Protist

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Protist

A protist (/ˈproʊtɪst/ PROH-tist) or protoctist is any eukaryotic organism that is not an animal, land
plant, or fungus. Protists do not form a natural group, or clade, but are a polyphyletic grouping of
several independent clades that evolved from the last eukaryotic common ancestor.

Protists were historically regarded as a separate taxonomic kingdom known as Protista or


Protoctista. With the advent of phylogenetic analysis and electron microscopy studies, the use of
Protista as a formal taxon was gradually abandoned. In modern classifications, protists are spread
across several eukaryotic clades called supergroups, such as Archaeplastida (photoautotrophs that
includes land plants), SAR, Obazoa (which includes fungi and animals), Amoebozoa and Excavata.

Protists represent an extremely large genetic and ecological diversity in all environments, including
extreme habitats. Their diversity, larger than for all other eukaryotes, has only been discovered in
recent decades through the study of environmental DNA and is still in the process of being fully
described. They are present in all ecosystems as important components of the biogeochemical
cycles and trophic webs. They exist abundantly and ubiquitously in a variety of forms that evolved
multiple times independently, such as free-living algae, amoebae and slime moulds, or as important
parasites. Together, they compose an amount of biomass that doubles that of animals. They exhibit
varied types of nutrition (such as phototrophy, phagotrophy or osmotrophy), sometimes combining
them (in mixotrophy). They present unique adaptations not present in multicellular animals, fungi or
land plants. The study of protists is termed protistology.

Definition

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.[3]

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.[3] They have
different life cycles, trophic levels, modes of locomotion, and cellular structures.[4][5] Some protists
can be pathogens.[6]
Examples of basic protist forms that do not
Protists
represent evolutionary cohesive lineages
Temporal range:
include:[7]

Algae, which are photosynthetic protists.


Traditionally called "protophyta", they are found
within most of the big evolutionary lineages or
supergroups, intermingled with heterotrophic
protists which are traditionally called
"protozoa".[8] There are many multicellular and
colonial examples of algae, including kelp, red
algae, some types of diatoms, and some
lineages of green algae.

Flagellates, which bear eukaryotic flagella. They


are found in all lineages, reflecting that the
Examples of protists. Clockwise from top left: red
common ancestor of all living eukaryotes was a algae, kelp, ciliate, golden alga, dinoflagellate,
flagellated heterotroph. metamonad, amoeba, slime mold.

Amoebae, which usually lack flagella but move Scientific classification


through changes in the shape and motion of (paraphyletic)
their protoplasm[9] to produce pseudopodia. Domain: Eukaryota
They have evolved independently several times,
Supergroups[1]
leading to major radiations of these lifeforms.
Many lineages lack a solid shape ("naked Amorphea (including fungi & animals)
amoebae"). Some of them have special forms, Apusomonadida
such as the "heliozoa", amoebae with Archaeplastida (including land plants)
microtubule-supported pseudopodia radiating Breviatea
from the cell, with at least three independent CRuMs
origins. Others, referred to as "testate Cryptista
amoebae", grow a shell around the cell made Discoba
from organic or inorganic material. Haptista
Slime molds, which are amoebae capable of Hemimastigophora
producing stalked reproductive structures that Malawimonadida
bear spores, often through aggregative Metamonada
multicellularity (numerous amoebae Provora[2]
aggregating together). This type of SAR supergroup
Telonemia
multicellularity has evolved at least seven times Cladistically included but traditionally
[10]
among protists. excluded taxa

Fungus-like protists, which can produce


Animalia
hyphae-like structures and are often
Fungi
saprophytic. They have evolved multiple times,
Embryophyta (land plants)
often very distantly from true fungi. For
example, the oomycetes (water molds) or the
myxomycetes.

Parasitic protists, such as Plasmodium falciparum, the cause of malaria.[11]

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.[12][13]

Classification

Phylogenomic tree of eukaryotes, as regarded in 2020.


Supergroups are in color.

