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An ''endosymbiont'' or ''endobiont'' is any
organism In biology, an organism () is any living system that functions as an individual entity. All organisms are composed of cells ( cell theory). Organisms are classified by taxonomy into groups such as multicellular animals, plants, and ...
that lives within the body or cells of another organism most often, though not always, in a mutualistic relationship. (The term endosymbiosis is from the
Greek Greek may refer to: Greece Anything of, from, or related to Greece, a country in Southern Europe: *Greeks, an ethnic group. *Greek language, a branch of the Indo-European language family. **Proto-Greek language, the assumed last common ancestor ...
: ἔνδον ''endon'' "within", σύν ''syn'' "together" and βίωσις ''biosis'' "living".) Examples are nitrogen-fixing
bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...
(called
rhizobia Rhizobia are diazotrophic bacteria that fix nitrogen after becoming established inside the root nodules of legumes (Fabaceae). To express genes for nitrogen fixation, rhizobia require a plant host; they cannot independently fix nitrogen. In ...
), which live in the
root nodule Root nodules are found on the roots of plants, primarily legumes, that form a symbiosis with nitrogen-fixing bacteria. Under nitrogen-limiting conditions, capable plants form a symbiotic relationship with a host-specific strain of bacteria known ...
s of
legume A legume () is a plant in the family Fabaceae (or Leguminosae), or the fruit or seed of such a plant. When used as a dry grain, the seed is also called a pulse. Legumes are grown agriculturally, primarily for human consumption, for livestock fo ...
s, single-cell
algae Algae (; singular alga ) is an informal term for a large and diverse group of photosynthetic eukaryotic organisms. It is a polyphyletic grouping that includes species from multiple distinct clades. Included organisms range from unicellular m ...
inside reef-building
coral Corals are marine invertebrates within the class Anthozoa of the phylum Cnidaria. They typically form compact colonies of many identical individual polyps. Coral species include the important reef builders that inhabit tropical oceans and ...
s and bacterial endosymbionts that provide essential nutrients to
insect Insects (from Latin ') are pancrustacean Hexapoda, hexapod invertebrates of the class (biology), class Insecta. They are the largest group within the arthropod phylum. Insects have a chitinous exoskeleton, a three-part body (head, Thorax (ins ...
s. There are two types of symbiont transmissions. In
horizontal transmission Horizontal transmission is the transmission of organisms between biotic and/or abiotic members of an ecosystem that are not in a parent-progeny relationship. This concept has been generalized to include transmissions of infectious agents, symbiont ...
, each new generation acquires free living symbionts from the environment. An example is the nitrogen-fixing bacteria in certain plant roots.
Vertical transmission Vertical transmission of symbionts is the transfer of a microbial symbiont from the parent directly to the offspring.  Many metazoan species carry symbiotic bacteria which play a mutualistic, commensal, or parasitic role.  A symbiont is acquire ...
takes place when the symbiont is transferred directly from parent to offspring. It is also possible for both to be involved in a mixed-mode transmission, where symbionts are transferred vertically for some generation before a switch of host occurs and new symbionts are horizontally acquired from the environment. In vertical transmissions, the symbionts often have a reduced genome and are no longer able to survive on their own. As a result, the symbiont depends on the host, resulting in a highly intimate co-dependent relationship. For instance, pea aphid symbionts have lost genes for essential molecules, now relying on the host to supply them with nutrients. In return, the symbionts synthesize essential amino acids for the aphid host. Other examples include ''
Wigglesworthia ''Wigglesworthia glossinidia'' is a species of gram-negative bacteria which was isolated from the gut of the tsetse fly. ''W. glossinidia'' is a bacterial endosymbiont of the tsetse fly. Because of this relationship, ''Wigglesworthia'' has lost ...
'' nutritional symbionts of tse-tse flies, or in sponges. When a symbiont reaches this stage, it begins to resemble a cellular
organelle In cell biology, an organelle is a specialized subunit, usually within a cell, that has a specific function. The name ''organelle'' comes from the idea that these structures are parts of cells, as organs are to the body, hence ''organelle,'' the ...
, similar to
mitochondria A mitochondrion (; ) is an organelle found in the cells of most Eukaryotes, such as animals, plants and fungi. Mitochondria have a double membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which is u ...
or
chloroplasts A chloroplast () is a type of membrane-bound organelle known as a plastid that conducts photosynthesis mostly in plant and algal cells. The photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it in t ...
. Many instances of endosymbiosis are ''obligate''; that is, either the endosymbiont or the host cannot survive without the other, such as the gutless marine worms of the
genus Genus ( plural genera ) is a taxonomic rank used in the biological classification of living and fossil organisms as well as viruses. In the hierarchy of biological classification, genus comes above species and below family. In binomial no ...
''
Riftia ''Riftia pachyptila'', commonly known as the giant tube worm and less commonly known as the Giant beardworm, is a marine invertebrate in the phylum Annelida (formerly grouped in phylum Pogonophora and Vestimentifera) related to tube worms co ...
'', which get nutrition from their endosymbiotic bacteria. The most common examples of obligate endosymbioses are
mitochondria A mitochondrion (; ) is an organelle found in the cells of most Eukaryotes, such as animals, plants and fungi. Mitochondria have a double membrane structure and use aerobic respiration to generate adenosine triphosphate (ATP), which is u ...
and
chloroplast A chloroplast () is a type of membrane-bound organelle known as a plastid that conducts photosynthesis mostly in plant and algal cells. The photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it in ...
s. Some human parasites, e.g. ''
Wuchereria bancrofti ''Wuchereria bancrofti'' is a filarial (arthropod-borne) nematode (roundworm) that is the major cause of lymphatic filariasis. It is one of the three parasitic worms, together with '' Brugia malayi'' and '' B. timori'', that infect the lymphatic ...
'' and ''
Mansonella perstans ''Mansonella perstans'' is a filarial (arthropod-borne) nematode (roundworm), transmitted by tiny blood-sucking flies called midges. ''Mansonella perstans'' is one of two filarial nematodes that causes serous cavity filariasis in humans. The ...
'', thrive in their intermediate insect hosts because of an obligate endosymbiosis with ''
Wolbachia ''Wolbachia'' is a genus of intracellular bacteria that infects mainly arthropod species, including a high proportion of insects, and also some nematodes. It is one of the most common parasitic microbes, and is possibly the most common repro ...
spp.'' They can both be eliminated from hosts by treatments that target this bacterium. However, not all endosymbioses are obligate and some endosymbioses can be harmful to either of the organisms involved. Two major types of
organelle In cell biology, an organelle is a specialized subunit, usually within a cell, that has a specific function. The name ''organelle'' comes from the idea that these structures are parts of cells, as organs are to the body, hence ''organelle,'' the ...
in
eukaryotic cells Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bacter ...
, mitochondria and
plastid The plastid (Greek: πλαστός; plastós: formed, molded – plural plastids) is a membrane-bound organelle found in the cells of plants, algae, and some other eukaryotic organisms. They are considered to be intracellular endosymbiotic cya ...
s such as chloroplasts, are considered to be bacterial endosymbionts. This process is commonly referred to as
symbiogenesis Symbiogenesis (endosymbiotic theory, or serial endosymbiotic theory,) is the leading evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms. The theory holds that mitochondria, plastids such as chloroplasts, and possibly ...
.


