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Microbiology and Biotechnology Letters

Review(총설)

Environmental Microbiology (EM)  |  Microbial Ecology and Diversity

Microbiol. Biotechnol. Lett. 2024; 52(3): 233-254

https://doi.org/10.48022/mbl.2406.06007

Received: June 14, 2024; Revised: August 28, 2024; Accepted: August 30, 2024

An Overview of Extremophile: Microbial Diversity, Adaptive Strategies, and Potential Applications

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

Abstract

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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

Introduction

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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 (Thermococci sp) and haloalkaliphiles that withstand both a high concentration of salt and alkalinity (Chromatium and Thiospirillum sp). They are mostly composed of prokaryotes, such as archaea and bacteria, with a few examples classified as eukaryotes [6, 7].

Figure 1.Categories of extremophiles including halophiles, peizophiles, acidophiles, alkaliphiles, psychrophiles, thermophiles, metal tolerance and others based on salt, pressure, pH, temperature, metal concentration and other type of stress conditions. Their metabolic products find applications in red, gray and white biotechnology [124].

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.

Biodiversity of Extremophiles

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The term “extremophile” was coined by McElroy in 1974, they are predominantly classified within the domains Eucarya, Archaea, and Bacteria, with the majority belonging to the latter two domains [14, 15]. They included different phyla (Fig. 2), including Firmicutes, Actinobacteria, Deinococcus-Thermus, Bacteroidetes, Euryarchaeota Crenarchaeota, Proteobacteria, Ascomycota, and Basidiomycota; These phyla comprise diverse genera, such as Bacillus, Halobacillus, Halomonas, Alkalibacillus, Geobacillus, Thermobacillus, Thalassobacillus, Lysinibacillus, Arthrobacter, Haloferax, Desemzia, Burkholderia, Exiguobacterium, Flavobacterium, Jeotgalicoccus, Nitrincola, Oceanobacillus, Pontibacillus, Paenibacillus, Pseudomonas, Psychrobacter, Sediminibacillus, Rhodococcus, Sporosarcina, Staphylococcus, Streptomyces, Virgibacillus and Penicillium [16].

Figure 2.Relationship Among extremophilic microbes isolated from varied extreme environments revealed by pehylogenetic tree [16].

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).

Figure 3.Exploring Microbial Diversity. (A) Cultivation-based Approach: Traditional method for isolating and characterizing microbial species(serial dilution, genetic analysis, phenotypic evaluation, and biochemical studies); (B) Metagenomic approach: constructing a metagenomic library to identify microbial communities (sequence based screening) and molecules (activity-screening) [7].

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 (Bacteria and Archaea domains) and 18S (Eucarya domain) of ribosomal RNAs [20]. By sequencing the 16S rRNA gene, the researchers discovered a large taxonomic diversity within the extremophilic microbial communities, demonstrating this method's usefulness in identifying a large diversity of microbes within a single sample and workflow [21].

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 (Deinococcus radiodurans). These bacteria are not dependent on extreme environmental conditions for their life cycle. (iii) Obligate: These extremophiles are organisms that can only carry out their life cycle when vital parameters reach the known limits for life. They cannot survive outside of extreme conditions, and this is especially true for Bacteria and Archaea. For example, “extreme acidophiles”, “moderate acidophiles”, and “acid-tolerant” species; the same pattern can be observed with other environmental parameters, such as temperature, salinity, pressure, etc., where the number of species capable of tolerating or growing in extreme conditions decreases as the intensity of the stress factor increases [24].

