Environmental Microbiology (EM) | Microbial Ecology and Diversity
Microbiol. Biotechnol. Lett. 2024; 52(3): 233-254
https://doi.org/10.48022/mbl.2406.06007
Meglali Amina* and Ghellai Lotfi
Laboratory of Biotoxicology, Pharmacognosy and Biological Valorization of Plants (LBPVBP), Faculty of Natural and Life Sciences, Department of Biology, University of Saida – Dr. Moulay Tahar, 20000 Saida, Algeria
Correspondence to :
Amina Meglali, meglaliamina@gmail.com
The microorganisms that live under extreme conditions on Earth are known as extremophiles. They possess an extraordinary capability to endure extreme conditions, including salinity, temperature variations, pH, desiccation, and nutrient scarcity, among others. These organisms, including a vast array of bacteria, eukarya, and archaea, have evolved specialized structural and functional adaptations that make them capable of thriving in extremely selective environments in such a way that they showcase remarkable adaptations that push the limits of what we consider habitable. This capability results in valuable compounds with great potential for developing novel pharmaceuticals and biotechnological innovations. The present review paper aims to summarize current knowledge on the diversity of extremophilic microorganisms and the adaptive strategies employed to face such a range of extreme conditions. Particular attention will be given to temperature, salinity, pH, and desiccation adaptation. The review also highlights their potential applications, specifically focusing on pharmaceutical and biotechnological applications.
Keywords: Extremophiles, extreme conditions, diversity, adaptive strategies, pharmaceutical, biotechnological applications
Until microbiologists discovered that a great diversity of microorganisms occupied the earth's extreme environments, humans assumed that no organisms could live in such extreme parameters. Nevertheless, a wide array of extremophiles has been identified in recent times across various habitats, such as hot springs, deserts, hypersaline terrains, caves, and oil fields, among others [1−4].
Extreme ecosystems can be present all around the world. In addition to the previously mentioned habitats, those contain volcanoes, salterns, acid or alkaline lakes, frozen sites, and other habitats with high levels of environmental pollution occupied by a vast microbial biodiversity capable of withstanding toxic compounds [5].
Extremophiles, as the name suggests, are organisms that can survive in one or more harsh environmental conditions of low or high temperature (psychrophiles; thermophiles), high or low pH (alkaliphiles; acidophiles), salinity (halophiles), or low water content (xerophiles)(Fig. 1). Some microorganisms are adapted to multiple stresses simultaneously (polyextremophile); for example, thermoacidophiles bacteria that thrive at high temperatures and acidity (
Estimations suggest that less than 5% of all microbial diversity has been successfully isolated in pure cultures and examined for microbial characteristics. Consequently, 95% or more of these microbes have yet to be discovered or cannot be reliably cultivated in a laboratory [8]. Cultivating extreme environments in the laboratory is labor-intensive and expensive (various incubators, pressure systems, UV incubators, corrosion-resistant vessels from high acidity, alkalinity, and salinity), requiring specific equipment and knowledge of media components. Innovation culture technologies (microfluidics and cultivation chips) pose challenges for extreme ecosystems [9, 10].
Considering the difficulties encountered in obtaining pure cultures from environmental specimens and, as a result, knowing the microbial biodiversity of these specimens, these extremophilic microorganisms have piqued the interest of researchers worldwide due to their different strategies to survive in various hostile environmental conditions. When faced with unfavorable environments, they activate a stress response, altering gene expression to protect vital processes and restore cellular balance, increasing resistance to future challenges [11]. This ability to maintain internal balance while adjusting to diverse environmental stresses is called “homeostasis” [12]. This process includes the production of different bioactive compounds, enzymes, and proteins that have great interest in several fields due to their varied applications [1, 13].
This review presents a comprehensive overview of life under extreme environmental conditions, focusing on the diversity of extremophilic microorganisms, their habitats, and their adaptation mechanisms, with a special focus on the adaptation of temperature, salinity, pH, and desiccation. Furthermore, the review covers the potential industrial applications of these microorganisms in various sectors, including pharmaceutical and biotechnological areas.
The term “extremophile” was coined by McElroy in 1974, they are predominantly classified within the domains
Long ago, most microorganisms were considered “uncultured” because they could not be successfully grown in laboratory culture conditions. However, over time, some of these microorganisms were transferred to the “cultivated” category as cultivation techniques improved. We only later realized the true extent of microbial diversity, with the cultured microorganisms representing only a small fraction, usually between 1 and 5%, of the total microbial diversity [17].
