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Dormancy

Dormancy is a reversible physiological state in which organisms temporarily reduce or suspend their metabolic activity to survive periods of environmental stress, such as extreme temperatures, desiccation, or nutrient scarcity.^[1] This adaptation enables the preservation of genetic information and cellular integrity without active growth or reproduction, distinguishing it from death or permanent quiescence.^[1] Across the tree of life, dormancy manifests in diverse forms tailored to specific taxa and ecological niches. In microorganisms, it often involves the production of resilient structures like endospores in bacteria, which can endure harsh conditions for millennia while maintaining viability. For instance, Bacillus species form these spores in response to nutrient limitation, creating microbial "seed banks" that facilitate long-term persistence in fluctuating environments.^[2] In plants, dormancy is prominently observed as seed dormancy, an innate dormancy mechanism that inhibits germination even under favorable conditions until specific cues like cold stratification or scarification break it.^[3] This ensures seedlings emerge at optimal times, enhancing survival rates.^[3] Animals exhibit dormancy through strategies like hibernation, torpor, and diapause, which allow energy conservation during seasonal hardships. Hibernation, seen in mammals such as bears and ground squirrels, involves profound metabolic depression and lowered body temperature to minimize energy expenditure over winter.^[4] Diapause, a developmental arrest common in insects and other invertebrates, suspends growth or reproduction in response to photoperiod or temperature signals, as in the overwintering eggs of mosquitoes.^[5] In trees and perennial plants, dormancy synchronizes with seasonal cycles, where buds enter a protected state during autumn to withstand cold, resuming growth in spring upon warming cues.^[6] Ecologically, dormancy plays a crucial role in population dynamics by buffering against disturbances, promoting dispersal, and maintaining biodiversity through temporal staggering of life cycles.^[1] It forms ecological seed banks—reservoirs of dormant individuals that can revive under improved conditions—thus stabilizing communities amid climate variability.^[2] Evolutionarily, dormancy likely originated early in life's history, possibly as a chemical stabilization mechanism, and has driven diversification by enabling survival in extreme habitats, from deep-sea vents to polar regions.^[1] With ongoing climate change, shifts in dormancy cues may alter phenology and species interactions, posing challenges to ecosystems.^[7]

General Principles

Definition and Characteristics

Dormancy is a temporary state in which organisms enter a reversible phase of minimized metabolic activity and suspended growth or development to survive adverse environmental conditions, thereby enhancing long-term viability.^[1] This adaptive strategy allows organisms to conserve resources and withstand stresses such as extreme temperatures, desiccation, or nutrient scarcity without succumbing to death.^[8] Unlike permanent states like senescence, dormancy preserves the potential for resumption of normal functions once conditions improve.^[1] Key characteristics of dormancy include significantly reduced respiration and energy expenditure, often accompanied by slowed or halted cellular processes while maintaining cellular integrity and viability.^[8] For instance, metabolic rates can drop by 90-99% in small hibernating mammals relative to basal levels, enabling prolonged survival on stored reserves.^[9] The state is inherently reversible, with organisms reactivating metabolism and growth upon sensing favorable cues, ensuring no irreversible damage occurs.^[1] These traits distinguish dormancy from mere inactivity, as it involves coordinated physiological adjustments that protect against environmental insults.^[7] A critical distinction exists between quiescence and dormancy proper: quiescence represents a direct, reversible arrest in response to immediate environmental stress, such as low water availability inhibiting seed germination, whereas dormancy involves an anticipatory, internally regulated suspension with built-in barriers that prevent activation even under seemingly suitable conditions. This internal programming in dormancy ensures timing aligns with predictable seasonal cycles, adding a layer of adaptive precision.^[7] Evolutionarily, dormancy serves as a pivotal adaptive trait that has facilitated the origin, diversification, and persistence of life across fluctuating environments by buffering against stochastic extinctions and promoting dispersal of viable propagules.^[1] Observed in diverse taxa from microorganisms to vertebrates, it underscores a conserved mechanism for enduring unpredictable stresses, contributing to ecological resilience and species longevity.^[1]