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 extremophilesGrowth characteristicSpeciesReferences
ThermophilesHigh temperatures 45-70℃Streptomyces mutabilis
Thermus aquaticus,
T. litoralis
Thermodesulfobacterium,
T. thermophiles,
Staphylothermus marinus		[27] [28]
PsychrophilesLow temperatures 0-25C° (optimum 15℃)Cryptococcuscylindricus
Cladosporium sp		[29] [30]
HalophilesHigh Salinity 1-20% (w/v) (optimum at 10-12%)Halobacterium sp. NRC-1
Bacillus subtilis LR-1
Halomonaselongata		[31] [32] [33]
Acidophileslow pH 0-5 (optimum 3-5)Thiobacillus thiooxidans,
Thermoplasmaacidophilum,
Thiobacillus acidophilus,
Ferrimicrobiumacidiphilum		[24]
AlkaliphilesHigh pH 9-12 (optimum around 10)Bacillusalcalophilus
Bacillus circulans
Bacillusclausii221(ATCC21522)		[8]
PiezophilesHigh Pressure >10 MPaThermococcus barophilus
Piezobacterthemophilus		[34]
XerophilesLow water activity and high desiccation (Aw 0.7-0.9)Xeromycesbisporus[35]
MetallophilesHigh metals conditions (Zn, Cd, Cu, Cr, Co, Ag, Pb, Hg…)FerroplasmaacidiphilumYt
Pseudomonas sp. W6		[36] [37]
RadiophilesIntense ionizing/non-ionizingradiations (X and Gamma rays/Ultraviolet)Deinococcusradiophilus, D. radiodurans,
Thermococcusradiotelerans.		[38]

Adaptation Mechanisms

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Salinity

Halophiles are diverse organisms that thrive in salty environments, including bacteria, archaea, and eukarya [39]. They can be found in habitats with a wide range of salt concentrations, from 0.3 M to 5.1 M. These environments can vary from moderately salty marine settings to highly saline areas such as salt lakes, mines, and unique locations like the Dead Sea [40]. Salt significantly impacts the stability, solubility, and shape of proteins, affecting their functional abilities [41]. Over time, halophiles have developed sophisticated strategies to cope with, adapt to, and survive the intense osmotic pressures in their environments through a process known as haloadaptation [42]. The study of halophiles' adaptive responses to high salinity reveals various mechanisms for managing osmotic stress from their external environment [43]. There are different adaptation strategies among halophiles, with some accumulating high levels of intracellular salt to match the external environment, while others, including halotolerant or moderate halophiles, exclude salt and produce organic solutes to achieve osmotic balance [44] (Fig. 4).

Figure 4.Adaptations of halophiles to high salinity conditions. (A) Macromolecules in non-halophilic organisms are destabilized, leading to water efflux from the cell and creating a turgor loss. (B) Moderate halophiles produce compatible organic solutes to preserve cellular function. (C) Extreme halophiles achieve adaptation in highly saline environments through equilibrium [39].

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 Halobacterium salinarium demonstrating a chemotactic response to acquire external compatible solutes [50]. Beyond their primary role, these solutes are utilized in various biotechnological applications, enhancing biomolecular stability, stress resistance, therapeutics, cosmeceuticals, cryoprotection, and facilitating gene transfer for increased osmotolerance in non-halotolerant species [51].

Halophile and halotolerant microorganisms have developed versatile molecular mechanisms to cope with saline stress. In this context, Zhou et al. have explored the mechanisms of halotolerant in six-type strains of Allopontixanthobacter and Pontixanthobacter by comparative genome analysis. Some genes that are directly linked to halotolerant are those involved in osmolyte synthesis, ions transport, membrane permeability control, polysaccharide biosynthesis, intracellular signaling, and SOS response (mutagenesis system that activates in response to DNA damage caused by high salt concentrations) [52].

Furthermore, the proteome comparison of the halotolerant Staphylococcus aureus under multiple osmotic stress conditions showed the differentially expressed proteins (DEPs) implicated in glycine betaine/proline transportation and biosynthesis, stress tolerance, fatty acid and cell wall biosynthesis, and the Krebs cycle, which may contribute to their osmotic stress tolerance. Also, halophiles have diverse DNA methylation and restriction-modification systems that regulate gene expression, restrict foreign DNA, and facilitate genome rearrangements and recombination in high-salt conditions [53].

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, Ferroplasma acidarmanus forms complex, multi-layered biofilms as a defensive strategy against saline conditions [55]. This multifaceted adaptation approach underscores halophiles' complexity and ingenuity in navigating their challenging habitats.

Temperature

Thermophiles, a category of extremophiles primarily composed of bacteria, archaea, and certain molds, thrive at high temperatures. They are categorized based on their optimal growth temperatures: moderate thermophiles (45℃ to 65℃), extreme thermophiles (up to 80℃), and hyperthermophiles (above 80℃) [56]. Despite sharing the same essential macromolecular components, RNA, DNA, proteins, and lipids as their mesophilic counterparts, thermophiles utilize several mechanisms to stabilize these molecules at elevated temperatures (Fig. 5A).

