Emmons, C. | bioRxiv Science

bioRxiv2025

Fifteen-year microbiome survey of endangered killer whales (Orcinus orca) reveals declining diversity and population differences

The endangered Southern Resident killer whale (Orcinus orca) (SRKW) population is burdened by multiple anthropogenic stressors with limited non-invasive approaches for health surveillance. The gut microbiome is interconnected with host physiology and can be characterized using remotely collected fecal samples, creating unique opportunities to integrate environmental and individualized host-associated features of health. In this study, we used fecal samples collected over a 15-year period (2005-2019) from 77% of the living, wild SRKW population (56 individuals, 1-17 time points per individual), as well as fecal samples from the conspecific Northern and Alaska Resident killer whale populations, to characterize distal gut microbiota structure and genomic composition. SRKW microbiotas were individualized and distinct from those of the nearby Northern and Alaska Resident populations, both of which exhibit consistently higher fecundity and survivorship. During the study period, SRKW fecal microbiota species richness declined, despite stability over periods of time less than or equal to 1 year. Several potential bacterial pathogens, such as Fusobacterium spp., achieved dominance in the fecal microbiotas of SRKW individuals sampled within 6 months of death. These findings demonstrate the feasibility and value of harnessing non-invasively collected fecal samples and microbiome profiles for longitudinal killer whale health surveillance.

microbiology↗

bioRxiv2024

Widespread parasite infections in living resident killer whales in the Northeast Pacific Ocean

Multiple populations of resident ecotype killer whales (Orcinus orca ater) inhabit the Northeast Pacific, but the southern resident killer whale (SRKW) population is the most at-risk. SRKWs were listed as endangered in the United States in 2005 and have since shown little sign of recovery. Several factors have been identified as key threats to this population, and previously published studies suggest the population may be energetically stressed. Underlying health risks, such as parasitism, may be contributing to this populations failure to recover, but little is known about parasite infections in living individuals from natural killer whale populations. To assess the prevalence of internal parasite infections in Northeastern Pacific killer whales, we examined scat from endangered SRKW (n = 25) compared to two conspecific populations of resident killer whales that are not in decline: northern resident (NRKW, n = 2) and southern Alaska resident killer whales (SARKW, n = 7), and one offshore killer whale (OKW, n = 1). We analyzed 35 fecal samples collected from 27 wild killer whales using both microscopic identification of parasite eggs and genetic detection of parasites through DNA metabarcoding. We used body condition indices derived from concurrent aerial photogrammetry to evaluate whether parasite infection status was associated with individual body condition. We found that most individuals sampled (94%) were positive for Anisakis spp. - a parasitic nematode known to inhabit the intestines of cetaceans. These infections were detected across populations, and were not correlated with body condition, based on limited paired data. These results suggest that Anisakis infection is widespread among resident killer whales of the Northeast Pacific. The widespread detections of Anisakis among the samples examined here emphasizes the need for further work to understand the potential health impacts of parasitic infections on individual killer whales, and potential synergistic effects with other environmental stressors.

ecology↗