Variation in Metabolite Profiles of Amphibian Skin Bacterial Communities Across Elevations in the Neotropics

Medina, Daniel; Hughey, Myra C.; Becker, Matthew H.; Walke, Jenifer B.; Umile, Thomas P.; Burzynski, Elizabeth A.; Iannetta, Anthony A.; Minbiole, Kevin P. C.; Belden, Lisa K.

doi:10.1007/s00248-017-0933-y

Cited by 28 publications

(20 citation statements)

References 81 publications

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“…Differences in an individual bacterial isolate's interactions with the environment and other microbes are also known to alter bacterial metabolite production (Daskin et al, 2014;Wolz et al, 2017;Medina et al, 2017a;Bird et al, 2018). Thus, another consideration is whether Bd is present and when is it most active, as changes in microbial community composition have been linked with the onset of Bd infection (Pullen et al, 2010;Longo et al, 2015;Clare et al, 2016;Varela et al, 2018).…”

Section: Spatial and Temporal Variation Within Genera And Speciesmentioning

confidence: 99%

Predicting Microbiome Function Across Space Is Confounded by Strain-Level Differences and Functional Redundancy Across Taxa

Barnes

Carter

2020

Front. Microbiol.

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Variation in the microbiome among individual organisms may play a critical role in the relative susceptibility of those organisms to infection, disease, and death. However, predicting microbiome function is difficult because of spatial and temporal variation in microbial diversity, and taxonomic diversity is not predictive of microbiome functional diversity. Addressing this issue may be particularly important when addressing pandemic diseases, such as the global amphibian die-off associated with Bd. Some of the most important factors in probiotic development for disease treatment are whether bacteria with desired function can be found on native amphibians in the local environment. To address this issue, we isolated, sequenced, and assayed the cutaneous bacterial communities of Plethodon cinereus along a gradient of land use change. Our results suggest that cutaneous community composition, but not overall diversity, change with changes in land use, but this does not correspond to significant change in Bd-inhibitory function. We found that Bd-inhibition is a functionally redundant trait, but that level of inhibition varies over phylogenetic, spatial, and temporal scales. This research provides further evidence for the importance of continued examination of amphibian microbial communities across environmental gradients, including biotic and abiotic interactions, when considering disease dynamics.

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Section: Spatial and Temporal Variation Within Genera And Speciesmentioning

confidence: 99%

Predicting Microbiome Function Across Space Is Confounded by Strain-Level Differences and Functional Redundancy Across Taxa

Barnes

Carter

2020

Front. Microbiol.

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“…Sample and sequence data processing DNA from the skin swabs was extracted following the manufacturer's protocol of the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA) including an initial lysozyme incubation step at 37 C for 1 h, as described in previous studies Walke et al, 2015;Medina et al, 2017). The extracted DNA was used as template for the detection and quantification of Bd mentioned earlier, and to conduct amplicon sequencing to determine the skin bacterial (previously done for a subset of the samples) and fungal (in the present study, with samples prepped in 2015) communities.…”

Section: Sample Collectionmentioning

confidence: 99%

Amphibian skin fungal communities vary across host species and do not correlate with infection by a pathogenic fungus

Medina

Hughey

Walke

et al. 2019

Environmental Microbiology

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Summary Amphibian population declines caused by the fungus Batrachochytrium dendrobatidis (Bd) have prompted studies on the bacterial community that resides on amphibian skin. However, studies addressing the fungal portion of these symbiont communities have lagged behind. Using ITS1 amplicon sequencing, we examined the fungal portion of the skin microbiome of temperate and tropical amphibian species currently coexisting with Bd in nature. We assessed cooccurrence patterns between bacterial and fungal OTUs using a subset of samples for which bacterial 16S rRNA gene amplicon data were also available. We determined that fungal communities were dominated by members of the phyla Ascomycota and Basidiomycota, and also by Chytridiomycota in the most aquatic amphibian species. Alpha diversity of the fungal communities differed across host species, and fungal community structure differed across species and regions. However, we did not find a correlation between fungal diversity/community structure and Bd infection, though we did identify significant correlations between Bd and specific OTUs. Moreover, positive bacterial–fungal cooccurrences suggest that positive interactions between these organisms occur in the skin microbiome. Understanding the ecology of amphibian skin fungi, and their interactions with bacteria will complement our knowledge of the factors influencing community assembly and the overall function of these symbiont communities.

