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

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Design of genus-specific semi-nested primers for simple and accurate identification of Enterobacter strains
(BioMed Central, 2025-07) Jordan, Sara; Pothier, Joel F.; De Maayer, Pieter; Broders, Kirk; Kvitko, Brian H.; Coutinho, Teresa A.; Smits, Theo H. .
BACKGROUND : The genus Enterobacter, in the family Enterobacteriaceae, is of both clinical and environmental importance. This genus has undergone frequent taxonomic changes, making it challenging to identify taxa even at genus level. This study aimed to design Enterobacter genus-specific primers that can be used for simple PCR identification of large sets of putative Enterobacter isolates. RESULTS : Comparative genomic approaches were employed to identify genes that were universally present on Enterobacter genomes but absent from the genomes of other members of the family Enterobacteriaceae, based on an initial set of 89 genomes. The presence of these genes was further confirmed in 4,276 Enterobacter RefSeq genomes. While no strictly genus-specific genes were identified, the hpaB gene demonstrated a restricted distribution outside of the genus Enterobacter. Semi-nested primers were designed for hpaB and its flanking gene hpaC (hpaBC) and evaluated on 123 strains in single-tube PCR reactions. All taxa showing positive reactions belonged to the genus Enterobacter. For Enterobacter strains the PCR yielded two amplicons at 110 bp and at 370 bp, while strains only displaying the 110 bp amplicon were classified as Leclercia pneumoniae. A blind-test on 120 strains accessioned as Enterobacter sp. from the USDA-ARS culture collection (NRRL), revealed that one third of the strains had an incorrect genus assignment. Comparison of gene trees of the hpaBC fragment sequences with marker genes frequently used for single-gene barcoding or multi-locus sequence analysis (MLSA) further demonstrated its potential for preliminary species identification. CONCLUSIONS : The nested PCR assay represents a rapid and cost-effective approach for preliminary identification of Enterobacter species. As the primer design was based on large-scale genomic comparison, including currently undescribed species clades, it will remain valid even after taxonomic changes within the genus.
A novel Arthrobotrys species : taxonomic characterization, nematicidal activity, and multi-omics insights into nematode predation
(Elsevier, 2025-09) Gao, Mengting; Yan, Zhaoqi; Liu, Zexin; Jiang, Yunxia; Liu, Tengteng; Miao, Xingjun; Dai, Meixue; Bose, Tanay; tanay.bose@fabi.up.ac.za
ursaphelenchus xylophilus, the pinewood nematode (PWN), is a devastating invasive pest responsible for widespread mortality in global conifer forests. During a survey of bark beetle-associated fungi, a nematode-trapping fungus was isolated from an empty beetle gallery in Pinus thunbergii. ITS sequence analysis suggested it represented a novel species. This study aimed to characterize the fungus taxonomically and evaluate its biocontrol potential against PWN. Multi-locus phylogenetic analyses (ITS, TEF1-α, RPB2) confirmed the isolate as a new species, Arthrobotrys byssisimilis sp. nov. Morphological examination revealed adhesive trapping networks and distinctive ellipsoidal conidia. Enzymatic assays demonstrated chitinase and protease activity, with optimal conditions defined for pH and temperature. Culture filtrates, protein extracts, and secondary metabolites showed rapid, dose-dependent nematicidal effects, achieving 100 % PWN mortality within 10–30 min. The fungus exhibited strong tolerance to pine-derived volatiles (α-pinene, β-pinene, turpentine, and ethanol), indicating high adaptability to the host environment. Whole-genome sequencing revealed a 36.97 Mb genome with 8,354 predicted genes, including 104 proteases, 8 chitinases, and diverse secondary metabolite biosynthesis clusters. Transcriptomic profiling after nematode exposure identified 638 differentially expressed genes, including virulence-related enzymes (proteases, CAZymes), cytochrome P450s, and PHI factors, with evidence of stage-specific regulation. Arthrobotrys byssisimilis is the first Arthrobotrys species reported from a bark beetle gallery, expanding the ecological scope of the genus. The integrated in vitro nematicidal activity, physiological adaptability, and multi-omics data suggest A. byssisimilis warrants further evaluation as a potential biocontrol agent against PWN, while its unique genomic features provide new molecular targets for investigating fungal-nematode interactions. HIGHLIGHTS • Discovered novel nematode-trapping fungus Arthrobotrys byssisimilis. • Achieved 100% pinewood nematode kill in 10–30 mins using culture filtrates and extracts. • Shows strong tolerance to pine volatiles, ensuring better field adaptability. • Genome shows 104 proteases, 8 chitinases as major virulence factors. • Found 638 genes differentially expressed under nematode stress, stage-specific virulence.
