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

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Profiling the diversity of the village chicken faecal microbiota using 16S rRNA gene and metagenomic sequencing data to reveal patterns of gut microbiome signatures
(Frontiers Media, 2025-02) Nene, Mxolisi; Kunene, Nokuthula W.; Pierneef, Rian; Hadebe, Khanyisile
INTRODUCTION: The production environment of extensively raised village chickens necessitates their adaptability to low-resource systems. The gut microbiome plays a critical role in supporting this adaptability by influencing health and productivity. This study aimed to investigate the diversity and functional capacities of the faecal microbiome in village chickens from Limpopo and KwaZulu-Natal provinces of South Africa. METHODS: Using a combination of 16S rRNA gene sequencing and shotgun metagenomic sequencing technologies, we analysed 98 16S rRNA and 72 metagenomic datasets. Taxonomic profiles and functional gene annotations were derived, focusing on microbial diversity, antibiotic resistance genes (ARGs), and potential zoonotic pathogens. RESULTS: Taxonomic analysis showed that the predominant phyla in both provinces were Firmicutes, Bacteroidota, Proteobacteria, and Actinobacteria. At the genus level, Escherichia and Shigella were prevalent, with Escherichia coli and Shigella dysenteriae identified as major contributors to the gut microbiome. ARGs were identified, with MarA, PmrF, and AcrE detected in KwaZulu-Natal, and cpxA, mdtG, and TolA in Limpopo. These genes primarily mediate antibiotic efflux and alteration. DISCUSSION: The detection of zoonotic bacteria such as Escherichia coli and Streptococcus spp. highlights potential health risks to humans through the food chain, emphasizing the importance of improved household hygiene practices. This study underscores the role of the gut microbiome in village chicken health and adaptability, linking microbial diversity to production efficiency in lowresource settings. Targeted interventions and further research are crucial for mitigating zoonotic risks and enhancing sustainability in village chicken farming.
Gene transfer between fungal species triggers repeated coffee wilt disease outbreaks
(Public Library of Science, 2024-12-06) Wingfield, Brenda D.; Wingfield, Michael J.; brenda.wingfield@fabi.up.ac.za
Two outbreaks of coffee wilt disease have devastated African coffee production. A PLOS Biology study suggests that horizontal gene transfer via large Starship transposons between 2 fungal species played a key role in the repeated emergence of the disease.
Genomic diversity and antimicrobial susceptibility of invasive Neisseria meningitidis in South Africa, 2016–2021
(Oxford University Press, 2024-12-15) Mikhari, Rito L.; Meiring, Susan; De Gouveia, Linda; Chan, Wai Yin; Jolley, Keith A.; Van Tyne, Daria; Harrison, Lee H.; Marjuki, Henju; Ismail, Arshad; Quan, Vanessa; Cohen, Cheryl; Walaza, sibongile; Von Gottberg, Anne; Du Plessis, Mignon
Please read abstract in the article.
Growth rate extremes of a Sciaenid in an ocean-warming hotspot
(Elsevier, 2025-05) Jagger, Charmaine E.; Potts, Warren M.; Pringle, Brett A.; Bordbar, M. Hadi; Henriques, Romina; McKeown, Niall J.; Wilhelm, Margit R.
Argyrosomus inodorus is a cool water Sciaenid, important to the recreational and commercial coastal fishery in Namibia, the northern Benguela. Given recent findings on the northern Benguela as an ocean-warming hotspot and A. inodorus being more sensitive to warm temperatures than its congeneric A. coronus, it is important to study long-term growth responses of this Sciaenid. We developed a 34-year otolith biochronology for A. inodorus. The linear mixed-effects models fitted to A. inodorus’ otolith biochronology indicated that the best linear unbiased predictor of growth was significantly positively correlated with mean sea surface temperatures (SSTs) in September of the year of formation and significantly negatively correlated with mean summer SSTs (November y-1), in the central Namibian area (20–24◦S, 12–14◦E). Thus, faster annual growth was observed during warmer winter/spring temperatures (up to 16℃) and slower growth was noted during warmer summer temperatures (> 16℃). These results indicate that the species has a narrow range of thermal plasticity, and highlight the recent reductions in growth of this species in response to rapid thermal change observed in the ocean warming hotspot. Our findings suggest that A. inodorus would not be able to adapt readily with future climate warming predicted to happen and already happening along the northernmost part of the Namibian coast.
