Investigating soil microbial interactions of Portulacaria afra
- Authors: Fulmaka, Aviwe
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54598 , vital:26592
- Description: Portulacaria afra commonly known as Spekboom contributes significantly to carbon sequestration and has been widely planted in degraded areas of the Eastern Cape. Approximately 50% of planted cuttings do not survive although the cause of this decline is unknown. Like many indigenous plants, Spekboom forms a symbiotic relationship with mycorrhizal fungi and the interaction with rhizobacteria may enhance and improve plant growth and establishment. This study aims to investigate these relationships which will include a survey of the arbuscular mycorrhizal (AM) fungal populations associated with Spekboom, determination of the causal agent of Spekboom decline, isolation and identification of the associated rhizobacteria and investigation of their plant growth promotion properties and assessing the ability of arbuscular mycorrhizal fungi and selected rhizobacteria to enhance establishment and growth of Spekboom. Soil and root samples from selected trial sites were used to assess AM fungal spore abundance and colonisation; isolation, characterization, and identification of rhizobacteria and determine the interaction of the microbes on Spekboom growth and tolerance to Fusarium. AM spore abundance and percentage root colonisation did not differ between the three Spekboom plots. Molecular analyses of the SSU region from the plots showed 4 families of AM fungi and were identified as Ambisporaceae, Glomeraceae, Claroideoglomeraceae and Paraglomeraceae. A suspected Fusarium pathogen was isolated and molecularly identified. Pathogenicity tests indicated reduced Spekboom growth with poor root development. Thirty four rhizobacterial isolates were tested for various plant growth promoting abilities. Of these, 6 were able to produce IAA which may promote plant root growth, 27 siderophores and 23 were phosphate solubilisers. Bacterial isolates were molecularly identified to be from various species of Bacillus, with some Arthrobacter, Enterobacter, Pseudomonas and Microbacterium. Inoculation of Spekboom cuttings with mycorrhizal fungi and selected rhizobacterial isolates significantly improved shoot height. Spekboom cuttings challenged with Fusarium and inoculated with mycorrhizal fungi and two rhizobacterial isolates significantly improved growth. The inoculation of cuttings in the nursery with mycorrhizal fungi and selected rhizobacteria is recommended prior to establishing Spekboom in the field.
- Full Text:
- Authors: Fulmaka, Aviwe
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54598 , vital:26592
- Description: Portulacaria afra commonly known as Spekboom contributes significantly to carbon sequestration and has been widely planted in degraded areas of the Eastern Cape. Approximately 50% of planted cuttings do not survive although the cause of this decline is unknown. Like many indigenous plants, Spekboom forms a symbiotic relationship with mycorrhizal fungi and the interaction with rhizobacteria may enhance and improve plant growth and establishment. This study aims to investigate these relationships which will include a survey of the arbuscular mycorrhizal (AM) fungal populations associated with Spekboom, determination of the causal agent of Spekboom decline, isolation and identification of the associated rhizobacteria and investigation of their plant growth promotion properties and assessing the ability of arbuscular mycorrhizal fungi and selected rhizobacteria to enhance establishment and growth of Spekboom. Soil and root samples from selected trial sites were used to assess AM fungal spore abundance and colonisation; isolation, characterization, and identification of rhizobacteria and determine the interaction of the microbes on Spekboom growth and tolerance to Fusarium. AM spore abundance and percentage root colonisation did not differ between the three Spekboom plots. Molecular analyses of the SSU region from the plots showed 4 families of AM fungi and were identified as Ambisporaceae, Glomeraceae, Claroideoglomeraceae and Paraglomeraceae. A suspected Fusarium pathogen was isolated and molecularly identified. Pathogenicity tests indicated reduced Spekboom growth with poor root development. Thirty four rhizobacterial isolates were tested for various plant growth promoting abilities. Of these, 6 were able to produce IAA which may promote plant root growth, 27 siderophores and 23 were phosphate solubilisers. Bacterial isolates were molecularly identified to be from various species of Bacillus, with some Arthrobacter, Enterobacter, Pseudomonas and Microbacterium. Inoculation of Spekboom cuttings with mycorrhizal fungi and selected rhizobacterial isolates significantly improved shoot height. Spekboom cuttings challenged with Fusarium and inoculated with mycorrhizal fungi and two rhizobacterial isolates significantly improved growth. The inoculation of cuttings in the nursery with mycorrhizal fungi and selected rhizobacteria is recommended prior to establishing Spekboom in the field.
