DNA metabarcoding reveals unexpected predator-prey-microbial dynamics in the southern right whale (Eubalaena australis)

Southern right whale (Eubalaena australis; SRW) populations are recovering from the impacts of commercial whaling, however, recovery has been spatially variable, with strong associations between reproduction and prey availability. The diet of SRWs has not been widely examined, and with SRW foraging shifting away from high-latitude foraging grounds dominated by krill, it is essential to understand their diet at different locations. The gut microbiome is closely linked to diet, and characterising gut bacterial composition can help evaluate long-term changes in prey and ecosystem dynamics. We used DNA metabarcoding to characterise the diet and faecal microbiome of SRWs from three calving/socialising grounds and a low-latitude foraging ground. SRW feeding was more opportunistic than previously documented. Decapoda emerged as a key component of the SRW diet, being consistently detected at higher frequency and relative read abundance than euphausiids and copepods in whales from both calving/socialising and foraging grounds. The expected prey of Calanoida were also prominent in whales from the foraging ground, as were Stomatopoda, Cumacea and Semaeostomeae. A significant correlation between diet composition and faecal bacterial composition was observed, with euphausiids being the strongest predictor of bacterial variation. Our findings provide a new understanding of the breadth and diversity of the diet of SRWs. We also provide a baseline for monitoring diet-gut microbiome interactions. Collectively, these results offer a glimpse into the trophic dynamics of a Southern Ocean predator being impacted by climate-driven changes in zooplankton distribution, with implications for long-term population recovery.