Authors: Geneviève Marchand, Cara McCreary, and Katie Goldenhar

Let’s start with the confusing part… I’m sure many growers have heard of Phomopsis. But how many are familiar with Diaporthe? We’ll just settle this right here and now. The Phomopsis species discussed in this blog post were renamed and now belong to the genus Diaporthe. (We are so grateful for taxonomists, but it’s hard to keep up with name changes sometimes!).

What is Diaporthe?

Diaporthe is a genus of filamentous fungi. The first species was described by Fuckel (1867) and was found on dead branches of alders. This genus contains many species, with the current estimate over 1,000 (Hongsanan et al. 2023). They can wear several hats, as their lifestyles can be:

• saprotrophic (contributing to the decomposition of decaying organic matter)
• endophytic (colonizing the vascular vessels of plants without necessarily causing them harm)
• pathogenic (infecting plant hosts and having a negative impact on plant health) (Gomes et al. 2013)

Many Diaporthe species are economically important pathogens of cultivated crops. For example, on soybean they can cause seed decay and blight. Some Diaporthe species used to be in the genus Phomopsis, and you may come across references to this in historical scientific and extension publications and reports. To make a long story short, the currently accepted name is Diaporthe…

Also, as for many fungal species, the scientific study of relationships between Diaporthe species is rapidly evolving due to advances in genetic sequencing, and this often leads to s pathogens being renamed. This is confusing for growers, extension specialists, and plant pathologists alike!

Diaporthe species of concern for greenhouse crops

Two Diaporthe species have been known for decades as pathogens of greenhouse cucumbers. More detailed description of symptoms and management practices can be found in Menzies & Jarvis (1994), chapter 22 of Diseases and Pests of Vegetable Crops in Canada – a copy can be accessed here.

Black root rot (Diaporthe sclerotioides)

This disease was first described in the Netherlands, in the 1960s (Van Kesteren 1967), with subsequent reports in the United Kingdom (Wiggell and Simpson 1969), Denmark, Norway, France (Ebben & Last 1973), and Canada (Ormrod & Christie 1972), in glasshouses where crops were grown in soil or straw bales amended with organic substrates. Crop symptoms included root rot and wilt. The causal agent was described as Phomopsis sclerotioides, and the initiation of disease, from contaminated soil. Management options explored included soil sterilization using steam and soil treatments with biocontrol agents and fungicides, as well as grafting on resistant rootstock of Cucurbita ficifolia (gourd). In modern greenhouse production, the disease has the potential to occur if nutrient solution or growth media become contaminated with infested soil, and preventative measures (your typical biosecurity and sanitation recommendations) should be taken to avoid this.

Phomopsis black rot of cucurbits (Diaporthe cucurbitae)

This species was first described by Mckeen (1957) as occurring on greenhouse cucumber crops in Ontario, Canada, in the 1950s. Symptoms resembled those of gummy stem blight and were initially attributed to this other fungal disease. (Note that this still seems to be happening today – it looks so similar and we are used to seeing gummy so it makes perfect sense). Microscopic examination of the pathogen’s fruiting bodies was required to determine that this was a new disease and causal agent, and it was initially described as the fungus Phomopsis cucurbitae.

Disease initiation often appeared to result from the infection of aerial plants parts and senescent tissue – tendrils, peduncles, petioles, and suckers, followed by the invasion of vascular tissue by the pathogen, causing plant wilt. Soil inoculation assays resulted in symptoms on cotyledons, hypocotyl and lower stem of young plants, but transmission pathways between crops remained unclear. The author hypothesized that the pathogen may have been seed-borne, but this did not match the presentation in some outbreaks (plants only showing symptoms at maturity and on upper internodes).

To summarize, the roots look healthy (Figure 1), and lesions may appear along the stem often at wound sites or nodes (Figure 2) resulting in wilted cucumber plants.

Figure 1. Healthy cucumber roots. Photo credit: Bri-Anna Jaksic, BioWorks Inc.

Figure 2. Stem lesions cause by Diaporthe sp. Photo credit: Bri-Anna Jaksic, BioWorks Inc.

A follow-up study (Atkinson 1982) showed disease reduction when inoculated soils were treated with thiophanate-methyl or benomyl. There are few official reports of disease caused by this species in modern greenhouse production. Suggestions for management practices include adequate ventilation and climate management to promote rapid drying of plant wounds and limit the development of the pathogen in the host. Splashing of water on hands and tools has been hypothesized to contribute to transmission within a crop, due to the morphology of spore production by the pathogen.   

Complicating matters even further

I’m sure you are thinking the same thing we were… Please tell me there aren’t other possible Diaporthe species that cause disease on greenhouse cucumbers?