- Full Text:
Investigating the use of Arbuscular Mycorrhizas and Plant Growth Promoting Bacteria to improve the drought tolerance of maize (Zea mays L.)
- Authors: Moore, Nicolle Maureen
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54587 , vital:26591
- Description: Maize (Zea mays L.) is a direct staple food crop in Africa and remains an essential component of global food security, with maize crops accounting for over 60% of the total harvested area of annual food crops. Stress caused by drought and high soil salinity limits crop growth and productivity more than any other single environmental factor, with grain yield reductions up to 76% depending on the severity of the drought and the plant growth stage. Arbuscular mycorrhizal (AM) fungi and Plant Growth Promotion Rhizobacteria (PGPR) have previously been shown to improve tolerance of plants to drought stress through a number of chemical and physiological processes. The aim of this investigation was to determine whether mycorrhizal fungi and rhizobacteria adapted to drought and saline conditions and possessing plant growth promoting (PGP) traits were able to stimulate plant growth responses when applied to Zea mays seeds growing under greenhouse conditions Bacterial isolates selected were tolerant to concentrations of NaCl up to 600 mM and maintained 50% growth at low water potentials (-1.44 MPa). They were positive for Indole Acetic Acid (IAA) production, phosphate solubilisation and secretion of siderophores. Bacterial isolates showing plant growth promoting potential were identified using 16S rDNA gene sequencing as Achromobacter xylosoxidans strains A8 and C54 and Klebsiella oxytoca strain M1. Mixed inoculum was prepared from indigenous communities of mycorrhizas in soils sampled from the Cerebos Salt Pan and the Kalahari Desert. Mycorrhizal diversity was investigated using 454-Pyrosequencing which revealed that the community composition was dominated by species in the Ambispora, Glomus and Paraglomus genera with a rare component represented by species in the Redeckera, Archaeospora and Geosiphon genera. Microscopic examination of plant roots at the end of the trial revealed the presence of diagnostic mycorrhizal structures within the root cells, confirming that colonization was successful. Plant growth response to microbial inoculation was assessed by monitoring changes in plant photosynthetic capacity over the duration of a 7 week pot trial. A significant difference in photosynthetic and biomass data was observed between drought and well-watered groups but no mycorrhizal or bacterial treatment effect was evident within the groups, despite the high levels of colonization by mycorrhizas. These results suggest that the beneficial effects of mycorrhizal colonization may be primarily attributed to improved nutrient and mineral uptake in conditions where nutrients are limiting, resulting in improved growth. The improved growth may then have secondary effects on the plant‟s ability to withstand drought. Having controlled for nutrient deficiency, it was not evident in this study that mycorrhizal fungi were able to stimulate a change in plant physiology and confer drought tolerance under the conditions imposed.
- Full Text:
- Authors: Moore, Nicolle Maureen
- Date: 2016
- Language: English
- Type: text , Thesis , Masters , MSc
- Identifier: http://hdl.handle.net/10962/54587 , vital:26591
- Description: Maize (Zea mays L.) is a direct staple food crop in Africa and remains an essential component of global food security, with maize crops accounting for over 60% of the total harvested area of annual food crops. Stress caused by drought and high soil salinity limits crop growth and productivity more than any other single environmental factor, with grain yield reductions up to 76% depending on the severity of the drought and the plant growth stage. Arbuscular mycorrhizal (AM) fungi and Plant Growth Promotion Rhizobacteria (PGPR) have previously been shown to improve tolerance of plants to drought stress through a number of chemical and physiological processes. The aim of this investigation was to determine whether mycorrhizal fungi and rhizobacteria adapted to drought and saline conditions and possessing plant growth promoting (PGP) traits were able to stimulate plant growth responses when applied to Zea mays seeds growing under greenhouse conditions Bacterial isolates selected were tolerant to concentrations of NaCl up to 600 mM and maintained 50% growth at low water potentials (-1.44 MPa). They were positive for Indole Acetic Acid (IAA) production, phosphate solubilisation and secretion of siderophores. Bacterial isolates showing plant growth promoting potential were identified using 16S rDNA gene sequencing as Achromobacter xylosoxidans strains A8 and C54 and Klebsiella oxytoca strain M1. Mixed inoculum was prepared from indigenous communities of mycorrhizas in soils sampled from the Cerebos Salt Pan and the Kalahari Desert. Mycorrhizal diversity was investigated using 454-Pyrosequencing which revealed that the community composition was dominated by species in the Ambispora, Glomus and Paraglomus genera with a rare component represented by species in the Redeckera, Archaeospora and Geosiphon genera. Microscopic examination of plant roots at the end of the trial revealed the presence of diagnostic mycorrhizal structures within the root cells, confirming that colonization was successful. Plant growth response to microbial inoculation was assessed by monitoring changes in plant photosynthetic capacity over the duration of a 7 week pot trial. A significant difference in photosynthetic and biomass data was observed between drought and well-watered groups but no mycorrhizal or bacterial treatment effect was evident within the groups, despite the high levels of colonization by mycorrhizas. These results suggest that the beneficial effects of mycorrhizal colonization may be primarily attributed to improved nutrient and mineral uptake in conditions where nutrients are limiting, resulting in improved growth. The improved growth may then have secondary effects on the plant‟s ability to withstand drought. Having controlled for nutrient deficiency, it was not evident in this study that mycorrhizal fungi were able to stimulate a change in plant physiology and confer drought tolerance under the conditions imposed.
