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

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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.
Diversity of environmental Escherichia coli in subtropical freshwater systems of South Africa
Seale, Tarren; Brözel, Volker Siegfried; Potgieter, Sarah Catherine; Rupp, Oliver; Blom, Jochen; Steenkamp, Emma Theodora; Venter, S.N. (Stephanus Nicolaas) (Springer, 2025-07)
Escherichia coli is widely used as an indicator of faecal contamination, as it is assumed that faeces from warm-blooded animals is the primary source of E. coli in the environment. However, various studies have shown that E. coli can survive and multiply in environmental niches, including soil, sand and sediment. E. coli can be assigned to eight main phylogroups but environmental E. coli are associated primarily with phylogroups A and B1. In this study, 410 E. coli were isolated from different niches within two peri-urban catchments in the Gauteng province of South Africa. To represent the E. coli circulating within the human population, E. coli was also isolated from sewage before treatment and released into these reservoirs. To capture the diversity of E. coli among these isolates, the β-D-glucuronidase (uidA) and mismatch repair (mutS) genes were sequenced. While isolates linked to phylogroup B1 dominated as was expected, the recovery of many isolates linked to phylogroup B2, the second most dominant group, was unanticipated. To further investigate this observation, the genomes of representative phylogroup B2 isolates were sequenced and subjected to phylogenetic and functional analyses. The results showed that phylogroup B2 isolates formed a distinct phylogenetic cluster, apparently independent of niche or geographic origin. Our findings also showed that while isolates seem to be associated with environmental samples, they could have the ability to colonize the gut and cause disease as they harboured several virulence factors associated with extraintestinal E. coli.
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.
High-resolution climate downscaling using terrain features and global circulation models : applications for species suitability in the management of plantation forestry
Van der Merwe, Jaco Pierre; Van Heerden, Elane; Germishuizen, Ilaria; Christie, Nanette; Kok, James; Ncongwane, Thandekile H.; Spencer, Katharine; Melane, Mandlakazi; Mansfield, Shawn D.; Ernst, Yolandi (Springer, 2026)
The forestry landscape is being climatically redefined due to global warming. Limited knowledge is available on whether introduced pine species will be viable for plantation forestry in South Africa. Existing global circulation models were scaled down to a finer resolution by incorporating historical climate data, global positioning, and terrain conditions (terrain scaling). Terrain scaling of mean annual maximum temperature (MAT-max), minimum temperature (MAT-min), and median annual precipitation rainfall (MAP-median) was statistically significant, achieving R2 values of 0.70, 0.78 and 0.90, respectively. Decadal climate change was analyzed for the period ranging from 2020 to 2060. Future decadal temperatures were found to increase and were generally greater in high-altitude regions compared to low-altitude regions. MAT-max increased by up to 1.7 °C and MAT-min by 0.4 °C by 2060. MAP-median decreased by up to 10% by 2060, with high-rainfall areas in low-altitude regions being more greatly impacted. Climate suitability was determined for Pinus elliottii, P. taeda, P. patula and the hybrid P. patula × P. tecunumanii by harnessing existing species-specific climate threshold models for the region. Current and future conditions were found to be most suitable for P. patula × P. tecunumanii plantations. Isolated climate niches with warmer, drier conditions were best suited for P. patula plantations, while warm, humid conditions favoured P. elliottii plantations. None of the current and future climatic conditions were suitable for P. taeda plantations. A similar approach can be applied to forestry regions globally to enable pre-emptive tree breeding and the introduction of new forest species due to climate change.
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.
