Acid Mine Drainage Environments Research Articles

Characterization of a pH-Tolerant Strain Cobetia sp. SASS1 and Its Phenol Degradation Performance Under Salinity Condition.

Biological treatment of complex saline phenolic wastewater remains a great challenge due to the low activity of bacterial populations under stressful conditions. Acid mine drainage (AMD) as a typically extreme environment, shaped unique AMD microbial communities. Microorganisms survived in the AMD environment have evolved various mechanisms of resistance to low pH, high salinity and toxic heavy metals. The primary goal of this work was to determine whether a strain isolated from an AMD could degrade phenol under stressful conditions such as low pH, high salinity and heavy metals. The results suggested that the strain Cobetia sp. SASS1 isolated from AMD presented different physiological characteristics in comparison with five most closely related species. SASS1 can efficiently degrade phenol at wide ranges of pH (3.0–9.0) and NaCl concentration (0–40 g/L), as well as the existence of Cu2+ and Mn2+. Specifically, the SASS1 could completely degrade 1500 mg/L phenol in 80 h at 10 g/L NaCl. Meanwhile, mineralization of phenol was achieved with complete degradation of 900 mg/L phenol and simultaneously COD decreasing from 2239 mg/L to 181.6 mg/L in 36 h. Based on biodegradation metabolites identification and enzyme activities analysis, both ortho-cleavage pathway and benzoic acid pathway for phenol degradation were proposed. These findings suggested that SASS1 was an efficient phenol degrader under salinity and acidic conditions, and could be considered as key population for bioremediation of industrial phenolic wastewaters under stressful conditions.

Solid and Aqueous Speciation of Yttrium in Passive Remediation Systems of Acid Mine Drainage.

Yttrium belongs to the rare earth elements (REEs) together with lanthanides and scandium. REEs are commonly used in modern technologies, and their limited supply has made it necessary to look for new alternative resources. Acid mine drainage (AMD) is a potential resource since it is moderately enriched in REEs. In fact, in passive remediation systems, which are implemented to minimize the environmental impacts of AMD, REEs are mainly retained in basaluminite, an aluminum hydroxysulfate precipitate. In this study, the solid and liquid speciation and the local structure of yttrium are studied in high-sulfate aqueous solutions, basaluminite standards, and samples from remediation columns using synchrotron-based techniques and molecular modeling. Pair distribution function (PDF) analyses and ab initio molecular dynamics density functional theory models of the yttrium sulfate solution show that the YSO4+ ion pair forms a monodentate inner-sphere complex. Extended X-ray absorption fine structure (EXAFS) and PDF analyses show that Y is retained by basaluminite, forming a monodentate inner-sphere surface complex on the aluminum hydroxide surface. EXAFS of the column samples shows that more than 72% of their signal is represented by the signal of basaluminite with which YSO4+ forms an inner-sphere complex. The atomic view of the REE configuration in AMD environments could facilitate a deeper research of REE recovery from waste generated in AMD remediation systems.

Microbial Communities of Polymetallic Deposits' Acidic Ecosystems of Continental Climatic Zone With High Temperature Contrasts.

