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

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Diversity and functionality of soil prokaryotic communities in antarctic volcanic soils : insights from penguin-influenced environments
(Springer, 2024-09) Segura, Diego; Jordaan, Karen; Diez, Beatriz; Tamayo-Leiva, Javier; Doetterl, Sebastian; Wasner, Daniel; Cifuentes-Anticevic, Jeronimo; Casanova-Katny, Angelica
In the nutrient-limited Antarctic terrestrial habitat, penguins transfer a significant amount of nutrients from the marine to the terrestrial ecosystem through their depositions (i.e., guano). This guano influences soil physicochemical properties, leading to the formation of ornithogenic soil rich in nutrients and organic matter. We hypothesize that soil prokaryotic communities will be strongly influenced by the contribution of nitrogenous nutrients from penguin rookeries, maintaining the influence over long distances. The objective was to establish how the soil prokaryotic diversity and community structure change with distance from a penguin colony, which provides large amounts of guano and nitrogenous compounds, and to study the effects of these nutrients on the functional role of these communities. Methods include volcanic soil sampling along a 1200 m transect from the penguin active rookery and the characterization of soil nutrient content and soil prokaryotic communities using 16S rRNA high-throughput amplicon sequencing. In contrast to our hypothesis, the results showed that the impact of guano from the penguin colony was restricted to the first 300 m. Probably because the penguin rookery was sheltered, strong wind and wind direction did not affect the transport of nutrients from the penguin rookery. Areas close to the penguin rookery were dominated by Proteobacteria and Bacteroidetes, while areas situated further away were dominated by Acidobacteria, Actinobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, and Planctomycetes. Beta diversity analysis among the soil prokaryotic communities revealed a high degree of community heterogeneity, strongly associated with N compound characteristics (NH4, NO3, and %N), C, and pH. Inferences from N metabolism genes suggest a high potential of the microbial community for dissimilatory nitrate reduction genes (DNRA) to ammonium, assimilatory nitrate reduction (ANR), and denitrification. Although it is assumed that the nitrogenous compounds of the penguin colonies reach long distances and affect the prokaryotic community, this effect can vary with wind directions or the morphology of the site, reducing the impact of the guano over long distances, as our results indicate. On the other hand, functional predictions give some clues about the main actors in nitrogen cycling, through processes like dissimilatory nitrate reduction, assimilatory nitrate reduction, and denitrification.
Carbon dynamics in termite mounds : the effect of land use on microbial oxalotrophy
(Elsevier, 2025-06) Nel, Teneille; Clarke, Catherine E.; Francis, Michele L.; Babenko, Darya; Botha, Alf; Breecker, Daniel O.; Cowan, Don A.; Gallagher, Timothy; Lebre, Pedro Humberto; McAuliffe, Joseph R.; Reinhardt, Alyssa N.; Trindade, Marla
The semi-arid western region of South Africa hosts extensive earthen mounds known as heuweltjies, which are inhabited by Microhodotermes viator termites and play a critical role in soil biogeochemical cycling. These mounds accumulate significant stores of soil organic and inorganic carbon (C), including pedogenic calcium carbonate, which may form through microbially induced calcite precipitation. In this study, the effects of land use change on C dynamics in heuweltjie soils were assessed by examining soil biogeochemistry and apparent respiratory quotient (ARQ, based on soil pore gas composition). We investigated the oxalate-carbonate pathway (OCP) as a potential mechanism of C sequestration. Topsoils were collected from one pristine and one cultivated termite mound in a semi-arid region of South Africa and incubated for one week. The carbon dioxide (CO2) and oxygen concentrations of soil pore gas as well as chemical properties of soils treated with termite frass (excrement) or calcium oxalate (CaOx) were monitored. Increases in pH and the calcite saturation index in both CaOx- and frass-treated soils suggested the potential occurrence of the OCP. The ARQ values did not reflect geochemical changes associated with OCP due to competing metabolic pathways, such as potential lignin degradation in frass-treated soils. Higher ARQ values in uncultivated versus cultivated CaOx-treated soils may indicate higher carbon use efficiency in uncultivated soils or destabilization of existing C in cultivated soils. Respiration in frass-treated soils was higher than control and CaOx-treated soils and resulted in production of bicarbonate (via dissociation of carbonic acid formed by dissolution of respired CO2 in water). This implies that termite-affected landscapes may sequester C in inorganic form. Increased total C in both cultivated and uncultivated soils treated with frass suggests that microbial CO2-fixation may occur in termite-affected landscapes, necessitating further investigation of pathways responsible for this process. HIGHLIGHTS • Frass of Microhodotermes viator increased fertility of termite mound soils. • Microbial respiration increased dissolved carbon concentrations in soils. • Calcite saturation index increased in soils supplemented with calcium oxalate. • Lower respiratory quotients may suggest degradation of lignin in frass. • Cultivation may destabilize organic matter and reduce microbial biomass production.
