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

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First record of the white root rot fungus Dematophora necatrix on indigenous South African trees
(Springer, 2025-05) Balocchi, Felipe; Wingfield, Michael J.; Paap, Trudy; felipe.balocchi@fabi.up.ac.za
The soilborne fungus Dematophora (=Rosellinia) necatrix and causal agent of white root rot, has a wide host range that includes many tree species of economic importance. The pathogen has a worldwide distribution, including reports from commercial orchards in South Africa since the 1970s. During tree health surveys conducted as part of a sentinel plant project, we detected the pathogen on two symptomatic individuals from the indigenous South African tree species Diospyros whyteana and Noronhia foveolata subsp. major. Observed symptoms included wilting and root rot, with characteristic white mycelium present under the bark. Dematophora necatrix was isolated from both hosts and its identity confirmed by sequencing two gene regions (ITS and actin). Pathogenicity was confirmed through inoculation tests under semi-controlled conditions by inoculating the soil with bamboo sticks colonized with the fungus. Plants of both species developed similar symptoms to those observed naturally, and the fungus was successfully recovered from all symptomatic plants. This is the first record in South Africa of D. necatrix on indigenous species and outside of commercial orchards. Given the environmental threat posed we recommend the fungus is considered for regulation in South Africa.
Medicinal chemistry progression of sapanisertib, the anticancer and dual Plasmodium phosphatidylinositol 4-kinase beta and cGMP-dependent protein kinase inhibitor, for malaria
(American Chemical Society, 2025-06) Gachuhi, Samuel; Kamunya, Stephanie; Fienberg, Stephen; Wambua, Lynn; Salomane, Nicolaas; Mayoka, Godfrey; Taylor, Dale; Coertzen, Dina; Van der Watt, Mariette Elizabeth; Reader, Janette; Birkholtz, Lyn-Marie; Wittlin, Sergio; Krugmann, Liezl; Coulson, Lauren B.; Chibale, Kelly
We recently demonstrated that the anticancer human mTOR inhibitor sapanisertib displays antimalarial activity in a malaria mouse model of infection and inhibits multiple Plasmodium kinases, including the high-value targets phosphatidylinositol 4-kinase type III beta (PI4Kβ) and cGMP-dependent protein kinase (PKG). Herein, we explore structure-activity relationships for sapanisertib analogues with benzyl and pyridyl substituents at the 7-position of the pyrazolopyrimidine core. New analogues with improved safety profiles were identified, including analogues with dual Plasmodium PI4Kβ and PKG inhibitory activity (exemplified by 19), as well as potent Plasmodium PI4Kβ inhibitors with minimal inhibitory activity against PKG (exemplified by 20). Compound 19 displayed potent antiplasmodium activity, high microsomal metabolic stability, and a good safety profile (hERG IC50 > 30; cytotoxicity selectivity index = 99). In vivo proof-of-concept, where a 4 × 50 mg kg-1 oral dose of 19 resulted in an 80% reduction in parasitemia in P. berghei-infected mice, further demonstrated the lead potential of this series. against respiratory-related infections with economic potential.
The synthesis and investigation of novel 3-benzoylbenzofurans and pyrazole derivatives for anti-HIV activity
(Royal Society of Chemistry, 2025-05) Khuzwayo, Sinothile S.; Selepe, Mamoalosi A.; Meyer, Debra; Gama, Ntombenhle Hlengiwe
Please read abstract in the article.
Microbial landscapes in Trinervitermes trinervoides termite colonies are affected by mound compartments and soil properties but not by symbiotic Podaxis fungi
(Elsevier, 2024-11-24) Bodawatta, Kasun H.; Maccario, Lorrie; Peereboom, Nils; Conlon, Benjamin H.; Li, Guangshuo; Plaszko, Tamas; Vinagre-Izquierdo, Celia; Jonsson, Knud A.; Vesala, Risto M.; De Beer, Z. Wilhelm
Termites are important ecosystem engineers and play key roles in modulating microbial communities within and outside their mounds. Microbial diversity within termite mounds is generally lower than surrounding soils, due to termite-associated antimicrobial compounds and active sanitary behaviours. Microbial symbionts of termites can also influence the microbial landscape, by inhibiting or out-competing other microbes. Certain members of the arid habitat fungal genus Podaxis (Agaricomycetes; Agaricaceae) are symbiotic with savannah specialist grass-cutting termites, and have the potential to influence mound-associated microbiomes. To test this, we characterized fungal (ITS2) and bacterial (16S rRNA) communities within and outside 49 Trinervitermes trinervoides mounds with and without Podaxis fruiting bodies across a 1000 km transect in South Africa. We predicted that Podaxis would be a dominant member of the fungal communities in mounds and negatively impact microbial diversity. Further, we explored how environmental variables shaped microbial communities, including whether soil elemental composition affected Podaxis presence. As expected, we observed less diverse fungal communities, but not bacterial communities, within than outside mounds, while microbial communities differed by sampling regions and mound compartments. Podaxis sequences were present in 48 out of 49 mounds in low relative abundances, and neither fruiting body presence nor sequence abundance were associated with microbial diversity or composition. There was, however, an overall association between the presence of Podaxis fruiting bodies and elemental composition, with different elements displaying varying associations depending on geographic region. Both environmental variables and soil elements were associated with fungal and bacterial taxa, indicating that they are key drivers of microbial community composition. Taken together, our findings suggest that microbial landscapes in termite mounds are not strongly influenced by Podaxis but mainly driven by termite filtering and regional abiotic variables and elemental compositions.
