Nest Material Shapes Eggs Bacterial Environment

Pollution-related changes in nest microbiota: Implications for growth and fledging in three passerine birds

Non-ferrous smelters emit toxic metals into the environment, posing a threat to wildlife health. Despite the acknowledged role of microbes in host health, the impact of such emissions on host-associated microbiota, especially in wild birds, remains largely unexplored. This study investigates the associations of metal pollution, fitness, and nest microbiota (serving as a proxy for early-life microbial environment) which may influence the nestling health and development. Our study focuses on three passerine birds, the great tit (Parus major), blue tit (Cyanistes caeruleus), and pied flycatcher (Ficedula hypoleuca), within control and metal-polluted sites around a Finnish copper-nickel smelter. The polluted sites had been contaminated with arsenic (As), cadmium (Cd), copper (Cu), nickel (Ni), and zinc (Zn). We performed bacterial 16S rRNA sequencing and metal analyses on 90 nests and monitored nestling body mass, fledging success, and various biotic and abiotic factors. Our findings revealed species-specific responses to metal exposure in terms of both fitness and nest microbiota. P. major and C. caeruleus showed sensitivity to pollution, with decreased nestling growth and fledging in the polluted zone. This was accompanied by a shift in the bacterial community composition, which was characterized by an increase in some pathogenic bacteria (in P. major and C. caeruleus nests) and by a decrease in plant-associated bacteria (within C. caeruleus nests). Conversely, F. hypoleuca and their nest microbiota showed limited responses to pollution, indicating greater tolerance to pollution-induced environmental changes. Although pollution did not correlate with nest alpha diversity or the most abundant bacterial taxa across all species, certain potential pathogens within the nests were enriched in polluted environments and negatively correlated with nestling fitness parameters. Our results suggest that metal pollution may alter the nest bacterial composition in some bird species, either directly or indirectly through environmental changes, promoting pathogenic bacteria and potentially impacting bird survival.

Pioneer access of the foam nest bacterial community of Leptodactylidae frogs and its biotechnological potential

Many anuran amphibians deposit their eggs in foam nests, biostructures that help protect the eggs and tadpoles from predators. Currently, there are no other identification and description studies of the cultivable microbiota role in the nests of the Leptodactylid frogs such as Physalaemus cuvieri, Leptodactylus vastus and Adenomera hylaedactyla. This study aimed to isolate and identify the culturable bacteria from these three anuran species' nests, as well as to prospect enzymes produced by this microbiota. Foam nests samples and environmental samples were diluted and viable cell count was determined. Bacterial morphotypes from foam nest samples were isolated through spread plate technique. Isolates' DNAs were extracted followed by rRNA 16S gene amplification and Sanger sequencing. To evaluate their enzymatic potential, the isolates were cultured in ATGE medium supplemented with starch (0.1% w/v), gelatin (3% w/v) and skimmed milk (1% w/v), to verify amylase and protease activity. A total of 183 bacterial morphotypes were isolated, comprising 33 bacterial genera. Proteobacteria phylum was the most abundant in all the three nests (79%). The genera Pseudomonas and Aeromonas were the most abundant taxon in P. cuvieri and L. vastus. In A. Hylaedactyla, were Enterobacter and Bacillus. Regarding enzymatic activities, 130 isolates displayed protease activity and 45 isolates were positive for amylase activity. Our results provide unprecedented information concerning culturable bacterial microbiota of the foam nests of the Leptodactylid frogs, as well as their potential for biomolecules of biotechnological interest.

The reproductive microbiome and maternal transmission of microbiota via eggs in Sceloporus virgatus

Maternal transmission of microbes occurs across the animal kingdom and is vital for offspring development and long-term health. The mechanisms of this transfer are most well-studied in humans and other mammals but are less well-understood in egg-laying animals, especially those with no parental care. Here, we investigate the transfer of maternal microbes in the oviparous phrynosomatid lizard, Sceloporus virgatus. We compared the microbiota of three maternal tissues-oviduct, cloaca, and intestine-to three offspring sample types: egg contents and eggshells on the day of oviposition, and hatchling intestinal tissue on the day of hatching. We found that maternal identity is an important factor in hatchling microbiome composition, indicating that maternal transmission is occurring. The maternal cloacal and oviductal communities contribute to offspring microbiota in all three sample types, with minimal microbes sourced from maternal intestines. This indicates that the maternal reproductive microbiome is more important for microbial inheritance than the gut microbiome, and the tissue-level variation of the adult S. virgatus microbiota must develop as the hatchling matures. Despite differences between adult and hatchling communities, offspring microbiota were primarily members of the Enterobacteriaceae and Yersiniaceae families (Phylum Proteobacteria), consistent with this and past studies of adult S. virgatus microbiomes.

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.

Does nest occupancy by birds influence the microbial composition?

Nest microbiota plays a vital role in the breeding and development of birds, which not only provides protection to bird hosts but also negatively affects the host. At present, it is unclear whether the composition of the microbes in the nests is affected by nesting. For this reason, we hung artificial nest boxes to simulate the natural nesting environment and combined 16S rRNA and ITS high-throughput sequencing technology to further study the differences in microbial composition and richness between used nests and control nests of Japanese tits (Parus minor). The study found that the bacteria in used nests and control nests showed significant differences at the phylum level (p < 0.05). It is also worth noting that the predominant bacteria in used nests were Proteobacteria (51.37%), Actinobacteria (29.72%), Bacteroidetes (6.59%), and Firmicutes (3.82%), while the predominant bacteria in control nests were Proteobacteria (93.70%), Bacteroidetes (2.33%), and Acidobacteria (2.06%). Both used nests and control nests showed similar fungi at the phylum level, which consisted mainly of Ascomycota and Basidiomycota, although significant differences were found in their relative abundance between both groups. The results of alpha diversity analysis showed significant differences in bacteria between the two groups and not in fungi. However, the beta diversity analysis showed significant differences between both bacteria and fungi. In summary, our results showed that the used nests had a higher abundance of beneficial microbiota and a lower presence of pathogenic microbiota. Therefore, we speculate that birds will change the characteristics of the nest microbial composition in the process of nest breeding to ensure their smooth reproductive development.

Effects of insect host chemical secretions on the entomopathogenic nematode Steinernema carpocapsae

Given the threat presented by parasites and pathogens, insects employ various defences to protect themselves against infection, including chemical secretions. The red flour beetle Tribolium castaneum releases a secretion containing the benzoquinones methyl-1,4-benzoquinone (MBQ) and ethyl-1,4-benzoquinone (EBQ) into the environment. These compounds have known antimicrobial effects; however, their role in defence against macroparasites is not known. Entomopathogenic nematodes, such as Steinernema carpocapsae, present a serious threat to insects, with successful infection leading to death. Thus, quinone-containing secretions may also aid in host defence. We tested how exposure to the individual components of this quinone secretion, as well as a mix at naturally-occurring proportions, affected the survival and thrashing behaviour of S. carpocapsae, as well as their virulence to a model host (Galleria mellonella). Exposure to high concentrations of MBQ and EBQ, as well as the quinone mix, significantly increased nematode death but did not consistently reduce thrashing, which would otherwise be expected given their toxicity. Rather, quinones may act as a host cue to S. carpocapsae by triggering increased activity. We found that exposure to quinones for 24 or 72 hours did not reduce nematode virulence, and surviving nematodes remained infective after non-lethal exposure. Our results indicate that quinone secretions likely serve as a defence against multiple infection threats by reducing S. carpocapsae survival, but further research is required to contextualize their roles by testing against other nematodes, as well as other helminths using insects as hosts.

