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

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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.
A global atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts
(Nature Research, 2024-07) Graham, Emily B.; Camargo, Antonio Pedro; Wu, Ruonan; Neches, Russell Y.; Nolan, Matt; Paez-Espino, David; Kyrpides, Nikos C.; Jansson, Janet K.; McDermott, Jason E.; Hofmockel, Kirsten S.; Blanchard, Jeffrey L.; Liu, Xiao Jun A.; Rodrigues, Jorge L. Mazza; Freedman, Zachary B.; Baldrian, Petr; Stursova, Martina; DeAngelis, Kristen M.; Lee, Sungeun; Godoy-Vitorino, Filipa; Yeoh, Yun Kit; Cadillo-Quiroz, Hinsby; Tringe, Susannah G.; Chauhan, Archana; Cowan, Don A.; Van Goethem, Marc W.; Woyke, Tanja; Dove, Nicholas C.; Konstantinidis, Konstantinos T.; Juenger, Thomas E.; Hart, Stephen C.; Myrold, David D.; Onstott, Tullis C.; Bohannan, Brendan J.M.; Schmer, Marty R.; Palmer, Nathan A.; Nusslein, Klaus; Makhalanyane, Thulani P.; Dynarski, Katherine A.; Nas, Neslihan; Nicol, Graeme W.; Hazard, Christina; Scully, Erin D.; Jain, Kunal R.; Madamwar, Datta; Bissett, Andrew; Constant, Philippe; Oliveira, Rafael S.; Takacs-Vesbach, Cristina; Cregger, Melissa A.; Carrell, Alyssa A.; Klingeman, Dawn M.; Pietrasiak, Nicole
Historically neglected by microbial ecologists, soil viruses are now thought to be critical to global biogeochemical cycles. However, our understanding of their global distribution, activities and interactions with the soil microbiome remains limited. Here we present the Global Soil Virus Atlas, a comprehensive dataset compiled from 2,953 previously sequenced soil metagenomes and composed of 616,935 uncultivated viral genomes and 38,508 unique viral operational taxonomic units. Rarefaction curves from the Global Soil Virus Atlas indicate that most soil viral diversity remains unexplored, further underscored by high spatial turnover and low rates of shared viral operational taxonomic units across samples. By examining genes associated with biogeochemical functions, we also demonstrate the viral potential to impact soil carbon and nutrient cycling. This study represents an extensive characterization of soil viral diversity and provides a foundation for developing testable hypotheses regarding the role of the virosphere in the soil microbiome and global biogeochemistry.
A comprehensive molecular phylogeny of Cephalotrichum and Microascus provides novel insights into their systematics and evolutionary history
(Naturalis Biodiversity Center and Centraalbureau voor Schimmelcultures, 2024-06) Wei, T.P.; Wu, Y.M.; Zhang, X.; Zhang, H.; Crous, Pedro W.; Jiang, Y.L.
The genera Cephalotrichum and Microascus contain ecologically, morphologically and lifestyle diverse fungi in Microascaceae (Microascales, Sordariomycetes) with a world-wide distribution. Despite previous studies having elucidated that Cephalotrichum and Microascus are highly polyphyletic, the DNA phylogeny of many traditionally morphology-defined species is still poorly resolved, and a comprehensive taxonomic overview of the two genera is lacking. To resolve this issue, we integrate broad taxon sampling strategies and the most comprehensive multi-gene (ITS, LSU, tef1 and tub2) datasets to date, with fossil calibrations to address the phylogenetic relationships and divergence times among major lineages of Microascaceae. Two previously recognised main clades, Cephalotrichum (24 species) and Microascus (49 species), were re-affirmed based on our phylogenetic analyses, as well as the phylogenetic position of 15 genera within Microascaceae. In this study, we provide an up-to-date overview on the taxonomy and phylogeny of species belonging to Cephalotrichum and Microascus, as well as detailed descriptions and illustrations of 21 species of which eight are newly described. Furthermore, the divergence time estimates indicate that the crown age of Microascaceae was around 210.37 Mya (95 % HPD: 177.18–246.96 Mya) in the Late Triassic, and that Cephalotrichum and Microascus began to diversify approximately 27.07 Mya (95 % HPD: 20.47–34.37 Mya) and 70.46 Mya (95 % HPD: 56.96–86.24 Mya), respectively. Our results also demonstrate that multigene sequence data coupled with broad taxon sampling can help elucidate previously unresolved clade relationships.
