa. Based on our findings, we propose a model of how tidal water affects the composition and activity of the Fe-cycling taxa, playing an important role in the transport of HMs (e.g., As, Cd, Cr, and Pb) along the Rio Tinto. IMPORTANCE The estuary of the Rio Tinto is a unique environment in which extremely acidic, heavy metal-rich, and especially iron-rich river water is mixed with seawater. Due to the mixing events, the estuarine water is characterized by a low pH, almost seawater salinity, and high concentrations of bioavailable iron. The unusual hydrogeochemistry maintains unique microbial communities in the estuarine water and in the sediment. These communities include halotolerant iron-oxidizing microorganisms which typically inhabit acidic saline environments and marine iron-oxidizing microorganisms which, in contrast, are not typically found in acidic environments. Furthermore, highly saline estuarine water favored the prosperity of acidophilic heterotrophs, typically inhabiting brackish and saline environments. The Rio Tinto estuarine sediment harbors a diverse microbial community with both acidophilic and neutrophilic members that can mediate the iron cycle and, in turn, can directly impact the mobility and transport of heavy metals in the Rio Tinto estuary.

Ferric Iron Reduction in Extreme Acidophiles

Biochemical processes are a key element of natural cycles occurring in the environment and enabling life on earth. With regard to microbially catalyzed iron transformation, research predominantly has focused on iron oxidation in acidophiles, whereas iron reduction played a minor role. Microbial conversion of ferric to ferrous iron has however become more relevant in recent years. While there are several reviews on neutrophilic iron reducers, this article summarizes the research on extreme acidophilic iron reducers. After the first reports of dissimilatory iron reduction by acidophilic, chemolithoautotrophic Acidithiobacillus strains and heterotrophic Acidiphilium species, many other prokaryotes were shown to reduce iron as part of their metabolism. Still, little is known about the exact mechanisms of iron reduction in extreme acidophiles. Initially, hypotheses and postulations for the occurring mechanisms relied on observations of growth behavior or predictions based on the genome. By comparing genomes of well-studied neutrophilic with acidophilic iron reducers (e.g., Ferroglobus placidus and Sulfolobus spp.), it became clear that the electron transport for iron reduction proceeds differently in acidophiles. Moreover, transcriptomic investigations indicated an enzymatically-mediated process in Acidithiobacillus ferrooxidans using respiratory chain components of the iron oxidation in reverse. Depending on the strain of At. ferrooxidans, further mechanisms were postulated, e.g., indirect iron reduction by hydrogen sulfide, which may form by disproportionation of elemental sulfur. Alternative scenarios include Hip, a high potential iron-sulfur protein, and further cytochromes. Apart from the anaerobic iron reduction mechanisms, sulfur-oxidizing acidithiobacilli have been shown to mediate iron reduction at low pH (< 1.3) under aerobic conditions. This presumably non-enzymatic process may be attributed to intermediates formed during sulfur/tetrathionate and/or hydrogen oxidation and has already been successfully applied for the reductive bioleaching of laterites. The aim of this review is to provide an up-to-date overview on ferric iron reduction by acidophiles. The importance of this process in anaerobic habitats will be demonstrated as well as its potential for application.

Towards Bioleaching of a Vanadium Containing Magnetite for Metal Recovery

Vanadium - a transition metal - is found in the ferrous-ferric mineral, magnetite. Vanadium has many industrial applications, such as in the production of high-strength low-alloy steels, and its increasing global industrial consumption requires new primary sources. Bioleaching is a biotechnological process for microbially catalyzed dissolution of minerals and wastes for metal recovery such as biogenic organic acid dissolution of bauxite residues. In this study, 16S rRNA gene amplicon sequencing was used to identify microorganisms in Nordic mining environments influenced by vanadium containing sources. These data identified gene sequences that aligned to the Gluconobacter genus that produce gluconic acid. Several strategies for magnetite dissolution were tested including oxidative and reductive bioleaching by acidophilic microbes along with dissimilatory reduction by Shewanella spp. that did not yield significant metal release. In addition, abiotic dissolution of the magnetite was tested with gluconic and oxalic acids, and yielded 3.99 and 81.31% iron release as a proxy for vanadium release, respectively. As a proof of principle, leaching via gluconic acid production by Gluconobacter oxydans resulted in a maximum yield of 9.8% of the available iron and 3.3% of the vanadium. Addition of an increased concentration of glucose as electron donor for gluconic acid production alone, or in combination with calcium carbonate to buffer the pH, increased the rate of iron dissolution and final vanadium recoveries. These data suggest a strategy of biogenic organic acid mediated vanadium recovery from magnetite and point the way to testing additional microbial species to optimize the recovery.

Insights into Autotrophic Activities and Carbon Flow in Iron-Rich Pelagic Aggregates (Iron Snow)

Pelagic aggregates function as biological carbon pumps for transporting fixed organic carbon to sediments. In iron-rich (ferruginous) lakes, photoferrotrophic and chemolithoautotrophic bacteria contribute to CO₂ fixation by oxidizing reduced iron, leading to the formation of iron-rich pelagic aggregates (iron snow). The significance of iron oxidizers in carbon fixation, their general role in iron snow functioning and the flow of carbon within iron snow is still unclear. Here, we combined a two-year metatranscriptome analysis of iron snow collected from an acidic lake with protein-based stable isotope probing to determine general metabolic activities and to trace ¹³CO₂ incorporation in iron snow over time under oxic and anoxic conditions. mRNA-derived metatranscriptome of iron snow identified four key players (Leptospirillum, Ferrovum, Acidithrix, Acidiphilium) with relative abundances (59.6-85.7%) encoding ecologically relevant pathways, including carbon fixation and polysaccharide biosynthesis. No transcriptional activity for carbon fixation from archaea or eukaryotes was detected. ¹³CO₂ incorporation studies identified active chemolithoautotroph Ferrovum under both conditions. Only 1.0-5.3% relative ¹³C abundances were found in heterotrophic Acidiphilium and Acidocella under oxic conditions. These data show that iron oxidizers play an important role in CO₂ fixation, but the majority of fixed C will be directly transported to the sediment without feeding heterotrophs in the water column in acidic ferruginous lakes.

