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A protist ( ) or protoctist is any Eukaryote organism that is not an animal, Embryophyte, or fungus. Protists do not form a Clade, or clade, but are a Paraphyly group encompassing the entire eukaryote tree of life, from which land plants, animals, and fungi evolved. They are primarily single-celled, exhibiting a wide range of forms such as amoebae, ciliates, thick-walled microalgae and, more commonly, flagellates. Several transitions to multicellularity have occurred among protists, from colonies with alternating cell types to giant slime molds, fungus-like organisms, and seaweeds with differentiated tissues.
Protists were historically regarded as a separate taxonomic rank kingdom known as Protista or Protoctista, or were lumped as part of the traditional plant and animal kingdoms as algae and protozoa, respectively. With the advent of molecular phylogenetics and electron microscopy studies, some protists were shown to be more closely related to animals or plants than to other protists, and algae were found to be intermixed with protozoa. The classification suffered major revisions, as seemingly unrelated forms were found to be evolutionarily related, and viceversa.
In modern classifications, protists are spread across several large clades known as supergroups, many of them containing disparate forms. For example, the Archaeplastida includes mostly phototrophs like Red algae and green algae, from which land plants evolved. Opisthokonta groups fungi, animals, and their single-celled relatives. Amoebozoa and Rhizaria harbor the majority of amoeboid organisms, such as testate amoebae, foraminifers and radiolarians. Stramenopiles and Alveolata are diverse groups of flagellates, many of which have evolved into major parasites (e.g., oomycetes, apicomplexans) or phototrophs (diatoms, brown algae, dinoflagellates). The earliest diverging groups, collectively known as Excavata (e.g., euglenids, metamonads), are flagellates that represent the ancestral traits of the last eukaryotic common ancestor (LECA). Despite the comparatively low number of described species, protists compose the majority of eukaryotic diversity as indicated by environmental DNA studies. Most protists are yet undescribed.
Protists encompass almost all of the seen in eukaryotes, and many exhibit unique adaptations. These include a range of nutritional modes through specialized feeding structures (phagotrophy, osmotrophy, myzocytosis) or chloroplasts (phototrophy), often mixing both as mixotrophy. Cellular respiration also varies due to modifications of their mitochondria. Almost all protists have a complex cytoskeleton composed of relatively Plesiomorphic structures across evolution, namely a flagellar apparatus with basal bodies from which microtubules emerge and support the remaining cellular structures. Many protists have unique organelles that serve other functions, such as contractile vacuoles for homeostasis, or eyespots for light perception. Protist cells tend to host symbionts such as bacteria and archaea, usually to support their metabolism and nutrition. Although traditionally presumed to be asexual, protists are capable of sexual reproduction, and can exhibit diverse and complex life cycles with different generations and life stages.
Protists are abundantly present in all , including extreme habitats, as important components of the biogeochemical cycles and . As producers, they are responsible for a large portion of global primary production and carbon fixation. As consumers and decomposers, they regulate fungal and bacterial populations, and release nutrients to other trophic levels. Some form mutualistic relationships with other protists or animals such as corals and termites. Others are important parasites. Pathogenic protists cause many well-known human and animal diseases such as malaria and toxoplasmosis, or significant plant diseases like clubroot and potato blight. Free-living protists can also negatively impact aquatic life as harmful algal blooms.
The early evolution of protists corresponds with the evolution of eukaryotes, which split from archaea around 3 billion years ago and eventually gave rise to a common ancestor (LECA) with essential traits such as mitochondria and a complex endomembrane system, some time during the Paleoproterozoic or Mesoproterozoic eras. In the gap between these two events, fossils are often interpreted as Crown group eukaryotes, with intermediate traits. Following the appearance of LECA, its descendants (crown-group eukaryotes) experienced a rapid diversification in the span of 300 million years that originated the modern supergroups. Still, their abundance in the fossil record remained low until the Neoproterozoic, when the first fossils of opisthokonts, amoebae, and multicellular algae appear. Throughout the Phanerozoic, protists evolved into the forms that dominate ecosystems today, leaving an extensive fossil record of primarily siliceous and calcareous shells.
