Research Articles (Forestry and Agricultural Biotechnology Institute (FABI))

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Pinus-derived membrane vesicles disrupt pathogenic metabolism in fungi
Kunene, Sithembile; Mmushi, Tshepo Joseph; Steenkamp, Emma Theodora; Motaung, Thabiso Eric (Wiley, 2026)
• Much of what we know about the biological impacts of vesicles (MVs) is derived from Arabidopsis thaliana. Our study focused on vesicles from species in the non-model plant group, Pinus (pine) (P. elliottii, P. radiata, and P. patula × Pinus tec (hybrid)). These plants have tougher tissues and strong, acicular-shaped leaves (needles). • Herein, we first developed a protocol to guide effective collection of juice fluid from needles and roots in a clean and efficient manner. The effects of these vesicles were characterized in terms of the global nutrient profile of the pine pitch canker fungus, Fusarium circinatum, generated from growing fungal spores on ~400 substrates embedded across BioLog phenotypic microarray (PM) plates (PM1, PM2A: carbon sources; PM3B: nitrogen sources; PM9: osmolytes/pH; PM24C: chemicals). • Our findings revealed that MVs, specifically needle-derived MVs (ndMVs) from P. elliottii, disrupt metabolite assimilation in several important pathways, including carbon and nitrogen metabolism. The PM data were also strongly correlated with observed phenotypic effects, including reduced viability and germination of spores in liquid media, as well as impaired filamentous growth on solid media. Importantly, these MV-induced phenotypic effects were reproducible in other filamentous pathogens (e.g., Botrytis cinerea, Chrysoporthe cubensis and F. graminearum) and during a glasshouse trial conducted with F. circinatum-infected P. elliottii seedlings, demonstrating the stable biological effects of ndMVs. • Cumulatively, our results suggest that plant-derived vesicles can disrupt metabolism in pathogenic fungi and, therefore, serve as a cost-effective and sustainable source of novel plant protection molecules.
Genome resources of Xanthomonas vasicola strains from various hosts : reference-guided chromosome and plasmid assemblies for enhanced pathogen genomics
Zim, Nomakula Y.; Yssel, Anna E.J.; Coutinho, Teresa A. (Springer, 2026)
No abstract available.
Genome and transcriptome-based identification and expression profiling of chemosensory gene families across developmental stages and tissues in Sirex noctilio (Hymenoptera: Siricidae)
Postma, Alisa; Klynsmith, Leandri; Duong, Tuan A.; Allison, Jeremy D.; Smidt, Werner; Waterhouse, Robert M.; Lesny, Peter; Oeyen, Jan Philip; Petersen, Malte; Martin, Sebastian; Liu, Shanlin; Zhou, Xin; Ziesmann, Tanja; Donath, Alexander; Mayer, Christoph; Misof, Bernhard; Niehuis, Oliver; Peters, Ralph S.; Podsiadlowski, Lars; Coetzee, Martin Petrus Albertus; Joubert, Fourie; Slippers, Bernard (Wiley, 2026)
The Sirex woodwasp (Sirex noctilio; Hymenoptera: Siricidae) is among the most destructive invasive pests affecting Pinus plantations worldwide. Chemosensory systems offer promising targets for pest control strategies. The identification and characterization of chemosensation genes in non-model, economically significant insects such as S. noctilio, is an important first step towards the development of such control methods. Here we sequenced and assembled a draft genome of S. noctilio and performed RNA-sequencing of 15 olfactory and non-olfactory tissues to study the expression patterns of chemosensation-related genes. Specific genes, such as SnocOR16 and SnocSNMP1, displayed tissue- and sex-specific expression patterns, making them particularly intriguing for their potential roles in chemosensation and oviposition. As woodwasps and their related lineages form a sister group to the majority of other Hymenoptera, including Apocrita, insights into their gene repertoires are crucial for tracing the evolutionary history of chemosensory multigene families of this ecologically and economically significant insect order. This study enhances our understanding of the molecular mechanisms underlying S. noctilio chemosensation, paving the way for further research in chemical ecology and the functional characterization of S. noctilio chemosensation genes.