Figure 5.An overview of adaptations in thermophiles (A) and psychrophiles (B) [56].

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 Escherichia coli (Ec) proteins GroES and GroEL, respectively, which aid in folding, stabilize the intermediate conformational states, prevent the aggregation or misfolding of proteins in the cells, and restore their functions [65, 66]. Moreover, around 80% of the soluble protein in the thermophilic Pyrodictium occultum, grown at 108℃, 2℃ below its optimal growth limit, is a chaperone protein complex known as the thermosome, which preserves the other cellular proteins in a functional conformation [67].

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 Psychromonas ingrahamii might form biofilms as a defense against the cold, the specifics of their quorum-sensing systems remain unidentified [71].

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 Streptococcus thermophilus and ice, forming a dense protective layer on the outer membrane that regulates the molecular structure of extracellular ice crystals, which results in increased intracellular metabolic activity, depressed apoptosis, and reduced extracellular membrane damage [75]. The buildup of compatible solutes such as glycerol, mannitol, trehalose, sucrose, and glycine betaine helps to prevent cellular dehydration and shrinkage under subzero temperatures [73]. Polar carotenoids play a significant role in modulating membrane stability and fluidity [76]. They also act as antioxidants against reactive oxygen species (ROS), as photoprotectants against UV radiation, photosynthetic components, cryoprotectants, antimicrobials, and conferring resistance to low temperatures (meo-viscosity in temperature fluctuations)[77]. Psychrophiles may suppress primary metabolic processes for enduring survival, including the electron transport chain, glycolysis, and the pentose phosphate pathway [78] (Fig. 5B).

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].

pH

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].

Figure 6.Possible mechanisms for pH regulation in wide pH tolerant [98].

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 (i.e., ATPases, symporters, and antiporters), which are identified in the sequenced acidophile genomes of Bacillus acidocaldarius and Thermoplasma acidophilum. Therefore, acid tolerance potential increases when ATPase activity and levels are higher [88]. One of the critical characteristics of acidophilic archaea is the monolayer membrane, typically composed of large amounts of GDGTs (Glycerol dialkyl glycerol tetraether lipids), which are highly impermeable to protons [89]. The dominance of secondary transporters, which use the transmembrane electrochemical gradient of sodium ions or protons to drive transport; was discovered in the genome of acidophilic microorganisms, suggesting their importance in pH homeostasis [84]. Also, these adaptations include cytoplasmic buffers rich in basic amino acids like histidine, lysine, and arginine, which help neutralize excess protons. Bacteria employ this system to adapt to changes in pH value (in Streptococcus agalactiae) using an arginine deaminase system (ADI) to provide acid tolerance to the microbe [90].

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 Acidithiobacillus caldus [91]. Certain bacteria and archaea use sulfur compounds (e.g., sulfides, sulfates, elemental sulfur) in their metabolic processes to withstand highly acidic conditions, alongside small organic molecules (e.g., oxalic acid, lactic acid, acetic acid, proline) to regulate internal pH [92−94].

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 Picrophilus torridus genome has been shown to contain many genes that determine DNA repair proteins [88]. It is also noticeable that genes for protein “holdase chaperones” in acidophiles like Acidobacteriota, Bacillota, and Actinomycetota were clustered with genes encoding proteases, demonstrating a coordinated regulation of activities related to protein degradation and protection, thus avoiding the toxicity and accumulation of unfolded proteins [95]. Genome reduction in acidophiles has been discussed as a mechanism to minimize energy costs to survive in highly acidic environments where organisms must deploy various energy-intensive acid resistance mechanisms to keep their cytoplasmic pH neutral. The genomes of different acidophilic microorganisms, such as Leptospirillum, Ferrovum, Methylacidiphilum (Bacteria domain) and Picrophilus (Archaea domain), have been reported to be smaller (2.3, 1.9, 2.3 and 1. 5 Mb, respectively) compared to their closest phylogenetic relatives neutrophils [96].

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 Escherichia coli under alkaline pH conditions, and changes in the gene encoding Na+/ H+ anti-porters make it unable to grow in low hydrogen concentrations [99]. Furthermore, alkaliphiles use a reversed chemical gradient to facilitate ATP synthesis. The low concentration of H+ in the external environment makes it challenging to maintain a pH gradient for ATP production. The electrochemical gradient facilitates the retention of H+ close to the membrane surface and contributes to ATP production [100].