Inhibitors of malaria parasite cyclic nucleotide phosphodiesterases block asexual blood-stage development and mosquito transmission
(American Association for the Advancement of Science, 2024-10-06) Gomez-Gonzalez, Paula-Josefina; Gupta, Antima; Drought, Laura G.; Patel, Avnish; Okombo, John; Van der Watt, Mariette Elizabeth; Walker-Gray, Ryan; Schindler, Kyra A.; Burkhard, Anna Y.; Yeo, Tomas; Narwal, Sunil K.; Bloxham, Talia S.; Flueck, Christian; Walker, Eloise M.; Rey, Joshua A.; Fairhurst, Kate J.; Reader, Janette; Park, Heekuk; Pollard, Harry G.; Stewart, Lindsay B.; Brandner-Garrod, Luke; Kristan, Mojca; Sterk, Geert-Jan; Van Nuland, Youri M.; Manko, Emilia; Van Schalkwyk, Donelly A.; Zheng, Yang; Leurs, Rob; Dechering, Koen J.; Aguiar, Anna Caroline C.; Guido, Rafael V.C.; Pereira, Dhelio B.; Tumwebaze, Patrick K.; Nosbya, Samuel L.; Rosenthal, Philip J.; Cooper, Roland A.; Palmer, Mike; Parkinson, Tanya; Burrows, Jeremy N.; Uhlemann, Anne-Catrin; Birkholtz, Lyn-Marie; Small-Saunders, Jennifer L.; Duffy, James; Fidock, David A.; Brown, Alan; Gardner, Mark; Baker, David A.
Cyclic nucleotide–dependent phosphodiesterases (PDEs) play essential roles in regulating the malaria parasite life cycle, suggesting that they may be promising antimalarial drug targets. PDE inhibitors are used safely to treat a range of noninfectious human disorders. Here, we report three subseries of fast-acting and potent Plasmodium falciparum PDEβ inhibitors that block asexual blood-stage parasite development and that are also active against human clinical isolates. Two of the inhibitor subseries also have potent transmission-blocking activity by targeting PDEs expressed during sexual parasite development. In vitro drug selection experiments generated parasites with moderately reduced susceptibility to the inhibitors. Whole-genome sequencing of these parasites detected no mutations in PDEβ but rather mutations in downstream effectors: either the catalytic or regulatory subunits of cyclic adenosine monophosphate–dependent protein kinase (PKA) or in the 3-phosphoinositide-dependent protein kinase that is required for PKA activation. Several properties of these P. falciparum PDE inhibitor series make them attractive for further progression through the antimalarial drug discovery pipeline.
Metagenomic evaluation of food hygiene practices in the National School Nutrition Programme in KwaZulu Natal, South Africa
(AOSIS, 2025-06) Madlala, Sithembile S.; Mchunu, Nokuthula; Dalasile, Monica; Pierneef, Rian Ewald; Reddy, Poovendhree
BACKGROUND : The National School Nutrition Programme (NSNP) provides meals to schools in low-income areas in South Africa, implemented by the Department of Basic Education (DBE) with food safety monitored by Municipal Health Services. AIM : To assess compliance of school kitchens with general hygiene requirements (R638 of 2018) and detect food pathogens on food contact surfaces using amplified metagenomics. SETTING : The study was conducted in quintile 1 and 2 primary schools in Vryheid, KwaZulu-Natal. METHODS : A quantitative cross-sectional study assessed the safety compliance of food preparation and storage areas in 33 primary schools against national legislation standards. Fifteen samples of food contact surfaces were collected from four schools and analysed using Illumina sequencing to identify prevalent bacterial genera. RESULTS : None of the schools possessed a Certificate of Acceptability. Significant structural issues include poor pest control, inadequate sanitary facilities, a lack of food safety training and inadequate waste management. Taxonomic analysis revealed several dominant bacterial genera, including Pseudomonas, Stenotrophomonas, Acinetobacter and Pantoea, indicating potential routes for food contamination and subsequent risks for foodborne illnesses. CONCLUSION : The study highlighted critical inadequacies in food preparation and storage areas requiring urgent intervention to ensure safe meal preparation. It emphasised the need for improved food safety monitoring and compliance in schools in low-income areas. Next-generation sequencing (NGS) techniques identified a broad spectrum of pathogens, offering a robust method for assessing environmental hygiene. CONTRIBUTION : This study provides insights into food safety risks in the NSNP, informing policies and interventions to improve food safety and reduce foodborne illnesses in schools.