Microbial infection risk predicts antimicrobial potential of avian symbionts

Symbiotic bacteria on animal hosts can prevent pathogenic bacterial infections by several mechanisms. Among them, symbiotic bacteria can indirectly enhance host’s immune responses or, directly, produce antimicrobial substances against pathogens. Due to differences in life-style, different host species are under different risks of microbial infections. Consequently, if symbiotic bacteria are somewhat selected by genetically determined host characteristics, we would expect the antimicrobial properties of bacterial symbionts to vary among host species and to be distributed according to risk of infection. Here we have tested this hypothesis by measuring the antimicrobial ability of the bacterial strains isolated from the uropygial-gland skin of 19 bird species differing in nesting habits, and, therefore, in risk of microbial infection. In accordance with our predictions, intensity and range of antimicrobial effects against the indicator strains assayed varied among bird species, with hole-and open-nesters showing the highest and the lowest values, respectively. Since it is broadly accepted that hole-nesters have higher risks of microbial infection than open nesters, our results suggest that the risk of infection is a strong driver of natural selection to enhance immunocompetence of animals through selecting for antibiotic-producing symbionts. Future research should focus on characterizing symbiotic bacterial communities and detecting coevolutionary processes with particular antibiotic-producing bacteria within-host species.

Incubation determines favorable microbial communities in Chinese alligator nests

Nest materials are a major heat source due to rotting promoted by microbial activity. Additionally, they are a potential microbial source given their direct contact with eggshells. Microbial dynamics during incubation have been studied in wild birds; however, similar studies in reptiles remain elusive. Here, the study characterized microbial communities in the nest materials of Chinese alligator (Alligator sinensis) using high-throughput sequencing of bacterial 16S rRNA genes and fungal internal transcribed spacer (ITS) region sequences. The results showed that significant changes in the diversity and structure of microbial communities according to different incubation periods. The diversity and richness of bacterial species increased significantly over time, but the relative abundance of the most dominant bacteria in pre-incubation period, including some pathogenic bacteria, declined after incubation. In contrast, fungal species diversity and richness decreased significantly with time. Additionally, nest material composition significantly influenced microbial community structure rather than species diversity and richness. Notably, the fungal community structure showed a stronger response than bacteria to nest material composition, which varied due to differences in plant litter composition. Our results demonstrate the significant response of microbial community diversity and structure to differences in incubation periods and nest material composition in reptiles. It is further emphasized that the importance of incubation period in the conservation of the Chinese alligator and could inform similar studies in other reptiles and birds.

The extended avian urban phenotype: anthropogenic solid waste pollution, nest design, and fitness

Solid waste pollution (garbage discarded by humans, such as plastic, metal, paper) has received increased attention given its importance as a global threat to biodiversity. Recent studies highlight how animals incorporate anthropogenic materials into their life-cycle, for example in avian nest construction. While increasingly monitored in natural areas, the influence of solid waste pollution on wildlife has been seldom explored in the urban habitat. There is limited data on the relationship between anthropogenic solid waste pollution, nest design, and reproductive success in an urban context. We address this knowledge gap (i) by investigating the presence of environmental solid waste pollution in the breeding habitats of great tits Parus major and blue tits Cyanistes caeruleus reproducing in a gradient of urbanisation, and (ii) by quantifying (ii) the contribution of different anthropogenic materials in their nests. We further examine potential drivers of solid waste pollution by inferring three distinct properties of the urban space: environmental solid waste pollution on the ground, human presence, and the intensity of urbanisation (e.g impervious surfaces) in nestbox vicinity. Finally, (iii) we explore the relationship between anthropogenic nest materials and reproductive success. We found that environmental solid waste pollution was positively associated with human presence and urbanisation intensity. There was also a positive relationship between increased human presence and the amount of anthropogenic materials in great tit nests. Interestingly, in both species, anthropogenic nest materials covaried negatively with nest materials of animal origin (fur and feathers). We suggest that fur and feathers - key insulating materials in nest design - may be scarcer in areas with high levels of human presence, and are consequently replaced with anthropogenic nest materials. Finally, we report a negative relationship between anthropogenic nest materials and blue tit reproductive success, suggesting species-specific vulnerability of urban birds to solid waste pollution.