The distinction between protists and other kingdoms was blurry before genetic analysis. Organisms that are unquestionably known as protists include a wide range of photosynthetic species, known as "algae", including various types of macroalgae that have a similar complexity to plants. Other protists have a fungus-like nutrition or appearance, such as the oomycetes. The remaining Heterotroph protists are often called "protozoa". Some minuscule animals (the Myxozoa) and the "lower" fungi (namely the Aphelida, Rozellida and Microsporidia, collectively the Opisthosporidia) were traditionally classified as protists, and some algae (particularly Red algae and green algae) were lumped with plants.
According to the current consensus, the label 'protist' specifically excludes animals, Embryophyte (land plants) —meaning that all eukaryotic algae fall under this label— and all fungi. Opisthosporidians are considered part of a larger fungal kingdom, although they are studied by Protistologist and Mycologist alike.
Other single-celled algae exist in forms beyond the motile flagellates. Some are non-motile and encased in hard cell walls (coccoid, like ) or embedded in a mucilage matrix (capsalean, like ); others are amoeboid, like the reticulose chlorarachniophytes. (2026). 9780986393549, LJLM Press. ISBN 9780986393549
Multicellularity has evolved numerous times to various degrees among protists, resulting in organisms built either by cells aggregating together (aggregative) or by cells dividing without separating (clonal). For example:
Other multicellular protists include amoebae that fuse into large networks, and colonial heliozoa and ciliates with new features not seen in solitary cells. The ciliate Haplozoon is interpreted to have animal-like embryonic development and cell type differentiation. Choanoflagellates, the closest living relatives of animals, include alternating cell types that are interpreted as early stages of animal multicellularity.
During the 19th century, after several waves of naturalist studies, it became clear that these microorganisms were distinct from animals and plants. John Hogg and Ernst Haeckel proposed a separate kingdom of life, named Protoctista or Protista, From p. 215: "VII. Character des Protistenreiches." (VII. Character of the kingdom of Protists.) respectively, to accommodate the predominantly unicellular eukaryotes, and initially bacteria, which were later excluded. The classical framework of protist classification was established, as exemplified by the works of Otto Bütschli, where they were grouped according to morphological and locomotive features, such as Mastigophora (flagellates), Rhizopoda (amoebae), Sporozoa (spore-forming parasites), and Infusoria (ciliates). However, Bütschli retained a division between the Protozoa (animal-like protists) and Protophyta (plant-like). This dogma remained dominant throughout the early 20th century.
From the mid-20th century, eukaryotes were firmly split from bacteria (prokaryotes) due to the presence of the cell nucleus, and protists (or protoctists) were more popularly accepted as a separate kingdom of eukaryotes. (2026). 9780123736215, AP. ISBN 9780123736215 The advent of electron microscopy shifted the methods of classification, as it revealed previously unrecognized cellular characteristics (i.e., ultrastructure, particularly of the flagellar apparatus and the cytoskeleton) that suggested evolutionary affinities between superficially disparate lineages. For example, the tripartite flagellar were used to group ochrophyte, and into the Stramenopiles; the discovery of cortical alveoli showed affinities between and , which now belong to the Alveolata; and disc-shaped mitochondrial cristae were shared by and , now united as Euglenozoa. The algae-protozoa dichotomy became obsolete.
Since the 1990s, molecular phylogenetic analyses based primarily on the SSU rRNA gene demonstrated that protists were a paraphyletic assemblage of clades spanning the entire eukaryotic tree of life, from which the other three "kingdoms" (animals, plants, and fungi) had evolved. Beginning in the 2000s, single-cell sequencing and phylogenomics technologies progressively improved the resolution of deeper evolutionary relationships. Altogether, these innovations led to successive revisions of protist classification, such as the ones published by the International Society of Protistologists. Eukaryotes could no longer be divided into four monophyletic kingdoms, and instead are arranged in "supergroups", each often encompassing an unexpected variety of morphologies and lifestyles that do not resemble one another. New deep-branching groups are added to the tree at a rate of nearly one per year.
