Protist Temporal range: Paleoproterozoic – Present Pha. Proterozoic Archean Had.
Scientific classification
Domain:	Eukaryota
Supergroups[1]
Amoebozoa Apusomonadida Archaeplastida (including land plants) Breviatea CRuMs Cryptista Discoba Haptista Hemimastigophora Malawimonadida Metamonada Meteora sporadica[2] Opisthokonta (including fungi & animals) Provora[3] SAR supergroup Telonemia
Cladistically included but traditionally excluded taxa
Animalia Fungi Embryophyta (land plants)

A protist (/ˈproʊtɪst/ PROH-tist) is any eukaryotic organism (that is, an organism whose cells contain a cell nucleus) that is not an animal, plant, or fungus. Protists, along with other eukaryotes, all descend from the last eukaryotic common ancestor.^[4] Protists do not form a natural group, or clade; any unicellular eukaryote may be described as a protist,^[5] in addition to some cases of multicellular protists such as slime molds, brown algae and xenophyophorean forams.^[6] The study of protists is termed protistology.^[7]

What is a protist?

There is not a single accepted definition of what protists are. As a paraphyletic assemblage of diverse biological groups, they have historically been regarded as a catch-all taxon that includes any eukaryotic organism (i.e. living beings whose cells possess a nucleus) that is not an animal, a land plant or a dikaryon fungus. Because of this definition by exclusion, protists encompass almost all of the broad spectrum of biological characteristics expected in eukaryotes.^[8]

They are generally unicellular, microscopic eukaryotes that can be purely phototrophic, which are generally called algae, or purely heterotrophic, which are traditionally called protozoa, but there is a wide range of mixotrophic protists where phagotrophy and phototrophy coexist.^[8] They have different life cycles, trophic levels, modes of locomotion, and cellular structures.^[9][10] Some protists can be pathogens.^[11]

Examples of basic protist forms, that do not represent evolutionary cohesive lineages, include:^[6]

• Algae, which are photosynthetic protists. Traditionally called “protophyta”, they are found within most of the big evolutionary lineages or supergroups, intermingled with heterotrophic protists which are traditionally called “protozoa”.^[12] There are many multicellular and colonial examples of algae: kelp, red algae, some types of diatoms, some lineages of green algae, etc.
• Flagellates, which bear eukaryotic flagella. They are found in all lineages, reflecting that the common ancestor of all living eukaryotes was a flagellated heterotroph.
• Amoebae, which lack flagella but move through changes in the shape and motion of their protoplasm^[13] to produce pseudopodia. They have evolved independently several times, leading to major radiations of these lifeforms. Many lineages lack a solid shape (“naked amoebae”). Some of them have special forms, such as the “heliozoa”, amoebae with microtubule-supported pseudopodia radiating from the cell, with at least three independent origins. Others, referred to as “testate amoebae”, grow a shell around the cell made from organic or inorganic material.
• Slime molds, which are amoebae capable of producing stalked reproductive structures that bear spores, often through aggregative multicellularity (numerous amoebae aggregating together). This type of multicellularity has evolved at least seven times among protists.^[14]
• Fungus-like protists, which can produce hyphae-like structures and are often saprophytic. They have evolved multiple times, often very distantly from true fungi. For example, the oomycetes (water molds) or the myxomycetes.
• Parasitic protists, such as Plasmodium falciparum, the cause of malaria.

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 ICN and the ICZN codes.^[15][16]

Diversity

The evolutionary relationships of protists have been elucidated 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 current tree is divided into various clades informally named supergroups:^[6][1]

Archaeplastida diversity

• Archaeplastida^[a] — consists of photosynthetic groups that have evolved from a common ancestor that obtained chloroplasts directly through a single event of endosymbiosis with a cyanobacterium:
  • Picozoa (1 species), non-photosynthetic predators.^[18]
  • Glaucophyta (26 species), unicellular algae found in freshwater and terrestrial environments.^[19]
  • Rhodophyta (5,000–6,000 species), mostly multicellular marine algae that lost chlorophyll and only harvest light energy through phycobiliproteins.^[19]
  • Viridiplantae or Chloroplastida, containing both green algae and land plants which are not protists. 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).^[6]