Effect of nest composition, experience and nest quality on nest-building behaviour in the Bonelli's Eagle

In bi-parentally built nests, there is evidence to suggest that nests are extended phenotypic signals that accurately indicate the quality of the building parent/s. Raptors often use a variety of materials to build their nests (natural, such as branches, but also non-natural objects), presumably due to their insulating properties, their suitability to advertise occupancy of the nest, and to decrease pathogen and parasite loads. However, in raptors where both sexes collaborate in nest construction, it is unclear whether nest building (taking the amount of material carried to the nest as the potential predictor) is an indicator of parental quality, and whether the effort expended by both sexes could constitute an honest signal of parental quality to their partners. Between 2011 and 2016, we monitored 16 nests of Bonelli’s Eagles (Aquila fasciata), and we examined data on sex, type of material brought to the nest, breeding experience, nest quality, timing, and nest-building investment prior to egg-laying from 32 identifiable Bonelli’s Eagles during the pre-laying period to investigate the relative contribution of the sexes to the amount of nest material gathered. Our results indicate that sex is not a determining factor in nest-building effort, and that females did not increase their parental effort in response to the male’s contribution, and supply of materials did not increase during the pre-laying period. In contrast, our models showed that: (1) the type of material supplied to the nest by both sexes varied significantly throughout the pre-laying period and (2) nest-building effort was determined by individual experience and nest quality. Therefore, our study suggests that male nest-building behaviour and investment by Bonelli’s Eagles cannot be considered as an extended phenotypic signal. The differential use of hard and green material by both sexes in the early and late stages of nest-building period, and the fact that the more experienced individuals contributed a larger amount of material on low quality nests, are discussed in the contexts of signaling nest occupancy to conspecifics and competitors and the decrease of ectoparasite loads during the pre-laying period.

Composition of the Wild Rabbit Nest and Its Implication for Domestic Rabbit Breeding

Wild European rabbits (Oryctolagus cuniculus) give birth in an underground nursery burrow where the kits are hermetically closed into the nest chamber for several weeks except for the three minutes of daily nursing. Given this confinement, the nest quality seems to be crucial in affecting the kits’ survival. The situation is less critical in rabbitries where the domesticated descendants are kept and give birth in separate nest boxes where the temperature and humidity conditions are less extreme and nests consist of fur and wood shavings or straw. However, nesting behaviour of domestic does still reflects several aspects of the ancestors, and providing conditions close to their biological needs is advised. The present study aimed to understand the factors contributing to the nest material choice of rabbits by analysing the composition of wild rabbit nests and testing naive domestic does in controlled laboratory settings for their preferences in constructing their nests. We were able to collect 21 just abandoned nests in their natural habitat and found they contained rabbit fur and hay, of which 85% was dry grass, mostly long leaves of Calamagrostis sp. Using domesticated rabbit does, we then tested if there is a preference for the features of the wild rabbit nests or whether the above-mentioned finding was either an accidental consequence of grass availability or ageing of the nest material. Two-way choice tests revealed that primiparous domestic does preferred the dry grass over green and long leaves over short grass bunches for nest building. Ageing of the nest material was rather negligible and did not contribute to the high level of dry grass content. We concluded that long dry grass is recommended as it seems to fulfil basic needs of this domesticated animal.

Temperature-induced changes in egg white antimicrobial concentrations during pre-incubation do not influence bacterial trans-shell penetration but do affect hatchling phenotype in Mallards

