Independent Consultant: Microbial communities associated with Pasture Dieback in Queensland 2016-2017
Meat and Livestock Australia
Queensland University of Technology
Project managers: Greg Palmer, Prof Carrie Hauxwell
Research team: Andrew Dickson, Ray Morgan
What is pasture dieback?
"Pasture dieback is a condition which causes the death of sown and native pastures by affecting plant health and function, reducing the productivity of affected properties. It has been observed in a range of soil types and plant species across Queensland and northern NSW."
The condition occurs episodically, with the current outbreak first identified in early 2015 and spreading across eastern Queensland in subsequent years. In early 2020, pasture dieback was also confirmed in northern NSW." - MLA
Read more here
Project Summary
I approached MLA in 2016 to see if my previous experience with dieback might be useful for determining what is causing this syndrome in pastures across Queensland. Having previously done biological consulting I had some experience in setting up this small project. My experience extended to a talent for being able to explain complex scientific protocols and concepts to collaborators with a variety of backgrounds, including cattle breeders, corporate executives and council members
I proposed conducting a multiplex microbial sequencing analysis of the microbiome associated with healthy and dieback-affected pasture species. This was based on the final chapter of my PhD thesis wherein I describe a potential workflow for diagnosing dieback in plants
This would investigate the importance of beneficial endophytes (microbes living in plants) and also focus on pathogens that may exist in pasture, or that are introduced by insects like mealybugs
We used next-generation Illumina MiSeq sequencing at QUT's CARF (one of only a few such platforms in Australia available for commercial use), to sequence specific genes that target the fungi and bacteria living in healthy pasture grass and soil, and compared these species to those living in dieback-affected grass. We also sequenced genes from a group of fungi-like organisms called Oomycetes which are renowned for causing dieback in other plants, but have not yet been found to associate with grasses
The raw data produced by the MiSeq platform (in the form of millions of DNA bases) were put through a data analysis pipeline which assigned the identities of the sequenced microorganisms by comparing each DNA sequence with the publicly available genetic database, GenBank. The data analysis pipeline also converted the raw sequence data to relative abundance data.
Knowing which species are found in dieback-affected grass and how prevalent they are will help to identify the species associated with dieback-occurrence. The results will show what pathogens are most likely involved, whether there may be “protective” or “beneficial” microorganisms protecting the healthy grass. These could be the focus of management options
At this stage, the causal agent of pasture dieback is pointing to a tiny soil-dwelling mealy bug (Heliococcus sp.) as the likely cause. The data from the sequencing was added to all other analyses to try to work out correlations with dieback occurrence (publications pending) and what a management options are available.