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Tallgrass prairies have some of the deepest and most fertile topsoil on earth. Widespread conversion of these grasslands to agriculture has decreased soil Carbon (C) storage by exacerbating erosion and disrupting aggregates that protect C from decomposition, coupled with lower plant C inputs. Thus, a primary goal of some grassland restorations is to improve soil structure and functioning. Conversion of cultivated systems to perennial grasslands often increases soil C, microbial biomass, and soil aggregate size and stability. A few studies have documented changes in soil microbial community structure after restoration. The objective of this work was two fold: 1) to explore the importance of soil texture and 2) determine plant diversity effects on recovery of soil biotic and abiotic properties. In the first study changes in soil microbial phospholipid fatty acid (PLFA) profiles and soil aggregates were examined in two 0-19 year chronosequences of restored grasslands in Nebraska on soils differing in texture, silty clay loam (SCL) and loamy fine sand (LFS), and compared them to native prairie. Soil was collected from the 0-10 cm soil depth at each site in May of 2007 and 2008. The SCL chronosequence exhibited increases in total PLFA biomass P<0.05, r2=0.29), PLFA richness (P<0.0001, r2=0.25), fungi (P<0.0001, r2=0.65), fungal:bacterial ratio (P<0.0001, r2=0.67), Gram (+) bacteria (P=0.02, r2=0.22), Gram (-) bacteria (P=0.05, r2=0.16), and actinomycetes (P=0.02, r2=0.23). Average soil aggregate diameter also increased (p=0.0002, r2=0.52). However, LFS sites showed no change across the chronosequence for any parameter. Total PLFA biomass (ANOVA, P<0.0001), richness (P<0.0001), and fungi (P=0.005) were greater on SCL restorations than LFS, but LFS had greater fungal:bacterial ratios (P=0.02). Soil microbial groups and soil aggregates were highly correlated, especially in the LFS choronosequence indicating that structural recovery is key to microbial community recovery. The second study investigated high diversity restorations with low diversity restorations on silty clay loam. In this study, high diversity and low diversity restorations in southeast Nebraska, aged 4 and 8 years were compared. The quantity of forbs seeded was too low and high diversity communities were a mixture of dominant C4 grasses (Andropogon gerardii Vitman, Schizachyrium scoparium (Michx.) Nash, Panicum virgatum L., Bouteloua curtipendula (Michx.) Torr. and Sorghastrum nutans (L.) Nash) and subdominant C3 grasses (Elymus canadensis L., Pascopyrum smithii (Rybd.) A. Löve, and Elymus virginicus L.). Eight year old plantings had greater root biomass, root C storage, root C:N ratio (P<0.05 for all), microbial biomass (low diversity only, PC<0.1, PN<0.05), PLFA richness (low diversity only, P<0.05), mycorrhizal fungi (P<0.05), and C mineralization (low diversity only, P<0.05) than 4 year old plantings. Low diversity plantings, which contained almost exclusively dominant C4 prairie grasses, had greater root C storage (P<0.1), mycorrhizal fungi (8 years only, P<0.1), and C mineralization (8 years only, P<0.05). Thus, C4 grasses and their associated arbuscular mycorrhizal fungi seem to drive recovery of soil C, soil respiration, and soil microbial communities over time. Overall, this work indicates that rates and success of belowground recovery are dependent on both abiotic and biotic factors in restoration. Restored plant communities affected soil recovery as dominant C4 grasses appeared to drive belowground recovery, but recovery depended on soil texture.

M.Tech. (Medical Technology) / Please refer to full text to view abstract

The purpose of this study was to determine the effect of substrate levels and different types of substrates on population changes of mixed cultures of Serratia marcescens and Saccharomyces cerevisiae, as compared to pure cultures.

Laboratory and field investigations during the past ten years have demonstrated that certain microorganisms can cause deleterious effects in jet fuel tank systems. These investigations have brought about new concepts concerning the mechanisms of utilization of certain constituents in jet fuel tanks by microorganisms. Since the presence of microorganisms is inevitable in fuel systems, research efforts have been directed towards identification and determination of the types of microorganisms which can utilize jet fuel hydrocarbons, fuel additives, polyurethane foam structural materials, and particular hydrocarbons present in the fuel.

