Protist

A protist (/ˈproʊtɪst/ PROH-tist) or protoctist is any eukaryotic organism that is not an animal, land plant, or fungus. Protists do not form a natural group, or clade, but are a paraphyletic grouping of all descendants of the last eukaryotic common ancestor excluding land plants, animals, and fungi.

Protists were historically regarded as a separate taxonomic kingdom known as Protista or Protoctista. With the advent of phylogenetic analysis and electron microscopy studies, the use of Protista as a formal taxon was gradually abandoned. In modern classifications, protists are spread across several eukaryotic clades called supergroups, such as Archaeplastida (photoautotrophs that includes land plants), SAR, Obazoa (which includes fungi and animals), Amoebozoa and "Excavata".

Protists represent an extremely large genetic and ecological diversity in all environments, including extreme habitats. Their diversity, larger than for all other eukaryotes, has only been discovered in recent decades through the study of environmental DNA and is still in the process of being fully described. They are present in all ecosystems as important components of the biogeochemical cycles and trophic webs. They exist abundantly and ubiquitously in a variety of mostly unicellular forms that evolved multiple times independently, such as free-living algae, amoebae and slime moulds, or as important parasites. Together, they compose an amount of biomass that is double that of animals. They exhibit varied types of nutrition (such as phototrophy, phagotrophy or osmotrophy), sometimes combining them (in mixotrophy). They present unique adaptations not present in multicellular animals, fungi or land plants. The study of protists is termed protistology.

Protists are a diverse group of eukaryotes that are primarily single-celled and microscopic and exhibit a wide variety of shapes and life strategies. They have different life cycles, trophic levels, modes of locomotion, and cellular structures.^[2][3] Although most protists are unicellular, there is a considerable range of multicellularity amongst them; some form colonies or multicellular structures visible to the naked eye. The term 'protist' refers to all eukaryotes that are not animals, land plants or fungi, the three traditional eukaryotic kingdoms.^[a][12] Because of this definition by exclusion, protists compose a paraphyletic group that includes the ancestors of those three kingdoms.^[13]

Protists exist in diverse shapes and sizes.^[14]: 27 While most are single-celled, others have evolved various forms of multicellularity, ranging from simple colonies of cells to large, complex organisms like giant kelp and slime molds.^[15] Single-celled protists are traditionally grouped by their shape and how they move, into four broad caetgories.^[16]: 5

• Flagellates are the most common protists, and very likely the most abundant eukaryotes on Earth.^[17] They move using one or more whip-like structures called flagella.^[b] Most are heterotrophic (known as zooflagellates), feeding on bacteria or other organisms, ranging from filter feeders like choanoflagellates to active predators like provorans. Many are photo- or mixotrophic (known as phytoflagellates) and are studied as algae, like the dinoflagellates.^[21][22]

• Amoebae are known for their often flexible shape and ability to form extensions of the cytoplasm known as pseudopodia. These extensions come in various forms, such as lobose (blunt, rounded, as in Amoeba), filose (thin, tapering, as in cercozoans), or reticulose (branching networks, as in foraminifers). Some, called axopodia, take the shape of radiating projections supported by microtubules, characteristic of heliozoa and radiolaria.^[14]: 23 Some amoebae can grow to sizes visible to the naked eye, reaching up to 20 cm.^[23] Amoeboflagellates can produce both pseudopodia and flagella within the same life cycle.^[24]

• Ciliates have larger cells with two types of nuclei and rows of small flagella, known as cilia.^[b] They are often at the top of the microbial food web. Although ciliates compose a single lineage,^[25] some protists have evolved unusual large ciliate-like cells, such as the opalines.^[26]

• Certain parasitic protists traditionally described as sporozoa^[27] are immobile in their adult stage and reproduce through thick-walled spores, such as haplosporidians and apicomplexans. This term also included fungi and animals that have evolved a similar lifestyle—microsporidians and myxozoans, respectively. Other than their lifestyle, they have very little in common, and have evolved in distantly related groups.^{[4][16]: 8–9}

