PERSPECTIVE
published: 21 October 2016
doi: 10.3389/fmicb.2016.01647
Frontiers in Microbiology | www.frontiersin.org 1 O
ctober 2016 | Volume 7 | Article 1647
Edited by:
Thomas Carl Bosch,
University of Kiel, Germany
Reviewed by:
Carolin Frank,
University of California, Merced, USA
Christian Robert Voolstra,
King Abdullah University of Science
and Technology, Saudi Arabia
*Correspondence:
Jonathan L. Klassen
jonathan.klassen@uconn.edu
Specialty section:
This article was submitted to
Microbial Symbioses,
a section of the journal
Frontiers in Microbiology
Received: 30 June 2016
Accepted: 04 October 2016
Published: 21 October 2016
Citation:
Kopac SM and Klassen JL (2016) Can
They Make It on Their Own? Hosts,
Microbes, and the Holobiont Niche.
Front. Microbiol. 7:1647.
doi: 10.3389/fmicb.2016.01647
Can They Make It on Their Own?
Hosts, Microbes, and the Holobiont
Niche
Sarah M. Kopac and Jonathan L. Klassen
*
Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
Virtually all multicellular organisms host a community of symbionts composed
of mutualistic, commensal, and pathogenic microbes, i.e., their microbiome. The
mechanism of selection on host-microbe assemblages remains contentious, particularly
regarding whether selection acts differently on hosts and their microbial symbionts. Here,
we attempt to reconcile these viewpoints using a model that describes how hosts and
their microbial symbionts alter each other’s niche and thereby fitness. We describe how
host-microbe interactions might change the shape of the host niche and/or reproductive
rates within it, which are directly related to host fitness. A host may also alter the niche
of a symbiotic microbe, although this depends on the extent to which that microbe is
dependent on the host for reproduction. Finally, we provide a mathematical model to
test whether interactions between hosts and microbes are necessary to describe the
niche of either partner. Our synthesis highlights the phenotypic effects of host-microbe
interactions while respecting the unique lifestyles of each partner, and thereby provides a
unified framework to describe how selection might act on a host that is associated with
its microbiome.
Keywords: niche, symbiosis, selection, microbiome, reproductive rate, fitness, holobiont
INTRODUCTION
Virtually all multicellular organisms host a diverse collection of mutualistic, commensal, and/or
pathogenic microbial symbionts, i.e., their microbiome (McFall-Ngai et al., 2013; note that we
define “symbiosis” as “two organisms living together” regardless of the nature of this interaction,
following De Bary, 1879). These symbiotic communities are assembled through vertical transfer
between host generations and/or horizontal transfer from external environments, either neutrally
or with host selection (Ebert, 2013). The long evolutionary association of hosts with microbes and
the diverse phenotypes resulting from these interactions reinforce the broad influence of microbes
on host fitness (McFall-Ngai et al., 2013). Despite this realization, how to best describe the evolution
of hosts and their symbiotic microbes remains controversial.
One emerging paradigm to describe how hosts evolve alongside their microbial symbionts
considers both hosts and their microbes as a single integrated unit, i.e., a holobiont (Zilber-
Rosenberg and Rosenberg, 2008; Rosenberg and Zilber-Rosenberg, 2013; Bordenstein and Theis,
2015; Theis et al., 2016). Several aspects of this approach have been criticized, particularly the degree
to which it presumes co-evolution between hosts and their microbes and whether selection on the
holobiont supersedes selection on hosts and their symbionts individually (Moran and Sloan, 2015;
Douglas and Werren, 2016). Although this debate remains unresolved, there is broad co
nsensus
that the impacts of microbial symbionts on host fitness need to be accounted for to comprehensively
describe host evolution.
Kopac and Klassen Hosts, Microbes, and the Holobiont Niche
Models that des cribe how host fitness is modified by microbial
symbioses are often rooted in evolutionary biology, perhaps
reflecting a long history of co-evolutionary studies in host-
microbe symbioses and proposed links to population genetics,
e.g., via the “hologenome” (comprising both host and microbial
genes; Zilber-Rosenberg and Rosenberg, 2008; Bordenstein and
Theis, 2015) . Here, we develop a complementary model rooted
in ecological niche theory to describe how microbes alter host
fitness. This framework advantageously accounts for the impacts
of interactions between hosts and their microbial symbionts
while respecting the distinct lifestyles and evolutionary interests
of each partner. Based on this framework, we propose
a mathematical model to determine if symbiotic microbes
affect host fitness and illustrate experimental approaches
that test this model. By accommodating the independent
lifestyles of both hosts and their microbial partners while still
allowing for emergent properties resulting from host-microbe
interactions, niche-based models provide a useful framework to
comprehensively describe host-microbe ecology and evolution.
