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

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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.
Prospecting, production and thermodynamic profiling of feather degrading keratinolytic protease from Bacillus subtilis GH2
Alamnie, Getachew; Bekele, Tigabu; Girma, Abayeneh; Malgas, Samkelo (Elsevier, 2026-04)
Please read abstract in the article. HIGHLIGHTS • Dialysis and ammonium sulfate purification gave a purification yield of 1.99%. • Kinetic properties showed that the keratinase can bind to its substrate. • Thermodynamic parameters suggest that the enzyme is relatively thermostable.
An evidence-based protocol for developing lists for tree planting
Potgieter, Luke J.; Cadotte, Marc W.; Kumschick, Sabrina; Paap, Trudy; Roets, Francois; Wilson, John R.U.; Richardson, David M. (Pensoft Publishers, 2025-11)
Tree-planting is increasingly being promoted for urban greening, carbon sequestration, and to enhance biodiversity. However, poorly planned and executed tree-planting schemes can inadvertently contribute to biological invasions with detrimental effects on local ecosystems, economies, and human well-being. Therefore, sustainable, rigorous, repeatable, and transparent species selection strategies are needed. We developed a strategic decision protocol for identifying tree taxa suitable for planting schemes, using a multi-criterion approach that integrates national lists of regulated invasive plant species, global evidence of invasiveness, and susceptibility to key pests. Using the Polyphagous Shot Hole Borer (PSHB) invasion in the City of Cape Town, South Africa as a case study, we illustrate the protocol’s application and potential for informing planting decisions. 444 tree taxa currently planted in Cape Town were assessed. Of these, 85 are regulated nationally as invasive species (and are prohibited from use), while 49 met all suitability criteria and were identified as candidates for a planting list (i.e., a safe list). This protocol provides evidence-based guidance for tree-planting to mitigate the risk of tree invasions and to reduce the spread and impact of associated pests and pathogens. This protocol is replicable and adaptable for use in other regions and can support environmental planners and managers in making informed decisions to safeguard ecosystems and optimise ecosystem services (e.g., which trees to plant in restoration initiatives).
Advancing the taxonomy of Sclerotinia (Helotiales, Sclerotiniaceae) : a review and recommendations for an important plant-pathogenic genus
Thomas, Chanel; Wilken, Pieter Markus; Coetzee, Martin Petrus Albertus; Visagie, Cobus M. (Pensoft Publishers, 2026)
Sclerotinia is a fungal genus of significant agricultural and scientific importance, as it includes multiple plant pathogens and provides an informative case study for mechanisms of host generalism. However, the taxonomy of this group remains unsettled, which hinders research on these pathogens. The last monographic treatment of Sclerotinia was published more than 40 years ago and was centered on the morphological data available at that time. Here, we examine that revision alongside other pivotal publications to trace the taxonomic history of Sclerotinia and to evaluate the morphological traits used to identify Sclerotinia species. We also briefly assess the composition of genera in the family Sclerotiniaceae, emphasising the need for a modern taxonomic investigation of the broader group. Thirteen new Sclerotinia species have been described since the last taxonomic revision, including Sclerotinia antarctica, S. asari, S. atrostipitata, S. cirsii-spinosissimi, S. ginseng, S. glacialis, S. himalayensis, S. nivalis, S. pseudoplatani, S. subarctica, S. tetraspora, S. trillii, and S. verrucispora. These species are evaluated here. Finally, several recommendations are made regarding how future taxonomic research on Sclerotinia should incorporate molecular data. We highlight potential obstacles and opportunities for this research, including the limitations of the internal transcribed spacer rDNA region (ITS) as a DNA barcode and the untapped potential of genomic data for the genus. By outlining the gaps that need to be addressed, this review charts a course toward a clearer understanding of taxonomic relationships among Sclerotinia species. This understanding will facilitate research into other aspects, such as pathogenicity and host generalism, and may ultimately contribute to improved management of the devastating diseases caused by these pathogens.
