Microbiology

Biological diversity is being lost at unprecedented rates, with admixture and introgression presenting major threats to species' conservation. To this end, our ability to accurately identify introgression is critical to manage species, obtain insights into evolutionary processes, and ultimately contribute to the Aichi Targets developed under the Convention on Biological Diversity. A case in hand concerns roan antelope, one of Africa's most iconic large mammal species. Despite their large size, these antelope are sensitive to habitat disturbance and interspecific competition, leading to the species being listed as Least Concern but with decreasing population trends, and as extinct over parts of its range. Molecular research identified the presence of two evolutionary significant units across their sub-Saharan range, corresponding to a West African lineage and a second larger group which includes animals from East, Central and Southern Africa. Within South Africa, one of the r...

The escalating growth in illegal wildlife trade and anthropogenic habitat changes threaten the survival of pangolin species worldwide. All eight extant species have experienced drastic population size reductions globally with a high extinction risk in Asia. Consequently, forensic services have become critical for law enforcement, with a need for standardised and validated genetic methods for reliable identifications. The seizure of three tonnes of pangolin scales, believed to have originated from Africa, by Hong Kong Customs Authorities provided an opportunity for the application of DNA barcoding in identifying scales. Three mitochondrial DNA gene regions (COI, Cyt b, and D-loop) were amplified for a subsample of the confiscated material and compared with taxonomically verified references. All four African species were recovered as monophyletic with high interspecific uncorrected p-distance estimates (0.048–0.188) among genes. However, only three of four African species (Phataginus ...

Here, we present the draft genome sequence (∼4.7 Mb) of the endopyhtic bacterium Pantoea agglomerans strain R6, which was isolated from surface-sterilized roots of Lactuca serriola (prickly lettuce). ABSTRACT Here, we present the draft genome sequence (∼4.7 Mb) of the endopyhtic bacterium Pantoea agglomerans strain R6, which was isolated from surface-sterilized roots of Lactuca serriola (prickly lettuce).

Here, we present the draft genome sequence (;4.7Mb) of the endopyhtic bacterium Pantoea agglomerans strain R6, which was isolated from surfacesterilized roots of Lactuca serriola (prickly lettuce). P antoea agglomerans is a Gram-negative aerobic bacillus that belongs to the family Erwiniaceae and can be isolated from a wide variety of environments (1, 2). In plants, various strains were found to be either pathogens or commensals (3) and possess many beneficial agricultural traits (4). In this study, P. agglomerans strain R6 was isolated from surface-sterilized roots of Lactuca serriola. The L. serriola root tissues were collected from the University of the Western Cape in Bellville, South Africa (33°56906.00S, 18°37941.00E), in April 2019. Clean root samples were sterilized with 70% ethanol for 3 min, 2.5% sodium perchlorate for 5 min, and 70% ethanol for 1 min and washed 5 times with autoclaved distilled water. The sterilized roots were crushed using a sterile mortar and pestle in ...

Pickersgill’s Reed Frog (Hyperolius pickersgilli) is an Endangered (IUCN, 2016) species, endemic to South Africa and restricted to the KwaZulu-Natal coastal region. The species occurs in fragmented patches of Indian Ocean Coastalbelt Wetland, a Critically Endangered habitat type threatened by urbanisation, agriculture, mining, and forestry. We used a 16S rRNA Next Generation Sequencing approach to characterize the bacterial skin microbiome of 20 adult Pickersgill’s Reed Frog from three localities, and to determine the prevalence of anti-Batrachochytrium dendrobatidis (Bd) associated bacteria. Results from three different populations were found to harbour similar skin microbial communities, dominated by a common core set of bacterial taxa that included Proteobacteria (39.67% of total amplicon sequence variants (ASVs), Actinobacteria (14.83%) and Firmicutes (11.21%). Anti-Bd associated bacterial communities were identified at all three localities (4.12-15.47%) of total ASVs), that may...

Canine distemper virus (CDV) causes a severe contagious disease in a broad range of hosts. This is the first study to genetically characterise CDV strains from four different wildlife species in South Africa. The phylogenetic diversity of CDV is examined, using the haemagglutinin gene. The South African wildlife CDV isolates showed a high degree of similarity to CDV in South African domestic dogs. Phylogenetic analyses confirmed the presence of 12 geographical lineages with CDV strains from South African wildlife falling within the Southern African lineage. The study reveals two possible co-circulating sub-genotypes corresponding to the northern and southern regions of South Africa respectively. CDV strains from the non-canid species were distinct, but similar to CDV isolates from domestic dog and wild canids. Residues at amino acid sites of the SLAM binding region support the notion that CDV strains encoding 519I / 549H are better adapted to non-canid species than canid species. The amino acids present at site 530 are conserved regardless of host species. Strains from South African wild carnivores showed no difference between host species with all strains presenting 530N. All non-canid strains in this study presented the combination 519I/549H. No evidence of host adaptation or lineage grouping was observed for the Nectin-4 binding region. Further studies should include CDV strains isolated from various hosts from a wider geographical range in South Africa.

Grateful thanks to the staff of the Rand Afrikaans University, especially Rita Kellerman (for talking me into this), Jannie Zaaiman (for supervising my dissertation) and Karel Stanz (for his dual roles as the project manager of the course and as a fellow student).

Understanding what drives “radicalisation” of people, and specifically how they are voluntarily drawn into violent enterprise in sub-Saharan Africa will help us develop more specific ways to counteract this. At present we are constrained by approaches developed in Europe, which may not be entirely applicable elsewhere.

The literature on the causes of this phenomenon (Radicalisation to Violent Extremism, RVE) is fragmented, and no one theory dominates. We are not sure if the same pathway to violence is followed in different geographies, nor are we certain of the degree of consistency and homogeneity of the various underlying factors of radicalisation into
extremist violence. In fact, according to a long-running project at the University of Amsterdam entitled SAFIRE (Scientific Approach to Finding Indicators for & Responses to Radicalisation) “...more than 200 different factors have been identified by research which could play a role in
the radicalisation process” (SAFIRE, 2013).

The research itself focuses, as best as possible, on examining studies of the causes of individuals becoming radicalised to the commission of acts of extremist politico-religious violence, omitting far-right; far-left and criminal violence.
This study draws for methodology on work done analysing processual models of radicalisation by Stephanie De Coensel (2018); derives a meta-model of the factors influencing RVE for the Western World (as applied in Europe) and compares it with what we know of sub-Saharan Africa.
Clear differences were found between the meta-model derived for RVE in Europe and the general themes emerging from the studies in sub-Saharan Africa, most notably in the factors pushing individuals toward a pathway leading to radicalisation to extremist violence. This provides indications for the need to have different approaches to counter-extremism interventions in the two regions.