INTERSPECIFIC INTERACTIONS AND THE
ECOLOGICAL NICHE
In his landmark “Concluding Remarks” paper, Hutchinson
defined a species’ fundamental niche as the sum of all
environmental factors that allow that species to reproduce and
maintain a stable population over time (
Hutchinson, 1957).
Outside of this fundamental niche, the population death rate
exceeds the population reproductive rate and, ba rring other
forces, ultimately causes extinction. The fundamental niche can
be represented as an n-dimensional vector that defines regions
in niche space where a population will grow (r > 0, where r is
the net reproductive rate), and regions where that population will
ultimately go extinct (r < 0). The first two dimensions of such a
vector are illustrated in Figure 1A, with solid lines representing
the r = 0 isocline that separates the regions where r > 0 and
r < 0. This isocline represents the boundary of a species’
fundamental niche.
The fundamental niche represents an idealized situation
without interspecific interactions. Accordingly, Hutchinson
further defined the “realized niche” as a subset of the
fundamental niche where a species is not outcompeted by other
taxa (
Hutchinson, 1957). Subsequent work has extended this
idea to include mutualistic interactions that can expand t he
realized niche beyond the boundaries of the fundamental niche
(Bruno et al., 2003). The structure of a host’s realized niche
therefore depends on the outcome of symbiotic interactions,
including the entire symbiotic spectrum from pathogens to
mutualists. It therefore follows that changes in such symbiotic
interactions might change the structure of a species’ realized
niche (Figures 1B,C).
The realized niche describes where a species is likely to
persist, having a net reproductive rate r > 0. Although a species
will persist within this region, r will almost certainly not be
equal t hroughout it. For example, different genotypes within a
population will be better adapted to some parts of a niche but
FIGURE 1 | The ecological niche and its relationship to reproductive
rate. (A) A simplified niche projected along two axes, bounded by a solid line
representing the isocline where a species’ net reproductive rate (r) equals 0.
Stable population growth only occurs within this isocline, although net
reproductive rates differ within this region as represented by different shades of
blue. (B-D): Niche boundaries may change relative to past conditions (dashed
line) via expansion (B) or contraction (C). The distribution of net reproductive
rates may also change within a set of unchanging niche boundaries (D),
exemplified by the addition a second region of this niche having a high net
reproductive rate. Although not shown in the figure, trade-offs may exist where
niche boundaries both expand and contract in different parts of a species’
niche alongside multiple changes in net reproductive rate.
not others. Alternatively, some regions of the niche will remain
incompletely filled because of dispersal limitation and/or low
population density, and organisms will temporarily occur in
regions where r < 0 due to source-sink dynamics (
Pulliam, 2000;
Holt, 2009). Thus, niche shape may change via differences in
net reproduction rate, even within a constant niche boundary
(defined by the r = 0 isocline; Figure 1D). Such changes in
reproductive rate directly correspond t o a species’ evolutionary
(Malthusian) fitness (Orr, 2009). In this way, understanding the
shape of a species’ niche and how it is altered by ecological
interactions directly informs models of that species’ fitness and
evolution.
MICROBIAL MODIFICATION OF THE HOST
NICHE
The previous section describes how symbiotic microbes might
alter the structure of the host niche, and thereby the host fitness
landscape on which selection can act. Do such microbially-
mediated niche alterations actually occur? Perhaps the most naïve
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Kopac and Klassen Hosts, Microbes, and the Holobiont Niche
test of this hypothesis is to compare microbe-free hosts to their
colonized counterparts. These experiments often indicate that
microbes modify the host niche, in the sense that growth rates
and/or their proxies (e.g., development, disease susceptibility)
differ between sterile and colonized hosts (
Smith et al., 2007).
However, such experiments cannot test if changes in the
microbiota change the shape of the host niche because all
hosts are colonized by microbes during birth, highlighting
the artificiality of the gnotobiotic niche. Stronger evidence for
microbially-mediated niche shifts comes from comparing natural
host populations with different microbially-mediated phenotypes
that effect host reproductive rate and/or related proxies. Ideally,
these host phenotypes can be re capitulated in different host
populations after switching microbes, thereby providing strong
evidence that microbes alter the niches of their hosts.
