Niloofar Vaghefi

Charcoal rot, caused by Macrophomina phaseolina , is a major constraint to soybean ( Glycine max ) production worldwide, particularly in warm and drought-prone environments. This review synthesizes current knowledge on the biology, epidemiology, diversity, and economic impact of M. phaseolina in soybean and identifies key knowledge gaps relevant to disease management. Our functional data analysis of long-term field data in Australia identified a significant impact of charcoal rot on soybean yield, with both high maximum air temperatures and low rainfalls significantly associated with high levels of charcoal rot in soybean fields. Misconceptions about host range and microsclerotia longevity, combined with contradictory findings from earlier studies, have contributed to a perception that agronomic practices such as crop rotation and cover cropping are ineffective for managing charcoal rot, thus eroding confidence in these approaches. However, inconsistencies in previous research may stem from pathogen misidentification as well as context-dependent interactions between local Macrophomina populations, crop genotypes, and environmental conditions. It is now recognized that management outcomes are influenced by the genetic variability of both the local pathogen populations and locally adapted host genotypes, as well as site-specific factors. M. phaseolina is likely composed of both “generalist” and “specialist” subpopulations with differing levels of aggressiveness and host specialization. Considering these findings, traditional agronomic practices should not be dismissed but re-evaluated under local conditions, using locally adapted pathogen populations and host genotypes.

Citrus is an important fruit crop worldwide and Colletotrichum species are important pathogens of this crop. Colletotrichum species infect a wide range of citrus tissue such as leaves, twigs, flower petals, immature and mature fruit, causing substantial losses in yield, fruit quality, and marketability. This review is a critical assessment of the major Colletotrichum species associated with citrus diseases, their global diversity, distribution, and biosecurity implications. This review also identifies areas in need of further research. Thirty-nine Colletotrichum species have been reported in association with citrus globally. Most Colletotrichum species are plant pathogens, while several are saprobes or exhibit endophytic or latent lifestyles. They also vary in host range, aggressiveness, and environmental adaptation. Several species can infect citrus hosts or tissues beyond those from which they were originally isolated, while some also infect plants from other genera. The nature of infection by Colletotrichum species highlights the need to include non-wound inoculation in bioassays designed to assess the ability of Colletotrichum isolates to penetrate the cuticle and epidermis and cause infection. Accurate identification, pathogenicity testing, and rapid molecular detection are therefore important for disease management, quarantine inspection, and plant biosecurity risk assessment.

Citrus is an important fruit crop worldwide and Colletotrichum species are important pathogens of this crop. Colletotrichum species infect a wide range of citrus tissue such as leaves, twigs, flower petals, immature and mature fruit, causing substantial losses in yield, fruit quality, and marketability. This review is a critical assessment of the major Colletotrichum species associated with citrus diseases, their global diversity, distribution, and biosecurity implications. This review also identifies areas in need of further research. Thirty-nine Colletotrichum species have been reported in association with citrus globally. Most Colletotrichum species are plant pathogens, while several are saprobes or exhibit endophytic or latent lifestyles. They also vary in host range, aggressiveness, and environmental adaptation. Several species can infect citrus hosts or tissues beyond those from which they were originally isolated, while some also infect plants from other genera. The nature of infection by Colletotrichum species highlights the need to include non-wound inoculation in bioassays designed to assess the ability of Colletotrichum isolates to penetrate the cuticle and epidermis and cause infection. Accurate identification, pathogenicity testing, and rapid molecular detection are therefore important for disease management, quarantine inspection, and plant biosecurity risk assessment.

Agrobacterium tumefaciens -mediated transformation (ATMT) has been widely used in filamentous fungi for gene functional studies and for the introduction of fluorescent markers to investigate infection biology. In pyrethrum ( Tanacetum cinerariifolium ), the foliar pathogens Didymella tanaceti and Stagonosporopsis tanaceti cause significant yield losses. However, the infection biology of D. tanaceti remains poorly understood. In this study, ATMT was used to generate fluorescently labelled strains of D. tanaceti and S. tanaceti expressing mNeonGreen and tdTomato, respectively. Transformants were characterised for fluorescence stability, morphology, growth, and pathogenicity. Whole-genome sequencing revealed predominantly single-copy T-DNA insertions, with occasional partial insertions and small genomic rearrangements. Despite variation in fluorescence intensity among D. tanaceti transformants, stable expression of fluorescent proteins was confirmed in both species. Detached leaf assays demonstrated that transformed strains exhibited infection patterns comparable to their respective wild types. In D. tanaceti , germination occurred by 24 hours after inoculation (HAI), followed by hyphal growth and direct epidermal penetration by 72 HAI, leading to mesophyll colonisation. No major differences in infection timing or colonisation patterns were observed between wild type and transformed strains. In S. tanaceti , infection dynamics were consistent with previous descriptions, supporting the suitability of transformed strains for in planta studies. Fluorescently labelled strains of D. tanaceti and S. tanaceti a re valuable tools for investigating infection biology and provide the first visual insights into early infection processes of D. tanaceti in pyrethrum. These findings lay the foundation for future studies incorporating quantitative approaches to better understand pathogen dynamics and interactions.

