Browsing by Author "Conradie, Tersia Andrea"

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    The abundance and diversity of Acidobacteria in fynbos soil: a closer look at culturability and function
    (Stellenbosch : Stellenbosch University, 2021-04) Conradie, Tersia Andrea; Jacobs, Karin; Stellenbosch University. Faculty of Science. Dept. of Microbiology.
    ENGLISH SUMMARY: The Acidobacteria are considered to be one of the most widespread and highly abundant soil bacterial phyla. This phylum was first described in 1997 with only three cultured representatives. Currently, the Acidobacteria is divided into 15 class-level subdivisions, of which only 5 subdivisions contain the 62 successfully cultured and fully described species in the Acidobacteria. The reason for their low representation in culture collections, is partly due to their unculturable, or difficult to culture nature. The application of 16S rRNA gene techniques has revealed that this phylum can represent almost 50% of the soil bacterial community, averaging around 10-20% of the global soil bacteria. Their proliferation in soils suggests that the Acidobacteria play an important role in biogeochemical processes. Microorganisms are an essential part of the terrestrial environment and are important in maintaining ecological functions. These functions are especially important in biomes where nutrient availability is low, and plants depend on their symbiotic relationships with the soil microbiome. One example of such an environment include the fynbos biome in the Cape Floristic Region (CFR) of South Africa. Despite the dominant presence of the Acidobacteria in several habitats, little is still known about their diversity and distribution in the fynbos biome. The aim of this study, therefore, was to explore the Acidobacterial communities in fynbos soils with the use of 16S rRNA gene sequencing, and how they respond to environmental change, as well as agricultural practices. Further, we aimed to isolate as many species as possible from the fynbos biome, and taxonomically characterise novel species. In Chapter 2, we explored the distribution patterns of the Acidobacteria in different fynbos soils from native conservation areas, and in Chapter 3 how the Acidobacteria responds to seasonal changes and the cultivation of Aspalathus linearis (rooibos) and Cyclopia spp. (honeybush), two indigenous plants used in commercial agriculture. A total of 27 soil samples were collected at three nature reserves, namely Jonkershoek, Hottentots Holland, and Kogelberg. In addition, data from two previous studies from our research group, with GenBank accession numbers DRA003953 for Cyclopia spp. (honeybush) and DRA004000 for Aspalathus linearis (rooibos), were included in our analysis. A total of 33 acidobacterial operational taxonomic units (OTUs) were identified in the nature reserve samples, and a total of 32 and 31 OTUs were identified for honeybush and rooibos, respectively. The majority of OTUs in all samples were classified as representatives of subdivisions 1, 2, and 3. Significant differences were observed in the distribution and composition of these OTUs between nature reserves, between seasons for both honeybush and rooibos, as well as between the agricultural practices in some cases. Several OTUs and subdivisions correlated significantly with soil pH, potassium, phosphorus, and in some instances carbon and calcium. In Chapter 4, we successfully isolated two novel species, both within subdivision 1. We proposed the classification of strain HDX4T as the type strain of Edaphobacter sabuleum nom. prov., and strain ADX1T as the type strain of Terriglobus capensi nom. prov. Based on the genome sequences, both strains had the genomic potential for several complete carbohydrate metabolic pathways, organic nitrogen metabolism, as well as several survival mechanisms that contributes to their survival in the soil environment. In short, this study has contributed greatly to our knowledge of the Acidobacteria and their distribution and diversity in the fynbos biome. The successful isolation of two novel species were added to the list of cultivated Acidobacteria from around the globe.
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    The application of astaxanthin producing bacteria in poultry feed
    (Stellenbosch : Stellenbosch University, 2017-03) Conradie, Tersia Andrea; Jacobs, Karin; Pieterse, Elsje; Stellenbosch University. Faculty of Science. Dept. of Microbiology.
