Wild Avian Gut Microbiome at a Small Spatial Scale: A Study from a Mediterranean Island Population of Alectoris rufa

SIMPLE SUMMARY: Our study is one of the few comparative and within-a-species descriptions of microbiomes in wild non-passerine birds. Particularly, it focuses on red-legged partridges, which are medium-sized gamebirds inhabiting open dry countryside and low-intensity cultivations with a mix of fallow and uncultivated areas in southwestern Europe. We wanted to study microbes living in their gut as their occurrence and diversity may affect both survival and reproduction of these birds. We collected fresh red-legged partridge fecal pellets at different sites located on both the western (two) and eastern (one) sides of Elba Island (central Italy). Although most represented bacteria were the same in all the three sites, we found differences between western and eastern Elban subpopulations in terms of microbiome composition and diversity. This result might be related to locally diverging individual physiological needs and/or to different intensities in past releases of captive-bred birds between the two sides of Elba. Overall, we suggest that the two partridge subpopulations should be managed separately to avoid any loss or significant variation in their microbiome structure. ABSTRACT: This research is one of the few comparative descriptions at an intraspecific level of wild non-passerine microbiomes. We investigated for the first time the gut microbiome of red-legged partridges (Alectoris rufa) using fecal pellets in order to provide a more informed management. We focused on a small Italian population consisting of two demes (WEST, EAST) separated by about 20 km on the opposite sides of Elba Island. Given the small spatial scale, we set up a sampling protocol to minimize contamination from environmental bacteria, as well as differences due to variations in—among others—habitat, season, and age of feces, that could possibly affect the investigation of the three Elban sites. We found a significant divergence between the WEST and EAST Elban subpopulations in terms of microbial composition and alpha diversity. Although most represented bacterial phyla were the same in all the sites (Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes), microbiomes displayed a much higher diversity in western than in eastern partridges. This result might be related to locally diverging individual physiological needs and/or to different intensities in past releases of captive-bred birds between the two sides of Elba. We suggest that the two subpopulations should be treated as distinct management units.