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

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Assessing Gonipterus defoliation levels using multispectral unmanned aerial vehicle (UAV) data in Eucalyptus plantations
Nzuza, Phumlani; Schröder, Michelle L.; Heim, Rene J.; Daniels, Louis; Slippers, Bernard; Hurley, Brett Phillip; Germishuizen, IIaria; Sivparsad, Benice; Roux, Jolanda; Maes, Wouter H. (Elsevier, 2025-12)
Invasive insect pest Gonipterus sp. n. 2 (Coleoptera: Curculionidae) threatens Eucalyptus species, causing defoliation and yield loss through adult and larval feeding. Early detection is important for early intervention to prevent pest outbreaks. As conventional insect pest monitoring methods are time-consuming and spatially restrictive, this study assessed the potential of UAV monitoring. Multispectral imagery was obtained with Unmanned Aerial Vehicles (UAVs) across six different stands of young Eucalyptus dunnii with varying levels of Gonipterus sp. n. 2 infestations. Some stands were revisited, a total of 9 datasets were covered. Reference damage levels were obtained through visual assessments of (n = 89–100) trees at each site. Across sites, a decrease in canopy reflectance in both the visual and the near-infrared domains with increasing damage levels was consistently observed. Several vegetation indices showed consistent patterns, but none showed site independence. XGBoost, Support Vector Machine and Random Forest (RF) were used to predict damage levels using five input spectral data types. XGBoost performed best, closely followed by RF. Both models consistently selected very similar features. The best-performing models included reflectance, vegetation indices and grey-level co-occurrence matrix data. When data from 10 different wavelengths were used, the highest classification accuracy was 92 % across all sites in classifying defoliation levels. With a classical 5-band multispectral camera, accuracy was 88 %, but distinguishing medium damage from low remained challenging. However, the method was less reliable when trained and validated on separate fields. This study highlights the potential of multi-site datasets in increasing the model's generalization, using UAV based multispectral imagery to assess Gonipterus sp. n. 2 damage and demonstrating reliable upscaling from individual tree assessments to stand scale. However, it also recognises the difficulty of generating a robust model that performs well on untrained sites. HIGHLIGHTS • Canopy damage from Gonipterus sp. n. 2 was assessed across stands using UAV imagery, capturing defoliation, chlorophyll reduction. • The 5-band imagery perfomed comparable to the 10-band but was less effective at detecting subtle low vs no damage defoliation. • Similar pattern was observed across sites but absolute reflectance and vegetation indices are site specific.
Enhancing plantation forest sustainability : a review of Eucalyptus defence mechanisms to foliar fungal pathogens
Solis, Myriam; Hammerbacher, Almuth; Wingfield, Michael J.; Naidoo, Saloshnee (Springer, 2025-02)
PURPOSE OF THE REVIEW : In this review, we synthesize knowledge generated over many decades on the main defence responses of Eucalyptus to fungal leaf pathogens with the aim of identifying targets for breeding disease tolerant trees. We highlight physiological and molecular traits associated with host defence in relation to pathogen life-style. Overall, the purpose of this review is to identify resistance mechanisms that offer improved resilience of Eucalyptus plantations in the face of increasing threats by foliar fungal pathogens. The broad aim is to promote sustainable forestry through appropriate selection of resistance traits in trees that are widely planted for commercial timber production. RECENT FINDINGS : Eucalyptus is among the most important tree genera planted for commercial timber production worldwide. Numerous foliar pathogens have been reported on these trees in the last 30 years with numbers of recent reports increasing exponentially. The majority of these diseases affect the leaves and shoots of the trees. Knowledge on resistance traits in Eucalyptus to fungal foliar pathogens is limited. This is in part due to the high intra- and inter-species variation in molecular and physiological responses of the host and variation in responses to different pathogens, especially those with different trophic modes. A well-founded understanding of such host responses will provide valuable knowledge required to maintain healthy, sustainable Eucalyptus plantations, especially in the face of changing environmental conditions, where new diseases are caused by fungi previously not considered relevant. SUMMARY : Foliar diseases are among the most important challenges for Eucalyptus plantations globally. The effects of climate change and new or more serious outbreaks present an important threat to the sustainability of Eucalyptus plantations worldwide. Due to restrictions on the use of chemicals, more feasible solutions for disease management lie in selecting planting material with resistance traits. To achieve that goal, it is essential to understand the most important physiological and molecular responses of Eucalyptus to infection by pathogens that infect their foliar tissues. In this review we summarise the available knowledge of the main physiological defence barriers and genetic traits that play key roles in the broad defence against foliar fungal pathogens. Furthermore, we consider defence pathways that are specifically related to the lifestyle and trophic mode of the pathogens. In order to ensure the future sustainability of Eucalyptus plantations, it will be necessary to understand how disease resistance is affected by climate change, as well as the adaptability of the hosts and pathogens to newly emerging environmental conditions.
