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

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Kinship and network analysis of two South African beef cattle breeds using pedigree and high-density SNP markers
Khanyile, Khulekani S.; Maiwashe, Azwihangwisi; Magagula, Nozipho A.; Van Marle-Koster, Este; Zwane, Avhashoni A. (MDPI, 2026-03-19)
Accurate genealogical records are essential in livestock breeding for maintaining genetic diversity, preventing inbreeding, and mapping of economically important traits in beef production. This study aimed to assess parent–offspring relationships within South African Bonsmara and Nguni cattle populations using both traditional pedigree records and genomic data. Hair samples from 119 Nguni and 311 Bonsmara cattle were genotyped using the BovineSNP50 array, and these were imputed to Illumina BovineHD BeadChip using updated SNP coordinates from the assembly genome (ARC—UCSD 1.2). Quality control and data filtering were performed using PLINK v1.9, while relationship inference was conducted using KING v2.2.8 and PLINK v1.9 software for principal component analysis, IBD metrics and Mendelian error-based exclusion. Categories of relatedness through network relationship analysis revealed a predominance of half-sibling relationships in both breeds, with 2317 such relationships identified in Nguni and 1221 in Bonsmara. Inference of parent–offspring pairs showed discrepancies with the recorded pedigrees, with 49 inferred pairs compared to 47 recorded pairs in Nguni, and 62 inferred pairs compared to 75 pairs recorded in Bonsmara. Relationships based on IBD using PLINK with a ‘PI-HAT’ threshold greater than 0.45 revealed unique parent–offspring inferences that differed from those obtained using KING v2.2.8. Phylogenetic network analysis assigned each individual’s genomic origin independent of the pedigree records, supporting the efficiency of SNP data for genetic assignment. These results demonstrated that SNP-based pedigree verification can accurately identify parent–offspring and half-sibling relationships, providing a reliable foundation for recombination analysis and supporting precise trait mapping and informed selection in breeding programs.
Silent invaders : the hidden threat of asymptomatic phytobiomes to forest biosecurity
Tanney, Joey B.; Kemler, Martin; Vivas, Maria; Wingfield, Michael J.; Slippers, Bernard (Wiley, 2025-07)
Populations of diverse, unknown, and potentially pathogenic fungi and fungus-like organisms are continuously introduced into new locations via asymptomatic infections (e.g. as endophytes or latent pathogens) within internationally traded live plants. Interactions between these asymptomatic fungi and novel recipient host trees can be unpredictable, and urban introductions may act as bridgeheads into natural and managed forests. Historical examples of novel, highly destructive forest tree diseases highlight the potential threat of this pathway. As the trade in live plants continues to expand, the likelihood of high-impact incursions increases. This has led to calls for more proactive management, including more stringent treatment and regulatory standards, and even the phasing out of trade in plants determined to be an untenable risk to forest ecosystems. In this review, we discuss how biosecurity systems should consider advances in understanding the diversity and ecology of phytobiomes associated with asymptomatic plants and what measures can be considered to reduce this threat to global forest health.
Leaf bleaching is associated with extensive transcriptional reprogramming in avocado trees with sunblotch disease
Joubert, Melissa; Van den Berg, Noelani; Theron, Jacques; Swart, Velushka; Theron, Jacques.; (Elsevier, 2026-07)
Avocado sunblotch viroid (ASBVd), the type member of the family Avsunviroidae, causes avocado sunblotch disease; marked by the appearance of distinct chlorotic symptoms on fruit, stems and/or leaves of infected trees. Despite the economic impact of the disease, limited information is available regarding the molecular interactions underlying ASBVd infection of avocado. However, studies of other host-viroid pathosystems have revealed large-scale changes to plant gene expression in response to viroid infection. To elucidate molecular changes associated with sunblotch symptom development, we used next-generation sequencing to investigate the global gene expression differences associated with leaf bleaching symptoms in avocado. A total of 3169 genes were differentially expressed in yellow (chlorotic) tissues of bleached leaves compared to asymptomatic leaves from the same ASBVd-infected trees, with most of these genes being upregulated in chlorotic samples. Grouping of genes by predicted function identified substantial alterations to expression of genes involved in genetic information processing, host immune responses, and photosynthesis. Notably, downregulation of chloroplast-associated genes was linked to the manifestation of leaf bleaching. This is the first study to report on global transcriptome changes associated with a symptomatic avsunviroid infection, and provides new insights into the molecular mechanisms underpinning ASBVd-induced chlorosis. HIGHLIGHTS • Leaf bleaching was associated with transcriptome changes in ASBVd-infected avocado. • Bleached leaf tissues contained >3000 differentially expressed genes. • Functional classification showed gene expression changes across multiple pathways. • Photosynthesis-related genes were notably downregulated in bleached leaf tissues.