Expanding the toolkit for ploidy manipulation in Chlamydomonas reinhardtii
(Wiley, 2025) Van de Vloet, Antoine; Prost-Boxoen, Lucas; Bafort, Quinten; Paing, Yunn Thet; Casteleyn, Griet; Jomat, Lucile; Lemaire, Stephane D.; De Clerck, Olivier; Van de Peer, Yves
Whole-genome duplications, widely observed in plant lineages, have significant evolutionary and ecological impacts. Yet, our current understanding of the direct implications of ploidy shifts on short- and long-term plant evolution remains fragmentary, necessitating further investigations across multiple ploidy levels. Chlamydomonas reinhardtii is a valuable model organism with profound potential to study the impact of ploidy increase on the longer term in a laboratory environment. This is partly due to the ability to increase the ploidy level. We developed a strategy to engineer ploidy in C. reinhardtii using noninterfering, antibiotic, selectable markers. This approach allows us to induce higher ploidy levels in C. reinhardtii and is applicable to field isolates, which expands beyond specific auxotroph laboratory strains and broadens the genetic diversity of parental haploid strains that can be crossed. We implement flow cytometry for precise measurement of the genome size of strains of different ploidy. We demonstrate the creation of diploids, triploids, and tetraploids by engineering North American field isolates, broadening the application of synthetic biology principles in C. reinhardtii. However, our newly formed triploids and tetraploids show signs of rapid aneuploidization. Our study greatly facilitates the application of C. reinhardtii to study polyploidy, in both fundamental and applied settings.
Asymmetric genome merging leads to gene expression novelty through nucleo-cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids
(Wiley, 2025-01) Prost-Boxoen, Lucas; Bafort, Quinten; Van de Vloet, Antoine; Almeida-Silva, Fabricio; Paing, Yunn Thet; Casteleyn, Griet; D'hondt, Sofie; De Clerck, Olivier; Van de Peer, Yves
Genome merging is a common phenomenon causing a wide range of consequences on phenotype, adaptation, and gene expression, yet its broader implications are not well-understood. Two consequences of genome merging on gene expression remain particularly poorly understood: dosage effects and evolution of expression. We employed Chlamydomonas reinhardtii as a model to investigate the effects of asymmetric genome merging by crossing a diploid with a haploid strain to create a novel triploid line. Five independent clonal lineages derived from this triploid line were evolved for 425 asexual generations in a laboratory natural selection experiment. Utilizing fitness assays, flow cytometry, and RNA-Seq, we assessed the immediate consequences of genome merging and subsequent evolution. Our findings reveal substantial alterations in genome size, gene expression, protein homeostasis, and cytonuclear stoichiometry. Gene expression exhibited expression-level dominance and transgressivity (i.e. expression level higher or lower than either parent). Ongoing expression-level dominance and a pattern of ‘functional dominance’ from the haploid parent was observed. Despite major genomic and nucleo-cytoplasmic disruptions, enhanced fitness was detected in the triploid strain. By comparing gene expression across generations, our results indicate that proteostasis restoration is a critical component of rapid adaptation following genome merging in Chlamydomonas reinhardtii and possibly other systems.
