An endosymbiont is any organism that lives within the body or cells of another organism, i.e. forming an endosymbiosis (Greek: endo = inner, sym = together and biosis = living). Examples are nitrogen-fixing bacteria (called rhizobia) which live in root nodules on legume roots, single-celled algae inside reef-building corals, and bacterial endosymbionts that provide essential nutrients to about 10%–15% of insects.
Many instances of endosymbiosis are obligate, that is neither the endosymbiont nor the host can survive without the other, such as the gutless marine worms of the genus Riftia, which get nutrition from their endosymbiotic bacteria. However, not all endosymbioses are obligate. Also, some endosymbioses can be harmful to either of the organisms involved. See symbiosis for further discussion of this issue.
It is generally agreed that certain organelles of the eukaryotic cell, especially mitochondria and plastids such as chloroplasts, originated as bacterial endosymbionts. This theory is called the endosymbiotic theory, confirmed and popularized by Lynn Margulis.
The endosymbiont theory and mitochondria and chloroplasts
Is a close association between different types of organisms over an extended time. However, more specifically, the relationship was endosymbiotic, meaning that one of the organisms (the bacteria) lived within the other (the prokaryotic cells).
According to the endosymbiont theory, an anaerobic cell probably ingested an aerobic bacterium but failed to digest it. The aerobic bacterium flourished within the cell because the cell’s cytoplasm was abundant in half-digested food molecules. The bacterium digested these molecules with oxygen and gained great amounts of energy. Because the bacterium had so much energy, it probably leaked some of it as ATP into the cell’s cytoplasm. This benefited the anaerobic cell because it enabled it to digest food aerobically. Eventually, the aerobic bacterium could no longer live independently from the cell, and it therefore became a mitochondrion. The origin of the chloroplast is very similar to that of the mitochondrion. A cell must have captured a photosynthetic cyanobacterium and failed to digest it. The cyanobacterium thrived in the cell and eventually evolved into the first chloroplast. Other eukaryotic organelles may have also evolved through endosymbiosis. Scientists believe that cilia, flagella, centrioles, and microtubules may have come from a symbiosis between a spirilla-like bacterium and an early eukaryotic cell.
There are several examples of evidence that support the endosymbiont theory. Mitochondria and chloroplasts contain their own small supply of DNA, which may be remnants of the genome the organelles had when they were independent aerobic bacteria. The single most convincing evidence of the descent of organelles from bacteria is the position of mitochondria and plastid DNA sequences in phylogenetic trees of bacteria. Mitochondria have sequences that clearly indicate origin from a group of bacteria called the alpha-Proteobacteria. Plastids have DNA sequences that indicate origin from the cyanobacteria (blue-green algae). In addition, there are organisms alive today, called living intermediates, that are in a similar endosymbiotic condition to the prokaryotic cells and the aerobic bacteria. Living intermediates show that the evolution proposed by the endosymbiont theory is possible. For example, the giant amoeba Pelomyxa lacks mitochondria but has aerobic bacteria that carry out a similar role. A variety of corals, clams, snails, and one species of Paramecium permanently host algae in their cells. Many of the insect endosymbionts have been shown to have ancient associations with their hosts, involving strictly vertical inheritance. In addition, these insect symbionts have similar patterns of genome evolution to those found in true organelles: genome reduction, rapid rates of gene evolution, and bias in nucleotide base composition favoring adenine and thymine, at the expense of guanine and cytosine.
Further evidence of endosymbiosis are the prokaryotic ribosomes found within chloroplasts and mitochondria as well as the double membrane enclosing them. The inner membrane is thought to be the original membrane of the once independent prokaryote, while the outer one is thought to be the food vacuole it was enclosed in initially. Triple or quadruple membranes are found among certain algae, probably resulting from repeated endosymbiosis (although little else was retained of the engulfed cell).
These modern organisms with endosymbiotic relationships with aerobic bacteria have verified the endosymbiotic theory, which explains the origin of mitochondria and chloroplasts from bacteria. Researchers in molecular and evolutionary biology no longer question this theory, although some of the details, such as the mechanisms for loss of genes from organelles to host nuclear genomes, are still being worked out.
Bacterial endosymbionts in marine oligochaetes
Some marine oligochaeta (e.g Olavius or Inanidrillus) 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).
Bacterial endosymbionts in other marine invertebrates
Extracellular endosymbionts are also represented in all 5 extant classes of Echinodermata (Crinoidea, Ophiuroidea, Asteroidea, 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 alpha group of the class Proteobacteria, 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.
Symbiodinium dinoflagellate endosymbionts in marine metazoa and protists
Dinoflagellate endosymbionts of the genus Symbiodinium, commonly known as zooxanthellae, are found in corals, mollusks (esp. giant clams, the Tridacna), sponges, and foraminifera. These endosymbionts drive the amazing formation of coral reefs by capturing sunlight and providing their hosts with energy for carbonate deposition.
Previously thought to be a single species, molecular phylogenetic 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. 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 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.
Endosymbionts in 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.
Bacterial obligate endosymbionts in 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 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 haemolymph of the insects (not specialized bacteriocytes, see below), and are not obligate.
Among primary endosymbionts of insects, the best studied are the pea aphid (Acyrthosiphon pisum) and its endosymbiont Buchnera sp. APS, 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 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, 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 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 acids that the aphid cannot acquire from its natural diet of plant sap. Similarly, the primary role of Wigglesworthia is probably 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 which constitutes a bulk of the termites' diet.
