Research Articles (Biochemistry, Genetics and Microbiology (BGM))

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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.
Cross-continental soil prokaryotic traits driven by precipitation regime and land cover
Donhauser, Jonathan; Han, Xingguo; Doménech-Pascual, Anna; Jordaan, Karen; Casas-Ruiz, Joan P.; Ramond, Jean-Baptiste; Romaní, Anna Maria; Frossard, Aline; Priemé, Anders (Nature Research, 2026-01)
Trade-offs among traits determine microbial community dynamics and affect soil carbon-cycling feedback to climate change. Here, we determined soil prokaryotic traits based on a novel marker gene-based workflow using cross-continental temperature and aridity gradients. Genome streamlining and high 16S rRNA gene copy numbers per genome (RRN) conferred high maximal growth rates, possibly by allowing for smaller cells with higher surface to volume ratio. Small genomes and high maximal growth rates were found under high precipitation seasonality and in barren soils. Large genomes and low maximal growth rates were found in forests, characterized by high water availability and by abundant and complex organic resources. Our findings suggest that large genomes confer versatility to cope with resource fluctuations and moderate climatic fluctuations while extreme climatic fluctuations and scarcity of resources promote genome streamlining. Seasonal fluctuations in water availability were associated with the ability to form spores and with rapid resuscitation, promoted by high RRN. Moreover, Prokaryotes were less dispersal limited compared to Fungi, presumably due to their smaller size, but within Prokaryotes, small taxa were not more ubiquitous. Our trait-based framework highlights that particularly changes in precipitation patterns and vegetation type will cause changes in microbial processes under future climate.
Did the WHO recognition of snakebite as a neglected tropical disease impact national NTD master plans in 15 African countries?
Stienstra, Ymkje; Clevering, Ymkje; Kokhuis, Sanne; Amuasi, John Humphrey; Padidar, Sara; Schurer, Janna M.; Mijumbi-Deve, Rhona M.; Thomson, Rachael; Oluoch, George O.; Mbonigaba, Jean Bosco; Lalloo, David G. (Elsevier, 2026-02)
In 2018, the World Health Organization (WHO) acknowledged Snakebite Envenoming (SBE) as a Neglected Tropical Disease (NTD). The WHO set a target for 2030 to halve the number of snakebite victims and published a roadmap to assist affected countries with drafting national SBE policies. These national SBE policies define the course of action to reach country specific and global goals. In order to review the policy environment needed to reduce the burden, we studied if SBE policy was included in national NTD programmes and if it included the four WHO SBE policy aims and a vision for the integration of NTDs. National NTD masterplans were reviewed and combined with in-depth interviews focusing on stakeholders' experience with the integration of SBE in NTD programmes, and the influence of the inclusion of SBE on the NTD list. Only 18 % (2 out of 11) of 2015-2020 NTD masterplans mentioned SBE whereas all twelve countries who published masterplans for 2020-2025 included SBE and the need for an integrated approach between NTD programmes. Information on the type of activities allowing integration or the organizational aspects of an integrated approach was often missing. The extent to which the core policy aims of the WHO SBE roadmap has been elaborated differs considerably from country to country. In the interviews, several stakeholders raised the importance of improving the quality of epidemiological data to convince policy makers of its importance, to base antivenom distribution and to facilitate overall policy making. The path of improvement that has been taken since the recognition of SBE as an NTD must be continued and benefits from a closer collaboration between policymakers, researchers and healthcare workers to reduce the evidence gap and, ultimately, to improve care. HIGHLIGHTS • After the acknowledgment of SBE as NTD the national NTD masterplans more commonly included SBE. • The level of detail of SBE plans in the policy documents was low. • Stakeholders emphasized the lack of robust data on the SBE burden to lead to challenges in developing national policies.
