Protist

Protists Temporal range: Paleoproterozoic–present Pha. Proterozoic Archean Had.
Examples of protists. Clockwise from top left: red algae, kelp, ciliate, golden alga, dinoflagellate, metamonad, amoeba, slime mold.
Scientific classification (paraphyletic)
Domain:	Eukaryota
Supergroups[1]
Amorphea Amoebozoa Obazoa (including fungi and animals) CRuMs Ancyromonadida Discoba Malawimonadida Metamonada Hemimastigophora Provora[2] Diaphoretickes Archaeplastida (including plants) Cryptista Haptista TSAR supergroup Telonemia Stramenopiles Alveolata Rhizaria
Cladistically included but traditionally excluded taxa
Animalia Fungi Embryophyta (land plants)

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 polyphyletic grouping of several independent clades that evolved from the last eukaryotic common ancestor.

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 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 doubles 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 (organisms whose cells possess a nucleus) that are primarily single-celled and microscopic but exhibit a wide variety of shapes and life strategies. They have different life cycles, trophic levels, modes of locomotion, and cellular structures.^[3][4] 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' is defined as a paraphyletic group of all eukaryotes that are not animals, plants or fungi.^[5] Because of this definition by exclusion, protists encompass almost all of the broad spectrum of biological characteristics expected in eukaryotes.^[6]

The distinction between protists and the other three eukaryotic kingdoms has been difficult to settle. Historically, the heterotrophic protists, known as protozoa, were considered part of the animal kingdom, while the phototrophic ones, called algae, were studied as part of the plant kingdom. Even after the creation of a separate protist kingdom, some minuscule animals (the myxozoans)^[7] and 'lower' fungi (namely the aphelids, rozellids and microsporidians, collectively known as Opisthosporidia) were studied as protists,^[8][9] and some algae (particularly red and green algae) remained classified as plants.^[10] According to the current consensus, the term 'protist' specifically excludes animals, embryophytes (land plants) —meaning that all algae fall under this category— and all fungi, although lower fungi are often studied by protistologists and mycologists alike.^[1]

The names of some protists (called ambiregnal protists), because of their mixture of traits similar to both animals and plants or fungi (e.g. slime molds and flagellated algae like euglenids), have been published under either or both of the botanical (ICN) and the zoological (ICZN) codes of nomenclature.^[11][12]

Protists display a wide range of distinct morphologies that have been used to classify them for practical purposes, although most of these categories do not represent evolutionary cohesive lineages or clades and have instead evolved independently several times. The most recognizable types are:^[13]

• Amoebae. Characterized by their irregular, flexible shapes, these protists move by extending portions of their cytoplasm, known as pseudopodia, to crawl along surfaces.^[14] Many groups of amoebae are naked, but testate amoebae and foraminifera grow a shell around their cell made from digested material or surrounding debris. Some, known as radiolarians and heliozoans, have special spherical shapes with microtubule-supported pseudopodia radiating from the cell.^[13] Some amoebae are capable of producing stalked multicellular stages that bear spores, often by aggregating together; these are known as slime molds.^[15] The main clades containing amoebae are Amoebozoa (including various slime molds and testate amoebae) and Rhizaria (including famous groups such as foraminifera and radiolarians, as well as a few testate amoebae).^[16][17] Even some individual amoebae can grow to giant sizes visible to the naked eye.^[18][19]

• Flagellates. These protists are equipped with one or more whip-like appendages called cilia, undulipodia or eukaryotic flagella,^[a] which enable them to swim or glide freely through the environment. Flagellates are found in all lineages, reflecting that the common ancestor of all living eukaryotes was a flagellate. They usually exhibit two cilia (e.g., in Provora, Telonemia, Stramenopiles, Alveolata, Obazoa and most excavates), but there are a number of flagellate groups with a high number of cilia (such as Hemimastigophora and other excavates).^[13] Some groups, such as the well-known ciliates and the parasitic opalinids, have a cell surface covered in rows of cilia that beat rhythmically. A few groups of amoebae have retained their flagella, making them amoeboflagellates.^[23]

• Algae. They are the photosynthetic protists, and can be found in most of the main clades, completely intermingled with heterotrophic protists which are traditionally called protozoa.^[24] Algae exhibit the most diverse range of morphologies, from single flagellated or coccoid cells (e.g., cryptophytes, haptophytes, dinoflagellates, chromerids, many green algae, ochrophytes, euglenophytes) to amoeboid cells (chlorarachniophytes) to colonial and multicellular macroscopic forms (e.g., red algae, some green algae, and some ochrophytes such as kelp).^[25]

• Fungus-like protists. Several clades of protists have evolved an appearance similar to fungi through hyphae-like structures and a saprophytic nutrition. They have evolved multiple times, often very distantly from true fungi (e.g., the oomycetes, labyrinthulomycetes and hyphochytrids, in Stramenopiles; the myxomycetes, in Amoebozoa; the phytomyxeans, in Rhizaria; the perkinsozoans, in Alveolata).^[26][27]

• Sporozoa. This category traditionally included parasitic protists that reproduced via spores (the apicomplexans, microsporidians, myxozoans and ascetosporeans).^[7] Its current use is restricted to the apicomplexans,^[28] such as Plasmodium falciparum, the cause of malaria.^[29]

In general, protists are typical eukaryotic cells that follow the same principles of physiology and biochemistry described for those cells within the "higher" eukaryotes (animals, fungi or plants): they are aerobic organisms that consume oxygen to produce energy through mitochondria, and those with chloroplasts perform carbon fixation through photosynthesis in chloroplasts. ^[30] However, many have evolved a variety of unique physiological adaptations that do not appear in the remaining eukaryotes.^[31]

