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

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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.
Heavy metals pollution in low quality water irrigated soil and their impact on bacterial abundance and diversity in the rhizosphere of Swiss chard (Beta Vulgaris L.) seedlings
Manegabe, Bahati J.; Msagati, Titus Am.; Ntabugi, Kikongo Marie-Mediatrice; Maree, Johannes P.; Pierneef, Rian Ewald; De Bruyn, Karin; Raletsena, Maropeng V. (Springer, 2026-01)
Substandard irrigation water impacts the chemical characteristics of soil, which may subsequently modify the shape of soil bacterial communities. Five categories of water, including the river water (RW), acid mine drainage (AMD), untreated wastewater (UTWW), treated wastewater (TWW), and tap water (TW), were utilized as irrigation water samples. Soil and water samples were examined for heavy metals, such as Chromium (Cr), Cobalt (Co), Zinc (Zn), Arsenic (As), Cadmium (Cd), and Lead (Pb), using ICP-MS. The V1-9 region of bacterial 16S rRNA was PCR-amplified to evaluate the effects of heavy metals in low-quality irrigated soil on bacterial diversity and abundance in the rhizosphere of Swiss chard seedlings. Approximately 88.9% of heavy metals in water, with concentrations ranging from 0.03 to 432.8 mg/L, were detected at low levels in TW. Conversely, about 83.3% of heavy metals, with the concentrations between 0.38 and 553.78 mg/kg, were detected at low levels in TW irrigated soil (TS1). The electrical conductivity (EC), pH, and organic matter (OM) fluctuated based on the irrigation water and soil samples. Bacterial diversity and abundance in soils differed according on the quality of irrigation water samples. Blastoccus, Microlunatus, Nocardioides, Solirubrobacter, and Streptomyces exhibited higher relative abundance in soil subjected to low-quality water compared to soil irrigated with TW (TS1). Redundancy analysis (RDA) demonstrated that bacterial community structure in the rhizosphere of Swiss chard seedlings were influenced by heavy metals, EC, pH and OM. This indicates that the introduction of heavy metals into the soil can select sensitive bacteria, whereas soil OM can supply nutrients that enhances resistant/tolerant bacterial multiplication, thereby influencing seedling growth.
Wind direction and strength determine the genetic structure of an insect-pollinated plant across heterogeneous landscape
Deng, Jun-Yin; Fu, Rong-Hua; Compton, Stephen G.; Yuan, Chuan; Kling, Matthew M.; Chen, Xiao-Yong; Song, Yao-Bin; Jiang, Kai; Liu, Mei; Greeff, Jacobus Maree; Chen, Yan (Wiley, 2025-06)
AIM : Dispersal of plant propagules and their genes is crucial for plant responses to landscape heterogeneities, yet the mechanisms behind this dispersal remain unclear. Ficus species depend on wind-borne fig wasps for pollination, but research on airflow effects on Ficus genetic structure has produced conflicting results. Our study aims to clarify the role of wind in shaping the genetic structure of such plants with wind-borne insect pollinators by examining how geomorphological complexity interacts with air movements to influence genetic structures. LOCATION : Southwest China: Sichuan, Yunnan, Guangxi and Guizhou provinces. TAXON : Ficus tikoua Bur., Ficus, Moraceae. METHODS : We sampled 56 F. tikoua sites across southwest China, characterised by high geomorphologic complexity. River basins and predominant winds were visualised across the sampled regions. Wind connectivity between sampled sites during the main pollination season was modelled based on hourly daily wind data. The maternal and biparental genetic structure of sites were reconstructed using chloroplast DNA (cpDNA) and nuclear SSR (nuSSR) markers. Links between genetic structure, location, and wind parameters were estimated by Mantel or partial Mantel tests. RESULTS : The plant's maternal genetic structure was defined by river systems, with two distinct cpDNA groups located in the Yangtze and Pearl River basins, respectively. The boundaries for nuclear variation were less clearly delimited geographically. Sites with mixtures of nuSSR groups were concentrated where prevailing winds arrived from several directions. Stronger between-site air flows increased nuSSR geneflow and genetic similarities, while populations receiving more wind flow were also more genetically variable. MAIN CONCLUSIONS : Our study reveals how plant gene dispersal reflects air and water movements that in turn respond to geomorphologic complexity, thereby directly demonstrating the effects of wind on gene flow of plants with wind-borne insect pollinators. Wind data matching pollinator flight times and large sample sizes are crucial for testing wind effects.
