Statistical associations identified in historical datasets

A geospatial database was developed and three years of field assessed cotton pathology data and management practices were collected. Multivariate analyses of survey data were performed to test for any effect of previous crop and cotton trash present on early and late season diseases. Further correlation network analyses were performed on the data to identify relationships between diseases and yield and diseases themselves in the whole data set and in each state. 

Key findings include the impact of previous cropping on disease in the subsequent cotton crop. For example, Verticillium wilt was significantly higher following winter cereal crops than cotton. Seed rot was significantly lower following a fallow or winter cereals, boll rot was significantly higher following summer grains, and tight-lock was significantly lower following fallow and winter cereals, than cotton. Tight-lock had the strongest negative relationship with yield in the data set, providing statistical support of anecdotal findings. The amount of cotton trash present in the field did not have any significantly detectable effect on disease in the analyses performed on these data. Given the impact of previous crop on disease incidence, an estimation of crop residues other than cotton may provide insight to how other crops influence disease, such as maintaining inoculum levels through asymptomatic colonisation or providing a suitable carbon source for saprophytic growth. Hence, these findings provide direction for research to investigate cropping rotations that potentially will decrease/increase disease incidence of important diseases of cotton. The groundwork achieved in this project has provided the foundation knowledge and critical directions to improve the collection and storage of data, and to build on the analyses already conducted.

Disease suppression potential of cotton soils from different cotton growing regions

Composition and abundance of microbial communities were analysed for soils collected from different regions with different cropping histories and varying disease incidences. Results from the long-term experiments indicate that (i) the diversity and abundance of soil fungal communities varied significantly by crop management history and (ii) fungal communities in suppressive cotton soils were characterized by higher diversity and higher connectedness. The high level of organization along with higher diversity in the soil fungal community in the suppressive soils would provide the cotton plant with a stable microbial reservoir across varied seasonal environmental conditions. 

Changes in the microbial diversity and activity in the short-term rotation experiment clearly indicated the significant and important contribution of soil microbiome (bacteria and fungi) for the suppression of Verticillium disease in cotton. The influence of rotation crops such as sorghum and corn could be attributed to (i) increased microbial catabolic diversity and activity (ii) higher diversity of bacteria and fungi, (iii) increased abundances of specific groups of microorganisms involved in antibiosis, antifungal (cell-wall degradation) and plant growth promoting capabilities, and (iv) lower pathogen levels. These changes would have contributed to the suppression of the pathogen, disease incidence and impact. Whereas the fallow treatment caused a significant decline in the total microbial activity and catabolic diversity, genetic diversity of bacteria and fungi resulting in lower pathogen suppression capacity. Although the lower pathogen levels would help in the reduction of disease incidence, long-term adoption of such management practices would not benefit in maintaining or improving the overall soil biological health. The traditional continuous cotton system seems to promote the growth of pathogenic fungi such as V. dahliae and result in lower microbial diversity and abundances of beneficial microorganisms.

A laboratory based pathogen suppression potential assay was developed which provides a quantitative measure of a cotton soils ability to support or inhibit soil-borne fungal pathogens such as V. dahliae. 

Results from this study clearly indicate the presence of a genetically diverse fungal community in cotton soils and distinct variation in the community composition and diversity between fields in different cotton regions. Actinobacteria were the most dominant bacteria in cotton soils and bacterial community composition was significantly different in fields from some regions e.g. Darling Downs vs. Lochlan and Namoi vs. Theodore.

Verticillium wilt research

The management of Verticillium wilt requires an integrated approach that ultimately reduces soil inoculum levels with deleterious effects on overall soil biological health.  The field trials conducted in this project have shown that rotation can reduce disease but needs to be longer than one year out of cotton where Verticillium levels are high.  Two years of rotation to either non-hosts (sorghum and corn) or a bare fallow significantly reduced Verticillium levels compared to growing three years of continuous cotton.  One year of rotation (corn, sorghum or fallow) on the other hand was not long enough to significantly lower disease levels.  The assessment of microbial changes in the soil under the different rotations sequences suggest that management of this disease through cropping to other non-host crops that may also promote disease suppressive microorganisms may be a better option than fallow as they reduce disease incidence but also maintain overall soil biological health.  A decline in overall microbial populations in the long term could potentially make soils more conducive to soil borne diseases.

V. dahliae has one of the widest host ranges of any fungal pathogen, including over 400 susceptible crop and weed hosts.  It may cause classic characteristic symptoms but also has the ability to develop asymptomatic, endophytic infections.  The susceptibility of some rotation crops commonly grown in the Australian cotton farming system has been largely unknown to date.  Our studies have shown that grain sorghum is a non-host (previous study) and that faba bean (previous study) and cultivars of chickpea, mungbean, wheat and barley are all susceptible symptomatic hosts with some differential cultivar and strain reactions observed in some of these crops.  While the susceptibility of these crops has not been proven under natural field conditions there is clearly the potential for infection to occur and close monitoring of field plants of these alternative hosts should be carefully monitored and assessed when grown in fields known to have a history of Verticillium. 

To conclude, these analyses of laboratory and field based research, have provided a wealth of knowledge to address systems questions on disease management. Research to understand management strategies that promote microbial diversity, increase specific groups of beneficial microorganisms, and reduce pathogen capability to cause disease, is required.