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

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Fungal Planet description sheets : 1697–1780
(Westerdijk Fungal Biodiversity Institute, 2024-12-06) Crous, Pedro W.; Wingfield, Michael J.; Jurjević, Ž.; Balashov, S.; Osieck, E.R.; Marin-Felix, Y.; Luangsa-ard, J.J.; Mejía, L.C.; Cappelli, A.; Parra, L.A.; Lucchini, G.; Chen, J.; Moreno, G.; Faraoni, M.; Zhao, R.L.; Weholt, Ø.; Borovička, J.; Jansen, G.M.; Shivas, R.G.; Tan, Y.P.; Akulov, A.; Alfenas, A.C.; Alfenas, R.F.; Altés, A.; Avchar, R.; Barreto, R.W.; Catcheside, D.E.A.; Chi, T.Y.; Esteve-Raventós, F.; Fryar, S.C.; Hanh, L.T.M.; Larsbrink, J.; Oberlies, N.H.; Olsson, L.; Pancorbo, F.; Raja, H.A.; Thanh, V.N.; Thuy, N.T.; Ajithkumar, K.; Akram, W.; Alvarado, P.; Angeletti, B.; Arumugam, E.; Atashi Khalilabad, A.; Bandini, D.; Baroni, T.J.; Barreto, G.G.; Boertmann, D.; Akram, W.; Alvarado, P.; Angeletti, B.; Arumugam, E.; Atashi Khalilabad, A.; Bandini, D.; Baroni, T.J.; Barreto, G.G.; Boertmann, D.; Bose, Tanay; Castañeda Ruiz, R.F.; Couceiro, A.; Cykowska-Marzencka, B.; Dai, Y.C.; Darmostuk, V.; Da Silva, S.B.G.; Dearnaley, J.D.W.; De Azevedo Santiago, A.L.C.M.; Declercq, B.; De Freitas G. , L.W.S.; De la Peña-Lastra, S.; Delgado, G.; De Lima, C.L.F.; Dhotre, D.; Dirks, A.C.; Eisvand, P.; Erhard, A.; Ferro, L.O.; García, D.; García-Martín, A.; Garrido-Benavent, I.; Gené, J.; Ghobad-Nejhad, M.; Gore, G.; Gunaseelan, S.; Gusmão, L.F.P.; Hammerbacher, Almuth; Hernández-Perez, A.T.; Hernández-Restrepo, M.; Hofmann, T.A.; Hubka, V.; Jiya, N.; Kaliyaperumal, M.; Keerthana, K.S.; Ketabchi, M.; Kezo , K.; Knoppersen, Rosa; Kolarczyková, D.; Kumar, T.K.A.; Læssøe, T.; Langer, E.; Larsson, E.; Lodge, D.J.; Lynch, M.J.; Maciá-Vicente, J.G.; Mahadevakumar, S.; Mateos, A.; Mehrabi-Koushki, M.; Miglio, B.V.; Noor, A.; Oliveira, J.A.; Pereira, O.L.; Piątek, M.; Pinto, A.; Ramírez, G.H.; Raphael, B.; Rawat, G.; Renuka, M.; Reschke, K.; Ruiz Mateo, A.; Saar, I.; Saba, M.; Safi, A.; Sánchez, R.M.; Sandoval-Denis, M.; Savitha, A.S.; Sharma, A.; Shelke, D.; Sonawane, H.; Souza, M.G.A.P.; Stryjak-Bogacka, M.; Thines, M.; Thomas, A.; Torres-Garcia, D.; Traba, J.M.; Vauras, J.; Vermaas, M.; Villarreal, M.; Vu, D.; Whiteside, E.J.; Zafari, D.; Starink-Willemse, M.; Groenewald, J.Z.; Akram
Novel species of fungi described in this study include those from various countries as follows: Antarctica, Leuconeurospora bharatiensis from accumulated snow sediment sample. Argentina, Pseudocercospora quetri on leaf spots of Luma apiculata. Australia, Polychaetomyces verrucosus on submerged decaying wood in sea water, Ustilaginoidea cookiorum on Scleria levis, Xylaria guardiae as endophyte from healthy leaves of Macaranga tanarius. Belgium, Iodophanus taxi on leaf of Taxus baccata. Belize, Hygrocybe mirabilis on soil. Brazil, Gongronella irregularis from soil, Linodochium splendidum on decaying sheath of Euterpe oleracea, Nothophysalospora agapanthi (incl. Nothophysalospora gen. nov.) on flower stalks of Agapanthus praecox, Phaeosphaeria tabebuiae on leaf of Tabebuia sp., Verrucohypha endophytica (incl. Verrucohypha gen. nov.) from healthy roots of Acrocomia aculeata. Estonia, Inosperma apricum on soil under Quercus robur. Greece, Monosporascus solitarius isolated from surface-sterilised, asymptomatic roots of Microthlaspi perfoliatum. India, Diaporthe neocapsici on young seedling stems of Capsicum annuum, Fuscoporia naditirana on dead wood, Sebacina spongicarpa on soil, Torula kanvae from the gut of a Copris signatus beetle. Iran, Sarcinomyces pruni from twig and petiole tissues of Prunus persica and Prunus armeniaca, Xenodidymella quercicola from leaf spots of Quercus brantii. Italy, Agaricus aereiceps on grass, Agaricus bellui in meadows, Agaricus fabrianensis in urban grasslands, Beaucarneamyces muscorum on moss growing in forest, Xenoanthostomella quercus on leaf litter of Quercus ilex. Netherlands, Alfaria neerlandica on stem lesions of Cortaderia selloana, Neodictyosporium juncicola on culms of Juncus maritimus, Penicillium geertdesnooi from soil under Papaver rhoeas, Russula abscondita on rich calcareous soil with Quercus, Russula multiseptata on rich clay soil with Quercus, Russula purpureopallescens on soil with Populus, Sarocladium caricicola on leaves of Carex riparia. Pakistan, Circinaria shimlaensis on limestone rocks. Panama, Acrocalymma philodendri on leaf spots of Philodendron sp., Caligospora panamaensis on leaf litter, Chlamydocillium simulans associated with a Xylaria sp., Corynesporina panamaensis on leaf litter, Cylindromonium panamaense on twig litter of angiosperm, Cyphellophora panamaensis on twig litter of angiosperm, Microcera panamensis on leaf litter of fern, Pseudotricholoma pusillum