Research Articles (Plant Production and Soil Science)

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A collection containing some of the full text peer-reviewed/ refereed articles published by researchers from the
Department of Plant Production and Soil Science

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Restoring degraded mine landscapes in Sub-Saharan Africa : plant facilitatory mechanisms, strategies and knowledge gaps
Owiny, Arthur A.; Chirwa, Paxie W.; Zekeng, Jules Christian; Mwamba, Theodore Mulembo; Syampungani, Stephen (Elsevier, 2026-01)
Facilitation is an important process for restructuring plant communities in degraded areas. However, little is known about its role in enhancing tree recruitment in mine wastelands. We reviewed and synthesised studies investigating the facilitation process in recovering degraded landscapes and critically analysed the prospects of its application in mine-generated wastelands. Our findings show that, although there are examples of application of facilitation in the restoration of tropical forest landscapes, little is known about its application in the recovery of mine wastelands. In mine wastelands, facilitation can improve vegetation recovery by driving plant structural dynamics and enhancing soil quality through litterfall and root activities, such as root interactions among leguminous trees and other plants. Facilitation also enhances nitrogen transfer, the exchange of essential nutrients and carbon through mycorrhizal fungi, and the improvement of microclimatic conditions by increasing water and nutrient availability. Furthermore, facilitation supports hydraulic lift and provides shade, reducing temperature and evapotranspiration in the understory. This, in turn, improves water status and promotes plant survival and growth under dry conditions. This review highlights the research gaps and proposes areas that require further investigation. These include studies on (1) the facilitation of dominant tree species for the long-term reclamation across different mine wastelands, (2) assisted restoration for naturally and planted dominant tree species in mine-affected areas, and (3) understanding which species best facilitates the existence of other species, their interactions during restoration, the role of functional traits in successful outcomes, and the potential impact of climate change on the suitability of dominant species for restoration efforts. Additionally, several drawbacks associated with facilitation are highlighted in this review. However, we propose suggestions that might help address these challenges and invigorate interest in this line of research. This review examines the existing gaps and summarises the fundamental mechanisms of optimizing facilitation. Furthermore, the practical potential of facilitations for future development and the application of mine wastelands restoration is emphasised, highlighting their role in accelerating ecosystem recovery.
Petalidium saxatile (Acanthaceae), a new species from Namibia
Swanepoel, Wessel; Dexter , Kyle G.; Adamo, Martino; Manzitto-Tripp, Erin A.; Van Wyk, Abraham Erasmus (Braam) (Magnolia Press, 2025-09-03)
Petalidium saxatile, hitherto confused with P. canescens, and the widespread P. setosum, is here described as a new species. It is a range-restricted species, only known from the vicinity of Palmwag and southwards to the Bergsig area with an outlier population to the south of Khorixas in the Kaokoveld Centre of Endemism, northwestern Namibia. It grows mainly among basaltic rocks of the Etendeka Group on arid hillsides and along ephemeral riverbeds and drainage lines. Diagnostic characters for P. saxatile include the pale green appearance of the plants, vegetative parts with a dense white indumentum of relatively short dendritic trichomes appearing matted on young leaves, flowers borne in compact dichasia, and long simple eglandular trichomes on the bracts visible to the naked eye. The flowers of P. saxatile are distinctive in having the corolla lobes inside (adaxially) distinctly bicolorous: the upper and lateral lobes are pink or brown-pink, while the anterior lobe is yellow. Additionally, all lobes are discolorous in being much paler outside (abaxially). Furthermore, analyses of genetic data across many nuclear loci, generated using a ddRADseq approach, show the species to be genetically distinct from P. canescens. A comparison of key morphological features distinguishing P. saxatile from P. canescens and P. setosum, is provided. Based on IUCN Red List criteria, a provisional conservation assessment of Endangered (EN) is recommended for the new species. It is suggested that the Etendeka Tableland, to which P. saxatile is largely confined, may serve as a local subcentre of plant endemism within the larger Kaokoveld Centre of Endemism, at least for species in the genus Petalidium.
Tree composition, diversity, and structural complexity of the Cryptosepalum forests of North-Western Zambia : implications for conservation and sustainable management
Chishaleshale, Mwale; Chirwa, Paxie W.; Zekeng, Jules Christian; Syampungani, Stephen (Elsevier, 2026-05)
Please read abstract in the article. HIGHLIGHTS • Tree composition, diversity and structure were assessed in the Cryptosepalum forest (CF), across sites and across canopy types in Zambia. • The CF is dominated by the endemic Cryptosepalum exfoliatum species. • Co-existence of the Cryptosepalum exfoliatum with the Guibourtia coleosperma (Rosewood) threatens biodiversity of the CF. • Beta diversity was mainly driven by nestedness across forest canopy types. • Structural complexity varied across sites, reflecting disturbance and succession. • Forest canopy type shaped species diversity and evenness more than soil nutrients and elevation.