In recent decades, the diversity of microorganisms living in extreme environments has been extensively researched. Both culture-dependent and culture-independent methods (Both conventional cultivation-based and modern non-cultivation-based techniques) have been used in this research to investigate these microbial communities [18] (Fig. 3).
Recently, there have been significant advances in sequencing techniques and data analysis, leading to an increased use of the “Omics” approach studying microorganisms. This approach has been increasingly employed not only for mesophilic (non-extreme) microorganisms but also for extremophilic microorganisms [19]. They enabled a more accurate description of microorganisms and the introduction of a new classification system based on a comparison of the gene sequences encoding the 16S subunits (
Daniel Prieur, a microbiologist specializing in the microbiology of extreme environments, defined three categories of extremophiles related to the living conditions and resistance to the environment of these microorganisms [2, 22, 23]: (i) Passives: The life cycle proceeds under normal conditions until a vital parameter value exceeds the limits of the species. At this point, the organism develops a form of resistance (spores of certain Gram-positive bacteria) that allows it to wait to return to more normal conditions without dividing and with a prolonged metabolism. (ii) Actives: They can use cellular and molecular mechanisms that allow them to resist significant changes in environmental conditions (
Extremophiles comprise various microorganisms adapted to live and flourish under extreme conditions and severe environments. These include hot niches, icy environments, high salinity, acidic, and alkaline environments; they have also been found in environments contaminated with toxic waste, organic solvents or heavy metals [25]. Extremophiles can be categorized into different classes based on the specific extreme conditions in which they thrive, including halophiles, psychrophiles, thermophiles, acidophiles, alkalophiles, xerophiles, and others [26]. The main categories of extremophiles, their physicochemical characteristics (temperature, salinity, acidity, water activity, etc.) and some common classes are listed in Table 1.
Table 1 . Various categories of extremophiles, their growth characteristics and major species.
Group of extremophiles | Growth characteristic | Species | References |
---|---|---|---|
Thermophiles | High temperatures 45-70℃ | [27] [28] | |
Psychrophiles | Low temperatures 0-25C° (optimum 15℃) | [29] [30] | |
Halophiles | High Salinity 1-20% (w/v) (optimum at 10-12%) | [31] [32] [33] | |
Acidophiles | low pH 0-5 (optimum 3-5) | [24] | |
Alkaliphiles | High pH 9-12 (optimum around 10) | [8] | |
Piezophiles | High Pressure >10 MPa | [34] | |
Xerophiles | Low water activity and high desiccation (Aw 0.7-0.9) | [35] | |
Metallophiles | High metals conditions (Zn, Cd, Cu, Cr, Co, Ag, Pb, Hg…) | [36] [37] | |
Radiophiles | Intense ionizing/non-ionizingradiations (X and Gamma rays/Ultraviolet) | [38] |
Halophiles are diverse organisms that thrive in salty environments, including
Haloarchaea, for example, adopts a ‘salt-in’ strategy, aligning their intracellular KCl levels with the external NaCl concentrations, which their enzymes can tolerate or even require at 4−5 M concentrations [45, 46]. Conversely, halophilic eukaryotes and bacteria generally follow a ‘salt-out’ strategy, removing salt and generating or acquiring compatible solutes like glycerol, polyols, glycine betaine, and other zwitterionic compounds to maintain cellular equilibrium [47, 48]. These solutes help balance osmotic pressure and are crucial for cell metabolism compatibility [49]. Some halophiles cannot produce these solutes themselves. Instead, they have developed systems to uptake solutes produced by other organisms, with
Halophile and halotolerant microorganisms have developed versatile molecular mechanisms to cope with saline stress. In this context, Zhou
Furthermore, the proteome comparison of the halotolerant
Moreover, Halophilic proteins employ different adaptation mechanisms. They have a biased amino acid composition to remain active and stable at high ionic strength. They typically have excess acidic amino acids (e.g., aspartate and glutamate) on their surface, and their negative charges bind significant amounts of hydrated ions, thus decreasing the tendency to aggregate and reducing their surface hydrophobicity at high salt concentrations [54].
