Lessons from Extremophiles: Functional Adaptations and Genomic Innovations across the Eukaryotic Tree of Life

Abstract

From hydrothermal vents, to glaciers, to deserts, research in extreme environments has reshaped our understanding of how and where life can persist. Contained within the genomes of extremophilic organisms are the blueprints for a toolkit to tackle the multitude of challenges of survival in inhospitable environments. As new sequencing technologies have rapidly developed, so too has our understanding of the molecular and genomic mechanisms that have facilitated the success of extremophiles. Although eukaryotic extremophiles remain relatively understudied compared to bacteria and archaea, an increasing number of studies have begun to leverage ’omics tools to shed light on eukaryotic life in harsh conditions. In this perspective paper, we highlight a diverse breadth of research on extremophilic lineages across the eukaryotic tree of life, from microbes to macrobes, that are collectively reshaping our understanding of molecular innovations at life's extremes. These studies are not only advancing our understanding of evolution and biological processes but are also offering a valuable roadmap on how emerging technologies can be applied to identify cellular mechanisms of adaptation to cope with life in stressful conditions, including high and low temperatures, limited water availability, and heavy metal habitats. We shed light on patterns of molecular and organismal adaptation across the eukaryotic tree of life and discuss a few promising research directions, including investigations into the role of horizontal gene transfer in eukaryotic extremophiles and the importance of increasing phylogenetic diversity of model systems.

Significance.

The study of eukaryotes in extreme environments has uncovered important insights into eukaryotic adaptation and physiology, but these insights have largely been considered separately within different lineages and extreme conditions. Using research generated from recent advances in genomic and transcriptomic sequencing, we synthesize the patterns of physiological strategies and genomic signatures of diverse extremophile eukaryotes to forward our understanding of eukaryotic evolution and propose future directions for the field.

This Perspective is part of a series of articles celebrating 40 years of Society for Molecular Biology and Evolution journals. It is accompanied by virtual issues on this topic published by Genome Biology and Evolution and Molecular Biology and Evolution, which can be found at our 40th anniversary website.

Introduction

Research in extreme environments has dramatically expanded our understanding of how and where eukaryotic life can persist. From predatory ciliates that live in deep sea vents (Hu et al. 2021), to red algae that can inhabit high-temperature acidic geothermal springs (Cho et al. 2023), to Atacama-endemic plants that thrive in the driest of deserts (Eshel et al. 2021), organisms across the tree of life live in the harshest of places. Extreme environments have at least one condition that limits the survival of most life, leading to reduced species diversity (Weber et al. 2007; Shu and Huang 2022). What is extreme to most is the only option for some, but we consider extremophiles to be organisms needing, preferring, or tolerating extreme abiotic conditions, including, but not limited to, temperature, pH, salinity, heavy metals, radiation, darkness, pressure, aridity, and anoxia. Some examples of extreme environments are permafrost ice, acid mine drainage, salterns, and outer space, but there are a multitude of other naturally occurring and human-made extremes.

Although extreme environments have long been appreciated as key ecosystems to study how life evolves and adapts, advances in sequencing technology and computational pipelines have provided new ways to understand molecular-level adaptations to extreme environments, yielding insight into the evolution, physiology, and adaptations of extremophiles. The scientific impacts from this renaissance in extremophile biology in the past decade have been well documented in bacterial and archaeal lineages (Hedlund et al. 2014; de la Haba et al. 2022). Here, we seek to highlight some of the major ways in which our understanding of eukaryotic biology has also been revised.

These technological advances have made an increasing number of eukaryotic genomes and transcriptomes available. The resulting data sets facilitated comparative studies of mesophile and extremophile eukaryotes (Kelley et al. 2016; Birkeland et al. 2020; Wang et al. 2020), offered a window into the often complex evolutionary history of genes (Kelley et al. 2016; Ip et al. 2021; Fleming et al. 2024; Van Etten et al. 2024), and enabled new insights on the adaptive metabolic processes of eukaryotes (Hawkins et al. 2017; Zhang et al. 2019).

