As the global population rises to an estimated 9.4bn by 2050, the pressure for food, fuel and freshwater will continue to increase. Current renewable energy technologies are not widely applicable to the transport sector, which requires energy dense liquid fuels that drop into our existing infrastructure. Algal biofuels promise significantly higher yields than plants, without the displacement of valuable agricultural resources and have the potential to meet the global demand for transport fuel. Fossil fuel energy is largely ‘a legacy of algal photosynthesis’, with algae accounting for ~50% of global CO2 fixation today. In addition, these curious organisms show remarkable diversity in form, behaviour and composition. Recently there has been a global resurgence of interest in microalgae as a resource of biomass and novel products. With the present level of technology, knowledge and experience in commercial scale aquaculture, the capital cost and energy investment for algal biomass production is high. Culturing, harvesting and disrupting microalgal cells account for the largest energy inputs with more positive energy balances requiring low energy designs for culture, dewatering and extraction, efficient water and nutrient recycling with minimal waste. Little is known about the variable cell wall of microalgae, which presents a formidable barrier to the extraction of microalgal products. Staining, transmission electron microscopy (TEM) and enzymatic digestion were all utilised in an attempt to visualise, digest and characterise the cell wall of stock strains of Chlorella spp. and Pseudochoricystis ellipsoidea. The presence of algaenan, a highly resistant biopolymer, rendered staining and enzymatic digestion techniques ineffective. TEM revealed that algaenan is present in the outer walls of microalgae in a variety of conformations which appeared to impart strength to cells. A preliminary investigation utilising Fusarium oxysporum f.sp. elaeidis as a novel source of enzymes for the digestion of algaenan has also been described. Methods were developed for the mutagenesis of Chlorella emersonii and P. ellipsoidea using EMS and UV with the intent of generating cell-wall mutants. Although no viable cell wall mutants were produced, a viable pale mutant of C. emersonii was recovered 5 from UV mutagenesis. Growth rates of the pale mutant were significantly slower than the wild type, yet FAME profile was largely unaffected. Fluorescence activated cell sorting (FACS) was also investigated as a means for the rapid screening of mutagenized cells for cell wall mutants. In an attempt to reduce cooling costs of closed-culture systems, temperature tolerant species of microalgae were sought by bioprospecting the thermal waters of the Roman Baths. Numerous methods for isolation and purification of microalgae from the Baths were employed, ultimately yielding seven diverse isolates including cyanobacterial, eukaryotic, filamentous and single celled species. Despite some species possessing an increased tolerance to higher temperatures, none showed marked temperature tolerance coupled with high productivity. Further improvements to the culture conditions may have improved the productivity at higher temperatures. All seven isolates were deposited to the Culture Collection of Algae and Protozoa (CCAP). A variety of extraction methods including soxhlet, beadbeating, sonication and microwaving was investigated for efficacy of extracting fatty acid methyl esters (FAMEs) from C. emersonii. Beadbeating proved most effective in the extraction of FAMEs from C. emersonii. Microwaving showed potential as a rapid method of extraction yet was coupled with degradation of FAMEs, requiring further method development to resolve this issue. Method development has been a significant component of the work described in this thesis.