Additionally, exopolymeric substance (EPS) production to form biofilm emerges as another vital adaptive mechanism for halophiles, enabling them to withstand high saline stress. For instance,
Thermophiles, a category of extremophiles primarily composed of
For DNA stability, thermophiles employ DNA-binding proteins to compact and condense DNA into nucleosomes and DNA repair proteins to remove any alkylated, deaminated, primary site, or oxidized base and cross-linked products. Additionally, thermophiles tend to have smaller genomes than mesophiles, with shorter protein sequences, which are believed to reduce cellular energy costs during division [57, 58]. A higher G-C to A-T ratio in the rRNA and tRNA of thermophiles contributes to the stability of these molecules due to the stronger bond of G-C pairs [58]. Furthermore, the DNA of thermophiles contains reverse DNA gyrase, which assists in raising the melting point by producing positive supercoils in the DNA. The polyamines and osmolytes in the cell also help stabilize the DNA and protect proteins by shifting their equilibrium toward the native state [59]. Metabolically, thermophiles adapt by up-regulating glycolysis-related proteins and down-regulating respiration-associated proteins, such as electron transfer proteins and NADH dehydrogenase [60, 61]. Membrane adaptations include an increase in saturated and long-chain fatty acids to enhance membrane rigidity [62−64].
In addition to the above strategies, Thermophilic actinomycetes, bacteria and archaea adapt to high temperatures by increasing their proteins’ disulfide, electrostatic, and hydrophobic interactions; also, certain specialized proteins are produced by these organisms, known as “chaperones” consist of Cpn10, a homoheptameric dome-shaped ring (10 kDa subunits) and Cpn60, a homotetra-decameric doublering cylinder (57 kDa subunits). Paradigms for Cpn10 and Cpn60 are the
Conversely, psychrophilic bacteria exhibit adaptations to cold environments through structural, physiological, and molecular changes, including the thickening of their outer cell layers, notably the lipopolysaccharide (negative-Gram) and the peptidoglycan layer (positive-Gram) [68, 69]. These bacteria adjust their membrane phospholipid composition to increase the polyunsaturated to saturated fatty acid ratio, ensuring membrane permeability and fluidity through homeoviscous adaptation [70].
These extremophiles can synthesize cold-shock proteins, which are believed to increase translation efficiency by destabilizing secondary structures in mRNA. Additionally, cryoprotectants produced by psychrophiles increase the ability for nutrition absorption. Compared to mesophile proteins, psychrophilic proteins show decreased hydrogen bonds and ionic interactions and possess less hydrophobic groups, longer surface loops, and more charged groups on their surface [59]. Quorum sensing is also crucial for psychrophiles, facilitating survival at low temperatures through the production of extracellular polysaccharides, which may lower the freezing point around the cell. Although it hypothesizes that psychrophiles like
Moreover, psychrophiles employ several strategies to navigate the harsh conditions of the Antarctic environment, including the synthesis of ice-binding proteins, accumulation of compatible osmolytes, production of pigments, and metabolic adjustments [72, 73]. Ice-binding proteins, known as antifreeze proteins (AFPs), attach to ice to reduce the freezing point and prevent ice-crystal growth [74]. It demonstrates that a recombinant anti-freeze peptide (rsfAFP) interacts with the peptidoglycan and extracellular capsular polysaccharides of
Comparative genomic analyses among mesophiles, psychrophiles, and thermophiles have uncovered that a set of coordinated genetic modifications are associated with an organism's optimal growth temperature (OGT), influencing its survival in extreme conditions. These modifications include variations in the arrangement and frequency of secondary structures, folding patterns, and differences in tRNAs and their G+C content. Previous studies on the sequence and structural data across different bacterial types have established a relationship between an organism's OGT and the dinucleotide composition of its DNA [79].
Acidophiles are microorganisms that thrive at pH levels of 3 or below yet maintain a nearly neutral internal pH. Conversely, alkaliphiles can live in environments with pH levels between 9 and 11, maintaining an internal pH around 9 [80, 81]. Surviving in such pH extremes necessitates sophisticated cellular adaptations to overcome various eco-physiological challenges (Fig. 6). These organisms exhibit unique structural and functional adaptations to regulate internal pH levels [82, 83]. Despite their external environment's extreme acidity, acidophiles cannot sustain such acidic conditions internally without compromising macromolecular stability. This limitation has driven the evolution of mechanisms to expel acid from the cell, preserving neutral to slightly acidic conditions internally [84, 85].