Chromosome-level assemblies for the pine pitch canker pathogen Fusarium circinatum
(MDPI, 2024-01) De Vos, Lieschen; Van der Nest, Magrieta Aletta; Santana, Quentin C.; Van Wyk, Stephanie; Leeuwendaal, Kyle; Wingfield, Brenda D.; Steenkamp, Emma Theodora; emma.steenkamp@fabi.up.ac.za
The pine pitch canker pathogen, Fusarium circinatum, is globally regarded as one of the most important threats to commercial pine-based forestry. Although genome sequences of this fungus are available, these remain highly fragmented or structurally ill-defined. Our overall goal was to provide high-quality assemblies for two notable strains of F. circinatum, and to characterize these in terms of coding content, repetitiveness and the position of telomeres and centromeres. For this purpose, we used Oxford Nanopore Technologies MinION long-read sequences, as well as Illumina short sequence reads. By leveraging the genomic synteny inherent to F. circinatum and its close relatives, these sequence reads were assembled to chromosome level, where contiguous sequences mostly spanned from telomere to telomere. Comparative analyses unveiled remarkable variability in the twelfth and smallest chromosome, which is known to be dispensable. It presented a striking length polymorphism, with one strain lacking substantial portions from the chromosome’s distal and proximal regions. These regions, characterized by a lower gene density, G+C content and an increased prevalence of repetitive elements, contrast starkly with the syntenic segments of the chromosome, as well as with the core chromosomes. We propose that these unusual regions might have arisen or expanded due to the presence of transposable elements. A comparison of the overall chromosome structure revealed that centromeric elements often underpin intrachromosomal differences between F. circinatum strains, especially at chromosomal breakpoints. This suggests a potential role for centromeres in shaping the chromosomal architecture of F. circinatum and its relatives. The publicly available genome data generated here, together with the detailed metadata provided, represent essential resources for future studies of this important plant pathogen.
Sex pheromone receptor Ste2 orchestrates chemotropic growth towards pine root extracts in the pitch canker pathogen Fusarium circinatum
(MDPI, 2024-05) Ramaswe, J.B.; Steenkamp, Emma Theodora; De Vos, Lieschen; Fru, Felix Fon; Adegeye, O.O.; Wingfield, Brenda D.; emma.steenkamp@fabi.up.ac.za
In ascomycetous fungi, sexual mate recognition requires interaction of the Ste2 receptor protein produced by one partner with the α-factor peptide pheromone produced by the other partner. In some fungi, Ste2 is further needed for chemotropism towards plant roots to allow for subsequent infection and colonization. Here, we investigated whether this is also true for the pine pitch canker fungus, Fusarium circinatum, which is a devastating pathogen of pine globally. Ste2 knockout mutants were generated for two opposite mating-type isolates, after which all strains were subjected to chemotropism assays involving exudates from pine seedling roots and synthetic α-factor pheromone, as well as a range of other compounds for comparison. Our data show that Ste2 is not required for chemotropism towards any of these other compounds, but, in both wild-type strains, Ste2 deletion resulted in the loss of chemotropism towards pine root exudate. Also, irrespective of mating type, both wild-type strains displayed positive chemotropism towards α-factor pheromone, which was substantially reduced in the deletion mutants and not the complementation mutants. Taken together, these findings suggest that Ste2 likely has a key role during the infection of pine roots in production nurseries. Our study also provides a strong foundation for exploring the role of self-produced and mate-produced α-factor pheromone in the growth and overall biology of the pitch canker pathogen.
Inconsistencies within the proposed framework for stabilizing fungal nomenclature risk further confusion
(American Society for Microbiology, 2024-04) Kidd, Sarah E.; Hagen, Ferry; Halliday, Catriona L.; Abdolrasouli, Alireza; Boekhout, Teun; Crous, Pedro W.; Ellis, David H.; Elvy, Juliet; Forrest, Graeme N.; Groenewald, Marizeth; Hahn, Rosane C.; Houbraken, Jos; Rodrigues, Anderson M.; Scott, James; Sorrell, Tania C.; Summerbell, Richard C.; Tsui, Clement K.M.; Yurkov, Andrey M.; Chen, Sharon C.-A.
We read with interest the recent publication by de Hoog and colleagues in the Journal of Clinical Microbiology (1) and support the goal to stabilize fungal nomenclature. Although we recognize the importance of stable naming, we offeroffercomments on the need for clarity around the concepts introduced, consistency of the recommended nomenclature, process issues regarding the endorsement by professional groups and societies and the proposed oversight committee (working group), and the relationship between the proposed database and existing, officially recognized nomenclatural repositories.
FEP augmentation as a means to solve data paucity problems for machine learning in chemical biology
(American Chemical Society, 2024-04-23) Burger, Pieter B.; Hu, Xiaohu; Balabin, Ilya; Muller, Morne; Stanley, Megan; Joubert, Fourie; Kaiser, Thomas M.
