Disentangling the role of prokaryotes in regulating export flux via suspended and sinking organic matter in the southern ocean
- Authors: Dithugoe, Choaro David
- Date: 2022-10-14
- Subjects: Microbial ecology , Bioinformatics , Biochemistry , Oceanography , Metagenomics , Carbon cycle (Biogeochemistry) , Prokaryotes
- Language: English
- Type: Academic theses , Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/365745 , vital:65782 , DOI https://doi.org/10.21504/10962/365745
- Description: The role of phytoplankton in regulating atmospheric carbon dioxide in the marine environment has been the subject of extensive research. We lack, however, comparative insights regarding the functional contributions of bacteria, archaea, fungi, and viruses (the microbiota) to organic matter export especially in understudied polar marine environments such as the Southern Ocean. This knowledge deficit is in part due to the high levels of microbial diversity which obscures efforts to study the relationship between diversity and ecosystem functions including their roles in the sequestration of carbon and nitrogen. Elucidating their precise contributions to organic matter export may be central to potential ecosystems feedbacks to global climate change. We examined several factors which may influence organic matter export to depth including net primary production, phytoplankton biomass, temperature, and prokaryotic functional capacity in the Southern Ocean. A Marine Snow Catcher was used to collect suspended and sinking material 10 metres below mixed layer depth at Southern Ocean Time Series (SOTS) in autumn (March-April) and in the Atlantic sector of the Southern Ocean in winter (July-August) and spring (October-November) 2019. The suspended and sinking material was used to determine the particulate organic carbon and nitrogen concentrations which were then used to calculate fluxes and export ratio ((e-ratio) - particulate organic carbon flux divided by net primary production). Additionally, genomic DNA was extracted from the suspended and sinking material and sequenced to obtain Shotgun metagenomic data which was employed to reconstruct metagenome assembled genome (MAGs) and their functional capacity using bioinformatic tools such as DRAM. Data from the Atlantic sector of the Southern Ocean, demonstrate that net primary production and temperature were inversely related to the e-ratio which is consistent with previous findings from the northern region of the Southern Ocean. Genomic functional capacity from SOTS suggested that r-strategist (organisms adapted to live in unstable environments) bacteria (e.g., Gammaproteobacteria) were prominent in the suspended pool. By contrast, the sinking particle-pool appeared to be dominated by K- strategists (organisms adapted to stable environment). The opposite was true for the archaea. This finding (i.e., bacteria) differs from a previous study in the northern region of the Southern Ocean, showing that microbes with K-strategists were more abundant in the suspended fraction. K-strategists typically degrade sinking organic matter into suspended organic matter or dissolved organic matter reducing the organic carbon export efficiency. Furthermore, Data from the Atlantic sector of the Southern Ocean revealed that seasonal temperature changes might dictate the rate of regional prokaryotic degradation across the zones. Resulting in rapid degradation at the northerly warmer regions and slow degradation further south. The data further provide evidence of chemolithoautotrophic mechanisms, with prokaryotes harbouring key pathways, required to transform dissolved inorganic carbon into complex organic forms, including recalcitrant dissolved organic carbon. Collectively, the SOTS and Atlantic sector of the Southern Ocean data suggest that shifts in prokaryotic community structure and functional capacity may regulate (either degradation or synthesis of organic matter) carbon export to depth. , Thesis (PhD) -- Faculty of Science, Zoology and Entomology, 2022
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- Date Issued: 2022-10-14
Effects of genetically modified maize (MON810) and its residues on the functional diversity of microorganisms in two South African soils
- Authors: Puta, Usanda
- Date: 2011
- Subjects: Genetically modified foods -- South Africa , Transgenic plants -- South Africa , Crops -- Genetic engineering -- South Africa , Soil microbiology -- South Africa , Microorganisms , Microbial ecology , Rhizosphere -- Microbiology , Vesicular-arbuscular mycorrhizas , Corn -- South Africa
- Language: English
- Type: Thesis , Masters , MSc (Microbiology)
- Identifier: vital:11250 , http://hdl.handle.net/10353/419 , Genetically modified foods -- South Africa , Transgenic plants -- South Africa , Crops -- Genetic engineering -- South Africa , Soil microbiology -- South Africa , Microorganisms , Microbial ecology , Rhizosphere -- Microbiology , Vesicular-arbuscular mycorrhizas , Corn -- South Africa
