Article
Plant Sciences
Bernard Reynaud, Patrick Turpin, Florencia M. Molinari, Martial Grondin, Solene Roque, Frederic Chiroleu, Alberto Fereres, Helene Delatte
Summary: Huanglongbing (HLB) is a serious disease of citrus worldwide, caused by three non-cultivable bacteria. The African psyllid Trioza erytreae is capable of efficiently acquiring and transmitting the bacteria, highlighting the high risk of spread of the disease in Europe.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Plant Sciences
John da Graca, Glynnis Cook, Inusa J. Ajene, Tim G. Grout, Gerhard Pietersen, Ronel Roberts, Rachelle Bester, Mathys C. Pretorius, Hans J. Maree
Summary: It has been almost 100 years since citrus growers in the northern provinces of South Africa first noticed the symptoms of a disease called greening or huanglongbing (HLB), which later became a global pandemic. The disease is caused by a transmissible pathogen called 'Candidatus Liberibacter africanus'. This review focuses on the African form of HLB, discussing its bacterial species and subspecies, insect vector, geographic distribution, and management strategies.
Article
Agronomy
Ronel Roberts, Hong Lin, Gerhard Pietersen
Summary: By analyzing microsatellites of 167 'Candidatus Liberibacter africanus' (Laf) isolates from different regions in South Africa, it was found that most sources belong to two major genetic groups with 25 distinct haplotypes. The study also revealed that Laf populations in SA are formed by geographic locality, indicating a high genetic diversity within Laf in the country.
EUROPEAN JOURNAL OF PLANT PATHOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Jinhui Wang, Minna Haapalainen, Anne I. Nissinen, Minna Pirhonen
Summary: The study revealed that the interaction between carrot and 'Candidatus Liberibacter solanacearum' haplotype C led to the up-regulation or down-regulation of various immune-related genes, as well as observed leaf yellowing, cell regeneration, and differential gene expression of the bacteria at different infection stages.
MOLECULAR PLANT-MICROBE INTERACTIONS
(2021)
Review
Agriculture, Multidisciplinary
Anne Nissinen, Minna Haapalainen, Hannu Ojanen, Minna Pirhonen, Lauri Jauhiainen
Summary: Carrot cultivation in Europe is facing infections from Candidatus Liberibacter solanacearum (CLso), a psyllid-transmitted bacterial pathogen. Field experiments in Finland revealed that psyllid feeding damage and CLso infection significantly affect carrot growth, with the impact of CLso infection on yield being strongly dependent on weather conditions in the Nordic region.
ANNALS OF APPLIED BIOLOGY
(2021)
Article
Entomology
Arnaud Ameline, Alain Karkach, Thomas Denoirjean, Martial Grondin, Florencia Molinari, Patrick Turpin, Helene Delatte, Bernard Reynaud
Summary: This study investigated the effects of Candidatus Liberibacter asiaticus (CLas), the pathogen causing Huanglongbing, on the behavior, physiology, and biochemistry of the African psyllid, Trioza erytreae. The results showed minimal effects on the psyllid's probing behavior prior to acquisition of CLas, but significant changes in behavior, physiology, and biochemistry were observed in psyllids that completed their development on CLas-infected plants.
Article
Plant Sciences
Nabil Killiny
Summary: In this study, it was found that the infection of 'Candidatus Liberibacter asiaticus' led to a significant decrease in organic acids in the phloem sap of sweet orange and periwinkle plants. It was hypothesized that bacterial growth induced the mitochondrial tricarboxylic acid cycle to produce these compounds as a carbon source, which may explain the unequal distribution of the bacteria within infected trees.