Choi Li Si. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2003. / Includes bibliographical references (leaves 156-168). / Abstracts in English and Chinese. / Acknowledgements --- p.i / Abstract --- p.ii / Contents --- p.v / List of Tables --- p.ix / List of Figures --- p.xi / Chapter Chapter 1: --- General Introduction / Chapter 1.1 --- Introduction --- p.1 / Chapter 1.2 --- The distribution and growth of coral and algae in Hong Kong --- p.3 / Chapter 1.3 --- Objectives --- p.6 / Chapter 1.4 --- Study Site --- p.7 / Chapter 1.5 --- Coral species chosen for the experiment --- p.10 / Chapter 1.6 --- Thesis outline --- p.11 / Chapter Chapter 2: --- "General Survey on Changes in Percentage Coverage of Coral and Fleshy Macroalgae in AMW and AYW, Tung Ping Chau, over Time" / Chapter 2.1 --- Introduction --- p.18 / Chapter 2.2 --- Methods and Materials --- p.26 / Chapter 2.2.1 --- In-situ survey methods --- p.26 / Chapter 2.2.2 --- Comparison of coral cover in the presence or absence of algae --- p.26 / Chapter 2.2.3 --- Environmental parameters --- p.27 / Chapter 2.2.4 --- "Image, data and statistical analysis" --- p.28 / Chapter 2.3 --- Results --- p.28 / Chapter 2.3.1 --- Coral coverage in AMW and AYW --- p.28 / Chapter 2.3.2 --- Percentage algal cover in AMW and AYW --- p.29 / Chapter 2.3.3 --- Dominating fleshy algal species in AMW and AYW --- p.30 / Chapter 2.3.4 --- Comparison of the coral coverage before and after the algal removal --- p.30 / Chapter 2.3.5 --- Water temperature --- p.31 / Chapter 2.3.6 --- Nutrient levels --- p.32 / Chapter 2.3.7 --- Further observation on the health of the corals during fleshy macroalgal bloom --- p.34 / Chapter 2.4 --- Discussion --- p.35 / Chapter Chapter 3 --- "The Effects of Algal-Coral Interactions on the Photosynthetic Ability of the Coral, Porites lobata in AMW and AYW, Tung Ping Chau" / Chapter 3.1 --- Introduction --- p.59 / Chapter 3.2 --- Methods and Materials --- p.66 / Chapter 3.2.1 --- Settings of the permanent corals --- p.66 / Chapter 3.2.2 --- Measurement of the seasonal changes in the photosynthetic ability of the corals --- p.66 / Chapter 3.2.3 --- Measurement of the diurnal changes in the photochemical efficiency of Porites lobata --- p.67 / Chapter 3.2.4 --- Correlation of quantum yield with the zooxanthellae density and the chlorophyll a concentrations --- p.68 / Chapter 3.2.5 --- Evaluation of zooxanthellae and chlorophyll-a densities --- p.68 / Chapter 3.2.6 --- Statistical analysis --- p.69 / Chapter 3.2.6.1 --- Monthly measurement of the photosynthetic ability of the corals --- p.69 / Chapter 3.2.6.2 --- Diurnal measurements of the photosynthetic ability of the corals in May and July2002 --- p.70 / Chapter 3.2.6.3 --- Relationships between quantum yield and zooxanthellae and chlorophyll a concentrations --- p.70 / Chapter 3.3 --- Results --- p.70 / Chapter 3.3.1 --- The photosynthetic activities of corals --- p.70 / Chapter 3.3.2 --- The photochemical quenching (qP) of the corals --- p.72 / Chapter 3.3.3 --- Diurnal fluctuations in the photosynthetic ability of Porites lobata and the Photo synthetically Active Radiation (PAR) --- p.73 / Chapter 3.3.3.1 --- Photosynthetic quantum yield of Porites lobata --- p.74 / Chapter 3.3.3.2 --- Diurnal changes in the Photo synthetically Active Radiation (PAR) --- p.75 / Chapter 3.3.4 --- The relationship between the photosynthetic ability of the corals and their chlorophyll-a and zooxanthellae densities --- p.76 / Chapter 3.3.5 --- Correlation between photosynthetic activities of corals and eenvironmental parameters --- p.76 / Chapter 3.3.5.1 --- Heights of coral colonies --- p.76 / Chapter 3.3.5.2 --- Photosynthetic ability of the corals and the presence of the drifting algae --- p.77 / Chapter 3.3.5.3 --- Photosynthetic ability of the corals and sea water temperature --- p.77 / Chapter 3.4 --- Discussion --- p.78 / Chapter 3.4.1 --- The photosynthetic activities of the corals --- p.78 / Chapter 3.4.2 --- The photochemical quenching of the corals --- p.80 / Chapter 3.4.3 --- Diurnal changes in the photosynthetic efficiencies of the P. lobata --- p.81 / Chapter 3.4.4 --- Relationship between the fluorescence yield and the chlorophyll-a and zooxanthellae densities --- p.82 / Chapter Chapter 4 --- The effects of drifting fleshy macroalgae on the corals: A caging manipulation of their effect on the photosynthetic activities of the corals / Chapter 4.1 --- Introduction --- p.114 / Chapter 4.2 --- Methods and Materials --- p.115 / Chapter 4.2.1 --- Setting up of the cages --- p.115 / Chapter 4.2.2 --- Setting up of the corals --- p.116 / Chapter 4.2.3 --- Measurement of the photosynthetic activities of the corals --- p.117 / Chapter 4.2.4 --- Data and statistical analysis --- p.117 / Chapter 4.3 --- Results --- p.117 / Chapter 4.3.1 --- The photosynthetic ability of the corals under different treatments --- p.117 / Chapter 4.3.2 --- The photosynthetic activities of different regions of the corals in each treatment --- p.119 / Chapter 4.4 --- Discussion --- p.120 / Chapter Chapter 5 --- "Interactions between corals, filamentous algal turf and encrusting coralline algae in Tung Ping Chau" / Chapter 5.1 --- Introduction --- p.135 / Chapter 5.2 --- Methods and Materials --- p.138 / Chapter 5.3 --- Results --- p.139 / Chapter 5.3.1 --- Coral-algal turf interactions --- p.139 / Chapter 5.3.2 --- Coral-coralline algae interactions --- p.140 / Chapter 5.3.3 --- General observations on the growth of the algal turf and the CCA on corals --- p.141 / Chapter 5.4 --- Discussion --- p.141 / Chapter Chapter 6 --- Summary and Perspectives --- p.152 / References --- p.156