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:[7][1]

Archaeplastida[a] — consists of groups that have evolved from a photosynthetic common


ancestor that obtained chloroplasts directly through a single event of endosymbiosis with a
cyanobacterium:
Picozoa (1 species), non-photosynthetic predators.[15]
Glaucophyta (26 species), unicellular algae found in freshwater and terrestrial
environments.[16]

Rhodophyta (5,000–6,000 species), mostly multicellular marine algae that lost chlorophyll
and only harvest light energy through phycobiliproteins.[16]

Rhodelphidia (2 species), predators with non-photosynthetic plastid.[17]

Viridiplantae or Chloroplastida, containing both green algae and land plants which are not
protists. The green algae comprise many lineages of varying diversity, such as Chlorophyta
(7,000), Prasinodermophyta (10), Zygnematophyceae (4,000), Charophyceae (877),
Klebsormidiophyceae (48) or Coleochaetophyceae (36).[7]
Sar, SAR or Harosa – a clade of three highly diverse lineages exclusively containing protists.
Stramenopiles is a wide clade of photosynthetic and heterotrophic organisms that evolved
from a common ancestor with hairs in one of their two flagella. The photosynthetic
stramenopiles, called Ochrophyta, are a monophyletic group that acquired chloroplasts from
secondary endosymbiosis with a red alga. Among these, the best known are: the unicellular
or colonial Bacillariophyta (>60,000 species),[18] known as diatoms; the filamentous or
genuinely multicellular Phaeophyta (2,000 species),[19] known as brown algae; and the
Chrysomonadea (>1,200 species). The heterotrophic stramenopiles are more diverse in
forms, ranging from fungi-like organisms such as the Hyphochytrea, Oomycota and
Labyrinthulea, to various kinds of protozoa such as the flagellates Opalinata and
Bicosoecida.[7]

Alveolata contains three of the most well-known groups of protists: Apicomplexa, a parasitic
group with species harmful to humans and animals; Dinoflagellata, an ecologically important
group as a main component of the marine microplankton and a main cause of algal blooms;
and Ciliophora (4,500 species),[20] the extremely diverse and well-studied group of mostly
free-living heterotrophs known as ciliates.[7]

Rhizaria is a morphologically diverse lineage mostly comprising heterotrophic amoebae,


flagellates and amoeboflagellates, and some unusual algae (Chlorarachniophyta) and spore-
forming parasites. The most familiar rhizarians are Foraminifera and Radiolaria, groups of
large and abundant marine amoebae, many of them macroscopic. Much of the rhizarian
diversity lies within the phylum Cercozoa, filled with free-living flagellates which usually have
pseudopodia, as well as Phaeodaria, a group previously considered radiolarian. Other groups
comprise various amoebae like Vampyrellida or are important parasites like Phytomyxea,
Paramyxida or Haplosporida.[7]
Haptista — includes the Haptophyta algae and the heterotrophic Centrohelida, which are
"heliozoan"-type amoebae.[7]
Cryptista — closely related to Archaeplastida, it includes the Cryptophyta algae, with a plastid of
red algal origin, and two obscure relatives with two flagella, katablepharids and Palpitomonas.[7]
Discoba — includes many lineages previously grouped under the paraphyletic "Excavata": the
Jakobida, flagellates with bacterial-like mitochondrial genomes; Tsukubamonas, a free-living
flagellate; and the Discicristata clade, which unites well-known phyla Heterolobosea and
Euglenozoa. Heterolobosea includes amoebae, flagellates and amoeboflagellates with complex
life cycles, and the unusual Acrasida, a group of slime molds. Euglenozoa encompasses a clade
of algae with chloroplasts of green algal origin and many groups of anaerobic, parasitic or free-
living heterotrophs.[7]
Metamonada — a clade of completely anaerobic protozoa, primarily flagellates. Some are gut
symbionts of animals, others are free-living (for example, Paratrimastix pyriformis), and others are
well-known parasites (for example, Giardia lamblia).[7]
Amorphea — unites two huge clades:
Amoebozoa (2,400 species) is a large group of heterotrophic protists, mostly amoebae. Many
lineages are slime molds that produce spore-releasing fruiting bodies, such as Myxogastria,
Dictyostelia and Protosporangiida, and are often studied by mycologists. Within the non-
fruiting amoebae, the Tubulinea contain many naked amoebae (such as Amoeba itself) and a
well-studied order of testate amoebae known as Arcellinida. Other non-fruiting amoebozoans
are Variosea, Discosea and Archamoebae.[7]

Obazoa includes the two kingdoms Metazoa (animals) and Fungi,[b] and their closest protist
relatives inside a clade known as Opisthokonta. The opisthokont protists are Nucleariida,
Ichthyosporea, Pluriformea, Filasterea, Choanoflagellata and the elusive Tunicaraptor (1
species).[24] They are flagellated or amoeboid heterotrophs of vital importance in the search
for the genes that allow animal multicellularity. Sister groups to Opisthokonta are
Apusomonadida (28 species)[25] and Breviatea (4 species).[7]