Adjuvant-driven modulation of epitope recognition and protective immunity in Bm86 vaccinated Holstein-Friesian cattle
Bishop, Laura Jane; Stutzer, Christian; Crafford, Jannie; Maritz-Olivier, Christine (Elsevier, 2026)
Livestock production is vital to the economies and food security of African countries. Rising global demand for livestock-derived products intensifies the challenge of managing ticks and tick-borne diseases. This study aimed to optimize a Bm86-based vaccine for controlling Rhipicephalus microplus. Commercial Bm86-based vaccines show variable efficacy (0–100 %), reflecting incomplete understanding of the antigen and the immune response elicited. To address this, homologous challenge was conducted in Holstein-Friesian calves with Bm86 formulated with Montanide™ ISA 71 VG (referred to as Montanide™) and a novel Alum-based adjuvant alternative in two separate vaccine trials. Antibody responses were determined utilising indirect ELISA. Vaccine efficacy was assessed through controlled R. microplus challenge. Immunoinformatics mapped the antigenic regions of Bm86, followed by ex vivo validation using antisera from vaccinated cattle. Both adjuvant formulations induced high levels of Bm86-specific total IgG antibodies. However, only the Montanide™ formulation induced a protective response of 88.2 %, which correlated with total IgG antibody levels (r = 0.86). In contrast, the Alum-based adjuvant formulation induced low efficacy (2.3 %) with a strong inverse correlation with total IgG antibodies (r = −0.95). Both formulations induced an IgG1-biased (i.e. T-helper 2) antibody response, but the Montanide™ formulation conferred a more balanced IgG1/IgG2 response. The efficacy induced by the Montanide™ formulation strongly correlated with the levels of IgG2 antibodies (r = 0.91), suggesting that a balanced Th1/Th2 response plays a key role in protection. Despite its efficacy, the Montanide™ formulation caused adverse injection site effects, highlighting the need for safer alternatives. Epitope mapping identified similar linear B-cell epitope regions recognised by total IgG antibodies induced by vaccination with both adjuvant formulations. These findings suggest that Bm86 vaccination activates broader immune pathways than previously understood, emphasizing the need for exploration of additional immune markers to improve vaccine performance. HIGHLIGHTS • IgG2 levels and a balanced Th1/Th2 response are critical for Bm86 vaccine efficacy. • Bm86 in Montanide™ adjuvant provided 88.2 % efficacy but caused adverse injection site effects. • Bm86 in Alum-based adjuvant induced high IgG antibody levels but did not provide effective tick protection. • A coincident epitope group was identified for synthetic peptide-based vaccine development. • In silico tools and ex vivo validation was integrated for improved Bm86 epitope identification.
A weighted gene co-expression network analysis characterises the common defence responses of Eucalyptus to diverse biotic challenges
Swanepoel, Shae; Naidoo, Sanushka (Nature Research, 2026-02)
Eucalyptus is a globally important forestry genera cultivated for paper, pulp and biofuel production. These trees are increasingly threatened by a range of emerging pests and pathogens. While previous studies have focused on the transcriptomes of single Eucalyptus-pathogen interactions, the core transcriptional networks underlying defence across multiple biotic challenges remain poorly understood. Here we integrated 180 Eucalyptus-biotic stress RNA-sequencing libraries to characterise the common defence gene network during interactions with five distinct pathosystems. We constructed a comprehensive weighted gene co-expression network and identified 38 modules of highly co-expressed genes consisting of between 40 and 3,328 genes. The network revealed distinct modules that were induced by pathogen infection, enriched for defence responses including salicylic acid signalling and secondary metabolite biosynthesis and notably nitrate transport and responses, suggesting a potential link between nitrogen metabolism and immunity. Transcription factor enrichment analysis highlighted WRKY family genes as key regulators of induced responses, with WRKY6 emerging as a candidate hub gene in broad-spectrum resistance. Together, this study provides the first integrative transcriptome network of Eucalyptus responses to diverse biotic stressors, and offers candidate genes and pathways for future functional validation to enhance disease resistance resource in long-lived trees.