So Ka Yi Erica. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2005. / Includes bibliographical references (leaves 243-255). / Abstracts in English and Chinese. / Acknowledgements --- p.i / Abstract --- p.iii / Contents --- p.ix / List of Tables --- p.xii / List of Figures --- p.xix / Chapter Chapter 1 --- General Introduction / Chapter 1.1 --- Introduction --- p.1 / Chapter 1.2 --- General Objectives --- p.11 / Chapter 1.3 --- Study Site --- p.12 / Chapter 1.4 --- Organization of the Thesis --- p.13 / Chapter Chapter 2 --- "General Surveys on the Abundance of Algae and Herbivores in A Ma Wan, A Ye Wan and Lung Lok Shui, Tung Ping Chau, Hong Kong" / Chapter 2.1 --- Introduction --- p.16 / Chapter 2.2 --- Materials and Methods --- p.20 / Chapter 2.2.1 --- Study site --- p.20 / Chapter 2.2.2 --- Measurement of water temperature --- p.21 / Chapter 2.2.3 --- Measurement of algal percentage cover --- p.22 / Chapter 2.2.4 --- Measurement of herbivore density --- p.22 / Chapter 2.2.5 --- Investigation on the species richness and diversity of algae and herbivores --- p.23 / Chapter 2.2.6 --- Statistical analysis --- p.24 / Chapter 2.3 --- Results --- p.27 / Chapter 2.3.1 --- Measurement of algal abundance and diversity --- p.27 / Chapter 2.3.1.1 --- Percentage cover and morphology --- p.28 / Chapter 2.3.1.2 --- Species richness --- p.29 / Chapter 2.3.1.3 --- Species diversity --- p.29 / Chapter 2.3.1.4 --- Dominance and composition --- p.30 / Chapter 2.3.2 --- Measurement of herbivore abundance and diversity --- p.32 / Chapter 2.3.2.1 --- Density of herbivores --- p.32 / Chapter 2.3.2.2 --- Species richness --- p.33 / Chapter 2.3.2.3 --- Species diversity --- p.34 / Chapter 2.3.2.4 --- Dominance and composition --- p.34 / Chapter 2.3.3 --- Relationships between algae and herbivores --- p.37 / Chapter 2.3.3.1 --- Pairwise Pearson Correlation between algae and herbivores in different sites --- p.37 / Chapter 2.3.3.2 --- Canonical correlations between algal and herbivorous species --- p.38 / Chapter 2.3.4 --- "Water temperature and its relationships with the abundance, richness and diversity of algae and herbivores" --- p.39 / Chapter 2.4 --- Discussion --- p.40 / Chapter 2.4.1 --- Spatial distribution of algae and herbivores --- p.40 / Chapter 2.4.2 --- Seasonal distributions of algae and herbivores --- p.46 / Chapter 2.4.3 --- Interactions between algae and herbivores --- p.50 / Chapter Chapter 3 --- Growth of Algae in Herbivore-exclusion Manipulative Experiment / Chapter 3.1 --- Introduction --- p.106 / Chapter 3.2 --- Materials and Methods --- p.111 / Chapter 3.2.1 --- Study site --- p.111 / Chapter 3.2.2 --- Manipulative experiment --- p.111 / Chapter 3.2.3 --- Investigation on the manipulative experiment --- p.112 / Chapter 3.2.3.1 --- Species composition of algae and herbivores --- p.113 / Chapter 3.2.3.2 --- Percentage cover of algae and density of herbivores --- p.113 / Chapter 3.2.3.3 --- Sizes of herbivores --- p.113 / Chapter 3.2.4 --- Detecting the cage effect --- p.114 / Chapter 3.2.5 --- Statistical analyses --- p.114 / Chapter 3.3 --- Results --- p.117 / Chapter 3.3.1 --- Algae --- p.117 / Chapter 3.3.1.1 --- Percentage cover --- p.117 / Chapter 3.3.1.2 --- Species richness --- p.120 / Chapter 3.3.1.3 --- Composition between treatments --- p.121 / Chapter 3.3.1.4 --- Compositions between set-ups --- p.121 / Chapter 3.3.1.5 --- Effects from caging and clearing --- p.122 / Chapter 3.3.2 --- Herbivores --- p.123 / Chapter 3.3.2.1 --- Density --- p.123 / Chapter 3.3.2.2 --- Species richness --- p.124 / Chapter 3.3.2.3 --- Compositions between treatments --- p.124 / Chapter 3.3.2.4 --- Compositions between set-ups --- p.125 / Chapter 3.3.3 --- Relationships between algae and herbivores --- p.125 / Chapter 3.3.3.1 --- Abundance --- p.125 / Chapter 3.3.3.2 --- Composition --- p.126 / Chapter 3.3.4 --- Sizes of herbivores --- p.128 / Chapter 3.3.5 --- Irradiance between treatments --- p.128 / Chapter 3.4 --- Discussion --- p.129 / Chapter 3.4.1 --- Effects of clearing on algal and herbivore dynamics --- p.130 / Chapter 3.4.2 --- Effects of caging on algal and herbivore dynamics --- p.135 / Chapter 3.4.3 --- Effects of seasonality of clearing on algal and herbivore dynamics --- p.139 / Chapter 3.4.4 --- Interactions of algae and herbivores --- p.142 / Chapter Chapter 4 --- Feeding Behavior of Common Herbivores in the Artificial Food Experiment / Chapter 4.1 --- Introduction --- p.216 / Chapter 4.2 --- Materials and Methods --- p.218 / Chapter 4.2.1 --- Sample collections --- p.218 / Chapter 4.2.2 --- Production of artificial foods --- p.219 / Chapter 4.2.3 --- Feeding experiments --- p.219 / Chapter 4.2.4 --- Statistical analysis --- p.220 / Chapter 4.3 --- Results --- p.221 / Chapter 4.4 --- Discussion --- p.222 / Chapter Chapter 5 --- Summary and Conclusion --- p.233 / References --- p.243

