Dietary Carotenoid Supplementation Enhances the Cutaneous Bacterial Communities of the Critically Endangered Southern Corroboree Frog (Pseudophryne corroboree)

Skin microbiomes of frogs vary among body regions, revealing differences that reflect known patterns of chytrid infection

Introduction

The amphibian skin microbiome is an important line of defense against pathogens including the deadly chytrid fungus, Batrachochytrium dendrobatidis (Bd). Bd is known to preferentially infect ventral skin surfaces and feet of host amphibians, often leaving dorsal surfaces like the back uninfected. Within-individual variation in infection distribution across the skin, therefore, may relate to differences in microbiomes among skin regions. However, microbiome heterogeneity within amphibian individuals remains poorly characterized.

Methods

We utilized 16S rRNA gene amplicon sequencing to compare microbiomes of 10 body regions from nine captive Rana sierrae individuals and their tank environments. These individuals were naive to Bd, allowing us to assess whether microbiomes differed among body regions prior to any impacts that may be caused by infection.

Results

We found that frog skin and tank environments harbored distinct microbial communities. On frog skin, the bacterial families Burkholderiaceae (phylum Proteobacteria) and Rubritaleaceae (phylum Verrucomicrobia) were dominant, driven in large part by relative abundances of undescribed members of these families that were significantly higher on frogs than in their environment. Within individuals, we detected differences between microbiomes of body regions where Bd infection would be expected compared to regions that infrequently experience infection. Notably, putative Bd-inhibitory relative abundance was significantly higher on body regions where Bd infection is often localized.

Discussion

These findings suggest that microbiomes in certain skin regions may be predisposed for interactions with Bd. Further, our results highlight the importance of considering intraindividual heterogeneities, which could provide insights relevant to predicting localized interactions with pathogens.

Skin microbiomes of frogs vary among individuals and body regions, revealing differences that reflect known patterns of chytrid infection

The amphibian skin microbiome is an important line of defense against pathogens including the deadly chytrid fungus, Batrachochytrium dendrobatidis (Bd). Intra-species variation in disease susceptibility and intra-individual variation in infection distribution across the skin, therefore, may relate to differences in skin microbiomes. However, characterization of microbiome variation within and among amphibian individuals is needed. We utilized 16S rRNA gene amplicon sequencing to compare microbiomes of ten body regions from nine captive R. sierrae individuals and their tank environments. While frogs harbored distinct microbial communities compared to their tank environments, tank identity was associated with more variation in frog microbiomes than individual frog identity. Within individuals, we detected differences between microbiomes of body regions where Bd infection would be expected compared to regions that infrequently experience infection. Notably, the bacterial families Burkholderiaceae (phylum Proteobacteria) and Rubritaleaceae (phylum Verrucomicrobia) were dominant on frog skin, and the relative abundances of undescribed members of these families were important to describing differences among and within individuals. Two undescribed Burkholderiaceae taxa were found to be putatively Bd-inhibitory, and both showed higher relative abundance on body regions where Bd infection is often localized. These findings highlight the importance of considering intrapopulation and intraindividual heterogeneities, which could provide insights relevant to predicting localized interactions with pathogens.

Skin Bacterial and Fungal Microbiome Responses to Diet Supplementation and Rewilding in the Critically Endangered Southern Corroboree Frog

The composition and dynamics of the skin bacterial and fungal microbiome is thought to influence host-pathogen defence. This microbial community is shaped by host captivity, diet, and microbial interactions between bacterial and fungal components. However, there remains little understanding of how specific micronutrients influence bacterial and fungal microbiome composition and their inter-domain interactions during rewilding of captive-bred animals. This study experimentally investigated the effect of dietary beta-carotene supplementation and subsequent field release on bacterial and fungal microbiome composition and dynamics using the Southern Corroboree frog (Pseudophryne corroboree) as a model system. We found large-scale diversification of bacterial communities post-release and similar diversification of fungal communities. The rewilded fungal mycobiome was more transient and demonstrated stronger temporal and micro-spatial fluctuations than the bacterial microbiome. Accounting for temporal and spatial factors, we found strong residual associations between bacterial members, yet limited evidence for inter-domain associations, suggesting that co-occurrence patterns between bacterial and fungal communities are largely a result of shared responses to the environment rather than direct interactions. Lastly, we found supplementation of dietary beta-carotene in captivity had no impact on post-release microbiome diversity, yet was associated with approximately 15% of common bacterial and fungal genera. Our research demonstrates that environmental factors play a dominant role over dietary beta-carotene supplementation in shaping microbiome diversity post-release, and suggest inter-domain interactions may also only exert a minor influence. Further research on the function and ecology of skin bacterial and fungal microbiomes will be crucial for developing strategies to support survival of endangered amphibian species.