Exploring the diversity of leafrollers (Lepidoptera: Tortricidae) associated with eucalypts in South African forestry nurseries and plantations, with a new report of Strepsicrates sp.
(Taylor and Francis, 2024-11-08) Makunde, Privilege Tungamirai; Slippers, Bernard; Hurley, Brett P.; privilege.makunde@fabi.up.ac.za
A number of insect pests cause damage to eucalypts in South Africa. Their accurate identification is a key part of managing and controlling these pests. The aims of this study were to identify leafroller insect species in South African eucalypt nurseries and plantations, and to determine whether the species were native insects that had developed new host associations with eucalypts or introduced non-native species. A section of the mitochondrial cytochrome c-oxidase subunit 1 (CO1) gene of multiple specimens from nurseries and plantations was sequenced. The sequence data were compared and validated using sequences available in BOLD systems and GenBank databases. Results revealed the presence of an introduced non-native Strepsicrates sp. in both nurseries and plantations. In addition, the native species Choristoneura occidentalis and Eccopsis incultana were confirmed as present in plantations only and the native species Lozotaenia capensana was confirmed as present in one of the nurseries. Eucalypts are reported as host plants of C. occidentalis, E. incultana and Lozotaenia capensana for the first time. The findings contribute valuable insights into the identification and diversity of leaf rollers in eucalypt plantations in South Africa, with potential implications for pest management.
DNA sequence data confirms the presence of two closely related cypress-feeding aphid species on African cypress (Widdringtonia spp.) in South Africa
(Taylor and Francis, 2024-12) Wondafrash, Mesfin; Wingfield, Michael J.; Hurley, Brett Phillip; Slippers, Bernard; Mutitu, Eston K.; Jenya, Herbert; Paap, Trudy
Aphids in the genus Cinara (Hemiptera: Aphididae) are pests of coniferous trees globally. Some of these aphids have become invasive in various parts of the world and have led to significant economic and environmental damage. During surveys conducted as part of a sentinel plant project, severe aphid infestations were observed on Widdringtonia trees in the Kirstenbosch National Botanical Garden, Cape Town, South Africa. In addition, planted Widdringtonia wallichii Endl. ex Carrière trees within their natural range of the Cederberg Wilderness Area, Western Cape, South Africa were found infested with aphids. In this study, we investigated the species identity of the aphids using DNA sequence data for the mitochondrial cytochrome coxidase (COI) gene. The results revealed the presence of two closely related aphid species, the cypress aphid, Cinara cupressi (Buckton) and the cypress pine aphid, Cinara tujafilina (Del Guercio) infesting Widdringtonia spp. in South Africa. Both aphid species are alien to South Africa. While this is not the first report for either species in the country, the current study provides evidence of impact, with severe infestations leading to branch dieback and tree death. This finding supports the regulation of Cinara spp. in South Africa and highlights that management is urgently needed.
High genetic diversity and limited regional population differentiation in populations of Calonectria pseudoreteaudii from Eucalyptus plantations
(American Phytopathological Society, 2025-01) Li, WenWen; Liu, Feifei; Chen, ShuaiFei; Wingfield, Michael J.; Duong, Tuan A.
