Endosymbiont

Endosymbiosis comes from the Greek: ἔνδον endon "within", σύν syn "together" and βίωσις biosis "living".

File:Endosymbiotic theory.svgSymbiogenesis theory holds that eukaryotes evolved via absorbing prokaryotes. Typically, one organism envelopes a bacterium and the two evolve a mutualistic relationship. The absorbed bacterium (the endosymbiont) eventually lives exclusively within the host cells. This fits the concept of observed organelle development.{{cite journal |vauthors=Moore KR, Magnabosco C, Momper L, Gold DA, Bosak T, Fournier GP |date=2019 |title=An Expanded Ribosomal Phylogeny of Cyanobacteria Supports a Deep Placement of Plastids |journal=Frontiers in Microbiology |volume=10 |pages=1612 |doi=10.3389/fmicb.2019.01612 |pmc=6640209 |pmid=31354692 |doi-access=free}}{{cite journal |vauthors=McCutcheon JP |title=The Genomics and Cell Biology of Host-Beneficial Intracellular Infections |journal=Annual Review of Cell and Developmental Biology |volume=37 |issue=1 |pages=115–142 |date=October 2021 |pmid=34242059 |doi=10.1146/annurev-cellbio-120219-024122 |s2cid=235786110 |doi-access=free }}{{cite journal |vauthors=Callier V |title=Mitochondria and the origin of eukaryotes |journal=Knowable Magazine |date=8 June 2022 |doi=10.1146/knowable-060822-2 |doi-access=free |url=https://knowablemagazine.org/article/living-world/2022/mitochondria-origin-eukaryotes |access-date=18 August 2022}}{{cite journal |vauthors=Sagan L |title=On the origin of mitosing cells |journal=Journal of Theoretical Biology |volume=14 |issue=3 |pages=255–274 |date=March 1967 |pmid=11541392 |doi=10.1016/0022-5193(67)90079-3 |author-link=Lynn Margulis |bibcode=1967JThBi..14..225S }}{{cite journal |vauthors=Gabaldón T |title=Origin and Early Evolution of the Eukaryotic Cell |journal=Annual Review of Microbiology |volume=75 |issue=1 |pages=631–647 |date=October 2021 |pmid=34343017 |doi=10.1146/annurev-micro-090817-062213 |s2cid=236916203 }}

Typically the endosymbiont's genome shrinks, discarding genes whose roles are displaced by the host. For example, the Hodgkinia genome of Magicicada cicadas is much different from that of the prior freestanding bacteria. The cicada life cycle involves years of stasis underground. The symbiont produces many generations during this phase, experiencing little selection pressure, allowing their genomes to diversify. Selection is episodic (when the cicadas reproduce). The original Hodgkinia genome split into three much simpler endosymbionts, each encoding only a few genes—an instance of punctuated equilibrium producing distinct lineages. The host requires all three symbionts.{{cite journal |vauthors=Campbell MA, Łukasik P, Simon C, McCutcheon JP |title=Idiosyncratic Genome Degradation in a Bacterial Endosymbiont of Periodical Cicadas |journal=Current Biology |volume=27 |issue=22 |pages=3568–3575.e3 |date=November 2017 |pmid=29129532 |pmc=8879801 |doi=10.1016/j.cub.2017.10.008 |doi-access=free |bibcode=2017CBio...27E3568C }}

{{Main|Horizontal transmission|Vertical transmission}}

Symbiont transmission is the process where the host acquires its symbiont. Since symbionts are not produced by host cells, they must find their own way to reproduce and populate daughter cells as host cells divide. Horizontal, vertical, and mixed-mode (hybrid of horizonal and vertical) transmission are the three paths for symbiont transfer.

Horizontal symbiont transfer (horizontal transmission) is a process where a host acquires a facultative symbiont from the environment or another host. The Rhizobia-Legume symbiosis (bacteria-plant endosymbiosis) is a prime example of this modality. The Rhizobia-legume symbiotic relationship is important for processes such as the formation of root nodules. It starts with flavonoids released by the legume host, which causes the rhizobia species (endosymbiont) to activate its Nod genes.{{Cite journal |last=Gage |first=Daniel J. |date=June 2004 |title=Infection and Invasion of Roots by Symbiotic, Nitrogen-Fixing Rhizobia during Nodulation of Temperate Legumes |journal=Microbiology and Molecular Biology Reviews |language=en |volume=68 |issue=2 |pages=280–300 |doi=10.1128/MMBR.68.2.280-300.2004 |issn=1092-2172 |pmc=419923 |pmid=15187185}} These Nod genes generate lipooligosaccharide signals that the legume detects, leading to root nodule formation.{{cite journal |vauthors=Shigenobu S, Watanabe H, Hattori M, Sakaki Y, Ishikawa H |date=September 2000 |title=Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS |journal=Nature |volume=407 |issue=6800 |pages=81–86 |bibcode=2000Natur.407...81S |doi=10.1038/35024074 |pmid=10993077 |doi-access=free}} This process bleeds into other processes such as nitrogen fixation in plants. The evolutionary advantage of such an interaction allows genetic exchange between both organisms involved to increase the propensity for novel functions as seen in the plant-bacterium interaction (holobiont formation).{{Cite journal |last1=Chrostek |first1=Ewa |last2=Pelz-Stelinski |first2=Kirsten |last3=Hurst |first3=Gregory D. D. |last4=Hughes |first4=Grant L. |date=2017 |title=Horizontal Transmission of Intracellular Insect Symbionts via Plants |journal=Frontiers in Microbiology |volume=8 |page=2237 |doi=10.3389/fmicb.2017.02237 |issn=1664-302X |pmc=5712413 |pmid=29234308 |doi-access=free }}

Vertical transmission takes place when the symbiont moves directly from parent to offspring.{{cite journal |vauthors=McCutcheon JP |date=October 2021 |title=The Genomics and Cell Biology of Host-Beneficial Intracellular Infections |journal=Annual Review of Cell and Developmental Biology |volume=37 |issue=1 |pages=115–142 |doi=10.1146/annurev-cellbio-120219-024122 |pmid=34242059 |s2cid=235786110 |doi-access=free}}{{cite journal |vauthors=Callier V |date=8 June 2022 |title=Mitochondria and the origin of eukaryotes |url=https://knowablemagazine.org/article/living-world/2022/mitochondria-origin-eukaryotes |journal=Knowable Magazine |doi=10.1146/knowable-060822-2 |access-date=18 August 2022 |doi-access=free}} In horizontal transmission each generation acquires symbionts from the environment. An example is nitrogen-fixing bacteria in certain plant roots, such as pea aphid symbionts. A third type is mixed-mode transmission, where symbionts move horizontally for some generations, after which they are acquired vertically.{{cite journal |vauthors=Wierz JC, Gaube P, Klebsch D, Kaltenpoth M, Flórez LV |date=2021 |title=Transmission of Bacterial Symbionts With and Without Genome Erosion Between a Beetle Host and the Plant Environment |journal=Frontiers in Microbiology |volume=12 |pages=715601 |doi=10.3389/fmicb.2021.715601 |pmc=8493222 |pmid=34630349 |doi-access=free}}{{cite journal |vauthors=Ebert D |date=23 November 2013 |title=The Epidemiology and Evolution of Symbionts with Mixed-Mode Transmission |url=https://doi.org/10.1146/annurev-ecolsys-032513-100555 |journal=Annual Review of Ecology, Evolution, and Systematics |language=en |volume=44 |issue=1 |pages=623–643 |doi=10.1146/annurev-ecolsys-032513-100555 |issn=1543-592X |access-date=19 August 2022}}{{cite journal |vauthors=Bright M, Bulgheresi S |date=March 2010 |title=A complex journey: transmission of microbial symbionts |journal=Nature Reviews. Microbiology |volume=8 |issue=3 |pages=218–230 |doi=10.1038/nrmicro2262 |pmc=2967712 |pmid=20157340}}

