Molecular characterization of copper and cadmium resistance determinants in the biomining thermoacidophilic archaeon Sulfolobus metallicus

Potential applications of extremophilic bacteria in the bioremediation of extreme environments contaminated with heavy metals

Protecting the environment from harmful pollutants has become increasingly difficult in recent decades. The presence of heavy metal (HM) pollution poses a serious environmental hazard that requires intricate attention on a worldwide scale. Even at low concentrations, HMs have the potential to induce deleterious health effects in both humans and other living organisms. Therefore, various strategies have been proposed to address this issue, with extremophiles being a promising solution. Bacteria that exhibit resistance to metals are preferred for applications involving metal removal due to their capacity for rapid multiplication and growth. Extremophiles are a special group of microorganisms that are capable of surviving under extreme conditions such as extreme temperatures, pH levels, and high salt concentrations where other organisms cannot. Due to their unique enzymes and adaptive capabilities, extremophiles are well suited as catalysts for environmental biotechnology applications, including the bioremediation of HMs through various strategies. The mechanisms of resistance to HMs by extremophilic bacteria encompass: (i) metal exclusion by permeability barrier; (ii) extracellular metal sequestration by protein/chelator binding; (iii) intracellular sequestration of the metal by protein/chelator binding; (iv) enzymatic detoxification of a metal to a less toxic form; (v) active transport of HMs; (vi) passive tolerance; (vii) reduced metal sensitivity of cellular targets to metal ions; and (viii) morphological change of cells. This review provides comprehensive information on extremophilic bacteria and their potential roles for bioremediation, particularly in environments contaminated with HMs, which pose a threat due to their stability and persistence. Genetic engineering of extremophilic bacteria in stressed environments could help in the bioremediation of contaminated sites. Due to their unique characteristics, these organisms and their enzymes are expected to bridge the gap between biological and chemical industrial processes. However, the structure and biochemical properties of extremophilic bacteria, along with any possible long-term effects of their applications, need to be investigated further.

Hyperthermophile diversity microbes in the Calientes geothermal field, Tacna, Peru

Hyperthermophile microorganisms have been discovered worldwide, and several studies regarding biodiversity and the potential biotechnological applications have been reported. In this work, we describe for the first time the diversity of hyperthermophile communities in the Calientes Geothermal Field (CGF) located 4400 m above sea level in Tacna Region, Perú. Three hot springs were monitored and showed a temperature around 84 to 88 °C, for the microbiome analyzed was taken by sampling of sediment and water (pH 7.3-7.6). The hyperthermophile diversity was determined by PCR, DGGE, and DNA sequencing. The sediments analyzed showed a greater diversity than water samples. Sediments showed a more abundant population of bacteria than archaea, with the presence of at least 9 and 5 phylotypes, respectively. Most interestingly, in some taxa of bacteria (Bacillus) and archaea (Haloarcula and Halalkalicoccus), any of operational taxonomic units (OTUs) have not been observed before in hyperthermophile environments. Our results provide insight in the hyperthermophile diversity and reveal the possibility to develop new biotechnological applications based on the kind of environments.

Sessile Lifestyle Offers Protection against Copper Stress in Saccharolobus solfataricus

Some archaea from the genus Sulfolobus are important for bioleaching of copper, where metal resistant microorganisms are required. Biofilm generation is one of the ways microorganisms cope with some stimuli in nature, including heavy metals. The response to external factors, particularly in the biofilm form of life, is still underexplored in archaea. To explore how model thermoacidophilic archaeon Saccharolobus solfataricus faces copper stress during this lifestyle, changes in biofilms were studied using crystal violet staining, confocal fluorescence microscopy, and qPCR approaches. It was found that biofilm formation reached a maximum at 0.5 mM Cu, before starting to decrease at higher metal concentrations. The morphology of biofilms at 0.5 mM Cu was observed to be different, displaying lower thickness, different sugar patterns, and higher amounts of cells compared to standard growing conditions. Furthermore, copA, which is responsive to intracellular Cu concentration, was downregulated in biofilm cells when compared with planktonic cells exposed to the same metal concentration. The latest results suggests that cells in biofilms are less exposed to Cu than those in planktonic culture. In a PolyP-deficient strain, Cu was not able to induce biofilm formation at 0.5 mM. In summary, the findings reported here suggest that the biofilm form of life confers S. solfataricus advantages to face stress caused by Cu.Biofilm formation remains a relatively unexplored topic in archaeal research. Therefore, this knowledge in model organisms such as S. solfataricus, and how they use it to face stress, could be of great importance to engineer organisms with improved capabilities to be applied in biotechnological processes, such as bioleaching of metals.