Calonectria pseudoreteaudii causes a serious and widespread disease known as Calonectria leaf blight in Eucalyptus plantations of southern China. Little is known regarding the population biology or reproductive biology of this pathogen in the affected areas. The aims of this study were to investigate the genetic diversity, population structure, and reproductive mode of C. pseudoreteaudii from affected Eucalyptus plantations of southern China. Ten polymorphic simple sequence repeat markers were developed for the species and were used to genotype 311 isolates from eight populations. The mating types of all isolates were identified using the MAT gene primers. The results revealed a high level of genetic diversity of the pathogen in all investigated populations. Of the 90 multilocus genotypes detected, 10 were shared between at least two populations. With the exception of one population from HuiZhou, GuangDong (7HZ), the most dominant genotype was shared in the seven remaining populations. Discriminant analysis of principal components and population differentiation analyses showed that the 7HZ population was well differentiated from the others and that there was no significant differentiation between the remaining populations. Analysis of molecular variance suggested that most molecular variation was within populations (86%). Index of association analysis was consistent with a predominantly asexual life cycle for C. pseudoreteaudii in the studied regions. Although both mating types were detected in seven of the eight populations, the MAT1-1/MAT1-2 ratios in these populations deviated significantly from the 1:1 ratio expected in a randomly mating population.
Advancing forest pathology : the need for community-driven molecular experimental model systems
(Wiley, 2025-08) Oostlander, Anne G.; Fleissner, Andre; Slippers, Bernard; bernard.slippers@fabi.up.ac.za
Forests world-wide are under escalating threat from emerging and invasive fungal and oomycete pathogens, driven by globalization and shifting climate dynamics. Effective strategies to manage the current scale and rate of changes in forest health remain hindered by our limited ability to study the underlying mechanisms of pathogen–host and pathogen–microbiome interactions, especially at a molecular and cellular level, compared to general plant pathology, where experimental and model systems exist. Such models facilitate the integration of diverse methodologies from a broader base of the research community, allowing for a more holistic and deeper examination of complex research questions. Here, we propose a framework for the development of such model systems also for forest pathology. This goal is more feasible than ever, thanks to rapid technological advancements, increasing open data availability and a globally interconnected research community. These factors create a unique opportunity to integrate ecosystem-focused research in forest pathology with a unified model organism strategy. Achieving this goal will require a dedicated community effort in the coming years, as such model systems are not discovered but built.
First report of pepper ringspot virus on potato (Solanum tuberosum) in South Africa
(Springer, 2025-05) Espach, A.; Esterhuizen, L.; Africander, N.; Thiart, S.; Read, David Alan; Pietersen, Gerhard
No abstract available.
Expanding ISME communications to taxonomy and nomenclature
(Oxford University Press, 2025-06) Chuvochina, Maria; Palmer, Marike; Venter, S.N. (Stephanus Nicolaas)
Research in microbial ecology is often accompanied by the classification and naming of new taxa, typically included as part of the results section of an ecological study. Bold and beautiful, Latin names are more than labels—they are essential tools for scientific communication. Nested within a hierarchical system, they populate public databases and enable researchers to search for organisms, retrieve associated sequences and metadata, and explore related taxa across various taxonomic levels. In recognition of the vital role that naming and classification play in ecological studies, ISME Communications is proud to introduce Taxonomy and Nomenclature as part of its scope.
First report of Clavibacter nebraskensis causing Goss's bacterial leaf blight on maize (Zea mays) in South Africa
(American Phytopathological Society, 2025-07) Coertze, Sonja; Coetzee, Beatrix; Basson, Elaine; De Villiers, Dore; Makhura, Tjitjila; Mostert, Diane; Slippers, Bernard; Rose, Lindy J.; Visagie, Cobus M.; Read, David Alan
No abstract available.
