Weeds and crop stubble as a pathogen ‘host’ or reservoir. What species are involved with what crop impact ‐ implications for management

Author: Sue Thompson (University of Southern Queensland, PhD candidate, University of Qld), Stephen Neate (University of Southern Queensland), Yu Pei Tan and Roger Shivas (Ecosciences Precinct Herbarium, DAF Qld) and Elizabeth Aitken (University of Qld) | Date: 01 Mar 2016

Take home message

1. Green and Brown Bridges are aiding survival of some pathogens.

2. Dead weeds as well as crop stubble and live crop and weed alternative hosts can provide an inoculum reservoir for pathogens.

3. Diaporthe/Phomopsis species can have multiple hosts and more than one species can infect a single host.

4. Familiarisation with the pathogens in each crop of the rotation and their means of survival, plus a whole of farming system overview is essential to minimise build-up of pathogens.

A study initially investigating the pathogen(s) responsible for damaging lesions on sunflower has revealed an unexpected twist which highlights not only the role of live plants as alternative hosts but also dead weeds left in and around zero and low till cropping systems.

Diaporthe/Phomopsis species are known to cause serious stem cankers on sunflower and soybean, pod and stem blight in soybeans, cankers on many other crops such as grapes, roses and lupins in Australia and overseas, plus a range of other diseases on a wide variety of plants. A serious outbreak of stem canker on sunflower on the Liverpool Plains in 2010 was the catalyst for investigations to quantify the diversity of Diaporthe species initially on sunflower but then on other crops, to gain an understanding of the host range of these species and to study different modes of survival in northern farming systems.

To date, eleven new Diaporthe species have been described from this study including the highly virulent D. gulyae (Persoonia Journal Thompson et al. 2011, Thompson et al. 2015). Glasshouse inoculations revealed that D. gulyae was the most virulent species on sunflower, and highly virulent on soybean, chickpea, safflower, lupin and a range of other potential crop hosts.

Since the commencement of this study, 1700+ isolates of Diaporthe from both living plants and dead stubble of crops and common weeds have been collected, purified, stored, and most have been identified using both morphological and molecular techniques. As well as the eleven newly described species, another 10+ will be formally described in the future. In Australia, to date 13 Diaporthe described or new species have now been isolated from sunflower stem cankers, and 11 species associated with live soybean plants. Diaporthe helianthi, a highly damaging species on sunflower in the United States and Europe, has not been found in Australia.

From a management perspective, identifying alternative hosts and the pathogenicity of these new and known Diaporthe species for each host is of importance. Using a combination of isolations from field grown plants and crop residues from infection trials at Gatton, field crop and weed plants, crop and weed residues and artificial inoculations in glasshouses and growth cabinets, it has been revealed that all of these new species have a range of crop hosts (Table 1).

Table 1. Some examples of moderately- and highly-virulent Diaporthe species isolated from field grown live (L) and dead (D) plants or stubble and seeds (S) of crops and weeds


Diaporthe species










L, D, S


L, S

L, D




L, D










bathurst burr

L, D

bishop’s weed


bitou bush


cobblers peg




noogoora burr

L, D

saffron thistle










L, D

L, D

D, L



For example,

(i) D. gulyae is highly virulent on sunflower, chickpea, soybean and mungbean, and has been isolated from naturally-infected, field grown plants of soybean, sunflower and mungbean.

(ii) D. kongii is highly virulent on chickpea, sunflower and mungbean, and has been isolated from naturally infected plants of chickpea, sunflower and mungbean.

(iii) D. masirevicii is highly virulent on chickpea, soybean, sunflower, lupin, and mungbean, and has been isolated from field grown plants of all except lupin.

(iv) Multiple Diaporthe species have been isolated from seed (sunflower, soybean, sorghum, lupin, other crops) -– of significance for broadening the distribution of seed borne pathogens.

Diaporthe kongii, D. gulyae and D. masirevicii have been isolated from symptomless, field grown plants of maize suggesting that these species may form an endophytic association with maize plants, which is highly significant from the context of aiding survival on ‘non-host’ crops in the rotation.

The wide host range of many of these Diaporthe species also extends to live and dead plants as well as residues of common weeds in the northern region (Table 1). For example, D. gulyae, the most virulent of all species discovered during this study has been isolated from lesions on live plants of the crops sunflower, soybean, and mungbean as well as the weeds bathurst burr, noogoora burr, saffron thistle and sesbania and cobblers peg, and from dead plants of bathurst burr, bishop’s weed, cobbler’s peg, noogoora burr, thornapple and turnipweed.  Another new species, Diaporthe masirevicii, which has moderate virulence on soybean and sunflower, has also been isolated from living plants of the weeds bitou bush, sesbania and turnip weed.

Other recognised Diaporthe species have also been identified from a range of hosts. The first record of Diaporthe novem in Australia was recorded from a sunflower crop on the Darling Downs. This species has subsequently been found associated with a range of crop and weed hosts including thornapple and turnip weed and is also highly virulent soybean and a range of other potential crop hosts.

