Robigalia Roundup LXXXVI: The rice pathogen that thrives as the world warms

Hello {{first_name | Robigalia readers}},

If you're an early-career researcher in plant pathology, there's a new network worth knowing about.

The Mediterranean Phytopathological Union (MPU), a regional society of plant pathologists affiliated with the International Society for Plant Pathology, is establishing a dedicated Early-Career Researchers Committee.

The network is open to undergraduate and graduate students, PhD candidates, postdoctoral researchers, and scientists up to 35 years of age. Its focus is professional development, networking, and building connections across the plant pathology community.

Three early representatives are already in place. Fatma Zohra Sennoun and Marah Abu Khmaish are both PhD students working through joint programmes between their respective universities and CIHEAM Bari, the Italian headquarters of an intergovernmental agricultural research organisation with strong ties to Mediterranean food and plant health science. Chiara Aglietti is based at the University of Florence, working within the plant pathology and entomology section of the Faculty of Agriculture.

The network is currently collecting expressions of interest. If you'd like to get involved, or know someone who would, the contact is [email protected].

The launch of the MPU network got me thinking, how connected are to to the global plant pathology community?

Now, onto this week’s edition:

Let’s dive in!

Wheat yellow rust has long been managed through genetic resistance, but the usefulness of many resistance genes has eroded as new, more virulent pathogen races have emerged. Environmental conditions such as cold exposure may offer another layer of protection, and the mechanisms underlying it remain only partially understood.

A paper by Livbjerg et al., published in Plant Pathology, examines the histological basis of cold-induced resistance to yellow rust (Puccinia striiformis f. sp. tritici) in winter wheat.

The researchers vernalised seedlings of three winter wheat varieties (Anja, Elixer and Tonnage) at 5°C for eight weeks, then challenged them with the Warrior race of P. striiformis f. sp. tritici alongside non-vernalised controls at the same developmental stage. Infection was assessed phenotypically at 18 days after inoculation (DAI) using a 0–9 infection type scale.

To investigate underlying mechanisms, the team used fluorescent microscopy with wheat germ agglutinin staining to track fungal development at 2, 4, and 11 DAI; aniline blue staining to quantify callose deposition at 11 and 18 DAI; and trypan blue staining to assess cell death at 2 and 4 DAI.

Vernalisation reduced infection type scores across all three varieties, with Elixer and Tonnage showing the strongest responses. On vernalised second leaves, median infection type scores dropped from 6–7 to 2. Anja remained susceptible throughout, confirming its role as a negative control. At the cellular level, germinated spore counts and leaf colonisation were significantly lower on vernalised plants across all varieties at multiple time points, suggesting resistance operates from the earliest stages of infection.

Critically, neither callose deposition nor hypersensitive cell death appeared to drive this response. Callose levels in vernalised leaves tracked colonisation levels rather than representing an induced defence, and cell death was sporadic with no significant increase following vernalisation.

The authors propose that altered leaf surface morphology, including changes to epidermal roughness and cell wall composition documented in cold-treated cereals, may reduce spore adhesion and penetration rather than triggering classical immune pathways.

The resistance phenotypes observed in Elixer and Tonnage are more consistent with quantitative than qualitative resistance, and the fact that third leaves developed after vernalisation also showed reduced susceptibility suggests the response is systemic and potentially epigenetic in nature.

Toxoflavin has a long and strange history. Isolated in the 1930s during investigations into fatal food poisonings in Indonesia, it was later identified as the primary weapon of Burkholderia glumae, the bacterium behind one of the most damaging diseases in global rice production. The connection between a decades-old toxicological curiosity and the pathogen causing up to 75% yield losses in infected rice fields is a reminder that plant pathology has a habit of circling back.

Burkholderia glumae is a Gram-negative, beta-proteobacterium belonging to the family Burkholderiaceae. First described in Japan in 1956 as the cause of bacterial grain rot and seedling rot in flooded rice, it was initially placed in Pseudomonas before reclassification. Its primary virulence factor, toxoflavin, is a bright yellow phytotoxin whose production is controlled by quorum sensing and generates hydrogen peroxide in plant tissue, causing cell death. Toxoflavin synthesis is temperature-dependent, rising sharply above 30°C and becoming negligible below 25°C. That relationship between heat and pathogenicity sits at the centre of why this disease is becoming harder to ignore.

The primary host is rice (Oryza sativa), though B. glumae has been recovered from tomatoes, peppers, eggplants, sesame and potatoes. On rice, infection is seedborne: the bacterium persists epiphytically through the vegetative stages, then migrates to developing panicles at booting. Infected florets initially show light green to brown discolouration at the base of the glumes, developing a reddish-brown margin as the grain aborts. Severely infected panicles remain upright rather than drooping under grain weight, a field sign that experienced scouts quickly learn to read. Seedling rot presents separately, causing wilting and collapse in young plants emerging from contaminated seed.

Burkholderia glumae is now found across all major rice-growing regions, including Asia, Africa, Central and South America, and the southern United States. Disease pressure correlates strongly with warm, humid conditions at flowering, and modelling suggests a worsening trajectory under climate projections for tropical and subtropical rice systems.

Management remains genuinely difficult. No commercially acceptable levels of resistance exist in current varieties, and chemical options are limited. Copper-based bactericides offer partial suppression, and biocontrol strains, particularly Bacillus velezensis, are under active investigation for their ability to compete with B. glumae in the rhizosphere and reduce endophytic populations. Certified clean seed is the most important preventive tool available. The search for durable host resistance, and for a better understanding of the quorum sensing pathways that regulate toxoflavin production, remains one of the more active frontiers in rice pathology.

This week's plant pathologist knows rice pathology well. Alifia Nur Ayusma's Master's research at Universitas Gadjah Mada spans bacterial disease management in rice and the evaluation of Bacillus-based biocontrol agents in the field.

Keep reading to meet her.

This week, we meet Alifia Nur Ayusma, a plant pathologist completing her Master's degree at Universitas Gadjah Mada in Indonesia, whose path into the discipline began not with a textbook but with a family farm.

Alifia grew up in a household closely connected to horticultural crops, ornamental plants, and the plants her family used in traditional Indonesian medicine. Her parents kept a small farm in their village. Watching them tend it, with patience rather than force, shaped how she thinks about plant disease management. “When we plant crops, our task is not to command them to grow, but to remove the obstacles that interfere with their growth process.” She studied plant protection at Universitas Gadjah Mada, specialising in phytopathology.

Her Master's research has focussed on bacterial plant diseases. Her thesis examines the use of essential oils for the management of bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae, exploring how natural compounds might be incorporated into more environmentally friendly disease management strategies. Alongside this, she contributed to a molecular identification study of Onion Yellow Dwarf Virus (OYDV) in Allium fistulosum and Allium schoenoprasum in Indonesia, broadening her experience across bacterial and viral pathogens and reinforcing her interest in connecting diagnosis with practical management.

As a teaching assistant for the Prokaryotic Plant Pathogens practicum, she worked directly with bacterial isolates and guided students through applied disease identification. Through the department's community service programme, she spent time in rice paddies monitoring disease and agronomy parameters, installing pest management infrastructure, preparing Bacillus-based biocontrol agents, and supporting undergraduate and postgraduate students as they carried out their own field research. Research, in her view, becomes meaningful when it helps address the challenges farmers are actually facing.

You can connect with Alifia on LinkedIn and follow her work as she completes her degree.

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P.S. Why Robigalia? The name originates from the Ancient Roman festival dedicated to crop protection. You can read all about the history here: