Molecular Assessment of Soil Microbial Function and Community Response Under Differing Soil Management Practices

Abstract

<p>The cotton production belt in Australia covers vast areas from subtropical to temperate and grassland regions. Land management practices in these regions vary. Cotton producers often grow cotton in rotation with other crops, such as wheat, beans and corn. Soil fertilisation also varies, with a number of growers using organic amendments, such as manure or compost prior to planting, as a supplementary source of nutrients. Soil microorganisms play a central role in many of the processes that enhance nutrient availability to crops and support their health and productivity, either by assisting in nutrient uptake by plants, or by increasing the availability of nutrients in the rhizosphere. Thus, agricultural management strategies targeted to support microbial activity should deliver additional benefits.</p> <p>The objective of this study is to understand the influence of various land management strategies on soil microbial communities and soil microbial function. This information will assist producers to make decisions that can improve soil quality (soil health) and help sustain high crop yields. This thesis examines both the short- and longterm impacts of different management strategies, focusing on the impact of using soil organic amendments (manure and compost) versus use of commercial fertilisers only. To assess the long-term impacts of these management strategies, soil samples were collected from broad-acre cotton fields in four locations for analysis. To assess the short-term impacts of different management strategies glasshouse experiments were carried out with soils being supplemented with different combinations and concentrations of commercial fertilisers and/or organic amendments.</p> <p>A variety of approaches were taken to analyze the composition and function of microbial communities in soils under different management practices. Quantitative-PCR has been used to estimate the abundance of functional genes involved in the nitrogen, methane and sulfur cycles. The metabolic profiles of soil microbial communities were assessed using the Biolog Ecoplate system. Finally, microbial diversity of soils was assessed using next generation sequencing (V3–V4 16S rRNA gene region). Physiochemical properties of soils were also assessed, including amount of soil organic matter, and levels of nutrients including available nitrogen, phosphorous, manganese, potassium, iron, copper, nitrate and ammonium.</p> <p>The results of the functional gene assays showed that soil supplemented with organic amendments had a greater abundance of key genes involved in the nitrogen, methane and sulfur cycles, suggesting that addition of organic material increases the potential for these process to take place in soils. Moreover, metabolic analyses using the Biolog Ecoplate system showed that soils treated with organic amendments were able to utilise a more diverse range of carbon sources than untreated soils. This suggests that the regular use of organic amendments can contribute to increased microbial diversity and improved soil function. The results of next generation sequencing using 16S rRNA showed the phyla Proteobacteria and Bacteroidetes were consistently more abundant in soils supplemented with organic amendments, compared to soil supplemented with commercial fertiliser only. Conversely, the phyla Actinobacteria Gemmatimonadetes, Acidobacteria, Firmicutes and Chloroflexi were more abundant in soils under commercial fertilisation. These results suggest that management practices can have a significant impact on the composition of soil microbial communities, which in turn will impact on soil processes, nutrient availability, and soil productivity. </p> <p>Taken together, the results of this study suggest that supplementing soil with organic amendments (such as manure and compost) can increase microbial diversity and enhance the potential for cycling of key nutrients. Given that soil microbial communities play a key role in soil health and function, it is suggested that the use of organic amendments can contribute to the long-term sustainability of agricultural soils such as those used for production of cotton in Australia.</p>