in tropical montane forest dominated by Quercus spp., Striaticonidium panamaense on leaf litter, Yunnanomyces panamaensis on leaf litter. Poland, Albocremella abscondita (incl. Albocremella gen. nov.) from rhizoids of liverwort Conocephalum salebrosum. Portugal, Agaricus occidualis in meadows. South Africa, Alternaria elsarustiae on culms of unidentified Poaceae, Capronia capensis on dead twig of unidentified angiosperm, Codinaeella bulbinicola on dead leaves of Bulbine frutescens, Cytospora carpobroticola on leaf of Carpobrotus quadrifidus, Neophaeomoniella watsoniae on leaf of Watsonia sp., Neoplatysporoides aloigena on leaf of Aloe khamiesensis, Nothodactylaria comitabilis on living leaf of Itea rhamnoides, Nothopenidiella beaucarneae (incl. Nothopenidiella gen. nov.) on dead leaves of Beaucarnea stricta, Orbilia kirstenboschensis on dead flower stalks of Agapanthus praecox, Phragmocephala agapanthi on dead flower stalks of Agapanthus praecox, Podocarpigena hagahagaensis (incl. Podocarpigena gen. nov.) on leaf spots of Podocarpus falcatus, Sporisorium enterogonipteri from the gut of Gonipterus sp., Synnemapestaloides searsiae on leaf of Searsia populifolia, Xenophragmocapnias diospyri (incl. Xenophragmocapnias gen. nov.) on leaf spots of Diospyros sp., Yunnanomyces hagahagaensis on leaf spots of Sideroxylon inerme. Spain, Agaricus basicinctus in meadows, Agaricus quercetorum among leaf litter in oak forests, Coprinopsis palaciosii on degraded woody debris, Inocybe complutensis in calcareous loamy soil, Inocybe tanitiae in calcareous sandy soil, Mycena subfragosa on dead leaves of Salix atrocinerea, Pseudobaeospora cortegadensis in laurel forests, Trichoderma sedimenticola from fluvial sediments. Sweden, Inocybe badjelanndana on calcareous soil. Ukraine, Beaucarneamyces lupini on overwintered stems of Lupinus polyphyllus, Protocreopsis globulosa on thallus and apothecia of Lecania cyrtella on bark of Populus sp., Thyridium tiliae on dead twigs of Tilia sp. USA, Cladosporium louisianense, Cyphellophora americana from a bedroom vent, Extremus massachusettsianus from lyse buffer, Myxotrichum tapetae on carpet in basement, Neospissiomyces floridanus (incl. Neospissiomyces gen. nov.) on swab from hospital, Polychaetomyces marinus (incl. Polychaetomyces gen. nov.) on submerged driftwood in sea water, Steccherinum fragrans on hardwood fallen on the beach, Steinbeckomyces carnegieae (incl. Steinbeckomyces gen. nov.) on Carnegiea gigantea, Tolypocladium pennsylvanicum from air sampled in basement. Vietnam, Acidomyces ducanhii from Aglaia flowers, Acidomyces paludis from dead bark of Acacia sp., Phakopsora sageretiae on Sageretia theezans, Puccinia stixis on Stixis scandens. Morphological and culture characteristics are supported by DNA barcodes
The VP7 protein of the African horse sickness virus core particle facilitates binding to Culicoides sonorensis cells in an RGD-independent manner
(Elsevier, 2025-11) Buyens, Ariel Renée Monique; Van Staden, Vida; Theron, Jacques; jacques.theron@up.ac.za
African horse sickness, caused by African horse sickness virus (AHSV) that is transmitted by midges of the Culicoides genus, leads to rapid mortality among horses. Proteases in the saliva of Culicoides midges cleave the VP2 outer capsid protein, resulting in infectious sub-virus particles that have increased infectivity for the Culicoides vector insect and Culicoides-derived cells (KC cells). The AHSV VP7 protein has an arginine-glycine-aspartate (RGD) motif, but the functional relevance of this protein and motif in facilitating binding to insect cells is unknown. To investigate, core-like particles (CLPs) were produced using the baculovirus expression system through the co-expression of VP3 and sVP7, which is a soluble version of the AHSV-4 VP7 protein. Insect cell binding assays indicated that the CLPs bind to KC cells, suggesting a role for VP7 in this interaction. Subsequently, recombinant baculoviruses expressing mutant sVP7 proteins were synthesized, in which the RGD motif was either deleted or mutated. All RGD-mutated sVP7 proteins, except for the deletion of the RGD motif, formed trimers and, when co-expressed with VP3, assembled into CLPs that retained the ability to bind to insect cells. These findings indicate that VP7 facilitates the binding of CLPs to insect cells through an RGD-independent mechanism. HIGHLIGHTS • VP7 is the outermost protein of AHSV core particles and possesses an RGD motif. • AHSV CLPs, formed by VP3 and VP7 proteins, bind to Culicoides-derived insect cells. • RGD-mutant CLPs retain the ability to bind to insect cells. • VP7 acts as an attachment protein for insect cells, independent of the RGD motif. • The findings provide new insights into early AHSV–insect vector interactions.
