Protists represent an extremely largegenetic andecological diversity in all environments, including extreme habitats. Theirdiversity, larger than for all other eukaryotes, has only been discovered in recent decades through the study ofenvironmental DNA and is still in the process of being fully described. They are present in allecosystems as important components of thebiogeochemical cycles andtrophic webs. They exist abundantly and ubiquitously in a variety of mostly unicellular forms that evolved multiple times independently, such as free-livingalgae,amoebae andslime moulds, or as importantparasites. Together, they compose an amount of biomass that doubles that of animals. They exhibit varied types of nutrition (such asphototrophy,phagotrophy orosmotrophy), sometimes combining them (inmixotrophy). They present unique adaptations not present in multicellular animals, fungi or land plants. The study of protists is termedprotistology.
Protists display a wide range of distinctmorphological types that have been used to classify them for practical purposes, although most of these categories do not represent evolutionary cohesive lineages orclades and have insteadevolved independently several times. The most recognizable types are:[17]
Amoebae. Characterized by their irregular, flexible shapes, these protists move by extending portions of theircytoplasm, known aspseudopodia, to crawl along surfaces.[18] Many groups of amoebae are naked, buttestate amoebae andforaminifera grow a shell around theircell made from digested material or surrounding debris. Some, known asradiolarians andheliozoans, have special spherical shapes with microtubule-supported pseudopodia radiating from the cell.[17] Some amoebae are capable of producing stalked multicellular stages that bear spores, often by aggregating together; these are known asslime molds.[19] The main clades containing amoebae areAmoebozoa (including various slime molds and testate amoebae) andRhizaria (including famous groups such asforaminifera and radiolarians, as well as a few testate amoebae).[20][21] Even some individual amoebae can grow to giant sizes visible to the naked eye.[22][23]
Difference between morphological (A) and genetic (B) view of total eukaryotic diversity. Protists dominateDNA barcoding analyses, but constitute a minority of catalogued species.[34]
Thespecies diversity of protists is severely underestimated by traditional methods that differentiate species based onmorphological characteristics. The number of described protistspecies is very low (ranging from 26,000[35] to over 76,000)[c] in comparison to thediversity 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 asenvironmentalDNA barcoding have revealed a vast diversity of undescribed protists that accounts for the majority of eukaryotic sequences oroperational taxonomic units (OTUs), dwarfing those from land plants, animals and fungi.[34] As such, it is considered that protists dominate eukaryotic diversity.[37]
"Excavata" is a group that encompasses diverse protists, mostly flagellates, ranging from aerobic and anaerobic predators to phototrophs and heterotrophs.[42]: 597 The common name 'excavate' refers to the common characteristic of a ventral groove in the cell used forsuspension feeding, which is considered to be an ancestral trait present in thelast eukaryotic common ancestor.[43] The "Excavata" is composed of three clades:Discoba,Metamonada andMalawimonadida, each including 'typical excavates' that are free-living phagotrophic flagellates with the characteristic ventral groove.[44] According to most phylogenetic analyses, this group isparaphyletic,[40] with some analyses placing the root of the eukaryote tree within Metamonada.[45]
Discoba includes three major groups:Jakobida,Euglenozoa andPercolozoa.[d] 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.[47] They are best known for their bacterial-like mitochondrial genomes.[17] Euglenozoa is a rich (>2,000 species)[48] group of flagellates with very different lifestyles, including: the free-living heterotrophic (both osmo- and phagotrophic)[42] and photosyntheticeuglenids (e.g., theeuglenophytes, with chloroplasts originated from green algae); the free-living and parasitickinetoplastids (such asTrypanosoma); the deep-sea anaerobicsymbiontids; and the elusivediplonemids.[49] Percolozoa[d] (~150 species) are a collection of amoebae, flagellates and amoeboflagellates with complex life cycles, among which are some slime molds (acrasids).[17][46] The two clades Euglenozoa and Percolozoa aresister taxa, united under the nameDiscicristata, in reference to theirmitochondrial cristae shaped like discs.[9] The speciesTsukubamonas 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.[47]
Themetamonads (Metamonada) are a phylum of completelyanaerobic ormicroaerophilic protozoa, primarilyflagellates. Some aregut symbionts of animals such astermites, others are free-living, and others are parasitic. They include three main clades:Fornicata,Parabasalia andPreaxostyla.[17] Fornicata (>140 species)[36] encompasses thediplomonads, with twonuclei (e.g.,Giardia), and several smaller groups of free-living, commensal and parasitic protists (e.g.,Carpediemonas,retortamonads).[17] Parabasalia (>460 species)[36] is a varied group of anaerobic, mostly endobiotic organisms, ranging from small parasites (likeTrichomonas) to giant intestinal symbionts with numerous flagella and nuclei found in wood-eating termites andcockroaches.[17] Preaxostyla (~140 species) includes the anaerobic and endobioticoxymonads, with modified (or completely lost)[50][51]mitochondria, and two genera of free-living microaerophilic bacterivorous flagellatesTrimastix andParatrimastix, with typical excavate morphology.[51][52] Two genera of anaerobic flagellates of recent description and unique cell architecture,Barthelona andSkoliomonas, are closely related to the Fornicata.[53]
Themalawimonads (Malawimonadida) are a small group (three species) of freshwater or marine suspension-feeding bacterivorous flagellates[54] with typical excavate appearance, closely resembling Jakobida and some metamonads but not phylogenetically close to either in most analyses.[17]
Diaphoretickes includes nearly all photosynthetic eukaryotes. TheSAR supergroup gathers a colossal diversity of protists. It includesStramenopiles,Alveolata andRhizaria.[55] Another highly diverse clade within Diaphoretickes isArchaeplastida, which housesland plants and a variety of algae. In addition, three smaller groups,Telonemia,Haptista andCryptista, also belong to Diaphoretickes.[2]TSAR is a possible clade that would comprise Telonemia and SAR,[56] although Telonemia may branch with Haptista instead of SAR.[57][58] Telonemia shares some cellular similarities with the SAR supergroup.[55]
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 andGyrista, although themonophyly of Bigyra is being questioned.[59] Branching outside both Bigyra and Gyrista is a single species of enigmatic heterotrophic flagellates,Platysulcus tardus.[59] Much of the diversity of heterotrophic stramenopiles is still uncharacterized, known mostly from lineages of genetic sequences known as MASTs (MArine STramenopiles),[59] of which only a few species have been described.[60][61]
The phylum Gyrista includes the photosyntheticOchrophyta or Heterokontophyta (>23,000 species),[48] which contain chloroplasts originated from ared alga. Among these are many lineages of algae that encompass a wide range of structures and morphologies. The three most diverse ochrophyte classes are: thediatoms, unicellular or colonial organisms encased in silica cell walls (frustules) that exhibit widely different shapes and ornamentations and comprise much of themarine phytoplankton;[17][62] thebrown algae, filamentous or 'truly' multicellular (with differentiated tissues) macroalgae that constitute the basis of many temperate and cold marine ecosystems, such askelp forests;[63] and thegolden algae, unicellular or colonial flagellates that are mostly present in freshwater habitats.[64] Inside Gyrista, the sister clade to Ochrophyta are the predominantlyosmotrophic and filamentouspseudofungi (>1,200 species),[65] which include three distinct lineages: the parasiticoomycetes or water moulds (e.g.,Phytophthora), which encompass most of the pseudofungi species; the less diverse non-parasitichyphochytrids that maintain a fungus-like lifestyle; and thebigyromonads, a group of bacterivorous or eukaryovorous phagotrophs.[59] A small group of heliozoan-like heterotrophic amoebae,Actinophryida, has an uncertain position, either within or as the sister taxon of Ochrophyta.[66]
