Protist

Brief history

Starting in the 17th and 18th centuries, after the discovery of microscopic life by Antonie van Leeuwenhoek, the classification of single-celled protists was largely based on observations under light microscopy. Protists were incorporated into the traditional dichotomy that defined all life as either plant or animal: non-motile algae were considered part of the plant kingdom, and all other protists joined the animal kingdom.^[39][40] They were popularly known as "infusion animals" or infusoria, together with bacteria and small invertebrates. Otto Friedrich Müller was the first to introduce microbial protists to the Linnean system of binomial nomenclature.^[41][42]

During the 19th century, after several waves of naturalist studies,^[42] it became clear that these microorganisms were distinct from animals and plants. John Hogg and Ernst Haeckel proposed a separate kingdom of life, named Protoctista^[43] or Protista,^[44] respectively, to accommodate the predominantly unicellular eukaryotes, and initially bacteria, which were later excluded.^[39] The classical framework of protist classification was established, as exemplified by the works of Otto Bütschli, where they were grouped according to morphological and locomotive features, such as Mastigophora (flagellates), Rhizopoda (amoebae), Sporozoa (spore-forming parasites), and Infusoria (ciliates).^[40] However, Bütschli retained a division between the Protozoa (animal-like protists) and Protophyta (plant-like). This dogma remained widely accepted throughout the early 20th century.^[39]

From the mid-20th century, eukaryotes were firmly split from bacteria (prokaryotes) due to the presence of the cell nucleus,^[45] and protists (or protoctists) were more widely accepted as a separate kingdom.^[46][47][48] The advent of electron microscopy shifted the methods of classification, as it revealed previously unrecognized cellular characteristics (i.e., ultrastructure, particularly of the flagellar apparatus and the cytoskeleton) that suggested evolutionary affinities between superficially disparate lineages. For example, the tripartite flagellar mastigonemes were used to group heterokont algae, oomycetes and opalines into the Stramenopiles; the discovery of cortical alveoli showed affinities between dinoflagellates and ciliates, which now belong to the Alveolata; and disc-shaped mitochondrial cristae were shared by kinetoplastids and euglenids, now united as Euglenozoa. The algae-protozoa dichotomy became obsolete.^[49][50][40]

Since the 1990s, molecular phylogenetic analyses based primarily on the SSU rRNA gene demonstrated that protists were a paraphyletic assemblage of clades spanning the entire eukaryotic tree of life, from which the other three "kingdoms" (animals, plants, and fungi) had evolved.^[51][40] Beginning in the 2000s, single-cell sequencing and phylogenomics technologies progressively improved the resolution of deeper evolutionary relationships. Altogether, these innovations led to successive revisions of protist classification,^[40] such as the ones published by the International Society of Protistologists.^[52][53][9] Eukaryotes could no longer be divided into four monophyletic kingdoms,^[c] and instead are arranged in "supergroups", each often encompassing an unexpected variety of morphologies and lifestyles that do not resemble one another. New deep-branching groups are added to the tree at a rate of nearly one per year.^{[56][57][58][59]}

Modern classification and diversity

Protists are currently divided among a number of clades informally named supergroups. Most of these supergroups fall under either of two large clades of eukaryotes: Amorphea and Diaphoretickes. The animals and fungi belong to the Opisthokonta supergroup in the Amorphea clade, along with several other groups of protists (e.g., Amoebozoa).^[9] Diaphoretickes contains the diverse supergroups Archaeplastida (including plants), Stramenopiles, Alveolata, Rhizaria (combined as the SAR supergroup), and the less species-rich Cryptista, Haptista, Telonemia, and Disparia.^[60][61][62] Outside of these larger clades, various groups of protists with primitive cell architecture (Discoba, Metamonada, and Malawimonadida) are collectively known as the excavates or "Excavata". The name 'excavate' refers to the shared characteristic of a ventral groove in the cell used for feeding, which is considered an ancestral trait present in the last eukaryotic common ancestor.^{[63][64]: 597 [65]}

The following table lists estimated numbers of described extant species for all known protist supergroups, and provides an overview of their diversity in terms of morphologies, habitats, and nutritional modes. For large groups, the overview is not exhaustive and only mentions the most characteristic members.

More information Clade, Supergroup ...