Microbes can expand the niche boundary of many host
species, as illustrated by Figure 1B. For example, defensive
mutualists protect a host from infection by pathogens that
would otherwise exclude it from the areas of its fundamental
niche space containing those pathogens (reviewed in
Oliver
et al., 2014). Similarly, thermotolerance is conferred to
the panic grass Dichanthelium lanuginosum via the fungus
Curvularia protuberata when it is infected by the Curvularia
thermal tolerance virus, thereby extending th is grass’s niche to
include geothermally-heated soil (Márquez et al., 2007). This
phenotype can be transferred to naïve tomato plants in cross-
colonization experiments, highlighting the microbial etiology
of thermotolerance (Rodriguez et al., 2008). Finally, many
symbionts allow hosts to use substrates t hat they would otherwise
be unable to live off of, e.g., plant sap lacking essential amino
acids, animal blood lacking B vitamins, or inorganic ions emitted
from deep-sea vents (
Dubilier et al., 2008; Douglas, 2009). Niche
expansion mediated by symbiotic microbes therefore occurs in
many hosts and environmental contexts.
Microbes can also contract a host’s niche, as illustrated by
Figure 1C. An extreme example is pathogens t hat have driven
their hosts extinct, such as malarial parasites of native Hawaiian
birds (Warner, 1968 ; van Riper et al., 1986). Following the
introduction of these pathogens, the realized niche of these hosts
contracted to contain only pathogen-free regions. In a nother
example, Wolbachia can cause cytoplasmic incompatibility
in many insect hosts that prevent males from producing
viable offspring with infected females (
Werren, 1997), thereby
reducing the infec ted host’s niche to where uninfected mates
are present. On a longer timescale, persistent associations with
different nutritional mutualists have led to convergent losses
of arginine biosynthetic genes in pea aphids (The International
Aphid Genomics Consortium, 2010) and fungus growing ants
(Nygaard et al., 2011; Suen et al., 2011), restricting these hosts
to an obligately symbiotic lifestyle. This reflects a trade-off
where niche expansion to use previously inaccessible nutrients
was accompanied by niche contraction via diet restriction.
Interestingly, microbes have also experienced niche contraction
in these examples, e.g., via the loss of amino acid biosynthetic
enzymes in Buchnera that leaves it dependent on its aphid host
(
Russell et al., 201 3). Together, these examples demonstrate how
niches can contract through parasitism and specialization.
The above examples highlight incidences where microbes
change the host niche boundary, i.e., the r = 0 isocline
(Figure 1). However, microbes may more often cause subtler
changes in host net reproductive rate while leaving the niche
boundary unaltered. For example, most pathogens do not drive
their host extinct because pathogen fitness is dependent on
successful transmission between infective and naïve hosts (
Bull
and Lauring, 2014). Instead, pathogen fitness is maximized
when some but not all of their h osts are infected, i.e., host
net reproductive rate is decreased but r > 0. In a second
example, pea aphids reproduce twice as well on clover plants
when infected with Regiella insecticola symbionts (Ts uchida et al.,
2004), matching the occurrence of these Regiella only in regions
where pea aphids colonized clover (Tsuchida et al., 2002). Thus,
these aphids have increased fitness in a part of their niche that
they occupy with r > 0 regardless of the presence of Regiella.
Overall, we hypothesize that microbially-mediated changes in
host net reproductive rates are more common than changes in
host niche boundaries, especially for widely distributed species
with broad environmental niches like humans. However, any
change in niche shape can alter host evolution because of the
direct relationship between net reproductive rate and Malthusian
fitness (
Orr, 2009).
HOST MODIFICATION OF THE MICROBIAL
NICHE
The preceding section describes how changes in a host’s microbial
symbionts can alter the host’s realized niche. Might the reciprocal
also be true, i.e., do associations with different hosts signifi cantly
alter the realized niche of a microbe? This depends on the
fraction of a microbe’s realized niche that depends on host
association. At one extreme, obligate symbionts (e.g., Buchnera
nutritional mutualists of aphids) lack any known life stage outside
of their host; their realized niche is therefore entirely defined
by host association (
Douglas, 2009). In contrast, horizontally-
transmitted microbes may replicate more frequently in non-
host environments t han host-associated ones (Mushegian and
Ebert, 2016). For example, microbes that retain activity in
the human gut after ingestion with food only briefly associate
with hosts but reproduce extensively in food-associated niches
(
Derrien and van Hylckama Vlieg, 2015). Obligate symbionts
and food-associated microbes represent extremes on a spectrum
with many lifestyles in between. For example, Xenorhabdus
symbionts of entomopathogenic Steinernema nematodes must
balance carriage by the nematode against pathogenic potential
toward prey insects (Chapuis et al., 2012). Such trade-offs are
likely common for microbes that are horizontally transferred
between hosts . In summary, the degree to which a host defines
a microbe’s niche is contingent upon on how much that microbe
depends on that host to suc cessfully replicate.
