Stubble retention is a key component of conservation agricultural (CA) practices in Australian broad-acre agriculture, providing benefits such as soil moisture conservation, protection from soil erosion, and as a carbon source for soil health. However, the preservation of crop residues supports the build-up and carryover the primary inoculum source for stubble-borne diseases, including crown rot (Fusarium pseudogramineurum, Fp) of wheat. Moreover, the large pathogen population size enhances the probability of evolution to overcome crop genetic resistance and chemical controls. The resultant disease epidemics and yield loss represent a rapidly emerging and increasingly wicked problem for farmers, threatening the sustainability and profitability of CA and requiring the development of novel control approaches. The aim of the project is to culture, characterise and vigorously combine microbes with lignocellulolytic, pathogen suppressive and nitrogen fixing traits to identify potential synergistic interactions that enhance the breakdown of diseased crop residues whilst simultaneously building soil carbon. The combined function of synthetic communities will be assessed in a high throughput assay.
As a first step, we have generated a collection of microbes with specific target traits prior to creating synthetic communities.
To date, culturable bacteria and fungi have been isolated from samples at the start and end (98 d) of degradation experiments conducted under controlled conditions (optimal moisture and temperature) using wheat stubble infected with Fp and soil collected from a continuously cropped commercial field managed under conservation agriculture. Bacteria and fungi cultured on formulated wheat straw and synthetic media were identified using amplicon sequencing (16S and ITS) and functionality characterised for degradation of lignocellulose and antimicrobial activity against Fp.
A total of 220 bacterial strains and 85 fungal isolates were collected, comprising of 54 genera of bacteria and eight genera of fungi, were successfully characterised. Microbial diversity at the start and end (98 d) of degradation experiments was not significantly different but additional genera were cultured at 98 d. Most microbes, including Fp degraded all the major polysaccharides (cellulose, xylan and lignin) but at different rates, suggesting that they specialise in degradation of some compounds. Some microbes in the genera Clonostachys, Chaetomium, Trichoderma and Penicillium had antimicrobial activity against Fp. Overall, a greater diversity of microbes were cultured from the formulated wheat straw media.
Future research will focus on creating synthetic communities and investigating their ability to suppress Fp in wheat stubble, whilst simultaneously degrading stubble in controlled conditions in a high throughput assay.