The pine pathogen Diplodia sapinea : expanding frontiers
Wingfield, Michael J.; Slippers, Bernard; Barnes, Irene; Duong, Tuan A.; Wingfield, Brenda D. (Springer, 2025)
PURPOSE OF REVIEW : This review offers a thorough examination of the pine pathogen Diplodia sapinea, tracing its historical significance from its initial impact on South African non-native Pinus plantations to its recent emergence as a major threat to forests, particularly in Europe. It also highlights recent findings regarding its taxonomic position, genetic studies, and shifts from being perceived as a wound-infecting pathogen to an endophyte in healthy Pinus species that causes disease after stress. RECENT FINDINGS : Recent years have witnessed a dramatic increase in the damage caused by D. sapinea in natural and planted forests. This escalation is apparently strongly linked to climate change. The pathogen’s previously confused taxonomic position has been clearly resolved in the Botryosphaeriaceae, alongside several sibling species. Diplodia sapinea is now well-understood as an endophyte in healthy trees, which has significant implications for studies aimed at understanding its biology. Importantly, robust techniques including those utilizing genome sequences, are now available for rapid identification and population genetic studies of the pathogen and the factors that drive disease outbreaks. SUMMARY : Over the past century, D. sapinea has transitioned from a localized problem in South African non-native plantations to a global threat to both natural and planted forests, particularly in Europe. This review underscores the importance of historical context in understanding the evolution of the pathogen’s impact. It also lays the foundation for future research endeavours, leveraging modern technologies to address key questions surrounding its biology and ecology.
Extracting protoplasts from filamentous fungi using extralyse, an enzyme used in the wine industry
Wilson, Andi M.; Van Dijk, Alida; Marx, Bianke; Du Plessis, Deanne; Terblanche, Grant; Bornman, Simoné; Wilken, Pieter Markus; Duong, Tuan A.; De Fine Licht, Henrik H.; Wingfield, Brenda D. (Wiley, 2025-03)
The ability to extract protoplasts has contributed significantly to the study of fungi and plants. Protoplasts have historically been used to determine chromosome number via pulsed-field electrophoresis and for the functional characterization of genes via protoplast transformation. More recently, protoplasts have been used to extract the high-molecular-weight DNA required for long-read sequencing projects. The availability of efficient protoplast extraction protocols is thus integral to the study and experimental manipulation of model and non-model fungi. One major hurdle to the development of such protocols has been the discontinuation of enzymes and enzyme cocktails used to digest the fungal cell wall. Here, we provide five protoplast extraction protocols for use in various filamentous ascomycete species spanning the genera Ceratocystis, Fusarium, Metarhizium, Ophiostoma, and Sclerotinia. These protocols all use an inexpensive, readily available enzyme cocktail called Extralyse, a commercially available product commonly used in the wine making industry. Using this enzyme cocktail overcomes reliance on the laboratory-grade enzymes that have frequently been discontinued and are often cost prohibitive at the concentrations required. The protocols described here will allow further research, including genome editing, to be conducted in these fungal genera. Importantly, these protocols also provide a starting point for the development of protoplast extraction techniques in other filamentous fungi. This resource can therefore be used to expand the molecular toolkits available for fungi beyond the species described here, including those with relevance in both medical and biotechnological industries. Basic Protocol 1: Protoplast extractions from Ceratocystis eucalypticola and Ceratocystis fimbriata. Basic Protocol 2: Protoplast extractions from Fusarium circinatum. Basic Protocol 3: Protoplast extractions from Metarhizium acridum, Metarhizium brunneum, and Metarhizium guizhouense. Basic Protocol 4: Protoplast extractions from Ophiostoma novo-ulmi. Basic Protocol 5: Protoplast extractions from Sclerotinia sclerotiorum.