Whole-genome sequencing reveals genomic diversity and selection signatures for adaptation in South African Afrikaner and Bonsmara cattle
Alberts, Daniélle; Van Marle-Koster, Este; Joubert, F.; Berry, Donagh P. (Frontiers Media, 2026-02)
The indigenous Afrikaner and composite Bonsmara cattle breeds are hardy and adapted to the diverse South African climate and biomes. Both breeds have been successfully used in the South African stud and commercial industries. This study explored the genomic diversity and population structure, as well as identified selection signatures within and between the Afrikaner and Bonsmara breeds with a focus on signatures related to adaptation traits. Short-read whole genome sequencing data of 42 Afrikaner and 43 Bonsmara cattle were analysed. Diversity analysis revealed comparable nucleotide diversity levels in the Afrikaner and Bonsmara populations, with the Bonsmara having weaker average linkage disequilibrium between adjacent single nucleotide polymorphisms as well as having fewer runs of homozygosity. Furthermore, genetic structure analysis revealed distinct clustering of both populations, with the exception of a subset of Afrikaner individuals having been infused with Bonsmara genetics. Between and within breed selection signatures were detected using the fixation index and integrated haplotype score approaches, respectively. Several gene ontology terms were described based on the detected selection signatures, with the most significant being nervous system development and multicellular organismal processes. Finally, functional annotation of the candidate genes from the within-breed selection signature analysis revealed several genes (B3GLCT, HSPA2, HSPH1, STING1) relating to adaptive traits in both populations. The location of the within and between breed selection signatures in this study population is consistent with the performance and adaptive characteristics of both breeds and may enhance future breeding strategies with the inclusion of these breeds in crossbreeding programs. Furthermore, a comprehensive genomic characterization of these breeds through whole genome sequencing data is important as these adapted breeds are valuable reservoirs of genetic variation.
Pinus-derived membrane vesicles disrupt pathogenic metabolism in fungi
Kunene, Sithembile; Mmushi, Tshepo Joseph; Steenkamp, Emma Theodora; Motaung, Thabiso Eric (Wiley, 2026)
• Much of what we know about the biological impacts of vesicles (MVs) is derived from Arabidopsis thaliana. Our study focused on vesicles from species in the non-model plant group, Pinus (pine) (P. elliottii, P. radiata, and P. patula × Pinus tec (hybrid)). These plants have tougher tissues and strong, acicular-shaped leaves (needles). • Herein, we first developed a protocol to guide effective collection of juice fluid from needles and roots in a clean and efficient manner. The effects of these vesicles were characterized in terms of the global nutrient profile of the pine pitch canker fungus, Fusarium circinatum, generated from growing fungal spores on ~400 substrates embedded across BioLog phenotypic microarray (PM) plates (PM1, PM2A: carbon sources; PM3B: nitrogen sources; PM9: osmolytes/pH; PM24C: chemicals). • Our findings revealed that MVs, specifically needle-derived MVs (ndMVs) from P. elliottii, disrupt metabolite assimilation in several important pathways, including carbon and nitrogen metabolism. The PM data were also strongly correlated with observed phenotypic effects, including reduced viability and germination of spores in liquid media, as well as impaired filamentous growth on solid media. Importantly, these MV-induced phenotypic effects were reproducible in other filamentous pathogens (e.g., Botrytis cinerea, Chrysoporthe cubensis and F. graminearum) and during a glasshouse trial conducted with F. circinatum-infected P. elliottii seedlings, demonstrating the stable biological effects of ndMVs. • Cumulatively, our results suggest that plant-derived vesicles can disrupt metabolism in pathogenic fungi and, therefore, serve as a cost-effective and sustainable source of novel plant protection molecules.