To maintain the pH homeostasis of the cell, acidophiles employ different adaptation strategies: improving the efflux of the proton, increasing the expression of secondary transporters, reducing the proton permeability of cell membrane, and enhancing cytoplasmic buffering [84, 86, 87]. Acidophiles remove excess protons from the cytoplasm by active proton pumping using several candidate proton efflux systems (
Furthermore, acidophiles possess various protein structure adaptations to maintain enzyme and protein stability in acidic conditions, including changes in the surface charges by increased negative surface charge, thus enhancing their peptide insertions and acidic amino acid content. It has been reported that higher expression of proteins that use protons also contributes to acid tolerance in certain microorganisms, including
Genome sequencing has revealed the importance of protein and DNA repair systems and possibly a smaller genome size in adapting to low pH environments [84]. The
Almost all alkaliphilic bacteria maintain a specific cytoplasmic pH, comparatively lower than the high pH of the surrounding environment, and usually maintain a pH difference of approximately two units [97]. They counteract alkaline stress primarily through cellular physiological responses, using sodium and proton ion pumps for ATP production and pH regulation [98]. The H+/Na+ antiporters are the most well-known mechanism for Na+ extrusion. They use a proton gradient by exchanging external H+ with the internal Na+ and utilizing the H+-ATPase, which catalyzes the translocation of Na+ across the membrane, resulting in pH homeostasis. This system has been discovered to be critical for the survival of
Cell walls and membranes are critical in managing pH stress, with microbes adopting strategies to modulate proton permeability and surface charges. Alkaliphiles, for instance, develop a negatively charged cell wall to mitigate high external pH levels, effectively lowering the surrounding pH [56]. This highly negatively charged cell wall structure interacts with cations such as H+, reducing the rapid loss of H+ from the cell surface due to the equilibration process of the alkaline bulk phase in the environment, which contributes considerably to alkali-phile pH homeostasis and bioenergetics [101]. For example,
Utilizing deaminase (enzymatic approach) and polyamines in the cytoplasm are other mechanisms associated with the survival of the alkaliphile. Many alkaliphiles have been found to produce acids in the cytoplasm with the help of enzymes like amino acid deaminase, ATP synthase, oxidoreductases, and by fermentation of different sugars. It was observed that when
In addition, the significant contribution of adaptations to any environment is the unique set of genes present in the organism’s genome. Some alkaliphiles contain a higher rich sequence and extra-chromosomal genetic materials (plasmids), providing added advantages for survival and the tolerance of environmental extremities [97]. In haloalkaliphilic archaeon
The capability of prokaryotes to divide is significantly hindered at water activity (aw) levels below 0.91, and fungi generally cease metabolic activity at aw less than 0.7. however, Research in extreme environments has uncovered microorganisms that effectively manage to endure and function at aw levels considerably lower than these benchmarks [105]. Termed “xerophiles,” these organisms are specialized to proliferate in arid and moisture-deprived conditions [80]. Their ecological niches are often found in hot deserts, where conditions include minimal rainfall, vast temperature variations, and intense UV radiation, presenting formidable abiotic challenges. However, xerophiles have developed sophisticated adaptive mechanisms across various taxa, allowing them not just to survive but to prosper in these inhospitable environments [106−108].
To counteract desiccation, cells deploy ingenious strategies to shield against protein and DNA damage by generating and accumulating salts and osmoprotectants that not only substitute for water in stabilizing macro-molecules and membranes but also inhibit the formation of hydroxyl radicals through reduced intracellular diffusion rates, enhancing their capacity to retain water, averting water loss, curtailing energy expenditure, and expressing of DNA-binding and repair proteins that serve as protective barriers [109]. Additionally, the use of alternative carbon sources like fatty acids, generate higher ATP yields as metabolic activity transitions to energy preservation. Concurrently, photosynthesis is suppressed to limit oxygen accumulation and the resultant production of reactive oxygen species (ROS), major contributors to DNA damage during desiccation; at the same time, ROS scavengers such as catalases and superoxide dismutase (SOD) are elevated in response [110](Fig. 7).