Wigglesworthia, a tsetse fly symbiont, is vertically transmitted (via mother's milk). In vertical transmission, the symbionts do not need to survive independently, often leading them to have a reduced genome. For instance, pea aphid symbionts have lost genes for essential molecules and rely on the host to supply them. In return, the symbionts synthesize essential amino acids for the aphid host. When a symbiont reaches this stage, it begins to resemble a cellular organelle, similar to mitochondria or chloroplasts. Such dependent hosts and symbionts form a holobiont. In the event of a bottleneck, a decrease in symbiont diversity could compromise host-symbiont interactions, as deleterious mutations accumulate.{{Cite journal |last1=Smith |first1=Noel H. |last2=Gordon |first2=Stephen V. |last3=de la Rua-Domenech |first3=Ricardo |last4=Clifton-Hadley |first4=Richard S. |last5=Hewinson |first5=R. Glyn |date=September 2006 |title=Bottlenecks and broomsticks: the molecular evolution of Mycobacterium bovis |url=https://www.nature.com/articles/nrmicro1472 |journal=Nature Reviews Microbiology |language=en |volume=4 |issue=9 |pages=670–681 |doi=10.1038/nrmicro1472 |pmid=16912712 |s2cid=2015074 |issn=1740-1534}}

The best-studied examples of endosymbiosis are in invertebrates. These symbioses affect organisms with global impact, including Symbiodinium (corals), or Wolbachia (insects). Many insect agricultural pests and human disease vectors have intimate relationships with primary endosymbionts.{{Cite journal |last1=Eleftherianos |first1=Ioannis |last2=Atri |first2=Jaishri |last3=Accetta |first3=Julia |last4=Castillo |first4=Julio C. |date=2013 |title=Endosymbiotic bacteria in insects: guardians of the immune system? |journal=Frontiers in Physiology |volume=4 |page=46 |doi=10.3389/fphys.2013.00046 |issn=1664-042X |pmc=3597943 |pmid=23508299 |doi-access=free }}

File:Cospeciation (5 processes) - with key.png

Scientists classify insect endosymbionts as Primary or Secondary. Primary endosymbionts (P-endosymbionts) have been associated with their insect hosts for millions of years (from ten to several hundred million years). They form obligate associations and display cospeciation with their insect hosts. Secondary endosymbionts more recently associated with their hosts, may be horizontally transferred, live in the hemolymph of the insects (not specialized bacteriocytes, see below), and are not obligate.{{cite book |vauthors=Baumann P, Moran NA, Baumann L |chapter=Bacteriocyte-associated endosymbionts of insects |veditors=Dworkin M |title=The prokaryotes |publisher=Springer |location=New York |date=2000 |chapter-url=http://link.springer.de/link/service/books/10125/ }}

Among primary endosymbionts of insects, the best-studied are the pea aphid (Acyrthosiphon pisum) and its endosymbiont Buchnera sp. APS,{{cite journal |vauthors=Douglas AE |title=Nutritional interactions in insect-microbial symbioses: aphids and their symbiotic bacteria Buchnera |journal=Annual Review of Entomology |volume=43 |pages=17–37 |date=January 1998 |pmid=15012383 |doi=10.1146/annurev.ento.43.1.17 |s2cid=29594533 }} the tsetse fly Glossina morsitans morsitans and its endosymbiont Wigglesworthia glossinidia brevipalpis and the endosymbiotic protists in lower termites. As with endosymbiosis in other insects, the symbiosis is obligate. Nutritionally enhanced diets allow symbiont-free specimens to survive, but they are unhealthy, and at best survive only a few generations.{{Cite web |title=Figure 5—figure supplement 2. KEGG metabolic reconstructions based on the intact genes present in the Acromyrmex, Solenopsis, Apis mellifera and Anopheles gambiae genomes, together constituting the urea cycle. |url=https://elifesciences.org/articles/39209/figures#fig5s2 |doi=10.7554/elife.39209.022 |doi-access=free }}

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, as in Buchnera; in others like Wigglesworthia, they are transmitted via milk to the embryo. In termites, the endosymbionts reside within the hindguts and are transmitted through trophallaxis among colony members.{{Cite journal |last=Nalepa |first=Christine A. |date=2020 |title=Origin of Mutualism Between Termites and Flagellated Gut Protists: Transition From Horizontal to Vertical Transmission |journal=Frontiers in Ecology and Evolution |volume=8 |doi=10.3389/fevo.2020.00014 |issn=2296-701X |doi-access=free }}

Primary endosymbionts are thought to help the host either by providing essential nutrients or by metabolizing insect waste products into safer forms. For example, the putative primary role of Buchnera is to synthesize essential amino acids that the aphid cannot acquire from its diet of plant sap. The primary role of Wigglesworthia is to synthesize vitamins that the tsetse fly does not get from the blood 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 predators and competition from other bacterial species, the ample supply of nutrients and relative environmental stability inside the host.

Primary endosymbionts of insects have among the smallest of known bacterial genomes and have lost many genes commonly found in closely related bacteria. One theory claimed 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 of bacteria and insects was inferred supports the assumption hat primary endosymbionts are transferred only vertically.{{cite journal |vauthors=Wernegreen JJ |title=Endosymbiosis: lessons in conflict resolution |journal=PLOS Biology |volume=2 |issue=3 |pages=E68 |date=March 2004 |pmid=15024418 |pmc=368163 |doi=10.1371/journal.pbio.0020068 |df=dmy |doi-access=free }}{{cite journal |vauthors=Moran NA |title=Accelerated evolution and Muller's rachet in endosymbiotic bacteria |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=93 |issue=7 |pages=2873–2878 |date=April 1996 |pmid=8610134 |pmc=39726 |doi=10.1073/pnas.93.7.2873 |doi-access=free |bibcode=1996PNAS...93.2873M }}

Attacking obligate bacterial endosymbionts may present a way to control their hosts, many of which are pests or human disease carriers. For example, aphids are crop pests and the tsetse fly carries the organism Trypanosoma brucei that causes African sleeping sickness.{{cite journal |vauthors=Aksoy S, Maudlin I, Dale C, Robinson AS, O'Neill SL |title=Prospects for control of African trypanosomiasis by tsetse vector manipulation |journal=Trends in Parasitology |volume=17 |issue=1 |pages=29–35 |date=January 2001 |pmid=11137738 |doi=10.1016/S1471-4922(00)01850-X }} Studying insect endosymbionts can aid understanding the origins of symbioses in general, as a proxy for understanding endosymbiosis in other species.