Patterns of population genomic variation and evolutionary history of European hake in the Northeastern Atlantic
Pujolar, Jose Martin; Gardiner, Courtney E.C.; Von der Heyden, Sophie; Robalo, Joana I.; Castilho, Rita; Cunha, Regina L.; Meldrup, Dorte; Henriques, Romina; Nielsen, Einar E. (Wiley, 2026-02)
Climate change is driving species to shift their distribution ranges, potentially altering the level of genomic structuring and connectivity between populations. Additionally, fishing practices might further reduce genomic diversity and limit the potential adaptability of species to environmental changes. We use whole-genome sequencing for the first time to explore current and historical patterns of genomic diversity in European hake (Merluccius merluccius) from the Northeast Atlantic, focusing on the recently expanded distribution range in the North Sea. Genomic data revealed a complex scenario in the North Sea and neighbouring regions, with three distinct populations: North Sea, Celtic Sea and Portugal. Individuals from the Kattegat, Skagerrak and west coast of Denmark were highly differentiated from those in the Celtic Sea and waters around Ireland. The Northern North Sea appears as a transition zone, with individuals from higher latitudes assigned to the Celtic Sea group and those from lower latitudes to the North Sea group. The more distant Portuguese individuals appeared as a third distinct population. Although the differentiation among these populations was shallow when the entire dataset was used, a subset of 99,364 outlier markers revealed a much deeper divergence. Demographic analyses indicated that these populations are relatively young and have large effective population sizes and thus without sufficient time to build a signature of differentiation by genetic drift. At the same time, selection for local adaptation is strong enough to overcome the effects of contemporary gene flow. Our findings have important implications for managing the European hake stocks in the Northeastern Atlantic, highlighting the need for management measures that address shifts in species and population distribution due to climate change, as well as needing to account for different populations contributing to fisheries within a single stock. Preserving the genomic diversity within and among fish stocks is crucial for maintaining the long-term resilience of marine ecosystems and the services they provide.
Advances and shortfalls in knowledge of Antarctic terrestrial and freshwater biodiversity
Pertierra, Luis R.; Convey, P.; Barbosa, A.; Biersma, E.M.; Cowan, Don A.; Diniz, J.A.F.; De los Rios, A.; Escribano-Alvarez, P.; Fraser, C.I.; Fontaneto, D.; Greve, Michelle; Griffiths, H.J.; Harris, Mathew Andrew; Hughes, K.A.; Lynch, H.J.; Ladle, R.J.; Liu, X.P.; Le Roux, Peter Christiaan; Majewska, R.; Molina-Montenegro, M.A.; Peck, L.S.; Quesada, A.; Ronquillo, C.; Ropert-Coudert, Y.; Sancho, L.G.; Terauds, A.; Varliero, Gilda; Vianna, J.A.; Wilmotte, A.; Chown, S.L.; Olalla-Tárraga, M.A.; Hortal, J. (American Association for the Advancement of Science, 2025-02)
Antarctica harbors many distinctive features of life, yet much about the diversity and functioning of Antarctica’s life remains unknown. Evolutionary histories and functional ecology are well understood only for vertebrates, whereas research on invertebrates is largely limited to species descriptions and some studies on environmental tolerances. Knowledge on Antarctic vegetation cover showcases the challenges of characterizing population trends for most groups. Recent community-level microbial studies have provided insights into the functioning of life at its limits. Overall, biotic interactions remain largely unknown across all groups, restricted to basic information on trophic level placement. Insufficient knowledge of many groups limits the understanding of ecological processes on the continent. Remedies for the current situation rely on identifying the caveats of each ecological discipline and finding targeted solutions. Such precise delimitation of knowledge gaps will enable a more aware, representative, and strategic systematic conservation planning of Antarctica.