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, Bacillus alcalophilus reports producing the enzyme phosphoserine aminotransferase, which increases the percentage content of hydrophobic interactions and negatively charged amino acids at the interface; the alkaline stability stays enhanced [102].

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 E. coli is grown in higher pH conditions, it produces more organic acids in the cytoplasm, which help to maintain pH homeostasis and thereby prevent cellular damage [97]. In the case of obligate alkaliphilic fungi Sodiomyces alkaline (Ascomycota), it was found that it regulates their internal pH through the accumulation of polyamines (PA) in their cytoplasm to survive in extremely high pH of soda lakes [103].

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 Natrialba magadii, it was found that the GC content of the genome of the archaeon is relatively high (around 61.42%) and codes for some of the proteins which help in the homeostasis of pH (trehalose, spermidine, etc.). Sinorhizobium medicae WSM419 is another alkaliphile that has two plasmids, pSMED02 (1.24 Mb), and pSMED01 (1.57 Mb) that code for the genes that provide adaptive features to stress responses along with amino acid synthesis and energy conversion. Instead, the abundance of integrases, transposons, and other mobile elements in most alkaliphile plasmids suggests they also indicate an essential role in the plasticity and adaptability of alkaliphile genomes [97, 104].

Desiccation

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).

Figure 7.Adaptive mechanisms of xerotolerant bacteria [110].

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 Erwinia stewartii, Acinetobacter calcoaceticus, and E. coli, which exhibit up to a six-fold reduction in survival rates under desiccating conditions [117]. Some xerophiles adopt a state of dormancy to survive desiccation. For example, genera such as Clostridium and Bacillus can differentiate into spores, which are resilient to not only desiccation but also extreme temperatures, pressures, and radiation [118]. Non-sporulating prokaryotes may enter a meta-bolic dormancy or a viable but non-culturable (VBNC) state as a strategy against desiccation, a phenomenon observed in several species, including Salmonella enterica, Legionella pneumophila, and Sinorhizobium meliloti [119, 120].

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 S. enterica and E. coli. These organisms have signal transduction mechanisms that detect low aw and other environmental stressors, triggering regulatory activities that modulate gene expression and protein synthesis. Specifically, the induction of alternative sigma factors plays a crucial role in activating protective genes [111]. For example, Bacillus megaterium FDU301 was observed to upregulate 1422 genes under xeric stress: DNA protecting protein “dps”; biosynthesis of osmoprotectant ectoine “ectB, ectA”; genes regulating the oxidative stress response “perR”, “fur”, and “tipA”; catalase “katE”; genes involved in sporulation phase II “spoIIB, spoIIE, spoIIGA”; genes related to Fe2+ “feoB”; and small acid-soluble spore proteins “sspD” [112, 121]. Furthermore, Bradyrhizobium japonicum was observed to increase the expression of twelve transposases in response to arid conditions, highlighting the adaptive potential of microbial communities when they respond to extreme environmental conditions [87].

Other Extremes

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].

Potential Applications of Extremophiles

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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].

Pharmaceutical potentials

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 Ectothiorhodospira halochloris and has also been found in other bacterial species, including actinobacteria and alpha/gamma proteobacteria [125]. This ingredient is used for eye and skin care. Ectoin is an anti-inflammatory and can protect skin cells from damage caused by ionizing radiation. This is achieved through its ability to absorb ultraviolet radiation and prevent breaks in DNA strands [126].

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 Saccharothrix violacea sp. nov, which was first found in Kongju, Korea, in a gold mine cave. This bacterium shows strong antibacterial properties against Staphylococcus aureus, Bacillus subtilis, among others, Streptomyces murinus, and Micrococcus luteus, as well as antifungal activity against Saccharomyces cerevisiae, Candida albicans, and Aspergillus niger [127]. It has been known to produce many structurally diverse secondary metabolites, such as saccharomicins (hepta-decaglycoside), saccharothrixones (angucyclinones), saccharothriolides (10-membered macrolides), and saccharochelins (tetrapeptides) [128].