Clade	Supergroup		Example	Brief description of morphology, lifestyle and habitat	Living species
Diaph.	SAR	Stramenopiles		Ancestrally flagellates distinguished by two 'heterokont' (unequal) flagella, one with tripartite mastigonemes. Present in virtually all habitats. The most species-rich lineage, the ochrophytes, are algae of diverse morphologies, ranging from flagellates (like golden algae) to walled ornamented cells (like diatoms, pictured) to truly multicellular macroalgae with differentiated tissues (brown algae such as kelp). All other lineages are composed of heterotrophs: bacterivorous flagellates (e.g., bicosoecids, bigyromonads), fungus-like osmotrophs (oomycetes, hyphochytrids, and labyrinthulomycetes), heliozoan amoebae (actinophryids), and ciliate-like obligate symbionts of animals (opalinids).[66]	over 100,000[67]
		Alveolata		Ancestrally flagellated predators with cortical alveoli. The colponemids represent these ancestral characteristics.[68] The most diverse group are the ciliates (pictured), with large cells covered in rows of cilia, usually at the top of the microbial food chain.[69] The remaining alveolates belong to the clade Myzozoa and are ancestrally photosynthetic; some have retained their photosynthetic ability (chromerids and many dinoflagellates), while others have evolved into parasites of animals and algae (apicomplexans, perkinsozoans, and some dinoflagellates).[70][9][71][72]	over 10,000[68]
		Rhizaria		Amoebae with filose or reticulose pseudopodia.[73] The most species-rich group is Retaria, home to conspicuous marine amoebae encased in hard skeletons (radiolarians) or multichambered tests (foraminifers, pictured). Secondly is Cercozoa, with an extreme diversity of morphologies: small flagellates, amoeboflagellates, aggregative slime molds,[74] testate amoebae, heliozoa, and massive radiolarian-like cells (phaeodarians);[75] some are capable of photosynthesis (e.g., chlorarachniophytes). Lastly, Endomyxa contains both free-living predatory amoebae (e.g., vampyrellids) and obligate parasites of animals, plants, and algae (e.g., phytomyxeans and ascetosporeans).[76][9]	over 11,000[77]
	Telonemia			Free-living flagellates with a unique cytoskeleton and a combination of cell structures. Present in all marine and freshwater environments feeding on bacteria.[78]	10[79][80]
	Haptista			Two groups of different free-living single-celled protists: centrohelids—predatory heliozoan amoebae, widespread in aquatic and soil environments[81]—and haptophytes—coccoid or flagellated photosynthetic algae, mostly marine (e.g., coccolithophores, pictured).[82] Both can produce an outer coat of complex mineralized scales.[9]	over 600
	Pancryptista			Free-living flagellates, except one species of heliozoan amoebae, Microheliella maris.[83] Almost all of the flagellates are distinguished by specialized ribbon-shaped extrusomes known as ejectisomes. Many are photosynthetic, known as cryptomonads (pictured), while the rest are phagotrophs, consumers of bacteria. Present in aquatic environments worldwide.[84][9]	over 100
	Archaeplastida*			Algae with chloroplasts derived from primary endosymbiosis with a cyanobacterium. Found in all environments. Almost entirely photosynthetic, with the exception of two small groups of phagotrophic flagellates, rhodelphids[85] and picozoans.[86] The two major groups, red algae and green algae (pictured), exhibit diverse morphologies, ranging from single cells—coccoid, palmelloid, sarcinoid, flagellated—to colonies, simple filaments, and macroscopic thalli with varying degrees of complexity (e.g., coralline algae, sea lettuce, stoneworts). Also included are glaucophytes, rare blue-green algae found in surface waters.[87]	over 20,500[88]*
	Disparia			Three lineages of free-living predatory flagellates with unique cytoskeletons. These are: Hemimastigophora, with two rows of flagella, present in soils and aquatic sediments;[56] Provora, fast-swimming predators of other protists through a strong feeding apparatus resembling jaws, found in low abundance in marine environments globally;[89][90] and Caelestes (pictured), rare inhabitants of the marine benthos whose cells protrude arms or stalks used for movement or prey capture.[62]	20
Amorph.	Amoebozoa			Amoebae of diverse morphologies, with lobose or filose pseudopodia, and sometimes with flagella. Most are free-living phagotrophs found across terrestrial and aquatic environments, such as the archetypal genus Amoeba itself,[91][92][93] or the testate amoebae Arcellinida, one of the most conspicuous groups of protists.[94] Numerous groups have independently evolved fungus-like fruiting bodies,[95] such as myxomycetes (pictured).[96] Some of the free-living amoebae are important vectors of pathogenic bacteria or are pathogenic themselves (e.g., Acanthamoeba).[97] Others are anaerobic intestinal symbionts (e.g., Entamoeba).[9]	over 2,400[98]
	Breviatea			Anaerobic free-living amoeboflagellates with fine pseudopodia and modified mitochondria. Present only in low-oxygen marine and brackish sediments, their growth depends on mutualistic interactions with prokaryotes.[99]	4[100]
	Apusomonadida			Free-living flagellates distinguished by a proboscis, a sleeve-like structure that envelops one of their two flagella.[100] Found gliding on wet soil and aquatic sediments worldwide.[101]	28[101]
	Opisthokonta**			Flagellates distinguished by a single posterior flagellum, many with complex life cycles and varying degrees of multicellularity.[96] Some are entirely amoeboid, with fine pseudopodia (e.g., filastereans and nucleariids, including slime molds),[102][103] while others become amoeboid temporarily (e.g., choanoflagellates, pictured).[104] Most species are free-living filter-feeders or predators,[105][103][106][107] but some lineages (e.g., ichthyosporids) evolved into osmotrophic parasites of animals.[108][109]	approx. 300[77]**
Excavat.	Discoba			Flagellates with very different lifestyles, present in aquatic and terrestrial environments, ranging from aerobes to anaerobes. The most diverse group, Euglenozoa, includes free-living osmotrophs, phagotrophs, phototrophs (euglenophytes, pictured), and pathogens (kinetoplastids).[64][110] The less diverse Heterolobosea are primarily amoeboflagellates, and include some slime molds (acrasids) and well-known opportunistic parasites (e.g., Naegleria fowleri).[26] The smallest group, Jakobida, consume bacteria by suspension feeding.[111]	over 2,200[112][113]
	Metamonada			Anaerobic or microaerophilic flagellates, amoebae, or amoeboflagellates,[114] with reduced or completely lost[115] mitochondria. A few are free-living, found in aquatic hypoxic sediments, but most species are obligate parasites (e.g., Giardia, pictured) or commensals in animal intestines (e.g., parabasalids). Many have a high number of flagella.[116][114][9]	approx. 800[77]
	Malawimonadida			Free-living bacterivorous flagellates that feed by suspension feeding, present in marine or fresh waters.[117]	3[117]
Other	Ancyromonadida			Tiny free-living aquatic flagellates composed of flattened cells with an inflexible pellicle and a lateral rostrum with extrusomes. Found in most aquatic habitats.[118]	over 20[100][118]
	CRuMs			Free-living flagellates and filose amoebae with a pellicle underneath the cell membrane. Almost all flagellated members can produce filose pseudopodia. Found in aquatic environments.[40]	14[40]
*Excluding plants. **Excluding animals and fungi.