Quality and quantity losses of tomatoes grown by small-scale farmers under different production systems
Molelekoa, Tintswalo; Karoney, Edwin M.; Siyoum, Nazareth; Gokul, Jarishma Keriuscia; Korsten, Lise (MDPI, 2025-08-01)
Postharvest losses amongst small-scale farmers in developing countries are high due to inadequate resources and infrastructure. Among the various affected crops, tomatoes are particularly vulnerable; however, studies on postharvest losses of most fruits and vegetables are limited. Therefore, this study aimed to assess postharvest tomato losses under different production systems within the small-scale supply chain using the indirect assessment (questionnaires and interviews) and direct quantification of losses. Farmers reported tomato losses due to insects (82.35%), cracks, bruises, and deformities (70.58%), and diseases (64.71%). Chemical sprays were the main form of pest and disease control reported by all farmers. The direct quantification sampling data revealed that 73.07% of the tomatoes were substandard at the farm level, with 47.92% and 25.15% categorized as medium-quality and poor-quality, respectively. The primary contributors to the losses were decay (39.92%), mechanical damage (31.32%), and blotchiness (27.99%). Postharvest losses were significantly higher under open-field production systems compared to closed tunnels. The fungi associated with decay were mainly Geotrichum, Fusarium spp., and Alternaria spp. These findings demonstrate the main drivers behind postharvest losses, which in turn highlight the critical need for intervention through training and support, including the use of postharvest loss reduction technologies to enhance food security.
From Lake Victoria to the tap : antibiotic resistance and pathogenic contamination of Kisumu City water supply and wastewater network
Reva, Oleg N.; Sifuna, Anthony; Orata, Francis; Omolo, Caroline; Iramiot, Jacob Stanley; Enright, Mark C.; Mutshembele, Awelani; Zhou, Jian; Shivoga, William A. (Wiley, 2026)
Waterborne diseases and antimicrobial resistance (AMR) pose mounting public health threats across sub-Saharan Africa, particularly in rapidly urbanising regions dependent on untreated or poorly treated surface waters. This study applied shotgun metagenomic sequencing to characterise microbial communities, virulence factors and antibiotic resistance genes (ARGs) in water samples collected from Lake Victoria, River Wigwa, Dunga Water Treatment Plant, Nyalenda Wastewater Stabilisation Ponds and the tap water outlet in post-treatment supply pipe in Kisumu city (Kenya). Bacterial taxa dominated all metagenomes, with 121 classes represented. Cyanobacteria, particularly Planktothrix, were highly abundant in lake and tap water, whereas wastewater and river samples exhibited greater taxonomic diversity. Major human pathogens, including Pseudomonas aeruginosa, Klebsiella pneumoniae, Escherichia coli, Acinetobacter baumannii and Bacillus cereus/anthracis, were detected in nearly all samples, with unexpectedly high prevalence in tap water. Viral indicators of faecal contamination (adenoviruses, enteroviruses and torque teno viruses) corroborated widespread wastewater influence. Functional gene profiling revealed a rich resistome comprising aminoglycoside-modifying enzymes, β-lactamases, vancomycin-resistance operons and disinfectant-resistance determinants. The highest ARG and virulence gene frequencies occurred in tap and treatment-plant water, suggesting that incomplete disinfection and biofilm persistence promote the proliferation and exchange of ARGs between environmental and pathogenic taxa. In contrast, Lake Victoria water exhibited lower ARG abundance, reflecting natural self-purification processes. These findings underscore the inadequate water treatment and open wastewater systems create ecological ‘hotspots’ for ARG selection and horizontal gene transfer. Metagenomic surveillance integrated into One Health frameworks can enhance risk forecasting and guide interventions to mitigate AMR emergence and dissemination in freshwater systems serving over 35 million people across the Lake Victoria basin.
Genome resources of Xanthomonas vasicola strains from various hosts : reference-guided chromosome and plasmid assemblies for enhanced pathogen genomics
Zim, Nomakula Y.; Yssel, Anna E.J.; Coutinho, Teresa A. (Springer, 2026)
No abstract available.