Electro-impedimetric detection of human anti-mycolate antibody biomarkers of TB before, during, and after treatment
Baumeister, Carl Robert; Verschoor, Jan Adrianus; Ueckermann, Veronica; Molatseli, Mosa; Sesing, Thoriso; Khuboni, Nomthandazo; Fourie, Bernard P. (Taylor and Francis, 2025)
Efficient TB management requires rapid and accurate diagnosis of active pulmonary and extrapulmonary TB at the point-of-care. Blood-based antibody biomarker assays may be ideal if unaffected by HIV co-infection and antibody memory from prior TB or vaccination. AIM : This study assessed electro-impedimetric detection (EIS-MARTI) of anti-mycolate antibodies (AMAb) in TB patients before, during, and after treatment, compared to sputum culture (MGIT) as the gold standard. METHODS : A prospective pilot study enrolled 15 confirmed TB patients and 73 healthy controls at a Pretoria hospital (2016–2017). A prospective monitoring study followed 25 confirmed TB patients over 6 months of treatment at a Pretoria clinic (2019–2020) to evaluate biomarker behavior. Outcomes were analyzed using descriptive statistics, wherein diagnostic accuracy and predictive values were assessed by ROC curve analysis. RESULTS : EIS-MARTI detected 14/15 true TB-positive cases independent of HIV co-infection and 68/73 true TB-negatives in the pilot study. In the monitoring study, EIS-MARTI correlated with culture in 7/8 cases at treatment end, but not during the first 2 months. CONCLUSION : AMAbs arise independently of HIV co-infection in active TB, recede during treatment, and are rapidly detected by a hand-held EIS-MARTI device. While suitability for treatment monitoring remains uncertain, EIS-MARTI shows promise for rapid, accurate TB diagnosis and confirming cure. PLAIN LANGUAGE SUMMARY : The purpose of this work was to investigate anti-mycolate antibodies as a suitable biomarker for diagnosing tuberculosis, monitoring treatment, and screening people at risk for TB.
Resolving the population structure and demographic history of the European anchovy in the Northeast Atlantic : tracking historical and contemporary environmental changes
Pujolar, Jose Martin; Gardiner, Courtney E.C.; Von Der Heyden, Sophie; Robalo, Joana I.; Castilho, Rita; Cunha, Regina; Henriques, Romina; Nielsen, Einar E. (Wiley, 2025-07)
The spatial distribution of the European anchovy has expanded in the northern part of its range in the Northeast Atlantic in recent decades. However, whether this results from a northward range shift of southern conspecifics or the expansion of a local northern population is unknown. Using for the first time whole-genome sequencing, we explore current patterns of genetic diversity and population sub-structuring of European anchovy in the Northeast Atlantic, with special focus on recently expanded North Sea areas. Genomic data suggested three distinct groups: Northern (North Sea and Kattegat), Southern (Ireland and Central Portugal) and Cadis (South Portugal). Despite most of the genome being homogenised by high levels of gene flow characteristic of small pelagic fish, several large regions of high genetic differentiation were observed. This suggests that genomic population boundaries might be maintained by local adaptation within chromosome structural variants (inversions). Admixture analysis indicates that the ongoing northern range shift involves both migrants of southern origin and expansion of the local North Sea population. Historical demographic inference suggests that anchovies survived the last glacial period with small population sizes, followed by a split into the current Northern and Southern groups at the end of the last glacial maximum. The Southern group then expanded into the North Sea as the ice sheets retreated, in an expansion involving a large number of individuals, which is consistent with the retention of most of the genetic diversity. In comparison with other small pelagic fish, the genetic patterns found in anchovies (deeply divergent groups, no loss of genetic diversity during expansion, mixing between groups) align well with those found in European sprat, while sardines fit the pattern of expansion of a leading-edge population, with reduced genetic diversity and much shallower divergence between populations. This study contributes to a better understanding of population structure, range shifts and local adaptation in small pelagic fish under climate change, informing conservation and management efforts.
