The ephemeral microbiota: Ecological context and environmental variability drive the body surface microbiota composition of Magellanic penguins across subantarctic breeding colonies

Environmental microbes routinely colonize wildlife body surface microbiota. However, animals experience dynamic environmental shifts throughout their daily routine. Yet, the effect of ecological shifts in wildlife body surface microbiota has been poorly explored. Here, we sequenced the hypervariable region V3–V4 of the 16S rRNA gene to characterize the body surface microbiota of wild Magellanic penguins (Spheniscus magellanicus) under two ecological contexts: (1) Penguins walking along the coast and (2) Penguins sheltered underground in their nest, across three subantarctic breeding colonies in the Magellan Strait, Chile. Despite ecological contexts, our results revealed that Moraxellaceae bacteria were the most predominant and abundant taxa associated with penguin body surfaces. Nevertheless, we detected colony-specific core bacteria associated with penguin bodies. The most abundant were: Deinococcus in the Contramaestre colony, Fusobacterium in the Tuckers 1 colony, and Clostridium sensu stricto 1 in the Tuckers 2 colony. Our results give a new perspective on the niche environmental hypothesis for wild seabirds. First, the ecological characteristics of each colony were associated with the microbial communities from the nest soil and the body surface of penguins inside the nests. For example, in the colonies with heterogenous vegetation cover (i.e. the Tuckers Islets), there was a similar microbial composition between the nest soil and the body surface of penguins. In contrast, on the more arid colony (Contramaestre), we detected differences in the microbial communities between the nest soil and the body surface of penguins.