Symbiogenesis and organelles

Symbiogenesis explains the origins of
eukaryote Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bact ...
s, whose cells contain two major kinds of organelle: mitochondria and chloroplasts. The theory proposes that these organelles evolved from certain types of bacteria that eukaryotic cells engulfed through
phagocytosis Phagocytosis () is the process by which a cell uses its plasma membrane to engulf a large particle (≥ 0.5 μm), giving rise to an internal compartment called the phagosome. It is one type of endocytosis. A cell that performs phagocytosis is ...
. These cells and the bacteria trapped inside them entered an endosymbiotic relationship, meaning that the bacteria took up residence and began living exclusively within the eukaryotic cells. Numerous insect species have endosymbionts at different stages of symbiogenesis. A common theme of symbiogenesis involves the reduction of the genome to only essential genes for the host and symbiont collective genome. A remarkable example of this is the fractionation of the '' Hodgkinia'' genome of ''
Magicicada The term periodical cicada is commonly used to refer to any of the seven species of the genus ''Magicicada'' of eastern North America, the 13- and 17-year cicadas. They are called periodical because nearly all individuals in a local population ...
''
cicadas The cicadas () are a superfamily, the Cicadoidea, of insects in the order Hemiptera (true bugs). They are in the suborder Auchenorrhyncha, along with smaller jumping bugs such as leafhoppers and froghoppers. The superfamily is divided into tw ...
. Because the cicada life cycle takes years underground,
natural selection Natural selection is the differential survival and reproduction of individuals due to differences in phenotype. It is a key mechanism of evolution, the change in the heritable traits characteristic of a population over generations. Char ...
on endosymbiont populations is relaxed for many bacterial generations. This allows the symbiont genomes to diversify within the host for years with only punctuated periods of selection when the cicadas reproduce. As a result, the ancestral '' Hodgkinia'' genome has split into three groups of primary endosymbiont, each encoding only a fraction of the essential genes for the symbiosis. The host now requires all three sub-groups of symbiont, each with degraded genomes lacking most essential genes for bacterial viability.


Bacterial endosymbionts of invertebrates

The best-studied examples of endosymbiosis are known from
invertebrate Invertebrates are a paraphyletic group of animals that neither possess nor develop a vertebral column (commonly known as a ''backbone'' or ''spine''), derived from the notochord. This is a grouping including all animals apart from the chorda ...
s. These symbioses affect organisms with global impact, including ''
Symbiodinium : ''This is about the genus sometimes called Zoox. For the company, see Zoox (company)'' ''Symbiodinium'' is a genus of dinoflagellates that encompasses the largest and most prevalent group of endosymbiotic dinoflagellates known. These unicellu ...
'' of corals, or ''
Wolbachia ''Wolbachia'' is a genus of intracellular bacteria that infects mainly arthropod species, including a high proportion of insects, and also some nematodes. It is one of the most common parasitic microbes, and is possibly the most common repro ...
'' of insects. Many insect agricultural pests and human disease vectors have intimate relationships with primary endosymbionts.


Endosymbionts of insects

Scientists classify insect endosymbionts in two broad categories, 'Primary' and 'Secondary'. Primary endosymbionts (sometimes referred to as P-endosymbionts) have been associated with their
insect Insects (from Latin ') are pancrustacean Hexapoda, hexapod invertebrates of the class (biology), class Insecta. They are the largest group within the arthropod phylum. Insects have a chitinous exoskeleton, a three-part body (head, Thorax (ins ...
hosts for many millions of years (from 10 to several hundred million years in some cases). They form obligate associations (see below), and display cospeciation with their insect hosts. Secondary endosymbionts exhibit a more recently developed association, are sometimes horizontally transferred between hosts, live in the
hemolymph Hemolymph, or haemolymph, is a fluid, analogous to the blood in vertebrates, that circulates in the interior of the arthropod (invertebrate) body, remaining in direct contact with the animal's tissues. It is composed of a fluid plasma in which ...
of the insects (not specialized bacteriocytes, see below), and are not obligate.


Primary endosymbionts

Among primary endosymbionts of insects, the best-studied are the pea
aphid Aphids are small sap-sucking insects and members of the superfamily Aphidoidea. Common names include greenfly and blackfly, although individuals within a species can vary widely in color. The group includes the fluffy white woolly aphids. A ...
(''
Acyrthosiphon pisum ''Acyrthosiphon pisum'', commonly known as the pea aphid (and colloquially known as the green dolphin, pea louse, and clover louse), is a sap-sucking insect in the family Aphididae. It feeds on several species of legumes (plant family Fabaceae) w ...
'') and its endosymbiont '' Buchnera sp.'' APS, the
tsetse fly Tsetse ( , or ) (sometimes spelled tzetze; also known as tik-tik flies), are large, biting flies that inhabit much of tropical Africa. Tsetse flies include all the species in the genus ''Glossina'', which are placed in their own family, Glos ...
''Glossina morsitans morsitans'' and its endosymbiont '' Wigglesworthia glossinidia brevipalpis'' and the endosymbiotic
protists A protist () is any eukaryotic organism (that is, an organism whose cells contain a cell nucleus) that is not an animal, plant, or fungus. While it is likely that protists share a common ancestor (the last eukaryotic common ancestor), the excl ...
in lower
termite Termites are small insects that live in colonies and have distinct castes ( eusocial) and feed on wood or other dead plant matter. Termites comprise the infraorder Isoptera, or alternatively the epifamily Termitoidae, within the order Blatt ...
s. As with endosymbiosis in other insects, the symbiosis is obligate in that neither the bacteria nor the insect is viable without the other. Scientists have been unable to cultivate the bacteria in lab conditions outside of the insect. With special nutritionally-enhanced diets, the insects can survive, but are unhealthy, and at best survive only a few generations. In some insect groups, these endosymbionts live in specialized insect cells called bacteriocytes (also called ''mycetocytes''), and are maternally-transmitted, i.e. the mother transmits her endosymbionts to her offspring. In some cases, the bacteria are transmitted in the
egg An egg is an organic vessel grown by an animal to carry a possibly fertilized egg cell (a zygote) and to incubate from it an embryo within the egg until the embryo has become an animal fetus that can survive on its own, at which point t ...
, as in ''Buchnera''; in others like ''Wigglesworthia'', they are transmitted via milk to the developing insect embryo. In termites, the endosymbionts reside within the hindguts and are transmitted through
trophallaxis Trophallaxis () is the transfer of food or other fluids among members of a community through mouth-to-mouth ( stomodeal) or anus-to-mouth ( proctodeal) feeding. Along with nutrients, trophallaxis can involve the transfer of molecules such as pher ...
among colony members. The primary endosymbionts are thought to help the host either by providing nutrients that the host cannot obtain itself or by metabolizing insect waste products into safer forms. For example, the putative primary role of ''Buchnera'' is to synthesize
essential amino acid An essential amino acid, or indispensable amino acid, is an amino acid that cannot be synthesized from scratch by the organism fast enough to supply its demand, and must therefore come from the diet. Of the 21 amino acids common to all life form ...
s that the aphid cannot acquire from its natural diet of plant sap. Likewise, the primary role of ''Wigglesworthia'', it is presumed, is to synthesize
vitamin A vitamin is an organic molecule (or a set of molecules closely related chemically, i.e. vitamers) that is an essential micronutrient that an organism needs in small quantities for the proper functioning of its metabolism. Essential nutri ...
s that the tsetse fly does not get from the
blood Blood is a body fluid in the circulatory system of humans and other vertebrates that delivers necessary substances such as nutrients and oxygen to the cells, and transports metabolic waste products away from those same cells. Blood in th ...
that it eats. In lower termites, the endosymbiotic protists play a major role in the digestion of lignocellulosic materials that constitute a bulk of the termites' diet. Bacteria benefit from the reduced exposure to
predator Predation is a biological interaction where one organism, the predator, kills and eats another organism, its prey. It is one of a family of common feeding behaviours that includes parasitism and micropredation (which usually do not kill t ...
s and competition from other bacterial species, the ample supply of nutrients and relative environmental stability inside the host. Genome sequencing reveals that obligate bacterial endosymbionts of insects have among the smallest of known bacterial genomes and have lost many genes that are commonly found in closely related bacteria. Several theories have been put forth to explain the loss of genes. It is presumed that some of these genes are not needed in the environment of the host insect cell. A complementary theory suggests that the relatively small numbers of bacteria inside each insect decrease the efficiency of natural selection in 'purging' deleterious mutations and small mutations from the population, resulting in a loss of genes over many millions of years. Research in which a parallel
phylogeny A phylogenetic tree (also phylogeny or evolutionary tree Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA.) is a branching diagram or a tree showing the evolutionary relationships among various biological sp ...
of bacteria and insects was inferred supports the belief that the primary endosymbionts are transferred only vertically (i.e., from the mother), and not horizontally (i.e., by escaping the host and entering a new host). Attacking obligate bacterial endosymbionts may present a way to control their insect hosts, many of which are pests or carriers of human disease. For example, aphids are crop pests and the tsetse fly carries the organism ''
Trypanosoma brucei ''Trypanosoma brucei'' is a species of parasitic kinetoplastid belonging to the genus '' Trypanosoma'' that is present in sub-Saharan Africa. Unlike other protozoan parasites that normally infect blood and tissue cells, it is exclusively extracell ...
'' that causes African
sleeping sickness African trypanosomiasis, also known as African sleeping sickness or simply sleeping sickness, is an insect-borne parasitic infection of humans and other animals. It is caused by the species ''Trypanosoma brucei''. Humans are infected by two ty ...
. Other motivations for their study involve understanding the origins of symbioses in general, as a proxy for understanding e.g. how chloroplasts or mitochondria came to be obligate symbionts of
eukaryotes Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bact ...
or plants.