• Osmoregulation. Freshwater protists without cell walls are able to regulate their osmosis through contractile vacuoles, specialized organelles that periodically excrete fluid high in potassium and sodium through a cycle of diastole and systole. The cycle stops when the cells are placed in a medium with different salinity, until the cell adapts.^[31]

• Energetic adaptations. 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.^[31]

• Sensory adaptations. 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": (1) receptors with light antennae, found in many green algae, dinoflagellates and cryptophytes; (2) receptors with opaque screens; and (3) complex ocelloids with intracellular lenses, found in one group of predatory dinoflagellates, the Warnowiaceae. Additionally, 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.^[31]

• Endosymbiosis. 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.^[31]

Protists generally reproduce asexually under favorable environmental conditions, but 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.^[33]

Eukaryotes emerged in evolution more than 1.5 billion years ago.^[34] The earliest eukaryotes were protists. Although sexual reproduction is widespread among multicellular eukaryotes, it seemed unlikely until recently, that sex could be a primordial and fundamental characteristic of eukaryotes. The main reason for this view was that sex appeared to be lacking in certain pathogenic protists whose ancestors branched off early from the eukaryotic family tree. However, several of these "early-branching" protists that were thought to predate the emergence of meiosis and sex (such as Giardia lamblia and Trichomonas vaginalis) are now known to descend from ancestors capable of meiosis and meiotic recombination, because they have a set core of meiotic genes that are present in sexual eukaryotes.^[35][36] Most of these meiotic genes were likely present in the common ancestor of all eukaryotes,^[37] which was likely capable of facultative (non-obligate) sexual reproduction.^[38]

This view was further supported by a 2011 study on amoebae. Amoebae have been regarded as asexual organisms, but the study describes evidence that most amoeboid lineages are ancestrally sexual, and that the majority of asexual groups likely arose recently and independently.^[39] Even in the early 20th century, some researchers interpreted phenomena related to chromidia (chromatin granules free in the cytoplasm) in amoebae as sexual reproduction.^[40]

Some commonly found protist pathogens such as Toxoplasma gondii are capable of infecting and undergoing asexual reproduction in a wide variety of animals – which act as secondary or intermediate host – but can undergo sexual reproduction only in the primary or definitive host (for example: felids such as domestic cats in this case).^[41][42][43]

Some species, for example Plasmodium falciparum, have extremely complex life cycles that involve multiple forms of the organism, some of which reproduce sexually and others asexually.^[44] However, it is unclear how frequently sexual reproduction causes genetic exchange between different strains of Plasmodium in nature and most populations of parasitic protists may be clonal lines that rarely exchange genes with other members of their species.^[45]

The pathogenic parasitic protists of the genus Leishmania have been shown to be capable of a sexual cycle in the invertebrate vector, likened to the meiosis undertaken in the trypanosomes.^[46]

The 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^[48] to 74,400^[47] as of 2012) in comparison to the diversity of plants, animals and fungi, which are historically and biologically well-known and studied. The predicted number of species also varies greatly, ranging from 1.4×10⁵ to 1.6×10⁶, 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 plants, animals and fungi.^[47] As such, it is considered that protists dominate eukaryotic diversity.^[6]

Protist phylogeny

Eukarya Diaphoretickes  TSAR SAR Stramenopiles Alveolata Rhizaria Telonemia Haptista Pancryptista Microhelida Cryptista Archaeplastida1 Provora Hemimastigophora Meteora sporadica Discoba Metamonada Ancyromonadida Malawimonadida Podiata CRuMs Amorphea Amoebozoa Obazoa Breviatea Apusomonadida Opisthokonta2

One possible topology for the eukaryotic tree of life.[49][2][50][51] Excavate groups are shown in green. 1Includes land plants. 2Includes animals and fungi.

The evolutionary relationships of protists have been explained through molecular phylogenetics, the sequencing of entire genomes and transcriptomes, and electron microscopy studies of the flagellar apparatus and cytoskeleton. New major lineages of protists and novel biodiversity continue to be discovered, resulting in dramatic changes to the eukaryotic tree of life. The newest classification systems of eukaryotes do not recognize the formal taxonomic ranks (kingdom, phylum, class, order...) and instead only recognize clades of related organisms, making the classification more stable in the long term and easier to update. In this new cladistic scheme, the protists are divided into various branches informally named supergroups. Most photosynthetic eukaryotes fall under the Diaphoretickes clade, which contains the supergroups Archaeplastida (which includes plants) and TSAR (including Telonemia, Stramenopiles, Alveolata and Rhizaria), as well as the phyla Cryptista and Haptista.^[13] The animals and fungi fall into the Amorphea supergroup, which contains the phylum Amoebozoa and several other protist lineages. Various groups of eukaryotes with primitive cell architecture are collectively known as the Excavata.^[1]

Excavata is a group that encompasses diverse protists, mostly flagellates, ranging from aerobic and anaerobic predators to phototrophs and heterotrophs.^[52]: 597 The common name 'excavate' refers to the common characteristic of a ventral groove in the cell used for suspension feeding, which is considered to be an ancestral trait present in the last eukaryotic common ancestor.^[53] The Excavata is composed of three clades: Discoba, Metamonada and Malawimonadida, each including 'typical excavates' that are free-living phagotrophic flagellates with the characteristic ventral groove.^[54] According to most phylogenetic analyses, this group is paraphyletic, with some analyses placing the root of the eukaryote tree within Metamonada.^[55]

