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Global biodiversity and ecosystem function are the result of complex networks of interactions and feedbacks between animals and their environments, which in turn are affected by the interactions and feedbacks between animals and the organisms they host. Understanding these complex networks, including the main drivers of and responses to ecological and environmental changes and their global implications, requires adopting a systems-based perspective. We advocate for this approach by characterizing a framework centered around bats, a globally-distributed mammalian order, and their dual roles as both inhabitants of ecosystems and as habitats themselves. Like other organisms, bats interact with habitats by providing ecosystem services that impact the survival and distribution of other species, and may be affected by such factors as land use change, climate change, fluctuations in food availability, and hunting pressure. Habitat conditions (e.g. food availability, temperature, etc.) can affect the physiological condition of individuals, which in turn can affect the prevalence and/or virulence of hosted organisms and potential pathogens (e.g. ectoparasites, bacteria, viruses, fungi, and protozoa). In addition, the interactions among individuals (e.g. co-roosting, migration, etc.) influence the habitat connectivity for their hosted organisms (e.g. opportunities for dispersal). Bats have a unique relationship with infectious disease, both biological and cultural. With this in mind, when applied to bats this framework has special importance to how we understand and apply the One Health concept, whereby healthy natural environments foster both human and animal health, which in turn also promotes healthy environments. By leveraging a hierarchical approach among these different levels of biological organization, we can arrive at a clearer picture of the specific threats facing bats—as well as the risk of pathogen spillover to humans and other domesticated and wild animals generated by disrupting this delicate balance—and identify possible measures to mitigate adverse impacts. Thus, to understand these complex interactions and their implications for conservation, ecosystem health, and human health, we need a new ecological framework that recognizes that changes in habitats not only affect macrofauna and the ecosystem services they provide, but also have the potential to cascade through the diversity and evolution of the organisms they host. This review provides a case study for the application of this framework, which is extensible to other organisms with their own unique relationships with habitats and as habitats. 

Abstract Understanding biodiversity patterns as well as drivers of population declines, and range losses provides crucial baselines for monitoring and conservation. However, the information needed to evaluate such trends remains unstandardised and sparsely available for many taxonomic groups and habitats, including the cave-dwelling bats and cave ecosystems. We developed the DarkCideS 1.0 ( https://darkcides.org/ ), a global database of bat caves and species synthesised from publicly available information and datasets. The DarkCideS 1.0 is by far the largest database for cave-dwelling bats, which contains information for geographical location, ecological status, species traits, and parasites and hyperparasites for 679 bat species are known to occur in caves or use caves in part of their life histories. The database currently contains 6746 georeferenced occurrences for 402 cave-dwelling bat species from 2002 cave sites in 46 countries and 12 terrestrial biomes. The database has been developed to be collaborative and open-access, allowing continuous data-sharing among the community of bat researchers and conservation biologists to advance bat research and comparative monitoring and prioritisation for conservation.