Several new microbial natural products were discovered from the Streptosporangium genus, including anti-biotics (vancomycin, erythromycin, and daptomycin), anticancer agents (bleomycin), and immune-suppressants (FK506) [129]. A new species named Streptosporangium becharense sp. Nov. selected in the Saharan region of Algeria. This species shows antibacterial and fungal effects against Bacillus subtili, S. aureus, Listeria monocytogens, E. coli, Micrococcus luteus, Pseudomonas fluorescens, Mycobacterium smegmatis, Candida albicans, Aspergillus carbonarius, Saccharomyces cerevisiae, and Mucor ramannianus [130]. Moreover, two strains of Streptomyces sp isolated from the Salar de Huasco polyextreme ecosystem (Chili) showed a strong and broad spectrum of antimicrobial efficacy against various Gram-negative and Gram-positive bacteria, alongside significant cytotoxic effects against a human liver cancer cell line, producing lanthipeptides and two novel class of lasso peptides named as huascopeptin and citrulassin C [131].

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 et al., the antibacterial properties of diverse pathogenic bacteria, including those found in various aquatic environments (Vibrio harveyi, Aeromonas hydrophila, Vibrio parahaemolyticus, and Pseudomonas aeruginosa), were observed in organic compounds derived from Halomonas salifodinae MPM-TC. Furthermore, these extracts demonstrated antiviral efficacy against the white spot syndrome virus in vitro [132]. However, Chen et al. conducted research highlighting the bioactivity of halophilic Bacillus species and other moderately halophilic bacterial strains. Of the 45 strains investigated, 23 showed growth inhibition against Bacillus subtilis, while two displayed inhibitory effects on Pseudomonas fluorescens, and one strain inhibited E. coli. Nearly all halophilic strains demonstrated inhibitory effects on one or multiple indicator fungal strains. One strain was found to be related to the Bacillus genus, while 12 strains were associated with the Halobacillus genus based on phylogenetic analysis [133].

More and colleagues isolated an acidophilic Bacillus subtilis from the saline soda lake of Lonar in India. This microorganism was reported for phospholipid antimicrobial compound synthesis, which exhibited high activity against common Gram-negative and positive pathogenic bacteria, alongside Candida parapsilosis. Thus, this compound suggest its utility against infections caused by Pseudomonas aeruginosa, E. coli, and S. aureus [134]. Furthermore, the alkaliphilic Nocardiopsis sp. Strain YIM 80133 has been reported to produce a new pyranonaphthoquinone, known as griseusin D, which possesses cytotoxic activity on human leukaemia and lung adenocarcinoma cell lines [135]. An additional multi-faced compound “Pyrocoll”, originating from the alkaliphilic Streptomyces sp. AK409, was effective against a variety of Arthrobacter strains and filamentous fungi, and it was also reported to have antimalarial effect against Plasmodium falciparum, and other antiparasitic activity against Trypanosoma cruzi [136].

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 Serratia proteamaculans which isolated from a soil sample in Isla de los Estados, Argentina, and was termed to be the first cold-active antimicrobial compound, with mode of action was proposed to involve either inhibition of the septation process or blocking DNA replication [137]. Also, subtilomycin, class I bacteriocin (Type I lantibiotic) produced by B. subtilis MMA7, isolated from the marine sponge Haliclona simulans along the western Irish coast. The peptide usually compromises the cell membranes of susceptible bacteria, either by inhibiting poreforming or membrane biosynthesis, results in good antibacterial activity, and has also demonstrated significant antibacterial efficacy against vancomycin-resistant E. coli, vancomycin-intermediate S. aureus (VISA), methicillin-resistant S. aureus (MRSA), and different pathogenic Candida species [138].

Moreover, the bioactive metabolites produced by deep-sea fungi have demonstrated a diverse spectrum in inhibiting the growth of cancer cells (Alkaloid from Penicillium commune SD-118), bacteria (Citromycetin Analogue from Ascomycota sp. Ind19F07), and viruses (Polyketides from Cladosporium sphaerospermum 2005-01-E3) [139]. In addition, polysaccharides secreted by microorganisms such as Aphanothece halophytica GR02 have been shown to have remarkable anti-cancer, anti-inflammatory, antioxidant, anti-ageing and other medicinal values [32, 140, 141]. Besides, Frigocyclinone, a new angucyclinone antibiotic, extracted from the psychrotolerant Streptomyces griseus strain NTK 97, isolated from Terra Nova Bay soil in Antarctica, and showed antibacterial efficacy against Gram-positive bacteria such as B. subtilis and S. aureus. The psychrotolerant Penicillium algidum (IBT 22067) is another fungus, isolated from the East Oksestien soil, Greenland, was identified to synthesize psychrophilin D, which showed cytotoxic activity against murine leukaemia P-388 cells [135]. These findings indicate that extreme environments are promising for discovering new and valuable microorganisms with significant pharmaceutical potential.