The following table lists estimated numbers of described extant species for all known protist supergroups, and provides an overview of their diversity in terms of morphologies, habitats, and nutritional modes. For large groups, the overview is not exhaustive and only mentions the most characteristic members.
| Diaphoretickes | SAR supergroup | Stramenopiles | Ancestrally flagellates distinguished by two 'heterokont' (unequal) flagella, one with tripartite mastigonemes. Present in virtually all habitats. The most species-rich lineage, the Ochrophyte, are algae of diverse morphologies, ranging from flagellates (like golden algae) to walled ornamented cells (like diatoms, pictured) to truly multicellular macroalgae with differentiated tissues (brown algae such as kelp). All other lineages are composed of heterotrophs: bacterivorous flagellates (e.g., Bicosoecid, Bigyromonad), fungus-like osmotrophs (oomycetes, hyphochytrids, and labyrinthulomycetes), heliozoan amoebae (Actinophryid), and ciliate-like obligate symbionts of animals (Opalinata). | (2009). 9780123739445 ISBN 9780123739445 | |
| Alveolata | Ancestrally flagellated predators with cortical alveoli. The represent these ancestral characteristics. The most diverse group are the ciliates ( pictured), with large cells covered in rows of cilia, usually at the top of the microbial food chain. The remaining alveolates belong to the clade Myzozoa and are ancestrally photosynthetic; some have retained their photosynthetic ability (Chrompodellid and many dinoflagellates), while others have evolved into parasites of animals and algae (apicomplexans, Perkinsea, and some dinoflagellates). | ||||
| Rhizaria | Amoebae with filose or reticulose pseudopodia. The most species-rich group is Retaria, home to conspicuous marine amoebae encased in hard skeletons (radiolarians) or multichambered tests (foraminifers, pictured). Secondly is Cercozoa, with an extreme diversity of morphologies: small flagellates, amoeboflagellates, aggregative slime molds, testate amoebae, heliozoa, and massive radiolarian-like cells (Phaeodarea); some are capable of photosynthesis (e.g., chlorarachniophytes). Lastly, Endomyxa contains both free-living predatory amoebae (e.g., Vampyrellid) and obligate parasites of animals, plants, and algae (e.g., Phytomyxea and Ascetosporea). | ||||
| Telonemia | Free-living flagellates with a unique cytoskeleton and a combination of cell structures. Present in all marine and freshwater environments feeding on bacteria. | ||||
| Haptista | Two groups of different free-living single-celled protists: centrohelids—predatory heliozoan amoebae, widespread in aquatic and soil environments—and —coccoid or flagellated photosynthetic algae, mostly marine (e.g., Coccolithophore, pictured). Both can produce an outer coat of complex mineralized scales. | ||||
| Pancryptista | Free-living flagellates, except one species of heliozoan amoebae, Microheliella maris. Almost all of the flagellates are distinguished by specialized ribbon-shaped extrusomes known as ejectisomes. Many are photosynthetic, known as Cryptomonad ( pictured), while the rest are phagotrophs, consumers of bacteria. Present in aquatic environments worldwide. | ||||
| Archaeplastida* | Algae with chloroplasts derived from primary endosymbiosis with a cyanobacterium. Found in all environments. Almost entirely photosynthetic, with the exception of two small groups of phagotrophic flagellates, Rhodelphidia and Picozoa. The two major groups, red algae and green algae ( pictured), exhibit diverse morphologies, ranging from single cells—coccoid, palmelloid, sarcinoid, flagellated—to colonies, simple filaments, and macroscopic thalli with varying degrees of complexity (e.g., coralline algae, sea lettuce, stoneworts). Also included are Glaucophyte, rare blue-green algae found in surface waters. | * | |||
