Surveillance, Diversity and Vegetative Compatibility Groups of Fusarium oxysporum f. sp. vasinfectum Collected in Cotton Fields in Australia (2017 to 2022)

Cotton (Gossypium hirsutum) is a billion-dollar crop in regional New South Wales (NSW) and Queensland, Australia. Fusarium wilt (FW) caused by Fusarium oxysporum f. sp. vasinfectum (Fov) is an economically important disease. Initial disease losses of up to 90% when the disease was first detected resulted in fields being taken out of cotton production. The disease is now well-managed due to the adoption of highly resistant varieties. However, annual disease surveys recently revealed that the disease dynamic has changed in the past few seasons. With relatively mild and wet weather conditions during the 2021/22 growing season, FW was detected in eight surveyed valleys in NSW and Queensland, with the disease incidence as high as 44.5% and 98.5% in individual fields in early and late seasons, respectively. Fov is genetically distinct and evolved from local Fusarium oxysporum strains. Additionally, the pathogen was reported to evolve rapidly under continuous cotton cropping pressure. However, our knowledge of the genetic composition of the prevailing population is limited. Sequences of the translation elongation factor alpha 1 (TEF1) revealed that 94% of Fusarium isolates recovered from FW-infected cotton were clustered together with known Australian Fov and relatively distant related to overseas Fov races. All these isolates, except for nine, were further confirmed positive with a specific marker based on the Secreted in Xylem 6 (SIX6) effector gene. Vegetative compatibility group (VCG) analyses of 166 arbitrarily selected isolates revealed a predominance of VCG01111. There was only one detection of VCG01112 in the Border Rivers valley where it was first described. In this study, the exotic Californian Fov race 4 strain was not detected using a specific marker based on the unique Tfo1 insertion in the phosphate (PHO) gene. This study indicated that the prevalence and abundance of Fov across NSW and Queensland in the past five seasons was probably independent of its genetic diversity

Verticillium wilt - rotation crops

Verticillium wilt continues to be a major disease problem for cotton production in Australia. Disease incidence is related to the soil population of Verticillium dahliae, so management strategies that can lower this population are required. Non-host rotation crops can be beneficial in aiding this reduction compared to continually planting susceptible hosts. A field trial located near North Star in northern NSW investigated the incidence of disease in cotton following a crop of sorghum, corn, cotton or fallow by monitoring flagged plants for external disease symptoms over time. A hot summer resulted in a lack of visible symptoms of Verticillium until a period of cooler, overcast wet weather and reduced temperatures occurred in mid-March. Expression of disease symptoms then became obvious very quickly. When assessed prior to harvest disease incidence was greatest where cotton was planted after cotton, compared to after fallow and lowest disease occurred where cotton followed either one crop of sorghum or corn. Both 2A and 1A strains of the pathogen were confirmed from the field. Additionally, soil plating and DNA quantification will provide further information on the effect different cropping rotations are having on soil populations of V. dahliae

The importance of cotton disease surveys in Queensland for monitoring endemic diseases and detecting new pathogens and pests

The cotton industry in Australia funds biannual disease surveys conducted by plant pathologists. The objective of these surveys is to monitor the distribution and importance of key endemic pests and record the presence or absence of new or exotic diseases. Surveys have been conducted in Queensland since 2002/03, with surveillance undertaken by experienced plant pathologists. Monitoring of endemic diseases indicates the impact of farming practices on disease incidence and severity. The information collected gives direction to cotton disease research. Routine diagnostics has provided early detection of new disease problems which include 1) the identification of Nematospora coryli, a pathogenic yeast associated with seed and internal boll rot; and 2) Rotylenchulus reniformis, a plant-parasitic nematode. This finding established the need for an intensive survey of the Theodore district revealing that reniform was prevalent across the district at populations causing up to 30% yield loss. Surveys have identified an exotic defoliating strain (VCG 1A) and non-defoliating strains of Verticillium dahliae, which cause Verticillium wilt. An intensive study of the diversity of V. dahliae and the impact these strains have on cotton are underway. Results demonstrate the necessity of general multi-pest surveillance systems in broad acre agriculture in providing (1) an ongoing evaluation of current integrated disease management practices and (2) early detection for a suite of exotic pests and previously unknown pests

Reoccurring wilt: The Eutypella story

Reoccurring wilt is a recently described lethal disease of cotton, first detected in Central Queensland in the 2017/18 season. Pathogen identification was established on sequences of the ITS region of rDNA, revealing the presence of two novel Eutypella species. In Qld, the disease has since been detected in St George, Darling Downs, and Border Rivers region. Sequencing of roots and rhizosphere soil from diseased field grown cotton and the adjacent soil, indicated that the pathogen dominated the root microbiome but was not present in the rhizosphere or surrounding soil. Spore traps were strategically placed in-field to determine the presence of Eutypella ascospores. The source of inoculum and transfer of pathogen will be discussed. This study expands current knowledge on epidemiology of Eutypella spp. and provides information for developing management strategies against Reoccurring wilt