Discoba includes three major groups: Jakobida, Euglenozoa and Percolozoa.^[b] Jakobida are a small group (~20 species) of free-living heterotrophic flagellates, with two cilia, that primarily eat bacteria through suspension feeding; most are aquatic aerobes, with some anaerobic species, found in marine, brackish or fresh water.^[58] They are best known for their bacterial-like mitochondrial genomes.^[13] Euglenozoa is a rich (>2,000 species)^[59] group of flagellates with very different lifestyles, including: the free-living heterotrophic (both osmo- and phagotrophic)^[52] and photosynthetic euglenids (e.g., the euglenophytes, with chloroplasts originated from green algae); the free-living and parasitic kinetoplastids (such as the trypanosomes); the deep-sea anaerobic symbiontids; and the elusive diplonemids.^[60] Percolozoa^[b] (~150 species) are a collection of amoebae, flagellates and amoeboflagellates with complex life cycles, among which are some slime molds (acrasids).^[13][56] The two clades Euglenozoa and Percolozoa are sister taxa, united under the name Discicristata, in reference to their mitochondrial cristae shaped like discs.^[57] The species Tsukubamonas globosa is a free-living flagellate whose precise position within Discoba is not yet settled, but is probably more closely related to Discicristata than to Jakobida.^[58]

The metamonads (Metamonada) are a phylum of completely anaerobic or microaerophilic protozoa, primarily flagellates. Some are gut symbionts of animals such as termites, others are free-living, and others are parasitic. They include three main clades: Fornicata, Parabasalia and Preaxostyla.^[13] Fornicata (>140 species)^[61] encompasses the diplomonads, with two nuclei (e.g., Giardia, genus of well-known parasites of humans), and several smaller groups of free-living, commensal and parasitic protists (e.g., Carpediemonas, retortamonads).^[13] Parabasalia (>460 species)^[61] is a varied group of anaerobic, mostly endobiotic organisms, ranging from small parasites (like Trichomonas vaginalis, another human pathogen) to giant intestinal symbionts with numerous flagella and nuclei found in wood-eating termites and cockroaches.^[13] Preaxostyla (~140 species) includes the anaerobic and endobiotic oxymonads, with modified mitochondria, and two genera of free-living microaerophilic bacterivorous flagellates Trimastix and Paratrimastix, with typical excavate morphology.^[62] Two genera of anaerobic flagellates of recent description and unique cell architecture, Barthelona and Skoliomonas, are closely related to the Fornicata.^[63]

The malawimonads (Malawimonadida) are a small group (3 species) of freshwater or marine suspension-feeding bacterivorous flagellates^[64] with typical excavate appearance, closely resembling Jakobida and some metamonads but not phylogenetically close to either in most analyses.^[13]

Diaphoretickes includes nearly all photosynthetic eukaryotes. Within this clade, the TSAR supergroup gathers a colossal diversity of protists. The most basal branching member of the TSAR clade is Telonemia, a small (7 species) phylum of obscure phagotrophic predatory flagellates, found in marine and freshwater environments. They share some cellular similarities with the remaining three clades: Rhizaria, Alveolata and Stramenopiles, collectively known as the SAR supergroup.^[65] Another highly diverse clade within Diaphoretickes is Archaeplastida, which houses land plants and a variety of algae. In addition, two smaller groups, Haptista and Cryptista, also belong to Diaphoretickes.^[1]

The Stramenopiles, also known as Heterokonta, are characterized by the presence of two cilia, one of which bears many short, straw-like hairs (mastigonemes). They include one clade of phototrophs and numerous clades of heterotrophs, present in virtually all habitats. Stramenopiles include two usually well-supported clades, Bigyra and Gyrista, although the monophyly of Bigyra is being questioned.^[66] Branching outside both Bigyra and Gyrista is a single species of enigmatic heterotrophic flagellates, Platysulcus tardus.^[66] Much of the diversity of heterotrophic stramenopiles is still uncharacterized, known almost entirely from lineages of genetic sequences known as MASTs (MArine STramenopiles),^[66] of which only a few species have been described.^[67][68]

The phylum Gyrista includes the photosynthetic Ochrophyta or Heterokontophyta (>23,000 species),^[59] which contain chloroplasts originated from a red alga. Among these are many lineages of algae that encompass a wide range of structures and morphologies. The three most diverse ochrophyte classes are: the diatoms, unicellular or colonial organisms encased in silica cell walls (frustules) that exhibit widely different shapes and ornamentations, responsible for a big portion of the oxygen produced worldwide, and comprising much of the marine phytoplankton;^[13][69] the brown algae, filamentous or 'truly' multicellular (with differentiated tissues) macroalgae that constitute the basis of many temperate and cold marine ecosystems, such as kelp forests;^[70] and the golden algae, unicellular or colonial flagellates that are mostly present in freshwater habitats.^[71] Inside Gyrista, the sister clade to Ochrophyta are the predominantly osmotrophic and filamentous Pseudofungi (>1,200 species),^[72] which include three distinct lineages: the parasitic oomycetes or water moulds (e.g., Phytophthora infestans, the agent behind the Irish Potato Famine), which encompass most of the pseudofungi species; the less diverse non-parasitic hyphochytrids that maintain a fungus-like lifestyle; and the bigyromonads, a group of bacterivorous or eukaryovorous phagotrophs.^[66] A small group of heliozoan-like heterotrophic amoebae, Actinophryida, has an uncertain position, either within or as the sister taxon of Ochrophyta.^[73]

The little studied phylum Bigyra is an assemblage of exclusively heterotrophic organisms, most of which are free-living. It includes the Labyrinthulomycetes, among which are single-celled amoeboid phagotrophs, mixotrophs, and fungus-like filamentous heterotrophs that create slime networks to move and absorb nutrients, as well as some parasites. Also included in Bigyra are the bicosoecids, phagotrophic flagellates that consume bacteria, and the closely related Placidozoa, which consists of several groups of heterotrophic flagellates (e.g., the deep-sea halophilic Placididea) as well as the intestinal commensals known as Opalinata (e.g., the human parasite Blastocystis, and the highly unusual opalinids, composed of giant cells with numerous nuclei and cilia, originally misclassified as ciliates).^[66]

