A new multi locus variable number of tandem repeat analysis scheme for epidemiological surveillance of Xanthomonas vasicola pv. musacearum, the plant pathogen causing bacterial wilt on banana and enset

Xanthomonas vasicola pv. musacearum (Xvm) which causes Xanthomonas wilt (XW) on banana (Musa accuminata x balbisiana) and enset (Ensete ventricosum), is closely related to the species Xanthomonas vasicola that contains the pathovars vasculorum (Xvv) and holcicola (Xvh), respectively pathogenic to sugarcane and sorghum. Xvm is considered a monomorphic bacterium whose intra-pathovar diversity remains poorly understood. With the sudden emergence of Xvm within east and central Africa coupled with the unknown origin of one of the two sublineages suggested for Xvm, attention has shifted to adapting technologies that focus on identifying the origin and distribution of the genetic diversity within this pathogen. Although microbiological and conventional molecular diagnostics have been useful in pathogen identification. Recent advances have ushered in an era of genomic epidemiology that aids in characterizing monomorphic pathogens. To unravel the origin and pathways of the recent emergence of XW in Eastern and Central Africa, there was a need for a genotyping tool adapted for molecular epidemiology. Multi-Locus Variable Number of Tandem Repeat Analysis (MLVA) is able to resolve the evolutionary patterns and invasion routes of a pathogen. In this study, we identified microsatellite loci from nine published Xvm genome sequences. Of the 36 detected microsatellite loci, 21 were selected for primer design and 19 determined to be highly typeable, specific, reproducible and polymorphic with two- to four- alleles per locus on a sub-collection. The 19 markers were multiplexed and applied to genotype 335 Xvm strains isolated from seven countries over several years. The microsatellite markers grouped the Xvm collection into three clusters; with two similar to the SNP-based sublineages 1 and 2 and a new cluster 3, revealing an unknown diversity in Ethiopia. Five of the 19 markers had alleles present in both Xvm and Xanthomonas vasicola pathovars holcicola and vasculorum, supporting the phylogenetic closeliness of these three pathovars. Thank to the public availability of the haplotypes on the MLVABank database, this highly reliable and polymorphic genotyping tool can be further used in a transnational surveillance network to monitor the spread and evolution of XW throughout Africa.. It will inform and guide management of Xvm both in banana-based and enset-based cropping systems. Due to the suitability of MLVA-19 markers for population genetic analyses, this genotyping tool will also be used in future microevolution studies

The Southern African Society for Plant Pathology : 1962–2020

Scientific societies play an enormously valuable role in promoting important disciplines. This role is perhaps even greater in countries that are relatively isolated from the rest of the world, such as those in the southern hemisphere, with no long histories of scientific endeavour nor well-established networks of communication. In this regard, scientific societies in South Africa are crucially important; in our view, their value is often under-appreciated. This might also be true for the Southern African Society for Plant Pathology (SASPP), which has drawn together and coordinated the activities of plant pathologists for almost 60 years. In so doing, the SASPP has contributed substantially to the health of plants that sustain agriculture and forestry and food security, and those that constitute one of the most biodiverse and fascinating flora on earth, the Cape Floristic Region.http://www.sajs.co.zaam2021BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Elderly and Polypharmacy: Physiological and Cognitive Changes

Population ageing is one of the most significant social transformations of the twenty-first century. The increase in average life expectancy was a successful challenge achieved in the modern world. However, nowadays a new challenge arises for all society: achieving a better quality of life for increasing people’s life. The comorbidities associated with ageing make elderly prone to polypharmacy. On the other hand, physiological and cognitive changes interfere with drugs’ pharmacodynamics and pharmacokinetics contributing to drug-related problems which have been reported to account for a large percentage of emergency treatment and hospitalizations of older people, increasing the costs with health in the most aged regions. In order to reduce the use of potentially inappropriate medicines in this population, strategies and tools have been developed in recent years to assess the appropriateness medication use in the elderly

A highly specific tool for identification of Xanthomonas vasicola pv. musacearum based on five Xvm-specific coding sequences

