Purpose The microbiome is increasingly recognised as a contributor to pancreatic ductal adenocarcinoma (PDAC) pathogenesis, presenting opportunities for biomarker discovery and therapeutic intervention. Characterising microbial signatures associated with PDAC could improve early detection to improve survival outcomes. Experimental Design While previous studies on the PDAC microbiome have focused primarily on faecal samples, this study employed 16S rRNA gene amplicon sequencing to profile the bacteriome across 226 biospecimens ( n = 111 PDAC, n = 115 control) collected from the mouth, stomach, duodenum, bile and pancreas. We assessed alpha and beta diversity, taxonomic composition, relative abundance and prevalence of bacterial communities across these upper gastrointestinal tract sites. Results Microbial diversity was significantly higher in the PDAC cohort, particularly in the stomach, duodenum and bile, with the latter showing unexpectedly high richness. While five dominant phyla (Pseudomonadota, Bacillota, Actinomycetota, Bacteroidota and Fusobacteriota) were shared between cohorts, the PDAC cohort harboured a greater number of unique low‐abundance taxa and displayed distinct site‐specific microbial profiles compared with control samples. Notable microbial shifts included enrichment of Pseudomonas , Acinetobacter , Geobacillus and Corynebacterium , genera previously implicated in inflammation, immune modulation and tumour persistence. Microbial clustering was strongly influenced by anatomical site and moderately by ethnicity, suggesting complex host–microbiome interactions in PDAC. Conclusions This study demonstrates distinct, site‐specific microbial variation in PDAC and supports an association for the microbiome in PDAC development and progression, warranting further mechanistic investigation.

Barley grain quality is influenced by nitrogen content and storage conditions; however, their impact on the composition and function of the grain microbiome is not well understood. This study combined metataxonomic (16S rRNA and ITS) profiling, metagenome sequencing, and metaproteome analyses to characterize the structure and function of the barley grain microbiome. Grains with high (> 1.5%) and low (< 1.5%) nitrogen content from a single barley cultivar (Kadie) were sampled at harvest and after 3, 6, and 9 months of storage. Amplicon sequencing revealed a community dominated by Proteobacteria, Firmicutes, and Ascomycota, while metagenomics confirmed the abundance of genera such as Erwinia, Pantoea, and Pseudomonas, aligning with previous reports of barley endophytes. While a consistent set of core microbial genera was identified, their relative abundances varied throughout storage. Metagenomic analysis revealed the high-nitrogen grain microbiome had potential for rapid metabolic activity that declined post-harvest, whereas the low nitrogen grain community sustained prolonged metabolic potential. Metaproteomics confirmed that these functional shifts revealed a temporal transition from active growth to stress tolerance. Findings from this work contribute to a better understanding of the barley grain microbiome during prolonged storage, offering insights that could help optimize storage for malting and brewing.

The Southern Ground Hornbill (SGH – Bucorvus leadbeateri) is one of the largest hornbill species worldwide, known for its complex social structures and breeding behaviours. This bird has been of great interest due to its declining population and disappearance from historic ranges in southern Africa. Despite being the focus of numerous conservation efforts, with research forming an integral part of these initiatives, there is still a substantial lack of knowledge regarding the molecular biology aspects of this bird species. In this study, whole genome sequencing of the SGH was achieved using Illumina short-read (NovaSeq 6000) and Pacific Biosciences long-read technologies. A hybrid de novo genome assembly followed by reference-based refinement produced a 1.16 Gb high-quality draft genome assembly of the SGH comprised of 1,672 contigs (N50 value of 40.45 Mb). The availability of this genome will aid in improving our current understanding of this bird at a genomic level and provide a pivotal foundation for comparative genomic analysis with other hornbill species.

Cryptococcus gattii and its medical implications have been extensively studied. There is, however, a significant knowledge gap regarding cryptococcal survival in its environmental niche, namely woody material, which is glaring given that infection is linked to environmental populations. A gene from C. gattii (WM276), the predominant global molecular type (VGI), has been sequenced and annotated as a putative cellulase. It is therefore, of both medical and industrial intertest to delineate the structure and function of this enzyme. A homology model of the enzyme was constructed as a fusion protein to a maltose binding protein (MBP). The CGB_E4160W gene was overexpressed as an MBP fusion enzyme in Escherichia coli T7 cells and purified to homogeneity using amylose affinity chromatography. The structural and functional character of the enzyme was investigated using fluorescence spectroscopy and enzyme activity assays, respectively. The optimal enzyme pH and temperature were found to be 6.0 and 50 °C, respectively, with an optimal salt concentration of 500 mM. Secondary structure analysis using Far-UV CD reveals that the MBP fusion protein is primarily α-helical with some β-sheets. Intrinsic tryptophan fluorescence illustrates that the MBP-cellulase undergoes a conformational change in the presence of its substrate, CMC-Na+. The thermotolerant and halotolerant nature of this particular cellulase, makes it useful for industrial applications, and adds to our understanding of the pathogen's environmental physiology.