Responses of fruit flies (Diptera: Tephritidae) to protein bait : effects of tree canopy, species, physiological state and weather
Ramaoka, Msizi Ronald; Manrakhan, Aruna; Weldon, Christopher W. (Elsevier, 2025-11)
The application of protein baits forms the core of fruit fly (Diptera: Tephritidae) control measures in many orchard environments. Protein baits target adult fruit flies, which need protein for reproductive maturation. A proper understanding of the factors influencing fruit fly responses to protein is required to optimise control outcomes. In this study, responses to protein bait by three fruit fly species, Ceratitis capitata (Wiedemann), C. cosyra (Walker), and Bactrocera dorsalis (Hendel), were investigated. This was done in two field cages erected over lemon trees within an orchard. The response of each species to protein bait presented as a station and positioned at different heights within the tree canopy was evaluated. For each species, effects of fly age, sex, and nutritional status were evaluated under conditions of varying temperature and relative humidity. The highest response occurred when protein baits were placed in the middle to upper tree canopy. Species, nutritional status, sex and age also affected protein foraging. Ceratitis capitata responded more to bait compared to B. dorsalis and C. cosyra. The lowest response to protein bait was by one-day-old protein fed flies, while 10-day-old protein-deprived flies were most responsive. Protein deprived females were more attracted to protein than males fed the same diet. Flies responded to bait when temperatures were between 20 and 30 °C. Based on the results, the success of protein baits in controlling fruit flies in a tree canopy is height dependent and can be lower in areas with alternative protein sources.
Short communication: Elevated testosterone correlates with enhanced innate immune function in a cooperatively breeding rodent
Wallace, Kyra Mary Elizabeth; Venter, S.N. (Stephanus Nicolaas); Bennett, Nigel Charles; Hart, Daniel William (Elsevier, 2025-10)
In many vertebrates, elevated testosterone is believed to compromise the immune function, reflecting a trade-off between reproduction and survival. However, such trade-offs may potentially be relaxed in cooperative breeders, where social conflict and sexual selection are reduced. We investigated the relationship between testosterone, cortisol, and innate immunity in captive male Damaraland mole-rats (Fukomys damarensis), a eusocial rodent with minimal aggression-driven reproductive competition. Using microbial killing assays (MKAs) and white blood cell counts as proxies of immune function, we found that urinary testosterone concentration was positively correlated with immune strength. Males with higher urinary testosterone concentrations exhibited significantly greater antimicrobial capacity and elevated total white blood cell counts. However, urinary testosterone was unrelated to independent immune cell differentials. While, reproductive status, age, body mass, and urinary cortisol concentrations had a limited effect on any immune metric. These findings, while correlative, challenge traditional endocrine-immune trade-off models and infer that, in this species, testosterone may signal condition rather than impose immunosuppressive costs.
Myco-ecological warfare with Meloidogyne species
Ramatsitsi, Ndivhuwo; Manyevere, Alen; Motloba, Tuelo (Taylor and Francis, 2025)
Root-knot nematodes (RKNs), Meloidogyne, are the most widely distributed plant-parasitic nematodes. This group of soil-borne pests represents one of the largest causes of plant biotic stress that are challenging to manage, deeming them economically important. Using fungal bio-control agents (BCAs) is considered economic and ecologically friendly. This review illuminates how fungal BCAs generally decrease the negative impacts of RKNs, i.e. either via antagonistic activities or by modifying effects on plant root morphology and physiology. Of the 38 reviewed BCAs, the most studied were Arthrobotrys, Aspergillus, Lecanicillium, Purpureocillium, Trichoderma, Pochonia and Fusarium endophytes. Of the several studied fungal BCAs, approximately 10 are globally marketed. Based on literature, an understanding of the intricate interactions between fungal BCAs and Meloidogyne is a prerequisite for carrying out an appropriate method for formulation of bio-control products. The major challenge in commercialising fungal BCAs has been attributed to inconsistency concerns under different conditions, incompatibilities of BCAs species and formulation procedures that result in reduced effectiveness.
