Hot Springs as Reservoirs of Valuable Microbes, Metabolites, and Minerals with Ecological, Biotechnological and Bioeconomic Perspectives

Abstract

Hot springs represent unique geothermal ecosystems where extreme physicochemical conditions intersect with remarkable microbial diversity and metabolic innovation. These natural laboratories harbor specialized communities of thermophilic and hyperthermophilic microorganisms that have evolved exceptional adaptations to elevated temperatures, extreme pH, and high salinity. This review synthesizes current understanding of hot spring systems as multifunctional natural resources, examining their roles in fundamental microbiology, biotechnology, and sustainable development. We explore the ecological principles governing microbial community assembly, the taxonomic and functional diversity of prokaryotic and eukaryotic microorganisms, and the genomic mechanisms underlying thermophilic adaptation. Hot springs yield enzymes revolutionizing molecular biology and industrial catalysis, bioactive metabolites with pharmaceutical potential, and novel bioremediation capabilities including plastic degradation. Beyond biological significance, these systems contain valuable minerals and rare earth elements, supporting an emerging bioeconomy integrating wellness tourism, bioprospecting, and sustainable resource extraction. However, critical knowledge gaps remain regarding viral ecology, horizontal gene transfer, eukaryotic diversity, and climate change impacts. We emphasize that hot springs merit renewed interdisciplinary attention as model systems for understanding extremophile physiology, early life evolution, and the development of nature-based biotechnological solutions. Realizing their full potential requires balanced management strategies that preserve ecosystem integrity while enabling responsible utilization of these irreplaceable geobiological resources.

1. Introduction

1.1. Hot Springs as Natural Laboratories

Hot springs are geothermal features where subsurface fluids emerge at temperatures exceeding 50 °C or at least 10 °C above mean annual air temperature [1]. These ecosystems function as accessible natural laboratories for studying life under extreme conditions, offering unique advantages over other extreme environments such as deep-sea hydrothermal vents. Their accessibility, visible microbial communities, and well-defined physicochemical gradients make hot springs ideal model systems for investigating extremophile physiology, community ecology and metabolic innovation [2,3].

Globally, over 15,000 documented hot springs occur concentrated along tectonic plate boundaries, particularly the Pacific Ring of Fire and Alpine-Himalayan belt [4]. Despite their abundance, hot springs remain undersampled relative to their scientific importance. Taxonomic discovery rates have increased from approximately 8 novel thermophilic species annually during 2000–2010 to approximately 20 species annually during 2010–2024, with this accelerating trend continuing through 2025 as cultivation-independent metagenomic approaches reveal vast hidden diversity [5,6].

A landmark 2025 metagenomic study recovered nearly 3000 archaeal genomes from 152 terrestrial geothermal springs, spanning 12 phyla, with 19% representing entirely new taxa and 70% lacking formal nomenclature [6]. This massive genomic dataset confirms that these ecosystems harbor immense undiscovered microbial diversity with profound implications for understanding extremophile evolution, metabolic innovation, and biotechnological potential [7].

1.2. Evolutionary and Economic Significance

The study of hot spring microbiomes extends beyond contemporary ecology to questions of deep evolutionary significance. Early life forms are hypothesized to have been hyperthermophiles that colonized hydrothermal environments approximately 3.8–4.0 billion years ago [8,9]. The phylogenetic positioning of thermophilic lineages near the roots of both bacterial and archaeal domains supports this hypothesis, suggesting that thermophily represents an ancestral trait rather than a derived adaptation. Understanding thermophilic adaptation mechanisms thus illuminates both the origins of life on Earth and potential forms of life on other planetary bodies with geothermal activity [7].

While hot springs serve as windows into early Earth and potential extraterrestrial life, they also function as contemporary resources supporting human health and economic development. The global thermal springs tourism market, valued at USD 57.27 billion in 2024, is projected to reach USD 130.78 billion by 2030, representing a robust compound annual growth rate (CAGR) of 14.8% from 2025 to 2030 [10]. This substantial growth is driven by post-pandemic demand for natural healing experiences, increasing consumer awareness of health benefits, and growing preference for wellness-focused travel. The Asia-Pacific region, accounting for 46.83% of global revenues in 2023, leads market growth due to the cultural significance of hot springs in countries such as Japan, China, and South Korea. Europe is projected to grow at a CAGR of 14.0% from 2024 to 2030, driven by its established thermal bath culture and spa heritage. As of 2024, there are 35,099 thermal and mineral springs establishments across 130 countries, with 140-plus new projects in the pipeline, reflecting strong 18% annual growth projections through 2025 [11]. This economic significance underscores the urgent need for science-based management frameworks that preserve microbial diversity and ecosystem integrity while enabling sustainable utilization.

This review synthesizes current knowledge of hot springs as integrated natural resource systems at the intersection of microbiology, geochemistry, biotechnology, and economics. We address geological and geochemical foundations; ecological principles governing microbial community assembly; taxonomic diversity of prokaryotic and eukaryotic communities; biotechnological applications; economic resources, including minerals and rare earth elements; and critical knowledge gaps and research priorities. We emphasize cultivation-independent genomic approaches that are revolutionizing our understanding of hot spring microbial diversity and functional potential.

Figure 1. Two common types of natural and man-made hot springs used for leisure or health therapy are schematically represented on the scale of minerals and beneficial microorganisms for human health.

Figure 1. Two common types of natural and man-made hot springs used for leisure or health therapy are schematically represented on the scale of minerals and beneficial microorganisms for human health.

2. Geological and Geochemical Foundations

2.1. Formation Mechanisms and Energy Sources

Hot springs form where geothermally heated subsurface fluids reach Earth’s surface through permeable fracture networks and faults [12]. The fundamental process begins with meteoric water penetrating deep into Earth’s crust. In tectonically active regions, this water is heated by proximity to magmatic bodies or elevated geothermal gradients [13]. These fluids, reaching temperatures of 150–350 °C at depth, undergo prolonged interaction with host rocks under elevated temperature and pressure, dissolving minerals through thermally enhanced hydrolysis (Figure 1) [14].

This geothermal circulation creates distinctive aqueous chemical environments laden with dissolved constituents that both sustain microbial life and record geological processes. The emergent fluids carry electron donors, including hydrogen, hydrogen sulfide, and ferrous iron; electron acceptors, including sulfate and nitrate; essential nutrients, including phosphate and trace metals; and dissolved gases, including carbon dioxide, methane, and noble gases [15]. Upon reaching the surface, rapid cooling, degassing, atmospheric mixing, and biological activity drive mineral precipitation, creating characteristic terraces, pools, and fumaroles.

