Metatranscriptomic insights into microbial diversity among avian species on the Chatham Islands, New Zealand

Accelerating biodiversity loss highlights the urgent need to monitor the emergence of pathogens in vulnerable species. We used metatranscriptomics to investigate the infectomes of seven bird species, including the threatened black robin (Petroica traversi), on the Chatham Islands archipelago, New Zealand. These avian populations, residing in a geographically isolated ecosystem, face threats from introduced species, habitat loss, and climate change. Total RNA sequencing was performed on swab samples collected from seven bird species across Mangere Island and Rangatira Island to uncover the diversity of pathogens and shed light on the microbiomes of these island-endemic birds. Phylogenetic analysis unveiled 21 distinct and likely novel avian viruses across 10 viral taxa. Notably, black robins harboured viruses from the Flaviviridae, Herpesviridae, and Picornavirales, while starlings (Sturnus vulgaris) and seabirds (Procellariiformes) carried viruses from an additional six families. We also found evidence of cross-species transmission between native and introduced host species. Furthermore, non-viral microbes revealed microbial genera linked to disease outbreaks in other avian species in New Zealand. Multivariate analysis showed host taxonomy and sampling location to significantly influence microbial compositions. Overall, these findings provide insights into the avian infectomes of Chatham Islands, contributing to the broader field of conservation and enhancing our understanding of disease dynamics in isolated ecosystems.