Distance-based variations in tree seedling species regeneration in traditional agroforestry of the Vhembe Biosphere Reserve, South Africa
Makhubele, Lucky; Chirwa, Paxie W. (Elsevier, 2026-07)
Seedling regeneration and β-diversity are critical for maintaining tree structure, biodiversity, and ecosystem functioning in traditional agroforestry landscapes (TAL). This study assessed regeneration seedling density (<5 cm DBH), species richness, and β-diversity across a spatial gradient in the Vhembe Biosphere Reserve, South Africa. Sampling was conducted in 675 subplots nested within 135 plots across three distance classes: immediate (0–1 km), intermediate (1–5 km), and far (5–10 km). A total of 4693 seedlings representing 117 species were recorded. Diversity patterns were analysed using SIMPER, PERMDISP, PERMANOVA, and distance-based linear modelling (DISTLM). Significant differences (p < 0.05) in regeneration attributes were observed across distance classes. Seedling density increased with distance from settlements, with the highest values at far distances, while species richness and β-diversity peaked at intermediate distances. Species composition differed significantly among distance levels, with the greatest dissimilarity between the immediate and far zones. A few resilient and multipurpose species, including Tabernaemontana elegans, Grewia microthyrsa, and Combretum molle, were consistently abundant across all distance levels. DISTLM identified distance, elevation, slope gradient, and grazing as key drivers of regeneration patterns, with distance being the most influential. Higher disturbance near settlements, associated with harvesting, grazing, and land-use pressure, reduced regeneration density and diversity. The findings show that although TAL systems support substantial biodiversity and reflect community-based conservation of indigenous trees, regeneration is constrained by anthropogenic disturbances. Sustainable management, including reduced disturbance, regulated grazing, and protection of natural regeneration, is essential for long-term sustainability.
Bird community patterns and indicator species for monitoring fragmented Miombo and Mopane woodlands in southern Zambia
Laumonier, Yves; Simamora, Trifosa Iin; Siachoono, Stanford; Moombe, Kaala B.; Syampungani, Stephen; Ickowitz, Amy (Elsevier, 2026-07)
Biodiversity loss in subtropical dry forests and woodlands is accelerating, particularly where agricultural expansion has transformed woodland mosaics in human-modified landscapes outside protected areas. In Southern Zambia, the dry woodland biome is dominated by Miombo and locally by Mopane formations, which differ markedly in floristic composition, structure, soils, and disturbance regimes. We assessed bird assemblages across three woodland types (Hilly Miombo, Plateau Miombo, and Mopane woodland patches), compared diversity patterns among sites, and evaluated the potential of bird species as ecological indicators for long-term ecosystem monitoring. Combining community-level analyses (NMDS, diversity indices, rank–abundance distributions) with species-level approaches (IndVal and N-mixture models), we recorded 10,292 individuals from 212 species, representing about 70% of the region’s woodland avifauna. Indicator species analysis identified six candidate species strongly associated with Mopane and six with Hilly Miombo, whereas Plateau Miombo, characterized by long-term disturbance and community homogenization, yielded only one indicator species. N-mixture models produced 98 significant detections and 78 statistically significant abundance estimates, providing detection-corrected population baselines. Our findings demonstrate that fragmented woodland mosaics still support substantial bird diversity, despite sustained anthropogenic pressures. The identified indicator species, coupled with abundance-based modelling, offer a practical foundation for long-term monitoring of habitat change and guiding conservation and land-use planning in Zambia’s dry forest landscapes. HIGHLIGHTS • Bird communities vary among Hilly Miombo, Plateau Miombo, and Mopane woodlands. • Twelve habitat-specific indicator species were identified using IndVal analysis. • Plateau Miombo showed community homogenization, yielding only one indicator species. • N-mixture models produced 78 detection-corrected abundance estimates for monitoring. • Results support long-term biodiversity monitoring in Zambia’s fragmented woodland mosaics.