Close

There are also many protists of uncertain position because their DNA has not been sequenced, and consequently their phylogenetic affinities are unknown.^[9]

Predicted diversity

The total species diversity of protists is severely underestimated by traditional methods that differentiate species based on morphological characteristics. The number of described protist species is very low (ranging from 26,000^[119] to over 76,000)^[d] in comparison to the diversity of land plants, animals and fungi, which are historically and biologically well-known and studied. The predicted number of species also varies greatly, ranging from 140,000 to 1,600,000, and in several groups the number of predicted species is arbitrarily doubled. Most of these predictions are highly subjective. Molecular techniques such as environmental DNA barcoding have revealed a vast diversity of undescribed protists that accounts for the majority of eukaryotic sequences or operational taxonomic units (OTUs), dwarfing those from land plants, animals and fungi.^[98] As such, it is considered that protists dominate eukaryotic diversity.^[120]

Nutrition

Protists display a wide variety of food preferences and feeding mechanisms.^[9][123] According to the nutrient source, they can be divided into autotrophs (or phototrophs,^[124] producers, traditionally algae), which photosynthesize their own organic molecules, and heterotrophs (consumers, traditionally protozoa), which obtain organic molecules from the environment, either by passive feeding of small particles (i.e., osmotrophs) or by engulfing whole cells or parts of cells of other organisms (phagotrophs).^[125] Phagotrophic protists may consume prokaryotes (i.e., bacterivores) or other eukaryotes (eukaryovores), including single-celled protists (cytotrophs), algae (phycotrophs),^[9] fungi (mycophages or mycotrophs),^[126] nematodes (nematophages),^[127] or tissues of larger animals (histophages).^[128]

Phagotrophy

Phagotrophic protists feed by phagocytosis, a process unique to eukaryotes^[129] where food particles or cells are digested into a vacuole, the phagosome.^[123] This is the general mode of nutrition for protists, and has resulted in a diverse array of strategies for hunting and digestion.^[129] Usually, digestion occurs at a specialized mouth-like region of the cell, the cytostome, which may be followed by the cytopharynx,^[130] a tract supported by microtubules.^[123] In amoebae, phagocytosis takes place anywhere on the cell surface.^[128]

According to the method of digestion, protists can be divided into filter, raptorial, or diffusion feeders. Filter feeders accumulate small suspended particles into the cytostome by filtering them through pseudopodia or rigid tentacles, like choanoflagellates, or by generating water currents around the cytostome, like ciliates.^[9] Raptorial feeders capture whole cells, either grazing on surfaces like bacterial lawns or actively preying on larger cells of other organisms.^[128][9] Diffusion feeders, like suctorian ciliates and heliozoans, passively engulf prey that happen to collide with their tentacles or pseudopodia and are immobilized.^[128] Certain protists exhibit a variation of predation known as myzocytosis, where they perforate the prey cell and suck out its contents or ingest them from the inside, leaving behind an empty shell; this is the case for vampyrellids, viridiraptorids, and many alveolates.^[129][9]

Different predatory protists have sophisticated structures for capturing prey, such as the ventral groove of excavates, the hood-like extension or 'pallium' of some dinoflagellates, or the expandable oral pocket of ciliates. Many euglenids have a system of rods and vanes that grab and pull in prey cells, similarly to a Chinese finger trap.^[129]