Article
Biochemistry & Molecular Biology
Houriiyah Tegally, Eduan Wilkinson, Richard J. Lessells, Jennifer Giandhari, Sureshnee Pillay, Nokukhanya Msomi, Koleka Mlisana, Jinal N. Bhiman, Anne von Gottberg, Sibongile Walaza, Vagner Fonseca, Mushal Allam, Arshad Ismail, Allison J. Glass, Susan Engelbrecht, Gert Van Zyl, Wolfgang Preiser, Carolyn Williamson, Francesco Petruccione, Alex Sigal, Inbal Gazy, Diana Hardie, Nei-yuan Hsiao, Darren Martin, Denis York, Dominique Goedhals, Emmanuel James San, Marta Giovanetti, Jose Lourenco, Luiz Carlos Junior Alcantara, Tulio de Oliveira
Summary: The study identified 16 new lineages of SARS-CoV-2 in South Africa between March and August 2020, with unique mutations not found elsewhere. Three lineages (B.1.1.54, B.1.1.56, and C.1) dominated during the country's first wave, accounting for approximately 42% of all infections. The C.1 lineage, with 16 nucleotide mutations including the D614G spike protein change, became the most geographically widespread by August 2020. Genomic surveillance played a crucial role in identifying the 501Y.V2 variant in South Africa in December 2020.
Article
Genetics & Heredity
Osiel Silva Goncalves, Ralph Bonandi Barreiros, Sumaya Martins Tupy, Mateus Ferreira Santana
Summary: 'Candidatus Liberibacter' species have a dependency on essential nutrients and metabolites from the host cell, and their metabolism is closely linked to the host.
Article
Plant Sciences
Cheryl M. Armstrong, Lijuan Zhou, Weiqi Luo, Ozgur Batuman, Olufemi J. Alabi, Yongping Duan
Summary: In this study, researchers identified an 8.3 kb DNA region of the Las genome that was not present in the Las str. psy62 genome. This region, containing eight putative open reading frames, was found to be a unique genetic element associated with genome plasticity/instability. Through the use of specific primers, the presence and absence of this region in Las populations were studied in various samples including psyllids, periwinkle, and citrus plants.
Article
Multidisciplinary Sciences
Takalani Nelufule, Mark P. Robertson, John R. U. Wilson, Katelyn T. Faulkner
Summary: This article presents the first consolidated inventory of 'native-alien populations' in South Africa and provides an overview of the data it contains. Data was gathered through literature searches and expert consultations, and scored using a newly developed protocol. The inventory includes 77 native species forming 132 native-alien populations across different environments. While rare compared to alien species from other countries, these populations pose specific challenges for regulators and managers, and their importance is expected to increase with global change. The data will be integrated with an existing alien species list to address the issue.
Article
Microbiology
Yasser E. Ibrahim, Jorge R. Paredes-Montero, Mohammed A. Al-Saleh, Arya Widyawan, Ruifeng He, Mahmoud H. El Komy, Hathal M. Al Dhafer, Noel Kitchen, David R. Gang, Judith K. Brown
Summary: This study investigated the citrus greening disease in Saudi Arabia and found that it is caused by the Asian citrus psyllid transmitting the Candidatus Liberibacter asiaticus. The study also analyzed the genetic makeup of the psyllids and identified two major lineages of the pathogen.