Argyrolobium legumes from an African centre of endemism associate with novel Bradyrhizobium species harbouring unique sets of symbiosis genes
(Elsevier, 2026-01) Maake, Mabodiba Masutane; Beukes, Chrizelle Winsie; Van der Nest, Magrieta Aletta; Avontuur, Juanita R.; Muema, Esther K.; Stȩpkowski, Tomasz M.; Venter, Stephanus N.; Steenkamp, Emma Theodora; emma.steenkamp@up.ac.za
Given that several, mainly endemic South African Genisteae genera occupy basal positions in legume phylogenetic trees, this region of Africa is considered a primaeval centre of diversification of this legume tribe. Despite the importance of South Africa in Genisteae evolution, almost all studies have focused on rhizobia nodulating Genisteae in their centres of diversity in either the Mediterranean Basin or the Americas. Therefore, this study aimed to identify and characterize rhizobial strains associated with Argyrolobium species native to areas of the Grassland biome associated with the Great Escarpment, which dominates the subcontinent’s eastern landscape, and compare these to bradyrhizobia nodulating Genisteae in other centres of diversity. Phylogenetic analyses of five housekeeping genes (dnaK, glnII, gyrB, recA, and rpoB) separated the 18 Bradyrhizobium strains examined into five well-supported groups. Three of these were conspecific with B. arachidis, B. brasilense/B. australafricanum and B. ivorense, while the remaining two appeared to be new to science. After confirming their novelty using Average Nucleotide Identity, a metric for genome relatedness, and certain phenotypic traits, we recognized them as novel species for which we proposed the names B. spitzkopense sp. nov. (Arg816Ts) and B. mpumalangense sp. nov. (Arg237LTs). Phylogenetic analyses of nodA gene sequences showed that about half of the strains examined, irrespective of their species identity, harboured alleles known only from the Grassland biome along the Great Escarpment that were previously detected in Bradyrhizobium strains nodulating Crotalarieae endemic to this region. Genome-based analyses of data from this and previous studies further showed that strains with these unique nodA alleles typically encode the nodH gene, the product of which adds a sulfate moiety to the Nod factor (the signalling molecule for establishing the nitrogen-fixing symbiosis). The remaining strains had nodA alleles commonly encountered elsewhere in South Africa and other tropical regions of the world. Also, the genomes of these other strains lacked nodH but encoded nodZ, the gene involved in the fucosylation of the Nod factor. Our findings, therefore, showed that the root nodules of Genisteae (and its sister tribe Crotalarieae) native to the Grassland biome along the Great Escarpment are often related Bradyrhizobium strains that are distinct from bradyrhizobia nodulating Genisteae in the Mediterranean and the Americas. HIGHLIGHTS • Diverse bradyrhizobia, including two novel species, nodulate Argyrolobium in the Grassland biome along the Great Escarpment of South Africa. • New species were named Bradyrhizobium spitzkopense and B. mpumalangense, using their genome data as nomenclatural types. • Argyrolobium-nodulating Bradyrhizobium species from this region have unusual sets of host-specific nodulation genes. • The reducing end of their Nod factor is likely sulfated and not fucosylated as is common for bradyrhizobia occurring elsewhere in the world.
A single centre audit of genetic testing in early-onset breast cancer
(Medpharm Publications, 2025-03) Pillay, C.A.; Ngwisanyi, W.; Benn, C.A.
BACKGROUND : This paper serves to audit the number of women who received genetic testing after diagnosis with breast cancer ≤ 35 years. Patients were diagnosed or sought treatment at the Breast Care Centre of Excellence (BCCE), a private accredited specialist breast unit in Johannesburg, South Africa. This study focuses specifically on genetic testing for pathogenic variants of the BRCA 1 and BRCA 2 genes. METHODS : Files of patients diagnosed ≤ 35 years were retrieved, and medical information was extracted. These patient files were then compared to records from the University of the Witwatersrand genetic service facility and the GC Network Pty (Ltd) genetic service facility, and genetic service data was recorded. All data was then compiled and analysed. RESULTS : Over 10 years, 196 patients were diagnosed with breast cancer ≤ 35 years, while only 5 received genetic testing. CONCLUSION : In order to understand the relationship between BRCA1/2 genetic diagnosis and cancer diagnosis, greater emphasis must be placed on the availability of genetic services and testing. Ensuring that these services are available, accessible, and funded by either the State or medical insurance will greatly enhance the understanding between BRCA diagnosis, breast cancer diagnosis, risk reduction procedures, and quality of life in many young women.
Bacterial fruit tree quarantine pathogens – a threat to biosecurity in South Africa
(Academy of Science of South Africa, 2025-09) Coutinho, Teresa A.; teresa.coutinho@up.ac.za
Quarantine bacterial plant pathogens present a serious threat to the biosecurity of South Africa’s fruit tree industry, posing significant risks to agricultural productivity, trade and biodiversity. Pathogens such as Candidatus Liberobacter asiaticus, Xanthomonas citri pv. citri, Erwinia amylovora and Xylella fastidiosa can cause widespread economic losses in fruit crops, including citrus, apples, pears, grapes and olives. Managing these pathogens is challenging due to their ability to spread rapidly, often by the movement of infected plant material and/or by insect vectors. Limited diagnostic capabilities, few chemical control options, and the emergence of pathogen resistance also hamper effective management. This review highlights the importance of an integrated approach should an incursion occur, which would initially involve eradication, improved surveillance and public awareness. Strengthening these biosecurity practices is essential in safeguarding the agricultural sector and ensuring continued fruit trade viability. SIGNIFICANCE : • This review highlights the significant threat posed by quarantine bacterial fruit tree pathogens to South Africa’s agricultural biosecurity. These pathogens endanger essential fruit crops, and an outbreak could lead to severe losses, trade restrictions, and socio-economic impacts. • The review also highlights the challenges that would likely be faced if an incursion should occur. It advocates for an integrated management approach including eradication, surveillance, public awareness, and robust phytosanitary measures, legislative support and inter-agency collaboration. This approach could ensure that we safeguard the agricultural sector and mitigate potential crises.