In the realm of medicinal chemistry, the primary objective is to swiftly optimize a multitude of chemical properties of a set of compounds to yield a clinical candidate poised for clinical trials. In recent years, two computational techniques, machine learning (ML) and physics-based methods, have evolved substantially and are now frequently incorporated into the medicinal chemist’s toolbox to enhance the efficiency of both hit optimization and candidate design. Both computational methods come with their own set of limitations, and they are often used independently of each other. ML’s capability to screen extensive compound libraries expediently is tempered by its reliance on quality data, which can be scarce especially during early-stage optimization. Contrarily, physics-based approaches like free energy perturbation (FEP) are frequently constrained by low throughput and high cost by comparison; however, physics-based methods are capable of making highly accurate binding affinity predictions. In this study, we harnessed the strength of FEP to overcome data paucity in ML by generating virtual activity data sets which then inform the training of algorithms. Here, we show that ML algorithms trained with an FEP-augmented data set could achieve comparable predictive accuracy to data sets trained on experimental data from biological assays. Throughout the paper, we emphasize key mechanistic considerations that must be taken into account when aiming to augment data sets and lay the groundwork for successful implementation. Ultimately, the study advocates for the synergy of physics-based methods and ML to expedite the lead optimization process. We believe that the physics-based augmentation of ML will significantly benefit drug discovery, as these techniques continue to evolve.
Plasmid DNA-based reverse genetics as a platform for manufacturing of bluetongue vaccine
(American Society for Microbiology, 2025-04) Mlingo, Tendai A.M.; Theron, Jacques; Mokoena, Nobalanda B.
Control of bluetongue disease is predominantly through vaccination with licensed inactivated or live-attenuated vaccines (LAVs). Manufacturing of LAVs in endemic countries requires formulation with a high number of serotypes for effective protection. Herein, we evaluated a plasmid DNA-based reverse genetics platform for manufacturing a multivalent vaccine. The synthetic vaccine was characterized by a common BTV1 backbone, with exchange of outer capsid proteins. Recombinant South African vaccine serotypes 1, 5, and 14 were rescued by exchanging the VP2 protein on the backbone. BTV6 rescue was achieved following the exchange of VP2 and VP5 proteins. The particle sizes were comparable to commercial vaccines of respective serotypes. BTV1, BTV5, and BTV6 had distinct growth profiles compared to commercial vaccines, while BTV14 was indistinguishable. Stability and shelf-life determination under various storage conditions showed that commercial vaccines were more stable. Formulated antigens were evaluated for vaccine safety and immunogenicity in sheep. Serotyped BTV1 monovalent vaccine was safe, as no clinical signs were observed. Neutralizing antibodies (nAbs) were induced on day 14 and peaked at 32 on day 28. The multivalent synthetic vaccine containing four serotypes elicited BTV6 nAbs from day 21 with a titer of 52, which decreased to 33 by day 42. BTV1 elicited a weak immune response with a titer of 1 on day 42. No nAbs were detected against BTV5 and BTV14. This is a first report comparing reverse genetics-derived antigens with commercial vaccines. Data generated on production yields, stability, and immunogenicity demonstrated that some serotypes can be implemented as novel synthetic vaccines using this platform. IMPORTANCE : Vaccination is the most effective control strategy for viral diseases that affect livestock. To date, only live-attenuated and inactivated vaccines have been licensed for control of bluetongue (BT). This study demonstrated the use of reverse genetics as a possible platform for BTV vaccine production. Data generated in the study contribute toward the advancement of an alternative manufacturing platform for licensing of BT vaccines. Information on production yields and stability of synthetic vaccines in comparison to the conventional products demonstrated that optimization is required for some serotypes to fully translate the reverse genetics platform for manufacturing the BTV vaccine. The study highlighted the safety and immunogenicity of vaccines manufactured using the plasmid DNA-based reverse-genetics platform.
