Assessment of Bacterial Communities Associated With the Skin of Costa Rican Amphibians at La Selva Biological Station

Abstract

Amphibian skin is a suitable environment for rich communities of microorganisms, both beneficial and detrimental to the host. The amphibian cutaneous microbiota has been hypothesized to play an important role as symbionts, protecting their hosts against disease. Costa Rica has one of the most diverse assemblages of amphibians in the world and we know very little about the microbiota of these tropical animals. For comparison with other studies, we explore the diversity of the skin bacterial communities employing16S rRNA amplicon sequencing of swab samples from twelve species of frogs at La Selva Biological Station in Sarapiquí, Heredia province. The predominant phylum detected in our studies was Proteobacteria, followed by Bacteroidetes and Actinobacteria, with these three phyla representing 89.9% of the total bacterial taxa. At the family level, Sphingobacteriaceae and Comamonadaceae were highly represented among samples. Our results suggest that host species and host family are significant predictors of the variation in microbiota composition. This study helps set the foundation for future research about microbiota composition and resilience to unfavorable conditions, leading to improvement in managing strategies for endangered amphibian species.

Moving Beyond the Host: Unraveling the Skin Microbiome of Endangered Costa Rican Amphibians

“…This genus plays an important role in maintaining gut homeostasis (Wexler and Goodman, 2017) and therefore could be relevant for supporting the health of L. vibicarius . This species-specific microbiome pattern is congruent with other studies in the tropics, such as in low- and mid-elevations of Costa Rica and Panama (Belden et al, 2015; Rebollar et al, 2016b; Abarca et al, 2018) and in the temperate region (McKenzie et al, 2011; Kueneman et al, 2014; Bletz et al, 2017). The family Alcaligenaceae and genus Chryseobacterium were also the most common taxa in the bacterial communities of Agalychnis callidryas , Leptodactylus savagei , and Pristimantis ridens from the lowlands of Costa Rica (Abarca et al, 2018).…”

“…This species-specific microbiome pattern is congruent with other studies in the tropics, such as in low- and mid-elevations of Costa Rica and Panama (Belden et al, 2015; Rebollar et al, 2016b; Abarca et al, 2018) and in the temperate region (McKenzie et al, 2011; Kueneman et al, 2014; Bletz et al, 2017). The family Alcaligenaceae and genus Chryseobacterium were also the most common taxa in the bacterial communities of Agalychnis callidryas , Leptodactylus savagei , and Pristimantis ridens from the lowlands of Costa Rica (Abarca et al, 2018). In this study, we have not evaluated the mechanisms driving variation in the skin microbiome; however, we suspect that a distinct antimicrobial peptide composition among our species, as has been observed in other amphibians, plays a role as a selective force that determines which microbial genotypes can grow on each host’s skin (Woodhams et al, 2007a; Franzenburg et al, 2013).…”

“…We caution that this does not necessarily mean that these bacterial strains possess anti- Bd properties, rather that they are strong candidates. The use of this database to detect putatively anti- Bd bacterial strains has been used in previous amphibian microbiome studies (e.g., Kueneman et al, 2015; Abarca et al, 2018; Muletz-Wolz et al, 2019). We visualized the presence and relative abundance patterns with a Venn diagram and heatmaps using the R packages “Vennerable” and “ggplot2,” respectively.…”

The skin microbiome of Xenopus laevis and the effects of husbandry conditions

“…Skin-related microbial communities influence host resistance to infection, as reviewed in [13]. In amphibians, skin plays an important role in respiration, thermoregulation, osmoregulation, pigmentation and protection from predators and pathogens [14][15][16][17]. It is characterized by a thin mucosal surface produced by granular glands that secrete oils and other substances [14,15], and due to its moist nature sustains a wide microbial community composed of bacteria, archaea, fungi and protozoans [18,19].…”

Evaluation of the bacterial and fungal microbiome on the skin ofAnaxyrus boreas,Rhinella marina, andXenopus laevisand implications related toBatrachochytrium dendrobatidissusceptibility

“…A few studies have attempted to characterize the natural cutaneous microbiota of amphibians by culture-independent means (Abarca et al, 2018;Edwards, Byrne, Harlow, & Silla, 2017;Federici et al, 2015;Lauer et al, 2008;Madison, Ouellette, Schmidt, & Kerby, 2019). Cutaneous microbiota of certain amphibians are capable of producing antifungal compounds which may prevent Bd infection, and only a very limited proportion of resident host 5 microbes can be identified with culture dependent methods (Abarca et al, 2018;Dowd, Sun, Secor, et al, 2008;Edwards et al, 2017;Federici et al, 2015;Lauer et al, 2008;Madison et al, 2019). In addition, a comparison of the cutaneous microbiota between resistant and non-resistant amphibians to Bd would be especially helpful in characterizing potential key players in Bd resistance.…”