Skin microbiome correlates with bioclimate and Batrachochytrium dendrobatidis infection intensity in Brazil's Atlantic Forest treefrogs

Gene functions of the Ambystoma altamirani skin microbiome vary across space and time but potential antifungal genes are widespread and prevalent

Amphibian skin microbiomes can play a critical role in host survival against emerging diseases by protecting their host against pathogens. While a plethora of biotic and abiotic factors have been shown to influence the taxonomic diversity of amphibian skin microbiomes it remains unclear whether functional genomic diversity varies in response to temporal and environmental factors. Here we applied a metagenomic approach to evaluate whether seasonality, distinct elevations/sites, and pathogen presence influenced the functional genomic diversity of the A. altamirani skin microbiome. We obtained a gene catalogue of 92 107 nonredundant annotated genes and a set of 50 unique metagenome assembled genomes (MAGs). Our analysis showed that genes linked to general and potential antifungal traits significantly differed across seasons and sampling locations at different elevations. Moreover, we found that the functional genomic diversity of A. altamirani skin microbiome differed between B. dendrobatidis infected and not infected axolotls only during winter, suggesting an interaction between seasonality and pathogen infection. In addition, we identified the presence of genes and biosynthetic gene clusters (BGCs) linked to potential antifungal functions such as biofilm formation, quorum sensing, secretion systems, secondary metabolite biosynthesis, and chitin degradation. Interestingly genes linked to these potential antifungal traits were mainly identified in Burkholderiales and Chitinophagales MAGs. Overall, our results identified functional traits linked to potential antifungal functions in the A. altamirani skin microbiome regardless of variation in the functional diversity across seasons, elevations/sites, and pathogen presence. Our findings suggest that potential antifungal traits found in Burkholderiales and Chitinophagales taxa could be related to the capacity of A. altamirani to survive in the presence of Bd, although further experimental analyses are required to test this hypothesis.

Host phylogeny and environment shape the diversity of salamander skin bacterial communities

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 sampling habitats, whereas phylogenetic effects appear to be weak. However, the relative strength of phylogenetic and environmental effects on salamander skin microbiomes remains poorly understood. Here, we analysed sequence data from 1164 adult salamanders of 44 species to characterise and compare the diversity and composition of skin bacteria. We assessed the relative contribution of climate, host sampling habitat, and host phylogeny to the observed patterns of bacterial diversity. We found that bacterial alpha diversity was mainly associated with host sampling habitat and climate, but that bacterial beta diversity was more strongly associated with host taxonomy and phylogeny. This phylogenetic effect predominantly occurred at intermediate levels of host divergence (0-50 Mya). Our results support the importance of environmental factors shaping the diversity of salamander skin microbiota, but also support host phylogenetic history as a major factor shaping these bacterial communities.

Climate change is not just global warming: Multidimensional impacts on animal gut microbiota

Climate change has rapidly altered many ecosystems, with detrimental effects for biodiversity across the globe. In recent years, it has become increasingly apparent that the microorganisms that live in and on animals can substantially affect host health and physiology, and the structure and function of these microbial communities can be highly sensitive to environmental variables. To date, most studies have focused on the effects of increasing mean temperature on gut microbiota, yet other aspects of climate are also shifting, including temperature variation, seasonal dynamics, precipitation and the frequency of severe weather events. This array of environmental pressures might interact in complex and non-intuitive ways to impact gut microbiota and consequently alter animal fitness. Therefore, understanding the impacts of climate change on animals requires a consideration of multiple types of environmental stressors and their interactive effects on gut microbiota. Here, we present an overview of some of the major findings in research on climatic effects on microbial communities in the animal gut. Although ample evidence has now accumulated that shifts in mean temperature can have important effects on gut microbiota and their hosts, much less work has been conducted on the effects of other climatic variables and their interactions. We provide recommendations for additional research needed to mechanistically link climate change with shifts in animal gut microbiota and host fitness.