Xanthomonas vasicola pv. musacearum (Xvm) is a bacterial pathogen responsible for the economically important Xanthomonas wilt disease on banana and enset crops in Sub-Saharan Africa. Given that the symptoms are similar to those of other diseases, molecular diagnosis is essential to unambiguously identify this pathogen and distinguish it from closely related strains not pathogenic on these hosts. Currently, Xvm identification is based on polymerase chain reaction (PCR) with GspDm primers, targeting the gene encoding general secretory protein D. Experimental results and examination of genomic sequences revealed poor specificity of the GspDm PCR. Here, we present and validate five new Xvm-specific primers amplifying only Xvm strains

Seed treatment with selected plant growth-promoting rhizobacteria increases maize yield in the field

Maize, Zea mays is the most important grain crop in South Africa and is a staple food in many African countries. The beneficial effects of plant growth-promoting rhizobacteria on crop growth and yield have been well documented, but obtaining reproducible results under field conditions is often difficult. In the current study, five selected rhizobacterial strains that showed plant growth-promoting activities in pilot studies were evaluated for potential enhancement of maize yield under field conditions. The five strains together with a commercial standard were assessed as seed treatments of maize over three seasons in four different soil types. The strains were identified on the basis of 16S rRNA sequencing as Lysinibacillus sphaericus (T19), Paenibacillus alvei (T29), Bacillus safensis (S7) Bacillus pumilus (A26) and Brevundimonas vesicularis (A40). The best yield increases in maize were obtained during the 2011/2012 and 2012/2013 seasons in the Shortlands ecotope with the rhizobacterial strains T19, T29 and S7, resulting in yield increases ranging from 24% to 34%. Strain T19 rendered the most consistent yield increases during the three successive field trials amounting to 33% and 24% in Shortlands ecotope and 12% in Clovalley ecotope, respectively. During 2013/2014 a consortium of three strains, viz. T19, S7 and A26 gave a 32% yield increase in Clovalley ecotope. All the rhizobacterial strains solubilised phosphate in vitro except T19. Strain T29 showed the best nitrogen-fixing activity in vitro, proliferating on a nitrogen-free substrate and also producing ammonia. All the strains tested positive for indole acetic acid production. The current study demonstrates the ability of rhizobacterial strains T19, T29, S7 and A26 applied as seed treatments to significantly enhance maize yield in the field, making development and commercialisation of these strains a viable option.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1744-73482018-09-30hj2017Forestry and Agricultural Biotechnology Institute (FABI)Microbiology and Plant PathologyPlant Production and Soil Scienc

Roles of plant volatiles in defence against microbial pathogens and microbial exploitation of volatiles

Plants emit a large variety of volatile organic compounds during infection by pathogenic microbes, including terpenes, aromatics, nitrogen‐containing compounds, and fatty acid derivatives, as well as the volatile plant hormones, methyl jasmonate, and methyl salicylate. Given the general antimicrobial activity of plant volatiles and the timing of emission following infection, these compounds have often been assumed to function in defence against pathogens without much solid evidence. In this review, we critically evaluate current knowledge on the toxicity of volatiles to fungi, bacteria, and viruses and their role in plant resistance as well as how they act to induce systemic resistance in uninfected parts of the plant and in neighbouring plants. We also discuss how microbes can detoxify plant volatiles and exploit them as nutrients, attractants for insect vectors, and inducers of volatile emissions, which stimulate immune responses that make plants more susceptible to infection. Although much more is known about plant volatile–herbivore interactions, knowledge of volatile–microbe interactions is growing and it may eventually be possible to harness plant volatiles to reduce disease in agriculture and forestry. Future research in this field can be facilitated by making use of the analytical and molecular tools generated by the prolific research on plant–herbivore interactions.A. H. and T. A. are funded by South African National Research Council Incentive Funds (2019) and the University of Pretoria, and J. G. is funded by the Max Planck Society.https://wileyonlinelibrary.com/journal/pce2020-10-01hj2020BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant PathologyZoology and Entomolog