Avocado rhizosphere community profiling : white root rot and its impact on microbial composition
(Frontiers Media, 2025-05) Magagula, Phinda; Swart, Velushka; Fourie, Arista; Vermeulen, Alicia; Nelson, Johannes Harold; Van Rooyen, Zelda; Van den Berg, Noelani; noelani.vdberg@fabi.up.ac.za
INTRODUCTION : The avocado rhizosphere supports diverse microbial communities essential for plant health and defence against pathogens. This study aimed to investigate the impact of Dematophora necatrix, the causal agent of white root rot (WRR), on the microbial composition and soil physicochemical properties of infected and non-infected avocado trees in two South African orchards. METHODS : ITS and 16S metabarcoding was used to compare the composition and diversity of the rhizosphere microbiome. Soil physicochemical properties were also assessed, and culturable bacterial and fungal isolates from the rhizosphere were screened for antagonistic activity against D. necatrix. RESULTS : We found that D. necatrix did not significantly alter overall microbial diversity but influenced relative abundance of specific taxa. In Orchard A, dominant bacterial genera included Sphingomonas, Rokubacteriales and Lysobacter, while Orchard B featured Sphingomonas and Acidothermus while beneficial microbes such as Streptomyces and Bacillus were enriched in WRR non-infected (WRR-N) soils. The fungal profiles revealed Trichoderma and Penicillium as potential biocontrol agents enriched in WRR-N soils. Furthermore, dual-culture assays demonstrated that Bacillus, Pseudomonas, Penicillium and Trichoderma isolates inhibited D. necatrix, highlighting their biocontrol potential. Key parameters, such as soil pH and iron (Fe), correlated strongly with microbial composition, suggesting they play an important role in pathogen resilience. DISCUSSION : These findings underscore the complexity of the avocado rhizosphere and its role in managing WRR, offering a foundation for developing integrated disease management strategies to enhance avocado productivity.
Classification of Nostoc-like cyanobacteria isolated from paddy soil into Aliinostoc, Aulosira, and Desmonostoc
(Frontiers Media, 2025-05) Pham, Hang T.L.; Ngo, Trang T.; Tran, Thang V.; Duong, Tuan A.; Tran, Long D.; Tran, Anh T.T.; Nguyen, Van T.H.; Nguyen, Sang V.
Accurate identification of cyanobacterial strains is an essential step for subsequent research to be performed on these organisms. The classification of cyanobacteria in Nostocaceae remains a significant challenge due to the lack of reference data for type species and robust morphological characters for each genus. This study aims to classify 38 new isolated Nostoc–like strains at the genus level. The relationship between phylogenetic classification and morphological characteristics at the genus level was also investigated. The 16S rRNA gene sequences served as primary data for phylogenetic classification, supporting the designation of 18 isolates into the Aliinostoc, 7 isolates into the Aulosira, and 13 isolates into the Desmonostoc. Subsequently, we used these isolates as living materials to discover the most distinct features at each genus level of Aliinostoc, Aulosira, and Desmonostoc. As a result, the morphological characteristics of the three genera became distinguishable when grown in the BG110 medium. There, the mature vegetative cells of all isolated strains in the Aliinostoc were gray or brown, the strains in the Aulosira exhibited basal heterocysts at the beginning of cultivation, and the Desmonostoc strains showed the appearance of akinetes in the life cycle as an alternative reproduction. All isolated strains exhibited heterocysts, indicating their ability to fix nitrogen and potentially improve nutrient availability in paddy soil, especially in nitrogen-deficient conditions. This study provides a dataset of 16S rRNA gene sequences and morphological characteristics of Nostoc morphotypes, contributing to cyanobacterial taxonomy.