Barley (Hordeum vulgare) is essential to global food systems and the brewing industry. Its physiological traits and microbial communities determine malt quality. Although microbes influence barley from seed health to fermentation, there is a gap in metagenomic insights during seed storage. Crucially, elucidating the changes in microbial composition associated with barley seeds is imperative for understanding how these fluctuations can impact seed health and ultimately, influence both agricultural yield and quality of barley-derived products. Whole metagenomes were sequenced from eight barley seed samples obtained at different storage time points from harvest to nine months. After binning, 82 metagenome-assembled genomes (MAGs) belonging to 26 distinct bacterial genera were assembled, with a substantial proportion of potential novel species. Most of our MAG dataset (61%) showed over 90% genome completeness. This pioneering barley seed microbial genome retrieval provides insights into species diversity and structure, laying the groundwork for understanding barley seed microbiome interactions at the genome level.

© The Author(s) 2022. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http:// creat iveco mmons. org/ licen ses/ by/4. 0/. IMA GENOME‐F 16A Draft genome assembly of Fusarium marasasianum Introduction Many plants are thought to have at least one Fusariumassociated disease with more than 80% of economically important plants affected by at least one Fusarium disease (Leslie and Summerell 2006). The socioeconomic importance of Fusarium is particularly evident when considering the Fusarium fujikuroi species complex (FFSC, sensu Geiser et al. 2021). This monophyletic group contains 65 species and numerous cryptic species (Yilmaz et al. 2021). More than 50 species in the FFSC have publicly available genomes (www. ncbi. nlm. nih. gov), indicative of their economic importance. A number of recent studies showed that the FFSC complex contains four large clades (Herron et al. 2015; Sandoval-Denis et al. 2018; Yilmaz et al. 2021). One of these corresponds to the so-called “American” clade that was initially proposed to reflect the biogeography of the species it contains (O’Donnell et al. 1998). For example, Fusarium circinatum, the pine pitch canker pathogen, is thought to be native to Mexico and Central America (Drenkhan et al. 2020), where it likely co-evolved with its Pinus hosts (Herron et al. 2015; O’Donnell et al. 1998; Wikler and Gordon 2000). The American clade also includes five additional species associated with Pinus species in Colombia. These species are F. fracticaudum, F. pininemorale, F. parvisorum, F. marasasianum, and F. sororula, of which F. parvisorum, F. marasasianum, and F. sororula displayed levels of pathogenicity that were comparable to those of F. circinatum on susceptible Pinus species (Herron et al. 2015). The risk that the various American clade species pose to forestry in Colombia and globally has provided the impetus for projects aiming to sequence their genomes. To complement the genomic resources available for F. circinatum (Fulton et al. 2020; van der Nest et al. 2014a; Van Wyk et al. 2018; Wingfield et al. 2012, 2018a), the genomes of F. pininemorale (Wingfield et al. 2017), F. fracticaudum (Wingfield et al. 2018b) and F. sororula (van der Nest et al. 2021) have been published. Here we present the whole genome sequence for the pine pathogen F. marasasianum, named after the late South African professor Walter “Wally” F.O. Marasas (Wingfield and Crous 2012) who specialised in the taxonomy of Fusarium species and their associated mycotoxins.

Mobile genetic elements (MGEs) contribute to instability of the host genome and plasmids. Previously, removal of the prophages in the industrial amino acid producer Corynebacterium glutamicum ATCC 13 032 resulted in strain MB001 which showed better survival under stress conditions and increased transformability. Still, eight families of Insertion Sequence (IS) elements with 27 potentially active members remain in MB001, two of which were demonstrated to be detrimental in biotechnological processes. In this study, systematical deletion of all complete IS elements in MB001 resulted in the MGE-free strain CR101. CR101 shows growth characteristics identical to the wildtype and the increased transformability of MB001. Due to its improved genome stability, we consider this strain to be an optimal host for basic research and biotechnology. As a “zero-background” host, it is also an ideal basis to study C. glutamicum IS elements. Re-sequencing of CR101 revealed that only five spontaneous point mutations had occurred during the construction process, highlighting the low mutation rate of C. glutamicum on the nucleotide level. In a second step, we developed an easily applicable ISCg1-based transposon mutagenesis system to randomly transpose a selectable marker. For optimal plasmid stability during cloning in Escherichia coli, the system utilizes a genetic switch based on the phage integrase Bxb1. Use of this integrase revealed the presence of a functional attB site in the C. glutamicum genome. To avoid cross-talk with our system and increase ease-of-use, we removed the attB site and also inserted the Bxb1 encoding gene into the chromosome of CR101. Successful insertion of single markers was verified by sequencing randomly selected mutants. Sequencing pooled mutant libraries revealed only a weak target site specificity, seemingly random distribution of insertion sites and no general strand bias. The resulting strain, ML103, together with plasmid pML10 provides a easily customizable system for random mutagenesis in an otherwise genomically stable C. glutamicum. Taken together, the MGE-free C. glutamicum strain CR101, the derivative ML103, and the plasmid pML10 provide a useful set of tools to study C. glutamicum in the future.