Other single-celled algae exist in forms beyond the motile flagellates. Some are non-motile and encased in hard cell walls (coccoid, like diatoms) or embedded in a mucilage matrix (capsalean, like glaucophytes);^[28] others are amoeboid, like the reticulose chlorarachniophytes.^[29][30]

Multicellularity has evolved numerous times to various degrees among protists, resulting in organisms built either by cells aggregating together (aggregative) or by cells dividing without separating (clonal).^[15] For example:

• Fungus-like protists, traditionally studied by mycologists, are osmotrophic and produce macroscopic fruiting bodies for dispersal (sorocarps if aggregative, sporocarps if clonal). They may have hyphae-like bodies, or they may be slime molds, composed of individual amoebae until they form fruiting bodies.^[31][32][33] Some can reach lengths of several meters.^[14]: 29

• Multicellular algae range from simple filaments and coenocytes to the highly complex brown algae, which have fully differentiated tissues (parenchymatous) resembling those of plants, or the red algae, with only partial differentiation (pseudoparenchymatous).^[30][34] In green algae alone multicellularity is thought to have evolved over 20 separate times, with some groups like the stoneworts developing specialized reproductive organs.^[35][15]

Other multicellular protists include amoebae that fuse into large networks, and colonial heliozoa and ciliates with new features not seen in solitary cells. The ciliate Haplozoon is interpreted to have animal-like embryonic development and cell type differentiation.^[15] Choanoflagellates, the closest living relatives of animals, include alternating cell types that are interpreted as early stages of animal multicellularity.^[36]

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.^[37][38] 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.^[39][40]

During the 19th century, after several waves of naturalist studies,^[40] 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^[41] or Protista,^[42] respectively, to accommodate the predominantly unicellular eukaryotes, and initially bacteria, which were later excluded.^[37] 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).^[38] 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.^[37]

From the mid-20th century, eukaryotes were firmly split from bacteria (prokaryotes) due to the presence of the cell nucleus,^[43] and protists (or protoctists) were more widely accepted as a separate kingdom.^[44][45][46] 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.^[47][48][38]

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.^[49][38] 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,^[38] such as the ones published by the International Society of Protistologists.^[50][51][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.^{[54][55][56][57]}

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.^[58][59][60] 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.^{[61][62]: 597 [63]}

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.

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

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^[117] 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.^[96] As such, it is considered that protists dominate eukaryotic diversity.^[118]

In general, protists have typical eukaryotic cells that follow the same principles of biology described for those cells within the "higher" eukaryotes (animals, fungi and land plants).^[119] However, many have evolved a variety of unique physiological adaptations that do not appear in the remaining eukaryotes,^[120] and in fact protists encompass almost all of the broad spectrum of biological characteristics expected in eukaryotes.^[118]

Protists display a wide variety of food preferences and feeding mechanisms.^[9][121] According to the nutrient source, they can be divided into autotrophs (or phototrophs,^[122] 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).^[123]

Phagotrophic protists feed by phagocytosis, a process unique to eukaryotes^[124] where food particles or cells are digested into a vacuole, the phagosome.^[121] This is the general mode of nutrition for protists, and has resulted in a diverse array of strategies for hunting and digestion.^[124] Usually, digestion occurs at a specialized mouth-like region of the cell, the cytostome, which may be followed by the cytopharynx,^[125] a tract supported by microtubules.^[121] In amoebae, phagocytosis takes place anywhere on the cell surface.^[126]

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.^[126][9] Diffusion feeders, like suctorian ciliates and heliozoans, passively engulf prey that happen to collide with their tentacles or pseudopodia and are immobilized.^[126] 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.^[124][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.^[124]