Effects of cadmium and diethylhexyl phthalate on skin microbiota of Rana chinensis tadpoles

Skin microbiotas play a crucial role in the health, homeostasis, and immune function of amphibians. The contaminants in water could affect the structure and composition of microbial communities. The effects of coexisting pollutants on frogs cannot be adequately explained by a single exposure due to the coexistence of Cd and DEHP in the environment. Following exposure to Cd and/or DEHP, we examined the histological characteristics of Rana chensinensis tadpoles. We also used the 16S rRNA gene sequencing technique to assess the relative abundance of skin microbial communities among tadpoles from each treatment group. Our findings indicate that R. chensinensis' skin experienced some degree of injury due to exposure to Cd and DEHP, which led to the imbalance of their skin microbial community homeostasis and thus interfered with the normal trial status of the host. That may eventually lead to the decline of the amphibian population.

Low microbiome diversity in threatened amphibians from two biodiversity hotspots

Microbial diversity positively influences community resilience of the host microbiome. However, extinction risk factors such as habitat specialization, narrow environmental tolerances, and exposure to anthropogenic disturbance may homogenize host-associated microbial communities critical for stress responses including disease defense. In a dataset containing 43 threatened and 90 non-threatened amphibian species across two biodiversity hotspots (Brazil's Atlantic Forest and Madagascar), we found that threatened host species carried lower skin bacterial diversity, after accounting for key environmental and host factors. The consistency of our findings across continents suggests the broad scale at which low bacteriome diversity may compromise pathogen defenses in species already burdened with the threat of extinction.

Forgotten fungi: the importance of the skin mycobiome

The mosaic ecosystems of microbes that live on our skin encompass not only bacteria but also fungi, microeukaryotes, and viruses. As the second most prevalent group, unique fungal communities are found across the dry, moist, and oily microenvironments of human skin, and alterations of these communities are largely driven by changes in skin physiology throughout an individual's lifespan. Fungi have also been associated with infection and dermatological disorders, resulting from the disrupted balance between fungal-bacterial networks on the skin. Mechanisms of colonization resistance toward fungi in the skin microbiome of animals have advanced our understanding in conservation strategies, yet in the human skin, the fungal microbiome (mycobiome) remains vastly unexplored. Here, we review recent studies on the role of fungi in the skin microbiome, emphasizing how fungal-bacterial interactions at the skin surface play an important ecological function in vertebrate hosts.

Pathogenesis: How a killer fungus targets its host

The cellular signals that trigger pathogen recognition of its target hosts are critical components in the infection cycle. A new study describes the amphibian host cues that induce spore germination in the deadly pathogen that causes chytridiomycosis.

Signatures of functional bacteriome structure in a tropical direct-developing amphibian species

Background

Host microbiomes may differ under the same environmental conditions and these differences may influence susceptibility to infection. Amphibians are ideal for comparing microbiomes in the context of disease defense because hundreds of species face infection with the skin-invading microbe Batrachochytrium dendrobatidis (Bd), and species richness of host communities, including their skin bacteria (bacteriome), may be exceptionally high. We conducted a landscape-scale Bd survey of six co-occurring amphibian species in Brazil’s Atlantic Forest. To test the bacteriome as a driver of differential Bd prevalence, we compared bacteriome composition and co-occurrence network structure among the six focal host species.

Results

Intensive sampling yielded divergent Bd prevalence in two ecologically similar terrestrial-breeding species, a group with historically low Bd resistance. Specifically, we detected the highest Bd prevalence in Ischnocnema henselii but no Bd detections in Haddadus binotatus. Haddadus binotatus carried the highest bacteriome alpha and common core diversity, and a modular network partitioned by negative co-occurrences, characteristics associated with community stability and competitive interactions that could inhibit Bd colonization.

Conclusions

Our findings suggest that community structure of the bacteriome might drive Bd resistance in H. binotatus, which could guide microbiome manipulation as a conservation strategy to protect diverse radiations of direct-developing species from Bd-induced population collapses.