Phosphite inhibits Phytophthora cinnamomi by downregulating oxidoreductases and disrupting energy metabolism
Prabhu, Sreedhara Ashok; Naicker, Previn; Duong, Tuan A.; Govender, Ireshyn Selvan; Engelbrecht, Juanita; Backer, Robert; Stoychev, Stoyan Hristov; Van den Berg, Noelani (Frontiers Media, 2025-08-25)
Phytophthora root rot caused by the hemibiotrophic oomycete, Phytophthora cinnamomi is a major biotic hindrance in meeting the ever-increasing demand for avocados. In addition, the pathogen is a global menace to agriculture, horticulture and forestry. Phosphite trunk injections and foliar sprays remain the most effective chemical management strategy used in commercial avocado orchards against the pathogen. Phosphite is known to counter P. cinnamomi both directly and indirectly through fortification of host defense. However, phosphite's direct mode of action is still not understood completely. This study identified a P. cinnamomi isolate GKB4 sensitive to phosphite (EC50 of 27.9 μg/mL) and investigated the direct impact of phosphite on this isolate through label-free quantitative SWATH-MS. Proteomics data analysis of untreated vs. phosphite-treated samples revealed that the xenobiotic affects the pathogen's growth by targeting the oxidoreductases whose abundance is significantly reduced. Further, perturbations in the energy metabolism and membrane/transmembrane proteins and transporters, and oxidative stress contribute to growth inhibition. The current study also identified increased putrescine biosynthesis, a polyamine, that when present at non-optimal concentrations could be cytostatic/cytotoxic. The differential expression of enzymes involved in the biosynthesis of secondary metabolites and the intermediates/precursors involved in their biosynthesis is an interesting finding that needs further investigation to ascertain their role in phosphite-induced stress. The pathogen's attempt to counter phosphite's growth-inhibitory effects—through upregulation of alternate bioenergetics pathways (amino acid catabolism and β-oxidation of fatty acids), mitochondrial translation and translocation machinery, peroxisomal proteins, and antioxidants—appears ineffective. This research furthers our limited understanding of the direct in vitro effects of phosphite on P. cinnamomi and has identified potential candidates for molecular functional investigation. HIGHLIGHTS • A phosphite-sensitive P. cinnamomi isolate (PcGKB4) was identified. • Label-free quantitative proteomics identified that phosphite inhibits PcGKB4 predominantly by downregulating oxidoreductases and glycolysis. • Phosphite increased the biosynthesis of putrescine. Depending on its intracellular levels it could promote growth or act as a cytostatic/cytotoxic agent. • Enhanced production of proteins involved in alternative energy metabolism, mitochondrial translation, peroxisomal proteins and antioxidants is a futile countereffort by the pathogen to revive growth.
Estimation of breed composition of South African sheep affected with wet carcass syndrome
Kooverjee, Bhaveni B.; Van der Nest, Magrieta Aletta; MacNeil, Michael D.; Scholtz, Michiel M.; Neser, Frederick W.C.; Soma, Pranisha (Frontiers Media, 2025-07-21)
Wet carcass syndrome (WCS), a condition that negatively affects the quality of carcasses after slaughter, is seriously threatening the South African sheep industry. Despite its economic impact, the underlying genetic mechanisms of WCS remain unknown. Initially, WCS was predominantly observed in Dorper sheep, leading to speculation that the condition was breed-specific. However, recent reports indicate WCS has occurred in various sheep breeds. This study aimed to determine whether WCS is breed-specific and whether breed composition influences its incidence. Meat samples from 164 WCS-affected and 83 unaffected sheep were collected and genotyped using the Ovine 50K SNP Bead Chip. Principal Component Analysis (PCA) and ancestry matrix assessments revealed that WCS-affected and unaffected sheep belonged to different commercial breeds. Additionally, crossbred animals were affected. These findings suggest that WCS is strongly associated with breed and that Dorper and Merino-types show heightened susceptibility. The genetic diversity of the affected animals suggests a multifactorial etiology, potentially involving environmental and managerial factors. Future studies should also explore the physiological mechanisms underlying WCS, including metabolic and stress-related pathways, to develop effective prevention strategies.