Our effort here also seeks to unite diverse areas of eukaryotic extremophile research that are usually viewed as separate research “silos” despite the shared ancestry of eukaryotes. Although exciting advances in extremophile genome biology are occurring in many lineages, including diverse metazoa (Fontanillas et al. 2017; Papetti et al. 2021; Fleming et al. 2024), plants (Hawkins et al. 2017; Wang et al. 2020; Gupta et al. 2024), fungi (Zajc et al. 2013; Coleine et al. 2022; Touchette et al. 2022), algae (Foflonker et al. 2018; Zhang et al. 2019; Van Etten et al. 2023), and other microbial lineages, such as flagellates (Harding et al. 2016) and diatoms (Bar Dolev et al. 2016), these findings are rarely considered collectively in an evolutionary context (Fig. 1). We highlight the need for this evolutionary framework due to the distinctness of eukaryotic cells and their evolutionary processes as compared to bacteria and archaea. Such efforts will aid in the development of a broader understanding of the molecular and physiological toolkit that eukaryotes possess. Extremophiles have already been identified in most major lineages. Here, we highlight representative examples of some of the most well-studied extremophile lineages across the eukaryotic tree. We begin to integrate evolutionary perspectives with molecular studies from genome-scale data across eukaryotes in an effort to uncover the myriad of similar and unique solutions to cope with life in Earth's harshest environments.

Fig. 1.

Simplified tree of eukaryotes highlighting the broad phylogenetic diversity of major lineages. Popouts show diversity of multicellular lineages, not to scale (based on Burki et al. 2020; Jamy et al. 2022; Streptophyta based on Finet et al. 2010; Metazoa based on Laumer et al. 2019; Fernández and Gabaldón 2020; Laumer et al. 2019; Fungi based on Spatafora et al. 2017). The majority of eukaryotic lineages are microbial. The Streptophyta lineage includes land plants and most green algae. Rhodophyta are known as red algae. Bolded lineages with cartoons are discussed in this article and include many of the representative extremophile eukaryotic lineages that have been most studied via genome-scale data in extreme environments. Major eukaryotic clades are colored.

In the first section, we highlight ’omics studies that have expanded our understanding of the metabolic and physiological innovations that extremophile organisms possess to cope with extremes in environmental parameters, including temperature, pH, salinity, and water availability. In the second section, we synthesize studies that have investigated the underlying genomic and molecular signatures of extremophiles and how they have evolved across a diverse suite of eukaryotic lineages. We also highlight how interactions with bacteria and archaea have expanded the capabilities of eukaryotes to adapt to extremes. Finally, we discuss the key methodological challenges and opportunities and identify emerging directions that could help shape eukaryotic research in extreme environments.

Diverse Physiological Strategies Uncovered across Extremophile Eukaryotes from Genome-Scale Data

A suite of eukaryotic organisms (Fig. 1) flourish in a wide range of stressful environments through diverse physiological strategies. In this section, we discuss two prominent types of physiological strategies that showcase the breadth of metabolic innovations across extremophile eukaryotic lineages uncovered from genome-scale data: (i) the evolution of specialized proteins (e.g. heat shock and ice-binding) and (ii) the maintenance of homeostasis through cellular transport and physical protective states (exemplified in Fig. 2). We showcase diverse eukaryotic innovations, including anhydrobiosis of tardigrades, cell wall structure of halophilic (salt-loving) fungi, and flexible metabolism of red algae (Fig. 2), and compare these strategies to the ways in which bacteria and archaea cope with similar abiotic conditions.

Fig. 2.

Emerging eukaryotic model organisms have yielded new insights to our understanding of the cellular and physiological changes and underlying genetic and genomic signatures of these adaptations. a) Poecilia mexicana species complex live-bearing fish live in streams with elevated hydrogen sulfide. While a background set of genes does not cluster by environment across populations, sulfide-processing genes from individually adapted sulfidic populations cluster (adapted from Ryan et al. 2023). b) Cyanidiophyceae red algae inhabit hot springs with extreme heat, acidity, and heavy metal accumulation. Detoxification of arsenic and mercury, along with other mechanisms of survival in these environments, in part come from horizontally transferred genes from extremophilic bacteria and archaea, as well as subtelomeric gene duplications (Cho et al. 2023). c) Wallemia ichthyophaga fungi live in high-salt environments like salterns. They have highly compact genomes in comparison to the average basidiomycete fungus and deal with osmotic stress in part from 3-fold cell wall thickening (Zajc et al. 2013). d) Tardigrades live in a variety of environments from marine to moss and have had multiple independent transitions to a terrestrial lifestyle going along with multiple independent duplications and losses of heat-soluble protein families like CAHS (adapted from Fleming et al. 2024). They enter a state of anhydrobiosis to withstand extremes, such as radiation, freezing, and desiccation (adapted from Møbjerg and Neves 2021).

