The rhizobiome of Vachellia (Acacia) woodlands surrounding Witwatersrand gold and uranium mine tailings
Buck, Michelle Toni
Phytoremediation of mine tailings and surrounding areas provide the most cost-effective means of alleviating their pollutant effects. Research has shown that successful revegetation of mine tailings and surrounding areas can be optimised by providing appropriate microbial symbionts for the plants. Microorganisms are beneficial to plant growth and health which is essential for revegetation and phytoremediation of contaminated sites. The aim of this study was to assess the microbial status of Vachellia karroo rhizosphere currently growing on the surrounding areas of two mining operations, namely Vaal River (VR) and West Wits (WW) Operations. Metataxonomy is the study/use of genetic material isolated from field/environmental samples. It has been reported from metataxonomy studies that a large amount of microbial biodiversity had been missed by cultivation-based methods. Metataxonony allows for an unbiased genetic analysis from all members of the sampled community since it is a PCR directed sequencing approach for identification. Root and soil samples were collected in spring, roots were removed and physio-chemical analyses were preformed on the soil, including pH, conductivity, cation exchange capacity and XRF analysis. The soil samples were then prepared for DNA extraction by mixing/bulking 5 g of soil for each niche site and control. Then 500 mg of soil was used to extract DNA using the DNeasy® PowerSoil® Kit (Qiagen). Target genes, namely the 16S rRNA V1-V3 hypervariable region and the ITS2 hypervariable region, were sequenced at Molecular Research LP MR DNA (http://www.mrdnalab.com), Texas. The rhizosphere bacterial communities of V. karroo from VR Operations was predominantly comprised of Acidobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia, Firmicutes, Planctomycetes, Gemmatimonadetes, (between 1 % and 47 % depending on the niche sites and controls) and the remainder of the phyla (Chloroflexi, Armatimonadetes, Nitrospirae, Candidatus Saccharibacteria, candidate division WPS-1 and candidate division WPS-2) were less than 1 %. The numbers all represent the average percentage of sequences across 14 phyla. For WW Operations the bacterial communities were predominantly comprised of Actinobacteria, Acidobacteria, Planctomycetes, Verrucomicrobia, Proteobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, (between 0.7 % and 41.4 % depending on the niche sites and controls) and the remainder of the phyla (candidate division WPS-1, candidate division WPS-2, Armatimonadetes, Candidatus Saccharibacteria, Nitrospirae and Cyanobacteria/Chloroplast) were around 1 %. The numbers all iii represent the average percentage of sequences across 15 phyla. The rhizosphere fungal communities of V. karroo from VR Operations was predominantly comprised of Ascomycota (Sordariomycetes, Dothideomycetes, Eurotiomycetes, Ascomycota_unidentified, Leotiomycetes and Incertae_sedis_14); Zygomycota (Incertae_sedis_10); Basidiomycota, Agaricomycetes, Atractiellomycetes, Tremellomycetes (between 0.01 % and 77.1 % depending on the niche sites and controls) and to a lesser degree Glomeromycota (Glomeromycetes) and Fungi_unidentified (between 0.2-6 % depending on the niche sites and controls). The numbers all represent the average percentage of sequences across 12 classes. For WW Operations the fungal communities were predominantly comprised of Ascomycota (Sordariomycetes, Dothideomycetes, Eurotiomycetes, Ascomycota_unidentified, Leotiomycetes and Archaeorhizomycetes), Zygomycota (Incertae_sedis_10), Basidiomycota, Agaricomycetes, Tremellomycetes, Atractiellomycetes, Basidiomycota_unidentified, Fungi_unidentified and Glomeromycota (Glomeromycetes) (between 0.01 % and 91.42 % depending on the niche sites and controls). The numbers all represent the average percentage of sequences across 13 classes. The study represents a first report utilising metataxonomic tools in the analysis of the rhizobiome of V. karroo from areas around mine tailings. The results will assist in making decisions about future microbial surveys and applying microbial inoculum in revegetation of mine waste sites and the affected areas.
A thesis submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfillment for the degree of Doctor of Philosophy, 2018
Buck, Michelle Toni, (2018) The rhizobiome of Vachellia (Acacia) woodlands surrounding Witwatersrand gold and uranium mine tailings, University of the Witwatersrand, Johannesburg, https://hdl.handle.net/10539/27400.