Triggers and Regulation

Dormancy in organisms is initiated and maintained through a combination of exogenous and endogenous triggers, which collectively ensure survival under adverse conditions. Exogenous triggers are direct environmental cues that signal the onset of stress, such as temperature extremes, drought, changes in photoperiod, and nutrient scarcity, prompting physiological adjustments across plants, animals, and microorganisms.^[10] These cues often act as immediate sensors, with low temperatures or prolonged darkness, for instance, inhibiting metabolic activity to prevent energy depletion.^[11] In contrast, endogenous triggers involve internal physiological and genetic timers that synchronize dormancy with seasonal or developmental cycles, independent of immediate external changes but calibrated by prior exposures.^[12] This distinction allows organisms to anticipate unfavorable periods, with exogenous factors providing rapid responses and endogenous mechanisms ensuring precise timing.^[10] Hormonal regulation plays a central role in transducing these triggers into sustained dormancy states. In plants, abscisic acid (ABA) accumulates in response to stress signals like drought or cold, promoting dormancy by inhibiting growth processes and enhancing stress tolerance through gene expression networks.^[13] Similarly, in animals, melatonin acts as a key seasonal regulator, rising during shorter photoperiods to induce torpor or diapause by modulating metabolic and reproductive pathways.^[14] In microorganisms, particularly bacteria, cyclic di-GMP serves as a second messenger that shifts cellular behavior toward persistence, reducing replication and increasing resistance to antibiotics or starvation by altering biofilm formation and motility.^[15] These hormones integrate exogenous cues with endogenous rhythms, maintaining low metabolic rates until conditions improve. At the genetic and molecular level, dormancy is controlled by stress-response pathways and circadian clock components. Clock genes such as PER and TIM form feedback loops that align dormancy entry with photoperiodic changes, repressing growth-related transcription during unfavorable times in both animals and plants.^[16] The target of rapamycin (TOR) signaling pathway, responsive to nutrient availability, suppresses anabolic processes under scarcity, linking energy status to dormancy induction and promoting longevity-like states.^[17] These mechanisms ensure coordinated downregulation of metabolism, with TOR inhibiting translation and clock genes fine-tuning temporal responses to prevent premature reactivation.^[18] Dormancy release occurs when opposing signals overcome these barriers, often through prolonged environmental shifts. Vernalization, a cold-requiring process, epigenetically silences dormancy-promoting genes like FLC in plants, allowing growth resumption upon warming, while similar chilling fulfills release requirements in animal and microbial systems.^[19] Rehydration serves as a critical trigger for desiccation-induced dormancy, reactivating enzymes and metabolic pathways in seeds and bacteria by restoring cellular water balance and diluting inhibitors.^[20] These release mechanisms reverse hormonal and genetic controls, transitioning organisms back to active states with minimal lag.^[21]

