The Hologenome Concept: Helpful or Hollow? — TEI-tagged view

Nancy A. MoranpersName, Daniel B. SloanpersName (2015date). “The Hologenome Concept: Helpful or Hollow?.” PLOS Biologytitle·j.

Object of study — the hologenometerm·dom concept in the evolution of host-microbe associations

Research question — what evidence is needed to claim coevolutionterm·dom within holobiontsterm·dom and selectionterm·dom at the holobiontterm·dom level

Contribution — argues that hologenome-level selectionterm·dom should not be the null hypothesisterm for host-symbiont features

Full text — tagged

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The Hologenometerm·dom Concept: Helpful or Hollow?

Abstract With the increasing appreciation for the crucial roles that microbial symbiontsterm·key play in the development and fitness of plant and animal hosts, there has been a recent push to interpret evolution through the lens of the “hologenometerm·dom”—the collective genomic content of a host and its microbiometerm·key. But how symbiontsterm·key evolve and, particularly, whether they undergo natural selectionterm·dom to benefit hosts are complex issues that are associated with several misconceptions about evolutionary processes in host-associated microbial communities. Microorganisms can have intimate, ancient, and/or mutualistic associations with hosts without having undergone natural selectionterm·dom to benefit hosts. Likewise, observing host-specific microbial community composition or greater community similarity among more closely related hosts does not imply that symbiontsterm·key have coevolved with hosts, let alone that they have evolved for the benefit of the host. Although selectionterm·dom at the level of the symbiotic community, or hologenometerm·dom, occurs in some cases, it should not be accepted as the null hypothesisterm for explaining features of host–symbiontterm·key associations.

The ubiquity and importance of microorganisms in the lives of plants and animals are ever more apparent, and increasingly investigated by biologists. Suddenly, we have the aspiration and tools to open up a new, complicated world, and we must confront the realization that almost everything about larger organisms has been shaped by their history of evolving from, then with, microorganisms [ 1 ]. This development represents a dramatic shift in perspective—arguably a revolution—in modern biology.

Do we need to revamp basic tenets of evolutionary theory to understand how hosts evolve with associated microorganisms? Some scientists have suggested that we do [ 2 ], and the recently introduced terms “holobiontterm·dom” and “hologenometerm·dom” encapsulate what has been described as an “emerging postmodern synthesis” [ 3 ]. Holobiontterm·dom was initially used to refer to a host and a single inherited symbiontterm·key [ 4 ] but was later extended to a host and its community of associated microorganisms, specifically for the case of corals [ 5 ]. The idea of the holobiontterm·dom is that a host and its associated microorganisms must be considered as an integrated unit in order to understand many biological and ecological features.

The later introduction of the term hologenometerm·dom [ 2 , 6 , 7 ] sought to describe a holobiontterm·dom by its genetic composition. The term has been used in different ways by different authors, but in most contexts a hologenometerm·dom is considered a genetic unit that represents the combined genomes of a host and its associated microorganisms [ 8 ]. This non-controversial definition of hologenometerm·dom is linked to the idea that this entity has a role in evolution. For example, Gordon et al. [ 1 , 9 ] state, "The genome of a holobiontterm·dom, termed the hologenometerm·dom, is the sum of the genomes of all constituents, all of which can evolve within that context." That last phrase is sufficiently general that it can be interpreted in any number of ways. Like physical conditions, associated organisms can be considered as part of the environment and thus can be sources of natural selectionterm·dom, affecting evolution in each lineage.

But a more sweeping and problematic proposal is given by originators of the term, which is that "the holobiontterm·dom with its hologenometerm·dom should be considered as the unit of natural selectionterm·dom in evolution" [ 2 , 7 ] or by others, that “an organism’s genetics and fitness are inclusive of its microbiometerm·key” [ 3 , 4 ]. The implication is that differential success of holobiontsterm·dom influences evolution of participating organisms, such that their observed features cannot be fully understood without considering selectionterm·dom at the holobiontterm·dom level. Another formulation of this concept is the proposal that the evolution of host–microbe systems is “most easily understood by equating a gene in the nuclear genome to a microbe in the microbiometerm·key” [ 8 ]. Under this view, interactions between host and microbial genotypes should be considered as genetic epistasisterm·dom (interactions among alleles at different loci in a genome) rather than as interactions between the host’s genotype and its environment.