Stramenopiles diversity

• Sar, SAR or Harosa — a clade of three highly diverse lineages exclusively containing protists.
  • Stramenopiles is a wide cade of photosynthetic and heterotrophic organisms that evolved from a common ancestor with hairs in one of their two flagella. The photosynthetic stramenopiles, called Ochrophyta, are a monophyletic group that acquired chloroplasts from secondary endosymbiosis with a red alga. Among these, the best known are the unicellular or colonial Bacillariophyta (>60,000 species),^[20] known as diatoms, and the filamentous or genuinely multicellular Phaeophyta (2,000 species),^[21] known as brown algae. The heterotrophic stramenopiles are more diverse, ranging from fungi-like organisms such as the Hyphochytrea, Oomycota and Labyrinthulea, to various kinds of protozoa such as the Opalinata and Bigyra.^[6]
  • Alveolata contains three of the most well-known groups of protists: Apicomplexa, a parasitic group with species harmful to humans and animals; Dinoflagellata, an ecologically important group as a main component of the marine microplankton and a main cause of algal blooms; and Ciliophora (4,500 species),^[22] the extremely diverse and well-studied group of mostly free-living heterotrophs known as ciliates.^[6]
  • Rhizaria is a morphologically diverse lineage mostly comprised of heterotrophic amoebae, flagellates and amoeboflagellates, and some unusual algae (Chlorarachniophyta) and spore-forming parasites. The most familiar rhizarians are Foraminifera and Radiolaria, groups of large and abundant marine amoebae. Much of the rhizarian diversity lies within the phylum Cercozoa, filled with free-living flagellates which usually have pseudopodia, as well as Phaeodaria, a group previously considered radiolarian. Other groups are comprised of various amoebae like Vampyrellida or are important parasites like Phytomyxea, Paramyxida or Haplosporida.^[6]

• Haptista — includes the Haptophyta algae and the heterotrophic Centrohelida, which are “heliozoan”-type amoebae.^[6]

• Cryptista — closely related to Archaeplastida, it includes the Cryptophyta algae, with a plastid of red algal origin, and two obscure relatives with two flagella, katablepharids and Palpitomonas.^[6]

• Discoba — includes many lineages previously grouped under the paraphyletic "Excavata": the Jakobida, flagellates with bacterial-like mitochondrial genomes; Tsukubamonas, a free-living flagellate; and the Discicristata clade, which unites well-known phyla Heterolobosea and Euglenozoa. Heterolobosea includes amoebae, flagellates annd amoeboflagellates with complex life cycles, and the unusual Acrasida, a group of slime molds. Euglenozoa encompasses a clade of algae with chloroplasts of green algal origin and many groups of anaerobic, parasitic or free-living heterotrophs.^[6]

• Metamonada — a clade of completely anaerobic protozoa, primarily flagellates. Some are gut symbionts of animals, others are free-living, and others are well-known parasites (for example, Giardia lamblia).^[6]

• Amorphea — unites two huge clades:
  • 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.^[6]
  • Obazoa includes the two kingdoms Metazoa (animals) and Fungi,^[b] 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).^[26] 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)^[27] and Breviatea (4 species).^[6]

Many lineages do not belong to any of these supergroups, and are usually poorly known groups with limited data. Some, such as the CRuMs clade, Malawimonadida and Ancyromonadida, appear to be related to Amorphea.^[6] Others, like Hemimastigophora (10 species)^[28] and Provora (7 species), appear to be related to or within Diaphoretickes, a clade that unites SAR, Archaeplastida, Haptista and Cryptista.^[3]

Although the root of the tree is still unresolved, one possible topology of the eukaryotic tree of life is:^[29][3]

Protist phylogeny
Eukaryota Diaphoretickes TSAR SAR Stramenopiles Alveolata Rhizaria Telonemia Haptista Provora Hemimastigophora Cryptista Archaeplastida Discoba Metamonada Ancyromonadida Malawimonadida Podiata CRuMs Amorphea Amoebozoa Obazoa Breviatea Apusomonadida Opisthokonta

History of classification

Early concepts of protists

Goldfuss' system of life, introducing the Protozoa within animals.