Resolving the stasis-dynamism paradox : genome evolution in tree ferns
Wei, Zuoying; Chen, Hengchi; Feng, Chao; Xia, Zengqiang; Van de Peer, Yves; Kang, Ming; Wang, Jing (Oxford University Press, 2025-10)
The paradox of evolutionary stasis and dynamism—how morphologically static lineages persist through deep geological periods despite environmental fluctuations—remains unresolved in evolutionary biology. Here, we present chromosome-scale genomes for three ecologically divergent species (including both arborescent and nonarborescent growth forms) within Cyatheaceae, an ancient tree fern family characterized by morphological conservation dating back to the Jurassic era. Our results revealed substantial yet cryptically regulated genomic dynamism. A shared Jurassic whole-genome duplication (∼154 Ma) conferred dual adaptive advantages: initially buffering tree ferns against Late Jurassic climatic extremes through retention of stress-response genes, and subsequently facilitating niche diversification and phenotypic innovation via lineage-specific repurposing of duplicate genes. Arborescent lineages preferentially retained duplicates involved in cell wall biogenesis, essential for structural reinforcement and lignification, while nonarborescent forms conserved paralogs linked to metabolic resilience and defense. Alongside slow substitution rates, we detected cryptic genome dynamism mediated primarily by bursts of transposable elements, leading to genome size variations, chromosomal rearrangements, and localized innovation hotspots with elevated evolutionary rates. The concerted expansion and expression of lignification-related genes, coordinated with light signaling components, suggest a potential evolutionary mechanism integrating light perception with shade adaptation and lignification, facilitating arborescent adaptation in angiosperm-dominated understories. Our findings redefine evolutionary stasis as a dynamic equilibrium, sustained by regulatory plasticity and localized genomic innovation within a conserved morphological framework. This study offers a novel genomic perspective on the long-term persistence and evolution of ancient plant lineages, demonstrating how regulated genomic dynamism enables adaptive diversification while sustaining morphological conservatism.
SeqWord motif mapper : a tool for rapid statistical analysis and visualization of epigenetic modifications in bacterial genomes
Lefebvre, Christophe M.J.; Pierneef, Rian Ewald; Reva, Oleg N. (Elsevier, 2025-10)
Genomic methylation in bacteria plays a crucial role in gene regulation, chromosome replication, pathogenicity, and defense against phages. While single-molecule real-time (SMRT) sequencing technologies have advanced the detection of epigenetically modified bases, the statistical analysis of their distribution and the possible roles they play in bacterial cells remains challenging. To address this gap, we developed SeqWord Motif Mapper (SWMM), a computational tool designed for the statistical analysis and visualization of bacterial methylation patterns. SWMM utilizes PacBio sequencing data to identify sequence coverage, methylation motif distribution, and putative functional associations. Implemented in Python 3.9, the tool is platform-independent and requires minimal dependencies, making it accessible to a wide range of users. The SWMM command-line interface and a web-based version of the program facilitate the exploration of epigenetic modifications across bacterial genomes. Through case studies on different bacterial and archaeal taxa, we demonstrated that genome methylation in microorganisms extends beyond canonical sites and possibly influences gene expression, adaptation, and genome architecture. The tool enables detailed statistical evaluation of methylation motif distribution and provides insights into the potential regulatory roles of epigenetic modifications in bacterial genomes. SWMM is freely available at https://begp.bi.up.ac.za, with source code hosted on GitHub at https://github.com/chrilef/BactEpiGenPro. HIGHLIGHTS • Visualizes bacterial methylation using PacBio sequencing data. • Detects canonical and non-canonical methylation motif distributions. • Highlights strand-biased and replicon-specific methylation patterns. • Includes statistical analysis of motif bias in coding and non-coding regions. • Open-source and web-based tool for epigenetic data exploration.