Microbiome formation and assemblage are essential processes influencing proper embryonal and early-life development in neonates. In birds, transmission of microbes from the outer environment into the egg’s interior has been found to shape embryo viability and hatchling phenotype. However, microbial transmission may be affected by egg-white antimicrobial proteins (AMPs), whose concentration and antimicrobial action are temperature-modulated. As both partial incubation and clutch covering with nest-lining feathers during the pre-incubation period can significantly alter temperature conditions acting on eggs, we experimentally investigated the effects of these behavioural mechanisms on concentrations of both the primary and most abundant egg-white AMPs (lysozyme and avidin) using mallard (Anas platyrhychos) eggs. In addition, we assessed whether concentrations of egg-white AMPs altered the probability and intensity of bacterial trans-shell penetration, thereby affecting hatchling morphological traits in vivo. We observed higher concentrations of lysozyme in partially incubated eggs. Clutch covering with nest-lining feathers had no effect on egg-white AMP concentration and we observed no association between concentration of egg-white lysozyme and avidin with either the probability or intensity of bacterial trans-shell penetration. The higher egg-white lysozyme concentration was associated with decreased scaled body mass index of hatchlings. These outcomes demonstrate that incubation prior to clutch completion in precocial birds can alter concentrations of particular egg-white AMPs, though with no effect on bacterial transmission into the egg in vivo. Furthermore, a higher egg white lysozyme concentration compromised hatchling body condition, suggesting a potential growth-regulating role of lysozyme during embryogenesis in precocial birds.

Shifting microbiomes complement life stage transitions and diet of the bird parasite Philornis downsi from the Galapagos Islands

Domestication disconnects an animal from its natural environment and diet, imposing changes in the attendant microbial community. We examine these changes in Philornis downsi (Muscidae), an invasive parasitic fly of land birds in the Galapagos Islands. Using a 16S rDNA profiling approach we studied the microbiome of larvae and adults of wild and laboratory-reared populations. These populations diverged in their microbiomes, significantly more so in larval than in adult flies. In field-collected second-instar larvae, Klebsiella (70.3%) was the most abundant taxon, while in the laboratory Ignatzschineria and Providencia made up 89.2% of the community. In adults, Gilliamella and Dysgonomonas were key members of the core microbiome of field-derived females and males but had no or very low representation in the laboratory. Adult flies harbour sex-specific microbial consortia in their gut, as male core microbiomes were significantly dominated by Klebsiella. Thus, P. downsi microbiomes are dynamic and shift correspondingly with life cycle and diet. Sex-specific foraging behaviour of adult flies and nest conditions, which are absent in the laboratory, may contribute to shaping distinct larval, and adult male and female microbiomes. We discuss these findings in the context of microbe-host co-evolution and the implications for control measures.

Lining the nest with more feathers increases offspring recruitment probability: Selection on an extended phenotype in the blue tit

Birds, among various other taxa, construct nests. Nests form an extended phenotype of the individual building it. Nests are used to extend control over the conditions in which offspring develop, and are therefore commonly considered to be shaped by selection. Nevertheless, scarcely any scientific evidence exist that nest composition is under selection. Here, we demonstrate with data from over 400 blue tit (Cyanistes caeruleus) nests collected over 8 years that a higher proportion of feathers in the nest lining is positively associated with the probability of offspring to recruit as a breeding adult later in life. Strikingly, the extended phenotype (nest) was associated stronger with recruitment probability than phenotypic traits that have typically been considered important in selection (laying date, and female size and condition). Our findings suggest that the choice of nest material could be a maternal behavior with potential lifelong effects on her offspring.

Genomic characterization of multidrug-resistant ESBL-producing Escherichia coli ST58 causing fatal colibacillosis in critically endangered Brazilian merganser (Mergus octosetaceus)