Protein Adaptations in Extreme Temperatures

Managing protein stability is critical to survival in extreme temperatures. Eukaryotic organisms have adaptations that aid in the stabilization and activity of proteins in extreme habitats. High heat and UV radiation can denature proteins, and heat shock protein chaperones and thermostable enzymes aid in the preservation of the protein structure (Hu et al. 2022). In many diverse eukaryotes, including the thermophilic red algae, Cyanidioschyzon merolae (Rhodophyta; Kobayashi et al. 2014), and the hydrothermal vent dwelling, Alvinellid polychaete worm, Alvinella pompejana (Annelida; Fontanillas et al. 2017), these proteins bind unfolding proteins during heat stress. Red algae also use thermostable enzymes, such as alpha-xylosidase, associated with extreme heat (Rossoni et al. 2019; Van Etten et al. 2023), and Alvinellid worms have many amino acid differences that have led to global protein structural differences similar to thermophilic bacteria and archaea (Fontanillas et al. 2017). Despite the myriad ways in which eukaryotes manage protein stability at high temperatures, it is hypothesized that eukaryotes cannot survive at temperatures greater than 60 to 62 °C due to the limitations of forming thermostable organellar membranes, a challenge that is unique to eukaryotes (Tansey and Brock 1972). In contrast, some hyperthermophile bacteria and archaea can withstand temperatures of up to 130 °C (archaeon Geogemma barrossii; Kashefi and Lovley 2003; Merino et al. 2019) and grow at temperatures up to 122 °C (archaeon Methanopyrus kandleri; Takai et al. 2008; Merino et al. 2019). While archaeal thermophiles are successful at hotter temperatures than eukaryotes, similar protein folding systems are employed to ensure protein stability (Laksanalamai et al. 2004). Both archaeal and eukaryotic thermophiles use chaperone networks, with many protein-folding components in hyperthermophilic archaea having corresponding proteins in eukaryotes (Laksanalamai et al. 2004).

At the other end of the temperature spectrum, many psychrophilic eukaryotes use ice-binding proteins (IBPs), which are a diverse collection of proteins with different origins that mitigate threats of cell or environmental freezing (reviewed in Bar Dolev et al. 2016). IBPs include antifreeze proteins, which are present in some fish, insects, and crustaceans, such as marine teleost fish, snow fleas, and copepods, and lower the freezing point of their body fluids to live in subzero conditions (Duman et al. 2004; Kiko 2010; Bar Dolev et al. 2016). IBPs in plants (Griffith and Yaish 2004) and polar fungi like Antarctomyces psychrotrophicus (Ascomycota; Arai et al. 2019) prevent the growth of dangerously large ice crystals from ice recrystallization. Algae, such as Chlorella vulgaris (Chlorophyta) and Fragilariopsis diatoms (Ochrophyta), secrete IBPs to maintain a liquid environment around their cells (Raymond et al. 2009; Wang et al. 2020). Across eukaryotes, IBPs have different structures but a shared ligand (Bar Dolev et al. 2016). While bacterial IBPs have also been identified, our understanding of their diversity and function remains limited (Cid et al. 2016). Bacterial IBPs share some functions with eukaryotes (antifreeze and maintaining liquid environment) and functions not used by eukaryotes, such as adhesion to the ice structure (Garnham et al. 2008). The continued research of IBPs in eukaryotes will further resolve the structural and functional diversity of these proteins.

Some organisms have protein families or single proteins that facilitate survival in multiple conditions. Tardigrades (Tardigrada) have a set of heat-soluble protein families that are involved in the survival of both high and low temperatures (Fig. 2d), as well as desiccation and radiation resistance (Fleming et al. 2024). Some of these protein families are tardigrade specific, including cytosolic abundant heat-soluble (CAHS) proteins, mitochondrial abundant heat-soluble proteins, and secretory abundant heat-soluble proteins, hypothesized to have played a role in the tardigrade movement to land (Fleming et al. 2024). Heat-shock proteins are also used to cope with other stressors, such as salinity stress in Artemia brine shrimp (Arthropoda; Clegg 2005) and drought stress in Portulacineae plants (Angiospermae; Wang et al. 2019), highlighting the diverse uses of similar adaptations. Protein adaptation to multiple extremes is essential for polyextremophiles with a wide range of tolerance. The thermophilic mold, Myceliophthora thermophila BJA (Ascomycota), has an endoglucanase protein (cellulose metabolism) with a wide tolerance of pH and temperature, remaining stable at temperatures well above the limit for eukaryotic survival (Phadtare et al. 2017; Brininger et al. 2018). It is already clear that protein adaptations in eukaryotes have evolutionary implications for niche expansion through a wide range of tolerance.