Application of monoclonal anti-mycolate antibodies in serological diagnosis of tuberculosis
(MDPI, 2024-11-06) Truyts, Alma; Du Preez, Ilse; Maesela, Eldas M.; Scriba, Manfred R.; Baillie, Les; Jones, Arwyn T.; Land, Kevin J.; Verschoor, Jan Adrianus; Lemmer, Yolandy; jan.verschoor@up.ac.za
Patient loss to follow-up caused by centralised and expensive diagnostics that are reliant on sputum is a major obstacle in the fight to end tuberculosis. An affordable, non-sputum biomarker-based, point-of-care deployable test is needed to address this. Serum antibodies binding the mycobacterial cell wall lipids, mycolic acids, have shown promise as biomarkers for active tuberculosis. However, anti-lipid antibodies are of low affinity, making them difficult to detect in a lateral flow immunoassay—a technology widely deployed at the point-of-care. Previously, recombinant monoclonal anti-mycolate antibodies were developed and applied to characterise the antigenicity of mycolic acid. We now demonstrate that these anti-mycolate antibodies specifically detect hexane extracts of mycobacteria. Secondary antibody-mediated detection was applied to detect the displacement of the monoclonal mycolate antibodies by the anti-mycolic acid antibodies present in tuberculosis-positive guinea pig and human serum samples. These data establish proof-of-concept for a novel lateral flow immunoassay for tuberculosis provisionally named MALIA—mycolate antibody lateral flow immunoassay.
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.
Unveiling the hidden allies in the fight against antimicrobial resistance—medicinal plant endophytes
(MDPI, 2025-06) Kayode, Adeoye John; Igwaran, Aboi; Banji-Onisile, Folasade; Akwu, Nneka A.; Unuofin, John O.; Osunla, Ayodeji C.; Egbewale, Samson O.; Purnobasuki, Hery
Medicinal plants have long been a vital source of various natural products in the form of pure compounds or standardized extracts. The World Health Organization estimated that 80% of populations in Africa, Asia, and Latin America rely on traditional medicine for primary health care. In recent decades, endophytic microorganisms living within plants have gained attention for their ability to produce bioactive compounds with significant therapeutic potential. This review explores the diversity of medicinal plant endophytes, focusing on their pharmacological significance, including antimicrobial, anticancer, antidiabetic, and antioxidant properties. Additionally, we discuss the application of nanotechnology and computational tools in enhancing the potency and screening of endophyte-derived metabolites. Despite the promising potential, challenges such as scalability, safety, and commercial viability remain. Future research should prioritize optimizing production, elucidating biosynthetic pathways, and integrating advanced technologies to effectively harness these bioactive compounds for novel drug development.
Soil functions are shaped by aridity through soil properties and the microbial community structure
(Elsevier, 2025-09) Domenech-Pascual, Anna; Rodriguez, Luciana Chavez; Han, Xingguo; Casas-Ruiz, Joan Pere; Ferriol-Ciurana, Joan; Donhauser, Jonathan; Jordaan, Karen; Allison, Steven D.; Frossard, Aline; Prieme, Anders; Ramond, Jean-Baptiste; Romani, Anna M.