A Large-Scale Multiple Genome Comparison of Acidophilic Archaea (pH ≤ 5.0) Extends Our Understanding of Oxidative Stress Responses in Polyextreme Environments

Acidophilic archaea thrive in anaerobic and aerobic low pH environments (pH < 5) rich in dissolved heavy metals that exacerbate stress caused by the production of reactive oxygen species (ROS) such as hydrogen peroxide (H2O2), hydroxyl radical (OH) and superoxide (O2−). ROS react with lipids, proteins and nucleic acids causing oxidative stress and damage that can lead to cell death. Herein, genes and mechanisms potentially involved in ROS mitigation are predicted in over 200 genomes of acidophilic archaea with sequenced genomes. These organisms are often be subjected to simultaneous multiple stresses such as high temperature, high salinity, low pH and high heavy metal loads. Some of the topics addressed include: (1) the phylogenomic distribution of these genes and what this can tell us about the evolution of these mechanisms in acidophilic archaea; (2) key differences in genes and mechanisms used by acidophilic versus non-acidophilic archaea and between acidophilic archaea and acidophilic bacteria and (3) how comparative genomic analysis predicts novel genes or pathways involved in oxidative stress responses in archaea and likely horizontal gene transfer (HGT) events.

Structure and function of aerotolerant, multiple-turnover THI4 thiazole synthases

Plant and fungal THI4 thiazole synthases produce the thiamin thiazole moiety in aerobic conditions via a single-turnover suicide reaction that uses an active-site Cys residue as sulfur donor. Multiple-turnover (i.e. catalytic) THI4s lacking an active-site Cys (non-Cys THI4s) that use sulfide as sulfur donor have been biochemically characterized —– but only from archaeal methanogens that are anaerobic, O₂-sensitive hyperthermophiles from sulfide-rich habitats. These THI4s prefer iron as cofactor. A survey of prokaryote genomes uncovered non-Cys THI4s in aerobic mesophiles from sulfide-poor habitats, suggesting that multiple-turnover THI4 operation is possible in aerobic, mild, low-sulfide conditions. This was confirmed by testing 23 representative non-Cys THI4s for complementation of an Escherichia coli ΔthiG thiazole auxotroph in aerobic conditions. Sixteen were clearly active, and more so when intracellular sulfide level was raised by supplying Cys, demonstrating catalytic function in the presence of O₂ at mild temperatures and indicating use of sulfide or a sulfide metabolite as sulfur donor. Comparative genomic evidence linked non-Cys THI4s with proteins from families that bind, transport, or metabolize cobalt or other heavy metals. The crystal structure of the aerotolerant bacterial Thermovibrio ammonificans THI4 was determined to probe the molecular basis of aerotolerance. The structure suggested no large deviations compared with the structures of THI4s from O₂-sensitive methanogens, but is consistent with an alternative catalytic metal. Together with complementation data, use of cobalt rather than iron was supported. We conclude that catalytic THI4s can indeed operate aerobically and that the metal cofactor inserted is a likely natural determinant of aerotolerance.

The biology of thermoacidophilic archaea from the order Sulfolobales

Thermoacidophilic archaea belonging to the order Sulfolobales thrive in extreme biotopes, such as sulfuric hot springs and ore deposits. These microorganisms have been model systems for understanding life in extreme environments, as well as for probing the evolution of both molecular genetic processes and central metabolic pathways. Thermoacidophiles, such as the Sulfolobales, use typical microbial responses to persist in hot acid (e.g. motility, stress response, biofilm formation), albeit with some unusual twists. They also exhibit unique physiological features, including iron and sulfur chemolithoautotrophy, that differentiate them from much of the microbial world. Although first discovered >50 years ago, it was not until recently that genome sequence data and facile genetic tools have been developed for species in the Sulfolobales. These advances have not only opened up ways to further probe novel features of these microbes but also paved the way for their potential biotechnological applications. Discussed here are the nuances of the thermoacidophilic lifestyle of the Sulfolobales, including their evolutionary placement, cell biology, survival strategies, genetic tools, metabolic processes and physiological attributes together with how these characteristics make thermoacidophiles ideal platforms for specialized industrial processes.

