Dante L. Adorada

Ustiloxins are toxic cyclic peptides produced by the rice false smut fungus Ustilaginoidea virens . False smut disease turns rice grains into yellow‐orange spores later turned into greenish‐black smut balls, significantly reducing yield and grain quality. Due to their hydrophilic nature ustiloxins leach from spore balls and contaminate paddy soil, water, and rice products. They block eukaryotic cell division by binding tubulin and inhibit microtubule polymerization. This review provides information on advances in ustiloxin biology and control. It summarizes ribosomally synthesized and post‐translationally modified peptides (RiPPs) biosynthesis and recent insights into pathway genes, regulatory networks including target of rapamycin (TOR) signaling, and comparative fungal genomics. Environmental occurrence is reviewed with emphasis on persistence in soil, water and translocation into rice grains. Ecotoxicological evidence is consolidated, spanning phytotoxicity, effects on beneficial microbes, aquatic organisms, and mammalian toxicity supported by in vivo and mechanistic studies. Progress in detection is outlined with improved LC–MS/MS, immunoassays, and emerging biosensors for field diagnostics. Management strategies are evaluated, including resistant cultivars, disease forecasting, fungicidal and biological controls, and post‐harvest detoxification via enzymatic and physical approaches. A dedicated risk assessment discusses human dietary exposure, regulatory status, and the need for maximum limits. The review concludes by highlighting research priorities such as multi‐omics, spread modeling, and biotechnological interventions, to close key knowledge gaps and enable effective monitoring and mitigation toward an ustiloxin‐free rice agroecosystem.

Charcoal rot, caused by the pathogen Macrophomina, is becoming an increasing challenge in Australia’s northern cropping systems, with few effective management options available. The use of non-indigenous biocontrol agents raises ecological and regulatory concerns, which highlights the need to identify locally adapted microbial antagonists. In this study, indigenous Trichoderma isolates were collected from rhizosphere soils across Queensland and northern New South Wales and characterised using multilocus sequencing (ITS, tef-1α, rpb2) coupled with phylogenetic analysis. Twenty-six isolates were resolved into six species, dominated by T. azevedoi and T. afroharzianum. Dual-culture assays revealed substantial variation in antagonistic capacity, with several isolates achieving >70% inhibition of Macrophomina growth and maintaining consistent performance across pathogen genotypes. Functional screening indicated that enzyme-associated antibiosis was widespread, whereas volatile-mediated inhibition was restricted to a small subset of isolates. These findings demonstrate that biocontrol potential in indigenous Trichoderma populations is highly strain-dependent rather than species-driven. By integrating multilocus identification with functional screening, this study provides a practical framework for selecting locally adapted biocontrol candidates. This work establishes a foundation for developing region-specific biological control strategies and supports a shift toward targeted, strain-level selection for effective management of charcoal rot.

Aflatoxins are carcinogenic secondary metabolites produced by Aspergillus flavus and Aspergillus parasiticus. These two fungi are ubiquitous in soil and are often found in agricultural fields. Four aflatoxin variants commonly found in infected crops are: AFB₁, AFB₂, AFG₁, and AFG₂. Aspergillus parasiticus can produce all aflatoxin variants, with A. flavus only able to produce the aflatoxin B variants. Production of aflatoxins typically occurs as pre-harvest contamination in the Australian peanut-growing regions of Queensland. This study analysed geographic variations in aflatoxin component variants using the HPLC method for the 2020–2024 season peanuts. Aflatoxin-G was found as most common aflatoxin variant across three of the four peanut-growing regions. This study also evaluated diversity of A. flavus and A. parasiticus across the four peanut-growing regions, using post-harvest soil samples from the 2023–2024 growing season. Aspergillus parasiticus was found to be most prevalent (97% isolates) across the regions, whereas A. flavus was least prevalent (3% isolates) and only found in the Tolga region. The North Burnett had no Aspergillus colonies identified from the soil samples in the current year of collection. The data suggests the aflatoxin G variant is most predominant in Australian peanuts and also that there is large variation between the growing regions for prevalence of Aspergillus species.