The best-studied ant endosymbionts are Blochmannia bacteria, which are the primary endosymbiont of Camponotus ants. In 2018 a new ant-associated symbiont, Candidatus Westeberhardia Cardiocondylae, was discovered in Cardiocondyla. It is reported to be a primary symbiont.{{cite journal |display-authors=6 |vauthors=Klein A, Schrader L, Gil R, Manzano-Marín A, Flórez L, Wheeler D, Werren JH, Latorre A, Heinze J, Kaltenpoth M, Moya A, Oettler J |date=February 2016 |title=A novel intracellular mutualistic bacterium in the invasive ant Cardiocondyla obscurior |journal=The ISME Journal |volume=10 |issue=2 |pages=376–388 |bibcode=2016ISMEJ..10..376K |doi=10.1038/ismej.2015.119 |pmc=4737929 |pmid=26172209 |doi-access=free}}

File:HEMI Aphididae Aphidius attacking pea aphid.png

The pea aphid (Acyrthosiphon pisum) contains at least three secondary endosymbionts, Hamiltonella defensa, Regiella insecticola, and Serratia symbiotica. Hamiltonella defensa defends its aphid host from parasitoid wasps.{{cite journal |vauthors=Oliver KM, Campos J, Moran NA, Hunter MS |title=Population dynamics of defensive symbionts in aphids |journal=Proceedings. Biological Sciences |volume=275 |issue=1632 |pages=293–299 |date=February 2008 |pmid=18029301 |pmc=2593717 |doi=10.1098/rspb.2007.1192 }} This symbiosis replaces lost elements of the insect's immune response.{{cite journal |title=Genome sequence of the pea aphid Acyrthosiphon pisum |journal=PLOS Biology |volume=8 |issue=2 |pages=e1000313 |date=February 2010 |pmid=20186266 |pmc=2826372 |doi=10.1371/journal.pbio.1000313 |author1=International Aphid Genomics Consortium |doi-access=free }}

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 flies. In Drosophila neotestacea, S. poulsonii has spread across North America owing to its ability to defend its fly host against nematode parasites.{{cite journal |vauthors=Jaenike J, Unckless R, Cockburn SN, Boelio LM, Perlman SJ |title=Adaptation via symbiosis: recent spread of a Drosophila defensive symbiont |journal=Science |volume=329 |issue=5988 |pages=212–215 |date=July 2010 |pmid=20616278 |doi=10.1126/science.1188235 |s2cid=206526012 |bibcode=2010Sci...329..212J }} This defence is mediated by toxins called "ribosome-inactivating proteins" that attack the molecular machinery of invading parasites.{{cite journal |vauthors=Hamilton PT, Peng F, Boulanger MJ, Perlman SJ |title=A ribosome-inactivating protein in a Drosophila defensive symbiont |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=113 |issue=2 |pages=350–355 |date=January 2016 |pmid=26712000 |pmc=4720295 |doi=10.1073/pnas.1518648113 |doi-access=free |bibcode=2016PNAS..113..350H }}{{cite journal |vauthors=Ballinger MJ, Perlman SJ |title=Generality of toxins in defensive symbiosis: Ribosome-inactivating proteins and defense against parasitic wasps in Drosophila |journal=PLOS Pathogens |volume=13 |issue=7 |pages=e1006431 |date=July 2017 |pmid=28683136 |pmc=5500355 |doi=10.1371/journal.ppat.1006431 |doi-access=free }} These toxins represent one of the first understood examples of a defensive symbiosis with a mechanistic understanding for defensive symbiosis between an insect endosymbiont and its host.{{cite journal |vauthors=Ballinger MJ, Perlman SJ |date=July 2017 |title=Generality of toxins in defensive symbiosis: Ribosome-inactivating proteins and defense against parasitic wasps in Drosophila |journal=PLOS Pathogens |volume=13 |issue=7 |pages=e1006431 |doi=10.1371/journal.ppat.1006431 |pmc=5500355 |pmid=28683136 |doi-access=free }}

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 do not report a correlation between evolution of Sodalis and tsetse.Aksoy, S., Pourhosseini, A. & Chow, A. 1995. Mycetome endosymbionts of tsetse flies constitute a distinct lineage related to Enterobacteriaceae. Insect Mol Biol. 4, 15–22. Unlike Wigglesworthia, Sodalis has been cultured in vitro.{{cite journal |vauthors=Welburn SC, Maudlin I, Ellis DS |title=In vitro cultivation of rickettsia-like-organisms from Glossina spp |journal=Annals of Tropical Medicine and Parasitology |volume=81 |issue=3 |pages=331–335 |date=June 1987 |pmid=3662675 |doi=10.1080/00034983.1987.11812127 }}

Cardinium and many other insects have secondary endosymbionts.{{cite journal |vauthors=Zchori-Fein E, Perlman SJ |title=Distribution of the bacterial symbiont Cardinium in arthropods |journal=Molecular Ecology |volume=13 |issue=7 |pages=2009–2016 |date=July 2004 |pmid=15189221 |doi=10.1111/j.1365-294X.2004.02203.x |bibcode=2004MolEc..13.2009Z |s2cid=24361903 }}{{cite journal |vauthors=Wernegreen JJ |title=Genome evolution in bacterial endosymbionts of insects |journal=Nature Reviews. Genetics |volume=3 |issue=11 |pages=850–861 |date=November 2002 |pmid=12415315 |doi=10.1038/nrg931 |s2cid=29136336 }}

Extracellular endosymbionts are represented in all four extant classes of Echinodermata (Crinoidea, Ophiuroidea, Echinoidea, and Holothuroidea). Little is known of the nature of the association (mode of infection, transmission, metabolic requirements, etc.) but phylogenetic analysis indicates that these symbionts belong to the class Alphaproteobacteria, 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.{{cite journal |vauthors=Burnett WJ, McKenzie JD |title=Subcuticular bacteria from the brittle star Ophiactis balli (Echinodermata: Ophiuroidea) represent a new lineage of extracellular marine symbionts in the alpha subdivision of the class Proteobacteria |journal=Applied and Environmental Microbiology |volume=63 |issue=5 |pages=1721–1724 |date=May 1997 |pmid=9143108 |pmc=168468 |doi=10.1128/AEM.63.5.1721-1724.1997 |bibcode=1997ApEnM..63.1721B }}

Some marine oligochaeta (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).{{cite journal |vauthors=Dubilier N, Mülders C, Ferdelman T, de Beer D, Pernthaler A, Klein M, Wagner M, Erséus C, Thiermann F, Krieger J, Giere O, Amann R |display-authors=6 |title=Endosymbiotic sulphate-reducing and sulphide-oxidizing bacteria in an oligochaete worm |journal=Nature |volume=411 |issue=6835 |pages=298–302 |date=May 2001 |pmid=11357130 |doi=10.1038/35077067 |s2cid=4420931 |bibcode=2001Natur.411..298D }}

The sea slug Elysia chlorotica's endosymbiont is the algae Vaucheria litorea. The jellyfish Mastigias have a similar relationship with an algae. Elysia chlorotica forms this relationship intracellularly with the algae's chloroplasts. These chloroplasts retain their photosynthetic capabilities and structures for several months after entering the slug's cells.{{cite journal |vauthors=Mujer CV, Andrews DL, Manhart JR, Pierce SK, Rumpho ME |title=Chloroplast genes are expressed during intracellular symbiotic association of Vaucheria litorea plastids with the sea slug Elysia chlorotica |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=93 |issue=22 |pages=12333–12338 |date=October 1996 |pmid=8901581 |pmc=37991 |doi=10.1073/pnas.93.22.12333 |bibcode=1996PNAS...9312333M |doi-access=free }}

Trichoplax have two bacterial endosymbionts. Ruthmannia lives inside the animal's digestive cells. Grellia lives permanently inside the endoplasmic reticulum (ER), the first known symbiont to do so.{{Cite web|url=https://phys.org/news/2019-06-deceptively-simple-minute-marine-animals.html|title=Deceptively simple: Minute marine animals live in a sophisticated symbiosis with bacteria|first=Max Planck|last=Society|website=phys.org}}

Paracatenula is a flatworm which have lived in symbiosis with an endosymbiotic bacteria for 500 million years. The bacteria produce numerous small, droplet-like vesicles that provide the host with needed nutrients.{{Cite web|url=https://phys.org/news/2019-04-bacterium-entire-flatworm.html|title=How a bacterium feeds an entire flatworm|first=Max Planck|last=Society|website=phys.org}}

Dinoflagellate endosymbionts of the genus Symbiodinium, commonly known as zooxanthellae, are found in corals, mollusks (esp. giant clams, the Tridacna), sponges, and the unicellular foraminifera. These endosymbionts capture sunlight and provide their hosts with energy via carbonate deposition.{{cite journal |author=Baker AC |s2cid=35278104 |title=Flexibility and Specificity in Coral-Algal Symbiosis: Diversity, Ecology, and Biogeography of Symbiodinium |journal=Annual Review of Ecology, Evolution, and Systematics |volume=34 |pages=661–89 |date=November 2003 |doi=10.1146/annurev.ecolsys.34.011802.132417 }}

Previously thought to be a single species, molecular phylogenetic evidence reported diversity in Symbiodinium. In some cases, the host requires a specific Symbiodinium clade. More often, however, the distribution is ecological, with symbionts switching among hosts with ease. When reefs become environmentally stressed, this distribution is related to the observed pattern of coral bleaching and recovery. Thus, the distribution of Symbiodinium on coral reefs and its role in coral bleaching is an important in coral reef ecology.