Insights on Cadmium Removal by Bioremediation: The Case of Haloarchaea

Although heavy metals are naturally found in the environment as components of the earth’s crust, environmental pollution by these toxic elements has increased since the industrial revolution. Some of them can be considered essential, since they play regulatory roles in different biological processes; but the role of other heavy metals in living tissues is not clear, and once ingested they can accumulate in the organism for long periods of time causing adverse health effects. To mitigate this problem, different methods have been used to remove heavy metals from water and soil, such as chelation-based processes. However, techniques like bioremediation are leaving these conventional methodologies in the background for being more effective and eco-friendlier. Recently, different research lines have been promoted, in which several organisms have been used for bioremediation approaches. Within this context, the extremophilic microorganisms represent one of the best tools for the treatment of contaminated sites due to the biochemical and molecular properties they show. Furthermore, since it is estimated that 5% of industrial effluents are saline and hypersaline, halophilic microorganisms have been suggested as good candidates for bioremediation and treatment of this kind of samples. These microorganisms, and specifically the haloarchaea group, are of interest to design strategies aiming the removal of polluting compounds due to the efficiency of their metabolism under extreme conditions and their significant tolerance to highly toxic compounds such as heavy metals, bromate, nitrite, chlorate, or perchlorate ions. However, there are still few trials that have proven the bioremediation of environments contaminated with heavy metals using these microorganisms. This review analyses scientific literature focused on metabolic capabilities of haloarchaea that may allow these microbes to tolerate and eliminate heavy metals from the media, paying special attention to cadmium. Thus, this work will shed light on potential uses of haloarchaea in bioremediation of soils and waters negatively affected by heavy metals, and more specifically by cadmium.

The Role of Polyphosphate in Motility, Adhesion, and Biofilm Formation in Sulfolobales

Polyphosphates (polyP) are polymers of orthophosphate residues linked by high-energy phosphoanhydride bonds that are important in all domains of life and function in many different processes, including biofilm development. To study the effect of polyP in archaeal biofilm formation, our previously described Sa. solfataricus polyP (−) strain and a new polyP (−) S. acidocaldarius strain generated in this report were used. These two strains lack the polymer due to the overexpression of their respective exopolyphosphatase gene (ppx). Both strains showed a reduction in biofilm formation, decreased motility on semi-solid plates and a diminished adherence to glass surfaces as seen by DAPI (4′,6-diamidino-2-phenylindole) staining using fluorescence microscopy. Even though arlB (encoding the archaellum subunit) was highly upregulated in S. acidocardarius polyP (−), no archaellated cells were observed. These results suggest that polyP might be involved in the regulation of the expression of archaellum components and their assembly, possibly by affecting energy availability, phosphorylation or other phenomena. This is the first evidence indicating polyP affects biofilm formation and other related processes in archaea.

CopR, a Global Regulator of Transcription to Maintain Copper Homeostasis in Pyrococcus furiosus

Although copper is in many cases an essential micronutrient for cellular life, higher concentrations are toxic. Therefore, all living cells have developed strategies to maintain copper homeostasis. In this manuscript, we have analyzed the transcriptome-wide response of Pyrococcus furiosus to increased copper concentrations and described the essential role of the putative copper-sensing metalloregulator CopR in the detoxification process. To this end, we employed biochemical and biophysical methods to characterize the role of CopR. Additionally, a copR knockout strain revealed an amplified sensitivity in comparison to the parental strain towards increased copper levels, which designates an essential role of CopR for copper homeostasis. To learn more about the CopR-regulated gene network, we performed differential gene expression and ChIP-seq analysis under normal and 20 μM copper-shock conditions. By integrating the transcriptome and genome-wide binding data, we found that CopR binds to the upstream regions of many copper-induced genes. Negative-stain transmission electron microscopy and 2D class averaging revealed an octameric assembly formed from a tetramer of dimers for CopR, similar to published crystal structures from the Lrp family. In conclusion, we propose a model for CopR-regulated transcription and highlight the regulatory network that enables Pyrococcus to respond to increased copper concentrations.

Unlocking Survival Mechanisms for Metal and Oxidative Stress in the Extremely Acidophilic, Halotolerant Acidihalobacter Genus

Microorganisms used for the biohydrometallurgical extraction of metals from minerals must be able to survive high levels of metal and oxidative stress found in bioleaching environments. The Acidihalobacter genus consists of four species of halotolerant, iron–sulfur-oxidizing acidophiles that are unique in their ability to tolerate chloride and acid stress while simultaneously bioleaching minerals. This paper uses bioinformatic tools to predict the genes and mechanisms used by Acidihalobacter members in their defense against a wide range of metals and oxidative stress. Analysis revealed the presence of multiple conserved mechanisms of metal tolerance. Ac. yilgarnensis F5^T, the only member of this genus that oxidizes the mineral chalcopyrite, contained a 39.9 Kb gene cluster consisting of 40 genes encoding mobile elements and an array of proteins with direct functions in copper resistance. The analysis also revealed multiple strategies that the Acidihalobacter members can use to tolerate high levels of oxidative stress. Three of the Acidihalobacter genomes were found to contain genes encoding catalases, which are not common to acidophilic microorganisms. Of particular interest was a rubrerythrin genomic cluster containing genes that have a polyphyletic origin of stress-related functions.