Fusarium oxysporum Species Complex (FOSC) includes important soil‐borne pathogens of a range of crops worldwide. In Victoria and New South Wales, Australia, FOSC has been identified as the cause of stunting and poor growth in processing tomato fields, resulting in significant yield losses. A total of 40 FOSC isolates were obtained from symptomatic tomato plants, irrigation water samples and culture collections, which were confirmed to be FOSC by multigene phylogenetic analyses based on four genomic loci: β‐tubulin, calmodulin, the second largest subunit of nuclear RNA polymerase II and translation elongation factor 1‐α. There was a high level of genetic diversity among isolates, with multiple phylogenetic lineages detected. Glasshouse bioassays demonstrated that all tested isolates were pathogenic to processing tomato, resulting in significant reductions in plant growth, with above‐ground height reduced by 11%–26% and root dry weight by 44%–83% compared with the control ( p < 0.05). Although aggressiveness varied among isolates, growth reduction occurred irrespective of their phylogenetic placement. Moreover, the shared genetic background of isolates from irrigation water and plant samples highlights the role of irrigation water as a potential source of inoculum in Fusarium epidemics, underscoring its significance for disease management in Australian processing tomato systems.

Australia is the largest producer of Pyrethrum ( Tanacetum cinerariifolium ) globally. Amongst the constraints on production are the fungal pathogens Didymella tanaceti and Stagonosporopsis tanaceti, which pose a significant threat to the industry, causing substantial yield losses. While the infection biology of S. tanaceti is well characterised, knowledge of D. tanaceti and its potential interaction with S. tanaceti on plants remains limited, hindering disease management. We developed fluorescently labelled strains of both pathogens via Agrobacterium tumefaciens -mediated transformation (ATMT). Binary vectors carrying the mNeonGreen or tdTomato fluorescent protein genes were introduced into D. tanaceti and S. tanaceti , respectively, and expression of the fluorescent proteins was confirmed by microscopy. Genome sequencing revealed single-copy T-DNA insertions in all transformants, with minor genomic rearrangements at insertion sites. Detached leaf assays demonstrated that transformed strains retained pathogenicity, producing disease symptoms indistinguishable from those of the wild type. These fluorescently labelled variants enabled detailed visualisation of D. tanaceti infection biology and its interactions with S. tanaceti , including co-infection dynamics. Co-infection assays using fluorescent strains further facilitated simultaneous visualisation and differentiation of both pathogens within host tissues. Importantly, these tools also allowed the first description of the early stages of infection by D. tanaceti in pyrethrum leaves. This study represents the first successful transformation of D. tanaceti and S. tanaceti , providing valuable resources to investigate their infection processes.

Colletotrichum species are important fungal plant pathogens associated with citrus pre- or postharvest disease globally. Seventy-three Colletotrichum isolates were collected from diseased leaves, fruits, and twigs of lime, tangerine, and pomelo in the provinces of Chiang Mai, Nakhon Pathom, and Lampang in Thailand. Colletotrichum siamense, C. gloeosporioides, C. fructicola, C. gigasporum, C. kokhaense sp. nov., C. plurivorum, and C. tropicicola were identified using morphological characters and multigene phylogenetic analysis (combinations of internal transcribed spacer, glyceraldehyde-3-phosphate dehydrogenase, Apn2–Mat1–2 intergenic spacer and partial mating type, glutamine synthetase, β-tubulin, actin, and histone depending on the species complex). C. siamense was the most prevalent species in Thailand, C. gigasporum was reported for the first time as a pathogen of citrus globally, and the new species C. kokhaense in the magnum species complex was described. Pathogenicity tests confirmed that C. siamense, C. gloeosporioides, C. gigasporum, C. kokhaense sp. nov., and C. plurivorum were pathogenic to citrus fruits, seedlings, and in planta shoots, with C. gigasporum being the most aggressive species. The non–wound inoculation technique provided good discrimination between high and low aggressive species compared with wound inoculation, where most species appeared to be very aggressive. Knowledge of Colletotrichum species causing citrus disease and their pathogenic ability will assist the development of effective disease management strategies.