Skin Microbiomes of California Terrestrial Salamanders Are Influenced by Habitat More Than Host Phylogeny.

Alicia K Bird,Sofia R Prado-Irwin,Andrew G Zink,Vance T Vredenburg

doi:10.3389/fmicb.2018.00442

Abstract

A multitude of microorganisms live on and within plant and animal hosts, yet the ecology and evolution of these microbial communities remains poorly understood in many taxa. This study examined the extent to which environmental factors and host taxonomic identity explain microbiome variation within two salamander genera, Ensatina and Batrachoseps, in the family Plethodontidae. In particular, we assessed whether microbiome differentiation paralleled host genetic distance at three levels of taxonomy: genus and high and low clade levels within Ensatina eschscholtzii. We predicted that more genetically related host populations would have more similar microbiomes than more distantly related host populations. We found that salamander microbiomes possess bacterial species that are most likely acquired from their surrounding soil environment, but the relative representation of those bacterial species is significantly different on the skin of salamanders compared to soil. We found differences in skin microbiome alpha diversity among Ensatina higher and lower clade groups, as well as differences between Ensatina and Batrachoseps. We also found that relative microbiome composition (beta diversity) did vary between Ensatina lower clades, but differences were driven by only a few clades and not correlated to clade genetic distances. We conclude this difference was likely a result of Ensatina lower clades being associated with geographic location and habitat type, as salamander identity at higher taxonomic levels (genus and Ensatina higher clades) was a weak predictor of microbiome composition. These results lead us to conclude that environmental factors are likely playing a more significant role in salamander cutaneous microbiome assemblages than host-specific traits.

Highlights

Just as plants and animals have evolved and adapted to particular habitats, forming complex interconnected communities, microbial species have evolved to form communities that are well-suited to specific environments
Among the 118 salamander samples and the 41 soil samples we analyzed, we found a large degree of variation in operational taxonomic units (OTUs) richness among individual samples within each of the sample categories
Soil had significantly greater alpha diversity for all metrics when compared to salamander samples as a whole

Summary

Introduction

Just as plants and animals have evolved and adapted to particular habitats, forming complex interconnected communities, microbial species have evolved to form communities that are well-suited to specific environments. These unique microbial communities (here on referred to as microbiomes) can be found in a range of environments from hot springs. Skin Microbiome Conserved in Plethodontids (Jackson et al, 2001) to vertebrate digestive tracts (Ley et al, 2008a,b). These microbiomes can play a crucial role in the health and well-being of their host (Moloney et al, 2014). Technological advancements in DNA sequencing have made it possible to get a more complete picture of microbiome community composition (Petrosino et al, 2009), and begin answering questions about variation in the host–microbiome relationship (Spor et al, 2011; Council et al, 2016; Moeller et al, 2016)

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