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.[7] Others, like
Hemimastigophora (10 species)[26] and Provora (7 species), appear to be related to or within
Diaphoretickes, a clade that unites SAR, Archaeplastida, Haptista and Cryptista.[2]

Although the root of the tree is still unresolved, one possible topology of the eukaryotic tree of life
is:[27][2]
Protist phylogeny


Stramenopiles



⁠ AR ⁠Alveolata
S
⁠ ⁠
⁠TSAR
⁠ ⁠Rhizaria
⁠ ⁠
⁠⁠
⁠⁠ ⁠ Telonemia
⁠ ⁠

⁠Diaphoretickes ⁠ Haptista
⁠ ⁠

⁠⁠ ⁠
Provora
⁠ ⁠

Hemimastigophora

⁠ Cryptista


⁠⁠
Archaeplastida


⁠Eukaryota Discoba


⁠Metamonada

⁠ Ancyromonadida


Malawimonadida

⁠ CRuMs

⁠ Amoebozoa


⁠⁠ ⁠
Breviatea
⁠ ⁠Podiata ⁠
⁠ ⁠Amorphea
⁠ Apusomonadida

⁠Obazoa ⁠
⁠ ⁠
⁠⁠
Opisthokonta

History

Early concepts

Goldfuss' system of life, introducing


the Protozoa within animals.

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,[c] his Danish contemporary Otto Friedrich Müller was
the first to introduce protists to the binomial nomenclature system.[28][29]

In the early 19th century, German naturalist Georg August Goldfuss introduced Protozoa (meaning
'early animals') as a class within Kingdom Animalia,[30] 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).[31]
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.[8]
Origin of the protist kingdom

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 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.[32][8]

Haeckel's 1866 tree of life, with the


third kingdom Protista.

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[33] (Kingdom Protista) as the third kingdom of life, comprising primitive forms that
were "neither animals nor plants". He grouped both bacteria[34] 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.[35][36] 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.[8]

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.[8]

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.[8][37] This classification was the
basis for Whittaker's later definition of Fungi, Animalia, Plantae and Protista as the four kingdoms of
life.[38]

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,[38] recognized the fundamental division of life
between the prokaryotic Monera and the eukaryotic kingdoms: Animalia (ingestion), Plantae
(photosynthesis), Fungi (absorption) and the remaining Protista.[39][40][8]
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.[41] 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.[42]

Phylogenetics and modern concepts

Phylogenetic and symbiogenetic tree


of living organisms, showing the
origins of eukaryotes

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.[43] Today, protists are not treated as a formal taxon, but the
term is commonly used for convenience in two ways:[44]

Phylogenetic definition: protists are a paraphyletic group.[45] A protist is any eukaryote that is not
an animal, land plant or fungus,[46] thus excluding many unicellular groups like the fungal
Microsporidia, Chytridiomycetes and yeasts, and the non-unicellular Myxozoan animals included
in Protista in the past.[47]

Functional definition: protists are essentially those eukaryotes that are never multicellular,[44] that
either exist as independent cells, or if they occur in colonies, do not show differentiation into
tissues.[48] 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).[49]
Kingdoms Protozoa and Chromista

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:[d] Bacteria, Animalia, Plantae, Fungi, Protozoa and Chromista.[14][50] In his context,
paraphyletic groups take preference over clades:[14] 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.[21]

Diversity

Species diversity

Difference between morphological (A) and


genetic (B) view of total eukaryotic diversity.
Protists dominate DNA barcoding analyses,
but constitute a minority of catalogued
species.[51]

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[52] to 74,400[51] as of 2012) in comparison to the diversity of plants, animals and fungi, which
are historically and biologically well-known and studied. The predicted number of species also
varies greatly, ranging from 1.4×105 to 1.6×106, and in several groups the number of predicted
species is arbitrarily doubled. Most of these predictions are highly subjective.[51]
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.[51]

Biomass

Protists make up a large portion of the biomass in both marine and terrestrial ecosystems. It has
been estimated that protists account for 4 gigatons (Gt) of biomass in the entire planet Earth. This
amount is smaller than 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.[53]

Ecology

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.[54]

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.[54]
Marine

Marine diatoms are important oxygen


producers.

Marine protists are highly diverse, have a fundamental impact on biogeochemical cycles
(particularly, the carbon cycle)[55] and are at the base of the marine trophic networks as part of the
plankton.[56]

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.[54] 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.[57]

Prymnesium, a
constitutive mixotroph
that participates in toxic
algal blooms.

