Research Articles (Forestry and Agricultural Biotechnology Institute (FABI))

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Influence of season, sex, and interspecific interactions on the diel activity patterns of two sympatric African small carnivores
(Nature Research, 2024-11-29) Carvalho, Filipe; Galantinho, Ana; Somers, Michael J.; Do Linh San, Emmanuel
Animal activity patterns vary seasonally and between species, facilitating species coexistence. In Africa, however, factors affecting the activity of many small carnivores remain poorly understood, especially for congeneric and sympatric species whose similar sizes may lead to interspecific competition. Here, we investigated differences and variations in the activity patterns of two sympatric Viverridae species in a seasonal African landscape. We continuously radio-tracked 15 small-spotted genets (Genetta genetta) and five Cape genets (G. tigrina) over 24-h cycles throughout the year. We analysed the effects of season, sex, and interspecific interactions on circadian rhythms using multi-cosinor regression models. Both species maintained a nocturnal activity pattern year-round, decreasing activity significantly during the cold-dry season. This pattern aligns with the thermoregulatory hypothesis—especially for species with an elongated body like genets—suggesting decreased activity under extreme cold weather conditions to conserve energy. Females in both species were less active than males, possibly due to their smaller home ranges, especially during the cold-dry season. These effects were particularly pronounced in Cape genets, which primarily inhabit riverine forests. Female Cape genets adjusted their activity onset, possibly to minimize encounters with males, mostly during the hot-wet season when caring for their offspring. Small-spotted genets shifted their activity onset and peak in riverine forests—areas of potential contact with Cape genets—compared to areas without Cape genets. Overall, our study underscores the critical role of seasonal environmental changes and interspecific interactions in shaping the activity patterns of two carnivore species within a semi-arid Albany Thicket landscape.
In vitro infection of bovine erythrocytes with Theileria annulata merozoites as a key step in completing the T. annulata life cycle in vitro
(Nature Research, 2024-02-13) Elati, Khawla; Tajeri , Shahin; Mugo , Robert M.; Obara , Isaiah; Darghouth, Mohamed Aziz; Zweygarth, Erich; Nijhof, Ard Menzo
Theileria annulata is a protozoan parasite with a complex life cycle involving a bovine host and a tick vector. It is transmitted by Hyalomma ticks and is the causative agent of tropical theileriosis, a debilitating and often fatal disease in southern Europe, northern Africa and large parts of Asia. Understanding the biology of different life cycle stages is critical for the control of tropical theileriosis and requires the use of experimental animals which poses an ethical concern. We present for the first time the in vitro infection of red blood cells (RBCs) with T. annulata differentiated schizonts. The Ankara cell line of T. annulata was cultured at 41 °C for nine days to induce merogony and subsequently incubated with purified RBCs for one to three days. Percentage of parasitized erythrocyte (PPE) over the short culture period was estimated by Giemsa staining (0.007–0.01%), Flow cytometry activated sorting (FACS) (0.02–1.1%) and observation of FACS sorted cells by confocal microscopy (0.05–0.4%). There was a significant difference in the PPE between FACS and the two other techniques (one-way ANOVA followed by Tukey test, P = 0.004) but no significant difference was observed between the confocal imaging and Giemsa staining methods (ANOVA one-way followed by Tukey test, P = 0.06). Importantly, all three complementary methods confirmed the invasion of RBCs by T. annulata merozoites in vitro. Although the experimental conditions will require further optimization to increase the PPE, the in vitro infection of RBCs by T. annulata merozoites is pivotal in paving the way for the eventual completion of the T. annulata life cycle in vitro when combined with artificial tick feeding.
Improving the antinutritional profiles of common beans (Phaseolus vulgaris L.) moderately impacts carotenoid bioaccessibility but not mineral solubility
(Nature Research, 2024-05-24) Alvarado‑Ramos , Katherine; Bravo‑Nunez , Angela; Halimi , Charlotte; Maillot , Matthieu; Icard‑Verniere, Christele; Forti, Chiara; Preite, Chiara; Ferrari, Luisa; Sala, Tea; Losa, Alessia; Cominelli, Eleonora; Sparvoli, Emanuela Camilli Francesca; Lisciani, Stefania Marconi Silvia; Georgé, Stephane; Mouquet-Rivier, Claire; Kunert, Karl J.
