An endosymbiont is any organism that lives within the body or cells of another organism, i.e. forming an endosymbiosis (Greek: endo = inner and biosis = living). For instance, some nitrogen fixing bacteria (known as rhizobia) live in root nodules on legume roots, reef-building corals contain single-celled algae, and several insect species contain bacterial endosymbionts. Many other examples of endosymbiosis exist.

Many instances of endosymbiosis are obligate, where neither the endosymbiont nor the host can survive without the other, such as gutless marine worms 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.

It is generally agreed that certain organelles of the eukaryotic cell, especially mitochondria and chloroplasts, originated as bacterial endosymbionts. This theory is known as the endosymbiotic theory, confirmed and popularized by Lynn Margulis.

The endosymbiont theory and mitochondria and chloroplasts

The endosymbiont theory explains the origins of organelles such as mitochondria and chloroplasts in eukaryotic cells. The theory proposes that chloroplasts and mitochondria evolved from certain types of bacteria that prokaryotic cells engulfed through endophagocytosis. These cells and the bacteria trapped inside them entered a symbiotic relationship, 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, chloroplasts, and centrioles contain their own small supply of DNA, which may be remnants of the DNA the organelles had when they were independent aerobic bacteria. 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.

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 suggest that the endosymbiont theory, which explains the origin of mitochondria and chloroplasts, is accurate.

Bacterial endosymbionts in marine oligochaetes

Some marine oligochaetes (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.

Paramecium bursaria, a species of ciliate, has a mutualistic symbiotic relationship with green alga called Zoochlorella. The algae live inside the cell, in the cytoplasm.

Bacterial obligate endosymbionts in insects

Among bacterial endosymbionts of insects, the best studied are the pea aphid Acyrthosiphon pisum and its endosymbiont Buchnera sp. APS, and the tsetse fly Glossina morsitans morsitans and its endosymbiont Wigglesworthia glossinidia brevipalpis. 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.

The 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.

The bacteria are thought to help the host by either synthesizing nutrients that the host cannot make itself, or by metabolizing insect waste products into safer forms. For example, the primary role of Buchnera is thought to be to synthesize essential amino acids that the aphid cannot acquire from its natural diet of plant sap. The evidence is (1) when aphids' endosymbionts are killed using antibiotics, they appear healthier when their plant sap diet is supplemented with the appropriate amino acids, and (2) after the Buchnera genome was sequenced, analysis uncovered a large number of genes that likely code for amino acid biosynthesis genes; most bacteria that live inside other organisms do not have such genes, so their existence in Buchnera is noteworthy. Similarly, the primary role of Wigglesworthia is probably to synthesize vitamins that the tsetse fly does not get from the blood that it eats.

The benefit for the bacteria is that it is protected from the environment outside the insect cell, and presumably receives nutrients from the insect. 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 other bacteria. Presumably these genes are not needed in the environment of the host insect cell. (A complementary theory as to why the bacteria may have lost genes, Muller's ratchet, is that since the endosymbionts are maternally transmitted and have no opportunity to exchange genes with other bacteria, it is more difficult to keep good genes in all individuals in a population of these endosymbionts.) Research in which a parallel phylogeny of bacteria and insects was inferred supports the belief that the obligate 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 (trypanosome protozoa) 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.