| Disparia | Three lineages of free-living predatory flagellates with unique cytoskeletons. These are: Hemimastigophora, with two rows of flagella, present in soils and aquatic sediments; Provora, fast-swimming predators of other protists through a strong feeding apparatus resembling jaws, found in low abundance in marine environments globally; and Caelestes ( pictured), rare inhabitants of the marine benthos whose cells protrude arms or stalks used for movement or prey capture. | ||||
| Amorphea | Amoebozoa | Amoebae of diverse morphologies, with lobose or filose pseudopodia, and sometimes with flagella. Most are free-living phagotrophs found across terrestrial and aquatic environments, such as the archetypal genus Amoeba itself, or the testate amoebae Arcellinida, one of the most conspicuous groups of protists. Numerous groups have independently evolved fungus-like fruiting bodies, such as myxogastrid ( pictured). Some of the free-living amoebae are important vectors of pathogenic bacteria or are pathogenic themselves (e.g., Acanthamoeba). Others are anaerobic intestinal symbionts (e.g., Entamoeba). | |||
| Breviatea | Anaerobic free-living amoeboflagellates with fine pseudopodia and modified mitochondria. Present only in low-oxygen marine and brackish sediments, their growth depends on mutualistic interactions with prokaryotes. | ||||
| Apusomonadida | Free-living flagellates distinguished by a proboscis, a sleeve-like structure that envelops one of their two flagella. Found gliding on wet soil and aquatic sediments worldwide. | ||||
| Opisthokonta** | Flagellates distinguished by a single posterior flagellum, many with complex life cycles and varying degrees of multicellularity. Some are entirely amoeboid, with fine pseudopodia (e.g., Filasterea and nucleariids, including slime molds), while others become amoeboid temporarily (e.g., choanoflagellates, pictured). Most species are free-living filter-feeders or predators, (2026). 9783319281476, Springer. ISBN 9783319281476 but some lineages (e.g., Ichthyosporea) evolved into osmotrophic parasites of animals. | ** | |||
| Excavata | Discoba | Flagellates with very different lifestyles, present in aquatic and terrestrial environments, ranging from aerobes to anaerobes. The most diverse group, Euglenozoa, includes free-living osmotrophs, phagotrophs, phototrophs (Euglenophyceae, pictured), and pathogens (kinetoplastids). The less diverse Heterolobosea are primarily amoeboflagellates, and include some slime molds (Acrasid) and well-known opportunistic parasites (e.g., Naegleria fowleri). (2026). 9783319281476, Springer. ISBN 9783319281476 The smallest group, Jakobida, consume bacteria by suspension feeding. (2026). 9783319281476, Springer. ISBN 9783319281476 | |||
| Metamonada | Anaerobic or microaerophilic flagellates, amoebae, or amoeboflagellates, with reduced or completely lost mitochondria. A few are free-living, found in aquatic hypoxic sediments, but most species are obligate parasites (e.g., Giardia, pictured) or commensals in animal intestines (e.g., Parabasalid). Many have a high number of flagella. | ||||
| Malawimonadida | Free-living bacterivorous flagellates that feed by suspension feeding, present in marine or fresh waters. | ||||
| Other | Ancyromonadida | Tiny free-living aquatic flagellates composed of flattened cells with an inflexible pellicle and a lateral rostrum with extrusomes. Found in most aquatic habitats. | |||
| CRuMs | Free-living flagellates and filose amoebae with a pellicle underneath the cell membrane. Almost all flagellated members can produce filose pseudopodia. Found in aquatic environments. | ||||
| *Excluding plants. **Excluding animals and fungi. | |||||
There are also many protists of uncertain position because their DNA has not been DNA sequencing, and consequently their phylogenetic affinities are unknown.
