Introduction
Deforestation has well-documented, devastating consequences on species survival [1], global warming [2], and zoonotic disease emergence [3, 4]. This is particularly worrying in tropical forests, which lost 6% of in their global area between 1990 and 2015 [5]. For example, the Atlantic Forest of Brazil, one of the world’s most biodiverse regions, occupies only 28% of its original extent [6]. The consequences of this habitat loss have primarily been examined in macroorganisms, but we do not yet understand the extent to which microorganisms like bacteria, viruses, fungi, and single-cell eukaryotes respond to deforestation, especially those microorganisms that are obligately associated with a living host. These microorganisms are integral members of wildlife communities; changes in their presence or abundance may alter the function of communities [7], the health of individuals and species [8], and the transmission of pathogens between members of the community [9].
Here, we examine the bacterial microbiome within ectoparasites of bats in forest fragments of varying area and isolation as a model for testing the hypothesis that habitat loss affects host-associated microbial communities (Figure 1A). We use island biogeography theory as a null hypothesis for the way we expect microbiomes to behave if the environment is driving community composition instead of the host. This theory states that small, isolated habitats will support low-diversity communities that are a subset of the species found in larger source communities [10]. Historically, studies of the island biogeography of parasites have treated hosts as suitable habitat, not the broader environment where the host and parasite live [11, 12]. There are two limitations to this thinking: only an extremely small subset of parasites spend their entire lifespan on the body of a single host individual, and this idea ignores the impact that the environment has on parasite microbiomes that may subsequently impact parasite survival [13]. Hosts are not islands that perfectly constrain their parasites, and parasites are not islands that perfectly constrain their microbes. Previous research suggests that the environment influences microbiome composition following expectations of island biogeography [14, 15]. In other cases, the environment does not dictate microbiome composition [16, 17]. Variation in the ability of the environment to filter members of the microbiome community is a reflection of the complexity and diversity of microorganisms themselves [16, 18]. This diversity makes it difficult to tease apart the impacts of host and environment on microbiome community composition.