Even though antimicrobial‐resistant bacteria have begun to be detected in wildlife, raising important issues related to their transmission and persistence of clinically important pathogens in the environment, little is known about the role of these bacteria on wildlife health, especially on endangered species. The Brazilian merganser (Mergus octosetaceus) is one of the most threatened waterfowl in the world, classified as Critically Endangered by the International Union for Conservation of Nature. In 2019, a fatal case of sepsis was diagnosed in an 8‐day‐old Brazilian merganser inhabiting a zoological park. At necropsy, major gross lesions were pulmonary and hepatic congestion. Using microbiologic and genomic methods, we identified a multidrug‐resistant (MDR) extended‐spectrum β‐lactamase (ESBL) CTX‐M‐8‐producing Escherichia coli (designed as PMPU strain) belonging to the international clone ST58, in coelomic cavity, oesophagus, lungs, small intestine and cloaca samples. PMPU strain harboured a broad resistome against antibiotics (cephalosporins, tetracyclines, aminoglycosides, sulphonamides, trimethoprim and quinolones), domestic/hospital disinfectants and heavy metals (arsenic, mercury, lead, copper and silver). Additionally, the virulence of E. coli PMPU strain was confirmed using a wax moth (Galleria mellonella) infection model, and it was supported by the presence of virulence genes encoding toxins, adherence factors, invasins and iron acquisition systems. Broad resistome and virulome of PMPU contributed to therapeutic failure and death of the animal. In brief, we report for the first time a fatal colibacillosis by MDR ESBL‐producing E. coli in critically endangered Brazilian merganser, highlighting that besides colonization, critical priority pathogens are threatening wildlife. E. coli ST58 clone has been previously reported in humans, food‐producing animals, wildlife and environment, supporting broad adaptation and persistence at human–animal–environment interface.

The Nidobiome: A Framework for Understanding Microbiome Assembly in Neonates

The importance of microbial associations to animals' development, physiology, and fitness is widely recognized. In most animals, these microbial associations must be developed anew with every generation, making microbiome assembly a critical ecological and evolutionary process. To fully understand neonate microbial colonization, we need to study the interacting effects of neonate, parents, nest, and external environment. We propose an integrative approach based on the concept of the 'nidobiome', a new unit of microbiome-host interactions, which brings together these key elements. We discuss the contribution of each element on microbial colonization at different stages of host development, and we provide a framework based on key developmental events to compare microbiome assembly across animal species.

Antimicrobial activity of nest-lining feathers is enhanced by breeding activity in avian nests

The use of feathers as nest material has been proposed as a kind of self-medication strategy because antimicrobial-producing microorganisms living on feathers may defend offspring against pathogenic infections. In this case, it is expected that density of antimicrobial-producing bacteria, and their antimicrobial effects, are higher in feathers that line the nests than in eggshells. Moreover, we know that feather pigmentation and breeding activity may influence density and antimicrobial production of bacteria. To test these predictions, we analyzed bacterial densities and antimicrobial activity of bacterial colonies isolated from bird eggshells and nest-lining feathers against bacterial strains comprising potential pathogens. Samples were collected from spotless starling (Sturnus unicolor) nests, and from artificial nests to isolate the effects of breeding activity on bacterial communities. The composition of feathers lining the nests was experimentally manipulated to create groups of nests with pigmented feathers, with unpigmented feathers, with both types of feathers or without feathers. Although we did not detect an effect of experimental feather treatments, we found that bacterial colonies isolated from feathers were more active against the tested bacterial strains than those isolated from eggshells. Moreover, bacterial density on feathers, keratinolytic bacteria on eggshells and antimicrobial activity of colonies isolated were higher in starling nests than in artificial nests. These results suggest that antimicrobial activity of bacteria growing on nest-lining feathers would be one of the mechanisms explaining the previously detected antimicrobial effects of this material in avian nests, and that breeding activity results in nest bacterial communities with higher antimicrobial activity.

Different incubation patterns affect selective antimicrobial properties of the egg interior: experimental evidence from eggs of precocial and altricial birds