Osmotrophy

Osmotrophic protists absorb soluble^[125] or very small (under 0.5 μm) molecules by diffusion, membrane channels and carriers, or pinocytosis, where nutrients are engulfed into small vacuoles or endosomes.^[9][123] Some osmotrophs, known as saprotrophs or lysotrophs, perform external digestion by releasing digestive enzymes into the environment and decomposing organic matter^[9] into simpler molecules that can be absorbed, allowing finer control over substances that enter the cell and minimizing the risk of harmful substances or infection.^[132] Probably all eukaryotes are capable of osmotrophy, but some have no alternative of acquiring nutrients. Obligate osmotrophs include the aphagean euglenids, some green algae, the human parasite Blastocystis, some metamonads,^[9] the parasitic trypanosomatids,^[133] and the fungus-like oomycetes and hyphochytrids.^[132]

Mixotrophy

Rapaza viridis is a species of obligate specialist mixotrophs: it survives through the predation of Tetraselmis algae and acquisition of their chloroplasts. It rejects any other prey cells. Even when well fed, it cannot survive without a light source, as it needs to photosynthesize with those chloroplasts.^[134]

Most photosynthetic protists are mixotrophs,^[135] as they combine photosynthesis with phagocytosis.^[e] While some mixotrophs already have chloroplasts (i.e., algae), others acquire chloroplasts by stealing them from their prey, a process known as kleptoplasty. Kleptoplastic protists may be generalists, able to steal chloroplasts from a variety of prey, like some ciliates, or they may be specialists, only capable of obtaining chloroplasts from very specific prey. Specialists may keep the entire prey inside of their cells, as do many foraminifers and radiolarians, or they may only engulf the plastids and discard the rest.^[137][138]

Among exclusively heterotrophic protists, variation of nutritional modes is also observed. The diplonemids, which inhabit deep waters where photosynthesis is absent, can flexibly switch between osmotrophy and bacterivory depending on the environmental conditions.^[139]

Osmoregulation

Many freshwater protists need to osmoregulate (i.e., remove excess water volume to adjust the ion concentrations) because non-saline water enters in excess from the environment.^[140][130] Osmoregulation is done through ion transporters of the cell membrane and through contractile vacuoles, specialized organelles unique to protists that periodically excrete fluid high in potassium and sodium through a cycle of contractions.^[122] These vacuoles are surrounded by the spongiome, a system of vesicles or tubes that slowly collect fluid from the cytoplasm into the vacuoles, which then contract and discharge the fluid through a pore. The mechanism, location, and structure of this system vary across protists. For example, ciliates contract the vacuoles by actin and microtubule filaments; dinoflagellates contract it through a sheath formed by a flagellar rootlet, known as the pusule. Marine, parasitic, or thick-walled protists lack these vacuoles.^[140]

Respiration

The last eukaryotic common ancestor was aerobic, bearing mitochondria for oxidative metabolism. Many lineages of free-living and parasitic protists have independently evolved and adapted to inhabit anaerobic or microaerophilic habitats, by modifying the early mitochondria into hydrogenosomes, organelles that generate ATP anaerobically through fermentation of pyruvate. In a parallel manner, in the microaerophilic trypanosomatid protists, the fermentative glycosome evolved from the peroxisome.^[122]

Sensory perception

Many flagellates and probably all motile algae exhibit a positive phototaxis (i.e. they swim or glide toward a source of light). For this purpose, they exhibit three kinds of photoreceptors or "eyespots": simple receptors with light antennae, found in many green algae, dinoflagellates and cryptophytes; receptors with opaque screens; and complex ocelloids with intracellular lenses, found in one family of predatory dinoflagellates, the Warnowiaceae.^[122][141]

Some ciliates orient themselves in relation to the Earth's gravitational field while moving (geotaxis), and others swim in relation to the concentration of dissolved oxygen in the water.^[122]

Endosymbionts

Protists have an accentuated tendency to include endosymbionts in their cells, and these have produced new physiological opportunities. Some associations are more permanent, such as Paramecium bursaria and its endosymbiont Chlorella; others more transient. Many protists contain captured chloroplasts, chloroplast-mitochondrial complexes, and even eyespots from algae. The xenosomes are bacterial endosymbionts found in ciliates, sometimes with a methanogenic role inside anaerobic ciliates.^[122]

Asexual reproduction

Protists typically reproduce asexually under favorable environmental conditions,^[143] allowing for rapid exponential population growth with minimal genetic variation. This occurs through mitosis and has historically been considered the main reproductive mode in protists.^[142] Unicellular protists often multiply via binary fission, like bacteria;^[142] they can also divide through budding, similarly to yeasts, or through multiple fissions, a process known as schizogony.^[144] In multicellular protists, this process is often known as vegetative reproduction, only performed by the 'vegetative stage' or individual. It can take the form of fragmentation of body parts, or specialized propagules composed of numerous cells (e.g., in red algae).^[145]

