Suitable habitat fragment size, isolation, and distance from a source are important variables influencing community composition of plants and animals, but the role of these environmental factors in determining composition and variation of host-associated microbial communities is poorly known. In parasite-associated microbial communities, it is hypothesized that evolution and ecology of an arthropod parasite will influence its microbiome more than broader environmental factors, but this hypothesis has not been extensively tested. To examine the influence of the broader environment on the parasite microbiome, we applied high-throughput sequencing of the V4 region of 16S rRNA to characterize the microbiome of 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. Parasite species identity is the strongest driver of microbiome composition. To a lesser extent, reduction in habitat fragment area, but not isolation, is associated with an increase in connectance and betweenness centrality of bacterial association networks driven by changes in the diversity of the parasite community. Controlling for the parasite community, bacterial network topology covaries with habitat patch area and exhibits parasite-species specific responses to environmental change. Taken together, habitat loss may have cascading consequences for communities of interacting macro- and microorgansims.  

Understanding the processes that enable species coexistence has important implications for assessing how ecological systems will respond to global change. Morphology and functional similarity increase the potential for competition, and therefore, co-occurring morphologically similar but genetically unique species are a good model system for testing coexistence mechanisms. We used DNA metabarcoding and High Throughput Sequencing to characterise for first time the trophic ecology of two recently-described cryptic bat species with parapatric ranges, Myotis escalerai and Myotis crypticus. We collected faecal samples from allopatric and sympatric regions and locations to describe the diet both taxonomically and functionally and compare prey consumption with prey availability. The two bat species had similar diets characterised by high arthropod diversity, particularly Lepidoptera, Diptera and Araneae, and a high proportion of prey that is not volant at night, which points to extensive use of gleaning. Diet overlap at the prey-item level was lower in locally sympatric than allopatric locations, supporting trophic shift under fine-scale sympatry. Furthermore, locally sympatric samples of M. escalerai had a marginally lower proportion of not nocturnally volant prey, suggesting that the shift in diet may be driven by a change in foraging mode. Our findings suggest that fine-scale coexistence mechanisms can have implications for maintaining broad-scale diversity patterns. This study highlights the importance of including both allopatric and sympatric populations and choosing meaningful spatial scales for detecting ecological patterns. We conclude that a combination of high taxonomic resolution with a functional approach helps identify patterns of niche shift.

El Niño is a major driver of fluctuations in tropical precipitation and fruiting production, with cascading effects on frugivores. As places get wetter, mutualistic networks tend to become more modular and less nested. In order to test the impact of severe floods and droughts caused by the El Niño cycle of 2015-2016 on nestedness and modularity of mutualistic networks, we determined the links between frugivorous bats and the plants in their diets by DNA barcoding bat faeces and used null models for our network comparisons. Despite the contrasting effects of droughts and floods in the dry forest and rainforest, respectively, we observed similar changes in network structure for both forests. We found higher values of modularity, but lower of nestedness for most networks comparisons. Over all we found higher nestedness in the dry forest than the rainforest and minimal difference between wet and dry season in the dry forest. A lower nestedness might reduce the number of species supported by the habitat as well as increase species competition. Although the increase in modularity might reduce the number of coexisting species in the environment, higher network compartmentalization leads to greater stability, slower spread of disturbance and smaller chances of having trophic cascades. Therefore, changes in network structure promoted by El Niño are likely to have dual effects on networks with some effects leading to greater stability while others to increasing competition.