A protist or protoctist is any eukaryotic organism that is not an animal, land plant, or fungus. Protists do not form a natural group, or clade, but are a polyphyletic grouping of several independent clades that evolved from the last eukaryotic common ancestor.
Protists were historically regarded as a separate taxonomic kingdom known as Protista or Protoctista. With the advent of phylogenetic analysis and electron microscopy studies, the use of Protista as a formal taxon was gradually abandoned. In modern classifications, protists are spread across several eukaryotic clades called supergroups, such as Archaeplastida (photoautotrophs that includes land plants), SAR, Obazoa (which includes fungi and animals), Amoebozoa and Excavata.
Protists represent an extremely large genetic and ecological diversity in all environments, including extreme habitats. Their diversity, larger than for all other eukaryotes, has only been discovered in recent decades through the study of environmental DNA and is still in the process of being fully described. They are present in all ecosystems as important components of the biogeochemical cycles and trophic webs. They exist abundantly and ubiquitously in a variety of forms that evolved multiple times independently, such as free-living algae, amoebae and slime moulds, or as important parasites. Together, they compose an amount of biomass that doubles that of animals. They exhibit varied types of nutrition (such as phototrophy, phagotrophy or osmotrophy), sometimes combining them (in mixotrophy). They present unique adaptations not present in multicellular animals, fungi or land plants. The study of protists is termed protistology.
There is not a single accepted definition of what protists are. As a paraphyletic assemblage of diverse biological groups, they have historically been regarded as a catch-all taxon that includes any eukaryotic organism (i.e., living beings whose cells possess a nucleus) that is not an animal, a land plant or a dikaryon fungus. Because of this definition by exclusion, protists encompass almost all of the broad spectrum of biological characteristics expected in eukaryotes.
They are generally unicellular, microscopic eukaryotes. Some species can be purely phototrophic (generally called algae), or purely heterotrophic (traditionally called protozoa), but there is a wide range of mixotrophic protists which exhibit both phagotrophy and phototrophy together. They have different life cycles, trophic levels, modes of locomotion, and cellular structures.[1] [2] Some protists can be pathogens.
Examples of basic protist forms that do not represent evolutionary cohesive lineages include:
The names of some protists (called ambiregnal protists), because of their mixture of traits similar to both animals and plants or fungi (e.g. slime molds and flagellated algae like euglenids), have been published under either or both of the ICN and the ICZN codes.
The evolutionary relationships of protists have been explained through molecular phylogenetics, the sequencing of entire genomes and transcriptomes, and electron microscopy studies of the flagellar apparatus and cytoskeleton. New major lineages of protists and novel biodiversity continue to be discovered, resulting in dramatic changes to the eukaryotic tree of life. The newest classification systems of eukaryotes, revised in 2019, do not recognize the formal taxonomic ranks (kingdom, phylum, class, order...) and instead only recognize clades of related organisms, making the classification more stable in the long term and easier to update. In this new cladistic scheme, the protists are divided into various wide branches informally named supergroups:
Many smaller lineages do not belong to any of these supergroups, and are usually poorly known groups with limited data, often referred to as 'orphan groups'. Some, such as the CRuMs clade, Malawimonadida and Ancyromonadida, appear to be related to Amorphea. Others, like Hemimastigophora (10 species) and Provora (7 species), appear to be related to or within Diaphoretickes, a clade that unites SAR, Archaeplastida, Haptista and Cryptista.
Although the root of the tree is still unresolved, one possible topology of the eukaryotic tree of life is:
From the start of the 18th century, the popular term "infusion animals" (later infusoria) referred to protists, bacteria and small invertebrate animals. In the mid-18th century, while Swedish scientist Carl von Linnaeus largely ignored the protists, his Danish contemporary Otto Friedrich Müller was the first to introduce protists to the binomial nomenclature system.
In the early 19th century, German naturalist Georg August Goldfuss introduced Protozoa (meaning 'early animals') as a class within Kingdom Animalia, to refer to four very different groups: infusoria (ciliates), corals, phytozoa (such as Cryptomonas) and jellyfish. Later, in 1845, Carl Theodor von Siebold was the first to establish Protozoa as a phylum of exclusively unicellular animals consisting of two classes: Infusoria (ciliates) and Rhizopoda (amoebae, foraminifera). Other scientists did not consider all of them part of the animal kingdom, and by the middle of the century they were regarded within the groupings of Protozoa (early animals), Protophyta (early plants), Phytozoa (animal-like plants) and Bacteria (mostly considered plants). Microscopic organisms were increasingly constrained in the plant/animal dichotomy. In 1858, the palaeontolgist Richard Owen was the first to define Protozoa as a separate kingdom of eukaryotic organisms, with "nucleated cells" and the "common organic characters" of plants and animals, although he also included sponges within protozoa.