Bryophytes hold a larger gene family space than vascular plants
Dong, Shanshan; Wang, Sibo; Li, Linzhou; Yu, Jin; Zhang, Yongxia; Xue, Jia-Yu; Chen, Hengchi; Ma, Jianchao; Zeng, Yuying; Cai, Yuqing; Huang, Wei; Zhou, Xuping; Wu, Jiayi; Li, Jianyou; Yao, Yifeng; Hu, Ruoyang; Zhao, Tao; Villarreal A, Juan Carlos; Dirick, Leon; Liu, Li; Ignatov, Michael; Jin, Minghui; Ruan, Jue; He, Yikun; Wang, Haifeng; Xu, Bo; Rozzi, Ricardo; Wegrzyn, Jill; Stevenson, Dennis William; Renzaglia, Karen S.; Chen, Hongfeng; Zhang, Li; Zhang, Shouzhou; Mackenzie, Roy; Moreno, Javier E.; Melkonian, Michael; Wei, Tong; Gu, Ying; Xu, Xun; Rensing , Stefan A.; Huang, Jinling; Long, Manyuan; Goffinet, Bernard; Bowman, John L.; Van de Peer, Yves; Liu , Huan; Liu, Yang (Nature Research, 2025-10)
After 500 million years of evolution, extant land plants compose the following two sister groups: the bryophytes and the vascular plants. Despite their small size and simple structure, bryophytes thrive in a wide variety of habitats, including extreme conditions. However, the genetic basis for their ecological adaptability and long-term survival is not well understood. A comprehensive super-pangenome analysis, incorporating 123 newly sequenced bryophyte genomes, reveals that bryophytes possess a substantially greater diversity of gene families than vascular plants. This includes a higher number of unique and lineage-specific gene families, originating from extensive new gene formation and continuous horizontal transfer of microbial genes over their long evolutionary history. The evolution of bryophytes’ rich and diverse genetic toolkit, which includes new physiological innovations like unique immune receptors, likely facilitated their spread across different biomes. These newly sequenced bryophyte genomes offer a valuable resource for exploring alternative evolutionary strategies for terrestrial success.
Estimated timeline for the evolution of symbiotic nitrogen fixing Paraburkholderia
Mavima, Lazarus; Steenkamp, Emma Theodora; Beukes, Chrizelle Winsie; Palmer, Marike; De Meyer, Sofie E.; James, Euan K.; Venter, S.N. (Stephanus Nicolaas); Coetzee, Martin Petrus Albertus (Elsevier, 2025-12)
The nitrogen-fixing and nodule-forming symbionts of legumes, which belong to the class Betaproteobacteria, are informally known as beta-rhizobia. Thus far, members of this group have only been found in the genera Paraburkholderia, Trinickia and Cupriavidus. In this study, we investigate the poorly characterized evolutionary history of this trait in the predominant beta-rhizobial genus, Paraburkholderia. This was determined in the context of the current evolutionary theories and date estimates of rhizobia, the genus Paraburkholderia and the earth. Evolutionary divergence dates of rhizobial Paraburkholderia as well as their ancestral nodulation states were estimated using over 800 diverse proteobacterial genomes. Molecular dating was carried out using the software BEAST (Bayesian Evolutionary Analysis Sampling Trees) and APE (using the ‘chronopl’ function). Our results showed that the most recent common ancestor (MRCA) of the extant beta-rhizobial species emerged between 2744 and 1752 million years ago (Ma) and later (2135–514 Ma) diverged into the lineages Cupriavidus, Trinickia and Paraburkholderia. However, major diversifications of rhizobial Paraburkholderia occurred in three phases: (i) during the Permian and Triassic periods (400–200 Ma) when Pangaea was fully assembled and its landmass filling up with flora and fauna, (ii) during the Jurassic period (200–150 Ma) when fauna and flora were flourishing in Pangaea, and (iii) during the Cretaceous and Paleogene periods (150–23 Ma) when Gondwana was breaking up. Furthermore, Paraburkholderia were estimated to have acquired their precursor nodulation loci that evolved into their current nodulation loci from different sources between 103 and 48 Ma. Accordingly, our study describes the evolutionary history of rhizobial Paraburkholderia, thus enabling us to understand the past environmental factors that shaped the current geographical distribution of these agriculturally important bacteria, and to identify locations potentially rich in beta-rhizobia.