A novel approach for treating acid mine drainage through forming schwertmannite driven by a mixed culture of Acidiphilium multivorum and Acidithiobacillus ferrooxidans prior to lime neutralization

As the predominant treatment approach of acid mine drainage (AMD), lime neutralization often exhibits inefficiencies since the abundance of iron and sulfate in AMD usually form iron hydroxide and gypsum precipitate coatings on the surface of lime. In this study, a novel approach of biomineralization prior to lime neutralization for treating AMD was proposed, in which iron and sulfate were biologically precipitated as schwertmannite through iron biological reduction-oxidation driven by a culture mixed with Acidiphilium multivorum JZ-6 and Acidithiobacillus ferrooxidans LX5. It was found that only five cycles of iron reduction by A. multivorum JZ-6 followed by iron oxidation by A. ferrooxidans LX5 could remove completely iron and nearly 40% of sulfate in AMD, while non-ferrous metals (Al, Mn, Cu, Ni, and Zn) were hardly removed. Consequently, the amounts of lime required and sludge generated in the subsequent lime neutralization process were reduced by 56% and 68%, respectively. As a result, the content of non-ferrous metals in the sludge was increased by 3.2 folds. The level of Al was increased surprisingly to 19% (wt/wt), a level similar to the commercially valuable bauxite. The novel process of biomineralization prior to lime neutralization provides a sustainable way for AMD treatment.

High Representation of Archaea Across All Depths in Oxic and Low-pH Sediment Layers Underlying an Acidic Stream

Parys Mountain or Mynydd Parys (Isle of Anglesey, United Kingdom) is a mine-impacted environment, which accommodates a variety of acidophilic organisms. Our previous research of water and sediments from one of the surface acidic streams showed a high proportion of archaea in the total microbial community. To understand the spatial distribution of archaea, we sampled cores (0-20 cm) of sediment and conducted chemical analyses and taxonomic profiling of microbiomes using 16S rRNA gene amplicon sequencing in different core layers. The taxonomic affiliation of sequencing reads indicated that archaea represented between 6.2 and 54% of the microbial community at all sediment depths. Majority of archaea were associated with the order Thermoplasmatales, with the most abundant group of sequences being clustered closely with the phylotype B_DKE, followed by "E-plasma," "A-plasma," other yet uncultured Thermoplasmatales with Ferroplasma and Cuniculiplasma spp. represented in minor proportions. Thermoplasmatales were found at all depths and in the whole range of chemical conditions with their abundance correlating with sediment Fe, As, Cr, and Mn contents. The bacterial microbiome component was largely composed in all layers of sediment by members of the phyla Proteobacteria, Actinobacteria, Nitrospirae, Firmicutes, uncultured Chloroflexi (AD3 group), and Acidobacteria. This study has revealed a high abundance of Thermoplasmatales in acid mine drainage-affected sediment layers and pointed at these organisms being the main contributors to carbon, and probably to iron and sulfur cycles in this ecosystem.

Characterization of an acid rock drainage microbiome and transcriptome at the Ely Copper Mine Superfund site

The microbial oxidation of metal sulfides plays a major role in the formation of acid rock drainage (ARD). We aimed to broadly characterize the ARD at Ely Brook, which drains the Ely Copper Mine Superfund site in Vermont, USA, using metagenomics and metatranscriptomics to assess the metabolic potential and seasonal ecological roles of microorganisms in water and sediment. Using Centrifuge against the NCBI "nt" database, ~25% of reads in sediment and water samples were classified as acid-tolerant Proteobacteria (61 ± 4%) belonging to the genera Pseudomonas (2.6-3.3%), Bradyrhizobium (1.7-4.1%), and Streptomyces (2.9-5.0%). Numerous genes (12%) were differentially expressed between seasons and played significant roles in iron, sulfur, carbon, and nitrogen cycling. The most abundant RNA transcript encoded the multidrug resistance protein Stp, and most expressed KEGG-annotated transcripts were involved in amino acid metabolism. Biosynthetic gene clusters involved in secondary metabolism (BGCs, 449) as well as metal- (133) and antibiotic-resistance (8501) genes were identified across the entire dataset. Several antibiotic and metal resistance genes were colocalized and coexpressed with putative BGCs, providing insight into the protective roles of the molecules BGCs produce. Our study shows that ecological stimuli, such as metal concentrations and seasonal variations, can drive ARD taxa to produce novel bioactive metabolites.

Molecular Mechanisms Underpinning Aggregation in Acidiphilium sp. C61 Isolated from Iron-Rich Pelagic Aggregates

Iron-rich pelagic aggregates (iron snow) are hot spots for microbial interactions. Using iron snow isolates, we previously demonstrated that the iron-oxidizer Acidithrix sp. C25 triggers Acidiphilium sp. C61 aggregation by producing the infochemical 2-phenethylamine (PEA). Here, we showed slightly enhanced aggregate formation in the presence of PEA on different Acidiphilium spp. but not other iron-snow microorganisms, including Acidocella sp. C78 and Ferrovum sp. PN-J47. Next, we sequenced the Acidiphilium sp. C61 genome to reconstruct its metabolic potential. Pangenome analyses of Acidiphilium spp. genomes revealed the core genome contained 65 gene clusters associated with aggregation, including autoaggregation, motility, and biofilm formation. Screening the Acidiphilium sp. C61 genome revealed the presence of autotransporter, flagellar, and extracellular polymeric substances (EPS) production genes. RNA-seq analyses of Acidiphilium sp. C61 incubations (+/− 10 µM PEA) indicated genes involved in energy production, respiration, and genetic processing were the most upregulated differentially expressed genes in the presence of PEA. Additionally, genes involved in flagellar basal body synthesis were highly upregulated, whereas the expression pattern of biofilm formation-related genes was inconclusive. Our data shows aggregation is a common trait among Acidiphilium spp. and PEA stimulates the central cellular metabolism, potentially advantageous in aggregates rapidly falling through the water column.

An integrated microbiological and electrochemical approach to determine distributions of Fe metabolism in acid mine drainage-induced "iron mound" sediments

Fe(III)-rich deposits referred to as “iron mounds” develop when Fe(II)-rich acid mine drainage (AMD) emerges at the terrestrial surface, and aeration of the fluids induces oxidation of Fe(II), with subsequent precipitation of Fe(III) phases. As Fe(III) phases accumulate in these systems, O₂ gradients may develop in the sediments and influence the distributions and extents of aerobic and anaerobic microbiological Fe metabolism, and in turn the solubility of Fe. To determine how intrusion of O₂ into iron mound sediments influences microbial community composition and Fe metabolism, we incubated samples of these sediments in a column format. O₂ was only supplied through the top of the columns, and microbiological, geochemical, and electrochemical changes at discrete depths were determined with time. Despite the development of dramatic gradients in dissolved Fe(II) concentrations, indicating Fe(II) oxidation in shallower portions and Fe(III) reduction in the deeper portions, microbial communities varied little with depth, suggesting the metabolic versatility of organisms in the sediments with respect to Fe metabolism. Additionally, the availability of O₂ in shallow portions of the sediments influenced Fe metabolism in deeper, O₂-free sediments. Total potential (E_H + self-potential) measurements at discrete depths in the columns indicated that Fe transformations and electron transfer processes were occurring through the sediments and could explain the impact of O₂ on Fe metabolism past where it penetrates into the sediments. This work shows that O₂ availability (or lack of it) minimally influences microbial communities, but influences microbial activities beyond its penetration depth in AMD-derived Fe(III) rich sediments. Our results indicate that O₂ can modulate Fe redox state and solubility in larger volumes of iron mound sediments than only those directly exposed to O₂.