In 1860, British naturalist John Hogg proposed Protoctista (meaning 'first-created beings') as the name for a fourth kingdom of nature (the other kingdoms being Linnaeus' plant, animal and mineral) which comprised all the lower, primitive organisms, including protophyta, protozoa and sponges, at the merging bases of the plant and animal kingdoms.
In 1866 the 'father of protistology', German scientist Ernst Haeckel, addressed the problem of classifying all these organisms as a mixture of animal and vegetable characters, and proposed Protistenreich (Kingdom Protista) as the third kingdom of life, comprising primitive forms that were "neither animals nor plants". He grouped both bacteria and eukaryotes, both unicellular and multicellular organisms, as Protista. He retained the Infusoria in the animal kingdom, until German zoologist Otto Butschli demonstrated that they were unicellular. At first, he included sponges and fungi, but in later publications he explicitly restricted Protista to predominantly unicellular organisms or colonies incapable of forming tissues. He clearly separated Protista from true animals on the basis that the defining character of protists was the absence of sexual reproduction, while the defining character of animals was the blastula stage of animal development. He also returned the terms protozoa and protophyta as subkingdoms of Protista.
Butschli considered the kingdom to be too polyphyletic and rejected the inclusion of bacteria. He fragmented the kingdom into protozoa (only nucleated, unicellular animal-like organisms), while bacteria and the protophyta were a separate grouping. This strengthened the old dichotomy of protozoa/protophyta from German scientist Carl Theodor von Siebold, and the German naturalists asserted this view over the worldwide scientific community by the turn of the century. However, British biologist C. Clifford Dobell in 1911 brought attention to the fact that protists functioned very differently compared to the animal and vegetable cellular organization, and gave importance to Protista as a group with a different organization that he called "acellularity", shifting away from the dogma of German cell theory. He coined the term protistology and solidified it as a branch of study independent from zoology and botany.
In 1938, American biologist Herbert Copeland resurrected Hogg's label, arguing that Haeckel's term Protista included anucleated microbes such as bacteria, which the term Protoctista (meaning "first established beings") did not. Under his four-kingdom classification (Monera, Protoctista, Plantae, Animalia), the protists and bacteria were finally split apart, recognizing the difference between anucleate (prokaryotic) and nucleate (eukaryotic) organisms. To firmly separate protists from plants, he followed Haeckel's blastular definition of true animals, and proposed defining true plants as those with chlorophyll a and b, carotene, xanthophyll and production of starch. He also was the first to recognize that the unicellular/multicellular dichotomy was invalid. Still, he kept fungi within Protoctista, together with red algae, brown algae and protozoans.[7] This classification was the basis for Whittaker's later definition of Fungi, Animalia, Plantae and Protista as the four kingdoms of life.[8]
In the popular five-kingdom scheme published by American plant ecologist Robert Whittaker in 1969, Protista was defined as eukaryotic "organisms which are unicellular or unicellular-colonial and which form no tissues". Just as the prokaryotic/eukaryotic division was becoming mainstream, Whittaker, after a decade from Copeland's system,[8] recognized the fundamental division of life between the prokaryotic Monera and the eukaryotic kingdoms: Animalia (ingestion), Plantae (photosynthesis), Fungi (absorption) and the remaining Protista.[9]
In the five-kingdom system of American evolutionary biologist Lynn Margulis, the term "protist" was reserved for microscopic organisms, while the more inclusive kingdom Protoctista (or protoctists) included certain large multicellular eukaryotes, such as kelp, red algae, and slime molds.[10] Some use the term protist interchangeably with Margulis' protoctist, to encompass both single-celled and multicellular eukaryotes, including those that form specialized tissues but do not fit into any of the other traditional kingdoms.[11]
The five-kingdom model remained the accepted classification until the development of molecular phylogenetics in the late 20th century, when it became apparent that protists are a paraphyletic group from which animals, fungi and plants evolved, and the three-domain system (Bacteria, Archaea, Eukarya) became prevalent. Today, protists are not treated as a formal taxon, but the term is commonly used for convenience in two ways:
There is, however, one classification of protists based on traditional ranks that lasted until the 21st century. The British protozoologist Thomas Cavalier-Smith, since 1998, developed a six-kingdom model: Bacteria, Animalia, Plantae, Fungi, Protozoa and Chromista. In his context, paraphyletic groups take preference over clades: both protist kingdoms Protozoa and Chromista contain paraphyletic phyla such as Apusozoa, Eolouka or Opisthosporidia. Additionally, red and green algae are considered true plants, while the fungal groups Microsporidia, Rozellida and Aphelida are considered protozoans under the phylum Opisthosporidia. This scheme endured until 2021, the year of his last publication.
