Curious Discovery: A Quarantine Plant Pathogen Infection in Australia’s Most Endangered Western Ground Parrot/Kyloring
Posted on September 5, 2023 by Dr Subir Sarker
Dr Subir Sarker takes us behind the scenes of their latest publication, 'A discovery down under: decoding the draft genome sequence of Pantoea stewartii from Australia’s Critically Endangered western ground parrot/kyloring (Pezoporus flaviventris' published in Microbial Genomics.
I am Dr Subir Sarker, a Senior Lecturer in Microbiology within the College of Public Health, Medical and Veterinary Sciences at James Cook University in Townsville, Australia.
I wish to draw attention to Pantoea stewartii, a Gram-negative bacterium that plays a pivotal role in the development of Stewart's vascular wilt and leaf blight in maize. While this disease holds substantial implications for global crop yield losses, affecting crops ranging from sweet corn and jackfruit to rice and sudangrass, it’s important to note that there have been no reported cases of this disease affecting animals. The severity of this matter underscores the necessity for a comprehensive evaluation.
The European Food Safety Authority Plant Health Panel recently conducted a comprehensive risk evaluation concerning the potential entry of P. stewartii into maize populations. Their conclusion underscores the urgency, as the pathogen fulfils the criteria warranting consideration as a Union quarantine pest.
It is worth noting that more than 60 countries have implemented stringent quarantine measures on maize seeds to thwart the infiltration of P. stewartii. Several examples highlight the global scope of this concern: European and Mediterranean Plant Protection Organisation has recognised the pathogen as a quarantine pest since 1975, followed by Brazil, China, Israel, New Zealand, Russia, South Africa and Turkey.
Our comprehension of how bacterial pathogens induce diseases is in a constant state of evolution. Currently, we have gained substantial insights indicating that numerous bacterial infections in both plants and animals are linked with larger 'host' organisms. This revelation has led to the recognition that many diseases, previously attributed to a single primary host, stem from intricate interactions between multiple taxa and the host organism. In reality, the diversity and roles of these organisms associated with the host are incredibly varied and remain only partially understood. Even in cases where a primary agent can be pinpointed, its impact is frequently influenced by other symbiotic organisms.
This study centres around identifying potential pathogens associated with a perplexing situation involving an endangered Western Ground Parrot (WGP) located in Western Australia. It’s crucial to emphasise that the WGP population is already under multiple threats in its natural habitat, including challenges such as habitat loss, predation and the impacts of a small population (~150 of these birds left in their natural habitat). Given these circumstances, the conservation of the WGP population heavily relies on supplementation through a managed captive translocation program. Consequently, diligent health monitoring and assessment of WGPs are of paramount importance before their release into the wild. In this context, the WGP in question had been in quarantine for an extended period and underwent testing, yielding negative results for significant pathogens like beak and feather disease virus (a pathogen of biosecurity concern that is particularly abundant in psittacine birds), chlamydia, polyoma virus, psittacine herpesvirus as well as parasites as of May 2021. To effectively address this case, Sarker’s laboratory proposes the utilisation of a metagenomic approach using a high-through next-generation sequencing (NGS) technology. This innovative technique, relatively new in its application, enables the comprehensive detection and characterisation of entire microbiomes, encompassing both bacteria and viruses.
Dr Rhys White is a skilled computational biologist in the Institute of Environmental Science and Research, Wellington, New Zealand who focuses on using genomics to investigate pathogenic microorganisms. Dr White and his team analysed the NGS data generated in Sarker’s laboratory. We were pleasantly surprised with an unexpected and significant discovery: the presence of P. stewartii in the critically endangered Western Ground Parrot in Australia. This finding marks a groundbreaking milestone, as it represents the inaugural reported instance of a P. stewartii genome originating from an avian source and the first reported P. stewartii genome within Australia. Employing whole-genome sequencing and phylogenomic analysis of this novel strain of P. stewartii has illuminated fresh insights into the genetic diversity and potential avenues for transmission beyond the realms of insects and plants, where P. stewartii has traditionally been the focal point of study. As the cost of sequencing continues to drop, and more high-throughput sequencing instruments are being installed, the approach we’ve described is becoming increasingly feasible, time-sensitive and a routine practice.
Ensuring the well-being of these exceptional birds carries significant importance, not solely for their individual welfare but also for the wider ecosystem they inhabit. We are confident that this study presents a potential avenue for advancing our understanding of the challenges confronting the WGP population, thereby making a meaningful contribution to the ongoing conservation endeavours. Crucially, by adopting this approach, we aim to illuminate the enigmatic circumstances surrounding these birds. Simultaneously, we endeavour to gain insights into potential pathogens that impact not only these creatures but also extend to our ecosystems, plant life and even human health. In essence, this observation underscores the critical relevance, particularly in relation to the biosecurity risks associated with P. stewartia in Australia, demanding urgent investigation.