Exposure to outdoor aerospora and associated respiratory health risks among adults in Potchefstroom, North-West province, South Africa
(Frontiers Media, 2025-04) Gharbi, Dorra; Neumann, Frank Harald; Podile, Keneilwe; Mcdonald, Marinda; Linde, Jo-hanne; Frampton, Megan; Liebenberg, Jennifer Leigh; Cilliers, Sarel; Mmatladi, Tshiamo; Nkosi, Phumelele; Paledi, Keamogestswe; Piketh, Stuart; Staats, Jurgens; Burger, Roelof P.; Havenga, Henno; Garland, Rebecca M.; Bester, Petra; Lebre, Pedro Humberto
BACKGROUND : Data on allergic rhinitis and respiratory health metrics are limited for South Africa, with grass pollen as a key outdoor aeroallergen. Exotic trees such as plane trees and ragweed produce highly allergenic pollen, dominating indigenous trees and weeds. Pollen allergy prevalence data is lacking in cities of North-West province such as Potchefstroom. OBJECTIVES : This study aimed to (i) assess the prevalence of allergies to major aeroallergens, including Poaceae (grasses), Cupressus/Hesperocyparis (cypresses), Platanus (plane tree), Ulmus (elm), Quercus (oak), Betula (birch), Olea (olive), Artemisia (sagebrush), Amaranthus (amaranth), Plantago (plantain), Morus (mulberry), and Ambrosia (ragweed), along with fungal spores such as Alternaria, Cladosporium, and Penicillium/Aspergillus, and (ii) investigate the monthly incidence of major aeroallergens and reactivity levels in sensitized adults in Potchefstroom. METHODS : Skin prick tests (SPTs) were performed on 202 adults aged 18–64 years with confirmed allergic symptoms during a field campaign at North-West University (NWU)'s Potchefstroom campus. A test panel of grass, weed, tree, and fungal spore extracts previously identified via aerobiological monitoring was used. Symptom scores were recorded using ISAAC questionnaires; Spearman's statistical correlation between symptom frequency and monthly aeroallergen concentrations were analyzed. RESULTS : Among the participants, 184 (91%) exhibited positive SPT reactions: 104 (57%) are monosensitized to pollen, 45 (24%) to fungal spores, and 35 (19%) are polysensitized. Aeroallergen prevalence was higher in females (73%) than in males (27%). The most common pollen allergens were Cynodon dactylon (Bermuda grass) (85%), Zea mays (maize) (46%), Platanus spp. (plane tree) (35%), and Ulmus campestris (field elm) (33%). Among fungal spores, Alternaria was the most common (93%), followed by Cladosporium (27%). A significant and positive statistical correlation was found between allergic rhinitis symptoms and monthly pollen concentrations of Betula, Morus, Platanus, and Quercus. DISCUSSION AND CONCLUSION : This pilot study linked aeroallergens detected in Potchefstroom with allergy profiles of local residents. The findings highlight the need for more comprehensive regional studies that integrate allergen testing with aerobiological data. Raising awareness and implementing health strategies are essential for managing allergic rhinitis in South Africa. More affordable and available SPTs kits, adapted to allergy prevalence in South Africa, are strongly suggested.
Removal of organic biomass in Eucalyptus plantations has a greater impact on fungal than on bacterial networks
(Elsevier, 2025-06) Bose, Tanay; Vivas, Maria; Slippers, Bernard; Roux, Jolanda; Dovey, Steven; Kemler, Martin; Begerow, Dominik; Witfeld, Frederick; Brachmann, Andreas; Wingfield, Michael J.; Hammerbacher, Almuth; tanay.bose@fabi.up.ac.za
Complex and stable soil microbial networks are essential for productivity in plantation forestry, but their response to disturbances from harvesting and replanting is not well understood. This study assessed the impact of treatments designed to mitigate these disturbances on microbial biodiversity and networks in Eucalyptus plantation soils at three South African sites. We used high-throughput sequencing to catalogue fungal and bacterial biodiversity from 108 soil samples across three treatments: (i) retention of harvest residues (retained), (ii) removal of residues (removed), and (iii) removal of residues with added fertilizer (fertilized). Bioinformatic and statistical analyses of the sequence data revealed treatment-specific variations in microbial OTU richness, network structure and taxon associations at order-level. Microbiome richness was highest in ‘retained’ plots, and treatment-specific microbial diversity was evident in both fungal and bacterial communities. Network comparisons revealed that treatments to mitigate disturbances caused by harvesting significantly affected fungal networks but not bacterial networks. Fungal networks in ‘retained’ plots exhibited the highest complexity and stability compared to plots where the entire crop was removed. However, bacterial networks did not show significant differences in network structure among treatments. The associations between fungal and bacterial nodes were consistent in the three treatments, as indicated by similar Jaccard indices. However, distinct fungal hub nodes were found when comparing the 'retained' and 'removed' treatments. These findings highlight that retaining harvest residues enhances microbial richness and stabilizes fungal networks, making it a better strategy for managing soil disturbances than residue removal or fertilization.