According to molecular data, protists dominate eukaryotic diversity, accounting for a vast majority of environmental DNA sequences or operational taxonomic units (OTUs). However, their species diversity is severely underestimated by traditional methods that differentiate species based on morphological characteristics. The number of described protistan species is very low (ranging from 26,000 to 74,400 as of 2012) in comparison to the diversity of plants, animals and fungi, which are historically and biologically well-known and studied. The predicted number of species also varies greatly, ranging from 1.4×10 to 1.6×10, and in several groups the number of predicted species is arbitrarily doubled. Most of these predictions are highly subjective.
Molecular techniques such as DNA barcoding are being used to compensate for the lack of morphological diagnoses, but this has revealed an unknown vast diversity of protists that is difficult to accurately process because of the exceedingly large genetic divergence between the different protistan groups. Several different molecular markers need to be used to survey the vast protistan diversity, because there is no universal marker that can be applied to all lineages.
Protists make up a large portion of the biomass in both marine and terrestrial ecosystems. It has been estimated that protists account for 4 gigatons (Gt) of biomass in the entire planet Earth. This amount is smaller than 1% of all biomass, but is still double the amount estimated for all animals (2 Gt). Together, protists, animals, archaea (7 Gt) and fungi (12 Gt) account for less than 10% of the total biomass of the planet, because plants (450 Gt) and bacteria (70 Gt) are the remaining 80% and 15% respectively.
Protists are highly abundant and diverse in all types of ecosystems, especially free-living (i.e. non-parasitic) groups. An unexpectedly enormous, taxonomically undescribed diversity of eukaryotic microbes is detected everywhere in the form of environmental DNA or RNA. The richest protist communities appear in soil, followed by ocean and freshwater habitats.
Phagotrophic protists (consumers) are the most diverse functional group in all ecosystems, with three main taxonomical groups of phagotrophs: Rhizaria (mainly Cercozoa in freshwater and soil habitats, and Radiolaria in oceans), ciliates (most abundant in freshwater and second most abundant in soil) and non-photosynthetic stramenopiles (third most represented overall, higher in soil than in oceans). Phototrophic protists (producers) appear in lower proportions, probably constrained by intense predation. They exist in similar abundance in both oceans and soil. They are mostly dinophytes in oceans, chrysophytes in freshwater, and Archaeplastida in soil.
Marine protists are highly diverse, have a fundamental impact on biogeochemical cycles (particularly, the carbon cycle) and are at the base of the marine trophic networks as part of the plankton.
Phototrophic marine protists located in the photic zone as phytoplankton are vital primary producers in the oceanic systems. They fix as much carbon as all terrestrial plants together. The smallest fractions, the picoplankton (<2 μm) and nanoplankton (2–20 μm), are dominated by several different algae (prymnesiophytes, pelagophytes, prasinophytes); fractions larger than 5 μm are instead dominated by diatoms and dinoflagellates. The heterotrophic fraction of marine picoplankton encompasses primarily early-branching stramenopiles (e.g. bicosoecids and labyrinthulomycetes), as well as alveolates, ciliates and radiolarians; protists of lower frequency include cercozoans and cryptophytes.
Mixotrophic marine protists, while not very researched, are present abundantly and ubiquitously in the global oceans, on a wide range of marine habitats. In metabarcoding analyses, they constitute more than 12% of the environmental sequences. They are an important and underestimated source of carbon in eutrophic and oligotrophic habitats. Their abundance varies seasonally. Planktonic protists are classified into various functional groups or 'mixotypes' that present different biogeographies:
Freshwater planktonic protist communities are characterized by a higher "beta diversity" (i.e. highly heterogeneous between samples) than soil and marine plankton. The high diversity can be a result of the hydrological dynamic of recruiting organisms from different habitats through extreme floods.[18] The main freshwater producers (chrysophytes, cryptophytes and dinophytes) behave alternatively as consumers (mixotrophs). At the same time, strict consumers (non-photosynthetic) are less abundant in freshwater, implying that the consumer role is partly taken by these mixotrophs.