Increasing aridity poses a threat to soil functionality, as it affects the key players -prokaryotes and fungi- responsible for these functions. Studying microbial diversity and functions in soils from different aridity conditions is crucial to understanding potential adaptations and response mechanisms to climate change, which may ultimately affect soil ecosystem multifunctionality. Here, we used a natural humid-to-arid climate gradient to determine: (1) if and how soil functions and microbial communities change across the aridity gradient; and (2) the main drivers of soil function variability along the gradient. We sampled soils (0–10 cm depth) from 12 sites across the Iberian Peninsula and analyzed their prokaryotic and fungal diversity and biomass as well as soil functions (aerobic respiration and extracellular enzyme activities linked to organic carbon, nitrogen and phosphorus degradation), together with soil physicochemical characteristics. Our results showed that increasing aridity resulted in a gradual change in the microbial community structure and a decrease in fungal diversity. However, soil functions did not show clear changes in response to aridity itself. Instead, microbial respiration and enzyme activities depended mainly on the local soil properties (i.e. organic matter quantity and quality, soil texture and pH) rather than on aridity. Overall, results indicated that in long-term climate-adapted soils, microbial functions are primarily driven by soil edaphology with aridity influencing them indirectly by shaping the microbial community composition and the intrinsic soil characteristics. HIGHLIGHTS • Aridity directly shapes soil microbial structure but not soil functionality. • Functional redundancy may support microbial functional resistance to aridity. • Soil functions main drivers are related to organic matter or soil texture variables.
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.
Polyploid-diploid coexistence in the greater duckweed Spirodela polyrhiza
(Wiley, 2025) Mortier, Frederik; Van de Peer, Yves; Bonte, Dries
Polyploidy is widespread among plants and is often associated with stressful environments that can facilitate their establishment. Successful new polyploids must overcome competitive disadvantages against their progenitors or benefit from negative frequency-dependent growth. We tested the invasion of neotetraploid duckweed strains (Spirodela polyrhiza) into populations of their diploid progenitors in control and salt stress conditions in replicated microcosms. We also tested the reverse scenario: invasion of diploids in neotetraploid populations, to examine the impact of the initial tetraploid proportion. Tetraploid proportions declined in all tetraploid and diploid invasions, with different rates than predicted from only intrinsic growth rate differences. Salt stress affected the decline in a strain-specific manner. We found evidence for negative frequency-dependent growth that, nonetheless, was insufficient to overcome competitive disadvantages of neopolyploids. SYNTHESIS. Our findings demonstrate the crucial role of competition and frequency dependence on neopolyploid establishment. Therefore, we caution against inferring neopolyploid success based solely on intrinsic growth rates.
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.
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.
In silico docking and ADMET studies on clinical targets for type 2 diabetes correlated to in vitro inhibition of pancreatic alpha-amylase and alpha-glucosidase by rutin, caffeic acid, p-coumaric acid, and vanillin
(Springer, 2025-03) Mcmillan, Jamie; Bester, Megan Jean; Apostolides, Zeno; u16016760@tuks.co.za
Please read abstract in the article.
The population genetic structure of Ficus craterostoma in South Africa
(Elsevier, 2025-03) Deng, Jun-Yin; Van Noort, Simon; Compton, Stephen G.; Chen, Yan; Greeff, Jacobus Maree; jaco.greeff@up.ac.za
In the eastern part of its distribution, Ficus craterostoma occurs in Afromontane forests whereas it also occurs in low-lying scarp and Indian Ocean coastal belt forests in South Africa. Ficus craterostoma must have dispersed to these low-lying forests from the Afromontane forests, even though forests became highly fragmented during the Pleistocene. To understand how these ancient changes have impacted the distribution and population structure of F. craterostoma we quantified the genetic variation in its slow-evolving chloroplast DNA with limited dispersal ability via seeds, and its highly variable nuclear microsatellites that reflect exceptional pollen flow. The chloroplast variation was highly structured and frequently monomorphic in nearby forests while the nuclear variation showed little structure and isolation by distance. From these data we reach several conclusions. Ficus craterostoma may have become extinct from South Africa's northern Afromontane forests during the Pleistocene. These forests were possibly subsequently recolonized from southern forests that may have been scarp or Afromontane in nature. Additionally, there was one scarp and one Indian Ocean coastal belt forest refugium, both of which were very isolated and small. Nuclear gene flow caused by pollen flow is very effective along the western part of the South African population, knitting together Afromontane and scarp forest fragments, dispersed over 1000 km, into one genetic population. Conversely, the Indian Ocean coastal belt forest refugium appears to have been isolated in terms of gene flow, but more recent gene flow with two nearby inland forests may have started to homogenize their genetic variation. Due to the unusual pollination system of fig trees, other forest tree species may display very different dynamics. HIGHLIGHTS • In South Africa Ficus craterostoma inhabits Afromontane, scarp and coastal forests. • Genetic data suggest that F. craterostoma was affected profoundly by the ice ages. • Large F. craterostoma populations survived in southern scarp forests. • This tree may have recolonized Afromontane forests from the south. • Coastal forest populations of F. craterostoma are isolated and unique.