Understanding Stress Response to High-Arsenic Gold-Bearing Sulfide Concentrate in Extremely Metal-Resistant Acidophile Sulfobacillus thermotolerans

Biooxidation of gold-bearing arsenopyrite concentrates, using acidophilic microbial communities, is among the largest commercial biohydrometallurgical processes. However, molecular mechanisms of microbial responses to sulfide raw materials have not been widely studied. The goal of this research was to gain insight into the defense strategies of the acidophilic bacterium Sulfobacillus thermotolerans, which dominates microbial communities functioning in industrial biooxidation processes at >35 °C, against the toxic effect of the high-arsenic gold-bearing sulfide concentrate. In addition to extreme metal resistance, this acidophile proved to be one of the most As-tolerant microorganisms. Comparative proteomic analysis indicated that 30 out of 33 differentially expressed proteins were upregulated in response to the ore concentrate, while the synthesis level of the functional proteins required for cell survival was not negatively affected. Despite a high level of cellular metal(loid) accumulation, no specific metal(loid)-resistant systems were regulated. Instead, several proteins involved in the metabolic pathways and stress response, including MBL fold metallo-hydrolase, sulfide:quinone oxidoreductase, and GroEL chaperonin, may play crucial roles in resistance to the sulfide ore concentrate and arsenic, in particular. This study provides the first data on the microbial responses to sulfide ore concentrates and advances our understanding of defense mechanisms against toxic compounds in acidophiles.

Sulfobacillus thermotolerans: new insights into resistance and metabolic capacities of acidophilic chemolithotrophs

The first complete genome of the biotechnologically important species Sulfobacillus thermotolerans has been sequenced. Its 3 317 203-bp chromosome contains an 83 269-bp plasmid-like region, which carries heavy metal resistance determinants and the rusticyanin gene. Plasmid-mediated metal resistance is unusual for acidophilic chemolithotrophs. Moreover, most of their plasmids are cryptic and do not contribute to the phenotype of the host cells. A polyphosphate-based mechanism of metal resistance, which has been previously unknown in the genus Sulfobacillus or other Gram-positive chemolithotrophs, potentially operates in two Sulfobacillus species. The methylcitrate cycle typical for pathogens and identified in the genus Sulfobacillus for the first time can fulfill the energy and/or protective function in S. thermotolerans Kr1 and two other Sulfobacillus species, which have incomplete glyoxylate cycles. It is notable that the TCA cycle, disrupted in all Sulfobacillus isolates under optimal growth conditions, proved to be complete in the cells enduring temperature stress. An efficient antioxidant defense system gives S. thermotolerans another competitive advantage in the microbial communities inhabiting acidic metal-rich environments. The genomic comparisons revealed 80 unique genes in the strain Kr1, including those involved in lactose/galactose catabolism. The results provide new insights into metabolism and resistance mechanisms in the Sulfobacillus genus and other acidophiles.

Bioinformatics Analysis of Metabolism Pathways of Archaeal Energy Reserves

Energy storage compounds play crucial roles in prokaryotic physiology. Five chemical compounds have been identified in prokaryotes as energy reserves: polyphosphate (polyP), polyhydroxyalkanoates (PHAs), glycogen, wax ester (WE) and triacylglycerol (TAG). Currently, no systematic study of archaeal energy storage metabolism exists. In this study, we collected 427 archaeal reference sequences from UniProt database. A thorough pathway screening of energy reserves led to an overview of distribution patterns of energy metabolism in archaea. We also explored how energy metabolism might have impact on archaeal extremophilic phenotypes. Based on the systematic analyses of archaeal proteomes, we confirmed that metabolism pathways of polyP, PHAs and glycogen are present in archaea, but TAG and WE are completely absent. It was also confirmed that PHAs are tightly related to halophilic archaea with larger proteome size and higher GC contents, while polyP is mainly present in methanogens. In sum, this study systematically investigates energy storage metabolism in archaea and provides a clear correlation between energy metabolism and the ability to survive in extreme environments. With more genomic editing tools developed for archaea and molecular mechanisms unravelled for energy storage metabolisms (ESMs), there will be a better understanding of the unique lifestyle of archaea in extreme environments.