Soil protist communities are ecologically the richest. This may be due to the complex and highly dynamic distribution of water in the sediment, which creates extremely heterogenous environmental conditions. The constantly changing environment promotes the activity of only one part of the community at a time, while the rest remains inactive; this phenomenon promotes high microbial diversity in prokaryotes as well as protists. Only a small fraction of the detected diversity of soil-dwelling protists has been described (8.1% as of 2017). Soil protists are also morphologically and functionally diverse, with four major categories:
Parasitic protists represent around 15–20% of all environmental DNA in marine and soil systems, but only around 5% in freshwater systems, where chytrid fungi likely fill that ecological niche. In oceanic systems, parasitoids (i.e. those which kill their hosts, e.g. Syndiniales) are more abundant. In soil ecosystems, true parasites (i.e. those which do not kill their hosts) are primarily animal-hosted Apicomplexa (Alveolata) and plant-hosted oomycetes (Stramenopiles) and plasmodiophorids (Rhizaria). In freshwater ecosystems, parasitoids are mainly Perkinsea and Syndiniales (Alveolata), as well as the fungal Chytridiomycota. True parasites in freshwater are mostly oomycetes, Apicomplexa and Ichthyosporea.
Some protists are significant parasites of animals (e.g.; five species of the parasitic genus Plasmodium cause malaria in humans and many others cause similar diseases in other vertebrates), plants[19] [20] (the oomycete Phytophthora infestans causes late blight in potatoes)[21] or even of other protists.[22] [23]
Around 100 protist species can infect humans. Two papers from 2013 have proposed virotherapy, the use of viruses to treat infections caused by protozoa.[24] [25]
Researchers from the Agricultural Research Service are taking advantage of protists as pathogens to control red imported fire ant (Solenopsis invicta) populations in Argentina. Spore-producing protists such as Kneallhazia solenopsae (recognized as a sister clade or the closest relative to the fungus kingdom now)[26] can reduce red fire ant populations by 53–100%.[27] Researchers have also been able to infect phorid fly parasitoids of the ant with the protist without harming the flies. This turns the flies into a vector that can spread the pathogenic protist between red fire ant colonies.[28]
While, in general, protists are typical eukaryotic cells and follow the same principles of physiology and biochemistry described for those cells within the "higher" eukaryotes (animals, fungi or plants),[29] they have evolved a variety of unique physiological adaptations that do not appear in those eukaryotes.
Protists generally reproduce asexually under favorable environmental conditions, but tend to reproduce sexually under stressful conditions, such as starvation or heat shock. Oxidative stress, which leads to DNA damage, also appears to be an important factor in the induction of sex in protists.[30]
Eukaryotes emerged in evolution more than 1.5 billion years ago.[31] The earliest eukaryotes were protists. Although sexual reproduction is widespread among multicellular eukaryotes, it seemed unlikely until recently, that sex could be a primordial and fundamental characteristic of eukaryotes. The main reason for this view was that sex appeared to be lacking in certain pathogenic protists whose ancestors branched off early from the eukaryotic family tree. However, several of these "early-branching" protists that were thought to predate the emergence of meiosis and sex (such as Giardia lamblia and Trichomonas vaginalis) are now known to descend from ancestors capable of meiosis and meiotic recombination, because they have a set core of meiotic genes that are present in sexual eukaryotes.[32] [33] Most of these meiotic genes were likely present in the common ancestor of all eukaryotes,[34] which was likely capable of facultative (non-obligate) sexual reproduction.[35]
This view was further supported by a 2011 study on amoebae. Amoebae have been regarded as asexual organisms, but the study describes evidence that most amoeboid lineages are ancestrally sexual, and that the majority of asexual groups likely arose recently and independently.[36] Even in the early 20th century, some researchers interpreted phenomena related to chromidia (chromatin granules free in the cytoplasm) in amoebae as sexual reproduction.[37]
Some commonly found protist pathogens such as Toxoplasma gondii are capable of infecting and undergoing asexual reproduction in a wide variety of animals – which act as secondary or intermediate host – but can undergo sexual reproduction only in the primary or definitive host (for example: felids such as domestic cats in this case).[38] [39] [40]
Some species, for example Plasmodium falciparum, have extremely complex life cycles that involve multiple forms of the organism, some of which reproduce sexually and others asexually.[41] However, it is unclear how frequently sexual reproduction causes genetic exchange between different strains of Plasmodium in nature and most populations of parasitic protists may be clonal lines that rarely exchange genes with other members of their species.[42]
The pathogenic parasitic protists of the genus Leishmania have been shown to be capable of a sexual cycle in the invertebrate vector, likened to the meiosis undertaken in the trypanosomes.[43]
See main article: Protists in the fossil record.