Sand and Pebbles: The Study of Portuguese Raw Materials for Provenance Archaeological Glass

grant number 125421 UID/00729/2020Portuguese archaeological excavations dated to the 17th century onwards are extremely rich in glass artefacts, with this being a reality from the north to the south of the territory. Contrasting with this reality, no glass production locations from this period have been discovered or excavated so far, which makes the provenance attribution a challenging endeavour. One specific archaeological location, the Monastery of Santa Clara-a-Velha in Coimbra, held one of the largest glass archaeological assemblages dated to the 17th century unearthed in Portugal so far. Due to the large variety of objects’ shapes, glass colours and decorative features, this assemblage is a valuable candidate to hold glass artefacts produced in Portugal. Lacking archaeological excavation on glass furnaces in Portugal, the study of glassmaking raw materials is the most promising research line to investigate the provenance of glass circulating in Portugal. In this study, sand and pebbles from six different locations in the north/centre of Portugal were collected and melted to produce glass samples. The resulting glass samples were chemically characterised using LA-ICP-MS, to obtain the composition of the samples in major, minor and trace elements. The obtained results were compared with the composition of 37 historical samples from the Monastery of Santa Clara-a-Velha previously studied. Additionally, the thermal properties of selected synthesised glasses were analysed by Differential Scanning Calorimetry, allowing new insights on melting temperatures and glass workability. Results indicate that three artefacts with stylistic features attributed to a Portuguese production were locally made with sands collected in Coimbra.publishersversionpublishe

Draft genome sequences for the onion center roth pathogen Pantoea ananatis PA4 and maize brown stalk rot pathogen P. ananatis BD442

Pantoea ananatis is an emerging phytopathogen that infects a broad spectrum of plant hosts. Here, we present the genomes of two South African isolates, P. ananatis PA4, which causes center rot of onion, and BD442, isolated from brown stalk rot of maize

Editorial : Emergence and re-emergence of plant diseases caused by Xanthomonas species

No abstract available.https://www.frontiersin.org/journals/microbiologyam2023BiochemistryGeneticsMicrobiology and Plant Patholog

Comparative genomic analysis of the secondary flagellar (flag-2) system in the order Enterobacterales

BACKGROUND : The order Enterobacterales encompasses a broad range of metabolically and ecologically versatile bacterial taxa, most of which are motile by means of peritrichous flagella. Flagellar biosynthesis has been linked to a primary flagella locus, flag-1, encompassing ~ 50 genes. A discrete locus, flag-2, encoding a distinct flagellar system, has been observed in a limited number of enterobacterial taxa, but its function remains largely uncharacterized. RESULTS : Comparative genomic analyses showed that orthologous flag-2 loci are present in 592/4028 taxa belonging to 5/8 and 31/76 families and genera, respectively, in the order Enterobacterales. Furthermore, the presence of only the outermost flag-2 genes in many taxa suggests that this locus was far more prevalent and has subsequently been lost through gene deletion events. The flag-2 loci range in size from ~ 3.4 to 81.1 kilobases and code for between five and 102 distinct proteins. The discrepancy in size and protein number can be attributed to the presence of cargo gene islands within the loci. Evolutionary analyses revealed a complex evolutionary history for the flag-2 loci, representing ancestral elements in some taxa, while showing evidence of recent horizontal acquisition in other enterobacteria. CONCLUSIONS : The flag-2 flagellar system is a fairly common, but highly variable feature among members of the Enterobacterales. Given the energetic burden of flagellar biosynthesis and functioning, the prevalence of a second flagellar system suggests it plays important biological roles in the enterobacteria and we postulate on its potential role as locomotory organ or as secretion system.Additional file 1: Table S1. Presence/absence of flag-2 loci among 4028 strains belonging to eight families and 72 genera. The presence of flag-1 loci is also indicated. The previous taxonomy denotes the taxonomy according to the NCBI genome database, while the current taxonomy is according to the Genome Taxonomy Database (GTDB). The isolation source as well as habitat/lifestyles of the different strains are given. Table S2. Molecular characteristics of the flag-2 loci among 592 taxa in the Enterobacterales. The sizes of the flag-2 loci, variable regions VR1 and VR2, their G + C contents (%) and G + C deviation (%) from the genome are shown. The number of predicted proteins encoded on each of these flag-2 fractions are also shown. Table S3. Characteristics of the cargo genes encoded in the variable regions VR1 and VR2 and elsewhere in the enterobacterial flag-2 loci. The number of strains and the families/ genera in which each protein occurs within the flag-2 loci are indicated, as well as the average amino acid identities among enterobacterial orthologues. Conserved domains present in each cargo protein as determined by BlastP analysis against the Conserved Domain Database are shown.The National Research Foundation of South Africahttps://bmcgenomics.biomedcentral.comam2020Forestry and Agricultural Biotechnology Institute (FABI