Remediation of multiple heavy metal-contaminated soil through the combination of soil washing and in situ immobilization

The remediation of heavy metal-contaminated soils is a great challenge for global environmental sciences and engineering. To control the ecological risks of heavy metal-contaminated soil more effectively, the present study focused on the combination of soil washing (with FeCl₃) and in situ immobilization (with lime, biochar, and black carbon). The results showed that the removal rate of Cd, Pb, Zn, and Cu was 62.9%, 52.1%, 30.0%, and 16.7%, respectively, when washed with FeCl₃. After the combined remediation (immobilization with 1% (w/w) lime), the contaminated soils showed 36.5%, 73.6%, 70.9%, and 53.4% reductions in the bioavailability of Cd, Cu, Pb, and Zn (extracted with 0.11M acetic acid), respectively, than those of the soils washed with FeCl₃ only. However, the immobilization with 1% (w/w) biochar or 1% (w/w) carbon black after washing exhibited low effects on stabilizing the metals. The differences in effects between the immobilization with lime, biochar, and carbon black indicated that the soil pH had a significant influence on the lability of heavy metals during the combined remediation process. The activity of the soil enzymes (urease, sucrase, and catalase) showed that the addition of all the materials, including lime, biochar, and carbon black, exhibited positive effects on microbial remediation after soil washing. Furthermore, lime was the most effective material, indicating that low soil pH and high acid-soluble metal concentrations might restrain the activity of soil enzymes. Soil pH and nutrition were the major considerations for microbial remediation during the combined remediation. These findings suggest that the combination of soil washing and in situ immobilization is an effective method to amend the soils contaminated with multiple heavy metals.

Role of microbial activity in Fe(III) hydroxysulfate mineral transformations in an acid mine drainage-impacted site from the Dabaoshan Mine

Fe(III) hydroxysulfate minerals are secondary minerals commonly found in acid mine drainage (AMD) sites and have a major impact on water and soil quality in these environments. While previous studies showed that the Fe(III) hydroxysulfate mineral transformation could be mediated by some bacterial strains under laboratory conditions, the role of indigenous microbial activity in Fe(III) hydroxysulfate mineral transformation in natural environment has received little attention. In this study, microcosms were constructed with AMD-affected river water and sediment from the Dabaoshan Mine that was either left unamended or enriched with nutrients (lactate, nitrogen, and phosphorus (LNP)) and biosynthetic minerals (schwertmannite or jarosite). The results show that microbial activity played a decisive role in the mineralogical transformation of schwertmannite/jarosite in the AMD-contaminated site when organic carbon was available. The accumulation of Fe(II) and sulfide in microcosms amended with LNP indicates that schwertmannite/jarosite transformation is mediated by microbial reduction. XRD, SEM and FTIR analyses suggest that schwertmannite was completely transformed to goethite in the Sch-LNP microcosms at the end of their incubation. Jarosite in the Jar-LNP microcosms was also transformed to goethite, but at a much slower rate than schwertmannite. Bacterial community analysis reveals that the stimulated indigenous bacteria promote the mineralogical transformation of schwertmannite/jarosite. Most of these bacteria, including Geobacter, Desulfosporosinus, Geothrix, Desulfurispora, Desulfovibrio, and Anaeromyxobacter, are known to reduce iron and/or sulfate. The mineralogical transformation of schwertmannite and jarosite exerts significant control on the geochemistry of AMD-contaminated systems.

Effectiveness of phosphate removal during anaerobic digestion of waste activated sludge by dosing iron(III)

Phosphate-Fe(II) precipitation induced by Fe(III) reduction during the anaerobic digestion of excess activated sludge was investigated for the removal of phosphorus and its possible recovery. The experiments were conducted with three Fe(III) sources at 35 °C and 55 °C. The results show that ferrihydrite-Fe(III) was effectively reduced during the anaerobic sludge digestion by 63% and 96% under mesophilic and thermophilic conditions, respectively. Whereas FeCl₃-Fe(III) was only mesophilically reducible and the reduction of hematite-Fe(III) was unnoticeable at either temperature. Efficient precipitation of vivianite was not observed although high saturation index values, e.g., >14 (activity reduction not considered), had been reached. This reveals the complexity of vivianite precipitation in anaerobic digestion systems; for example, Fe(II) complexation and organic interference could not be ignored. With ferrihydrite amendments at a Fe/TP of 1.5, methane production from sludge digestion was reduced by 35.1% at 35 °C, and was unaffected when the digestion temperature went up to 55 °C. But, acidic FeCl₃ severely inhibited the methane production and consequently the sludge biomass degradation.

Sticking together: inter-species aggregation of bacteria isolated from iron snow is controlled by chemical signaling

Marine and lake snow is a continuous shower of mixed organic and inorganic aggregates falling from the upper water where primary production is substantial. These pelagic aggregates provide a niche for microbes that can exploit these physical structures and resources for growth, thus are local hot spots for microbial activity. However, processes underlying their formation remain unknown. Here, we investigated the role of chemical signaling between two co-occurring bacteria that each make up more than 10% of the community in iron-rich lakes aggregates (iron snow). The filamentous iron-oxidizing Acidithrix strain showed increased rates of Fe(II) oxidation when incubated with cell-free supernatant of the heterotrophic iron-reducing Acidiphilium strain. Amendment of Acidithrix supernatant to motile cells of Acidiphilium triggered formation of cell aggregates displaying similar morphology to those of iron snow. Comparative metabolomics enabled the identification of the aggregation-inducing signal, 2-phenethylamine, which also induced faster growth of Acidiphilium. We propose a model that shows rapid iron snow formation, and ultimately energy transfer from the photic zone to deeper water layers, is controlled via a chemically mediated interplay.