{{Further|Microbial loop}}

In marine environments,{{Cite journal|vauthors=Villareal T |date=1994|title=Widespread occurrence of the Hemiaulus-cyanobacterial symbiosis in the southwest North Atlantic Ocean |journal=Bulletin of Marine Science|volume=54|pages=1–7}}{{Cite journal |vauthors=Carpenter EJ, Montoya JP, Burns J, Mulholland MR, Subramaniam A, Capone DG |date=20 August 1999 |title=Extensive bloom of a N2-fixing diatom/cyanobacterial association in the tropical Atlantic Ocean|journal=Marine Ecology Progress Series |volume=185 |pages=273–283 |doi=10.3354/meps185273|bibcode=1999MEPS..185..273C|doi-access=free |hdl=1853/43100 |hdl-access=free }}{{Cite journal|vauthors=Foster RA, Subramaniam A, Mahaffey C, Carpenter EJ, Capone DG, Zehr JP |s2cid=53504106 |date=March 2007 |title=Influence of the Amazon River plume on distributions of free-living and symbiotic cyanobacteria in the western tropical north Atlantic Ocean|journal=Limnology and Oceanography |volume=52|issue=2|pages=517–532|doi=10.4319/lo.2007.52.2.0517|bibcode=2007LimOc..52..517F |doi-access=free}}{{cite journal |vauthors=Subramaniam A, Yager PL, Carpenter EJ, Mahaffey C, Björkman K, Cooley S, Kustka AB, Montoya JP, Sañudo-Wilhelmy SA, Shipe R, Capone DG |display-authors=6 |title=Amazon River enhances diazotrophy and carbon sequestration in the tropical North Atlantic Ocean |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=105 |issue=30 |pages=10460–10465 |date=July 2008 |pmid=18647838 |pmc=2480616 |doi=10.1073/pnas.0710279105 |doi-access=free }} endosymbiont relationships are especially prevalent in oligotrophic or nutrient-poor regions of the ocean like that of the North Atlantic.{{cite journal |vauthors=Goebel NL, Turk KA, Achilles KM, Paerl R, Hewson I, Morrison AE, Montoya JP, Edwards CA, Zehr JP |display-authors=6 |title=Abundance and distribution of major groups of diazotrophic cyanobacteria and their potential contribution to N₂ fixation in the tropical Atlantic Ocean |journal=Environmental Microbiology |volume=12 |issue=12 |pages=3272–3289 |date=December 2010 |pmid=20678117 |doi=10.1111/j.1462-2920.2010.02303.x |bibcode=2010EnvMi..12.3272G }} In such waters, cell growth of larger phytoplankton such as diatoms is limited by (insufficient) nitrate concentrations.{{cite journal |vauthors=Foster RA, Kuypers MM, Vagner T, Paerl RW, Musat N, Zehr JP |title=Nitrogen fixation and transfer in open ocean diatom-cyanobacterial symbioses |journal=The ISME Journal |volume=5 |issue=9 |pages=1484–1493 |date=September 2011 |pmid=21451586 |pmc=3160684 |doi=10.1038/ismej.2011.26 |bibcode=2011ISMEJ...5.1484F }} Endosymbiotic bacteria fix nitrogen for their hosts and in turn receive organic carbon from photosynthesis. These symbioses play an important role in global carbon cycling.{{Cite journal|vauthors=Scharek R, Tupas LM, Karl DM |date=11 June 1999|title=Diatom fluxes to the deep sea in the oligotrophic North Pacific gyre at Station Aloha |journal=Marine Ecology Progress Series |volume=182|pages=55–67|doi=10.3354/meps182055|bibcode=1999MEPS..182...55S|doi-access=free|hdl=10261/184131|hdl-access=free}}

One known symbiosis between the diatom Hemialus spp. and the cyanobacterium Richelia intracellularis has been reported in North Atlantic, Mediterranean, and Pacific waters.{{cite journal |vauthors=Zeev EB, Yogev T, Man-Aharonovich D, Kress N, Herut B, Béjà O, Berman-Frank I |title=Seasonal dynamics of the endosymbiotic, nitrogen-fixing cyanobacterium Richelia intracellularis in the eastern Mediterranean Sea |journal=The ISME Journal |volume=2 |issue=9 |pages=911–923 |date=September 2008 |pmid=18580972 |doi=10.1038/ismej.2008.56 |doi-access=free |bibcode=2008ISMEJ...2..911Z }} Richelia is found within the diatom frustule of Hemiaulus spp., and has a reduced genome.{{cite journal |vauthors=Hilton JA, Foster RA, Tripp HJ, Carter BJ, Zehr JP, Villareal TA |title=Genomic deletions disrupt nitrogen metabolism pathways of a cyanobacterial diatom symbiont |journal=Nature Communications |volume=4 |issue=1 |pages=1767 |date=23 April 2013 |pmid=23612308 |pmc=3667715 |doi=10.1038/ncomms2748 |bibcode=2013NatCo...4.1767H }} A 2011 study measured nitrogen fixation by the cyanobacterial host Richelia intracellularis well above intracellular requirements, and found the cyanobacterium was likely fixing nitrogen for its host. 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 nitrogen-replete areas.

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.{{Cite journal|vauthors=Villareal TA |date=December 1989 |title=Division cycles in the nitrogen-fixingRhizosolenia(Bacillariophyceae)-Richelia(Nostocaceae) symbiosis |journal=British Phycological Journal |volume=24 |issue=4 |pages=357–365 |doi=10.1080/00071618900650371|doi-access=free }} 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 Chaetoceros spp. and UNCY-A in prymnesiophyte microalga.{{cite journal |vauthors=Zehr JP |title=EVOLUTION. How single cells work together |journal=Science |volume=349 |issue=6253 |pages=1163–1164 |date=September 2015 |pmid=26359387 |doi=10.1126/science.aac9752 |s2cid=206641230 }} The Chaetoceros-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).