Dormancy in Animals

Hibernation

Hibernation is a form of seasonal dormancy characterized by profound torpor in certain endothermic animals, primarily mammals and some birds, during periods of cold and food scarcity in winter. In this state, body temperature drops to within a few degrees of ambient levels, often approaching 2–4°C in small mammals, while metabolic rate, heart rate, and other physiological functions are drastically suppressed to conserve energy.^[22] This adaptation allows hibernators to survive extended periods without feeding by relying on stored fat reserves, distinguishing it from shorter daily torpor bouts. Prior to entering hibernation, animals undergo a preparation phase involving hyperphagia, a period of excessive feeding to accumulate substantial fat deposits that serve as the primary energy source throughout torpor. Physiological adjustments also occur, including a reduction in thyroid hormone levels, which helps suppress metabolism and facilitate the transition to low-energy states. These pre-hibernation changes, driven by environmental cues like shortening photoperiods, ensure the animal can endure months of inactivity without external resources.^[23] During hibernation, hibernators experience repeated cycles of torpor bouts lasting days to weeks, interrupted by periodic arousals to euthermic temperatures (around 37°C) for several hours, presumably to restore physiological balance and eliminate metabolic wastes. Heart rate plummets to as low as 2–5 beats per minute, and oxygen consumption decreases by approximately 90–99%, reflecting the minimal energy demands of this hypometabolic state. These arousals, which consume up to 80% of the total hibernation energy budget, are essential but energetically costly.^[24]^[25] Classic examples include the thirteen-lined ground squirrel (Ictidomys tridecemlineatus), which hibernates for up to 7–8 months in northern regions, and black bears (Ursus americanus), which enter a milder form of hibernation lasting 4–7 months with less extreme temperature drops but similar metabolic suppression. While hibernation provides key benefits such as efficient energy conservation for winter survival, it also poses risks including temporary immune suppression to reduce energy expenditure and potential bone density challenges, though many hibernators exhibit adaptations that mitigate significant loss in bone strength during prolonged immobility.^[22]^[26]^[27]

Diapause

Diapause represents a mandatory or facultative suspension of growth and development at specific life stages, such as eggs, larvae, or pupae, primarily in insects and certain crustaceans, allowing survival through periods of environmental adversity. This hormonally mediated arrest differs from other dormancy forms by its precise timing to unfavorable seasons, often synchronized with photoperiod cues that integrate environmental signals through neuroendocrine pathways.^[28] Induction of diapause is highly sensitive to photoperiod, where shortening day lengths suppress the release of key hormones like juvenile hormone (JH) and ecdysone, preventing further development or reproduction. In many species, low JH titers maintain the diapause state by downregulating insulin signaling, while ecdysone suppression halts metamorphic processes, as observed in beetles like Colaphellus bowringi.^[28] This endocrine regulation ensures diapause entry aligns with predictable seasonal challenges, such as winter in temperate regions. Diapause manifests in various types, including embryonic (e.g., in eggs of the silkworm Bombyx mori), larval (e.g., in larvae of the European corn borer Ostrinia nubilalis), pupal (e.g., in pupae of flesh flies like Sarcophaga crassipalpis), and reproductive (e.g., in adults of the monarch butterfly Danaus plexippus during migration). In the monarch butterfly, reproductive diapause is facultative, triggered by autumn photoperiods, leading to suppressed ovarian development and enhanced lipid reserves for long-distance flight to overwintering sites.^[28] These types reflect adaptations to life cycle stages most vulnerable to seasonal stress. During diapause, metabolic rates decline dramatically, often by 90% or more, accompanied by behavioral quiescence and increased tolerance to stressors like desiccation and cold. Gene expression shifts include upregulation of heat shock proteins (HSPs), such as HSP70 and HSP90, which stabilize cellular proteins and enhance cryoprotection, as demonstrated in diapausing flesh fly pupae. Energy conservation occurs through lipid accumulation and reduced feeding, with adipokinetic hormones mobilizing stored trehalose for osmotic balance under low temperatures.^[28] Termination of diapause requires specific environmental cues, typically prolonged exposure to cold temperatures that accumulate over weeks or months to break the arrest. This chill accumulation resets hormonal balances, restoring JH and ecdysone levels to resume development, as seen in post-diapause emergence of insects in spring.^[28] In some cases, additional signals like increasing photoperiod reinforce termination, ensuring synchronization with favorable conditions.^[29]

