Cutaneous Microbial Ecology of Giant Salamanders: Implications for Conservation and Management

Obed Hernandez-Gomez, Purdue University

Abstract

Microbial symbionts impact important host physiological processes such as immunity and metabolic regulation. As a result, describing microbial communities is useful for a holistic understanding of host health. The amphibian skin serves as an excellent model for understanding the influence of the microbiome on host fitness. Within this class, the skin is a vital organ used for respiration, osmoregulation and immunity. In addition, the amphibian skin harbors diverse microbial communities that provide protection against common amphibian pathogens. In efforts to combat amphibian declines associated with pathogens, researchers are characterizing the cutaneous microbiome as a resource for disease management. Hellbender salamanders (Cryptobranchus alleganiensis) provide an ideal system to evaluate skin microbial communities under the scope of conservation. Hellbenders are threatened across their range, and conservation programs require information on ways to mitigate disease spread associated with translocations and re-introductions. In addition, the Ozark hellbender subspecies (C. a. bishopi) exhibits chronic wounds associated with bacterial infections, whereas the eastern hellbender (C. a. alleganiensis) does not. As a result, there is a need to evaluate the structure of the cutaneous microbiota of hellbenders, to investigate the microbiome composition of Ozark hellbender wound tissue, and to determine the genetic and evolutionary factors that influence microbial community composition. I characterized the skin microbiome of hellbenders across the range of both subspecies which are located in the eastern United States. I obtained microbiota samples from the dorsal skin of both hellbender subspecies and from the chronic wounds in wild Ozark hellbenders. I applied 16S rRNA gene amplicon sequencing and bioinformatics pipelines to describe the bacterial communities of all samples. In addition, I obtained estimates of allele frequency and diversity for the immune system major histocompatibility complex (MHC) IIB gene for individuals from both hellbender subspecies. To evaluate evolutionary-associated differentiation in the skin microbiome, I compared the microbiome composition of eastern and Ozark hellbender subspecies. I also evaluated differences in community composition between wounds and the healthy skin of Ozark hellbenders. Within each subspecies’ range, I estimated the effect of population genetic structure and geographical location on operational taxonomic unit (OTU) turnover and community differentiation. Finally, I measured MHC-IIB allele diversity within each subspecies, and assessed linkages between the MHC and microbiome diversity and composition. Microbiome analysis and immune gene characterization derived substantial results important for the conservation of this species. First, I observed significant differentiation of hellbender skin communities among populations driven by clumped operational taxonomic unit turnover. In addition, there were pronounced differences in the composition of bacterial communities on the skin of Ozark and eastern hellbenders. These patterns indicate that co-evolutionary adaptations have occurred between the host subspecies and their microbiome. In contrast to the Ozark hellbender healthy skin, bacterial community samples on chronic wounds had increased community richness. While the results of my investigations do not identify specific bacterial pathogens, richness differences between wounds and healthy skin suggest that symbiont and environmental bacteria opportunistically colonize exposed wound tissue. Ozark hellbenders also possessed reduced diversity in the MHC IIB gene compared to the eastern subspecies. Reduced immunocompetence due to loss of MHC divergence is among the first concrete explanations for the presence of chronic wounds in Ozark hellbenders. Finally, common MHC-IIB allele presence and divergence were noted to significantly define differences in microbiome composition among individuals in both subspecies. Thus, cutaneous immunity in amphibians is dependent on synergistic contributions by host and microbial traits. I provide a guide for the incorporation of MHC and microbiome data into current conservation practices. Current hellbender management practices should continue to prioritize the maintenance of genome-wide diversity in captive/wild populations. Moreover, preservation of MHC diversity in captive/wild populations should be a secondary goal given the presence of disease in wild populations. Additionally, if differences in the cutaneous microbiome exist between source and supplemented populations, there is a need to evaluate ways to reduce dysbiosis caused by management approaches (e.g., sterile captive environment). It is necessary to investigate how genetic/microbial diversity management can benefit the efforts of captive breeding and rearing programs in hellbenders and other amphibian species. Incorporating a holistic approach into amphibian management has great potential to improve the success of current and future conservation efforts worldwide.

Degree

Ph.D.

Advisors

Williams, Purdue University.

Subject Area

Genetics|Conservation biology

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