Genome analyses reveal two novel species of Seiridium from Acacia mearnsii
Aylward, Janneke; Visagie, Cobus M.; Roets, Francois; Wingfield, Brenda D.; Wingfield, Michael J. (Springer, 2026-02)
Seiridium is a genus of Sordariomycetes (Amphisphaeriales, Sporocadaceae), primarily known for species that cause cypress canker on Cupressaceae trees. However, most species in this genus have been reported from angiosperms, including many species in the native range of their hosts. Several unidentified Seiridium strains, collected > 20 years ago from Acacia mearnsii trees in eastern South Africa and southeastern Australia, were recently recovered from a collection of preserved cultures. We considered the phylogenetic position of these Seiridium strains and assessed their pathogenicity on A. mearnsii. Maximum likelihood analysis of three concatenated gene regions revealed four well-supported clades. Two closely related clades corresponded to Australian and South African origins, whereas two other clades representing South African isolates formed a monophyletic group with S. kartense, a species known from Eucalyptus cladocalyx on Kangaroo Island in Australia. Genome-wide average pairwise nucleotide identity and genetic differentiation analysis supported three species, including isolates considered conspecific with S. kartense and two that we consider to represent new species. These are described and named here as Seiridium mearnsii sp. nov. and Seiridium rouxiae sp. nov. Inoculations with South African isolates failed to produce evidence of pathogenicity. Seiridium species from A. mearnsii have likely been introduced into South Africa from Australia, along with the planting material used to establish A. mearnsii forestry.
A haplotype-resolved reference genome for Eucalyptus grandis
Lötter, Anneri; Bruna, Tomas; Duong, Tuan A.; Barry, Kerrie; Lipzen, Anna; Daum, Chris; Yoshinaga, Yuko; Grimwood, Jane; Jenkins, Jerry W.; Talag, Jayson; Borevitz, Justin; Lovell , John T.; Schmutz, Jeremy; Wegrzyn, Jill L.; Myburg, Alexander A. (Oxford University Press, 2025-07)
Eucalyptus grandis is a hardwood tree used worldwide as pure species or hybrid partner to breed fast-growing plantation forestry crops that serve as feedstocks of timber and lignocellulosic biomass for pulp, paper, biomaterials, and biorefinery products. The current v2.0 genome reference for the species served as the first reference for the genus and has helped drive the development of molecular breeding tools for eucalypts. Using PacBio HiFi long reads and Omni-C proximity ligation sequencing, we produced an improved, haplotype-phased assembly (v4.0) for TAG0014, an early-generation selection of E. grandis. The 2 haplotypes are 571 Mbp (HAP1) and 552 Mbp (HAP2) in size and consist of 37 and 46 contigs scaffolded onto 11 chromosomes (contig N50 of 28.9 and 16.7 Mbp), respectively. These haplotype assemblies are 70–90 Mbp smaller than the diploid v2.0 assembly but capture all except one of the 22 telomeres, suggesting that substantial redundant sequence was included in the previous assembly. A total of 35,929 (HAP1) and 35,583 (HAP2) gene models were annotated, of which 438 and 472 contain long introns (>10 kbp) in gene models previously (v2.0) identified as multiple smaller genes. These and other improvements have increased gene annotation completeness levels from 93.8 to 99.4% in the v4.0 assembly. We found that 6,493 and 6,346 genes are within tandem duplicate arrays (HAP1 and HAP2, respectively, 18.4 and 17.8% of the total) and >43.8% of the haplotype assemblies consists of repeat elements. Analysis of synteny between the haplotypes and the E. grandis v2.0 reference genome revealed extensive regions of collinearity, but also some major rearrangements, and provided a preview of population and pangenome variation in the species.