Mixotricha paradoxa is a protozoan that lacks mitochondria. However, spherical bacteria live inside the cell and serve the function of the mitochondria. Mixotricha has three other species of symbionts that live on the surface of the cell.{{Cite journal |last1=Wenzel |first1=Marika |last2=Radek |first2=Renate |last3=Brugerolle |first3=Guy |last4=König |first4=Helmut |date=2003-01-01 |title=Identification of the ectosymbiotic bacteria of Mixotricha paradoxa involved in movement symbiosis |url=https://www.sciencedirect.com/science/article/pii/S0932473904700802 |journal=European Journal of Protistology |volume=39 |issue=1 |pages=11–23 |doi=10.1078/0932-4739-00893 |issn=0932-4739}}

Paramecium bursaria, a species of ciliate, has a mutualistic symbiotic relationship with green alga called Zoochlorella. The algae live in its cytoplasm.{{cite journal | pmc=3413206 | year=2012 | last1=Dziallas | first1=C. | last2=Allgaier | first2=M. | last3=Monaghan | first3=M. T. | last4=Grossart | first4=H. P. | title=Act together—implications of symbioses in aquatic ciliates | journal=Frontiers in Microbiology | volume=3 | page=288 | doi=10.3389/fmicb.2012.00288 | pmid=22891065 | doi-access=free }}

Platyophrya chlorelligera is a freshwater ciliate that harbors Chlorella that perform photosynthesis.{{Cite book |last=Joint |first=Ian |url=https://books.google.com/books?id=883qCAAAQBAJ&q=Platyophrya%2520chlorelligera&pg=PA103 |title=Molecular Ecology of Aquatic Microbes |date=2013-06-29 |publisher=Springer Science & Business Media |isbn=978-3-642-79923-5 |language=en}}{{cite journal | url=https://pubmed.ncbi.nlm.nih.gov/23196282/ | pmid=23196282 | year=1991 | last1=Kawakami | first1=H. | title=An endosymbiotic Chlorella-bearing ciliate: Platyophrya chlorelligera Kawakami 1989 | journal=European Journal of Protistology | volume=26 | issue=3–4 | pages=245–255 | doi=10.1016/S0932-4739(11)80146-X }}

Strombidium purpureum is a marine ciliate that uses endosymbiotic, purple, non-sulphur bacteria for anoxygenic photosynthesis.{{Cite journal |doi=10.1111/j.1574-6968.1993.tb06289.x |title=Endosymbiotic purple non-sulphur bacteria in an anaerobic ciliated protozoon |year=1993 |last1=Fenchel |first1=Tom |last2=Bernard |first2=Catherine |journal=FEMS Microbiology Letters |volume=110 |pages=21–25 |s2cid=86458030 |doi-access=free }}{{Cite book |last1=Paracer |first1=Surindar |url=https://books.google.com/books?id=OmZ6CfHQIZ8C&q=Strombidium%2520purpureum&pg=PA47 |title=Symbiosis: An Introduction to Biological Associations |last2=Ahmadjian |first2=Vernon |date=2000-07-06 |publisher=Oxford University Press |isbn=978-0-19-802788-1 |language=en}}

Paulinella chromatophora is a freshwater amoeboid that has a cyanobacterium endosymbiont.

Many foraminifera are hosts to several types of algae, such as red algae, diatoms, dinoflagellates and chlorophyta.{{cite book|author1=Joseph Seckbach|author2=Patrick Kociolek|title=The Diatom World|url=https://books.google.com/books?id=Va35Mtn9VGYC&pg=PA439|year=2011|publisher=Springer Science & Business Media|isbn=978-94-007-1327-7|page=439}} 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 gametes, they need to acquire algae horizontally following sexual reproduction.{{cite thesis | url=https://theses.hal.science/tel-01760725 | title=Origins and early evolution of photosynthetic eukaryotes | date=5 March 2018 | publisher=Université Paris-Saclay | last1=Toledo | first1=Rafael Isaac Ponce |s2cid=89705815}}

Several species of radiolaria have photosynthetic symbionts. In some species the host digests algae to keep the population at a constant level.{{cite book|author1=Surindar Paracer|author2=Vernon Ahmadjian|title=Symbiosis: An Introduction to Biological Associations|url=https://books.google.com/books?id=Z3Y8DwAAQBAJ&pg=PA155|year=2000|publisher=Oxford University Press|isbn=978-0-19-511807-0|page=155}}

Hatena arenicola is a flagellate protist with a complicated feeding apparatus that feeds on other microbes. When it engulfs a green Nephroselmis alga, the feeding apparatus disappears and it becomes photosynthetic. During mitosis the algae is transferred to only one of the daughter cells, while the other cell restarts the cycle.

In 1966, biologist Kwang W. Jeon found that a lab strain of Amoeba proteus had been infected by bacteria that lived inside the cytoplasmic vacuoles.{{cite journal |vauthors=Jeon KW, Jeon MS |title=Endosymbiosis in amoebae: recently established endosymbionts have become required cytoplasmic components |journal=Journal of Cellular Physiology |volume=89 |issue=2 |pages=337–344 |date=October 1976 |pmid=972171 |doi=10.1002/jcp.1040890216 |s2cid=32044949 }} This infection killed almost all of the infected protists. After the equivalent of 40 host generations, the two organisms become mutually interdependent. A genetic exchange between the prokaryotes and protists occurred.{{cite web|url=https://bcmb.utk.edu/people/emeritus/kwang-w-jeon/|title=Kwang W. Jeon {{!}} Biochemistry & Cellular and Molecular Biology – UTK BCMB|date=28 April 2014|access-date=14 May 2019|archive-date=31 August 2018|archive-url=https://web.archive.org/web/20180831181533/https://bcmb.utk.edu/people/emeritus/kwang-w-jeon/|url-status=dead}}{{cite book|author1=Luigi Nibali|author2=Brian Henderson|title=The Human Microbiota and Chronic Disease: Dysbiosis as a Cause of Human Pathology|url=https://books.google.com/books?id=sQ6lDAAAQBAJ&pg=PA165|year=2016|publisher=John Wiley & Sons|isbn=978-1-118-98287-7|page=165}}K. Jeon, "Amoeba and X-bacteria: Symbiont Acquisition and Possible Species Change," in: L. Margulis and R. Fester, eds., Symbiosis as a Source of Evolutionary Innovation (Cambridge, Mass.: MIT Press), c. 9.

The spotted salamander (Ambystoma maculatum) lives in a relationship with the algae Oophila amblystomatis, which grows in its egg cases.{{cite journal |vauthors=Kerney R, Kim E, Hangarter RP, Heiss AA, Bishop CD, Hall BK |title=Intracellular invasion of green algae in a salamander host |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=108 |issue=16 |pages=6497–6502 |date=April 2011 |pmid=21464324 |pmc=3080989 |doi=10.1073/pnas.1018259108 |doi-access=free |bibcode=2011PNAS..108.6497K }}

All vascular plants harbor endosymbionts or endophytes in this context. They include bacteria, fungi, viruses, protozoa and even microalgae. Endophytes aid in processes such as growth and development, nutrient uptake, and defense against biotic and abiotic stresses like drought, salinity, heat, and herbivores.{{cite journal |vauthors=Baron NC, Rigobelo EC |year=2022 |title=Endophytic fungi: a tool for plant growth promotion and sustainable agriculture |journal=Mycology |volume=13 |issue=1 |pages=39–55 |doi=10.1080/21501203.2021.1945699 |pmc=8856089 |pmid=35186412}}

