For sustainable cotton production, Australian cotton farming systems need to promote and optimize soil biological functions to by improving nutrient use efficiency, increasing biological nitrogen inputs, reducing disease impacts and maintaining environmental health. Currently cotton farming systems involve management practices such as reduced tillage, crop rotation, residue retention, compost and fertilizer addition and reduced insecticide use all of which can potentially alter key soil microbial functions. This project addressed three key areas of soil microbial community and biological processes with an aim to improve current knowledge and evaluate the impact of management, soil and environmental factors affecting them. They include:

1. Determined the effect of management practices including rotation, stubble retention and organic manure application on microbial communities involved in C and N cycling, free-living (FL) N fixation and carbon turnover.

2. Characterized the genetic diversity of soil fungal communities as influenced by management practices and linked it with disease incidence and suppression.

3. Quantified the effect of compost addition materials on soil biological fertility.

This project utilized on-going field experiments at ACRI and in Queensland which demonstrated significant effects of management practices on N cycling and uptake, disease incidence and crop yields. These studies were completed with targeted glass-house and laboratory incubation experiments. Therefore, new knowledge of key biological processes from long-term experiments can be effectively linked with management systems under field conditions.

Briefly, the advancement of knowledge provided in this project includes:

• In cotton soils, crop rotation and fertilizer management have a significant influence on the microbial community and biological processes involved in N and C cycling processes. Populations of FL N-fixing bacteria were significantly higher in the D1 experiment compared to that in the F6E experiment indicating the effect of stubble management type and timing of fertilizer application. In both the experiments, grain legume rotation crops (e.g. vetch and fababean) significantly improved microbial activity, catabolic diversity and N mineralization potential in surface soils, however the magnitude of effect varied significantly. Microbial activity and microbial biomass levels were lowest in the Continuous Cotton rotation suggesting rotation based management of N availability and fertilizer efficiency is possible.

• Soil type and environment (location) and cropping history have a significant influence on the diversity, genetic composition and fungal community in the surface 0-10 cm cotton soils. A total of 370 genera were found in the 5 cotton experimental sites, however, a few groups (20 families) were dominant. Fungal community composition varied significantly between the cotton growing regions and was also influenced by crop rotation. Lower diversity and abundance of total fungi were associated with higher disease incidence in intensively managed cotton systems e.g. rotations including brassica crops and Continuous Cotton rotation.

• Composts vary in their chemical composition significantly in terms of major nutrients and trace elements and biologically available carbon (BDOC). In a long-term field experiment, four years of compost addition on a Vertosol had no significant effect on microbial and nutrient properties. In controlled environment experiments, addition of composts increased microbial activity for two week only. The magnitude of the effect on biological functions and microbial diversity varied between different composts both in the laboratory and field experiments. Thus long-term effects of repeated compost application would depend upon amount and frequency of application esp. for a change in microbial diversity and plant beneficial functions. Therefore, chemical analysis of the compost material before application is recommended to more fully consider its’ potential benefits. These effects need to be evaluated in different soil types and environments.

Overall, the new knowledge on the dynamics of microbial community and biological processes suggest that some of the key microbial groups and functions in cotton soils are regionally specific and can influenced by management. Thus a designer management may need to be applied to better harness specific biological benefits and is the foundation for building and managing more resilient cotton production systems.