Both synergism and interaction diversity explain the mixtures of defensive monoterpenes in spruce oleoresin
Zaman, Rashaduz; Jain, Akanksha; Hammerbacher, Almuth; Gershenzon, Jonathan; Kandasamy, Dineshkumar (Wiley, 2025-09)
1. Chemical defences, such as the monoterpenes of conifer oleoresin, frequently occur as complex blends of many components, but the selective pressures that maintain these mixtures are not yet known. Several theories attempt to explain the existence of chemical defence mixtures in plants. However, due to limited empirical evidence, it is unclear which theories might best apply. 2. Here, we tested the vapour phase activity of 12 individual Norway spruce monoterpenes and their naturally occurring mixtures to two types of natural spruce enemies, the adult Eurasian spruce bark beetles, Ips typographus, and their three major symbiotic fungi, using survival and growth bioassays. Next, we evaluated whether spruce trees could alter their monoterpene profile in response to fungal infection. 3. Individual monoterpenes had generally opposite effects on bark beetles compared to symbiotic fungi. The compounds that were most toxic to beetles were the least inhibitory to fungal growth and vice versa. The least abundant monoterpenes had the strongest activity against beetles or fungi, while the most abundant monoterpenes showed intermediate activity against both groups of enemies. Additionally, the activity of monoterpene mixtures was significantly stronger against beetles and some symbiotic fungi than the additive effects of individual compounds. Among the symbiotic fungi tested, one (Grosmannia penicillata) exhibited high tolerance to monoterpenes, and its growth was even stimulated by the monoterpenes most toxic to the beetle. Interestingly, spruce bark responded to G. penicillata inoculation by accumulating higher concentrations of specifically fungistatic monoterpenes. 4.Our results support the predictions of the interaction diversity hypothesis, which posits that defence mixtures are maintained in plants because the individual components target different attackers, as well as the synergy hypothesis, which predicts that mixtures will exhibit stronger activity than single compounds. Thus, these two theories may deserve increased emphasis in explaining the widespread occurrence of mixtures in plant chemical defence.
The effects of host and habitat preferences in mate location of Monochamus maculosus, Monochamus notatus, and Monochamus scutellatus (Coleoptera: Cerambycidae)
Andrade, Samara M.M.; Dutkiewicz, David; Borges, Marcelo E.; Smith, Sandy M.; Allison, Jeremy D. (Cambridge University Press, 2026-02)
Several Monochamus species (Coleoptera: Cerambycidae) use monochamol as an aggregation-sex pheromone, raising questions about how they maintain reproductive isolation. Herbivorous insects use host plant semiochemicals as cues for mate location and, with or without habitat cues, these could confer reproductive isolation among sympatric Monochamus spp. To test this hypothesis, host and habitat preferences in mate location were examined for sympatric populations of Monochamus maculosus, Monochamus notatus, and Monochamus scutellatus in the Algoma District, Ontario, Canada. Field experiments were performed to investigate whether differences in host preference, vertical distribution across the forest canopy, spatial distribution within down and standing dead trees, or any combination of these factors could minimise cross-attraction to monochamol. Results showed that more M. maculosus were attracted to monochamol combined with jack pine foliage than with balsam fir or white spruce, whereas no differences in host attractivity were observed for the other species. Vertical abundance of M. maculosus and M. scutellatus was similar across forests. Spatial distribution provided limited evidence for species segregation within hosts. No evidence was found that host or habitat preferences contribute to reproductive isolation in M. maculosus, M. notatus, or M. scutellatus, suggesting that vertical distribution could be driven by resource availability.
Proteomic and secretomic response of an African Armillaria species to iron
Narh, Deborah L.; Wingfield, Brenda D.; Coetzee, Martin Petrus Albertus (American Chemical Society, 2026-03)
Armillaria species have attracted considerable research interest, because they are widely distributed, mostly plant-pathogenic, and exhibit unique characteristics. Abiotic factors influence intra- and interspecies variations in pathogenicity and/or virulence of these fungi. However, the mechanisms involved in causing these variations are not well understood. Iron is an indispensable element in several molecular and biological processes. Yet, excessive abundance of iron can be toxic to organisms due to Fenton-like reactions. This study aimed to gain insights into the type and extent of iron-responsive proteomic and secretomic changes in Armillaria sp. strain CMW4456 cultured in liquid media supplemented with iron using a multiomics approach. Significant iron-dependent alterations of proteins involved in metabolism and growth were observed in the proteomes and secretomes. Iron supplementation at 100 μM did not elicit an oxidative stress response by the fungus. Our analyses revealed three putative siderophore biosynthetic gene clusters (BGCs) in the genome and expression of proteins encoded by some BGC genes in the proteome. This knowledge contributes to a better understanding of the mechanisms employed by an Armillaria sp. in response to iron, gives insights into possible modes for inhibiting or attenuating the pathogenicity and/or virulence of Armillaria spp., and can be valorized for more biotechnological applications.