Pathogenicity of Pythium myriotylum on Acacia crassicarpa and Acacia mangium x Acacia auriculiformis clones in Indonesia
(Taylor and Francis, 2025) Tarigan, Marthin; Wingfield, Michael J.; Jami, Fahimeh; Oliveira, Leonardo S.S.; Saha, Muhammad A.; Duran, Alvaro; Pham, Nam Q.; nam.pham@fabi.up.ac.za
The oomycete Pythium myriotylum is an important pathogen of several crops, causing wilt and damping-off during nursery propagation. The pathogen was recently reported as the causal agent of wilt and damping-off on Acacia crassicarpa plants in nurseries located in Riau, Indonesia. The aim of this study was to evaluate the relative pathogenicity of P. myriotylum on different clones of A. crassicarpa and Acacia mangium × Acacia auriculiformis hybrids. Based on the results, greater tolerance was found on the A. mangium × A. auriculiformis hybrid clones than on those of pure A. crassicarpa. The different Acacia clones also displayed different levels of tolerance of infection. Overall the results showed that screening for tolerance to infection by P. myriotylum will be important in the Acacia breeding programme and make it possible to produce sufficient nursery stock for plantation establishment.
Exploring meiotic recombination and its potential benefits in South African beef cattle : a review
(MDPI, 2025-07) Magagula, Nozipho A.; Ncube, Keabetswe T.; Zwane, Avhashoni Agnes; Mtileni, Bohani
Meiotic recombination is a key evolutionary process that generates novel allele combinations during prophase I of meiosis, promoting genetic diversity and enabling the selection of desirable traits in livestock breeding. Although its molecular mechanisms are well-characterised in model organisms such as humans and mice, studies in African indigenous cattle, particularly South African breeds, remain scarce. Key regulators of recombination, including PRDM9, SPO11, and DMC1, play essential roles in crossover formation and genome stability, with mutations in these genes often linked to fertility defects. Despite the Bonsmara and Nguni breeds’ exceptional adaptability to arid and resource-limited environments, little is known about how recombination contributes to their unique genetic architecture and adaptive traits. This review synthesises the current knowledge on the molecular basis of meiotic recombination, with a focus on prophase I events and associated structural proteins and enzymes. It also highlights the utility of genome-wide tools, particularly high-density single nucleotide polymorphism (SNP) markers for recombination mapping. By focusing on the underexplored recombination landscape in South African beef cattle, this review identifies key knowledge gaps. It outlines how recombination studies can inform breeding strategies aimed at enhancing genetic improvement, conservation, and the long-term sustainability of local beef production systems. SIMPLE SUMMARY By generating novel allele combinations during prophase I of meiosis, meiotic recombination is a fundamental evolutionary mechanism that enhances genetic diversity and supports the selection of desirable traits in livestock breeding. This process is crucial for improving the genetic potential of livestock through selective breeding. While recombination has been studied in commercial cattle breeds from Europe and North America, it remains unexplored and not understood in South African beef cattle, especially the Bonsmara and Nguni breeds. These indigenous breeds are highly valued for their adaptability to harsh, resource-limited environments, yet the genetic mechanisms underlying their resilience and productivity are not well characterised. This review explores how genome-wide technologies, especially those using high-density single nucleotide polymorphism (SNP) markers, can be used to map recombination patterns and identify genes involved in key traits. Applying these tools to South African cattle could enhance breeding strategies by improving the accuracy of selecting animals with a superior genetic merit. Understanding recombination in these breeds will also support their conservation and sustainable use. Ultimately, this knowledge has significant implications for advancing food security, promoting rural development, and ensuring the long-term adaptability of South African beef cattle under climate change.
The re-identification of Penicillium and Talaromyces (Eurotiales) catalogued in South African culture collections
(National Herbarium of the Netherlands, 2024-12) Visagie, Cobus M.; Houbraken, J.; Yilmaz, Neriman; cobus.visagie@fabi.up.ac.za
The taxonomy of Penicillium and Talaromyces has been modernized in the past decade, resulting in more robust and accurate identifications, while hundreds of new species were described from around the world. South Africa has emerged as somewhat of a biodiversity hotspot for these genera, with 48 new species being described in recent years. The aim of this current project was to re-identify Penicillium and Talaromyces strains held in South African culture collections, including the National Collections of Fungi (PPRI) and the Medical Research Council (MRC). A total of 295 PPRI and 56 MRC strains were revived and identified using β-tubulin (BenA) gene sequences. For new or rarely found species, we also sequenced the rDNA internal transcribed spacer regions (ITS), calmodulin (CaM), and RNA polymerase second largest subunit (RPB2) genes. The strains were identified to 99 Penicillium and 25 Talaromyces species, among them eight new Penicillium and three new Talaromyces species. Morphological comparisons with close relatives confirmed the novelty of these species, and they are formally described here as P. drakensteinense, P. kirstenboschense, P. limpopoense, P. lydenburgense, P. mbombelaense, P. potchefstroomense, P. roodeplaatense, P. silvertonense, T. gautengensis, T. macrodendroideus, and T. mzansiensis. This study provides a much-needed update on species diversity captured in South African culture collections and makes an important contribution to international knowledge on these important genera.
