Symbioses are close associations between organisms. These associations typically are between different species. They generally last for intervals of one or more generations for at least one of the participants—predator-prey interactions thus typically are not described as symbioses. Symbioses, broadly, can be considered to include not just interactions where both species benefit (mutualisms), but also ones in which only one benefits (commensalisms), and even interactions where one participant benefits while the other is harmed (parasitism, i.e., the parasite gains while the host is harmed). My emphasis in this chapter will be on mutualisms, or potential commensalisms, where parasitism instead is considered in the chapter titled, "Virulence". In addition to distinguishing symbiotic relationships in terms of costs and benefits, it is also profitable to distinguish symbioses into those between microbes and macrobes, i.e., where one species is big and the other small; those between microbes and other microbes; and those that can be described as endosymbioses (where the symbiont lives intracellularly within the host). In this chapter I consider these phenomena especially as examples of interspecific cooperation.

Vocabulary

Table: Important Terms and Concepts Related to Symbioses.
Term	Definition/Discussion
Amensalism	Symbiotic interaction in which one organism is negatively impacted but the other organism is neither helped nor harmed.
	With amensalisms, that is, the second organism is not appreciably impacted in a manner that affects the fitness of that organism. Consequently, there are costs to one organisms that result from the interaction but no gains for the other organism. Contrast especially parasitism where the second organism, the parasite, instead is impacted positively in association with costs to the other (the host). Contrast also commensalism where one organism is not affected (the host) while the other gains (the symbiont)
Antagonistic coevolution	Evolutionary interactions between species where adaptations in one species that negatively affect the other species are countered by adaptations in the second species that negatively impact the first species.
	Also described as arms races, these coevolutionary interactions involve offensive or defensive adaptations by one participant that are countered, evolutionarily, by the adaptations of the other. Host resistance to parasites, and parasites in turn evolutionarily overcoming host resistance, which is then countered by the evolution of additional resistance mechanisms in the host, can be seen as examples of antagonistic coevolution. Contrast this concept with coadaptation.
Coadaptation	Evolutionary interactions between entities where adaptive changes occur such that one entity positively impacts the functioning of the other and vice versa.
	Coevolution towards a mutual benefit and particularly as it occurs under circumstances where the replication or transmission of the participants is in some manner physically linked. Such coevolution particularly occurs when each entity is dependent in some manner on the proper functioning of the other. Genomes can be viewed as consisting of a large number of potentially beneficially coevolved entities where non-beneficial components instead tend to become degraded over time due to mutational processes unless those entities possess some means of replication enhancement relative to that of the genome. Contrast coadaptation with antagonistic coevolution.
Coevolution	Evolutionary interactions between entities where adaptive changes occur such that one entity impacts the functioning of the other and vice versa.
	This includes evolutionary modification of one organism in response to the evolutionary modification of a second organism. The term can be used more broadly than that to include, for example, the evolutionary modification of one gene in response to the evolutionary modification of another gene. Thus, entities can and do evolve in response to how other entities are evolving, and often the responses are two-way. See coadaptation and antagonistic coevolution as different aspects of coevolutionary change.
Commensalism	Interspecific interaction in which one organism gains whereas the other organism neither gains nor loses.
	A symbiosis in which the host neither benefits nor is harmed by the relationship can be described as a commensalism. The symbiont, by contrast, benefits from the interaction in some manner. A commensalism can be difficult to experimentally define explicitly as commensalistic, however, since it can be difficult to demonstrate that the unaffected organism truly is not affected.
Cross feeding	Interaction between two distinct species where the wastes of one species serves as nourishment for the other.
	Cross feeding serves as a key underpinning of microbial consortia as well as various mutualisms between smaller and larger organisms. Contrast, however, with "farming" where the other organism itself is consumed rather than its waste products. Indeed, contrast also with predation as well as parasitism. Cross feeding is also known as syntrophy and note that cross feeding need not be reciprocal between the two organisms involved.