Sexual reproduction

Sexual reproduction is a fundamental characteristic of eukaryotes.^[146][147] It involves meiosis (a specialized nuclear division enabling genetic recombination) and syngamy (the fusion of nuclei from two parents),^[142] two processes thought to have been present in the last eukaryotic common ancestor,^[148] which likely had the ability to reproduce sexually on a facultative (non-obligate) basis.^[149] Even protists that no longer reproduce sexually still retain a core set of meiosis-related genes, reflecting their descent from sexual ancestors.^[150][151] For example, although amoebae are traditionally considered asexual organisms, most asexual amoebae likely arose recently and independently from sexually reproducing amoeboid ancestors.^[152] Even in the early 20th century, some researchers interpreted phenomena related to chromidia (chromatin granules free in the cytoplasm) in amoebae as sexual reproduction.^[153] Three distinguishable sexual cycles are observed in protists depending on the ploidy^[f] of the individual or vegetative stage:^[142]

• Haploid cycle (as in most fungi): the individual is haploid and differentiates through mitosis into haploid gametes, which fuse into a zygote that immediately undergoes meiosis to generate new haploid individuals.^[142] This is the case for some green algae (such as volvocine algae), most dinoflagellates, dictyostelids, some metamonads, and apicomplexans.^{[130]: 26 [154]} Zygnematophytes, a group of green algae, fuse vegetative cells directly by conjugation instead of producing gametes.^[155]

• Diploid cycle (as in animals): the individual is diploid and undergoes meiosis to generate haploid gametes, which fuse into a zygote that develops as a new individual.^[142] This is the case for some metamonads, heliozoans, many green algae, diatoms, and labyrinthulids.^{[130]: 26 [154]} Ciliates are also diploid, but instead of producing gametes they divide their micronucleus into two haploid nuclei, exchange one of them by conjugation with another ciliate, and fuse the two nuclei into a new diploid nucleus.^[156]
• Haplo-diploid cycle (as in land plants): there are two alternating generations of individuals. One, the diploid agamont (or sporophyte), undergoes meiosis to generate haploid cells (called spores) that develop into the other generation, the haploid gamont (or gametophyte). The gamont then generates gametes by mitosis, which fuse to form the diploid zygote that develops into the agamont.^[142] This is the case for many foraminifera and many algae.^[130]: 26 Depending on the relative growth and lifespan of one generation compared to the other, life cycles may be haploid-dominant, diploid-dominant, or with equally dominant generations. Brown algae exhibit the full range of these modes.^[157] Many red algae have a three-generational cycle with a carposporophyte, whose spores germinate into a tetrasporophyte, whose spores develop into the gametophyte.^[158]

Cycles in pathogenic protists

Pathogenic protists tend to have extremely complex life cycles that involve multiple forms of the organism, some of which reproduce sexually and others asexually.^[160] The stages that feed and multiply inside the host are generally known as trophozoites (from Greek trophos 'nutrition' and zoia 'animals'), but the names of each stage vary depending on the protist group^[144] (e.g., sporozoites and merozoites in apicomplexans;^[161][147] primary and secondary zoospores in phytomyxeans).^[162]

Some pathogenic protists undergo asexual reproduction in a wide variety of organisms – which act as secondary or intermediate hosts – but can undergo sexual reproduction only in the primary or definitive host (e.g., Toxoplasma gondii in felids such as domestic cats).^[163] Others, such as Leishmania, are capable of performing syngamy in the secondary vector.^[164] In apicomplexans, sexual reproduction is obligatory for parasite transmission.^[165]

Despite undergoing sexual reproduction, it is unclear how frequently there is genetic exchange between different strains of pathogenic protists, as most populations may be clonal lines that rarely exchange genes with other members of their species.^[166]

Biomass

Protists are abundant in nearly all habitats. They contribute an estimated 4 gigatons (Gt) to Earth's biomass—double that of animals (2 Gt), but less than 1% of the total. Combined, protists, animals, archaea (7 Gt), and fungi (12 Gt) make up less than 10% of global biomass, with plants (450 Gt) and bacteria (70 Gt) dominating.^[167]

Habitat distribution

Protist diversity, as detected through environmental DNA surveys, is vast in every sampled environment, but it is mostly undescribed.^[168] The richest protist communities appear in soils, followed by oceanic and lastly freshwater habitats, mostly as part of the plankton.^[169] Freshwater protist communities are characterized by a higher "beta diversity" (i.e. highly heterogeneous between samples) than soil and marine plankton. The high diversity can be a result of the hydrological dynamic of recruiting organisms from different habitats through extreme floods.^[170]

Soil-dwelling protist communities are ecologically the richest, possibly due to the complex and highly dynamic distribution of water in the sediment, which creates extremely heterogenous environmental conditions. The constantly changing environment promotes the activity of only one part of the community at a time, while the rest remains inactive; this phenomenon promotes high microbial diversity in prokaryotes as well as protists.^[169]

Extreme habitats

Examples of extremophilic protists

a) Frontonia, a ciliate from soda lakes in Kenya.
b) Chlamydomonas pitschmanii, a green alga from hot spring soils.
c) Tetramitus thermacidophilus, an amoeboflagellate from an acidic geothermal lake in California.
d) Galdieria sulphuraria, a thermoacidophilic red alga.
e) Halocafeteria seosinensis, a flagellate from a saltern in Korea.

