Seed-borne pathogens and the bean weevil (Acanthoscelides obtectus) in bean (Phaseolus vulgaris) seed and their effect on seed germination and vigour.

Thesis (M.Sc.)-University of Natal, Pietermaritzburg, 2003.Two semi-selective media, MT and MSP, were compared for their ability to recover cells of the bacteria Xanthomonas axonopodis pv. phaseoli (Xap) and Pseudomonas syringae pv. phaseolicola (Psp), the causal organisms of bean common and halo blights respectively. Isolates Sx70 and Sp75 (for Xap and Psp respectively) were plated on the media by dilution plating. Greater number of Xap colonies on MT than on MSP was obtained, but the number of Psp colonies was not significantly different on the two media. Four media, XCP1, MT, MT(new), and TSM were also compared for the number of contaminants and Xap colonies grown on them, using data obtained from ISTA/ISHI Comparative test for Xap (2002), which was conducted at the Agricultural Research Council (ARC) in Roodeplaat, north of Pretoria. In most cases, the number of colonies was similar in XCPI, MT, MT(new), but bigger in TSM. The number of contaminants was smaller in MT than in MT(new). Bean plants (Phaseolus vulgaris), variety PAN 146, were grown and inoculated with the bacteria Xap and Psp, and two virus isolates of bean common mosaic virus (BCMV). Uninoculated controls were also grown. Germination and vigour tests were conducted on the seeds harvested from these plants. Germination was significantly lower for seeds harvested from Psp inoculated plants, while seed vigour was reduced both for seeds harvested from Psp and Xap inoculated plants. Neither germination nor vigour was affected for seeds from BCMV inoculated plants. Late and early matured seeds from the BCMV inoculated plants were compared for the virus transmission and emergence. There was greater virus transmission and reduced emergence in the late matured seeds than in the early matured ones. Seeds harvested from Psp and BCMV inoculated plants and uninoculated controls were unexpectedly found to be infested with the bean weevil (Acanthoscelides obtectus (Say)). The BCMV infected batch of seeds appeared to repel weevil attack, whereas 25% of the uninfected batch of seeds were attacked

Penicillium air mycoflora in postharvest fruit handling environments associated with the pear export chain

Penicillium is a well-known airborne fungal contaminant that is prevalent in indoor air. In this study, the total air mycoflora was determined in postharvest fruit handling environments. The study included eleven indoor environments from the packhouse to the final retail outlet. Standard active and passive air sampling methods were used over a period of three years to obtain a profile of air quality. A total of 6047 and 5849 Penicillium colonies were counted of which 1123 and 508 isolates were obtained using active and passive sampling methods respectively. Ultimately, 25 dominant Penicillium spp. were identified from active air samples. The five most prevalent species isolated were: P. glabrum (31.88%); P. expansum (14.18%); P. crustosum (13.42%); P. chrysogenum (10.35%) and P. brevicompactum (10.25%). Furthermore, a total of 22 Penicililum spp. were isolated from passive air samples with P. glabrum (23.72%); P. italicum (16.45%); P. brevicompactum (14.22%); P. crustosum (13.80%) and P. chrysogenum (11.76%) being most prevalent. The presence of pathogenic Penicillium spp. in the air of fruit handling environments was profiled. Counts of total air mycoflora were significantly higher in the re-pack facilities than in all other environments sampled and are significantly higher than the proposed baseline threshold value. This study clearly shows the importance of air quality in facilities that regularly handle different fruit types. Re-pack and retail facilities should therefore be cleaned more effectively to reduce the potential air inoculum that can induce decay of fruit at the market-end. Finally we propose an air quality standard for fresh produce environments.The National Research Foundation (NRF), Technology and Human Resources for Industry Programme, the South African Apple and Pear Producers Association (administered by Fruitgro Science), the Department of Science and Technology, Fresh Produce Exporters Forum, Postharvest Innovation Programme PHi and the University of Pretoria.http://www.elsevier.com/locate/postharvbio2018-06-01hj2018Plant Production and Soil Scienc

Prevalence of Botrytis cinerea at different phenological stages of table grapes grown in the northern region of South Africa