Extremophilic Microfactories: Applications in Metal and Radionuclide Bioremediation

Metals and radionuclides (M&Rs) are a worldwide concern claiming for resilient, efficient, and sustainable clean-up measures aligned with environmental protection goals and global change constraints. The unique defense mechanisms of extremophilic bacteria and archaea have been proving usefulness towards M&Rs bioremediation. Hence, extremophiles can be viewed as microfactories capable of providing specific and controlled services (i.e., genetic/metabolic mechanisms) and/or products (e.g., biomolecules) for that purpose. However, the natural physiological plasticity of such extremophilic microfactories can be further explored to nourish different hallmarks of M&R bioremediation, which are scantly approached in the literature and were never integrated. Therefore, this review not only briefly describes major valuable extremophilic pathways for M&R bioremediation, as it highlights the advances, challenges and gaps from the interplay of ‘omics’ and biological engineering to improve extremophilic microfactories performance for M&R clean-up. Microfactories’ potentialities are also envisaged to close the M&R bioremediation processes and shift the classical idea of never ‘getting rid’ of M&Rs into making them ‘the belle of the ball’ through bio-recycling and bio-recovering techniques.

Advances in concrete materials for sewer systems affected by microbial induced concrete corrosion: A review

Microbial induced concrete corrosion (MICC) is recognized as one of the main degradation mechanisms of subsurface infrastructure worldwide, raising the demand for sustainable construction materials in corrosive environments. This review aims to summarize the key research progress acquired during the last decade regarding the understanding of MICC reaction mechanisms and the development of durable materials from an interdisciplinary perspective. Special focus was laid on aspects governing concrete - micoorganisms interaction since being the central process steering biogenic acid corrosion. The insufficient knowledge regarding the latter is proposed as a central reason for insufficient progress in tailored material development for aggressive wastewater systems. To date no cement-based material exists, suitable to withstand the aggressive conditions related to MICC over its entire service life. Research is in particular needed on the impact of physiochemical material parameters on microbial community structure, growth characteristics and limitations within individual concrete speciation. Herein an interdisciplinary approach is presented by combining results from material sciences, microbiology, mineralogy and hydrochemistry to stimulate the development of novel and sustainable materials and mitigation strategies for MICC. For instance, the application of antibacteriostatic agents is introduced as an effective instrument to limit microbial growth on concrete surfaces in aggressive sewer environments. Additionally, geopolymer concretes are introduced as highly resistent in acid environments, thus representing a possible green alternative to conventional cement-based construction materials.

Global effect of the lack of inorganic polyphosphate in the extremophilic archaeon Sulfolobus solfataricus: A proteomic approach

Inorganic polyphosphates (polyP) are present in all living cells and several important functions have been described for them. They are involved in the response to stress conditions, such as nutrient depletion, oxidative stress and toxic metals amongst others. A recombinant strain of Sulfolobus solfataricus unable to accumulate polyP was designed by the overexpression of its endogenous ppx gene. The overall impact of the lack of polyP on this S. solfataricus polyP (-) strain was analyzed by using quantitative proteomics (isotope-coded protein label, ICPL). Stress-related proteins, such as peroxiredoxins and heat shock proteins, proteins involved in metabolism and several others were produced at higher levels in the ppx expression strain. The polyP deficient strain showed an increased copper sensitivity and an earlier transcriptional up-regulation of copA gene coding for the P-type copper-exporting ATPase. This implies a complementary function of both copper resistance systems. These results strongly suggests that the lack of polyP makes this hyperthermophilic archaeon more sensitive to toxic conditions, such as an exposure to metals or other harmful stimuli, emphasizing the importance of this inorganic phosphate polymers in the adaptations to live in the environmental conditions in which thermoacidophilic archaea thrive. SIGNIFICANCE: Inorganic polyphosphate (polyP) are ubiquitous molecules with many functions in living organisms. Few studies related to these polymers have been made in archaea. The construction of a polyP deficient recombinant strain of Sulfolobus solfataricus allowed the study of the global changes in the proteome of this thermoacidophilic archaeon in the absence of polyP compared with the wild type strain. The results obtained using quantitative proteomics suggest an important participation of polyP in the oxidative stress response of the cells and as having a possible metabolic role in the cell, as previously described in bacteria. The polyP deficient strain also showed an increased copper sensitivity and an earlier transcriptional up-regulation of copA, implying a complementary role of both copper resistance systems.