Secondary endosymbionts

The pea aphid (''
Acyrthosiphon pisum ''Acyrthosiphon pisum'', commonly known as the pea aphid (and colloquially known as the green dolphin, pea louse, and clover louse), is a sap-sucking insect in the family Aphididae. It feeds on several species of legumes (plant family Fabaceae) w ...
'') is known to contain at least three secondary endosymbionts, ''
Hamiltonella defensa ''Hamiltonella defensa'' (''H. defensa'') is a species of bacteria. It is maternally or sexually transmitted and lives as an endosymbiont of whiteflies and aphids, meaning that it lives within a host, protecting its host from attack. It does thi ...
'', '' Regiella insecticola'', and '' Serratia symbiotica''. ''Hamiltonella defensa'' defends its aphid host from parasitoid wasps. This defensive symbiosis improves the survival of aphids, which have lost some elements of the insect immune response. One of the best-understood defensive symbionts is the spiral bacteria '' Spiroplasma poulsonii''. ''Spiroplasma sp.'' can be reproductive manipulators, but also defensive symbionts of ''
Drosophila ''Drosophila'' () is a genus of flies, belonging to the family Drosophilidae, whose members are often called "small fruit flies" or (less frequently) pomace flies, vinegar flies, or wine flies, a reference to the characteristic of many specie ...
'' flies. In '' Drosophila neotestacea'', ''S. poulsonii'' has spread across North America owing to its ability to defend its fly host against nematode parasites. This defence is mediated by toxins called "ribosome-inactivating proteins" that attack the molecular machinery of invading parasites. These ''Spiroplasma'' toxins represent one of the first examples of a defensive symbiosis with a mechanistic understanding for defensive symbiosis between an insect endosymbiont and its host. '' Sodalis glossinidius'' is a secondary endosymbiont of tsetse flies that lives inter- and intracellularly in various host tissues, including the midgut and hemolymph. Phylogenetic studies have not indicated a correlation between evolution of '' Sodalis'' and tsetse. Unlike tsetse's primary symbiont ''Wigglesworthia'', though, ''Sodalis'' has been cultured ''in vitro''. Many other insects have secondary endosymbionts not reviewed here.


Endosymbionts of ants


Bacteriocyte-associated symbionts

The most well studied endosymbiont of ants are bacteria of the genus Blochmannia, which are the primary endosymbiont of Camponotus ants. In 2018 a new ant-associated symbiont was discovered in
Cardiocondyla ''Cardiocondyla'' is an Old World genus of ants in the subfamily Myrmicinae. Distribution Approximately 70 species are currently recognized as belonging to this genus, most of which are distributed in the Old World tropics and subtropics, but a ...
ants. This symbiont was named Candidatus Westeberhardia Cardiocondylae and it is also believed to be a primary symbiont.


Endosymbionts of marine invertebrates

Extracellular endosymbionts are also represented in all four extant classes of
Echinodermata An echinoderm () is any member of the phylum Echinodermata (). The adults are recognisable by their (usually five-point) radial symmetry, and include starfish, brittle stars, sea urchins, sand dollars, and sea cucumbers, as well as the sea l ...
(
Crinoidea Crinoids are marine animals that make up the class Crinoidea. Crinoids that are attached to the sea bottom by a stalk in their adult form are commonly called sea lilies, while the unstalked forms are called feather stars or comatulids, which ar ...
,
Ophiuroidea Brittle stars, serpent stars, or ophiuroids (; ; referring to the serpent-like arms of the brittle star) are echinoderms in the class Ophiuroidea, closely related to starfish. They crawl across the sea floor using their flexible arms for locomo ...
,
Echinoidea Sea urchins () are spiny, globular echinoderms in the class Echinoidea. About 950 species of sea urchin live on the seabed of every ocean and inhabit every depth zone from the intertidal seashore down to . The spherical, hard shells ( tests) o ...
, and
Holothuroidea Sea cucumbers are echinoderms from the class Holothuroidea (). They are marine animals with a leathery skin and an elongated body containing a single, branched gonad. Sea cucumbers are found on the sea floor worldwide. The number of holothuri ...
). Little is known of the nature of the association (mode of infection, transmission, metabolic requirements, etc.) but
phylogenetic In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups o ...
analysis indicates that these symbionts belong to the class
Alphaproteobacteria Alphaproteobacteria is a class of bacteria in the phylum Pseudomonadota (formerly Proteobacteria). The Magnetococcales and Mariprofundales are considered basal or sister to the Alphaproteobacteria. The Alphaproteobacteria are highly diverse an ...
, relating them to ''Rhizobium'' and ''Thiobacillus''. Other studies indicate that these subcuticular bacteria may be both abundant within their hosts and widely distributed among the Echinoderms in general. Some marine
oligochaeta Oligochaeta () is a subclass of animals in the phylum Annelida, which is made up of many types of aquatic and terrestrial worms, including all of the various earthworms. Specifically, oligochaetes comprise the terrestrial megadrile earthwor ...
(e.g., '' Olavius algarvensis'' and '' Inanidrillus spp.'') have obligate extracellular endosymbionts that fill the entire body of their host. These marine worms are nutritionally dependent on their symbiotic chemoautotrophic bacteria lacking any digestive or excretory system (no gut, mouth, or
nephridia The nephridium (plural ''nephridia'') is an invertebrate organ, found in pairs and performing a function similar to the vertebrate kidneys (which originated from the chordate nephridia). Nephridia remove metabolic wastes from an animal's body. Neph ...
). The sea slug '' Elysia chlorotica'' lives in endosymbiotic relationship with the algae '' Vaucheria litorea'', and the jellyfish '' Mastigias'' have a similar relationship with an algae.