Editorial : Forest microbiome : dynamics and interactions in the anthropocene era
Chakraborty, Amrita; Roy, Amit; He, Shulin; Castellano-Hinojosa, Antonio; Asiegbu, Fred O.; Coutinho, Teresa A. (Frontiers Media, 2025-11-21)
Forests represent one of the most complex and biodiverse ecosystems on Earth, with intricate networks linking trees, vegetation strata, insects, microbial communities, and soil processes. These networks, sustained by feedback loops and finely tuned ecological balances, form the foundation of global biogeochemical cycles and biodiversity conservation. At the core of these dynamics lies the forest microbiome, including a vast, often invisible consortium of bacteria, fungi, archaea, and viruses that mediates nutrient turnover, supports tree health, and shapes interactions across trophic levels (Baldrian, 2017; Asiegbu and Kovalchuk, 2021).
Outbreaks of a native jewel beetle, Agrilus grandis (Coleoptera: Buprestidae), on commercial black wattle, Acaciamearnsii, plantations in South Africa
Nel, Wilma Janine; Jali, Sandisiwe; Barnes, Irene; Wondafrash, Mesfin; Hurley, Brett Phillip (Entomological Society of Southern Africa, 2026-02)
In early 2024, an outbreak of an unknown wood-borer was observed in Acacia mearnsii De Wild (black wattle) compartments in the Midlands of KwaZulu-Natal, South Africa, causing symptoms of excessive resin production. Larvae uncovered beneath the bark were morphologically identified as a flathead borer, prompting urgent investigation due to the historically low impact of wood-borers on black wattle in South Africa. DNA sequencing of the COI and CytB regions of the larvae failed to yield conclusive matches, so infested logs were collected and the infesting insects reared, resulting in the emergence of three adult beetles. Morphological examination of the adults revealed them as being Agrilus grandis Gory & Laporte 1839, a native African jewel beetle. Comparison to historical specimens housed in the FABI Insect Reference Collection based at the University of Pretoria revealed a previous, unpublished outbreak of the same species in Acacia mearnsii in 1974. However, this is the first official report of A. grandis infestations on A. mearnsii in South Africa.
Vulnerabilities of parasitoid-mediated biocontrol to climate stress
Lyberger, Kelsey P.; Machekano, Honest; Khan, Md Kawsar (Elsevier, 2026-06)
Climate change threatens vital ecosystem services, including biological control mediated by parasitoids. As higher-trophic-level organisms, parasitoids, compared to their hosts, are disproportionately vulnerable to climatic stress because their survival depends on both their own physiology and that of their hosts. This review synthesizes how rising temperatures reconfigure host–parasitoid interactions, with outcomes that are system-dependent. Common disruptions include reduced parasitism success due to narrower parasitoid thermal tolerance, phenological mismatches that desynchronize life cycles, and altered overwintering activity. As these shifts can undermine both natural and artificial biological control, elevating pest outbreak risks and threatening agroecosystem stability, we discuss how mitigating them may require adapting current biocontrol strategies. HIGHLIGHTS • Parasitoids often exhibit narrower thermal windows than their hosts. • Warming differentially alters host and parasitoid development and longevity, increasing chances of phenological mismatch. • Climate change may reduce overwintering survival in parasitoids and their ability to regulate host populations. • Warming may reduce parasitism success, impacting both artificial and natural biocontrol.
Draft genome sequences of Rahnella perminowiae, R. aceris, and R. aquatilis isolated from onion bulbs (Allium cepa L.) displaying symptoms of bacterial rot
Mnguni, Fanele Cabangile; Shin, Gi Yoon; Aegerter, Brenna J.; Du Toit, Lindsey J.; Derie, Michael L.; Coutinho, Teresa A. (Springer, 2026-02)
Onions (Allium cepa L.) are among the most widely produced vegetables globally, and their cultivation plays an important role in food security (Schwartz et al. 2007). However, the emergence of opportunistic bacterial plant pathogens, such as Rahnella species, which are not fully understood yet, poses a threat to onion production (Asselin et al. 2019; Brady et al. 2022). Rahnella species are Gram-negative, facultative anaerobes within the Yersiniaceae family, part of the order Enterobacteriales (Adeolu et al. 2016). According to the List of Prokaryotic Names with Standing in Nomenclature (LPSN), the genus consists of 15 described species that are isolated from various environments and are considered validly characterised (Guo et al. 2012; Brady et al. 2014; Lee et al. 2019; Liang et al. 2020).
