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

Permanent URI for this collectionhttp://hdl.handle.net/2263/1756

Browse

Now showing 1 - 20 of 1289

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.
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.
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.
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.
Harnessing benzamides as plant stress inhibitors, growth promoters and in management of crop resilience-a review
Koetle, M.J.; Motaung, Thabiso Eric; Amoo, S.O. (Wiley, 2026)
Benzamides have emerged as potent stress inhibitors and growth promoters in plant biotechnology, particularly in the management of crop resilience. This review delves into the mechanisms of action, applications, and potential benefits of benzamides, especially focusing on their role as poly(ADP-ribose) polymerase (PARP) inhibitors. Benzamides modulate stress responses by inhibiting PARP activity, which is crucial for DNA repair and maintaining genomic stability. This inhibition prevents excessive poly(ADP-ribosyl)ation, conserving cellular energy and enhancing stress tolerance. Additionally, benzamides promote alternative DNA repair pathways, contributing to the timely repair of DNA lesions and reducing mutation accumulation. In plant stress management, classical PARP inhibitors like 3-methoxybenzamide (3-MBA) and 3-aminobenzamide (3-AB) have demonstrated efficacy in enhancing resistance to abiotic stresses, improving plant growth, and increasing transformation efficiency. This review also highlights the antimicrobial, herbicidal, and insecticidal properties of benzamides, which enhance plant defence mechanisms against various pests and diseases. In summary, benzamides offer multiple approaches to enhancing crop resilience and stress management, with significant implications for sustainable agriculture.
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.
The 2022 Fusarium head blight outbreak in Ethiopia : emerging pathogens, mixed mycotoxins, and interspecies interactions
DeGenring, Liza M.; Gemechu, Ashenafi; Rafiei, Vahideh; Broz, Karen; Regasa, Gizachew H.; Munsamy, Kiara; Yilmaz, Neriman; Dong, Yanhong; Rouse, Matthew N.; Drott, Milton T. (American Phytopathological Society, 2026-03)
As Ethiopia pushes toward self-sufficiency in wheat production, it has escaped large outbreaks of Fusarium head blight (FHB), a disease that threatens wheat production globally. However, in 2022, FHB incidences in Ethiopia rose to 80%, with some areas experiencing 100% disease severity. Here we provide insights into the etiology of this disease outbreak and point toward future directions to mitigate the emerging threat of FHB on a global scale. Although most wheat samples from 2022 exhibited low trichothecene levels, 26% exceeded recommended thresholds and several contained multiple trichothecene variants. We obtained 64 isolates from the outbreak and identified diverse members of the Fusarium graminearum species complex (FGSC) and many Epicoccum species. The FGSC species contributing to the outbreak are rare on a global scale. Genomic analyses reveal that Fusarium aethiopicum has persisted in Ethiopia for decades and shares ancient ancestry with a newly emerged novel species in the FGSC that we formally described as Fusarium kistleri. Single-nucleotide polymorphism–based analyses suggest high clonal fraction among FGSC isolates in Ethiopia, raising questions about a recent population expansion. Our findings reveal that although Epicoccum alone causes minimal disease on wheat, its presence can have a small but synergistic impact on disease symptoms when F. graminearum has already infected. The unique diversity and species composition of the 2022 Ethiopian outbreak underscores the importance of addressing emerging threats in a globalized agricultural economy to secure food safety, food security, and global food equity.