By definition, all eukaryotes before the existence of plants, animals and fungi are considered protists. For that reason, this section contains information about the deep ancestry of all eukaryotes.
All living eukaryotes, including protists, evolved from the last eukaryotic common ancestor (LECA). Descendants of this ancestor are known as "crown-group" or "modern" eukaryotes. Molecular clocks suggest that LECA originated between 1200 and more than 1800 million years ago (Ma). Based on all molecular predictions, modern eukaryotes reached morphological and ecological diversity before 1000 Ma in the form of multicellular algae capable of sexual reproduction, and unicellular protists capable of phagocytosis and locomotion. However, the fossil record of modern eukaryotes is very scarce around this period, which contradicts the predicted diversity.
Instead, the fossil record of this period contains "stem-group eukaryotes". These fossils cannot be assigned to any known crown group, so they probably belong to extinct lineages that originated before LECA. They appear continuously throughout the Mesoproterozoic fossil record (1650–1000 Ma). They present defining eukaryote characteristics such as complex cell wall ornamentation and cell membrane protrusions, which require a flexible endomembrane system. However, they had a major distinction from crown eukaryores: the composition of their cell membrane. Unlike crown eukaryotes, which produce "crown sterols" for their cell membranes (e.g. cholesterol and ergosterol), stem eukaryotes produced "protosterols", which appear earlier in the biosynthetic pathway.
Crown sterols, while metabolically more expensive, may have granted several evolutionary advantages for LECA's descendants. Specific unsaturation patterns in crown sterols protect against osmotic shock during desiccation and rehydration cycles. Crown sterols can also receive ethyl groups, thus enhancing cohesion between lipids and adapting cells against extreme cold and heat. Moreover, the additional steps in the biosynthetic pathway allow cells to regulate the proportion of different sterols in their membranes, in turn allowing for a wider habitable temperature range and unique mechanisms such as asymmetric cell division or membrane repair under exposure to UV light. A more speculative role of these sterols is their protection against the Proterozoic changing oxygen levels. It is theorized that all of these sterol-based mechanisms allowed LECA's descendants to live as extremophiles of their time, diversifying into ecological niches that experienced cycles of desiccation and rehydration, daily extremes of high and low temperatures, and elevated UV radiation (such as mudflats, rivers, agitated shorelines and subaerial soil).
In contrast, the named mechanisms were absent in stem-group eukaryotes, as they were only capable of producing protosterols. Instead, these protosterol-based life forms occupied open marine waters. They were facultative anaerobes that thrived in Mesoproterozoic waters, which at the time were low on oxygen. Eventually, during the Tonian period (Neoproterozoic era), oxygen levels increased and the crown eukaryotes were able to expand to open marine environments thanks to their preference for more oxygenated habitats. Stem eukaryotes may have been driven to extinction as a result of this competition. Additionally, their protosterol membranes may have posed a disadvantage during the cold of the Cryogenian "Snowball Earth" glaciations and the extreme global heat that came afterwards.
Modern eukaryotes began to appear abundantly in the Tonian period (1000–720 Ma), fueled by the proliferation of red algae. The oldest fossils assigned to modern eukaryotes belong to two photosynthetic protists: the multicellular red alga Bangiomorpha (from 1050 Ma), and the chlorophyte green alga Proterocladus (from 1000 Ma).[44] Abundant fossils of heterotrophic protists appear later, around 900 Ma, with the emergence of fungi.[44] For example, the oldest fossils of Amoebozoa are vase-shaped microfossils resembling modern testate amoebae, found in 800 million-year-old rocks. Radiolarian shells are found abundantly in the fossil record after the Cambrian period (~500 Ma), but more recent paleontological studies are beginning to interpret some Precambrian fossils as the earliest evidence of radiolarians.[45] [46] [47]