Biofilm characterisation of the maize rot-causing pathogen, Fusarium verticillioides
(Taylor and Francis, 2025) Peremore, Chizne; Van't Hof, Cairin; Nkosi, Cebo-LeNkosi; Tshiyoyo, Kadima Samuel; Ratsoma, Francinah M.; Kola, Wisely; Malgas, Samkelo; Santana, Quentin C.; Wingfield, Brenda D.; Steenkamp, Emma Theodora; Motaung, Thabiso Eric; thabiso.motaung@up.ac.za
Biofilm formation was investigated in a maize rot-causing pathogen, Fusarium verticillioides. This work revealed that in vitro cultures produce structured, adherent communities with a dense extracellular matrix (ECM) surrounding hyphae that makes up the biomass of a matured biofilm. Pellicle containing exopolysaccharide had a hydrodynamic diameter of 4.19 nm and a low viscosity (0.022 dl/g). The exopolysaccharide was composed of amino sugars and unordered, facilitating stability through complexation with the anionic eDNA. Biofilm formation varied over different pH and temperature values, emphasising its role in promoting adaption, survival, and persistence in F. verticillioides, potentially contributing to its pathogenicity in maize. Collectively, the results provide valuable insights into biofilm structure and stress resistance in this fungus, and will serve as a foundation for future studies incorporating in planta infection systems.
Small RNAs derived from avocado sunblotch viroid and their association with bleaching symptoms : implications for pathogenesis in avocado sunblotch disease
(Springer, 2025-09) Joubert, Melissa; Van den Berg, Noelani; Theron, Jacques; Swart, Velushka; velushka.swart@fabi.up.ac.za
Avocado sunblotch viroid (ASBVd) is a structured RNA molecule responsible for sunblotch disease of avocado, characterised by distinct chloroses of fruit, leaves, and stems. Despite its impact on avocado, the mechanism by which ASBVd elicits sunblotch symptoms remains unknown. Previous studies on other avsunviroids have shown that viroid-derived small RNAs (vd-sRNAs) with specific sequence mutations can trigger leaf chlorosis via RNA silencing of host genes. Building on this knowledge, we aimed to shed light on the molecular basis of ASBVd pathogenesis by analysing ASBVd sequence variants and ASBVd-sRNAs from bleached and asymptomatic leaf tissues of sunblotch-affected avocado trees. Sequencing of ASBVd clones revealed that variants carrying the pathogenic determinant for bleaching were present in both green and yellow leaf tissues. Next-generation sequencing (NGS) identified ASBVd-sRNAs that varied in abundance between symptomatic and asymptomatic leaf tissues, correlating with viroid titre. We discovered 64 vd-sRNAs spanning the pathogenic region of the ASBVd genome, which were almost exclusively found in yellow tissues. The ASBVd-sRNAs containing the bleaching-associated mutation were predicted to target numerous avocado transcripts for degradation, with 25 of these transcripts significantly downregulated in bleached tissues. Notably, one of these genes, encoding a chloroplastic protein, demonstrated strong evidence of ASBVd-sRNA-guided RNA silencing, presenting a promising candidate for future research into the molecular trigger for ASBVd-induced bleaching symptoms. This study is the first to investigate ASBVd-sRNAs in bleached leaves using NGS. Our findings support the role of RNA silencing in sunblotch symptom development and reveal a unique silencing trigger compared to other avsunviroids.
Revisiting the description of Atractoscion macrolepis (Perciformes: Sciaenidae) : another argument for comprehensive taxonomy
(Magnolia Press, 2024-10-24) Gouws, Gavin; Kruger, Jerraleigh L.; Smale, Malcolm; Henriques, Romina; Potts, Warren M.; romina.henriques@up.ac.za
Atractoscion macrolepis was described as a species separate to A. aequidens, distinguished by a geographically-separated distribution, genetic evidence and a diagnostic meristic character: the number of pored lateral line scales. However, the distinction of these species and description of A. macrolepis were based on the examination of a limited number of specimens, some of which were incorrectly catalogued and possibly wrongly identified. Moreover, earlier data, demonstrating the overlap of the supposedly diagnostic character, were overlooked or not considered fully. The present study aimed to reconsider the distinction of these two species and to highlight characters for identification, using a more extensive representation of specimens, additional character sets and multivariate analyses. Seven meristic characters, 24 morphometric measurements and nine otolith variables were examined from up to 33 specimens of A. aequidens and 52 specimens of A. macrolepis. These were compared among the species and subjected to univariate and multivariate analyses, including Principal Component Analyses (PCAs) and Discriminant Function Analyses (DFAs). No meristic characters, including the number of lateral line scales, could distinguish the species, with modes being identical or with nodes differing, but ranges overlapping. While the PCA of size-transformed morphometric data revealed some separation of the two species, the DFA indicated significant and reliable discrimination. Considering the otolith variables, the PCA showed weak separation of the two species, while fair discrimination was observed in the DFA. ANOVAs indicated a number of significant differences for some transformed otolith measurements, but there were no clear trends with respect to proportions that would discriminate the species. Further exploration of those morphometric variables highlighted as contributing to separation in the PCA and DFA provided a number of variables that, when expressed as a proportion of SL and used in combination, discriminate A. aequidens and A. macrolepis: HL, MCL, PFL, AFL and PLFL. The present study does not contest the taxonomic status of A. macrolepis, the distinction of which has been demonstrated repeatedly, but does refute the characters regarded as diagnostic. In light of this, an updated key is provided for the five species of the genus. The study demonstrates the value of increased specimen representation and having data fully available rather than in summary.