Host specificity and host stage preference of Psyllaephagus species (Hymenoptera: Encyrtidae) towards invasive eucalypt psyllids (Hemiptera: Aphalaridae)
(Wiley, 2025-08) Makunde, Privilege Tungamirai; Slippers, Bernard; Bush, Samantha J.; Hurley, Brett Phillip; privilege.makunde@up.ac.za
Invasive eucalypt psyllids pose a threat to the long-term production of eucalypts worldwide. In order to reduce their economic impact, classical biological control using Psyllaephagus species has been used successfully. The objectives of this study were to determine the host specificity and host stage preference of Psyllaephagus blastopsyllae, Psyllaephagus pilosus and Psyllaephagus bliteus using related eucalypt-feeding psyllids, Blastopsylla occidentalis, Ctenarytaina eucalypti, Glycaspis brimblecombei and Spondyliaspis cf. plicatuloides. To determine host specificity, three Psyllaephagus species were collected locally from their hosts. Five-day-old parasitoids were exposed to all five developmental stages (I–V) of host and non-host psyllids in choice and non-choice tests. Similar bioassays were used to assess parasitoid preferences for specific nymphal stages, identifying their preferred developmental stages of potential hosts. Glycaspis brimblecombei was identified as a potential host for P. blastopsyllae, and S. cf. plicatuloides as an alternate host for P. bliteus, though emergence rates were three to four times lower than for their known hosts. Psyllaephagus pilosus showed no interest in non-host psyllids. Female parasitoids displayed stage-specific preferences for both known and newly identified hosts. The current findings indicate that some Psyllaephagus species attack hosts within an ecological niche, whereas others are highly host specific. Additionally, the distinction between potential host range observed in laboratory conditions and ecological host range in field conditions should be considered, as laboratory tests typically exhibit a broader host range.
Pheromonal variation and mating between two mitotypes of fall armyworm (Spodoptera frugiperda) in Africa
(Nature Research, 2024) Sisay, Birhanu; Tamiru, Amanuel; Subramanian, Sevgan; Weldon, Christopher William; Khamis, Fathiya; Green, Kristina Karlsson; Anderson, Peter; Torto, Baldwyn
In the Americas, the fall armyworm (Spodoptera frugiperda) exists in two genetically distinct strains, the corn (C) and rice (R) strains. Despite their names, these strains are not associated with host plant preferences but have been shown to vary in pheromone composition and male responses. Recently, S. frugiperda was detected in Africa as an invasive species, but knowledge about variation in strain types, pheromone composition and inter-strain mating of populations of the pest in the continent has not been fully examined. Therefore, this study aimed to investigate variations, if any in the pheromone composition of female moths, male moth responses, and mating between C and R mitotypes of S. frugiperda populations in Kenya, as well as their geographic distribution. Strains (mitotypes) of S. frugiperda were identified using mitochondrial DNA (mtDNA) markers, and their pheromonal composition determined by coupled gas chromatography-mass spectrometric (GC-MS) analysis. Male moth responses to these compounds were evaluated using GC-electroantennographic detection (EAD), electroantennogram (EAG), and wind tunnel assays. Oviposition assays were used to determine whether R and C mitotype moths could mate and produce eggs. The results showed that both the R and C mitotypes were present, and there were no statistically significant differences in their distribution across all sampled locations. Five pheromone compounds including (Z)-7-dodecenyl acetate (Z7-12:OAc), (Z)-7-tetradecenyl acetate (Z7-14:OAc), (Z)-9-tetradecenyl acetate (Z9-14:OAc), (Z)-11-tetradecenyl acetate (Z11-14:OAc) and (Z)-11-hexadecenyl acetate (Z11-16:OAc), were detected in the pheromone glands of female moths of both mitotypes, with Z9-14:OAc being the most abundant. The relative percentage composition of Z9-14:OAc was similar in both mitotypes. However, the R mitotype had a 2.7 times higher relative percentage composition of Z7-12:OAc compared to the C mitotype moth, while the C mitotype moth had a 2.4 times higher relative percentage composition of Z11-16:OAc than the R mitotype moth. Male moths of both mitotypes exhibited similar responses to the pheromone compounds, showing the strongest responses to Z9-14:OAc and Z7-12:OAc in electrophysiological and behavioural assays. There was mating between R and C mitotypes with egg production comparable to mating within the same mitotype. Our results revealed that differences between the two S. frugiperda mitotypes are characterized by female moth pheromone composition rather than male moth responses to the pheromones, and that this does not prevent hybridisation between the mitotypes, which may have implications for their management.