In silico and in vitro evaluation of flavonoid derivatives for diabetes management : molecular dynamics, and enzyme kinetics for pancreatic alpha-amylase and alpha-glucosidase
McMillan, Jamie; Bester, Megan Jean; Apostolides, Zeno (Springer, 2025-11)
Please read abstract in the article.
Draft genome sequences of Rahnella perminowiae, R. aceris, and R. aquatilis isolated from onion bulbs (Allium cepa L.) displaying symptoms of bacterial rot
Mnguni, Fanele Cabangile; Shin, Gi Yoon; Aegerter, Brenna J.; Du Toit, Lindsey J.; Derie, Michael L.; Coutinho, Teresa A. (Springer, 2026-02)
Onions (Allium cepa L.) are among the most widely produced vegetables globally, and their cultivation plays an important role in food security (Schwartz et al. 2007). However, the emergence of opportunistic bacterial plant pathogens, such as Rahnella species, which are not fully understood yet, poses a threat to onion production (Asselin et al. 2019; Brady et al. 2022). Rahnella species are Gram-negative, facultative anaerobes within the Yersiniaceae family, part of the order Enterobacteriales (Adeolu et al. 2016). According to the List of Prokaryotic Names with Standing in Nomenclature (LPSN), the genus consists of 15 described species that are isolated from various environments and are considered validly characterised (Guo et al. 2012; Brady et al. 2014; Lee et al. 2019; Liang et al. 2020).
Launching the IUCN Microbial Conservation Specialist Group as a global safeguard for microbial biodiversity
Gilbert, Jack A.; Peixoto, Raquel S.; Scholz, Amber Hartman; Dominguez Bello, Maria Gloria; Korsten, Lise; Berg, Gabriele; Singh, Brajesh; Boetius, Antje; Wang, Fengping; Greening, Chris; Wrighton, Kelly; Bordenstein, Seth; Jansson, Janet K.; Lennon, Jay T.; Souza, Valeria; Thomas, Torsten; Cowan, Don A.; Crowther, Thomas W.; Nguyen, Nguyen; Harper, Lucy; Haraoui, Louis-Patrick; Ishaq, Suzanne L.; Redford, Kent (Nature Research, 2025-10)
Despite its importance, microbial life is largely absent from global conservation frameworks. Launched in July 2025, the Microbial Conservation Specialist Group (MCSG) was established as a Species Survival Commission (SSC) by the International Union for Conservation of Nature (IUCN). The IUCN is the world’s leading authority in environmental science and policy, renowned for shaping conservation priorities across governments, non-governmental organizations and international treaties. The MCSG convenes a coalition of microbiologists, ecologists, traditional knowledge experts and conservation leaders to develop and advocate for conservation tools, strategies and policies that explicitly integrate microbiology into global biodiversity governance. Despite the importance of microorganisms for ecosystem function, their role has been seen as too abstract or complex to integrate into policy. Elevating microbial perspectives within global conservation has required overcoming a deep-rooted tendency to overlook the invisible.