Acid mine drainage (AMD) systems are globally widespread and are an important source of metal pollution in riverine and coastal systems. Microbial AMD communities have been extensively studied for their ability to thrive under extremely acidic conditions and for their immense contribution to the dissolution of metal ores. However, little is known on microbial inhabitants of AMD systems subjected to extremely contrasting continental seasonal temperature patterns as opposed to maritime climate zones, experiencing much weaker annual temperature variations. Here, we investigated three types of AMD sites in Eastern Transbaikalia (Russia). In this region, all surface water bodies undergo a deep and long (up to 6 months) freezing, with seasonal temperatures varying between −33 and +24°C, which starkly contrasts the common well-studied AMD environments. We sampled acidic pit lake (Sherlovaya Gora site) located in the area of a polymetallic deposit, acidic drainage water from Bugdaya gold-molybdenum-tungsten deposit and Ulan-Bulak natural acidic spring. These systems showed the abundance of bacteria-derived reads mostly affiliated with Actinobacteria, Acidobacteria, Alpha- and Gammaproteobacteria, chloroplasts, Chloroflexi, Bacteroidetes, and Firmicutes. Furthermore, candidate taxa “Ca. Saccharibacteria” (previously known as TM7), “Ca. Parcubacteria” (OD1) and WPS-2 were represented in substantial quantities (10–20%). Heterotrophy and iron redox cycling can be considered as central processes of carbon and energy flow for majority of detected bacterial taxa. Archaea were detected in low numbers, with Terrestrial Miscellaneous Euryarchaeal Group (TMEG), to be most abundant (3%) in acidic spring Ulan-Bulak. Composition of these communities was found to be typical in comparison to other AMD sites; however, certain groups (as Ignavibacteriae) could be specifically associated with this area. This study provides insight into the microbial diversity patterns in acidic ecosystems formed in areas of polymetallic deposits in extreme continental climate zone with contrasting temperature parameters.

Macroscopic and Microscopic Morphological Features of Stromatolites Related To Activity of Eukaryote-Dominated Biofilms in an Acid Mine Drainage Environment: Biosignatures and Understanding Preservation of Stromatolites as Trace Fossils

Euglena-, diatom-, and algae-dominated biofilms are the principal producers of iron-rich biolaminates that result in biosedimentary structures, or stromatolites, in an acid mine drainage (AMD) environment in Indiana. These structures are considered trace fossils because they are produced by organism-sediment interactions and record physicochemical conditions of the environment. Our purpose was to link the biofilm types to specific micro- and micromorphological features and the physicochemical conditions under which they were formed. Analyses revealed that Euglena-dominated biofilm produced thin, porous microlaminae by trapping, binding, and relocating AMD precipitates as the biofilm kept pace with chemical sedimentation. More massive microlaminae were produced by high rates of chemical sedimentation brought on by increased discharge and dilution of acidity. Diatom- and algae-dominated biofilms produced thick, mm–cm-scale, porous, spongelike micro- to macrolaminae through oxygenic photosynthesis and/or metal uptake in extracellular polymeric substances, which promoted mineral precipitation on cell walls to create a rigid, porous structure. The variations in biolaminate textures within the stromatolites record seasonal changes in the microbial populations and physicochemical conditions of the AMD environment. These iron-rich stromatolites represent trace fossils that record morphological biosignatures of eukaryote-dominated microbial biofilms and may serve as appropriate proxies in the search for similar evidence of eukaryotic life in other iron-rich paleoenvironments, such as those on early Earth and Mars.

Iron and sulfur oxidation pathways of Acidithiobacillus ferrooxidans.

Acidithiobacillus ferrooxidans is a gram-negative, autotrophic and rod-shaped bacterium. It can gain energy through the oxidation of Fe(II) and reduced inorganic sulfur compounds for bacterial growth when oxygen is sufficient. It can be used for bio-leaching and bio-oxidation and contributes to the geobiochemical circulation of metal elements and nutrients in acid mine drainage environments. The iron and sulfur oxidation pathways of A. ferrooxidans play key roles in bacterial growth and survival under extreme circumstances. Here, the electrons transported through the thermodynamically favourable pathway for the reduction to H2O (downhill pathway) and against the redox potential gradient reduce to NAD(P)(H) (uphill pathway) during the oxidation of Fe(II) were reviewed, mainly including the electron transport carrier, relevant operon and regulation of its expression. Similar to the electron transfer pathway, the sulfur oxidation pathway of A. ferrooxidans, related genes and operons, sulfur oxidation mechanism and sulfur oxidase system are systematically discussed.