While biologists would agree that microorganisms have important roles in host evolution, this statement is a far cry from the claim that they are fused with hosts to form the primary units of selectionterm·dom, or that hosts and microorganisms provide different portions of a unified genome. Broadly, the hologenometerm·dom concept contends, first, that participating lineages within a holobiontterm·dom affect each other’s evolution, and, second, that that the holobiontterm·dom is a primary unit of selectionterm·key. Our aim in this essay is to clarify what kinds of evidence are needed for each of these claims and to argue that neither should be assumed without evidence. We point out that some observations that superficially appear to support the concept of the hologenometerm·dom have spawned confusion about real biological issues ( Box 1 ).

Box 1. Misconceptions Related to the Hologenometerm·dom Concept Misconception #1 : Similarities in microbiomesterm·key between related host species result from codiversificationterm·dom.

Reality : Related species tend to be similar in most traits. Because microbiometerm·key composition is a trait that involves living organisms, it is tempting to assume that these similarities reflect a shared evolutionary history of host and symbiontsterm·key. This has been shown to be the case for some symbioses (e.g., ancient maternally inherited endosymbionts in insects). But for many interactions (e.g., gut microbiota), related hosts may have similar effects on community assembly without any history of codiversificationterm·dom between the host and individual microbial species ( Fig 1B ).

Misconception #2 : Parallel phylogenies of host and symbiontterm·key, or intimacy of host and symbiontterm·key associations, reflect coevolutionterm·dom.

Reality : Coevolutionterm·dom is defined by a history of reciprocal selectionterm·dom between parties. While coevolutionterm·dom can generate parallel phylogenies or intimate associations, these can also result from many other mechanisms.

Misconception #3: Highly intimate associations of host and symbiontsterm·key, involving exchange of cellular metabolites and specific patterns of colonization, result from a history of selectionterm·dom favoring mutualistic traits.

Reality: The adaptive basis of a specific trait is difficult to infer even when the trait involves a single lineage, and it is even more daunting when multiple lineages contribute. But complexity or intimacy of an interaction does not always imply a long history of coevolutionterm·dom nor does it imply that the nature of the interaction involves mutual benefit.

Misconception #4 : The essential roles that microbial species/communities play in host development are adaptations resulting from selectionterm·dom on the symbiontsterm·key to contribute to holobiontterm·dom function.

Reality : Hosts may adapt to the reliable presence of symbiontsterm·key in the same way that they adapt to abiotic components of the environment, and little or no selectionterm·dom on symbiontterm·key populations need be involved.

Misconception #5 : Because of the extreme importance of symbiontsterm·key in essential functions of their hosts, the integrated holobiontterm·dom represents the primary unit of selectionterm·key.

Reality : The strength of natural selectionterm·dom at different levels of biological organization is a central issue in evolutionary biology and the focus of much empirical and theoretical research. But insofar as there is a primary unit of selectionterm·key common to diverse biological systems, it is unlikely to be at the level of the holobiontterm·dom. In particular cases, evolutionary interests of host and symbiontsterm·key can be sufficiently aligned such that the predominant effect of natural selectionterm·dom on genetic variation in each party is to increase the reproductive success of the holobiontterm·dom. But in most host–symbiontterm·key relationships, contrasting modes of genetic transmission will decouple selectionterm·dom pressures.

Alternative evolutionary processes can result in related host species harboring similar symbiontterm·key communities. Left panel: Individual symbiontterm·key lineages retain fidelity to evolving host lineages, through co-inheritance or other mechanisms, with some gain and loss of symbiontterm·key lineages over evolutionary time. Right panel: As host lineages evolve, they shift their selectivity of environmental microbes, which are not evolving in response and which may not even have been present during host diversification. In both cases, measures of community divergence will likely be smaller for more closely related hosts, but they reflect processes with very different implications for hologenometerm·dom evolution. Image credit : Nancy MoranpersName and Kim Hammond , University of Texas at Austin .