In adapting to the environmental shifts accompanying desiccation, prokaryotes modulate their metabolic pathways, transitioning from constructive (anabolic) to degradative (catabolic) metabolism [111]. When glucose availability dwindles, cells reallocate glucose for the synthesis of trehalose. This adaptation leads to the utilization of fatty acid oxidation as a highly efficient alternate energy source, yielding a more significant number of ATP molecules per carbon atom than glucose [112, 113]; this metabolic adjustment also results in the reduction of energy-intensive functions, such as flagellar motility, to conserve energy [110]. Moreover, they adjust to reduced water activity by altering their lipid composition, specifically by increasing the ratio of trans- to cis-mono-unsaturated fatty acids and saturated to unsaturated fatty acids. They also augment the levels of negatively charged phospholipids in their membranes [114, 115]. This adjustment in lipid composition aid in maintaining the membranés liquid crystalline state during moderate desiccation, thereby preserving the structural integrity of the membrane bilayer [114, 116].
In addition, these organisms enhance their survival in dry conditions by forming biofilms and boosting the production of exopolysaccharides (EPS), leveraging EPS's ability to retain water and thus create a more hydrated microenvironment [108]. It has been demonstrated that mutations affecting EPS biosynthesis can significantly reduce desiccation tolerance, as seen in
Research involving transcriptomic and proteomic analysis of microorganisms under desiccation stress has shown an increase in transcriptional regulator activity, such as “rpoS”, which regulates the DNA protection protein “Dps”, the trehalose synthesis gene “otsAB”, and other genes involved in counteracting oxidative damage, and “rpoE” which regulates exopolysaccharide synthesis and secretes protein misfolding across different species like
It is crucial to highlight that several organisms referred to as extremophiles do not belong to the categories mentioned earlier. Examples of such organisms include radiotolerant species, which exhibit remarkable tolerance to radiation due to their efficient DNA repair systems, making them potential candidates for bioremediation in areas contaminated with radioactivity. Additionally, organisms capable of thriving in environments with high concentrations of heavy metals or exposure to toxic compounds like hexachlorobenzenes have also been contemplated for roles in bioremediation. Similarly, there is a consideration for piezophiles or occasionally barophiles, which can adapt to extreme barometric pressure, in the context of their potential roles [122].
Microorganisms that thrive under extreme conditions have developed different and remarkable survival mechanisms. These unique properties make extremophiles particularly interesting for the biotechnology and pharmaceutical industries. Although numerous applications have already been discovered, the extensive possibilities and potential have yet to be fully explored [123].
With the rise of multidrug-resistant pathogens, the discovery of new antibiotics and bioactive microbial metabolites has become a priority. As a result, scientists are actively researching microorganisms isolated from extreme habitats in search of new antibiotics [3]. Under stress conditions, extremophiles produce organic compounds called extremolytes (carbohydrates, amino acids, exopolysaccharides, etc.). These extremolytes have been used in the pharmaceutical industry, particularly in areas such as cosmetics and therapeutics. They can potentially develop pharmacophores with anti-inflammatory and anti-proliferative effects, as well as chemo-preventive agents [124]. Ectoine, for example, was first isolated from the halophilic
Extremophilic organisms are increasingly being researched for natural substances, particularly those with antimicrobial effects against multi-resistant pathogens [38]. New bacterial species with remarkable biological activities have been identified and proposed, including
Several new microbial natural products were discovered from the
In addition to their antibacterial and antifungal activities, halophilic microorganisms have also shown other bioactivities producing halocins, cyclopeptides, alkaloids, and other metabolites. According to Velmurugane
More and colleagues isolated an acidophilic
Explorations into marine microorganisms have high-lighted their potential in pharmaceutical development, focusing on psychrophiles as a potential candidate for new antimicrobial drugs, such as the bacteriocin compound serraticin A, synthesized by
Moreover, the bioactive metabolites produced by deep-sea fungi have demonstrated a diverse spectrum in inhibiting the growth of cancer cells (Alkaloid from
Around a decade ago, extremophiles were considered unusual species and studied by a few researchers world-wide. Today, enzymologists are researching and utilizing these microbes in various industrial applications, which has become a promising field for them [21].