Endophytic and epiphytic microorganisms as biocontrol agents : mechanisms, applications, and metagenomic approaches in tomato cultivation
Rakhalaru, Phathutshedzo; Mampholo, Beverly Mmakatane; Mamphogoro, Tshifhiwa Paris; Thantsha, Mapitsi Silvester (MDPI, 2025-09-19)
Tomato (Solanum lycopersicum) is an essential crop worldwide, yet it remains highly vulnerable to severe fungal and bacterial diseases. Traditional chemical-based disease management strategies, aimed at controlling these diseases face increasing scrutiny, due to concerns regarding pathogen resistance, environmental degradation, and potential health risks to humans. This has catalyzed the exploration of sustainable alternatives, with biological control emerging as a viable and promising strategy. Endophytic and epiphytic microorganisms are pivotal as biocontrol agents (BCAs), employing diverse strategies, such as generating antimicrobial substances, enzymes, and volatile organic compounds (VOCs), to suppress pathogen growth and enhance plant health. The efficacy of these antagonistic microorganisms is influenced by the cultivation systems employed, with significant variations observed between soil and hydroponic environments. Factors such as nutrient dynamics and microbial interactions play crucial roles in determining the success of BCAs in these different settings. The advent of metagenomic tools has transformed the landscape of microbial community research, facilitating the identification of functional genes associated with antagonistic activities and the adaptation of these microorganisms to diverse environmental conditions. This review aims to elucidate the potential of endophytic and epiphytic microorganisms in biological control, examining their mechanisms of action, the impact of cultivation systems on their effectiveness, and the application of metagenomics to optimize their use in sustainable disease management strategies for tomato crops.
Diversity and distribution of Lophodermium species on non‑native Pinus species in the Southern Hemisphere
Theron, Cobus; Wingfield, Michael J.; Ahumada, R.; Carnegie, A.J.; Fraser, S.; Rodas, Carlos A.; Barnes, Irene (Springer, 2025-07-04)
Lophodermium species are amongst the most commonly isolated endophytic fungi on the needles and cones of pines. Of the 38 species reported on these trees, only Lophodermium seditiosum is considered a major pathogen. Species of Pinus have been widely established as non-natives in Southern Hemisphere countries, and several Lophodermium species have been reported on the needles of these trees. However, most of these reports are based on morphology alone. In this study, we considered the biogeography of Lophodermium species across the Southern Hemisphere by obtaining and identifying isolates from non-native Pinus species planted in Australia, Chile, Colombia, New Zealand, and South Africa. A multi-locus phylogenetic approach was used to delineate the species, and characteristic morphological features were evaluated against the resulting phylogeny. Phylogenetic analyses revealed the presence of five Lophodermium taxa on Pinus species in the Southern Hemisphere. A species belonging to the L. conigenum-australe complex was found in all countries except Chile. Lophodermium indianum and L. molitoris were found only in Colombian and New Zealand collections, respectively. Two distinct lineages of L. pinastri emerged from Chile, New Zealand, and Australia. None of the morphological features could distinguish between the different taxa of Lophodermium found, with several of the traits varying by host or location. Overall, the results support the fact that various cryptic Lophodermium species occur on the sampled Pinus species and suggest that several independent introductions of these fungi have occurred in Southern Hemisphere countries.
