The skin microbiome of humpback whales harbours diverse microbial communities that play a crucial role in host skin protection and environmental interaction. However, studies on cetacean skin microbiomes in the Southern Hemisphere focus on feeding grounds, with limited information on microbiome dynamics at breeding grounds and during migration across contrasting habitats. We characterised the skin microbiome of 46 humpback whales from two seasonal habitats: the Magellan Strait feeding ground and the Ecuadorian coast breeding ground, comparing age, sex, environmental conditions, and seawater. Amplicon sequencing of the 16S rRNA gene revealed no differences in alpha diversity, but habitat-specific compositional shifts were found. Psychrobacter was detected in both regions, with higher abundance in the feeding ground, while Tenacibaculum remained abundant across sites. Additional taxa exhibited habitat-specific patterns, including bacteria associated with thermal sensitivity and ultraviolet radiation-tolerance in the Magellan Strait, and lactic acid bacteria in Ecuador. Skin microbiomes were similar between age classes and sexes, but distinct from seawater. Our findings show that geographic and environmental factors, such as superficial seawater temperature and maximum ultraviolet B radiation, shape the skin microbiome of humpback whales, with certain taxa reflecting migratory behaviour across seasonal habitats.
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