The slow pandemic : emergence of antimicrobial resistance in the postadvent of SARS-CoV-2 pandemic
(Wiley, 2025-04) Osunla, Ayodeji; Oloye, Femi; Kayode, Adeoye John; Femi-Oloye, Oluwabunmi; Okiti, Ayomide; Servos, Mark; Giesy, John
BACKGROUND : The unprecedented outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has dramatically changed the global approach to public health, emphasizing the importance of measures to control and prevent infections. In response to the COVID-19 crisis, stringent hygiene practices and surface disinfection have become the norm, with an unprecedented surge in the use of disinfectants and antiseptics (DAs). MAIN TEXT : While these measures have been crucial in curbing the spread of the virus, an emerging concern has taken center stage: the potential impact of the prolonged and widespread use of antimicrobial compounds in these products on the development of antibiotic resistance. Antimicrobial resistance (AMR) has long been recognized as one of the most pressing global health threats. Quaternary ammonium compounds (QAC) such as benzalkonium chloride, benzethonium chloride, and cetylpyridinium chloride, which are extensively used in DAs formulations, have gained less attention in the context of AMR. CONCLUSION : A high abundance of QACs was detected in wastewater, and certain bacteria such as Pseudomonas aeruginosa, Acinetobacter baumannii, and Enterococcus species developed resistance to these compounds over time. We analyzed the available evidence from the scientific literature, examining the presence and concentrations of QACs in different water sources, and their resistance mechanisms. This review aimed to shed light on the multifaceted challenges that arise from the dual battle against the COVID-19 pandemic and the ongoing global fight against AMR.
Uncovering cryptic species diversity of Ophiocordyceps (Ophiocordycipitaceae) associated with Coleoptera from Thailand
(Westerdijk Fungal Biodiversity Institute, 2024-12) Mongkolsamrit, S.; Noisripoom, W.; Tasanathai, K.; Khonsanit, A.; Thanakitpipattana, D.; Lamlertthon, S.; Himaman, W.; Crous, Pedro W.; Stadler, M.; Luangsa-ard, J.J.
This study advances our understanding of Ophiocordyceps, an extensively studied entomopathogenic fungus within the Ophiocordycipitaceae, particularly in Thailand. We introduce seven novel species associated with Coleoptera - O. albostroma, O. brunnea, O. capilliformis, O. kohchangensis, O. phitsanulokensis, O. pseudovariabilis, and O. ratchaburiensis. Remarkably, O. brunnea, O. kohchangensis, and O. ratchaburiensis exhibit ascomata on the subterminal region of the stromata, with the asexual form appearing at the apex of the stipe, reminiscent of O. brunneipunctata. In contrast, O. phitsanulokensis produces its ascomata in the upper region of the stipe. Shared traits include immersed perithecia and part-spores production. Ophiocordyceps albostroma and O. pseudovariabilis produce pseudo-immersed perithecia, with the former producing ascospores breaking into four part-spores, and the latter displaying 32 part-spores. Ophiocordyceps capilliformis is also introduced due to morphological distinctions from closely related species. Phylogenetic analyses based on multigene loci (LSU, TEF1, RPB1, RPB2) robustly confirm the placement of these new species within Ophiocordyceps. Additionally, we report a new record of O. clavata in Thailand.
A phylogenetic assessment of Akanthomyces sensu lato in Cordycipitaceae (Hypocreales, Sordariomycetes) : introduction of new genera, and the resurrection of Lecanicillium
(Westerdijk Fungal Biodiversity Institute, 2024-12) Khonsanit, A.; Thanakitpipattana, D.; Mongkolsamrit, S.; Kobmoo, N.; Phosrithong, N.; Samson, R.A.; Crous, Pedro W.; Luangsa-ard, J.J.