Botrytis cinerea, is one of the major causal agents of postharvest decay in table grapes, contributing to 20% losses world-wide. The aim of this study was to determine the prevalence of B. cinerea at different phenological growth stage (full bloom, pea size and fully mature berries) and the impact of agro-climatic sites on pathogen incidence. Droplet digital polymerase chain reaction (ddPCR) was used simultaneously with culture based methods to detect and quantify B. cinerea. Botrytis cinerea was detected at different phenological stages on asymptomatic grape samples. Prevalence and level of B. cinerea differed between phenological stages and sites. Full bloom stage of site B showed the highest prevalence of B. cinerea (82.9%) compared to site A (33.3%). For the latter phenological stages (pea size and mature stage), site A had the highest prevalence (100% for both), compared to 35.2% and 44.4% observed at site B, respectively. Furthermore, the B. cinerea concentration varied between stages within the two sites. The concentration of B. cinerea at site A showed a threefold increase from pea size (2.67 copies μL−1 of DNA) to mature berry stage (9.16 copies μL−1 of DNA), compared with the decline noted for similar growth stages at site B. Botrytis cinerea inoculum build up on asymptomatic grapes could be effectively monitored as the berry develops at critical phenological stages. Preharvest monitoring of the pathogen can help growers improve well-established cultural and management practices, hence limit the risk of postharvest decay.The Department of Science and Technology in partnership with the Fresh Produce Exporters’ Forum, Post-harvest Innovation Programme and the South African table grape industry.http://www.elsevier.com/locate/scihorti2019-09-15hj2018Plant Production and Soil Scienc

Characterization of fungal communities of developmental stages in table grape grown in the northern region of South Africa

AIMS : To determine fungal communities that characterize table grapes during berry development. METHODS AND RESULTS : Two agro-ecologically different table grape commercial farms (site A and B) were used in this study. Samples were collected at full bloom, pea size and mature stages, from three positions (inside centre, eastern and western peripheral ends) per site. Total DNA extraction, Illumina sequencing and analysis of 18 pooled samples for fungal diversity targeting ITS1-2 generated a total of 2 035 933 high-quality sequences. The phylum Ascomycota (77.0%) and Basidiomycota (23.0%) were the most dominant, while the genera, Alternaria (33.1%) and Cladosporium (24.2%) were the overall dominant postharvest decay causing fungi throughout the developmental stages. Inside centre of site A were more diverse at full bloom (3.82) than those at the peripheral ends (<3.8), while at site B, the peripheral ends showed better diversity, particularly the eastern part at both full bloom (3.3) and pea size (3.7). CONCLUSION : Fungal population diversity varies with different phenological table grape growth stages and is further influenced by site and vine position within a specific vineyard. SIGNIFICANCE AND IMPACT OF THE STUDY : The information on fungal diversity and succession in table grapes during preharvest growth stages is critical in the development of a more targeted control strategy, to improve postharvest quality of table grapes.The Post-Harvest Innovation (PHI) Programme and the South African Table Grape Industry (SATI). The PHI Programme is a public–private partnership between the Department of Science and Technology and the Fresh Produce Exporters’ Forum, whereas SATI is an industry partner of the PHI Programme.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1365-26722018-11-30hj2017Plant Production and Soil Scienc

Exploring the microbial communities associated with Botrytis cinerea during berry development in table grape with emphasis on potential biocontrol yeasts

Table grapes harbour a wide diversity of microbes, some of which are potential biocontrol agents that may be responsible for the control of fungal pathogens in the phyllosphere. This study evaluated the diversity of microbial communities associated with naturally present Botrytis cinerea inoculum, with special emphasis on populations of potential biocontrol yeasts during berry development in table grapes. Samples were collected from two agro-ecological habitats in South Africa (Northern Province), characterised by low rainfall (site A) and high rainfall (site B). The phenological development samples included those at full bloom, pea size and mature berry stages. Within the group of yeasts known to be natural antagonists, Aureobasidium, Cryptococcus, Rhodotorula and Sporobolomyces could be cultured, while pathogenic fungal genera from asymptomatic samples included Cladosporium, Alternaria, and Aspergillus. Botrytis cinerea could only be cultured at the harvest stage from symptomatic and asymptomatic berries. Overall, the study showed the highest prevalence of Alternaria (35.6%), Cladosporium (27.2%) and Rhodoturula (21.2%). In conclusion, the study reveals a diverse pathogenic and beneficial naturally-known yeast genera in the presence of B. cinerea. Such information and knowledge can be further explored to manipulate potential antagonistic populations to prevent establishment of pathogenic populations and secure dominance of antagonistic populations at the harvest stage.The Department of Science and Technology in partnership with the Fresh Produce Exporters’ Forum, Post-harvest Innovation Programme.https://link.springer.com/journal/106582020-03-11hj2020Plant Production and Soil Scienc