Targeting Aurora kinases as essential cell-cycle regulators to deliver multi-stage antimalarials against Plasmodium falciparum
Langeveld, Henrico; Maree, Marche; Thibaud, Jessica L.; Salomane, Nicolaas; Bridgwater, Rosie; Famodimu, Mufuliat T.; Godoy, Luiz C.; Pasaje, Charisse Flerida A.; Boonyalai, Nonlawat; Laureano de Souza, Mariana; Fong, Justin; Rabie, Tayla Anne; Van der Watt, Mariette Elizabeth; Birkholtz, Lyn-Marie (Wiley, 2025-12)
Kinases play critical roles in the development and adaptation of Plasmodium falciparum and present novel opportunities for chemotherapeutic intervention. Mitotic kinases that regulate the proliferation of the parasites by controlling nuclear division, segregation, and cytokinesis. We evaluated the potential of human Aurora kinase (Aur) inhibitors to prevent P. falciparum development by targeting members of the Aurora-related kinase (Ark) family in this parasite. Several human AurB inhibitors exhibited multistage potency (< 250 nM) against all proliferative stages of parasite development, including asexual blood stages, liver schizonts, and male gametes. The most potent compounds, hesperadin, TAE684, and AT83, exhibited > 1000x selectivity towards the parasite. Importantly, we identified PfArk1 as the principal vulnerable Ark family member, with specific inhibition of PfArk1 as the primary target for hesperadin. Hesperadin’s wholecell and protein activity validates it as a unique PfArk1 tool compound. Inhibition of PfArk1 results in the parasite’s inability to complete mitotic processes, presenting with unsegregated, multi-lobed nuclei caused by aberrant microtubule organization. This suggests PfArk1 is the main Aur mitotic kinase in proliferative stages of Plasmodium, characterized by bifunctional AurA and B activity. This paves the way for drug-discovery campaigns based on hesperadin targeting PfArk1.
Influence of the Benguela Upwelling System on the genetic connectivity of blacktail seabream Diplodus capensis across southern Africa
Olivier, W.F.; Potts, W.M.; Childs, A.-R.; Santos, C.; Shaw, P.W.; Henriques, Romina (Taylor and Francis, 2025-12-22)
Oceanographic features such as upwelling cells and currents contribute to shaping the evolutionary history of marine fishes, including species that may be important socio-economic resources. However, the impacts of these barriers are often cryptic and may change, particularly in a rapidly changing climate. Hence, sustainable fisheries management strategies need to take into consideration the influence of oceanographic barriers to the genetic structure of populations. Here, we evaluated the influence of the Benguela Upwelling System, a known barrier for warm-temperate fishes, on the evolutionary history of the blacktail seabream Diplodus capensis (family Sparidae), using eight microsatellite loci in conjunction with DNA barcoding of the cytochrome c oxidase 1 gene. Diplodus capensis is an important recreational and small-scale fishery species, distributed across southern Africa. Overall, there was significant genetic differentiation across the region, but the level of divergence varied with the genetic marker. Our results identified two isolated populations—in the northern and southern subsystems of the Benguela Upwelling System—with limited contemporary gene flow, and no sub-structuring detected within the subsystems. Because the species is vulnerable to exploitation, with declines in South Africa, our results suggest that management policies should aim at regional levels for the northern population (off Angola and Namibia), whereas the southern population (off South Africa) was identified as an isolated and highly connected population.
Subgenome partitioning and polyploid genome evolution in the Loach Family Botiidae (order Cypriniformes)
Lv, Yunyun; Li, Jia; Li, Yanping; Huang, Yu; Lai, Qiang; Wen, Zhengyong; Wang, Jun; He, Yang; Shi, Jinrong; Huang, Zejin; Jiang, Ying; Van de Peer, Yves; Shi, Qiong; Xie, Biwen; Wang, Yongming (Wiley, 2025-09)