Pathogens can evolve rapidly, leading to the emergence of novel strains that can overcome commercially deployed host plant resistance. Understanding the genetic and phenotypic diversity and population dynamics of plant pathogens is crucial to inform breeding programs targeting resistance. Tan spot, otherwise known as bacterial wilt, caused by Curtobacterium flaccumfaciens pv. flaccumfaciens, is an increasingly significant pathogen affecting beans and mungbean worldwide. Since the 1990s, several mungbean cultivars with partial resistance to tan spot have been released in Australia; however, cultivars initially rated as moderately resistant were later rated as moderately susceptible to tan spot. This study investigated the genetic and phenotypic diversity and temporal evolutionary dynamics of C. flaccumfaciens pv. flaccumfaciens in Australian mungbean fields. Whole-genome sequencing of 119 isolates collected from mungbean and other legumes (1986 to 2019) enabled analyses of pathogen evolution in Australia and in a global context. The results revealed that clonal expansion from standing genetic variation, rather than introduction of novel genotypes, has driven the evolution of this pathogen in Australia since the 1980s. Glasshouse trials confirmed the role of a plasmid in the pathogenicity of C. flaccumfaciens pv. flaccumfaciens but found no significant differences in aggressiveness between clonal lineages. Our research provides insights into the genetic and phenotypic diversity of this important plant pathogen and temporal changes in its population structure in Australia and highlights the need for further studies on the competitive fitness of isolates and characterization of private alleles linked to dominant clonal lineages.

The emerging sesame (Sesamum indicum L.) industry in Australia faces potential threats from multiple pre-harvest diseases and pests, which will necessitate an initiative-taking approach for pest management. Here we assess the diseases and pests most likely to impede the development of a viable Australian sesame industry. Drawing on the international literature, we also consider the management approaches most likely to be viable and identify key research gaps necessary for effective and sustainable crop protection. More than sixty-seven plant pathogens have been identified worldwide that cause diseases in sesame, with some being observed to be major in Australia. Part of this review aims to provide an extensive overview of previous research on sesame and its diseases, shedding light on the evolving knowledge within sesame research, emerging trends, and the current state of understanding on the topic as it applies to Australia. Among the hundreds of pests reported to attack sesame internationally, this review identifies fifty-six pest taxa that are established in, or native to, Australia. We rank those most likely to be serious based on overseas damage levels and observations from recent trial plantings in Northern Australia. Chemical control methods have demonstrated efficacy overseas but are associated with concerns over resistance and environmental impact. Extremely limited numbers of pesticides are currently registered for pest or disease control in sesame by the Australian Pesticides and Veterinary Medicines Authority so non-chemical methods will be important. These include botanical, biological, cultural, and physical control approaches. This review underscores the need for continued research and tailored plant protection strategies to optimize sesame.

Terminal drought is the major constraint for chickpea production, leading to yield losses of up to 90% in tropical environments. Understanding the morphological, phenological, and physiological traits underlying drought tolerance is crucial for developing resilient chickpea genotypes. This study elucidates the drought-tolerant traits of eight kabuli chickpea genotypes under a controlled environment using polyvinyl chloride (PVC) lysimeters. Terminal drought was imposed after the flowering stage, and the response was assessed against non-stress (well-watered) treatment. Drought stress significantly impacted gas-exchange parameters, reducing the stomatal conductance (16–35%), chlorophyll content (10–22%), carbon assimilation rate (21–40%) and internal carbon concentration (7–14%). Principal component analysis (PCA) indicated three groups among these eight genotypes. The drought-tolerant group included two genotypes (AVTCPK#6 and AVTCPK#19) with higher water use efficiency (WUE), deep-rooted plants, longer maturity, and seed yield stability under drought stress. In contrast, the drought-susceptible group included two genotypes (AVTCPK#1 and AVTCPK#12) that were early-maturing and low-yielding with poor assimilation rates. The intermediate group included four genotypes (AVTCPK#3, AVTCPK8, AVTCPK#24, and AVTCPK#25) that exhibited medium maturity and medium yield, conferring intermediate tolerance to terminal drought. A significantly strong positive correlation was observed between seed yield and key physiological traits (stomatal conductance (gsw), leaf chlorophyll content (SPAD) and carbon assimilation rate (A_sat)) and morphological traits (plant height, number of pods, and root biomass). Conversely, carbon discrimination (Δ¹³C) and intrinsic WUE (iWUE) showed a strong negative correlation with seed yield, supporting Δ¹³C as a surrogate for WUE and drought tolerance and a trait suitable for the selection of kabuli chickpea genotypes for drought resilience.