Bacteria benefit from the reduced exposure to predators, 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. Presumably 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 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 that causes African sleeping sickness. Other motivations for their study is to understand symbiosis, and to understand how bacteria with severely depleted genomes are able to survive, thus improving our knowledge of genetics and molecular biology.
Less is known about secondary endosymbionts. The pea aphid (Acyrthosiphon pisum) is known to contain at least three secondary endosymbionts, Hamiltonella defensa, Regiella insecticola, and Serratia symbiotica. H. defensa aids in defending the insect from parasitoids. Sodalis glossinidius is a secondary endosymbiont 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 P-symbiont Wigglesworthia, though, Sodalis has been cultured in vitro.
Viral endosymbionts, endogenous retrovirus(or ERV)
During pregnancy in vivipary mammals(only exception the Monotremes), a ERVs are activated and produced in high quantities during the implantation of the embryo.In one hand they act as immunodepressors,and protect the embryo from the immune system of the mother and in the other hand viral fusion proteins cause the formation of the placental syncytium in order to limit the exchange of migratory cells between the developing embryo and the body of the mother,an epithelium wont do because certain blood cells are specialized to be able to insert themselves between adjacent epithelial cells. The ERV is a similar type of virus as HIV (causing AIDS in humans), the immunodepressive action was the initial normal behavior of the virus,in a similar way as HIV,the fusion proteins was a way to spread the infection to other cells by simply merging them with the infected one(HIV does this too). It is beleaved that the ancestors of modern vivipary mammals evolved after an accidental infection to an ancestor to this virus, that permitted to the fetus to survive the immune system of the mother. 
The human genome project found several thousand ERVs comprise by 24 families.
- Douglas, A E (1998). "Nutritional interactions in insect-microbial symbioses: Aphids and their symbiotic bacteria Buchnera". Annual Review of Entomology 43: 17-38. ISSN 00664170. Retrieved on 2007-05-16.
- 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.
- Welburn, S.C., Maudlin, I. & Ellis, D.S. 1987. In vitro cultivation of rickettsia-like-organisms from Glossina spp. Ann. Trop. Med. Parasitol. 81, 331-335.
-  The Viruses That Make Us: A Role For Endogenous Retrovirus In The Evolution Of Placental Species (by Luis P. Villarreal)
-  Persisting Viruses Could Play Role in Driving Host Evolution
Obligate bacterial endosymbiosis in marine oligochaetes:
- Endosymbiotic sulphate-reducing and sulphide-oxidizing bacteria in an oligochaete worm. Dubilier N., Mülders C.,Ferdelman T., De Beer D.,Pernthaler A.,Klein M., Wagner M., Erseus C., Thiermann F., Krieger J., Giere O & Amann R. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11357130
Bacterial endosymbionts in echinoderms:
- 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. Burnett, W J and J D McKenzie http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=168468&rendertype=abstract
Symbiodinium dinoflagellate endosymbionts in marine metazoa and protists
- Excellent review paper covering the role of Symbiodinium in reef ecology and the current state of research: FLEXIBILITY AND SPECIFICITY IN CORAL-ALGAL SYMBIOSIS: Diversity, Ecology, and Biogeography of Symbiodinium. Andrew C. Baker, Annual Review of Ecology, Evolution, and Systematics 2003 34, 661-689
Obligate bacterial endosymbionts in insects:
- PLOS Biology Primer- Endosymbiosis: lessons in conflict resolution http://www.plosbiology.org/plosonline/?request=get-document&doi=10.1371/journal.pbio.0020068
- A general review of bacterial endosymbionts in insects. P. Baumann, N. A. Moran and L. Baumann, Bacteriocyte-associated endosymbionts of insects in M. Dworkin, ed., The prokaryotes, Springer, New York, 2000. http://link.springer.de/link/service/books/10125/
- An excellent review of insect endosymbionts that focuses on genetic issues. Jennifer J. Wernegreen (2002), Genome evolution in bacterial endosymbionts of insects, Nature Reviews Genetics, 3, pp. 850-861. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12415315&dopt=Abstract
- A review article on aphids and their bacterial endosymbionts. A. E. Douglas (1998), Nutritional interactions in insect-microbial symbioses: Aphids and Their Symbiotic Bacteria Buchnera, Annual Reviews of Entomology, 43, pp. 17-37.
- Describes possible methods to control the human pathogen causing African sleeping sickness, which is transmitted by tsetse flies. Focuses on methods using the primary and secondary endosymbionts of the tsetse fly. Serap Aksoy, Ian Maudlin, Colin Dale, Alan S. Robinsonand and Scott L. O’Neill (2001), Prospects for control of African trypanosomiasis by tsetse vector, TRENDS in Parasitology, 17 (1), pp. 29-35. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11137738&dopt=Abstract
- Announces and analyzes the full genome sequence of Buchnera sp. APS, the endosymbiont of the pea aphid, and the first endosymbiont to have its genome sequenced. S. Shigenobu, H. Watanabe, M. Hattori, Y. Sakaki and H. Ishikawa (2000), Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS, Nature, 407, pp. 81-86. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10993077&dopt=Abstract
- An article that presents for the first time a theory on how obligate endosymbionts may have their genomes degraded, in a freely-available journal. Nancy A. Moran (1996), Accelerated evolution and Muller’s ratchet in endosymbiotic bacteria, Proceedings of the National Academy of Sciences of the USA, 93, pp. 2873-2878. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8610134&dopt=Abstract