    ENGLISH ABSTRACT: In the food industry, the colour of the product is important to the consumer as it gives an indication of the freshness and quality of the product. Hens are not able to produce pigments and absorb pigments through their diet. This has led to a rapidly emerging trend in poultry farming to enhance egg yolk colour as the yolk colour is influenced by the diet of the hen. Over the years, natural or synthetic carotenoids have been added to poultry feed. Several studies have focused on using astaxanthin producing microorganisms, such as the microalga, Haematococcus pluvialis, and yeast, Xanthophyllomyces dendrorhous. However, the production costs are expensive and the thick cell walls of the microalga and yeast limits its whole cell application as a feed additive. Some bacterial species are also able to produce astaxanthin, including the bacterium Paracoccus marcusii, and have previously not been used as a feed additive to enhance yolk colour. The purpose of this study was, therefore, to determine the whole cell application of P. marcusii as a feed additive to enhance egg yolk colour, without the need to homogenise the cells or extract the pigment. In the first experimental chapter (Chapter 2), the growth conditions and astaxanthin production of P. marcusii was optimised. Furthermore, the stability of the astaxanthin molecule under different storage conditions, namely lyophilisation and microencapsulation, was determined. The optimum growth conditions for P. marcusii and for astaxanthin production was at 26 °C in a specialised medium containing yeast extract (5 g/L), bacteriological peptone (10 g/L) and NaCl (3%) at a pH between 6 – 7. Astaxanthin is a valuable compound with several health promoting benefits for humans and animals. However, the molecule is unstable when exposed to oxygen, light and temperature. After lyophilisation in sucrose (10% m/v), there was an 85% loss in astaxanthin concentration after 3 weeks. However, the loss in cell viability was low. When P. marcusii was microencapsulated in calcium alginate beads, cell viability significantly decreased when stored at 20 °C compared to 4 °C. However, only 30% of the total astaxanthin concentration was lost after 3 weeks at both storage temperatures. The microencapsulation significantly improved the stability of astaxanthin under storage. The highest concentration of astaxanthin obtained was 24.25 μg/g dry cell weight. Chapter 3 examined the pigmentation effect of P. marcusii when fed to laying hens to enhance egg yolk colour. Paracoccus marcusii was fed to hens daily either in a sucrose solution (10% m/v) or microencapsulated in calcium alginate beads. After the pilot study, it was clear that a diet free of all pigments was needed to effectively determine the pigmentation effect of P. marcusii. In all the experimental trials there was a significant increase in yolk colour and no negative effect on egg quality, laying rate or hen weight was observed. There was also an increase in whole egg and yolk weight when compared to the control groups. Furthermore, the microbial communities of the duodenum and caeca were investigated after a prolonged feeding of P. marcusii to detect any changes that might have occurred (Chapter 4). The microbial community of the hen’s gastro-intestinal tract (GIT) starts out as a simple community in the small intestines which becomes increasingly diverse and complex further down the intestinal tract. The findings in this study revealed a similar pattern when considering the results obtained from the Shannon diversity index and total number of operational taxonomic units (OTUs). Starting in the duodenum, the index ranged between 2.14 – 2.59 and increased in the caeca to between 2.45 – 3.03. OTUs increased from 21.44 – 28.60 in the duodenum to 28.30 – 38.00 in the caeca. A significant difference was only observed for the OTUs of the experimental group compared to the control groups in both the duodenum and caeca. There was no significant difference observed in the microbial community structure of the duodenum. However, distinct patterns and clusters formed in the caeca between the experimental diet group compared to the control diet groups. Since no mortalities were recorded during the trial and all hens appeared in excellent health, it is safe to assume that the change in microbial community structure of the caeca was not negative. Therefore, P. marcusii is safe to use as a feed additive for laying hens. Finally, Chapter 5 evaluated the costs associated with the small-scale production of P. marcusii microencapsulated in calcium alginate beads and its feasibility in the poultry industry. Based on the economic assessment, the total cost for one month’s production of 210 g calcium alginate beads is estimated at R2912.88. This is too expensive and not practical to be used by poultry farmers. Possible solutions can include the use of inexpensive peptones, production on a larger scale and also increasing the concentration of bacterium encapsulated in the bead.
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    Distribution patterns of Acidobacteriota in different fynbos soils
    (Public Library of Science, 2021-03-22) Conradie, Tersia Andrea; Jacobs, Karin
    Abstract The Acidobacteriota is ubiquitous and is considered as one of the major bacterial phyla in soils. The current taxonomic classifications of this phylum are divided into 15 class-level subdivisions (SDs), with only 5 of these SDs containing cultured and fully described species. Within the fynbos biome, the Acidobacteriota has been reported as one of the dominant bacterial phyla, with relative abundances ranging between 4–26%. However, none of these studies reported on the specific distribution and diversity of the Acidobacteriota within these soils. Therefore, in this study we aimed to first determine the relative abundance and diversity of the Acidobacteriota in three pristine fynbos nature reserve soils, and secondly, whether differences in the acidobacterial composition can be attributed to environmental factors, such as soil abiotic properties. A total of 27 soil samples were collected at three nature reserves, namely Jonkershoek, Hottentots Holland, and Kogelberg. The variable V4- V5 region of the 16S rRNA gene was sequenced using the Ion Torrent S5 platform. The mean relative abundance of the Acidobacteriota were 9.02% for Jonkershoek, 14.91% for Kogelberg, and most significantly (p<0.05), 18.42% for Hottentots Holland. A total of 33 acidobacterial operational taxonomic units (OTUs) were identified. The dominant subdivisions identified in all samples included SDs 1, 2, and 3. Significant differences were observed in the distribution and composition of these OTUs between nature reserves. The SD1 were negatively correlated to soil pH, hydrogen (H+), potassium (K+) and carbon (C). In contrast, SD2, was positively correlated to soil pH, phosphorus (P), and K+, and unclassified members of SD3 was positively correlated to H+, K, and C. This study is the first to report on the specific acidobacterial distribution in pristine fynbos soils in South Africa.