The father of protistology, Anton van Leeuwenhoek, is thought to be the first person to observe a variety of free-living protists, which he referred to as “very little animalcules” in 1674.^[30]

From the start of the 18th century, the popular term “infusion animals” was introduced by Ledermuller in 1763 to refer to these small organisms, and was later formalized as the Infusoria by Wrisberg in 1765. In the mid-18th century, while Carl von Linnaeus largely ignored the protists,^[c] his contemporary Otto Friedrich Müller was the first to introduce protists to the binomial system of nomenclature. The Infusoria included not only protists but also bacteria and many groups of small invertebrate animals.^[30][31]

In the early 19th century, the German naturalist Georg August Goldfuss introduced the word “Protozoa” (early animals) as a class within Kingdom Animalia,^[32] to refer to four groups of very different organisms: Infusoria (the modern ciliates of today), Lithozoa (corals), Phytozoa (such as Cryptomonas) and Medusinae (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).^[33] Other scientists, such as Louis Agassiz, did not consider all of these organisms to be part of the animal kingdom, and by the middle of the century they were generally 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 dichotomy between plant and animal. In 1858, the palaeontolgist Richard Owen was the first to define Protozoa as a separated kingdom of eukaryotic organisms, with “nucleated cells” and the “common organic characters” of plants and animals, although he also included sponges within this definition.^[12]

Origin of Kingdom Protista or Protoctista

John Hogg's illustration of the Four Kingdoms of Nature, showing "Regnum Primigenum" (Protoctista) as a greenish haze at the base of the Animals and Plants, 1860

In 1860, naturalist John Hogg proposed Protoctista (first-created beings) as the name for a fourth kingdom of nature, “Regnum Primigenum” (primigenal kingdom), the other kingdoms being Linnaeus' plant, animal and mineral. This kingdom comprised all the lower, primitive organisms, including Protophyta, Protozoa and Armophoctista (sponges), at the merging bases of the plant and animal kingdoms.^[34][12]

Haeckel's 1866 tree of life, with the third kingdom Protista.

In 1866 the 'father of protistology', Ernst Haeckel, addressed the problem of classifying all these organisms as a mixture of animal and vegetable characters, and proposed Protistenreich (Kingdom Protista) as the third kingdom of life, comprising primitive forms that were “neither animals nor plants”. He grouped both bacteria^[35] and eukaryotes, both unicellular and multicellular organisms, as Protista. He retained the Infusoria in the animal kingdom, until Otto Butschli demonstrated that they were unicellular.^[36][37] 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.^[12]

Otto Butschli 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 von Siebold, and the German naturalists asserted this view over the worldwide scientific community by the turn of the century. However, 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.^[12]

In 1938, 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.^[12][38] This classification was the basis for Whittaker's later definition of Fungi, Animalia, Plantae and Protista as the four kingdoms of life.^[39]

In the popular five-kingdom scheme published by 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,^[39] recognized the fundamental division of life between the prokaryotic Monera and the eukaryotic kingdoms: Animalia (ingestion), Plantae (photosynthesis), Fungi (absorption) and the remaining Protista.^[40][41][12]

In the five-kingdom system of 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.^[42] Some use the term protist interchangeably with Margulis's 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.^[43]

Phylogenetics and the modern definition

Phylogenetic and symbiogenetic tree of living organisms, showing the origins of eukaryotes

Phylogenomic tree of eukaryotes, as regarded in 2020. Supergroups are in color.

The five-kingdom models remained the accepted classification until the development of molecular phylogenetics in the late 20th century, when it became apparent that neither protists nor monera were single groups of related organisms (they were not monophyletic groups), and the three-domain system (Bacteria, Archaea, Eukarya) became prevalent.^[44]

Today, Protista is not treated as a formal taxon, but the term "protist" is still commonly used for convenience in two ways.^[45] The most popular contemporary definition is a phylogenetic one, that recognizes protists as a paraphyletic group:^[46] a protist is any eukaryote that is not an animal, (land) plant, or (true) fungus; this definition^[47] excludes many unicellular groups, like the Microsporidia, Chytridiomycetes and yeast (fungi), and a non-unicellular group included in Protista in the past, the Myxozoa (animals).^[48]

The other definition describes protists primarily by functional or biological criteria: protists are essentially those eukaryotes that are never multicellular,^[45] that either exist as independent cells, or if they occur in colonies, do not show differentiation into tissues.^[49]

Because the protists are paraphyletic, the monophyletic kingdoms Animalia, Plantae and Fungi evolved from them. The newest classification systems of eukaryotes do not recognize the formal taxonomic ranks (phylum, class, order...) and instead only recognize the group that are clades of related organisms. This is intended to make the classification more stable in the long term and easier to update. In this new cladistic scheme, the protists are divided into wide branches or supergroups, such as the SAR supergroup, Opisthokonta (animals, fungi and all related protists), Archaeplastida (true plants and related protists), Amoebozoa (containing slime molds), Discoba (containing most excavates), and others.^[1]