New genera, species, combinations, and synonyms of saprobic Dothideomycetes and Sordariomycetes from subtropical Texas, USA
(Taylor and Francis, 2025) Delgado, Gregorio; Miller, Andrew N.; Crous, Pedro W.; Koukol, Ondrej
As a result of long-term field work in subtropical Texas, USA, three novel genera and three new species are introduced in Pezizomycotina to accommodate new or previously described taxa lacking DNA sequence data. In the Dothideomycetes, Piepenbringia, gen. nov. is established for Taeniolella multiplex (Pleosporales incertae sedis) distant from the type species T. exilis in Kirschsteiniotheliales. Ernakulamia americana, sp. nov. (Tetraplosphaeriaceae, Pleosporales), collected on dead leaves of Sabal minor (Arecaceae), forms a distinct monophyletic lineage distant from representative strains of E. cochinensis, the type species. In the Sordariomycetes, Pseudotaeniolella, gen. nov. is introduced for Taeniolella sabalicola in Distoseptisporaceae (Distoseptisporales), also distant from T. exilis in the Dothideomycetes. Parapenzigomyces ampelinus, gen. et sp. nov. collected on dead stems of hanging vines, forms a strongly supported lineage in Xylariales distant from the type species of Penzigomyces, P. nodipes, in Chaetosphaeriales. A new combination in Parapenzigomyces is proposed for P. flagellatus after examination of ex-type material. Sporidesmina is expanded to accommodate Stanjehughesia floridensis and a few other stanjehughesia-like fungi that cluster together in a distinct lineage incertae sedis in Xylariales. They are distant from St. hormiscioides, the type species in Chaetosphaeriales; therefore, five new combinations in Sporidesmina are proposed. Acrodictys holubovae, sp. nov. (Acrodictyaceae, Sordariomycetes incertae sedis), collected on dead culms of Arundinaria sp. (Poaceae), is phylogenetically distant from other Acrodictys species having clavate or pyriform conidia with 3–4 transverse septa and distinct pores. The identity of Solicorynespora foveolata is revised due to its similarity to several Distoseptispora species. The new combination D. foveolata is proposed, and the name D. bambusae is reduced to its synonym. The genus is also expanded to include previously overlooked tretic conidiogenesis. Pleopunctum ellipsoideum, D. euseptata, and D. meilingensis are newly recorded from North America. Novel phylogenetic placements are provided for Sporidesmium fragilissimum and Tubeufia berkeleyi.
Opportunistic bacterial pathogens in bioaerosols emitted at municipal wastewater treatment plants, South Africa
(Nature Research, 2025-03) Poopedi, Evida; Pierneef, Rian Ewald; Singh, Tanusha; Gomba, Annancietar
Aeration tanks at wastewater treatment plants (WWTPs) emit significant amounts of bioaerosols containing potentially hazardous infectious material. Occupational exposure to airborne pathogens can pose health risks to WWTP workers. Bioaerosol samples collected at aeration tanks of two typical municipal WWTPs that use different aeration modes were analysed to investigate the composition and diversity of airborne bacteria in wastewater environments, using the Illumina MiSeq platform. Thirty-six potential airborne bacterial pathogens were identified in the air samples, and these were dominated by Bacillus, Enterococcus, Clostridium, Streptococcus, Acinetobacter, Enterobacter, Pseudomonas, Bacteroides fragilis, Acinetobacter baumannii, and Escherichia/Shigella. Bioaerosols from mechanical aeration tanks (72%, 26/36) had a relatively higher richness and diversity of airborne bacterial pathogens than diffused aeration tanks (17%, 6/36). Furthermore, most of the identified airborne bacterial pathogens (78%, 28/36) were classified as Risk Group 2 according to the revised South African Regulation for Hazardous Biological Agents, 2022, and up to 70% of these were gram-negative bacteria. The presence of potentially pathogenic bacteria in the ambient air at WWTPs suggests an elevated risk of bioaerosol exposure for workers. Therefore, further research and site-specific risk assessments are recommended to guide the implementation of effective bioaerosol strategies to protect workers’ health, with special attention paid to WWTPs that use mechanical aerators.
Ewingella allii sp. nov. isolated from a diseased onion plant in the Columbia Basin of Washington State, USA
(Springer, 2025-07) Mnguni, Fanele Cabangile; Shin, Gi Yoon; Du Toit, Lindsey J.; Derie, Michael L.; Coutinho, Teresa A.; teresa.coutinho@up.ac.za
Please read abstract in the article.
Enhanced gram-negative membrane disruption and in vivo efficacy via lysine-arginine enrichment of Opis16a
(American Chemical Society, 2025-05) Van der Walt, Mandelie; Oosthuizen, Carel B.; Serian, Miruna; Lorenz, Christian D.; Mason, A. James; Bester, Megan Jean; Gaspar, Anabella Regina Marques; anabella.gaspar@up.ac.za
Infections complicate burn wound care, especially with the rise of antimicrobial resistance. Antimicrobial peptides (AMPs) offer the potential for advancing wound care by combating persistent infections. Opis16a, a scorpion venom-derived AMP, exhibits potent antibacterial activity by targeting Gram-negative membranes, causing rapid membrane disruption and bacterial cell death. Here, four novel Opis16a analogues were developed with improved membrane targeting and antibacterial efficacy. One analogue shows particular promise for topical application in Gram-negative burn wound infections. Enhanced peptide–lipid hydrogen bonding increases conformational stability, membrane insertion, and permeabilization rates. Substituting lysine residues in the C-terminal with arginine leads to the most consistent improvement in activity, selectivity for pathogen over HaCat cells, and stability in serum. In an in vivo Galleria mellonella burn wound model, a 5 mg/kg topical dose provides better protection than Opis16a against Enterobacter cloacae NICD 16103. These findings highlight the potential of optimized bactericidal AMPs to improve burn wound care.