Artificial Gene Amplification in Escherichia coli Reveals Numerous Determinants for Resistance to Metal Toxicity

When organisms are subjected to environmental challenges, including growth inhibitors and toxins, evolution often selects for the duplication of endogenous genes, whose overexpression can provide a selective advantage. Such events occur both in natural environments and in clinical settings. Microbial cells-with their large populations and short generation times-frequently evolve resistance to a range of antimicrobials. While microbial resistance to antibiotic drugs is well documented, less attention has been given to the genetic elements responsible for resistance to metal toxicity. To assess which overexpressed genes can endow gram-negative bacteria with resistance to metal toxicity, we transformed a collection of plasmids overexpressing all E. coli open reading frames (ORFs) into naive cells, and selected for survival in toxic concentrations of six transition metals: Cd, Co, Cu, Ni, Ag, Zn. These selections identified 48 hits. In each of these hits, the overexpression of an endogenous E. coli gene provided a selective advantage in the presence of at least one of the toxic metals. Surprisingly, the majority of these cases (28/48) were not previously known to function in metal resistance or homeostasis. These findings highlight the diverse mechanisms that biological systems can deploy to adapt to environments containing toxic concentrations of metals.

Genome analysis of the thermoacidophilic archaeon Acidianus copahuensis focusing on the metabolisms associated to biomining activities

Background

Several archaeal species from the order Sulfolobales are interesting from the biotechnological point of view due to their biomining capacities. Within this group, the genus Acidianus contains four biomining species (from ten known Acidianus species), but none of these have their genome sequenced. To get insights into the genetic potential and metabolic pathways involved in the biomining activity of this group, we sequenced the genome of Acidianus copahuensis ALE1 strain, a novel thermoacidophilic crenarchaeon (optimum growth: 75 °C, pH 3) isolated from the volcanic geothermal area of Copahue at Neuquén province in Argentina. Previous experimental characterization of A. copahuensis revealed a high biomining potential, exhibited as high oxidation activity of sulfur and sulfur compounds, ferrous iron and sulfide minerals (e.g.: pyrite). This strain is also autotrophic and tolerant to heavy metals, thus, it can grow under adverse conditions for most forms of life with a low nutrient demand, conditions that are commonly found in mining environments.

Results

In this work we analyzed the genome of Acidianus copahuensis and describe the genetic pathways involved in biomining processes. We identified the enzymes that are most likely involved in growth on sulfur and ferrous iron oxidation as well as those involved in autotrophic carbon fixation. We also found that A. copahuensis genome gathers different features that are only present in particular lineages or species from the order Sulfolobales, some of which are involved in biomining. We found that although most of its genes (81%) were found in at least one other Sulfolobales species, it is not specifically closer to any particular species (60–70% of proteins shared with each of them). Although almost one fifth of A. copahuensis proteins are not found in any other Sulfolobales species, most of them corresponded to hypothetical proteins from uncharacterized metabolisms.

Conclusion

In this work we identified the genes responsible for the biomining metabolisms that we have previously observed experimentally. We provide a landscape of the metabolic potentials of this strain in the context of Sulfolobales and propose various pathways and cellular processes not yet fully understood that can use A. copahuensis as an experimental model to further understand the fascinating biology of thermoacidophilic biomining archaea.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3828-x) contains supplementary material, which is available to authorized users.

Microbial copper resistance: importance in biohydrometallurgy

Industrial biomining has been extensively used for many years to recover valuable metals such as copper, gold, uranium and others. Furthermore, microorganisms involved in these processes can also be used to bioremediate places contaminated with acid and metals. These uses are possible due to the great metal resistance that these extreme acidophilic microorganisms possess. In this review, the most recent findings related to copper resistance mechanisms of bacteria and archaea related to biohydrometallurgy are described. The recent search for novel metal resistance determinants is not only of scientific interest but also of industrial importance, as reflected by the genomic sequencing of microorganisms present in mining operations and the search of those bacteria with extreme metal resistance to improve the extraction processes used by the biomining companies.

Thermophilic microorganisms in biomining

Biomining is an applied biotechnology for mineral processing and metal extraction from ores and concentrates. This alternative technology for recovering metals involves the hydrometallurgical processes known as bioleaching and biooxidation where the metal is directly solubilized or released from the matrix for further solubilization, respectively. Several commercial applications of biomining can be found around the world to recover mainly copper and gold but also other metals; most of them are operating at temperatures below 40-50 °C using mesophilic and moderate thermophilic microorganisms. Although biomining offers an economically viable and cleaner option, its share of the world´s production of metals has not grown as much as it was expected, mainly considering that due to environmental restrictions in many countries smelting and roasting technologies are being eliminated. The slow rate of biomining processes is for sure the main reason of their poor implementation. In this scenario the use of thermophiles could be advantageous because higher operational temperature would increase the rate of the process and in addition it would eliminate the energy input for cooling the system (bioleaching reactions are exothermic causing a serious temperature increase in bioreactors and inside heaps that adversely affects most of the mesophilic microorganisms) and it would decrease the passivation of mineral surfaces. In the last few years many thermophilic bacteria and archaea have been isolated, characterized, and even used for extracting metals. This paper reviews the current status of biomining using thermophiles, describes the main characteristics of thermophilic biominers and discusses the future for this biotechnology.