The case study is to alert all health care workers and the public alike to the dangers of ingesting wild mushrooms. We describe an incidence of Amanita phalloides poisoning in Johannesburg, South Africa, where three different outcomes were experienced. A pregnant mother recovered with conservative management while her unborn foetus died, and her three-year-old daughter required an emergency liver transplant. We outline the clinical course, management options and principles of mushroom identification and toxicology to increase awareness of the presence of Amanita phalloides and its toxic relatives in South Africa. We highlight that early recognition, prompt treatment and referral to a transplant service is life-saving.

Knowledge of the environmental prevalence of members of the Ctyptococcus neoformans/Cryptococcus gattii species complex is important, since cryptococcal infection is acquired from the environment. We determined whether trees located in two South African recreational areas harboured pathogenic cryptococci and compared the isolates to clinical isolates obtained from Western Cape hospitals with molecular typing techniques. The majority of isolates originating from trees in a public park in Cape Town (PPCT) were C. gattii sensu stricto, followed by C neoformans sensu stricto genotype AFLP1/VNI. The PPCT trees might be a source of infection, since all genotype AFLP1/VNI isolates from these trees and one clinical isolate belonged to the same sequence type (ST), i.e. ST23. Recombination and basidiospore production might be occurring in PPCT trees that contained C gattii s.s. isolates belonging to both mating types. The presence of C gattii s.s. in PPCT trees might therefore pose a risk to human health. (C) 2017 Elsevier Ltd and British Mycological Society. All rights reserved.

A total of 36 Cryptococcus neoformans strains originating from South Africa were screened for wood degrading enzymes. All strains tested positive for cellulase activity while none where capable of xylan degradation. Three C. neoformans var. grubii strains, originating from clinical and environmental samples, representing the same genotype (VNI/AFLP1—C. neoformans var. grubii) and MATα, were evaluated for growth on debris of two common tree species in South Africa: Acacia mearnsii and Eucalyptus camaldulensis. The mating capability of all the C. neoformans strains was evaluated on similar debris. Strains grown on A. mearnsii yielded substantially greater yeast populations. A total of 26%, 6%, 46%, and 80% of the 36 C. neoformans strains tested were either able to mate or develop filaments when crossed on A. mearnsii and E. camaldulensis debris, V8 juice, and yeast carbon base (YCB) agar, respectively. Filamentation and monokaryotic fruiting was observed in 3% of strains when C. neoformans was cultured on either A. mearnsii, E. camaldulensis debris, or YCB. The results indicate that this fungus is capable of completing its life cycle and can produce basidiospores on woody debris. In the future, these findings should be considered when studying the epidemiology, microbial ecology, and proposed infection process of this global pathogen.

Climate has been proposed as an explanation for the present-day distribution of closely-related melanistic and non-melanistic cordylid species in the southwestern Cape of South Africa. However, diet may also contribute towards shaping geographic distributions. We present preliminary data on diet composition based on analyses of faecal pellets of Cordylus cordylus (non-melanistic), C. niger (melanistic) and C. oelofseni (melanistic). Coleoptera were the most common prey ingested both in summer and early spring for all species, followed by Hymenoptera for all species in summer. The overlap in other arthropod taxa ingested was low across species and seasons, suggesting an opportunistic component to their foraging behaviour. We distinguished plant matter in faecal samples of all species in all seasons, reflecting either voluntary or accidental ingestion. The results of this study suggest that the generalist diets of these cordylid species should not constrain their distributions despite the common preference for coleopterans.