Maintaining Homeostasis in Extremes

In extremes, such as pH, salinity, and heavy metal environments, eukaryotic organisms need to maintain homeostasis. Mounting genome evidence has uncovered three prominent strategies eukaryotes use to regulate their internal environment in extreme conditions: altered cellular transport, detoxification and solute accumulation, and whole-organism structural protections. Proton pumps and ion transport play key roles in maintaining a stable cell condition in the face of toxicity or hypertonicity. Portulacineae desert plants are specialized for the import of water during drought through plasma membrane intrinsic proteins (Wang et al. 2019). Proton pumps are also used in response to extreme acidity and sometimes high salt for red algae (Van Etten et al. 2023). Likewise, potassium ion transporters relieve salt stress in the extremely halophilic fungus, Wallemia ichthyophaga (Basidiomycota; Zajc et al. 2013). Ion channels relieve alkalinity stress from Cypriniformes fish in the extremely alkaline Lake Dali Nur (Chordata; Zhou et al. 2023). Live-bearing Poeciliidae fish transport oxidized sulfur in their hydrogen sulfide-rich environments (Chordata; Kelley et al. 2016), and Caulanthus annual mustard (Angiospermae) transport out heavy metals in serpentine soils (Hawkins et al. 2017). Similarly, magnesium transporters in Antarctic lichen, such as Cladonia borealis, maintain homeostasis in the high-magnesium Antarctic environment (Ascomycota; Cho et al. 2024). Acidophilic bacteria (e.g. Acidithiobacillus ferrooxidans, optimal pH 1.8) and archaea (e.g. Thermoplasma acidophilum, optimal pH 1.4) also have proton efflux systems, withstanding similar low pH to acidophilic eukaryotes, such as red algae, which are found in pH 0.2 to 5 (Baker-Austin and Dopson 2007). Several archaeal acidophiles, including T. acidophilum, Ferroplasma acidiphilum, and Sulfolobus solfataricus, have cell membranes bound with tetraether lipids, which additionally resists the entry of protons (Baker-Austin and Dopson 2007).

Eukaryotes also use strategies of detoxification and organic solute accumulation to neutralize toxins and respond to harmful conditions. Detoxification reduces the reactivity of heavy metals, such as arsenic, mercury, hydrogen sulfide, and free radicals in distantly related eukaryotes, including Cyanidiophyceae red algae, Poeciliidae fishes, Alvinellid worms, Arctic Brassicaceae plants (Angiospermae), and Chlamydomonas green algae (Chlorophyta) (Kelley et al. 2016; Fontanillas et al. 2017; Brown et al. 2018; Zhang et al. 2019; Birkeland et al. 2020; Van Etten et al. 2023). Other organisms accumulate compatible solutes to handle tonic stress. Haberlea resurrection plants (Angiospermae), named for their ability to recover from fully drying out, and Aureobasidium (desert fungi; Ascomycota) accumulate raffinose and trehalose sugars as part of their desiccation responses (Jiang et al. 2018; Gupta et al. 2024). Halophilic flagellates, such as Halocafeteria seosinensis (Stramenopiles; Opalozoa) and Pharyngomonas kirbyi (Discoba), accumulate organic solutes like myoinositol (Harding et al. 2016). Xerophilic (low water) Aspergillus penicilloides fungi (Ascomycota) and halophilic W. ichthyophaga fungi accumulate glycerol and other polyols (Zajc et al. 2013; Coleine et al. 2022). In contrast, while the accumulation of organic solutes is common for many bacteria and archaea, many extremely halophilic bacteria and archaea use the “salt-in” strategy, accumulating salt (K⁺ and Cl⁻) inside their cells instead of keeping it out (Kempf and Bremer 1998; Oren 2008; Czech and Bremer 2018).