Structural insights into WY domain SLiM-containing conserved RxLR effectors : a case study of five important Phytophthora species
Salasini, Brenda Chisanga; Chepsergon, Jane; Nxumalo, Celiwe Innocentia; Moleleki, Lucy Novungayo (American Phytopathological Society, 2026)
Pathogenicity in Phytophthora species is in part underpinned by a sophisticated arsenal of RxLR effectors, which function as molecular determinants of host immune manipulation. Among these, conserved RxLR effectors (CREs) represent an evolutionarily conserved subset that is indispensable for virulence. However, the structural basis of their function remains poorly understood. Here, we conducted in silico analysis of CREs across five agriculturally significant Phytophthora species, revealing a conserved subset that integrates WY domains with embedded short linear motifs (SLiMs), a previously recognized architectural feature with functional implications. Notably, our findings indicate that despite the canonical association of SLiMs with intrinsically disordered regions, their incorporation within the structured WY domain preserves domain integrity while potentially expanding the effector's interactome within host cells. To explore the functional relevance of this domain organization, we characterized Phytophthora nicotianae RxLR6 (PpRxLR6), a representative WY-SLiM CRE identified in this study. Using Agrobacterium-mediated transient expression assays, we demonstrate that PpRxLR6 activates key immune defense networks in Nicotiana and Solanum species, suggesting a role in modulating host immune signaling. Structural predictions further reveal that PpRxLR6 harbors its SLiM within a well-ordered WY-like helical core region, suggesting that SLiM-mediated interactions may occur within structured effector domains rather than being confined to intrinsically disordered regions. These findings enhance our understanding of the effector domain architecture of PpRxLR6, illustrating how structured domains in CREs may serve as scaffolds for SLiM-mediated interactions. This structural arrangement may represent an adaptive strategy in Phytophthora evolution, potentially enhancing effector versatility in host interactions and immune modulation.
Phenotypic profiling of carbon utilization of Pectobacterium brasiliense (Pbr1692)
Bokhale, Mamokete; Njage, Patrick M. K.; Wambui, Joseph; Moleleki, Lucy Novungayo (Oxford University Press, 2025-10-30)
Pectobacterium brasiliense 1692 (Pbr1692) is a necrotrophic pathogen that infects many crops such as potatoes and ornamental plants and derives nutrients from degraded plant tissue. Previous studies have identified Pbr1692 genes required for ecological fitness and virulence, however there is a lack of information on nutrient utilization in Pbr1692. Carbon source utilization profiling in Pbr1692 could provide a platform to decipher its metabolic flexibility and adaptation. This study assessed the nutrient utilization of Pbr1692 in different carbon sources, using Biolog Phenotypic Microarray (PM). An array of carbon sources utilized by Pbr1692 were identified, 32 carbohydrates and 8 carboxylic acids were among the preferred carbon nutrients utilized by Pbr1692. The PM results also revealed that the citric acid cycle, amino acid metabolism, and pentose phosphate metabolic pathways might be used to produce energy for Pbr1692. In addition, growth of Pbr1692 cells in minimal medium supplemented with citric acid, glucose, and aspartic acid retained the typical rod shape, suggesting that nutrient variation did not influence Pbr1692 cell morphology adaptation. This study provides an understanding on the adaptation of Pbr1692 and lays a foundation for understanding carbon metabolism of Pbr1692.