Even when hosts strongly define a microbe’s re alize d niche,
switching between different hosts may or may not shift this
microbe’s niche. For example, a generalist microbe may be active
and equally adapted to multiple hosts, with equal reproductive
rates in e ach. Alternatively, microbes may colonize non-target
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Kopac and Klassen Hosts, Microbes, and the Holobiont Niche
hosts ( e.g., as zoonotic pathogens) in which they replicate
poorly. Such colonization may be selectively favored if it is a
byproduct of adaptations to another more common host, or
selectively neutral if it happens at low frequency. Having said
this, clear examples of horizontally-transferred microbes t hat
are specialized to a particular host exist and represent instances
where a specific host association dominates the structure of a
microbe’s niche (e.g.,
Kodaman et al., 2014). However, ecological
forces such as drift and dispersal limitation must be ruled
out as alternative explanations for such patterns of host-
microbe specificity (Alt h off et al., 2014). Explicitly differentiating
between adaptive and non-adaptive reasons for host-microbe
specialization is an important topic for future research.
SELECTION ON THE HOST AND ITS
MICROBIAL SYMBIONTS
All hosts are colonized by microbial symbionts. Rece nt t h eories
have suggested that both the host and its symbiotic microbes
together form a single “holobiont” on which selection acts
(Zilber-Rosenberg and Rosenberg, 2008; Rosenberg and Zilber-
Rosenberg, 2013; Bordenstein and Theis, 2015; Theis et al., 2016).
Expressed in terms of our niche-based framework, selection will
follow t h e fitness landscape defined by the net host reproductive
rates within its realized niche, as shaped by interactions with its
microbial symbionts. The contributions of microbes to the host
niche can therefore be formalized by t he following equation:
N
holo
= N
apo
+ A (1)
Here, a vector N
holo
describes the realized niche of the holobiont
(holo- indicating whole, the h ost while associated with its
microbial symbionts). This N
holo
vector can be decomposed
into two other vectors, N
apo
describing the niche of the host
lacking its microbiota (apo- indicating separate, the host without
microbial symbionts) and A describing how N
apo
is modified
by this microbiota. Experimentally, N
apo
can be observed as the
niche occupied by a sterile host, and A represents how N
apo
differs from N
holo
. A can itself be decomposed into vectors
describing the impact of individual members of a microbiome
on the host niche and how interactions between these microbes
alter the host niche. For example, gypsy moths are only sensitive
to toxins produced by Bacillus thuringiensis when the moths
are colonized by their natural gut microbes (
Broderick et al.,
2006). Thus, the interaction between B. thuringiensis and these
gut microbes is required to describe how microbial symbionts
together alter the moth’s niche (as represented by A). Equation (1)
and its derivatives therefore mathematically describe how a host’s
realized niche is structured by interactions with its microbial
symbionts, including emergent properties caused by interactions
between multiple partners.
Equation (1) has several interesting properties. First, it
provides an empirical measure to assess whether the holobiont
might be a significant unit of selection according to the
magnitude and shape of the host-microbe interaction vector
A. If selection acts along niche axes that are modified by A,
then selection on the host cannot be accurately represented
without considering the influence of its symbiotic microbes.
Thus, measuring the shape of A is a critical test of the holobiont
as a unit on which selection might act. For example, differences
between axenic hosts and those colonized by their microbes
would define the value of A and indicate that microbes alter
the shape of the host niche. Importantly, this vector describes
changes in host net reproductive rate that are caused by microbes,
which directly relates to host fitness. The ability of selection to
maximize holobiont fitness must also be weighed against other
ecological forces that impact reproductive rates within a niche,
e.g., population density and dispersal rates.