Capturing the fungal diversity hidden in Eastern Cape dairy pastures
Dewing, Claudette; Yilmaz, Neriman; Steenkamp, Emma Theodora; Wingfield, Brenda D.; Visagie, Cobus M. (Springer, 2025-06-21)
Fungi in dairy pastures impact cattle health, yet the diversity of fungal species present in South African pastures remains understudied. Following an outbreak of Sporidesmin-Induced Liver Disease (SILD; caused by the mycotoxin sporidesmin produced by Pseudopithomyces toxicarius) in the Eastern Cape in 2020, we collected mixed pasture samples from 14 dairy farms affected by this disease. Our aim was to investigate what fungal species are present in communities and whether species like Ps. toxicarius are present that may play a role in cattle health. A total of 708 strains were isolated from 95 mixed pasture samples and identified based on DNA sequence data to 132 species representing 55 genera. Fusarium was the most isolated (207 strains; 21 species; 55 samples), followed by Penicillium (75 strains; 22 species; 27 samples), Pseudopithomyces (69 strains; 2 species; 21 samples), Cladosporium (54 strains; 6 species; 23 samples), Epicoccum (52 strains; 6 species; 24 samples) and Bipolaris (38 strains; 3 species; 19 samples). Several strains could not be identified and represent potentially new or previously uncharacterised species. Additionally, phylogenetic analyses revealed the presence of Ps. palmicola and Ps. toxicarius in the Eastern Cape dairy pastures. Our findings underscore the ecological complexity of pasture environments and raise important questions about the role of fungal diversity in livestock health.
Three new species of Fusarium (Nectriaceae, Hypocreales) isolated from Eastern Cape dairy pastures in South Africa
Dewing, Claudette; Visagie, Cobus M.; Steenkamp, Emma Theodora; Wingfield, Brenda D.; Yilmaz, Neriman (Pensoft Publishers, 2025-03-20)
A survey of the fungal diversity associated with mixed pastures from Eastern Cape dairy farms in South Africa led to the isolation of 155 Fusarium strains that belong to the Fusarium incarnatum-equiseti species complex (FIESC). Using single and multigene phylogenies based on partial sequences of the translation elongation factor 1-alpha (TEF), calmodulin (CaM), and the partial RNA polymerase second largest subunit (RPB2) genes, we identified 11 species. They included F. brevicaudatum, F. clavus, F. coffeatum, F. croceum, F. goeppertmayerae, and F. heslopiae, with five species that were found to be new. Based on morphological and phylogenetic data, three new species are formally described here as F. cumulatum, F. mariecurieae, and F. pascuum. We also provided a description for F. goeppertmayerae, as the authors who identified and named this species did not include one. We have chosen to not describe the remaining species, as our cultures lack proper morphological structure development. This study shows that mixed pastures harbour a diverse range of Fusarium species and highlights the need for further studies into their potential to impact animal health.
Four novel endolichenic fungi from Usnea spp. (Lecanorales, Parmeliaceae) in Yunnan and Guizhou, China : taxonomic description and preliminary assessment of bioactive potentials
Chang, Runlei; Yan, Zhaoqi; Jiang, Jibo; Wang, Yichen; Si, Hongli; Bose, Tanay; Miao, Congcong (Pensoft Publishers, 2025-06-02)
Usnea is one of the largest and most diverse genera of fruticose lichens with global distribution. Endolichenic fungi, which thrive within lichen thalli, have emerged as a promising source of bioactive compounds, with the ability to synthesise a variety of metabolites with biopharmaceutical potential. In this study, four isolates of endolichenic fungi isolated from Usnea spp. were identified using comprehensive multi-gene phylogenetic analyses. These isolates were evaluated for their anticancer, antifungal, and antibacterial properties, as well as for their ability to produce extracellular enzymes. Our findings revealed that the isolates represent four novel species, named as Amphisphaeria falcata, Kirschsteiniothelia tumidula, Neoroussoella annulata, and Veronaea brunneicolor. Our screening assay showed N. annulata and V. brunneicolor exhibited cytotoxic effects against the H460 human lung cancer cell line, with moderate inhibitory activity at a concentration of 100 μg/mL. The four fungal isolates exhibited distinct antifungal profiles against phytopathogens: Amphisphaeria falcata specifically inhibited Fusarium graminearum, while Veronaea brunneicolor showed broad-spectrum activity against Botrytis cinerea, F. graminearum, and Alternaria alternata. No antibacterial effects were detected in any isolates. These fungi exhibited a diverse array of extracellular enzyme activities, including amylase, protease, gelatinase, glucose oxidase, and cellulase. Collectively, these results underscore the considerable biotechnological potential of endolichenic fungi as sources of bioactive compounds with applications in drug discovery, agriculture, and environmental management. These findings also highlight the ecological importance of endolichenic fungi, suggesting that they may play multifaceted roles in lichen symbioses and their environments. Continued exploration of these fungi is essential for unlocking their full pharmacological and industrial potential.