Diversity and functionality of soil prokaryotic communities in antarctic volcanic soils : insights from penguin-influenced environments
(Springer, 2024-09) Segura, Diego; Jordaan, Karen; Diez, Beatriz; Tamayo-Leiva, Javier; Doetterl, Sebastian; Wasner, Daniel; Cifuentes-Anticevic, Jeronimo; Casanova-Katny, Angelica
In the nutrient-limited Antarctic terrestrial habitat, penguins transfer a significant amount of nutrients from the marine to the terrestrial ecosystem through their depositions (i.e., guano). This guano influences soil physicochemical properties, leading to the formation of ornithogenic soil rich in nutrients and organic matter. We hypothesize that soil prokaryotic communities will be strongly influenced by the contribution of nitrogenous nutrients from penguin rookeries, maintaining the influence over long distances. The objective was to establish how the soil prokaryotic diversity and community structure change with distance from a penguin colony, which provides large amounts of guano and nitrogenous compounds, and to study the effects of these nutrients on the functional role of these communities. Methods include volcanic soil sampling along a 1200 m transect from the penguin active rookery and the characterization of soil nutrient content and soil prokaryotic communities using 16S rRNA high-throughput amplicon sequencing. In contrast to our hypothesis, the results showed that the impact of guano from the penguin colony was restricted to the first 300 m. Probably because the penguin rookery was sheltered, strong wind and wind direction did not affect the transport of nutrients from the penguin rookery. Areas close to the penguin rookery were dominated by Proteobacteria and Bacteroidetes, while areas situated further away were dominated by Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, and Planctomycetes. Beta diversity analysis among the soil prokaryotic communities revealed a high degree of community heterogeneity, strongly associated with N compound characteristics (NH4, NO3, and %N), C, and pH. Inferences from N metabolism genes suggest a high potential of the microbial community for dissimilatory nitrate reduction genes (DNRA) to ammonium, assimilatory nitrate reduction (ANR), and denitrification. Although it is assumed that the nitrogenous compounds of the penguin colonies reach long distances and affect the prokaryotic community, this effect can vary with wind directions or the morphology of the site, reducing the impact of the guano over long distances, as our results indicate. On the other hand, functional predictions give some clues about the main actors in nitrogen cycling, through processes like dissimilatory nitrate reduction, assimilatory nitrate reduction, and denitrification.
Carbon dynamics in termite mounds : the effect of land use on microbial oxalotrophy
(Elsevier, 2025-06) Nel, Teneille; Clarke, Catherine E.; Francis, Michele L.; Babenko, Darya; Botha, Alf; Breecker, Daniel O.; Cowan, Don A.; Gallagher, Timothy; Lebre, Pedro Humberto; McAuliffe, Joseph R.; Reinhardt, Alyssa N.; Trindade, Marla
The semi-arid western region of South Africa hosts extensive earthen mounds known as heuweltjies, which are inhabited by Microhodotermes viator termites and play a critical role in soil biogeochemical cycling. These mounds accumulate significant stores of soil organic and inorganic carbon (C), including pedogenic calcium carbonate, which may form through microbially induced calcite precipitation. In this study, the effects of land use change on C dynamics in heuweltjie soils were assessed by examining soil biogeochemistry and apparent respiratory quotient (ARQ, based on soil pore gas composition). We investigated the oxalate-carbonate pathway (OCP) as a potential mechanism of C sequestration. Topsoils were collected from one pristine and one cultivated termite mound in a semi-arid region of South Africa and incubated for one week. The carbon dioxide (CO2) and oxygen concentrations of soil pore gas as well as chemical properties of soils treated with termite frass (excrement) or calcium oxalate (CaOx) were monitored. Increases in pH and the calcite saturation index in both CaOx- and frass-treated soils suggested the potential occurrence of the OCP. The ARQ values did not reflect geochemical changes associated with OCP due to competing metabolic pathways, such as potential lignin degradation in frass-treated soils. Higher ARQ values in uncultivated versus cultivated CaOx-treated soils may indicate higher carbon use efficiency in uncultivated soils or destabilization of existing C in cultivated soils. Respiration in frass-treated soils was higher than control and CaOx-treated soils and resulted in production of bicarbonate (via dissociation of carbonic acid formed by dissolution of respired CO2 in water). This implies that termite-affected landscapes may sequester C in inorganic form. Increased total C in both cultivated and uncultivated soils treated with frass suggests that microbial CO2-fixation may occur in termite-affected landscapes, necessitating further investigation of pathways responsible for this process. HIGHLIGHTS • Frass of Microhodotermes viator increased fertility of termite mound soils. • Microbial respiration increased dissolved carbon concentrations in soils. • Calcite saturation index increased in soils supplemented with calcium oxalate. • Lower respiratory quotients may suggest degradation of lignin in frass. • Cultivation may destabilize organic matter and reduce microbial biomass production.