Impacts of detrital nano- and micro-scale particles (dNP) on contaminant dynamics in a coal mine AMD treatment system

Pollutants in acid mine drainage (AMD) are usually sequestered in neoformed nano- and micro-scale particles (nNP) through precipitation, co-precipitation, and sorption. Subsequent biogeochemical processes may control nNP stability and thus long-term contaminant immobilization. Mineralogical, chemical, and microbiological data collected from sediments accumulated over a six-year period in a coal-mine AMD treatment system were used to identify the pathways of contaminant dynamics. We present evidence that detrital nano- and micron-scale particles (dNP), composed mostly of clay minerals originating from the partial weathering of coal-mine waste, mediated biogeochemical processes that catalyzed AMD contaminant (1) immobilization by facilitating heterogeneous nucleation and growth of nNP in oxic zones, and (2) remobilization by promoting phase transformation and reductive dissolution of nNP in anoxic zones. We found that dNP were relatively stable under acidic conditions and estimated a dNP content of ~0.1g/L in the influent AMD. In the AMD sediments, the initial nNP precipitates were schwertmannite and poorly crystalline goethite, which transformed to well-crystallized goethite, the primary nNP repository. Subsequent reductive dissolution of nNP resulted in the remobilization of up to 98% of S and 95% of Fe accompanied by the formation of a compact dNP layer. Effective treatment of pollutants could be enhanced by better understanding the complex, dynamic role dNP play in mediating biogeochemical processes and contaminant dynamics at coal-mine impacted sites.

Ecological roles of dominant and rare prokaryotes in acid mine drainage revealed by metagenomics and metatranscriptomics

High-throughput sequencing is expanding our knowledge of microbial diversity in the environment. Still, understanding the metabolic potentials and ecological roles of rare and uncultured microbes in natural communities remains a major challenge. To this end, we applied a 'divide and conquer' strategy that partitioned a massive metagenomic data set (>100 Gbp) into subsets based on K-mer frequency in sequence assembly to a low-diversity acid mine drainage (AMD) microbial community and, by integrating with an additional metatranscriptomic assembly, successfully obtained 11 draft genomes most of which represent yet uncultured and/or rare taxa (relative abundance <1%). We report the first genome of a naturally occurring Ferrovum population (relative abundance >90%) and its metabolic potentials and gene expression profile, providing initial molecular insights into the ecological role of these lesser known, but potentially important, microorganisms in the AMD environment. Gene transcriptional analysis of the active taxa revealed major metabolic capabilities executed in situ, including carbon- and nitrogen-related metabolisms associated with syntrophic interactions, iron and sulfur oxidation, which are key in energy conservation and AMD generation, and the mechanisms of adaptation and response to the environmental stresses (heavy metals, low pH and oxidative stress). Remarkably, nitrogen fixation and sulfur oxidation were performed by the rare taxa, indicating their critical roles in the overall functioning and assembly of the AMD community. Our study demonstrates the potential of the 'divide and conquer' strategy in high-throughput sequencing data assembly for genome reconstruction and functional partitioning analysis of both dominant and rare species in natural microbial assemblages.

Depth-dependent geochemical and microbiological gradients in Fe(III) deposits resulting from coal mine-derived acid mine drainage

We evaluated the depth-dependent geochemistry and microbiology of sediments that have developed via the microbially-mediated oxidation of Fe(II) dissolved in acid mine drainage (AMD), giving rise to a 8–10 cm deep “iron mound” that is composed primarily of Fe(III) (hydr)oxide phases. Chemical analyses of iron mound sediments indicated a zone of maximal Fe(III) reducing bacterial activity at a depth of approximately 2.5 cm despite the availability of dissolved O₂ at this depth. Subsequently, Fe(II) was depleted at depths within the iron mound sediments that did not contain abundant O₂. Evaluations of microbial communities at 1 cm depth intervals within the iron mound sediments using “next generation” nucleic acid sequencing approaches revealed an abundance of phylotypes attributable to acidophilic Fe(II) oxidizing Betaproteobacteria and the chloroplasts of photosynthetic microeukaryotic organisms in the upper 4 cm of the iron mound sediments. While we observed a depth-dependent transition in microbial community structure within the iron mound sediments, phylotypes attributable to Gammaproteobacterial lineages capable of both Fe(II) oxidation and Fe(III) reduction were abundant in sequence libraries (comprising ≥20% of sequences) from all depths. Similarly, abundances of total cells and culturable Fe(II) oxidizing bacteria were uniform throughout the iron mound sediments. Our results indicate that O₂ and Fe(III) reduction co-occur in AMD-induced iron mound sediments, but that Fe(II)-oxidizing activity may be sustained in regions of the sediments that are depleted in O₂.

Fe biogeochemistry in reclaimed acid mine drainage precipitates--implications for phytoremediation

At a 50-year-old coal mine drainage barrens in central Pennsylvania, USA, we evaluated the biogeochemistry of acidic, Fe(III)oxy(hydr)oxide precipitates in reclaimed plots and compared them to untreated precipitates in control areas. Reclaimed plots supported successional vegetation that became established after a one-time compost and lime treatment in 2006, while control plots supported biological crusts. Precipitates were sampled from moist yet unsaturated surface layers in an area with lateral subsurface flow of mine drainage above a fragipan. Fe(II) concentrations were three- to five-fold higher in reclaimed than control precipitates. Organically bound Fe and amorphous iron oxides, as fractions of total Fe, were also higher in reclaimed than control precipitates. Estimates of Fe-reducing and Fe-oxidizing bacteria were four- to tenfold higher in root-adherent than both types of control precipitates. By scaling up measurements from experimental plots, total Fe losses during the 5-yr following reclamation were estimated at 45 t Fe ha(-1) yr(-1).

Parallel changes of taxonomic interaction networks in lacustrine bacterial communities induced by a polymetallic perturbation

Heavy metals released by anthropogenic activities such as mining trigger profound changes to bacterial communities. In this study we used 16S SSU rRNA gene high-throughput sequencing to characterize the impact of a polymetallic perturbation and other environmental parameters on taxonomic networks within five lacustrine bacterial communities from sites located near Rouyn-Noranda, Quebec, Canada. The results showed that community equilibrium was disturbed in terms of both diversity and structure. Moreover, heavy metals, especially cadmium combined with water acidity, induced parallel changes among sites via the selection of resistant OTUs (Operational Taxonomic Unit) and taxonomic dominance perturbations favoring the Alphaproteobacteria. Furthermore, under a similar selective pressure, covariation trends between phyla revealed conservation and parallelism within interphylum interactions. Our study sheds light on the importance of analyzing communities not only from a phylogenetic perspective but also including a quantitative approach to provide significant insights into the evolutionary forces that shape the dynamic of the taxonomic interaction networks in bacterial communities.