Genomic features and evolution of lifestyles support the recognition of distinct genera among fusarioid fungi
Ulaszewski, Bartosz; Sandoval‑Denis, Marcelo; Groenewald, Johannes Z.; Costa, Marileide M.; Mishra, Bagdevi; Ploch, Sebastian; Crous, Pedro W.; Thines, Marco (Springer, 2025-02-24)
The family Nectriaceae (Hypocreales, Sordariomycetes) includes saprobes, endophytes and numerous important pathogens, several of which are of high commercial interest. Presently there are numerous genera scattered throughout the Nectriaceae that have a fusarioid asexual morph (i.e., genera with fusarium-like macroconidia). Fusarioid fungi encompass diverse lifestyles, including plant, human, and animal pathogens or associates, saprobes, lichenicolous species, endophytes, and mycophilic taxa. The fusarioid genera in Nectriaceae do not only differ in their sexual morphs, but also in their asexual morphology and biology, although their ecology has remained rather unclear. While genome data are available for numerous species, this has been mostly focused on Fusarium sensu stricto, as the genus encompasses most of the economically important species in this generic complex. To compliment this, we expanded the sampling, and generated whole genome sequences for 40 isolates representing the genera Atractium, Bisifusarium, Cinnamomeonectria, Corinectria, Cosmospora, Cyanonectria, Cylindrodendrum, Dialonectria, Fusarium, Fusicolla, Geejayessia, Ilyonectria, Macroconia, Macronectria, Microcera, Neocosmospora, Neonectria, Pseudofusicolla, Rectifusarium, Rugonectria, Scolecofusarium, Thelonectria, and Tumenectria. Phylogenomic ancestral reconstructions showed that plant pathogenicity is most likely ancestral to Fusarium and cylindrocarpioid genera, and revealed multiple and frequent lifestyle transitions. Although many species are prolific generalists, several genera appear to be more specialised, being primarily plant pathogens, mycophilic, or insect associated, while endophytism or plant pathogenicity evolved several times, and more recently in Fusarium. The broadly sampled Nectriaceae genomes supported morphological differences between most genera of Nectriaceae, mirrored by genome sizes, lactic enzymes, biosynthetic gene clusters, and small secreted proteins. Furthermore, it also supported a narrow circumscription of Fusarium in Nectriaceae that equals its morphology (Gibberella sexual morphs), and biology.
From description to implementation : key takeaways from the 3rd African Microbiome Symposium
Marsh, Charissa C.; Van Zyl, Kristien Nel; Babalola, Olubukola Oluranti; Bohmer, Reinhard; Cowan, Don A.; Moganedi, Kgabo L.M.; Moroenyane, Itumeleng; Naidoo, Jerolen; Delgado,12 ,13 ,14 , Abigail Nieves; Posma, Joram M.; Segal, Leopoldo N.; Setati, Mathabatha E. (American Society for Microbiology, 2025-12)
The 3rd African Microbiome Symposium was held in Cape Town, South Africa, from 20 to 22 November 2024. The symposium featured a diverse range of local and international microbiome research and provided a platform for 79 researchers, students, and industry members to engage in discussions on the microbiome within an African context and focusing on translational research. This meeting review shares highlights, findings, and recommendations derived from the event. Insights from two panel discussions revealed key barriers to microbiome research in Africa, including limited funding, infrastructure gaps, and a shortage of trained local scientists. Recommendations centered on increased investment, institutional training, adherence to ethical guidelines, and the fostering of equitable global partnerships.