Plant symbionts can be categorized into epiphytic, endophytic, and mycorrhizal. These relations can also be categorized as beneficial, mutualistic, neutral, and pathogenic.{{cite journal |display-authors=6 |vauthors=Hardoim PR, van Overbeek LS, Berg G, Pirttilä AM, Compant S, Campisano A, Döring M, Sessitsch A |date=September 2015 |title=The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes |journal=Microbiology and Molecular Biology Reviews |volume=79 |issue=3 |pages=293–320 |doi=10.1128/MMBR.00050-14 |pmc=4488371 |pmid=26136581}}{{cite journal |vauthors=Khare E, Mishra J, Arora NK |date=2018 |title=Multifaceted Interactions Between Endophytes and Plant: Developments and Prospects |journal=Frontiers in Microbiology |volume=9 |pages=2732 |doi=10.3389/fmicb.2018.02732 |pmc=6249440 |pmid=30498482 |doi-access=free}} Microorganisms living as endosymbionts in plants can enhance their host's primary productivity either by producing or capturing important resources.{{cite journal |vauthors=de Sassi C, Müller CB, Krauss J |date=May 2006 |title=Fungal plant endosymbionts alter life history and reproductive success of aphid predators |journal=Proceedings. Biological Sciences |volume=273 |issue=1591 |pages=1301–1306 |doi=10.1098/rspb.2005.3442 |pmc=1560287 |pmid=16720406}} These endosymbionts can also enhance plant productivity by producing toxic metabolites that aid plant defenses against herbivores.{{cite journal |vauthors=Schardl CL, Leuchtmann A, Spiering MJ |date=2004-06-02 |title=Symbioses of grasses with seedborne fungal endophytes |journal=Annual Review of Plant Biology |volume=55 |issue=1 |pages=315–340 |doi=10.1146/annurev.arplant.55.031903.141735 |pmid=15377223}}{{Cite journal |vauthors=Hunter MD, Price PW |date=1992 |title=Playing Chutes and Ladders: Heterogeneity and the Relative Roles of Bottom-Up and Top-Down Forces in Natural Communities |url=https://www.jstor.org/stable/1940152 |journal=Ecology |volume=73 |issue=3 |pages=724–732 |bibcode=1992Ecol...73..724H |doi=10.2307/1940152 |issn=0012-9658 |jstor=1940152 |s2cid=54005488}}

Plants are dependent on plastid or chloroplast organelles. The chloroplast is derived from a cyanobacterial primary endosymbiosis that began over one billion years ago. An oxygenic, photosynthetic free-living cyanobacterium was engulfed and kept by a heterotrophic protist and eventually evolved into the present intracellular organelle.{{cite journal |vauthors=Qiu H, Yoon HS, Bhattacharya D |title=Algal endosymbionts as vectors of horizontal gene transfer in photosynthetic eukaryotes |journal=Frontiers in Plant Science |volume=4 |pages=366 |date=September 2013 |pmid=24065973 |pmc=3777023 |doi=10.3389/fpls.2013.00366 |doi-access=free }}

Mycorrhizal endosymbionts appear only in fungi.

Typically, plant endosymbiosis studies focus on a single category or species to better understand their individual biological processes and functions.{{cite journal |vauthors=Porras-Alfaro A, Bayman P |title=Hidden fungi, emergent properties: endophytes and microbiomes |journal=Annual Review of Phytopathology |volume=49 |issue=1 |pages=291–315 |date=2011-09-08 |pmid=19400639 |doi=10.1146/annurev-phyto-080508-081831 }}

Fungal endophytes can be found in all plant tissues. Fungi living below the ground amidst plant roots are known as mycorrhiza, but are further categorized based on their location inside the root, with prefixes such as ecto, endo, arbuscular, ericoid, etc. Fungal endosymbionts that live in the roots and extend their extraradical hyphae into the outer rhizosphere are known as ectendosymbionts.{{Cite journal |vauthors=Salhi LN, Bustamante Villalobos P, Forget L, Burger G, Lang BF |date=Sep 2022 |title=Endosymbionts in cranberry: Diversity, effect on plant growth, and pathogen biocontrol |journal=Plants, People, Planet |language=en |volume=4 |issue=5 |pages=511–522 |doi=10.1002/ppp3.10290 |s2cid=250548548 |issn=2572-2611|doi-access=free }}{{cite journal |vauthors=Roth R, Paszkowski U |title=Plant carbon nourishment of arbuscular mycorrhizal fungi |journal=Current Opinion in Plant Biology |volume=39 |pages=50–56 |date=October 2017 |pmid=28601651 |doi=10.1016/j.pbi.2017.05.008 |series=39 Cell signalling and gene regulation 2017 |bibcode=2017COPB...39...50R }}

Arbuscular mycorrhizal fungi or AMF are the most diverse plant microbial endosymbionts. With exceptions such as the Ericaceae family, almost all vascular plants harbor AMF endosymbionts as endo and ecto as well. AMF plant endosymbionts systematically colonize plant roots and help the plant host acquire soil nutrients such as nitrogen. In return it absorbs plant organic carbon products. Plant root exudates contain diverse secondary metabolites, especially flavonoids and strigolactones that act as chemical signals and attracts the AMF.{{cite journal |vauthors=Oldroyd GE, Harrison MJ, Paszkowski U |title=Reprogramming plant cells for endosymbiosis |journal=Science |volume=324 |issue=5928 |pages=753–754 |date=May 2009 |pmid=19423817 |doi=10.1126/science.1171644 |bibcode=2009Sci...324..753O |s2cid=206518892 }} AMF Gigaspora margarita lives as a plant endosymbiont and also harbors further endosymbiont intracytoplasmic bacterium-like organisms.{{cite journal |vauthors=Bianciotto V, Bandi C, Minerdi D, Sironi M, Tichy HV, Bonfante P |title=An obligately endosymbiotic mycorrhizal fungus itself harbors obligately intracellular bacteria |journal=Applied and Environmental Microbiology |volume=62 |issue=8 |pages=3005–3010 |date=August 1996 |pmid=8702293 |pmc=168087 |doi=10.1128/aem.62.8.3005-3010.1996 |bibcode=1996ApEnM..62.3005B }} AMF generally promote plant health and growth and alleviate abiotic stresses such as salinity, drought, heat, poor nutrition, and metal toxicity.{{cite journal |vauthors=Begum N, Qin C, Ahanger MA, Raza S, Khan MI, Ashraf M, Ahmed N, Zhang L |display-authors=6 |title=Role of Arbuscular Mycorrhizal Fungi in Plant Growth Regulation: Implications in Abiotic Stress Tolerance |journal=Frontiers in Plant Science |volume=10 |pages=1068 |date=2019 |pmid=31608075 |pmc=6761482 |doi=10.3389/fpls.2019.01068 |doi-access=free }} Individual AMF species have different effects in different hosts – introducing the AMF of one plant to another plant can reduce the latter's growth.{{cite journal |vauthors=Herre EA, Mejía LC, Kyllo DA, Rojas E, Maynard Z, Butler A, Van Bael SA |date=March 2007 |title=Ecological implications of anti-pathogen effects of tropical fungal endophytes and mycorrhizae |journal=Ecology |volume=88 |issue=3 |pages=550–558 |bibcode=2007Ecol...88..550H |doi=10.1890/05-1606 |pmid=17503581}}