Dissimilatory iron and sulfate reduction by native microbial communities using lactate and citrate as carbon sources and electron donors

The bacterial (dissimilatory) iron and sulfate reduction (BIR and BSR) are intimately linked to the biogeochemical cycling of C, Fe, and S in acid mine drainage (AMD) environments. This study examined the response of native microbial communities to the reduction of iron and sulfate in bench experimental systems. Results showed that the reduction of ferric iron and sulfate took place when the electron acceptors coexist. Existence of Fe(III) can postpone the reduction of sulfate, but can enhance the reduction rate. Cultures grown in the presence of 10 mM iron can reach the final level of sulfate bio-reduction rate (~100%) after 35 days incubation. 16 S rDNA -based microbial community analysis revealed that the three genera Anaeromusa, Acinetobacter and Bacteroides were dominated in the ferric-reducing conditions. SRB (Desulfobulbus, Desulfosporosinus and Desulfovibrio) were dominated in the sulfate reduction process. Results in this study highlighted the highly coupled nature of C, Fe, and S biogeochemical cycles in AMD and provided insights into the potential of environmental remediation by native microbial.

Thiocyanate-induced labilization of schwertmannite: Impacts and mechanisms

Schwertmannite is an amorphous iron(III)-oxyhydroxysulfate that forms in acid mine drainage (AMD) environments. The characteristic of high heavy metal adsorption capability makes schwertmannite a potentially useful, environmentally friendly material in wastewater treatment. Unstable schwertmannite is prone to recrystallization. Understanding the mechanisms that induce schwertmannite labilization and affect its capacity to remove heavy metals are of great environmental and geochemical significance. Thiocyanate (SCN¯) is a hazardous pseudohalide that is also normally found in AMD. However, little is known about the impact of Fe(III)-binding ligand SCN¯ on schwertmannite stability and its subsequent capacity to bind trace elements. Here, we investigated the adsorption of SCN¯ on schwertmannite and subsequent mineral transformation to characterize this little-known process. The appearance of Fe2+ indicated that the interactions between schwertmannite and SCN¯ may involve complexation and reduction reactions. Results showed that the majority of the adsorbed-SCN¯ was immobilized on schwertmannite during the 60-days transformation. The transformation rates of schwertmannite increased with increasing concentrations of SCN¯. Goethite was detected as the dominant transformation product with or without SCN¯. The mechanisms of SCN¯-promoted dissolution of schwertmannite can be described as follows: (1) formation of Fe(III)–NCS complexes on the schwertmannite surface and in solution, a process which increases the reactivity of solid phase Fe(III); (2) the extraction of Fe(III) from schwertmannite by SCN¯ and subsequent schwertmannite dissolution; and (3) the formation of secondary minerals from extracted Fe(III). These findings may improve AMD treatment strategies and provide insight into the use and potential reuse of schwertmannite as a trace element sorbent.

Transformation of cadmium-associated schwertmannite and subsequent element repartitioning behaviors.

Schwertmannite is an important sink for cadmium (Cd) in acid mine drainage (AMD) environments and is unstable when environmental conditions change. However, the release and redistribution of Cd during schwertmannite transformation with respect to pre-bound Cd are poorly understood. In this work, the transformation of cadmium-associated schwertmannite and subsequent Cd repartitioning behaviors were investigated. The way of schwertmannite associated with Cd was predominant by absorption, and the diffuse layer model (DLM) showed that Cd2+ existed as monodentate complexes ≡Fe(1)OCd+ and ≡Fe(2)OCd+ on schwertmannite surfaces. Kinetics of SO42- release and mineralogical characterization both showed that the mineral transformation rates decreased and more lepidocrocite aggregated with increasing adsorbed Cd levels. The shrinking core model revealed that Fe(II)-induced process would affect mineral dissolution by changing surface reaction-controlled step to internal diffusion-controlled step, and significantly promote the dissolution rate of Cd-adsorbed schwertmannite. Adsorbed Cd blocked the surface sites for later Fe(II) adsorption and the Fe(II)-Fe(III) electron transfer, then resulted in the decelerated transformation and the accumulation of intermediate phase lepidocrocite. The maximum release of aqueous Cd occurred after 1mM Fe2+ addition, then over 69% of initial added Cd(aq) re-bound to solid-phase accompanying with mineral transformation, and finally, Cd was mainly associated with the secondary minerals by complexation with surficial OH groups. These findings are useful for developing the strategies for treating Cd contamination in AMD affected areas.