Coevolutionterm·dom Versus Codiversificationterm·dom Versus Phylosymbiosisterm·key Host associations with microorganisms often display several features that seem, at first glance, to support the view that they have evolved together as a unit. A particular host species often associates with a characteristic set of microbial species, and related hosts tend to have similar microbiota, suggesting the possibility of shared evolutionary history of the host and its microbial communities. Often, the relationships are intimate and highly specific, in the sense that microorganisms colonize specific tissues and exchange metabolites with hosts. What do such observations truly imply about the occurrence of host–microorganism coevolutionterm·dom or shared evolutionary history? By definition [ 10 , 11 ], coevolutionterm·dom requires that each lineage undergoes evolutionary change due to selective forces imposed by the other lineages. So how can we recognize when holobiontsterm·dom are shaped by the coevolutionterm·dom of participants, and furthermore whether this coevolutionterm·dom reflects selectionterm·dom at the level of the holobiontterm·dom unit?

Coevolutionterm·dom is often assumed based on observing intimate associations between hosts and microorganisms, but intimacy of an association does not require a history of coevolutionterm·dom. In some cases, microorganisms colonize a host in an intimate and characteristic manner, and have a major impact on host fitness, yet are not evolving in response to the host. For example, Pseudomonas aeruginosa colonization of the human lung, associated with cystic fibrosis, impacts the host even though the lung is probably not a significant habitat for P . aeruginosa , which is primarily a soil-dwelling organism. Even relationships that bear striking similarities to highly coevolved mutualisms may not actually involve coevolutionterm·dom. For example, photosynthetic sea slugs are able to capture chloroplasts from specific algal food sources and maintain them for up to months at a time [ 12 ]. While it is tempting to imagine that the algae and their chloroplasts have somehow evolved to facilitate this spectacular example of a symbiotic interaction, this is entirely inconsistent with the current understanding of this relationship as an evolutionary dead-end for the algae.

Coevolutionterm·dom appears more likely when lineages have a shared evolutionary history, as evidenced by a pattern of codiversificationterm·dom (also called cospeciationterm·dom or parallel phylogenesis) where symbiontterm·key and host lineages show matching phylogenetic trees ( Fig 1A ). By itself, however, codiversificationterm·dom does not imply coevolutionterm·dom. In fact, organisms with no interaction at all sometimes diversify in parallel if subjected to the same series of geographic isolation events [ 13 ]. Codiversificationterm·dom can also reflect unidirectional selectionterm·dom, in which a symbiontterm·key or parasite adaptively tracks changes in hosts but not vice versa. An example might be Helicobacter pylori , which has evolved in parallel with human populations [ 1 , 14 ]. Whether human populations have evolved in response is not evident. A strong pattern of codiversificationterm·dom—perfect matching of phylogenies of numerous species of host and associated symbiontterm·key—supports some type of shared history but does not demonstrate coevolutionterm·dom.

In fact, coevolutionterm·dom is hard to prove. This is illustrated by its past contentiousness among researchers of plant–animal interactions. Under one view, plants produce toxic molecules as metabolic side-products and specialized insect herbivores adapt to overcome these [ 2 , 15 ]. Alternatively, insects and plants have coevolved: toxins evolve as defensive adaptations and insects reciprocate with adaptations to neutralize these toxins. But strong evidence for coevolutionterm·dom is not impossible. In the case of insects and plants, coevolutionterm·dom has been strongly supported by studies showing sequential evolution of defenses and counter-defenses in butterflies and their food plants [ 3 , 16 ] and recent changes in toxin content in plant populations differing in herbivore exposure [ 4 , 17 ].