Protozoa and Chromista

There is, however, one classification of protists based on traditional ranks that lasted until the 21st century. The protozoologist Thomas Cavalier-Smith, since 1998, developed a six-kingdom model:^[d] Bacteria, Animalia, Plantae, Fungi, Protozoa and Chromista.^[17][50] In his context, paraphyletic groups take preference over clades:^[17] both protist kingdoms Protozoa and Chromista contain paraphyletic phyla such as Apusozoa, Eolouka or Opisthosporidia. Additionally, in Cavalier-Smith's system, red and green algae are considered true plants, while the fungal phyla Microsporidia, Rozellida and Aphelida are considered protozoans. This scheme endured until 2021, the year of his last publication.^[23]

Reproduction

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.^[51]

The demonstration of sex in protists

Eukaryotes emerged in evolution more than 1.5 billion years ago.^[52] 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.^[53][54] Most of these meiotic genes were likely present in the common ancestor of all eukaryotes,^[55] which was likely capable of facultative (non-obligate) sexual reproduction.^[56]

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.^[57] Even in the early 20th century, some researchers interpreted phenomena related to chromidia (chromatin granules free in the cytoplasm) in amoebae as sexual reproduction.^[58]

Sexual reproduction in pathogenic protists

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).^[59][60][61]

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.^[62] 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.^[63]

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.^[64]

Ecology

Free-living protists occupy almost any environment that contains liquid water. Many protists, such as algae, are photosynthetic and are vital primary producers in ecosystems, particularly in the ocean as part of the plankton. Other protists include pathogenic species, such as the kinetoplastid Trypanosoma brucei, which causes sleeping sickness, and species of the apicomplexan Plasmodium, which cause malaria.

Biomass

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 0.01% 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) only 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.^[65]

Metabolism

Nutrition can vary according to the type of protist. Most eukaryotic algae are autotrophic, but the pigments were lost in some groups.^[vague] Other protists are heterotrophic, and may present phagotrophy, osmotrophy, saprotrophy or parasitism. Some are mixotrophic. Some protists that do not have / lost chloroplasts/mitochondria have entered into endosymbiontic relationship with other bacteria/algae to replace the missing functionality. For example, Paramecium bursaria and Paulinella have captured a green alga (Zoochlorella) and a cyanobacterium respectively that act as replacements for chloroplast. Meanwhile, a protist, Mixotricha paradoxa that has lost its mitochondria uses endosymbiontic bacteria as mitochondria and ectosymbiontic hair-like bacteria (Treponema spirochetes) for locomotion.

Many protists are flagellate, for example, and filter feeding can take place where flagellates find prey. Other protists can engulf bacteria and other food particles, by extending their cell membrane around them to form a food vacuole and digesting them internally in a process termed phagocytosis.

For most important cellular structures and functions of animal and plants, it can be found a heritage among protists.^[66]

Parasitism: role as pathogens

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^[67][68] (the oomycete Phytophthora infestans causes late blight in potatoes)^[69] or even of other protists.^[70][71] Protist pathogens share many metabolic pathways with their eukaryotic hosts. This makes therapeutic target development extremely difficult – a drug that harms a protist parasite is also likely to harm its animal/plant host. A more thorough understanding of protist biology may allow these diseases to be treated more efficiently. For example, the apicoplast (a nonphotosynthetic chloroplast but essential to carry out important functions other than photosynthesis) present in apicomplexans provides an attractive target for treating diseases caused by dangerous pathogens such as plasmodium.

Recent papers have proposed the use of viruses to treat infections caused by protozoa.^[72][73]

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)^[74] can reduce red fire ant populations by 53–100%.^[75] 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.^[76]

Fossil record

Many protists have neither hard parts nor resistant spores, and their fossils are extremely rare or unknown. Examples of such groups include the apicomplexans, most ciliates, some green algae (the Klebsormidiales), choanoflagellates, oomycetes, brown algae, yellow-green algae, Excavata (e.g., euglenids). Some of these have been found preserved in amber (fossilized tree resin) or under unusual conditions (e.g., Paleoleishmania, a kinetoplastid).

Others are relatively common in the fossil record, as the diatoms, golden algae, haptophytes (coccoliths), silicoflagellates, tintinnids (ciliates), dinoflagellates, green algae, red algae, heliozoans, radiolarians, foraminiferans, ebriids and testate amoebae (euglyphids, arcellaceans). Some are even used as paleoecological indicators to reconstruct ancient environments.

More probable eukaryote fossils begin to appear at about 1.8 billion years ago, the acritarchs, spherical fossils of likely algal protists. Another possible representative of early fossil eukaryotes are the Gabonionta.