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.[56] Their abundance varies seasonally.[58]
Planktonic protists are classified into various functional groups or 'mixotypes' that present different
biogeographies:
Constitutive mixotrophs, also called 'phytoplankton that eat', have the innate ability to
photosynthesize. They have diverse feeding behaviors: some require phototrophy, others
phagotrophy, and others are obligate mixotrophs.[56] They are responsible for harmful algal
blooms. They dominate the eukaryotic microbial biomass in the photic zone, in eutrophic and
oligotrophic waters across all climate zones, even in non-bloom conditions. They account for
significant, often dominant predation of bacteria.[59]

Noctiluca, a specialist non-


constitutive mixotroph that
photosynthesizes through
endosymbionts.

Non-constitutive mixotrophs acquire the ability to photosynthesize by stealing chloroplasts from


their prey. They can be divided into two: generalists, which can use chloroplasts stolen from a
variety of prey (e.g. oligotrich ciliates), or specialists, which have developed the need to only
acquire chloroplasts from a few specific prey. The specialists are further divided into two:
plastidic, those which contain differentiated plastids (e.g. Mesodinium, Dinophysis), and
endosymbiotic, those which contain endosymbionts (e.g. mixotrophic Rhizaria such as
Foraminifera and Radiolaria, dinoflagellates like Noctiluca).[59] Both plastidic and generalist non-
constitutive mixotrophs have similar biogeographies and low abundance, mostly found in
eutrophic coastal waters. Generalist ciliates can account for up to 50% of ciliate communities in
the photic zone. The endosymbiotic mixotrophs are the most abundant non-constitutive type.[56]

Freshwater

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.[60] 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.[54]
Soil

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).[54] Soil protists are also morphologically
and functionally diverse, with four major categories:[61]

Dictyostelids are fungus-like protists


present in soil.

Cercomonads (Rhizaria) are


important phagotrophic protists in
soil.

Photoautotrophic soil protists, or algae, are as abundant as their marine counterparts. Given the
importance of marine algae, soil algae may provide a larger contribution to the global carbon
cycle than previously thought, but the magnitude of their carbon fixation has yet to be
quantified.[54] Most soil algae belong to the supergroups Stramenopiles (diatoms, Xanthophyceae
and Eustigmatophyceae) and Archaeplastida (Chlorophyceae and Trebouxiophyceae). There is
also the presence of environmental DNA from dinoflagellates and haptophytes in soil, but no
living forms have been seen.[61]
Fungus-like protists are present abundantly in soil. Most environmental sequences belong to the
Oomycetes (Stramenopiles), an osmotrophic and saprotrophic group that contains free-living and
parasitic species of other protists, fungi, plants and animals. Another important group in soil are
slime molds (found in Amoebozoa, Opisthokonta, Rhizaria and Heterolobosea), which reproduce
by forming fruiting bodies known as sporocarps (originated from a single cell) and sorocarps
(from aggregations of cells).[61]
Phagotrophic protists are abundant and essential in soil ecosystems. As bacterial grazers, they
have a significant role in the foodweb: they excrete nitrogen in the form of NH3, making it
available to plants and other microbes.[62] Many soil protists are also mycophagous, and
facultative (i.e. non-obligate) mycophagy is a widespread evolutionary feeding mode among soil
protozoa.[63] Amoeboflagellates like the glissomonads and cercomonads (in Rhizaria) are among
the most abundant soil protists: they possess both flagella and pseudopodia, a morphological
variability well suited for foraging between soil particles. Testate amoebae (e.g. arcellinids and
euglyphids) have shells that protect against desiccation and predation, and their contribution to
the silica cycle through the biomineralization of shells is as important as that of forest trees.[61]
Parasitic soil protists (in Apicomplexa) are diverse, ubiquitous and have an important role as
parasites of soil-dwelling invertebrate animals. In Neotropical forests, environmental DNA from
the apicomplexan gregarines dominates protist diversity.[61]

Parasitic

Blastocystis (Stramenopiles) is a
prevalent intestinal parasite in
humans.