Redox Transformations of Iron at Extremely Low pH: Fundamental and Applied Aspects

Many different species of acidophilic prokaryotes, widely distributed within the domains Bacteria and Archaea, can catalyze the dissimilatory oxidation of ferrous iron or reduction of ferric iron, or can do both. Microbially mediated cycling of iron in extremely acidic environments (pH < 3) is strongly influenced by the enhanced chemical stability of ferrous iron and far greater solubility of ferric iron under such conditions. Cycling of iron has been demonstrated in vitro using both pure and mixed cultures of acidophiles, and there is considerable evidence that active cycling of iron occurs in acid mine drainage streams, pit lakes, and iron-rich acidic rivers, such as the Rio Tinto. Measurements of specific rates of iron oxidation and reduction by acidophilic microorganisms show that different species vary in their capacities for iron oxido-reduction, and that this is influenced by the electron donor provided and growth conditions used. These measurements, and comparison with corresponding data for oxidation of reduced sulfur compounds, also help explain why ferrous iron is usually used preferentially as an electron donor by acidophiles that can oxidize both iron and sulfur, even though the energy yield from oxidizing iron is much smaller than that available from sulfur oxidation. Iron-oxidizing acidophiles have been used in biomining (a technology that harness their abilities to accelerate the oxidative dissolution of sulfidic minerals and thereby facilitate the extraction of precious and base metals) for several decades. More recently they have also been used to simultaneously remediate iron-contaminated surface and ground waters and produce a useful mineral by-product (schwertmannite). Bioprocessing of oxidized mineral ores using acidophiles that catalyze the reductive dissolution of ferric iron minerals such as goethite has also recently been demonstrated, and new biomining technologies based on this approach are being developed.

Iron and arsenic cycling in intertidal surface sediments during wetland remediation

The accumulation and behavior of arsenic at the redox interface of Fe-rich sediments is strongly influenced by Fe(III) precipitate mineralogy, As speciation, and pH. In this study, we examined the behavior of Fe and As during aeration of natural groundwater from the intertidal fringe of a wetland being remediated by tidal inundation. The groundwater was initially rich in Fe(2+) (32 mmol L(-1)) and As (1.81 μmol L(-1)) with a circum-neutral pH (6.05). We explore changes in the solid/solution partitioning, speciation and mineralogy of Fe and As during long-term continuous groundwater aeration using a combination of chemical extractions, SEM, XRD, and synchrotron XAS. Initial rapid Fe(2+) oxidation led to the formation of As(III)-bearing ferrihydrite and sorption of >95% of the As(aq) within the first 4 h of aeration. Ferrihydrite transformed to schwertmannite within 23 days, although sorbed/coprecipitated As(III) remained unoxidized during this period. Schwertmannite subsequently transformed to jarosite at low pH (2-3), accompanied by oxidation of remaining Fe(2+). This coincided with a repartitioning of some sorbed As back into the aqueous phase as well as oxidation of sorbed/coprecipitated As(III) to As(V). Fe(III) precipitates formed via groundwater aeration were highly prone to reductive dissolution, thereby posing a high risk of mobilizing sorbed/coprecipitated As during any future upward migration of redox boundaries. Longer-term investigations are warranted to examine the potential pathways and magnitude of arsenic mobilization into surface waters in tidally reflooded wetlands.

Heavy metal tolerance of Fe(III)-reducing microbial communities in contaminated creek bank soils

Fe(III)-reducing soil enrichment cultures can tolerate 100 μM Cu and Cd, 150 μM Co, 600 μM Ni, and 2,500 μM Zn. Metal-tolerant cultures were dominated by Geobacter-related Deltaproteobacteria and Gram-positive Firmicutes spp. (Clostridia and Sedimentibacter). A Cd- and Cu-tolerant Fe(III)-reducing coculture of Desulfosporosinus and Desulfitobacterium indicated the importance of the Firmicutes for Fe(III) reduction in the presence of metals.

Ecophysiology of Fe-cycling bacteria in acidic sediments

Using a combination of cultivation-dependent and -independent methods, this study aimed to elucidate the diversity of microorganisms involved in iron cycling and to resolve their in situ functional links in sediments of an acidic lignite mine lake. Using six different media with pH values ranging from 2.5 to 4.3, 117 isolates were obtained that grouped into 38 different strains, including 27 putative new species with respect to the closest characterized strains. Among the isolated strains, 22 strains were able to oxidize Fe(II), 34 were able to reduce Fe(III) in schwertmannite, the dominant iron oxide in this lake, and 21 could do both. All isolates falling into the Gammaproteobacteria (an unknown Dyella-like genus and Acidithiobacillus-related strains) were obtained from the top acidic sediment zones (pH 2.8). Firmicutes strains (related to Bacillus and Alicyclobacillus) were only isolated from deep, moderately acidic sediment zones (pH 4 to 5). Of the Alphaproteobacteria, Acidocella-related strains were only isolated from acidic zones, whereas Acidiphilium-related strains were isolated from all sediment depths. Bacterial clone libraries generally supported and complemented these patterns. Geobacter-related clone sequences were only obtained from deep sediment zones, and Geobacter-specific quantitative PCR yielded 8 × 10(5) gene copy numbers. Isolates related to the Acidobacterium, Acidocella, and Alicyclobacillus genera and to the unknown Dyella-like genus showed a broad pH tolerance, ranging from 2.5 to 5.0, and preferred schwertmannite to goethite for Fe(III) reduction. This study highlighted the variety of acidophilic microorganisms that are responsible for iron cycling in acidic environments, extending the results of recent laboratory-based studies that showed this trait to be widespread among acidophiles.

Bioremediation of acidic oily sludge-contaminated soil by the novel yeast strain Candida digboiensis TERI ASN6

BACKGROUND, AIM, AND SCOPE

Primitive wax refining techniques had resulted in almost 50,000 tonnes of acidic oily sludge (pH 1-3) being accumulated inside the Digboi refinery premises in Assam state, northeast India. A novel yeast species Candida digboiensis TERI ASN6 was obtained that could degrade the acidic petroleum hydrocarbons at pH 3 under laboratory conditions. The aim of this study was to evaluate the degradation potential of this strain under laboratory and field conditions.

MATERIALS AND METHODS

The ability of TERI ASN6 to degrade the hydrocarbons found in the acidic oily sludge was established by gravimetry and gas chromatography-mass spectroscopy. Following this, a feasibility study was done, on site, to study various treatments for the remediation of the acidic sludge. Among the treatments, the application of C. digboiensis TERI ASN6 with nutrients showed the highest degradation of the acidic oily sludge. This treatment was then selected for the full-scale bioremediation study conducted on site, inside the refinery premises.