Protists can survive a broad range of extreme conditions, including extreme temperatures (thermophiles or psychrophiles), salinity (halophiles), and pH (alkaliphiles or acidophiles). Most of the extremophilic eukaryotes are algae, specifically chlorophytes, followed by fungi. Other extremophile-abundant groups are heterolobose amoebae, red algae, stramenopiles, and ciliates.^[171]

Eukaryotic algae are well-known to withstand high temperatures; for example, the red alga Cyanidioschyzon merolae persists up to 60°C, similarly to the most extreme thermophilic fungi. Lesser-known thermophilic amoebae and amoeboflagellates (e.g., Echinamoeba thermarum) are repeatedly found in hot environments, including artificially heated systems. While less successful than algae or amoebae, ciliates have also been found in hydrothermal vents up to 52°C. This is still lower than prokaryotes, some of which grow above 80°C.^[171]

In terms of pH and salinity, protists can withstand similar extremes relative to prokaryotes and fungi, and also persist in polyextreme environments (polyextremophiles). The record for acidophily is the red alga C. merolae, with an observed minimum growth of pH 0. Besides red algae, some species of green algae and amoeboflagellates are found in high-temperature, low-pH geothermal springs. Alkaliphilic protists, primarily ciliates, resist up to pH 10.48, higher than the most alkalophilic bacterium.^[171]

Protists are remarkably successful in extreme salinity due to their salt-out strategy, which consists of accumulating organic solutes in the cell instead of ions to counterbalance the hypertonic environment. Examples include the alga Dunaliella salina and the flagellate Halocafeteria seosinensis, which is able to tolerate up to 36.3% salinity, higher than the maximum reported in bacteria (35%) and fungi (30%).^[171]

Ecological roles

Protists are indispensable to modern ecosystems worldwide. They also have been the only eukaryotic component of all ecosystems for much of Earth's history, which allowed them to evolve a vast functional diversity that explains their critical ecological significance. They are essential as primary producers, as intermediates in multiple trophic levels, as key regulating parasites or parasitoids, and as partners in diverse symbioses.^[120]

Consumers

Phagotrophic protists are the most diverse functional group in all ecosystems, primarily represented by cercozoans (dominant in freshwater and soils), radiolarians (dominant in oceans), non-photosynthetic stramenopiles (with higher abundance in soils than in oceans), and ciliates.^[169]

Contrary to the common division between phytoplankton and zooplankton, much of the marine plankton is composed of mixotrophic protists, which pose a largely underestimated importance and abundance (around 12% of all marine environmental DNA sequences). Mixotrophs have varied presence due to seasonal abundance^[177] and depending on their specific type of mixotrophy. Constitutive mixotrophs are present in almost the entire range of oceanic conditions, from eutrophic shallow habitats to oligotrophic subtropical waters but mostly dominating the photic zone, and they account for most of the predation of bacteria. They are also responsible for harmful algal blooms. Plastidic and generalist non-constitutive mixotrophs have similar biogeographies and low abundance, mostly found in eutrophic coastal waters, with generalist ciliates dominating up to half of ciliate communities in the photic zone. Lastly, endosymbiotic mixotrophs are by far the most widespread and abundant non-constitutive type, representing over 90% of all mixotroph sequences (mostly radiolarians).^[138][137]

In the trophic webs of soils, protists are the main consumers of both bacteria and fungi, the two main pathways of nutrient flow towards higher trophic levels.^[178] Amoeboflagellates like the glissomonads and cercomonads are among the most abundant soil protists: they possess both flagella and pseudopodia, a morphological variability well suited for foraging between soil particles. Testate amoebae are also acclimated to the soil environment, as their shells protect against desiccation.^[176] As bacterial grazers, they have a significant role in the foodweb: they excrete nitrogen in the form of NH₃, making it available to plants and other microbes.^[178] Traditionally, protists were considered primarily bacterivorous due to biases in cultivation techniques, but many (e.g., vampyrellids, cercomonads, gymnamoebae, testate amoebae, small flagellates) are omnivores that feed on a wide range of soil eukaryotes, including fungi and even some animals such as nematodes. Bacterivorous and mycophagous protists amount to similar biomasses.^[126]

Biogeochemical cycles

Marine protists have a fundamental impact on biogeochemical cycles, particularly the carbon cycle.^[186] As phytoplankton, they fix as much carbon as all terrestrial plants combined.^[169] Soil protists, particularly testate amoebae, contribute to the silica cycle as much as forest trees through the biomineralization of their shells.^[176]