During entomopathogenic fungal surveys conducted in Thailand, 15 specimens tentatively classified under Akanthomyces sensu lato were identified. To gain a comprehensive understanding of their taxonomy, molecular phylogenies using combined LSU, TEF1, RPB1, and RPB2 sequence data, together with morphological examination of several Akanthomyces spp. from previous studies were conducted. The analyses revealed distinct clades representing independent lineages within the Cordycipitaceae. These clades were further characterized by different asexual morph types and the respective hosts they parasitize. In this context, we resurrected the genus Lecanicillium to accommodate 12 known species previously classified under Akanthomyces sensu lato, found on diverse hosts. We propose four new genera - Corniculantispora, Corpulentispora, Zarea, and Zouia - from species previously identified as Lecanicillium. Notably, certain Akanthomyces species associated with spiders and parasitic on Ophiocordyceps sinensis were reclassified into the new genera Arachnidicola and Kanoksria, respectively. Moreover, we introduce four novel species in Akanthomyces sensu stricto found across a diverse range of moth families: Ak. buriramensis, Ak. fusiformis, Ak. niveus, and Ak. phariformis. Additionally, we provide descriptions and illustrations of the sexual morph linked to Ak. laosensis and Ak. pseudonoctuidarum, along with a second type of synnemata seen in Ak. noctuidarum and Ak. pseudonoctuidarum. To assist with their identification, keys to the genera Akanthomyces, Arachnidicola, and Lecanicillium are provided, but should not be used to replace molecular identification
Endophytic diaporthe species from Brazil
(Westerdijk Fungal Biodiversity Institute, 2024-12) Ferro, L.O.; Bezerra, J.D.P.; Da Silva, T.M.; De Oliveira, C.S.; Nascimento, S.dosS.; Paiva, L.M.; Fan, x.; Crous, Pedro W.; Souza-Motta, C.M.
Diaporthe species can inhabit various hosts with different lifestyles and live as endophytes, pathogens, and saprobes. Our study analysed 180 endophytic Diaporthe isolates from Miconia sp. in the Atlantic Forest, Brosimum gaudichaudii in the Brazilian savanna (Cerrado), and Anacardium occidentale in the Caatinga forest and Cerrado in Brazil. Based on multi-locus phylogenetic analyses [β-tubulin (tub2), internal transcribed spacer regions and intervening 5.8S rRNA (ITS), translation elongation factor 1-alpha (tef1), calmodulin (cmdA), and histone (his3)] and morphological features, we are introducing seven new species (D. azevedoi, D. catimbauensis, D. coracoralinae, D. luizorum, D. pedratalhadensis, D. samambaiaensis, and D. vargemgrandensis) and reporting seven known species (D. fructicola, D. inconspicua, D. infertilis, D. paranensis, D. raonikayaporum, D. schini, and D. ueckeri). We also included a morphological description of D. infertilis and synonymised D. lutescens, D. pseudoinconspicua, and D. samaneae under D. inconspicua; D. neoraonikayoporum under D. raonikayaporum; and D. passifloricola, D. rosae, and D. vochysiae under D. ueckeri, based on limited nucleotide differences among DNA sequence data and overlapping morphological features. Our results highlight the importance of including endophytic isolates in the phylogeny of Diaporthe, and show how these data expand the geographic distribution and host relationships of known species.
First record of the white root rot fungus Dematophora necatrix on indigenous South African trees
(Springer, 2025-05) Balocchi, Felipe; Wingfield, Michael J.; Paap, Trudy; felipe.balocchi@fabi.up.ac.za
The soilborne fungus Dematophora (=Rosellinia) necatrix and causal agent of white root rot, has a wide host range that includes many tree species of economic importance. The pathogen has a worldwide distribution, including reports from commercial orchards in South Africa since the 1970s. During tree health surveys conducted as part of a sentinel plant project, we detected the pathogen on two symptomatic individuals from the indigenous South African tree species Diospyros whyteana and Noronhia foveolata subsp. major. Observed symptoms included wilting and root rot, with characteristic white mycelium present under the bark. Dematophora necatrix was isolated from both hosts and its identity confirmed by sequencing two gene regions (ITS and actin). Pathogenicity was confirmed through inoculation tests under semi-controlled conditions by inoculating the soil with bamboo sticks colonized with the fungus. Plants of both species developed similar symptoms to those observed naturally, and the fungus was successfully recovered from all symptomatic plants. This is the first record in South Africa of D. necatrix on indigenous species and outside of commercial orchards. Given the environmental threat posed we recommend the fungus is considered for regulation in South Africa.