Endosymbiont	Cell that lives inside of another cell, typically in a long-term relationship that is not damaging to the larger cell.
	Of an endosymbiosis, the endosymbiont is the smaller cell that either typically or always lives within the cytoplasm of the larger cell. Endosymbiosis often are mutualistic associations, and indeed can evolve into associations in which it can be difficult to define where one of the involved organisms ends and the other begins.
Endosymbiosis	Cell living within another cell, typically in a mutualistic relationship.
	A symbiosis in which the symbiont is present within the cell or cells of the host organism. Typically endosymbioses are mutualisms. Note that the word endosymbiosis describes a combination of host (or host cell) and endosymbiont.
"Farming"	Mutualism in which one species collectively has its fitness positively enhanced while some individuals of that same population nonetheless have their fitness severely curtailed so as to provide nourishment for the first species.
	A kind of mutualism in which one organism intentionally cultivates another for the sake of exploiting the cultivated organism, particularly so that the fitness of the cultivated organism is reduced in the course of the cultivating organism's gain. Thus, familiarly, food animals or plants commonly are killed in the course of harvesting or consumption, and this type of interaction is also seen among certain relationships that also can be described as symbioses. These relationships particularly are ones in which, for example, that host gains from the relationship at a cost to the symbiont, but not so much of a cost, measured across the symbiont's population, that the ongoing retention of the symbiotic relationship itself is threatened.
Genomic transfer	Permanent transfer of especially large amounts of DNA such as from cytoplasmic endosymbionts into nuclear chromosomes.
	Genomic transfer is part of the explanation for the erosion of mitochondrial and plasmid genome size, including in terms of gene loss, without commensurate losses in the functionality of these endosymbionts (the other key component of this story is that genes, once acquired by the nuclear genome, then can come to be expressed with their products returned to the endosymbiont). This term, however, does not appear to be sufficiently popular including in terms of this meaning for me to impose upon you its memorization. The process itself, however, is important.
Host	Larger organism that participates in a symbiotic relationship with a smaller organism.
	Hosts typically are the larger, longer-live organismal component of a symbiosis. The host can be helped, harmed, or display no change in fitness as a consequence of participating in the symbiosis. We describe the resulting symbioses as mutualisms, parasitisms, and commensalisms, respectively, i.e., depending on the impact of the symbiont on the host's fitness.
Microbial antagonism	Prevention of colonization by certain species due to the previous colonization of the same location by other species.
	The idea that the presence or actions of resident normal flora microorganisms can serve to inhibit colonization of hosts by other microorganisms. This idea is commonly conceptualized in terms of inhibition of colonization by pathogens. Nevertheless, microbial antagonism can occur in any environment, and in fact serves as the basis of food preservation via fermentation.
Microbial consortium	Intimate, mutualistic symbiosis between microorganisms.
	Microbial consortia typically do not consist of endosymbioses. Nonetheless, the interactions between species can be so close that it can be difficult to distinguish an individual consortium into multiple species except by molecular means, and distinctions can be further confused by physiological integration such as one sees with syntrophy, a.k.a., cross feeding. Certain microbial consortia have been hypothesized to be forerunners of modern endosymbioses such as of mitochondria and perhaps also Gram-negative bacteria.
Microbiome	Those microorganisms found in association with a given environment and particularly from the perspective of what genes they carry as well as what impact they have.
	The term 'microbiome' is constructed either from a combination of 'microbe' and the familiar '-ome' or from a combination of 'microbe' and 'biome'. Thus, one subset of meanings of microbiome is the some of the gene sequences associated with the microorganisms as found within a given environment such as may be gatherer using metagenomic techniques. Here, then, a microbiome would be the metagenome of the microorganisms associated with an environment, such as the human microbiome. Microbiome nevertheless is also used to describe simply those microorganisms that tend to be found within a given environment, just as "biome" describes those organisms more generally that tend to be found in association also with a given environment. The latter definition is equivalent to that of 'microbiota', as in normal microbiota.