Different predatory protists have sophisticated structures for capturing prey, such as the ventral groove of Excavata, the hood-like extension or 'pallium' of some dinoflagellates, or the expandable oral pocket of ciliates. Many euglenids have a system of rods and vanes that grab and pull in prey cells, similarly to a Chinese finger trap.
Preys of phagotrophic protists range from prokaryotes (i.e., bacterivores) to other eukaryotes, including single-celled protists, algae, fungi, nematodes, or tissues of larger animals. Prey specificity varies, with some groups specialized in eating only one type of organisms, or only a particular strain. Traditionally, protists were considered primarily bacterivorous due to biases in cultivation techniques, but most are omnivores.
Among exclusively heterotrophic protists, variation of nutritional modes is also observed. The , which inhabit deep waters where photosynthesis is absent, can flexibly switch between osmotrophy and bacterivory depending on the environmental conditions.
Certain protists have acidic organelles known as Acidocalcisome, which store high concentrations of phosphorus, calcium, and enzymes related to their metabolism. Among their proposed functions are osmoregulation and maintenance of pH and calcium homeostasis.
Mitochondrial cristae, foldings of the inner membrane, have been used to classify protists since the advent of electron microscopy. Flat cristae are the ancestral trait, tubular cristae are present in the SAR supergroup and Amoebozoa, and discoid cristae distinguish the Discoba.
The interior of the flagellum, the axoneme, consists of a common structure of nine pairs of microtubules surrounding two central microtubules, known as the 9+2 structure. At its base is a basal body or kinetosome, a complex proteic structure that forms the centrioles and behaves as the microtubule organizing center. Microtubules emerge from each basal body in the form of one or two 'roots'. The basic plan of the flagellar apparatus consists of two basal bodies (B1 and B2), one for each flagellum, followed by four primary microtubular 'roots' (named R1 through R4) and a 'singlet root' (SR) formed by a single microtubule and originating from B1. Attached to the R1 is a multilayered structure, also known as C fiber.
Each protist group has modifications or secondary losses of this standard organization. In groups where the standard structure is mostly untouched (e.g., Excavata, stramenopiles, and ), the R1, R2 and SR roots provide reinforcement for the ventral feeding groove, and the R3 supports the dorsal side of the cell. In , one flagellum and all the microtubular roots were lost, but both basal bodies remain. In , the SR and R2 supporting the feeding groove were lost, likely due to their shift to autotrophic nutrition. In certain protists the flagellar apparatus is physically linked to the cell nucleus, forming what is known as the karyomastigont. This connection is often done through different kinds of filamentous structures, variously called Rhizoplast or internal flagellar roots.
Several groups of protists host non-photosynthetic prokaryotes, often maintaining an anaerobic lifestyle through the metabolism of their symbionts. are bacterial endosymbionts with a methanogenic role, found in anaerobic ciliates. Symbiontid and select ciliates have sulfur-oxidizing bacteria living as on their surfaces. Similarly, breviatea have hydrogen-oxidizing epibiotic bacteria. Metamonads, particularly and found in the hindgut of termites, typically host methanogenic archaea as epi- or endobionts.
Some rare associations involve prokaryotes that defend the protist host against potential predators, namely in symbiontids and in the ciliate Euplotidium, where the epibionts are verrucomicrobia that eject genetic material as a defense mechanism. There are also some species of oxymonads whose epibionts function as chemosensors, providing their host with information on the surrounding chemical gradient.
Besides algae, occurrence of mutualistic eukaryotic symbionts is rare among protists. In the genus Neoparamoeba, some species have endosymbionts that resemble Perkinsela, a species of trypanosomatids. Although no benefits are yet known from this association, their coevolution, suggesting that the symbionts are inherited.
Several protists Synchronization their life cycles (namely the formation or release of gametes) according to environmental factors such as nutrient or light levels, resulting in synchronization with the day-night cycle, the lunar cycle, or the seasons. The malaria agent Plasmodium falciparum synchronizes its life cycle with the host's levels of melatonin.