Advanced analysis of single-molecule spectroscopic data
(Cell Press, 2024-09) Botha, Joshua Leon; Van Heerden, Bertus; Kruger, T.P.J. (Tjaart); tjaart.kruger@up.ac.za
We present Full SMS, a multipurpose graphical user interface (GUI)-based software package for analyzing single-molecule spectroscopy (SMS) data. SMS typically delivers multiparameter data—such as fluorescence brightness, lifetime, and spectra—of molecular- or nanometer-scale particles such as single dye molecules, quantum dots, or fluorescently labeled biological macromolecules. Full SMS allows an unbiased statistical analysis of fluorescence brightness through level resolution and clustering, analysis of fluorescence lifetimes through decay fitting, as well as the calculation of second-order correlation functions and the display of fluorescence spectra and raster-scan images. Additional features include extensive data filtering options, a custom HDF5-based file format, and flexible data export options. The software is open source and written in Python but GUI based so it may be used without any programming knowledge. A multi-process architecture was employed for computational efficiency. The software is also designed to be easily extendable to include additional import data types and analysis capabilities.
Molecular epidemiology of carbapenemase‑producing Klebsiella pneumoniae in Gauteng South Africa
(Nature Research, 2024-11-09) Salvador-Oke, Kafilat Taiwo; Pitout, Johann D.D.; Peirano, Gisele; Strydom, Kathy‑Anne; Kingsburgh, Chanel; Ehlers, Marthie Magdaleen; Ismail, Arshad; Takawira, Faustinos T.; Kock, Marleen M.; marleen.kock@up.ac.za
Klebsiella pneumoniae multidrug-resistant (MDR) high-risk clones drive the spread of antimicrobial resistance (AMR) associated infections, resulting in limited therapeutic options. This study described the genomic characteristics of K. pneumoniae MDR high-risk clones in Gauteng, South Africa. Representative carbapenem-resistant [K. pneumoniae carbapenemase (KPC)-2, New-Delhi metallo-beta (β)-lactamase (NDM)-1, oxacillinase (OXA)-181, OXA-232, OXA-48, Verona integron-encoded metallo-β-lactamase (VIM)-1] K. pneumoniae isolates (n = 22) obtained from inpatient and outpatient’s urine (n = 9) and inpatients rectal carriage (n = 13) were selected for short-read whole genome sequencing. Klebsiella pneumoniae population include sequence type (ST)-307 (n = 3), ST2497 (n = 5) and ST17 (n = 4). The ST17 strains were exclusively obtained from rectal screening. Ten isolates co-harboured carbapenemase genes including β-lactamase gene encoding KPC-2 + OXA-181, NDM-1 + OXA-48 and NDM-1 + OXA-181. One ST307 isolate (UP-KT-73CKP) co-harboured three carbapenemase genes (blaNDM-1 + blaOXA-48 + blaOXA-181), while all the ST2497 strains co-harboured (blaNDM-1 + blaOXA-232). Phenotypically, hypermucoviscosity was observed in a single ST307 isolate. The ST307 isolate UP-KT-151UKP harboured colibactin genotoxins. The following mobile genetic elements were detected: plasmids [incompatibility group (Inc)-FIB(K), IncX3], and bacteriophages [e.g. Klebsi_ST16_OXA48phi5.4_NC_049450, Klebsi_3LV2017_NC_047817(36)]. The study highlights the importance of local genomic surveillance systems to characterise K. pneumoniae MDR high-risk clones. This data will aid in designing infection and prevention measures for limiting the spread of carbapenemase-producing K. pneumoniae in Gauteng, South Africa.