- Full Text:
Soil microbial properties and apple tree performance under conventional and organic management
- Authors: Meyer, André Harold
- Date: 2016
- Subjects: Soil management South Africa Western Cape , Agricultural chemicals Environmental aspects , Soil microbiology South Africa Western Cape , Vesicular-arbuscular mycorrhizas , Enzymes Biotechnology , Apples Organic farming South Africa Western Cape
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/64545 , vital:28557
- Description: Conventional (CON) soil management that permits the use of agrochemicals is currently the most common form of management in Western Cape deciduous fruit orchards. There is increasing pressure to minimise or eliminate synthetic agrochemical usage due to its potentially harmful effect on the environment, particularly to non-target soil microorganisms, and to the functions and processes they perform or mediate. In apple orchards, organic (ORG) practices exclude the use of synthetic pesticides and herbicides making use instead of organic fertilisers and naturally derived products as defined by organic certification programs. ORG practices aim to improve nutrient availability, yield, and long-term orchard sustainability relative to CON orchard management practices. If ORG and CON orchard floor management practices affect orchard ecosystems differently, such differences should be measurable in terms of differences in microbiological parameters. In this thesis it is hypothesised that ORG practices would induce positive soil microbiological responses in Western Cape apple orchards relative to CON practices, and by inference general soil health and apple tree performance. To test this hypothesis a polyphasic approach was adopted. This involved measurement of soil microbial activities and functional diversities, by enzyme activity (using colorimetric assays) and carbon-substrate utilisation (using the BIOLOG™ system), respectively. With reference to the enzyme analyses, the performance of a literature-validated, enzyme-based soil health index was also tested. The analyses were supported by coarse-level comparisons of the magnitude of bacteria, fungi, actinobacteria and total heterotroph populations using traditional culturing techniques (dilution plating on growth media). The extent to which the microbial status differed between the applied ORG and CON treatments was thought likely to reflect such treatment-induced variables as soil nutrient status, apple tree nutritional response, tree growth and yield, all of which were determined. Because the root systems of deciduous fruit trees commonly extend to depths >60 cm in well-prepared soils, microbial enzyme activities in the soil depth intervals corresponding to the lower rootzone, were also investigated. This research was carried out in a randomized field trial. Finally, to gain a broader understanding of the effects of contrasting soil management systems on soil microbiology under a greater variety of environmental conditions, arbuscular mycorrhizal (AM) fungal dynamics were explored in a survey of commercial apple orchards. These orchards were selected to span the range of environmental conditions that occur in the apple production areas of the Western Cape. Orchard soils under ORG management promoted richer microbial ecosystems, and appeared to be better able to sustain community metabolic diversity and, by inference, the functions mediated by soil microbial communities, than those under CON management. This implies that ORG approaches possibly afford a better option to sustain critical ecosystem functions than CON management. This possibly explains why use of straw mulches and compost in accordance with ORG practices, compared with CON practices, promoted β-glucosidase, acid phosphatase and urease activities rather than affecting the abundance of the micro-organisms that produce these enzymes. Enzyme activities in the 0–30 cm soil intervals were also more effectively promoted by ORG than CON practices, although no differences were observed at lower depth intervals. ORG practices promoted functional AM associations more effectively than CON practices, but the abundance of glomalin, a beneficial by-product of AM fungi, was unaffected. The greater enzyme activities and higher root colonisation levels in the ORG treatments probably contributed to improved nutritional effects that caused greater vegetative growth, but lower yields, in the ORG treatments. Yield suppression was conceivably due to excessive vegetative growth induced by oversupply of compost and the mineral nutrients contained therein. The survey of Western Cape apple orchards suggested that neither glomalin nor root colonisation bore any specific relationship to production area, cultivation practice, scion x rootstock combination, or, in the case of root colonisation, with any chemical parameters. However, the effect of season on glomalin was conclusively shown, being higher in summer than in spring, as was the lack of any effect of year on glomalin and root colonisation. Collectively, these results showed that ORG soil management promote soil microbiology, soil nutrient status, and apple tree performance compared to CON management. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2016