Many enzymes are found in organisms that live under harsh conditions and could be applied as biological catalysts in a variety of industrial domains, including the manufacture of biofuels and food to the application of the paper industry, biological detergents, xenobiotic-biodegradation compounds, and molecular biology [123]. For instance, enzymes from thermophiles are employed to catalyze chemical processes at high temperature that are difficult for enzymes that function at normal temperatures. One of the most successful extremozymes is “Taq polymerase,” which was derived from the thermophilic bacteria “
Recent studies have focused on thermophiles as promising agents for redox stress during the dye degradation process in textile wastewater treatment. The thermophilic laccase from
Lipolytic enzymes, known for their broad versatility, are essential in various industrial sectors, particularly food and cosmetics. Cold-adapted lipolytic enzymes, renowned for their exceptional characteristics and high specific activity, find extensive application as additives in household dishwashers and contribute to flavor development [146]. Salt-tolerant and cold-adapted α-amylases have a particular appeal for use in the textile detergent sector. Because many textile stains contain a high salt content, salt-tolerant enzymes must be used to remove them effectively [123]. Besides, Thermostable Superoxide Dismutases (SOD) is increasingly incorporated into cosmetic products, serving as a constituent of skin care and topical hair treatments, where it helps wound recovery, prevent hair greying, protect against UV rays, help reduce facial lines, and promote hair growth. L’Oreal (France) was a pioneer in the application of this enzyme in cosmetics and registered a patent in 1973 for a marine-derived SOD. Numerous prestigious brands, such as Avêne and Estee Lauder, have also incorporated this enzyme into their product formulations as a vital component [143].
In industrial processes, a few halophilic enzymes are used; among them, the H nuclease of
Converting starch process requires the exposure of enzymes to extreme pH and temperatures; therefore, optimization using extremophiles is required [149]. Oli-gosaccharide syrups are produced from starch through a tri-phase procedure: initially, the starch slurry is gelatinized at temperatures ranging from 90−100℃; it is then liquefied using α-amylase; and finally, digestion is carried out with glucoamylase. Initial pH values of the native starch slurry typically are between 3 and 5, so Employing acidophilic amylases will negate the need to neutralize the starch slurry before liquefaction, thereby reducing the time and cost involved in deriving oligosaccharides from raw starch.
several reports have documented acidophilic glucoamylases and amylases; primarily produced by acido-thermophilic archaea (
Extremophiles offer potential benefits in producing biocatalysts and organic compounds for efficient industrial processes, enhancing efficiency and productivity, and becoming a good platform for developing the next generation of industrial biotechnology [153, 154]; we have reviewed various extremophiles, their bioactive compounds and their biotechnological importance, as shown in Table 2.
Table 2 . Overview of different extremophiles and their biotechnological applications.
Extremophiles | Bioactive compounds | Applications | References |
---|---|---|---|
Halophiles | lipases, proteases, amylases, cellulases, Compatible solutes Nucleases, Halophilic laccase | Functional ingredients in food, biomedicine, and pharmaceutical industries Bioremediation of oil-polluted cosmetics applications Delignification and waste treatment | [155] [156] |
Thermophiles | DNA polymerase Thermostable Amylase | PCR, molecular biology Bioethanol production | [157], [158] |
Psychrophiles | Neutralproteases Proteases Amylases | dairy production, cheese maturation, Polymer-degrading additives in detergents, pharmaceuticals applications | [153] |
Acidophiles | Glucoamylase, protease, cellulases | Feed component, Valuable metals recovery | [159] |
Alkaliphiles | Haloalkaline cellulase | Chemical bleach for paper and pulp industries | [160] |
Oligotrophes/Oligophiles | Whole microorganism | Bioassay of consumableorganic carbon in potable water | [159] |
Metalophiles | Whole microorganism, E xopolysaccharide | Ore-bioleaching, bioreme-diation, biomineralization | [161] |
Piezophiles | Whole microorganism | Antibiotics production | [38] |
Xerophiles | Whole microorganism | Enhancing water-management strategies in desert plants. | [162] |
As mentioned in this review paper, extremophilic microorganisms, spanning the phylogenetic domains of
While many different adaptation strategies have been discovered, a lot remains to be known. Thus, extensive research in the field of extremophiles is required to know how these microorganisms adapt, survive, and function in extreme environments.
Meglali Amina wrote the manuscript. Ghellai Lotfi reviewed the research.
The authors have no financial conflicts of interest to declare.
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