Article
Biochemistry & Molecular Biology
Houriiyah Tegally, Monika Moir, Josie Everatt, Marta Giovanetti, Cathrine Scheepers, Eduan Wilkinson, Kathleen Subramoney, Zinhle Makatini, Sikhulile Moyo, Daniel G. Amoako, Cheryl Baxter, Christian L. Althaus, Ugochukwu J. Anyaneji, Dikeledi Kekana, Raquel Viana, Jennifer Giandhari, Richard J. Lessells, Tongai Maponga, Dorcas Maruapula, Wonderful Choga, Mogomotsi Matshaba, Mpaphi B. Mbulawa, Nokukhanya Msomi, Yeshnee Naidoo, Sureshnee Pillay, Tomasz Janusz Sanko, James E. San, Lesley Scott, Lavanya Singh, Nonkululeko A. Magini, Pamela Smith-Lawrence, Wendy Stevens, Graeme Dor, Derek Tshiabuila, Nicole Wolter, Wolfgang Preiser, Florette K. Treurnicht, Marietjie Venter, Georginah Chiloane, Caitlyn McIntyre, Aine O'Toole, Christopher Ruis, Thomas P. Peacock, Cornelius Roemer, Sergei L. Kosakovsky Pond, Carolyn Williamson, Oliver G. Pybus, Jinal N. Bhiman, Allison Glass, Darren P. Martin, Ben Jackson, Andrew Rambaut, Oluwakemi Laguda-Akingba, Simani Gaseitsiwe, Anne von Gottberg, Tulio de Oliveira, Armand Phillip Bester, Mathilda Claassen, Deelan Doolabh, Innocent Mudau, Nokuzola Mbhele, Susan Engelbrecht, Dominique Goedhals, Diana Hardie, Nei-Yuan Hsiao, Arash Iranzadeh, Arshad Ismail, Rageema Joseph, Arisha Maharaj, Boitshoko Mahlangu, Kamela Mahlakwane, Ashlyn Davis, Gert Marais, Koleka Mlisana, Anele Mnguni, Thabo Mohale, Gerald Motsatsi, Peter Mwangi, Noxolo Ntuli, Martin Nyaga, Luicer Olubayo, Botshelo Radibe, Yajna Ramphal, Upasana Ramphal, Wilhelmina Strasheim, Naume Tebeila, Stephanie van Wyk, Shannon Wilson, Alexander G. Lucaci, Steven Weaver, Akhil Maharaj, Yusasha Pillay, Michaela Davids, Adriano Mendes, Simnikiwe Mayaphi
Summary: The genomic characterization of the SARS-CoV-2 Omicron lineages BA.4 and BA.5, responsible for the fifth wave of the COVID-19 pandemic in South Africa, reveals their continued viral diversification and sheds light on the potential mechanisms that allow these new lineages to outcompete their predecessors. These new lineages, BA.4 and BA.5, share identical spike proteins with BA.2 but have certain differences such as the presence of the 69-70 deletion, L452R, F486V, and the wild-type amino acid at Q493. They can be identified by the S-gene target failure, a proxy marker associated with the 69-70 deletion. BA.4 and BA.5 have rapidly replaced BA.2 and have become the dominant lineages in South Africa.
Article
Entomology
Jennifer Dahan, Erik J. Wenninger, Michael Thornton, Cesar A. Reyes Corral, Nora Olsen, Alexander Karasev
Summary: The study found that the potato psyllids were most abundant on bittersweet nightshade, with only 2.7% carrying Lso haplotype A or B, suggesting a limited role in the persistence of zebra chip disease. Field bindweed was found to be a transient host for potato psyllids of Northwestern, Western, and Central haplotypes late in the season, with a minor role, if any, in the persistence of Lso and field infestation by potato psyllids.
ENVIRONMENTAL ENTOMOLOGY
(2021)
Article
Public, Environmental & Occupational Health
Liping Gao, Canjun Zheng, Qi Shi, Lili Wang, Alie Tia, Jone Ngobeh, Zhiguo Liu, Xiaoping Dong, Zhenjun Li
Summary: COVID-19 pandemic in West Africa has been ongoing and evolving with multiple introduced lineages and a single native lineage. Nigeria has recorded the highest number of cases and deaths, while Liberia and Sierra Leone have the fewest. Eight SARS-CoV-2 variants have been found, indicating high diversity. Enhancing quarantine measures and implementing genome surveillance strategy are recommended to better understand the transmission dynamics.