Accurate identification and estimation of the population densities of microscopic, soil-dwelling plant-parasitic nematodes (PPNs) are essential, as PPNs cause significant economic losses in agricultural production systems worldwide. This study presents a comprehensive review of emerging techniques used for the identification of PPNs, including morphological identification, molecular diagnostics such as polymerase chain reaction (PCR), high-throughput sequencing, meta barcoding, remote sensing, hyperspectral analysis, and image processing. Classical morphological methods require a microscope and nematode taxonomist to identify species, which is laborious and time-consuming. Alternatively, quantitative polymerase chain reaction (qPCR) has emerged as a reliable and efficient approach for PPN identification and quantification; however, the cost associated with the reagents, instrumentation, and careful optimisation of reaction conditions can be prohibitive. High-throughput sequencing and meta-barcoding are used to study the biodiversity of all tropical groups of nematodes, not just PPNs, and are useful for describing changes in soil ecology. Convolutional neural network (CNN) methods are necessary to automate the detection and counting of PPNs from microscopic images, including complex cases like tangled nematodes. Remote sensing and hyperspectral methods offer non-invasive approaches to estimate nematode infestations and facilitate early diagnosis of plant stress caused by nematodes and rapid management of PPNs. This review provides a valuable resource for researchers, practitioners, and policymakers involved in nematology and plant protection. It highlights the importance of fast, efficient, and robust identification protocols and decision-support tools in mitigating the impact of PPNs on global agriculture and food security.

Chickpea is one of the economically important legume crops adapted for winter season production in tropical climates. This study evaluated the physiological, morphological, and biochemical traits of eight Kabuli chickpea genotypes in an Australian tropical environment. The result revealed significant differences between genotypes for seed emergence, plant height, primary shoots, leaf number, leaf area index, gas-exchange parameters, seed yield, carbon discrimination (Δ¹³C), and natural abundance for nitrogen fixation. Among the tested genotypes, AVTCPK#6 and AVTCPK#19 exhibited late flowering (60–66 days) and late maturity (105–107 days), and had higher leaf photosynthetic rate (A_sat) (28.4–31.2 µmol m⁻² s⁻¹), lower stomatal conductance (gsw) (516–756 mmol m⁻² s⁻¹), were associated with reduced transpiration rate (T) (12.3–14.5 mmol m⁻² s⁻¹), offered greater intrinsic water-use efficiency (iWUE) (2.1–2.3 µmol m⁻² s⁻¹/mmol m⁻² s⁻¹), and contributed a higher seed yield (626–746 g/m²) compared to other genotypes. However, a larger seed test weight (>60 g/100 seed) was observed for AVTCPK#24, AVTCPK#8, and AVTCPK#3. Similarly, a high proportion (45%) of larger seeds (>10–11 mm) was recorded for AVTCPK#24. Furthermore, a higher %Ndfa in AVTCPK#6 (71%) followed by AVTCPK#19 (63%) indicated greater symbiotic nitrogen fixation in high-yielding genotypes. Positive correlation was observed between %Ndfa and seed protein, as well as between seed yield and plant height, primary shoots, leaf count, leaf area index, leaf photosynthesis, stomatal conductance, transpiration rate at pod filling stage, biomass, and harvest index. An inverse correlation between (Δ¹³C) and iWUE, particularly in AVTCPK#6 and AVTCPK#19, indicates greater heat and drought tolerance, required for high-yielding Kabuli chickpea production in northern Australia.