Ecological success of extreme halophiles subjected to recurrent osmotic disturbances is primarily driven by congeneric species replacement
(Oxford University Press, 2024-11) Bustos-Caparros, Esteban; Viver, Tomeu; Gago, Juan F.; Rodriguez-R, Luis M.; Hatt, Janet K.; Venter, S.N. (Stephanus Nicolaas); Fuchs, Bernhard M.; Amann, Rudolf; Bosch, Rafael; Konstantinidis, Konstantinos T.; Rossello-Mora, Ramon
To understand how extreme halophiles respond to recurrent disturbances, we challenged the communities thriving in salt-saturated (∼36% salts) ∼230 L brine mesocosms to repeated dilutions down to 13% (D13 mesocosm) or 20% (D20 mesocosm) salts each time mesocosms reached salt saturation due to evaporation (for 10 and 17 cycles, respectively) over 813 days. Depending on the magnitude of dilution, the most prevalent species, Haloquadratum walsbyi and Salinibacter ruber, either increased in dominance by replacing less competitive populations (for D20, moderate stress conditions), or severely decreased in abundance and were eventually replaced by other congeneric species better adapted to the higher osmotic stress (for D13,strong stress conditions). Congeneric species replacement was commonly observed within additional abundant genera in response to changes in environmental or biological conditions (e.g. phage predation) within the same system and under a controlled perturbation of a relevant environmental parameter. Therefore, a genus is an ecologically important level of diversity organization, not just a taxonomic rank, that persists in the environment based on congeneric species replacement due to relatively high functional overlap (gene sharing), with important consequences for the success of the lineage, and similar to the success of a species via strain-replacement. Further, our results showed that successful species were typically accompanied by the emergence of their own viral cohorts, whose intra-cohort diversity appeared to strongly covary with, and likely drive, the intra-host diversity. Collectively, our results show that brine communities are ecologically resilient and continuously adapting to changing environments by transitioning to alternative stable states.
Managing wilding pines in the Cape Floristic Region, South Africa : progress and prospects
(Elsevier, 2025-02) Martin, Grant D.; Canavan, Kim; Chikowore, Gerald; Bugan, Richard; De Lange, Willem; Du Toit, Ben; Harding, Graham; Heath, Ronald; Hill, Martin; Hurley, Brett Phillip; Ivey, Philip; Muir, Debbie; Musedeli, Jufter; Richardson, David M.; Slippers, Bernard; Stafford, Louise; Turner, Andrew; Watson, Kirsten; Van Wilgen, Brian W.
The occurrence and continuing spread of wilding pines (genus Pinus) in the Cape Floristic Region (CFR), South Africa, impacts negatively on water resources, threatens the region's rich biodiversity, and increases the damage caused by uncontrolled wildfires. The invasive potential and threat of wilding pines has been regularly reported since the 1940s, leading to the development and implementation of various control strategies. The last substantial review of pine invasions and their management in the CFR (in 2012) recommended several actions, including securing more sustainable funding and adopting alternative control methods. We review the last 12 years of wilding pine research and management in the CFR, and provide updates on spread and impact, government funding, payments for ecosystems services initiatives, and contributions of the South African Forest industry. We note an increase in private funding, specifically to address invasion in priority catchment areas in the Greater Cape Town region, as well as a recent decline in government funding. Steps have also been taken to revive research aimed at biological control of pines originating from the Iberian Peninsula. The forest industry has deployed species with lower fecundity in some parts of the CFR and has also started experimenting with hybrids that could potentially be less invasive. New methods for applying herbicides may prove to be more efficient than currently used methods. We discuss five opportunities for addressing current shortcomings in the management of wilding pines, namely broadening sources of funding to increase sustainability, effectively integrating all available management techniques, accommodating the need for commercial forestry, focussing scarce funds on priority areas, and raising awareness. We stress that failure to contain rampant invasions by wilding pines will have far-reaching consequences for conservation in the CFR.
