Microbial and extracellular polymeric substance dynamics in arid–zone temporary pan ecosystems
- Authors: Bute, Tafara Frank
- Date: 2023-03-29
- Subjects: Extracellular polymeric substances , Biofilms , Vernal pools , Microbiomes , Sediment–water interface
- Language: English
- Type: Academic theses , Master's theses , text
- Identifier: http://hdl.handle.net/10962/422258 , vital:71925
- Description: Microbial communities of bacteria, viruses, algae, protozoans and fungi participate profoundly in aquatic systems, particularly in mediating processes such as primary production, decomposition, and biogeochemical cycles. In addition, microbiomes produce extracellular polymeric substances (EPS) which encompass a hydrated exopolymer mainly constituted of carbohydrates and proteins. The exopolymer aid proliferation and persistence of biofilms on their resident surfaces. There is however paucity of data on functional diversity of microbiomes in arid zone temporary wetlands with previous research having mainly focused on permanent systems in the northern hemisphere. In the face of ongoing climatic changes and anthropogenic threats to wetlands, it is imperative to assess the health status of aquatic systems in relation to microbial productivity dynamics. In this thesis, colorimetric methods and sequence–based metagenomics were conducted to quantify microbial EPS production and bacterial metagenome functions, respectively. This study was conducted in Khakhea–Bray region (North–West, South Africa) in June 2021 and January 2022 with a focus on evaluating microbial patterns of distribution between seasons (i.e., Dry and Wet) and varying depth i.e., deepest zones (Deep), intermediate depth (Mid) and shallowest regions (Edge). Additionally, potential relationships between EPS and either water content or organic matter content (OM content) were evaluated. In this study it was hypothesized that wet phases and deeper zones will have high EPS production and support more functions in comparison to shallowest regions and dry phases. Carbohydrates and proteins were quantified using the Dubois method and modified Lowry procedure, respectively. Carbohydrates generally occurred in higher proportions than proteins, suggesting that EPS found in these systems was largely diatom produced. The wet phases (wet season and inundation periods) supported more EPS production compared to the dry phases. The results of principal components analysis (PCA) and Spearman’s correlations suggested that EPS was highly correlated with sediment water content among other assessed variables. No significant associations were established between EPS and organic matter content. Spatial distribution of EPS demonstrated similar patterns between the deepest (Deep) and the intermediate depth zones (Mid) however the shallow regions (Edge) had significantly lower concentrations. Bacterial characterization was established by amplification of the 16S rRNA gene using illumina–sequencing protocol. Enzyme functions associated with biogeochemical pathways were predicted in PICRUSt2 bioinformatics pipeline. A total of 15 042 Unique Amplicon Sequence Variants (ASVs) were observed to be affiliated to 51 bacterial phyla and 1 127 genera. All top genera had commonality in heat tolerance. Firmicutes, dominated at phyla level with 59 % (mean ± sd, 19 ± 13 %) relative abundance followed by Actinobacteria and Proteobacteria both at 34 % (18 ± 7 %) and (18 ± 6 %), respectively. Microbial diversity matrices highlighted significant differences in beta diversity more than alpha diversity. Bacterial microbiomes were more distinct between seasons compared to within season, suggesting that functions were seasonally driven. These findings were supported by highest rates of denitrification, carbohydrate degradation and EPS production by core microbiomes in the wet season as compared to low rates of nitrogen mineralisation, carbon fixation and nitrification in the dry season. The present findings represent a first attempt in evaluating sequence–based metagenomics in semi–arid southern African temporary pan ecosystem. Both microbial EPS and bacterial functional potential were highly driven by water availability, with highest rates mainly associated with maximum inundation compared to dry states of pans. It can therefore be suggested that extended dry periods are threatening to microbially mediated processes in temporary wetlands, with implications to loss of biodiversity due to desiccation resulting in poor nutrient cycling. , Thesis (MSc) -- Faculty of Science, Zoology and Entomology, 2023
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- Date Issued: 2023-03-29