Avian eggs contend with omnipresent microorganisms entering the egg interior, where they affect embryo viability and hatchling phenotype. The incubation behaviour and deposition of egg white antimicrobial proteins (AMPs) vary highly across the avian altricial-precocial spectrum. Experimental evidence of how these alterations in avian reproductive strategies affect the antimicrobial properties of the precocial and altricial egg interior is lacking, however. Here, we tested the egg white antimicrobial activity in eggs of two representative model species, from each end of the avian altricial-precocial spectrum, against potentially pathogenic and beneficial probiotic microorganisms. Eggs were experimentally treated to mimic un-incubated eggs in the nest, partial incubation during the egg-laying period, the onset of full incubation and the increased deposition of two main egg white AMPs, lysozyme and ovotransferrin. We moreover assessed to what extent egg antimicrobial components, egg white pH and AMP concentrations varied as a result of different incubation patterns. Fully incubated precocial and altricial eggs decreased their antimicrobial activity against a potentially pathogenic microorganism, whereas partial incubation significantly enhanced the persistence of a beneficial probiotic microorganism in precocial eggs. These effects were most probably conditioned by temperature-dependent alterations in egg white pH and AMP concentrations. While lysozyme concentration and pH decreased in fully incubated precocial but not altricial eggs, egg white ovotransferrin increased along with the intensity of incubation in both precocial and altricial eggs. This study is the first to experimentally demonstrate that different incubation patterns may have selective antimicrobial potential mediated by species-specific effects on antimicrobial components in the egg white.

Ectoparasite Activity During Incubation Increases Microbial Growth on Avian Eggs

While direct detrimental effects of parasites on hosts are relatively well documented, other more subtle but potentially important effects of parasitism are yet unexplored. Biological activity of ectoparasites, apart from skin injuries and blood-feeding, often results in blood remains, or parasite faeces that accumulate and modify the host environment. In this way, ectoparasite activities and remains may increase nutrient availability that may favour colonization and growth of microorganisms including potential pathogens. Here, by the experimental addition of hematophagous flies (Carnus hemapterus, a common ectoparasite of birds) to nests of spotless starlings Sturnus unicolor during incubation, we explore this possible side effect of parasitism which has rarely, if ever, been investigated. Results show that faeces and blood remains from parasitic flies on spotless starling eggshells at the end of incubation were more abundant in experimental than in control nests. Moreover, eggshell bacterial loads of different groups of cultivable bacteria including potential pathogens, as well as species richness of bacteria in terms of Operational Taxonomic Units (OTUs), were also higher in experimental nests. Finally, we also found evidence of a link between eggshell bacterial loads and increased embryo mortality, which provides indirect support for a bacterial-mediated negative effect of ectoparasitism on host offspring. Trans-shell bacterial infection might be one of the main causes of embryo death and, consequently, this hitherto unnoticed indirect effect of ectoparasitism might be widespread in nature and could affect our understanding of ecology and evolution of host-parasite interactions.

Eggshells as hosts of bacterial communities: An experimental test of the antimicrobial egg coloration hypothesis

Oviparous animals have evolved multiple defenses to prevent microbes from penetrating their eggs and causing embryo mortality. In birds, egg constituents such as lysozyme and antibodies defend against microbial infestation, but eggshell pigments might also impact survival of bacteria. If so, microbes could exert an important selective pressure on the evolution of eggshell coloration. In a previous lab experiment, eggshell protoporphyrin caused drastic mortality in cultures of Gram positive, but not Gram negative, bacteria when exposed to light. Here, we test this "photodynamic antimicrobial hypothesis" in a field experiment. In a paired experimental design, we placed sanitized brown, protoporphyrin-rich chicken eggs alongside white eggs that lack protoporphyrin. We deployed eggs for 48 hr without incubation, as can occur between laying and incubation, when microbial infection risk is highest. Eggs were placed on the open ground exposed to sunlight and in dark underground storm-petrel burrows. We predicted that the proportion of Gram-positive bacteria on brown eggs should be lower when exposed to sunlight than when kept in the dark, but we expected no such difference for white eggs. Although our data revealed variation in bacterial community composition, the proportion of Gram-positive bacteria on eggshells did not vary by egg color, and there was no interaction between egg color and location. Instead, Gram-positive bacteria were proportionally more common on eggs on the ground than eggs in burrows. Overall, our experiment did not support the photodynamic antimicrobial hypothesis. The diverse range of avian egg colors is generated by just two pigments, but over 10 hypotheses have been proposed for the evolution of eggshell color. If our results are generalizable, eggshell protoporphyrin might not play a substantial role in defending eggs against microbes, which narrows the field of candidate hypotheses for the evolution of avian eggshell coloration.