The alveolates (Alveolata) are characterized by the presence of cortical alveoli, cytoplasmic sacs underlying the cell membrane of unknown physiological function.^[52]: 599 Among them are three of the most well-known groups of protists: apicomplexans, dinoflagellates and ciliates. The ciliates (Ciliophora) are a highly diverse (>8,000 species) and probably the most thoroughly studied^[13] group of protists. They are mostly free-living microbes characterized by large cells covered in rows of cilia and containing two kinds of nuclei, micronucleus and macronucleus (e.g., Paramecium, a model organism).^[74] Free-living ciliates are usually the top heterotrophs and predators in microbial food webs, feeding on bacteria and smaller eukaryotes, present in a variety of ecosystems, although a few species are kleptoplastic. Others are parasitic of numerous animals.^[75] Ciliates have a basal position in the evolution of alveolates, together with a few species of heterotrophic flagellates with two cilia collectively known as colponemids.^[76]

The remaining alveolates are grouped under the clade Myzozoa, whose common ancestor acquired chloroplasts through a secondary endosymbiosis from a red alga.^[77] One branch of Myzozoa contains the apicomplexans and their closest relatives, a small clade of flagellates known as Chrompodellida where phototrophic and heterotrophic flagellates, called chromerids and colpodellids respectively, are evolutionarily intermingled.^[77] In contrast, the apicomplexans (Apicomplexa) are a large (>6,000 species) and highly specialized group of obligate parasites who have all secondarily lost their photosynthetic ability (e.g., Plasmodium falciparum, cause of malaria). Their adult stages absorb nutrients from the host through the cell membrane, and they reproduce between hosts via sporozoites, which exhibit an organelle complex (the apicoplast) evolved from non-photosynthetic chloroplasts.^{[78][52]: 600}

The other branch of Myzozoa contains the dinoflagellates and their closest relatives, the perkinsids (Perkinsozoa), a small group (26 species) of aquatic intracellular parasites which have lost their photosynthetic ability similarly to apicomplexans.^[77] They reproduce through flagellated spores that infect dinoflagellates, molluscs and fish.^[79] In contrast, the dinoflagellates (Dinoflagellata) are a highly diversified (~4,500 species)^[80] group of aquatic algae that have mostly retained their chloroplasts, although many lineages have lost their own and instead either live as heterotrophs or reacquire new chloroplasts from other sources, including tertiary endosymbiosis and kleptoplasty.^[81] Most dinoflagellates are free-living and compose an important portion of phytoplankton, as well as a major cause of harmful algal blooms due to their toxicity; some live as symbionts of corals, allowing the creation of coral reefs. Dinoflagellates exhibit a diversity of cellular structures, such as complex eyelike ocelli, specialized vacuoles, bioluminescent organelles, and a wall surrounding the cell known as the theca.^[80]

Rhizaria is a lineage of morphologically diverse organisms, composed almost entirely of unicellular heterotrophic amoebae, flagellates and amoeboflagellates,^[13] commonly with reticulose (net-like) or filose (thread-like) pseudopodia for feeding and locomotion.^{[82][52]: 604} It was the last supergroup to be described, because it lacks any defining characteristic and was discovered exclusively through molecular phylogenetics.^[83] Three major clades are included, namely the phyla Cercozoa, Endomyxa and Retaria.^[1]

Retaria contains the most familiar rhizarians: forams and radiolarians, two groups of large free-living marine amoebae with pseudopodia supported by microtubules, many of which are macroscopic.^[13] The radiolarians (Radiolaria) are a diverse group (>1,000 living species) of amoebae, often bearing delicate and intricate siliceous skeletons.^[84] The forams (Foraminifera) are also diverse (>6,700 living species),^[85] and most of them are encased in multichambered tests constructed from calcium carbonate or agglutinated mineral particles.^[13] Both groups have a rich fossil record, with tens of thousands of described fossil species.^[85][86]

Cercozoa (also known as Filosa) is an assemblage of free-living protists with very different morphologies. Cercozoan amoeboflagellates are important predators of other microbes in terrestrial habitats and the plant microbiota (e.g., cercomonads and paracercomonads and glissomonads, collectively known as class Sarcomonadea),^[87] and a few can generate slime molds (e.g., Helkesea).^[88] Many cercozoans are testate or scale-bearing amoebae, namely the elusive Kraken and the two classes Imbricatea (e.g., the euglyphids) and Thecofilosea.^[87] Thecofilosea also contains the Phaeodaria (~400–500 species), a group of skeleton-bearing marine amoebae previously classified as radiolarians,^[86] and both classes include some non-scaly naked flagellates (e.g., spongomonads in Imbricatea and thaumatomonads in Thecofilosea).^[89] Among the basal-branching cercozoans are the pseudopodia-lacking thecate flagellates of Metromonadea, the heliozoan-like Granofilosea^[89] and the photosynthetic chlorarachniophytes, whose chloroplasts originated from a secondary endosymbiosis with a green alga.^[13]

Endomyxa contains two major clades of parasitic protists: Ascetosporea are sporozoan-type parasites of marine invertebrates,^[90] while Phytomyxea are obligate pathogens of plants and algae, divided into the terrestrial plasmodiophorids and the marine phagomyxids.^[91] Also included in Endomyxa are the order of predatory amoebae Vampyrellida (48 species)^[92] and two genera of marine amoebae, the thecate Gromia and the naked Filoreta.^[1]

Besides these three phyla, Rhizaria includes numerous enigmatic and understudied lineages of uncertain evolutionary position. One such clade is the Gymnosphaerida, which includes heliozoan-type protists.^[93] Several clades labeled as Novel Clades (NC) are entirely composed of environmental DNA from uncultured protists, although a few have slowly been resolved over the decades with the description of new taxa (e.g., Tremulida and Aquavolonida, formerly NC11 and NC10 respectively, with a deep-branching position in Rhizaria).^[94]