Fungal diversity and community composition of wheat rhizosphere and non-rhizosphere soils from three different agricultural production regions of South Africa

Understanding complex interactions among plant genotypes, environmental conditions and microbiome structure provides crucial information for sustainable farming practices towards disease control in agriculture. In this study, fungal diversity and composition in wheat rhizosphere and non-rhizosphere soils were investigated. Special emphasis was placed on pathogenic and beneficial genera. Wheat rhizosphere and non-rhizosphere soil from three different wheat growing regions were analyzed using Illumina high-throughput sequencing. The analysis showed a significant decline in the fungal diversity and richness from non-rhizosphere to rhizosphere soils. Ascomycota and Basidiomycota were the dominant fungal phyla detected in both rhizosphere and non-rhizosphere soils across the three test sites. Genera known to include wheat pathogens detected included Fusarium, Phoma and Colletotrichum genera while, beneficial groups included Trichoderma, Aureobasidium and Acaulospora. The presence of Fusarium was observed to be inversely proportional to that of Aureobasidium, a well-known antagonist of the Fusarium spp. This information could provide new opportunities to explore the potential of manipulating natural fungal antagonistic microorganisms for use in controlling soil-borne pathogenic fungi in wheat.Supplementary Table A1. Permutational multivariate analysis of variance (PERMANOVA) of main factors tested and their interactions for wheat rhizosphere and non-rhizosphere soil from the same field sites.Supplementary Table A2. Descriptive statistics on OUT richness (Chao 1) and species diversity (Shannon-Weaver).Supplementary Fig. A1. Overall relative abundance of fungal class on SST88 and Kariega rhizosphere (R), and non-rhizosphere (NR) soil at Site A, Kariega rhizosphere (R) and non-rhizosphere soil at site B and Eland rhizosphere and non-rhizosphere soil at Site C wheat growing area. SST88_A, SST88 rhizosphere soil at Site A; Kariega_A, Kariega rhizosphere soil at Site A; NR_A, Non- rhizosphere soil at Site A; Kariega_B, Kariega rhizosphere soil at Site B; NR_B, Non- rhizosphere soil at Site B; Eland_C, Eland rhizosphere soil at Site C; NR_C, Non- rhizosphere soil at Site C.Supplementary Fig. A2. Overall relative abundance of fungal order on cv. SST88 wheat rhizosphere (R) at site A.Supplementary Fig. A3. Overall relative abundance of fungal order on cv. Kariega wheat rhizosphere (R) at site A.The National Research Foundation (NRF) and the Centre of Excellence (“CoE”) in Food Security sponsored by the Department of Science, Technology and Innovation and administered by the NRF.http://www.elsevier.com/locate/apsoil2021-07-01hj2020Plant Production and Soil Scienc

Microbial succession in white button mushroom production systems from compost and casing to a marketable packed product