Another strategy to maintain homeostasis is to strengthen the protection between the organism and the environment or to enter a protective state during particular stress. Eukaryotes use different mechanisms with similar outcomes. Wallemia fungi thicken their cell wall 3-fold as the most halophilic known fungi (Zajc et al. 2013; Fig. 2c), and Cypriniformes fish protect their egg coats, with genes encoding egg coat proteins recently identified (Xu et al. 2017). Tardigrades are potentially the most famed for their cryptobiotic state, called “tun,” where metabolism is nearly paused, and the animals can withstand most extremes besides high heat (Møbjerg and Neves 2021; Fig. 2d). Antarctic midge larvae (Arthropoda) enter a similar anhydrobiotic state during frozen periods (Goto et al. 2015). Animals like Artemia brine shrimp and many protist lineages spanning the tree of eukaryotes, including ciliates, amoebae, and diatoms, can enter protective cysts to withstand adverse conditions (Clegg 2005; Schaap and Schilde 2018; Fig. 1). As for protective states, many groups of bacteria form protective endospores (Firmicutes), exospores (Actinobacteria), budding spores (Chloroflexi), or dormant akinetes (Cyanobacteria) in response not only to stress, primarily low nutrients but also unfavorable abiotic conditions (Beskrovnaya et al. 2021). Critically, because research into these states of low metabolic activity has taken place in separate fields, these processes have not been well connected and use different terminologies. Comparative genomic and transcriptomic data from these diverse lineages present an exciting opportunity to illuminate the physiological and underlying genetic similarity of these protective states.

Genomic Signatures and the Genetic Basis of Adaptation across Diverse Eukaryotic Lineages

Advances in ’omics tools have not only shed light on the physiological adaptations of eukaryotes in extreme environments but also uncovered many genome-level changes and, in some cases, the genetic basis of adaptation associated with extremophiles. Below, we synthesize how genetic information has been shaped in eukaryotic extremophiles across scales from individual sequences to genomic signatures.

At the sequence level, similar to bacterial and archaeal extremophiles (Foerstner et al. 2005; Arias et al. 2023), there are a suite of attributes associated with eukaryotes, including the rates of substitution, percent GC content, and signatures of selection (Jain et al. 2014; Xu et al. 2017; Eshel et al. 2021). Galdieria sulphuraria has the fastest mitochondrial substitution rate of red algae and an extremely high GC skew (Jain et al. 2014). Thermophilic and hyperthermophilic bacteria and archaea are known to have a high GC content, influencing DNA and tRNA stability (Arias et al. 2023). Elevated substitution rates are also displayed in Cypriniformes fish in long terminal repeats (LTRs), regions inserted by viruses (Xu et al. 2017). Substitutions are maintained in cases of positive selection where new traits may be beneficial to survival. Positive selection on different genes related to abiotic stress has resulted in convergent phenotypes in multiple Arctic Brassicaceae plants (Birkeland et al. 2020), psychrophilic algae (Zhang et al. 2019), and live-bearing Poecilia fish (Ryan et al. 2023; Fig. 2a). There is also evidence of a positive selection for drought tolerance in plants in the Atacama Desert (Eshel et al. 2021) and Caulanthus annual mustard plants (Hawkins et al. 2017). In other cases, such as the mitogenomes of Antarctic ice fish (Papetti et al. 2021) and the thermostable genes of Alvinellid vent worms (Fontanillas et al. 2017), purifying selection may have preserved ancestral traits that are beneficial to survival in extremes.

From an increasing number of comparative transcriptomic studies on extreme organisms and closely related mesophilic counterparts, it is clear that shifts in gene expression and transcriptional regulation can also facilitate success in extreme environments. For example, multiple populations of Poecilia mexicana fish that live in hydrogen sulfide springs upregulate genes involved in hydrogen sulfide detoxification and maintenance of homeostasis relative to nonsulfidic populations (Kelley et al. 2016). Haberlea resurrection species show the upregulation of genes not only particularly involved in their desiccation response but also in response to darkness (Gupta et al. 2024), and halophilic protists have upregulation of genes involved in their organic osmolyte metabolism and transport (Harding et al. 2016). As both sequencing technologies and bioinformatics pipelines continue to improve in accuracy and capture of transcripts (particularly from low input samples), comparative transcriptomic studies present an exciting avenue to uncover the importance of differential gene regulation of metabolic processes in facilitating species persistence.