Aestivation

Aestivation, also known as estivation, is a form of summer dormancy observed primarily in ectothermic animals, where individuals enter a state of reduced metabolic activity to survive periods of high temperatures, drought, and desiccation.^[30] This hypometabolic strategy involves behavioral adaptations such as burrowing into soil or mud, or encasing the body in a protective mucus cocoon or seal to minimize water loss and exposure to environmental stressors.^[30] Unlike other dormancy forms, aestivation is triggered specifically by heat and aridity rather than cold, allowing animals in seasonal or tropical environments to conserve energy and water during unfavorable hot-dry periods.^[31] Physiologically, aestivation features a profound depression in metabolic rate, often reducing it to 10-30% of the standard resting level, which extends survival time by limiting energy expenditure and preventing dehydration.^[31] In some species, such as African lungfish, metabolic suppression can exceed 70%, coupled with the accumulation of urea as an osmoprotectant to maintain cellular hydration and detoxify ammonia waste without frequent urination.^[32] These adaptations include downregulated glycolysis, reduced protein synthesis, and enhanced antioxidant defenses to counteract oxidative stress from prolonged inactivity.^[30] Prominent examples include the African lungfish (Protopterus spp.), which burrow into riverbeds and form a mucus-lined cocoon during the dry season, remaining dormant for up to several years until water returns.^[30] Land snails, such as the milk snail (Otala lactea), seal their shells with a calcium-rich epiphragm and lower their metabolic rate below 30% to endure desiccation.^[30] Amphibians like the African clawed frog (Xenopus laevis) and burrowing frogs (Cyclorana spp.) embed in mud aestivation chambers, tolerating up to 30-40% body water loss while suppressing activity.^[30] The duration of aestivation is closely linked to the length of drought, ranging from weeks in amphibians to months or years in lungfish.^[31] From an evolutionary perspective, aestivation represents a conserved adaptation to arid and semi-arid climates, enabling ectotherms to exploit ephemeral habitats by bridging dry intervals without migration.^[31] This strategy has independently evolved across diverse taxa, including fish, amphibians, and mollusks, highlighting its role in enhancing survival in fluctuating tropical and desert ecosystems.^[30] Aestivation concludes with reawakening triggered by environmental cues such as rainfall, cooling temperatures, or increased humidity, which prompt metabolic reactivation, urea excretion, and resumption of normal behaviors.^[30]

Brumation

Brumation refers to a state of winter dormancy observed in many reptiles, such as snakes, lizards, and turtles, as well as certain amphibians, characterized by prolonged inactivity and suppression of metabolic processes in response to cold temperatures. Unlike true sleep, animals in brumation remain alert to environmental stimuli and may periodically rouse for limited activity, particularly on warmer days.^[33] This adaptation allows ectothermic (poikilothermic) species to conserve energy when prey is scarce and temperatures limit mobility.^[34] As autumn progresses and ambient temperatures decline below approximately 15°C, reptiles and amphibians begin preparations for brumation by seeking out protective hibernacula, such as underground burrows, rock fissures, or submerged sites in water bodies.^[35] For instance, timber rattlesnakes (Crotalus horridus) aggregate in communal dens within rocky outcrops or caves starting in early October, where they cluster to share body heat and maintain microclimates above freezing.^[35] These sites provide insulation against extreme cold, and animals often fast in the weeks prior, relying on previously accumulated energy reserves rather than building extensive fat stores as seen in mammalian hibernators.^[33] During brumation, physiological processes slow dramatically due to the direct influence of low environmental temperatures on ectothermic metabolism, following the Q10 temperature coefficient, which typically indicates a twofold reduction in metabolic rate for every 10°C decrease.^[33] In squamate reptiles, standard metabolic rates can drop by up to 70% at 12°C compared to summer levels, with the Q10 value increasing from about 4.4 in active seasons to 7.7 in winter, reflecting heightened thermal sensitivity.^[33] Heart rates also decline substantially; for example, in some lizards and turtles, rates can halve or reduce further, from around 20-30 beats per minute in mild conditions to 5-10 beats per minute or less during deep cold exposure.^[36] Unlike mammals, there is no active regulation of body temperature to achieve profound hypothermia; instead, metabolic depression predominates, enabling survival on minimal energy without significant fat mobilization.^[33] Examples of brumation include alligators (Alligator mississippiensis), which retreat to swampy burrows or underwater, and various lizards like the western rattlesnake (Crotalus oreganus), which utilize subterranean refugia while occasionally emerging on mild winter days.^[35] In amphibians, species such as certain frogs partially bury in mud or leaf litter, tolerating near-freezing conditions through supercooling. However, inadequate hibernacula depth poses risks, including tissue freezing and mortality if temperatures fall below -2°C to -5°C without sufficient insulation, as seen in exposed snakes or turtles.^[35] Brumation differs from mammalian hibernation in lacking controlled endothermic torpor, resulting in no periodic deep hypothermia or complex arousal cycles; instead, arousal is more opportunistic and tied to ambient warming, allowing sporadic activity without full metabolic reactivation.^[33] This shallower dormancy reflects the ectothermic reliance on passive thermal conformity rather than active physiological suppression independent of temperature.^[36]