The aim of the study was to investigate microbial succession in the mushroom supply chain from compost, casing to fruit body formation and mushroom growth to the point of harvested, packing and point of sale. The microbial population dynamics of compost, casing and mushrooms were determined using a plate count technique, denaturing gradient gel electrophoresis (DGGE) and sequencing of 16S and 18S rDNA. Plating revealed greater abundance of bacteria, fungi and yeasts in mushroom compost compared to casing and fresh mushroom samples. The viable count method also showed that bacteria and yeasts increased significantly after harvest and during cold storage. Sequencing revealed a more diverse culturable bacterial population in casing and on the mushrooms than in the compost. Phylogenetic analysis revealed a general trend of grouping of species from the same sources. In contrast, a higher microbial diversity was recorded in compost when using the DGGE method, which reflects cultural and non- culturable microorganisms. For compost and casing bacteria studied using DGGE, several species formed separate lineages, demonstrating highly diverse communities in these samples. Fungi were shown to be less abundant and less diverse compared to bacteria and yeasts. The study provides baseline knowledge of microbial populations and -succession trends in mushroom production systems using viable and non- viable methods. The information provided in this study may be useful for microbial ecology studies and to identify and develop biocontrol systems for pathogen control during production or to enhance pinning stimulation by knowing when to apply Pseudomonas spp. to ensure increased yield. Finally an insight is provided into microbial survival during cold storage and marketing of mushrooms. Potential antagonistic populations known to prevent spoilage, quality deterioration and extend shelf life are listed in this paper.This research was funded by the South African Mushroom Farmers Association (SAMFA), National Research Foundation (NRF) and the Technology and Human Resources for Industry Programme (THRIP) (a partnership programme funded by the Department of Trade and Industry and managed by the NRF).http://link.springer.com/journal/132132017-03-31hb2016Plant Production and Soil SciencePlant Scienc

Bacterial profiling of casing materials for white button mushrooms (Agaricus bisporus) using denaturing gradient gel electrophoresis

Commercial producers of white button mushrooms utilise a casing material to cover the spawn run compost, which stimulates the mushrooms’ reproductive stage. Certain bacteria in this casing are responsible for this stimulation, which is known as pinning. Bacterial species richness and diversity within peat and peat-based casing mixtures made from industrial waste materials (i.e. those containing coir, wattle bark, bagasse and filter cake) were examined using denaturing gradient gel electrophoresis (DGGE) at three phases of mushroom growth: (1) casing, (2) pinning and (3) harvesting. Results from the DGGE established that higher bacterial species richness occurred at pinning and harvesting than at casing. Increases in bacterial population density at pinning were greater in the peat-based mixtures, which contained industrial waste materials, than in peat alone. Peat mixtures containing these alternative materials are therefore favourable substrates for bacterial growth. The DGGE profiles for pasteurised casing materials reflected their ability to rapidly reestablish the original bacterial community. The bacteria found to be dominant in casing materials during pinning were closely related to Pseudomonas, Flavobacterium, alpha-Proteobacterium, beta-Proteobacterium, gamma-Proteobacterium, delta-Proteobacterium and uncultured species

Global research network analysis of fresh produce postharvest technology : innovative trends for loss reduction

DATA AVAILABILITY : Data will be made available on request.Globally, fruit and vegetables (fresh produce) are important for nutrition, health, food security, and economic growth. However, this type of produce is highly impacted by huge global postharvest losses ranging between 28 % and 55 % annually with low and middle-income countries (LMICs) being the most affected. Tremendous efforts have been made in terms of research and innovation to address the issue of fresh produce postharvest losses over time. Hence, this study aimed to understand the trends in fresh produce postharvest research focusing on innovations for loss reduction over the last three decades using bibliographic network analysis. This involved the retrieval of postharvest-related research documents on fruit and vegetables from the Web of Science database published between January 1990 and December 2020. The retrieved documents were used to generate maps using the VOS viewer software to visualise the key research areas and technology trends towards reducing fruit and vegetables postharvest losses as well as collaborations among countries. The study results showed an exponential increase in postharvest research on fresh produce over the past three decades with around 65 % of the work happening in the last decade (2010–2020). Research trends showed that postharvest loss reduction (PHLR) innovations focus has shifted from common chemical control to search for alternative control strategies. Most notable is the shift towards plant-based compounds, edible coatings, and biofilms for disease control and fresh produce shelf-life extension. Study results showed that China and USA are the major global players in fresh produce postharvest research, while South Africa and Egypt are the key players in Africa. Despite the milestones in fresh produce postharvest research, LMICs still experience high postharvest losses shifting the debate on access to information and the adoption of novel technologies. The study recommends the need to strengthen PHLR research investment and collaboration, particularly among LMICs to reduce the burden of food losses and waste and strengthen food security. This can be achieved by increasing adoption of the novel technologies by the industries.https://www.elsevier.com/locate/postharvbio2025-11-09hj2024Plant Production and Soil ScienceSDG-02:Zero Hunge