Hot springs generate abundant thermodynamic disequilibrium through continuous delivery of reduced compounds into oxidizing surface environments [16]. Thermophilic microorganisms harness diverse energy sources: phototrophy in photic zones below approximately 73 °C, where cyanobacteria perform oxygenic photosynthesis [17]; aerobic chemolithotrophy, where hydrogen oxidation, sulfide oxidation, and iron oxidation support chemolithoautotrophic communities [18]; anaerobic respiration utilizing alternative electron acceptors; and fermentation of organic matter. This metabolic diversity creates tightly coupled biogeochemical cycles where products of one metabolic guild become substrates for others, establishing complex food webs fundamentally powered by geothermal energy rather than solar radiation [19].

2.2. Chemical Diversity and Classification

Hot spring chemistry exhibits remarkable diversity controlled by source fluid composition, water-rock interaction conditions, host rock mineralogy, and near-surface processes. The most widely applied geochemical classification recognizes four principal types: neutral-chloride springs originating from deep circulation systems with chloride-rich waters; acid-sulfate springs where volcanic gases dissolve in shallow groundwater producing extremely acidic conditions (pH < 3); acid-sulfate-chloride springs representing hybrid systems; and bicarbonate springs developing in peripheral zones with shallow circulation [20,21].

Each geochemical type presents unique selective pressures that filter microbial colonization, resulting in chemically predictable community assemblages. Acidic hot springs impose extreme selective pressure through low pH, high concentrations of dissolved metals, and limited nutrient availability, typically supporting low-diversity communities dominated by archaea of the order Sulfolobales and acidophilic bacteria, including Acidithiobacillus [22]. Neutral to alkaline springs harbor substantially higher bacterial diversity spanning multiple phyla, including Aquificae, Deinococcus-Thermus, Chloroflexi, and Proteobacteria [23,24].

2.3. Geothermal Gases and Biogeochemical Connections

Gases dissolved in geothermal fluids exsolve upon pressure reduction during ascent, creating visible fumaroles and influencing dissolved gas content. Gas composition provides critical information on subsurface processes [25]. Major gases include nitrogen, carbon dioxide, hydrogen sulfide, methane, hydrogen, helium, argon, and ammonia [26]. Noble gases provide powerful tracers for subsurface processes, while carbon and sulfur isotopes distinguish magmatic, thermogenic, and biogenic sources [27].

Geothermal gases fuel chemolithoautotrophic primary production, sustaining hot spring ecosystems independent of photosynthesis. Hydrogen oxidation, sulfide oxidation, and methanogenesis establish geochemical-biological linkages coupling deep-Earth processes to surface ecosystem functioning, demonstrating that hot spring food webs are fundamentally supported by geothermal energy rather than solar radiation [18,28].

3. Ecological Organization and Community Assembly

3.1. Microbial Life in Hot Springs

The 3.5-billion-year-old Archean fossil hot spring stromatolites of Western Australia’s Pilbara region exemplify the origin of microbial life from geothermal environments [29,30]. Geothermal activity dissolves minerals through heat and pressure, creating a unique chemical milieu enriched with sulfur, iron, and nitrogen—essential nutrients providing redox energy for microbial growth and metabolism [31]. Hot springs fulfill universal life attributes: thermodynamic disequilibrium utilization, covalently bonded molecules (N, P, O, S), liquid solvent availability, and capacity for Darwinian evolution [32,33] (Figure 2). Three essential niches—biofilms, water column, and sediments—harbor nutritionally distinct microbiota. Biofilms exhibit sulfur-related functions and multilayered photosynthetic communities; water contains heavy metal-oxidizing bacteria dependent on dissolved organic matter; sediments harbor thermophilic archaea and eukaryotes adapted to low-oxygen, high-pressure conditions [34,35,36]. This niche interplay creates diverse, interdependent microbial communities [37] (Figure 2).

3.2. Spatial Structure and Habitat Types

Hot spring microbial communities exhibit pronounced spatial organization driven by physicochemical gradients and biological interactions. Three primary habitat types host distinct microbiota: biofilms, water column communities, and sediments (Figure 3) [38].

Biofilms represent the most biomass-rich habitat, consisting of stratified microbial communities encased in extracellular polymeric substances (EPS). These self-organized structures range from less than 1 mm to greater than 10 cm in thickness, depending on conditions. In photic zones, cyanobacterial phototrophs dominate surface layers, performing oxygenic photosynthesis that generates organic carbon and molecular oxygen [38]. Deeper strata harbor chemolithotrophs oxidizing reduced inorganic compounds and heterotrophs consuming organic matter. The physical structure creates microenvironments with steep gradients in oxygen concentration, pH, and redox potential across millimeter scales, enabling coexistence of metabolically incompatible organisms, obligate aerobes and obligate anaerobes within the same macroscopic structure [39].

Groundbreaking studies from Yellowstone National Park published in January 2025 revealed that cyanobacterial Synechococcus species and filamentous Chloroflexus species actively cooperate to enhance community fitness through interspecies behavioral coordination [40]. Using a binary consortium model with Synechococcus OS-B′ and Chloroflexus MS-CIW-1 isolated from hot spring mats, researchers demonstrated that these distantly related microbes exhibit cooperative motility toward light, enhanced colonization capabilities, and construction of more robust biofilm structures compared to either species alone. Individual species displayed distinct behaviors: Chloroflexus MS-CIW-1 formed bundles of filaments moving in all directions with no directional light bias, while Synechococcus OS-B′ exhibited positive phototaxis but was slightly less motile. When combined, the consortium moved further distances than either species individually and formed ordered arrays where both species aligned with the light source. This cooperative behavior was abolished when a nonmotile pilB mutant of Synechococcus OS-B′ was used, confirming the essential role of cyanobacterial motility in driving collective behavior. Electron microscopy revealed close interspecies physical associations, and the binary consortium produced more adherent biofilms than individual species, demonstrating that physical interactions and behavioral coordination between taxonomically distant microbes enhance survival and ecosystem functioning. This discovery challenges the traditional view of hot spring microbial mats as static assemblages of independently functioning cells competing for resources, revealing instead dynamic cooperative systems where metabolite exchange, physical interactions, and coordinated motility between evolutionarily divergent organisms enhance niche colonization and biofilm robustness [41].

Water column communities comprise planktonic microorganisms exhibiting markedly lower biomass compared to biofilms but maintaining distinct phylogenetic composition [42,43]. These free-living populations occupy the pelagic zone of hot spring pools and channels, experiencing different selective pressures than biofilm-associated microbes. Water column communities include chemolithoautotrophic bacteria oxidizing dissolved reduced compounds (hydrogen, sulfide, ferrous iron) as well as heterotrophic bacteria metabolizing dissolved organic carbon released from biofilms or produced by planktonic phototrophs in moderate-temperature zones [44]. The taxonomic composition of water column communities differs substantially from adjacent biofilm populations, with enrichment of motile, fast-growing taxa adapted to nutrient acquisition in dilute aqueous environments [42,45]. These planktonic populations serve as dispersal agents for colonization of new surfaces and play critical roles in biogeochemical cycling by processing dissolved chemical species in the water column before they reach biofilm surfaces [46].