Microalgal-bacterial flocs and extracellular polymeric substances for optimum function of integrated algal pond systems
- Authors: Jimoh, Taobat Adekilekun
- Date: 2021-10-29
- Subjects: Flocculation , Extracellular polymeric substances , Water Purification , Sewage Purification Anaerobic treatment , Integrated algae pond systems (IAPS) , Microalgal-bacterial flocs
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/191214 , vital:45071 , 10.21504/10962/191214
- Description: Despite the dire state of sanitation infrastructures, water scarcity, and the dwindling reserve of natural resources due to ever-increasing population growth, implementation of a suitable technology that can provide a solution to all these issues continues to be ignored. The integrated algal pond system (IAPS) is a wastewater treatment technology that combines the processes of anaerobic digestion and photosynthetic oxygenation to achieve wastewater treatment and facilitate the recovery of treated water and resources in the form of biogas and microalgal-bacterial biomass. The natural process of bioflocculation through microalgal-bacterial mutualism and production of extracellular polymeric substances (EPS) in high rate algal oxidation ponds (HRAOPs) of an IAPS increases efficiency of wastewater treatment and potentially enhances harvestability and biomass recovery, which could contribute significantly to the successful establishment of a biorefinery. Using a 500 PE pilot-scale IAPS supplied domestic sewage coupled with laboratory experiments, this study investigated the importance and function of in situ EPS production and MaB-floc formation in HRAOP. A metagenomic study revealed the biological components of the biomass or mixed liquor suspended solids (MLSS) produced in HRAOP and showed that the suspended biomass is composed largely of eukaryotes that were dominated by the colonial microalgae Pseudopediastrum sp. and Desmodesmus sp., and a diverse range of prokaryotes including bacteria and cyanobacteria. Dominance, within the bacterial population, by a sulphur-oxidizing bacterium, Thiothrix which comprised up to 80% of the prokaryotes, coincided with a period of poor flocculation and was therefore rationalized to have contributed to bulking and poor biomass settleability. Otherwise, good flocs were formed in the MLSS with settleability up to 95% and, within 1 h. The formation of MaB-flocs appeared to be dependent on EPS concentration of the mixed liquor due to the observed positive correlation between soluble EPS (S-EPS), biomass concentration, and settleability. The contribution and role of MLSS components towards the formation and sustenance of MaB-flocs were further demonstrated in laboratory experiments using pure strains of microalgae, cyanobacteria, and bacteria. Results showed that pure cultures of dominant microalgae in MLSS, Pseudopediastrum sp. and Desmodesmus sp. achieved a rapid 92 and 75% settleability within 3 h. A self-flocculating filamentous cyanobacterium, Leptolyngbya strain ECCN 20BG was isolated, characterized, and shown to achieve 99% settleability within 5 min by forming large tightly aggregated flocs. In further experiments, this strain was found to improve the settleability of MLSS by an average of 20%. Bacterial strains identified as Bacillus strain ECCN 40b, Bacillus strain ECCN 41b, Planococcus strain ECCN 45b, and Exiguobacterium strain ECCN 46b were also observed to produce sticky EPS-like materials in pure cultures that could also contribute to the aggregation of cells in a mixed environment. Given these results, various factors and/or mechanisms that might enhance microbial aggregation and biomass recovery from HRAOP MLSS were identified in this study and include; (1) dominance by larger colonial microalgae prevents disintegration of MaB-flocs and enhances recovery of biomass from MLSS by gravity sedimentation, (2) presence of filamentous cyanobacteria species that can self-flocculate to form an interwoven network of filaments may play an important role in the structural stability and settleability of MaB-flocs in MLSS, and (3) production of EPS to form the matrix or scaffold whereon all microbial components aggregate to develop a microenvironment. Indeed, all forms of EPS, except for that produced by Bacillus strain ECCN 41b, showed bioflocculating property and were able to serve as flocculants for the recovery of Chlorella, an alga known for its poor settleability. A combination of biochemical analyses and FTIR spectroscopy revealed the importance of carbohydrate enrichment of these biopolymers. Carbohydrate concentration in all forms of EPS was between 12 and 41% suggesting that production of these compounds by microbes within the MLSS contributed