MALDI-TOF Mass Spectrometry Characterization of Culturable Microbiota Associated with the Skin of Amphibians from the Southern Andes Mountains of Ecuador

Abstract

Ecuador is recognized for having a high diversity of anuran species, which are distributed mainly south of the Andes mountains. However, due to their geographic location and accessibility, there are few studies related to the culturable microbiota of these amphibians in this region. The objective of this study was to explore the bacterial and fungal biodiversity present on the skin of wild anuran species in the southern Andes of Ecuador and to observe whether geographical barriers in the region could increase the variability of the culturable microbiota through MALDI-TOF mass spectrometry. This analysis revealed the presence of 29 bacterial taxa and 9 fungal taxa, consisting mainly of: Pseudomonas chlororaphis (28%), Acinetobacter iwoffii (14%), Pseudomonas fluorescens (14%), and Hortaea werneckii (26.4%), Fusarium solani (20.5%), Syncephalastrum spp. (20.5%), respectively. Diversity varied across the five sampling locations, with geographic location proving to be a significant driver of diversity. Some of the most abundant bacterial and fungal genera have important associations with skin diseases in wildlife and humans. This work represents a glimpse into the complex biodiversity of bacteria and fungi that inhabit the skin substrate, and further studies will be needed to better understand bacterial and fungal biodiversity with potential implications for establishing conservation strategies, along with the development of necessary animal protection measures.

Keywords: Andes; Anura; Bacteria; Fungi; MALDI-TOF mass spectrometry.

Fig. 1

The left side shows the location of the sampling sites south of the Andes mountain range in the areas corresponding to the provinces of (A) Zamora Chinchipe, (B) Loja, (C) Cañar (D) Azuay, and (E) Morona Santiago. At the bottom, a map of the Republic of Ecuador is shown

Fig. 2

Total abundance of the species observed in the provinces of Zamora Chinchipe, Loja, Cañar, Azuay, and Morona Santiago. (A) Ring diagram illustrating the relative percentage abundance of sampled anuran species, with color codes and percentages next to each taxonomic name. (B) Horizontal bar graph showing the percentage proportion of isolated bacterial species, sorted by decreasing abundance, with the x-axis indicating the total percentage of bacterial abundance. C) Horizontal bar graph presenting the percentage abundance of culturable fungal species, with the x-axis representing the total percentage of fungal abundance. All axes include comparable numerical scales

Fig. 3

General abundance at the species level recorded on the skin of anuran spp. in the locations of (A) Azuay, (B) Morona Santiago, (C) Loja, (D) Zamora Chinchipe and (E) Cañar (Ecuador)

Fig. 4

Relative abundances of bacteria at the phylum level, recorded on the skin of anuran spp. in the locations of Azuay, Morona Santiago, Loja, Cañar and Zamora Chinchipe (Ecuador)

Fig. 5

Relative abundances at the class level, recorded on the skin of anuran species in the locations of Azuay, Morona Santiago, Loja, Cañar and Zamora Chinchipe (Ecuador)

Fig. 6

Alpha diversity metrics (Observed, Shannon, and Simpson) assessed in five provinces south of the Andes in Ecuador (Azuay, Cañar, Loja, Morona Santiago, and Zamora Chinchipe). Richness (Observed), heterogeneity (Shannon), and dominance (Simpson) indices are shown, spatially correlated with sampling locations. Data arrangement allows for comparisons of microbial biodiversity patterns across high Andean zones. (**) indicates significant differences between locations according to the Kroskal-Wallis test for each index. Observed variability values (P = < 0.05)

Fig. 7

Estimated alpha diversity in fungi for the sampling locations (Azuay, Cañar, Loja, Morona Santiago and Zamora Chinchipe). Richness (Observed), heterogeneity (Shannon), and dominance (Simpson) indices are shown, spatially correlated with sampling locations. Data arrangement allows for comparisons of microbial biodiversity patterns across high Andean zones. (**) show significant differences between the three groups according to the Kruskal–Wallis test for each index. Observed variability values (P = < 0.05)

Fig. 8

Principal coordinate analysis (PCoA) based on Bray–Curtis distances of bacterial communities on the skin of anuran spp. divided according to the sampling location (Azuay, Cañar, Loja, Morona Santiago and Zamora Chinchipe)

Fig. 9

Comparative heatmap of the bacterial community in the localities of Azuay, Cañar, Loja, Morona Santiago, and Zamora Chinchipe. Color intensities (light, low dissimilarity—dark, high dissimilarity) reflect variations in the relative abundance of taxa, highlighting clusters through dendrograms

Fig. 10

Principal coordinate analysis (PCoA) based on Bray–Curtis distances of the fungal communities on the skin of anuran spp. divided according to sampling location (Azuay, Cañar, Loja, Morona Santiago and Zamora Chinchipe)

Fig. 11

The comparative Bray–Curtis dissimilarity matrix (Heatmap) illustrates the variation in fungal composition among localities (Azuay, Cañar, Loja, Morona Santiago, and Zamora Chinchipe). The color gradient, from light (low dissimilarity) to dark (high dissimilarity), reflects differences in the abundance and presence of taxa