Optimization and characterization of the antimalarial activity of N-aryl acetamides that are susceptible to mutations in ROM8 and CSC1
Nguyen, William; Boulet, Coralie; Dans, Madeline G.; Loi, Katie; Jarman, Kate E.; Barnes, Claudia B.G.; Yeo, Tomas; Sheth, Tanaya; Mukherjee, Partha; Chakraborty, Arnish; Famodimu, Mufuliat T.; Delves, Michael J.; Pollard, Harry; Sutherland, Colin J.; Coyle, Rachael; Sevilleno, Nicole; Boonyalai, Nonlawat; Lee, Marcus C.S.; Rabie, Tayla Anne; Birkholtz, Lyn-Marie; Baud, Delphine; Brand, Stephen; Chowdury, Mrittika; De Koning-Ward, Tania F.; Fidock, David A.; Gilson, Paul R.; Sleebs, Brad E. (American Chemical Society, 2025-07)
New antimalarials are needed due to the threat of emerging resistance against existing antimalarial therapies. A phenotypic screen uncovered the N-aryl acetamide class that inhibits the development of P. falciparum asexual ring-stage parasites. The structure–activity relationship of this class was investigated, and key modifications were introduced that produced WEHI-326 with potent antimalarial activity. Enhancing the metabolic stability of this class will be a future challenge to achieve efficacy in a malaria mouse model. WEHI-326 was found to have a moderate barrier to resistance and a moderate rate of asexual kill, potently inhibited gametocyte and gamete development, and in turn, blocked the transmission of parasites to the mosquito. Forward genetics and cross-resistance profiling determined that parasites resistant to N-aryl acetamides had mutations in rhomboid protease 8 (ROM8) and the putative cation channel, CSC1. WEHI-326 will be an important tool in unraveling the role of ROM8 and CSC1 in P. falciparum development.
Novel inhibitors of Plasmodium Phosphatidylinositol 4-kinase IIIβ with low propensity for resistance : life cycle stage activity and in vivo efficacy in a humanized mouse malaria infection model
Dziwornu, Godwin A.; Mmonwa, Mmakwena M.; Coertzen, Dina; Krugmann, Liezl; Salomane, Nicolaas; Leshabane, Meta; Thomas, Jean Argyle; Da Rocha, Shanté; Reader, Janette; Masike, Keabetswe; Njoroge, Mathew; Sevilleno, Nicole; Coyle, Rachael; Boonyalai, Nonlawat; Mayville, Emily; Lee, Marcus C.S.; Fidock, David A.; Coulson, Lauren B.; Woodland, John G.; Wicht, Kathryn J.; Ghorpade, Sandeep R.; Birkholtz, Lyn-Marie; Chibale, Kelly (American Chemical Society, 2025-08)
Please read abstract in the article.
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.
Persistence of pathogens and biocontrol potential in the bell pepper fruit mycobiome from flowering to postharvest
Karoney, Edwin M.; Gokul, Jarishma Keriuscia; Siyoum, Nazareth Afewerki; Molelekoa, Tintswalo; Korsten, Lise (Frontiers Media, 2025-08-19)
INTRODUCTION : Several postharvest strategies have been explored to prevent postharvest losses of fruit and vegetables in small-scale production environments that are caused by fungal spoilage during storage; however, the losses remain persistent. In the bell pepper industry for instance, approximately 40% of the total global production is lost annually, highlighting a need to understand pathogen dynamics at the preharvest stage that could contribute to tissue breakdown at storage. This study therefore aimed to explore fungal community shifts during bell pepper fruit development from flowering to storage. METHODS : The samples of flowers, small fruits, mature fruits at harvest and storage were processed to identify the fungal composition using next-generation sequencing of the internal transcribed spacer region. RESULTS : The results showed that bell pepper harbored 346 fungal genera across all fruit stages mainly from the phyla Ascomycota (83.9%) and Basidiomycota (15.3%). The fungal community comprised both pathogenic and beneficial taxa: Cladosporium, Alternaria, and Fusarium were among the most abundant probable pathogenic taxa, while Aureobasidium, Filobasidium, and Sampaiozyma represented potential biocontrol agents (BCAs). Trend and correlation analysis showed an antagonistic relationship between the BCAs and pathogenic fungi, possibly explaining their dynamic composition across the fruit stages. DISCUSSION : The analysis showed interaction likelihood between pathogenic taxa, giving insights into co-infection, as well as among beneficial taxa with biocontrol potential, highlighting their synergistic effect against pathogens. Based on redundancy analysis, fruit physiological changes across the developmental stages may have accounted for approximately 8.53% of the total microbial variation observed and could favor growth of spoilage pathogens at storage. The overall analysis confirmed that primary infection at the early fruit developmental stage was the source of the bell pepper decay at postharvest. This highlights the critical need to refocus postharvest spoilage management on reducing preharvest infection, particularly those relating to quiescent infections. The antagonistic characteristics in the bell pepper mycobiome can be harnessed for the development of biocontrol consortia targeting dual/multiple infections. These findings offer a new approach to the management of postharvest losses while aligning with sustainable agricultural production and food security by promoting the use of naturally occurring beneficial microbes for crop protection.