Sometimes coevolutionterm·dom or shared evolutionary history is presumed because particular host species associate with characteristic microbial species or communities. But this also does not imply that host and microorganisms have evolved in response to one another, or even that they have evolved in the presence of one another. For example, it has been demonstrated that showerheads are colonized by characteristic microbial communities that represent a highly selective subset of all water-borne microorganisms [ 5 , 18 ]. This is expected, as showerheads provide a distinctive habitat and resources, suitable for particular sets of organisms. But showerheads and microorganisms have not coevolved. Likewise, a host may be highly selective, permitting only a small subset of environmental organisms to colonize, without sharing any evolutionary history with them.

Often microbial communities are more similar among closely related hosts than among more distantly related ones [ 2 , 6 , 7 , 19 – 21 ]. “Phylosymbiosisterm·key” is a term coined recently for the idea that microbial communities change in a way that reflects host phylogeny [ 8 , 22 ]. But a relationship of host phylogeny to symbiontterm·key community composition can arise from two very different processes. First, ancestral associated microorganisms may diversify in parallel with the host, through continuous association of evolving lineages; i.e., they codiversify ( Fig 1A ). This is the case for organelles and eukaryotic cells, and for obligate symbiontsterm·key and their host insects, such as Buchneraterm·key and aphids [ 23 ]. In this case, changes in microbiota during host evolution are due to fixation of mutations in evolving symbiontterm·key lineages, and the pattern supports long-term associations of symbiontsterm·key with host lineages. Potentially, though not necessarily, this is linked to their acting on one another as reciprocal selective forces, i.e., coevolving. Alternatively, more related host species may simply be colonized by similar sets of microbial species from the environment ( Fig 1B ) [ 1 , 9 , 19 , 22 ]. In this case, changes in microbiota composition are due to differences in community assembly rather than genealogy. The microorganisms themselves need not have evolved at all, and need not have shared a long history with their hosts. In fact, this second pattern, that closely related host species share similar microbial communities, is expected under most evolutionary scenarios. Closely related species typically have greater resemblance than distantly related species for any phenotypic feature, be it genetic, behavioral, or ecological. Thus, this situation suggests nothing one way or the other about whether host and symbiontsterm·key have coevolved or have a shared evolutionary history.

Hologenomesterm·dom As the Units of Selectionterm·dom Although sometimes hard to demonstrate, coevolutionterm·dom and codiversificationterm·dom are likely common for hosts and associated microorganisms. But the proposals that the hologenometerm·dom is the primary unit of selectionterm·key and that microbes can be equated to genes within a larger genome are far more sweeping claims. They imply that selectionterm·dom on constituent genomes acts primarily to increase fitness at the level of the holobiontterm·dom, that is, that conflicts between the evolutionary interests of host and symbiontsterm·key are suppressed due to selectionterm·dom at the higher level. Even demonstrating coevolutionterm·dom does not necessarily imply that hologenomesterm·dom are a significant unit of selectionterm·key. In fact, most documented cases of interspecific coevolutionterm·dom involve antagonistic changes such as those of hosts and pathogens, or plants and herbivores.

A host’s survival depends on its interactions with microorganisms, and hosts are, therefore, under selectionterm·dom to encourage colonization by beneficial bacteria and to discourage colonization by harmful ones. However, such selectionterm·dom can often be interpreted in the simple context of a host adapting to the microorganisms in its environment, including those involved in antagonistic coevolutionterm·dom. For the hologenometerm·dom to be the primary unit of selectionterm·key, the evolution of microbial lineages must also be contributing to increased holobiontterm·dom fitness. This view has many parallels with the idea of group selectionterm: that natural selectionterm·dom acts on groups of individuals within a species, and not only on the individuals. Group selectionterm can and does occur in some circumstances, but the required conditions are restrictive and often depend on groups that consist of genetic relatives [ 2 , 7 , 24 ] or the enforcement of a system of mutual policing to limit cheating [ 3 , 4 , 25 ]. Early and oversimplified views of group selectionterm (e.g., that ungulate herds have evolved to avoid overexploiting rangeland plants, so as to conserve resources for future generations [ 8 , 26 ]) failed to recognize that population-level adaptations are unstable under most circumstances, due to susceptibility to invasion by selfish individuals (e.g., that eat more than their share and thereby reproduce more [ 10 , 11 , 27 ]). Many of the same issues arise for the proposal that hologenomesterm·dom are the primary units of selectionterm·dom: what mechanisms are there to limit the tendency of microorganisms to evolve selfish traits at the expense of fitness of the holobiontterm·dom?