Schwertmannite transformation via direct or indirect electron transfer by a sulfate reducing enrichment culture

Understanding the mechanism of the microbial transformation of Fe(III)-oxyhydroxysulfate minerals is of considerable interest, because this transformation plays an important role in controlling the behaviour of toxic metals from acid mine drainage (AMD). In this study, we examined a sulfate reducing enrichment culture from AMD-contaminated sediments and predicted the possible pathway of electron transfer when incubated with schwertmannite, a common Fe(III)-oxyhydroxysulfate occurring in the AMD environment. Experiments were designed to distinguish the mechanisms by which bacteria facilitate direct (i.e., bacteria allowed to adhere to the mineral) or indirect (i.e., bacteria separated from the mineral by dialysis bag) electron transfer to reduce the mineral. The effects of adding anthraquinone-2,6-disulfonate (AQDS) as an exogenous electron shuttle were also investigated. Vivianite was detected as the main product of schwertmannite transformation. Reduction of sulfate and iron were more pronounced in direct treatments, while more non-reductive dissolution were observed in indirect treatments. The addition of AQDS lead to the production of more dissolved Fe2+ over 20 d than in the absence of AQDS. Microbial community composition differed in direct and indirect treatments, while the addition of AQDS did not significantly affect the community structure in each treatment. After incubation for 20 d, the growth of Desulfovibrio exceeded that of the originally dominant Citrobacter in direct treatments, while an unknown genus most closely related to Citrobacter within Enterobacteriaceae was predominant in indirect treatments. This monodominant community in indirect treatments was assumed not to transfer electron directly to schwertmannite but to rely on shuttling mechanism. PICRUSt results implied that bacteria in indirect treatment have potential to produce shuttling compounds or complexing agents. The absence of dsr genes and the putative fermentative process suggested that the Enterobacteriaceae might indirectly facilitate the dissolution and transformation of schwertmannite.

Natural occurrence of nanocrystalline Al-hydroxysulfates: Insights on formation, Al solubility control and As retention

Nanocrystalline basaluminite [Al4OH10(SO4)·(H2O)3–5] and aggregation of the ε-Keggin polyoxocation [Al12(AlO4)(OH)24(H2O)12]7+, referred to as Al13, have both been described to form in acid mine drainage environments. Although the chemical composition is quite similar, their crystalline varieties significantly differ, demonstrating that various types of Al-hydroxysulfates can form under similar conditions and that their respective formation is not fully understood yet. Here, we report the occurrence of nanocrystalline precipitates that form naturally in a small alpine catchment in Switzerland where an acidic mountainous stream (pH ∼ 4) is neutralized successively after mixing with several neutral tributaries. The stepwise neutralization in conjunction with the large amount of precipitates provide an ideal setting for obtaining new insights into (i) the structure of naturally forming Al-hydroxysulfates, (ii) their formation mechanism, (iii) their role in controlling the solubility of Al, and (iv) their ability to lower the mobility of As. Synchrotron-based high-energy X-ray diffraction and subsequent pair distribution function analyses demonstrate that these precipitates are structurally identical to basaluminite samples obtained from acid mine drainage sites. In contrast, only minor amounts of tetrahedrally coordinated Al, as present in Al13, were identified by nuclear magnetic resonance spectroscopy. The precipitates are further characterized by elevated As concentrations up to 600 μg/g, whereas other heavy metals are at background concentrations only. Given the low As concentrations in the stream from which precipitation occurs (<0.03 mg/L), high As concentrations confirm that basaluminite serves as a highly efficient As sink, which is attributed to its high anion-exchange capacity. Chemical analysis of streamwater samples in combination with geochemical modeling show that precipitation occurs instantaneously upon mixing with neutral streams. Moreover, our data reveal that the precipitation of basaluminite exerts a strong solubility control on dissolved Al concentrations as manifested by the quasi-constant basaluminite ion activity product observed during neutralization from pH 5 to pH 5.9. We hypothesize that in our field system, high fluoride and sulfate concentrations on the order of 100 and 1–2 mg/L, respectively, as well as low water temperatures (<8 °C) favor the formation of basaluminite instead of Al13-bearing sulfate precipitates.