Dormancy in Plants

Seed Dormancy

Seed dormancy refers to the temporary inhibition of embryo growth and germination in viable seeds under otherwise favorable conditions, ensuring that seedlings emerge only when environmental factors support survival and establishment.^[37] This adaptive trait prevents premature germination during dispersal or unfavorable periods, such as drought or winter, and is distinct from quiescence, where germination is simply delayed by current conditions.^[38] Seed dormancy is classified into several types based on underlying mechanisms. Physical dormancy (PY) arises from an impermeable seed coat that blocks water uptake, common in species like legumes and malvaceous plants.^[39] Physiological dormancy (PD), the most prevalent type across angiosperms, involves internal inhibition of embryo growth, often mediated by high levels of abscisic acid (ABA) and low gibberellic acid (GA), as seen in model species like Arabidopsis thaliana.^[40] Morphological dormancy (MD) occurs when the embryo is underdeveloped and requires time to mature before germination can proceed, typically in temperate woodland herbs.^[39] Combinational dormancy integrates multiple mechanisms, such as PY combined with PD (PY+PD), allowing nuanced responses to complex environments.^[39] Dormancy is broken by specific environmental or artificial cues that counteract inhibitory mechanisms. For PY, scarification—mechanical abrasion or chemical treatment of the seed coat—allows water imbibition, as applied to hard-coated crop seeds.^[41] PD is often released through stratification, involving exposure to cold, moist conditions that degrade inhibitors over weeks or months, mimicking winter.^[40] In fire-prone ecosystems, smoke-derived karrikins activate germination signaling pathways, requiring GA synthesis and light, as demonstrated in diverse post-fire flora.^[42] Examples illustrate dormancy's ecological roles, such as in desert annuals like those in the Sonoran Desert, where seeds form long-lived soil banks persisting for decades and germinating en masse after rare rains to exploit brief windows of productivity.^[38] Agriculturally, persistent dormant seed banks of weeds like Amaranthus species challenge control efforts, as viable seeds can remain viable for years, necessitating strategies like tillage or herbicide timing to induce and deplete banks.^[43] Evolutionarily, seed dormancy provides a bet-hedging advantage by synchronizing germination with seasonal optima, reducing risk in variable climates and promoting diversification, particularly through PD as an adaptive hub.^[38]