Vertebrates have undergone two rounds of whole-genome duplication (WGD), termed 1R and 2R, with a third, teleost-speciﬁc duplication (TSGD or 3R) occurring in ray-ﬁnned ﬁshes. In the order Cypriniformes, additional lineage-speciﬁc WGDs have further contributed to species diversiﬁcation. While polyploidy is well characterized in species like common carp and goldﬁsh, other polyploid taxa—particularly loaches—remain understudied. Here, high-quality, chromosome-level genome assemblies are presented fortwo loach species: Sinibotia superciliaris (Golden Chinese Loach) and Parabotia fasciatus (Yichang Sand Loach). By integrating these genomes into a comparative framework with 20 other cypriniform species, key phylogenetic relationships are reconstructed, and introduce a novel subgenome partitioning method (M3). Unlike previous approaches, M3 uses diﬀerential sequence divergence to accurately and rapidly assign subgenomes, completing partitioning within minutes and outperforming existing tools. Applying M3, a markedly reduced subgenome is uncovered in the Golden Chinese Loach, with lineage-speciﬁc molecular changes in several candidate genes, suggesting potential adaptive signiﬁcance. This study oﬀers a comprehensive view of polyploidy and subgenome evolution in loaches, highlighting the genomic complexity shaped by repeated WGDs in Cypriniformes and providing valuable resources for future research on vertebrate genome evolution and adaptation
Investigation of the potential of phytochemicals derived from citrus peels to inhibit digestive enzymes : an overture to the management of lifestyle diseases
Moloi, Lebohang; Samson, Sana; Tshiyoyo, Kadima Samuel; Maluleke, Kamogelo C.; Oberholzer, Marni; Baloyi, Itumeleng Tsebang; Malgas, Samkelo (Taylor and Francis, 2025-12)
The food industry relies on citrus fruits for juice, canned fruit, and jam, creating significant waste from peels, seeds, and pomace. This waste contains valuable phytochemicals like carotenoids, essential oils, (poly)phenols, pectin, and vitamins, which can be used as nutraceuticals or key ingredients in functional foods for managing diabetes and obesity. Repurposing citrus peel waste offers an excellent opportunity to advance biorefineries and the bioeconomy. Compounds derived from citrus have attracted attention for their potential therapeutic effects on diabetes and obesity, and their effectiveness depends on various mechanisms. This review summarises citrus-derived phytochemicals that inhibit α-glucosidase and pancreatic lipase in vitro, highlighting their potential as anti-diabetic and anti-obesity compounds. We also discuss progress in using molecular docking screening against key drug targets linked to type II diabetes and obesity. This review explores novel citrus phytochemicals for the development of nutraceuticals and functional food ingredients with enhanced health benefits.
Tundrisphaera macrotermitis sp. nov., a novel member of the family Isosphaeraceae isolated from the gut of a fungus-growing termite
Kallscheuer, Nicolai; Carlstedt, Kim-Loreen; Hammer, Jonathan; Haufschild, Tom; Benndorf, René; De Beer, Z. Wilhelm; Poulsen, Michael; Beemelmanns, Christine; Jogler, Christian (Nature Research, 2025-11)
A pink-pigmented, neutrophilic and mesophilic strain, TA3T, was isolated from the hindgut of a fungus-growing termite of the species Macrotermes natalensis. Phylogenetic analysis placed the strain in the family Isosphaeraceae, order Isosphaerales, class Planctomycetia, phylum Planctomycetota. The isolate turned out to be an aerobic chemoorganoheterotroph capable of growth under microaerobic conditions. Cells are non-motile, spherical, and either form shapeless aggregates or grow as single cells. The average cell size (length x width) is 2.5 ± 0.3 μm x 2.3 ± 0.2 μm. Cells divide asymmetrically by budding. Optimum pH and temperature for growth are 7.5 (range 6.0–9.0) and 24 °C (range 18–28 °C), respectively. The strain has a genome size of 7.23 Mbp with 69.3% DNA G + C content and it contains four plasmids. Since the genome of the currently known closest relative Tundrisphaera lichenicola has not been sequenced, the previously characterized type strain P12T was included for genome sequencing. A comparison based on established phylogenetic markers yielded a 16S rRNA gene sequence similarity of 94.8%, an average nucleotide identity of 78.4% and a digital DNA-DNA hybridization (dDDH) value of 20.3%, suggesting a relationship of the two strains on the level of the same genus. Differences in genome-encoded features, e.g. carbohydrate-active enzymes, secondary metabolite-associated biosynthetic gene clusters and plasmid-located genes were analyzed using comparative genomics. Together with whole genome-based phylogenetic analyses and differences in phenotypic characteristics, the data justifies the delineation of the novel isolate from the sole known species in the genus Tundrisphaera. We therefore introduce Tundrisphaera macrotermitis sp. nov. that is represented by TA3T (= CECT 30560T = STH00997T) as the type strain.