Parental heat stress has transgenerational physiological- but not ecological-progeny fitness advantage in the larger grain borer
Mlambo, Shaw; Machekano, Honest; Mvumi, Brighton Marimanzi; Nyamukondiwa, Casper (Emerald, 2026-03)
Climate change forecasts predict that global temperature and variability will continue rising owing to anthropogenic activities. This poses significant stress on ectotherms, whose bodily function depends on ambient temperatures. The ability of species to adapt within and/or across generations through phenotypic plasticity is thus a critical ecological topic. We investigated transgenerational thermal plasticity of the larger grain borer, Prostephanus truncatus, a devastating postharvest maize pest. Specifically, we tested the effects of parental exposure to sublethal heat stress (35 and 38 °C for 2 h; 80 % RH) on progeny thermal— and ecological—performance. Following acclimation, the colonies were separately maintained on shelled maize at optimum conditions of 32 °C at 65 ± 10 % RH. After 21 d, adult beetles were removed and the emerging progeny respectively labelled as F1 treatments (F1_35 °C and F1_38 °C). Subcultures from these 2 × F1 treatments were sampled in the same manner to obtain F2 (F2_35 °C and F2_38 °C) and subsequently F3 (F3_35 °C and F3_38 °C) generations which were then evaluated against parental (control) cultures maintained at optimal conditions 32 °C (P_32 °C). Our results showed that parental heat acclimation: (i) had transgenerational physiological— but not ecological-progeny fitness advantage; (ii) decreased critical thermal limit ranges; (iii) had cross-protection improvement in cold tolerance; and (iv) had transgenerational physiological responses that may last generations. Transgenerational plastic responses may help in understanding how species and ecosystems adapt to environmental temperature changes. This is the first report documenting transgenerational heat tolerance plasticity in P. truncatus. HIGHLIGHTS • Parental heat acclimation had transgenerational physiological- but not ecological-progeny fitness advantage. • Parental heat acclimation decreased progeny critical thermal limit ranges. • Parental heat acclimation had cross protective improvement in progeny cold tolerance. • Transgenerational physiological responses may last generations.
Climate change and the antinutrient–antioxidant puzzle in common bean seeds
Vorster, Juan; Cominelli, Eleonora; Sparvoli, Francesca; Losa, Alessia; Sala, Tea; Kunert, Karl J. (Wiley, 2026-02)
Non-proteinaceous and proteinaceous antinutrients in common bean (Phaseolus vulgaris L.) seeds can negatively affect human nutrition by reducing mineral bioavailability and impairing protein digestibility during digestion, respectively. However, many of these compounds also possess strong antioxidant properties that can help protect the plant from oxidative stress. While strategies to reduce antinutrient levels have been proposed to enhance the nutritional value of beans, less attention has been given to their potential protective functions, particularly under abiotic stress conditions. In the context of ongoing global climate change - marked by more frequent and prolonged drought and heat stress - there is a significant research gap concerning the influence of these environmental stresses on the accumulation and function of seed antinutrients in common beans. This perspective paper reviews current knowledge on the production of antioxidative antinutrients in response to abiotic stress and highlights the dual role of these compounds. It also outlines key research directions needed to better understand how climate-induced stress may alter antinutrient levels, and the implications this may have for both human nutrition and plant resilience. © 2025 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Thermotolerance and post-fire growth in Rhizina undulata is associated with the expansion of heat stress-related protein families
Wilson, Andi M.; Wingfield, Michael J.; Duong, Tuan A.; Wingfield, Brenda D. (BioMed Central, 2025-11-13)
BACKGROUND : Rhizina undulata is an important tree pathogen, infecting a wide variety of conifer species, including those in the genus Pinus. The fungus relies on heat shock-mediated activation of its ascospores, which require high temperatures to initiate germination. Consequently, disease due to R. undulata often occurs after fire events in both natural and managed forests. The genetic mechanisms contributing to the pyrophilous nature of R. undulata have not been investigated. We sought to identify key genes that may be responsible for thermotolerance in the fungus. A comparative genomics approach was used, by sequencing the genome of R. undulata for the first time and comparing its predicted proteome to those from other Pezizomycetes, both with and without known associations with fire. RESULTS : Three protein families were shown to be expanded in R. undulata; heat shock protein 20 (HSP20), glutathione-S transferases (GST), and aromatic compound dioxygenases (ACD). While HSP20 was uniquely over-represented in R. undulata, the expansions of the GST and ACD families were also identified in other fire-associated species. CONCLUSION : HSP20s are known to protect cells against heat stress, GSTs are involved in the detoxification of reactive oxygen species, and ACDs play a role in the metabolism of recalcitrant compounds present in post-fire environments. The expansion of these families thus suggests that they may play an important role in protecting and stimulating R. undulata ascospores during and after fire-induced heat shock, activating the fungus, and enabling it to colonise the root systems of conifers.