Dinoflagellate endosymbionts

Dinoflagellate The dinoflagellates ( Greek δῖνος ''dinos'' "whirling" and Latin ''flagellum'' "whip, scourge") are a monophyletic group of single-celled eukaryotes constituting the phylum Dinoflagellata and are usually considered algae. Dinoflagellates ...
endosymbionts of the genus ''Symbiodinium'', commonly known as
zooxanthella Zooxanthellae is a colloquial term for single-celled dinoflagellates that are able to live in symbiosis with diverse marine invertebrates including demosponges, corals, jellyfish, and nudibranchs. Most known zooxanthellae are in the genus ''Symbi ...
e, are found in
corals Corals are marine invertebrates within the class (biology), class Anthozoa of the phylum Cnidaria. They typically form compact Colony (biology), colonies of many identical individual polyp (zoology), polyps. Coral species include the important C ...
,
mollusk Mollusca is the second-largest phylum of invertebrate animals after the Arthropoda, the members of which are known as molluscs or mollusks (). Around 85,000  extant species of molluscs are recognized. The number of fossil species is es ...
s (esp.
giant clam The giant clams are the members of the clam genus ''Tridacna'' that are the largest living bivalve mollusks. There are actually several species of "giant clams" in the genus ''Tridacna'', which are often misidentified for ''Tridacna gigas'', t ...
s, the ''Tridacna''),
sponges Sponges, the members of the phylum Porifera (; meaning 'pore bearer'), are a basal animal clade as a sister of the diploblasts. They are multicellular organisms that have bodies full of pores and channels allowing water to circulate through th ...
, and
foraminifera Foraminifera (; Latin for "hole bearers"; informally called "forams") are single-celled organisms, members of a phylum or class of amoeboid protists characterized by streaming granular ectoplasm for catching food and other uses; and commonly a ...
. These endosymbionts drive the formation of
coral reefs A coral reef is an underwater ecosystem characterized by reef-building corals. Reefs are formed of colonies of coral polyps held together by calcium carbonate. Most coral reefs are built from stony corals, whose polyps cluster in groups. C ...
by capturing sunlight and providing their hosts with energy for
carbonate A carbonate is a salt of carbonic acid (H2CO3), characterized by the presence of the carbonate ion, a polyatomic ion with the formula . The word ''carbonate'' may also refer to a carbonate ester, an organic compound containing the carbonate g ...
deposition. Previously thought to be a single species, molecular
phylogenetic In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups o ...
evidence over the past couple decades has shown there to be great diversity in ''Symbiodinium''. In some cases, there is specificity between host and ''Symbiodinium''
clade A clade (), also known as a monophyletic group or natural group, is a group of organisms that are monophyletic – that is, composed of a common ancestor and all its lineal descendants – on a phylogenetic tree. Rather than the English term, ...
. More often, however, there is an ecological distribution of ''Symbiodinium'', the symbionts switching between hosts with apparent ease. When reefs become environmentally stressed, this distribution of symbionts is related to the observed pattern of
coral bleaching Coral bleaching is the process when corals become white due to various stressors, such as changes in temperature, light, or nutrients. Bleaching occurs when coral polyps expel the zooxanthellae (dinoflagellates that are commonly referred to as al ...
and recovery. Thus, the distribution of ''Symbiodinium'' on coral reefs and its role in coral bleaching presents one of the most complex and interesting current problems in reef
ecology Ecology () is the study of the relationships between living organisms, including humans, and their physical environment. Ecology considers organisms at the individual, population, community, ecosystem, and biosphere level. Ecology overlaps ...
.


Endosymbionts of phytoplankton

In marine environments, bacterial endosymbionts have more recently been discovered. These endosymbiotic relationships are especially prevalent in
oligotrophic An oligotroph is an organism that can live in an environment that offers very low levels of nutrients. They may be contrasted with copiotrophs, which prefer nutritionally rich environments. Oligotrophs are characterized by slow growth, low rates o ...
or nutrient-poor regions of the ocean like that of the North Atlantic. In these oligotrophic waters, cell growth of larger phytoplankton like that of
diatom A diatom (New Latin, Neo-Latin ''diatoma''), "a cutting through, a severance", from el, διάτομος, diátomos, "cut in half, divided equally" from el, διατέμνω, diatémno, "to cut in twain". is any member of a large group com ...
s is limited by low nitrate concentrations.  Endosymbiotic bacteria fix nitrogen for their diatom hosts and in turn receive organic carbon from photosynthesis. These symbioses play an important role in global carbon cycling in oligotrophic regions. One known symbiosis between the diatom '' Hemialus'' spp. and the cyanobacterium ''Richelia intracellularis'' has been found in the North Atlantic, Mediterranean, and Pacific Ocean. The ''Richelia'' endosymbiont is found within the diatom frustule of ''Hemiaulus'' spp., and has a reduced genome likely losing genes related to pathways the host now provides.  Research by Foster et al. (2011) measured nitrogen fixation by the cyanobacterial host ''Richelia intracellularis'' well above intracellular requirements, and found the cyanobacterium was likely fixing excess nitrogen for Hemiaulus host cells. Additionally, both host and symbiont cell growth were much greater than free-living ''Richelia intracellularis'' or symbiont-free ''Hemiaulus'' spp. The ''Hemaiulus''-''Richelia'' symbiosis is not obligatory especially in areas with excess nitrogen (nitrogen replete). ''Richelia intracellularis'' is also found in ''Rhizosolenia'' spp., a diatom found in oligotrophic oceans. Compared to the ''Hemaiulus'' host, the endosymbiosis with ''Rhizosolenia'' is much more consistent, and ''Richelia intracellularis'' is generally found in ''Rhizosolenia''. There are some asymbiotic (occurs without an endosymbiont) Rhizosolenia, however there appears to be mechanisms limiting growth of these organisms in low nutrient conditions. Cell division for both the diatom host and cyanobacterial symbiont can be uncoupled and mechanisms for passing bacterial symbionts to daughter cells during cell division are still relatively unknown. Other endosymbiosis with nitrogen fixers in open oceans include Calothrix in Chaetocerous spp. and UNCY-A in prymnesiophyte microalga.  The Chaetocerous-Calothrix endosymbiosis is hypothesized to be more recent, as the Calothrix genome is generally intact. While other species like that of the UNCY-A symbiont and Richelia have reduced genomes. This reduction in genome size occurs within nitrogen metabolism pathways indicating endosymbiont species are generating nitrogen for their hosts and losing the ability to use this nitrogen independently. This endosymbiont reduction in genome size, might be a step that occurred in the evolution of organelles (above).