Mineralogical controls on mobility of rare earth elements in acid mine drainage environments

Rare earth elements (REE) were analyzed in river waters, acid mine waters, and extracts of secondary precipitates collected in the Iberian Pyrite Belt. The obtained concentrations of the REE in river water and mine waters (acid mine drainage - AMD) were in the range of 0.57 μg/L (Lu) and 2579 μg/L (Ce), which is higher than previously reported in surface waters from the Iberian Pyrite Belt, but are comparable with previous findings from AMD worldwide. Total REE concentrations in river waters were ranged between 297 μg/L (Cobica River) and 7032 μg/L (Trimpancho River) with an average of 2468 μg/L. NASC (North American Shale Composite) normalized REE patterns for river and acid mine waters show clear convex curvatures in middle−REE (MREE) with respect to light- and heavy−REE.During the dissolution experiments of AMD-precipitates, heavy−REE and middle−REE generate the most enriched patterns in the solution. A small number of precipitates did not display MREE enrichment (an index Gdn/Lun < 1.0) in NASC normalized pattern and produced relatively lower REE concentrations in extracts. Additionally, very few samples, which mainly contained aluminum sulfates, e.g., pickeringite and alunogen, displayed light−REE enrichment relative to heavy−REE (HREE). In general, the highest retention of REE occurs in samples enriched in magnesium (epsomite or hexahydrite) and aluminum sulfates, mainly pickeringite.

Examination of effects of acid and metals on benthic algae in streams using chemical diffusing substrata

Acid mine drainage environments have multiple stressors, making it difficult to isolate effects of individual contaminants on benthic algal communities in situ in order to develop more specific indicators. Additionally, responses to AMD contaminants may be dependent on the abiotic and biotic conditions within the affected stream. We examined the efficacy of using chemical diffusing substrata (CDS) to determine how acid and metals interact to affect benthic algae in 2 streams with different trophy. CDS containing Mn, Fe, Al, acid, Mn + acid, Fe + acid, and Al + acid were deployed in a flow-through system to determine flux from the liquid media. Flux values for metals ranged from 1.0 to 18.1 µg/cm2/d for 5 days, and 0.5–7.4 µg/cm2/d for 21 days. Flux values for H+ were 467 (5 day) and 212 (21 day) µg/cm2/d. Corresponding water column concentrations that would produce the same flux as CDS metal treatments were estimated to be in the low to mid toxicity range for Al, low range for Fe, and nontoxic range for Mn. Acid treatments were estimated to be equivalent to a stream pH of 2.1–2.5. Five replicates of each CDS treatment, and a water control, were placed into a high-alkalinity, eutrophic stream (Wolf Creek) for 5 days and a low-alkalinity, oligotrophic stream (Silver Creek) for 21 days, respectively. In Silver Creek, all treatments except circumneutral Fe and circumneutral Mn had significantly lower algal cell densities than control treatments. Cell densities were significantly lower on Al + acid and Mn + acid than on the acid-only treatment, indicating synergistic effects. Cell densities were not significantly different among treatments in Wolf Creek. Higher alkalinity, nutrients, and productivity in this stream likely increased neutralization and detoxification processes within the biofilm. However, significantly lower chlorophyll a and higher phaeophytin concentrations of communities on treatments containing acid indicated sublethal effects. Significantly more acid tolerant taxa occurred on treatments with acid in Silver Creek, and significantly more metal-tolerant taxa occurred on metal treatments in Wolf Creek. However, treatment effects on taxonomic composition appeared to be constrained by the species pool within each stream, as these indicator taxa made up less than 4% of any community. Although equating CDS flux of contaminants to water column concentrations requires assumptions, and flux decreases over the exposure period, this study indicates that in situ experiments using CDS can separate out effects of individual toxic components on benthic algae, and determine context-dependent responses.