Sediments accumulate at pool bottoms, creating redox stratification with oxic surface layers overlying anoxic zones that harbor sulfate-reducing bacteria, methanogens, and fermentative bacteria [47]. Sediment communities perform critical ecosystem functions, including organic matter decomposition, nutrient regeneration, and terminal electron-accepting processes [48]. The upper sediment layers (0–2 mm) contain aerobic heterotrophs and facultative anaerobes, while deeper zones (>2 mm) become progressively more reducing, supporting obligate anaerobes that conduct sulfate reduction, methanogenesis, and fermentation [49]. Thermophilic archaea dominate the deepest, hottest sediment zones, where temperatures may exceed water column temperatures by 5–15 °C due to conductive heating from below. Eukaryotic thermophiles, including thermotolerant fungi and protists, also colonize sediments, where they function as decomposers and grazers [50]. Sediment communities exhibit the highest phylogenetic diversity of the three habitats, reflecting the multitude of microniches created by vertical chemical gradients, particle surfaces, and microbial microcolonies [51]. The sediments serve as a reservoir for dormant cells and genetic diversity, with some thermophiles existing in spore or cyst forms that can persist for extended periods. Biogeochemical cycling in sediments is tightly coupled to overlying water chemistry and biofilm productivity, with organic matter produced by photoautotrophs and chemoautotrophs in biofilms ultimately mineralized in sediments, completing nutrient cycles and regenerating electron acceptors for chemolithotrophic metabolism [52].

The interplay between these three habitat types creates functionally integrated ecosystems. Organic matter produced by photoautotrophs in biofilms is consumed by heterotrophs within biofilms, released as dissolved organic carbon to water columns, and ultimately deposited in sediments, where it fuels anaerobic food webs [53]. Reduced compounds produced by anaerobic sediment communities (sulfide, methane, ammonium) diffuse upward to oxic zones where they are oxidized by chemolithotrophs, closing biogeochemical cycles [54]. This spatial organization and functional integration create diverse, interdependent microbial communities where ecological processes at one spatial scale influence community structure and function at adjacent scales [55].

3.3. Environmental Drivers of Community Composition

Microbial community composition responds to three primary environmental gradients: temperature, pH, and salinity that act as hierarchical filters on community assembly. Temperature exerts the strongest selective pressure. Mesophilic zones below 40 °C are dominated by conventional soil and aquatic bacteria. Thermophilic zones (40–75 °C) host specialized thermophiles, while hyperthermophilic zones above 75 °C are exclusively inhabited by archaea and the most thermally adapted bacteria [56,57]. This temperature-driven taxonomic turnover reflects fundamental thermodynamic constraints on protein stability, membrane fluidity, and nucleic acid structure.

pH shapes community composition through multiple mechanisms: direct physiological stress on cellular membranes and proteins; modulation of metal speciation and bioavailability; and alteration of transmembrane electrochemical gradients affecting energy metabolism. Acidic hot springs with pH below 3 typically support low-diversity, specialist-dominated communities composed of acidophilic archaea and bacteria that have evolved specialized proton-pumping mechanisms [58,59]. Neutral to alkaline springs harbor substantially higher bacterial diversity, reflecting reduced selective pressure and broader physiological compatibility [23].

Salinity creates osmotic stress requiring specialized adaptations, including synthesis of compatible solutes and accumulation of potassium ions [60]. Thermophiles accumulate unusual compatible solutes such as di-myo-inositol-phosphate and mannosylglycerate in response to osmotic stress, enabling them to maintain cellular function under combined thermal and osmotic challenges.

This ecological organization—spanning multiple spatial scales, metabolic guilds, and trophic levels creates multifunctional systems that support both fundamental research and applied innovation. The biofilms that serve as model systems for microbial cooperation also produce enzymes with industrial value. The chemolithoautotrophs that reveal principles of energy metabolism also remediate toxic pollutants. Understanding these fundamental ecological principles is thus inseparable from realizing hot springs’ biotechnological potential.

4. Prokaryotic Diversity and Thermophilic Adaptations

4.1. Classification and Thermo-Adaptation Mechanisms

Thermophilic prokaryotes are classified based on growth temperature ranges (Figure 4): facultative thermophiles capable of growth at both mesophilic and thermophilic temperatures (25–50 °C); moderate thermophiles with optimal growth at 40–70 °C; obligate thermophiles requiring temperatures of 50–80 °C; and hyperthermophiles growing optimally at 65–113 °C [8]. The current temperature record holder is Methanopyrus kandleri strain 116, an anaerobic methanogen isolated from deep-sea hydrothermal sediments that grows at 122 °C [61], approaching the theoretical upper temperature limit for life estimated at 130–150 °C based on thermodynamic constraints on protein stability and the hydrolysis of key biological molecules.

Survival at extreme temperatures requires coordinated molecular adaptations across all cellular systems. Figure 5 illustrates how these six major adaptation categories—(A) genomic features, (B) proteomic modifications, (C) RNA stabilization, (D) membrane composition, (E) molecular chaperones, and (F) DNA repair pathways—are coordinated through integrated regulatory networks. This multidimensional regulatory system enables maintenance of cellular homeostasis under conditions that would denature most proteins within seconds, representing one of the most remarkable examples of biological adaptation to extreme environments. These adaptations operate at multiple biological scales and are integrated through complex regulatory networks:

Genomic Adaptations: Thermophile genomes exhibit structural features enhancing DNA stability, including reverse gyrase—a unique topoisomerase that introduces positive supercoils (overwound DNA structure) to prevent thermal denaturation [62]—DNA-binding proteins that compact chromosomes and protect DNA from thermal damage [63,64], and optimized codon usage favoring thermally stable tRNAs. While elevated genomic GC content has been associated with thermophily in some lineages [65], this feature is not universal across all thermophiles [66]. For instance, the hyperthermophile Pyrococcus furiosus, which grows optimally at 100 °C [67], possesses a genomic GC content of only 41% [68]. This exception demonstrates that thermostability results from coordinated multi-level adaptations rather than relying on any single mechanism such as GC content elevation [69]. The interplay of reverse gyrase activity, DNA-binding proteins [70], enhanced repair systems, and structural modifications to proteins, membranes, and RNAs collectively enables survival at extreme temperatures, with different thermophilic lineages emphasizing different combinations of these mechanisms based on their evolutionary history and specific environmental conditions [71].