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.
Gene expression divergence following gene and genome duplications in spatially resolved plant transcriptomes
Almeida-Silva, Fabricio; Van de Peer, Yves (Oxford University Press, 2025-10)
Gene and genome duplications expand genetic repertoires and facilitate functional innovation. Segmental or whole-genome duplications generate duplicates with similar and somewhat redundant expression profiles across multiple tissues, while other modes of duplication create genes that show increased divergence, leading to functional innovations. How duplicates diverge in expression across cell types in a single tissue remains elusive. Here, we used high-resolution spatial transcriptomic data from Arabidopsis thaliana, Glycine max, Phalaenopsis aphrodite, Zea mays, and Hordeum vulgare to investigate the evolution of gene expression following gene duplication. We found that genes originating from segmental or whole-genome duplications display increased expression levels, expression breadths, spatial variability, and number of co-expression partners. Duplication mechanisms that preserve cis-regulatory landscapes typically generate paralogs with more preserved expression profiles, but such differences generated by mode of duplication fade or disappear over time. Paralogs originating from large-scale (including whole-genome) duplications display redundant or overlapping expression profiles, indicating functional redundancy or sub-functionalization, while most small-scale duplicates diverge asymmetrically, consistent with neofunctionalization. Expression divergence also depends on gene functions, with dosage-sensitive genes displaying highly preserved expression profiles and genes involved in more specialized processes diverging more rapidly. Our findings offer a spatially resolved view of expression divergence following duplication, elucidating the tempo and mode of gene expression evolution, and helping understand how gene and genome duplications shape cell identities.
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.
Whole genome characterization of Listeria welshimeri isolates recovered from cattle abattoirs and retailers in Gauteng province in South Africa
Gana, James; Pierneef, Rian Ewald; Gcebe, Nomakorinte; Moerane, Rebone; Adesiyun, Abiodun Adewale (Springer, 2025-06)
The study used whole-genome sequencing (WGS) to characterize 12 isolates of L. welshimeri recovered from the beef production chain in Gauteng province, South Africa. Two sequence types (STs) were identified, with ST3294 accounting for 75% (9/12) and ST1084 for 16.7% (2/12) of the isolates. Antimicrobial resistance (AMR) plasmids detected included conjugative plasmid (MOBP2; T_virB11; virb4) in 58.3% and AMR plasmid (NFO33156) in 41.7% of the isolates. Two AMR genes, fosX (25%) and vga (G) (100%), along with 11 virulence factors, were present in all 12 isolates of L. welshimeri. The phylogenomic tree of L. welshimeri clustering based on the ST according to the source, type, and class of beef and beef products revealed three groups: ST3294 (n = 9), ST1084 (n = 2), and unassigned ST (n = 1). The findings of this study demonstrate the potential for transferring genetic materials from non-pathogenic L. welshimeri to pathogenic L. monocytogenes within the same ecological niche.
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.

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