Common beans are a common staple food with valuable nutritional qualities, but their high contents in antinutritional factors (ANFs) can decrease the bioavailability of (i) fat-soluble micronutrients including carotenoids and (ii) minerals. Our objective was to select ANF-poor bean lines that would not interfere with carotenoid and mineral bioavailability. To achieve this objective, seeds of commercial and experimental Phaseolus vulgaris L. bean lines were produced for 2 years and the bean’s content in ANFs (saponins, phytates, tannins, total polyphenols) was assessed. We then measured carotenoid bioaccessibility and mineral solubility (i.e. the fraction of carotenoid and mineral that transfer into the aqueous phase of the digesta and is therefore absorbable) from prepared beans using in vitro digestion. All beans contained at least 200 mg/100 g of saponins and 2.44 mg/100 g tannins. The low phytic acid (lpa) lines, lpa1 and lpa12 exhibited lower phytate levels (≈ − 80%, p = 0.007 and p = 0.02) than their control BAT-93. However, this decrease had no significant impact on mineral solubility. HP5/1 (lpa + phaseolin and lectin PHA-E free) bean line, induced an improvement in carotenoid bioaccessibility (i.e., + 38%, p = 0.02, and + 32%, p = 0.005, for phytofluene bioaccessibility in 2021 and 2022, respectively). We conclude that decrease in the phytate bean content should thus likely be associated to decreases in other ANFs such as tannins or polyphenols to lead to significant improvement of micronutrient bioaccessibility.
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.
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.
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.
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.
Thermal performance drifts between the egg parasitoid Telenomus remus and the fall armyworm may threaten the efficacy of biological control under climate change
(Wiley, 2025-05) Mubayiwa, Macdonald; Machekano, Honest; Mvumi, Brighton M.; Opio, Winnifred A.; Segaiso, Bame; Chidawanyika, Frank; Nyamukondiwa, Casper
The fall armyworm, Spodoptera frugiperda J.E. Smith, is a significant global agricultural pest known for its rapid invasion and devastating impact on crops. While pesticides may be effective for controlling the pest in the short-term, they cause several socioeconomic and ecological costs that highlight the need for more sustainable management strategies. Telenomus remus (Nixon) is a promising egg parasitoid for its biological control. For the parasitoid to provide effective ecosystem services, it should be able to survive and coexist within the same ecological niches as its host. However, there is limited information regarding the potential responses of T. remus to thermal changes. In the context of the changing climate environments, it is key to understand the parasitoid's overall environmental fitness in relation to its host. We investigated the effects of short-term (2 h) and long-term (6 h) acclimation pretreatment of T. remus adults and S. frugiperda eggs to high and low temperatures (18°C and 32°C, respectively) in comparison with the control (28°C). Telenomus remus thermal fitness (critical thermal maxima [CTmax], heat knockdown time and critical thermal minima [CTmin]), parasitism rates, and adult emergence were determined. Pretreated S. frugiperda eggs were assessed for hatchability under the control conditions. Acclimation at low (18°C) and high (32°C) temperatures significantly reduced and increased heat tolerance, respectively. Both temperatures, however, reduced cold tolerance. The parasitoid thermal tolerance polygons following acclimation pretreatment, showed significant heat- but not cold-tolerance gains. Fall armyworm eggs short-term acclimated to 32°C had significantly higher (p < 0.05) but comparable hatchability to the control treatment. Similarly, parasitism and adult emergence rates were significantly lower (p < 0.001) following long-term acclimation of host eggs and the parasitoid to 32°C. These findings suggest that high temperatures may decouple the T. remus-fall armyworm ecological relationship, threatening its success in warming regions. The findings provide valuable insights into the potential environmental resilience and suitability of T. remus as a biological control agent across different climates or geographies.
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 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.
In silico characterisation of the avocado WAK/WAKL gene family with a focus on genes involved in defence against Phytophthora cinnamomi
(Frontiers Media, 2025-01) Harvey, Aaron Thomas; Van den Berg, Noelani; Swart, Velushka; velushka.swart@up.ac.za
The avocado industry faces a significant threat from the hemibiotrophic oomycete pathogen Phytophthora cinnamomi. A variably expressed defence gene during an avocado infection trial was a Wall-associated kinase (WAK). WAK and WAK-Like (WAKL) proteins are known to bind to fragmented pectin (oligogalacturonides) produced during pathogen penetration, thereby activating downstream defence-related pathways. To better understand the P. cinnamomi-avocado defence interaction, this gene family was assessed using in silico methods. In this study, previously generated RNA-sequencing data were used to associate genes with the defence response, followed by promoter- and phylogenetic analysis of these genes/proteins. The predicted proteins from these genes were modelled with AlphaFold2, and structural similarity across different rootstocks, as well as their binding affinity for oligogalacturonides, were assessed. The analysis identified 14 Persea americana (Pa)WAKs and 62 PaWAKLs across the West-Indian (pure accession reference), Dusa®, Leola™ and R0.12 avocado rootstock genomes. These genes showed distribution across the West-Indian genome’s chromosomes, with MCScanX analyses predicting tandem duplications. PaWAK/WAKL expression profiles were compared, implicating five PaWAK/WAKLs in defence. Phylogenetic and promoter analyses were conducted to predict associated defence-related pathways, focusing on stress and phytohormone-responsive pathways. Structural differences and varying oligogalacturonide binding affinities of PaWAK/WAKLs were predicted across rootstocks. These defence-related genes could be incorporated into a molecular screening tool to improve the development of resistant avocado rootstocks.

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