Graduation date: 2003

Viruses or viruslike particles of eukaryotic algae are ubiquitous in aquatic habitats, however, suprisingly little is known about them. The research presented here focused on one such virus which infects a multicellular filamentous brown alga of the genus Feldmannia. Although preliminary studies had been performed on the genome structure of the Feldmannia sp. Virus (FsV), little was known. The purpose of this study was to analyze the structure of the FsV genome in detail. During the experiments aimed at mapping the FsV genome, cross-hybridization was observed among five BamHI-fragments of the digested FsV DNA. Sequence analysis of one of those fragments revealed the presence of 173 by direct repeats. There are two FsV genomes of different size-classes (158 and 178 kbp). The 173 by repeats in the cross-hybridizing BamHI-fragments were confined to a small region of each virus genome. The number of these repeats in the 178 kbp genome was estimated to be about 109 and in the 158 kbp genome to be about 41. in the 178 kbp genome, the repeats are contained within a 22 kbp region and in the 1.58 kbp genome, the repeats are contained within a 10 kbp region. These viruses are actively replicated in sporophyte plants. A family of related 173 by direct repeats was discovered in an encrypted FsV genome. The family of repeats estimated to be greater than 50 kbp in length were found inserted into a protein kinase gene encoded within the 3.6 kbp viral BamHI-fragment Z. Southern analysis indicates that these repeats in the encrypted FsV genome are distinct from the previously characterized repeats in the amplified FsV genome. The translated protein kinase shares highest homologies to the SNF1 subfamily of serine/threonine protein kinases and contains a potential autophosphorylation site in a region unique to this protein kinase. A DNA polymerase gene was identified in the FsV genome. The predicted peptide sequence of the FsV DNA polymerase gene contains all of the conserved motifs found in B-family (a-like) DNA polymerases. A TTTTTNT sequence motif shown to be a transcription termination signal for Vaccinia virus early genes is found at the 3' end of the DNA polymerase gene. Phylogenetic analysis of the FsV DNA polymerase gene and other viral DNA polymerase genes indicates that FsV belongs to a group of algal viruses recently defined as Phycodnaviridae. / Graduation date: 1998