These findings are very significant and have important implications for northern farming systems. Firstly, Diaporthe/Phomopsis species have been shown to be capable of being:

(i) pathogens of a range of crop and weed species causing stem lesions (in mungbean, sunflower, soybean and weeds)

(ii) lodging and yield loss in sunflower when conditions are conducive, and early senescence, pod infection and yield loss in soybean

(iii) saprophytes by invading and surviving on dead plant residues of many crops and weeds,

(iv) potential endophytes which invade plants of certain hosts, eg., D. gulyae in maize without displaying symptoms.

Consequently, depending on the Diaporthe species, living volunteer plants of crop hosts and living plants of weeds in paddocks and adjacent areas can act as the “green bridge” between highly susceptible crops, while colonised dead plants and stubble of crop and weed hosts can act as the dead or “brown bridge” between major crops. Almost 30 months after the severe Diaporthe lodging event in sunflower crops on the Liverpool Plains, D. gulyae was isolated from the ‘brown bridge’ of sunflower and noogoora burr stubble lying on the soil surface after zero till farming practices and two cereal crops planted into the sunflower stubble.

Although this study has focussed on the Diaporthe/Phomopsis species, many other known pathogens have also been identified. This indicates that crop and weed residues are also aiding survival of other genera such as the Fusarium spp. (eg.root, leaf and head infection in sorghum), Colletotrichum spp. (eg. leaf, stem and pod infection of soybeans), Sclerotinia spp.(500+ crop and weed hosts), Macrophomina spp. (charcoal rot of sorghum, sunflower, mungbeans and soybeans) and Alternaria spp. (leaf spots multiple crop hosts).

In some cases, species are also surviving in non-damaging infection sites such as small necrotic spots on the ‘green bridges’ of crop plants and weeds. For example, Fusarium andiyazi, one of the sorghum stalk rot pathogens, was identified from a leaf spot on a live plant of the weed vetch on the edge of a cultivation at Moree; D. ambigua (damaging lesions on stone fruit trees overseas and not previously recorded in Australia) was isolated from small lesions on sunflowers at Nobby in Qld, noogoora burr at North Star and thornapple stubble near Caroona in NSW.

This study reveals that Diaporthe/Phomopsis species have wider host ranges than previously thought and suggests it is considered likely that the same will be found for other groups of pathogens such as the Fusarium species which are also opportunistic colonisers of both live and dead plant tissues.

It is apparent that these fungi form a group of pathogens/saprophytes that are potentially capable of surviving on both “brown” and “green” bridges between growing seasons in the northern region and that the role of weed stubble in aiding survival has been largely unrecognised. Since the introduction of zero and minimum tillage systems, crop and weed stubble is commonly found across the various cropping systems of the northern region. An inoculum reservoir can be found in these residues regardless of the presence of the primary crop host.

The impact of strategic tillage on the survival of these groups of pathogens in crop and weed residues under Australian conditions is largely unstudied. Crown rot researchers, (Simpendorfer et al. NSWDPI) have looked at the role of tillage for the Fusarium crown rot pathogen in Australia and multiple tillage investigations have been completed by overseas researchers.

A GRDC funded project has been initiated with the aim of looking more intensively at alternative hosts and survival of the Fusarium species on sorghum as well as early studies on the impact of burial on infected sorghum. (J White, USQ. DAQ00186).

Generally, it is well recognised that the incidence of stubble borne pathogens is increasing in the northern region farming systems – this Diaporthe/Phomopsis case study reveals that infected weed stubble, as well as the more commonly accepted crop stubble left on the soil surface, is providing inoculum reservoirs for significant crop pathogens across northern region farming systems. It also highlights the importance of considering a whole of farming systems approach for the control of pathogens rather than concentrating on the pathogens of each crop individually.

Collaboration between Ms Thompson and the SARDI team led by Dr Alan MacKay has led to the development of primers and probes for six Diaporthe/Phomopsis species which infect a range of crops. When complete, the PreDicta B® type test will allow stubble testing for Diaporthe gulyae, kongii, novem, sojae, masirevicii as well as a biosecurity tool for the exotic D. helianthi. Initial validation tests for D. gulyae and D. kongii in sunflower and soybean stubble will commence in the near future. These probes have the potential to be used for commercial sunflower and soybean production and have the potential to expand into other crops.


The research undertaken as part of this project is made possible by the significant contributions of growers through both trial cooperation and the support of the GRDC which funded this work and to USQ and UQ for their continued support.

Additionally, the authors would like to thank Pacific Seeds (Advanta) for provision of a trial site and upkeep over a number of years – without this site much of this work could not have been successfully undertaken.

We also thank Nuseed and KB Ornamentals, PB Agrifoods, NSWDPI researchers and extension personell and the DAF Hermitage Pulse Team for their ongoing support and generous assistance as well as the many growers and advisors in all regions who have enthusiastically provided samples for analysis and access to sites for inspection.

To the Australian Sunflower Association and Australian Oilseeds Federation – thank-you for your long term moral support and monetary assistance for attendance to disseminate the results of this study at many conferences and meetings, state, national and international, over many years.

Contact details

Sue Thompson
CCH, University of Southern Queensland
West St, Toowoomba Q 4350
Mb:  0477 718 593
Email: sue.thompson@usq.edu.au

Reviewed by: Prof. Stephen Neate, Centre for Crop Health, USQ. Toowoomba. Qld.

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