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.
Multilocus sequence typing and antimicrobial susceptibility of Listeria monocytogenes isolated from foods surveyed in Kosovo
(MDPI, 2024-12) Jashari, Besart; Stessl, Beatrix; Felix, Benjamin; Cana, Armend; Bisha, Bledar; Jankuloski, Dean; Blagoevska, Katerina; Kayode, Adeoye John
In the absence of data on the reporting of L. monocytogenes resistance to antibiotics, we sought to determine which clonal complexes (CCs)/sequence types (STs) circulate in the food chain in Kosovo and to determine their antibiogram profiles to a panel of 18 antibiotics. From a total of 114 isolates, 21 different typical STs were identified by multilocus sequence typing (MLST). Each isolate derived from the food categories was subjected to tests to verify its susceptibility to the selected antibiotics according to the designed Sensititre GPN3F panel. Among the different STs that were identified, CC9-ST9 was more abundant in meat products (38.75%) while CC29-ST29 was more abundant (24.0%) in dairy products. Moreover, these isolates showed marked resistance against levofloxacin (22.8%), gentamicin and rifampicin (17.5%), quinupristin/dalfopristin (14.9%), erythromycin (11.4%), penicillin (7.89%), tetracycline (1.75%), and streptomycin (0.88%). A total of 27 multiple antibiotic resistance (MAR) phenotypes were observed amongst the isolates, which ranged from 3 to 12. The ARI of the food category including meat and meat products (MMP, 0.22) and fish meat products (FMP, 0.26) were >0.2, the permissible Krumperman threshold. The number of strains with MAR values >0.2 was 34, (29.8%). The identification of typical multidrug-resistant STs among L. monocytogenes isolates in Kosovo constitutes a potential threat to food safety and public health, which requires
Synergizing ecotoxicology and microbiome data is key for developing global indicators of environmental antimicrobial resistance
(Springer, 2024-12) Makumbi, John Paul; Leareng, Samuel K.; Pierneef, Rian Ewald; Makhalanyane, Thulani Peter
The One Health concept recognises the interconnectedness of humans, plants, animals and the environment. Recent research strongly supports the idea that the environment serves as a significant reservoir for antimicrobial resistance (AMR). However, the complexity of natural environments makes efforts at AMR public health risk assessment difficult. We lack sufficient data on key ecological parameters that influence AMR, as well as the primary proxies necessary for evaluating risks to human health. Developing environmental AMR ‘early warning systems’ requires models with well-defined parameters. This is necessary to support the implementation of clear and targeted interventions. In this review, we provide a comprehensive overview of the current tools used globally for environmental AMR human health risk assessment and the underlying knowledge gaps. We highlight the urgent need for standardised, cost-effective risk assessment frameworks that are adaptable across different environments and regions to enhance comparability and reliability. These frameworks must also account for previously understudied AMR sources, such as horticulture, and emerging threats like climate change. In addition, integrating traditional ecotoxicology with modern ‘omics’ approaches will be essential for developing more comprehensive risk models and informing targeted AMR mitigation strategies.

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