The little studied phylum Bigyra is an assemblage of exclusively heterotrophic organisms, most of which are free-living. It includes thelabyrinthulomycetes, 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 and a few testate amoebae (Amphitremida). Also included in Bigyra are thebicosoecids, phagotrophic flagellates that consume bacteria, and the closely relatedPlacidozoa, which consists of several groups of heterotrophic flagellates (e.g., the deep-sea halophilicPlacididea) as well as the intestinalcommensals known asOpalinata (e.g., the human parasiteBlastocystis, and the highly unusualopalinids, composed of giant cells with numerous nuclei and cilia, originally misclassified as ciliates).[59]
Thealveolates (Alveolata) are characterized by the presence ofcortical alveoli, cytoplasmic sacs underlying thecell membrane of unknown physiological function.[42]: 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[17] 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. 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 arekleptoplastic. Others are parasitic of numerous animals.[67] Ciliates have a basal position in the evolution of alveolates, together with a few species of heterotrophic flagellates with two cilia collectively known ascolponemids.[68]
The remaining alveolates are grouped under the cladeMyzozoa, whose common ancestor acquired chloroplasts through a secondary endosymbiosis from a red alga.[69] One branch of Myzozoa contains the apicomplexans and their closest relatives, a small clade of flagellates known asChrompodellida where phototrophic and heterotrophic flagellates, calledchromerids andcolpodellids respectively, are evolutionarily intermingled.[69] 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). Their adult stages absorb nutrients from the host through the cell membrane, and they reproduce between hosts via sporozoites, which exhibit anorganelle complex (theapicoplast) evolved from non-photosynthetic chloroplasts.[70][42]: 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.[69] They reproduce through flagellated spores that infect dinoflagellates,molluscs andfish.[71] In contrast, the dinoflagellates (Dinoflagellata) are a highly diversified (~4,500 species)[72] 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 andkleptoplasty.[73] Most dinoflagellates are free-living and compose an important portion of phytoplankton, as well as a major cause ofharmful 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 thetheca.[72]
Rhizaria is a lineage of morphologically diverse organisms, composed almost entirely of unicellular heterotrophic amoebae, flagellates and amoeboflagellates,[17] commonly with reticulose (net-like) or filose (thread-like)pseudopodia for feeding and locomotion.[75][42]: 604 It was the last supergroup to be described, because it lacks anydefining characteristic and was discovered exclusively throughmolecular phylogenetics.[76] Three major clades are included, namely the phylaCercozoa,Endomyxa andRetaria.[2]
Retaria contains the most familiar rhizarians:forams andradiolarians, two groups of large free-living marine amoebae with pseudopodia supported bymicrotubules, many of which are macroscopic.[17] The radiolarians (Radiolaria) are a diverse group (>1,000 living species) of amoebae, often bearing delicate and intricate siliceous skeletons.[77] The forams (Foraminifera) are also diverse (>6,700 living species),[78] and most of them are encased in multichambered tests constructed from calcium carbonate or agglutinated mineral particles.[17] Both groups have a rich fossil record, with tens of thousands of described fossil species.[78][79]
Cercozoa (also known asFilosa) 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 andparacercomonads andglissomonads, collectively known as classSARcomonadea),[80] and a few can generate slime molds (e.g.,Helkesea).[81] Many cercozoans are testate or scale-bearing amoebae, namely the elusiveKraken and the two classesImbricatea (e.g., theeuglyphids) andThecofilosea.[80] Thecofilosea also contains thePhaeodaria (~400–500 species), a group of skeleton-bearing marine amoebae previously classified as radiolarians,[79] and both classes include some non-scaly naked flagellates (e.g.,spongomonads in Imbricatea andthaumatomonads in Thecofilosea).[82] Among the basal-branching cercozoans are the pseudopodia-lacking thecate flagellates ofMetromonadea, the heliozoan-likeGranofilosea[82] and the photosyntheticchlorarachniophytes, whose chloroplasts originated from a secondary endosymbiosis with a green alga.[17]
Endomyxa contains two major clades of parasitic protists:Ascetosporea are sporozoan-type parasites of marine invertebrates,[83] whilePhytomyxea are obligate pathogens of plants and algae, divided into the terrestrialplasmodiophorids and the marinephagomyxids.[84] Also included in Endomyxa are the order of predatory amoebaeVampyrellida (48 species)[85] and two genera of marine amoebae, the thecateGromia and the nakedFiloreta.[2]
Besides these three phyla, Rhizaria includes numerous enigmatic and understudied lineages of uncertain evolutionary position. One such clade is theGymnosphaerida, which includes heliozoan-type protists.[86] Several clades labeled as Novel Clades (NC) are entirely composed ofenvironmental DNA from uncultured protists, although a few have slowly been resolved over the decades with the description of new taxa (e.g.,Tremulida andAquavolonida, formerly NC11 and NC10 respectively, with a deep-branching position in Rhizaria).[87]
Globorotalia, a genus of forams visible to the naked eye
Cladococcus cell, showing the intricate radiolarian skeleton
Haptista andCryptista are two similar phyla of single-celled protists previously thought to be closely related, and collectively known asHacrobia.[88] However, the monophyly of Hacrobia was disproven, as the two groups originated independently.[89] Molecular analyses place Cryptista next to Archaeplastida, forming the hypothesizedCAM clade,[39] and Haptista next to the Telonemia and the SAR clade[40] (Telonemia may either be the sister group to SAR, forming the hypothesized TSAR clade,[90] or to Haptista, forming a common sister clade to SAR[91][39][92]). Within the CAM clade, the closest relative of Cryptista is the speciesMicroheliella maris, together composing the cladePancryptista.[39]
The phylum Haptista includes two distinct clades with mineralized scales:haptophytes andcentrohelids.[17] The haptophytes (Haptophyta) are a group of over 500 living species[48] 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 thecoccolithophores, 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.[93] The centrohelids (Centroplasthelida) are a small (~95 species)[94] but widespread group of heterotrophic heliozoan-type amoebae, usually covered in scale-bearing mucous, that form an important component of benthic food webs of aquatic habitats, both marine and freshwater.[95]
The phylum Cryptista is a clade of three distinct groups of unicellular protists:cryptomonads,katablepharids, and the speciesPalpitomonas bilix.[2] The cryptomonads (>100 species), also known as cryptophytes, are flagellated algae found in aquatic habitats of diverse salinity, characterized by extrusive organelles orextrusomes called ejectisomes. Their chloroplasts, of red algal origin, contain anucleomorph, a remnant of the eukaryotic nucleus belonging to the endosymbiotic red alga.[96] The katablepharids, the closest relatives of cryptomonads, are heterotrophic flagellates with two cilia, also characterized by ejectisomes.[88][2] The speciesPalpitomonas bilix is the most basal-branching member of Cryptista, a marine heterotrophic flagellate with two cilia, but unlike the remaining members it lacks ejectisomes.[97]
Archaeplastida is the clade containing those photosynthetic groups whoseplastids were likely obtained through a single event of primaryendosymbiosis with acyanobacterium. It containsland plants (Embryophyta) and a big portion of the diversity of algae, most of which are thegreen algae, from which plants evolved, and thered algae.[98] A third lineage of algae, theglaucophytes (25 species),[48] contains rare and obscure species found in surfaces of freshwater and terrestrial habitats.[98]
