Management practices in current Australian cotton farming systems, e.g. reduced tillage, crop rotation, residue retention, organic manure application and reduced insecticide use, can change the levels of key soil microbial functions. They need to be optimised to promote soil biological functions to sustain cotton production, improve nutrient use efficiency, reduce soilborne diseases and maintain environmental health. Preliminary results from research at ACRI suggest that management systems can be manipulated to optimise microbial functions to improve N and C cycling processes and improve soil biological health. Diseases such as Fusarium wilt, Black root rot and Verticillium wilt have significant impact on cotton production. Crop rotation, stubble retention and tillage can either reduce the levels of pathogen inoculum or modify pathogen-soil microbe interactions thereby influencing disease. Currently the management of diseases is through the selection of genetically resistant cultivars (where available), agrochemical application and rotation with non-host crops. But even in our current high F-rank cultivars significant losses can occur from Fusarium disease under the right environmental conditions (Stiller W 2012 FUSCOM). Soil fungal community has been shown to have capacity to affect pathogen inoculum levels and their disease causing potential. Examples of enhanced biological disease suppression have been suggested in cotton (suppression of black root rot). Biological mechanisms behind disease suppression in high-input cotton soils are not known and we are unable to extend individual observations to other sites or develop management options that promote biological disease suppression. In the lower carbon cotton soils, composts can provide a source of organic carbon and nutrients for soil biota and increase soil fertility as well as provide other biological and structural benefits. But little is known about the effects of compost addition to cotton soils on soil biological health and fertility. Long-term rotation trials at ACRI and in Qld provided a valuable resource to quantify management effects on key beneficial microbial communities and processes. In collaboration with these projects/experiments this project provided new knowledge on the underlying biological mechanisms that promote soil biological health.