Characterization of the soil resistome and mobilome in Namib Desert soils
(Springer, 2024-08) Naidoo, Yashini; Pierneef, Rian Ewald; Cowan, Don A.; Valverde, Angel; don.cowan@up.ac.za
The study of the soil resistome is important in understanding the evolution of antibiotic resistance and its dissemination between the clinic and the environment. However, very little is known about the soil resistome, especially of those from deserts. Here, we characterize the bacterial communities, using targeted sequencing of the 16S rRNA genes, and both the resistome and the mobilome in Namib Desert soils, using shotgun metagenomics. We detected a variety of antibiotic resistance genes (ARGs) that conferred resistance to antibiotics such as elfamycin, rifampicin, and fluoroquinolones, metal/biocide resistance genes (MRGs/BRGs) conferring resistance to metals such as arsenic and copper, and mobile genetic elements (MGEs) such as the ColE1-like plasmid. The presence of metal/biocide resistance genes in close proximity to ARGs indicated a potential for co-selection of resistance to antibiotics and metals/biocides. The co-existence of MGEs and horizontally acquired ARGs most likely contributed to a decoupling between bacterial community composition and ARG profiles. Overall, this study indicates that soil bacterial communities in Namib Desert soils host a diversity of resistance elements and that horizontal gene transfer, rather than host phylogeny, plays an essential role in their dynamics.
An integrative re-evaluation of the Fusarium sambucinum species complex
(Westerdijk Fungal Biodiversity Institute, 2025-03) Sandoval-Denis, M.; Costa, M.M.; Broders, K.; Becker, Y.; Maier, W.; Yurkov, A.; Kermode, A.; Buddie, A.G.; Ryan, M.J.; Schumacher, R.K.; Groenewald, J.Z.; Crous, Pedro W.
The species-rich Fusarium sambucinum species complex (FSAMSC; Fusarium, Nectriaceae, Hypocreales) is well-known for including devastating plant pathogens and toxigenic species. However, this group of grass-loving fungi also accommodates soil saprobes, endophytes, mycoparasites and rare opportunistic pathogens of humans and other animals. Recent publications have highlighted the vast phylogenetic and biochemical diversity of the FSAMSC, although a large number of taxa in FSAMSC have not been systematically described and still lack Latin binomials. In this study we established the phylogenetic breadth of the FSAMSC using an integrative approach including morphological, multilocus phylogenetic, and coalescence analyses based on five gene regions (calmodulin, RNA polymerase II largest and second largest subunits, translation elongation factor 1-α, and β-tubulin). Results obtained support the recognition of 75 taxa in FSAMSC, including all the currently known species segregates of the Fusarium head-blight pathogen F. graminearum s. lat. Thirty novel species are formally described and illustrated, while four phylogenetic species remain undescribed. An epitype is proposed for the generic type of Fusarium, F. sambucinum, from recently collected material identified by means of morphology, phylogenetics and mating experiments, fixing the phylogenetic application of the name. Additional notes are included on the typification of Fusisporium cerealis (syn. Fusarium cerealis).
Central nervous system infection by free-living nematode Cephalobus cubaensis in a human host in Africa
(MDPI, 2025-02) Sriruttan-Nel, Charlotte; Cairns, Chelline; Boughan, Shareen; Moodley, Bhavani; Sun, Lisa Ming; Chan, Wai Yin; Ismail, Arshad; Mwazha, Absalom; Bennimahadeo, Praniel; Manickchund, Nithendra; Moyo, Mthabisi; Nkwanyana, Thabani; Msimang, Mpumelelo Z.; Essa, Ahmed; Frean, John; Moosa, Mahomed-Yunus
BACKGROUND : Human central nervous system infections due to free-living nematodes, although extremely rare, are usually fatal. Immunodeficiency has not been a feature of most of these cases, unlike the situation pertaining to disseminated Strongyloides stercoralis infection. CASE REPORT : An elderly immunocompetent man presented with a history of tinnitus and otalgia, progressing to central nervous system involvement with confusion, weakness, and other neurological signs. Examination revealed a unilateral external auditory canal soft tissue mass and radiological evidence of ipsilateral temporal bone destruction and brain parenchymal disease. A biopsy of the ear canal mass revealed the presence of an unidentified nematode species, and treatment with anthelminthics was started. The patient’s clinical condition deteriorated and he died shortly after admission to the intensive care unit. The immediate cause of death was bronchopneumonia. During the autopsy, an extensive involvement of the right middle cranial fossa was found, with destruction of the squamous and petrous parts of the temporal bone. RESULTS : We identified adult, larval, and egg stages of a free-living nematode in the antemortem external auditory canal tissue mass and the post-mortem brain samples. Polymerase chain reaction assays, with Sanger and whole-genome sequencing, identified Cephalobus cubaensis. This is a free-living species not previously known to be pathogenic to humans, although nematodes of the same genus have caused mastitis in horses. CONCLUSIONS : Microscopic appearance and the invasive behaviour of the pathogen evoked a putative diagnosis of Halicephalobus gingivalis, the most frequently reported free-living nematode infecting humans. However, this nematode’s size and anatomical features, and the clinical presentation and duration of illness, prompted the consideration of an alternative species. We speculate that an initial bacterial otitis externa provided the opportunity for colonization by the nematode from an environmental source and subsequent invasion.