Mitigation of opportunistic pathogens in hot water systems : a review focused on premise plumbing in South Africa
(Water Research Commission, 2025-05) Moodley, S.J.; Venter, S.N. (Stephanus Nicolaas); Muchesa, P.; Barnard, T.G.; Singh, A.
Water reticulation systems (i.e., premise plumbing) serve as a reservoir for opportunistic premise plumbing pathogens (OPPPs) to survive within these premise systems. OPPPs can be transmitted to individuals mainly via inhalation of aerosols from these water systems. These OPPPs can adapt, thrive and survive under a range of different conditions, which include high temperatures and low oxygen levels during stagnation, conditions often associated with household plumbing systems, including hot water systems (HWS). Hospitals are of specific concern as infections caused by OPPPs predominantly affect individuals who have underlying illnesses or health conditions. The current South African National Standard (SANS) 241 for drinking water does not provide information regarding testing for the presence of OPPPs, while the SANS 893 and 893-1 standards only provide a guideline for Legionella in water systems. The presence of OPPPs within HWS and premise plumbing is a concern, and a need exists to establish remediation and mitigation measures to control the presence of OPPPs in buildings. This review addresses risk analysis, evaluation and measures, which include the control of geyser temperatures and training of plumbers, as well as sampling and detection of OPPPs. This should limit the number of infections amongst individuals and will thus lessen the financial burden on health care systems and the economy.
Water lily pond : a multiomics database for water lilies
(Oxford University Press, 2025-06) Zhao, Chengjun; Zhang, Ji; Chen, Yayu; Yang, Lishuang; Chen, Hongliang; Liang, Yufan; Wang, Wenquan; He, Shuang; Luo, Yunqing; Zhang, Junyu; Zhang, Hongbin; Yang, Shuting; Guo, Guilian; Dai, Wenbai; Yang, Zhijuan; Chen, Junhao; Zhou, Yuhan; Khan, Wasi Ullah; Liu, Guanhua; Jiang, Yifan; Zhu, Tianlong; Xu, Yingchun; Garcia-Caparros, Pedro; Van de Peer, Yves; Xue, Jia-yu; Chen, Chengjie; Zhang, Liangsheng; Chen, Fei
No abstract available.
Oxalate content of vegetation and termite frass in western South Africa
(Wiley, 2025-05) Nel, T.; Clarke, C.E.; Francis, M.L.; Babenko, D.; Breecker, D.; Cowan, Don A.; Gallagher, T.; McAuliffe, J.R.; Trindade, M.
Please read abstract in the article.
Investigating the antimicrobial and anticancer potential of culturable fungal endophytes isolated from the stems of Kirkia acuminata Oliv
(BioMed Central, 2025-05) Magagula, Mfundo; Motaung, Thabiso Eric; Mbita, Zukile; Dithebe, Khumiso
BACKGROUND : Fungal endophytes produce various structurally and chemically diverse bioactive secondary metabolites including those that are similar to their host plants. However, fungal endophytes from South African medicinal plants are relatively under-explored. The medicinal plant, Kirkia acuminata Oliv., is on the decline in the natural environment due to overharvesting. This necessitates the search for novel alternatives to sustainably obtain the plant’s bioactive metabolites. Thus, fungal endophytes may serve as suitable candidates as they can produce host-similar bioactive compounds. RESULTS : Eighteen morphologically distinct fungal endophytes were isolated from the surface-sterilised stems of K. acuminata Oliv. Sequencing of the internal transcribed spacer (ITS) region revealed that the isolates were distributed among three genera, namely Diaporthe, Neofusicoccum and Pseudofusicoccum. The broth micro-dilution assay showed that 17 of the 18 ethyl acetate crude extracts exhibited inhibitory activity with minimum inhibitory concentration (MIC) values ranging from 0.31 to 2.5 mg/mL and 1.25 to 2.5 mg/mL against bacterial pathogens and Candida albicans, respectively. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay revealed that most of the crude extracts had dose-dependent cytotoxicity against non-cancerous human embryonic kidney (HEK-293) cells, with the crude extracts of the N. parvum KaS-3, D. macadamiae KaS-4, P. olivaceum KaS-5 and D. neotheicola KaS-6 isolates demonstrating safety against the non-cancerous cells. The alamarBlue assay revealed that the four non-cytotoxic crude extracts had moderate anticancer activity against cervical cancer ME-180 and melanoma A375 cancerous cell lines. Moreover, mycochemical analysis of the non-cytotoxic crude extracts using colourimetric quantification methods revealed that the observed cytotoxic effect could be attributed to the high total phenolic content in the crude extracts. CONCLUSION : The study highlights that the fungal endophytes inhabiting the stems of K. acuminata Oliv. produce secondary metabolites that may serve as leads for novel antimicrobial and non-toxic anticancer agents.