Synergistic effects of bioactive plant extract mixtures on methane reduction and rumen fermentation of Eragrostis curvula hay in vitro
Akanmu, Abiodun Mayowa; Hassen, Abubeker; Van Marle-Koster, Este; Azaizeh, Hassan; Apostolides, Zeno; Landau, Serge Yan (Nature Research, 2025-10-07)
Building on prior research indicating the methane-mitigating potential of specific medicinal plants for ruminant animals. This study aimed to investigate the associative effects of combining six medicinal plant extracts known for their methane-reducing properties: Aloe vera (AV), Carica papaya (CP), Azadirachta indica (AZ), Tithonia diversifolia (TD), Jatropha curcas (JA), and Moringa oleifera (MO). Methanolic extracts of the plants were combined in equal proportions into two-way mixtures and applied at a concentration of 50 mg/L to 400 mg Eragrostis curvula hay, followed by a 48-hour in vitro incubation. Phytochemical profiling of individual plant extracts was performed using LC-MS and HPLC methods. Evaluated parameters included methane (CH4) production, total gas production (TGP), in vitro organic matter digestibility (IVOMD), ammonia nitrogen, and volatile fatty acids (VFA). Phytochemical profiling revealed diverse bioactive compounds such as flavonoids, saponins, anthraquinones, phenols, alkaloids, and terpenoids in all extracts, with AZ showing the highest phenolic content. The mixtures significantly reduced CH4 production by over 50%, individual plant extracts generally showed greater improvements in IVOMD compared to mixtures. Moreover, the mixture displayed positive associative effects on various parameters, including TVFA, CH4/IVOMD, CH4/TGP, and CH4/TVFA production. Two-way mixture containing AV or CP (AV + CP, AV + JA) notably increased propionic acid concentration, differentiating them from single plant extracts, monensin, and control treatments. The study highlights that specific combinations of these medicinal plant extracts can significantly reduce methane emissions while positively modulating rumen fermentation parameters, indicating their potential as natural additives for sustainable livestock production.
From chaos to tranquillity : a modern approach to the identification, nomenclature and phylogeny of Aspergillus, Penicillium and other Eurotiales, including an updated accepted species list
Visagie, Cobus M.; Houbraken, J.; Overy, D.P.; Sklenář, F.; Bensch, K.; Frisvad, J.C.; Mack, J.; Perrone, G.; Samson, R.A.; Van Vuuren, Nicole Innike; Yilmaz, Neriman; Hubka, V. (Westerdijk Fungal Biodiversity Institute, 2025)
Eurotiales is a diverse and speciose order and includes economically important genera like Aspergillus, Penicillium, Paecilomyces and Talaromyces. Historically, species identifications based on morphology are challenging. The publication of accepted species lists and the availability of representative DNA sequences for type strains have contributed greatly towards accurate species identification and facilitated the description of many new species. However, despite current advancements, a proportion of newly described species within these taxonomically challenging genera represent, in fact, existing species, which raises obvious concerns. This study thus aimed to further modernise the taxonomy of Eurotiales by addressing key challenges in species identification and classification. Our study objectives were threefold: 1) to review species described after 2023, 2) update the accepted species list, and 3) release a curated DNA sequence dataset to facilitate future species identifications. We conclude that a move to a phylogenetic species concept is necessary but continue to support the inclusion of morphological descriptions and, where possible, associated secondary metabolite, exoenzyme, physiology and ecological data when introducing new species. Based on our phylogenetic analyses, we accept 130 of 171 species described since 2023 but reduce 41 to synonyms. Furthermore, we also reduced 17 species described pre-2023 to synonyms. Our list now contains 1393 species classified into four families and 26 genera, with Aspergillus (n = 465), Penicillium (n = 598) and Talaromyces (n = 236) containing the most species. To aid sequence-based identifications and species descriptions under a phylogenetic species concept, we release a curated DNA reference sequence database containing 18837 DNA sequences (3867 ITS, 5277 BenA, 5110 CaM and 4583 RPB2) generated from 5325 strains. Sequences were selected to best cover the infraspecies variation under our current understanding of each species. The species list and sequence database will be kept up to date as new information becomes available and will remain available at https://doi.org/10.5281/zenodo.16605949. This manuscript presents a major leap towards our goal to facilitate work with Eurotiales, while providing the taxonomic framework to support research excellence related to this important fungal group.