Proteomic Adaptations: Thermostable proteins resist thermal denaturation through multiple structural modifications: increased hydrophobic amino acid content in protein cores that strengthens hydrophobic interactions; enhanced networks of ion pairs (salt bridges) on protein surfaces that stabilize tertiary structure; shorter and more rigid loop regions that reduce conformational flexibility; increased proline content that restricts backbone mobility; and oligomerization to form multimeric complexes with enhanced thermal stability [72,73]. These modifications work synergistically to maintain protein structure and catalytic activity at temperatures that would denature mesophilic proteins within seconds [74].

RNA Modifications: Ribosomal RNAs and transfer RNAs contain extensive post-transcriptional modifications, including pseudouridines and methylations that enhance thermal stability [75,76]. Thermophiles also exhibit enhanced secondary structure in RNAs through increased base pairing, creating more stable RNA conformations resistant to thermal denaturation [77].

Membrane Adaptations: Archaeal thermophiles employ ether-linked lipids—which exhibit superior chemical stability compared to the ester-linked lipids of bacteria—while hyperthermophiles utilize tetraether lipids that span the entire membrane as monolayer structures, eliminating the fluid bilayer that would become unstable at extreme temperatures [78,79,80]. Bacterial thermophiles increase membrane fatty acid saturation and adjust fatty acid chain length to maintain optimal membrane fluidity [81].

Molecular Chaperones: Heat shock proteins, including Hsp70 and Hsp90 families, are constitutively expressed at high levels in thermophiles, providing continuous protein quality control by assisting in proper folding, preventing aggregation, and refolding damaged proteins [82,83]. This constitutive expression contrasts with mesophiles, which only upregulate heat shock proteins under stress conditions [84].

DNA Repair Pathways: Enhanced DNA repair systems operate with exceptional efficiency to counteract the accelerated rates of spontaneous DNA damage (depurination, deamination, strand breaks) that occur at elevated temperatures [85,86]. Thermophiles possess highly efficient base excision repair, nucleotide excision repair, and SOS response systems that rapidly detect and repair DNA lesions [87,88,89].

Compatible Solutes: Thermophiles accumulate unusual compatible solutes such as di-myo-inositol-phosphate, mannosylglycerate, and diglycerol phosphate in response to both thermal and osmotic stress [90,91,92]. These organic solutes stabilize proteins through preferential exclusion mechanisms, maintain cellular hydration, and enable growth under combined high temperature and high salinity conditions common in many geothermal environments [93,94].

This multidimensional regulatory network—spanning genome architecture, protein engineering, RNA stability, membrane composition, protein quality control, DNA maintenance, and osmotic adaptation—enables maintenance of cellular homeostasis under conditions that would denature most proteins, melt DNA, and disrupt membranes within seconds [95,96,97]. The evolutionary convergence of these diverse mechanisms across phylogenetically distant thermophilic lineages demonstrates the profound selective pressure imposed by high-temperature environments and the remarkable plasticity of cellular biochemistry in responding to extreme thermal stress [98,99].

However, universal adaptation mechanisms may not be observed; adaptation mechanisms are usually associated with species and their habitats. In many cases, the cell undergoes global physiological changes, thereby achieving survival at elevated temperatures [100,101].

Figure 5. Multi-level diagram showing six adaptation categories coordinated through omics networks: genomic adaptations including elevated GC content and codon optimization; proteomic adaptations including amino acid substitutions, disulfide bonds, and oligomerization; RNA modifications including rRNA modifications and enhanced secondary structure; lipid adaptations including archaeal ether lipids, saturation, and membrane composition; cellular chaperones including heat shock proteins Hsp70/90; and DNA repair pathways including SOS response and nucleotide excision repair. Arrows indicate coordinated regulation across adaptation levels.

Figure 5. Multi-level diagram showing six adaptation categories coordinated through omics networks: genomic adaptations including elevated GC content and codon optimization; proteomic adaptations including amino acid substitutions, disulfide bonds, and oligomerization; RNA modifications including rRNA modifications and enhanced secondary structure; lipid adaptations including archaeal ether lipids, saturation, and membrane composition; cellular chaperones including heat shock proteins Hsp70/90; and DNA repair pathways including SOS response and nucleotide excision repair. Arrows indicate coordinated regulation across adaptation levels.

Archaeal thermophiles employ ether-linked lipids that provide superior chemical stability, while tetraether lipids spanning the entire membrane as monolayers characterize hyperthermophiles [102]. Heat shock proteins are constitutively expressed at high levels, DNA repair systems operate with exceptional efficiency, and compatible solutes stabilize proteins and maintain cellular hydration [60,103]. This multidimensional regulatory network enables maintenance of cellular homeostasis under conditions that would denature most proteins within seconds.

4.2. Bacterial and Archaeal Diversity

Having examined the molecular mechanisms enabling thermophily, we now turn to the question of how many thermophilic lineages have evolved these adaptations and where they occur across the tree of life. The diversity of thermophilic prokaryotes has only recently become apparent through cultivation-independent approaches that bypass the limitations of traditional culturing.

Hot spring bacterial diversity has been revolutionized by cultivation-independent metagenomics, revealing that less than 1% of hot spring bacteria are readily cultivable using standard techniques [104]. Between 2015–2025, an average of 18–20 novel thermophilic bacterial species has been formally described annually, confirming that hot springs remain significantly undersampled reservoirs of microbial diversity. This accelerating discovery rate reflects both improved cultivation techniques and the widespread adoption of cultivation-independent metagenomic approaches that reveal the vast uncultured majority of thermophilic bacteria [105].

Key bacterial phyla include Aquificae, comprising obligate chemolithoautotrophs oxidizing hydrogen and sulfur; Deinococcus-Thermus, including the biotechnologically significant genus Thermus; Chloroflexi, ubiquitous in biofilms; Firmicutes spanning diverse metabolisms; and thermophilic representatives of Proteobacteria [7,106,107]. Recent discoveries include Thermomonas species from Asian geothermal systems, Sporanaerobium hydrogeniformans producing hydrogen gas, and Thermus parvatiensis, reinforcing Thermus as a prolific source of thermostable enzymes [108,109]. The extensive prokaryotic diversity documented above represents only part of hot spring microbial communities [110,111]. While archaea and bacteria dominate environments above 70 °C, eukaryotic microorganisms become increasingly abundant and functionally important at lower temperatures, performing critical roles as grazers, decomposers, and primary producers that shape ecosystem structure and nutrient cycling (

Table 1. Representative Thermophilic Bacterial Species from Hot Springs (2000–2025).