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“…In the present study, the number and taxonomic classification of the indicator OTUs associated with R2A and dR2A suggests that R2A is the most appropriate media to recover a high diversity of the culturable members of the amphibian skin community. In addition, R2A also recovers some of the most abundant and prevalent taxa occurring on amphibian skin, based on studies of tropical and temperate species (Kueneman et al, 2013 ; Walke et al, 2014 ; Becker et al, 2015 ; Belden et al, 2015 ; Rebollar et al, 2016b ; Medina et al, 2017 ). For example, we identified several indicator OTUs from the families Nocardiaceae, Enterobacteriaceae, Pseudomonadaceae, Sphingomonadaceae and Xanthomonadaceae associated with R2A and dR2A that were the most abundant and prevalent bacterial taxa on these individual toads according to 16S rRNA amplicon data (Walke et al, 2015a ).…”

Section: Discussionmentioning

confidence: 91%

Culture Media and Individual Hosts Affect the Recovery of Culturable Bacterial Diversity from Amphibian Skin

et al. 2017

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One current challenge in microbial ecology is elucidating the functional roles of the large diversity of free-living and host-associated bacteria identified by culture-independent molecular methods. Importantly, the characterization of this immense bacterial diversity will likely require merging data from culture-independent approaches with work on bacterial isolates in culture. Amphibian skin bacterial communities have become a recent focus of work in host-associated microbial systems due to the potential role of these skin bacteria in host defense against the pathogenic fungus Batrachochytrium dendrobatidis (Bd), which is associated with global amphibian population declines and extinctions. As there is evidence that some skin bacteria may inhibit growth of Bd and prevent infection in some cases, there is interest in using these bacteria as probiotic therapy for conservation of at-risk amphibians. In this study, we used skin swabs from American toads (Anaxyrus americanus) to: (1) assess the diversity and community structure of culturable amphibian skin bacteria grown on high and low nutrient culture media, (2) determine which culture media recover the highest proportion of the total skin bacterial community of individual toads relative to culture-independent data, and (3) assess whether the plated communities from the distinct media types vary in their ability to inhibit Bd growth in in-vitro assays. Overall, we found that culture media with low nutrient concentrations facilitated the growth of more diverse bacterial taxa and grew distinct communities relative to media with higher nutrient concentrations. Use of low nutrient media also resulted in culturing proportionally more of the bacterial diversity on individual toads relative to the overall community defined using culture-independent methods. However, while there were differences in diversity among media types, the variation among individual hosts was greater than variation among media types, suggesting that swabbing more individuals in a population is the best way to maximize culture collections, regardless of media type. Lastly, the function of the plated communities against Bd did not vary across culture media type or between high and low nutrient media. These results inform current efforts for developing a probiotic-based approach for amphibian conservation and help to ensure that culture collections are capturing the majority of the important diversity in these systems.

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Variation in Metabolite Profiles of Amphibian Skin Bacterial Communities Across Elevations in the Neotropics

Cited by 28 publications

References 81 publications

Predicting Microbiome Function Across Space Is Confounded by Strain-Level Differences and Functional Redundancy Across Taxa

Predicting Microbiome Function Across Space Is Confounded by Strain-Level Differences and Functional Redundancy Across Taxa

Amphibian skin fungal communities vary across host species and do not correlate with infection by a pathogenic fungus

Culture Media and Individual Hosts Affect the Recovery of Culturable Bacterial Diversity from Amphibian Skin

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