Haptista and Cryptista are two similar phyla of single-celled protists previously thought to be closely related, and collectively known as Hacrobia.^[95] However, the monophyly of Hacrobia was disproven, as the two groups originated independently.^[96] Molecular analyses place Cryptista next to Archaeplastida, forming the hypothesized "CAM" clade, and Haptista next to the TSAR clade.^[50][51]

The phylum Haptista includes two distinct clades with mineralized scales: haptophytes and centrohelids.^[13] The haptophytes (Haptophyta) are a group of ~330 species of flagellated or coccoid algae that have acquired chloroplasts from a secondary endosymbiosis. They are mostly marine, comprise an important portion of oceanic plankton, and include the coccolithophores, whose calcified scales ('coccoliths') contribute to the formation of sedimentary rocks and the biogeochemical cycles of carbon and calcium. Some species are capable of forming toxic blooms.^[97] The centrohelids (Centroplasthelida) are a small (~95 species)^[98] but widespread group of heterotrophic heliozoan-type amoebae, usually covered in scale-bearng mucous, that form an important component of benthic food webs of aquatic habitats, both marine and freshwater.^[99]

The phylum Cryptista is a clade of three distinct groups of unicellular protists: cryptomonads, katablepharids, and the species Palpitomonas bilix.^[1] The cryptomonads (>100 species), also known as cryptophytes, are flagellated algae found in aquatic habitats of diverse salinity, characterized by extrusive organelles or extrusomes called ejectisomes. Their chloroplasts, of red algal origin, contain a nucleomorph, a remnant of the eukaryotic nucleus belonging to the endosymbiotic red alga.^[100] The katablepharids, the closest relatives of cryptomonads, are heterotrophic flagellates with two cilia, also characterized by ejectisomes.^[95][1] The species Palpitomonas bilix is the most basal-branching member of Cryptista, a marine heterotrophic flagellate with two cilia, but unlike the remaining members it lacks ejectisomes.^[101]

The Archaeplastida or Plantae^[c] consists of groups that have evolved from a common photosynthetic ancestor that obtained chloroplasts directly through a single event of endosymbiosis with a cyanobacterium. These are:

• Glaucophyta (26 species), unicellular algae found in freshwater and terrestrial environments.^[102]
• Picozoa (1 species), non-photosynthetic predators.^[103]
• Rhodophyta (5,000–6,000 species), mostly multicellular marine algae that lost chlorophyll and only harvest light energy through phycobiliproteins.^[102]
• Rhodelphidia (2 species), predators with non-photosynthetic plastid.^[103]
• Viridiplantae or Chloroplastida, containing both green algae and land plants. The green algae comprise many lineages of varying diversity, such as Chlorophyta (7,000), Prasinodermophyta (10), Zygnematophyceae (4,000), Charophyceae (877), Klebsormidiophyceae (48) or Coleochaetophyceae (36).^[13]

The phylum Amoebozoa (2,400 species) is a large group of heterotrophic protists, mostly amoebae. Many lineages are slime molds that produce spore-releasing fruiting bodies, such as Myxogastria, Dictyostelia and Protosporangiida, and are often studied by mycologists. Within the non-fruiting amoebae, the Tubulinea contain many naked amoebae (such as Amoeba itself) and a well-studied order of testate amoebae known as Arcellinida. Other non-fruiting amoebozoans are Variosea, Discosea and Archamoebae.^[13]

Obazoa includes the two kingdoms Metazoa (animals) and Fungi,^[d] and their closest protist relatives inside a clade known as Opisthokonta. The opisthokont protists are Nucleariida, Ichthyosporea, Pluriformea, Filasterea, Choanoflagellata and the elusive Tunicaraptor (1 species).^[106] They are flagellated or amoeboid heterotrophs of vital importance in the search for the genes that allow animal multicellularity. Sister groups to Opisthokonta are Apusomonadida (28 species)^[107] and Breviatea (4 species).^[13]

Many smaller lineages do not belong to any of these supergroups, and are usually poorly known groups with limited data, often referred to as 'orphan groups'. Some, such as the CRuMs clade, Malawimonadida and Ancyromonadida, appear to be related to Amorphea.^[13] Others, like Hemimastigophora (10 species)^[108] and Provora (7 species), appear to be related to or within Diaphoretickes, a clade that unites SAR, Archaeplastida, Haptista and Cryptista.^[2] A mysterious protist species, Meteora sporadica, is more closely related to the latter two of these orphan groups.^[51]

Protists make up a large portion of the biomass in both marine and terrestrial ecosystems. It has been estimated that protists account for 4 gigatons (Gt) of biomass in the entire planet Earth. This amount is smaller than 1% of all biomass, but is still double the amount estimated for all animals (2 Gt). Together, protists, animals, archaea (7 Gt) and fungi (12 Gt) account for less than 10% of the total biomass of the planet, because plants (450 Gt) and bacteria (70 Gt) are the remaining 80% and 15% respectively.^[109]

Protists are highly abundant and diverse in all types of ecosystems, especially free-living (i.e. non-parasitic) groups. An unexpectedly enormous, taxonomically undescribed diversity of eukaryotic microbes is detected everywhere in the form of environmental DNA or RNA. The richest protist communities appear in soil, followed by ocean and freshwater habitats.^[110]

Phagotrophic protists (consumers) are the most diverse functional group in all ecosystems, with three main taxonomical groups of phagotrophs: Rhizaria (mainly Cercozoa in freshwater and soil habitats, and Radiolaria in oceans), ciliates (most abundant in freshwater and second most abundant in soil) and non-photosynthetic stramenopiles (third most represented overall, higher in soil than in oceans). Phototrophic protists (producers) appear in lower proportions, probably constrained by intense predation. They exist in similar abundance in both oceans and soil. They are mostly dinophytes in oceans, chrysophytes in freshwater, and Archaeplastida in soil.^[110]