Sr. No.	Species	Location	Country	T (°C)	pH	Energy Source	Primary Metabolism	O2 Requirement	Reference
1	Tenuifilum osseticum sp. nov.	Hydrothermal spring	Russia (North Ossetia)	55	6.8–7.2	Chemoorganotroph	Fermentation, polysaccharide metabolism	Anaerobe	[112]
2	Thermomonas flagellata sp. nov.	Hot spring sediments, Yunnan	China	45	7.0	Chemoorganotroph	Respiration	Aerobic	[113]
3	Marmoricola caldifontis sp. nov.	Hot spring sediment, Tibet	China	35–50	6.5–8.0	Chemoorganotroph	Respiration	Aerobic	[114]
4	Arenimonas fontis sp. nov.	Geothermal spring, Chukotka	Russia (Arctic)	50	6.0–9.5	Chemoorganoheterotroph	Polysaccharide metabolism	Aerobic	[115]
5	Crenotalea thermophila gen. nov.	Sulfur-turf biofilm, Okuhodaka	Japan	45–50	5.5–7.5	Chemolithotroph/Chemoorganotroph	Fermentation, nitrate respiration	Aerobic	[116]
6	Thermotoga profunda sp. nov.	Terrestrial hot spring	Japan	65	7.4	Chemoheterotroph	Thiosulfate-reduction	Anaerobe	[117]
7	Fontisphaera persica gen. nov.	Hot spring water, Baikal	Russia	45	6.8	Chemoorganoheterotroph	Polysaccharide metabolism	Facultative anaerobe	[118]
8	Sporanaerobium hydrogeniformans gen. nov.	Aravali hot spring, Ratnagiri	India	42	8.0	Chemoorganotroph	Anaerobic fermentation, H2 production	Obligate anaerobe	[119]
9	Chelatococcus albus sp. nov.	Microbial mat, Tengchong	China (Yunnan)	37	6.0	Chemoorganotroph	Aerobic respiration	Aerobe	[120]
10	Micromonospora solifontis sp. nov.	Hot spring soil, Chiang Rai	Thailand	30	5.0–8.0	Chemoorganotroph	Aerobic respiration	Aerobe	[121]
11	Microbacterium neungamense sp. nov.	Hot spring, Chungju	South Korea	35	6.0–10.0	Chemoorganotroph	Aerobic respiration	Aerobe	[122]
12	Elioraea tepida sp. nov.	Microbial mats, Mushroom Spring	USA (Yellowstone)	47	7.0–7.5	Chemoheterotroph/Photoheterotroph	Aerobic respiration, photophosphorylation	Aerobe	[123]
13	Cohnella caldifontis sp. nov.	Hot spring soil, Tengchong	China (Yunnan)	45	7.0	Chemoorganotroph	Aerobic respiration, sulfur metabolism	Obligate aerobe	[121]
14	Athalassotoga saccharophila gen. nov.	Acidic hot spring, Oku-Shiobara	Japan	55	5.5–6.0	Heterotroph	Iron oxidation	Anaerobic	[124]
15	Caldisericum exile gen. nov.	Hot spring	Japan	65	5.5–7.5	Chemoheterotroph	Sulfur-reduction	Anaerobe	[125]
16	Calditerrivibrio nitroreducens gen. nov.	Hot spring water, Yumata	Japan (Nagano)	55	7.25	Chemoorganoheterotroph	Nitrate-reduction	Anaerobe	[126]
17	Chloracidobacterium thermophilum gen. nov.	Microbial mats, Octopus Spring	USA (Yellowstone)	51	7.0	Photoheterotroph	Anoxygenic photosynthesis	Anoxygenic microaerophilic	[127]
18	Fervidobacterium riparium sp. nov.	Hot spring water, Kunashir Island	Russia	65	7.8	Chemoorganotroph	Fermentation	Anaerobe	[128]
19	Meiothermus granaticius sp. nov.	Hot spring, Furnas	Portugal (Azores)	47	7.5	Chemoorganoheterotroph	Nitrate-reduction, aerobic respiration	Aerobe	[128]
20	Meiothermus hypogaeus sp. nov.	Subsurface hot spring (1000 m)	Japan	50	7.6	Chemoorganoheterotroph	Nitrate-reduction, aerobic respiration	Aerobe	[125]
21	Meiothermus luteus sp. nov.	Hot spring sediment, Tengchong	China (Yunnan)	60	7.5	Chemoorganoheterotroph	Polysaccharide metabolism, aerobic respiration	Aerobe	[129]
22	Thermocrinis jamiesonii sp. nov.	Great Boiling Spring	USA (Nevada)	80	7.25	Chemolithoautotroph/Chemolithoheterotroph	Thiosulfate-oxidation	Microaerobe	[130]
23	Thermoflexus hugenholtzii gen. nov.	Great Boiling Spring	USA (Nevada)	73	7.25	Heterotroph	Fermentation	Facultative anaerobe	[131]
24	Venenivibrio stagnispumantis gen. nov.	Terrestrial hot spring, Waiotapu	New Zealand	70	5.4	Chemolithotroph	Hydrogen-oxidation	Microaerobe	[132]
25	Thermus parvatiensis sp. nov.	Hot spring, Manikaran	India (Himachal Pradesh)	70	7.2	Heterotroph	Polysaccharide metabolism, aerobic respiration	Aerobe	[133]
26	Thermus amyloliquefaciens sp. nov.	Hot spring, Niujie	China (Yunnan)	62	7.0	Heterotroph	Nitrate-reduction, aerobic respiration	Aerobe	[134]

).

The following tables present novel thermophilic and hyperthermophilic prokaryotes described since 2002, selected based on the following criteria: (i) formal taxonomic description with validly published names, (ii) isolation from terrestrial hot springs, (iii) representation of phylogenetic and metabolic diversity, and (iv) availability of comprehensive physiological characterization. The temporal scope reflects the acceleration of thermophile discovery following development of molecular phylogenetic and metagenomic methods. Classic thermophiles described before 2008 are included when they represent type species of genera or exhibit unique metabolic characteristics relevant to the biotechnological applications.

Archaea exhibit exceptional phylogenetic and metabolic diversity, occupying ecological niches across temperature ranges of 50–122 °C and pH values from 0 to 10 [8,135]. The phylum Thermoproteota dominates acidic, high-temperature springs with orders Sulfolobales and Desulfurococcales [136]. Euryarchaeota encompasses methanogens, thermoacidophilic archaea, and halophilic thermophiles [137]. Archaeal abundance relative to bacteria varies dramatically with environmental conditions, ranging from ratios of 1:1000 in moderate-temperature neutral-pH springs to 100:1 in hyperthermophilic acidic springs [135] (

Table 2. Representative Thermophilic Archaeal Species from Hot Springs (2000–2025).