Endosymbionts of protists

'' Mixotricha paradoxa'' is a protozoan that lacks mitochondria. However, spherical bacteria live inside the cell and serve the function of the mitochondria. ''Mixotricha'' also has three other species of symbionts that live on the surface of the cell. '' Paramecium bursaria'', a species of
ciliate The ciliates are a group of alveolates characterized by the presence of hair-like organelles called cilia, which are identical in structure to eukaryotic flagella, but are in general shorter and present in much larger numbers, with a different ...
, has a mutualistic symbiotic relationship with green alga called ''
Zoochlorella ''Zoochlorella'' is a ''nomen rejiciendum'' for a genus of green algae assigned to '' Chlorella''. The term zoochlorella (plural zoochlorellae) is sometimes used to refer to any green algae that lives symbiotically within the body of a freshwate ...
''. The algae live inside the cell, in the cytoplasm. '' Paulinella chromatophora'' is a freshwater
amoeboid An amoeba (; less commonly spelled ameba or amœba; plural ''am(o)ebas'' or ''am(o)ebae'' ), often called an amoeboid, is a type of cell or unicellular organism with the ability to alter its shape, primarily by extending and retracting pseudo ...
which has recently (evolutionarily speaking) taken on a
cyanobacterium Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, blue ...
as an endosymbiont. Many
foraminifera Foraminifera (; Latin for "hole bearers"; informally called "forams") are single-celled organisms, members of a phylum or class of amoeboid protists characterized by streaming granular ectoplasm for catching food and other uses; and commonly a ...
are hosts to several types of algae, such as
red algae Red algae, or Rhodophyta (, ; ), are one of the oldest groups of eukaryotic algae. The Rhodophyta also comprises one of the largest phyla of algae, containing over 7,000 currently recognized species with taxonomic revisions ongoing. The majority ...
,
diatom A diatom (New Latin, Neo-Latin ''diatoma''), "a cutting through, a severance", from el, διάτομος, diátomos, "cut in half, divided equally" from el, διατέμνω, diatémno, "to cut in twain". is any member of a large group com ...
s,
dinoflagellate The dinoflagellates ( Greek δῖνος ''dinos'' "whirling" and Latin ''flagellum'' "whip, scourge") are a monophyletic group of single-celled eukaryotes constituting the phylum Dinoflagellata and are usually considered algae. Dinoflagellates ...
s and
chlorophyta Chlorophyta or Prasinophyta is a taxon of green algae informally called chlorophytes. The name is used in two very different senses, so care is needed to determine the use by a particular author. In older classification systems, it refers to a ...
. These endosymbionts can be transmitted vertically to the next generation via asexual reproduction of the host, but because the endosymbionts are larger than the foraminiferal
gamete A gamete (; , ultimately ) is a haploid cell that fuses with another haploid cell during fertilization in organisms that reproduce sexually. Gametes are an organism's reproductive cells, also referred to as sex cells. In species that produce ...
s, they need to acquire new algae again after sexual reproduction. Several species of
radiolaria The Radiolaria, also called Radiozoa, are protozoa of diameter 0.1–0.2 mm that produce intricate mineral skeletons, typically with a central capsule dividing the cell into the inner and outer portions of endoplasm and ectoplasm. The ela ...
have photosynthetic symbionts. In some species the host will sometimes digest algae to keep their population at a constant level. '' Hatena arenicola'' is a flagellate protist with a complicated feeding apparaturs that feed on other microbes. But when it engulfs a green alga from the genus ''Nephroselmis'', the feeding apparatus disappears and it becomes photosynthetic. During
mitosis In cell biology, mitosis () is a part of the cell cycle in which replicated chromosomes are separated into two new nuclei. Cell division by mitosis gives rise to genetically identical cells in which the total number of chromosomes is maintai ...
the algae is transferred to only one of the two cells, and the cell without the algae needs to start the cycle all over again. In 1976, biologist Kwang W. Jeon found that a lab strain of ''
Amoeba proteus ''Amoeba proteus'' is a large species of amoeba closely related to another genus of giant amoebae, '' Chaos''. As such, the species is sometimes given the alternative scientific name ''Chaos diffluens''. This protozoan uses extensions called ps ...
'' had been infected by bacteria that lived inside the cytoplasmic
vacuoles A vacuole () is a membrane-bound organelle which is present in plant and fungal cells and some protist, animal, and bacterial cells. Vacuoles are essentially enclosed compartments which are filled with water containing inorganic and organic mo ...
. This infection killed all the protists except for a few individuals. After the equivalent of 40 host generations, the two organisms gradually became mutually interdependent. Over many years of study, it has been confirmed that a genetic exchange between the
prokaryotes A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Con ...
and protists had occurred.


Endosymbionts of vertebrates

The spotted salamander ('' Ambystoma maculatum'') lives in a relationship with the algae ''
Oophila amblystomatis ''Chlorococcum amblystomatis'', synonym ''Oophila amblystomatis'', commonly known as chlamydomonad algae or salamander algae, is a species of single-celled green algae. When placed in the genus ''Oophila'', it was the only species. The Latin ...
'', which grows in the egg cases.


Endosymbionts of plants

Plant Plants are predominantly photosynthetic eukaryotes of the kingdom Plantae. Historically, the plant kingdom encompassed all living things that were not animals, and included algae and fungi; however, all current definitions of Plantae ex ...
s are diverse
photosynthetic Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored in ...
eukaryote Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bact ...
s having wide variety of cell morphologies and lifestyles. Plants are considered one of the primary
producers Producer or producers may refer to: Occupations * Producer (agriculture), a farm operator *A stakeholder of economic production *Film producer, supervises the making of films **Executive producer, contributes to a film's budget and usually does n ...
. Plants with all photosynthetic eukaryotes are dependent on an intracellular
organelle In cell biology, an organelle is a specialized subunit, usually within a cell, that has a specific function. The name ''organelle'' comes from the idea that these structures are parts of cells, as organs are to the body, hence ''organelle,'' the ...
known as
plastid The plastid (Greek: πλαστός; plastós: formed, molded – plural plastids) is a membrane-bound organelle found in the cells of plants, algae, and some other eukaryotic organisms. They are considered to be intracellular endosymbiotic cya ...
or
chloroplast A chloroplast () is a type of membrane-bound organelle known as a plastid that conducts photosynthesis mostly in plant and algal cells. The photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it in ...
(in case of
plant Plants are predominantly photosynthetic eukaryotes of the kingdom Plantae. Historically, the plant kingdom encompassed all living things that were not animals, and included algae and fungi; however, all current definitions of Plantae ex ...
s and
green algae The green algae (singular: green alga) are a group consisting of the Prasinodermophyta and its unnamed sister which contains the Chlorophyta and Charophyta/Streptophyta. The land plants ( Embryophytes) have emerged deep in the Charophyte alga ...
). The chloroplast is derived from a cyanobacterial primary endosymbiosis over one billion years ago. The oxygenic photosynthetic free-living
cyanobacterium Cyanobacteria (), also known as Cyanophyta, are a phylum of gram-negative bacteria that obtain energy via photosynthesis. The name ''cyanobacteria'' refers to their color (), which similarly forms the basis of cyanobacteria's common name, blue ...
was engulfed and kept by a heterotrophic
protist A protist () is any eukaryotic organism (that is, an organism whose cells contain a cell nucleus) that is not an animal, plant, or fungus. While it is likely that protists share a common ancestor (the last eukaryotic common ancestor), the exclu ...
and eventually evolved into the present intracellular organelle over the course of many years.   The term
symbiosis Symbiosis (from Greek , , "living together", from , , "together", and , bíōsis, "living") is any type of a close and long-term biological interaction between two different biological organisms, be it mutualistic, commensalistic, or parasi ...
is defined as "living together" of unlike organisms. The
symbioses Symbiosis (from Greek , , "living together", from , , "together", and , bíōsis, "living") is any type of a close and long-term biological interaction between two different biological organisms, be it mutualistic, commensalistic, or parasit ...
have been recognized and studied since 1879. The plant
symbioses Symbiosis (from Greek , , "living together", from , , "together", and , bíōsis, "living") is any type of a close and long-term biological interaction between two different biological organisms, be it mutualistic, commensalistic, or parasit ...
can be categorized into
epiphytic An epiphyte is an organism that grows on the surface of a plant and derives its moisture and nutrients from the air, rain, water (in marine environments) or from debris accumulating around it. The plants on which epiphytes grow are called phoroph ...
,
endophytic An endophyte is an endosymbiont, often a bacterium or fungus, that lives within a plant for at least part of its life cycle without causing apparent disease. Endophytes are ubiquitous and have been found in all species of plants studied to date; h ...
, and
mycorrhiza   A mycorrhiza (from Greek μύκης ', "fungus", and ῥίζα ', "root"; pl. mycorrhizae, mycorrhiza or mycorrhizas) is a symbiotic association between a fungus and a plant. The term mycorrhiza refers to the role of the fungus in the plan ...
l. The mycorrhizal category is only used for
fungi A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from ...
. The
endosymbiosis An ''endosymbiont'' or ''endobiont'' is any organism that lives within the body or cells of another organism most often, though not always, in a mutualistic relationship. (The term endosymbiosis is from the Greek: ἔνδον ''endon'' "within" ...
relation of plants and endosymbionts can also be categorized into beneficial, mutualistic, neutral, and
pathogen In biology Biology is the scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of cells that process ...
ic. Typically, most of the studies related to plan symbioses or plant endosymbionts such as
endophytic An endophyte is an endosymbiont, often a bacterium or fungus, that lives within a plant for at least part of its life cycle without causing apparent disease. Endophytes are ubiquitous and have been found in all species of plants studied to date; h ...
bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...
or
fungi A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from ...
, are focused on a single category or
specie Specie may refer to: * Coins or other metal money in mass circulation * Bullion coins * Hard money (policy) * Commodity money * Specie Circular, 1836 executive order by US President Andrew Jackson regarding hard money * Specie Payment Resumption A ...
to better understand the biological processes and functions one at a time. But this approach is not helping to understand the complex endosymbiotic interactions and biological functions in natural
habitat In ecology, the term habitat summarises the array of resources, physical and biotic factors that are present in an area, such as to support the survival and reproduction of a particular species. A species habitat can be seen as the physical ...
.
Microorganism A microorganism, or microbe,, ''mikros'', "small") and ''organism'' from the el, ὀργανισμός, ''organismós'', "organism"). It is usually written as a single word but is sometimes hyphenated (''micro-organism''), especially in olde ...
s living in association as endosymbionts with plants can enhance the primary productivity of plants either by producing or capturing the limiting resources. These endosymbionts can also enhance the productivity of plants by the production of toxic metabolites helping plant defenses against
herbivore A herbivore is an animal anatomically and physiologically adapted to eating plant material, for example foliage or marine algae, for the main component of its diet. As a result of their plant diet, herbivorous animals typically have mouthp ...
s . Although, the role and potential of microorganisms in community regulations has been neglected since long, may because of the
microscopic The microscopic scale () is the scale of objects and events smaller than those that can easily be seen by the naked eye, requiring a lens or microscope to see them clearly. In physics, the microscopic scale is sometimes regarded as the scale bet ...
size and unseen lifestyle. Theoretically, all the vascular plants harbor endosymbionts (e.g., fungi and bacteria). these endosymbionts colonize the plants
cells Cell most often refers to: * Cell (biology), the functional basic unit of life Cell may also refer to: Locations * Monastic cell, a small room, hut, or cave in which a religious recluse lives, alternatively the small precursor of a monastery w ...
and tissue predominantly but not exclusively. Plant endosymbionts can be categorized into different types based on the function, relation and location, some common plant endosymbionts are discussed as follow.