The subordinate role of pseudogenization to recombinative deletion following polyploidization in angiosperms
Crombez, Ewout; Van de Peer, Yves; Li, Zhen (Nature Research, 2025-07-09)
Extensive gene loss is a hallmark of rediploidization following polyploidization, but its molecular basis remains unclear: whether it occurs primarily through pseudogenization or DNA deletion. Here, we examine pseudogenization in collinear segments from ancient whole-genome multiplications (WGMs) across 12 angiosperms. Although total pseudogenes are abundant, we find far fewer WGM-derived pseudogenes than expected if pseudogenization and DNA deletion contribute equally to gene loss. Simulations of neutrally evolving pseudogenes indicate that, if DNA deletion is absent, pseudogenes should be detectable for far longer than observed in the paleo-polyploid genomes, suggesting gene loss driven by DNA deletion. Analyses of three neo-autopolyploid genomes confirm this pattern: among substantial gene loss, DNA deletions occur on average 1.5 times more frequently than pseudogenization. Our findings imply that gene loss post-polyploidization primarily takes place via DNA deletion, enabled by a genomic environment with an elevated recombination rate created by WGMs. In contrast, small-scale duplications yield scattered duplicated genes, which appear less exposed to deletion and hence result in a high number of pseudogenes. This model is further reinforced by an enrichment of WGM-derived pseudogenes in high recombination regions. Moreover, some pseudogenes may govern a function, as indicated by non-neutral Ka/Ks ratios and overlap with lncRNAs.
Antibacterial potential of crude extracts from Cylindrospermum alatosporum NR125682 and Loriellopsis cavernicola NR117881
Ikhane, Albert Olufemi; Osunsanmi, Foluso Oluwagbemiga; Mosa, Rebamang Anthony; Opoku, Andrew Rowland (MDPI, 2025-01-19)
The challenges of antimicrobial resistance (AMR) to human health have pushed for the discovery of a new antibiotics agent from natural products. Cyanobacteria are oxygen-producing photosynthetic prokaryotes found in a variety of water habitats. Secondary metabolites are produced by cyanobacteria to survive extreme environmental stress factors, including microbial competition. This study presents the antibacterial activity and mechanism of the crude extracts from Cylindrospermum alatosporum NR125682 (A) and Loriellopsis cavernicola NR117881 (B) isolated from freshwater. The cyanobacteria were identified through 16S rRNA sequencing. Crude extracts were sequentially prepared using hexane, dichloromethane, and ethanol consistently. The minimum inhibition concentration (MIC), minimum bactericidal concentration (MBC) using the CSLI microdilution test protocol, and crude extract potential to inhibit the growth of the tested clinical bacteria strains were evaluated. The mechanism of action of the extracts including membrane damage, efflux pump, β-lactamase activity, DNA degradation, and extract–drug interaction was investigated using standard procedures. The hexane extract of B performed the best with a MIC (0.7–1.41 mg/mL) and MBC (1.41–2.81 mg/mL) range. All the crude extracts inhibited efflux pump activity against the bacteria tested. However, the extracts poorly inhibited β-lactamase. The ethanol extract of B exhibited the most appreciable antibacterial activity. The dichloromethane extract of B showed the highest significant DNA degradation potential, when compared with other samples. The extracts exhibited synergism when combined with erythromycin against some test bacteria, indicating primary microbial activity through membrane interactions. Hence, this study demonstrates the significance of cyanobacteria for antibiotic development.
Archaeal genomes linked to industrial wastewater and associated freshwater in South Africa
Makumbi, John Paul; Bezuidt, Keoagile Ignatius Oliver; Leareng, Leareng; Makhalayane, , T.P. (American Society for Microbiology, 2025-04)
Archaea provide important ecosystem services including the degradation of contaminants. Here, we present archaeal genomes from understudied South African wastewater treatment plants (WWTPs) and associated rivers receiving industrial effluents. Functional analysis revealed key genes implicated in heavy metal degradation, offering a valuable resource for mechanistic studies on archaeal metabolism.