Managing resistance : evaluating alternative herbicides for glyphosate-resistant smooth pigweed (Amaranthus hybridus) in the Republic of South Africa
Shabangu, Nhlanhla M.; Simelane, Nonduduzo Adelaide; Reinhardt, Carl Frederick (Charlie); Marais, Diana; Vorster, Barend Juan (Cambridge University Press, 2026)
Herbicide resistance poses a significant challenge due to the increasing number of weeds resistant to multiple sites of action (SOAs). Recently, smooth pigweed populations resistant to glyphosate have been confirmed in the KwaZulu-Natal Province in the Republic of South Africa. This study evaluated herbicide products with different SOAs as alternative options for controlling glyphosate-resistant (GR) smooth pigweed populations. Dose-response assays for preemergence and postemergence herbicides were conducted under greenhouse conditions at the University of Pretoria, in South Africa. Seeds of GR smooth pigweed populations from Bergville and Winterton, and a glyphosate-susceptible (GS) population from Hendrina, were used. To evaluate preemergence herbicides (mesotrione, atrazine, imazethapyr, and acetochlor), seeds were sown in pots and herbicides were applied 12 h after sowing. Postemergence herbicides (mesotrione, atrazine, tembotrione and atrazine tank mixture, and chlorimuron-ethyl) were tested on potted plants at the 6-leaf stage. Herbicides were applied at 0×, 0.5×, 1×, 2×, and 4×of the field-use rate for the herbicide products representing each SOA. Preemergence herbicides provided >90% control across all populations. Among postemergence herbicides, mesotrione effectively controlled all the GR populations, whereas the GS population exhibited reduced sensitivity (>50% survival). Atrazine was effective when applied to the GR populations at rates higher than the recommended field-use rate. The tank mixture of tembotrione and atrazine had an additive effect compared to sole applications of mesotrione and atrazine. Chlorimuron-ethyl was effective only against the GS population. These results suggest that incorporating effective preemergence and postemergence herbicides into weed management programs could improve control of GR populations of smooth pigweed.
Ploidy does not affect responses to increased soil nutrients and salinity in a perennial geophyte
Mtileni, Masingitla P.; Oberlander, Kenneth Carl; Glennon, Kelsey L. (University of Chicago Press, 2026-05)
PREMISE OF RESEARCH : Polyploidy can alter plant phenotypes and may enhance the ability of plants to take advantage of high soil nutrient concentrations in their environment or exhibit tolerance to saline conditions. Experimental studies are useful to test how polyploid and diploid plants differ in their growth and reproductive success in different soil nutrient and saline conditions. METHODOLOGY : Here, we used growth chambers and reciprocal transplants in field habitats to test whether different soil nutrient–supplemented (nitrogen [N] and phosphorus [P]) and saline (NaCl) conditions and natural field soil conditions affected the number of leaves and flowers, size of longest leaves, relative growth rate, reproductive output, and survival of diploid and tetraploid individuals of Rhodohypoxis baurii var. platypetala. PIVOTAL RESULTS : Tetraploidy was not associated with an increase in the number of leaves and flowers, size of longest leaves, and relative growth rate and increased reproductive output under N or P enrichment in growth chambers and did not increase survival rate under NaCl. Reciprocal transplants showed a similar survivorship and reproductive output between diploid and tetraploid individuals, suggesting that the different ploidies are capable of establishing in each other’s environment. CONCLUSIONS : Together, findings from this study indicate that polyploidy in R. baurii var. platypetala does not necessarily confer a growth or reproductive advantage or limitation under different soil nutrient levels in the growth chambers or in the field.
First report of the Eucalypt stem canker pathogen Teratosphaeria gauchensis in South Africa
Roux, Jolanda; Angel Salazar, Lina Del Mar; Barnes, Irene (Wiley, 2025-12)
Two species of eucalypt stem canker pathogens in the genus Teratosphaeria are known from Africa. Teratosphaeria zuluensis (as Coniothyrium zuluense) was described from Eucalyptus species in South Africa in the 1990s (Wingfield et al. 1996) and T. gauchensis was reported from the continent in 2006 when a multi-gene phylogenetic study of T. zuluensis isolates, including ones previously collected from Ethiopia and Uganda (Gezahgne et al. 2005), revealed the presence of a second species (then treated as Colletogloeopsis gauchensis) causing similar symptoms on eucalypts (Cortinas et al. 2006). To date, only T. zuluensis has been recorded from South Africa.