The root rot pathogen Phytophthora cinnamomi : a long-overlooked threat to the Cape Floristic Region of South Africa
(Springer, 2025-04) Paap, Trudy; Balocchi, Felipe; Wingfield, Michael J.; trudy.paap@fabi.up.ac.za
The globally important plant pathogen Phytophthora cinnamomi was first reported in South Africa in 1931, where it caused substantial damage to avocado orchards. Surprisingly, 40 years passed before the pathogen was recognised as a significant threat to South Africa’s natural ecosystems. This first became evident when P. cinnamomi caused a “quick decline” of the iconic silver trees (Leucadendron argenteum) in the Cape Floristic Region (CFR) of the Western Cape Province. Subsequent research has underscored the role of P. cinnamomi as a major root rot pathogen affecting numerous native species. Despite these findings, there has been limited research on the extent of the threat P. cinnamomi poses to Cape flora, leaving the risk of extinction for many species largely unknown. A recent observation of P. cinnamomi causing rapid mortality in Sorocephalus imbricatus, a Critically Endangered Proteaceae, underscores the urgent need for a comprehensive evaluation of this pathogen’s impact on Cape flora and the associated extinction risks. Given the high number of rare and threatened species in the CFR, many of which belong to families known to be vulnerable to P. cinnamomi, there is a pressing need to initiate an intensive local research programme to fill this critical gap. To address this, we propose a structured research programme that will guide targeted mitigation efforts against P. cinnamomi. Enhancing our understanding of P. cinnamomi’s threat to the CFR, a global biodiversity hotspot, will be essential to inform conservation strategies and to set restoration priorities in the region.
Molecular mechanisms underlying tree host-pathogen interactions under drought stress and subsequent rewatering in Eucalyptus grandis
(Elsevier, 2024-12-02) Teshome, Demissew Tesfaye; Zharare, Godfrey Elijah; Ployet, Raphael; Naidoo, Sanushka; sanushka.naidoo@up.ac.za
Abiotic stresses such as drought change plant-pathogen interactions by affecting both hosts and pathogens. Here, we aimed to unravel the molecular mechanisms underlying forest tree-pathogen interactions under drought stress and subsequent rewatering. We conducted glasshouse experiments involving infection by the stem canker-causing fungal pathogen Chrysoporthe austroafricana under drought stress and rewatering in Eucalyptus grandis and investigated host and pathogen transcriptomic changes using RNA-seq data from our current combined stress experiment as well as previous single stress studies. We found that mild drought stress enhances disease progression while, upon rewatering, pathogen infection delays recovery of leaf stomatal conductance. Transcriptomic changes in the host support increased susceptibility to the pathogen while the in planta fungal transcriptome suggests prioritization of survival in the drought-stressed host. Upon rewatering, changes in the host transcriptome suggest allocation of resources to stress responses at the expense of growth and carbohydrate storage while that of the pathogen indicate downregulation of some fungal metabolic pathways potentially because the pathogen takes advantage of changes in the host. Our study identified key molecular processes and genes that provide mechanistic insights into tree-pathogen interactions under abiotic stresses. This enables prediction of tree resilience under a changing climate and contributes towards future tree health improvement endeavours.
