Research question: Can the microbiome of Allium crops be manipulated through agronomic management practices and the incorporation of amendments to improve crop nutrient use efficiency and minimise nutrient loss pathways? Aims: - Determine current Allium agronomic practices to allow us to group farmers into major management categories. - Link agronomic practices with soil properties to understand the impact on the composition of the soil microbiome and its predicted functionality. - Link agronomic practices and soil properties to understand the impact on the colonisation of arbuscular mycorrhizal fungi (AMF) on Allium plant roots. Background: Soil microorganisms are a key component of agricultural systems; however, most are undescribed, and their functional roles are not understood (Bardgett 2005, Fierer 2017). Soil microbes are crucial in nutrient cycling, soil fertility and carbon sequestration and are impacted by abiotic and biotic factors (Fierer, 2017). This research will focus on the role of soil microorganisms in nutrient cycling. Soil microorganisms play an important role in the bioavailability of soil borne nutrients (Jacoby et al., 2017). Bacteria and fungi are usually the dominant microorganisms in soil and recent advances in DNA and RNA sequencing have allowed comprehensive understanding of phylogenetic and taxonomic structure of the soil microbiome. Predicted functionality of the soil microbiome can be estimated using PICRUST2, which is a bioinformatics software (Douglas et al., 2020). There are major gaps in knowledge of the strategies plants use to recruit microbes, and which particular microbes are best partners for improving plant nutrition from organic sources of N, P and S (Jacoby et al., 2017). Methodology: A survey of Allium farmers in south Queensland and northern New South Wales will be conducted to explore current farm agronomic practices. Plant tissue samples to examine AMF colonisation and soil tests for soil properties and the soil microbiome will be collected from farms. DNA extraction and sequencing will be used to determine the structure of the microbiome and bioinformatics software will be used to estimate the predicted functionality. Future experiments will examine microbes crucial to improving nutrient cycling and nutrient use efficiency in allium production systems. Outcomes: There is potential to manipulate the soil microbiome, including AMF, to improve the nutrient use efficiency and productivity of Allium crops. This could potentially improve crop production and reduce the amount of chemical inputs into the cropping system. Thus, improving the long-term sustainability of Allium production. References: Bardgett, R. D. 2005. The biology of soil : a community and ecosystem approach, New York, Oxford University Press. Douglas, G. M., Maffei, V. J., Zaneveld, J. R., Yurgel, S. N., Brown, J. R., Taylor, C. M., Huttenhower, C. & Langille, M. G. I. 2020. PICRUSt2 for prediction of metagenome functions. Nature Biotechnology, 38, 685-688. Fierer, N. 2017. Embracing the unknown: disentangling the complexities of the soil microbiome. Nature Reviews Microbiology, 15, 579-590. Jacoby, R., Peukert, M., Succurro, A., Koprivova, A. & Kopriva, S. 2017. The Role of Soil Microorganisms in Plant Mineral Nutri

Funding: Westpac Future Leaders Scholar RTP Scholarship

Project members

Jessie Harper

PHD candidate
School of Agriculture and Food Science