Soil and crop response to irrigation with untreated and partially treated acidic mine waters
Magwaza, Siboniso Ntabebi; Annandale, John George; Steyn, Martin Joachim; Tanner, Philip Dale (Springer, 2026)
Coal mines in the Mpumalanga Province of South Africa generate large volumes of acid mine drainage (AMD). The AMD is neutralised in high-density sludge (HDS) plants and then treated to potable standard in reverse osmosis (RO) plants. These processes are very expensive, energy intensive, and produce gypsiferous sludges and brines that need to be managed. Irrigation with partially treated or untreated AMD on soils amended with limestone is considered a potential alternative. To test the feasibility of this, two glasshouse pot experiments were conducted, one in the winter of 2023 with barley, wheat, and stooling rye, and the other with sorghum and soybean in the summer of 2023/24. The aim was to evaluate site-specific predictions of fitness for use of these waters using an irrigation water quality decision support system and to determine crop and soil responses to irrigation with untreated acidic waters (pH 2.5 and 3.5) and partially treated mine waters (pH 7.5, 8, and 9). The model predicted rapid soil accumulation of elements for untreated AMD, which was consistent with the pot experiment findings. Even with additional limestone applied to the soils irrigated with untreated AMD to counter the acidity, the soil pH, above-ground biomass, and yield were markedly reduced. Vegetative biomass remained unaffected when partially treated waters were used for irrigation; however, grain yield was slightly reduced. Grains from crops irrigated with highly acidic water exceeded Codex Alimentarius levels for mercury and lead, suggesting consideration of industrial crops that are not consumed, for irrigation with untreated AMD, if yield penalties and environmental impacts of such irrigation are acceptable.
Genome sequencing of Monilinia spp. and expression of Monilinia fructicola putative effector genes during infection of peach (Prunus persica) cultivars 'Royal Summer' and 'Messapia'
Landi, L.; D’Ortenzio, A.L.; Makau, Sarah Mojela; De Miccolis Angelini, R.M.; Romanazzi, G. (International Society for Horticultural Science, 2026-04-24)
Pathogen genome sequencing provides useful information for plant disease management. The genomes of Monilinia laxa, M. fructigena and M. fructicola were recently sequenced, and showed the evolutionary state of these species within Sclerotiniaceae family, as compared to Sclerotinia sclerotiorum and Botrytis cinerea. Such investigations provided data for studying the effectors of such pathogens, involved in plant-pathogen interactions. The in vivo involvement of putative effector genes of Monilinia fructicola predicted by genome investigations was validated. Five M. fructicola isolates were inoculated on two peach (Prunus persica) cultivars, ‘Royal Summer’ and ‘Messapia’, with intermediate and late ripening periods, respectively. The expression pattern of 17 candidate effector genes of M. fructicola having heterogenous functions with roles in both the host invasion and fungal life, and seven peach genes involved in the immune defense system, were examined at 0, 2, 6, 10, and 24 h post inoculation (hpi). The overall expression of the genes analyzed was regulated mainly at 2, 6, and 10 hpi when disease symptoms started to appear on the fruit surface. All fungal isolates showed a similar ability to induce lesions associated with brown rot on both cultivars, although effector genes were differentially expressed over time, depending on the fungal isolates and largely on the hosts, which suggested specialized functions for these effector activities. The salicylic acid and jasmonate/ethylene signaling pathways were in a different way modulated in the host independently from the fungal isolate. The M. fructicola effectors can suppress host immune responses during the early biotrophic phase of the infection and induce plant cell death in the host. Our work improves understanding of M. fructicola effectors function and provides useful information for the development of novel strategies for brown rot management.
Fast response of satellite fluorescence-derived plant physiology to drought stress
Tang, Zhi; Miralles, Diego G.; Guo, Zhongyang; Maes, Wouter H. (Nature Research, 2026-03-27)
The differences in response times between vegetation physiology and vegetation structure to water stress at the global scale remain unclear. Here, we integrate solar-induced chlorophyll fluorescence satellite observations, optical remote sensing indices, and hydrometeorological data to globally disentangle the sequence and related factors of vegetation physiological and structural responses to drought. We isolated fluorescence efficiency by normalizing solar-induced chlorophyll fluorescence by absorbed photosynthetically active radiation; We show that fluorescence efficiency is a robust proxy for ecosystem-level vegetation physiology and responds to drought within ~3 days, while structural changes emerge after ~12 days. The contrast in timing is clearest in humid regions, owing to the sustained soil moisture availability during the initial stage of drought. Physiological responses are more temporally aligned with changes in vapor pressure deficit, whereas structural changes coincide more with soil moisture dynamics, reflecting differing patterns of association under increasing drought stress. These findings advance mechanistic understanding of vegetation drought responses across the continuum from physiological to structural processes.