Transcriptomes of the Extremely Thermoacidophilic Archaeon Metallosphaera sedula Exposed to Metal "Shock" Reveal Generic and Specific Metal Responses

The extremely thermoacidophilic archaeon Metallosphaera sedula mobilizes metals by novel membrane-associated oxidase clusters and, consequently, requires metal resistance strategies. This issue was examined by "shocking" M. sedula with representative metals (Co(2+), Cu(2+), Ni(2+), UO2 (2+), Zn(2+)) at inhibitory and subinhibitory levels. Collectively, one-quarter of the genome (554 open reading frames [ORFs]) responded to inhibitory levels, and two-thirds (354) of the ORFs were responsive to a single metal. Cu(2+) (259 ORFs, 106 Cu(2+)-specific ORFs) and Zn(2+) (262 ORFs, 131 Zn(2+)-specific ORFs) triggered the largest responses, followed by UO2 (2+) (187 ORFs, 91 UO2 (2+)-specific ORFs), Ni(2+) (93 ORFs, 25 Ni(2+)-specific ORFs), and Co(2+) (61 ORFs, 1 Co(2+)-specific ORF). While one-third of the metal-responsive ORFs are annotated as encoding hypothetical proteins, metal challenge also impacted ORFs responsible for identifiable processes related to the cell cycle, DNA repair, and oxidative stress. Surprisingly, there were only 30 ORFs that responded to at least four metals, and 10 of these responded to all five metals. This core transcriptome indicated induction of Fe-S cluster assembly (Msed_1656-Msed_1657), tungsten/molybdenum transport (Msed_1780-Msed_1781), and decreased central metabolism. Not surprisingly, a metal-translocating P-type ATPase (Msed_0490) associated with a copper resistance system (Cop) was upregulated in response to Cu(2+) (6-fold) but also in response to UO2 (2+) (4-fold) and Zn(2+) (9-fold). Cu(2+) challenge uniquely induced assimilatory sulfur metabolism for cysteine biosynthesis, suggesting a role for this amino acid in Cu(2+) resistance or issues in sulfur metabolism. The results indicate that M. sedula employs a range of physiological and biochemical responses to metal challenge, many of which are specific to a single metal and involve proteins with yet unassigned or definitive functions.

IMPORTANCE

The mechanisms by which extremely thermoacidophilic archaea resist and are negatively impacted by metals encountered in their natural environments are important to understand so that technologies such as bioleaching, which leverage microbially based conversion of insoluble metal sulfides to soluble species, can be improved. Transcriptomic analysis of the cellular response to metal challenge provided both global and specific insights into how these novel microorganisms negotiate metal toxicity in natural and technological settings. As genetics tools are further developed and implemented for extreme thermoacidophiles, information about metal toxicity and resistance can be leveraged to create metabolically engineered strains with improved bioleaching characteristics.

Biotechnological applications of extremophiles, extremozymes and extremolytes

In the last decade, attention to extreme environments has increased because of interests to isolate previously unknown extremophilic microorganisms in pure culture and to profile their metabolites. Microorganisms that live in extreme environments produce extremozymes and extremolytes that have the potential to be valuable resources for the development of a bio-based economy through their application to white, red, and grey biotechnologies. Here, we provide an overview of extremophile ecology, and we review the most recent applications of microbial extremophiles and the extremozymes and extremolytes they produce to biotechnology.

Cadmium resistance in extremely halophilic archaeon Haloferax strain BBK2

Halophilic archaea are prevalent in highly saline habitats. Haloferax strain BBK2 is an orange pigmented, exopolysaccharide (EPS) producing extremely halophilic archaeon, isolated from solar salterns of Ribandar, Goa, India. It grew in varying pH (5-10) and NaCl concentration (10-30%). The isolate grew well in complex (NTYE) and minimal media (NGSM) in presence of heavy metal cadmium (Cd) up to 4.0 mM (805.28 mg L(-1)) concentration. The optimum growth in the presence and absence of Cd was seen at a pH range of 7-9 and salinity of 15-25%. The growth kinetics of the isolate in NTYE showed a specific growth rate (μmax) of 0.352 with generation time of 1.968 days. In presence of 1mM Cd, the μmax was 0.325 day(-1) and generation time was 2.132 days. In NGSM, the μmax decreased from 0.517 day(-1) (in control) to 0.265 day(-1) in 1mM Cd while, the doubling time increased from 1.34 days in control to 2.615 days in presence of 1 mM Cd. SDS PAGE of the whole cell protein extracts showed overexpressed proteins of 74.14 and 40 kDa. The scanning electron microscopy, energy dispersive X-ray spectroscopy (SEM-EDX) analysis of the intact cells and cells disrupted by dialysis revealed that Cd was bound onto the cells, which was further confirmed by AAS, FTIR and XRD analysis.