Mitochondria	The site of cellular respiration in eukaryotic cells.
	In eukaryotes the acquisition of mitochondria and their descendants is thought to represent the original primary endosymbiosis event. Mitochondria, in addition to other duties, are responsible for supplying respiratory pathways to their host cells, most notably as associated with oxidative phosphorylation. There are, however, descendants of mitochondria that are less familiarly endowed, in particular, not associated with oxidative phosphorylation, and indeed in certain circumstances not even associated with extra-nuclear genomes (i.e., hydrogenosomes and mitosomes).
Mutualism	Interspecific interaction in which both species benefit.
	A symbiosis in which the host benefits from the relationship. Evolutionarily one measures these costs or benefits in terms of host fitness. Contrast mutualism with parasitism (host is damaged by the relationship) as well as commensalism (host neither gains nor loses as a consequence of the relationship).
Normal flora	Those microorganisms consistently present within a specific environment.
	See normal microbiota. See too the concept of microbiome.
Normal microbiota	Microorganisms found in association especially with healthy organisms, such as animals and plants.
	Normal microbiota are those microorganisms that normally inhabit an environment, including the environment consisting of a larger-organism's body. In this case the normal microbiota would be indistinguishable from the 'normal' microbial symbionts of the larger organism. There is substantial and perhaps even complete overlap between the concepts of normal microbiota and normal flora. Normal microbiota as a descriptor, however, is not limited to those organisms that are found in association with a larger organisms, and nor is normal flora equivalently limited. Thus, one can speak, for example, of soil normal microbiota.
Obligatory intracellular parasite	Organism that can only reproduce when it is found inside of another cell.
	Particularly an obligatory intracellular parasite is a parasite that replicates only within the cell or cells of a host such that no replication can occur except during intracellular infection. Obligately intracellularly replicating organisms, however, are not limited to parasites, as symbionts, but instead this represents what in effect is a common characteristic of endosymbionts. Note that obligate intracellular parasite is used equivalently and in fact more often than obligately intracellular parasite.
Parasite	Organism that lives in or on other organisms from which it is stealing resources and to which it is causing harm.
	Parasites, broadly, are symbionts that can effect a reduction in host fitness. More narrowly, a parasite is a symbiont that induces diseases in host organisms. Note that disease is different from merely harm since in principle a symbiont can compensate for any harm it causes in its host, resulting in a relationship that is not exactly parasitic. A parasite thus in effect causes net harm to a host organism. Lastly, and most narrowly, the word parasite is often reserved to describe eukaryotic organisms involved in disease-causing infestations.
Parasitism	Act of taking advantage of a host organism by a symbiont.
	Parasitisms are symbioses in which the host is harmed by the relationship, particular in the course of the parasite's gain.
Pathogen	Disease-causing microorganism, and particularly a disease-causing bacterium or virus.
	A parasite, typically one that is not a eukaryotic organisms. That is, the word pathogen typically is used to describe bacteria or viruses that can causes diseases in host organisms. though not indicated, not too that fungi that cause disease also can be described as pathogens.
Plastids	Often photosynthetic endosymbiotic organelle associated with eukaryotic organisms such as algae and plants.
	In many photosynthetic eukaryotes, the photosynthetic organelles are known as plastids and these are products of either primary, secondary, or tertiary endosymbiosis events. Plastids can serve many roles in addition to catalyzing photosynthesis. In addition, plastid-containing eukaryotes also will contain mitochondria, where the latter is responsible for catalyzing oxidative phosphorylation in the same host cells.
Primary endosymbiosis	The taking up of intracellular mutualistic cells that consist of bacteria rather than of eukaryotic cells.