Do hosts and their associated microorganisms ever form new units of selectionterm·dom, resulting in phenotypes only understandable as arising from selectionterm·dom on hologenomesterm·dom? And, if so, when and how often? The answer to the first question is yes. Heritable obligate symbioses such as those of mitochondria and eukaryotes, or of insects and obligate bacterial symbiontsterm·key that provision nutrients, provide clear cases in which fitness of each party is directly dependent on fitness of the other. Furthermore, this codependence is maintained, in some cases, for many millions of generations through the co-transmission of genomes of both parties. In the aphid– Buchneraterm·key symbiosis, the bacterium Buchneraterm·key provides nutrients to aphid hosts and is passed directly from mother to progeny. Selectionterm·dom acts on Buchneraterm·key to increase female fecundityterm and on the aphid to maintain the Buchneraterm·key upon which it depends. Both the aphid and the Buchneraterm·key have specific features that can only be interpreted as adaptations to promote the fitness of the holobiontterm·dom: both parties cooperate in the production of a joint metabolism able to provide needed nutrients [ 2 , 6 , 7 , 12 , 28 – 30 ], and the aphid has evolved specialized mechanisms for housing and transmitting Buchneraterm·key [ 13 , 31 ]. In other insect groups, acquisitions of heritable bacteria and host adaptations for maintaining them appear to have been key adaptations in shifts between dietary niches, such as xylem versus phloem sap of plants [ 32 , 33 ]. Clearly, these systems are shaped by holobiont-level selectionterm·dom, acting both on gains and losses of heritable symbiontsterm·key and on mutational changes in symbiontterm·key and host genomes [ 8 ].

But even in these extreme cases of co-inherited genomes, selectionterm·dom at the level of the hologenometerm·dom fails to explain many features, which are understandable only by considering the distinct transmission routes and selective milieu of each partner. For mitochondria, the most intimate and coevolved example of symbiosis, traits sometimes oppose fitness interests of the “host,” resulting in cytonuclear conflictterm·dom [ 34 – 36 ]. Selectionterm·dom acts at multiple levels simultaneously, and heritable symbiontsterm·key can evolve as both helpers and antagonists. For example, maternally inherited symbiontsterm·key such as Wolbachia and Spiroplasma provide insect hosts with protection against natural enemies [ 37 , 38 ] but also inflict costs on hosts by manipulating their reproductive systems to favor female progeny [ 39 , 40 ].

Thus, even when symbiontsterm·key are vertically inherited and more readily regarded as part of the host genetics than as part of the environment, conflicts are rampant. To state that the hologenometerm·dom is the primary unit of selectionterm·key oversimplifies, and ignores a large body of theoretical and experimental work devoted to teasing apart how selectionterm·dom acts on these composite entities.

But the majority of microbial associations of multicellular animals and plants are non-heritable. Sometimes these too appear to involve selectionterm·dom on hologenomesterm·dom. In the bobtail squid– Vibrio fischeri symbiosis, hosts are colonized repeatedly during their lives and employ specific mechanisms for recognizing and admitting their symbiontsterm·key [ 41 ], and symbiontsterm·key retain features (luminescence) that benefit hosts. These cases are intriguing, as their stability suggests that hosts have evolved effective policing mechanisms that prevent “selfish” symbiontsterm·key from invading and spreading.