Sr. No.	Species	Phylum	Location	Country	T (°C)	pH	Energy Source	Primary Metabolism	O2 Requirement	Reference
1	Tardisphaera miroshnichenkoae gen. nov.	Thermoproteota	Mud spring, Kamchatka	Russia	58	4.2	Heterotroph	Polysaccharide metabolism	Facultative aerobe	[138]
2	Tardisphaera saccharovorans sp. nov.	Thermoproteota	Mud spring, Kamchatka	Russia	60	4.5	Heterotroph	Polysaccharide metabolism	Facultative aerobe	[138]
3	Pyrobaculum calidifontis sp. nov.	Crenarchaeota	Los Baños hot spring	Philippines	92.5	7.0	Heterotroph	Sulfur-reduction, proteinaceous metabolism	Facultative anaerobe	[139]
4	Pyrobaculum ferrireducens sp. nov.	Crenarchaeota	Uzon Caldera	Russia (Kamchatka)	85	6.5	Chemolithoautotroph	Proteinaceous metabolism	Anaerobe	[140]
5	Ignisphaera aggregans gen. nov.	Crenarchaeota	Hot springs, Rotorua/Tokaanu	New Zealand	93.5	6.4	Heterotroph	Fermentation	Anaerobe	[141]
6	Pyrobaculum oguniense sp. nov.	Crenarchaeota	Oguni-cho hot spring	Japan	92	6.5	Heterotroph	Sulfur-reduction, proteinaceous metabolism	Facultative anaerobe	[142]
7	Desulfurococcus kamchatkensis sp. nov.	Crenarchaeota	Uzon Caldera	Russia (Kamchatka)	85	6.5	Organotrophic	Sulfur-reduction	Anaerobe	[143]
8	Sulfolobus tengchongensis sp. nov.	Crenarchaeota	Acidic hot spring, Tengchong	China (Yunnan)	85	3.5	Lithotroph/Heterotroph	Sulfur-oxidation, aerobic respiration	Aerobe	[144]
9	Thermofilum adornatum sp. nov.	Crenarchaeota	Hot spring	Unknown	80	5.75	Chemoorganoheterotroph	Polysaccharide metabolism	Anaerobe	[145]
10	Saccharolobus caldissimus gen. nov.	Crenarchaeota	Hakone Ohwaku-dani	Japan	85	3.0	Chemolithotroph	Iron-reduction, polysaccharide metabolism	Facultative anaerobe	[146]
11	Thermogladius shockii gen. nov.	Crenarchaeota	Washburn hot spring	USA (Yellowstone)	84	5.5	Organoheterotroph	Fermentation	Anaerobe	[147]
12	Vulcanisaeta distributa gen. nov.	Crenarchaeota	Hot spring areas	Japan (Eastern)	87.5	4.25	Heterotroph	Sulfur-reduction, polysaccharide metabolism	Anaerobe	[148]
13	Thermofilum uzonense sp. nov.	Crenarchaeota	Kamchatka hot spring	Russia	85	6.25	Chemoorganotroph	Polysaccharide metabolism	Anaerobe	[149]
14	Acidilobus saccharovorans sp. nov.	Crenarchaeota	Acidic hot spring	Russia (Kamchatka)	82.5	3.75	Heterotroph	Fermentation	Anaerobe	[150]
15	Acidianus manzaensis sp. nov.	Crenarchaeota	Hot spring sample	China (Yunnan)	65	2.0	Heterotroph	Fermentation, monosaccharide metabolism	Facultative anaerobe	[151]
16	Sulfolobus tokodaii sp. nov.	Crenarchaeota	Beppu Hot Springs	Japan (Kyushu)	80	2.75	Chemoheterotroph	Sulfur-oxidation, aerobic respiration	Anaerobe	[152]
17	Caldisphaera lagunensis gen. nov.	Crenarchaeota	Mt Maquiling acidic hot spring	Philippines	72.5	3.75	Heterotroph	Fermentation, sulfate-reduction	Anaerobe	[153]
18	Metallosphaera cuprina sp. nov.	Crenarchaeota	Sulfuric hot spring, Tengchong	China (Yunnan)	70	3.0	Chemolithoautotroph	Aerobic respiration	Aerobe	[154]
19	Metallosphaera tengchongensis sp. nov.	Crenarchaeota	Sulfuric hot spring, Tengchong	China (Yunnan)	70	3.5	Chemolithoautotroph/Heterotroph	Aerobic respiration	Aerobe	[155]
20	Candidatus Nitrosocaldus islandicus *	Thaumarchaeota	Hot spring biofilm, Graendalur	Iceland	65	7.5	Chemolithoautotroph	Ammonia oxidation	Aerobe	[156]

* Note: The entry for Candidatus Nitrosocaldus islandicus represents a microorganism characterized through cultivation-independent genomic approaches (metagenomics and enrichment culture transcriptomics). While not formally isolated in pure culture, its metabolic functions and genomic characteristics are well-characterized, representing an important functional guild of thermophilic ammonia-oxidizing archaea [156].

).

4.3. Eukaryotic Microorganisms: Thermal Limits and Ecological Roles

While prokaryotes dominate hot spring communities at temperatures above 60 °C, diverse eukaryotic microorganisms colonize moderate-temperature zones and perform critical ecosystem functions, including grazing, decomposition, and primary production. Eukaryotic diversity remains poorly characterized, with fewer than 500 thermophilic or thermotolerant eukaryotic species formally described compared to over 2000 prokaryotic thermophiles [157,158]. This disparity reflects both methodological bias toward prokaryote-optimized techniques and the fundamental thermal constraints that limit eukaryotic growth above 62 °C.

Eukaryotic thermal limits differ fundamentally from those of prokaryotes. The maximum growth temperature for eukaryotes is approximately 62 °C, established by the red alga Cyanidioschyzon merolae [159], compared to 122 °C for archaea. This 60 °C differential reflects intrinsic constraints imposed by eukaryotic cellular complexity, including thermal instability of nuclear envelopes, spliceosomal machinery, tubulin-based cytoskeleton, and mitochondrial cristae membranes [160].

Despite limited research attention, hot spring eukaryotic diversity encompasses multiple kingdoms. Free-living amoebae such as Echinamoeba thermarum and Stenamoeba dejonckheerii function as bacterivores [161]. Amoeboflagellates like Tetramitus thermacidophilus exhibit remarkable tolerance to combined thermal and pH extremes. Thermophilic fungi contribute to organic matter decomposition and produce bioactive secondary metabolites, with Teratosphaeria acidotherma representing one of the most acidophilic eukaryotes known [162].

Thermophilic red algae of the class Cyanidiophyceae represent the upper thermal limits of photosynthetic eukaryotes, thriving in acidic hot springs where they perform oxygenic photosynthesis. Their adaptations include modified photosystem proteins resistant to thermal denaturation, enhanced photoprotective mechanisms, and acidic polysaccharide cell walls [162,163].

While often overlooked, eukaryotic diversity represents an untapped frontier for bioprospecting. Thermophilic fungi produce bioactive metabolites, thermotolerant algae offer genes for engineering crop heat tolerance, and protists may harbor novel biosynthetic pathways. Closing the research gap on eukaryotes is not merely an academic exercise but an economic imperative for maximizing hot springs’ contribution to the bioeconomy.