The red algae or Rhodophyta (>7,100 species) are a group of diverse morphologies, ranging from single cells tomulticellular filaments to giantpseudoparenchymatousthalli, all without flagella. They lackchlorophyll and only harvest light energy throughphycobiliproteins. Their life cycles are varied and may include two or three generations. They are present in terrestrial, freshwater and primarily marine habitats, from the intertidal zone to deep waters; some are calcified and are vital components of marine ecosystems such ascoral reefs.[99] Closely related to the red algae are two small lineages of non-photosynthetic predatory flagellates: the freshwater and marineRhodelphidia (3 species),[100] which still retain genetic evidence of relic plastids;[101] and the marinePicozoa (1 species), which lack any remains of plastids. The evolutionary position of Picozoa may indicate that there have been two separate events of primary endosymbiosis, as opposed to one.[102]
The green algae, unlike themonophyletic glaucophytes and rhodophytes, are aparaphyletic group from which land plants evolved. Together they compose theChloroplastida or Viridiplantae clade.[2] The earliest branching member is the phylumPrasinodermophyta (ten species), whose members are exclusively marine coccoid cells or small macroscopic thalli.[103] The remaining green algae are distributed in two major clades. One clade is the phylumChlorophyta (>7,900 species),[48] which includes numerous lineages of scaly unicellular flagellate algae known collectively asprasinophytes along with the Prasinodermophyta, but also includes a variety of morphologies such as coccoids, palmelloids, colonies, and macroscopic filamentous, foliose or tubular thalli, present in aquatic and terrestrial habitats.[2] The opposed clade isStreptophyta, which contains the land plants and a paraphyletic group of green algae collectively known as phylumCharophyta, composed of several classes:Zygnematophyceae (>4,300 species),[48] containing unicellular, colonial and filamentous flagella-lacking organisms found almost exclusively in freshwater habitats;[104]Charophyceae (450 living species),[48] also known as stoneworts, consisting of complex multicellular thalli only found in freshwater habitats;[105]Klebsormidiophyceae (52 species), with unbranched filamentous thalli;Coleochaetophyceae (36 species), containing branched filamentous thalli;Mesostigmatophyceae, composed of a single species of scaly flagellates; andChlorokybophyceae (five species), with sarcinoid forms.[106][48]
Amorphea is a group of exclusively heterotrophic organisms. It contains the fungi and animals, as well as most slime moulds, many amoebae and some flagellates.[107] Many of its protist members exhibit complex life cycles with different levels of multicellularity.[108] Amorphea is roughly equivalent to the concept of 'unikonts', meaning 'single cilium', although it currently contains several organisms with more cilia.[109] It is defined as the smallest clade containing the groupsAmoebozoa (containing mostly slime moulds and amoebae) andOpisthokonta (containing fungi, animals, and their closest relatives).[107][2] The closest relatives of Opisthokonta are two small lineages of single-celled protists with two cilia: the flagellateApusomonadida (28 species)[110] and the amoeboflagellate anaerobicBreviatea (four species).[17] Together with opisthokonts, these two groups form the cladeObazoa, the sister clade to Amoebozoa.[109]
The phylumAmoebozoa (2,400 species)[34] is a large group of morphologically diverse phagotrophic protists, mostly amoebae. A considerable portion of amoebozoans arelobose amoebae, meaning they produce round, blunt-ended pseudopods.[111] It includes the 'archetypal' amoebae, known as the naked lobose amoebae or 'gymnamoebae'[112] (such asAmoeba itself),[113] among which is a genus of sorocarp-forming slime moulds,Copromyxa.[114] Some gymnamoebae are important pathogens to animals (e.g.,Acanthamoeba).[115] Other relevant lobose amoebae are theArcellinida, a diverse order of testate amoebae and one of the most conspicuous protist groups overall.[116] The remaining, non-lobose amoebozoans include theEumycetozoa or 'true slime moulds', comprising the sorocarp-producing bacterivorousdictyostelids and the sporocarp-producing omnivorousmyxogastrids andprotosporangiids.[2] Due to the fungus-like appearance of their fruiting bodies, eumycetozoans are often studied by mycologists.[17] Closely related to the eumycetozoans are two lineages: theVariosea, a heterogeneous assortment of amoeboid, reticulate or flagellated organisms[113] (including some sorocarp-producing organisms);[117] and the anaerobicArchamoebae, some of which live as intestinal symbionts of some animals (e.g.,Entamoeba).[2]
Opisthokonta includes the animal and fungal kingdoms,[a] as well as their closest protist relatives. The branch leading to the fungi is known asNucletmycea or Holomycota, while the branch leading to the animals is calledHolozoa.[118] The Holomycota includes the closest relatives of fungi, thenucleariids, a small group (~50 species) of free-living naked or scale-bearing phagotrophic amoebae with filose pseudopodia, some of which can aggregate into slime moulds.[119] Within the wider definition of fungi, three groups are studied as protists by some authors:Aphelida (15 species),[12]Rozellida (27 species)[120] andMicrosporidia (~1,300 species),[121] collectively known asOpisthosporidia, as opposed to the 'true' or osmotrophic fungi. Both aphelids and rozellids are single-celled phagotrophic flagellates that feed in an endobiotic manner, penetrating the cells of their respective hosts. Microsporidians are obligate intracellular parasites that feed through osmotrophy, much like true fungi. Aphelids and true fungi are closest relatives, and generally feed on cellulose-walled organisms (many algae and plants). Conversely, rozellids and microsporidians form a separate clade, and generally feed on chitin-walled organisms (fungi and animals).[122]
The Holozoa includes various lineages with complex life cycles involving different cell types and associated with the origin of animal multicellularity.[17] The closest relatives to animals are thechoanoflagellates (~360 species), free-living flagellates that feed through a collar of microvilli surrounding a larger cilium and often form colonies.[123] TheIchthyosporea (>40 species), otherwise known as mesomycetozoans, are a group of fungus-like pathogenic holozoans specialized in infecting fish and other animals.[124] TheFilasterea (six species) are a heterogeneous group of free-living, endosymbiotic, or parasitic amoebae or flagellates.[125] Lastly, thePluriformea are two species of free-living holozoans with life cycles that include multicellular aggregates.[126] An elusive flagellate speciesTunicaraptor unikontum has an uncertain evolutionary position among these holozoan groups.[127]
Several smaller lineages do not belong to any of the three main supergroups, and instead have a deep-branching "kingdom-level" position in eukaryote evolution. They are usually poorly known groups with limited data and few species, often referred to as "orphan groups".[40] TheCRuMs clade, containing the free-swimmingCollodictyonidae (seven species) with two to four cilia, the amoeboidRigifilida (two species) with filose pseudopodia, and the glidingMantamonadidae (three species)[128] andGlissandridae (two species)[129][130] with two cilia, are the sister clade of Amorphea.[38] TheAncyromonadida (35 species)[131] are aquatic gliding flagellates with two cilia, positioned near Amorphea and CRuMs.[38] TheHemimastigophora (ten species), or hemimastigotes, are predatory flagellates with a distinctive cell morphology and two rows of around a dozen flagella.[132] TheProvora (eight species)[133] are predatory flagellates with an unremarkable morphology similar to that of excavates and other flagellates with two cilia. Both Hemimastigophora and Provora were thought to be related to or within Diaphoretickes,[3] although further analyses have placed them in a separate clade along with a mysterious species of predatory protists,Meteora sporadica. This species has a remarkable morphology: they lack flagella, are bilaterally symmetrical, project a pair of lateral "arms" that swing back and forth, and contain a system of motility unlike any other.[40]
There are also manygenera of uncertain affiliation among eukaryotes because their DNA has not beensequenced, and consequently their phylogenetic affinities are unknown.[2] One enigmatic heliozoan species is so large that it does not match the description of any known genus, and was consequently transferred to a separate genusBerkeleyaesol with an unclear position, although it probably belongs to Diaphoretickes along with all other heliozoa.[134] The organismParakaryon is harder to place, as it shares traits from both prokaryotes and eukaryotes.[135]