Ascochyta blight (AB) is a major threat to Kabuli-type chickpea production worldwide. This study aimed to identify AB-resistant Kabuli-type chickpea lines through combined phenotypic and genotypic screening. Twenty-six Kabuli-type chickpea lines were phenotyped at the seedling stage using spray inoculation with conidial suspension. Genotyping employed marker-aided selection (MAS) with markers linked to quantitative trait loci (QTL) for AB resistance. The allele-specific marker, CaETR, closely linked to QTLAR1, and the sequence-tagged microsatellite (STMS) markers GAA47, TAA146, and TA194 linked to QTLAR1, QTLAR2, and QTLAR3 were used to assess their utility in distinguishing between resistant and susceptible chickpea lines. The study revealed that none of the lines tested were completely resistant (R) phenotypically. However, some lines, such as AVTCPK#6 and AVTCPK#14, were found to be moderately resistant (MR). Of the two MR lines identified phenotypically, only AVTCPK#6 was found to have bands linked to QTLs for adult plant resistance. The other MR line for AB showed the presence of bands in only one or two of the four markers used. These MR lines can be further utilized in chickpea breeding programs for the development of AB-resistant chickpea cultivars. It is recommended that these results be verified through repeat experiments, using more diverse isolates, and including additional chickpea lines as reference checks for resistance and susceptibility. The allele-specific marker, CaETR, closely linked to QTL_AR1 and sequence-tagged microsatellite (STMS) markers GAA47, TAA146 and TA194 linked to QTL_AR1, QTL_AR2, and QTL_AR3 were used to explore these markers’ utility in discriminating between resistant and susceptible chickpea lines. The study showed that phenotypically, none of the lines tested are completely resistant (R). However, some lines, namely AVTCPK#6 and AVTCPK#14, were found to be moderately resistant (MR). Of the two MR lines identified phenotypically, only AVTCPK#6 was identified to have bands linked to QTLs for adult plant resistance. The other MR line for AB showed the presence of bands in only one or two markers among the four markers used. These MR lines can be exploited further in chickpea breeding programs for the development of AB-resistant chickpea cultivars. It is recommended that these results are verified by repeat experiments, using more as well as diverse isolates alongside additional chickpea lines for resistant and susceptible reference checks.

The cause of peanut kernel shrivel (PKS) syndrome, affecting peanut crops in Australia’s growing regions, is currently unknown. It is estimated that PKS is costing the peanut industry more than AUD 5 M p.a. and is a potential threat to the industry. Previous investigations have ruled out all abiotic factors and most biotic factors as the cause of PKS. This research aimed at investigating the scope, distribution, and cause of the PKS syndrome. The survey showed PKS symptoms to be present in peanut crops in all the growing regions surveyed. Based on our study of culturable microorganisms, there appears to be no clear-cut involvement of plant pathogenic bacteria and fungi; however, Fusarium spp. were revealed as the most prevalent fungi in affected plants. Moreover, the soil metagenomics study revealed Fusarium spp. as the most abundant fungal communities in the soil microbial profile, and they could contribute to the PKS syndrome. The consistent presence observed of the identified Fusarium oxysporum in PKS-affected samples could indicate a role for this pathogen in the syndrome, especially in conjunction with abiotic stressors. The pathogenicity testing of F. oxysporum resulted in very mild PKS symptoms. A separate report suggesting the involvement of phytoplasma in the PKS syndrome raises the possibility of an interplay of biotic factors in the development of this disease. Further investigation is warranted to determine the true cause or causes of this disease.