Evaluation of quenching and extraction procedures for performing metabolomics in Acidithiobacillus ferrooxidans

Acidithiobacillus ferrooxidans has a central role in the microbial community metabolism that drives production of acid mine drainage (AMD), a major environmental concern. Metabolomic profiling can offer insight into how At. ferrooxidans contributes to these processes. The unique biology of some organisms means that protocols for metabolomic profiling need to be species-specific. Current protocols have largely been optimized for neutrophilic model organisms and, presently, no protocol exists for studying acidophilic extremophiles such as At. ferrooxidans. An appropriate protocol was developed and applied to investigate At. ferrooxidans’ metabolomic capabilities in relation to the colonization of AMD sites. We quantified the overall effectiveness of three quenching solutions in combination with three extraction solutions, quantifying the amount of metabolite leakage, number of metabolites extracted and degradation of C13 labeled standards. We then used this method to quantify how the At. ferrooxidans metabolome differed between early and late stages in the logarithmic growth phase to investigate infer how the metabolism of the organism changes as it colonizes the AMD environment. An acidic methanol:water based quenching solution with ammonium formate salt used in conjunction with an isopropanol:methanol:water extraction solution produced the smallest amount of leakage, extracted the largest number of metabolites, and was most effective in recovering known standards. When this protocol was applied to the metabolomic fingerprinting of At. ferrooxidans in the beginning and end of its logarithmic growth phase, there was a clear separation in the metabolome at each growth point. Overall, 3% of the metabolome differed significantly.

Schwertmannite stability in anoxic Fe(II)-rich aqueous solution

Schwertmannite (SHM) is a powerful scavenger for As(III) leading to As(III)-enriched precipitates around acid mine drainage environments that may become exposed to aqueous Fe(II). In this study we have investigated the stability of pure SHM and SHM containing 0.92wt% As(III) under Fe(II)aq-rich (0.4–1.0mM) anoxic conditions using XRD, SEM, Mössbauer and FTIR spectroscopic techniques. Schwertmannite transformation proceeded through an alkalinity-driven pathway releasing sulfate and a Fe(II)-catalyzed pathway that generated lepidocrocite and goethite at pH 6 and 6.9 in the presence of 1mM Fe(II)aq. Lepidocrocite was found to be needle shaped if the SHM contained As(III) and platy for pure SHM. Goethite had a poor degree of crystallinity in As(III) containing SHM. Pre-adsorption of As(III) inhibited the extent of SHM transformation. Fe(II) sorption onto SHM was pH dependent and reflected a sorption edge with complete consumption at pH 6.9, while only ∼20% were adsorbed at pH 5. Surface coverage with Fe(II) appears to be the key parameter controlling extent and products of the transformation process. As(III) concentrations in solution are controlled by two mechanisms: (1) exchange of As(III) for sulfate upon alkalinity-driven transformation of schwertmannite and (2) re-adsorption to new phases formed upon Fe(II)-catalyzed transformation. The adsorbed As(III) has inhibited the extent of transformation and was partly released with the maximum release at pH 5 (0.5%) in the absence of Fe(II)aq.

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.

Unexpected Dominance of Elusive Acidobacteria in Early Industrial Soft Coal Slags.

Acid mine drainage (AMD) and mine tailing environments are well-characterized ecosystems known to be dominated by organisms involved in iron- and sulfur-cycling. Here we examined the microbiology of industrial soft coal slags that originate from alum leaching, an ecosystem distantly related to AMD environments. Our study involved geochemical analyses, bacterial community profiling, and shotgun metagenomics. The slags still contained high amounts of alum constituents (aluminum, sulfur), which mediated direct and indirect effects on bacterial community structure. Bacterial groups typically found in AMD systems and mine tailings were not present. Instead, the soft coal slags were dominated by uncharacterized groups of Acidobacteria (DA052 [subdivision 2], KF-JG30-18 [subdivision 13]), Actinobacteria (TM214), Alphaproteobacteria (DA111), and Chloroflexi (JG37-AG-4), which have previously been detected primarily in peatlands and uranium waste piles. Shotgun metagenomics allowed us to reconstruct 13 high-quality Acidobacteria draft genomes, of which two genomes could be directly linked to dominating groups (DA052, KF-JG30-18) by recovered 16S rRNA gene sequences. Comparative genomics revealed broad carbon utilization capabilities for these two groups of elusive Acidobacteria, including polysaccharide breakdown (cellulose, xylan) and the competence to metabolize C1 compounds (ribulose monophosphate pathway) and lignin derivatives (dye-decolorizing peroxidases). Equipped with a broad range of efflux systems for metal cations and xenobiotics, DA052 and KF-JG30-18 may have a competitive advantage over other bacterial groups in this unique habitat.

Genomic and transcriptomic analyses reveal adaptation mechanisms of an Acidithiobacillus ferrivorans strain YL15 to alpine acid mine drainage.

Acidithiobacillus ferrivorans is an acidophile that often occurs in low temperature acid mine drainage, e.g., that located at high altitude. Being able to inhabit the extreme environment, the bacterium must possess strategies to copy with the survival stress. Nonetheless, information on the strategies is in demand. Here, genomic and transcriptomic assays were performed to illuminate the adaptation mechanisms of an A. ferrivorans strain YL15, to the alpine acid mine drainage environment in Yulong copper mine in southwest China. Genomic analysis revealed that strain has a gene repertoire for metal-resistance, e.g., genes coding for the mer operon and a variety of transporters/efflux proteins, and for low pH adaptation, such as genes for hopanoid-synthesis and the sodium:proton antiporter. Genes for various DNA repair enzymes and synthesis of UV-absorbing mycosporine-like amino acids precursor indicated hypothetical UV radiation—resistance mechanisms in strain YL15. In addition, it has two types of the acquired immune system–type III-B and type I-F CRISPR/Cas modules against invasion of foreign genetic elements. RNA-seq based analysis uncovered that strain YL15 uses a set of mechanisms to adapt to low temperature. Genes involved in protein synthesis, transmembrane transport, energy metabolism and chemotaxis showed increased levels of RNA transcripts. Furthermore, a bacterioferritin Dps gene had higher RNA transcript counts at 6°C, possibly implicated in protecting DNA against oxidative stress at low temperature. The study represents the first to comprehensively unveil the adaptation mechanisms of an acidophilic bacterium to the acid mine drainage in alpine regions.

A novel uncultured bacterium of the family Gallionellaceae: Description and genome reconstruction based on metagenomic analysis of microbial community in acid mine drainage

Drainage waters at the metal mining areas often have low pH and high content of dissolved metals due to oxidation of sulfide minerals. Extreme conditions limit microbial diversity in- such ecosystems. A drainage water microbial community (6.5'C, pH 2.65) in an open pit at the Sherlovaya Gora polymetallic open-cast mine (Transbaikal region, Eastern Siberia, Russia) was studied using metagenomic techniques. Metagenome sequencing provided information for taxonomic and functional characterization of the micro- bial community. The majority of microorganisms belonged to a single uncultured lineage representing a new Betaproteobacteria species of the genus Gallionella. While no.acidophiles are known among the cultured members of the family Gallionellaceae, similar 16S rRNA gene sequences were detected in acid mine drain- ages. Bacteria ofthe genera Thiobacillus, Acidobacterium, Acidisphaera, and Acidithiobacillus,-which are com- mon in acid mine drainage environments, were the minor components of the community. Metagenomic data were -used to determine the almost complete (-3.4 Mb) composite genome of the new bacterial. lineage desig- nated Candidatus Gallionella acididurans ShG14-8. Genome analysis revealed that Fe(II) oxidation probably involved the cytochromes localized on the outer membrane of the cell. The electron transport chain included NADH dehydrogenase, a cytochrome bc1 complex, an alternative complex III, and cytochrome oxidases of the bd, cbb3, and bo3 types. Oxidation of reduced sulfur compounds probably involved the Sox system, sul- fide-quinone oxidoreductase, adenyl sulfate reductase, and sulfate adenyltransferase. The genes required for autotrophic carbon assimilation via the Calvin cycle were present, while no pathway for nitrogen fixation was revealed. High numbers of RND metal transporters and P type ATPases were probably responsible for resis- tance to heavy metals. The new microorganism was an aerobic chemolithoautotroph of the group of psychrotolerant iron- and sulfur-oxidizing acidophiles of the family Gallionellaceae, which are common in acid mine drainages.

