Developing a database of bio-markers for compost quality control to maximise mushroom production yield (MU17006)
What was it all about?
This project explored the role of microbiology in mushroom composting, creating a large-scale database of microbial biomarkers to better understand their influence on mushroom yield and quality. While the study identified promising bacterial candidates, variations in composting processes and market demands made it challenging to establish universal biomarkers for the Australian mushroom industry.
Challenge
Mushroom growers rely on high-quality compost for optimal yield and crop consistency, yet compost quality assessment methods have remained largely unchanged for four decades. With recent discoveries highlighting the importance of microbiology in composting, there was a need to better understand microbial dynamics.
However, identifying reliable microbial biomarkers proved challenging due to variations in composting techniques across different facilities, as well as external factors such as market-driven harvesting practices. Additionally, many of the bacteria identified were previously unknown or poorly characterised, making it difficult to use them as consistent indicators for improving crop management on an industry-wide scale.
Response
To address these challenges, researchers conducted a comprehensive sampling program across four Australian states, analysing microbial populations in 425 compost samples from 113 mushroom compost crops. Advanced DNA sequencing techniques were used to track bacterial and fungal succession, linking microbial diversity to compost quality and mushroom yield. The study revealed that bacterial communities at the end of Phase I composting were most strongly correlated with yield and quality, with Thermus emerging as a promising biomarker. While no universal biomarkers could be identified, the project established an extensive database of over 60 million DNA sequences, providing a foundation for future research.
Benefit
This research enhances the Australian mushroom industry’s understanding of compost microbiology, paving the way for improved compost management practices. The extensive microbial database created through this project offers a valuable resource for ongoing research, potentially leading to refined composting techniques that optimise yield and quality.
Although universal biomarkers were not established, the identification of microbial trends at key composting stages provides insights that can help individual composters refine their processes. Long-term, this research could contribute to more consistent crop production, better resource efficiency, and the potential for microbial-based compost quality assessments, benefiting growers and the wider industry.
The feasibility of the project was confirmed over the past six months, using a preliminary survey of three successive compost crops from multiple Australian composting facilities. The major sampling program (26 successive crops obtained from composters in four Australian states) commenced in October 2022, taking samples from four timepoints at every second compost crop. So far 86 samples have been received and processed (mixing, sub sampling, drying, grinding), making up 16 per cent of the total samples for the project. On site sampling by composters has been fairly reliable, and only four samples were not collected for operational reasons. This suggests that the overall database will be able to achieve the anticipated data resolution. DNA purification from the received samples is ongoing, and generation of microbial diversity data will commence once 50% per cent of the total samples have been processed. Work is ongoing to obtain mushroom crop yield and quality data from growers for the composts that have already been sampled.
The feasibility of the project was tested in a testing program using samples collected from three successive crops at four independent mushroom composting facilities across New South Wales, Victoria and South Australia.
Chemical compost quality markers in these samples (pH, moisture, total C and N, soluble C and N, microbial biomass, humification index, nitrification index) were compared with microbial diversity at four composting timepoints. Close chemical and biological reproducibility between successive crops at individual yards was confirmed.
There was more overall variation observed between yards, presumably due to differing feedstocks at widely different locations and differing process parameters used by individual computers, especially during Phase 1. Both biological and physicochemical variation was highest at bunker fill, but much less by the end of phase 2, especially for the microbial markers tested.
The results confirm the feasibility of developing biological indicators as a predictor of crop yield/quality, and a 12-month sampling effort has commenced to provide the depth of data needed to support this.
Since project commencement, progress has been severely impacted by COVID-19 travel restrictions, leading to a temporary pause in research activites.
Restarting in January 2021, the team focused on developing effective and reproducible compost sampling strategies.
The initial phase worked to assess changes in microbial diversity and other compost quality parameters in three successive compost crops from yards in three different States. With sampling almost complete, the analytical methods required for analysis have been optimised.
The results from this study are now being used to prepare methods for a much larger one-year study.
This project is a strategic levy investment in the Hort Innovation Mushroom Fund