RESULTS

The novel yeast strain TERI ASN6 could degrade 40 mg of eicosane in 50 ml of minimal salts medium in 10 days and 72% of heneicosane in 192 h at pH 3. The degradation of alkanes yielded monocarboxylic acid intermediates while the polycyclic aromatic hydrocarbon pyrene found in the acidic oily sludge yielded the oxygenated intermediate pyrenol. In the feasibility study, the application of TERI ASN6 with nutrients showed a reduction of solvent extractable total petroleum hydrocarbon (TPH) from 160 to 28.81 g kg(-1) soil as compared to a TPH reduction from 183.85 to 151.10 g kg(-1) soil in the untreated control in 135 days. The full-scale bioremediation study in a 3,280-m(2) area in the refinery showed a reduction of TPH from 184.06 to 7.96 g kg(-1) soil in 175 days.

DISCUSSION

Degradation of petroleum hydrocarbons by microbes is a well-known phenomenon, but most microbes are unable to withstand the low pH conditions found in Digboi refinery. The strain C. digboiensis could efficiently degrade the acidic oily sludge on site because of its robust nature, probably acquired by prolonged exposure to the contaminants.

CONCLUSIONS

This study establishes the potential of novel yeast strain to bioremediate hydrocarbons at low pH under field conditions.

RECOMMENDATIONS AND PERSPECTIVES

Acidic oily sludge is a potential environmental hazard. The components of the oily sludge are toxic and carcinogenic, and the acidity of the sludge further increases this problem. These results establish that the novel yeast strain C. digboiensis was able to degrade hydrocarbons at low pH and can therefore be used for bioremediating soils that have been contaminated by acidic hydrocarbon wastes generated by other methods as well.

Microbial communities in acid mine drainage

The dissolution of sulfide minerals such as pyrite (FeS2), arsenopyrite (FeAsS), chalcopyrite (CuFeS2), sphalerite (ZnS), and marcasite (FeS2) yields hot, sulfuric acid-rich solutions that contain high concentrations of toxic metals. In locations where access of oxidants to sulfide mineral surfaces is increased by mining, the resulting acid mine drainage (AMD) may contaminate surrounding ecosystems. Communities of autotrophic and heterotrophic archaea and bacteria catalyze iron and sulfur oxidation, thus may ultimately determine the rate of release of metals and sulfur to the environment. AMD communities contain fewer prokaryotic lineages than many other environments. However, it is notable that at least two archaeal and eight bacterial divisions have representatives able to thrive under the extreme conditions typical of AMD. AMD communities are characterized by a very limited number of distinct species, probably due to the small number of metabolically beneficial reactions available. The metabolisms that underpin these communities include organoheterotrophy and autotrophic iron and sulfur oxidation. Other metabolic activity is based on anaerobic sulfur oxidation and ferric iron reduction. Evidence for physiological synergy in iron, sulfur, and carbon flow in these communities is reviewed. The microbial and geochemical simplicity of these systems makes them ideal targets for quantitative, genomic-based analyses of microbial ecology and evolution and community function.

Auto- and heterotrophic acidophilic bacteria enhance the bioremediation efficiency of sediments contaminated by heavy metals

This study deals with bioremediation treatments of dredged sediments contaminated by heavy metals based on the bioaugmentation of different bacterial strains. The efficiency of the following bacterial consortia was compared: (i) acidophilic chemoautotrophic, Fe/S-oxidising bacteria, (ii) acidophilic heterotrophic bacteria able to reduce Fe/Mn fraction, co-respiring oxygen and ferric iron and (iii) the chemoautotrophic and heterotrophic bacteria reported above, pooled together, as it was hypothesised that the two strains could cooperate through a mutual substrate supply. The effect of the bioremediation treatment based on the bioaugmentation of Fe/S-oxidising strains alone was similar to the one based only on Fe-reducing bacteria, and resulted in heavy-metal extraction yields typically ranging from 40% to 50%. The efficiency of the process based only upon autotrophic bacteria was limited by sulphur availability. However, when the treatment was based on the addition of Fe-reducing bacteria and the Fe/S oxidizing bacteria together, their growth rates and efficiency in mobilising heavy metals increased significantly, reaching extraction yields >90% for Cu, Cd, Hg and Zn. The additional advantage of the new bioaugmentation approach proposed here is that it is independent from the availability of sulphur. These results open new perspectives for the bioremediation technology for the removal of heavy metals from highly contaminated sediments.

Isolation and characterization of ferrous- and sulfur-oxidizing bacteria from Tengchong solfataric region, China

Microbial oxidation and reduction of iron and sulfur are important parts of biogeochemical cycles in acidic environments such as geothermal solfataric regions. Species of Acidithiobacillus and Leptospirillum are the common ferrous-iron and sulfur oxidizers from such environments. This study focused on the Tengchong sofataric region, located in Yunnan Province, Southwest China. Based on cultivation, 9 strains that grow on ferrous-iron and sulfuric compounds were obtained. Analysis of 16S rRNA genes of the 9 strains indicated that they were affiliated to Acidithiobacillus, Alicyclobacillus, Sulfobacillus, Leptospirillum and Acidiphilium. Physiological and phylogenetic studies indicated that two strains (TC-34 and TC-71) might represent two novel members of Alicyclobacillus. Strain TC-34 and TC-71 showed 94.8%-97.1% 16S rRNA gene identities to other species of Alicyclobacillus. Different from the previously described Alicyclobacillus species, strains TC-34 and TC-71 were mesophilic and their cellular fatty acids do not contain omega-cyclic fatty acids. Strain TC-71 was obligately dependent on ferrous-iron for growth. It was concluded that the ferrous-iron oxidizers were diversified and Alicyclobacillus species were proposed to take part in biochemical geocycling of iron in the Tengchong solfataric region.

pH gradient-induced heterogeneity of Fe(III)-reducing microorganisms in coal mining-associated lake sediments

Lakes formed because of coal mining are characterized by low pH and high concentrations of Fe(II) and sulfate. The anoxic sediment is often separated into an upper acidic zone (pH 3; zone I) with large amounts of reactive iron and a deeper slightly acidic zone (pH 5.5; zone III) with smaller amounts of iron. In this study, the impact of pH on the Fe(III)-reducing activities in both of these sediment zones was investigated, and molecular analyses that elucidated the sediment microbial diversity were performed. Fe(II) was formed in zone I and III sediment microcosms at rates that were approximately 710 and 895 nmol cm(-3) day(-1), respectively. A shift to pH 5.3 conditions increased Fe(II) formation in zone I by a factor of 2. A shift to pH 3 conditions inhibited Fe(II) formation in zone III. Clone libraries revealed that the majority of the clones from both zones (approximately 44%) belonged to the Acidobacteria phylum. Since Acidobacterium capsulatum reduced Fe oxides at pHs ranging from 2 to 5, Acidobacteria might be involved in the cycling of iron [corrected]. PCR products specific for species related to Acidiphilium revealed that there were higher numbers of phylotypes related to cultured Acidiphilium or Acidisphaera species in zone III than in zone I. From the PCR products obtained for bioleaching-associated bacteria, only one phylotype with a level of similarity to Acidithiobacillus ferrooxidans of 99% was obtained. Using primer sets specific for Geobacteraceae, PCR products were obtained in higher DNA dilutions from zone III than from zone I. Phylogenetic analysis of clone libraries obtained from Fe(III)-reducing enrichment cultures grown at pH 5.5 revealed that the majority of clones were closely related to members of the Betaproteobacteria, primarily species of Thiomonas. Our results demonstrated that the upper acidic sediment was inhabited by acidophiles or moderate acidophiles which can also reduce Fe(III) under slightly acidic conditions. The majority of Fe(III) reducers inhabiting the slightly acidic sediment had only minor capacities to be active under acidic conditions.