A recent report from Ohio documents an outbreak of a disease caused by a potentially novel species of Diaporthe, in a hydroponic cucumber crop in a research greenhouse in 2021 (Moodispaw et al. 2023). This report is preliminary, and it remains unclear whether the causal agent could have been D. cucurbitae (Phomopsis black rot) or is truly a new species. Our understanding of Diaporthe species is rapidly evolving, and there are still limitations in available isolates and genetic sequences for comparison.

Recent advances in the taxonomy of the Diaporthe genus propose separating it into different species complexes, based on sequencing data (Udayanga et al. 2015, Norphanphoun et al. 2022). The known causal species of disease on greenhouse cucumbers (D. sclerotioides and D. cucurbitae) are included in the Diaporthe sojae species complex, which contains several Diaporthe species pathogenic to soybean. One of these (closely related) species is Diaporthe sojae and has been reported as pathogenic to cucurbits (melon; Hongsanan et al. 2023). It remains unclear whether this species, and others infecting soybean, may also be capable of infecting greenhouse cucumbers. But this is a potential concern, given the extent of soybean production in southwestern Ontario, and should be explored further.

Do you suspect Diaporthe in your cukes?

Even though it may not be a new disease per se, it seems to be popping up a bit more often over the last couple of years.

Precise identification of Diaporthe species is challenging and may require microscopic examination, culturing the pathogen, and genetic sequencing. Reach out to your trusted consultants, suppliers, extension specialists and diagnostic labs if you need help with identification and management. More research is needed, given the limited scientific understanding of these fungi and their impact on greenhouse crops.

As for management, in the absence of registered fungicides and details on sources of contamination and spread, we are left with some traditional approaches to managing fungal pathogens:

• SANITATION, SANITATION, SANITATION (it’s all about minimizing sources of inoculum)
• Disinfection of nutrient solutions (even though we don’t know if this is a source of Diaporthe spp., it’s still a good idea!)
• Minimize temperature and relative humidity fluctuations (day and night fluctuations in temperature and free moisture on the plants are ideal for many fungal pathogens)
• Good ventilation
• Deleaf early in the day in high-wire cucumbers to allow wounds to dry before night time
• Reduce plant stress/improve plant health

Here’s the BIG ASK: Growers can help advance our understanding and ability to help them by providing crop samples for further research. Please reach out with questions, comments or samples. And stay tuned for more updates!

Contacts

Cara McCreary, Greenhouse Vegetable IPM Specialist, Ontario Ministry of Agriculture, Food and Rural Affairs (OMAFRA): cara.mccreary@ontario.ca

Katie Goldenhar, Pathologist – Horticulture, OMAFRA: katie.goldenhar@ontario.ca

Geneviève Marchand, Research Scientist – Plant Pathology, Agriculture and Agri-Food Canada (AAFC): geneviève.marchand2@agr.gc.ca

References

Atkinson, R. G. (1980). “Control Of Phomopsis Black Rot Of Greenhouse Cucumbers By Soil Drenches.” Canadian Journal of Plant Science 60(2): 747-749.

Ebben, M. H. and F. T. Last (1973). “Cucumber black root rot caused by Phomopsis sclerotioides.” Annals of Applied Biology 73(3): 259-267.

Gomes, R., et al. (2013). “Diaporthe: a genus of endophytic, saprobic and plant pathogenic fungi.” Persoonia-Molecular Phylogeny and Evolution of Fungi 31(1): 1-41.

Hongsanan, S. et al. (2023). “Annotated notes on Diaporthe species.” Mycosphere 14(1): 918-1189.

McKeen, C. D. (1957). “Phomopsis Black Rot of Cucurbits.” Canadian Journal of Botany 35(1): 43-50.

Moodispaw, M., et al. (2023). “First Report of Diaporthe fruit rot and stem canker of hydroponic cucumber caused by Diaporthe sp. in the United States.” Plant Disease, online ahead of print

Norphanphoun, C., et al. (2022). “Diaporthe: Formalizing the species-group concept.” Mycosphere 13(1): 752-819.

Ormrod, D. and W. Christiel (1972). “Vol. 56, No. 1–PLANT DISEASE REPORTER–January 1972 53 Phomopsis Root Rot Of Greenhouse Cucumbers In British Columbia.” The Plant Disease Reporter 56: 53.

Udayanga, D., et al. (2015). “The Diaporthe sojae species complex: Phylogenetic re-assessment of pathogens associated with soybean, cucurbits and other field crops.” Fungal Biology 119(5): 383-407.

Van Kesteren, H. (1967). ““Black root rot” in Cucurbitaceae caused by Phomopsis sclerotioides nov. Spec. Zwartwortelrot bij Cucurbitaceae, veroorzaakt door Phomopsis sclerotioides nov. spec.” Netherlands Journal of Plant Pathology 73(4): 112-116.

Wiggell, P. and C. J. Simpson (1969). “Observations on the Control of Phomopsis Root Rot of Cucumber.” Plant Pathology 18(2): 71-77.