Determinants of mating success in a lek-mating species
Queffelec, Josephine; Allison, Jeremy D.; Slippers, Bernard; Greeff, Jacobus Maree (Wiley, 2025-11)
• Leks are male-biased aggregations formed for mating, where sperm is the only resource acquired by visiting females. • One of the many advantages of leks is the possibility to efficiently assess the quality of potential mates by comparing aggregated individuals of the same sex with one another. • When direct mate choice occurs in a lekking species, it is often exhibited by females, but some studies have also demonstrated the presence of male mate choice. • We investigate mate choice in the lek-forming European woodwasp, Sirex noctilio. • We determine the importance of age and size as predictors of mating success. • We demonstrate that mating is not random and that male and female traits affect mating success. • Age plays an important role in mating success in both males and females, with older males mating more and younger females being more attractive and more receptive to mating. • Relative male size seems to play a role in mating success, with males being more successful when attempting to mate with females that are larger than they are.
Bark and ambrosia beetle communities (Coleoptera: Curculionidae: Scolytinae: Platypodinae) across five mangrove forests in South Africa
Osorio, Jhon Alexander; Chara, Jenny (SpringerOpen, 2025-06)
BACKGROUND : Mangrove forests are of fundamental significance that support a diverse array of species, but despite their importance and the benefits they provide, the health of these trees is under constant threat. This is due to a variety of environmental and human factors, which lead to their weakening and susceptibility to colonization by insect pests. Although the diversity of bark and ambrosia beetles has been well documented worldwide, there is limited information available regarding their relationships with mangroves. To investigate the diversity and distribution of ambrosia and bark beetles associated with mangrove habitats in South Africa, extensive field surveys and species sampling across various mangrove sites were carried out, as well as Lindgren and Panel traps were installed along five estuaries in KwaZulu–Natal and one in the Eastern Cape Province, from October to December 2013 and January to February 2014. RESULTS : A total of 8677 individuals comprising 11 genera and 16 species of ambrosia and bark beetles were captured. Of these, the most abundant was Hypothenemus eruditus (n = 2178; 25.10%), followed by Ambrosiodmus natalensis (n = 863; 10.36%), Xyleborus affinis (n = 844; 9,73%) and Premnobius cavipennis (n = 833; 9,60%), respectively. The remaining species registered an incidence lower than 7%. From the analysis of representativeness by rarefaction curves, there was no trend toward an increase in species as the number of trajectories increased. CONCLUSIONS : This research contributes to understanding the biodiversity of ambrosia and bark beetle assemblages within South African mangrove ecosystems and underscores the importance of conserving these habitats in the face of environmental and anthropogenic pressures. The findings provide a valuable baseline for future studies and management strategies aimed at preserving mangrove health and monitoring beetle community dynamics in these critical coastal environments.
BISMiS Live : a digital platform for global communication among microbial systematists
Jangid, Kamlesh; Li, Wen-Jun; Venter, S.N. (Stephanus Nicolaas); Teo, Wee Fei Aaron; Whitman, William (Elsevier, 2025-09)
BISMiS Live, launched on March 20, 2021, emerged as a timely response to the disruption caused by the CoViD-19 pandemic, offering a global virtual platform for discourse in microbial systematics. Spearheaded by the Bergey's International Society for Microbial Systematics (BISMiS), this monthly webinar series hosted renowned experts and engaged thousands of participants across 84 countries. The initiative emphasized inclusivity, scientific depth, and digital accessibility, with sessions archived on YouTube (@BISMiS_) for broader impact. Behind each event lies a dedicated team managing speaker coordination, technical execution, and global outreach. BISMiS Live has grown into an educational resource, integrated into university curricula and inspiring the next generation of microbial taxonomists. With suggestions for future innovation, such as student lightning talks, thematic series, and podcast formats, the platform is poised to evolve further. BISMiS Live stands as a digital bridge connecting systematists worldwide, sustaining knowledge exchange and community through innovation and collaboration. HIGHLIGHTS • BISMiS Live is a global webinar series on microbial systematics to promote inclusive, digital scientific exchange. • Run by volunteers, it is a key education/outreach tool with top experts and archived sessions on YouTube @BISMiS_. • Participants from 84 countries include students, postdocs, and faculty with diverse backgrounds and expertise. • Future plans include student talks, theme series, and a podcast format for broader impact.