Endophytes

The term endophytic has been defined and discussed multiple times. Generally, the term implies to the organism that is living inside of the plant. More recently it is more focused on the
microorganism A microorganism, or microbe,, ''mikros'', "small") and ''organism'' from the el, ὀργανισμός, ''organismós'', "organism"). It is usually written as a single word but is sometimes hyphenated (''micro-organism''), especially in olde ...
that live inside the plant tissues and do no harm to the plant. According to the latest definition, the
endophyte An endophyte is an endosymbiont, often a bacterium or fungus, that lives within a plant for at least part of its life cycle without causing apparent disease. Endophytes are ubiquitous and have been found in all species of plants studied to date ...
s are those microorganisms which lives in the internal plant tissues for a major part of their life cycle and as long as they don’t induce any infectious or harmful effect to the host plant. These endophytes include includes
bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...
,
fungi A fungus ( : fungi or funguses) is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, separately from ...
,
virus A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Since Dmitri Ivanovsky' ...
es,
protozoa Protozoa (singular: protozoan or protozoon; alternative plural: protozoans) are a group of single-celled eukaryotes, either free-living or parasitic, that feed on organic matter such as other microorganisms or organic tissues and debris. His ...
and even
microalgae Microalgae or microphytes are microscopic algae invisible to the naked eye. They are phytoplankton typically found in freshwater and marine systems, living in both the water column and sediment. They are unicellular species which exist indiv ...
. Endophytes helps plant in biological processes such as growth and development, nutrient uptake and defense against biotic and abiotic stresses like
drought A drought is defined as drier than normal conditions.Douville, H., K. Raghavan, J. Renwick, R.P. Allan, P.A. Arias, M. Barlow, R. Cerezo-Mota, A. Cherchi, T.Y. Gan, J. Gergis, D.  Jiang, A.  Khan, W.  Pokam Mba, D.  Rosenfeld, J. Tierney, an ...
,
salinity Salinity () is the saltiness or amount of salt dissolved in a body of water, called saline water (see also soil salinity). It is usually measured in g/L or g/kg (grams of salt per liter/kilogram of water; the latter is dimensionless and equal t ...
, heat, herbivores etc. The endophytes are in mutualistic relation to the host plant which means that the endophytes are not only helping plants but also get benefits from plant. So, the endophytes can be described as plant endosymbionts.


Fungi as plant endosymbionts

All vascular plants have fungal and bacterial endophytes or endosymbionts which colonize predominantly but not exclusively, roots. Fungal endosymbionts can be found all out the plant tissues and based on their location in the plant, fungal endosymbionts can be defined in multiple ways like fungi living in plant tissues above the ground are termed as endophytes, while fungi living below the ground (roots) are known as mycorrhizal, but the mycorrhizal fungi also have different names based on their location inside the root which are ecto, endo, arbuscular, ericoid, etc. Furthermore, the fungal endosymbionts living in the roots and extending their extraradical hyphae into the outer rhizosphere are known as ectendosymbionts.


Arbuscular Mycorrhizal Fungi (AMF)

Among the plant microbial endosymbionts
arbuscular mycorrhizal fungi An arbuscular mycorrhiza (AM) (plural ''mycorrhizae'', a.k.a. ''endomycorrhiza'') is a type of mycorrhiza in which the symbiont fungus (''AM fungi'', or AMF) penetrates the cortical cells of the roots of a vascular plant forming arbuscules. (N ...
or AMF are the most diverse group. With some exceptions
Ericaceae The Ericaceae are a family of flowering plants, commonly known as the heath or heather family, found most commonly in acidic and infertile growing conditions. The family is large, with c.4250 known species spread across 124 genera, making it ...
family, almost all vascular plants are harboring the AMF endosymbionts both as endo and ecto as well. The AMF plant endosymbionts systematically colonize the
plant roots In vascular plants, the roots are the organs of a plant that are modified to provide anchorage for the plant and take in water and nutrients into the plant body, which allows plants to grow taller and faster. They are most often below the su ...
and helping plant host by soil
nutrient A nutrient is a substance used by an organism to survive, grow, and reproduce. The requirement for dietary nutrient intake applies to animals, plants, fungi, and protists. Nutrients can be incorporated into cells for metabolic purposes or excret ...
s and as a return it takes the plant organic carbon sources. Plant roots exudates contain a diversity of secondary metabolites especially flavonoids and strigolactones which acts as chemical signals and attracts the AMF. Arbuscular mycyrrizal fungus '' Gigaspora margarita'' not only lives as a plant endosymbiont but also harbor further endosymbiont intracytoplasmic bacterium-like organisms. By isolating the pure cultures of AMF endosymbionts, it has been reported that it has different effects to the different plant hosts. By introducing the AMF of one plant can reduce the net growth of the other plant host which might have to do something with already present AMF. Furthermore, the AMF are reported in numerous studies as plant health and growth promoting and as an alleviating agent for
abiotic stress Abiotic stress is the negative impact of non-living factors on the living organisms in a specific environment. The non-living variable must influence the environment beyond its normal range of variation to adversely affect the population performan ...
es like salinity, drought, heat, poor nutrition and
metal toxicity Metal toxicity or metal poisoning is the toxic effect of certain metals in certain forms and doses on life. Some metals are toxic when they form poisonous soluble compounds. Certain metals have no biological role, i.e. are not essential minerals ...
.


