Final Report Executive Summary

The sustainability of crop production is a key issue for agricultural systems. Maintaining soil

biodiversity is important for promoting soil health and sustainable crop production. The root zone

is rich with microorganisms and nutrients. Soil type and agricultural management practices have

great influence on soil biodiversity. Mixed vegetation contributes to an increase in soil

biodiversity, while intense mono-cropping supports the growth of only a subset of soil microbes and

suggested to be causing a decrease in biodiversity. Furthermore, increased use of fertilisers and

pesticides might compromise both the activity and survival of certain microbes in the soil. The

first aim of this study was to test cotton-growing soils in Australia that are under different

management strategies for the abundance of microbes involved in nitrogen fixation and

denitrification. It has been achieved using the quantitative PCR technique – extracting DNA from

soils and measuring the presence of nitrogen fixation genes (nifH) and denitrification genes (nirK,

nirS and nosZ). Soils that were relatively poor or rich in nitrogen cycling genes were identified.

It has been noted that soils richer in nitrogen cyclers had also a more intense and diverse carbon

utilization patters, indicating larger microbial community with higher biodiversity. Soil N content

did not vary much under the different management strategies, but higher soil organic carbon was

associated with increased functional capacity. Possible factors influencing the nitrogen cycler

community in the tested soils that should be further investigated are the use of organic

amendments, soil enhancers and rotation with other crops as well as the intensity of nitrogen

fertilisation.

Every soil has potential to promote plant growth, with the most important players being the soil

microbial communities. Plant growth promoting microbes contribute to biofertilization, biocontrol,

and phytostimulation. Cotton seedling-disease complexes reduce crop establishment and lead to yield

loss by causing stunted growth and, in severe cases, plant mortality. The period from seed

germination to the establishment of cotton seedling is a critical stage in plant development. The

seedling at this stage, lasting up until the development of two to four leaves, is particularly

susceptible to soil-borne diseases. Improved plant nutrition and use of plant growth promoting

microbes as inoculants could sustainably increase the success of crop establishment and reduce the

impact of soil-borne diseases in cotton growing systems. The second aim of this project was to

isolate indigenous plant growth promoting microbes from Australian cotton-growing soils with the

aim of developing successful isolates into inoculants for local soils. Methods for direct and rapid

isolation of pathogen-suppressive bacteria and fungi were developed in this project and used in an

related project for further isolation of a collection of microbes, suppressing black root rot

caused by Thielaviopsis basicola and pathogens of other seedling diseases such as Rhizoctonia and

Verticillium wilts. The collection is ready for testing under field conditions. Selecting for

indigenous beneficial microbes increase the chances of survival of the re- introduced microbes in

the soil. Other plant-growth-promoting microbes of interest were those that influence water

retention and soil aggregation, secrete plant growth hormones, mediate stress response, solubilise

phosphate or suppress pathogen growth. Methods for the isolation of such beneficial microbes were

optimised for cotton-growing soils and then fine- tuned and used in a related project for producing

a collection of beneficial bacteria is ready for testing under field conditions.

In recent years soil scientists have made enormous progress toward understanding soil organisms and

their roles in ecosystems. Nonetheless, much remains to be discovered to allow the development of

practices that will promote the sustainable use of soils. Understanding what causes changes in the

belowground biodiversity and how diversity is linked to soil function, as well as how it influences

crops, would contribute to sustainable

agriculture and restoration of ecosystems.