Evaluation of phosphite to protect a South African Proteaceae from Phytophthora root rot
Msweli, Dumsani; Geerts, Sjirk; Nndanduleni, Mashudu; Paap, Trudy (Springer, 2025-11)
Phytophthora cinnamomi is a globally recognised invasive plant pathogen, affecting approximately 5000 host species. In South Africa, previous research has linked P. cinnamomi to root rot in endemic Proteaceae, including Leucadendron argenteum. Recent observations have noted high mortality rates in L. argenteum, with P. cinnamomi readily isolated from the roots and collars of dying trees. Phosphite is commonly used to control Phytophthora diseases, but its efficacy in protecting native South African flora remains uncertain. To address this, trials were conducted to evaluate phosphite’s effectiveness against P. cinnamomi infection in L. argenteum. In the glasshouse trial, four-month-old seedlings were treated with 5 g/L phosphite and then inoculated with P. cinnamomi. Non-treated inoculated seedlings exhibited rapid wilting within three weeks, while treated seedlings showed significant disease reduction, with no difference in root weight and seedling height compared to non-inoculated controls. In the field trial, L. argenteum trees treated with 40 g/L and 50 g/L phosphite injections over 30 months showed no significant difference in survival rates compared to untreated controls. The lack of phosphite efficacy in the field trial was attributed to the presence of Armillaria spp. The study underscores the threat P. cinnamomi poses to L. argenteum populations and highlights the additional risk from Armillaria. While phosphite has demonstrated effectiveness against Phytophthora root rot, further investigation is needed to determine if P. cinnamomi and Armillaria spp. have synergistic effects on L. argenteum mortality. Additionally, exploring phosphite’s potential to protect plants from A. mellea at the seedling stage is warranted.
Ophiostoma ipsi-confusi sp. nov. six, Marinc. & Duong, a consistent symbiotic fungus of the pinyon ips bark beetle, ips confusus LeConte
Six, Diana L.; Marincowitz, Seonju; Duong, Tuan A. (Springer, 2026)
Several tree-killing bark beetle species have nutritional mutualisms with specific fungi. However, few secondary bark beetles (those that colonize weak or dying trees) have been investigated for symbiotic fungi and most are thought to have only incidental fungal associates and no dependence on fungi for nutritional or other benefits. In contrast to this supposition, we consistently isolated (> 97%) a fungus from adult Ips confusus (pinyon ips) collected from Pinus edulis (two-needle pinyon pine) from Arizona and New Mexico, USA. Using morphology and DNA sequences for three gene regions, we found the fungus is most closely related to an obligate mutualist fungus of Dendroctonus ponderosae (mountain pine beetle), Ophiostoma montium (Ascomycota: Ophiostomatales), but is morphologically and genetically distinct from it and other known species in Ophiostoma. It is also capable of growth at relatively high temperatures compared with other Ophiostoma, reflective of its southwestern USA distribution. The high frequency of its association with the beetle indicates it is symbiotic and suggests it may be a mutualist.
Global dominance of Haloquadratum walsbyi by a single genomovar with distinct gene content and viral cohorts from close relatives
Bustos-Caparros , Esteban; Viver , Tomeu; Gago, Juan F.; Avontuur, Juanita R.; Amiour, Souad; Baxter, Bonnie K .; Llames, María E.; Mutlu, Mehmet B.; Oren, Aharon; Ramírez, Ana S.; Stott, Matthew B.; Venter, S.N. (Stephanus Nicolaas); Santos , Fernando; Antón, Josefa; Rodriguez-R, Luis M.; Bosch, Rafael; Hedlund, Brian P.; Konstantinidis, Konstantinos T.; Rossello-Mora, Ramon (Oxford University Press, 2025-01)
Haloquadratum walsbyi is generally the dominant species in hypersaline ecosystems at salt saturation conditions. Here, we followed the dynamics of its genomovars and associated viruses during recurrent evaporation-dilution disturbances of varying intensities at the mesocosm scale over 813 days. The diversity observed within a single mesocosm was also compared with that in a global-scale inventory of hypersaline environments of thalassohaline origin. The 140 binned metagenome assembled genomes (MAGs) together with the genomes of the (only) two available of H. walsbyi isolates grouped into four highly related (98.25% > Average Nucleotide Identity [ANI] > 99.5%) dominant genomovars (intra-genomovar ANI > 99.5%). In mesocosm experiments, moderate disturbances (i.e. recurrent dilution from saturation to 20% salts) enhanced the abundance of the already-dominant genomovar Hqrw1, resulting in reduced intraspecific diversity. This genomovar also dominated in almost all sites sampled around the globe. In contrast, more intense disturbance (i.e. recurrent dilution from saturation to 13% salts) decreased the abundance of Hqrw1 to lower levels than genomovar Hqrw2 by the end of the incubation, which seems to resist better osmotic changes. Further, our results showed that genomovars were followed by their viral cohorts, who play a significant role in the global dominance of the four H. walsbyi genomovars and their replacement under unfavorable conditions. We propose that the global dominance of H. walsbyi in thalassohaline hypersaline sites is enabled by both the success of Hqrw1 in high but stable salinities and the larger resistance of Hqrw2 to extreme osmotic stress, safeguarding the presence of the species in the system.