In general, protists have typicaleukaryotic cells that follow the same principles ofbiology described for those cells within the "higher" eukaryotes (animals, fungi and land plants).[136] However, many have evolved a variety of unique physiological adaptations that do not appear in the remaining eukaryotes,[137] and in fact protists encompass almost all of the broad spectrum ofbiological characteristics expected in eukaryotes.[37]
Protists display a wide variety of food preferences and feeding mechanisms.[2][138] According to the source of their nutrients, they can be divided intoautotrophs (producers, traditionallyalgae) andheterotrophs (consumers, traditionallyprotozoa). Autotrophic protistssynthesize their own organic compounds from inorganic substrates through the process ofphotosynthesis, using light as the source of energy;[139]: 217 accordingly, they are also known asphototrophs.[140]
Heterotrophic protists obtain organic molecules synthesized by other organisms, and can be further divided according to the size of their nutrients. Those that feed on soluble molecules[139]: 218 or macromolecules under 0.5 μm in size are calledosmotrophs,[138] and they absorb them bydiffusion, ciliary pits,transport proteins of the cell membrane, and a type ofendocytosis (i.e., invagination of the cell membrane intovacuoles, calledendosomes) known aspinocytosis[2] or fluid-phase endocytosis.[138] Those that feed on organic particles over 0.5 μm in size or entire cells are calledphagotrophs, and they ingest them through a type of endocytosis known asphagocytosis.[138][139]: 218 Endocytosis is considered one of the most importantadaptations in the origin of eukaryotes because it increased the potential food supply, and phagocytosis allowed theendosymbiosis and development ofmitochondria andchloroplasts. In both osmotrophs and phagotrophs, endocytosis is often restricted to a specific region of the cell membrane, known as thecytostome, which may be followed by a cytopharynx, a specialized tract supported bymicrotubules.[138]
Osmotrophic protists acquire soluble nutrients throughmembrane channels andcarriers, but also throughpinocytosis: the nutrients are trapped in vesicles that merge into a digestive vacuole orendosome where digestion takes place.[141][138] Some osmotrophs, calledsaprotrophs orlysotrophs, perform external digestion by releasing enzymes into the environment and decomposing organic matter[2] into simpler molecules that can be absorbed. This external digestion has a distinct advantage: it allows greater control over the substances that are allowed to enter the cell, thus minimizing the intake of harmful substances or infection.[142]
Structure of the cytostome-cytopharynx complex inTrypanosoma cruzi. The food travels the pre-oral ridge from the flagellar pocket until it reaches the cytostome and enters the cell through the cytopharynx, where nutrients are presumably transported bymyosin proteins until they are enclosed in vesicles. The cytopharynx is supported by specific sets of microtubules.[144]
Phagotrophic feeding consists of two phases: the concentration of food particles in the environment, and the phagocytosis, which encloses the food particle in a vacuole (thephagosome)[138] where digestion takes place. Inciliates and most phagotrophicflagellates, digestion occurs at the oral region or cytostome, which is covered by a single membrane from which vacuoles are formed; the phagosomes then may be shuttled to the interior of the cell along the cytopharynx.[145] In amoebae, phagocytosis takes place anywhere on the cell surface. The average food particle size is around one tenth the size of the protist cell.[146]
Phagotrophic protists can be further classified according to how they approach the nutrients. Thefilter feeders acquire small, suspended food particles or prokaryotic cells and accumulate them by filtration into the cytostome (e.g.,choanoflagellates, somechrysomonads, most ciliates);[2] filter-feeding flagellates accumulate particles by propelling them with a flagellum through a collar of rigid tentacles or pseudopodia that act as a filter, while filter-feeding ciliates generate water currents through cilia and membranelle zones surrounding the cytostome. Theraptorial feeders (e.g.,bicosoecids, chrysomonads,kinetoplastids, some euglenids, manydinoflagellates and ciliates), instead of retaining all particles in bulk, capture each particle individually.[146] Among raptorial protists, thegrazers search and ingest prey from surfaces covered with potential food items such asbacterial lawns, while thepredators actively pursue scarce prey.[2] Predators that feed on filamentous algae or fungalhyphae either swallow the filaments entirely or penetrate the cell wall and ingest thecytoplasm (e.g.,Viridiraptoridae).[2] Predators may have adaptations to hunt prey, such as 'toxicysts' that immobilize prey cells. Certain ciliates have developed a specialized kind of raptorial feeding calledhistophagy, where they attack damaged but live animals (e.g., annelids and small crustaceans), enter the wounds, and ingest animal tissue. Large raptorial amoebae enclose their prey in a "food cup" of pseudopodia, prior to the formation of the food vacuole.[146] Lastly,diffusion feeders (e.g.,heliozoa,foraminifera and many other amoebae,suctorian ciliates) engulf prey that happen to collide with their pseudopods or, in the case of ciliates, tentacles that carry toxicysts or extrusomes to immobilize the prey.[146]
Consumers of prokaryotes are popularly calledbacterivores (e.g., most amoebae), while consumers (including osmotrophic parasites) of eukaryotes are known aseukaryovores. In particular, eukaryovores that feed on unicellular protists arecytotrophs (e.g.,colponemids,colpodellids, many amoebae, some ciliates); those that feed on fungi aremycophages ormycotrophs (e.g., the ciliate familyGrossglockneriidae of obligate mycophages);[147] those that prey onnematodes arenematophages;[148] and those that feed on algae arephycotrophs (e.g.,vampyrellids).[2]
Rapaza viridis is a species of obligate specialist mixotrophs: it survives through the predation ofTetraselmis algae and acquisition of their chloroplasts. It rejects any other prey cells. Even when well fed, it cannot survive without a light source, as it needs to photosynthesize with those chloroplasts.[149]
Most autotrophic protists aremixotrophs[150] and combine photosynthesis with phagocytosis.[e] They are classified into various functional groups or 'mixotypes'.[152][153]Constitutive mixotrophs have the innate ability tophotosynthesize through already present chloroplasts, and have diverse feeding behaviors, as some require phototrophy, others phagotrophy, and others are obligate mixotrophs (e.g., nanoflagellates such as somehaptophytes and dinoflagellates).Non-constitutive mixotrophs acquire the ability to photosynthesize by stealing chloroplasts from their prey, a process known askleptoplasty. Non-constitutives can be divided into two:generalists, which can steal chloroplasts from a variety of prey (e.g.,oligotrich ciliates), orspecialists, which can only acquire chloroplasts from a few specific prey (e.g.,Rapaza viridis can only steal fromTetraselmis cells).[149] The specialists are further divided into two types:plastidic, which only engulf theplastids (e.g.,Mesodinium,Dinophysis), andendosymbiotic, which keep the entire prey (e.g., mixotrophicRhizaria such asForaminifera andRadiolaria, dinoflagellates likeNoctiluca).[152]
Among exclusively heterotrophic protists, variation of nutritional modes is also observed. Thediplonemids, which inhabit deep waters where photosynthesis is absent, can flexibly switch between osmotrophy and bacterivory depending on the environmental conditions.[154]
Manyfreshwater protists need toosmoregulate (i.e., remove excess water volume to adjust the ion concentrations) because non-saline water enters in excess byosmosis from the environment[155] and by endocytosis when feeding.[145] Osmoregulation is done through active ion transporters of the cell membrane and throughcontractile vacuoles, specializedorganelles that periodically excrete fluid high inpotassium andsodium 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.[137]
The contractile vacuoles are surrounded by thespongiome, an array of cytoplasmic vesicles or tubes that slowly collect fluid from the cytoplasm into the vacuole. The vacuoles then contract and discharge the fluid outside of the cell through a pore. The contractile mechanism varies depending on the protist: in ciliates, the spongiome is composed of irregular tubules andactin filaments wind around the pore and over the vacuole surface, together with microtubules; in most flagellates and amoebae, the spongiome is composed of both vesicles and tubules; in dinoflagellates, a flagellar rootlet branches to form a contractile sheath around the vacuole (known as pusule).[145] The location and amount also varies: unicellular flagellated algae (cryptomonads, euglenids, prasinophytes, golden algae, haptophytes, etc.) typically have a single contractile vacuole in a fixed position; naked amoebae have numerous small vesicles that fuse into one vacuole and then split again after excretion. Marine or parasitic protists (e.g., metamonads), as well as those with rigid cell walls, lack these vacuoles.[155]