Marine protists are highly diverse, have a fundamental impact on biogeochemical cycles (particularly, the carbon cycle)^[111] and are at the base of the marine trophic networks as part of the plankton.^[112]

Phototrophic marine protists located in the photic zone as phytoplankton are vital primary producers in the oceanic systems. They fix as much carbon as all terrestrial plants together.^[110] The smallest fractions, the picoplankton (<2 μm) and nanoplankton (2–20 μm), are dominated by several different algae (prymnesiophytes, pelagophytes, prasinophytes); fractions larger than 5 μm are instead dominated by diatoms and dinoflagellates. The heterotrophic fraction of marine picoplankton encompasses primarily early-branching stramenopiles (e.g. bicosoecids and labyrinthulomycetes), as well as alveolates, ciliates and radiolarians; protists of lower frequency include cercozoans and cryptophytes.^[113]

Mixotrophic marine protists, while not very researched, are present abundantly and ubiquitously in the global oceans, on a wide range of marine habitats. In metabarcoding analyses, they constitute more than 12% of the environmental sequences. They are an important and underestimated source of carbon in eutrophic and oligotrophic habitats.^[112] Their abundance varies seasonally.^[114] Planktonic protists are classified into various functional groups or 'mixotypes' that present different biogeographies:

• Constitutive mixotrophs, also called 'phytoplankton that eat', have the innate ability to photosynthesize. They have diverse feeding behaviors: some require phototrophy, others phagotrophy, and others are obligate mixotrophs.^[112] They are responsible for harmful algal blooms. They dominate the eukaryotic microbial biomass in the photic zone, in eutrophic and oligotrophic waters across all climate zones, even in non-bloom conditions. They account for significant, often dominant predation of bacteria.^[115]

• Non-constitutive mixotrophs acquire the ability to photosynthesize by stealing chloroplasts from their prey. They can be divided into two: generalists, which can use chloroplasts stolen from a variety of prey (e.g. oligotrich ciliates), or specialists, which have developed the need to only acquire chloroplasts from a few specific prey. The specialists are further divided into two: plastidic, those which contain differentiated plastids (e.g. Mesodinium, Dinophysis), and endosymbiotic, those which contain endosymbionts (e.g. mixotrophic Rhizaria such as Foraminifera and Radiolaria, dinoflagellates like Noctiluca).^[115] Both plastidic and generalist non-constitutive mixotrophs have similar biogeographies and low abundance, mostly found in eutrophic coastal waters. Generalist ciliates can account for up to 50% of ciliate communities in the photic zone. The endosymbiotic mixotrophs are the most abundant non-constitutive type.^[112]

Freshwater planktonic 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.^[116] The main freshwater producers (chrysophytes, cryptophytes and dinophytes) behave alternatively as consumers (mixotrophs). At the same time, strict consumers (non-photosynthetic) are less abundant in freshwater, implying that the consumer role is partly taken by these mixotrophs.^[110]

Soil protist communities are ecologically the richest. This may be 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. Only a small fraction of the detected diversity of soil-dwelling protists has been described (8.1% as of 2017).^[110] Soil protists are also morphologically and functionally diverse, with four major categories:^[117]

• Photoautotrophic soil protists, or algae, are as abundant as their marine counterparts. Given the importance of marine algae, soil algae may provide a larger contribution to the global carbon cycle than previously thought, but the magnitude of their carbon fixation has yet to be quantified.^[110] Most soil algae belong to the supergroups Stramenopiles (diatoms, Xanthophyceae and Eustigmatophyceae) and Archaeplastida (Chlorophyceae and Trebouxiophyceae). There is also the presence of environmental DNA from dinoflagellates and haptophytes in soil, but no living forms have been seen.^[117]

• Fungus-like protists are present abundantly in soil. Most environmental sequences belong to the Oomycetes (Stramenopiles), an osmotrophic and saprotrophic group that contains free-living and parasitic species of other protists, fungi, plants and animals. Another important group in soil are slime molds (found in Amoebozoa, Opisthokonta, Rhizaria and Heterolobosea), which reproduce by forming fruiting bodies known as sporocarps (originated from a single cell) and sorocarps (from aggregations of cells).^[117]

• Phagotrophic protists are abundant and essential in soil ecosystems. 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.^[118] Many soil protists are also mycophagous, and facultative (i.e. non-obligate) mycophagy is a widespread evolutionary feeding mode among soil protozoa.^[119] Amoeboflagellates like the glissomonads and cercomonads (in Rhizaria) 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 (e.g. arcellinids and euglyphids) have shells that protect against desiccation and predation, and their contribution to the silica cycle through the biomineralization of shells is as important as that of forest trees.^[117]

• Parasitic soil protists (in Apicomplexa) are diverse, ubiquitous and have an important role as parasites of soil-dwelling invertebrate animals. In Neotropical forests, environmental DNA from the apicomplexan gregarines dominates protist diversity.^[117]

Parasitic protists represent around 15–20% of all environmental DNA in marine and soil systems, but only around 5% in freshwater systems, where chytrid fungi likely fill that ecological niche. In oceanic systems, parasitoids (i.e. those which kill their hosts, e.g. Syndiniales) are more abundant. In soil ecosystems, true parasites (i.e. those which do not kill their hosts) are primarily animal-hosted Apicomplexa (Alveolata) and plant-hosted oomycetes (Stramenopiles) and plasmodiophorids (Rhizaria). In freshwater ecosystems, parasitoids are mainly Perkinsea and Syndiniales (Alveolata), as well as the fungal Chytridiomycota. True parasites in freshwater are mostly oomycetes, Apicomplexa and Ichthyosporea.^[110]