Conservation gap analysis for Erica (Ericaceae)
Pirie, Michael D.; Bester, Stoffel P.; Blackhall-Miles, Robbie; Coetzee, Anina; Crowley, Dan; Ebrahim, Ismail; Elliott, Alan C.; Fagundez, Jaime; Forest, Felix; Forshaw, Nigel; Hoekstra, Rendert D.; Kandziora, Martha; Klopper, Ronell Renett; Koopman, Rupert; Musker, Seth D.; Nurk, Nicolai M.; Osborne, Jo; Pasta, Salvatore; Pipins, Sebastian; Quintana, Itxaso; Rebelo, Anthony G.; Rees, Paul; Rohrauer, Daniel; Le Roux, M. Marianne; Smit, Martin; Wilman, Victoria (Pensoft Publishers, 2026-04-06)
The flowering plant genus Erica (Ericaceae) includes well over 800 species and numerous formally described subspecies and varieties. Many of these are threatened in the wild. The Global Conservation Consortium (GCC) for Erica was established under Botanic Gardens Conservation International (BGCI) in order to collaboratively prevent species extinctions. To target this work, we need fundamental information on species distributions, conservation status in the wild, and representation in ex situ collections. In large, complex groups like Erica, such data are not necessarily available or easily accessible. Here, we document the current state of ex situ and in situ conservation of threatened Erica species, identify knowledge and resource gaps, and set out priorities for future work. We further developed and consolidated the large body of data on Erica nomenclature, taxonomy, and diversity now openly accessible as a result of collaborative efforts, in particular through the World Flora Online (WFO), the e-Flora of South Africa, and contributors to the Global Biodiversity Information Facility (GBIF). We obtained accessions data for living plant collections from BGCI’s PlantSearch and from botanic gardens directly, and wild distribution data from GBIF. We linked and summarised data in an updated version (4.03) of the openly available Erica Identification Aid to assist in prioritising work. Through discussions in thematic working groups of GCC Erica we identified further priorities for conservation action. The volume of openly available, georeferenced records for species has increased dramatically in recent years. Although fewer than half of threatened Erica taxa are in ex situ conservation collections, many more botanic gardens hold African/Cape species and could contribute to distributed meta-collections. The most urgent research gaps include undescribed and poorly understood diversity (particularly in South Africa and Madagascar) and shortfalls in up-to-date threat assessments. Between ex situ sites we need to establish accession-level comparisons of data and sharing of conservation grade material. We must improve knowledge of seed longevity and techniques for effective cultivation. We should secure species and collect data through collaboration with landowners and the public. Priority action in situ should include clearance of invasive alien plants as well as habitat restoration and reintroduction. Key statistics for Erica species: 1) Total: 830 species (excluding hybrids; plus 364 subspecies and varieties). South Africa: 747 species; Madagascar/Mascarenes: 41; Tropical Africa: 25; Europe/Mediterranean: 21. 2) 45% species revised taxonomically since 1965. 3) 77% species recorded on GBIF in the last 10 years. 4) 90% species threat assessed (38% in the last 10 years). 5) 46 Critically Endangered (CR), 48 Endangered (EN), 95 Vulnerable (VU) (23% threatened). 6) 47% of threatened species in ex situ collections.
From policy to practice : unpacking the implementation hurdles of South Africa’s R638 regulation on hygiene for handling food
Mkhwanazi, Ntombizethu Simphiwe; Adelle, Camilla; Korsten, Lise (Institute for African Alternatives, 2026-03)
This case study examines the implementation of Regulation R638, which outlines general hygiene requirements for food premises and the transport of food in South Africa. The regulation was introduced without stakeholder consultation due to the urgency of addressing public health concerns, particularly following the listeriosis outbreak across the country in 2017/18. This study explores the roles of various stakeholders, including government, industry, civil society, and research institutions, in the implementation of Regulation R638 and identifies significant challenges in enforcement. Key challenges include budgetary constraints, insufficient training, lack of institutional capacity, and non-compliance among food handlers. The findings highlight how the absence of stakeholder engagement during the regulation’s formulation has hindered effective implementation. Additionally, the study underscores the complexities of policy networks at different levels of government and the impact of resource allocation on food safety governance. The results suggest that the top-down approach adopted by the Department of Health, although necessary in response to a public health crisis, has led to difficulties in practical enforcement, underscoring the need for more inclusive and well-planned regulatory processes.