Many flagellates and probably all motile algae exhibit a positivephototaxis (i.e. they swim or glide toward a source of light). For this purpose, they exhibit three kinds ofphotoreceptors or "eyespots": (1) receptors with light antennae, found in manygreen algae,dinoflagellates andcryptophytes; (2) receptors with opaque screens; and (3) complexocelloids with intracellular lenses, found in one group of predatorydinoflagellates, theWarnowiaceae. Additionally, someciliates orient themselves in relation to the Earth'sgravitational field while moving (geotaxis), and others swim in relation to the concentration of dissolvedoxygen in the water.[137]
Protists have an accentuated tendency to includeendosymbionts in their cells, and these have produced new physiological opportunities. Some associations are more permanent, such asParamecium bursaria and its endosymbiontChlorella; others more transient. Many protists contain captured chloroplasts, chloroplast-mitochondrial complexes, and even eyespots from algae. Thexenosomes arebacterial endosymbionts found in ciliates, sometimes with amethanogenic role inside anaerobic ciliates.[137]
Consensus life cycle of free-living protists, includingsexual reproduction (red arrows),asexual reproduction (green arrows),colonial stages (blue), and formation ofcysts. Each protist group has a different sexual cycle (light purple) as well as different means of exiting the colonial stage.[157]
Protists exhibit a large range oflife cycles andstrategies involving multiple stages of different morphologies which have allowed them to thrive in most environments. Nevertheless, most of the knowledge concerning protist life cycles concernsmodel organisms and important parasites. Free-living uncultivated protists represent the majority, but knowledge on their life cycles remains fragmentary.[157]
Protists typically reproduce asexually under favorable environmental conditions,[158] allowing for rapid exponential population growth with minimal genetic diversification. Thisasexual reproduction, occurs throughmitosis and has historically been regarded as the primary reproductive mode in protists.[157] This process is also known asvegetative reproduction, as it is only performed by the 'vegetative stage' or individual.[159]
Unicellular protists often multiply viabinary fission, similarly to bacteria.[157] They can also divide throughbudding, similarly toyeasts, or through multiple fissions, a process known asschizogony.[160] In multicellular protists, vegetative reproduction can take the form offragmentation of body parts, or specializedpropagules composed of numerous cells (e.g., inred algae).[159]
While asexual reproduction remains the most common strategy among protists,sexual reproduction is also a fundamental characteristic of eukaryotes.[161][162] Sexual reproduction involvesmeiosis (a specialized nuclear division enablinggenetic recombination) andsyngamy (the fusion of nuclei from two parents).[157] These processes are thought to have been present in thelast eukaryotic common ancestor,[163] which likely had the ability to reproduce sexually on a facultative (non-obligate) basis.[164] Even protists that no longer reproduce sexually still retain a core set of meiosis-related genes, reflecting their descent from sexual ancestors.[165][166] For example, althoughamoebae are traditionally considered asexual organisms, most asexual amoebae likely arose recently and independently from sexually reproducing amoeboid ancestors.[167] Even in the early 20th century, some researchers interpreted phenomena related to chromidia (chromatin granules free in thecytoplasm) in amoebae as sexual reproduction.[168]
Every sexual cycle involves the events of syngamy and meiosis, which increase or decrease theploidy (i.e., number ofchromosome sets, represented by the lettern), respectively. Syngamy implies the fusion of two haploid (1n) reproductive cells, known asgametes, which generates a diploid (2n) cell calledzygote. The diploid cell then undergoes meiosis to generate haploid cells. Depending on which cells compose the individual or vegetative stage (i.e., the stage that grows by mitosis), there are three distinguishable sexual cycles observed in free-living protists:[157]
Two ciliates join during conjugation to exchange their haploid nuclei via a cytoplasm bridge.
In thediploid cycle, the individual is diploid and undergoes meiosis to generate haploid gametes, which in turn fuse with others to form a zygote that develops into a new individual.[157] This is the case for some metamonads,heliozoans, many green algae,diatoms, andciliates, as well asanimals.[145]: 26 Instead of generating gametes, ciliates divide their diploidmicronucleus into two haploid nuclei, exchange one of them byconjugation with another ciliate, and fuse the two nuclei into a new diploid nucleus.[67]
In thehaplo-diploid cycle, there are twoalternating generations of individuals. One generation is the diploid 'agamont', which undergoes meiosis to generate haploid cells (spores) that develop into the other generation, the haploid 'gamont'. The gamont then generates gametes by mitosis, which in turn fuse to form the zygote that develops into the agamont.[157] This is the case for manyforaminifera and many algae, as well asland plants.[145]: 26 There are three modes of this cycle depending on the relative growth and lifespan of one generation compared to the other: haploid-dominant, diploid-dominant, or equally dominant generations.Brown algae exhibit the full range of these modes.[169]
Free-living protists tend to reproduce sexually under stressful conditions, such as starvation or heat shock.Oxidative stress, which leads toDNA damage, also appears to be an important factor in the induction of sex in protists.[158]
Pathogenic protists tend to have extremely complex life cycles that involve multiple forms of the organism, some of which reproduce sexually and others asexually.[170] The stages that feed and multiply inside thehost are generally known astrophozoites (from Greek trophos'nutrition' and zoia'animals'), but the names of each stage vary depending on the protist group[160] (e.g.,sporozoites andmerozoites in apicomplexans;[70][162]primary andsecondary zoospores in phytomyxeans).[171]
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 infelids such asdomestic cats).[172] Others, such asLeishmania, are capable of performing syngamy in the secondary vector.[173] In apicomplexans, sexual reproduction is obligatory for parasite transmission.[174]
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.[175]
Protists are indispensable to modernecosystems worldwide. They also have been the only eukaryotic component of all ecosystems for much ofEarth's history, which allowed them to evolve a vast functional diversity that explains their critical ecological significance. They are essential asprimary producers, as intermediates in multipletrophic levels, as key regulatingparasites orparasitoids, and as partners in diversesymbioses.[37]
Protists are abundant and diverse 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.[176] Protist diversity, as detected throughenvironmental DNA surveys, is vast in every sampled environment, but it is mostly undescribed.[177] The richest protist communities appear insoils, followed byoceanic and lastlyfreshwater habitats, mostly as part of theplankton.[178] Freshwater protist communities are characterized by a higher "beta diversity" (i.e. highly heterogeneous between samples) than soil and marine plankton. The high diversity can be a result of the hydrological dynamic of recruiting organisms from different habitats through extremefloods.[179]Soil-dwelling protist communities are ecologically the richest, possibly be due to the complex and highly dynamic distribution of water in thesediment, 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 inprokaryotes as well as protists.[178]
a)Frontonia, a ciliate from soda lakes in Kenya. b)Chlamydomonas pitschmanii, a green alga from hot spring soils. c)Tetramitus thermacidophilus, an amoeboflagellate from an acidic geothermal lake in California. d)Galdieria sulphuraria, a thermoacidophilic red alga. e)Halocafeteria seosinensis, a flagellate from a saltern in Korea.