	Primary endosymbiosis is the acquisition of an endosymbiont-less cell by a second cell where the first cell subsequently serves as an endosymbiont of the second cell. The acquisition of mitochondria is commonly provided as an example of primary endosymbiosis as too is the acquisition of cyanobacteria as plastids. In fact, there exist a fairly large number of primary endosymbioses since there exist a fairly large number of non-mitochondrial or -plastid endosymbionts of bacterial origin (endosymbionts of eukaryotic origin essentially always are products of primary endosymbiosis since eukaryotes at a minimum consist of already mitochondria-containing cells). Contrast with secondary endosymbiosis but see also serial endosymbiosis.
Resident normal flora	Microorganism symbionts of larger organisms that are somewhat permanently ensconced within the larger organism.
	Resident normal flora are normal flora microorganisms that have formed long-term associations with host organisms. Resident normal flora often are thought of as displaying mutualistic or commensalistic relationships with their hosts though that perspective is certainly not the case given chronic infectious disease and otherwise may reflect an ignorance of the impact of specific normal flora members.
Secondary endosymbiosis	Possession or acquisition as well as relatively long-term intracellular retention by a cell of an additional, especially eukaryotic cell.
	Secondary endosymbiosis is the acquisition by a cell of an endosymbiont which itself is an endosymbiont-containing cell. Thus, a host cell surrounds an endosymbiont which in turn surrounds an endosymbiont. Plastids in certain algae are products of secondary endosymbiosis. Contrast with primary endosymbiosis, and contrast as well with tertiary endosymbiosis.
Serial endosymbiosis	Long-term acquisition of an intracellular, mutualistic microorganism by cells that already possess a long-term intracellular mutualistic microorganism.
	Serial endosymbiosis, that is, is the acquisition of an second or more endosymbiont by an already endosymbiont containing cell/species. This is distinct from secondary endosymbiosis which, at least in principle, could involve the acquisition of a symbiont by an organism that does not yet possess an endosymbiont (though, in fact, this example is highly unlikely given that endosymbiont-less organisms tend to be prokaryotes and prokaryotes tend to be much smaller than eukaryotic cells, though this distinction does not always hold). Another way of making this latter point is that serial endosymbiosis at a minimum requires the acquisition of two distinct and indeed independent endosymbionts by a single cell whereas secondary endosymbiosis involves the acquisition of more than one cell (a cell and its endosymbiont) that in fact are not independent of each other but instead where one is found within the other (i.e., the new endosymbiont and the pre-existing endosymbiont found within the new endosymbiont). Nevertheless, serial endosymbiosis can involve secondary endosymbiosis as occurs given the acquisition of eukaryotic algae as plastids by already mitochondria-containing eukaryotes.
Symbiont	Organism living in long-term, physically intimate association with another, much larger organism.
	The smaller, shorter-lived organismal component of a symbiosis is the symbiont, contrasting the host. The symbiont typically gains from participating in the symbiosis though these gains are not necessarily independent of the symbiont's impact on the host. Symbionts can be parasites, mutual, or commensals depending on whether they harm, help, or neither harm nor help the host.
Symbiosis	Long-term interaction between two organisms where "long-term" is defined in generations for at least one of the organisms and the interaction is physically intimate.
	Symbioses in many cases consist of interactions between symbionts and hosts, though in the case of microbial consortia the participants are less readily distinguished into a larger host and smaller symbiont.
Syntrophy	Cross feeding.
	Literally 'together nourishment'.
Tertiary endosymbiosis	Acquisition of the product of secondary endosymbiosis as an endosymbiont.
	Thus, in theory at least, a host cell surrounds an endosymbiont that surrounds an endosymbiont that surrounds an endosymbiont. Plastids in certain algae are products of tertiary endosymbiosis.
Transient microbiota	Microorganisms that are not a permanent part of a microbiome but nevertheless are present at least some of the time.
	Transient microbiota are normal flora microorganisms that either do not or have not formed long-term association with host organisms. Microorganisms that are only briefly in contact with hosts and subsequently shed or otherwise lost also are members of transient normal flora. Parasitic microorganisms typically are transient, though so too are microorganisms that either are not well adapted to colonizing the host that they have encountered or instead are blocked from colonizing such as due to microbial antagonism.