Horizon scanning the application of probiotics for wildlife

The provision of probiotics benefits the health of a wide range of organisms, from humans to animals and plants. Probiotics can enhance stress resilience of endangered organisms, many of which are critically threatened by anthropogenic impacts. The use of so-called 'probiotics for wildlife' is a nascent application, and the field needs to reflect on standards for its development, testing, validation, risk assessment, and deployment. Here, we identify the main challenges of this emerging intervention and provide a roadmap to validate the effectiveness of wildlife probiotics. We cover the essential use of inert negative controls in trials and the investigation of the probiotic mechanisms of action. We also suggest alternative microbial therapies that could be tested in parallel with the probiotic application. Our recommendations align approaches used for humans, aquaculture, and plants to the emerging concept and use of probiotics for wildlife.

Dietary carotenoid supplementation has long-term and community-wide effects on the amphibian skin microbiome

The amphibian skin microbiome plays a crucial role in host immunity and pathogen defence, yet we know little about the environmental drivers of skin microbial variation across host individuals. Inter-individual variation in the availability of micro-nutrients such as dietary carotenoids, which are involved in amphibian immunity, may be one factor that influences skin microbial assembly across different life history stages. We compared the effect of four carotenoid supplementation regimes during different life stages on the adult skin microbiome using a captive population of the critically endangered southern corroboree frog, Pseudophryne corroboree. We applied 16S rRNA sequencing paired with joint-species distribution models to examine the effect of supplementation on taxon abundances. We found that carotenoid supplementation had subtle yet taxonomically widespread effects on the skin microbiome, even 4.5 years post supplementation. Supplementation during any life-history stage tended to have a positive effect on the number of bacterial taxa detected, although explanatory power was low. Some genera were sensitive to supplementation pre-metamorphosis, but most demonstrated either additive or dominant effects, whereby supplementation during one life history stage had intermediate or similar effects, respectively, to supplementation across life. Carotenoid supplementation increased abundances of taxa belonging to lactic acid bacteria, including Lactococcus and Enterococcus, a group of bacteria that have previously been linked to protection against the amphibian fungal pathogen Batrachochytrium dendrobatidis (Bd). While the fitness benefits of these microbial shifts require further study, these results suggest a fundamental relationship between nutrition and the amphibian skin microbiome which may be critical to amphibian health and the development of novel conservation strategies.

Reintroduction modifies the intraspecific variations of symbiotic microbes in captive bred Chinese giant salamander

Microorganisms play as fundamental contributors to maintain hosts' fitness, which can be shaped by external environment. Moreover, symbiotic microbiome also varied within species (e.g., between sexes and developmental stages). However, we still need more studies to quantify whether the intraspecific variation patterns of symbiotic microbes can be modified with the change of environment. The Chinese giant salamander (CGS; Andrias davidianus) is a Critically Endangered species. Despite quantitative captive bred individuals were released to rebuild wild populations, the effectiveness is limited. More importantly, no studies have revealed the adaptation of released CGSs to the complex field conditions. In the present study, we explored whether reintroduction can reshape the intraspecific variations of symbiotic microbiota in captive bred CGSs using high-throughput amplicon sequencing of the16S rRNA gene. We found no significant difference of symbiotic microbiome in captive bred males and females, but released males and females differed significantly in skin microbiome. Juveniles had higher diversity of microbial symbiont than adults in hatchery, but lower diversity in field. Moreover, dominant bacterial taxa differed between juveniles and adults in both hatchery and field. Importantly, this symbiotic microbiome variations within species can be modified (alpha and beta diversity, and community composition) when captive bred individuals were released to the field. Overall, we observed a lower alpha diversity and higher relative abundance of Chryseobacterium, Plesiomonas, and Acinetobacter in the bacterial community of captive bred individuals. Instead, higher alpha diversity of symbiotic microbiota and higher relative abundance of S24-7 and Lactobacillus was detected in released individuals. These modifications may associate with the change of living environment, as well as the specific behavior within CGSs (e.g., movement patterns and foraging activities). Future studies can incorporate other approaches (e.g., blood physiology) to better evaluate the growth and health of reintroduced CGSs.

