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.