>Magister Scientiae - MSc / Approximately 50% of sorghum (Sorghum bicolour (L.) Moench) produced globally is used as human food, with 95% of its total consumption occurring in Africa. Unfortunately, sorghum crops are prone to pathogenic attack, notably leading to a reduction in production yields. Generally, chemical agents are used as fertilizers and/or biocides to increase crop production. However, these chemicals can have a detrimental environmental impact including the eutrophication of fresh water and marine ecosystems. Thus, there is increased interest in plant growth promoting rhizobacteria (PGPR), as an alternative to chemicals, to facilitate eco-friendly biological control of soil-borne pathogens. PGPRs colonize the plant root system (i.e rhizosphere and rhizoplane) and promote growth and production yields essentially via the biological control of plant pathogens and their role in the nutrient cycles (e.g N fixation). The aim of this study is to characterize the microbial communities associated with sorghum in South Africa, and to identify common bacteria which could further be developed and applied to improve sorghum growth and yield. Sorghum rhizospheric environments (rhizoplane and rhizosphere) were collected from three sites characterized by different agricultural practices (Free State, Limpopo and North West). Denaturing gradient gel electrophoresis (DGGE) and Terminal-restriction fragment length polymorphism (T-RFLP) were used to identify microbial community molecular fingerprints. Sorghum-associated microbial communities were found to be different in all rhizospheric soil samples which could be explained by differences in soil chemistry, agricultural practices and geographical location. The analyses also clearly demonstrated that the sorghum bacterial community structures were similar in the rhizoplane, indicating the strong influence that the sorghum plant has in determining the rhizoplane colonizers. The archaeal community structure from rhizoplane and rhizosphere in each sampling site were dissimilar, which could be explained by differences in soil type and/or agricultural practices. Both the T-RFLP and DGGE analyses revealed that Bacillus sp. were consistently associated with South African Sorghum, Arthrobacter sp. were detected in the rhizoplane, while Uncultured archaea were detected in the rhizoplane of sorghum. These microorganisms represent valuable targets for engineering to promote growth and yield in sorghum.

Macroalgae such as Ulva are living hosts that are known to perform essential roles in marine ecosystems, and are extensively utilised for several aquaculture operations, including in the integrated production of high value goods such as abalone. Intensive aquaculture operations along the coastline release effluent water into the surrounding coastal waters, which has adverse impact on the environment. As a means to bioremediate abalone effluent, several commercial abalone farms in South Africa use Ulva as a biofilter, after which the Ulva may serve as a feed source for the abalone. Advancements in gene sequencing technology has enabled the assessment of large scale 16S rRNA gene libraries of near full-length sequences. However, studies concerning the epiphytic bacterial communities present on macroalgae grown in effluent systems are scarce, and as a result several commercial farmers have become sceptical about utilising effluent grown Ulva as feed. This study addresses the biosecurity implications associated with the use of Ulva as a biofilter and feed within an integrated multitrophic aquaculture (IMTA) system along with the abalone Haliotis midae by assessing the bacterial communities associated with Ulva and its environment. Water and Ulva samples were collected from an integrated abalone farm along the Western Cape of South Africa and assessed via a culture and a non-culture-based approach. Samples were collected from both fertilised seawater tanks and abalone effluent wastewater raceways. The water samples were collected at the inlets and outlets of each tank/raceway and the Ulva was collected from within each system. The culture-based approach utilised three selective media for the isolation and quantification of culturable bacteria, namely Tryptic Soy Agar (TSA, a general growth media), thiosulfate-citrate-bile-sucrose (TCBS) agar (vibrio selective growth media), and Ulvan agar plates, where the primary carbohydrate of Ulva was utilized as the main carbohydrate source. Post isolation, selected bacteria underwent 16S rDNA gene analysis for identification. The non-culture-based approach utilised the next generation Illumina 16S Metagenomic Sequencing platform (MiSeq). Moreover, the Ulva was sequenced using the rbcL gene to identify the species grown in the aquaculture system. Phylogenetic analysis of Ulva suggests that it falls within the U. rigida clade. The sequenced Ulva cultivated at I&J abalone farm shared close similarity with Ulva rigida (KP233772) and Ulva scandinavica (EU484416) on the GenBank database, and hence was referred to with the name of its corresponding molecular synonym, i.e. U. rigida. The culture-based results indicate that bacterial numbers were significantly higher in the raceways receiving abalone effluent water when compared with the Ulva tanks receiving seawater that were fertilized. Bacterial abundance on all three selective media types was higher on the Ulva cultured in the abalone effluent raceways than on the Ulva cultured in the fertilized seawater tanks. Moreover, it was observed that the Ulva has the potential to significantly reduce the bacterial load of abalone effluent water raceways. Rarefaction results from the non-culture-based approach indicate that the Ulva in both the fertilised seawater and abalone effluent raceways had significantly lower bacterial alpha diversity than the water columns themselves. Principal co-ordinate analysis (PCoA) at phylum level showed that bacterial communities on the Ulva and in the water, columns shared similar phyla diversity. Alternatively, PCoA at genus level demonstrated that microbial communities residing on the Ulva (both effluent and fertilised seawater grown Ulva) had significant differences compared with the water samples obtained from both the inlets and outlets of the effluent and fertilised seawater systems. When assessing the differential abundant bacteria on the Ulva, general marine bacteria appear in high abundance and potentially pathogenic bacteria such as Vibrio appear in low abundance. Moreover, the presence of the Ulva within the wastewater seemed to decrease the bacterial abundance of Vibrio within the fertilised seawater tanks as well as the abalone effluent raceways. Despite the presence of potentially pathogenic bacteria within the abalone effluent raceways, the Ulva does not seem to act as a sink for potentially pathogenic bacteria indicating that feeding effluent grown Ulva to abalone is not of significant biosecurity concern. Even though several commercial abalone farmers consider recirculation within aquaculture feed systems high-risk technology, no papers have reported disease outbreaks due to the use of effluent grown Ulva as abalone feed. These results provide a general basis for the dynamic changes in the bacterial community profiles in a commercial abalone farm associated with utilising effluent grown Ulva as a feed additive for abalone. This effort to profile the bacteria associated with Ulva and its environment under fertilised and effluent conditions provides deeper insight on understanding the biosecurity implications of incorporating effluent grown Ulva into abalone feed.

