Differential effects of elevated nest temperature and parasitism on the gut microbiota of wild avian hosts

Early-life environmental effects on birds: epigenetics and microbiome as mechanisms underlying long-lasting phenotypic changes

Although the long-lasting effects of variation in early-life environment have been well documented across organisms, the underlying causal mechanisms are only recently starting to be unraveled. Yet understanding the underlying mechanisms of long-lasting effects can help us predict how organisms will respond to changing environments. Birds offer a great system in which to study developmental plasticity and its underlying mechanisms owing to the production of large external eggs and variation in developmental trajectories, combined with a long tradition of applied, physiological, ecological and evolutionary research. Epigenetic changes (such as DNA methylation) have been suggested to be a key mechanism mediating long-lasting effects of the early-life environment across taxa. More recently, changes in the early-life gut microbiome have been identified as another potential mediator of developmental plasticity. As a first step in understanding whether these mechanisms contribute to developmental plasticity in birds, this Review summarizes how changes in early-life environment (both prenatal and postnatal) influence epigenetic markers and the gut microbiome. The literature shows how both early-life biotic (such as resources and social environment) and abiotic (thermal environment and various anthropogenic stressors) factors modify epigenetic markers and the gut microbiome in birds, yet data concerning many other environmental factors are limited. The causal links of these modifications to lasting phenotypic changes are still scarce, but changes in the hypothalamic-pituitary-adrenal axis have been identified as one putative pathway. This Review identifies several knowledge gaps, including data on the long-term effects, stability of the molecular changes, and lack of diversity in the systems studied, and provides directions for future research.

Microbiology of the built environment: harnessing human-associated built environment research to inform the study and design of animal nests and enclosures

SUMMARYOver the past decade, hundreds of studies have characterized the microbial communities found in human-associated built environments (BEs). These have focused primarily on how the design and use of our built spaces have shaped human-microbe interactions and how the differential selection of certain taxa or genetic traits has influenced health outcomes. It is now known that the more removed humans are from the natural environment, the greater the risk for the development of autoimmune and allergic diseases, and that indoor spaces can be harsh, selective environments that can increase the emergence of antimicrobial-resistant and virulent phenotypes in surface-bound communities. However, despite the abundance of research that now points to the importance of BEs in determining human-microbe interactions, only a fraction of non-human animal structures have been comparatively explored. It is here, in the context of human-associated BE research, that we consider the microbial ecology of animal-built natural nests and burrows, as well as artificial enclosures, and point to areas of primary interest for future research.

Climate change is not just global warming: Multidimensional impacts on animal gut microbiota

Climate change has rapidly altered many ecosystems, with detrimental effects for biodiversity across the globe. In recent years, it has become increasingly apparent that the microorganisms that live in and on animals can substantially affect host health and physiology, and the structure and function of these microbial communities can be highly sensitive to environmental variables. To date, most studies have focused on the effects of increasing mean temperature on gut microbiota, yet other aspects of climate are also shifting, including temperature variation, seasonal dynamics, precipitation and the frequency of severe weather events. This array of environmental pressures might interact in complex and non-intuitive ways to impact gut microbiota and consequently alter animal fitness. Therefore, understanding the impacts of climate change on animals requires a consideration of multiple types of environmental stressors and their interactive effects on gut microbiota. Here, we present an overview of some of the major findings in research on climatic effects on microbial communities in the animal gut. Although ample evidence has now accumulated that shifts in mean temperature can have important effects on gut microbiota and their hosts, much less work has been conducted on the effects of other climatic variables and their interactions. We provide recommendations for additional research needed to mechanistically link climate change with shifts in animal gut microbiota and host fitness.

Elevated nest temperature has opposing effects on host species infested with parasitic nest flies

Environmental factors, such as elevated temperature, can have varying effects on hosts and their parasites, which can have consequences for the net outcome of this relationship. The individual direct effects of temperature must be disentangled to determine the net-effect in host-parasite relationships, yet few studies have determined the net-effects in a multi-host system. To address this gap, we experimentally manipulated temperature and parasite presence in the nests of two host species infested by parasitic blowflies (Protocalliphora sialia). We conducted a factorial experiment by increasing temperature (or not) and removing all parasites (or not) in the nests of eastern bluebirds (Sialia sialis) and tree swallows (Tachycineta bicolor). We then measured nestling morphometrics, blood loss, and survival and quantified parasite abundance. We predicted that if temperature had a direct effect on parasite abundance, then elevated temperature would cause similar directional effects on parasite abundance across host species. If temperature had a direct effect on hosts, and therefore an indirect effect on the parasite, parasite abundance would differ across host species. Swallow nests with elevated temperature had fewer parasites compared to nests without temperature manipulation. In contrast, bluebird nests with elevated temperatures had more parasites compared to nests without temperature manipulation. The results of our study demonstrate that elevated temperature can have differential effects on host species, which can impact infestation susceptibility. Furthermore, changing climates could have complex net-effects on parasite fitness and host health across multi-host-parasite interactions.

Characteristics of Wild Bird Resistomes and Dissemination of Antibiotic Resistance Genes in Interconnected Bird-Habitat Systems Revealed by Similarity of blaTEM Polymorphic Sequences

Wild birds are known to harbor and discharge antibiotic-resistant bacteria (ARB) and their associated antibiotic resistance genes (ARGs). However, assessments of their contribution to the dissemination of antibiotic resistance in the environment are limited to culture-dependent bacterial snapshots. Here, we present a high-throughput sequencing study that corroborates extensive ARG exchange between wild bird feces and their habitats and implies the need to scrutinize high-mobility birds as potential vectors for global propagation of ARGs. We characterized the resistome (281 ARGs) and microbiome of seven wild bird species and their terrestrial and aquatic habitats. The resistomes of bird feces were influenced by the microbial community structure, mobile genetic elements (MGEs), and residual antibiotics. We designated 33 ARGs found in more than 90% of the bird fecal samples as core ARGs of wild bird feces, among which 16 ARGs were shared as core ARGs in both wild bird feces and their habitats; these genes represent a large proportion of both the bird feces (35.0 ± 15.9%) and the environmental resistome (29.9 ± 21.4%). One of the most detected β-lactam resistance genes (bla_TEM, commonly harbored by multidrug resistant "superbugs") was used as molecular marker to demonstrate the high interconnectivity of ARGs between the microbiomes of wild birds and their habitats. Overall, this work provides a comprehensive analysis of the wild bird resistome and underscores the importance to consider genetic exchange between animals and the environment in the One Health approach.