β-Lactam antibiotics and β-lactamases : historical perspectives and a review of β-lactamase inhibitors derived from natural products
Moyo, Phanankosi; Albert, Ikhane O.; Hlungwani, Neo; Sibanda, Thulani; Lumu, Perfoy; Khorommbi, Ndivhuwo Kevin; Kaur, Gurleen; Calvopina Tapia, Karina; Siegwart, George; Buabeng, Nana Kwaku; Danquah, Cynthia A.; McGaw, Lyndy Joy; Cosa, Sekelwa; Schofield, Christopher J.; Maharaj, Vinesh J. (Royal Society of Chemistry, 2026)
The history of β-lactam antibiotics and, subsequently, β-lactamase inhibitors highlight the indispensable role of natural products in modern medicine. The isolation and testing of β-lactam bearing natural products led to world-changing therapeutic breakthroughs, yielding efficacious, safe, and cost-effective medicines that are still widely used today. The scientific triumph of β-lactams was, however, followed by a period of reduced research into new antibiotics, during which time bacterial pathogens acquired multiple mechanisms of resistance. The available evidence suggests that this situation is not irretrievable – whereas insufficient medicinal chemistry is currently being carried out to enable a renaissance in antibiotic development, our molecular understanding of antimicrobial modes of action and resistance mechanisms has improved dramatically. The history of β-lactams and many other drug classes suggests that natural product-based approaches will be critical in the future. Here, we summarise the history of β-lactams, focusing on natural product science. We then examine historical and recent efforts to identify new types of β-lactamase inhibitors using natural product-based screening approaches. We conclude by providing a perspective on how we can most efficiently discover β-lactamase inhibitors from microbial and plant-derived natural products.
In vitro assessment of essential oils as sustainable antifungal agents against Sclerotinia sclerotiorum causing lettuce drop
Tunc, Mehdiye; Piancatelli, Simone; Makau, Sarah Mojela; D'Ortenzio, Annamaria Lucrezia; Moumni, Marwa; Simonetti, Sara; Papi, Laura; Grassi, Eleonora; Bucci, Francesco; Romanazzi, Gianfranco (MDPI, 2026-02-16)
Sclerotinia sclerotiorum is a soilborne fungal pathogen, and it is a major threat to lettuce production, causing lettuce drop. This study evaluated the antifungal effectiveness of five essential oils (EOs) (Rosmarinus officinalis, R. officinalis var. verbenone, Lavandula hybrida, Origanum majorana, and Thymus vulgaris) at 0.1%, 1%, and 10%, along with their phytotoxic effect in the field on three different crops (lettuce, tomato, and chard) following foliar application. T. vulgaris EO completely inhibited S. sclerotiorum mycelial growth at all tested concentrations. R. officinalis, L. hybrida, and O. majorana also showed full inhibition at 1% and 10%, while R. officinalis var. verbenone achieved 80–100% inhibition. R. officinalis had the least phytotoxic effects, with only a minimal effect on chard at 1%. R. officinalis var. verbenone caused low/moderate phytotoxicity in lettuce and chard but had no toxic effect on tomato. L. hybrida and O. majorana had moderate to low effects, while T. vulgaris was the most phytotoxic, significantly affecting lettuce and tomato at 1%. Further field trials are needed to define EO application protocols toward sustainable lettuce drop management without risks of phytotoxicity.