The increasing availability of eukaryotic genomes has also led to the identification of genomic attributes associated with organisms in extreme environments, including genome expansion, reduction, and rearrangement. The gene family expansion of stress response genes in extremophiles has been particularly ubiquitous. For example, 89 gene families were significantly expanded in Haberlea rhodopensis resurrection plants compared to other land plants (Gupta et al. 2024), Cladonia lichens have 50 expanded gene families especially related to transporters (Cho et al. 2024), and gene family expansions have been identified in Portulacineae plants (Wang et al. 2019), deep-sea Vesicomyid clams (Mollusca; Ip et al. 2021), and halophilic Wallemia fungi (Zajc et al. 2013). Genomes are also expanded through gene duplications. Tardigrades have experienced many independent gene duplications (Fleming et al. 2024; Fig. 2d), along with Cactaceae (within Portulacineae) (Wang et al. 2019). Cyanidiophyceae red algae have specifically experienced subtelomeric gene duplications of genes related to functional adaptation (Cho et al. 2023; Fig. 2b). Cladonia borealis Antarctic lichens have expanded Copia transposable elements (TEs) (Cho et al. 2024), Cypriniformes fish have expanded LTRs (Xu et al. 2017), and Archevesica marissinica Vesicomyid clams have increased TEs potentially related to their gene family expansions (Ip et al. 2021). Gene duplications and gene family expansions are likely most common in eukaryotes and shown to be rare in bacteria and archaea (Treangen and Rocha 2011; Tria and Martin 2021).

In contrast, many extremophile genomes have also been reduced by gene loss. While Cladonia and tardigrades exhibit many gene family expansions, there are many losses as well (Cho et al. 2024; Fleming et al. 2024). Likewise, the mitogenome of the red alga, G. sulphuraria, is highly reduced (Jain et al. 2014) in addition to the broader genome reduction among all Cyanidiophyceae (Van Etten et al. 2023). The size of W. ichthyophaga and the predicted number of coding genes are much smaller compared to those of most fungi (Zajc et al. 2013; Fig. 2c), and the genome of halophilic Picochlorum costarvermella is very small for green algae (Chlorophyta; Foflonker et al. 2018). Furthermore, Picochlorum has arranged coding regions into “gene neighborhoods,” which function similarly to bacterial operons (Foflonker et al. 2018). Arctic notothenioid fishes have gene order rearrangements in their mitogenomes alongside purifying selection (Papetti et al. 2021). Such reductions and rearrangements may facilitate increased efficiency of transcription in extreme environments with variable conditions (Foflonker et al. 2018). Unlike genome expansion, genome reduction is well appreciated as a common strategy in bacteria and archaea. For example, thermoreduction has been observed in archaeal hyperthermophiles, including Sulfobacillus thermosulfidooxidans, Halobacterium NRC-1, and Methanosarcina species (Laksanalamai et al. 2004; Zhang et al. 2017). Likewise in bacteria, there has been a large-scale gene reduction of the psychrophilic bacterium, Exiguobacterium antarcticum (Dias et al. 2018), and a pattern of genome reduction in hyperthermophiles and thermophiles like Thermotoga maritima (Sabath et al. 2013).

Gene Transfer and Symbiosis Facilitate Success of Eukaryotic Extremophiles

While horizontal gene transfer (HGT) between bacteria and archaea is frequent, widespread, and well appreciated (Polz et al. 2013; Arnold et al. 2022), there is a growing appreciation for the ways in which cross-domain HGT has also shaped the metabolic capabilities of eukaryotic organisms (Soucy et al. 2015). Bacteria and archaea can also reshape eukaryotic metabolism and access to resources through symbiosis. Symbiosis is defined as the direct interaction between organisms with either one- or two-way dependency upon each other, although symbiosis is most often associated with mutually beneficial interactions (López-García et al. 2017). In some ways, symbiosis can be thought of as “borrowing” the metabolism of an entire organism, as opposed to individually transferred genes. Below, we discuss the ways in which both HGT and symbioses with bacteria and archaea (and occasionally, other eukaryotes) have shaped eukaryotic life in extreme environments.