Protists can survive a broad range of extreme conditions, including extreme temperatures (thermophiles orpsychrophiles), salinity (halophiles), andpH (alkaliphiles oracidophiles). Most of the extremophilic eukaryotes are algae, specifically chlorophytes, followed by fungi. Other extremophile-abundant groups areheterolobose amoebae, red algae, stramenopiles, and ciliates.[180]
Eukaryotic algae are well-known to withstand high temperatures; for example, the red algaCyanidioschyzon merolae persists up to 60°C, similarly to the most extreme thermophilicfungi. 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 inhydrothermal vents up to 52°C. This is still lower than prokaryotes, some of which grow above 80°C.[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 the red algaC. merolae, with an observed minimum growth of pH 0. Besides red algae, some species of green algae and amoeboflagellates are found in high-temperature, low-pH geothermal springs. Alkaliphilic protists, primarily ciliates, resist up to pH 10.48, higher than the most alkalophilic bacterium.[180]
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 thehypertonic environment. Examples include the algaDunaliella salina and the flagellateHalocafeteria seosinensis, which is able to tolerate up to 36.3% salinity, higher than the maximum reported in bacteria (35%) and fungi (30%).[180]
Microscopic phototrophic protists (ormicroalgae) are the main contributors to thebiomass andprimary production in nearly all aquatic environments, where they are collectively known asphytoplankton (together withcyanobacteria). In marine phytoplankton, 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 bydiatoms anddinoflagellates.[177] In freshwater phytoplankton,golden algae,cryptophytes and dinoflagellates are the most abundant groups.[178] Altogether, they are responsible for almost half of the global primary production.[181] They are the main providers of much of the energy and organic matter used bybacteria,archaea, and higher trophic levels (zooplankton andfish), including essential nutrients such asfatty acids.[182] Their abundance in the oceans depends mostly on the availability of inorganic nutrients, rather than temperature or sunlight; 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 theArctic Ocean and alongcontinental margins.[181] In freshwater habitats, most phototrophic protists aremixotrophic, meaning they also behave as consumers, while strict consumers (heterotrophs) are less abundant.[178] In extremely cold habitats, like snow and the arctic ocean, diatoms and green algae are the dominant phototrophs.[180]
Macroalgae (namelyred algae,green algae andbrown algae), unlike phytoplankton, generally require a fixation point, which limits their marine distribution to coastal waters, and particularly to rocky substrates. They support numerous herbivorous animals, especiallybenthic ones, as both food and refuge from predators. Some communities ofseaweeds exist adrift on the ocean surface, serving as a refuge and means of dispersal for associated organisms.[183][184]
Phagotrophic protists are the most diverse functional group in all ecosystems, primarily represented bycercozoans (dominant in freshwater and soils),radiolarians (dominant in oceans), non-photosyntheticstramenopiles (with higher abundance in soils than in oceans), andciliates.[178]
Contrary to the common division between phytoplankton and zooplankton, much of the marine plankton is composed ofmixotrophic protists, which pose a largely underestimated importance and abundance (around 12% of all marineenvironmental DNA sequences). Mixotrophs have varied presence due toseasonal abundance[186] and depending on their specific type of mixotrophy. Constitutive mixotrophs are present in almost the entire range of oceanic conditions, from eutrophic shallow habitats to oligotrophic subtropical waters but mostly dominating thephotic zone, and they account for most of the predation of bacteria. They are also responsible forharmful algal blooms. Plastidic and generalist non-constitutive mixotrophs have similar biogeographies and low abundance, mostly found in eutrophic coastal waters, with generalistciliates dominating up to half of ciliate communities in the photic zone. Lastly, endosymbiotic mixotrophs are by far the most widespread and abundant non-constitutive type, representing over 90% of all mixotroph sequences (mostlyradiolarians).[153][152]
Diagram of the soil food web, taking into account the diverse roles of protists as not just bacterivores, but also mycophages and omnivores.[147] Arrows show the flow of nutrients.
In thetrophic webs of soils, protists are the main consumers of bothbacteria andfungi, the two main pathways of nutrient flow towards higher trophic levels.[187] Amoeboflagellates like theglissomonads andcercomonads are among the most abundant soil protists: they possess both flagella and pseudopodia, a morphological variability well suited for foraging between soil particles. Testate amoebae are also acclimated to the soil environment, as their shells protect againstdesiccation.[185] As bacterial grazers, they have a significant role in the foodweb: they excretenitrogen in the form ofNH3, making it available to plants and other microbes.[187] Traditionally, protists were considered primarily bacterivorous due to biases in cultivation techniques, but many (e.g.,vampyrellids, cercomonads, gymnamoebae,testate amoebae, small flagellates) are omnivores that feed on a wide range of soil eukaryotes, including fungi and even some animals such asnematodes. Bacterivorous and mycophagous protists amount to similar biomasses.[147]
Necrophagy (the degradation of dead biomass) among microbes is mainly attributed to bacteria and fungi, but protists have a still poorly recognized role asdecomposers with specializedlyticenzymes.[188] In soils,fungus-like protists andslime molds (e.g.,oomycetes,myxomycetes,acrasids) are present abundantly asosmotrophs andsaprotrophs.[185] In marine and estuarine environments, the well-studiedthraustochytrids (part oflabyrinthulomycetes) are relevant saprotrophs that decompose various substrates, including dead plant and animal tissue. Various ciliates and testate amoebae scavenge on dead animals. Somenucleariid amoebae specifically consume the contents of dead or damaged cells, but not healthy cells. However, all these examples are only facultative necrophages that also feed on live prey. In contrast, the algivorous cercozoan familyViridiraptoridae, present in shallow bog waters, are broad-range but sophisticated necrophages that feed on a variety of exclusively dead algae, potentially fulfilling an important role in cleaning up the environment and releasing nutrients for live microbes.[188]
Parasitic protists occupy around 15–20% of all environmental DNA in marine and soil systems, but only around 5% in freshwater systems, wherechytrid fungi likely fill thatecological niche. In oceanic systems,parasitoids (i.e. those which kill their hosts, e.g.Syndiniales) are more abundant. In freshwater ecosystems, parasitoids are mainlyPerkinsea andSyndiniales (Alveolata), while true parasites (i.e. those which do not kill their hosts) in freshwater are mostlyoomycetes,Apicomplexa andIchthyosporea.[178] In soil ecosystems, true parasites are primarily animal-hostedapicomplexans and plant-hostedoomycetes andplasmodiophorids.[185] InNeotropical forest soils, apicomplexans dominate eukaryotic diversity and have an important role as parasites of small invertebrates, while oomycetes are very scarce in contrast.[189]
Some protists are significant parasites of animals (e.g.; five species of the parasitic genusPlasmodium causemalaria in humans and many others cause similar diseases in other vertebrates), land plants[190][191] (theoomycetePhytophthora infestans causeslate blight in potatoes)[192] or even of other protists.[193][194] Around 100 protist species can infect humans.[185]
In 1820, German naturalistGeorg August Goldfuss coined the term "Protozoa" (meaning 'early animals') as a class within Kingdom Animalia[198] that consisted of four groups:Infusoria (ciliates), Lithozoa (corals), Phytozoa, and Medusinae (jellyfish). Later, in 1845,Carl Theodor von Siebold used the term "Protozoa" as a phylum of exclusively unicellular animals consisting of two classes: Infusoria (ciliates) andRhizopoda (amoebae,foraminifera).[199] Other scientists did not consider all protozoans part of the animal kingdom, and by the middle of the century most biologists grouped microorganisms into Protozoa, Protophyta (primitive plants), Phytozoa (animal-like plants), andBacteria (mostly considered plants). In 1860, palaeontolgistRichard Owen was the first to define Protozoa as its own kingdom of eukaryotes, although he also includedsponges within his group.[28]
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, British naturalistJohn Hogg proposed "Protoctista" as the name for a fourth kingdom, (the other kingdoms being plant, animal and mineral) which he described as containing "all the lower creatures, or the primary organic beings", which included Protophyta, Protozoa andsponges.[200][28]
Haeckel's 1866 tree of life, with the third kingdom Protista.