Productivity drives leaf mycobiome diversity patterns at global and continental scales
Harris, Mathew Andrew; Kemler, Martin; Slippers, Bernard; Hassel, Nils; Tsamba, Joshua; Arthan, Watchara; Kellogg, Elizabeth A.; AuBuchon-Elder, Taylor; Vorontsova, Maria S.; Archibald, Sally; Hempson, Gareth P.; Lehmann, Caroline E.R.; Besnard, Guillaume; Begerow, Dominik; Brachmann, Andreas; Solofondranohatra, Cédrique L.; Greve, Michelle (Wiley, 2025-07)
AIM : Studies assessing large-scale patterns of microbial diversity have predominantly focused on free-living microorganisms, often failing to link observed patterns to established theories regarding the maintenance of global diversity patterns. We aimed to determine whether foliar fungi on two closely related grass hosts—Heteropogon contortus and Themeda triandra—display a commonly observed latitudinal gradient in species richness and determine whether host identity, energy (temperature and precipitation), climate seasonality, fire frequency and grass evolutionary history drive the observed patterns in species richness and composition. LOCATION : Paleotropical. TIME PERIOD: Contemporary. MAJOR TAXA STUDIED : Foliar fungi. METHODS : Foliar fungal diversity was quantified from 201 leaf samples of T. triandra and H. contortus collected across the distributional range of these species. Mixed effects models were used to quantify patterns of diversity and their correlates among and within continents. Ordinations were used to assess drivers of composition. RESULTS : Foliar fungi displayed consistent latitudinal diversity gradients in richness. Energy was a strong driver of richness at inter-continental and continental scales, while other factors had inconsistent impacts on richness among scales, hosts and guilds. Globally, richness was higher in regions of higher growing season temperatures and where hosts were present for longer periods. Composition was primarily structured by geographic region at the global scale, indicating that distance was a dominant driver of community composition. Within Australia, temperature and rainfall seasonality and the amount of growing season rainfall, were the dominant drivers of both richness and composition. MAIN CONCLUSIONS : We find some support for the idea that foliar fungal species diversity is governed by the same factors as many macro-organisms (energy availability and evolutionary history) at inter-continental scales, but also that fungal diversity and composition in the highly seasonal continent of Australia were driven by factors that shape tropical grassy ecosystems, namely climate seasonality and fire.
Novel amplified fragment length polymorphism (AFLP) markers for typing medically relevant Fusarium and allied fusarioid genera
Monteiro, R.C.; Yu, C.Z.; Dolatabadi, S.; Hagen, F.; Sandoval-Denis, M.; Crous, Pedro W.; Fisher, M.C.; Gonçalves, S.S.; De Camargo, Z.P.; Hofling-Lima, A.L.; Rodrigues, A.M. (Westerdijk Fungal Biodiversity Institute, 2025-06-25)
Fusariosis is an emerging mycosis caused by diverse Fusarium and allied fusarioid genera that are characterized by spindle-shaped macroconidia. These fungi possess a broad ecological distribution, causing infections in a wide diversity of hosts, spanning the animal and plant kingdoms. The spectrum of human fusariosis encompasses superficial lesions like keratitis and onychomycosis to invasive fungal diseases. Notable genera within the medically relevant fusarioid group include Neocosmospora, Fusarium s. str., and Bisifusarium. While Neocosmospora species (formerly F. solani species complex) are primary causative agents of human fusariosis, instances involving Fusarium s. str. and Bisifusarium (formerly F. dimerum species complex) have been reported. There is an urgent need for DNA-based markers to explore the epidemiology of these emerging fusarioid pathogens using molecular methods. We took advantage of fusarioid genomes available in NCBI (n = 20) to optimize the development of novel amplified fragment length polymorphism (AFLP) markers by conducting in-depth in silico analyses to refine their applicability for studies on these pathogens' genetic epidemiology. In-silico screening highlighted eight primer pair combinations (C1-C8) to be tested in vitro. The AFLP protocol was used for genotyping 40 medically relevant fusarioid fungi. Based on the overall scored AFLP markers (77-93 fragments), the values of polymorphism information content (PIC = 0.3474-0.3725), marker index (MI = 0.0038-0.0056), effective multiplex ratio (E = 26.3750-40.4750), resolving power (Rp = 40.1500-54.6000), discriminating power (D = 0.7978-0.8857), expected heterozygosity (H = 0.4476-0.4949), and mean heterozygosity (H avp = 0.0001) demonstrated the utility of these primer combinations for discriminating Neocosmospora, Fusarium s. str., and Bisifusarium species. Of relevance, some AFLP panels were better than others at studying genetic trends in Neocosmospora (#2 EcoRI-AT/MseI-TA, #3 EcoRI-AA/MseI-TT, and #5 EcoRI-AT/MseI-AG) or Fusarium s. str. (mainly #2 EcoRI-AT/MseI-TA and #6 EcoRI-GA/MseI-TT) and Bisifusarium (#1 EcoRI-GA/MseI-AG and #6 EcoRI-GA/MseI-TT), and these combinations will better resolve disease transmission routes. Our DNA fingerprint assay has proven effective by exhibiting rapidity, reproducibility, and high discriminatory capabilities, which represents a valuable asset in the ongoing efforts to combat fusariosis and enhance our scientific understanding of medically relevant Fusarium and allied fusarioid genera.