Adaptations of bacteria and archaea have often benefitted eukaryotes through HGT. Heavy metal detoxification genes, along with other adaptive traits of Cyanidiophyceae red algae, including pathways driving metabolic expansion and flexibility, likely result from HGT (Qiu et al. 2013; Rossoni et al. 2019; Cho et al. 2023; Van Etten et al. 2023; Fig. 2b). This is also likely the case for acidophilic green algae, such as Coccomyxa subellipsoidea, Chlamydomonas eustigma, and Chlamydomonas acidophila, aiding in their high tolerance of arsenic or cadmium (Chlorophyta; Hirooka et al. 2017). Halophilic Halocafeteria have genes involved in organic osmolyte (accumulated solute) synthesis derived from bacteria (Harding et al. 2016), and halophilic Picochlorum green algae have genes resulting from HGT involved in many adaptive functions, including osmolyte synthesis, metabolic flexibility, and salinity tolerance (Foflonker et al. 2018). Vesicomyid clams have 28 HGT events from bacteria (Ip et al. 2021), which are potentially related to their chemosymbiosis. Many IBPs discussed earlier are derived from HGT in Antarctic and some Arctic diatoms and green algae (Raymond and Kim 2012; Raymond 2014; Raymond and Morgan-Kiss 2017; and see summary in Van Etten and Bhattacharya 2020), Antarctic ciliate Euplotes focardii (Ciliophora; Pucciarelli et al. 2014), polar fungi (Arai et al. 2019), polar dinoflagellate Polarella glacialis (Dinoflagellata; Stephens et al. 2020), and potentially Antarctic copepods (Arthropoda; Kiko 2010). There are also cases of HGT from one extremophile eukaryote to another, as in the case of the Arctic algae transfer of IBP genes between distantly related algal clades (Dorrell et al. 2022).

Symbioses have likely facilitated the expansion of eukaryotic organisms into dark, high-pressure, high-heat, and anoxic environments through the chemosynthetic metabolism of deep-sea endosymbionts in animals like tube worms and Bathymodiolus mussels (Mollusca) as well as microbial eukaryotes like ciliates (Fontanillas et al. 2017; Sogin et al. 2020). Multiple groups of anaerobic amoebae also have documented symbioses with bacteria, such as Lenisia limosa (Breviatea) and its ectosymbiont bacteria (Hamann et al. 2016), Pelomyxa schiedti within Archamoeba (Evosea, Amoebozoa) and its multiple endosymbiont bacteria and a methanogen archaea (Treitli et al. 2023), and Anaeramoeba (Metamonada) and its sulfate-reducing bacterial ectosymbionts (Jerlström-Hultqvist et al. 2023). Both the amoebae and their symbionts benefit from hydrogen transfer or methanogenesis in their anoxic environments. The eugelonozoan subgroup of Symbiontida flagellates (Discoba) also has bacterial epibionts that may detoxify their sulfidic, low-oxygen environments (Edgcomb et al. 2011). Symbionts are not limited to bacteria and archaea. It is hypothesized that fungal symbionts help many plants withstand extreme conditions (Singh et al. 2011), such as the fungal symbionts of Antarctic vascular plants that mediate nitrogen uptake (Acuña-Rodríguez et al. 2020). Likewise, lichens (a symbiosis of multiple fungi plus a cyanobacteria or algae) can survive in more extreme environments than their symbionts individually (Armstrong 2017; Cho et al. 2024).

Biofilms and mats are symbioses that confer physical protection to many extremophile eukaryotes. Antarctic chlorophytes (Chlorophyta) often grow inside cyanobacterial mats, offering additional UV protection (Vincent et al. 2004). Cyanobacterial mats and bacterial biofilms are structures known to confer not only population protection, such as antibiotic resistance, but also likely community protection to their members from extremes, such as radiation (Enyedi et al. 2019). Similarly, living within a biofilm with bacteria also confers protection for many eukaryotes within extremes like acid mine drainage and the gelatinous “acid streamers” of acidic cave complexes (Zirnstein et al. 2012; Kay et al. 2013). It is already evident that symbioses with bacteria and transfer of genes have facilitated a diversity of eukaryotic life in extreme environments and increased sampling and comparative genomics will aid in a more resolved understanding of the frequency of these events and their phylogenetic distribution.

Challenges, Opportunities, and Emerging Research Areas

Research on eukaryotes in extreme environments has been limited in comparison to bacteria and archaea in part due to key methodological challenges. First, for microbial eukaryotes, culturing still presents a significant barrier due to complex nutrient requirements that remain unknown. For example, many heterotrophic protists have obligate interactions with other organisms (Faktorová et al. 2020). This challenge is likely compounded in many extreme environments, where eukaryotic taxa are reliant on symbioses with archaea and bacteria to persist in harsh conditions. Second, eukaryotic genomes remain notorious for their complexity and size. Although size varies greatly in both microbial and macrobial lineages, eukaryotic genomes can be many orders of magnitude larger (>160 Gb) than average bacteria or archaea (Blommaert 2020; Fernández et al. 2024). To complicate this further, eukaryotes (including microbial lineages) host their own “microbiome” of bacteria and archaea, resulting in a need for careful curation and removal of contaminant sequences. Third, only a handful of bioinformatic tools and pipelines are designed for diverse groups of eukaryotes, particularly for protists. Similarly, databases are often only relevant to specific model lineages (i.e. dictyBase, Saccharomyces Genome Database), and most eukaryotic lineages lack high-quality references, annotations, and gene models resulting in limited inferential power.