Micro(nano)plastics as an emerging risk factor to the health of amphibian: A scientometric and systematic review

Although the toxicity of microplastics (MPs) and nanoplastics (NPs) is recognized at different trophic levels, our know-how about their effects on amphibians is limited. Thus, we present and discuss the current state on studies involving amphibians and plastic particles, based on a broad approach to studies published in the last 5 years. To search for the articles, the ISI Web of Science, ScienceDirect, and Scopus databases were consulted, using different descriptors related to the topic of study. After the systematic search, we identified 848 publications. Of these, 12 studies addressed the relationship "plastic particles and amphibians" (7 studies developed in the laboratory and 5 field studies). The scientometric analysis points to geographic concentration of studies in Brazil and China; low investment in research in the area, and limited participation of international authors in the studies carried out. In the systematic approach, we confirm the scarcity of available data on the toxicity of plastic particles in amphibians; we observed a concentration of studies in the Anura order, only one study explored the toxicological effects of NPs and polystyrene and polyethylene are the most studied plastic types. Moreover, the laboratory tested concentrations are distant from those of the environmentally relevant; and little is known about the mechanisms of action of NPs/MPs involved in the identified (eco)toxicological effects. Thus, we strongly recommend more investments in this area, given the ubiquitous nature of NPs/MPs in aquatic environments and their possible consequences on the dynamics, reproduction, and survival of species in the natural environment.

TEMPERATURE AS A DRIVER OF THE PATHOGENICITY AND VIRULENCE OF AMPHIBIAN CHYTRID FUNGUS BATRACHOCHYTRIUM DENDROBATIDIS: A SYSTEMATIC REVIEW

Chytridiomycosis, caused by the chytrid fungus Batrachochytrium dendrobatidis (Bd), is a leading cause of global amphibian declines. Severe infections with Bd can lead to cardiac arrest, and mass deaths during epidemics have been reported. Temperature, pH, salinity, and moisture are important determinants of the survival, growth, reproduction, and pathogenicity of Bd, as well as its effect on amphibian populations. Here, we synthesize current knowledge on the role of temperature as a driver of the pathogenicity and virulence of Bd to better understand the effects of temperature on amphibian defense mechanisms against infection. This review advises on research direction and management approaches to benefit amphibian populations affected by Bd. We conclude by offering guidelines for four levels of temperature monitoring in amphibian field studies to improve consistency between studies: regional climate, habitat, microhabitat, and amphibian host.

Batrachochytrium fungi: stealth invaders in amphibian skin

Amphibian populations around the world have been affected by two pathogenic fungi within the phylum Chytridiomycota. Batrachochytrium dendrobatidis (Bd) has infected hundreds of species and led to widespread declines and some species extinctions. Batrachochytrium salamandrivorans (Bsal) has devastated some native European salamanders, especially the iconic fire salamanders (Salamandra salamandra). Comparative genomic studies show that Bd is more diverse and widespread than previously thought, and global lineages occur together allowing for the development of hybrid lineages. New studies raise the concern of greater pathogenesis if both Bd and Bsal infect the same host. Although amphibians possess robust immune defenses, co-infected and many single-infected hosts seem unable to mount effective immune responses. A strong defense may actually be harmful. Analysis of Bd and Bsal secretions documents small metabolites that signal high density to limit their growth and to suppress adaptive immune defenses, thus enabling a stealth presence in the skin compartment.

First line of defence: Skin microbiota may protect anurans from infective larval lungworms

Functional roles of the rich microbiota of the skin are not fully understood, but include protection against microbial diseases and other environmental challenges. In experimental studies, we show that reducing the microbiota from cane toad (Rhinella marina) skin by gently wiping with absorptive gauze resulted in threefold higher rates of infection by lungworms (Rhabdias pseudosphaerocephala) following standardised exposure to infective skin-penetrating larvae. Higher concentrations of microbial DNA were associated with lower rates of lungworm entry. Our data suggest that microbial activity on the anuran skin comprises an important line of defence against attack by macroparasites as well as by fungi and other microbes.