Endophytic Fungi

In addition to
mycorrhiza   A mycorrhiza (from Greek μύκης ', "fungus", and ῥίζα ', "root"; pl. mycorrhizae, mycorrhiza or mycorrhizas) is a symbiotic association between a fungus and a plant. The term mycorrhiza refers to the role of the fungus in the plan ...
l endosymbionts, the endophytic fungi are also catching the interest of scientist by showing so much potential not only in its mutualistic relation where it is benefiting host plant and taking advantages as well but also showing promising results in other domains like helping plant to grow in
polluted Pollution is the introduction of contaminants into the natural environment that cause adverse change. Pollution can take the form of any substance (solid, liquid, or gas) or energy (such as radioactivity, heat, sound, or light). Pollutants, the ...
environment such as high polluted environment with toxic metals. Fungal
endophyte An endophyte is an endosymbiont, often a bacterium or fungus, that lives within a plant for at least part of its life cycle without causing apparent disease. Endophytes are ubiquitous and have been found in all species of plants studied to date ...
s are taxonomically diverse group of omnipresent fungi which is divided into different categories based on mode of transmission,
biodiversity Biodiversity or biological diversity is the variety and variability of life on Earth. Biodiversity is a measure of variation at the genetic ('' genetic variability''), species ('' species diversity''), and ecosystem (''ecosystem diversity'') ...
, in planta colonization and host plant type. These categories are clavicipitaceous and non-clavicipitaceous, the former one systematically colonizes the temperate season grasses while the later one colonizes higher plants and even roots and that’s why can be divided into further categories. ''Bacillus amyloliquefaciens'' is a seed born endophytic fungi which produces gibberellins and promotes the physiology. ''
Bacillus amyloliquefaciens ''Bacillus amyloliquefaciens'' is a species of bacterium in the genus ''Bacillus'' that is the source of the BamHI restriction enzyme. It also synthesizes a natural antibiotic protein barnase, a widely studied ribonuclease that forms a famously ...
'' has been evaluated in a study for its growth promoting potential where it promotes the longer height of
transgenic A transgene is a gene that has been transferred naturally, or by any of a number of genetic engineering techniques, from one organism to another. The introduction of a transgene, in a process known as transgenesis, has the potential to change t ...
dwarf rice plants. Similarly, '' Aureobasidium ''and '' preussia'' species of endophytic fungi isolated from
Boswellia sacra ''Boswellia sacra'' (commonly known as frankincense or olibanum-tree) is a tree in the Burseraceae family. It is the primary tree in the genus ''Boswellia'' from which frankincense, a resinous dried sap, is harvested. It is native to the Arabian ...
are producing indole acetic acid hormone to promote plant health and development.
Aphid Aphids are small sap-sucking insects and members of the superfamily Aphidoidea. Common names include greenfly and blackfly, although individuals within a species can vary widely in color. The group includes the fluffy white woolly aphids. A ...
s are most common
insect Insects (from Latin ') are pancrustacean Hexapoda, hexapod invertebrates of the class (biology), class Insecta. They are the largest group within the arthropod phylum. Insects have a chitinous exoskeleton, a three-part body (head, Thorax (ins ...
s and can be found in most of the plants and carnivorous
ladybirds Coccinellidae () is a widespread family of small beetles ranging in size from . They are commonly known as ladybugs in North America and ladybirds in Great Britain. Some entomologists prefer the names ladybird beetles or lady beetles as they ...
are the specialized predators of the aphids. These ladybirds are used in different programs for the
pest control Pest control is the regulation or management of a species defined as a pest; any animal, plant or fungus that impacts adversely on human activities or environment. The human response depends on the importance of the damage done and will range ...
. A study conducted on the effect of plant-endophyte symbiosis on the population and fitness of carnivorous ladybirds. The plant endophytic fungus '' Neotyphodium lolii'' is producing
alkaloid Alkaloids are a class of basic, naturally occurring organic compounds that contain at least one nitrogen atom. This group also includes some related compounds with neutral and even weakly acidic properties. Some synthetic compounds of similar st ...
mycotoxins in response to
aphid Aphids are small sap-sucking insects and members of the superfamily Aphidoidea. Common names include greenfly and blackfly, although individuals within a species can vary widely in color. The group includes the fluffy white woolly aphids. A ...
invasions. The ladybirds picking on the aphids from the infected plants exhibited reduced rate of
fertility Fertility is the capability to produce offspring through reproduction following the onset of sexual maturity. The fertility rate is the average number of children born by a female during her lifetime and is quantified demographically. Ferti ...
and abnormal reproductive performance. Adult
ladybirds Coccinellidae () is a widespread family of small beetles ranging in size from . They are commonly known as ladybugs in North America and ladybirds in Great Britain. Some entomologists prefer the names ladybird beetles or lady beetles as they ...
were not significantly affected in terms of their body symmetries and size. But the consistently strong negative effects of endophytes overall fitness of ladybirds suggest that the mycotoxins are transmitted along the
food chain A food chain is a linear network of links in a food web starting from producer organisms (such as grass or algae which produce their own food via photosynthesis) and ending at an apex predator species (like grizzly bears or killer whales), ...
and effecting the top
predators Predation is a biological interaction where one organism, the predator, kills and eats another organism, its prey. It is one of a family of common feeding behaviours that includes parasitism and micropredation (which usually do not kill th ...
.


Endophytic Bacteria

Endophytic An endophyte is an endosymbiont, often a bacterium or fungus, that lives within a plant for at least part of its life cycle without causing apparent disease. Endophytes are ubiquitous and have been found in all species of plants studied to date; h ...
bacteria belong to a diverse group of plant endosymbionts and characterized by systematically colonization of plant internal tissues. Generally, the endophytic bacteria are isolated from the plant tissues by surface sterilization of the plant tissue in a sterile environment.  Moreover, the isolation of endophytic bacteria according to their essential needs in
niche Niche may refer to: Science * Developmental niche, a concept for understanding the cultural context of child development *Ecological niche, a term describing the relational position of an organism's species * Niche differentiation, in ecology, th ...
occupations has been explored. That’s why the endophytic bacterial community can be divided into "passenger" and "true"
endophyte An endophyte is an endosymbiont, often a bacterium or fungus, that lives within a plant for at least part of its life cycle without causing apparent disease. Endophytes are ubiquitous and have been found in all species of plants studied to date ...
s. The passenger endophytic bacteria are those who eventually colonize inner tissue of plant by
stochastic Stochastic (, ) refers to the property of being well described by a random probability distribution. Although stochasticity and randomness are distinct in that the former refers to a modeling approach and the latter refers to phenomena themselve ...
events while the true endophytes possess adaptive traits because of which they live in association with plants strictly. the in vitro cultivated endophytic
bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...
association with plant is considered a more intimate relationship where it helps plant acclimatize to the conditions and promotes health and growth. The endophytic bacteria are considered as plant's essential endosymbionts because virtually all plants harbor it, and these endosymbionts play essential roles in host plant survival. This plant-endosymbiont relation is important in terms of
ecology Ecology () is the study of the relationships between living organisms, including humans, and their physical environment. Ecology considers organisms at the individual, population, community, ecosystem, and biosphere level. Ecology overlaps ...
,
evolution Evolution is change in the heredity, heritable Phenotypic trait, characteristics of biological populations over successive generations. These characteristics are the Gene expression, expressions of genes, which are passed on from parent to ...
and diversity. Moreover, the endophytic bacteria such as ''
Sphingomonas ''Sphingomonas'' was defined in 1990 as a group of Gram-negative, rod-shaped, chemoheterotrophic, strictly aerobic bacteria. They possess ubiquinone 10 as their major respiratory quinone, contain glycosphingolipids (GSLs), specifically ceramide ...
'' sp. and ''
Serratia ''Serratia'' is a genus of Gram-negative, facultatively anaerobic, rod-shaped bacteria of the family Yersiniaceae. According to the List of Prokaryotic names with Standing Nomenclature (LPSN), there are currently 19 species of ''Serratia'' that ...
'' sp. being isolated from arid land plants regulate endogenous
hormone A hormone (from the Greek participle , "setting in motion") is a class of signaling molecules in multicellular organisms that are sent to distant organs by complex biological processes to regulate physiology and behavior. Hormones are required ...
content and promote growth in crop plants.


