Amphibian skin microbiota exhibits temporal variation in community structure but stability of predicted Bd-inhibitory function

Abstract

Host-associated microbiomes are increasingly recognized to contribute to host disease resistance; the temporal dynamics of their community structure and function, however, are poorly understood. We investigated the cutaneous bacterial communities of three newt species, Ichthyosaura alpestris, Lissotriton vulgaris and Triturus cristatus, at approximately weekly intervals for 3 months using 16S ribosomal RNA amplicon sequencing. We hypothesized cutaneous microbiota would vary across time, and that such variation would be linked to changes in predicted fungal-inhibitory function. We observed significant temporal variation within the aquatic phase, and also between aquatic and terrestrial phase newts. By keeping T. cristatus in mesocosms, we demonstrated that structural changes occurred similarly across individuals, highlighting the non-stochastic nature of the bacterial community succession. Temporal changes were mainly associated with fluctuations in relative abundance rather than full turnover of bacterial operational taxonomic units (OTUs). Newt skin microbe fluctuations were not correlated with that of pond microbiota; however, a portion of community variation was explained by environmental temperature. Using a database of amphibian skin bacteria that inhibit the pathogen Batrachochytrium dendrobatidis (Bd), we found that the proportion of reads associated with 'potentially' Bd-inhibitory OTUs did not vary temporally for two of three newt species, suggesting that protective function may be maintained despite temporal variation in community structure.

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

“…Studies on the distribution of bacteria and the variability of their function are limited (Kueneman et al, 2014;Becker et al, 2015;Bletz et al, 2017;Jiménez and Sommer, 2017;Kruger, 2019) but are increasingly relevant to the amphibian microbiome as changes in microbial community structure have been hypothesized to result in changes in anti-fungal function. In line with these studies, our results suggest that predicting microbiome function across space and time is difficult due to strain-level differences and functional redundancy across taxa.…”

Probiotic consortia are not uniformly effective against different amphibian chytrid pathogen isolates

“…These data support previous work suggesting B. dendrobatidis inhibition capability is distributed widely across bacterial genera (Antwis et al., ; Becker et al., ; Bletz, Myers, et al, ); several strains demonstrated at least weak inhibition for all 10 Bd GPLs but were spread across multiple genera with no clear pattern. That there is clear functional redundancy among genera in this host‐protective trait suggests it is not prudent to focus on any one genus in the search for beneficial probiotics (Becker et al., ), as highly divergent microbial communities can still possess similar functional traits (e.g., Bletz et al., ; Bletz, Perl, ).…”

Temporal changes in cutaneous bacterial communities of terrestrial‐ and aquatic‐phase newts (Amphibia)

“…Consequently, some of the temporal variation encountered might be explained by individuals temporarily entering terrestrial environments and acquiring different environmental bacteria there, or by us sampling individuals that had transitioned from terrestrial to aquatic adult phase at different points in time. Yet, another study on the related crested newt, T. cristatus , found substantial variation in skin microbiota composition even when monitoring the same aquatic individuals over time (Bletz et al ., ).…”