Experiments to establish if the use of GM cotton has an impact on the soil microbes that grow in association with the plant roots has shown that there are no differences in number or function when compared to non-GM conventional cotton under field conditions. However, varietal differences were observed in both the field and glasshouse.

Experiments were run in cotton field trials over three seasons at the Australian Cotton Research Institute, near Narrabri, NSW. Rhizosphere soil, the soil that makes contact with the root and is directly influenced by the plant, was routinely sampled. Bacteria and fungi were recovered from this soil using traditional cultural techniques on several selective agar media and found not to differ in numbers between GM and non-GM. Experiments to investigate activity (measured as respiration) and amount of microbes (assessed as biomass) also showed no differences between the GM and non-GM plants under our experimental conditions. A desk top environmental impact assessment of insecticide use, made during the project, also indicated that GM cotton is less environmentally damaging than it’s conventional counterpart and their associated pesticide usage. With these two considerations in mind, GM cotton would appear to be the more sustainable and less environmentally harmful option of cotton production currently available in Australia.

Despite no significant GM to non-GM differences being observed in microbial biomass and activity, cotton varietal differences were noted during the course of the project. Molecular work, using a technique known as DGGE to produce a ‘fingerprint’ of microbial communities, produced evidence that varieties were selecting specific microbial populations in association with their roots. This was apparent from glasshouse trials conducted in Narrabri and Adelaide, on both cotton and non-cotton soils. Lack of consistent differences under field conditions could be attributed to stresses due to environmental factors such as temperature, water availability and plant physiology differences between glasshouse and field.

Varietal differences were again noted when border cells produced by cotton cultivars were assessed. Border cells are produced at root tips and are involved in environmental sensing by the plant. Border cell numbers were much lower in many of the currently available GM and non-GM cotton varieties. Tested varieties produced between 2000 to 12000 border cells per root tip. Reasons for this varietal difference were unclear, but there was evidence that border cell number plays a role in Fusarium resistance.

Assessment of the impact of leaf drop following defoliation indicated that this sudden carbon deposit onto the soil significantly/dramatically increased adjacent soil biota. No consistent varietal differences in the microbial biomass levels were observed, however, the composition of microbial communities associated with decomposing leaf residues was influenced by variety. This work does raise questions regarding the functional significance of this explosion of biota and if management could alter or better utilise this process. Future research to fill this knowledge gap is recommended.

Establishing recommendations for improved farm management and soil conditioning through cotton variety selection is currently not possible. This is because we still know very little about the soil biological environment. Further investigation of the soil biota is warranted to develop tools to predict how soil responds to changes imposed upon it through either crop selection or management. Additionally, over the course of this project we have seen clear evidence that cotton variety choice can have an impact on the soil microbiota. With the yearly release of new varieties the extent and significance of this impact is difficult to gauge. Establishing the extent and nature of these variety differences and their significance for soil microbiota has formed the basis of a new CRDC funded project.