Despite these challenges, recent methodological advances in sequencing technologies and computational pipelines leave the field well poised to advance our understanding of the innovations that have enabled eukaryotic life to flourish in extreme environments. Single-cell genomics and transcriptomics are increasingly being used to obtain data from microbial eukaryotic lineages not in culture or currently uncultivable (Sieracki et al. 2019; Thomé et al. 2023; Li et al. 2024). The continued improvement of long-read sequencing technologies has also rapidly improved our ability to assemble high-quality eukaryotic genomes (Tedersoo et al. 2021; Cosma et al. 2022). Higher-quality genomes obtained from long-read and hybrid sequencing approaches are already improving detection of regulatory elements and HGT (Jian et al. 2024). The development of new bioinformatic tools to obtain and profile eukaryotic metatranscriptome and metagenome-resolved genomes (for example Cerón-Romero et al. 2019; Saary et al. 2020; Krinos et al. 2023) also present an exciting opportunity to assess species pangenomes and population-level dynamics in eukaryotes (Fan et al. 2020; Weiner et al. 2023).

When leveraging these methodological advances, it is critical that a broad phylogenetic diversity of lineages is targeted. Despite the increasing number of studies that have derived physiological and evolutionary insights from genome-scale data, most eukaryotic lineages that live in extreme environments lack a genome-scale representation (Oliverio et al. 2018; Coleine et al. 2022; Shain et al. 2022; Rappaport and Oliverio 2023). This is particularly notable for microbial eukaryotes (i.e. protists), which represent the bulk of eukaryotic phylogenetic diversity (Fig. 1). This has several important consequences. Increased phylogenetic sampling is critical for understanding the evolutionary history of genes, and molecular experiments are important to test hypotheses of function (Sibbald and Archibald 2017). Limited phylogenetic sampling can lead to misunderstanding of what constitutes common types of adaptations versus exceptions in eukaryotes. It can also result in limited resolution of whether functions have a shared genetic basis or are lineage specific (Fleming et al. 2024). As noted for vent worms (Fontanillas et al. 2017), but more broadly applicable, traits of extremophiles may not be derived but actually shared ancestrally and later lost in some lineages.

The study of extremophiles presents key opportunities to synthesize patterns of molecular and organismal adaptation across the eukaryotic tree of life (Fig. 1) and evolutionary processes that have led to these adaptations. Many examples of convergent evolution have already been identified across extremophile lineages (Zhang et al. 2019; Birkeland et al. 2020; Ryan et al. 2023), and synthesis efforts will shed light on the frequency of convergence across diverse lineages and if particular lineages are more likely to have similar adaptations. Another consideration is the relative importance of vertical versus HGT in facilitating adaptation across a wide range of lineages, along with mechanisms of selection for horizontally transferred genes (Van Etten and Bhattacharya 2020; Van Etten et al. 2024). Machine learning/artificial intelligence approaches have begun to be applied to synthesizing and predicting genome and protein structure of extremophilic bacteria and archaea (Khan and Patra 2018; Arias et al. 2023; Huang et al. 2023). These approaches may also be applied to the analysis of genomic signatures in eukaryotes to reveal patterns by environment and differentiate taxonomy.

It is clear that exciting current and emerging methodological approaches can be employed to explore eukaryotic adaptations to extreme environments. However, we also argue that the field needs to not only characterize individual extremophile lineages and clades but also make sense of these innovations from a broader conceptual framework. Eukaryotic extremophiles already show a complex history of structural and functional reductions and expansions, so there will not be a singular clear story of how eukaryotes have come to inhabit environments historically deemed too harsh for eukaryotic life. Yet, such frameworks will allow us to identify and explain patterns and trends in these solutions. This will facilitate a more integrative understanding of the frequency of uniquely evolved and independently replicated solutions and, more broadly, the evolution of genes and genomes across the tree of life.

Data Availability

No new data were generated for this manuscript.