Prevalence of aeroallergen sensitization in a polluted and industrialized area : a pilot study in South Africa's Vaal Triangle
(Springer, 2025-02) Gharbi, Dorra; Neumann, Frank Harald; Staats, Jurgens; Mcdonald, Marinda; Linde, Jo-hanné; Mmatladi, Tshiamo; Podile, Keneilwe; Piketh, Stuart; Burger, Roelof; Garland, Rebecca M.; Bester, Petra; Lebre, Pedro H.; Ricci, Cristian; rebecca.garland@up.ac.za
This pioneering study evaluates the prevalence of aeroallergens reactivity among atopic populations living in the Vaal Triangle Airshed Priority Area (VTAPA), South Africa. A total of 138 volunteers (51 males and 87 females), of African, colored, white, and Asian ethnicity, and with a mean (range) age of 22 (18–56) years were participating in the study. The study was conducted on the North-West University (NWU) campus in Vanderbijlpark/VTAPA. The International Study of Asthma and Allergies in Childhood questionnaire was utilized for pre-screening to identify individuals with probable allergic dispositions. Subsequently, skin prick testing was conducted using commercial aeroallergen extracts for all confirmed participants with allergy symptoms. One hundred six participants were clinically diagnosed with pollen and fungal spore allergies. The highest allergy prevalence was attributed to Cynodon dactylon ((L.) Pers) (Bermuda grass) (41.5%), followed by Lolium perenne (L.) (ryegrass), grass mix, and Zea mays (L.) (maize) (31.1%), respectively. Moreover, among the tree allergens, Olea (L.) (olive tree) was the most prevalent allergen (20; 18.8%), followed by Platanus (L.) (plane tree) (18; 16.9%). Among the weeds, 16 (15.1%) participants were allergic to the weed mix (Artemisia (L.) (wormwood), Chenopodium (Link) (goosefoot), Salsola (L.) (saltwort), Plantago (L.) (plantain), and 11 (10.3%) to Ambrosia (L.) (ragweed)). Regarding the fungal spores, Alternaria (Fr.) (9; 8.5%) followed by Cladosporium (Link) (5; 4.7%) had the highest skin sensitivity. In this pilot study, our findings provide insights into the prevalence of allergic responses in the study population—underlining the strong impact of allergens of exotic plants—and contribute to the existing aerobiological data in South Africa.
The functional and structural succession of mesic-grassland soil microbiomes beneath decomposing large herbivore carcasses
(Wiley, 2025-01) Fouche, Jacques; Lebre, Pedro H.; Melville, Haemish A.; Cowan, Don A.; don.cowan@up.ac.za
Plant detritus is abundant in grasslands but decomposes slowly and is relatively nutrient-poor, whereas animal carcasses are labile and nutrient-rich. Recent studies have demonstrated that labile nutrients from carcasses can significantly alter the long-term soil microbial function at an ecosystem scale. However, there is a paucity of knowledge on the functional and structural response and temporal scale of soil microbiomes beneath large herbivore carcasses. This study compared microbiome functions and structures of soil beneath Connochaetes taurinus (hereafter ‘wildebeest’) carcasses at various postmortem intervals of decomposition to matched control samples over 18 months. Microbial functions were compared by their community-level physiological profiles determined by sole-carbon substrate utilisation and structures by metagenomic sequences using 16S rRNA gene markers. Overall metabolism and metabolic diversity remained increased and functionally dissimilar to control soils throughout the experimental period, with successive sole-carbon substrate utilisation observed. Conversely, diversity was initially reduced and structurally dissimilar from the control soil but recovered within the experimental period. The study contributes to the knowledge of carcass decomposition by investigating the long-term soil microbiome dynamics resulting from large herbivore carcasses decomposing in a mesic grassland. Microbial functional succession and ecologically relevant bacterial biomarkers of soil beneath the decomposing carcasses were identified for various postmortem intervals.