Genome and transcriptome-based identification and expression profiling of chemosensory gene families across developmental stages and tissues in Sirex noctilio (Hymenoptera: Siricidae)
Postma, Alisa; Klynsmith, Leandri; Duong, Tuan A.; Allison, Jeremy D.; Smidt, Werner; Waterhouse, Robert M.; Lesny, Peter; Oeyen, Jan Philip; Petersen, Malte; Martin, Sebastian; Liu, Shanlin; Zhou, Xin; Ziesmann, Tanja; Donath, Alexander; Mayer, Christoph; Misof, Bernhard; Niehuis, Oliver; Peters, Ralph S.; Podsiadlowski, Lars; Coetzee, Martin Petrus Albertus; Joubert, Fourie; Slippers, Bernard (Wiley, 2026)
The Sirex woodwasp (Sirex noctilio; Hymenoptera: Siricidae) is among the most destructive invasive pests affecting Pinus plantations worldwide. Chemosensory systems offer promising targets for pest control strategies. The identification and characterization of chemosensation genes in non-model, economically significant insects such as S. noctilio, is an important first step towards the development of such control methods. Here we sequenced and assembled a draft genome of S. noctilio and performed RNA-sequencing of 15 olfactory and non-olfactory tissues to study the expression patterns of chemosensation-related genes. Specific genes, such as SnocOR16 and SnocSNMP1, displayed tissue- and sex-specific expression patterns, making them particularly intriguing for their potential roles in chemosensation and oviposition. As woodwasps and their related lineages form a sister group to the majority of other Hymenoptera, including Apocrita, insights into their gene repertoires are crucial for tracing the evolutionary history of chemosensory multigene families of this ecologically and economically significant insect order. This study enhances our understanding of the molecular mechanisms underlying S. noctilio chemosensation, paving the way for further research in chemical ecology and the functional characterization of S. noctilio chemosensation genes.
Genome analyses reveal two novel species of Seiridium from Acacia mearnsii
Aylward, Janneke; Visagie, Cobus M.; Roets, Francois; Wingfield, Brenda D.; Wingfield, Michael J. (Springer, 2026-02)
Seiridium is a genus of Sordariomycetes (Amphisphaeriales, Sporocadaceae), primarily known for species that cause cypress canker on Cupressaceae trees. However, most species in this genus have been reported from angiosperms, including many species in the native range of their hosts. Several unidentified Seiridium strains, collected > 20 years ago from Acacia mearnsii trees in eastern South Africa and southeastern Australia, were recently recovered from a collection of preserved cultures. We considered the phylogenetic position of these Seiridium strains and assessed their pathogenicity on A. mearnsii. Maximum likelihood analysis of three concatenated gene regions revealed four well-supported clades. Two closely related clades corresponded to Australian and South African origins, whereas two other clades representing South African isolates formed a monophyletic group with S. kartense, a species known from Eucalyptus cladocalyx on Kangaroo Island in Australia. Genome-wide average pairwise nucleotide identity and genetic differentiation analysis supported three species, including isolates considered conspecific with S. kartense and two that we consider to represent new species. These are described and named here as Seiridium mearnsii sp. nov. and Seiridium rouxiae sp. nov. Inoculations with South African isolates failed to produce evidence of pathogenicity. Seiridium species from A. mearnsii have likely been introduced into South Africa from Australia, along with the planting material used to establish A. mearnsii forestry.
Targeted protein degradation as a novel therapeutic strategy against infectious diseases
Birkholtz, Lyn-Marie; Olivier, Tiaan; Welcome, Tyrick; Strauss, Erick (Elsevier, 2026-04)
Targeted protein degradation (TPD) represents an emerging antimicrobial strategy that is predominantly still in preclinical development stages. Chimeric molecules (i.e., PROteolysis-TArgeting Chimera [PROTACs]) that can direct molecular targets for degradation by hijacking a cell's proteolytic machinery offer significant advantages over traditional small-molecule therapeutics. These include diversifying the druggable proteome by targeting previously 'undruggable' non-enzymatic and structural proteins, lowering the effective therapeutic concentration, enabling lower drug concentrations, and delaying resistance development. Recent reports of BacPROTACs that are active against Mycobacterium tuberculosis have set the stage to exploit TPD for antimicrobial drug development, yet despite its clear relevance to African-endemic diseases challenged by multidrug resistance-notably HIV, tuberculosis, and malaria-TPD-based infectious disease therapeutic development remains in its early stages. This review highlights the recent advances in the development and application of PROTACs as antimicrobials and provides an outlook for TPD's strategic value in addressing the growing threat posed by drug-resistant pathogens.
