INTRODUCTION
Microbiomes are both a trait of the host
(Benson et al., 2010) and
ecological communities comprised of microorganisms capable of complex
and dynamic interactions (Kodera et al. 2022). Ecological theory
provides specific hypotheses for testing and inferring rules of life
that apply to all organisms
(Koskella, Hall, & Metcalf,
2017), and ecological processes are essential to understanding the
composition, stability, and evolution of the microbiome
(Miller, Svanbäck, &
Bohannan, 2018). The Theory of Island Biogeography
(MacArthur & Wilson, 2001)
is an ecological theory that relates the size of an island and its
biodiversity through parameterizing factors such as immigration and
extinction (MacArthur &
Wilson, 2001). With larger islands, extinction events are predicted to
be less likely to occur due to the greater availability of space and
resources. With more isolated islands, the arrival of new immigrants is
predicted to be less likely and thus fewer new species come into the
space. Conceptualizing hosts as “islands” is reasonable: both
geographic islands and vertebrate hosts harbor complex biological
communities that are connected by ecological processes (e.g., dispersal
and immigration) and that are limited by resources and space.
Communities can be significantly impacted by random environmental events
and follow successional processes in the face of disturbance
(Karl et al., 2018). The
difference is scale. Another ecological theory, Metacommunity Theory
(Leibold et al., 2004),
incorporates scale in how communities interact with local and regional
processes (Miller et al.,
2018). According to Metacommunity Theory, communities exist in patches
that are connected by dispersal and are hierarchically nested within
larger patches. Importantly, both (1) properties of the physical space
and (2) traits of the organisms within the community impact successful
colonization of a new habitat and probability of survival
(Miller & Bohannan, 2019).
The consideration of hosts and their specific body sites as patches of
biodiversity that are affected by processes shared by all life is a
powerful way to test and identify “universal” rules of life
(Ma & Li, 2018;
Li et al., 2020;
L. Li & Ma, 2016). Body
size has been shown to positively correlate with bacterial richness,
implying adherence to Species-Area Relationships
(Sherrill-Mix et al., 2018),
although the non-independence of host species was not accounted for in
this case. The Theory of Island Biogeography has been demonstrated in
the human lung microbiota, where sites farther from the “mainland
source” are less diverse
(Dickson et al., 2015) and
tests of microbial composition against a neutral assembly model have
identified diseased lung microbiomes as under selection
(Venkataraman et al., 2015).
Birds (class: Aves) are important members of Earth’s biosphere and to
fully understand their biology requires knowledge of their microbiota.
Furthermore, bird body sizes span five orders of magnitude by weight,
making them an excellent clade for exploring species-area relationships
in host-associated microbiota. Larger birds exhibit a greater area for
microorganisms to occupy than smaller birds, which may provide increased
ecological niches and lead to fewer extinction events as bacteria are
less likely to compete for resources. Microbial colonization may also be
higher in larger birds due to intrinsic qualities and life history
traits (e.g. greater food requirements, larger territories), leading to
increased exposure to diverse microorganisms. Alternatively, higher
immune cell output of larger birds
(Ruhs, Martin, & Downs,
2020) may inhibit the establishment of new microbial colonizers.
The microbiome is not only an ecological community, it is also a trait
of its host (Benson et al.,
2010). To understand the evolution of any trait in a comparative
context, we must also consider the underlying phylogeny
(Felsenstein, 1985), as many
organismal traits are not independent of evolutionary relationships. To
appropriately test the relationship between island size and
(micro)biodiversity, and to ensure any correlations are not simply a
factor of the relatedness of the host species, we use phylogenetic
comparative analyses. Five body sites were the focus of our analyses:
four are distinct sites along the gastrointestinal tract connected to
each other through digestion (buccal, gizzard, intestines, cloaca) and
the fifth is blood. These sample types encompass diverse environmental
conditions and may follow Island Biogeography principles more or less
strongly. The buccal, gizzard, intestine, and cloacal samples are
frequently exposed to external microbes through the intake of food
containing distinct microbiota that may be able to newly colonize those
areas. The blood (and liver and spleen) sample types are in contact with
new microbes rarely and thus will have fewer potential “immigrants”
into their microbial communities.
There were several goals of this paper. First, we describe the taxonomic
composition and diversity of the microbiomes of hundreds of wild birds
at various body sites. Second, we compare the microbiota of the body
sites, and identify conserved and unique members. Third, we estimate the
phylogenetic signal of microbiome diversity using Pagel’s lambda, and
fourth, we address the relationship between host body size and
microbiome diversity using a phylogenetically controlled method.
Together, these aims expand what is known about the microorganisms, the
birds and the processes structuring the avian microbiome.