Preys of phagotrophic protists range from prokaryotes (i.e., bacterivores) to other eukaryotes, including single-celled protists, algae,^[9] fungi,^[127] nematodes,^[128] or tissues of larger animals.^[126] Prey specificity varies, with some groups specialized in eating only one type of organisms,^[127] or only a particular strain.^[129] Traditionally, protists were considered primarily bacterivorous due to biases in cultivation techniques, but most are omnivores.^[127]

Osmotrophic protists absorb soluble^[123] 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][121] 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.^[130] 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,^[131] and the fungus-like oomycetes and hyphochytrids.^[130]

Most photosynthetic protists are mixotrophs,^[132] 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.^[134][135]

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.^[136]

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.^[137][125] 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.^[120] 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.^[137]

The last eukaryotic common ancestor was aerobic, bearing mitochondria that synthesize ATP through oxidative respiration, which requires oxygen. Most protists are aerobes, but many lineages of free-living and parasitic protists have independently adapted to inhabit anaerobic or microaerophilic (low-oxygen) habitats by modifying their mitochondria into organelles collectively known as mitochondrion-related organelles (MROs). These exist in a continuum from lower to higher degrees of reduction. For example, hydrogenosomes have lost the electron transport chain used in respiration, as well as other features of classical mitochondria (their DNA, the Krebs cycle, etc.), but can still generate ATP anaerobically through the fermentation of pyruvate, releasing hydrogen gas as a byproduct. Mitosomes have lost both the respiratory chain and the production of ATP. One group of protists, the genus Monocercomonoides, has lost its mitochondria entirely.^{[120][138][139]} In a similar manner, the oxidative peroxisome evolved into a fermentative glycosome in trypanosomatids.^[120]

Besides metabolic reduction, the shape, composition, and number of mitochondria varies greatly across protists. Apicomplexans and kinetoplastids have a single large mitochondrion that divides synchronously with the cell, while some amoebae can present hundreds of mitochondria.^[140] Mitochondrial genomes (mitogenomes), typically composed of one circular chromosome, can appear as numerous linear chromosomes in many unrelated protists, such as Amoebidium, with hundreds of chromosomes.^[141] The large mitogenome of kinetoplastids is condensed into a kinetoplast, which is physically tied to the flagellar apparatus. The smallest known mitogenome belongs to the symbiotic alga Chromera velia.^[142]

Mitochondrial cristae, foldings of the inner membrane, have been used to classify protists since the advent of electron microscopy.^[47] Flat cristae are the ancestral trait, tubular cristae are present in the SAR supergroup and Amoebozoa, and discoid cristae distinguish the Discoba.^[143]

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 photoreceptors of varying degrees of complexity, from simple receptors with light antennae (as in the eyespot apparatus of many algae), to receptors with opaque screens, to complex ocelloids with intracellular lenses (as in the dinoflagellate family Warnowiaceae).^[120][144]

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.^[120]

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.^[120]

Protists exhibit a large variability of life cycles and strategies involving multiple stages of different morphologies which have allowed them to thrive in most environments. Nevertheless, most research concerning protist life cycles corresponds to model organisms and important parasites; knowledge on the life cycles of the free-living majority remains fragmentary.^[145]

Protists typically reproduce asexually under favorable environmental conditions,^[146] 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.^[145] Unicellular protists often multiply via binary fission, like bacteria;^[145] they can also divide through budding, similarly to yeasts, or through multiple fissions, a process known as schizogony.^[147] 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).^[148]

Sexual reproduction is a fundamental characteristic of eukaryotes.^[149][150] It involves meiosis (a specialized nuclear division enabling genetic recombination) and syngamy (the fusion of nuclei from two parents),^[145] two processes thought to have been present in the last eukaryotic common ancestor,^[151] which likely had the ability to reproduce sexually on a facultative (non-obligate) basis.^[152] Even protists that no longer reproduce sexually still retain a core set of meiosis-related genes, reflecting their descent from sexual ancestors.^[153][154] For example, although amoebae are traditionally considered asexual organisms, most asexual amoebae likely arose recently and independently from sexually reproducing amoeboid ancestors.^[155] Even in the early 20th century, some researchers interpreted phenomena related to chromidia (chromatin granules free in the cytoplasm) in amoebae as sexual reproduction.^[156] Three distinguishable sexual cycles are observed in protists depending on the ploidy^[f] of the individual or vegetative stage:^[145]