Low genotypic diversity and first reports of clinical Sporothrix from retrospective samples in South Africa
Fuchs, Taygen; Vismer, Hester F.; Visagie, Cobus M.; Wingfield, Brenda D.; Wingfield, Michael J. (Oxford University Press, 2025-11)
Sporotrichosis is a fungal infection caused by Sporothrix species. Some of the largest outbreaks of this disease have been recorded in South Africa, and the country is considered an endemic region for the pathogen. Previous work in the 1990s considered the etiological agents of the disease, with strains stored in various culture collections. In this study, we reconsidered the identity of these strains by polymerase chain reaction amplification and sequencing of three gene regions (ITS, BenA, and CaM) and assessed their genetic diversity by microsatellite typing. The results showed that the population included four species, S. schenckii (n = 69), S. globosa (n = 1), S. pallida (n = 1), and an uncharacterised taxon (n = 2). The mating type distribution of the S. schenckii population was predominantly of the MAT1-2 idiomorph (92%). Microsatellite markers revealed only four multi-locus genotypes, of which a single genotype represented 85% of the isolates. The results provide evidence for asexual proliferation of S. schenckii lineages in South Africa, and raise questions as to how they have been dispersed. Furthermore, the results highlight uncertainties regarding the relative significance of the other species reported here. PLAIN LANGUAGE SUMMARY : Sporotrichosis is a mammalian cutaneous traumatic infection caused by pathogenic Sporothrix fungi. Using genetic markers, we report several Sporothrix species in South Africa for the first time, and reveal the wide distribution of a closely related genetic lineage in the country.
Mycotoxins : an ongoing challenge to food safety and security
Yilmaz, Neriman; Verheecke-Vaessen, Carol; Ezekiel, Chibundu N. (Public Library of Science, 2025-11-10)
Mycotoxins have influenced human and animal health for centuries, often with serious and sometimes deadly consequences. The earliest known cases are outbreaks of ergotism in medieval Europe, caused by alkaloids from Claviceps purpurea growing on rye. These epidemics, called “St Anthony’s fire”, produced convulsions, gangrene and death. Ergot-infected grain has also been suggested as a possible factor behind the symptoms recorded during the Salem witch trials in 1692. During the Second World War, people in Russia consumed overwintered grain infected by trichothecene-producing Fusarium species. This led to the alimentary toxic aleukia epidemic, one of the best-documented examples of human mycotoxicosis. Such outbreaks demonstrate the longstanding impact of mycotoxins on societies.
Smallholder farmers’ knowledge, perception and management of Spodoptera frugiperda (Lepidoptera: Noctuidae) on Zea mays at irrigation schemes in Limpopo province, South Africa
Nethononda, Phophi D.; Hurley, Brett Phillip; Slippers, Bernard; Makhura, Moraka Nakedi (Elsevier, 2026-03)
The fall armyworm (Spodoptera frugiperda) was first detected in Limpopo province, South Africa, during the 2016/2017 cropping season and continues to cause significant damage to maize production in the region. Despite the significant damage caused by S. frugiperda to maize, there is a lack of documented information on smallholder farmers' responses and control practices in South Africa. This study investigated smallholder farmers' knowledge, perceptions, and management practices of S. frugiperda at the Dzindi and the Tshiombo irrigation schemes in Limpopo province, South Africa. In this study, an irrigation scheme refers to a communal water distribution system that channels water from a river to multiple plots under smallholder cultivation through furrows or canals. Data were collected through 16 focus group discussions with farmers from the two irrigation schemes. A total of 118 farmers participated in the interviews. Each was assigned a unique identifier, which allowed for the recording and analysis of individual responses where applicable. Thematic analysis was used to identify and summarize common themes from participants’ responses, while descriptive analysis using frequencies and percentages was employed to present the responses quantitively. Farmers perceived S. frugiperda as the most destructive insect pest, yet lacked knowledge of its biology, being unable to identify its eggs, pupae, or adult moths. Control was largely through insecticide use. At the Dzindi irrigation scheme, farmers adopted Bt maize but did not comply with resistance management practices. The findings underscore the urgent need for farmer education on insect biology, responsible pesticide use, and proper implementation of Bt maize. The study also highlights the importance of collective rather than individual efforts in managing S. frugiperda, as the consequences of mismanagement can affect all farmers. These findings reveal major gaps in Integrated Pest Management (IPM) practices among smallholder farmers in Limpopo province, South Africa. HIGHLIGHTS • First detection of Spodoptera frugiperda in Limpopo Province, South Africa, occurred during the 2016/2017 cropping season. • Smallholder farmers lack knowledge of the pest's biology, relying on insecticides for its management. • Concurrent use of insecticides and Bt maize raises concerns over the potential evolution of S. frugiperda resistance in the region.