Endophytic fungi in mutualistic relations directly benefit and benefit from their host plants. They also can help their hosts succeed in polluted environments such as those contaminated with toxic metals.{{cite journal |vauthors=Domka AM, Rozpaądek P, Turnau K |title=Are Fungal Endophytes Merely Mycorrhizal Copycats? The Role of Fungal Endophytes in the Adaptation of Plants to Metal Toxicity |journal=Frontiers in Microbiology |volume=10 |pages=371 |date=2019 |pmid=30930857 |pmc=6428775 |doi=10.3389/fmicb.2019.00371 |doi-access=free }} Fungal endophytes are taxonomically diverse and are divided into categories based on mode of transmission, biodiversity, in planta colonization and host plant type.{{cite journal |vauthors=Rodriguez RJ, White JF, Arnold AE, Redman RS |title=Fungal endophytes: diversity and functional roles |journal=The New Phytologist |volume=182 |issue=2 |pages=314–330 |date=Apr 2009 |pmid=19236579 |doi=10.1111/j.1469-8137.2009.02773.x |doi-access=free |bibcode=2009NewPh.182..314R }}{{Cite journal |vauthors=Purahong W, Hyde KD |date=2011-03-01 |title=Effects of fungal endophytes on grass and non-grass litter decomposition rates |url=https://doi.org/10.1007/s13225-010-0083-8 |journal=Fungal Diversity |language=en |volume=47 |issue=1 |pages=1–7 |doi=10.1007/s13225-010-0083-8 |s2cid=43678079 |issn=1878-9129}} Clavicipitaceous fungi systematically colonize temperate season grasses. Non-clavicipitaceous fungi colonize higher plants and even roots and divide into subcategories.{{Cite journal |date=2005-05-24 |title=Evolutionary Development of the Clavicipitaceae |url=https://www.taylorfrancis.com/chapters/edit/10.1201/9781420027891-33/evolutionary-development-clavicipitaceae |journal=The Fungal Community |language=en |pages=525–538 |doi=10.1201/9781420027891-33|isbn=9780429116407 }} Aureobasidium and preussia species of endophytic fungi isolated from Boswellia sacra produce indole acetic acid hormone to promote plant health and development.{{cite journal |vauthors=Khan AL, Al-Harrasi A, Al-Rawahi A, Al-Farsi Z, Al-Mamari A, Waqas M, Asaf S, Elyassi A, Mabood F, Shin JH, Lee IJ |display-authors=6 |title=Endophytic Fungi from Frankincense Tree Improves Host Growth and Produces Extracellular Enzymes and Indole Acetic Acid |journal=PLOS ONE |volume=11 |issue=6 |pages=e0158207 |date=2016-06-30 |pmid=27359330 |pmc=4928835 |doi=10.1371/journal.pone.0158207 |bibcode=2016PLoSO..1158207K |doi-access=free }}

Aphids can be found in most plants. Carnivorous ladybirds are aphid predators and are used in pest control. Plant endophytic fungus Neotyphodium lolii produces alkaloid mycotoxins in response to aphid invasions. In response, ladybird predators exhibited reduced fertility and abnormal reproduction, suggesting that the mycotoxins are transmitted along the food chain and affect the predators.

Endophytic bacteria belong to a diverse group of plant endosymbionts characterized by systematic colonization of plant tissues. The most common genera include Pseudomonas, Bacillus, Acinetobacter, Actinobacteria, Sphingomonas. Some endophytic bacteria, such as Bacillus amyloliquefaciens, a seed-born endophytic bacteria, produce plant growth by producing gibberellins, which are potent plant growth hormones. Bacillus amyloliquefaciens promotes the taller height of transgenic dwarf rice plants.{{cite journal |vauthors=Shahzad R, Waqas M, Khan AL, Asaf S, Khan MA, Kang SM, Yun BW, Lee IJ |display-authors=6 |title=Seed-borne endophytic Bacillus amyloliquefaciens RWL-1 produces gibberellins and regulates endogenous phytohormones of Oryza sativa |journal=Plant Physiology and Biochemistry |volume=106 |pages=236–243 |date=September 2016 |pmid=27182958 |doi=10.1016/j.plaphy.2016.05.006 |bibcode=2016PlPB..106..236S }} Some endophytic bacteria genera additionally belong to the Enterobacteriaceae family.{{Cite book |last1=Pirttilä |first1=Anna Maria |url={{google books|plainurl=y|id=10MZbnLKRJIC}} |title=Endophytes of Forest Trees: Biology and Applications |last2=Frank |first2=A. Carolin |date=2011-07-11 |publisher=Springer Science & Business Media |isbn=978-94-007-1599-8 |language=en}} Endophytic bacteria typically colonize the leaf tissues from plant roots, but can also enter the plant through the leaves through leaf stomata.Senthilkumar et al., 2011 Generally, the endophytic bacteria are isolated from the plant tissues by surface sterilization of the plant tissue in a sterile environment.{{Cite journal |vauthors=Quadt-Hallmann A, Kloepper JW, Benhamou N |date=2011-02-10 |title=Bacterial endophytes in cotton: mechanisms of entering the plant |url=https://cdnsciencepub.com/doi/10.1139/m97-081 |journal=Canadian Journal of Microbiology |volume=43 |issue=6 |pages=577–582 |language=en |doi=10.1139/m97-081}} Passenger endophytic bacteria eventually colonize inner tissue of plant by stochastic events while True endophytes possess adaptive traits because of which they live strictly in association with plants.{{cite journal |vauthors=Hardoim PR, van Overbeek LS, Elsas JD |title=Properties of bacterial endophytes and their proposed role in plant growth |language=English |journal=Trends in Microbiology |volume=16 |issue=10 |pages=463–471 |date=October 2008 |pmid=18789693 |doi=10.1016/j.tim.2008.07.008 |url=https://research.rug.nl/en/publications/c4338aca-07f5-4222-9ecc-75142f0dbdab }} The in vitro-cultivated endophytic bacteria association with plants is considered a more intimate relationship that helps plants acclimatize to conditions and promotes health and growth. Endophytic bacteria are considered to be plant's essential endosymbionts because virtually all plants harbor them, and these endosymbionts play essential roles in host survival.{{cite journal |vauthors=Bodył A, Mackiewicz P, Stiller JW |title=The intracellular cyanobacteria of Paulinella chromatophora: endosymbionts or organelles? |language=English |journal=Trends in Microbiology |volume=15 |issue=7 |pages=295–296 |date=July 2007 |pmid=17537638 |doi=10.1016/j.tim.2007.05.002 }} This endosymbiotic relation is important in terms of ecology, evolution and diversity. Endophytic bacteria such as Sphingomonas sp. and Serratia sp. that are isolated from arid land plants regulate endogenous hormone content and promote growth.{{Cite journal |vauthors=Asaf S, Khan MA, Khan AL, Waqas M, Shahzad R, Kim A, Kang S, Lee I |date=2017-01-01 |title=Bacterial endophytes from arid land plants regulate endogenous hormone content and promote growth in crop plants: an example of Sphingomonas sp. and Serratia marcescens |journal=Journal of Plant Interactions |language=en |volume=12 |issue=1 |pages=31–38 |doi=10.1080/17429145.2016.1274060 |s2cid=90203067 |issn=1742-9145|doi-access=free |bibcode=2017JPlaI..12...31A }}

Archaea are members of most microbiomes. While archaea are 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 amid biotic and abiotic stresses. However, few studies have investigated the role of archaea in plant health and its symbiotic relationships.{{cite journal |vauthors=Jung J, Kim JS, Taffner J, Berg G, Ryu CM |title=Archaea, tiny helpers of land plants |journal=Computational and Structural Biotechnology Journal |volume=18 |pages=2494–2500 |date=2020-01-01 |pmid=33005311 |pmc=7516179 |doi=10.1016/j.csbj.2020.09.005 }} Most plant endosymbiosis studies focus on fungal or bacteria using metagenomic approaches.{{cite journal |vauthors=Taffner J, Cernava T, Erlacher A, Berg G |title=Novel insights into plant-associated archaea and their functioning in arugula (Eruca sativa Mill.) |journal=Journal of Advanced Research |volume=19 |pages=39–48 |date=September 2019 |pmid=31341668 |pmc=6629838 |doi=10.1016/j.jare.2019.04.008 |series=Special Issue on Plant Microbiome |s2cid=155746848 }}

