Skin and gut microbiomes of tadpoles vary differently with host and water environment: a short-term experiment using 16S metabarcoding

Abstract

The host-microbiome community is influenced by several host and environmental factors. In order to disentangle the individual effects of host and environment, we performed a laboratory experiment to assess the effects of the exposure to different water sources on the skin and gut microbiome of two amphibian species (Pelophylax perezi and Bufo spinosus). We observed that the bacterial communities greatly varied with water environment and host identity. Tadpoles of B. spinosus collected from a waterbody with poorer bacterial diversity exhibited a more diverse skin and gut microbiome after exposed to a richer water source. Tadpoles of P. perezi, originally collected from a richer water environment, exhibited less marked alterations in diversity patterns independently of the water source but showed alterations in gut composition. These results highlight that environment alterations, such as the water source, combined with the host effect, impact the microbiome of amphibian species in different ways; the population history (e.g., previous water environment and habitat) of the host species may also influence future alterations on tadpole microbiome.

Figure 1

Graphical representation of the 4-week reciprocal translocation experiment carried out in this study using Pelophylax perezi and Bufo spinosus tadpoles. The experiment design consisted in four experimental groups (2 source waters × 2 host species) and one control group for each source water (aquaria without tadpoles). The figure displays the number of replicas per experimental group (× 1, × 2), the sampling events (Days) and the four types of samples collected at each day – skin (open circle), gut (closed circle), newly collected water from the waterbody (white drop), and water collected from the aquarium (black drop). Different colours represent different water sources: Gafanha (yellow), Lousada (green). Three tadpoles were sampled weekly from each group replicate, where skin swabs and gut were collected. At the sampling days 7, 14 and 21, we partially replaced the water of the aquaria (wave arrow), by mixing freshly-collected water from the waterbody (70%) with the 1-week old water of the respective aquarium (30%), to which tadpoles were exposed in the previous seven days (see Methods for details).

Figure 2

Skin-associated bacterial communities of tadpoles exposed to native and translocated waters sources over time: (a) phylogenetic α-diversity detected in each host species, Bufo spinosus (top) and Pelophylax perezi (bottom); and (b) β-diversity (using unweighted Unifrac distances) detected among tadpoles of each species. Yellow and green colour shades represent the water source (Gafanha and Lousada, respectively), ellipses denote the four experimental groups, and symbols indicate sampling events. P. perezi tadpoles were collected at Gafanha and B. spinosus tadpoles at Lousada, which correspond to their respective native source waters. Values of Linear Hypothesis test (LHT) and Power analysis for each GLMM are indicated within each α-diversity plot.

Figure 3

Gut-associated bacterial communities of tadpoles exposed to native and translocated waters sources over time: (a) phylogenetic α-diversity detected in each host species, Bufo spinosus (top) and Pelophylax perezi (bottom); and (b) β-diversity (using unweighted Unifrac distances) detected among tadpoles of each species. Yellow and green colour shades represent the water source (Gafanha and Lousada, respectively), ellipses denote the four experimental groups, and symbols indicate sampling events. P. perezi tadpoles were collected at Gafanha and B. spinosus tadpoles at Lousada, which correspond to their respective native source waters. Values of Linear Hypothesis test (LHT) and Power analysis for each GLMM are indicated within each α-diversity plot.

Figure 4

Abundance of the 10 most prevalent bacterial Phyla in the skin and gut communities of (a) Bufo spinosus and (b) Pelophylax perezi in comparison with those found in the water where tadpoles were reared at each sampling event (Day).

Figure 5

Abundance of the 10 most prevalent bacterial families in the skin and gut communities of (a) Bufo spinosus and (b) Pelophylax perezi in comparison with those found in the water where tadpoles were reared at each sampling event (Day).