- Full Text:
- Authors: Meyer, André Harold
- Date: 2016
- Subjects: Soil management South Africa Western Cape , Agricultural chemicals Environmental aspects , Soil microbiology South Africa Western Cape , Vesicular-arbuscular mycorrhizas , Enzymes Biotechnology , Apples Organic farming South Africa Western Cape
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/64545 , vital:28557
- Description: Conventional (CON) soil management that permits the use of agrochemicals is currently the most common form of management in Western Cape deciduous fruit orchards. There is increasing pressure to minimise or eliminate synthetic agrochemical usage due to its potentially harmful effect on the environment, particularly to non-target soil microorganisms, and to the functions and processes they perform or mediate. In apple orchards, organic (ORG) practices exclude the use of synthetic pesticides and herbicides making use instead of organic fertilisers and naturally derived products as defined by organic certification programs. ORG practices aim to improve nutrient availability, yield, and long-term orchard sustainability relative to CON orchard management practices. If ORG and CON orchard floor management practices affect orchard ecosystems differently, such differences should be measurable in terms of differences in microbiological parameters. In this thesis it is hypothesised that ORG practices would induce positive soil microbiological responses in Western Cape apple orchards relative to CON practices, and by inference general soil health and apple tree performance. To test this hypothesis a polyphasic approach was adopted. This involved measurement of soil microbial activities and functional diversities, by enzyme activity (using colorimetric assays) and carbon-substrate utilisation (using the BIOLOG™ system), respectively. With reference to the enzyme analyses, the performance of a literature-validated, enzyme-based soil health index was also tested. The analyses were supported by coarse-level comparisons of the magnitude of bacteria, fungi, actinobacteria and total heterotroph populations using traditional culturing techniques (dilution plating on growth media). The extent to which the microbial status differed between the applied ORG and CON treatments was thought likely to reflect such treatment-induced variables as soil nutrient status, apple tree nutritional response, tree growth and yield, all of which were determined. Because the root systems of deciduous fruit trees commonly extend to depths >60 cm in well-prepared soils, microbial enzyme activities in the soil depth intervals corresponding to the lower rootzone, were also investigated. This research was carried out in a randomized field trial. Finally, to gain a broader understanding of the effects of contrasting soil management systems on soil microbiology under a greater variety of environmental conditions, arbuscular mycorrhizal (AM) fungal dynamics were explored in a survey of commercial apple orchards. These orchards were selected to span the range of environmental conditions that occur in the apple production areas of the Western Cape. Orchard soils under ORG management promoted richer microbial ecosystems, and appeared to be better able to sustain community metabolic diversity and, by inference, the functions mediated by soil microbial communities, than those under CON management. This implies that ORG approaches possibly afford a better option to sustain critical ecosystem functions than CON management. This possibly explains why use of straw mulches and compost in accordance with ORG practices, compared with CON practices, promoted β-glucosidase, acid phosphatase and urease activities rather than affecting the abundance of the micro-organisms that produce these enzymes. Enzyme activities in the 0–30 cm soil intervals were also more effectively promoted by ORG than CON practices, although no differences were observed at lower depth intervals. ORG practices promoted functional AM associations more effectively than CON practices, but the abundance of glomalin, a beneficial by-product of AM fungi, was unaffected. The greater enzyme activities and higher root colonisation levels in the ORG treatments probably contributed to improved nutritional effects that caused greater vegetative growth, but lower yields, in the ORG treatments. Yield suppression was conceivably due to excessive vegetative growth induced by oversupply of compost and the mineral nutrients contained therein. The survey of Western Cape apple orchards suggested that neither glomalin nor root colonisation bore any specific relationship to production area, cultivation practice, scion x rootstock combination, or, in the case of root colonisation, with any chemical parameters. However, the effect of season on glomalin was conclusively shown, being higher in summer than in spring, as was the lack of any effect of year on glomalin and root colonisation. Collectively, these results showed that ORG soil management promote soil microbiology, soil nutrient status, and apple tree performance compared to CON management. , Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 2016
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