Alleviation of adverse effects associated with α-glucosidase inhibitors by Ocimum basilicum L., Matricaria chamomilla L., and Salvia officinalis L. reveals novel selective inhibition of Bacillus α-glucosidase by acarbose
Van der Merwe, Lané; Bester, Megan Jean; Serem, June Cheptoo; Apostolides, Zeno (Elsevier, 2026-04)
Ocimum basilicum L., Matricaria chamomilla L., and Salvia officinalis L. have literature-supported ethnobotanical claims of reducing hyperglycaemia and gastrointestinal discomfort. Thus, they contain potent potential for reducing gastrointestinal adverse side effects associated with the use of the type 2 diabetes medication, acarbose. The adverse effects are predominantly theorised to be caused by excess carbohydrate fermentation by gut bacteria. Therefore, the aim of this study was to subject herbal extracts as well as compounds identified in the herbs to in silico and in vitro investigation for selective inhibition of a gut bacterial enzyme, Bacillus α-glucosidase, compared with human α-glucosidase. In silico molecular docking was employed to filter and select top performing compounds that exhibited the highest selective Bacillus α-glucosidase inhibition, followed by pharmacokinetic examination of the selected compounds. In vitro enzyme kinetics, hepatocellular carcinoma cell line cytotoxicity and the reduction of hepatic lipid accumulation in a hepatocellular carcinoma/oleic acid cellular model of metabolic dysfunction-associated fatty liver disease was examined. A metabolomic study on the concentration of the selected compounds in the herbs as well as a comparative analysis on abundant metabolites between herbs were analysed through an ultra-performance liquid chromatography-mass spectrometry-based study. Molecular docking revealed cinnamic acid, coumaric acid, epicatechin, hesperetin, linalool, menthol, octenol, terpineol, umbelliferone, and vanillic acid as the top predicted compounds with the highest predicted selective inhibition of Bacillus α-glucosidase. These findings were validated through in vitro assessment, in which the primary finding and the most unexpected result was obtained through enzyme kinetics, where compared with all compounds, acarbose exhibited the most potent inhibition and selectivity towards Bacillus α-glucosidase. Only umbelliferone significantly reduced cell viability and therefore validated its predicted toxicity that was obtained through pharmacokinetic studies. O. basilicum, M. chamomilla, and S. officinalis were evaluated against Camellia sinensis (L.) Kuntze for cytotoxic effects, where only M. chamomilla produced a significantly higher EC50, substantiating the herbs potent anti-cancerous abilities. Compounds and herb extracts were not found to reduce hepatic lipid accumulation. The novel finding was related to acarbose inhibition and specifically its potent selectivity of Bacillus α-glucosidase which discredits and disproves the theory that excess bacterial fermentation is the cause behind acarbose's reported adverse effects. Thus, this research study rather proves that acarbose negatively affects gut bacterial enzymes, promoting microbiome dysbiosis and therefore future research should at the forefront focus on the rehabilitation of diabetic patients' gut microbiome and intestinal health. HIGHLIGHTS • Type 2 diabetes (T2D) medication, acarbose, causes adverse gastrointestinal side effects. • It is theorised this is due to excess carbohydrate fermentation by gut bacteria. • However, acarbose proved potent selective inhibition towards Bacillus α-glucosidase. • Disproving the theory, showing acarbose negatively affect gut bacterial enzymes. • Leading to possible future pathogenic Bacillus α-glucosidase inhibition by acarbose.
Structural insights into WY domain SLiM-containing conserved RxLR effectors : a case study of five important Phytophthora species
Salasini, Brenda Chisanga; Chepsergon, Jane; Nxumalo, Celiwe Innocentia; Moleleki, Lucy Novungayo (American Phytopathological Society, 2026)
Pathogenicity in Phytophthora species is in part underpinned by a sophisticated arsenal of RxLR effectors, which function as molecular determinants of host immune manipulation. Among these, conserved RxLR effectors (CREs) represent an evolutionarily conserved subset that is indispensable for virulence. However, the structural basis of their function remains poorly understood. Here, we conducted in silico analysis of CREs across five agriculturally significant Phytophthora species, revealing a conserved subset that integrates WY domains with embedded short linear motifs (SLiMs), a previously recognized architectural feature with functional implications. Notably, our findings indicate that despite the canonical association of SLiMs with intrinsically disordered regions, their incorporation within the structured WY domain preserves domain integrity while potentially expanding the effector's interactome within host cells. To explore the functional relevance of this domain organization, we characterized Phytophthora nicotianae RxLR6 (PpRxLR6), a representative WY-SLiM CRE identified in this study. Using Agrobacterium-mediated transient expression assays, we demonstrate that PpRxLR6 activates key immune defense networks in Nicotiana and Solanum species, suggesting a role in modulating host immune signaling. Structural predictions further reveal that PpRxLR6 harbors its SLiM within a well-ordered WY-like helical core region, suggesting that SLiM-mediated interactions may occur within structured effector domains rather than being confined to intrinsically disordered regions. These findings enhance our understanding of the effector domain architecture of PpRxLR6, illustrating how structured domains in CREs may serve as scaffolds for SLiM-mediated interactions. This structural arrangement may represent an adaptive strategy in Phytophthora evolution, potentially enhancing effector versatility in host interactions and immune modulation.

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