Exploring neopestalotiopsis diversity associated with blueberry leaf and twig blight in South African nurseries
Van der Vyver, Lourens Stefanus; De Bruin, Willeke; Siyoum, Nazareth Afewerki; Nsibo, David Livingstone; Groenewald, j.z.; Korsten, Lise (Westerdijk Fungal Biodiversity Institute, 2025-12)
New blueberry plantings in South Africa have increased dramatically since the year 2000, exceeding the global expansion rate. The crop is, however, impacted by several economically important fungal pathogens. Lesser-known fungi such as pestalotioid species can cause leaf and twig blight, and have the potential to become a global threat to blueberry production and expansion. This study aimed to assess the presence of such fungal species in blueberry nurseries in South Africa due to the industry’s exponential growth and mass introduction of new cultivars. Symptomatic leaf and twig samples were collected from six propagation nurseries, resulting in 180 pestalotioid isolates, of which a subset of 48 isolates were selected for molecular characterisation using multi-locus sequence analysis of the internal transcribed spacer region (ITS), partial translation elongation factor 1-α (TEF1) and partial β-tubulin (TUB2) gene regions. Phylogenetic analyses were performed using Maximum Likelihood, Maximum Parsimony and Bayesian Inference methods. Based on the phylogenetic analyses, all isolates clustered with three previously described species of Neopestalotiopsis, namely N. rosae, N. hispanica and N. longiappendiculata. Of these, 32 isolates were identified as N. rosae, followed by N. hispanica (12) and N. longiappendiculata (4). To the best of our knowledge, this is the first report of these species in South Africa. Based on phylogenetic analysis and morphological comparisons, we further recommend that N. vaccinii be considered a synonym of N. hispanica.
Effects of fire intensity on soil microbial ecology in a grassland ecosystem
Lebre, Pedro Humberto; Fouche, Jacques; Bosch, Jason; Pertierra, Luis R.; Varliero, Gilda; Frisby, Arnold Walter; Barker, Nigel; Greve, Michelle; Tichapondwa, Shepherd Masimba; Cowan, Don A. (Wiley, 2025-06)
In temperate grasslands, periodic or seasonal burning is considered critical for maintaining plant diversity and ecosystems. Under global change scenarios such as warmer and wetter climates and increasing alien invasions, fire is predicted to increase in intensity in many ecosystems. While the effects of fire on many terrestrial habitats (e.g., grassland, forest) have been extensively studied, less attention has been paid to the effects of fire intensity on the underlying soil microbiome. In this study, we used metagenomics, via 16S rRNA amplicon sequencing, coupled with functional assays and thermal profiling, to investigate the effects of increased fire intensity on the short‐ and medium‐term composition and functionality of grassland soil microbiomes. The results indicated that an increase in fire calorific output had a short‐term negative effect on soil microbial activity in grassland plots supplemented with plant biomass to simulate increases in fire intensity. In turn, the taxonomic profiling of soil microbial communities revealed that these plots were enriched in fast‐growing bacterial taxa 4 weeks after the fire event when compared to plots without biomass supplementation. This suggests that increased fire intensity exerts a medium‐term effect on the recovery of grassland soil microbiomes.
Cucumber production system as a reservoir for clinically important extended-spectrum beta-lactamase- and AmpC beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae strains
Dlangalala, Manana; Duvenage, Stacey; Du Plessis, Erika Margarete; Korsten, Lise (Wiley, 2026-02-13)
This study evaluated clinically significant extended-spectrum β-lactamase (ESBL)- and AmpC β-lactamase (AmpC)- producing Escherichia coli and Klebsiella pneumoniae in a cucumber production system, focusing on their potential sources and public health implications. Samples from water (n = 16) and cucumber (n = 12) yielded 40 potentially pathogenic isolates (E. coli: n = 17, K. pneumoniae n = 23), identified through matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF) analysis. All E. coli and K. pneumoniae isolates were phenotypically (Kirby Bauer disk diffusion) and genotypically [whole genome sequencing (WGS) (Illumina MiSeq)] characterized as multidrug resistant. Clinical relevance of these isolates is underscored by the pathogen probabilities (0.925–0.944 for E. coli and 0.534-0.897 K. pneumoniae isolates). The detection of K. pneumoniae ST985 in both the water source (Hartebeespoort Dam and preparation reservoir) and on the irrigated cucumbers highlights the importance of identifying the source of origin for more effective management and shows the potential that agricultural production environments can serve as conduits for the dissemination of clinically relevant antimicrobial-resistant bacteria. Understanding the presence of these clinically relevant organisms and antimicrobial resistance within the food system can lead to improved mitigation, on farm management and public health protection.

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