The microbiome in threatened species conservation: implications for the conservation of kākāpō and takahē.

Abstract

Continuing reductions in global biodiversity have seen threatened species increasingly brought under intensive management or into captivity. However, such efforts are often impeded by poor animal health and low reproductive success. Factors including habitat degradation and captivity can significantly alter the microbiomes of threatened species, though how these changes affect animal health remains poorly understood. My overarching thesis aim was to explore how microbiome research can inform conservation management of threatened species. Specifically, I used gene-targeted amplicon sequencing to determine how the gut (faecal) microbiotas of two threatened endemic birds of Aotearoa New Zealand vary with numerous factors, including conservation practices. The kākāpō is a flightless, critically endangered parrot under intensive conservation management. I built on previous research to investigate how development of the bacterial and fungal gut biotas in kākāpō chicks is affected by regular management practices and disease. A microbiota survey was then conducted for virtually the entire kākāpō species to assess associations between gut microbiota and host genomic diversity. Finally, for the first time, the bacterial diversity of the takahē gut was documented across eight separate sanctuaries. The takahē is a flightless, herbivorous rail that was considered extinct for 50 years until 1948. Captivity significantly influenced the bacterial gastrointestinal communities of both takahē and kākāpō chicks. Lactobacillus abundance was associated with supplemental feeding, particularly for hand-reared kākāpō chicks. However, neither aspergillosis infection nor removal of faecal material from kākāpō nests affected bacterial or fungal composition of the gut biota in kākāpō chicks. Besides hand-rearing, age had the greatest influence on gut microbiota diversity of kākāpō chicks, characterised by reduced species diversity over time. There were also significant associations between kākāpō gut bacterial diversity and kākāpō genes and functional pathways related to intestinal homeostasis, inflammation, immune response, and metabolism. Finally, bacterial diversity within the takahē gut varied substantially with location, associated with significantly reduced species diversity for captive individuals. This thesis improves our understanding of factors influencing the kākāpō gut microbiota, highlights substantial variation within the takahē gut microbiota, and contributes crucial knowledge relevant to their conservation management and to avian microbiome research more generally.