Posted on Authorea 12 Jun 2020 | The copyright holder is the author/funder. All rights reserved. No reuse without permission. | https://doi.org/10.22541/au.159200503.35915032 | This a preprint and has not been peer reviewed. Data may be preliminary. Parasite species identity and local community diversity mediate effects of habitat fragmentation on bacterial microbiomes. Kelly A. Speer 1 , Tiago Teixeira 2 , Alexis Brown 3 , Susan Perkins 1 , Katharina Dittmar 4 , Melissa Ingala 1 , Claudia Wultsch 1 , Konstantinos Krampis 5 , Carl Dick 6 , Marcos Vieira 7 , Ana Delciellos 7 , Spencer Galen 8 , Nancy Simmons 1 , and Elizabeth Clare 2 1 American Museum of Natural History 2 Queen Mary University of London 3 Stony Brook University Department of Ecology and Evolution 4 State University of New York at Buffalo 5 Hunter College CUNY 6 Western Kentucky University 7 Universidade Federal do Rio de Janeiro 8 The Academy of Natural Sciences of Drexel University June 12, 2020 Abstract Arthropod ectoparasites generally have nutrient-poor diets and are dependent on their bacterial symbionts for nutrient acqui- sition, development, and immune response initiation. As the body of research on parasite-microbiome interactions continues to grow, it is becoming more apparent that the parasite is not an island that physically and biologically constrains the microbiome. Suitable habitat fragment size, isolation, and distance from a source are important variables influencing community composition of plants and animals, but the role of the environment in determining composition and variation of host-associated microbial communities is poorly known. It is hypothesized that evolution and ecology of an arthropod parasite will influence its micro- biome more than broader environmental factors, but this hypothesis has not yet been tested. To compare the relative influence of the broader environment to that of phylogenetic constraint on the microbiome, we applied high-throughput sequencing of the V4 region of 16S rRNA from 222 obligate ectoparasitic bat flies (Streblidae and Nycteribiidae) collected from 155 bats (representing six species) from ten habitat fragments in the Atlantic Forest of Brazil. We find that parasite species identity is the strongest driver of microbiome composition. To a lesser extent, reduction in habitat fragment area is associated with a reduction in connectance of microbial interaction networks and an increase in modularity, but size-independent measures of network topology and bacterial taxon richness do not show an impact of the environment. Instead, habitat fragments that support more diverse bat and bat fly communities also support more connected bacterial interaction networks. Title: Parasite species identity and local community diversity mediate effects of habitat frag- mentation on bacterial microbiomes. Running Title: Island biogeography of parasite microbiomes Kelly A. Speer 1,2,3* , Tiago Souto Martins Teixeira 4 , Alexis M. Brown 5 , Susan L. Perkins 1,6,7 , Katharina Dittmar 8 , Melissa R. Ingala 1 , Claudia Wultsch 6,9 , Konstantinos Krampis 9,10 , Carl W. Dick 11,12 , Marcos Vin´ ıcuis Vieira 13 , Ana Cl´ audia Delciellos 13 , Spencer C. Galen 14 , Nancy B. Simmons 1,15 , and Elizabeth L. Clare 4 1 Richard Gilder Graduate School, American Museum of Natural History, New York, NY, USA 1