Multiple phenotypic traits predict male mating success in a critically endangered frog

Abstract

Complex sexual signals spanning multiple sensory modalities may be common in nature, yet few studies have explored how combinations of phenotypic traits influence male attractiveness and mating success. Here, we investigate whether combinations of multiple male phenotypic traits (both within and across sensory modalities) predict male mating and fertilization success in the critically endangered southern corroboree frog, Pseudophryne corroboree. We conducted breeding trials in a standardized captive environment where females were given the opportunity to choose between multiple males over the duration of the breeding season. For each male, we measured multiple call traits, aspects of coloration, body size, and age. We found that complex interactions between multiple traits best predicted male mating and fertilization success. In general, males with lower call frequency, lower call rate, and shorter call duration had the highest mating and fertilization success. Fertilization success was additionally linked to male body size and age. These findings suggest that female P. corroboree select mates based on a suite of acoustic traits, adding to a growing body of evidence that females use multiple traits to assess male quality. Our results also suggest that females may combine information from multiple signals non-additively. Moreover, our results imply that females gain direct fertility benefits from their mate choice decisions. We argue that understanding female mate choice based on various signals across multiple sensory modalities has important implications for the integration of mate choice into conservation breeding programs and needs to be considered when developing behavior-based captive breeding strategies.

Significance statement

Sexual signals are often highly complex, yet we know little about how multiple signal components both within and across various sensory modalities predict male mating success. We investigated whether combinations of multiple phenotypic traits (within and across sensory modalities) predicted male breeding success in threatened corroboree frogs. We conducted captive breeding trials in a homogeneous environment, where females could choose between multiple males over the duration of a single breeding season. We found that interactions between multiple male traits predicted mating and fertilization success. Males with lower call frequency, call rate, and duration had higher mating success. Fertilization success was also linked to acoustic signals, body size, and age. Understanding mate choice for multiple traits further elucidates the complexity of female mate choice. This study is one of the first to consider the conservation implications of multimodal signaling in mate choice.

The Role of Feed in Aquatic Laboratory Animal Nutrition and the Potential Impact on Animal Models and Study Reproducibility

Feed plays a central role in the physiological development of terrestrial and aquatic animals. Historically, the feeding practice of aquatic research species derived from aquaculture, farmed, or ornamental trades. These diets are highly variable, with limited quality control, and have been typically selected to provide the fastest growth or highest fecundity. These variations of quality and composition of diets may affect animal/colony health and can introduce confounding experimental variables into animal-based studies that impact research reproducibility.

Comparison of the gut microbiota of Rana amurensis and Rana dybowskii under natural winter fasting conditions

Rana amurensis and R. dybowskii occupy similar habitats. As temperatures decrease with the onset of winter, both species migrate to ponds for hibernation. Our goal was to determine whether different species possess different intestinal microbiota under natural winter fasting conditions. We used high-throughput Illumina sequencing of 16S rRNA gene sequences to analyse the diversity of intestinal microbes in the two species. The dominant gut bacterial phyla in both species were Bacteroidetes, Proteobacteria and Firmicutes. Linear discriminant analysis (LDA) effect size revealed significant enrichment of Proteobacteria in R. amurensis and Firmicutes in R. dybowskii. There were significant differences in the gut microbiota composition between the species. The core operational taxonomic unit numbers in R. amurensis and R. dybowskii shared by the two species were 106, 100 and 36. This study indicates that the intestinal bacterial communities of the two frog species are clearly different. Phylum-level analysis showed that R. amurensis was more abundant in Proteobacteria and Verrucomicrobia than R. dybowskii was This is the first study of the composition and diversity of the gut microbiota of these two species, providing important insights for future research on the gut microbiota and the role of these bacterial communities in frogs.