Bud Dormancy

Bud dormancy in plants refers to the cessation of growth in apical and lateral buds, a survival strategy in perennial species that enables them to endure adverse environmental conditions such as winter cold or summer drought. This dormancy is categorized into ecodormancy, where unfavorable external factors like low temperatures or water scarcity directly inhibit bud outgrowth; endodormancy, characterized by internal physiological constraints that prevent growth even under favorable conditions; and paradormancy, arising from inhibitory signals from other plant parts.^[44]^[45] The mechanisms regulating bud dormancy involve hormonal and environmental cues. In paradormancy and early endodormancy, correlative inhibition occurs through auxin transport from the shoot apex, which suppresses lateral bud activity by promoting the expression of dormancy-promoting genes and limiting nutrient allocation to subordinate buds. Endodormancy release typically requires a chilling period, often quantified as 400 to 2000 hours below 7°C depending on the species, which satisfies the plant's vernalization-like requirement and triggers epigenetic changes that allow growth resumption.^[46]^[47]^[48] Examples of bud dormancy are prominent in temperate trees and storage organs. In apple trees (Malus domestica), apical and lateral buds enter endodormancy in autumn, requiring around 800 to 1700 chilling hours for synchronized spring budbreak and flowering. Potato tubers (Solanum tuberosum) exhibit similar bud dormancy after harvest, where paradormant influences from the apical bud and hormonal balances maintain quiescence for weeks to months, preventing premature sprouting during storage. Paradormancy can also stem from competition among buds or between vegetative and reproductive organs, prioritizing resource allocation to the main shoot.^[48]^[49] Physiologically, dormant buds undergo adaptations for protection and stasis. Scales and bud coverings seal the meristem, reducing water loss and conferring resistance to desiccation and freezing temperatures down to -30°C in some species, while metabolic rates drop to minimize energy use. Post-chilling, dormancy breaks with hormonal shifts—such as increased gibberellins and cytokinins—leading to cell division, bud swelling, and outgrowth when combined with warming temperatures.^[50] Climate change poses challenges to bud dormancy by reducing winter chilling accumulation through milder temperatures, potentially delaying or desynchronizing budbreak and bloom timing in crops like apples, which could shorten growing seasons and increase vulnerability to late frosts. In regions like California, historical data show a decline in chill hours by up to 20% over recent decades, exacerbating uneven flowering and yield variability.^[51]^[52]

Dormancy in Microorganisms

Bacterial Dormancy

Bacterial dormancy encompasses adaptive strategies where cells enter low-metabolic states to endure adverse conditions, such as nutrient scarcity, oxidative stress, or antibiotic exposure. These states include endospore formation, the viable but non-culturable (VBNC) condition, and persister cells, enabling long-term survival without replication.^[53] Unlike active growth phases, dormant bacteria exhibit reduced transcription, translation, and energy production, preserving viability for reactivation when conditions improve.^[54] Endospore formation represents a highly resistant dormancy mechanism primarily in Gram-positive bacteria, such as Bacillus and Clostridium species. This process unfolds in seven morphological stages: axial filament formation, where chromosomes segregate and align along the cell's long axis (stage I); asymmetric septation that divides the cell into a forespore and mother cell (stage II); engulfment of the forespore by the mother cell (stage III); cortex formation with peptidoglycan layers around the forespore (stage IV); coat assembly for structural protection (stage V); and maturation with dipicolinic acid (DPA) accumulation complexed with calcium ions to confer heat and desiccation resistance (stage VI).^[55]^[56] The mother cell ultimately lyses to release the mature endospore (stage VII), which can remain viable for decades under extreme conditions like high temperatures or radiation.^[57] This sporulation is genetically regulated by sigma factors and response regulators, ensuring precise coordination.^[58] The VBNC state involves a reversible metabolic slowdown without morphological changes like sporulation, allowing bacteria to persist in non-growth conditions while retaining viability and potential pathogenicity. In this state, cells maintain low-level respiration and membrane integrity but fail to form colonies on standard media, often detected via viability stains or molecular assays.^[59] VBNC formation occurs across diverse species, including Escherichia coli and Vibrio cholerae, and differs from persister cells, which are transient subpopulations tolerant to antibiotics due to halted metabolism but capable of regrowth post-treatment.^[60] Unlike irreversible death, VBNC cells can resuscitate upon nutrient replenishment or stress relief.^[61] Common triggers for bacterial dormancy include nutrient depletion and starvation, which activate stringent response pathways via (p)ppGpp alarmone to downregulate growth.^[62] Oxidative stress from reactive oxygen species or hypoxia similarly induces dormancy, as seen in Mycobacterium tuberculosis, where low oxygen and nitric oxide exposure prompt non-replicating persistence, contributing to latent tuberculosis infections affecting billions worldwide.^[53] Antibiotic exposure selectively enriches persister and VBNC subpopulations, while environmental cues like temperature shifts or osmolarity changes can initiate endospore formation in Bacillus subtilis.^[63] These dormancy mechanisms have significant applications in food preservation and medicine. Endospores from pathogens like Clostridium botulinum resist thermal processing, necessitating advanced inactivation strategies such as high-pressure or pulsed electric fields to ensure food safety.^[64] In clinical contexts, persister cells and VBNC states underlie antibiotic tolerance in chronic infections, such as tuberculosis, prompting research into revival inhibitors or phage therapies to target dormant populations and improve treatment efficacy.^[65]