Several Seiridium species (Sporocadaceae: Xylariales) cause cypress canker in South Africa
(Elsevier, 2025-02) Aylward, Janneke; Atkins, Sydney; Roets, Francois; Wingfield, Brenda D.; Wingfield, Michael J.; janneke.aylward@fabi.up.ac.za
Cypress canker is an important fungal disease caused by at least seven different Seiridium species. The disease has been known on Cupressaceae trees in South Africa since the 1980's, but its relevance was recently accentuated with an outbreak on native Widdringtonia nodiflora trees in the Western Cape. The causal agent, S. neocupressi, was previously unknown in the country, highlighting a lack of information regarding the disease in South Africa. The aim of this study was to investigate the occurrence of cypress canker and its causal agents across the country by sampling diseased Cupressaceae trees and reconsidering the identity of Seiridium strains previously collected in the country. Phylogenetic analyses revealed five known cypress canker pathogens and two putatively novel species. Seiridium cardinale was the most frequently isolated species in the Western Cape. Only two isolates of S. neocupressi were found outside the outbreak on Widdringtonia. Seiridium unicorne was most frequently isolated in the Gauteng and Free State provinces. Seiridium cancrinum, S. kenyanum and the two undescribed species were each recovered only in localised areas. Stem inoculations on x Hesperotropsis leylandii using S. cardinale, S. neocupressi and S. unicorne strains confirmed the pathogenicity of S. cardinale and S. neocupressi. In contrast, S. unicorne strains exhibited variable levels of aggressiveness. This study represents the first extensive consideration of cypress canker in South Africa and one of few studies on this important disease in the Southern Hemisphere
Production of fusel alcohols and fusel acetates by pathogenic fungi in the Ceratocystidaceae
(Elsevier, 2025-08) Mailula, Dineo M.; Wingfield, Brenda D.; Van der Nest, Magrieta Aletta; Hammerbacher, Almuth; almuth.hammerbacher@fabi.up.ac.za
The family Ceratocystidaceae includes economically important plant pathogens that vary in host preference and lifestyle. These fungi are believed to attract insect vectors, for their dispersal through their floral and fruity scents. This study aimed to identify the volatiles produced by a subset of fungi within the Ceratocystidaceae using gas chromatography coupled with mass spectrometry. The primary volatiles produced by most genera in the family were fusel alcohols and fusel acetates, but their emission rates differed significantly between genera and isolates from a single species. Ceratocystis albifundus collected from Protea cynaroides produced higher levels of fusel acetates compared to isolates from Terminalia sericea. In addition, significant differences in volatile biosynthesis were observed between isolates grown under different temperatures. Results of this study demonstrate that Ceratocystidaceae exhibit varied volatile profiles, but further research is needed to understand the ecological and physiological mechanisms underlying this plasticity.
CRISPR-Cas9 genome editing reveals that the Pgs gene of Fusarium circinatum is involved in pathogenicity, growth and sporulation
(Elsevier, 2025-03) Van Dijk, Alida; Wilson, Andi M.; Marx, Bianke; Hough, Bianca; Swalarsk-Parry, Benedicta S.; De Vos, Lieschen; Wingfield, Michael J.; Wingfield, Brenda D.; Steenkamp, Emma Theodora; alida.vandijk@up.ac.za
Fusarium circinatum, the causal agent of pine pitch canker, is one of the most destructive pathogens of Pinus species worldwide. Infections by this pathogen result in serious mortality of seedlings due to root and root collar disease, and growth reduction in trees due to canker formation and dieback. Although much is known about the population biology, genetics, and genomics of F. circinatum, relatively little is known regarding the molecular basis of pathogenicity in F. circinatum. In this study, a protoplast-based transformation using CRISPR-Cas9-mediated genome editing was utilized to functionally characterize a putative pathogenicity gene in three different strains of the fungus. In silico analyses suggested the gene likely encodes a small secreted protein, and all isolates in which it was deleted displayed significantly reduced vegetative growth and asexual spore production compared to the wild-type isolates. In pathogenicity tests, lesions induced by the deletion mutants on detached Pinus patula branches were significantly shorter than those produced by the wild-types. The putative pathogenicity gene was named Pgs reflecting its role in pathogenicity, growth, and sporulation. Future research will seek to explore the molecular mechanisms underlying the mutant phenotypes observed. Overall, this study represents a significant advance in F. circinatum research as the development and application of a Cas9-mediated gene deletion process opens new avenues for functional gene characterization underlying many of the pathogen's biological traits.

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