Effects of Seasonal Hibernation on the Similarities Between the Skin Microbiota and Gut Microbiota of an Amphibian (Rana dybowskii)

Both the gut and skin microbiotas have important functions for amphibians. The gut microbiota plays an important role in both the health and evolution of the host species, whereas the role of skin microbiota in disease resistance is particularly important for amphibians. Many studies have examined the effects of environmental factors on the skin and gut microbiotas, but no study has yet explored the similarities between the skin and gut microbiotas. In this study, the gut and skin microbiotas of Rana dybowskii in summer and winter were investigated via high-throughput Illumina sequencing. The results showed that the alpha diversity of gut and skin microbiotas decreased significantly from summer to winter. In both seasons, the microbial composition and structure differed significantly between the gut and skin, and the similarities between these microbiotas differed between seasons. The pairwise distances between the gut and skin microbiotas were greater in winter than in summer. The ratio of core OTUs and shared OTUs to the sum of the OTUs in the gut and skin microbiotas in summer was significantly higher than that in winter. The similarities between the gut and skin microbiotas are important for understanding amphibian ecology and life history.

Fucoxanthin modulates cecal and fecal microbiota differently based on diet

Obesity is a major health concern worldwide and is considered to be associated with disruption of host-microbial homeostasis, especially microbiota composition in the gastrointestinal tract. Use of microbiota-directed foods or nutraceuticals therefore represents a promising approach for the control of obesity. Fucoxanthin, a marine carotenoid, has been proven to be one of the most effective anti-obesity natural products. However, its action mechanism is yet to be unraveled, especially with respect to its role in the modulation of gut microbiota composition. In the present study, profiles of microbiota in both the cecal and fecal samples from BALB/c mice given respectively the following treatments were examined: normal chow diet (NCD), NCD + fucoxanthin (NCDF), high-fat-diet (HFD), and HFD + fucoxanthin (HFDF). The results showed that fucoxanthin supplementation for 4 weeks significantly changed the composition of both cecal and fecal microbiota. In addition, a differential effect was observed between the supplementation to NCD and to HFD. The changes in the Firmicutes/Bacteroidetes ratio and the abundance of S24-7 and Akkermansia were identified to be among the major gut microbiota modulating events associated with the anti-obesity bioactivity of fucoxanthin. Hence, our results suggested that fucoxanthin could be a promising microbiota-targeted functional-food ingredient.

Dietary carotenoids affect the development of individual differences and behavioral plasticity

Nutritional conditions experienced during development are expected to play a key role in shaping an individual’s behavioral phenotype. The long term, irreversible effects of nutritional conditions on behavioral variation among and within individuals remains largely unexplored. This study aimed to investigate how long-term carotenoid availability (representing low vs. high quality nutritional conditions) during both larval and adult life stages influences the expression of among-individual variation (animal personality) and within-individual variation (behavioral plasticity). We tested for personality and plasticity along the exploration/avoidance behavioral axis in the Southern Corroboree frog (Pseudophryne corroboree). We predicted that treatment groups receiving carotenoids during early development would be more exploratory and have greater among- and within-individual variation compared with individuals that did not receive carotenoids (i.e., silver spoon hypothesis). Superior nutritional conditions experienced during development are expected to provide individuals with resources needed to develop costly behaviors, giving them an advantage later in life irrespective of prevailing conditions. Unexpectedly, frogs that did not receive carotenoids as larvae expressed greater among-individual variance in exploration behavior. Additionally, frogs that did not receive carotenoids at either life stage displayed greater within-individual variance. Our findings provide no support for the silver spoon hypothesis but suggest that inconsistent nutritional conditions between life stages may adversely affect the development of behavioral phenotypes. Overall, our results indicate that early and late life nutritional conditions affect the development of personality and plasticity. They also highlight that nutritional effects on behavior may be more complex than previously theorized.