• 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.^[145] This is the case for some green algae (such as volvocine algae), most dinoflagellates, dictyostelids, some metamonads, and apicomplexans.^{[125]: 26 [157]} Zygnematophytes, a group of green algae, fuse vegetative cells directly by conjugation instead of producing gametes.^[158]

• 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.^[145] This is the case for some metamonads, heliozoans, many green algae, diatoms, and labyrinthulids.^{[125]: 26 [157]} 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.^[159]
• 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.^[145] This is the case for many foraminifera and many algae.^[125]: 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.^[160] Many red algae have a three-generational cycle with a carposporophyte, whose spores germinate into a tetrasporophyte, whose spores develop into the gametophyte.^[161]

Free-living protists tend to reproduce sexually under stressful conditions, such as starvation or heat shock. Oxidative stress, which leads to DNA damage, also appears to be an important factor in the induction of sex in protists.^[146]

Several protists synchronize their life cycles (namely the formation or release of gametes) according to environmental factors such as nutrient or light levels, resulting in synchronization with the day-night cycle, the lunar cycle, or the seasons. The malaria agent Plasmodium falciparum synchronizes its life cycle with the host's levels of melatonin.^[162]

Pathogenic protists tend to have extremely complex life cycles that involve multiple forms of the organism, some of which reproduce sexually and others asexually.^[163] 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^[147] (e.g., sporozoites and merozoites in apicomplexans;^[164][150] primary and secondary zoospores in phytomyxeans).^[165]

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).^[166] Others, such as Leishmania, are capable of performing syngamy in the secondary vector.^[167] In apicomplexans, sexual reproduction is obligatory for parasite transmission.^[168]

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.^[169]

Protist diversity, as detected through environmental DNA surveys, is vast in every sampled environment, but it is mostly undescribed.^[170] The richest protist communities appear in soils, followed by oceanic and lastly freshwater habitats, mostly as part of the plankton.^[171]

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.^[171] Cercozoan amoeboflagellates like the glissomonads and cercomonads are among the most abundant soil protists, their morphological variability well suited for foraging between soil particles. Testate amoebae are also acclimated to the soil environment, as their shells protect against desiccation. Most soil algae are stramenopiles and green algae. Fungus-like protists and slime molds (e.g., oomycetes, myxomycetes, acrasids) are present abundantly as saprotrophs.^[172] The major parasites in land are the animal-associated apicomplexans^[173] and the plant-associated oomycetes and plasmodiophorids.^[172]

Marine protists are present in almost the entire range of oceanic conditions, mostly dominating the photic zone. Their abundance depends mostly on the availability of inorganic nutrients, rather than temperature or sunlight, and may vary seasonally.^[174] They are most abundant in coastal waters that receive nutrient-rich run-off from land, and areas where nutrient-rich deep ocean water reaches the surface, namely the upwelling zones in the Arctic Ocean and along continental margins.^[175] Radiolarians are widespread as the most dominant marine consumers.^{[135][134][171]} Macroalgae (namely red algae, green algae and brown algae), unlike plankton, generally require a fixation point, which limits their marine distribution to coastal waters, and particularly to rocky substrates.^[176] Some communities of seaweeds exist adrift on the ocean surface, serving as a refuge and means of dispersal for associated organisms.^[177] Parasitoids such as Syndiniales are abundant pathogens in oceans.^[171]

Freshwater protist communities are characterized by a higher beta diversity (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.^[178] In freshwater phytoplankton, golden algae, cryptophytes and dinoflagellates are the most abundant groups.^[171]

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.^[179]

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.^[179] In extremely cold habitats, like snow and the Arctic Ocean, diatoms and green algae are the dominant phototrophs.^[180]

