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

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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.
A haplotype-resolved reference genome for Eucalyptus grandis
Lötter, Anneri; Bruna, Tomas; Duong, Tuan A.; Barry, Kerrie; Lipzen, Anna; Daum, Chris; Yoshinaga, Yuko; Grimwood, Jane; Jenkins, Jerry W.; Talag, Jayson; Borevitz, Justin; Lovell , John T.; Schmutz, Jeremy; Wegrzyn, Jill L.; Myburg, Alexander A. (Oxford University Press, 2025-07)
Eucalyptus grandis is a hardwood tree used worldwide as pure species or hybrid partner to breed fast-growing plantation forestry crops that serve as feedstocks of timber and lignocellulosic biomass for pulp, paper, biomaterials, and biorefinery products. The current v2.0 genome reference for the species served as the first reference for the genus and has helped drive the development of molecular breeding tools for eucalypts. Using PacBio HiFi long reads and Omni-C proximity ligation sequencing, we produced an improved, haplotype-phased assembly (v4.0) for TAG0014, an early-generation selection of E. grandis. The 2 haplotypes are 571 Mbp (HAP1) and 552 Mbp (HAP2) in size and consist of 37 and 46 contigs scaffolded onto 11 chromosomes (contig N50 of 28.9 and 16.7 Mbp), respectively. These haplotype assemblies are 70–90 Mbp smaller than the diploid v2.0 assembly but capture all except one of the 22 telomeres, suggesting that substantial redundant sequence was included in the previous assembly. A total of 35,929 (HAP1) and 35,583 (HAP2) gene models were annotated, of which 438 and 472 contain long introns (>10 kbp) in gene models previously (v2.0) identified as multiple smaller genes. These and other improvements have increased gene annotation completeness levels from 93.8 to 99.4% in the v4.0 assembly. We found that 6,493 and 6,346 genes are within tandem duplicate arrays (HAP1 and HAP2, respectively, 18.4 and 17.8% of the total) and >43.8% of the haplotype assemblies consists of repeat elements. Analysis of synteny between the haplotypes and the E. grandis v2.0 reference genome revealed extensive regions of collinearity, but also some major rearrangements, and provided a preview of population and pangenome variation in the species.
Proteomic and secretomic response of an African Armillaria species to iron
Narh, Deborah L.; Wingfield, Brenda D.; Coetzee, Martin Petrus Albertus (American Chemical Society, 2026-03)
Armillaria species have attracted considerable research interest, because they are widely distributed, mostly plant-pathogenic, and exhibit unique characteristics. Abiotic factors influence intra- and interspecies variations in pathogenicity and/or virulence of these fungi. However, the mechanisms involved in causing these variations are not well understood. Iron is an indispensable element in several molecular and biological processes. Yet, excessive abundance of iron can be toxic to organisms due to Fenton-like reactions. This study aimed to gain insights into the type and extent of iron-responsive proteomic and secretomic changes in Armillaria sp. strain CMW4456 cultured in liquid media supplemented with iron using a multiomics approach. Significant iron-dependent alterations of proteins involved in metabolism and growth were observed in the proteomes and secretomes. Iron supplementation at 100 μM did not elicit an oxidative stress response by the fungus. Our analyses revealed three putative siderophore biosynthetic gene clusters (BGCs) in the genome and expression of proteins encoded by some BGC genes in the proteome. This knowledge contributes to a better understanding of the mechanisms employed by an Armillaria sp. in response to iron, gives insights into possible modes for inhibiting or attenuating the pathogenicity and/or virulence of Armillaria spp., and can be valorized for more biotechnological applications.
α-Glucosidase inhibitory potential of Citrus reticulata peel-derived flavonoids—a prelude for the management of type 2 diabetes
Baloyi, Itumeleng Tsebang; Rabbad, Ali H.; Gama, Ntombenhle Hlengiwe; Malgas, Samkelo (Wiley, 2026-02)
α-Glucosidase inhibitors (AGIs) are compounds used to treat type 2 diabetes (T2D) by preventing the breakdown of dietary starch into monosaccharides, which reduces their absorption by the body and lowers blood glucose levels. AGIs often cause gastrointestinal issues such as diarrhea and flatulence due to excessive α-amylase inhibition, leading to excess residual starch reaching the colon and being fermented by microbes. There is a need to prospect for novel AGIs that are effective and have fewer adverse effects. This study investigated the potential of citrus-derived flavonoids as AGIs targeting amylolytic enzymes: α-amylase and α-glucosidase. Firstly, flavonoids were extracted from Citrus reticulata (tangerines) peels using an ultrasound-assisted methanolic procedure, followed by C18 column-purification and profiling with liquid chromatography-mass spectrometry. Select citrus peel-derived flavonoids, quercetin (−9.2 kcal/mol) and rutin (−10.8 kcal/mol), and the commercial AGI, acarbose (−8.7 kcal/mol), showed strong binding affinities against α-glucosidase. Molecular dynamics simulations of the compounds were also assessed, revealing flexibility and stability in response to ligand interactions with the α-glucosidase. The in silico data correlated positively with the results from the in vitro inhibition assays; acarbose (Ki = 0.14 mg/mL), quercetin (Ki = 0.12 mg/mL) and rutin (Ki = 0.19 mg/mL) recorded low inhibition constant values. The cytotoxicity profile of the selected compounds was also conducted on Caco-2 cells, with flavonoids showing no significant cytotoxic effects. Flavonoids could be used as AGIs with minimal gastrointestinal impacts, reducing residual starch entering the colon and decreasing glucose uptake.