Biotechnological application

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 “Thermus aquaticus” and has already been used in PCR techniques, revolutionizing the field of molecular biology; similarly, thermophilic Geobacillus sp. Iso5 and Geobacillus spp. were isolated from thermal springs, and have been found to produce hyper-thermostable α-amylase, exhibiting optimal enzyme activities at temperatures of 140 and 90℃, respectively [142].

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 Bacillus sp. strain FNT has proven its efficacy in bio-decolorize eight recalcitrant synthetic dyes from three structurally diverse groups: anthraquinone, triarylmethane, and azo dyes [143], and is now commercially available for Research purposes (as an enzyme product) from Swissaustral LLC in the United States. In another study, the Acinetobacter baumannii strain was identified as a Reactive Red 198 degrader with 96.2% efficiency under hypersaline conditions. Also, a haloalkalophilic Bacillus albus DD1was investigated as a degrader of azo dye RB5, achieving a removal efficiency of 98% [144, 145].

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 Micrococcus varians subsp. Halophilus which is commercially applied to produce the flavoring agent 50-guanylic acid (50-GMP). This enzyme functions efficiently in conditions with 12%salt concentration and at temperatures around 60℃[147]. Also, halophilic peptidases and proteases from the halo-bacterium Nesterenkonia sp. F are noted for their organic solvent stability, such as toluene, benzene, and chloroform, which leads to a rapid reduction in salt concentration and, eventually, addresses the issue of metal corrosion attributed to salt residues [148].

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 (Sulfolobus, Picrophilus, Thermoplasma) and bacteria (Alicyclobacillus, Bacillus) and have maximal activities at pH between 3 and 6 [150]. As for Alkaliphiles, particularly their alkaline, cellulases, and amylases as biological detergents, they have had a significant impact on industrial applications [151]. Moreover, alkaliphilic xylanase has been employed in the bleaching process of soda pulps and kraft without the need for pH adjustment, enhancing the process's economic viability [143]. Regarding radiophilic enzymes, there are no reports regarding their isolation [150]. However, radiophilic microorganisms used as whole cells, such as Deinococcus radiodurans, which grow in environments with chronic radiation exposure up to 60 Gray/h, are used for decontamination and uranium bio-precipitation from the radioactive waste sites through the removal of uranyl ions [152].

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.

ExtremophilesBioactive compoundsApplicationsReferences
Halophileslipases, 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]
ThermophilesDNA polymerase
Thermostable Amylase		PCR, molecular biology
Bioethanol production		[157], [158]
PsychrophilesNeutralproteases
Proteases
Amylases		dairy production,
cheese maturation, Polymer-degrading additives
in detergents, pharmaceuticals applications		[153]
AcidophilesGlucoamylase, protease, cellulasesFeed component, Valuable metals recovery[159]
AlkaliphilesHaloalkaline cellulaseChemical bleach for paper and pulp industries[160]
Oligotrophes/OligophilesWhole microorganismBioassay of consumableorganic carbon in potable water[159]
MetalophilesWhole microorganism, E xopolysaccharideOre-bioleaching,
bioreme-diation,
biomineralization		[161]
PiezophilesWhole microorganismAntibiotics production[38]
XerophilesWhole microorganismEnhancing water-management strategies in desert plants.[162]

Conclusion

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As mentioned in this review paper, extremophilic microorganisms, spanning the phylogenetic domains of Bacteria, Archaea, and Eukarya, survive under harsh conditions such as cold, high temperatures, acidity, alkalinity, drought, and salinity. They are categorized according to the conditions in which they grow, including thermophiles, psychrophiles, alkalophiles, acidophiles, xerophiles, halophiles, etc., with the existence of polyex-tremophiles. These microorganisms employ diverse adaptation strategies involving structural, physiological, and molecular modifications, such as adaptations in membrane structure and metabolic processes, as well as modifications in proteins and nucleic acids. Their significance extends to both pure and applied research, particularly relevant in pharmaceutical and biotechnological applications.

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.

References

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