Diversification of an emerging bacterial plant pathogen; insights into the global spread of Xanthomonas euvesicatoria pv. perforans
Timilsina, Sujan; Iruegas-Bocardo, Fernanda; Jibrin, Mustafa O.; Sharma, Anuj; Subedi, Aastha; Kaur, Amandeep; Minsavage, Gerald V.; Huguet-Tapia, Jose C.; Klein-Gordon, Jeannie; Adhikari, Pragya; Adhikari, Tika B.; Cirvilleri, Gabriella; Tapia de la Barrera, Laura Belen; Bernal, Eduardo; Creswell, Tom C.; Doan, Tien Thi Kieu; Coutinho, Teresa A.; Egel, Daniel S.; Félix-Gastélum, Rubén; Francis, David M.; Kebede, Misrak; Ivey, Melanie Lewis; Louws, Frank J.; Luo, Laixin; Maynard, Elizabeth T.; Miller, Sally A.; Nguyen, Nga Thi Thu; Osdaghi, Ebrahim; Quezado-Duval, Alice M.; Roach, Rebecca; Rotondo, Francesca; Ruhl, Gail E.; Shutt, Vou M.; Thummabenjapone, Petcharat; Trueman, Cheryl; Roberts, Pamela D.; Jones, Jeffrey B.; Vallad, Gary E.; Goss, Erica M. (Public Library of Science, 2025-04-09)
Emerging and re-emerging plant diseases continue to present multifarious threats to global food security. Considerable recent efforts are therefore being channeled towards understanding the nature of pathogen emergence, their spread and evolution. Xanthomonas euvesicatoria pv. perforans (Xep), one of the causal agents of bacterial spot of tomato, rapidly emerged and displaced other bacterial spot xanthomonads in many tomato production regions around the world. In less than three decades, it has become a dominant xanthomonad pathogen in tomato production systems across the world and presents a compelling example for understanding diversification of recently emerged bacterial plant pathogens. Although Xep has been continuously monitored in Florida since its discovery, the global population structure and evolution at the genome-scale is yet to be fully explored. The objectives of this work were to determine genetic diversity globally to ascertain if different tomato production regions contain genetically distinct Xep populations, to examine genetic relatedness of strains collected in tomato seed production areas in East Asia and other production regions, and to evaluate variation in type III secretion effectors, which are critical pathogenicity and virulence factors, in relationship to population structure. We used genome data from 270 strains from 13 countries for phylogenetic analysis and characterization of type III effector gene diversity among strains. Our results showed notable genetic diversity in the pathogen. We found genetically similar strains in distant tomato production regions, including seed production regions, and diversification over the past 100 years, which is consistent with intercontinental dissemination of the pathogen in hybrid tomato production chains. Evolution of the Xep pangenome, including the acquisition and loss of type III secreted effectors, is apparent within and among phylogenetic lineages. The apparent long-distance movement of the pathogen, together with variants that may not yet be widely distributed, poses risks of emergence of new variants in tomato production.
Decoding Cryptococcus : from African biodiversity to worldwide prevalence
Coelho, Marco A.; David-Palma, Ma´rcia; Aylward, Janneke; Pham, Nam Q.; Visagie, Cobus M.; Fuchs, Taygen; Yilmaz, Neriman; Roets, Francois; Sun, Sheng; Taylor, John W.; Wingfield, Brenda D.; Fisher, Matthew C.; Wingfield, Michael J.; Heitman, Joseph (Public Library of Science, 2025-02-03)
Fungal pathogens cause millions of infections and deaths annually, while also contributing to global food insecurity [1]. Among them, basidiomycete Cryptococcus species—particularly C. neoformans (Cn; previously C. neoformans var. grubii, serotype A; lineages VNI, VNII, VNBI, and VNBII), C. deneoformans (Cd; previously C. neoformans var. neoformans, serotype D; lineage VNIV), and the C. gattii (Cg) species complex (Fig 1A)—are significant opportunistic and primary pathogens, especially in sub-Saharan Africa [2,3]. These pathogens primarily cause cryptococcosis, manifesting as severe pulmonary infections or life-threatening meningoencephalitis in both immunocompromised and apparently immunocompetent individuals. Exposures are typically thought to occur by inhalation of desiccated yeast cells or spores from the environment [4]. While Cryptococcus species vary in their occurrence worldwide, mounting evidence suggests an evolutionary origin in Africa for most of the pathogenic Cryptococcus species, where they occupy diverse ecological niches such as trees, pigeon guano, and mammalian middens (Fig 1B). While Cn, Cd, and Cg are pathogenic, nonpathogenic species within the genus (such as C. amylolentus, C. wingfieldii, and C. floricola; Fig 1A) occur either as African microendemic species or are known thus far from only a single isolate in the Canary Islands (C. floricola) [5,6]. This review explores the likely African origins of Cryptococcus, its ecological diversity, and how pathogenic species spread globally, transitioning from environmental microbes to human pathogens.