FRONTIERS IN PUBLIC HEALTH
(2022)
Article
Biochemistry & Molecular Biology
Juanita R. Avontuur, Marike Palmer, Chrizelle W. Beukes, Wai Y. Chan, Taponeswa Tasiya, Elritha van Zyl, Martin P. A. Coetzee, Tomasz Stepkowski, Stephanus N. Venter, Emma T. Steenkamp
Summary: This study isolated fourteen strains of Bradyrhizobium bacteria from root nodules of legumes in South Africa and determined their taxonomic position and possible novelty through gene sequence analysis. The existence of these novel species was supported by genome data and metabolic characteristics.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Microbiology
Esther K. Muema, Emma T. Steenkamp, Stephanus N. Venter
Summary: This study assessed the bacterial diversity in the rhizosphere soils of native and encroaching legumes in the Succulent Karoo Biome of South Africa. The results showed a diverse range of bacteria, including diazotrophic bacteria, that support plant growth in harsh environments. Vachellia karroo had the highest diversity and influence on soil microbes among the legume species studied.
Article
Biochemistry & Molecular Biology
Janneke Aylward, Minette Havenga, Brenda D. Wingfield, Michael J. Wingfield, Leanne L. Dreyer, Francois Roets, Emma T. Steenkamp
Summary: The presence of accessory MAT genes in different idiomorphs of Mycosphaerellaceae and Teratosphaeriaceae species, as well as the discovery of highly similar fragment sequences outside the MAT locus, provide important insights into the evolution and functionality of mating-type genes.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2022)
Article
Biotechnology & Applied Microbiology
Lazarus Mavima, Chrizelle W. Beukes, Marike Palmer, Sofie E. De Meyer, Euan K. James, Marta Maluk, Muthama A. Muasya, Juanita R. Avontuur, Wai Yin Chan, Stephanus N. Venter, Emma T. Steenkamp
Summary: This study investigates the taxonomic status of rhizobial isolates from South African legume hosts. The isolates were initially identified as P. tuberum but were classified into two putative species clusters. Analysis of nucleotide identity confirmed the high genome similarity between isolates of one cluster and P. tuberum sensu stricto. A new taxon, P. podalyriae sp. nov., was proposed for the members of the other cluster associated with a single species of Podalyria.
SYSTEMATIC AND APPLIED MICROBIOLOGY
(2022)
Article
Virology
David A. Read, Elrea Strydom, Bernard Slippers, Emma Steenkamp, Gerhard Pietersen
Summary: This study collected samples showing blotchy mottle symptoms from soybeans in South Africa and obtained the complete genome sequences of soybean blotchy mosaic virus (SbBMV) through high-throughput sequencing. The gene organization of SbBMV is similar to other cytorhabdoviruses but with low sequence identity. Based on the demarcation thresholds for rhabdoviruses, SbBMV is classified as a distinct member of the genus Cytorhabdovirus.
ARCHIVES OF VIROLOGY
(2022)
Article
Microbiology
Claudette Dewing, Magrieta A. Van der Nest, Quentin C. Santana, Robert H. Proctor, Brenda D. Wingfield, Emma T. Steenkamp, Lieschen De Vos
Summary: This study used comparative genomics to elucidate the mechanisms underlying the ability of grass-associated and pine-associated Fusarium species to colonize their respective plant hosts. The results showed that the genes associated with host range originated and were retained through various mechanisms during the evolution of Fusarium. These host-range-associated genes tended to be located towards the subtelomeric regions of chromosomes.
Article
Microbiology
Mkhululi N. Maphosa, Emma T. Steenkamp, Aquillah M. Kanzi, Stephanie van Wyk, Lieschen De Vos, Quentin C. Santana, Tuan A. Duong, Brenda D. Wingfield
Summary: In this study, the genomes of five isolates of Fusarium circinatum were sequenced and compared with previously published genomes. The results revealed genome plasticity in F. circinatum, with some genomic elements not being conserved within the isolates and some variants having high impact. This study is important for informing disease management strategies against this pathogen.
Article
Agronomy
Felix F. Fru, Michael J. Wingfield, Jolanda Roux, Emma T. Steenkamp
Summary: Pitch canker, a fungal disease caused by Fusarium circinatum, has been a threat to plantation-grown Pinus trees in South Africa. In this study, the population biology of F. circinatum in the region was investigated using microsatellite markers and mating-type assays. The results indicated high diversity and connectivity among populations, with shared genotypes across nursery and plantation sites. Outbreak populations showed dominance of certain genotypes and clonality as the main reproductive mode. The genetic variation of the pathogen could be attributed to multiple introductions into the country. These findings have important implications for Pinus disease management.