Maize edible‑legumes intercropping systems for enhancing agrobiodiversity and belowground ecosystem services
(Nature Research, 2024-06-21) Jalloh, Abdul A.; Mutyambai, Daniel Munyao; Yusuf, Abdullahi Ahmed; Subramanian, Sevgan; Khamis, Fathiya
Intensification of staple crops through conventional agricultural practices with chemical synthetic inputs has yielded positive outcomes in food security but with negative environmental impacts. Ecological intensification using cropping systems such as maize edible-legume intercropping (MLI) systems has the potential to enhance soil health, agrobiodiversity and significantly influence crop productivity. However, mechanisms underlying enhancement of biological soil health have not been well studied. This study investigated the shifts in rhizospheric soil and maize-root microbiomes and associated soil physico-chemical parameters in MLI systems of smallholder farms in comparison to maize-monoculture cropping systems (MMC). Maize-root and rhizospheric soil samples were collected from twenty-five farms each conditioned by MLI and MMC systems in eastern Kenya. Soil characteristics were assessed using Black oxidation and Walkley methods. High-throughput amplicon sequencing was employed to analyze fungal and bacterial communities, predicting their functional roles and diversity. The different MLI systems significantly impacted soil and maize-root microbial communities, resulting in distinct microbe sets. Specific fungal and bacterial genera and species were mainly influenced and enriched in the MLI systems (e.g., Bionectria solani, Sarocladium zeae, Fusarium algeriense, and Acremonium persicinum for fungi, and Bradyrhizobium elkanii, Enterobacter roggenkampii, Pantoea dispersa and Mitsuaria chitosanitabida for bacteria), which contribute to nutrient solubilization, decomposition, carbon utilization, plant protection, bio-insecticides/fertilizer production, and nitrogen fixation. Conversely, the MMC systems enriched phytopathogenic microbial species like Sphingomonas leidyi and Alternaria argroxiphii. Each MLI system exhibited a unique composition of fungal and bacterial communities that shape belowground biodiversity, notably affecting soil attributes, plant well-being, disease control, and agroecological services. Indeed, soil physico-chemical properties, including pH, nitrogen, organic carbon, phosphorus, and potassium were enriched in MLI compared to MMC cropping systems. Thus, diversification of agroecosystems with MLI systems enhances soil properties and shifts rhizosphere and maize-root microbiome in favor of ecologically important microbial communities.
Influence of season, sex, and interspecific interactions on the diel activity patterns of two sympatric African small carnivores
(Nature Research, 2024-11-29) Carvalho, Filipe; Galantinho, Ana; Somers, Michael J.; Do Linh San, Emmanuel
Animal activity patterns vary seasonally and between species, facilitating species coexistence. In Africa, however, factors affecting the activity of many small carnivores remain poorly understood, especially for congeneric and sympatric species whose similar sizes may lead to interspecific competition. Here, we investigated differences and variations in the activity patterns of two sympatric Viverridae species in a seasonal African landscape. We continuously radio-tracked 15 small-spotted genets (Genetta genetta) and five Cape genets (G. tigrina) over 24-h cycles throughout the year. We analysed the effects of season, sex, and interspecific interactions on circadian rhythms using multi-cosinor regression models. Both species maintained a nocturnal activity pattern year-round, decreasing activity significantly during the cold-dry season. This pattern aligns with the thermoregulatory hypothesis—especially for species with an elongated body like genets—suggesting decreased activity under extreme cold weather conditions to conserve energy. Females in both species were less active than males, possibly due to their smaller home ranges, especially during the cold-dry season. These effects were particularly pronounced in Cape genets, which primarily inhabit riverine forests. Female Cape genets adjusted their activity onset, possibly to minimize encounters with males, mostly during the hot-wet season when caring for their offspring. Small-spotted genets shifted their activity onset and peak in riverine forests—areas of potential contact with Cape genets—compared to areas without Cape genets. Overall, our study underscores the critical role of seasonal environmental changes and interspecific interactions in shaping the activity patterns of two carnivore species within a semi-arid Albany Thicket landscape.

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