to MaB-floc formation. EPS extracted from bulk MLSS and EPS produced by Bacillus strains possessed some surface-active properties that were comparable to Triton X-100, indicating potential application in bioremediation and recovery of oil from contaminated soil and water. In particular, EPS generated from Bacillus strain ECCN 41b displayed relatively distinct properties including the quantity produced (> 500 mg/L), increased viscosity, inability to flocculate microalgal cells, a rhamnolipid content of 32%, and a higher surface-activity. Based on these results, Bacillus strain ECCN 41b was rationalized to produce anionic EPS with potential application in metal or oil recovery. In addition to EPS production, the bacteria Planococcus strain ECCN 45b and Exiguobacterium strain ECCN 46b appeared pigmented. Based on partial characterization using UV/Vis spectrophotometry, thin-layer chromatography, FTIR, and NMR, the pigments produced by these two strains appeared to be identical and were tentatively identified as ketocarotenoids. This study successfully demonstrated the importance of EPS production and formation of MaB-flocs in the MLSS from HRAOP of an IAPS treating domestic sewage. It is evident that increased settleability of the biomass does contribute to the reported efficiency of wastewater treatment by IAPS and would reduce both total suspended solids (TSS) and chemical oxygen demand (COD). In addition, demonstration that this biomass contains products of value such as carotenoids and EPS with potential for commercial use strengthens the idea of using IAPS as a platform technology for innovation of the wastewater treatment process to a biorefinery. , Thesis (PhD) -- Faculty of Science, Institute for Environmental Biotechnology, 2021
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- Date Issued: 2021-10-29
Plant-fungal mutualism as a strategy for the bioremediation of hydrocarbon polluted soils
- Authors: Keshinro, Olajide Muritala
- Date: 2021-10-29
- Subjects: Mutualism (Biology) , Plant-fungus relationships , Bioremediation , Mucilage , Plant exudates , Extracellular polymeric substances , Laccase , Peroxidase , Phytoremediation , Ligninolytic enzymes
- Language: English
- Type: Doctoral theses , text
- Identifier: http://hdl.handle.net/10962/190918 , vital:45041 , 10.21504/10962/190918
- Description: Inasmuch as coal remains the linchpin for the generation of electricity and liquid petroleum products in South Africa, hydrocarbon waste and coal discard will continue to pose a threat to the environment. Therefore, the onus is on the associated industries to develop and implement efficient and sustainable strategies to mitigate the negative impacts of energy generating activities on the environment. Most conventional efforts in this regard, although successful for soil repair and the initiation of vegetation, have been deemed unsustainable. In an effort to find a sustainable remediation strategy a novel technology termed “FungCoal” was conceptualized and patented as a strategy for the rehabilitation of open cast coal mines, carbonaceous-rich spoils and coal wastes. This biotechnology, which exploits plant-fungal mutualism to achieve effective biodegradation of coal on discard dumps and the breakdown of the carbonaceous component in spoils, promotes revegetation to facilitate rehabilitation of mining-disturbed land. However, one limiting factor of the FungCoal bioprocess is that it requires oxidized weathered coal, a highly complex and variable resource for use as a co-substrate, for growth and proliferation of the coal degrading microorganisms. To fully exploit the potential of plant-fungal mutualism and its interaction for use in the remediation of coal contaminated soils, this study investigated the proposed relationship between plant roots, root exudate and the coal degrading fungus “Aspergillus sp.” (previously Neosartorya fischeri) strain 84 in more detail, in an effort to gain further insight into the mechanisms underpinning plant-fungal mutualism as a strategy for re-vegetation of coal discard dumps and the rehabilitation of hydrocarbon-contaminated soil using the FungCoal approach. A pot-on-beaker (PoB) method was developed for the easy cultivation and collection of extracellular polymeric substance (EPS)-containing exudates from Zea mays L. (maize) and Abelmuschus esculentus (okra). Characterisation of the EPS material from these exudates was carried out using a combination of physicochemical and biochemical methods. The results from analysis of phenolics and indoles showed that exudates contain some form of indoles and phenolic compounds, although in little proportions, which may fulfil a signalling