- Description: Genetically modified (GM) crops are commercially cultivated worldwide but there are concerns on their possible negative impacts on soil biodiversity. A glasshouse study was conducted to determine effects of Bt maize residues on soil microbial diversity. Residues of Bt maize (PAN 6Q-308B) and non-Bt maize (PAN 6Q-121) were incorporated into the soil and corresponding maize seeds planted. The treatments were replicated three times. Fertilizer and water application were similar for both treatments. Rhizosphere and bulk soil was destructively sampled from each treatment and analyzed for microbial community level physiological profiles using Biolog plates with 31 different carbon substrates. Absorbance in the Biolog plates was recorded after 72 h of incubation at 20oC. Arbuscular mycorrhizal fungi spore counts were also determined. Field studies were conducted at the University of Free State and University of Fort Hare Research Farms to determine the effects of growing Bt maize on soil microbial diversity. One Bt maize cultivar (PAN6Q-308B) and non-Bt maize (PAN6Q-121) were grown in a paired experiment at University of Free State farm, while two Bt maize (DKC61-25B and PAN6Q-321B) and their near-isogenic non-Bt maize lines (DKC61-24 and PAN6777) were grown in a randomized complete block design with three replicates. Fertilization, weed control and water application, were similar for both Bt maize cultivars and their non-Bt maize counterparts. Rhizosphere soil samples were collected by uprooting whole plants and collecting the soil attached to the roots. The samples were analysed for microbial diversity and for arbuscular mycorrhizae fungal spore counts. Principal component analysis showed that soil microbial diversity was affected more by sampling time whereas genetic modification had minimal effects. Presence of residues also increased the diversity of microorganisms. Mycorrhizal fungal spores were not affected by the presence of Bt maize residues. Growing Bt maize had no effect on the soil microbial diversity in the rhizosphere.
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- Date Issued: 2011
The microbial ecology of sulphidogenic lignocellulose degradation
- Authors: Clarke, Anna Maria
- Date: 2007
- Subjects: Microbial ecology , Lignocellulose , Sulfides , Lignin , Lignocellulose -- Biodegradation , Mines and mineral resources -- Waste disposal , Acid mine drainage
- Language: English
- Type: Thesis , Doctoral , PhD
- Identifier: vital:4094 , http://hdl.handle.net/10962/d1008181
- Description: Acid mine drainage is a well known environmental pollutant, not only in South Africa, but throughout the world, and the use of microbial processes in the treatment of these wastes has been the subject of investigation over past decades. Lignocellulose packed-bed reactors have been used in passive treatment systems, and, although effective initially, they show early decline in performance while the packing material remains largely un-utilized. Little is known about this phenomenon which remains a severe constraint in the development of efficient passive mine water treatment systems. It has been proposed that the degradation pathways of the complex lignocellulose substrate may be limited in some way in these systems during the manifestation of this effect. This study has addressed the problem using a molecular microbial ecology methodology in an attempt to relate trophic functions of the microbial population to the physico-chemical data of the system. A field-scale lignocellulose packed-bed reactor located at Vryheid Coronation Colliery (Northern Kwa-Zulu Natal province, South Africa) was monitored for six years and the results showed the classic profile of performance decline related to a slowdown in sulphate reduction and alkalinity production. The reactor was decommissioned , comprehensive samples were collected along the depth profile and the microbial populations investigated by means of 16S rRNA gene methodology. The population was found to include cellulolytic Clostridia spp., CytophagaIFlavobacterlBacteroidetes, Sphingomonadaceae and as yet uncultured microorganisms related to microbiota identified in the rumen and termite gut. These are all known to be involved as primary fermenters of cellulose. Oesulphosporosinus was present as sulphate reducer. A comparison of substrata sampling and population distribution suggested that spatial and temporal gradients within the system may become established over the course of its operation. Based on these findings, a laboratory-scale reactor was constructed to simulate the performance of the packed-bed reactor under controlled experimental conditions. The laboratory-scale reactor was operated for 273 days and showed comparable performance to that in the field in both biomolecular and physicochemical data. Clearly defined trophic niches were observed. These results suggested that a sequence of events does occur in lignocellulose degradation over time. Based on the spatial and temporal column studies, a descriptive model was proposed to account for these events. It was found that fermentative organisms predominate in the inlet zone of the system using easily extractable compounds from the wood, thus providing feedstock for sulphate reduction occurring in the succeeding compartments. Production of sulphide and alkalinity appears to be involved in the enhancement of lignin degradation and this, in turn, appears to enhance access to the cellulose fraction. However, once the readily extractables are exhausted, the decline in sulphide and alkalinity production leads inexorably to a decline in the overall performance of the system as a sulphate reducing unit operation. These observations led to the proposal that with the addition of a limited amount of a readily available carbon source, such as molasses, in the initial zone of the the reactor, the ongoing generation of sulphide would be sustained and this in turn would sustain the microbial attack on the lignocellulose complex. This proposal was tested in scale-up studies and positive results indicate that the descriptive model may, to some extent, provide an account of events occurring in these systems. The work on sustaining lignocellulose degradation through the maintenance of sulphate reduction in the initial stages of the reactor flow path has led to the development of the Degrading Packed-bed Reactor concept and that, has subsequently been successfully evaluated in the field.