Paleo- and Mesoproterozoic

Modern or crown-group eukaryotes originated from the last eukaryotic common ancestor (LECA) and emerged between 1600 and 2400 million years ago (Ma), during the Paleoproterozoic and Mesoproterozoic eras.^[1] However, the fossil record through this time is scarce and dominated by stem-group eukaryotes, extinct lineages preceding LECA. These lineages displayed early eukaryotic traits like flexible cell membranes and complex cell wall ornamentations, which require a flexible endomembrane system, but they lacked crown-group eukaryotes' advanced sterols (e.g., cholesterol), and instead produced simpler protosterols that require less oxygen during biosynthesis.^[188] Examples of these are: Trachyhystrichosphaera and Leiosphaeridia dated at 1100 Ma,^[189] Satka dated at 1300 Ma,^[190] Tappania and Shuiyousphaeridium dated at 1600 Ma,^[191] Grypania dated at 1800–1900 Ma, and Valeria which ranges from 1650 to 700 Ma.^[192]

Crown-group eukaryotes achieved significant morphological and ecological diversity before 1000 Ma, with multicellular algae capable of sexual reproduction and unicellular protists exhibiting modern phagocytosis and locomotion. Their advanced but metabolically expensive sterols likely provided numerous evolutionary advantages due to the increased membrane flexibility, including resilience to osmotic shock during desiccation and rehydration cycles, extreme temperatures, UV light exposure, and protection against changing oxygen levels. These adaptations allowed crown-group eukaryotes to colonize diverse and harsh environments (e.g., mudflats, rivers, agitated shorelines and land). In contrast, stem-group eukaryotes occupied the low-oxygen marine waters as anaerobes.^[188] The oldest definitive crown-group eukaryotic fossils include Rafatazmia and Ramathallus, both putative red algae, dated at 1600 Ma.^[1]

Neoproterozoic

As oxygen levels rose during the Tonian period, crown-group eukaryotes outcompeted stem-group eukaryotes, expanding into oxygen-rich marine environments that supported an aerobic metabolism enabled by their mitochondria. Stem-group eukaryotes may have gone extinct due to competition and the extreme climatic changes of the Cryogenian glaciations and subsequent global warming, cementing the dominance of crown-group eukaryotes.^[188] Crown-group eukaryotes began to appear abundantly in this era, fueled by the proliferation of red algae. The oldest fossils firmly assigned to existing protist groups include three multicellular algae: the rhodophyte Bangiomorpha (1047 Ma),^[193] the chlorophyte Proterocladus (1000 Ma),^[188] and the xanthophyte Paleovaucheria (1000 Ma).^[194][195] Also included are the oldest fossils of Opisthokonta: Ourasphaira giraldae (1010–890 Ma), interpreted as the earliest fungus,^[188] and Bicellum brasieri (1000 Ma), the earliest holozoan, showing traits associated with complex multicellularity.^[196]

Abundant fossils of heterotrophic protists appear significantly later, parallel to the emergence of fungi.^[188] Vase-shaped microfossils (VSMs), widespread rocks dated at 780–720 Ma (Tonian to Cryogenian), have been described as a variety of organisms across the decades (e.g., algae, chitinozoans, tintinnids), but current scientific consensus relates most VSMs to marine testate amoebae.^[197] As such, VSMs comprise the oldest known fossils of both filose (Cercozoa) and lobose (Amoebozoa) testate amoebae.^[198][199]

After the Gaskiers glaciation of the Late Ediacaran (~579 Ma), fossils of heterotrophic protists undergo diversification. Some fossils similar to VSMs are interpreted as the oldest fossils of Foraminifera dated at 548 Ma (e.g., Protolagena),^[197] but their foraminiferal affinity is doubtful. Other microfossils that are possibly foraminifera include some poorly preserved tubular shells from 716–635 Ma rocks.^[200]

Paleozoic

Radiolarian shells appear abundantly in the fossil record since the Cambrian, with the first definitive radiolarian fossils found at the very start of this period (~540 Ma) together with the first small shelly fauna.^[201] Radiolarian records from older Precambrian rocks have been disregarded due to the lack of reliable fossils.^{[202][203][204]} Around this time, between 540 and 510 Ma, the oldest Foraminifera shells appear, first multi-chambered and later tubular.^{[205][187][200]}

Following the Cambrian explosion and rapid diversification of animals, the Precambrian microbe-dominated ecosystems were replaced by primarily benthic and nekto-benthic communities, with most marine organisms (animals, foraminifers, radiolarians) limited to the depths of shallow water environments.^[206] Mirroring the animal radiation, there was a radiation of phytoplanktonic protists (i.e., acritarchs)^[207] around 520–510 Ma, followed by a decrease in diversity around 500 Ma.^[208] Later, the surviving acritarchs expanded in diversity and morphological innovation^[207] due to a decrease in predation from benthic animals (particularly trilobites and brachiopods), which suffered extinction due to various proposed environmental factors such as anoxia.^[209] Both phytoplankton and zooplankton (e.g., radiolarians) flourished, as signaled by an increase of organic carbon buried in the sediment known as the SPICE event (~497 Ma).^[206][209] This abundant biomass supported a second animal radiation known as the Great Ordovician Biodiversification Event (GOBE), where many animals switched to a planktonic lifestyle and pelagic predators first appeared (e.g., cephalopods, swimming arthropods). This event is also known as the 'Ordovician Plankton Revolution' due to the significant diversification of planktonic protists, and it spanned from the late Cambrian well into the Ordovician.^[206]