Some pathogenic protists undergo asexual reproduction in a wide variety of organisms – which act as secondary or intermediate hosts – but can undergo sexual reproduction only in the primary or definitive host (e.g., Toxoplasma gondii in such as ). (2026). 9780123964816, Academic Press. ISBN 9780123964816 Others, such as Leishmania, are capable of performing syngamy in the secondary vector. In apicomplexans, sexual reproduction is obligatory for parasite transmission.
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.
Soil-dwelling protist communities are ecologically the richest, possibly due to the complex and highly dynamic distribution of water in the sediment, which creates extremely heterogenous environmental conditions. The constantly changing environment promotes the activity of only one part of the community at a time, while the rest remains inactive; this phenomenon promotes high microbial diversity in prokaryotes as well as protists. Cercozoan amoeboflagellates like the and are among the most abundant soil protists, their morphological variability well suited for foraging between soil particles. Testate amoebae are also acclimated to the soil environment, as their shells protect against desiccation. Most soil algae are stramenopiles and green algae. Fungus-like protists and (e.g., , , ) are present abundantly as . The major parasites in land are the animal-associated apicomplexans and the plant-associated oomycetes and plasmodiophorids.
Marine protists are present in almost the entire range of oceanic conditions, mostly dominating the photic zone. Their abundance depends mostly on the availability of inorganic nutrients, rather than temperature or sunlight, and may vary seasonally. They are most abundant in coastal waters that receive nutrient-rich run-off from land, and areas where nutrient-rich deep ocean water reaches the surface, namely the upwelling zones in the Arctic Ocean and along continental margins. are widespread as the most dominant marine consumers. Macroalgae (namely red algae, green algae and brown algae), unlike plankton, generally require a fixation point, which limits their marine distribution to coastal waters, and particularly to rocky substrates. Some communities of exist adrift on the ocean surface, serving as a refuge and means of dispersal for associated organisms. Parasitoids such as Syndiniales are abundant pathogens in oceans.
Freshwater protist communities are characterized by a higher beta diversity (highly heterogeneous between samples) than soil and marine plankton. The high diversity can be a result of the hydrological dynamic of recruiting organisms from different habitats through extreme . In freshwater phytoplankton, golden algae, cryptomonad and dinoflagellates are the most abundant groups.
Eukaryotic algae are well-known to withstand high temperatures; for example, the red alga Cyanidioschyzon merolae persists up to 60°C, similarly to the most extreme thermophilic fungi. Lesser-known thermophilic amoebae and amoeboflagellates (e.g., Echinamoeba thermarum) are repeatedly found in hot environments, including artificially heated systems. While less successful than algae or amoebae, ciliates have also been found in hydrothermal vents up to 52°C. This is still lower than prokaryotes, some of which grow above 80°C. In extremely cold habitats, like snow and the Arctic Ocean, diatoms and green algae are the dominant phototrophs.
In terms of pH and salinity, protists can withstand similar extremes relative to prokaryotes and fungi, and also persist in polyextreme environments (polyextremophiles). The record for acidophily is also C. merolae, with an observed minimum growth of pH 0. Besides red algae, some species of green algae and amoeboflagellates are found in high-temperature, low-pH geothermal springs. Alkaliphilic protists, primarily represented by ciliates, resist up to pH 10.48, higher than the most alkalophilic bacterium.
Protists are remarkably successful in extreme salinity due to their salt-out strategy, which consists of accumulating organic solutes in the cell instead of ions to counterbalance the hypertonic environment. Examples include the alga Dunaliella salina and the flagellate Halocafeteria seosinensis, which is able to tolerate up to 36.3% salinity, higher than the maximum reported in bacteria (35%) and fungi (30%).
As part of the plant-associated microbiomes (rhizosphere near the roots, phyllosphere on the leaves), predatory protists such as cercomonads regulate the populations of bacteria and fungi, indirectly improving plant health and growth. They can also have a more direct impact by releasing proteins with antimicrobial activity.