Semiochemical-based strategies for sustainable management of the fall armyworm, Spodoptera frugiperda (J.E Smith) (Lepidoptera: Noctuidae)
Sisay, Birhanu; Nakamura, Akihiro; Mihretie, Aderajew; Tamiru, Amanuel; Weldon, Christopher William; Ashton, Louise A. (Springer, 2025-10)
Semiochemicals are produced by diverse taxa to mediate intra- and interspecific communication. These chemical cues are becoming increasingly important in integrated pest management (IPM) for manipulating key behaviors such as mating, foraging, and host selection in both plant–insect and insect-insect interactions. Semiochemical-based approaches regulate pest populations through techniques such as monitoring, mass trapping, and mating disruption. Understanding the chemical cues that mediate these interactions is crucial for developing sustainable and targeted pest management options. This review explores the role of semiochemicals in managing insect pests, with a focus on the fall armyworm (Spodoptera frugiperda), a globally significant pest native to the Americas. We discuss composition, variability, efficacy, specificity, and applications of plant volatiles and sex pheromones in pest management. Additionally, we address challenges associated with the adoption of semiochemical-based approaches and highlight emerging research directions to enhance their integration into IPM programs. By synthesizing current knowledge, this review underscores the potential of semiochemical-based strategies to reduce reliance on conventional insecticides while improving pest control efficiency. The strategic application of plant volatiles and sex pheromones in agricultural systems offers an opportunity to develop more ecologically sound and sustainable pest management practices, thereby fostering resilient cropping systems with minimal environmental impact.
Leaf area index-based phenotypic assessment of sweet potato varieties using UAV multispectral imagery and a hybrid retrieval approach
Tsele, Philemon; Ramoelo, Abel; Moleleki, Lucy Novungayo; Laurie, Sunette; Mphela, Whelma; Tshuma, Natasha (Elsevier, 2025-08)
Phenotyping based on the estimation of plant traits such as the leaf area index (LAI) could aid the identification and monitoring of the sweet potato health, growth status and gross primary productivity. Integrating radiative transfer models (RTMs), active learning algorithms and non-parametric regression methods using unmanned aerial vehicle (UAV) multispectral imagery have the potential for accurately estimating LAI across multiple crop varieties at varying growth stages. This study tested the boosted regression trees (BRT) and kernel ridge regression (KRR) for inversion of the PROSAIL RTM to retrieve LAI across 20 sweet potato varieties during peak growth stage. Furthermore, the study attempted to constrain the inversion process by using active learning (AL) techniques which ensured the selection of informative samples from a pool of RTM simulations. Results show that the most accurate LAI retrieval over the heterogeneous sweet potato canopy was achieved by integrating smaller PROSAIL simulations with the random sampling AL and KRR methods. The LAI retrieval accuracy had a coefficient of determination (R2) of 0.52, root mean squared error (RMSE) of 0.88 m2.m-2 and relative RMSE of 12.23 %. However, the BRT performance in-comparison to KRR, captured more spatial variability of observed LAI with a better prediction accuracy across the 20 sweet potato varieties. The hybrid approach developed in this study, show potential for accurate phenotyping of LAI dynamics across multiple sweet potato varieties during a matured growth stage. These findings have significant implications for sweet potato breeding programmes that are critical for developing new cultivars in South Africa.
Plant pathogen name game : Cross Kingdom Review for the naming of biotic agents associated with plants
Bull, Carolee T.; Salgado-Salazar, Catalina; Romberg, Megan K.; Allen, Cavan; Kantor, Mihail; Handoo, Zafar; Aboughanem-Sabanadzovic, Nina; Sabanadzovic, Sead; Coutinho, Teresa A. (Annual Reviews, 2025-09)
To communicate across scientific disciplines, regulatory bodies, and the agricultural community, the naming of plant pathogens assigned to specific taxa is critical. Here, we provide an overview of the nomenclatural systems governing the naming of plant-pathogenic nematodes, fungi, oomycetes, prokaryotes, and viruses. Although we focus on the nature of the nomenclatural codes, we briefly discuss fundamental principles of taxonomy, including classification and identification. Key elements of the codes of nomenclature that ensure stability and clarity when naming species of pathogens are defined. When comparing the practice of nomenclature across different kingdoms, the classification and nomenclatural systems differ, and thus unique challenges are faced. We provide guidance from the codes and current practice for naming novel species. When there are nomenclatural conflicts, international committees play a critical role in their resolution. They also play a role in updating the codes to reflect new advancements in science. With this review, we aim to assist plant pathologists, journal editors, and those in related fields by providing an entrée to the legalistic requirements of the codes. Authors must consult and follow the rules of the appropriate code for any proposal of new or new combinations of names. To those interested in naming new species (or renaming the current ones), we recommend collaborations with experts in the field of taxonomy to ensure that rules for accurate and consistent naming practices and procedures are followed and to increase the likelihood that the proposed nomenclature is correct and acceptable.