Archaea as plant endosymbionts

Archaea Archaea ( ; singular archaeon ) is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes. Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archae ...
are members of most microbiomes. While archaea are highly abundant in extreme environments, they are less abundant and diverse in association with eukaryotic hosts. Nevertheless, archaea are a substantial constituent of plant-associated ecosystems in the aboveground and belowground phytobiome, and play a role in host plant’s health, growth and survival in biotic and abiotic stresses. However, only a few studies have investigated the role of archaea in plant health and its potential symbiosis in ecosystems. Generally, most of the plant endosymbiont related studies focus on fungal or bacterial endosymbionts using metagenomic approaches. The characterization of archaea is not only limited to crop plants like
rice Rice is the seed of the grass species ''Oryza sativa'' (Asian rice) or less commonly '' Oryza glaberrima'' (African rice). The name wild rice is usually used for species of the genera '' Zizania'' and ''Porteresia'', both wild and domesticate ...
and
maize Maize ( ; ''Zea mays'' subsp. ''mays'', from es, maíz after tnq, mahiz), also known as corn ( North American and Australian English), is a cereal grain first domesticated by indigenous peoples in southern Mexico about 10,000 years ago. T ...
but also identified in many aquatic plant species. The abundance of archaea is different in different tissues for example archaea are more abundant in the
rhizosphere The rhizosphere is the narrow region of soil or substrate that is directly influenced by root secretions and associated soil microorganisms known as the root microbiome. Soil pores in the rhizosphere can contain many bacteria and other microo ...
than the
phyllosphere In microbiology, the phyllosphere is the total above-ground surface of a plant when viewed as a habitat for microorganisms. The phyllosphere can be further subdivided into the caulosphere (stems), phylloplane (leaves), anthosphere (flowers), a ...
and
endosphere Some microorganisms, such as endophytes, penetrate and occupy the plant internal tissues, forming the endospheric microbiome. The arbuscular mycorrhizal and other endophytic fungi are the dominant colonizers of the endosphere. Bacteria, and to so ...
. This archaeal abundance is highly associated with plant species type, environment and plant’s developmental stage. In a study conducted on the detection of plant-
genotype The genotype of an organism is its complete set of genetic material. Genotype can also be used to refer to the alleles or variants an individual carries in a particular gene or genetic location. The number of alleles an individual can have in a ...
specific archaeal and bacterial endophytes, 35% of archaeal sequences were detected in overall sequences (achieved using amplicon sequencing and verified by real time-PCR). The archaeal sequences belong to the phyla '' Thaumarchaeota'', ''
Crenarchaeota The Thermoproteota (also known as crenarchaea) are archaea that have been classified as a phylum of the Archaea domain. Initially, the Thermoproteota were thought to be sulfur-dependent extremophiles but recent studies have identified character ...
,'' and ''
Euryarchaeota Euryarchaeota (from Ancient Greek ''εὐρύς'' eurús, "broad, wide") is a phylum of archaea. Euryarchaeota are highly diverse and include methanogens, which produce methane and are often found in intestines, halobacteria, which survive extre ...
''.


Endosymbionts of bacteria

It has been observed that some Betaproteobacteria have
Gammaproteobacteria Gammaproteobacteria is a class of bacteria in the phylum Pseudomonadota (synonym Proteobacteria). It contains about 250 genera, which makes it the most genera-rich taxon of the Prokaryotes. Several medically, ecologically, and scientifically im ...
endosymbionts.


Endosymbionts of fungi

Fungi have been shown to harbor endohyphal bacteria; however, the effects of the bacteria on the fungi are not well studied. Many fungi that harbor these endohyphal bacteria in turn live within plants. These fungi are otherwise known as fungal
endophyte An endophyte is an endosymbiont, often a bacterium or fungus, that lives within a plant for at least part of its life cycle without causing apparent disease. Endophytes are ubiquitous and have been found in all species of plants studied to date ...
s. It is hypothesized that the fungi offers a safe haven for the
bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were am ...
, and diverse bacteria colonize these refugia creating a micro-ecosystem. These interactions are important because they may impact the way that fungi interact with the environment by modulating their phenotypes. The way in which the bacteria do this is by altering the gene expression of the fungi. For example, '' Luteibacter'' sp. has been shown to naturally infect the ascomycetous
endophyte An endophyte is an endosymbiont, often a bacterium or fungus, that lives within a plant for at least part of its life cycle without causing apparent disease. Endophytes are ubiquitous and have been found in all species of plants studied to date ...
'' Pestalotiopsis'' sp. isolated from '' Platycladus orientalis.'' The ''Luteibacter'' sp. influences the auxin and enzyme production within its host, which, in turn, may influence the effect the fungus has on its plant host''.'' Another interesting example of a bacteria living in symbiosis with a fungus is with the fungus '' Mortierella.'' This soil-dwelling fungus lives in close association with a toxin-producing bacteria, ''Mycoavidus'', which helps the fungus to defend against
nematode The nematodes ( or grc-gre, Νηματώδη; la, Nematoda) or roundworms constitute the phylum Nematoda (also called Nemathelminthes), with plant- parasitic nematodes also known as eelworms. They are a diverse animal phylum inhabiting a br ...
s. This is a very new, but potentially very important, area of study within the study of symbiosis.


Virus-host associations

The human genome project found several thousand
endogenous retrovirus Endogenous retroviruses (ERVs) are endogenous viral elements in the genome that closely resemble and can be derived from retroviruses. They are abundant in the genomes of jawed vertebrates, and they comprise up to 5–8% of the human genome (l ...
es, endogenous viral elements in the
genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ...
that closely resemble and can be derived from
retrovirus A retrovirus is a type of virus that inserts a DNA copy of its RNA genome into the DNA of a host cell that it invades, thus changing the genome of that cell. Once inside the host cell's cytoplasm, the virus uses its own reverse transcriptas ...
es, organized into 24 families.


See also

* Epibiont, organism living ''on the surface'' of another organism *
Anagenesis Anagenesis is the gradual evolution of a species that continues to exist as an interbreeding population. This contrasts with cladogenesis, which occurs when there is branching or splitting, leading to two or more lineages and resulting in separate ...
*
Endophyte An endophyte is an endosymbiont, often a bacterium or fungus, that lives within a plant for at least part of its life cycle without causing apparent disease. Endophytes are ubiquitous and have been found in all species of plants studied to date ...
*
Ectosymbiosis Ectosymbiosis is a form of symbiotic behavior in which a parasite lives on the body surface of the host, including internal surfaces such as the lining of the digestive tube and the ducts of glands.  The parasitic species is generally an i ...
* List of symbiotic organisms * List of symbiotic relationships * Multigenomic organism *
Protocell A protocell (or protobiont) is a self-organized, endogenously ordered, spherical collection of lipids proposed as a stepping-stone toward the origin of life. A central question in evolution is how simple protocells first arose and how they coul ...
* Fungal-bacterial endosymbiosis


References

{{Self-replicating organic structures Symbiosis Microbial population biology Environmental microbiology Endosymbiotic events