Article
Plant Sciences
David A. Read, Gerhard Pietersen, Bernard Slippers, Emma T. Steenkamp
Summary: This study reports the first discovery of chrysanthemum virus B (CVB) and chrysanthemum chlorotic mottle viroid (CChMVd) in Chrysanthemum x morifolium cultivars in South Africa. Molecular detection and sequencing confirmed the presence of these viruses.
AUSTRALASIAN PLANT DISEASE NOTES
(2022)
Article
Virology
David A. Read, Bernard Slippers, Emma Steenkamp
Summary: The complete RNA genome sequence of a novel potyvirus, Barleria repens mottle virus (BaRMoV), has been determined. BaRMoV was found infecting a plant showing virus-like leaf mosaic symptoms in South Africa. Phylogenetic analysis confirmed the relationship between BaRMoV and yam mosaic virus (YMV) of the family Potyviridae. This is the first identification of a member of the Potyviridae family in the Barleria species.
ARCHIVES OF VIROLOGY
(2023)
Article
Microbiology
Edwin I. Wanjofu, Stephanus N. Venter, Chrizelle W. Beukes, Emma T. Steenkamp, Eastonce T. Gwata, Esther K. Muema
Summary: This study evaluated the symbiotic effectiveness of different Mesorhizobium strains with various chickpea genotypes. The results showed that inoculation with compatible Mesorhizobium promoted chickpea growth. The globally sourced strains performed better in promoting plant growth compared to the South African field isolates.
Article
Microbiology
Benedicta S. Swalarsk-Parry, Emma T. Steenkamp, Stephanie van Wyk, Quentin C. Santana, Magriet A. van der Nest, Almuth Hammerbacher, Brenda D. Wingfield, Lieschen De Vos
Summary: The study investigated the molecular processes underlying the growth of Fusarium circinatum, an economically important pathogen of pine. By exploring the association between growth and the nutritional environment provided by the pine host, the study identified Quantitative Trait Loci (QTLs) associated with growth and characterized a significant QTL using available genome sequences. The study revealed that growth is a complex multilocus trait and raised the possibility of multiple small-effect QTLs dependent on genetic backgrounds. This study improved our knowledge of the genetic determinants of vegetative growth in F. circinatum and provided a foundation for further research on the genes and processes underlying its ability to colonize its host environment.
Article
Agronomy
Francina L. Bopape, Chrizelle W. Beukes, Kopotsa Katlego, Ahmed I. Hassen, Emma T. Steenkamp, Eastonce T. Gwata
Summary: Pigeonpea is an important grain legume with low productivity in South Africa. This study characterized indigenous rhizobial strains and tested their nodulation abilities on local and improved genotypes of pigeonpea. The results showed that the rhizobia mainly belonged to Rhizobium and Bradyrhizobium and were able to nodulate both genotypes. However, the locally sourced landrace performed better. Further screening and field trials are needed to identify elite nitrogen fixing rhizobial strains for enhancing pigeonpea production in South Africa.
Article
Infectious Diseases
S. N. Venter, M. Palmer, E. T. Steenkamp
Summary: The availability of multiple gene sequences has changed how taxonomists delineate microbial subspecies, and full genome sequence data is particularly important. Well-defined lineages with high genome similarity values are often described as subspecies, despite clear evidence of genetic isolation. The taxonomic category of subspecies has become irrelevant and its use should be discontinued. Variation within species based on the accessory genome information is biologically significant.
NEW MICROBES AND NEW INFECTIONS
(2022)
Meeting Abstract
Dermatology
C. Dewing, N. Yilmaz, E. T. Steenkamp, B. D. Wingfield, C. M. Visagie