Deferrization of Kaolinic Sand by Iron Oxidizing and Iron Reducing Bacteria

Iron oxidizing bacteria Acidithiobacillus ferrooxidans, iron reducing bacteria Acidiphilium spp. and their mixture were applied for leaching of iron impurities from quartz sand. The bacterial leaching was carried out in order to decrease the amount of colouring iron oxides and to improve the technological properties of the raw material. Mineralogical analysis confirmed the presence of siderite, iron-bearing muscovite and various amorphous and crystalline forms of iron oxides occurring both free and coating siderite and quartz particles. Mössbauer spectroscopy revealed various oxidation and magnetic states of iron ions, with the prevalence of reduced ionic species. Highest extraction of iron was achieved with pure culture of iron-reducing bacteria with ferrous iron as dominant species in the leaching liquor. Surprisingly, iron oxidizing bacteria caused passivation of the surface of iron-bearing minerals, resulting in the depression of iron leaching in comparison with abiotic control. Ferric iron was major species in the leaching solution containing the mixed culture of iron-oxidizing and iron-reducing bacteria. The mixture was far less efficient in iron extraction than pure culture of iron-reducing bacteria.

Identification and characterization of a novel acidotolerant Fe(III)-reducing bacterium from a 3,000-year-old acidic rock drainage site

Acidic, ochre-precipitating springs at Mam Tor, East Midlands, UK, are analogous to sites impacted by acid mine drainage over prolonged periods of time, and were studied for the presence of Fe(III)-reducing bacteria. From enrichment cultures inoculated with Mam Tor sediment, a facultative anaerobe capable of reducing Fe(III) at pH values as low as three was isolated. 16S rRNA gene analysis showed that this bacterium is a close relative of Serratia species and not previously shown to respire using Fe(III) as an electron acceptor. Direct cell counts of the isolate grown with Fe(III)-NTA coupled with protein assays suggest that this bacterium is able to conserve energy for growth through Fe(III) reduction.

Reduction of Cr(VI) under acidic conditions by the facultative Fe(lll)-reducing bacterium Acidiphilium cryptum

The potential for biological reduction of Cr(VI) under acidic conditions was evaluated with the acidophilic, facultatively metal-reducing bacterium Acidiphilium cryptum strain JF-5 to explore the role of acidophilic microorganisms in the Cr cycle in low-pH environments. An anaerobic suspension of washed A. cryptum cells rapidly reduced 50 microM Cr(VI) at pH 3.2; biological reduction was detected from pH 1.7-4.7. The reduction product, confirmed by XANES analysis, was entirely Cr(III) that was associated predominantly with the cell biomass (70-80%) with the residual residing in the aqueous phase. Reduction of Cr(VI) showed a pH optimum similar to that for growth and was inhibited by 5 mM HgCl2, suggesting that the reaction was enzyme-mediated. Introduction of O2 into the reaction medium slowed the reduction rate only slightly, whereas soluble Fe(III) (as ferric sulfate) increased the rate dramatically, presumably by the shuttling of electrons from bioreduced Fe(II) to Cr(VI) in a coupled biotic-abiotic cycle. Starved cells could not reduce Cr(VI) when provided as sole electron acceptor, indicating that Cr(VI) reduction is not an energy-conserving process in A. cryptum. We speculate, rather, that Cr(VI) reduction is used here as a detoxification mechanism.

Towards determining details of anaerobic growth coupled to ferric iron reduction by the acidophilic archaeon 'Ferroplasma acidarmanus' Fer1

Elucidation of the different growth states of Ferroplasma species is crucial in understanding the cycling of iron in acid leaching sites. Therefore, a proteomic and biochemical study of anaerobic growth in 'Ferroplasma acidarmanus' Fer1 has been carried out. Anaerobic growth in Ferroplasma spp. occurred by coupling oxidation of organic carbon with the reduction of Fe(3+); but sulfate, nitrate, sulfite, thiosulfate, and arsenate were not utilized as electron acceptors. Rates of Fe(3+) reduction were similar to other acidophilic chemoorganotrophs. Analysis of the 'F. acidarmanus' Fer1 proteome by 2-dimensional polyacrylamide gel electrophoresis revealed ten key proteins linked with central metabolic pathways > or =4 fold up-regulated during anaerobic growth. These included proteins putatively identified as associated with the reductive tricarboxylic acid pathway used for anaerobic energy production, and others including a putative flavoprotein involved in electron transport. Inhibition of anaerobic growth and Fe(3+) reduction by inhibitors suggests the involvement of electron transport in Fe(3+)reduction. This study has increased the knowledge of anaerobic growth in this biotechnologically and environmentally important acidophilic archaeon.

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.

Microbiology of a wetland ecosystem constructed to remediate mine drainage from a heavy metal mine

A pilot passive treatment plant (PPTP) was constructed to evaluate the potential of a composite wetland system to remediate acidic, metal-rich water draining the former Wheal Jane tin, in Cornwall, England. The treatment plant consists of three separate and controllable composite systems, each of which comprises a series of aerobic wetlands for iron oxidation and precipitation, a compost bioreactor for removing chalcophilic metals and to generate alkalinity, and rock filter ponds for removing soluble manganese and organic carbon. To understand the roles of microorganisms in remediating acid mine drainage (AMD) in constructed wetland ecosystems, populations of different groups of cultivatable acidophilic microbes in the various components of the Wheal Jane PPTP were enumerated over a 30-month period. Initially, moderately acidophilic iron-oxidising bacteria (related to Halothiobacillus neapolitanus) were found to be the major cultivatable microorganisms present in the untreated AMD, though later heterotrophic acidophiles emerged as the dominant group, on a numerical basis. Culturable microbes in the surface waters and sediments of the aerobic wetlands were similarly dominated by heterotrophic acidophiles, though both moderately and extremely acidophilic iron-oxidising bacteria were also present in significant numbers. The dominant microbial isolate in waters draining the anaerobic compost bioreactors was an iron- and sulfur-oxidising moderate acidophile that was closely related to Thiomonas intermedia. The acidophiles enumerated at the Wheal Jane PPTP accounted for 1% to 25% of the total microbial population. Phylogenetic analysis of 14 isolates from various components of the Wheal Jane PPTP showed that, whilst many of these bacteria were commonly encountered acidophiles, some of these had not been previously encountered in AMD and AMD-impacted environments.

