Host range of Verticillium dahliae and effect of rotations on overall soil health

Following pathogenicity testing in the glasshouse it was revealed numerous crop species were susceptible hosts to both defoliating and non-defoliating strains of Verticillium, which are the predominant strains causing wilt in Australian cotton.  These alternate host crops include mungbean, black gram, soybean, cowpea, lablab, pigeon pea, butterfly pea, chickpea, wheat, barley, oats, triticale and canary grass.  Like cotton there were differences in the severity of symptoms observed between the two strains of verticillium and between varieties of the one crop where multiple varieties were examined.  Varietal differences were observed in wheat, barley, chickpea, mungbean and lablab.  Crops that were proven to either aid in lowering inoculum levels or are non-hosts, based on field and glasshouse testing, include maize, sorghum, forage sorghum, Japanese millet, and white French millet.  Red panicum, Shirohie and Panorama millets were poor hosts under glasshouse conditions.  Symptomatic hosts supporting infection and being used as rotation crops potentially will aid in maintaining inoculum levels between cotton crops rather than providing a disease break.  Cereal residues, in particular wheat and barley, can support development of microsclerotia and V. dahliae is both seed-borne and transmissible in these crops.  This has potential implications in disease management and using cereals as a rotation crop in verticillium-infested cotton fields.  Both cereal residue and seed could act as reservoirs of further infection.  Despite infection of cereals not being observed under field conditions to date (possibly because of winter temperature), ground truthing being done currently for example by Crown Analytical, to determine inoculum loads before and after cereal and other crops will aid in a greater understanding of the potential risk these crops may pose in aiding inoculum carryover and/or disease spread.  Several plant species identified as hosts from this research should not be overlooked as possible bridging hosts for V. dahliae.

Change in the incidence and severity of cotton diseases

NSW

The annual cotton disease survey in NSW was first commenced in the 1983/84 season. The continuous surveillance program in NSW enabled us to monitor the disease prevalence, distribution and dynamics. Wilt diseases caused by Fusarium and Verticillium, and black root rot disease remained a major constraint for cotton production in NSW. With additional detection of a novel lethal wilt disease caused by a novel fungal Eutypella, the need for surveillance remains high. The disease was detected in many valleys in the past three seasons, except for Murrumbidgee and Lachlan. The disease survey program also allowed us for the first time to record a significant yield loss of up to 25% caused by Alternaria leaf spot in a dry land crop in NSW. Alternaria leaf spot has been long considered a minor disease, but this reaffirmed that under favourable conditions, a minor disease could result in a major loss. Similarly, a sporadic and under-studied boll rot also caused lots of yield loss concerns in the past three seasons due to wet weather conditions. 

Qld

At the completion of this project annual disease surveys in Queensland had been conducted consecutively for 20 years. Previously and within this project, the data collected has enabled an understanding of incidence, severity and distribution of those diseases present and insight was gained into emerging disease issues. Importantly, a new wilt disease named Reoccurring wilt was shown to be caused by two novel Eutypella species. The prevalence of this disease across regions was assessed by conducting annual disease surveys. The disease has been confirmed in Theodore, Emerald, St George, Darling Downs and the Border Rivers. In Queensland novel species 1 has been confirmed in Theodore, Moura, St George and Border Rivers, as well as Boggabilla and Mungindi in NSW. Novel species 2 has only been detected in Central Queensland. In Central Queensland, and particularly in the Dawson Callide, high reniform nematode pressure at planting has continued to impact seedling development. The presence of mungbean volunteers when planting back into cotton contributed to poor seedling growth since mungbean is a host of reniform. To date this nematode has not been detected in cotton fields outside of CQ. Fusarium wilt remains a key disease for the Darling Downs as well as fields in St George and Border Rivers region, with impacts felt early and late season due to highly conducive conditions. Verticillium wilt is prevalent in the Border Rivers, and the increase in incidence and impact continues to be of concern.  Areas on the Darling Downs were also significantly impacted by Verticillium wilt. Fields in the Border Rivers, St George and Darling Downs with both Fusarium and Verticillium wilt pathogens poses a significant management challenge. Environmental conditions are the key factors in determining infection rates of boll rots. In this study a low level of boll rots, in general, weas present, particularly when late-season rain was present. The most prevalent type of boll rot in Central Queensland was tight lock, whereas in the other regions of Queensland both boll rot and tight lock tended to occur. Leaf spots associated with several pathogens were detected on the Darling Downs and St George at a high incidence, and in some fields with high severity, occurring throughout the canopy as well as on young leaves. In some fields the complex of leaf spot pathogens was also associated with early senescence and significant leaf drop, hence there was grower concern of the potential impact of leaf spot diseases on yield. Fungi recovered from necrotic lesions included Alternaria alternata, Stemphylium lycopersici, Cercospora sp., Corynespora sp. and Pithomyces chartarum.  S. lycopersici and P. chartarum are not associated with leaf spot of cotton. Preliminary pathogenicity tests suggest that these fungi can initiate leaf spot on cotton leaves, however tests need to be replicated to confirm results. 