Region-based differences in the diversity and abundance of fungal community in cotton soils

Fungi are ubiquitous and account for more than 60% of microbial abundance in Australian soils including those under intensive cotton cropping. Plant associated fungal communities not only assist with crop nutrition but can also function as an important line of defence against fungal pathogens e.g. species-rich communities are more resistant to pathogen invasions. Their many roles in ecosystem processes, both beneficial and deleterious, have been identified but the determinants of their diversity and abundance in cotton soils as influenced by the biographical habitat are poorly understood. Surface 0-10 cm soils from farmer fields, monitoring cotton performance and disease incidence in 5 cotton growing regions in Queensland and New South Wales, collected during 2016 cotton season were analysed for the genetic diversity (ITS region sequencing) and abundance (qPCR) of fungi. Samples were also analysed for microbial catabolic diversity, microbial biomass and soil chemical properties. Briefly, Ascomycota are the most dominant group of fungi in all the soils accounting for 68 to 78% of total fungi followed by Basidiomycota (12 to 19%) and Zygomycota (1-9%). Fungal genera belonging to the Classes Sordariomycetes (43 to 53%), Agaricomycetes (9-21%) and Dothideomycetes (5 to 17%) were the major groups that showed distinct differences between locations. Members of Glomeromycetes fungi (mycorrhizal fungi) accounted for 2.2%), probably due to the P fertilization in cotton crops. Results also indicated significant differences in the abundance & diversity of fungal community, e.g. Shannon diversity index was lower in the soils from St. George and Emerald regions compared to that in the Darling Downs and Namoi region soils. Overall, these results suggest that soil ecological and environmental factors and management-related filtering processes related to substrate quality and availability play a significant role in shaping fungal communities and their functionality in cotton soils

Can reniform nematode (Rotylenchulus reniformis) in Australian cotton be managed by crop rotations?

Reniform nematode is an important pest in cotton production in Central Queensland. No reniform resistant cultivars are commercially available. Rotation to resistant or non-host crops is used overseas to manage this pest. The potential of non-hosts to reduce the population density of reniform nematode was investigated in a replicated strip trial over two seasons on a commercial farm in Theodore, Qld. A sorghum plant with biofumigation properties, grain sorghum, and two corn varieties were investigated. In the second year the effect of previous crop on soil population of reniform post-harvest was determined. In the 2014/15 season the four non-hosts significantly reduced soil nematode populations, with reductions of 98% compared with cotton in the top 15 cm of soil post-harvest. Deep coring showed that high populations of reniform were present at depth after cotton, confirming they survive deep in the soil profile. It is possible that re-colonisation of the planting zone could occur by drawing upon this population reservoir. In the 2015/16 season, pre-plant populations in the non-host plots were significantly lower than the cotton plots. Post-harvest however, reniform populations were extremely high in the top profile for all treatments. Fumig8tor forage sorghum was the only crop that significantly reduced the population in the top 15 cm compared to cotton. Soil populations under Fumig8tor were significantly lower than commercial corn 606. Researchers overseas have shown that a single rotation with a non-host may only suppress nematode populations, with economic thresholds being reached again by the end of the next cotton crop. Two successive rotations with a non-host crop are therefore recommended for improved production sustainability in such circumstances. Data from trial concurs, as large populations were observed after cotton for all treatments hence two years out of cotton is not sufficient to manage this pest

What influences fungal communities in cotton soils

Soilborne diseases such as Fusarium wilt, Black root rot and Verticillium wilt have significant impact on cotton production. Fungi are an important component of soil biota with capacity to affect pathogen inoculum levels and their disease causing potential. Very little is known about the soil fungal community structure and management effects in Australian cotton soils. We analysed surface soils from ongoing field experiments monitoring cotton performance and disease incidence in three cotton growing regions, collected prior to 2013 planting, for the genetic diversity and abundance as influenced by soil type, environment and management practices and link it with disease incidence and suppression. Results from the 28S LSU rRNA sequencing based analysis indicated a total of 370 fungal genera in all the cotton soils and the top 25 genera in abundance accounted for the major portion of total fungal community. There were significant differences in the composition and genetic diversity of soil fungi between the different field sites from the three cotton growing regions. Results for diversity indices showed significantly greater diversity in the long-term crop rotation experiment at Narrabri (F6E) and experiments at Cowan and Goondiwindi compared to the Biofumigation and D1 field experiments at ACRI, Narrabri. Diversity was lowest in the soils under brassica crop rotation in Biofumigation experiment. Overall, the diversity and abundance of soil fungal community varied significantly in the three cotton growing regions indicating soil type and environmental effects. These results suggest that changes in soil fungal community may play a notable role in soilborne disease incidence in cotton