Investigating the Effects of Fungal Community Structure and Interactions on Aspergillus fumigatus From Kākāpō (Strigops habroptilus) Nest Soils
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Kanis, Amber
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Perrott, John
Stephen, Archer
Petterson, Megan
Lacap-Bugler, Donnabella
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Auckland University of Technology
Abstract
New Zealand’s rare and endemic parrot species, kākāpō (Strigops habroptilus), have suffered aspergillosis outbreaks during their last two breeding seasons (2019 and 2022). The fungal causative agent, Aspergillus fumigatus, typically infects the airways of birds and mammals that are immunosuppressed or exposed to high spore loads. However, monitoring by the Department of Conservation found that A. fumigatus was almost undetected in 2019 nest soils, even in those linked to infected individuals. This prompted an investigation into other ecological drivers of disease proliferation in kākāpō. As microorganisms can co-infect, suppress host immunity, or alter metabolite production through competition, this thesis investigated how A. fumigatus may interact with other soil fungi within kākāpō nests and whether such interactions may help explain disease outcomes observed in kākāpō during recent aspergillosis outbreaks.
Aspergillus species and fungal communities within kākāpō nest soils were investigated using culture-based methods (viable counts), DNA community analysis (ITS amplicon sequencing), and experimental co-cultivation assays. Kākāpō nest soils were collected from two breeding islands, Whenua Hou (Codfish Island) and Pukenui (Anchor Island), across three nest microhabitats (cavity, entrance, and two metres away) during and after the 2019 and 2022 breeding seasons. Samples included soils from both aspergillosis-affected and unaffected nests, allowing comparisons between nests linked to infection and nests associated with healthy birds.
Across abundance analyses (viable abundance and DNA relative abundance), A. fumigatus was found at low abundances relative to other Aspergillus species and yeasts, despite being the confirmed disease-causing agent for the kākāpō aspergillosis outbreaks. Yeasts were highly abundant in 2022 nest soils (particularly within cavities and entrances), and their presence was negatively associated with Aspergillus spp. counts across both years, suggesting potential competitive interactions. Statistical modelling showed that nests associated with aspergillosis in 2019 contained higher overall Aspergillus loads, largely driven by A. niger and A. flavus rather than A. fumigatus, implying that infection may arise from complex community interactions rather than a single causal species.
Fungal community analyses revealed that richness and composition was more strongly driven by the nest microhabitat and island, than by disease status/outcome. Fungal richness increased with distance from nesting burrows on both islands, while fungal community composition differed between islands only within their nest microhabitat. This indicates that kākāpō nesting activity strongly effects fungal diversity and composition within nesting burrows. Dominant yeasts such as Apiotrichum, Debaryomyces, and Kazachstania were also prevalent in kākāpō faeces in a previous study, and their relative abundance decreased once chicks fledged and shifted diets, supporting the idea that diet influences the nest mycobiota.
Experimental co-cultivation assays confirmed that many of these nest-associated yeasts can suppress A. fumigatus and A. niger growth and conidiation (sporulation). Most isolates inhibited mycelial expansion and suppressed conidiation, with Meyerozyma guilliermondii showing the strongest inhibitory effect. These interactions may contribute to the low A. fumigatus loads observed in nest soils, though they also raise questions about the dual roles of yeasts as potential biological controls or contributors to disease risk (as opportunistic pathogens or enhancers of A. fumigatus pathogenicity).
Taken together, this thesis demonstrates that aspergillosis risk in kākāpō cannot be explained by A. fumigatus soil abundance alone, and that disease outcomes are likely shaped by complex ecological processes within the nest, including microbial interactions, host behaviour, and diet-driven changes. By integrating cultivation, sequencing, and competition assays, this work provides an ecological perspective on kākāpō nest fungi and delivers management-relevant insights for monitoring soils, dietary effects, and microbial interactions to help mitigate future aspergillosis outbreaks.