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.[54]

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[64][65] (the oomycete Phytophthora infestans causes late blight in potatoes)[66] or
even of other protists.[67][68]

Around 100 protist species can infect humans.[61] Two papers from 2013 have proposed
virotherapy, the use of viruses to treat infections caused by protozoa.[69][70]

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)[71] can reduce red fire ant populations by 53–100%.[72] 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.[73]

Biology

Physiological adaptations

Paramecium aurelia with


contractile vacuoles

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),[74] they have evolved a variety of unique physiological adaptations that do not appear in
those eukaryotes.[75]

Osmoregulation. Freshwater protists without cell walls are able to regulate their osmosis through
contractile vacuoles, specialized organelles that periodically excrete fluid high in potassium and
sodium through a cycle of diastole and systole. The cycle stops when the cells are placed in a
medium with different salinity, until the cell adapts.[75]

Light micrograph of an
ocelloid-containing
dinoflagellate. n: nucleus,
double arrowhead: ocelloid,
scale bar: 10 μm.[76]

Energetic adaptations. The last eukaryotic common ancestor was aerobic, bearing mitochondria
for oxidative metabolism. Many lineages of free-living and parasitic protists have independently
evolved and adapted to inhabit anaerobic or microaerophilic habitats, by modifying the early
mitochondria into hydrogenosomes, organelles that generate ATP anaerobically through
fermentation of pyruvate. In a parallel manner, in the microaerophilic trypanosomatid protists, the
fermentative glycosome evolved from the peroxisome.[75]
Sensory adaptations. Many flagellates and probably all motile algae exhibit a positive phototaxis
(i.e. they swim or glide toward a source of light). For this purpose, they exhibit three kinds of
photoreceptors or "eyespots": (1) receptors with light antennae, found in many green algae,
dinoflagellates and cryptophytes; (2) receptors with opaque screens; and (3) complex ocelloids
with intracellular lenses, found in one group of predatory dinoflagellates, the Warnowiaceae.
Additionally, some ciliates orient themselves in relation to the Earth's gravitational field while
moving (geotaxis), and others swim in relation to the concentration of dissolved oxygen in the
water.[75]
Endosymbiosis. Protists have an accentuated tendency to include endosymbionts in their cells,
and these have produced new physiological opportunities. Some associations are more
permanent, such as Paramecium bursaria and its endosymbiont Chlorella; others more transient.
Many protists contain captured chloroplasts, chloroplast-mitochondrial complexes, and even
eyespots from algae. The xenosomes are bacterial endosymbionts found in ciliates, sometimes
with a methanogenic role inside anaerobic ciliates.[75]
Sexual reproduction

Two similar-looking but


sexually distinct Coleps
partners connected at
their front ends exchange
genetic material via a
plasma bridge.

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.[77]

Eukaryotes emerged in evolution more than 1.5 billion years ago.[78] 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.[79][80] Most of these meiotic genes were likely present in the common ancestor
of all eukaryotes,[81] which was likely capable of facultative (non-obligate) sexual reproduction.[82]

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.[83] Even in
the early 20th century, some researchers interpreted phenomena related to chromidia (chromatin
granules free in the cytoplasm) in amoebae as sexual reproduction.[84]

Sex in pathogenic protists

Some commonly found protist pathogens such as Toxoplasma gondii are capable of infecting and
undergoing asexual reproduction in a wide variety of animals – which act as secondary or
intermediate host – but can undergo sexual reproduction only in the primary or definitive host (for
example: felids such as domestic cats in this case).[85][86][87]

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.[88]
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.[89]

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.[90]

Fossil record

Mesoproterozoic

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.[91]

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.[91]

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).[91]

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.[91]

Neoproterozoic

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).[91] Abundant fossils of heterotrophic protists
appear later, around 900 Ma, with the emergence of fungi.[91] For example, the oldest fossils of
Amoebozoa are vase-shaped microfossils resembling modern testate amoebae, found in 800
million-year-old rocks.[92][93] 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.[94][95][96]

See also

Evolution of sexual reproduction

Protist locomotion

Footnotes

a. According to some classifications,[14] all of Archaeplastida is treated as Kingdom Plantae, but others
consider the algae (or non-terrestrial "plants") to be protists.[7]

b. Under traditional classifications, the groups Microsporidia, Aphelida and Rozellida are considered to be
protists, commonly grouped by the name Opisthosporidia and treated as the immediate relative of
Eumycota or true fungi.[21] However, many researchers currently accept those three groups as part of a
larger Kingdom Fungi.[1][22][23]

c. Carl von Linnaeus did not mention a single protist genus until the tenth edition of Systema Naturae of
1758, where Volvox was recorded.[28]

d. In 2015, Cavalier-Smith's initial six-kingdom model was revised into a seven-kingdom model after the
inclusion of Archaea.[50]

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External links

UniEuk Taxonomy App (https://eukmap.unieuk.net/)

Tree of Life: Eukaryotes (http://tolweb.org/Eukaryotes/3)


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Hosei University.Protist Information Server (http://protist.i.hosei.ac.jp/) . Updated: March 22,
2016.

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