Second, equation (1) explicitly describes changes to the niche
of a single organism. Although holobiont theory was originally
described in terms of selection on the host (
Zilber-Rosenberg
and Rosenberg, 2008; Rosenberg and Zilber-Rosenberg, 2013;
Bordenstein and Theis, 2015; Theis et al., 2016), equation (1) can
equally be written to describe how a microbe’s niche is modified
by the host. Differences between host and microbial generation
times, population sizes, and life-cycle stages imply both that hosts
and their microbial symbionts have differently shaped niches,
and t hat the extent to which a microbe alters a host’s niche
(A
microbe
) differs from the extent to which a host alters a microbe’s
niche (A
host
). For example, horizontally-acquired microbes that
reproduce more frequently in non-host environments than while
host-associated (
Mushegian and Ebert, 2016) likely have niches
that remain unaltered by th eir host (A
host
≈ 0) despite these
microbes’ potential to impact th eir host’s niche (A
microbe
> 0).
Members of the microbiome may also differ in their impact
on their host’s niche, either individually or as a community.
Comparing A for different members of the microbiome and/or
A
host
may be useful to identify shared environmental niches
and/or coevolution between these partners.
Third, equation (1) can be easily expanded to describe how
changes in a host’s symbiotic microbes will change the niche of
the holobiont:
1N
holo
= 1N
apo
+ 1A (2)
Given that hosts have been colonized by microbes throughout
their evolutionary history, this is likely the most relevant question
to ask concerning host evolution. Equation (2) suggests a n
important experimental approach to determine how microbes
change the shape of the host niche. Microbially-mediated
alterations of the holobiont niche shape can be determined
by comparing the niche shape of a host species with different
microbial symbionts or vice versa. This approach has a lready
been applied in gnotobiotic experiments to determine the
microbial etiology of different phenotypes exhibited by the same
host genotype, i.e., where 1N
apo
= 0 (
Smith et al., 2007).
Similar exchanges using distinct host populations will allow
disambiguation of host and microbial contributions to changes
in a host population’s niche shape, as exemplified by experiments
describing how microbes facilitate diet specialization via toxin
degradation in different populations of Neotoma woodrats (
Kohl
and De aring, 2012; Kohl et al., 2014
).
Finnaly, the notation “holo” to describe the host plus
its microbes and “apo” to describe the host alone draws
Frontiers in Microbiology | www.frontiersin.org 4 October 2016 | Volume 7 | Article 1647
Kopac and Klassen Hosts, Microbes, and the Holobiont Niche
a direct parallel to the well-established nomenclature of
“holoenzyme” and “apoenzyme” in biochemistry. Here, a
holoenzyme comprises both an enzyme and its c atalytic cofactor
that together perform a biochemical function. In contrast,
an apoenzyme lacks this cofactor and does not perform the
biochemical function. Like hosts and their microbes, enzymes
and their cofactors have different evolutionary capacities and/or
tendencies, e.g., inorganic cofactors cannot evolve. Furth ermore,
the holoenzyme is not always the most relevant unit to
describe biochemical function. For example, human cytosolic
aconitase has enzymatic activity at high iron concentrations, but
disassembles its cofactor at low iron concentrations. At such
low-iron concentrations, this aconitase instead functions as an
iron-responsive element binding protein that stabilizes ferritin
mRNA and thereby increases its translation and ultimately
iron accumulation (Kennedy et al., 1992). Such “moonlighting
proteins” are common throughout biochemistry (
Jeffery, 1999).
Thus, like the holobiont, whether the holoenzyme is a relevant
functional unit depends on whether or not the process of interest
is affected by the presence of t he partner cofactor.
In summary, many cases exist where a host’s realized niche
is altered by the presence of its microbial symbionts. These
alterations can either increase or decrease the extent of the host’s
realized niche and reproductive rates within it, thereby altering
host fitness as the target of selection. Such a niche shift can be
identified by comparing sterile and colonized hosts (Smith et a l.,
2007), and/or using gnotobiotic systems that can experimentally
differentiate host- and microbially-mediated alterations of niche
shape (Kohl and Dearing, 2012; Koh l et al., 2014). A host might
similarly shift a microbe’s niche, although the strength and/or
direction of such changes likely differ between these partners.
We therefore consider hosts and microbes to comprise a single
evolutionary unit in the sense that both partners may be required
to faithfully describe their respective realized niches, and thereby
the context in which selection can act.
AUTHOR CONTRIBUTIONS
SK and JK both conceived, wrote, and edited the manuscript. All
authors have approved the final manuscript version.
FUNDING
This work was supported by funding to JK from the University of
Connecticut.
ACKNOWLEDGMENTS
We thank the members of the Klassen lab for helpful comments
on e arlier versions of this manuscript.
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