Parasitic protists are among the most well-known Human pathogen, causing diseases such as malaria, toxoplasmosis, amoebic meningoencephalitis, sleeping sickness, leishmaniasis, and several diarrheal illnesses like amoebiasis, cryptosporidiosis, and giardiasis. Several amoebae are amphizoic, normally free-living but capable of infection.
While parasitic protists are largely studied as protozoa, some are algae, such as the green alga Cephaleuros virescens which infects plant leaves. Hundreds of red algae species parasitize on other red algae, usually closely related species.
Certain non-parasitic protists can still be toxic to aquatic animals during periods of excessive growth, either by the release of potent toxins, the depletion of oxygen in the water, or mechanical damage to gills from piercing structures (like the skeletons of ).Nicola Haigh (2026). 9788799082773, International Society for the Study of Harmful Algae. . ISBN 9788799082773 These phenomena are known as harmful algal blooms, sometimes causing water discoloration (). The most common agents are diatoms and dinoflagellates. When toxins are involved, they can reach human consumption, leading to fish or shellfish poisoning like ciguatera.
Heterotrophic protists are prevalent members of the gut microbiome of animals, although research has focused almost exclusively on gut bacteria. The giant metamonad flagellates found in the hindgut of and allow them to digest wood. This is an obligate mutualism, as termites will starve if cleaned of these protists. However most gut protists are , such as the ciliates abundantly present in the rumen of , or the ciliate-like that inhabit amphibian and reptile guts.
, common to modern eukaryotic membranes (e.g., cholesterol), appear comparatively late in the fossil record in comparison to the molecular dating of LECA, suggesting that crown-group eukaryotes flourished relatively late. Instead, stem eukaryotes may have produced simpler protosterols that require less oxygen during biosynthesis. The advanced sterols of modern eukaryotes, although metabolically expensive, likely provided numerous advantages through increased membrane flexibility, such as resilience to osmotic shock during dessication-rehydration cycles, extreme temperatures, oxidative damage, and UV light exposure, allowing them to colonize diverse and harsh environments (e.g., , rivers, agitated shorelines and land). In contrast, stem eukaryotes remained in low-oxygen marine waters, although at higher abundances.
Following LECA, a series of ecological and evolutionary innovations took place in the span of 300 million years, between the Paleoproterozoic and Mesoproterozoic, resulting in a rapid radiation that originated all major eukaryotic supergroups. These events can be outlined in four broad stages. Firstly, the direct descendants of LECA, excavate-like flagellates feeding on bacteria by altering water currents, diversify and give rise to the most basal groups such as the anaerobic metamonads and the aerobic jakobids. Secondly, surface-associated protists emerge with the development of gliding motility and the cell plasticity to form thin pseudopodia, resulting in lineages such as ancyromonads, apusomonads and CRuMs (i.e., the Podiata), which pick bacteria directly off of surfaces. The third stage involves the lineage Diaphoretickes, in which agile swimming motility was prioritized and several adaptations led to an active predatory lifestyle (e.g., Provora, Telonemia) hunting both bacteria and, for the first time, other eukaryotes. In response, some prey might have developed stronger pellicles, as seen in rigifilids and apusomonads. Lastly, the fourth stage saw the appearance of both "super-predators" capable of hunting other eukaryovores (as in the SAR supergroup lineages), and more specialized bacterivores with amoeboid movement (as in amoebozoans and opisthokonts), resulting in a "mature" biosphere. Early amoebozoans of the Mesoproterozoic adapted to grazing on microbial mats, the dominant food source at the time, resulting in multiple losses of flagella and large amoeboid bodies.
Below is a consensus phylogenetic tree of eukaryotes, including all major supergroups that originated from this time period. The position of the root is still debated, hence the polytomy. Excavate groups are marked *.