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), plants^[120][121] (the oomycete Phytophthora infestans causes late blight in potatoes)^[122] or even of other protists.^[123][124]

Around 100 protist species can infect humans.^[117] Two papers from 2013 have proposed virotherapy, the use of viruses to treat infections caused by protozoa.^[125][126]

Researchers from the Agricultural Research Service are taking advantage of protists as pathogens to control red imported fire ant (Solenopsis invicta) populations in Argentina. Spore-producing protists such as Kneallhazia solenopsae (recognized as a sister clade or the closest relative to the fungus kingdom now)^[127] can reduce red fire ant populations by 53–100%.^[128] Researchers have also been able to infect phorid fly parasitoids of the ant with the protist without harming the flies. This turns the flies into a vector that can spread the pathogenic protist between red fire ant colonies.^[129]

From the start of the 18th century, the popular term "infusion animals" (later infusoria) referred to protists, bacteria and small invertebrate animals. In the mid-18th century, while Swedish scientist Carl von Linnaeus largely ignored the protists,^[e] his Danish contemporary Otto Friedrich Müller was the first to introduce protists to the binomial nomenclature system.^[130][131]

In the early 19th century, German naturalist Georg August Goldfuss introduced Protozoa (meaning 'early animals') as a class within Kingdom Animalia,^[132] to refer to four very different groups: infusoria (ciliates), corals, phytozoa (such as Cryptomonas) and jellyfish. Later, in 1845, Carl Theodor von Siebold was the first to establish Protozoa as a phylum of exclusively unicellular animals consisting of two classes: Infusoria (ciliates) and Rhizopoda (amoebae, foraminifera).^[133] Other scientists did not consider all of them part of the animal kingdom, and by the middle of the century they were regarded within the groupings of Protozoa (early animals), Protophyta (early plants), Phytozoa (animal-like plants) and Bacteria (mostly considered plants). Microscopic organisms were increasingly constrained in the plant/animal dichotomy. In 1858, the palaeontolgist Richard Owen was the first to define Protozoa as a separate kingdom of eukaryotic organisms, with "nucleated cells" and the "common organic characters" of plants and animals, although he also included sponges within protozoa.^[24]

In 1860, British naturalist John Hogg proposed Protoctista (meaning 'first-created beings') as the name for a fourth kingdom of nature (the other kingdoms being Linnaeus' plant, animal and mineral) which comprised all the lower, primitive organisms, including protophyta, protozoa and sponges, at the merging bases of the plant and animal kingdoms.^[134][24]

In 1866 the 'father of protistology', German scientist Ernst Haeckel, addressed the problem of classifying all these organisms as a mixture of animal and vegetable characters, and proposed Protistenreich^[135] (Kingdom Protista) as the third kingdom of life, comprising primitive forms that were "neither animals nor plants". He grouped both bacteria^[136] and eukaryotes, both unicellular and multicellular organisms, as Protista. He retained the Infusoria in the animal kingdom, until German zoologist Otto Bütschli demonstrated that they were unicellular.^[137][138] At first, he included sponges and fungi, but in later publications he explicitly restricted Protista to predominantly unicellular organisms or colonies incapable of forming tissues. He clearly separated Protista from true animals on the basis that the defining character of protists was the absence of sexual reproduction, while the defining character of animals was the blastula stage of animal development. He also returned the terms protozoa and protophyta as subkingdoms of Protista.^[24]

Bütschli considered the kingdom to be too polyphyletic and rejected the inclusion of bacteria. He fragmented the kingdom into protozoa (only nucleated, unicellular animal-like organisms), while bacteria and the protophyta were a separate grouping. This strengthened the old dichotomy of protozoa/protophyta from German scientist Carl Theodor von Siebold, and the German naturalists asserted this view over the worldwide scientific community by the turn of the century. However, British biologist C. Clifford Dobell in 1911 brought attention to the fact that protists functioned very differently compared to the animal and vegetable cellular organization, and gave importance to Protista as a group with a different organization that he called "acellularity", shifting away from the dogma of German cell theory. He coined the term protistology and solidified it as a branch of study independent from zoology and botany.^[24]

In 1938, American biologist Herbert Copeland resurrected Hogg's label, arguing that Haeckel's term Protista included anucleated microbes such as bacteria, which the term Protoctista (meaning "first established beings") did not. Under his four-kingdom classification (Monera, Protoctista, Plantae, Animalia), the protists and bacteria were finally split apart, recognizing the difference between anucleate (prokaryotic) and nucleate (eukaryotic) organisms. To firmly separate protists from plants, he followed Haeckel's blastular definition of true animals, and proposed defining true plants as those with chlorophyll a and b, carotene, xanthophyll and production of starch. He also was the first to recognize that the unicellular/multicellular dichotomy was invalid. Still, he kept fungi within Protoctista, together with red algae, brown algae and protozoans.^[24][139] This classification was the basis for Whittaker's later definition of Fungi, Animalia, Plantae and Protista as the four kingdoms of life.^[140]

In the popular five-kingdom scheme published by American plant ecologist Robert Whittaker in 1969, Protista was defined as eukaryotic "organisms which are unicellular or unicellular-colonial and which form no tissues". Just as the prokaryotic/eukaryotic division was becoming mainstream, Whittaker, after a decade from Copeland's system,^[140] recognized the fundamental division of life between the prokaryotic Monera and the eukaryotic kingdoms: Animalia (ingestion), Plantae (photosynthesis), Fungi (absorption) and the remaining Protista.^{[141][142][24]}

In the five-kingdom system of American evolutionary biologist Lynn Margulis, the term "protist" was reserved for microscopic organisms, while the more inclusive kingdom Protoctista (or protoctists) included certain large multicellular eukaryotes, such as kelp, red algae, and slime molds.^[143] Some use the term protist interchangeably with Margulis' protoctist, to encompass both single-celled and multicellular eukaryotes, including those that form specialized tissues but do not fit into any of the other traditional kingdoms.^[144]