Effect of carotenoid class and dose on the larval growth and development of the critically endangered southern corroboree frog

Dietary carotenoids are expected to improve vertebrate growth and development, though evidence for beneficial effects remains limited. One reason for this might be that few studies have directly compared the effects of carotenoids from different classes (carotenes versus xanthophylls) at more than one dose. Here, we tested the effect of two doses of dietary β-carotene and lutein (representing two different carotenoid classes) on the growth and development of larval southern corroboree frogs (Pseudophryne corroboree). Individuals were supplemented with either β-carotene or lutein at one of two doses (0.1 mg g^-1, 1 mg g^-1), or given a diet without carotenoids (control). Each dietary treatment included 36 replicate individuals, and individuals remained on the same diet until metamorphosis (25-39 weeks). We measured larval survival, larval growth (body length), time to metamorphosis, metamorphic body size (mass and SVL), and body condition. Lutein had no detectable effect on larval growth and development. However, larvae receiving a high dose (1 mg g^-1) of β-carotene metamorphosed significantly faster than all other dietary treatments, despite no significant differences in growth rate. This result indicates that β-carotene supplementation in P. corroboree has positive effects on development independent of growth effects. Our study provides new evidence for differential effects of carotenoid class and dose on vertebrate development. From a conservation perspective, our findings are expected to assist with the recovery of P. corroboree by expediting the generation of frogs required for the maintenance of captive insurance colonies, or the provision of frogs for release. More broadly, our study highlights the potential for dietary manipulation to assist with the ex situ management of threatened amphibian species worldwide.

Conservation biology needs a microbial renaissance: a call for the consideration of host-associated microbiota in wildlife management practices

The central aim of conservation biology is to understand and mitigate the effects of human activities on biodiversity. To successfully achieve this objective, researchers must take an interdisciplinary approach that fully considers the effects, both direct and indirect, of anthropogenic disturbances on wildlife physiology and health. A recent surge in research has revealed that host-associated microbiota-the archaeal, bacterial, fungal and viral communities residing on and inside organisms-profoundly influence animal health, and that these microbial communities can be drastically altered by anthropogenic activities. Therefore, conservation practitioners should consider the disruption of host-associated microbial diversity as a serious threat to wildlife populations. Despite the tremendous potential for microbiome research to improve conservation outcomes, few efforts have been made to truly integrate these fields. In this review, we call for the microbial renaissance of conservation biology, where biodiversity of host-associated microbiota is recognized as an essential component of wildlife management practices. Using evidence from the existing literature, we will examine the known effects of anthropogenic activities on the diversity of host-associated microbial communities and integrate approaches for maintaining microbial diversity to successfully achieve conservation objectives.

Probiotics as a tool for disease mitigation in wildlife: insights from food production and medicine

The use of beneficial microbes to improve host attributes, referred to as probiotic therapy, has been increasingly applied to industries, including aquaculture, agriculture, and human medicine, and is emerging in the field of wildlife medicine. However, there is a general lack of shared knowledge regarding successful practices as well as ecological processes that underlie host-microbe interactions. Presently, probiotics are being developed specifically for preventing and treating particular infectious diseases as an alternative to antibiotic treatments and chemotherapy. We review research on probiotics developed for mitigation of infectious disease in the aforementioned industries to gain insight into how probiotics may be effective in reducing wildlife disease risk. We examine the trends of successful in vivo probiotic applications for disease systems and identify common objectives to reduce intestinal pathogens and sexually transmitted and respiratory diseases, inhibit skin pathogens, and serve as environmental prophylaxis to reduce pathogen loads in the environment. We conclude by highlighting the frontier of wildlife probiotics research and identifying knowledge gaps where research is needed.