In 1866, the 'father of protistology', German scientistErnst Haeckel, addressed the problem of classifying all these organisms as a mixture of animal and vegetable characters, and proposedProtistenreich[201] (Kingdom Protista) as thethird kingdom of life, comprising primitive forms that were "neither animals nor plants". He grouped both bacteria[202] and eukaryotes, both unicellular and multicellular organisms, as Protista. He retained theInfusoria in the animal kingdom, until German zoologistOtto Bütschli demonstrated that they were unicellular.[203][204] At first, he includedsponges and fungi, but in later publications he explicitly restricted Protista to predominantly unicellular organisms or colonies incapable of formingtissues. He clearly separated Protista fromtrue animals on the basis that the defining character of protists was the absence ofsexual reproduction, while the defining character of animals was theblastula stage of animal development. He also returned the termsProtozoa andProtophyta as subkingdoms of Protista.[28]
Bütschli considered the kingdom to be toopolyphyletic and rejected the inclusion of bacteria. He fragmented the kingdom intoprotozoa (only nucleated, unicellular animal-like organisms), while bacteria and theprotophyta were a separate grouping. This strengthened the old dichotomy ofprotozoa/protophyta from German scientistCarl Theodor von Siebold, and the German naturalists asserted this view over the worldwide scientific community by the turn of the century. However, British biologistC. 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 termprotistology and solidified it as a branch of study independent fromzoology andbotany.[28]
In 1938, American biologistHerbert Copeland resurrected Hogg's label, arguing that Haeckel's termProtista included anucleated microbes such as bacteria, which the termProtoctista (meaning "first established beings") did not. Under hisfour-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 definingtrue plants as those withchlorophylla andb,carotene,xanthophyll and production ofstarch. He also was the first to recognize that the unicellular/multicellular dichotomy was invalid. Still, he kept fungi within Protoctista, together withred algae,brown algae andprotozoans.[28][205] This classification was the basis for Whittaker's later definition of Fungi,Animalia,Plantae and Protista as the four kingdoms of life.[206]
In the popularfive-kingdom scheme published by American plant ecologistRobert Whittaker in 1969, Protista was defined as eukaryotic "organisms which areunicellular or unicellular-colonial and which form notissues". Just as the prokaryotic/eukaryotic division was becoming mainstream, Whittaker, after a decade from Copeland's system,[206] recognized the fundamental division of life between the prokaryotic Monera and the eukaryotic kingdoms: Animalia (ingestion), Plantae (photosynthesis), Fungi (absorption) and the remaining Protista.[207][208][28]
In the five-kingdom system of American evolutionary biologistLynn Margulis, the term "protist" was reserved formicroscopic organisms, while the more inclusive kingdom Protoctista (orprotoctists) included certain largemulticellular eukaryotes, such askelp,red algae, andslime molds.[209] Some use the termprotist 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.[210]
Advances in electron microscopy and molecular phylogenetics
Phylogenomic tree of eukaryotes, as regarded in 2020.Supergroups are in color.
The five-kingdom model remained the accepted classification until the development ofmolecular phylogenetics in the late 20th century, when it became apparent that protists are aparaphyletic group from which animals, fungi and land plants evolved, and thethree-domain system (Bacteria,Archaea,Eukarya) became prevalent.[211] Today, protists are not treated as a formaltaxon, but the term is commonly used for convenience in two ways:[13]
Functional definition: protists are essentially those eukaryotes that are nevermulticellular,[13] that either exist as independent cells, or if they occur incolonies, do not show differentiation into tissues.[215] 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).[216]
Before the existence ofland plants,animals andfungi, alleukaryotes were protists. As a result, the early fossil record of protists is equivalent to the early record of eukaryotic life.[174] The protist fossil record is mainly represented by protists with fossilizable coverings, such as foraminifera, radiolaria, testate amoebae and diatoms, as well as multicellular algae.[218]
Crown-group eukaryotes achieved significantmorphological andecological diversity before 1000 Ma, with multicellular algae capable of sexual reproduction and unicellular protists exhibiting modernphagocytosis andlocomotion. Their advanced but metabolically expensive sterols likely provided numerousevolutionary advantages due to the increased membrane flexibility, including resilience toosmotic shock during desiccation and rehydration cycles, extreme temperatures,UV light exposure, and protection againstchanging oxygen levels. These adaptations allowed crown-group eukaryotes to colonize diverse and harsh environments (e.g.,mudflats, rivers, agitated shorelines and land). In contrast, stem-group eukaryotes occupied the low-oxygen marine waters asanaerobes.[219] The oldest definitive crown-group eukaryotic fossils includeRafatazmia andRamathallus, both putative red algae, dated at 1600 Ma.[1]
Abundant fossils ofheterotrophic protists appear significantly later, parallel to the emergence offungi.[219] Vase-shaped microfossils (VSMs), widespread rocks dated at 780–720 Ma (Tonian to Cryogenian), have been described as a variety of organisms across the decades (e.g., algae,chitinozoans,tintinnids), but current scientific consensus relates most VSMs to marinetestate amoebae.[228] As such, VSMs comprise the oldest known fossils of both filose (Cercozoa) and lobose (Amoebozoa) testate amoebae.[229][230]
After theGaskiers glaciation of theLate Ediacaran (~579 Ma), fossils of heterotrophic protists undergo diversification. Some fossils similar to VSMs are interpreted as the oldest fossils ofForaminifera dated at 548 Ma (e.g.,Protolagena),[228] but their foraminiferal affinity is doubtful. Other microfossils that are possibly foraminifera include some poorly preserved tubular shells from 716–635 Ma rocks.[231]
Radiolarian shells appear abundantly in the fossil record since theCambrian, with the first definitive radiolarian fossils found at the very start of this period (~540 Ma) together with the firstsmall shelly fauna.[232] Radiolarian records from olderPrecambrian rocks have been disregarded due to the lack of reliable fossils.[233][234][235] Around this time, between 540 and 510 Ma, the oldest Foraminifera shells appear, first multi-chambered and later tubular.[236][218][231]
Following theCambrian explosion and rapid diversification of animals, the Precambrian microbe-dominated ecosystems were replaced by primarilybenthic and nekto-benthic communities, with most marine organisms (animals, foraminifers, radiolarians) limited to the depths of shallow water environments.[237] Mirroring the animalradiation, there was a radiation of phytoplanktonic protists (i.e., acritarchs)[238] around 520–510 Ma, followed by a decrease in diversity around 500 Ma.[239] Later, the surviving acritarchs expanded in diversity and morphological innovation[238] due to a decrease in predation from benthic animals (particularlytrilobites andbrachiopods), which suffered extinction due to various proposed environmental factors such asanoxia.[240] Both phytoplankton and zooplankton (e.g., radiolarians) flourished, as signaled by an increase of organic carbon buried in the sediment known as theSPICE event (~497 Ma).[237][240] This abundantbiomass supported a second animal radiation known as theGreat Ordovician Biodiversification Event (GOBE), where many animals switched to a planktonic lifestyle and pelagic predators first appeared (e.g.,cephalopods, swimmingarthropods). This event is also known as the 'Ordovician Plankton Revolution' due to the significant diversification of planktonic protists, and it spanned from the late Cambrian well into theOrdovician.[237]