Application of monoclonal anti-mycolate antibodies in serological diagnosis of tuberculosis
(MDPI, 2024-11-06) Truyts, Alma; Du Preez, Ilse; Maesela, Eldas M.; Scriba, Manfred R.; Baillie, Les; Jones, Arwyn T.; Land, Kevin J.; Verschoor, Jan Adrianus; Lemmer, Yolandy; jan.verschoor@up.ac.za
Patient loss to follow-up caused by centralised and expensive diagnostics that are reliant on sputum is a major obstacle in the fight to end tuberculosis. An affordable, non-sputum biomarker-based, point-of-care deployable test is needed to address this. Serum antibodies binding the mycobacterial cell wall lipids, mycolic acids, have shown promise as biomarkers for active tuberculosis. However, anti-lipid antibodies are of low affinity, making them difficult to detect in a lateral flow immunoassay—a technology widely deployed at the point-of-care. Previously, recombinant monoclonal anti-mycolate antibodies were developed and applied to characterise the antigenicity of mycolic acid. We now demonstrate that these anti-mycolate antibodies specifically detect hexane extracts of mycobacteria. Secondary antibody-mediated detection was applied to detect the displacement of the monoclonal mycolate antibodies by the anti-mycolic acid antibodies present in tuberculosis-positive guinea pig and human serum samples. These data establish proof-of-concept for a novel lateral flow immunoassay for tuberculosis provisionally named MALIA—mycolate antibody lateral flow immunoassay.
Design of genus-specific semi-nested primers for simple and accurate identification of Enterobacter strains
(BioMed Central, 2025-07) Jordan, Sara; Pothier, Joel F.; De Maayer, Pieter; Broders, Kirk; Kvitko, Brian H.; Coutinho, Teresa A.; Smits, Theo H. .
BACKGROUND : The genus Enterobacter, in the family Enterobacteriaceae, is of both clinical and environmental importance. This genus has undergone frequent taxonomic changes, making it challenging to identify taxa even at genus level. This study aimed to design Enterobacter genus-specific primers that can be used for simple PCR identification of large sets of putative Enterobacter isolates. RESULTS : Comparative genomic approaches were employed to identify genes that were universally present on Enterobacter genomes but absent from the genomes of other members of the family Enterobacteriaceae, based on an initial set of 89 genomes. The presence of these genes was further confirmed in 4,276 Enterobacter RefSeq genomes. While no strictly genus-specific genes were identified, the hpaB gene demonstrated a restricted distribution outside of the genus Enterobacter. Semi-nested primers were designed for hpaB and its flanking gene hpaC (hpaBC) and evaluated on 123 strains in single-tube PCR reactions. All taxa showing positive reactions belonged to the genus Enterobacter. For Enterobacter strains the PCR yielded two amplicons at 110 bp and at 370 bp, while strains only displaying the 110 bp amplicon were classified as Leclercia pneumoniae. A blind-test on 120 strains accessioned as Enterobacter sp. from the USDA-ARS culture collection (NRRL), revealed that one third of the strains had an incorrect genus assignment. Comparison of gene trees of the hpaBC fragment sequences with marker genes frequently used for single-gene barcoding or multi-locus sequence analysis (MLSA) further demonstrated its potential for preliminary species identification. CONCLUSIONS : The nested PCR assay represents a rapid and cost-effective approach for preliminary identification of Enterobacter species. As the primer design was based on large-scale genomic comparison, including currently undescribed species clades, it will remain valid even after taxonomic changes within the genus.
A novel Arthrobotrys species : taxonomic characterization, nematicidal activity, and multi-omics insights into nematode predation
(Elsevier, 2025-09) Gao, Mengting; Yan, Zhaoqi; Liu, Zexin; Jiang, Yunxia; Liu, Tengteng; Miao, Xingjun; Dai, Meixue; Bose, Tanay; tanay.bose@fabi.up.ac.za
ursaphelenchus xylophilus, the pinewood nematode (PWN), is a devastating invasive pest responsible for widespread mortality in global conifer forests. During a survey of bark beetle-associated fungi, a nematode-trapping fungus was isolated from an empty beetle gallery in Pinus thunbergii. ITS sequence analysis suggested it represented a novel species. This study aimed to characterize the fungus taxonomically and evaluate its biocontrol potential against PWN. Multi-locus phylogenetic analyses (ITS, TEF1-α, RPB2) confirmed the isolate as a new species, Arthrobotrys byssisimilis sp. nov. Morphological examination revealed adhesive trapping networks and distinctive ellipsoidal conidia. Enzymatic assays demonstrated chitinase and protease activity, with optimal conditions defined for pH and temperature. Culture filtrates, protein extracts, and secondary metabolites showed rapid, dose-dependent nematicidal effects, achieving 100 % PWN mortality within 10–30 min. The fungus exhibited strong tolerance to pine-derived volatiles (α-pinene, β-pinene, turpentine, and ethanol), indicating high adaptability to the host environment. Whole-genome sequencing revealed a 36.97 Mb genome with 8,354 predicted genes, including 104 proteases, 8 chitinases, and diverse secondary metabolite biosynthesis clusters. Transcriptomic profiling after nematode exposure identified 638 differentially expressed genes, including virulence-related enzymes (proteases, CAZymes), cytochrome P450s, and PHI factors, with evidence of stage-specific regulation. Arthrobotrys byssisimilis is the first Arthrobotrys species reported from a bark beetle gallery, expanding the ecological scope of the genus. The integrated in vitro nematicidal activity, physiological adaptability, and multi-omics data suggest A. byssisimilis warrants further evaluation as a potential biocontrol agent against PWN, while its unique genomic features provide new molecular targets for investigating fungal-nematode interactions. HIGHLIGHTS • Discovered novel nematode-trapping fungus Arthrobotrys byssisimilis. • Achieved 100% pinewood nematode kill in 10–30 mins using culture filtrates and extracts. • Shows strong tolerance to pine volatiles, ensuring better field adaptability. • Genome shows 104 proteases, 8 chitinases as major virulence factors. • Found 638 genes differentially expressed under nematode stress, stage-specific virulence.

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