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 also 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 represented by ciliates, resist up to pH 10.48, higher than the most alkalophilic bacterium.^[179]

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%).^[179]

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.^[181]

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.^[118]

Phototrophic protists are the main contributors to the biomass and primary production in nearly all aquatic environments, as part of the phytoplankton.^[g] Altogether, they are responsible for almost half of the global primary production.^[175] They are the main providers of much of the energy and organic matter used by other trophic levels, including essential nutrients such as fatty acids.^[182] Macroalgae support numerous herbivorous animals, especially benthic ones, as both food and refuge from predators.^[176][177]

Phagotrophic protists are the most diverse functional group in all ecosystems.^[171] 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. 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.^[183]

As part of the plant-associated microbiomes (rhizosphere near the roots, phyllosphere on the leaves), predatory protists such as cercomonads regulate the populations of bacteria and fungi, indirectly improving plant health and growth. They can also have a more direct impact by releasing proteins with antimicrobial activity.^[184]

Necrophagy (the degradation of dead biomass) among microbes is mainly attributed to bacteria and fungi, but protists have a still poorly recognized role as decomposers with specialized lytic enzymes.^[185] In marine and estuarine environments, the well-studied thraustochytrids (a type of labyrinthulomycetes) are relevant saprotrophs that decompose various substrates, including dead plant and animal tissue. Various ciliates and testate amoebae scavenge on dead animals. Some nucleariid amoebae specifically consume the contents of dead or damaged cells, but not healthy cells. However, all these examples are of facultative necrophages that also feed on live prey. In contrast, the cercozoan family Viridiraptoridae, present in shallow bog waters, are obligate necrophages of dead algae, potentially fulfilling an important role in cleaning up the environment and releasing nutrients for other microbes.^[185]

Parasitic protists compose around 15–20% of all environmental DNA samples in marine and soil systems, but only around 5% in freshwater systems, where chytrid fungi likely fill that ecological niche.^[171] Some protists are significant parasites of animals (e.g.; five species of the parasitic genus Plasmodium cause malaria in humans and many others cause similar diseases in other vertebrates), land plants^[186][187] (the oomycete Phytophthora infestans causes potato blight)^[188] or even of other protists.^[189][190] Around 100 protist species can infect humans.^[172]

Marine protists have a fundamental impact on biogeochemical cycles, particularly the carbon cycle.^[191] As phytoplankton, they fix as much carbon as all terrestrial plants combined.^[171] Soil protists, particularly testate amoebae, contribute to the silica cycle as much as forest trees through the biomineralization of their shells.^[172]

Modern (or crown-group) eukaryotes originated from an endosymbiosis between an archaeon and at least one bacterium, leading to the last eukaryotic common ancestor (LECA), which had mitochondria (derived from said bacterium) and a complex endomembrane system.^[192] The origin of LECA is difficult to pinpoint due to technological limitations, artifacts, and a scarce fossil record,^[193] but is estimated to have occurred in the Paleoproterozoic,^[192] between 2.4 and 1.6 billion years ago.^[1] Prior to LECA is a relatively long gap of intermediate stem-group (extinct) eukaryotes that lacked one or more of the traits of crown eukaryotes.^[192][194]

Fossils of this time period are often interpreted as stem eukaryotes, as they display early eukaryotic traits like flexible cell membranes and complex cell wall ornamentations, which require a differentiated endomembrane system, but they lacked the sterols (e.g., cholesterol) seen in more advanced eukaryotes, and instead produced simpler protosterols that require less oxygen during biosynthesis. The advanced sterols of modern eukaryotes, although metabolically expensive, likely provided numerous advantages through increased membrane flexibility, such as resilience to osmotic shock during dessication-rehydration cycles, extreme temperatures and UV light exposure, allowing them to colonize diverse and harsh environments (e.g., mudflats, rivers, agitated shorelines and land). In contrast, stem-group eukaryotes remained in low-oxygen marine waters.^[195] Regardless of the possible stem- or crown- affinities of these early fossils, they lack the diagnostic features necessary to be assigned to known groups.^[192] As such, they are lumped as acritarchs (meaning uncertain origin).^[196] Examples of these are Tappania, Shuiyousphaeridium, and Grypania.^[195]