The potential of oleaginous yeast Rhodotorula glutinis for the sustainable production of biodiesel feedstock via fermentation of lignocellulosic biomass in pulp and paper wastewater as a fermentation media was investigated. The overall objective was to increase the levels of lipid feedstock in oleaginous yeast in order to reduce biodiesel production cost. To meet sustainable production of biodiesel, industrial wastewater and waste lignocellulose biomass were used as cultivation media and carbon source, respectively. Pulp and paper wastewater effluent was selected as a source of water and nutrients for the production of microbial lipids due to its environmental pollution as it creates large volume of wastewater discharge with high chemical oxygen demand (COD). Since medium composition and process fermentation condition can significantly affect the fermentative performance of oleaginous microorganisms, to find the optimum cultivation condition, design of experiment combined with RSM optimization technique was performed, which has been shown to be successful to predict the optimum condition for the biomass and lipid production in batch fermentation. In addition, lignocellulosic biomass hydrolysate was used as a substrate to improve the cost associated with feedstock fermentation. Lignocellulosic hydrolysate, a product of degradation of lignocelllosic biomass, contains degradation by-products such as 5- hydroxymethylfurfural (HMF), furfural and acetic acid that are known as major inhibitors that influences microorganism growth process. Therefore, their impacts on the fermentative performance and lipid productivity of oleaginous yeast were explored. A detailed operating condition and equipment design for the process of biocrude production from pulp and paper wastewater on a commercial scale was developed. A technological assessment of the process was performed to evaluate their technical benefits and limitations. Results show that pulp and paper wastewater can be used as a cultivation media for the production of microbial lipids using R. glutinis. However, its carbon content has to be improved. Analysis of the design and cost of the process showed that acid hydrolysis process using paper mill sludge as lignocellulosic biomass required the smallest process equipment units but at a higher raw material cost compared to fermentation process.

Bacillus subtilis capable of producing surfactin was cultured to evaluate effects of microbial cell mass on natural gas hydrate formation, dissociation, and stability characteristics. The direct molecular influences of microbial cell wall polymers inhibited gas hydrate formation significantly, decreased hydrate formation rates, and increased dissociation rates. Upon the introduction of bentonite, significant synergy was observed in the system in the form of a catalytic effect. Microbes cultured from seafloor seawater-saturated sediments collected from Mississippi Canyon 118 (MC-118) produced similar effects and generalized the observed trends. MC-118 cultures also produced biosurfactant in several culture media, which was shown to catalyze natural gas hydrate formation in porous media. Microorganisms inhabit gas hydrate macrostructures and consume hydrocarbons and other substrates from within. Sulfate reduction and anaerobic hydrocarbon oxidation occurred within gas hydrate during incubations with MC-118 indigenous consortia. A mathematical model was developed to explore the diffusion-reaction implications in massive seafloor gas hydrates.

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