Cryphonectriaceae : biodiverse and threatening tree pathogens in the tropics and southern hemisphere
Wingfield, Michael J.; Pham, Nam Q.; Marincowitz, Seonju; Wingfield, Brenda D. (Annual Reviews, 2025-09)
The chestnut blight pathogen Cryphonectria parasitica is well-known for the devastation it caused to North American forests. It is less well recognized that numerous other fungi in the Cryphonectriaceae are emerging as threats to native and planted forests in the tropics and Southern Hemisphere. Unlike C. parasitica, these fungi, such as Chrysoporthe cubensis, initially gained attention due to a canker disease in plantations of non-native Eucalyptus. More than four decades of research have revealed a wide diversity of Cryphonectriaceae species that infect many other tree genera in the Myrtales. These fungi often exist as endophytes but become problematic when trees are planted outside their native range. Growing numbers of species are also undergoing host shifts from native to susceptible trees such as Eucalyptus, posing serious risks to both natural and planted forests. These fungi provide an example of the biodiversity of tree-infecting fungi that is understudied, despite their significant potential to harm forest ecosystems.
Investigating bark, ambrosia and nitidulid beetle (Coleoptera : Scolytinae and Nitidulidae) communities and their potential role in the movement of Ceratocystis manginecans in commercial forestry plantations in Riau, Indonesia
Lynn, Kira Mary Theresa; Wingfield, Michael J.; Tarigan, Marthin; Duran, Alvaro; Santos, Samuel A.; Nel, Wilma Janine; Barnes, Irene (Wiley, 2025-11)
Ceratocystis Canker and Wilt Disease (CCWD), caused by the fungal pathogen Ceratocystis manginecans, poses a significant threat to Acacia and Eucalyptus plantations in Indonesia. Infections typically occur through wounds on the main stems of trees, and infected trees, particularly Acacia, are often co-infested by various wood-associated beetles. The aim of this study was to identify the beetle species associated with Ceratocystis-infected trees and to assess their potential role in dispersing C. manginecans. Beetle and frass samples were collected from Ceratocystis-infected compartments of Acacia and Eucalyptus propagated as monocultures in Riau, Indonesia, either by using traps or by direct collection from infected trees. The samples were screened for the presence and viability of Ceratocystis propagules using a quantitative polymerase chain reaction-high-resolution melting analysis (qPCR-HRMA) diagnostic tool and a carrot baiting technique, respectively. Fourteen beetle species, predominantly collected from traps, representing nine genera of the Scolytinae and Nitidulidae, were identified from the two plantation types. The qPCR tool detected the presence of Ceratocystis DNA on 13 of the 14 beetle species at concentrations as low as 0.015–0.0019 ng. However, viable Ceratocystis propagules could not be recovered from these beetles using culture-based methods. Of the 105 frass samples screened, qPCR detected Ceratocystis DNA in 67 samples; however, only one Ceratocystis isolate was obtained using the carrot baiting method. The results of this study suggest that the beetles and beetle frass can harbour Ceratocystis propagules, as indicated by the detection of fungal DNA. However, the viability of the propagules and the ability of the beetles and/or beetle frass to spread C. manginecans requires further investigation.