Editorial : Forest microbiome : dynamics and interactions in the anthropocene era
Chakraborty, Amrita; Roy, Amit; He, Shulin; Castellano-Hinojosa, Antonio; Asiegbu, Fred O.; Coutinho, Teresa A. (Frontiers Media, 2025-11-21)
Forests represent one of the most complex and biodiverse ecosystems on Earth, with intricate networks linking trees, vegetation strata, insects, microbial communities, and soil processes. These networks, sustained by feedback loops and finely tuned ecological balances, form the foundation of global biogeochemical cycles and biodiversity conservation. At the core of these dynamics lies the forest microbiome, including a vast, often invisible consortium of bacteria, fungi, archaea, and viruses that mediates nutrient turnover, supports tree health, and shapes interactions across trophic levels (Baldrian, 2017; Asiegbu and Kovalchuk, 2021).
Enhancing multi-season wheat yield through plant growth-promoting rhizobacteria using consortium and individual isolate applications
Breedt, Gerhardus; Korsten, Lise; Gokul, Jarishma Keriuscia (Springer, 2025-12)
In recent decades, there has been a growing interest in harnessing plant growth-promoting rhizobacteria (PGPR) as a possible mechanism to mitigate the environmental impact of conventional agricultural practices and promote sustainable agricultural production. This study investigated the transferability of promising PGPR research from maize to another Poaceae cereal crop, wheat. This multi-seasonal study evaluated the wheat grain yield effect of Lysinibacillus sphaericus (T19), Paenibacillus alvei (T29) when applied i. individually, ii. as a consortium with Bacillus safensis (S7), and iii. at a 75% reduced fertilizer rate. Whole genome sequencing allowed annotation of genes linked to plant growth promotion, providing potential genomic explanations for the observed in-field findings. Application of the consortium compared to a commercial PGPR showed significantly increased wheat yield by 30.71%, and 25.03%, respectively, in season one, and 63.92% and 58.45%, respectively, under reduced fertilizer rates in season two. Individual application of T19 and T29 showed varying results, with T19 increasing wheat yield by 9.33% and 16.22% during seasons three and four but a substantial reduction (33.39%) during season five. T29 exhibited yield increases during season three (9.31%) and five (5.61%) but led to a significant reduction (21.15%) in season four. Genomic analysis unveiled a spectrum of plant growth-promoting genes including those associated with ammonification, phosphate solubilization, ethylene, siderophore, catalase, and superoxide dismutase production. These findings offer valuable insights into the mechanisms behind observed field results, with potential implications for advancing sustainable agriculture and crop productivity in evolving agricultural landscapes.
Safeguarding microbial biodiversity : microbial conservation specialist group within the species survival commission of the International Union for conservation of nature
Gilbert, Jack A.; Scholz, Amber Hartman; Bello, Maria Gloria Dominguez; Korsten, Lise; Berg, Gabriele; Singh, Brajesh K.; Boetius, Antje; Wang, Fengping; Greening, Chris; Wrighton, Kelly; Bordenstein, Seth R.; Jansson, Janet; Lennon, Jay T.; Souza, Valeria; Allard, Sarah M.; Thomas, Torsten; Cowan, Don A.; Crowther, Thomas W.; Nguyen, Nguyen; Harper, Lucy; Haraoui, Louis-Patrick; Ishaq, Suzanne L.; McFall-Ngai, Margaret; Redford, Kent H.; Peixoto, Raquel (Oxford University Press, 2025-01)
No abstract available.