Uneven sequencing (coverage) depth can bias microbial intraspecies diversity estimates and how to account for it
Bustos-Caparros, Esteban; Viver, Tomeu; Gago, Juan F.; Venter, S.N. (Stephanus Nicolaas); Bosch, Rafael; Konstantinidis, Konstantinos T.; Rodriguez-R, Luis M.; Rossello-Mora, Ramon (Oxford University Press, 2025-01)
An unbiased and accurate estimation of intraspecies diversity, i.e. the extent of genetic diversity within species (or microdiversity), is crucial for clinical and environmental microbiome studies. Although it is well appreciated that sequencing depth (or coverage depth) below 10X can provide biased estimates of microdiversity, typically underestimating diversity due to the random sampling of alleles, there is a widely accepted convention that microdiversity estimates tend to be relatively stable at sequencing depth exceeding 10X. Therefore, discarding species with <10X or rarefying to 10-20X sequencing depth are generally used to compare microdiversity among taxa and samples. Our findings showed that these biases may persist even at depth levels above 50-200X for all popular sequencing platforms, including Illumina, PacBio, and Oxford Nanopore. The biases mostly, but not always, represent an underestimation of diversity and were attributable to the incomplete recovery of Single Nucleotide Variants (SNVs) at lower sequencing depth levels. To address this issue, we recommend using rarefaction-based approaches to standardize data at least 50X, and ideally at 200X sequencing depth, which reduces differences between observed and expected microdiversity values to <0.5%. Furthermore, the Average Nucleotide Identity of reads (ANIr) metric is significantly less sensitive to sequencing depth variability than nucleotide diversity (π), making it a robust alternative for estimating microdiversity at sequencing depth close or exceeding 10X, without a need to rarefying data. Therefore, the sequencing depth thresholds proposed herein provide a more standardized framework for direct comparisons of microdiversity across samples and studies.
Microscale assessment of brush packing mulch as a method for enhancing soil moisture content and promoting delayed grass seedling mortality of subtropical grasses
Mangani, Tshepiso; Monegi, Piet; Mangani, Robert (Wiley, 2026-04)
Recurring droughts in South Africa's dryland rangelands have profound effects on ecosystem health. Consequently, identifying sustainable soil moisture content techniques is critical for enhancing plant growth to support ecosystem function. Soil moisture content was measured daily for five weeks using the field capacity as a reference and compared within the two mulching densities, high and low versus bare soil. The effect thereof was evaluated on growth parameters: emergence, relative growth, and survival rate of three subtropical grasses (Cenchrus ciliaris, Chloris gayan, and Panicum maximum) in seedling trays under a greenhouse. Soil moisture content significantly differed in all the treatments (p < 0.05); the mulching treatments retained half their moisture compared to the no cover treatment, which lost more than 77% moisture. The evapotranspiration was cumulatively lowest in the high-density mulching. Overall, Chloris gayana and Panicum maximum had the highest emergence (> 40%) and relative growth in the mulching treatments, while Cenchrus ciliaris emerged better (56%) and had relative growth in the no cover. By Week 6, many seedlings did not survive; however, Panicum maximum persisted in the high-density mulching with almost 17% seedlings survival. The mulching effect improved soil moisture content, thus providing more conducive conditions for germination and survival, especially of understorey grasses. While this approach is effective for certain grass species, it has demonstrated ecologically significant enhancement for soil moisture content and reducing evaporation, potentially promoting good soil structure and health.