Fungal Dormancy

Fungal dormancy encompasses quiescent states in spores or hyphal structures that enable these eukaryotic microorganisms to endure environmental stresses including desiccation, ultraviolet radiation, and nutrient scarcity.^[66] This dormancy is metabolically quiescent, with low respiration rates and minimal macromolecular synthesis, allowing long-term viability.^[67] Key dormant structures include conidia, asexual spores adapted for short-term dispersal and survival; chlamydospores, thick-walled, melanized cells derived from hyphal segments that provide robust protection; and sclerotia, compact aggregates of hardened hyphae enriched with nutrient reserves for extended persistence.^[68]^[69]^[70] Mechanisms underlying fungal dormancy involve structural and biochemical adaptations that minimize damage from stressors. Thick cell walls, often multilayered and melanized, act as barriers against physical and chemical insults while maintaining structural integrity.^[71] Low intracellular water content, typically below 10-20% in dormant spores, suppresses enzymatic activity and prevents ice crystal formation during freezing.^[67] Additionally, accumulation of trehalose, a non-reducing disaccharide, stabilizes proteins and membranes under desiccation by forming protective glasses or hydration shells, enhancing tolerance to dehydration and oxidative stress.^[72] Representative examples illustrate dormancy's role in fungal survival and pathogenesis. In Aspergillus species, conidia persist in soil as dormant propagules, germinating only when moisture and nutrients become available to initiate growth or infection.^[73] Rust fungi, such as Puccinia spp., form teliospores as overwintering dormant structures that endure harsh conditions before producing basidiospores to infect crops, contributing to significant agricultural losses.^[74] Sclerotia in pathogens like Sclerotinia sclerotiorum can remain viable in soil for up to a decade, serving as reservoirs for disease outbreaks in plants.^[75] Ecologically, fungal dormancy facilitates persistence in extreme habitats, such as Antarctic soils, where spores and sclerotia withstand subzero temperatures, prolonged desiccation, and limited nutrients, enabling recolonization during brief favorable periods.^[76] This adaptation underscores fungi's role in nutrient cycling and microbial community resilience in polar ecosystems.^[77]