From pan-active to parasite-selective antiparasitic agents : a scaffold hopping approach
Borsari, Chiara; Santarem, Nuno; Coertzen, Dina; Mazzolari , Asia; Corfu, Alexandra Ioana; Coelho, Catarina; Barbosa, Francisca; Tamborini, Lucia; Birkholtz, Lyn-Marie; Raffellini , Lorenzo; Keminer, Oliver; Basilico, Nicoletta; Parapini, Silvia; Gul, Sheraz; Cordeiro-da-Silva, Anabela; Conti, Paola (Elsevier, 2025-12)
Vector-borne parasitic diseases (VBPDs) represent a major global public health concern, with human African trypanosomiasis (HAT), Chagas disease, leishmaniasis, and malaria collectively threatening millions of people, particularly in developing regions. Climate change may further influence their transmission and geographic spread, increasing the global burden. As drug resistance continues to rise, there is an urgent need for novel therapeutic agents to expand treatment options and limit disease progression. Exploiting a cell-based phenotypic approach, we had previously developed 1,3,4-oxadiazole derivatives, as broad-spectrum low-toxicity agents active against protozoan parasites including Plasmodium falciparum, Leishmania spp. and Trypanosoma brucei. Herein, we applied a scaffold-hopping approach to develop novel chemotypes by replacing the central 1,3,4-oxadiazole core with 1,2,4-oxadiazole and oxazole rings. A systematic investigation allowed us to generate two novel libraries of compounds and carry out extensive Structure-Activity-Relationship studies and early drug discovery pharmacological liability characterization. Starting from pan-active 1,3,4-oxadiazole-based antiparasitic agents, we identified two anti-kinetoplastid molecules bearing the 1,2,4-oxadiazole core and one promising anti-T. brucei agent featuring an oxazole core. Our work paves the way for the development of novel chemotypes to successfully fight parasitic infections.
Outbreaks of a native jewel beetle, Agrilus grandis (Coleoptera: Buprestidae), on commercial black wattle, Acaciamearnsii, plantations in South Africa
Nel, Wilma Janine; Jali, Sandisiwe; Barnes, Irene; Wondafrash, Mesfin; Hurley, Brett Phillip (Entomological Society of Southern Africa, 2026-02)
In early 2024, an outbreak of an unknown wood-borer was observed in Acacia mearnsii De Wild (black wattle) compartments in the Midlands of KwaZulu-Natal, South Africa, causing symptoms of excessive resin production. Larvae uncovered beneath the bark were morphologically identified as a flathead borer, prompting urgent investigation due to the historically low impact of wood-borers on black wattle in South Africa. DNA sequencing of the COI and CytB regions of the larvae failed to yield conclusive matches, so infested logs were collected and the infesting insects reared, resulting in the emergence of three adult beetles. Morphological examination of the adults revealed them as being Agrilus grandis Gory & Laporte 1839, a native African jewel beetle. Comparison to historical specimens housed in the FABI Insect Reference Collection based at the University of Pretoria revealed a previous, unpublished outbreak of the same species in Acacia mearnsii in 1974. However, this is the first official report of A. grandis infestations on A. mearnsii in South Africa.
Integrated analysis of gene expression, protein synthesis, and epigenetic modifications in Alcanivorax borkumensis SK2 under iron limitation
Smedile, Francesco; Denaro, Renata; Crisafi, Francesca; Giosa, Domenico; D'Auria, Giuseppe; Ferrer, Manuel; Rosselli, Riccardo; Staege, Martin S.; Yakimov, Michail M.; Giuliano, Laura; Reva, Oleg N. (Wiley, 2025-06)
This study aimed to understand the genetic and molecular mechanisms enabling Alcanivorax borkumensis SK2, a hydrocarbonoclastic marine bacterium, to thrive under iron‐limited conditions. Using SMRT PacBio whole‐genome sequencing, Illumina total RNA sequencing, and proteomics analysis, we examined the strain's response to iron‐rich and iron‐depleted media. Despite minimal impact on growth, significant changes in gene expression were observed when using n‐tetradecane or acetate under iron limitation. Iron scarcity, depending on the carbon source, affects energy metabolism, membrane transport, lipid metabolism, stress‐adaptive responses, and siderophore synthesis. We identified several methyltransferases (MTases) in the studied genome, including RS14230, which is a part of a fully functional restriction‐modification (RM) system causing bipartite cytosine methylation and DNA cleavage at AgGCcT sites. Another MTase, RS09425, controls bipartite adenine methylation at GaTNNNNNGtGG motifs; however, no restriction activity at these motifs has been detected. Many epigenetically modified nucleotides lacked canonical motifs, possibly due to MTase byproducts. Notably, non‐canonical modifications were statistically associated with transcriptional start sites and gene regulation, suggesting an indirect role in transcription via DNA conformation changes and its accessibility to MTases near actively transcribed genes.

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