Pseudoteratosphaeria supramediana sp. nov. (Teratosphaeriaceae, Mycosphaerellales), a new foliar pathogen on Eucalyptus in Indonesia
Pham, Nam Q.; Marincowitz, Seonju; Wingfield, Brenda D.; Crous, Pedro W.; Santos, Samuel A.; Duran, Alvaro; Tarigan, Marthin; Wingfield, Michael J. (Springer, 2026-02)
The Eucalyptus plantation industry in Indonesia has expanded rapidly during the last few decades. This growth is primarily attributed to the replacement of Acacia mangium, that was severely damaged by diseases. The rapid shift to large-scale monoculture plantations of Eucalyptus has introduced new challenges, particularly the emergence of new disease and pest problems. During routine Eucalyptus disease surveys in Indonesia, symptoms of a new leaf and shoot disease were observed on a single hybrid Eucalyptus grandis × pellita clone in Riau and Kalimantan. Leaf samples were collected, and isolations were made from the disease symptoms. Isolates were identified based on their morphological characteristics and DNA sequence data for seven loci. Phylogenetic analyses of the isolates revealed a novel species of Pseudoteratosphaeria, described here as Pseudoteratosphaeria supramediana sp. nov. A greenhouse pathogenicity test resulted in symptoms similar to those found under field conditions, and the inoculated fungus was consistently reisolated from the resulting lesions. Its appearance in two geographically distinct locations of Indonesia raises the possibility of multiple independent introductions of the pathogen.
Cold storage of Gonipterus platensis (Coleoptera: Curculionidae) eggs for Anaphes nitens (Hymenoptera: Mymaridae) rearing
Ribeiro, Murilo Fonseca; Cavallini, Gabriela; Solce, Gabriel Negri; Favoreto, Ana Laura; Passos, Jose Raimundo De Souza; Barbosa, Leonardo Rodrigues; Hurley, Brett Phillip; Wilcken, Carlos Frederico (PeerJ, Inc., 2026-03-13)
BACKGROUND : Anaphes nitens (Girault, 1928) (Hymenoptera: Mymaridae) is an egg parasitoid used for the biological control of Gonipterus spp. in regions where this pest is present. Cold storage of host eggs is a crucial strategy in biological control programs. This study aimed to evaluate the effects of cold storage on G. platensis eggs for laboratory rearing of both the host and its parasitoid, A. nitens. METHODS : Gonipterus platensis eggs, aged 1 and 3 days, were stored in a refrigerator at 7 ± 1 °C for 5, 10, 20, 30, 40, and 50 days in complete darkness. After each storage period, the eggs were transferred to a biochemical oxygen demand (BOD) chamber at 25 °C and hatching rates and larval survival were assessed. To evaluate parasitoid reproduction, fresh host eggs were stored at 7 ± 1 °C for 5, 10, 15, 20, and 25 days under dark conditions and subsequently exposed to A. nitens. Parasitism rate, sex ratio, and offspring longevity were recorded. RESULTS : Results showed that 1- and 3-day-old G. platensis eggs maintained the highest viability within the first 10 days of storage, with hatching rates exceeding 50% up to 20 days post-storage. A 20-day storage period was the longest duration that did not differ significantly from the non-stored eggs (control) considering A. nitens parasitism and progeny longevity when stored host eggs were offered. CONCLUSION : Therefore, storing host eggs for this period effectively supports colony maintenance while simultaneously facilitating parasitoid propagation.

Browse

Recent Submissions