The Ordovician also includes the oldesteuglenid fossil, known asMoyeria, which is found in rocks spanning from the middle Ordovician (~471 Ma) to theSilurian.[241] There are putative records of calcareous foraminifera from the Early Ordovician to the Silurian, but these are not widely accepted; the oldest trusted and well-known calcaerous foraminifera appear in the MiddleDevonian, the next geological period.[218][242]
In Early Devonian terrestrial ecosystems the first fossils of freshwater arcellinid testate amoebae are found (e.g.,Palaeoleptochlamys,Cangweulla),[243] as well as various types of freshwatergreen algae, includingcharophytes,volvocaceans anddesmids,[244] and some putative algal fossils that might representglaucophytes.[245] During the Devonian some benthic foraminifera acquired the ability of calcifying, and particularly the giantfusulinids became the dominant fossilizable protists. This time interval is also considered the molecular origin ofhaptophytes (~310 Ma) andsilicoflagellates (397–382 Ma), which did not leave fossil traces until later in theMesozoic. After theLate Devonian extinction (372 Ma),nassellarian-like radiolarians appeared for the first time, with a uniquebody plan among marine protists.[218]
During theCarboniferous period, no new fossilizable protists originated despite the major environmental changes. However, starting in the Late Carboniferous, radiolarian diversity and productivity increased, causing a large amount of biosiliceous sediment (chert) to be accumulated worldwide; this is known as the Radiolarian Optimum Event, which lasted primarily from the MiddlePermian until the EarlyCretaceous.[246][247][248] Around theCapitanian mass extinction event (262–259 Ma) of the Permian period,coccolithophores genetically diverged from the rest of haptophytes, possibly as a response to a reduction in atmospheric oxygen, and there was a faunal turnover from larger to smaller fusulinids.[218]Spumellarian radiolarians appear in the latest Permian.[246]
ThePermian-Triassic extinction event (~251.9 Ma) caused the extinction of many radiolarians, which manifests as a gap in the chert record.[246] The extinction is hypothesized as resulting in the molecular origin ofdiatoms and modern coccolithophores.[218] The Middle to LateTriassic period saw the acceleration of radiolarian diversity[246] and the appearance of several groups of calcaerous nannofossils. First, various nannofossils, some of which belonged todinocysts, appeared early at around 235 Ma. Later originated the oldest identifiable coccolithophore,Crucirhabdus minutus (205–201 Ma), as well as the oldest fossils ofPhaeodaria.[218] There's a variety of protozoa, including soft-bodiedciliates, and filamentous algae found inamber from the Late Triassic (220–230 Ma).[249]
Around the Early–MiddleJurassic, after the globalToarcian 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 betweenAcantharia radiolarians and lineages ofPhaeocystis haptophytes, as well as the appearance of planktonic foraminifera.[218] The period of low atmospheric oxygen ends in theAptian-Albian boundary during the EarlyCretaceous, and the first fossils of diatoms and silicoflagellates appear.[218] Samples ofamber from around 100 Ma contain the oldest fossil records ofapicomplexans (particularlymalarian agents andgregarines),trypanosomes,[250] andmetamonads—particularly mutualisticparabasalids ofcockroaches, representing the earliest record of mutualism between protists and animals.[251][252]
The diversification of coccolithophores, mixotrophic dinoflagellates, and later diatoms across the Mesozoic era caused an accelerated transfer of primary production into higher trophic levels. This evolutionary radiation of phytoplankton was, in turn, responsible for the animal "Mesozoic marine revolution", characterized by the appearance of widespread predation among most invertebrate phyla. Coccolithophores, dinoflagellates and especially diatoms became the dominating eukaryotic producers in oceans until today, as opposed tocyanobacteria and green algae which dominated earlier.[253]
TheCretaceous-Paleogene extinction event (~66 Ma) caused the extinction of many marine dinoflagellates, foraminifers, coccolithophores, and silicoflagellates; mesozoic types of these groups were substituted with types that dominate marine habitats today. Right after this event, putativeebridians begin appearing in the fossil record (e.g.,Ammodochium), but the oldest reliable ebridian fossils belong to the upper middleEocene (42–33.7 Ma).[218] Around this time, the oldest fossils ofSynurophyceae appear (~49–40 Ma).[254] Following theMiddle 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 andcollodarians.[218]
^abThe distinction between protists and the other three eukaryotic kingdoms has been difficult to settle. Historically, theheterotrophic protists, known asprotozoa, were considered part of theanimal kingdom, while thephototrophic ones, calledalgae, were studied as part of theplant kingdom. Even after the creation of a separate protist kingdom, some minuscule animals (themyxozoans)[6] and 'lower'fungi (namely theaphelids,rozellids andmicrosporidians, collectively known asOpisthosporidia) were studied as protists,[7][8][9] and some algae (particularlyred andgreen algae) remained classified as plants.[10] According to the current consensus, the label 'protist' specifically excludes animals,embryophytes (land plants) —meaning that all algae fall under this label— and all fungi. Opisthosporidians are considered part of a larger fungal kingdom, although they are often studied byprotistologists andmycologists alike.[2][11][12]
^The terms 'cilium' and 'eukaryotic flagellum' are interchangeable from a biological perspective. However, their usage depends on the author: some prefer to reserve cilia for shorter appendages and flagella for longer ones, while others prefer cilia for eukaryotes and flagella for prokaryotes. The term 'undulipodium' was proposed to unify the two concepts, as it refers specifically to thehomologousmicrotubular structure found in both, but not found inprokaryotic flagella.[24][25][26]
^A 2007 report on protist diversity included a table listing the described number of species for protist and fungal groups. The total sum of the listed species, excluding fungi, is 76,144.[36]
^abThe phylum Percolozoa is usually better known as Heterolobosea.[2][46] However, in the strictest sense, Heterolobosea refers only to a class within this phylum, containing the ordersAcrasida andSchizopyrenida. The name Percolozoa encompasses these and other related single-celled protists, not just the 'true' heteroloboseans.[9]
^The terms "mixotroph" and "mixoplankton" almost exclusively refer to protists that perform photosynthesis and phagocytosis (photo-phagotrophs). Osmotrophy is always present, but not taken into account. As such, "pure" phototrophs (incapable of phagocytosis) and "pure" phagotrophs (incapable of photosynthesis) are technically mixotrophic due to their innate ability for osmotrophy, but are not usually reported in this sense.[151]
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