The soil biota consist of a large number and range of micro- and macro-organisms and are the living part of soils. They interact with each other and with plants, directly providing nutrition and other benefits. They regulate their own populations as well as those of incoming microorganisms by biological control mechanisms. Microorganisms are responsible for organic matter decomposition and for the transformations of organically bound nitrogen and minerals to forms that are available to plants. Their physical structure and products contribute significantly to soil structure. Management practices have a significant impact on micro- and macro-organism populations and activities. Stubble retention, an increasing trend in Australia, provides an energy source for growth and activity. Significant increases in the sizes and activities of microbial biomass, including heterotrophic microorganisms, cellulolytic microorganisms, nitrogen-fixing bacteria and nitrifying and denitrifying bacteria have been observed. In addition, increases in protozoa and meso- and macro-fauna have been seen. Stubble retention provides a means of maintaining or increasing organic matter levels in soils. The way in which stubbles are managed may impact further on the activities of the soil biota and may alter the population balance, e.g. bacterial:fungal ratios. In general, no-tillage results in a concentration of microorganisms closer to the soil surface and causes least disruption of soil structure compared with conventionally tilled soils. Some plant diseases increase with stubble retention and with no-tillage, particularly where the next crop is susceptible to the same disease as the previous crop. However, the general increase in microbial populations resulting from stubble retention can exclude pathogens through competitive inhibition and predatory and parasitic activity. Cropping sequences may be used to break disease cycles. Crop rotations that include legumes may provide additional nitrogen and stimulate mineralization processes. Coupled with no-tillage in stubble retention systems is an increased usage of herbicides to control weeds. Continued herbicide use has been shown to significantly depress some groups of microorganisms and some of their activities but, in Australia, little information is available about the effects of herbicides on microbial populations. Although we know that micro- and macro-organisms are vital in maintaining ecosystem function, our knowledge about them is still very limited. New techniques in molecular microbial ecology promise further advances. Much more detailed information about the effects of specific managements on the size and activities of populations is needed. Soils and their processes are extremely complex and, in order to develop appropriate management practices, integration of new and existing information is necessary. This is now being made possible through computer simulation modelling.