Rhizosphere bacterial communities of Namib Desert plant species : evidence of specialised plant-microbe associations
Maphosa, Silindile; Steyn, Megan; Lebre, Pedro Humberto; Gokul, Jarishma Keriuscia; Convey, Peter; Marais, Eugene; Maggs-Kolling, Gillian; Cowan, Don A. (Elsevier, 2025-04)
Rhizosphere microbial communities are intimately associated with plant root surfaces. The rhizosphere microbiome is recruited from the surrounding soil and is known to impact positively on the plant host via enhanced resistance to pathogens, increased nutrient availability, growth stimulation and increased resistance to desiccation. Desert ecosystems harbour a diversity of perennial and annual plant species, generally exhibiting considerable physiological adaptation to the low-water environment. In this study, we explored the rhizosphere bacterial microbiomes associated with selected desert plant species. The rhizosphere bacterial communities of 11 plant species from the central Namib Desert were assessed using 16S rRNA gene-dependent phylogenetic analyses. The rhizosphere microbial community of each host plant species was compared with control soils collected from their immediate vicinity, and with those of all other host plants. Rhizosphere and control soil bacterial communities differed significantly and were influenced by both location and plant species. Rhizosphere-associated genera included 67 known plant growth-promoting taxa, including Rhizobium, Bacillus, Microvirga, Kocuria and Paenibacillus. Other than Kocuria, these genera constituted the ‘core’ rhizosphere bacterial microbiome, defined as being present in > 90 % of the rhizosphere communities. Nine of the 11 desert plant species harboured varying numbers and proportions of species-specific microbial taxa. Predictive analyses of functional pathways linked to rhizosphere microbial taxa showed that these were significantly enriched in the biosynthesis or degradation of a variety of substances such as sugars, secondary metabolites, phenolic compounds and antimicrobials. Overall, our data suggest that plant species in the Namib Desert recruit unique taxa to their rhizosphere bacterial microbiomes that may contribute to their resilience in this extreme environment.
High-quality metagenomic-assembled genomes from sea ice and seawater of the Southern Ocean
Buthelezi, Z.M.; Pierneef, Rian Ewald; Bezuidt, Keoagile Ignatius Oliver; Makhalanyane, T.P. (American Society for Microbiology, 2025-07)
We provide high-quality metagenome-assembled genomes (MAGs) derived from seawater and sea ice samples collected in the Southern Ocean. Several MAGs encode genes associated with dimethylsulfoniopropionate (DMSP) lyase activity and methane oxidation. This resource provides insights regarding the role of microbial communities in the production of key volatile compounds.
Harnessing exogenous membrane vesicles for studying Fusarium circinatum and its biofilm communities
Motaung, Thabiso Eric; Ratsoma, Manchela Francinah; Kunene, Sithembile; Santana, Quentin C.; Wingfield, Brenda D. (Elsevier, 2025-03)
Extracellular vesicles (EVs) are tiny messengers that convey bioactive molecules from donor to recipient cells, leading to changes in their physiology and function. We investigated the role of EVs in shaping growth and the biofilm biology of the tree pathogen Fusarium circinatum and its interaction with the susceptible host, Pinus patula. Vesicles were collected from fungal planktonic and biofilm cultures and from pine seedling needles and roots. The physical properties of these vesicles were analysed using nanoparticle tracking analysis and transmission electron microscopy, which revealed a diverse range of sizes and shapes, respectively. Furthermore, uptake of vesicles by conidia was conducted. The results demonstrated that F. circinatum EVs significantly but variably affected spore viability during the early phase (2–4 h) although they enhanced fungal biofilm integrity. In contrast, P. patula EVs greatly inhibited hyphal formation and biofilm biomass, but failed to inhibit matrix production in the fungal biofilm. Our results therefore show that conidial germination is essential for late fungal development including hyphal and biofilm formation while matrix production is a counter measure against harsh environmental conditions including the effects of plant-derived EVs.