Early detection of Phytophthora root rot in Eucalyptus using hyperspectral reflectance and machine learning
Esterhuizen, Hendrik J.; Slippers, Bernard; Bosman, Anna Sergeevna; Roux, Jolanda; Jones, Wayne; Bose, Tanay; Hammerbacher, Almuth (Elsevier, 2025-10)
The rising prevalence of Phytophthora diseases in forests highlights the need for rapid, non-invasive detection methods. Early-stage root infections are difficult to detect due to the absence of visible above-ground symptoms, while current diagnostics remain slow and invasive. This study investigated whether hyperspectral leaf reflectance could detect root rot caused by Phytophthora alticola in Eucalyptus benthamii. Nineteen commercially planted families were inoculated, and leaf spectra were collected using an ASD FieldSpec 4 sensor. A machine learning pipeline was developed to identify diagnostic spectral signals. Key wavelengths were identified using permutation importance, a genetic algorithm, and self-attention network (SAN) scores. Spectral signals linked to root rot revealed that infection was correlated with leaf pigment accumulation and moisture stress. Three algorithms, random forest (RF), support vector machine (SVM), and SAN, were trained on hyperspectral data to predict P. alticola infection. The SAN achieved 97 % accuracy on a reduced dataset, which included the diagnostic wavelengths from the feature selection step, surpassing the RF (96 %) and SVM (94 %) models. This study demonstrates hyperspectral sensing as an effective tool for detecting Phytophthora root rot using spectra from the foliage and highlights the application of advanced machine learning techniques for plant disease classification. HIGHLIGHTS • Hyperspectral sensing detects Phytophthora root rot before symptoms appear. • SAN model achieved 97 % accuracy using selected wavelengths from leaf spectra. • Key wavelengths correlated with pigment shifts and moisture stress in leaves. • Machine learning identified spectral markers for early disease detection. • Vegetation indices NDNI and MSI are strongly linked to infection status.
Chemodiversity of penicillium isolated from alpine and arctic environments, including ten new species
Overy, D.P.; Frisvad, J.C.; Witte, T.E.; Hicks, C.L.; Hermans, A.; Sproule, A.; Louis-Seize, G.; Seifer, K.A.; Yilmaz, Neriman; Price, Jodi; Van Vuuren, Nicole Innike; Visagie, Cobus M. (Westerdijk Fungal Biodiversity Institute, 2025-08-01)
Polar, high altitude montane and cold desert environments harbour only sparse plant life and often remain frozen for extended periods. Because of their remoteness, often combined with restricted access, such regions are rarely visited and the fungal biodiversity of the soils is scarcely studied. Despite this, when such studies are undertaken, psychrophilic Penicillium species are often reported and the isolates exhibit a high spectrum of biologically active compounds of biotechnological interest. Small molecule profiling by mass spectrometry (often called ‘metabolomics’) can supplement phylogenetic species concepts and provide information to characterize variation within species or populations. During large scale fungal isolation surveys exploring new psychrophilic fungi from high altitude alpine and arctic tundra soils, several undescribed Penicillium species were discovered. A polyphasic taxonomic approach was adopted to formally describe ten new species using multigene phylogenetic analyses and phenotypic characterizations including secondary metabolite production, colony characters, and microscopic analysis of morphological structures. Using untargeted metabolomics and molecular networking tools, an emphasis was made to characterize, compare and discuss in depth, the chemical diversity associated with these new Penicillium species.
Factors that influence the flight activity, abundance and infestation severity of the polyphagous shot hole borer beetle (PSHB, Euwallacea fornicatus) in an urban-agricultural fringe setting
Roberts, Elise; Paap, Trudy; Roets, Francois (Elsevier, 2025-10)
The polyphagous shot hole borer (PSHB, Euwallacea fornicatus) has invaded multiple countries, including South Africa. Along with its fungal mutualist, PSHB has caused the death of a wide range of tree species. Unmitigated costs of invasion in South Africa are estimated to be high. This study consisted of a 26-month PSHB monitoring programme using baited traps in an urban-agricultural fringe setting in the Western Cape province, focusing on revealing the factors most important to flight activity, beetle abundance, and infestation severity. It also tested the validity of felling infested trees as a management option to reduce beetle numbers (propagule pressure). More than half of the 94 study plots evaluated had PSHB-infested trees. Beetle flight activity was highest in summer and negligible in winter, with flight activity being positively correlated with temperature, beetle developmental degree days and beetle flight hours. The surrounding abundance of infested hosts was positively correlated with beetle abundance and infestation levels, though “saturation” in the infestation of a focal host tree may be a deterrent to dispersing beetles. Trees in plots that experience water stress (seasonal flooding) had higher dispersing beetle abundance and infestation levels, suggesting that tree stress might play a role in attracting beetles or making trees more vulnerable to infestation. Beetle activity during tree felling echoed the overall seasonal trend, and higher numbers of dispersing beetles on the day of tree felling in summer suggest that felling activities should best be conducted in winter. For three host tree species, infestation severity increased with decreasing tree size, which may be due to larger trees having thicker bark or other better defence systems. This study provides insight into the ecology of PSHB in this region of South Africa, which is important for developing monitoring and management strategies.

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