5. Biotechnological Applications

5.1. Thermostable Enzymes: Industrial Revolution

Thermostable enzymes from hot spring microorganisms have revolutionized molecular biology and catalyzed billion-dollar industries. The paradigmatic success is Taq DNA polymerase from Thermus aquaticus, isolated from Yellowstone hot springs in 1969, which enabled the polymerase chain reaction and generates over USD 2 billion in annual revenues from diagnostics, forensics, and research applications [164].

Beyond Taq polymerase, hot springs have yielded thermostable DNA ligases, restriction endonucleases, and high-fidelity DNA polymerases from Pyrococcus and Thermococcus species [165]. In industrial biocatalysis, thermostable proteases, lipases, and amylases function in detergent formulations, with the global market exceeding USD 2 billion annually [166]. Textile processing employs thermostable amylases and cellulases, while food and beverage industries utilize α-amylases, glucoamylases, xylanases, and pectinases [167,168].

An emerging frontier for thermostable enzymes is renewable energy production. Second-generation biofuels from lignocellulosic biomass require enzymatic saccharification. Thermophilic cellulases, xylanases, and accessory enzymes from genera including Caldicellulosiruptor, Thermotoga, and Clostridium thermocellum offer advantages including higher specific activity at 60–80 °C, reduced contamination risk, lower viscosity enabling improved mass transfer, and potential for consolidated bioprocessing [169,170]. Despite advantages, commercialization faces challenges including enzyme cost, substrate recalcitrance, and product inhibition [171]. While microbe-derived products represent high-value niche markets, hot springs also provide direct access to inorganic resources with strategic and industrial importance.

5.2. Bioactive Metabolites and Pharmaceuticals

The global antimicrobial resistance crisis has created urgent demand for novel antimicrobial compounds. Hot springs represent underexplored reservoirs of bioactive secondary metabolites, as extreme environmental pressures promote evolution of unique biosynthetic pathways and chemical scaffolds [172,173].

Thermophilic bacteria produce diverse antimicrobial compounds, including heat-stable bacteriocins active against both Gram-positive and Gram-negative pathogens [174]. Halothermophilic archaea synthesize halocins and archaeocins with activities against MRSA and VRE [173,175]. Hot spring fungi contribute additional chemical diversity through polyketides and peptide metabolites with antimicrobial, anticancer, and immunomodulatory activities [176].

Beyond antimicrobials, hot spring metabolites show promise for treating complex diseases. Cytotoxic peptides and polyketides demonstrate anticancer potential [177], while anti-inflammatory compounds inhibit pro-inflammatory cascades relevant to chronic disease [111]. Immunomodulators and antioxidants with radical-scavenging properties offer additional therapeutic applications [178].

Despite this promising diversity, most discoveries remain at early technology readiness levels. Translation to clinical applications requires structure elucidation, mechanism-of-action studies, optimization of bioactivity, toxicology studies, and scale-up of production systems [111]. To date, no hot spring-derived metabolites have reached clinical trials, highlighting the nascent state of this field and substantial opportunities for drug discovery. Despite the technological sophistication of enzyme production and mineral extraction, the economically dominant use of hot springs remains direct human utilization through wellness tourism and balneotherapy, which generates revenues exceeding all other applications combined.

5.3. Environmental Applications: Bioremediation

Beyond synthetic polymers, hot spring microorganisms demonstrate bioremediation potential for diverse pollutants. Thermophilic microorganisms produce enzymes capable of hydrolyzing synthetic polymers, including polyethylene terephthalate, polyethylene, polypropylene, and nylon [179,180]. Thermostable esterases and cutinases cleave ester bonds in PET, depolymerizing the plastic to recyclable monomers [181,182]. Reaction rates increase exponentially with temperature from 40 °C to 70 °C, with some enzymes remaining active at 80–90 °C.

Hot spring microorganisms exhibit robust tolerance and detoxification mechanisms for heavy metals, including arsenic, mercury, chromium, and cadmium [47,183]. Thermophilic bacteria and archaea reduce toxic soluble metal species to less toxic forms through respiratory reduction, oxidize reduced metals to precipitate insoluble oxides, and biosorb metals onto cell surfaces [184]. Thermophilic hydrocarbon-degrading bacteria metabolize alkanes, aromatics, and polycyclic aromatic hydrocarbons [185]. Thermophilic bioreactors treat high-temperature industrial wastewaters from textile dyeing, paper manufacturing, and food processing without cooling requirements, improving energy efficiency [186].

6. Economic Applications and the Hot Spring Bioeconomy

6.1. Therapeutic Applications of Mineral-Rich Waters

Hot spring waters are enriched with dissolved minerals derived from water-rock interactions under elevated temperature and pressure. These dissolved minerals underpin balneotherapy, with observational clinical studies documenting health benefits including alleviation of inflammatory conditions, improvement in cardiovascular function, respiratory benefits, and dermatological improvements [187,188] (

Table 3. Primary minerals from hot springs and their health applications.

Mineral	Chemical Form	Concentration (ppm)	Origin	Health Applications	Industrial Applications	Reference
Calcium	Ca2+	50–500	Limestone, carbonate rocks	Bone health, muscle function, neuromuscular transmission	Cement, glass, pharmaceuticals	[189]
Magnesium	Mg2+	20–200	Magnesium silicates, carbonates	Muscle relaxation, pain relief, sleep quality, stress reduction	Industrial catalysts, alloys	[190]
Sulfur (elemental/H2S)	S, H2S, SO42−	10–500	Sulfide mineral oxidation	Skin conditions, joint pain, arthritis relief, eczema	Chemical industry, disinfectants	[191]
Silica	SiO2 (colloidal)	50–300	Quartz dissolution	Skin health, collagen synthesis, hair/nail strength	Electronics, glass, cosmetics	[192]
Iron	Fe2+/Fe3+	5–50	Iron-rich minerals	Blood circulation, oxygen transport, anemia treatment	Steel production, catalysts	[193]
Sodium	Na+	100–1000	Salt minerals, halite	Electrolyte balance, nerve function	Chemical industry, salt production	[194]
Lithium	Li+	0.1–2	Lithium minerals	Mood stabilization, mental health, bipolar disorder treatment	Battery production, pharmaceuticals	[195]
Boron	B(OH)3, B(OH)4−	1–50	Borax, borate minerals	Bone health, joint function, brain cognition	Glass production, ceramics, cosmetics	[196]
Iodine	I−	0.1–1	Iodide minerals	Thyroid function, metabolic regulation	Chemical industry, disinfectants	[197]
Rare Earth Elements (La, Ce, Nd, etc.)	REE3+	0.01–50	Complex minerals	Emerging medical research	Catalysts, magnets, electronics, green technology	[198]

).