A highly divergent mitochondrial genome in extant Cape buffalo from Addo Elephant National Park, South Africa
(Wiley, 2025-01) De Jager, Deon; Moller, Marlo; Hoal, Eileen; Van Helden, Paul David; Glanzmann, Brigitte; Harper, Cindy Kim; Bloomer, Paulette; paulette.bloomer@up.ac.za
The reduced cost of next-generation sequencing (NGS) has allowed researchers to generate nuclear and mitochondrial genome data to gain deeper insights into the phylogeography, evolutionary history and biology of non-model species. While the Cape buffalo (Syncerus caffer caffer) has been well-studied across its range with traditional genetic markers over the last 25 years, researchers are building on this knowledge by generating whole genome, population-level data sets to improve understanding of the genetic composition and evolutionary history of the species. Using publicly available NGS data, we assembled 40 Cape buffalo mitochondrial genomes (mitogenomes) from four protected areas in South Africa, expanding the geographical range and almost doubling the number of mitogenomes available for this species. Coverage of the mitogenomes ranged from 154 to 1036X. Haplotype and nucleotide diversity for Kruger National Park (n = 15) and Mokala National Park (n = 5) were similar to diversity levels in southern and eastern Africa. Hluhluwe–iMfolozi Park (n = 15) had low levels of genetic diversity, with only four haplotypes detected, reflecting its past bottleneck. Addo Elephant National Park (n = 5) had the highest nucleotide diversity of all populations across Africa, which was unexpected, as it is known to have low nuclear diversity. This diversity was driven by a highly divergent mitogenome from one sample, which was subsequently identified in another sample via Sanger sequencing of the cytochrome b gene. Using a fossil-calibrated phylogenetic analysis, we estimated that this lineage diverged from all other Cape buffalo lineages approximately 2.51 million years ago. We discuss several potential sources of this mitogenome but propose that it most likely originated through introgressive hybridisation with an extinct buffalo species, either S. acoelotus or S. antiquus. We conclude by discussing the conservation consequences of this finding for the Addo Elephant National Park population, proposing careful genetic management to prevent inbreeding depression while maintaining this highly unique diversity.
Fungal biocontrol agents in the management of postharvest losses of fresh produce-a comprehensive review
(MDPI, 2025-01) Ramudingana, Phathutshedzo; Makhado, Ndivhuho; Kamutando, Casper Nyaradzai; Thantsha, Mapitsi Silvester; Mamphogoro, Tshifhiwa Paris; mapitsi.thantsha@up.ac.za
Postharvest decay of vegetables and fruits presents a significant threat confronting sustainable food production worldwide, and in the recent times, applying synthetic fungicides has become the most popular technique of managing postharvest losses. However, there are concerns and reported proofs of hazardous impacts on consumers’ health and the environment, traceable to the application of chemical treatments as preservatives on fresh produce. Physical methods, on the other hand, cause damage to fresh produce, exposing it to even more infections. Therefore, healthier and more environmentally friendly alternatives to existing methods for managing postharvest decays of fresh produce should be advocated. There is increasing consensus that utilization of biological control agents (BCAs), mainly fungi, represents a more sustainable and effective strategy for controlling postharvest losses compared to physical and chemical treatments. Secretion of antifungal compounds, parasitism, as well as competition for nutrients and space are the most common antagonistic mechanisms employed by these BCAs. This article provides an overview of (i) the methods currently used for management of postharvest diseases of fresh produce, highlighting their limitations, and (ii) the use of biocontrol agents as an alternative strategy for control of such diseases, with emphasis on fungal antagonists, their mode of action, and, more importantly, their advantages when compared to other methods commonly used. We therefore hypothesize that the use of fungal antagonists for prevention of postharvest loss of fresh produce is more effective compared to physical and chemical methods. Finally, particular attention is given to the gaps observed in establishing beneficial microbes as BCAs and factors that hamper their development, particularly in terms of shelf life, efficacy, commercialization, and legislation procedures.

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