Doctoral Degrees (Microbiology)

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Browsing Doctoral Degrees (Microbiology) by Subject "Acidobacteria -- Habitat"

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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.