LECA is widely hypothesized as having a typical excavate morphology, with two flagella and a ventral groove used for feeding on bacteria by phagocytosis.^[61][63] In addition, LECA was likely a facultative anaerobe which could live in both aerobic and, more commonly during this geological period, anaerobic environments.^[202][200] Based on the phylogeny of modern protists and their morphological and ecological traits, a hypothesis proposed in 2025 explains the early evolution of crown-group eukaryotes, outlined in four ecological stages.^[i] Stage 1 involved the direct descendants of LECA: excavate-like flagellates feeding on bacteria by altering water currents, giving rise to the most basal groups such as the anaerobic metamonads and the aerobic jakobids. Stage 2 saw the emergence of surface-associated protists that developed gliding motility and the cell plasticity to form thin pseudopodia, resulting in lineages such as ancyromonads, apusomonads and CRuMs (i.e., the podiates), which pick bacteria directly off of surfaces. Stage 3 involved the separate lineage Diaphoretickes, in which agile swimming motility was prioritized and several adaptations led to an active predatory lifestyle (e.g., provorans, telonemids) hunting both bacteria and, for the first time, other eukaryotes. In response, some prey might have developed stronger pellicles, as seen in rigifilids and apusomonads. Lastly, stage 4 saw the appearance of both "super-predators" capable of hunting other eukaryovores (as in the SAR lineages), and more specialized bacterivores with amoeboid movement (as in amoebozoans and opisthokonts), resulting in a "mature" biosphere.^[193] Early amoebozoans in the Mesoproterozoic adapted to grazing on microbial mats, the dominant food source at the time, resulting in multiple losses of flagella and large amoeboid bodies.^[203]

According to fossil data and molecular clock estimations, these events probably took place in the span of 300 million years, from the late Paleoproterozoic to the Mesoproterozoic, resulting in a radiation that originated all major eukaryotic supergroups.^[193] In the early Mesoproterozoic, at 1.6 billion years ago, the earliest fossils of multicellular algae are found: Rafatazmia and Ramathallus, regarded as possible red algae.^[1] Dinosterane, a biomarker associated with dinoflagellates or some other marine protists, also begins appearing at this time in the fossil record.^[204]

The presence of modern eukaryotes in the fossil record remained relatively modest until the Neoproterozoic, when biomarker molecules and microfossils became abundant.^[192] As oxygen levels rose during the Tonian period, crown eukaryotes outcompeted stem eukaryotes, expanding into oxygen-rich marine environments that supported an aerobic metabolism enabled by their mitochondria. Stem 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 eukaryotes which began to appear abundantly in this era, fueled by the proliferation of algae.^[205][195] The time period around 1 billion years ago includes the earliest fossils of multicellular algae, such as Bangiomorpha and Proterocladus,^[205] as well as the oldest fossils of opisthokonts: Ourasphaira giraldae, interpreted as the earliest fungus,^[195] and Bicellum brasieri, the earliest holozoan, showing traits associated with animal-like multicellularity such as different cell types.^[206]

Abundant fossils of heterotrophic protists appear later.^[195] Vase-shaped microfossils, dated at 780–720 million years ago (Mya), are considered marine testate amoebae,^[207] and as such comprise the oldest known fossils of both filose (Cercozoa) and lobose (Amoebozoa) amoebae.^[208][209] Other microfossils that are possibly foraminifers include some poorly preserved tubular shells from 716–635 Mya rocks.^[210] After the Gaskiers glaciation of the Late Ediacaran (~579 Mya), fossils of heterotrophic protists undergo diversification. Some fossils similar to VSMs are interpreted as the oldest fossils of foraminifers dated at 548 Mya (e.g., Protolagena),^[207] but their foraminiferal affinity is doubtful.^[210]