As oxygen levels rose, crown eukaryotes may have outcompeted stem eukaryotes, expanding into oxygen-rich marine environments that supported an aerobic metabolism enabled by their mitochondria. Stem eukaryotes may have gone extinct due to competition and the extreme climatic changes of the Cryogenian glaciations (720–635 Mya) and subsequent global warming, cementing the dominance of crown eukaryotes which began to appear abundantly in this era, fueled by the proliferation of algae. After the Gaskiers glaciation of the Ediacaran (ca. 579 Mya), fossils of heterotrophic protists diversify further. Some fossils at 548 Mya, similar to vase-shaped microfossils, are interpreted as the oldest traces of foraminifers (e.g., Protolagena), but their foraminiferal affinity is doubtful.
In the Devonian period, the first fossils of freshwater arcellinid testate amoebae are found (e.g., Palaeoleptochlamys, Cangweulla), as well as various types of freshwater green algae, including , volvocaceae and , and some fossils that might represent . Some benthic foraminifera acquired the ability of calcifying, (2026). 9784431551300, Springer Japan. ISBN 9784431551300 and particularly the giant Fusulinida became the dominant fossilizable protists. This period also includes the molecular origin of (~310 Mya) and (397–382 Mya), which did not leave fossil traces until later in the Mesozoic. After the Late Devonian extinction (372 Mya), -like radiolarians appeared for the first time, with a unique body plan among marine protists.
During the Carboniferous period, no new fossilizable protists originated despite the major environmental changes. However, radiolarian diversity and productivity increased, causing the accumulation of large amounts of biosiliceous sediment (chert) worldwide until the Early Cretaceous. (2026). 9780478099195, GNS Science. ISBN 9780478099195 Around the Capitanian mass extinction event (262–259 Mya) of the Permian period, 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. radiolarians appear in the latest Permian.
The Permian-Triassic extinction event (~251.9 Mya) caused the extinction of many radiolarians, which manifests as a gap in the chert record. The Triassic period saw the acceleration of radiolarian diversity and the appearance of several groups of calcaerous nannofossils, including dinocysts, the oldest identifiable coccolithophore Crucirhabdus minutus, and the oldest fossils of Phaeodaria. There's a variety of protozoa, including soft-bodied , and filamentous algae found in amber from the Late Triassic (220–230 Ma).
Around the Early–Middle Jurassic, after the global Toarcian Oceanic Anoxic Event there was a diversification of dinoflagellates and coccolithophores, in both species and abundance. This interval also saw the completion of a symbiosis between Acantharia radiolarians and lineages of Phaeocystis haptophytes, as well as the appearance of planktonic foraminifera. The period of low atmospheric oxygen ends in the Aptian-Albian boundary during the Early Cretaceous, and the first fossils of diatoms and silicoflagellates appear. Samples of amber from around 100 Ma contain the oldest fossil records of (particularly agents and ), Trypanosomatida, and —particularly mutualistic of cockroaches, representing the earliest record of mutualism between protists and animals.
Across the Mesozoic era, coccolithophores, dinoflagellates and later diatoms became the dominating eukaryotic producers in oceans until today, as opposed to cyanobacteria and green algae which dominated earlier. Their diversification caused an accelerated transfer of primary production into higher trophic levels, which in turn caused the animal "Mesozoic marine revolution", characterized by the appearance of widespread predation among most invertebrate phyla.
The Cenozoic era began with another extinction event (~66 Ma) that caused the replacement of mesozoic forms of dinoflagellates, foraminifers, coccolithophores, and silicoflagellates with forms that dominate marine habitats today. Right after this event, putative ebriid begin appearing in the fossil record (e.g., Ammodochium), but the oldest reliable ebridian fossils belong to the upper middle Eocene (42–33.7 Ma). Around this time, the oldest fossils of appear (~49–40 Ma). Following the Middle Eocene Climatic Optimum (~40 Ma), diatoms became the dominant agents of marine silicon precipitation as opposed to radiolarians, and the fossil record shows the first raphid diatoms and .
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