function, responsible for attracting soil microorganisms into the rhizosphere. Spectroscopic analysis of the exudates using FT-IR revealed vibrations corresponding to functional groups of alkanes, alkenes, alkynes, and carboxylic acids. These compounds likely provide an easily accessible source of carbon to soil microorganisms and are also a better alternative to the poly-aromatics which are an inherent component locked-up in the supposed recalcitrant coal material. The results from biochemical analyses also revealed the presence of carbohydrate, proteins, lipids, and low amounts of α-amino-nitrogen in the EPS of maize and okra. These components of EPS are all essential for the stimulation of enzymatic activities in soil microorganisms and, which may in turn aid biodegradation. The action of the root EPS from maize was further tested on three coal-degrading fungal isolates identified as Aspergillus strain ECCN 84, Aspergillus strain ECCN 225 and Penicillium strain ECCN 243 for manganese peroxidase (MnP) and laccase (LAC) activities. The results revealed that the Aspergillus species, strains ECCN 84 and ECCN 225, showed with or without EPS, observable black halos surrounding each of the colonies after 7d incubation indicative of positive MnP activity, while no activity was observed for the Penicillium sp. strain ECCN 243. Analysis for LAC revealed little or no activity in any of the coal degrading fungi following addition of pulverized coal to the growth medium. Interestingly, the addition of EPS-containing exudate to the coal-containing medium resulted in increased LAC activity for all fungal isolates. This finding affirmed the positive contribution of EPS to extracellular LAC activity, purported as an important enzyme in the coal biodegradation process. Finally, the impact of plant-derived exudate on the colonisation and biodegradation of coal was investigated in situ using rhizoboxes, to simulate a coal environment, and was carried out for 16 weeks. Microscopic examination of coal samples after termination of the experiment showed fungal proliferation and attachment to coal particles. All of the rhizoboxes that contained plants had higher medium pH and EC, and the concentration of phenolics, indoles and humic acids was greater than that of control treatments. These observations indicated better rhizosphere colonisation, substrate biodegradation and humification. Therefore, root exudate appears to play a significant role in coordination of soil microorganisms within the rhizosphere and likely serves both as a scaffold for rhizospheric interactions by providing microorganisms with accessible carbon and as a likely ‘trigger’ for induction of coal-degrading enzymes such as fungal LAC for mobilisation of recalcitrant carbon. This study has shown that EPS exuded from roots of Zea mays together with coal degrading fungus Aspergillus strain ECCN 84 can alkalinise the coal substrate and facilitate introduction of oxygen, possibly as a result of increased laccase activity, and increase availability of nutrients (as indicated by higher EC) in a coal-polluted rhizosphere, to provide plants and their associated mycorrhizae and presumably other beneficial microorganisms a more mesic environment for sustained phytoremediation with enhanced rehabilitation potential. In conclusion, this study confirms the positive role of root exudate in mediating a mutualistic rehabilitation strategy involving plants and fungi such as the FungCoal bioprocess. , Thesis (PhD) -- Faculty of Science, Institute for Environmental Biotechnology, 2021
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- Date Issued: 2021-10-29
Bacterial colonisation and degradation of geologically weathered and discard coal
- Authors: Olawale, Jacob Taiwo
- Date: 2018
- Subjects: Coal mine waste , Coal -- Biodegradation , Coal mines and mining -- Environmental aspects , Land degradation , Electron microscopy , Extracellular polymeric substances , Flagella (Microbiology) , Fourier transform infrared spectroscopy , Microbiologically influenced corrosion
- Language: English
- Type: text , Thesis , Doctoral , PhD
- Identifier: http://hdl.handle.net/10962/61625 , vital:28043