Gut-dwelling organisms are of particular interest, due to their potential to affect the health of animal hosts. To what extent are they selected at the hologenometerm·dom level? The fidelity to a host and transmission routes vary enormously among host species and among gut symbiontsterm·key. At one extreme, gut symbiontsterm·key are directly transferred from mothers to progeny through mechanisms such as the deposition of a symbiontterm·key mass that is ingested by newly hatched progeny (e.g., [ 42 ]). Alternatively, maternal behaviors or gregarious lifestyles may effect direct transfer of gut organisms between members of a host species. But in many cases, gut organisms are promiscuous: they are picked up from the environment or from unrelated host individuals every generation, or repeatedly during the lives of single individuals as they develop. In some cases, gut communities appear to consist of microbial species that are widespread in the environment, so natural selectionterm·dom associated with the host gut may be inconsequential for these organisms. In many insects, gut communities are a highly selected subset of microbial species ingested with food but nonetheless are variable among host individuals and habitats [ 43 – 46 ].

Across this spectrum, how can we determine if and when selectionterm·dom at the hologenometerm·dom level has an important evolutionary impact? Even in the highly dynamic cases, fitness interests of host and symbiontsterm·key can align: symbiontterm·key fitness may depend on host longevity and growth rate, which may correlate with opportunities for symbiontterm·key replication and dispersal. Thus, opportunity for selectionterm·dom at the hologenometerm·dom level exists, but it may be small or insignificant relative to selectionterm·dom on individual interacting genomes.

Reciprocal fitness benefits, i.e., mutualism, or developmental dependence of the host on its symbiontsterm·key are sometimes taken as evidence of selectionterm·dom at the hologenometerm·dom level. But even if microorganisms are effectively parasitic and provide no initial benefit to hosts, host development can evolve to become dependent on them. Thus, the striking finding that normal development of the vertebrate gut is dependent on microorganisms [ 47 ] does not imply that gut inhabitants have evolved to promote gut development, only that vertebrates have evolved dependence on a part of the environment that is reliably present. Just as day length is used by many plants as a cue for initiating flowering times, presence of particular organisms can provide useful developmental cues. Another example is the role of bacteria in promoting multicellularity in choanoflagellates [ 48 ]: this finding does not imply that the bacteria evolved to carry out this role, only that they have been adopted by choanoflagellates as a developmental cue.

What Is the Null Hypothesisterm?

Many features of eukaryotes, including ourselves, cannot be understood without taking into account microbial associates, which are themselves evolving. Clearly we need to study organisms in the context of these associations, but how should we formulate our questions and hypotheses? We argue that the wrong approach is to start with the assumption that associated organisms have evolved to function as a cooperative unit and that the task is simply to characterize mutually beneficial adaptations. This assumption is often incorrect, and embracing it uncritically will slow progress. A more parsimonious approach is to adopt the null hypothesisterm that interacting lineages have not evolved exceptional hologenome-selected traits, and to test specific hypotheses regarding such traits.

For many purposes, the issue of whether organisms have evolved due to selectionterm·dom on a hologenometerm·dom is irrelevant. For the purpose of understanding how symbiontsterm·key affect human health or productivity of agricultural crops, one may simply want to know the current effect of a symbiontterm·key on the host, whatever the evolutionary history may have been. But careful wording that does not invoke dubious evolutionary mechanisms is still important. Sometimes hosts and symbiontsterm·key have coadapted for mutual benefit, but even in these cases, an element of antagonism persists due to the differences in fitness interests of the interacting genomes. In other cases, hosts have evolved to be dependent on microorganisms, even though the latter have not evolved in response. The central claim of the hologenometerm·dom concept, that a host and its microbiometerm·key together form the primary unit of selectionterm·key, is sometimes true, and sometimes false; its validity will depend on the particular case. In answer to the question posed in the title, we suggest that the varied and often inconsistent interpretations of the hologenometerm·dom concept have been a source of more confusion than clarity in understanding the evolution of host–microbe interactions. Advances will come from empirical studies that start with rigorous assumptions and a clear framework for detecting coevolutionterm·dom and teasing apart levels of selectionterm·dom.