The characterization of archaea includes crop plants such as rice{{cite journal |vauthors=Ma M, Du H, Sun T, An S, Yang G, Wang D |title=Characteristics of archaea and bacteria in rice rhizosphere along a mercury gradient |journal=The Science of the Total Environment |volume=650 |issue=Pt 1 |pages=1640–1651 |date=February 2019 |pmid=30054090 |doi=10.1016/j.scitotenv.2018.07.175 |bibcode=2019ScTEn.650.1640M |s2cid=51727014 }} and maize, but also aquatic plants. The abundance of archaea varies by tissue type; for example archaea are more abundant in the rhizosphere than the phyllosphere and endosphere.{{cite journal |vauthors=Knief C, Delmotte N, Chaffron S, Stark M, Innerebner G, Wassmann R, von Mering C, Vorholt JA |display-authors=6 |title=Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice |journal=The ISME Journal |volume=6 |issue=7 |pages=1378–1390 |date=July 2012 |pmid=22189496 |pmc=3379629 |doi=10.1038/ismej.2011.192 |bibcode=2012ISMEJ...6.1378K }} This archaeal abundance is associated with plant species type, environment and the plant's developmental stage.{{cite journal |vauthors=Moissl-Eichinger C, Pausan M, Taffner J, Berg G, Bang C, Schmitz RA |title=Archaea Are Interactive Components of Complex Microbiomes |journal=Trends in Microbiology |volume=26 |issue=1 |pages=70–85 |date=January 2018 |pmid=28826642 |doi=10.1016/j.tim.2017.07.004 }} In a study on plant genotype-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, and Euryarchaeota.{{cite journal |vauthors=Müller H, Berg C, Landa BB, Auerbach A, Moissl-Eichinger C, Berg G |title=Plant genotype-specific archaeal and bacterial endophytes but similar Bacillus antagonists colonize Mediterranean olive trees |journal=Frontiers in Microbiology |volume=6 |pages=138 |date=2015 |pmid=25784898 |pmc=4347506 |doi=10.3389/fmicb.2015.00138 |doi-access=free }}

Some Betaproteobacteria have Gammaproteobacteria endosymbionts.Von Dohlen, Carol D., Shawn Kohler, Skylar T. Alsop, and William R. McManus. "Mealybug β-proteobacterial endosymbionts contain γ-proteobacterial symbionts." Nature 412, no. 6845 (2001): 433–436.

Fungi host endohyphal bacteria;{{cite journal |vauthors=Shaffer JP, Carter ME, Spraker JE, Clark M, Smith BA, Hockett KL, Baltrus DA, Arnold AE |display-authors=6 |title=Transcriptional Profiles of a Foliar Fungal Endophyte (Pestalotiopsis, Ascomycota) and Its Bacterial Symbiont (Luteibacter, Gammaproteobacteria) Reveal Sulfur Exchange and Growth Regulation during Early Phases of Symbiotic Interaction |journal=mSystems |volume=7 |issue=2 |pages=e0009122 |date=April 2022 |pmid=35293790 |pmc=9040847 |doi=10.1128/msystems.00091-22 |editor-first=Stephen R. |editor-last=Lindemann }} the effects of the bacteria are not well studied. Many such fungi in turn live within plants. These fungi are otherwise known as fungal endophytes. It is hypothesized that the fungi offers a safe haven for the bacteria, and the diverse bacteria that they attract create a micro-ecosystem.{{cite journal |vauthors=Arnold AE |title=Bacterial-fungal interactions: Bacteria take up residence in the house that Fungi built |journal=Current Biology |volume=32 |issue=7 |pages=R327–R328 |date=April 2022 |pmid=35413262 |doi=10.1016/j.cub.2022.02.024 |s2cid=248089525 |doi-access=free |bibcode=2022CBio...32.R327A }}

These interactions may impact the way that fungi interact with the environment by modulating their phenotypes. The bacteria do this by altering the fungi's gene expression. For example, Luteibacter sp. has been shown to naturally infect the ascomycetous endophyte 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 bacterium living in symbiosis with a fungus is the fungus Mortierella. This soil-dwelling fungus lives in close association with a toxin-producing bacteria, Mycoavidus, which helps the fungus defend against nematodes.{{cite journal |vauthors=Büttner H, Niehs SP, Vandelannoote K, Cseresnyés Z, Dose B, Richter I, Gerst R, Figge MT, Stinear TP, Pidot SJ, Hertweck C |display-authors=6 |title=Bacterial endosymbionts protect beneficial soil fungus from nematode attack |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=118 |issue=37 |pages=e2110669118 |date=September 2021 |pmid=34504005 |pmc=8449335 |doi=10.1073/pnas.2110669118 |bibcode=2021PNAS..11810669B |doi-access=free }}

In 2024, researchers injected individual cells of the bacterium Mycetohabitans rhizoxinica into cells of the fungus Rhizopus microsporus and were able to propagate the pair of cells for ten rounds using fluorescence-activated cell sorting to select fungal cells containing the bacterium. They found that the fungus's DNA changed during the rounds of propagation.{{Cite journal|url=https://www.nature.com/articles/s41586-024-08010-x|title=Inducing novel endosymbioses by implanting bacteria in fungi|first1=Gabriel H.|last1=Giger|first2=Chantal|last2=Ernst|first3=Ingrid|last3=Richter|first4=Thomas|last4=Gassler|first5=Christopher M.|last5=Field|first6=Anna|last6=Sintsova|first7=Patrick|last7=Kiefer|first8=Christoph G.|last8=Gäbelein|first9=Orane|last9=Guillaume–Gentil|first10=Kirstin|last10=Scherlach|first11=Miriam|last11=Bortfeld-Miller|first12=Tomaso|last12=Zambelli|first13=Shinichi|last13=Sunagawa|first14=Markus|last14=Künzler|first15=Christian|last15=Hertweck|first16=Julia A.|last16=Vorholt|date=28 November 2024|journal=Nature|volume=635|issue=8038|pages=415–422|via=www.nature.com|doi=10.1038/s41586-024-08010-x|pmc=11560845}} This was claimed to be the first time that endosymbiosis was artifically induced in a laboratory.{{Cite web|url=https://www.quantamagazine.org/scientists-re-create-the-microbial-dance-that-sparked-complex-life-20250102/|title=Scientists Re-Create the Microbial Dance That Sparked Complex Life|first=Molly|last=Herring|date=2 January 2025|website=Quanta Magazine}}

{{main|Endogenous retrovirus}}

The human genome project found several thousand endogenous retroviruses, endogenous viral elements in the genome that closely resemble and can be derived from retroviruses, organized into 24 families.{{cite journal |author=Villarreal LP |title=Persisting Viruses Could Play Role in Driving Host Evolution |journal=ASM News |date=October 2001 |url=http://newsarchive.asm.org/oct01/feature1.asp |url-status=dead |archive-url=https://web.archive.org/web/20090508113235/http://newsarchive.asm.org/oct01/feature1.asp |archive-date=8 May 2009 }}{{cite journal |vauthors=Belshaw R, Pereira V, Katzourakis A, Talbot G, Paces J, Burt A, Tristem M |title=Long-term reinfection of the human genome by endogenous retroviruses |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=101 |issue=14 |pages=4894–4899 |date=April 2004 |pmid=15044706 |pmc=387345 |doi=10.1073/pnas.0307800101 |doi-access=free |bibcode=2004PNAS..101.4894B }}

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• {{annotated link|Anagenesis}}
• {{annotated link|Cyanobiont}}
• {{annotated link|Ectosymbiosis}}
• {{annotated link|Endophyte}}
• {{annotated link|Epibiont}}
• {{annotated link|Fungal-bacterial endosymbiosis}}
• {{annotated link|List of symbiotic organisms}}
• {{annotated link|List of symbiotic relationships}}
• {{annotated link|Multigenomic organism}}
• {{annotated link|Nitroplast}}
• {{annotated link|Protocell}}

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{{reflist}}

{{Self-replicating organic structures}}

Category:Endosymbiotic events

Category:Environmental microbiology

Category:Microbial population biology

Category:Symbiosis