Fungal diversity as a key driver of soil multifunctionality along a European latitudinal gradient
Han, Xingguo; Domenech-Pascual, Anna; Donhauser, Jonathan; Zohner, Constantin M.; Mo, Lidong; Crowther, Thomas W.; Casas-Ruiz, Joan Pere; Jordaan, Karen; Ramond, Jean-Baptiste; Romaní, Anna M.; Prieme, Anders; Frossard, Aline (Elsevier, 2025-12)
Soils harbor a vast diversity of microorganisms and play a crucial role in global carbon and nutrients cycles. Yet, the extent and drivers of variations in soil microbial diversity and functioning across environmental gradients at continental scales remain poorly understood. Here, we investigated the diversity and network complexity of prokaryotic and fungal communities and their relationships with soil multifunctionality (SMF) – an integrative index for C-, N- and P-cycling functions – along a 3,000-km latitudinal transect across Europe (37° to 62°N), spanning biomes from Mediterranean drylands, temperate to boreal forests. We found that SMF followed a hump-shaped latitudinal pattern, peaking at mid-latitude temperate forests and declining toward the southern Mediterranean drylands and northern boreal forests. Fungal alpha-diversity, together with mean annual precipitation (MAP), mean annual temperature (MAT), and soil pH and C/N ratio, were key contributors to SMF across latitudes, while prokaryotic alpha-diversity had little effect. Both prokaryotic and fungal communities were predominantly structured by dispersal limitation, land cover, climate and soil properties, with fungal communities more strongly limited by spatial dispersion. Our study highlights the significant role of fungal diversity in sustaining SMF along the European latitudinal gradient and demonstrates the importance of both large-scale climatic and biogeographical factors and local edaphic and land cover variables in shaping microbial diversity. Our findings offer valuable insights for the conservation of ecosystem functions.
Sex-linked differentiation in commercially exploited fishes : rethinking population structure in dynamic marine environments
Gardiner, Courtney E.C.; Von der Heyden, Sophie; Matthee, Conrad A.; Nielsen, Einar E.; Pujolar, José M.; Castilho, Rita; Cunha, Regina L.; Robalo, Joana I.; Durholtz, Deon; Fairweather, Tracey P.; Kathena, Johannes N.; Henriques, Romina (Wiley, 2025)
Understanding how genomic structure links with ecological and evolutionary processes is critical for forecasting species responses to dynamic marine environments, especially in commercially exploited marine species, where fishing pressure can impact genomic integrity. Here we investigate Merluccius paradoxus, a commercially exploited demersal fish that appears to be undergoing a range expansion along the southern African coastline. Using whole-genome sequence data of individuals from across the species' distribution (n = 37), we reveal that sex-linked divergence, rather than geography, is the principal driver of genomic variation, challenging conventional assumptions of regional geographic population structure. Divergence was concentrated on autosomal regions (primarily large regions on Chromosomes 1 and 2), rather than known sex-determining (SD) regions (Chromosome 9), and did not have structural variants or extended linkage disequilibrium (LD). Instead, patterns were consistent with sex-specific directional selection acting on genes enriched for neuronal function, metabolism and muscle development, traits that are likely linked to behaviour, physiology and environmental tolerance. Males had reduced nucleotide diversity (π), low observed heterozygosity (Ho) and longer runs of homozygosity (ROH) in these regions, suggesting recent selective sweeps or a reduced effective population size (Ne). Together with spatial differences in sex distribution and genomic diversity metrics, results suggest that males and females may differ in both range dynamics and adaptive potential. As M. paradoxus continues to shift its distribution across geo-political boundaries, sex-biased adaptation may have important consequences for reproductive output, resilience and sustainable fisheries management under a changing climate. This study highlights the need to incorporate sex-linked genomic variation into conservation planning, particularly in transboundary systems vulnerable to cumulative pressures of fishing and environmental change.