Mulching of post-harvest residues and delayed planting improves fungal biodiversity in South African Eucalyptus plantations and enhances plantation productivity
(Elsevier, 2025-06) Bose, Tanay; Roux, Jolanda; Titshall, Louis; Dovey, Steven B.; Hammerbacher, Almuth; tanay.bose@fabi.up.ac.za
Short-rotation Eucalyptus plantations provide essential forest products, with productivity and soil health influenced by residue management and planting strategies. This study examined the effects of burning or mulching post-harvest residue followed by immediate versus delayed planting on soil fungal biodiversity, soil properties, and tree growth across four sites in KwaZulu-Natal, South Africa. Plots were planted either three months ('immediate') or six months ('delayed') after treatment implementation. Volume measurements assessed tree growth, and soil attributes, including moisture, temperature, and nutrient levels, were analyzed. Soil samples were collected in November 2019 and March 2022, and fungal communities were analyzed through high-throughput sequencing targeting the internal transcribed spacer 1 (ITS1) region. Data emerging from this study showed mulched plots had significantly higher tree volume, with delayed planting increasing productivity by 13.6 % at 24–36 months and 25 % at 36–48 months post-planting. Soil moisture was 1.3–2 times higher in mulched plots than in burnt plots. Mulching significantly reduced the maximum soil temperatures by 4.5–6.8 °C. Four months after treatment, burnt plots had higher pH (1.1-fold), carbon (2.2-fold), phosphate (1.6-fold) and manganese (2.5-fold). Initially, mulched plots had lower fungal biodiversity (0.81-fold) than burnt plots but surpassed them after 28 months (1.28-fold increase). Fungal community overlap declined from 83.28 % to 40.64 %, with mulching supporting higher saprotroph (1.3-fold) and symbiotroph (1.25-fold) abundances, while delayed planting increased pathotroph presence by 1.5-fold in burnt plots. These findings highlight the long-term benefits of mulching and delayed planting in enhancing fungal biodiversity, promoting beneficial microbial communities, and improving tree growth, contributing to more sustainable Eucalyptus plantation management.
Mesorhizobium salmacidum sp. nov. and Mesorhizobium argentiipisi sp. nov. are symbionts of the dry-land forage legumes Lessertia diffusa and Calobota sericea
(Springer, 2025-03) Muema, Esther K.; Van Lill, Melandre; Venter, S.N. (Stephanus Nicolaas); Chan, Wai Yin; Claassens, Ricu; Steenkamp, Emma Theodora
Legumes Lessertia diffusa and Calobota sericea, indigenous to South Africa, are commonly used as fodder crops with potential for sustainable livestock pasture production. Rhizobia were isolated from their root nodules grown in their respective soils from the Succulent Karoo biome (SKB) in South Africa, identified and characterized using a polyphasic approach. Sequence analysis of the 16S rRNA gene confirmed all isolates as Mesorhizobium members, which were categorized into two distinct lineages using five housekeeping protein-coding genes. Lineage I included 14 strains from both legumes, while Lineage II comprised a single isolate from C. sericea. Differences in phenotypic traits were observed between the lineages and corroborated by average nucleotide identity analyses. While all strains nodulated their original hosts, strains from C. sericea failed to effectively nodulate L. diffusa and vice versa. Phylogenetic analyses of nitrogen fixation (nifH) and nodulation (nodA, nodC) loci grouped all strains in a single clade, suggesting that unique symbiotic loci determine nodulation of these legumes. We designated Lineage I and II as Mesorhizobium salmacidum sp. nov. (Ld1326Ts; GCA_037179605.1Ts) and Mesorhizobium argentiipisi sp. nov. (Cs1330R2N1Ts; GCA_037179585.1Ts), using genome sequences as nomenclatural types according to the Nomenclatural Code for Prokaryotes using Sequence Data, thus avoiding complications with South Africa's biodiversity regulations. Identifying effective microsymbionts of L. diffusa and C. sericea is essential for conservation of Succulent Karoo Biome, where indigenous invasive species like Vachellia karroo and non-native Australian acacia species are present. Furthermore, targeted management practices using effective symbionts of the studied legumes can sustain the biome's socio-economic contribution through fodder provision.