Dormancy in Viruses

Viral Latency

Viral latency refers to a reversible state of non-productive infection in which the viral genome persists within the host cell either as an episome or integrated into the host genome as a provirus, without active replication or production of infectious virions.^[78] This dormancy allows the virus to evade host immune detection while maintaining long-term persistence, enabling potential reactivation under specific conditions.^[79] In eukaryotic viruses such as herpesviruses, latency is characterized by highly restricted gene expression, often limited to non-coding RNAs or a few latency-associated transcripts that support genome maintenance without triggering immune responses.^[80] Mechanisms of viral latency involve epigenetic silencing of the viral genome, including histone modifications like methylation that condense chromatin and repress transcription, as well as interference by host microRNAs (miRNAs) that target viral transcripts for degradation or translational inhibition.^[81] For instance, in herpes simplex virus type 1 (HSV-1), the viral genome establishes latency in sensory neurons, where latency-associated transcripts (LATs) and associated miRNAs promote silencing of lytic genes through epigenetic changes and evasion of apoptosis.^[82] Induction of latency often serves immune evasion during initial infection or under stress signals, such as nutrient limitation or cellular differentiation, while reactivation can be triggered by external stimuli including ultraviolet (UV) light exposure, hormonal fluctuations, or immunosuppression.^[80] In HSV-1, UV irradiation can trigger reactivation from latency, leading to viral gene expression and lesion formation.^[83] In bacteriophages, latency manifests as lysogeny, where the viral genome integrates into the bacterial chromosome as a prophage and is maintained by repressor proteins that inhibit lytic genes.^[84] The lambda phage exemplifies this through its CI repressor protein, which binds operator sites to autoregulate its expression and silence lytic promoters, ensuring stable propagation during host cell division.^[85] This state persists until environmental cues, such as DNA damage, induce the SOS response, cleaving the repressor and shifting to the lytic cycle.^[85] Pathological implications of viral latency include associations with oncogenesis, where persistent genomes can disrupt host cell regulation upon reactivation or through latent gene products.^[86] Epstein-Barr virus (EBV), for example, establishes latency in B lymphocytes via episomal persistence and expression of latent membrane proteins that promote cell proliferation, contributing to cancers such as Burkitt's lymphoma and nasopharyngeal carcinoma.^[87] These latency programs hijack host signaling pathways, underscoring the virus's role in malignant transformation while remaining dormant for extended periods.^[88]

Viral Persistence

Viral persistence refers to the long-term survival of a virus within a host organism, characterized by the virus's ability to evade immune clearance and maintain infection without causing immediate host cell destruction or overt disease. This form of viral dormancy allows the virus to reside in a quiescent or low-replicative state, often alternating between periods of minimal activity and reactivation. Unlike acute infections that are rapidly resolved, persistent viruses employ strategies to suppress host antiviral responses, ensuring their continued presence over months, years, or even a lifetime.^[89] Key mechanisms of viral persistence involve modulation of the host immune system to prevent effective antiviral activity. Viruses can down-regulate major histocompatibility complex (MHC) class I and co-stimulatory molecules on infected cells and antigen-presenting cells, such as dendritic cells, thereby impairing T cell recognition and activation. Additionally, persistent viruses induce T cell exhaustion or tolerance, where antiviral T cells become dysfunctional and fail to eliminate infected cells, a process that is reversible upon removal of the viral antigen. Non-cytolytic infection strategies further contribute, as viruses alter host cell functions—such as neurotransmitter or hormone production—without lysing the cell, allowing prolonged intracellular residence. These mechanisms collectively enable the virus to curtail innate and adaptive immune responses, synonymous with evasion of immunologic surveillance.^[90]^[90]^[90]^[90] In the context of dormancy, viral persistence represents a survival adaptation where the virus enters a metabolically subdued state, minimizing replication to avoid detection while preserving the potential for future propagation. This differs from strict latency by often involving low-level, ongoing viral gene expression or intermittent production of infectious particles, rather than complete transcriptional silencing. Persistence can occur in various host tissues, including immunologically privileged sites like the central nervous system, further shielding the virus from immune effectors.^[89]^[89] Representative examples illustrate these principles across virus families. The lymphocytic choriomeningitis virus (LCMV) persists in mice by inducing T cell exhaustion, leading to lifelong infection without clearance. Hepatitis B virus (HBV) establishes chronic persistence in hepatocytes through restricted antigen expression and immune suppression, contributing to liver cirrhosis and hepatocellular carcinoma in humans. Human retroviruses, such as HIV, maintain persistence via integration into host genomes and establishment of reservoirs in resting immune cells, despite antiretroviral therapy. These cases highlight how persistence facilitates viral transmission and chronic pathology while embodying a dormant phase in the viral life cycle.^[90]^[89]^[89]^[90]

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