No abstract

Background Microbiomes have been increasingly recognized as major contributors to host health and survival. In amphibians, bacterial members of the skin microbiota protect their hosts by inhibiting the growth of the fungal pathogen Batrachochytrium dendrobatidis (Bd). Even though several studies describe the influence of biotic and abiotic factors over the skin microbiota, it remains unclear how these symbiotic bacterial communities vary across time and development. This is particularly relevant for species that undergo metamorphosis as it has been shown that host physiology and ecology drastically influence diversity of the skin microbiome. Results We found that the skin bacterial communities of the axolotl A. altamirani are largely influenced by the metamorphic status of the host and by seasonal variation of abiotic factors such as temperature, pH, dissolved oxygen and conductivity. Despite high Bd prevalence in these samples, the bacterial diversity of the skin microbiota did not differ between infected and non-infected axolotls, although relative abundance of particular bacteria were correlated with Bd infection intensity. Conclusions Our work shows that metamorphosis is a crucial process that shapes skin bacterial communities and that axolotls under different developmental stages respond differently to environmental seasonal variations. Moreover, this study greatly contributes to a better understanding of the factors that shape amphibian skin microbiota, especially in a largely underexplored group like axolotls (Mexican Ambystoma species).

Chytridiomycosis, an emerging disease caused mostly by the pathogen Batrachochytrium dendrobatidis, has caused massive amphibian population declines and extinctions worldwide. The ecology of this disease is mainly explained by the interaction of environmental factors, pathogen biology, and host traits including development. For paedomorphic salamanders, differences in B. dendrobatidis infection may be explained by metamorphosis and water physicochemical conditions. In this study, we aimed to determine the influence of environmental and host factors on B. dendrobatidis prevalence and infection intensity in the facultative paedomorphic salamander Ambystoma altamirani. We determined B. dendrobatidis prevalence and infection load in four populations of A. altamirani along 1 year (four seasons) and assessed their relationship with environmental factors and host metamorphic status (gilled or non‐gilled). We found that B. dendrobatidis prevalence and infection load are largely explained by metamorphic status and environmental factors such as elevation, seasonality, water temperature, pH, conductivity, and dissolved oxygen. To our knowledge, this is the first study to empirically show the effect of metamorphosis on B. dendrobatidis infection status across locations and seasons. This information may be used to understand the temporal dynamics of B. dendrobatidis–host interactions and to identify potential disease outbreaks that may cause cryptic sublethal effects on salamander populations. Our results will help in the development of conservation strategies for paedomorphic salamanders that are already considered threatened by anthropogenic factors such as habitat loss and climate change.

Background: Microbiomes have been increasingly recognized as major contributors to host health and survival. In amphibians, bacterial members of the skin microbiota protect their hosts by inhibiting the growth of the fungal pathogen Batrachochytrium dendrobatidis (Bd). Even though several studies describe the influence of biotic and abiotic factors over the skin microbiota, it remains unclear how these symbiotic bacterial communities vary across time and development. This is particularly relevant for species that undergo metamorphosis as it has been shown that host physiology and ecology drastically influence diversity of the skin microbiome. Results: We found that the skin microbiota of the axolotl A. altamirani is largely influenced by the metamorphic status of the host and by seasonal variation of abiotic factors such as temperature, pH, dissolved oxygen, and conductivity. Despite high Bd prevalence in these samples, the bacterial diversity of the skin microbiota did not differ between infected and non-infected axolotls, although particular bacteria were correlated with Bd infection intensity. Conclusions: Our work shows that metamorphosis is a crucial process that shapes skin microbiota and that axolotls under different developmental stages response differently to environmental seasonal variations. Moreover, this study greatly contributes to a better understanding of the factors that shape amphibian skin microbiota, especially in a largely underexplored group like axolotls (Mexican Ambystoma species).

The composition and diversity of animal-associated microbial communities are shaped by multiple ecological and evolutionary processes acting at different spatial and temporal scales. Skin microbiomes are thought to be strongly influenced by the environment due to the direct interaction of the host’s skin with the external media. As expected, the diversity of amphibian skin microbiomes is shaped by climate and host habitats, whereas phylogenetic effects appear to be weak. However, the relative strength of phylogenetic and environmental effects on amphibian skin microbiomes remains poorly understood. Here, we analysed sequence data from 1,091 adult salamanders in 41 species to characterise and compare the diversity and composition of skin bacteria. We assessed the relative contribution of climate, host habitat, and host phylogeny to the observed patterns of bacterial diversity. We found that microbial alpha was mainly associated with host habitat and climate, but that microbial beta diversity was more strongly associated with host taxonomy and phylogeny. This phylogeny effect predominantly occurred at intermediate levels of host divergence (0–50 Mya). Our results support the importance of environmental factors shaping the diversity of amphibian skin microbiomes, but also support host phylogenetic history as a major factor shaping these microbial communities.