Establishing African genomics and bioinformatics programs through annual regional workshops
(Nature Research, 2024-08) Sharaf, Abdoallah; Nesengani, Lucky Tendani; Hayah, Ichrak; Kuja, Josiah Ochieng; Mdyogolo, Sinebongo; Omotoriogun, Taiwo Crossby; Odogwu, Blessing Adanta; Beedessee, Girish; Smith, Rae Marvin; Barakat, Abdelhamid; Moila, Acclaim M.; El Hamouchi, Adil; Benkahla, Alia; Boukteb, Amal; Elmouhtadi, Amine; Mafwila, Antoine Lusala; Abushady, Asmaa Mohammed; Elsherif, Assem Kadry; Ahmed, Bulbul; Wairuri, Charles; Ndiribe, Charlotte C.; Ebuzome, Chukwuike; Kinnear, Craig J.; Ndlovu, Deborah-Fay; Iraqi, Driss; El Fahime, Elmostafa; Assefa, Ermias; Ouardi, Faissal; Belharfi, Fatima Zohra; Tmimi, Fatim Zohra; Markey, Fatu Badiane; Radouani, Fouzia; Zeukeng, Francis; Mvumbi, Georges Lelo; Ganesan, Hamilton; Hanachi, Mariem; Nigussie, Helen; Charoute, Hicham; Benamri, Ichrak; Mkedder, Ikram; Haddadi, Imane; Meftah-Kadmiri, Issam; Mubiru, Jackson Franco; Domelevo Entfellner, Jean-Baka Kodjo; Rokani, Joan Bayowa; Ogwang, Joel; Daiga, Jude Bigoga; Omumbo, Judy; Ideozu, Justin Eze; Errafii, Khaoula; Labuschagne, Kim; Komi, Komi Koukoura; Tonfack, Libert Brice; Hadjeras, Lydia; Ramantswana, Madeleine; Chaisi, Mamohale; Botes, Marietjie W.; Kilian, Mariette; Kvas, Marija; Melloul, Marouane; Chaouch, Melek; Khyatti, Meriem; Abdo, Michael; Phasha-Muchemenye, Mmatshepho; Hijri, Mohamed; Mediouni, Mohammed Rida; Hassan, Mohammed Ahmed; Piro, Mohammed; Mwale, Monica; Maaloum, Mossaab; Mavhunga, Mudzuli; Olivier, Nicholas Abraham; Aminou, Oumaima; Arbani, Oumayma; Souiai, Oussema; Djocgoue, Pierre Francois; Mentag, Rachid; Zipfel, Renate Dorothea; Tata, Rolland Bantar; Megnekou, Rosette; Muzemil, Sadik; Paez, Sadye; Salifu, Samson Pandam; Kagame, Samuel Paul; Selka, Sarra; Edwards, Sean; Gaouar, Semir Bechir Suheil; Reda, Shaimaa Roshdy Abdullah; Fellahi, Siham; Khayi, Slimane; Ayed, Soumia; Madisha, Thabang; Sahil, Tulsi; Udensi, Ogbuagu Ugorji; Ras, Verena; Ezebuiro, Victor; Duru, Vincent C.; David, Xavier; Geberemichael, Yonas; Tchiechoua, Yves H.; Mungloo-Dilmohamud, Zahra; Chen, Zhiliang; Happi, Christian; Kariuki, Thomas; Ziyomo, Cathrine; Djikeng, Appolinaire; Badaoui, Bouabid; Mapholi, Ntanganedzeni; Muigai, Anne; Osuji, Julian O.; Ebenezer, ThankGod Echezona
The African BioGenome Project (AfricaBP) Open Institute for Genomics and Bioinformatics aims to overcome barriers to capacity building through its distributed African regional workshops and prioritizes the exchange of grassroots knowledge and innovation in biodiversity genomics and bioinformatics. In 2023, we implemented 28 workshops on biodiversity genomics and bioinformatics, covering 11 African countries across the 5 African geographical regions. These regional workshops trained 408 African scientists in hands-on molecular biology, genomics and bioinformatics techniques as well as the ethical, legal and social issues associated with acquiring genetic resources. Here, we discuss the implementation of transformative strategies, such as expanding the regional workshop model of AfricaBP to involve multiple countries, institutions and partners, including the proposed creation of an African digital database with sequence information relating to both biodiversity and agriculture. This will ultimately help create a critical mass of skilled genomics and bioinformatics scientists across Africa.
A revision of the family Cucurbitariaceae with additional new taxa from forest trees in Iran
(Springer, 2024-02) Eisvand, Payam; Mehrabi-Koushki, Mehdi; Crous, Pedro W.
The family Cucurbitariaceae is rich in species diversity and has a wide host range and geographic distribution. In this study, we identified 12 Cucurbitariaceae isolates which were obtained from disease symptoms in two forest trees in Khuzestan province, Iran. In addition, this family is reassessed using phylogenetic analyses based on DNA sequences from five nuclear regions (ITS, LSU, TUB2, TEF1α, and RPB2). The phylogenetic analyses showed that the present isolates represent one new genus, Nothocucurbitaria, and three new species, Allocucurbitaria galinsogisoli, Nothocucurbitaria izehica, and Parafenestella quercicola, which are described and illustrated. Furthermore, the genus Allocucurbitaria is emended to accommodate Seltsamia ulmi that grouped with the type species of Allocucurbitaria. Parafenestella pittospori and A. prunicola are recombined into the genera Neocucurbitaria and Nothocucurbitaria, respectively. Comparative analysis of single-locus trees revealed that the TUB2 and TEF1α can distinguish most genera and species in Cucurbitariaceae, while the ITS and LSU phylogenies show low resolution at both generic and species level. The best single-locus marker, RPB2, was able to distinguish all generic and most species lineages in Cucurbitariaceae.

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