Temporal evolution of bacterial communities associated with the in situ wetland-based remediation of a marine shore porphyry copper tailings deposit

Mine tailings are a serious threat to the environment and public health. Remediation of these residues can be carried out effectively by the activation of specific microbial processes. This article presents detailed information about temporal changes in bacterial community composition during the remediation of a section of porphyry copper tailings deposited on the Bahía de Ite shoreline (Peru). An experimental remediation cell was flooded and transformed into a wetland in order to prevent oxidation processes, immobilizing metals. Initially, the top oxidation zone of the tailings deposit displayed a low pH (3.1) and high concentrations of metals, sulfate, and chloride, in a sandy grain size geological matrix. This habitat was dominated by sulfur- and iron-oxidizing bacteria, such as Leptospirillum spp., Acidithiobacillus spp., and Sulfobacillus spp., in a microbial community which structure resembled acid mine drainage environments. After wetland implementation, the cell was water-saturated, the acidity was consumed and metals dropped to a fraction of their initial respective concentrations. Bacterial communities analyzed by massive sequencing showed time-dependent changes both in composition and cell numbers. The final remediation stage was characterized by the highest bacterial diversity and evenness. Aside from classical sulfate reducers from the phyla δ-Proteobacteria and Firmicutes, community structure comprised taxa derived from very diverse habitats. The community was also characterized by an elevated proportion of rare phyla and unaffiliated sequences. Numerical ecology analysis confirmed that the temporal population evolution was driven by pH, redox, and K. Results of this study demonstrated the usefulness of a detailed follow-up of the remediation process, not only for the elucidation of the communities gradually switching from autotrophic, oxidizing to heterotrophic and reducing living conditions, but also for the long term management of the remediation wetlands.

Schwertmannite in soil materials: Limits of detection of acidified ammonium oxalate method and differential X-ray diffraction

Schwertmannite is a secondary iron mineral, found in acid mine drainage (AMD) and acid sulfate soils (ASS), that generates acidity when it transforms to stable mineral phases. Acidity liberated during schwertmannite transformation can seriously diminish water quality and soil health. Acidified ammonium oxalate (AAO) extraction in the dark coupled with differential X-ray diffraction (DXRD) analysis is routinely used to identify and to quantify poorly crystalline iron oxide phases such as schwertmannite in AMD environments. However, management of ASS environments is largely impacted due to lack of reliable methods to identify/quantify schwertmannite in soil materials. Our study aimed to evaluate the 15min AAO extraction method to identify/quantify schwertmannite in soil materials. We extracted soil samples spiked with synthetic and natural schwertmannite (termed as natural organic rich schwertmannitic material) with acidified ammonium oxalate (AAO) for 15min. We also examined soil samples spiked with schwertmannite through the DXRD analysis under ideal conditions assuming that only schwertmannite would dissolve during the extraction. Our data show that synthetic schwertmannite dissolved partially during the 15min AAO extraction and as a result the recovered Fe content from schwertmannite-spiked soils was underestimated by ~20%. The data also show that soil materials could also influence the recovery of schwertmannite. Fe/S molar ratios of schwertmannite spiked at higher rates (2% and 5%) were closer to the expected ratios. In addition to schwertmannite, goethite and other unidentified minerals in natural organic rich schwertmannitic material also dissolved during the 15min extraction time. The DXRD analysis data show that schwertmannite in soil materials at contents >5% may be identifiable through this approach. Our findings highlight that both the 15min AAO extraction procedure and the DXRD analysis have limited applicability towards detecting schwertmannite accurately in soil materials.