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- Date Issued: 2007
The biology and molecular ecology of floating sulphur biofilms
- Authors: Bowker, Michelle Louise
- Date: 2002
- Subjects: Biofilms , Microbial ecology , Sulfur
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4056 , http://hdl.handle.net/10962/d1004117 , Biofilms , Microbial ecology , Sulfur
- Description: Floating sulphur biofilms have been observed to occur on sulphate-containing natural systems and waste stabilization ponds. It has been postulated that these biofilms form on the surface of the water because sulphate reducing bacteria present in the bottom layers of the water body reduce sulphate to sulphide which then diffuses upwards and is oxidized under the correct redox conditions to sulphur by sulphide oxidizing bacteria. Very little information exists on these complex floating systems and in order to study them further, model systems were designed. The Baffle Reactor was successfully used to cultivate floating sulphur biofilms. Conditions within the reactor could be closely scrutinized in the laboratory and it was found that sulphate levels decreased, sulphide levels increased and that sulphur was produced over a period of 2 weeks. The success of this system led to it being scaled-up and currently a method to harvest sulphur from the biofilm is under development. It is thought that biofilms are highly complex, heterogeneous structures with different bacteria distributed in different layers. Preliminary work suggested that bacteria were differentially distributed along nutrient and oxygen gradients within the biofilm. Biofilms are very thin structures and therefore difficult to study and Gradient systems were developed in an attempt to spatially separate the biofilm species into functional layers. Gradient Tubes were designed; these provided a gradient of high-sulphide, low oxygen conditions to high-oxygen, low-sulphide conditions. Bacteria were observed to grow in different layers of these systems. The Gradient Tubes could be sectioned and the chemical characteristics of each section as well as the species present could be determined. Silicon Tubular Bioreactors were also developed and these were very efficient at producing large amounts of sulphur under strictly controlled redox conditions. Microscopy and molecular methods including the amplification of a section of Ribosomal Ribonucleic acid by Polymerase Chain Reaction were used in an attempt to characterize the populations present in these biofilm systems. Denaturing Gradient Gel Electrophoresis was used to create band profiles of the populations; individual bands were excised from the gels and sequenced. Identified species included Ectothiorhodospira sp., Dethiosulfovibrio russensis, Pseudomonas geniculata, Thiobacillus baregensis and Halothiobacillus kellyi.
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- Date Issued: 2002
Studies on the ecology and molecular biology of transferable drug resistance factors in coliform bacteria
- Authors: Marcos, David
- Date: 1973
- Subjects: Enterobacteriaceae , Molecular biology , Microbial ecology , Bacteria -- Ecology , Ecology
- Language: English
- Type: Thesis , Masters , MSc
- Identifier: vital:4249 , http://hdl.handle.net/10962/d1007494 , Enterobacteriaceae , Molecular biology , Microbial ecology , Bacteria -- Ecology , Ecology
- Description: From Introduction: It was as early as 1904 that Paul Ehrlich propounded the idea of a “magic bullet”. This “magic bullet”, or chemotherapeutic agent, as he also called it, had to meet certain requirements: (a) a high activity against pathogenic micro-organisms; (b) easy absorption by the body; (c) activity in the presence of body fluids and tissue; (d) a low degree of toxicity; (e) must not allow the development of resistant micro-organisms. The discovery of the sulphonamide, Prentosil, by Domagk in 1935 was one of the initial steps in the search for this “magic bullet”. This, together with the production and purification of the antibiotics penicillin, by Fleming, Florey and Chain in 1942 and streptomycin, by Waksman in 1943, heralded a new era in the fight against bacterial infections. The majority of modern antibacterial agents have to a large extent met the requirements of Ehrlich’s ‘magic bullet”. They have however failed to prevent the development of resistant bacterial strains. This has been particularly noticeable in the past twenty years since the sudden emergence of multiple-resistant bacteria, many of which can transfer to several drugs in one step by a process of conjugation. This phenomenon which has serious medical implications has prompted numerous studies on the origin, epidemiology, biochemistry and genetics of transferable drug resistance.
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- Date Issued: 1973