- Description: Bacterial beneficiation of low-grade coal, coal discard, and waste has the potential to mitigate land degradation, water and soil pollution and, be a strategy for mining companies to responsibly extract and process coal with environmental sustainability. This study investigated the colonisation and biodegradation or depolymerisation of coal discard and geologically weathered coal by selected strains of bacteria, and an attempt has been made to describe the mechanisms associated with colonisation and biodegradation of this carbonaceous material. Ten bacterial strains, Bacillus strain ECCN 18b, Citrobacter strain ECCN 19b, Proteus strain ECCN 20b, Exiguobacterium strain ECCN 21b, Microbacterium strain ECCN 22b, Proteus strain ECCN 23b, Serratia strain ECCN 24b, Escherichia strain ECCN 25b, Bacillus strain ECCN 26b and Bacillus strain ECCN 41b, isolated from diesel-contaminated soil and coal slurry and identified using DNA sequencing, were rescreened and their coal biodegradation potential ranked. The ranking of the bacterial strains was undertaken using several indicators including; formation of brown halos on the plate culture (solid), change in colour intensity of the medium in liquid culture, change in culture media pH, and an increase in absorbance at 280nm and 450nm. Although, all the ten strains showed evidence of biodegradation of coal discard and geologically weathered coal based on the ranking employed, and the three strains considered the best candidates were Citrobacter strain ECCN 19b, Exiguobacterium strain ECCN 21b and Serratia strain ECCN 24b. The actions of the three bacterial strains were further studied and characterised in relation to coal degradation. Electron microscopy revealed that Citrobacter strain ECCN 19b, Exiguobacterium strain ECCN 21b and Serratia strain ECCN 24b attached to the surface of coal discard and geologically weathered coal by a process that appeared to involve extracellular polymeric substances (EPS), and flagella. The presence of flagella for Citrobacter strain ECCN 19b and Serratia strain ECCN 24b was confirmed by transmission electron microscopy. Bacterial degradation of coal discard and geologically weathered coal by these selected strains resulted in the release of soluble and insoluble products. Ultraviolet/ visible spectrophotometric (UV/VIS) analysis revealed that the soluble products resembled humic acid-like substances, which was confirmed following Fourier Transform Infrared (FTIR) spectroscopy. Analysis revealed that the coal-derived humic acid-like substances were similar to commercial humic acid extracted from bituminous coal. Elemental analysis of the insoluble product residue after bacterial biodegradation revealed the modification of the chemical compositions of the coal discard and geologically weathered coal substrates. Characterisation of the functional groups of the insoluble product using FTIR spectroscopy indicated changes, with the appearance of new peaks at 1737cm-1, 1366cm-1, 1228cm-1, and 1216cm-1 characteristic of aldehyde, ketones, carboxylic acids, esters, amines, and alkanes. Broad spectra regions of 3500 -3200cm-1, characteristic of alcohol and phenol, were also observed. Together, these results were taken as evidence for increased oxidation of the coal substrates, presumably as a consequence of bacterial catalysed biodegradation of coal discard and geologically weathered coal. During bacterial degradation of coal discard and geologically weathered coal, strains produced extracellular protein, which was detected and further investigated using sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS- PAGE). At least three protein bands with molecular mass 53 kDa, 72 kDa, and 82 kDa were common to the three bacterial strains. Following ammonium sulphate precipitation and gel filtration chromatography, additional bands with molecular mass 16 kDa, 33 kDa, 37 kDa, and 43 kDa were detected. An extracellular laccase activity was detected in cultures of Exiguobacterium strain ECCN 21b and Serratia strain ECCN 24b. Cytochrome P450 activity was detected in all the bacterial strains in the presence of both coal discard and geologically weathered coal. This is the first time that cytochrome P450 activity has been reported following exposure of these three bacterial strains to a coal substrate. Overall, this research has successfully demonstrated the partial degradation of coal discard and geologically weathered coal by Citrobacter strain ECCN 19b, Exiguobacterium strain ECCN 21b and Serratia strain ECCN 24b and the release of humic acid-like substances. Thus, the biodegradation process involved adherence to and growth of the bacteria on the surface of coal substrate and appeared to require the formation of alkaline substances and the combined activities of extracellular LAC and cytochrome P450. Since bacterial degradation of low-grade coal and discard appears to be viable, the bacteria isolated in this study can potentially be used either for conversion of discard into valuable chemicals or to mitigate the deleterious effects of stockpiled coal discard on the environment.
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- Date Issued: 2018