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Recent advances in the field of wild avian microbiome research have significantly deepened our understanding of the eco‐evolutionary dynamics of bird–microbe interactions. Consequently, the field is now approaching a pivotal moment in uncovering the ultimate factors shaping avian microbiome structure, especially in relation to birds' ecological, evolutionary, and dietary diversity. Yet, avian microbiome researchers face persistent methodological challenges. Based on discussions from a round table session at the 2023 European Ornithologists' Union Congress in Lund, Sweden, which brought together researchers studying host–microbe interactions across avian systems, here we highlight shared obstacles and potential solutions to strengthen the prospects of the field. This work outlines and discusses key challenges faced, and considerations to be taken into account by avian microbiome researchers throughout the scientific process, while pinpointing areas of research that need attention to advance the field. Disseminating these insights can foster innovation and collaboration, while providing a roadmap for young and new scientists who are interested in the field of avian microbiomes.

The choice of colony size may have profound consequences for individual fitness in colonially breeding birds, but at the same time it may require certain behavioural adaptations. Here, we aimed to examine behavioural divergence of common terns Sterna hirundo nesting in colonies of different size. For this purpose, we promoted establishment of small (<35 pairs) and large (>100 pairs) tern colonies under uniform ecological and environmental conditions by providing attractive patches of nesting substrate (floating rafts) at a single site. We combined video recording and GPS-tracking to assess communal and individual defence initiation rate, intra-specific aggression rate, and foraging flight characteristics. We found that birds from larger colonies more frequently engaged in communal defence and they performed longer foraging flights, while terns from smaller colonies more frequently showed individual defence behaviours. Also, intra-specific aggression rate was higher in smaller colonies, but this effect was primarily attributed to a higher proportion of edge breeding pairs, which were more aggressive. Our results suggest that various colony sizes may be associated with different behavioural syndromes, which comprise of diverse personality traits, such as social responsiveness, social tolerance, or propensity for aggression. It remains to be tested whether these behavioural differences reflect processes of phenotypic sorting among colonies of different size or whether they are a result of behavioural plasticity under different social contexts.

Extensive transformation of natural land cover into urbanized areas enhances accumulation of phenotypic differences between animals from urban and nonurban populations, but there is little information on whether these changes, especially in terms of animal behaviour and circadian rhythm, have a genetic basis. The aim of this study was to investigate genetic background of behavioural differences between four pairs of urban and nonurban populations of a common waterbird, the Eurasian coot Fulica atra . For this purpose, we quantified polymorphisms in personality‐related candidate genes, previously reported to be associated with avian circadian rhythms and behavioural traits that may be crucial for urban life. We found general associations between landscape urbanization level and polymorphisms in 3′UTR region of CREB1 gene encoding transcriptional factor, which participates in development of cognitive functions and regulation of circadian rhythm. We also found significant differentiation between urban and nonurban populations in the intronic region of CKIɛ gene responsible for regulation of circadian clock. Although we lacked evidence for linkage of this intronic variation with coding polymorphisms, genetic differentiation between urban populations was significantly stronger at CKIɛ intron compared with neutral microsatellite markers, suggesting possible local adaptations of CKIɛ expression regulation to specific urban sites. Our results indicate that behavioural differentiation between urban and nonurban coot populations may be the effect of habitat‐specific selective pressure resulting in genetic adaptations to urban environment and supporting the microevolutionary scenario. These adaptations, however, prevailed in non‐coding regulatory rather than coding gene regions and showed either general or local patterns, revealing high complexity of associations between behaviour and landscape urbanization in birds.

There is a growing body of evidence that urbanization can affect body condition and immune function in wild birds, although these effects may be complex and taxa-specific. Here, we assessed the effects of urbanization on body condition (size-corrected body mass and haemoglobin concentration) and innate immune defences (haemolysis–haemagglutination assay, haptoglobin concentration and bacterial killing assay) in 136 Eurasian coots (Fulica atra) from three urban and three non-urban populations across Poland. We also quantified the heterophil to lymphocyte ratio to control for the potential effect of physiological stress on immune defences. We found that urban coots showed significantly better condition than non-urban ones. At the same time, we found no relationship between any immune defence and urbanization or condition. Thus, our study offers no support for condition-dependent immune function. Our analyses also revealed significant differences between male and female coots in both condition and immune defences; however, we found no evidence for sex-specific responses to urbanization. In conclusion, our study provides correlative evidence that urban habitat enhances condition, but not immune defences in the Eurasian coot.

Abstract Long-distance host movements play a major regulatory role in shaping microbial communities of their digestive tract. Here, we studied gut microbiota composition during seasonal migration in five shorebird species (Charadrii) that use different migratory (stopover) habitats. Our analyses revealed significant interspecific variation in both composition and diversity of gut microbiome, but the effect of host identity was weak. A strong variation in gut microbiota was observed between coastal and inland (dam reservoir and river valley) stopover habitats within species. Comparisons between host age classes provided support for an increasing alpha diversity of gut microbiota during ontogeny and an age-related remodeling of microbiome composition. There was, however, no correlation between microbiome and diet composition across study species. Finally, we detected high prevalence of avian pathogens, which may cause zoonotic diseases in humans (e.g. Vibrio cholerae) and we identified stopover habitat as one of the major axes of variation in the bacterial pathogen exposure risk in shorebirds. Our study not only sheds new light on ecological processes that shape avian gut microbiota, but also has implications for our better understanding of host–pathogen interface and the role of birds in long-distance transmission of pathogens. Gut microbiota composition and prevalence of bacterial gut pathogens are related to stopover site habitat in shorebirds during autumn migration, suggesting a crucial role of environmental factors in shaping gut microbial community of migratory birds.

Abstract Most behavioral traits are known to be weakly heritable, possibly due to their extreme complexity and flexibility. Despite this general pattern, within-species variation in avian colony size choice has been reported to have a strong additive genetic component, but we are aware of no attempts to assess the heritability of avian sociality at the finer spatial scale. Here, we used an animal model and parent–offspring regression to quantify additive genetic variance in social phenotype (local nesting density) in a nonpasserine waterbird, the common tern Sterna hirundo. For this purpose, we used a novel experimental framework, where variation in the social environment was generated by providing birds with artificial patches of attractive nesting substrate that markedly varied in size. During 2011–2019, we collected data on social preferences for either low or high nesting density in over 250 individuals, either kin (mostly parent–offspring relationships) or non-kin recorded breeding multiple times across years. All heritability estimates of local nesting density were low (<0.10), irrespectively of fixed effects (sex and year) included in the models, data used in the modeling (all individuals vs. early recruits), or methodological approach (animal model vs. parent–offspring regression). We conclude that avian sociality, as measured at the local scale, may be much less heritable than colony size choice, as measured at the landscape level. Our study adds to the understanding of additive genetic variance in avian behavior, and it underlines a scale dependency in the heritability of behavioral traits.