The Ordovician also includes the oldest euglenid fossil, known as Moyeria, which is found in rocks spanning from the middle Ordovician (~471 Ma) to the Silurian.^[210] There are putative records of calcareous foraminifera from the Early Ordovician to the Silurian, but these are not widely accepted; the oldest trusted and well-known calcaerous foraminifera appear in the Middle Devonian, the next geological period.^[187][211]

In Early Devonian terrestrial ecosystems the first fossils of freshwater arcellinid testate amoebae are found (e.g., Palaeoleptochlamys, Cangweulla),^[212] as well as various types of freshwater green algae, including charophytes, volvocaceans and desmids,^[213] and some putative algal fossils that might represent glaucophytes.^[214] During the Devonian some benthic foraminifera acquired the ability of calcifying, and particularly the giant fusulinids became the dominant fossilizable protists. This time interval is also considered the molecular origin of haptophytes (~310 Ma) and silicoflagellates (397–382 Ma), which did not leave fossil traces until later in the Mesozoic. After the Late Devonian extinction (372 Ma), nassellarian-like radiolarians appeared for the first time, with a unique body plan among marine protists.^[187]

During the Carboniferous period, no new fossilizable protists originated despite the major environmental changes. However, starting in the Late Carboniferous, radiolarian diversity and productivity increased, causing a large amount of biosiliceous sediment (chert) to be accumulated worldwide; this is known as the Radiolarian Optimum Event, which lasted primarily from the Middle Permian until the Early Cretaceous.^{[215][216][217]} Around the Capitanian mass extinction event (262–259 Ma) of the Permian period, coccolithophores genetically diverged from the rest of haptophytes, possibly as a response to a reduction in atmospheric oxygen, and there was a faunal turnover from larger to smaller fusulinids.^[187] Spumellarian radiolarians appear in the latest Permian.^[215]

Mesozoic

The Permian-Triassic extinction event (~251.9 Ma) caused the extinction of many radiolarians, which manifests as a gap in the chert record.^[215] The extinction is hypothesized as resulting in the molecular origin of diatoms and modern coccolithophores.^[187] The Middle to Late Triassic period saw the acceleration of radiolarian diversity^[215] and the appearance of several groups of calcaerous nannofossils. First, various nannofossils, some of which belonged to dinocysts, appeared early at around 235 Ma. Later originated the oldest identifiable coccolithophore, Crucirhabdus minutus (205–201 Ma), as well as the oldest fossils of Phaeodaria.^[187] There's a variety of protozoa, including soft-bodied ciliates, and filamentous algae found in amber from the Late Triassic (220–230 Ma).^[218]

Around the Early–Middle Jurassic, after the global Toarcian Oceanic Anoxic Event there was a diversification of dinoflagellates and coccolithophores, in both species and abundance. This interval also saw the completion of a symbiosis between Acantharia radiolarians and lineages of Phaeocystis haptophytes, as well as the appearance of planktonic foraminifera.^[187] The period of low atmospheric oxygen ends in the Aptian-Albian boundary during the Early Cretaceous, and the first fossils of diatoms and silicoflagellates appear.^[187] Samples of amber from around 100 Ma contain the oldest fossil records of apicomplexans (particularly malarian agents and gregarines), trypanosomes,^[219] and metamonads—particularly mutualistic parabasalids of cockroaches, representing the earliest record of mutualism between protists and animals.^[220][221]

The diversification of coccolithophores, mixotrophic dinoflagellates, and later diatoms across the Mesozoic era caused an accelerated transfer of primary production into higher trophic levels. This evolutionary radiation of phytoplankton was, in turn, responsible for the animal "Mesozoic marine revolution", characterized by the appearance of widespread predation among most invertebrate phyla. Coccolithophores, dinoflagellates and especially diatoms became the dominating eukaryotic producers in oceans until today, as opposed to cyanobacteria and green algae which dominated earlier.^[222]

Cenozoic

The Cretaceous-Paleogene extinction event (~66 Ma) caused the extinction of many marine dinoflagellates, foraminifers, coccolithophores, and silicoflagellates; mesozoic types of these groups were substituted with types that dominate marine habitats today. Right after this event, putative ebridians begin appearing in the fossil record (e.g., Ammodochium), but the oldest reliable ebridian fossils belong to the upper middle Eocene (42–33.7 Ma).^[187] Around this time, the oldest fossils of Synurophyceae appear (~49–40 Ma).^[223] Following the Middle Eocene Climatic Optimum (~40 Ma), diatoms became the dominant agents of marine silicon precipitation as opposed to radiolarians, and the fossil record shows the first raphid diatoms and collodarians.^[187]