Primary minerals include calcium for bone health and cardiovascular regulation, magnesium for muscle relaxation and pain relief, sulfur for dermatological conditions and arthritis relief, silica for skin health and collagen synthesis, iron for blood circulation improvement, and bicarbonate for digestive health [199,200]. While therapeutic benefits are supported by clinical evidence, molecular and microbiological mechanisms remain incompletely understood [201,202].

Key research questions include whether immersion alters skin microbiome composition, what proportion of dissolved minerals penetrate intact skin, which molecular pathways mediate anti-inflammatory effects, and whether benefits result from thermal effects, chemical effects, or their synergistic combination [203]. Future research must move beyond observational data to controlled molecular studies elucidating host-mineral-microbe interactions, transforming balneotherapy from a traditional practice to evidence-based precision medicine.

6.2. Strategic Minerals and Rare Earth Elements

Beyond dissolved minerals with therapeutic applications, hot spring fluids contain strategically important elements with industrial and technological value. While therapeutic minerals serve the wellness economy, these strategic resources connect hot springs to emerging green technologies and national resource security.

Certain geothermal fluids contain appreciable concentrations of rare earth elements strategically critical for modern technologies, including permanent magnets, LED phosphors, catalysts, high-performance alloys, and emerging green technologies [204,205]. Geothermal extraction represents a potentially lower-impact alternative to conventional mining [206]. Proposed recovery technologies include selective precipitation, adsorption and ion exchange, membrane filtration, and biological recovery [207].

Current technology readiness is at proof-of-concept and laboratory validation levels. Barriers to commercialization include low concentrations requiring processing of enormous fluid volumes, competition from established mining operations, matrix complexity fouling recovery systems, regulatory frameworks requiring fluid reinjection, and price volatility [208,209]. Despite challenges, integrated geothermal-rare earth element systems represent long-term strategic opportunities as demand grows and environmental regulations tighten.

6.3. Sustainable Management Framework

The modern hot spring bioeconomy encompasses high-value tourism and wellness generating approximately USD 57 billion globally; bioprospecting for enzymes, metabolites, and genetic resources; and mineral and energy extraction [210,211]. Uncoordinated development threatens delicate microbial ecosystems, necessitating integrated management frameworks (Figure 6).

Sustainable development requires treating geothermal systems as non-renewable geobiological reserves [212]. Key management principles include: (i) spatial zoning with different use priorities; (ii) carrying capacity assessments based on ecological monitoring; (iii) benefit sharing where revenue supports conservation; (iv) ecosystem services valuation quantifying economic value of intact systems; and (v) international cooperation facilitating knowledge exchange [213,214]. When managed through integrated frameworks balancing economic utilization with ecosystem protection, hot springs can function as sustainable bioeconomy pillars providing long-term economic resilience.

7. Critical Knowledge Gaps and Research Priorities

Advancing hot spring science requires addressing gaps spanning three interconnected domains: fundamental biological processes, technological innovation, and environmental stewardship. Progress in each domain will amplify advances in the others, creating synergistic benefits for both basic science and applied applications.

7.1. Fundamental Biological Processes

Viral ecology and horizontal gene transfer: Viruses represent the most abundant biological entities in most ecosystems, yet viral diversity in hot springs remains severely understudied [215,216]. Preliminary viral metagenomics suggests these systems harbor novel viral lineages, with less than 10% of viral sequences matching known viruses [217]. Key research questions include which viral types dominate different environments, what are their host specificities, whether viruses regulate microbial densities through kill-the-winner dynamics, and how viruses mediate horizontal gene transfer.

Horizontal gene transfer via transformation, conjugation, and transduction enables rapid adaptation [218]. Thermophilic microorganisms exhibit evidence of extensive gene transfer, though rates, mechanisms, and ecological consequences remain poorly quantified [219]. Research priorities include quantifying transfer rates, cataloging mobile genetic element diversity, identifying barriers and hotspots, and assessing biocontainment risks for engineered thermophiles.

Eukaryotic microbiology: Strategic research priorities include targeted isolation using low-nutrient media and extended incubation times, deep amplicon sequencing cataloging global diversity, experimental manipulations quantifying top-down control, comparative genomics identifying genetic changes enabling heat tolerance, and systematic screening for biotechnological potential [220].

7.2. Technological and Methodological Innovation

Single-cell and spatial omics: Bulk sampling approaches obscure fine-scale spatial heterogeneity within biofilms exhibiting chemical gradients over micron to millimeter scales [221]. Emerging technologies include fluorescence in situ hybridization combined with Raman microspectroscopy, revealing metabolic activity at single-cell resolution; nanoscale secondary ion mass spectrometry (NanoSIMS), a technique that maps isotope distribution at subcellular resolution to track metabolic activity; single-cell genomics and transcriptomics reconstructing genomes from uncultivated organisms; and microfluidic cultivation creating picoliter-scale growth chambers mimicking natural microenvironments [222].

7.3. Environmental Change and Conservation

Climate change impacts: Global climate change may alter hot spring ecosystems through hydrological impacts affecting discharge rates, temperature shifts compressing habitable zones, altered biogeochemistry from changed precipitation chemistry, and permafrost thaw modifying groundwater flow paths [223,224]. Research needs include long-term monitoring, establishing permanent stations tracking temporal changes, manipulative experiments simulating climate scenarios, predictive modeling forecasting ecosystem responses, and paleoclimate records analyzing how geothermal ecosystems responded to previous climate fluctuations.

Conservation policy: Science-based conservation policies are increasingly urgent [225]. Priorities include protected area designation, establishing legal protections, access and benefit-sharing agreements implementing Nagoya Protocol provisions, environmental impact assessments before development, restoration ecology protocols for degraded springs, international cooperation for globally significant systems, and citizen science engaging public stakeholders in monitoring and conservation [226,227].

8. Conclusions

Hot springs constitute geobiological systems where geothermal energy, mineral-rich fluids, and biology interact to generate ecosystems of complexity. This review shows that hot springs are dynamic, structured environments illuminating core principles of microbial evolution, community assembly, and metabolic innovation. Advances in metagenomics, single-cell genomics, and spatially resolved methods reveal extensive taxonomic novelty and breadth among thermophiles and hyperthermophiles, reinforcing hot springs as model systems for probing early Earth conditions and the limits of life. Beyond fundamental insight, hot spring microorganisms deliver tangible societal value. Thermostable enzymes, distinctive secondary metabolites, and high-temperature bioremediation capacities underpin biotechnology, while mineral-rich waters and strategic elements connect geothermal systems to a growing bioeconomy. Yet accelerating tourism, resource extraction, and climate-driven hydrological change threaten ecosystem integrity. Future research should move from inventories to integrative frameworks coupling molecular ecology, geochemistry, and ecosystem modeling. Priority directions include viral–host dynamics, horizontal gene transfer, and eukaryotic roles, ensuring sustainable stewardship.