Dissimilatory Fe(III) and Mn(IV) reduction

Dissimilatory Fe(III) and Mn(IV) reduction has an important influence on the geochemistry of modern environments, and Fe(III)-reducing microorganisms, most notably those in the Geobacteraceae family, can play an important role in the bioremediation of subsurface environments contaminated with organic or metal contaminants. Microorganisms with the capacity to conserve energy from Fe(III) and Mn(IV) reduction are phylogenetically dispersed throughout the Bacteria and Archaea. The ability to oxidize hydrogen with the reduction of Fe(III) is a highly conserved characteristic of hyperthermophilic microorganisms and one Fe(III)-reducing Archaea grows at the highest temperature yet recorded for any organism. Fe(III)- and Mn(IV)-reducing microorganisms have the ability to oxidize a wide variety of organic compounds, often completely to carbon dioxide. Typical alternative electron acceptors for Fe(III) reducers include oxygen, nitrate, U(VI) and electrodes. Unlike other commonly considered electron acceptors, Fe(III) and Mn(IV) oxides, the most prevalent form of Fe(III) and Mn(IV) in most environments, are insoluble. Thus, Fe(III)- and Mn(IV)-reducing microorganisms face the dilemma of how to transfer electrons derived from central metabolism onto an insoluble, extracellular electron acceptor. Although microbiological and geochemical evidence suggests that Fe(III) reduction may have been the first form of microbial respiration, the capacity for Fe(III) reduction appears to have evolved several times as phylogenetically distinct Fe(III) reducers have different mechanisms for Fe(III) reduction. Geobacter species, which are representative of the family of Fe(III) reducers that predominate in a wide diversity of sedimentary environments, require direct contact with Fe(III) oxides in order to reduce them. In contrast, Shewanella and Geothrix species produce chelators that solubilize Fe(III) and release electron-shuttling compounds that transfer electrons from the cell surface to the surface of Fe(III) oxides not in direct contact with the cells. Electron transfer from the inner membrane to the outer membrane in Geobacter and Shewanella species appears to involve an electron transport chain of inner-membrane, periplasmic, and outer-membrane c-type cytochromes, but the cytochromes involved in these processes in the two organisms are different. In addition, Geobacter species specifically express flagella and pili during growth on Fe(III) and Mn(IV) oxides and are chemotactic to Fe(II) and Mn(II), which may lead Geobacter species to the oxides under anoxic conditions. The physiological characteristics of Geobacter species appear to explain why they have consistently been found to be the predominant Fe(III)- and Mn(IV)-reducing microorganisms in a variety of sedimentary environments. In comparison with other respiratory processes, the study of Fe(III) and Mn(IV) reduction is in its infancy, but genome-enabled approaches are rapidly advancing our understanding of this environmentally significant physiology.

Enumeration and characterization of iron(III)-reducing microbial communities from acidic subsurface sediments contaminated with uranium(VI)

Iron(III)-reducing bacteria have been demonstrated to rapidly catalyze the reduction and immobilization of uranium(VI) from contaminated subsurface sediments. Thus, these organisms may aid in the development of bioremediation strategies for uranium contamination, which is prevalent in acidic subsurface sediments at U.S. government facilities. Iron(III)-reducing enrichment cultures were initiated from pristine and contaminated (high in uranium, nitrate; low pH) subsurface sediments at pH 7 and pH 4 to 5. Enumeration of Fe(III)-reducing bacteria yielded cell counts of up to 240 cells ml(-1) for the contaminated and background sediments at both pHs with a range of different carbon sources (glycerol, acetate, lactate, and glucose). In enrichments where nitrate contamination was removed from the sediment by washing, MPN counts of Fe(III)-reducing bacteria increased substantially. Sediments of lower pH typically yielded lower counts of Fe(III)-reducing bacteria in lactate- and acetate-amended enrichments, but higher counts were observed when glucose was used as an electron donor in acidic enrichments. Phylogenetic analysis of 16S rRNA gene sequences extracted from the highest positive MPN dilutions revealed that the predominant members of Fe(III)-reducing consortia from background sediments were closely related to members of the Geobacteraceae family, whereas a recently characterized Fe(III) reducer (Anaeromyxobacter sp.) and organisms not previously shown to reduce Fe(III) (Paenibacillus and Brevibacillus spp.) predominated in the Fe(III)-reducing consortia of contaminated sediments. Analysis of enrichment cultures by terminal restriction fragment length polymorphism (T-RFLP) strongly supported the cloning and sequencing results. Dominant members of the Fe(III)-reducing consortia were observed to be stable over several enrichment culture transfers by T-RFLP in conjunction with measurements of Fe(III) reduction activity and carbon substrate utilization. Enrichment cultures from contaminated sites were also shown to rapidly reduce millimolar amounts of U(VI) in comparison to killed controls. With DNA extracted directly from subsurface sediments, quantitative analysis of 16S rRNA gene sequences with MPN-PCR indicated that Geobacteraceae sequences were more abundant in pristine compared to contaminated environments,whereas Anaeromyxobacter sequences were more abundant in contaminated sediments. Thus, results from a combination of cultivation-based and cultivation-independent approaches indicate that the abundance/community composition of Fe(III)-reducing consortia in subsurface sediments is dependent upon geochemical parameters (pH, nitrate concentration) and that microorganisms capable of producing spores (gram positive) or spore-like bodies (Anaeromyxobacter) were representative of acidic subsurface environments.

The microbiology of acidic mine waters

Acidic, metal-rich waters generated by the microbially accelerated dissolution of pyrite and other sulfide minerals, are frequently encountered in derelict mine sites, including many that have been long-abandoned. While these waters are major causes of environmental pollution and are toxic to the majority of prokaryotic and eukaryotic organisms, some life forms (mostly bacteria and archaea) thrive within them. "Acidophiles" comprise a surprisingly wide diversity (in terms of both physiology and phylogeny) of microorganisms. This article reviews current knowledge of the distribution and biodiversity of this group of extremophiles.