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High dispersal rates are known to homogenize host’s population genetic structure in panmictic species and to disrupt host local adaptation to the environment. Long-distance dispersal might also spread micro-organisms across large geographical areas. However, so far, to which extent selection mechanisms that shape host’s population genetics are mirrored in the population structure of the enteric microbiome remains unclear. High dispersal rates and horizontal parental transfer may homogenize bacterial communities between breeding sites (homogeneous hypothesis). Alternatively, strong selection from the local environment may differentiate bacterial communities between breeding sites (heterogeneous hypothesis). Furthermore, selection from age-specific environmental or physiological factors may differentiate the microbiome between juveniles and adults. Here, we analyzed the cloacal bacterial 16S rRNA gene of fledgling greater flamingos, Phoenicopterus roseus, across nine western Mediterranean breeding sites and four breeding seasons (n = 731) and adult birds (n = 27) from a single site. We found that fledgling cloacal microbiome, as measured by alpha diversity, beta diversity, the relative abundance of assigned sequence variants (ASVs) belonging to a phylum and genus composition within phylum, varied significantly between sampling sites and across time within site despite high adult dispersal rates. The spatio-temporal effects were stronger on individual ASV absence/presence than on ASV abundance (i.e., than on core microbiome composition). Spatial effects had a stronger effect than temporal effects, particularly on ASV abundance. Our study supports the heterogeneous hypothesis whereby local environmental conditions select and differentiate bacterial communities, thus countering the homogenizing effects of high-dispersing host species. In addition, differences in core microbiome between adult vs. fledgling samples suggests that differences in age-specific environmental and/or physiological factors result in differential selection pressure of core enteric microbiome between age classes, even within the same environment. In particular, the genus Corynebacterium, associated with both seasonal fat uptake and migration in previous studies, was much more abundant in high-dispersing fledglings than in more resident adults. To conclude, selection mechanisms that shape the host’s genetic structure cannot be extended to the genetic structure of the enteric microbiome, which has important implications regarding our understanding of both host local adaptation mechanisms and enteric microbiome population genetics.

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Environmental trace element composition can have an important impact on ecosystem and population health as well individual fitness. Therefore, carefully assessing bioaccumulation of trace elements is central to studies investigating the ecological impact of pollution. Colonial birds are important bioindicators since non‐invasive sampling can easily be achieved through sampling of chick feathers, which controls for some confounding factors of variability (age and environmental heterogeneity). However, an additional confounding factor, external contamination (ExCo), which remains even after washing feathers, has frequently been overlooked in the literature. We developed a new method to reliably interpret bioaccumulation of 10 trace elements (As, Cd, Cr, Cu, Hg, Ni, Pb, Se, Sn and Zn) in feathers using chicks of a colonial species: the Greater Flamingo, Phoenicopterus roseus. First, only shafts were used to remove ExCo retained in vanes. Secondly, we applied a thorough washing procedure. Thirdly, we applied a new analytical method to control for ExCo, which assumes that ExCo is mainly due to adhered sediment particles and that the relative concentration of each trace element will be similar to the sediment geochemical composition of sampling sites. We validated this new methodology by comparing trace element composition and particle composition (by scanning electron microscopy and mass spectrometry) of washed and unwashed feathers. The washing procedure removed >99% of K indicating that most of the ExCo from salt was removed. Scanning electron microscopy and mass spectrometry revealed that some sediment particles remained after washing, especially clays which are likely to severely bias bioaccumulation interpretation. We successfully controlled for ExCo by calculating the ratio of ExCo due to sediment using the geochemical fingerprint of sediment samples. Our methodology leads to conservative estimates of bioaccumulation for As, Cd, Cr, Cu, Hg, Ni, Pb, Se, Sn and Zn. We have validated a new more reliable method of analysing trace element concentrations in feathers, which effectively controls for ExCo, if geochemical sediment data can be meaningfully compared to ExCo of feathers. We have demonstrated that overlooking ExCo leads to potentially erroneous conclusions, and we urge that the method applied in this study be considered in future studies.