Genome sequence of Candidatus Nitrososphaera evergladensis from group I.1b enriched from Everglades soil reveals novel genomic features of the ammonia-oxidizing archaea

The activity of ammonia-oxidizing archaea (AOA) leads to the loss of nitrogen from soil, pollution of water sources and elevated emissions of greenhouse gas. To date, eight AOA genomes are available in the public databases, seven are from the group I.1a of the Thaumarchaeota and only one is from the group I.1b, isolated from hot springs. Many soils are dominated by AOA from the group I.1b, but the genomes of soil representatives of this group have not been sequenced and functionally characterized. The lack of knowledge of metabolic pathways of soil AOA presents a critical gap in understanding their role in biogeochemical cycles. Here, we describe the first complete genome of soil archaeon Candidatus Nitrososphaera evergladensis, which has been reconstructed from metagenomic sequencing of a highly enriched culture obtained from an agricultural soil. The AOA enrichment was sequenced with the high throughput next generation sequencing platforms from Pacific Biosciences and Ion Torrent. The de novo assembly of sequences resulted in one 2.95 Mb contig. Annotation of the reconstructed genome revealed many similarities of the basic metabolism with the rest of sequenced AOA. Ca. N. evergladensis belongs to the group I.1b and shares only 40% of whole-genome homology with the closest sequenced relative Ca. N. gargensis. Detailed analysis of the genome revealed coding sequences that were completely absent from the group I.1a. These unique sequences code for proteins involved in control of DNA integrity, transporters, two-component systems and versatile CRISPR defense system. Notably, genomes from the group I.1b have more gene duplications compared to the genomes from the group I.1a. We suggest that the presence of these unique genes and gene duplications may be associated with the environmental versatility of this group.

Metal resistance or tolerance? Acidophiles confront high metal loads via both abiotic and biotic mechanisms

All metals are toxic at high concentrations and consequently their intracellular concentrations must be regulated. Extremely acidophilic microorganisms have an optimum growth of pH <3 and proliferate in natural and anthropogenic low pH environments. Some acidophiles are involved in the catalysis of sulfide mineral dissolution, resulting in high concentrations of metals in solution. Acidophiles are often described as highly metal resistant via mechanisms such as multiple and/or more efficient active resistance systems than are present in neutrophiles. However, this is not the case for all acidophiles and we contend that their growth in high metal concentrations is partially due to an intrinsic tolerance as a consequence of the environment in which they live. In this perspective, we highlight metal tolerance via complexation of free metals by sulfate ions and passive tolerance to metal influx via an internal positive cytoplasmic transmembrane potential. These tolerance mechanisms have been largely ignored in past studies of acidophile growth in the presence of metals and should be taken into account.

Cd2+ resistance mechanisms in Methanosarcina acetivorans involve the increase in the coenzyme M content and induction of biofilm synthesis

To assess what defence mechanisms are triggered by Cd(2+) stress in Methanosarcina acetivorans, cells were cultured at different cadmium concentrations. In the presence of 100 μM CdCl2, the intracellular contents of cysteine, sulfide and coenzyme M increased, respectively, 8, 27 and 7 times versus control. Cells incubated for 24 h in medium with less cysteine and sulfide removed up to 80% of Cd(2+) added, whereas their cysteine and coenzyme M contents increased 160 and 84 times respectively. Cadmium accumulation (5.2 μmol/10-15 mg protein) resulted in an increase in methane synthesis of 4.5 times in cells grown on acetate. Total phosphate also increased under high (0.5 mM) Cd(2+) stress. On the other hand, cells preadapted to 54 μM CdCl2 and further exposed to > 0.63 mM CdCl2 developed the formation of a biofilm with an extracellular matrix constituted by carbohydrates, DNA and proteins. Biofilm cells were able to synthesize methane. The data suggested that increased intracellular contents of thiol molecules and total phosphate, and biofilm formation, are all involved in the cadmium resistance mechanisms in this marine archaeon.