Dematophora necatrix : from taxonomy to molecular advances
Carstens, Maryke; Pliego, Clara; Norval, Annabel; Van den Berg, Noelani (Elsevier, 2026-03)
Dematophora necatrix Hartig is a destructive soil-borne fungus responsible for White Root Rot (WRR), affecting more than 350 plant species across 51 countries, including many economically important crops. The pathogen's persistence in soil and broad host range makes it especially challenging to control. Over the past decade, molecular studies have significantly advanced our understanding of the pathogen's biology and its interactions with host plants. These developments underscore the need for a comprehensive review to consolidate recent scientific progress. First, we outline the taxonomy, biology, disease symptoms, hosts and global distribution, and current management strategies of D. necatrix. We then focus on recent molecular advances, highlighting how genomics, transcriptomics, proteomics and metabolomics studies have improved our understanding of the pathogen's virulence and pathogenicity. A high-quality, chromosome-level genome assembly has enabled more precise annotation and gene prediction. Transcriptomic analyses have identified candidate pathogenicity-related genes and putative effectors, while secretome proteomic studies suggest the production of antimicrobial proteins which may facilitate infection by suppressing microbial competitors. Secondary metabolites, such as cytochalasin E, have been implicated in virulence, although their precise roles in pathogenicity remain unresolved. Improved transformation protocols now permit targeted gene manipulation, creating new opportunities for functional studies. Lastly, this review highlights key knowledge gaps and calls for integrated multi-omics approaches to better understand D. necatrix pathogenicity and virulence, long-term survival, and environmental adaptation. Such insights are critical for the development of durable, targeted strategies to manage WRR.
Taxonomy, distribution and dispersal of Calonectria species : important pathogens of forestry, agricultural and horticultural crops
Liu, QianLi; Wingfield, Michael J.; Duong, Tuan A.; Wingfield, Brenda D.; Crous, Pedro W.; Chen, ShuaiFei (Springer, 2026-01-19)
PURPOSE OF THE REVIEW : Calonectria is a globally distributed genus of plant-pathogenic fungi causing destructive diseases across a wide range of woody and herbaceous hosts. This review synthesizes recent advances in the species delimitation, host range dynamics, reproductive strategies, and global dispersal patterns of Calonectria. Particular attention is given to the ecological adaptability, cryptic diversity, and climate-driven shifts in distribution of these important fungi. The review identifies key knowledge gaps and provides recent research regarding genome-based diagnostics, adaptive disease management, and forward-looking biosecurity measures. RECENT FINDINGS : Polyphasic taxonomic approaches and molecular systematics have substantially refined the classification of Calonectria, which now includes 136 species grouped into 11 species complexes. Some species, such as Ca. pseudonaviculata, exhibit strict host specificity; others like Ca. pauciramosa have wide host ranges and are globally invasive. Both sexual and asexual reproduction enhance persistence and facilitate dispersal, often via infected nursery stock and contaminated substrates. Climate change is projected to expand the distribution of multiple Calonectria species into new regions. Despite increasing reports of international spread, genomic surveillance remains limited, and diagnostic inconsistencies continue to hinder effective detection and containment. SUMMARY : The broad host range, complex reproductive biology, and environmental adaptability of Calonectria species enhances their growing threat to plant health worldwide. Their spread is accelerated by global trade and climate change, while unresolved taxonomic challenges and underdeveloped molecular tools constrain opportunities for their management. Integrated strategies that combine phylogenomics, risk modeling, and coordinated surveillance are urgently needed to mitigate its impact across agricultural, horticultural, and forest systems.
From beginning to end : the synecology of tree-killing bark beetles, fungi, and trees
Six, Diana L.; Hammerbacher, Almuth; Trowbridge, Amy; Bullington, Lorinda (Wiley, 2026-02)
Over a century of research has revealed an amazing complexity of behaviours and physiological adaptations that allow tiny bark beetles to overcome large trees, sometimes resulting in outbreaks that kill millions of trees. Turning a tree into a home and successfully raising offspring involves constant interactions among the beetles, the tree, its microbiome, and the beetles' associated microbes, all influenced by abiotic factors that can determine success or failure. While we have learned much about these systems, substantial knowledge gaps remain. This synthesis aims to clarify and integrate current understanding, identify gaps, challenge long-held assumptions, and address interpretative issues that impede progress toward a holistic understanding of these systems. We advocate for expanding perspectives using synecological approaches to understand these complex systems better. We encourage expanding research into how colonization by the bark beetle–fungi complex influences subsequent tree decay and forest carbon dynamics. An explicit goal is to provide a comprehensive resource for new researchers while encouraging them to question established hypotheses and to explore new avenues of enquiry.

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