At the very start of the Paleozoic era, the first definitive fossils of radiolarian^{[211][212][213]} and foraminiferal^{[214][204][210]} shells are found, alongside the first small shelly fauna.^[215] Following the Cambrian explosion of animals, the Precambrian microbe-dominated ecosystems were replaced by primarily benthic and nekto-benthic communities, with most marine organisms limited to the depths of shallow water environments.^[216] Mirroring the animal radiation, there was a radiation of phytoplanktonic protists (acritarchs)^[217] around 520–510 Ma, followed by a decrease in diversity around 500 Ma.^[218] The surviving acritarchs expanded in diversity and morphological innovation^[217] due to a decrease in predation from benthic animals, which suffered extinction due to various proposed environmental factors such as anoxia.^[219] 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 Mya).^[216][219] This abundant biomass supported a second animal radiation known as the Great Ordovician Biodiversification Event. This period is also known as the 'Ordovician Plankton Revolution' due to the significant diversification of planktonic protists.^[216] Starting in the middle Ordovician, the earliest fossils of eugelnids (Moyeria) appear.^[220]

In the Devonian period, the first fossils of freshwater arcellinid testate amoebae are found (e.g., Palaeoleptochlamys, Cangweulla),^[221] as well as various types of freshwater green algae, including charophytes, volvocaceans and desmids,^[222] and some fossils that might represent glaucophytes.^[223] Some benthic foraminifera acquired the ability of calcifying,^[204] and particularly the giant fusulinids became the dominant fossilizable protists. This period also includes the molecular origin of haptophytes (~310 Mya) and silicoflagellates (397–382 Mya), which did not leave fossil traces until later in the Mesozoic. After the Late Devonian extinction (372 Mya), nassellarian-like radiolarians appeared for the first time, with a unique body plan among marine protists.^[204]

During the Carboniferous period, no new fossilizable protists originated despite the major environmental changes. However, radiolarian diversity and productivity increased, causing the accumulation of large amounts of biosiliceous sediment (chert) worldwide until the Early Cretaceous.^{[224][225][226]} Around the Capitanian mass extinction event (262–259 Mya) 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.^[204] Spumellarian radiolarians appear in the latest Permian.^[224]

The Permian-Triassic extinction event (~251.9 Mya) caused the extinction of many radiolarians, which manifests as a gap in the chert record. The Triassic period saw the acceleration of radiolarian diversity^[224] and the appearance of several groups of calcaerous nannofossils, including dinocysts, the oldest identifiable coccolithophore Crucirhabdus minutus, and the oldest fossils of Phaeodaria.^[204] There's a variety of protozoa, including soft-bodied ciliates, and filamentous algae found in amber from the Late Triassic (220–230 Ma).^[227]

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.^[204] 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.^[204] Samples of amber from around 100 Ma contain the oldest fossil records of apicomplexans (particularly malarian agents and gregarines), trypanosomes,^[228] and metamonads—particularly mutualistic parabasalids of cockroaches, representing the earliest record of mutualism between protists and animals.^[229][230]

Across the Mesozoic era, coccolithophores, dinoflagellates and later diatoms became the dominating eukaryotic producers in oceans until today, as opposed to cyanobacteria and green algae which dominated earlier. Their diversification caused an accelerated transfer of primary production into higher trophic levels, which in turn caused the animal "Mesozoic marine revolution", characterized by the appearance of widespread predation among most invertebrate phyla.^[231]

The Cenozoic era began with another extinction event (~66 Ma) that caused the replacement of mesozoic forms of dinoflagellates, foraminifers, coccolithophores, and silicoflagellates with forms 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).^[204] Around this time, the oldest fossils of synurids appear (~49–40 Ma).^[232] 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.^[204]

• Chromista
• Evolution of sexual reproduction
• Marine protists
• Protist locomotion
• Protozoa