Recent studies have both shown and predicted that global climate change will have a substantial influence on biodiversity. This is true especially of a global biodiversity hotspot, the Cape Floristic Region. Although the effects of predicted changes have been widely assessed for plants, little is known about how insect diversity in the region might be affected. In particular, patterns in and the correlates of diversity in the region are poorly understood, and therefore the likely affects of a changing abiotic environment on this significant group of organisms are not clear. Therefore, we investigate patterns in, and correlates of, epigaeic beetle (Tenebrionidae and Carabidae) diversity in one of the most climate change-sensitive areas in the Cape Floristic Region, the Cederberg. In particular, we determine whether epigaeic beetle assemblage structure differs between the main vegetation types in the Cederberg (Strandveld, Mountain Fynbos and Succulent Karoo), how restricted these beetles are to specific vegetation types, and which environmental variables might be associated with site-related differences in beetle richness and abundance. Sampling was undertaken during October 2002 and 2003 across an altitudinal gradient ranging from sea level (Lambert's Bay) to approximately 2000 m above sea level (Sneeukop, Cederberg) and down again to 500 m above sea level (Wupperthal) using pitfall traps. The environmental correlates of abundance and species density in the epigaeic beetles were similar to those identified previously for ants across the transect, with both taxa being positively related to several temperature variables. Several species showed habitat specificity and fidelity, and clear distinctions existed between the vegetation types across the transect. A larger proportion of the variance in tenebrionid species density was explained by environmental variables and spatial factors than for carabids. The most likely explanation for this difference is that the correlates might well reflect collinear historical processes, rather than a causal relationship between contemporary environmental variables and species density. If this is the case, it suggests that caution should be exercised when interpreting environmental correlates of species density, and making climate change predictions based on these correlates.

Aim Climate-modelling exercises have demonstrated that the Cape Floristic Region is highly sensitive to climate change and will apparently lose much of its northern limits over the next few decades. Because there is little monitoring of diversity in this area, ant assemblage structure was investigated within the main vegetation types in the Greater Cederberg Biodiversity Corridor. In particular, we sought to determine how ant assemblage structure differs between the main vegetation types, how restricted ants - and in particular the major myrmecochores - are to the major vegetation types, and which environmental variables might underlie differences in the ant assemblages and in the specificity of species to particular areas. Location Northern Cape Floristic Region, Western Cape, South Africa. Methods Sampling was undertaken during October 2002 and March 2003 across an altitudinal gradient ranging from sea level (Lambert's Bay) to c. 2000 m a.s.l. (Sneeukop, Cederberg) and down again to 500 m a.s.l. (Wupperthal) in the Western Cape, South Africa. Pitfall traps were used to sample ants at 17 altitudinal bands, stretching over three vegetation types (Strandveld, Mountain Fynbos and Succulent Karoo). Biotic and abiotic environmental variables were collected at each sampling site. Generalized linear models were used to determine the relationships between species richness, density, abundance and the abundance of the major myrmecochores, and the environmental variables. Redundancy analysis was used to determine the relationship between ant assemblage structure and the environmental variables. The Indicator Value Method was used to identify characteristic ant species for each vegetation type and altitudinal site. Results Temperature explained significant proportions of the variation in species density and abundance, and, together with area and several vegetation variables, contributed significantly to the separation of the assemblages in the major vegetation types and biomes. Four major myrmecochores were identified (Anoplolepis sp. (cf. custodiens), Anoplolepis sp. (cf. steinergroeveri), Camponotus niveosetosus, Tetramorium quadrispinosum). The abundances of the two Anoplolepis species were related to vegetation variables, while the abundance of the other two species showed opposite relationships with temperature variables. Fourteen ant species were characteristic of certain vegetation types and altitudes. Several of these species contributed to the differences between the assemblages. Main conclusions There are likely to be substantial and complex changes to ant assemblages as climates change in the northern Cape Floristic Region. Moreover, the importance of ants for ecosystem functioning suggests that these responses are not only likely to be a response solely to vegetation changes, but might also precipitate vegetation changes. The changes that are predicted to take place in the next 50 years in the Cape Floristic Region could be substantially exacerbated by such synergistic effects, which have major implications for

High African elephant stocking rates in nature reserves in southern Africa have been shown to have significant impacts on vegetation structure and diversity. However, the direct and indirect effects of elephants on fauna, particularly invertebrates, remain poorly known. The Maputaland Centre of Endemism, an area of southern Mozambique and northern KwaZulu-Natal in South Africa, is undergoing rapid rates of habitat conversion. Sand Forest, the rarest vegetation type in the Centre, is threatened by human disturbance outside of protected areas and by elephant browsing pressure in Tembe Elephant Park, one of the few protected areas for Sand Forest. Here we examine the effects of elephant- and human-induced disturbance to Sand Forest on a functionally important component of invertebrate diversity, i.e. the dung beetle fauna. The dung beetle assemblage associated with elephant-disturbed Sand Forest was transitional between undisturbed Sand Forest and Mixed Woodland, whereas that associated with human disturbance was markedly different to either habitat type. Differences are attributed to a change in habitat structure under both disturbance types, as well as to changes in the quality and distribution of dung under human disturbance. Therefore, grazing impacts by elephant not only affect plant diversity, but also implement changes in invertebrate fauna. The maintenance of the integrity of the Sand Forest–Mixed Woodland matrix is considered critical for biodiversity conservation in the Maputaland Centre of Endemism. Management of elephant populations, as well as the protection of sufficient Sand Forest inside conservation areas must, therefore, necessarily form part of the conservation strategy for the Centre.