Soil microbial and biochemical elements that support and improve disease suppression potential of cotton soils

Surface soils from ongoing multi-year experiments and farmer fields from multiple cotton growing regions with different cropping histories and varying disease incidences were collected and analysed for the composition and abundance of microbial (bacteria and fungi) communities, microbial biomass, its catabolic potential and physico-chemical properties with an objective to determine the role of management practices on the disease suppression potential and overall soil biological health of cotton soils. 

Results from the multi-year field experiments indicate that (i) the inclusion of cover crops increased the catabolic potential, genetic diversity of soil fungal and bacterial community, total microbial biomass of cotton soils, (ii) cover crops and crop rotation with alternate crops caused a significant change in the composition of soil bacterial and fungal communities and (iii) fallow as part of crop rotation generally reduced microbial biomass and the diversity of microbial communities and abundance of soil fungal communities including plant pathogens. However, in spite of increases in microbial diversity not all cover crops, especially some crop mixes, improved suppression potential of soils to the soilborne fungal pathogen V. dahliae. Fungal communities in suppressive cotton soils were characterized by higher diversity and higher connectedness. Results on the high level of organization along with higher diversity in the soil fungal community in the suppressive soils developed due to long-term crop management or rotational crops such as Sorghum and Corn seem to provide the cotton plant with a stable microbial reservoir across varied seasonal environmental conditions. Overall, changes in microbial catabolic and genetic diversity would have contributed to the suppression of the pathogens such as V. dahliae, disease incidence and impact. Despite the observation of lower verticillium wilt pathogen levels after fallow would help in the reduction of disease incidence in the short-term, long-term adoption of such management practices would not benefit in maintaining or improving the overall soil biological health. This is especially important in cotton soils in Australia that seem to support microbial biomass levels that are below the threshold levels (i.e., MB levels <5% of soil organic carbon) and require regular C inputs to maintain biological functions essential for plant health and nutrition. 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. Fallows can also cause a significant decline in the amount of soil microbial biomass (the ‘engine’ for all biological functions), microbial activity and genetic diversity of bacteria and fungi i.e., overall soil biological health, resulting in lower pathogen suppression capacity and weaken the biological buffer to reduce the impact of the soilborne diseases on cotton growth and productivity.

Results from the analysis of farmer field soils in this project 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 confirming previous observations potentially requiring evaluation of management options across contrasting cotton growing regions.

The laboratory-based pathogen suppression potential assay developed for V. dahliae was further standardised and found suitable for soils from across different cotton regions. It provided a quantitative measure of a cotton soils ability to support or inhibit soil-borne fungal pathogens such as V. dahliae and found suitable to evaluate and identify different amendments that can potentially reduce pathogen growth. It presents a valuable tool to evaluate and/or identify potential management options to reduce pathogen growth as one of the measures to reduce disease incidence.

Eutypella – a new pathogen of cotton

This research characterised two novel Eutypella species recovered from diseased cotton and confirmed pathogenicity using Koch’s postulates. This is the first known report of a fungus from the Diatrypaceae family causing disease on cotton.  This new disease is referred to as Reoccurring wilt.

Bioassays using naturally infested field soil suggest that plant stress, such as that caused by drought, promotes infection and disease development. In addition, the disease was often first detected in areas of a field described as ‘poor’, due to soil constraints or other issues. Management that reduces plant stress and supports good growth such as well-formed beds, adequate and timely irrigations, and balanced nutrition, is recommended.

Four cotton cultivars evaluated for resistance to Eutypella under field conditions were all equally susceptible to the disease. However, multiple trials covering different regions to account for the different environmental conditions, pathogen diversity, and soil types, would need to be undertaken to fully understand varietal resistance to this pathogen before recommendations could be made.

It was observed in the field that root infection by the pathogen occurs and hypothesised that dead infected cotton trash is a potential source of inoculum. Removing dead wood from vineyards and tree crop plantations is known to reduce the likelihood of infection by pathogens belonging to the Diatrypaceae family, including Eutypella species. Hence management to reduce the quantity of cotton trash carrying over to the following season is proposed for the management of this disease. Crop rotation with non-hosts rather than back-to-back cotton is also recommended.

Roots from dead cotton plants exhibiting typical symptoms of Reoccurring wilt were analysed to determine their fungal community composition. The genus Eutypa represented by two Operational Taxonomic Unit of Eutypella scoparia were the most abundant fungi accounting for 45 to 99% of all sequences in the roots.  These results show that this pathogen can exclude other fungi from colonising the roots. Given this, the general microbial biological buffering may be weakened and could potentially increase infection by other opportunistic fungi. This raises the question, what impact might this have on the biology in field in the future crop if it is being reduced.