The five-kingdom model remained the accepted classification until the development of molecular phylogenetics in the late 20th century, when it became apparent that protists are a paraphyletic group from which animals, fungi and plants evolved, and the three-domain system (Bacteria, Archaea, Eukarya) became prevalent.^[145] Today, protists are not treated as a formal taxon, but the term is commonly used for convenience in two ways:^[5]

• Phylogenetic definition: protists are a paraphyletic group.^[146] A protist is any eukaryote that is not an animal, land plant or fungus,^[147] thus excluding many unicellular groups like the fungal Microsporidia, Chytridiomycetes and yeasts, and the non-unicellular Myxozoan animals included in Protista in the past.^[148]
• Functional definition: protists are essentially those eukaryotes that are never multicellular,^[5] that either exist as independent cells, or if they occur in colonies, do not show differentiation into tissues.^[149] While in popular usage, this definition excludes the variety of non-colonial multicellularity types that protists exhibit, such as aggregative (e.g. choanoflagellates) or complex multicellularity (e.g. brown algae).^[150]

There is, however, one classification of protists based on traditional ranks that lasted until the 21st century. The British protozoologist Thomas Cavalier-Smith, since 1998, developed a six-kingdom model:^[f] Bacteria, Animalia, Plantae, Fungi, Protozoa and Chromista.^[10][151] In his context, paraphyletic groups take preference over clades:^[10] both protist kingdoms Protozoa and Chromista contain paraphyletic phyla such as Apusozoa, Eolouka or Opisthosporidia. Additionally, red and green algae are considered true plants, while the fungal groups Microsporidia, Rozellida and Aphelida are considered protozoans under the phylum Opisthosporidia. This scheme endured until 2021, the year of his last publication.^[57]

By definition, all eukaryotes before the existence of plants, animals and fungi are considered protists. For that reason, this section contains information about the deep ancestry of all eukaryotes.

All living eukaryotes, including protists, evolved from the last eukaryotic common ancestor (LECA). Descendants of this ancestor are known as "crown-group" or "modern" eukaryotes. Molecular clocks suggest that LECA originated between 1200 and more than 1800 million years ago (Ma). Based on all molecular predictions, modern eukaryotes reached morphological and ecological diversity before 1000 Ma in the form of multicellular algae capable of sexual reproduction, and unicellular protists capable of phagocytosis and locomotion. However, the fossil record of modern eukaryotes is very scarce around this period, which contradicts the predicted diversity.^[152]

Instead, the fossil record of this period contains "stem-group eukaryotes". These fossils cannot be assigned to any known crown group, so they probably belong to extinct lineages that originated before LECA. They appear continuously throughout the Mesoproterozoic fossil record (1650–1000 Ma). They present defining eukaryote characteristics such as complex cell wall ornamentation and cell membrane protrusions, which require a flexible endomembrane system. However, they had a major distinction from crown eukaryores: the composition of their cell membrane. Unlike crown eukaryotes, which produce "crown sterols" for their cell membranes (e.g. cholesterol and ergosterol), stem eukaryotes produced "protosterols", which appear earlier in the biosynthetic pathway.^[152]

Crown sterols, while metabolically more expensive, may have granted several evolutionary advantages for LECA's descendants. Specific unsaturation patterns in crown sterols protect against osmotic shock during desiccation and rehydration cycles. Crown sterols can also receive ethyl groups, thus enhancing cohesion between lipids and adapting cells against extreme cold and heat. Moreover, the additional steps in the biosynthetic pathway allow cells to regulate the proportion of different sterols in their membranes, in turn allowing for a wider habitable temperature range and unique mechanisms such as asymmetric cell division or membrane repair under exposure to UV light. A more speculative role of these sterols is their protection against the Proterozoic changing oxygen levels. It is theorized that all of these sterol-based mechanisms allowed LECA's descendants to live as extremophiles of their time, diversifying into ecological niches that experienced cycles of desiccation and rehydration, daily extremes of high and low temperatures, and elevated UV radiation (such as mudflats, rivers, agitated shorelines and subaerial soil).^[152]

In contrast, the named mechanisms were absent in stem-group eukaryotes, as they were only capable of producing protosterols. Instead, these protosterol-based life forms occupied open marine waters. They were facultative anaerobes that thrived in Mesoproterozoic waters, which at the time were low on oxygen. Eventually, during the Tonian period (Neoproterozoic era), oxygen levels increased and the crown eukaryotes were able to expand to open marine environments thanks to their preference for more oxygenated habitats. Stem eukaryotes may have been driven to extinction as a result of this competition. Additionally, their protosterol membranes may have posed a disadvantage during the cold of the Cryogenian "Snowball Earth" glaciations and the extreme global heat that came afterwards.^[152]

Modern eukaryotes began to appear abundantly in the Tonian period (1000–720 Ma), fueled by the proliferation of red algae. The oldest fossils assigned to modern eukaryotes belong to two photosynthetic protists: the multicellular red alga Bangiomorpha (from 1050 Ma), and the chlorophyte green alga Proterocladus (from 1000 Ma).^[152] Abundant fossils of heterotrophic protists appear later, around 900 Ma, with the emergence of fungi.^[152] For example, the oldest fossils of Amoebozoa are vase-shaped microfossils resembling modern testate amoebae, found in 800 million-year-old rocks.^[153][154] Radiolarian shells are found abundantly in the fossil record after the Cambrian period (~500 Ma), but more recent paleontological studies are beginning to interpret some Precambrian fossils as the earliest evidence of radiolarians.^{[155][156][157]}

• Evolution of sexual reproduction
• Protist locomotion

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• UniEuk Taxonomy App
• Tree of Life: Eukaryotes
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