The hidden cost of open access : artificial intelligence, paywalls and the risk of knowledge inequity
Wingfield, Brenda D.; Wingfield, Beverly Jane (Academy of Science of South Africa, 2025-11)
SIGNIFICANCE : This Commentary underscores the urgency of rethinking how artificial intelligence systems and publishing models intersect. Rather than focusing solely on efficiency or access, we call attention to structural inequities that shape who is visible in the scholarly record. By highlighting the systemic risks of exclusion, we argue for proactive collaboration between policymakers, publishers and technologists to design frameworks that safeguard equity and inclusivity in the future of academic research.
Comparative genomics reveals adaptive traits in novel Antarctic lithic cyanobacteria
Van Goethem, Marc W.; Vikram, Surendra; Cowan, Don A.; Makhalanyane, Thulani P. (BioMed Central, 2025-11-05)
BACKGROUND : Terrestrial polar cyanobacteria persist at the cold limits of life, enduring a suite of extreme stressors including sub-zero temperatures, frequent freeze–thaw cycles, oligotrophic soils, variable light regimes with long periods of darkness, and desiccation. To survive, cyanobacteria have evolved diverse physiological strategies. A key adaptation among Antarctic terrestrial cyanobacteria is niche colonization: inhabiting the undersides of translucent quartz rocks (hypoliths) and the interior spaces of porous rocks (endoliths), which buffer environmental extremes and sustains the potential for photoautotrophic carbon fixation. However, the full genomic repertoire facilitating their resilience is incomplete. RESULTS : We cultivated cyanobacteria from endolithic and hypolithic niches in Victoria Valley, Eastern Antarctica, and recovered four near-complete genomes (100% completeness, < 1% contamination). Three hypolithic genomes showed near-identical sequence similarity (whole genome average nucleotide identity = 99.98%) and phylogenomic proximity to the genus Coleofasciculus, yet represent a novel species, Coleofasciculus caryii H7-2. The fourth genome, derived from an endolith, showed moderate similarity to Aliterella antarctica (whole genome average nucleotide identity = 79.1%), and is proposed as a new species, Aliterella bergstromii E5.1. C. caryii H7-2 possessed a larger genome (~ 6.1 Mbp) than A. bergstromii E5.1 (~ 5.4 Mbp). Both genomes encoded complete pathways for carbon fixation via oxygenic photosynthesis (RuBisCO and phosphoribulokinase), extensive phycobilisomes, and multiple photoprotective mechanisms. Predicted optimal growth temperatures were 21.7 °C and 23.2 °C, respectively. Shared stress-mitigation genes included those for osmotic, thermal and oxidative (superoxide dismutase) stress response. All genomes contained biosynthetic gene clusters associated with stressadaptive secondary metabolites, including heterocyst glycolipids, siderophores, phenazines, compounds related to nostopeptolide and merocyclophane. The C. caryii H7-2 genome encoded multiple CRISPR-Cas systems, suggesting adaptive immunity and historical phage exposure. In contrast, A. bergstromii E5.1 harboured a single prophage and an array of 24 plasmids. CONCLUSIONS : These finding reveal that the newly-described cyanobacteria possess a rich genomic repertoire of adaptations to withstand Antarctic extremes, emphasizing the resilience and ecological importance of lithobiontic cyanobacteria in polar deserts.
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.

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