Evolutionary Biology Needs Wild Microbiomes

The microbiome is a vital component to the evolution of a host and much of what we know about the microbiome derives from studies on humans and captive animals. But captivity alters the microbiome and mammals have unique biological adaptations that affect their microbiomes (e.g., milk). Birds represent over 30% of known tetrapod diversity and possess their own suite of adaptations relevant to the microbiome. In a previous study, we showed that 59 species of birds displayed immense variation in their microbiomes and host (bird) taxonomy and ecology were most correlated with the gut microbiome. In this Frontiers Focused Review, I put those results in a broader context by discussing how collecting and analyzing wild microbiomes contributes to the main goals of evolutionary biology and the specific ways that birds are unique microbial hosts. Finally, I outline some of the methodological considerations for adding microbiome sampling to the research of wild animals and urge researchers to do so. To truly understand the evolution of a host, we need to understand the millions of microorganisms that inhabit it as well: evolutionary biology needs wild microbiomes.

Ecoimmunology and microbial ecology: Contributions to avian behavior, physiology, and life history

Bacteria have had a fundamental impact on vertebrate evolution not only by affecting the evolution of the immune system, but also generating complex interactions with behavior and physiology. Advances in molecular techniques have started to reveal the intricate ways in which bacteria and vertebrates have coevolved. Here, we focus on birds as an example system for understanding the fundamental impact bacteria have had on the evolution of avian immune defenses, behavior, physiology, reproduction and life histories. The avian egg has multiple characteristics that have evolved to enable effective defense against pathogenic attack. Microbial risk of pathogenic infection is hypothesized to vary with life stage, with early life risk being maximal at either hatching or fledging. For adult birds, microbial infection risk is also proposed to vary with habitat and life stage, with molt inducing a period of increased vulnerability. Bacteria not only play an important role in shaping the immune system as well as trade-offs with other physiological systems, but also for determining digestive efficiency and nutrient uptake. The relevance of avian microbiomes for avian ecology, physiology and behavior is highly topical and will likely impact on our understanding of avian welfare, conservation, captive breeding as well as for our understanding of the nature of host-microbe coevolution.

Nest Bacterial Environment Affects Microbiome of Hoopoe Eggshells, but Not That of the Uropygial Secretion

The study of associations between symbiotic bacterial communities of hosts and those of surrounding environments would help to understand how bacterial assemblages are acquired, and how they are transmitted from one to another location (i.e. symbiotic bacteria acquisition by hosts). Hoopoes (Upupa epops) smear their eggshells with uropygial secretion (oily secretion produced in their uropygial gland) that harbors antibiotic producing bacteria. Trying to elucidate a possible role of nest material and cloaca microbiota in determining the bacterial community of the uropygial gland and the eggshells of hoopoes, we characterized bacterial communities of nest material, cloaca, uropygial gland and eggshells by the ARISA fingerprinting. Further, by adding material with scarce bacteria and antimicrobial properties, we manipulated the bacterial community of nest material and thus tested experimentally its effects on the microbiomes of the uropygial secretion and of the eggshells. The experiment did not influence the microbiome of the uropygial secretion of females, but affected the community established on eggshells. This is the first experimental evidence indicating that nest material influences the bacterial community of the eggshells and, therefore, probability of embryo infection. Some of the bacterial strains detected in the secretion were also in the bacterial communities of the nest material and of cloaca, but their occurrence within nests was not associated, which suggests that bacterial environments of nest material and cloaca are not sources of symbiotic bacteria for the gland. These results do not support a role of nest environments of hoopoes as reservoirs of symbiotic bacteria. We discuss possible scenarios explaining bacterial acquisition by hoopoes that should be further explored.