Hidden diversity behind the Lecanicillium-like white colony-forming mycoparasites on Hemileia vastatrix (coffee leaf rust)
Colman, A.A.; Araujo, J.P.M.; Evans, H.C.; Mansur, P.S. Correa; Salcedo-Sarmiento, S.; Silva, A.L.; Kapeua-Ndacnou, M.; Belachew-Bekele, B.K.; Pereira, C.M.; Crous, Pedro W.; Barreto, R.W. (Westerdijk Fungal Biodiversity Institute, 2025-12)
During surveys for fungal natural enemies of Hemileia vastatrix - the causal agent of coffee leaf rust (CLR) - in its African centre of origin (Cameroon, Ethiopia), as well as in its exotic South American range (Brazil, Paraguay), an eclectic and species-rich mycobiota was encountered. Here, we provide a comprehensive report on an assemblage of "white colony-forming fungi" (WCF), often treated in the earlier literature under the inadequate "label" Verticillium lecanii (=Lecanicillium lecanii). A total of 265 isolates of WCF were provisionally placed in this arbitrary group. We clarified the identity of our assemblage of Lecanicillium-like fungi using a combination of morphological characteristics and sequence data for the large subunit nuclear ribosomal DNA (LSU), translation elongation factor 1-α (TEF) and the largest subunits of RNA polymerase II (RPB1 and RPB2) regions. Fifteen WCF species belonging to eight genera across three hypocrealean families (Bionectriaceae, Clavicipitaceae and Cordycipitaceae) were found parasitizing pustules of CLR. Significantly, Lecanicillium lecanii was not found to be present amongst these taxa. Six species belonged to the known genera - Corniculantispora, Gamszarella, Lecanicillium, Ovicillium, Pleurodesmospora and Simplicillium. Two new genera are described, Bettiolomyces and Hemileiophthora, as well as seven new species, Bettiolomyces urediniophagus, Gamszarella uredinophila, Hemileiophthora denticulata, H. nodosa, Lecanicillium hemileiae, Pleurodesmospora hemileiae and Simplicillium hemileiae. The following known WCF species are recorded here for the first time on pustules of H. vastatrix: Corniculantispora dimorpha, Gamszarella buffelskloofina, Lecanicillium uredinophilum, Ovicillium attenuatum, Pleurodesmospora coccorum and Simplicillium subtropicum. Additionally, the new combination Bettiolomyces epiphytus is introduced for Verticillium epiphytum.
Inside the belly of the beast : exploring the gut bacterial diversity of Gonipterus sp. n. 2
Knoppersen, Rosa Sophie; Bose, Tanay; Coutinho, Teresa A.; Hammerbacher, Almuth (Springer, 2025-04-12)
The Eucalyptus snout beetle (Gonipterus sp. n. 2) is a destructive invasive pest of Eucalyptus plantations, responsible for significant defoliation and wood yield losses globally. Native to Australia, this beetle has adapted to thrive on diverse Eucalyptus hosts, overcoming their chemical defences. However, the mechanisms by which Gonipterus tolerates or utilises these plant defence metabolites remain poorly understood. In South Africa, Gonipterus sp. n. 2 poses a significant threat to Eucalyptus plantations by causing extensive defoliation and leading to substantial reductions in growth and wood production. This study investigates the relationship between diet, host Eucalyptus species, and the gut microbiome of Gonipterus sp. n. 2. Using controlled feeding experiments, beetles were reared on artificial, semi-artificial, and natural diets, as well as two Eucalyptus genotypes with distinct secondary metabolite profiles. High-throughput 16S rDNA sequencing and gas chromatography-mass spectrometry (GC–MS) revealed significant shifts in gut bacterial diversity and composition across diets. Natural diets supported the most diverse microbial communities, while artificial diets fostered a homogenised microbiome dominated by opportunistic taxa like Serratia. Host-specific effects were observed in frass microbiota, with substantial biotransformation of monoterpenes into less toxic derivatives. The results highlight the plasticity of Gonipterus gut microbiota, which enables metabolic adaptability and resilience in diverse environments. This microbial flexibility underpins the invasiveness of Gonipterus, emphasising the role of gut symbionts in overcoming host chemical defences. Understanding these interactions offers novel insights for microbiome-targeted pest management strategies, providing a sustainable approach to mitigate the impact of Gonipterus on global Eucalyptus forestry.

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