A BAC‑guided haplotype assembly pipeline increases the resolution of the virus resistance locus CMD2 in cassava
Cornet, Luc; Zaidi, Syed Shan‑e‑Ali; Li, Jia; Ngapout, Yvan; Shakir, Sara; Meunier, Loic; Callot, Caroline; Marande, William; Hanikenne, Marc; Rombauts, Stephane; Van de Peer, Yves; Vanderschuren, Hervé (BioMed Central, 2025-06-29)
BACKGROUND : Cassava is an important crop for food security in the tropics where its production is jeopardized by several viral diseases, including the cassava mosaic disease (CMD) which is endemic in Sub-Saharan Africa and the Indian subcontinent. Resistance to CMD is linked to a single dominant locus, namely CMD2. The cassava genome contains highly repetitive regions making the accurate assembly of a reference genome challenging. RESULTS : In the present study, we generate BAC libraries of the CMD-susceptible cassava cultivar (cv.) 60444 and the CMD-resistant landrace TME3. We subsequently identify and sequence BACs belonging to the CMD2 region in both cultivars using high-accuracy long-read PacBio circular consensus sequencing (ccs) reads. We then sequence and assemble the complete genomes of cv. 60444 and TME3 using a combination of ONT ultra-long reads and optical mapping. Anchoring the assemblies on cassava genetic maps reveals discrepancies in our, as well as in previously released, CMD2 regions of the cv. 60444 and TME3 genomes. A BAC-guided approach to assess cassava genome assemblies significantly improves the synteny between the assembled CMD2 regions of cv. 60444 and TME3 and the CMD2 genetic maps. We then performed repeat-unmasked gene annotation on CMD2 assemblies and identify 81 stress resistance proteins present in the CMD2 region, among which 31 were previously not reported in publicly available CMD2 sequences. CONCLUSIONS : The BAC-assessed approach improved CMD2 region accuracy and revealed new sequences linked to virus resistance, advancing our understanding of cassava mosaic disease resistance.
Chromosome-level genome assemblies for the latent pine pathogen, Diplodia sapinea, reveal two accessory chromosomes with distinct genomic features and evolutionary dynamics
Shaw, Preston Locke; Slippers, Bernard; Wingfield, Brenda D.; Laurent, Benoit; Penaud, Benjamin; Wingfield, Michael J.; Crous, Pedro W.; Bihon, Wubetu; Duong, Tuan A. (Oxford University Press, 2025-12)
Diplodia sapinea (Dothideomycetes) is a latent fungal pathogen with a global distribution that predominantly infects Pinus species. The impact of the fungus is increasing due to climate-driven range expansion and thus wide-scale disease outbreaks are occurring. With the aim of developing high-quality genome resources, we generated chromosome-level genome assemblies for 3 D. sapinea isolates and low-coverage Illumina genome data for 6 additional isolates. By comparing these genome assemblies, we identified 14 core chromosomes and 2 accessory chromosomes (ACs) in the pathogen. These 2 ACs encode 80 and 147 proteins, respectively, while 11,374 to 11,601 genes were identified in the core chromosomes. Both ACs had lower gene density and higher proportions of transposable elements compared to the core chromosomes. Sequence analysis indicated that genes on the ACs displayed more sequence variation compared to those on the core chromosomes, suggesting they serve as evolutionary hotspots in the species. Sequence homology analyses suggested that the ACs were possibly acquired horizontally, probably from a species in the Dothideomycetes. We designed PCR-based assays to detect the presence of ACs and applied these on a set of 37 isolates from 14 countries. One of the ACs was detected in 33 isolates from 13 countries, while the other AC was absent in all isolates tested. Pathogenicity trials on Pinus patula seedlings showed no correlation between the presence of ACs and isolate aggressiveness. The high-quality genomes provided here offer important resources for future research on this globally important pathogen, including the biological roles of the ACs.

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