Graduation date: 1992

Graduation date: 1992

This thesis reports the rheological properties of algae slurries as a function of cell concentration for three microalgae species: Nannochloris sp.,Chlorella vulgaris, and Phaeodactylum tricornutum. Rheological properties ofalgae slurries have a direct impact on the agitation and pumping power requirements as well as process design for producing algal biofuels. This study measures the rheological properties of eight diff erent concentrations of each species ranging from 0.5 to 80 kg dry biomass/m³. Strain-controlled steady rate sweep tests were performed for each sample with an ARES-TA rheometer using a double wall couette cup and bob attachment. Shear rates ranged from 5 - 270 s⁻¹, corresponding to typical expected conditions. The results showed that Nannochloris sp. slurry behaved as a Newtonian fluid for concentrations up to 20 kg/m³. Samples with concentrations above 40 kg/m³ behaved as a shear thinning non-Newtonian fluid. The effective viscosity increased with increased biomass concentration for a maximum value of 3.3x10⁻³ Pa-s. Similarly, C. vulgaris slurry behaved as a Newtonian fluid with concentrations of up to 40 kg/m³, above which it displayed a shear thinning non-Newtonianf behavior and a maximum eff ective viscosity of 3.5x10⁻² Pa-s. On the other hand, P. tricornutum slurry demonstrated solely Newtonian fluid behavior, with the dynamic viscosity increasing with increasing biomass concentration for a maximum value of 3.2x10⁻³ Pa-s. The maximum observed e ffective viscosity occurred at a concentration of 80 kg/m³ for all three species. Moreover, an energy analysis was performed where a non-dimensional bioenergy transport e ffectiveness was de termined as the ratio of the energy content of the transported algae biomass to the sum of the required pumping power and the harvesting power. The results show that the increase in major losses due to increase in viscosity was overcompensated by the increase in the transported biomass energy. Also, cultivating a more concentrated slurry requires less dewatering power and is the preferred option. The largest bioenergy transport eff ectiveness was observed for the slurries with the largest initial dry biomass concentrations. Finally, the relative viscosity of algae slurries was modeled using a Kelvin-Voit based model for dilute and concentrated viscoelastic par- ticle suspensions. The model, which depends primarily on the packing factor of the algae species, agrees with the measured viscosity with an average error of 18%, while the concentrated particle suspension model was slightly more accurate than the dilute suspension model. / text

published_or_final_version / Ecology and Biodiversity / Master / Master of Philosophy

As algae-derived biofuel is a promising renewable energy source, it is well-established that micro-algae have the potential to make a significant contribution to transportation fuel demand. Although it has many advantages including high areal productivity, there are many negative factors. One of these factors is the predation of algae by amoebas, protozoans, ciliates and rotifers, particularly in open pond systems. For example, the rotifer Brachionus plicatilis, is able to eat as much as 12,000 algae cells per hour and can be responsible for an entire pond crash within days. Thus, these higher organisms need to be controlled in order to satisfy large-scale algae crop and biofuel production demand. One method of predation control involves the introduction of a toxic chemical to an algal culture that the predator has a higher sensitivity to with respect to algae. Ideally, predation could be minimized or eliminated without a substantial effect on the algal culture growth. Chlorella kessleri was used as the algal culture and Brachionus calyciflorus as the source of predation. Research was conducted in five stages. First, chlorine dissipation tests were carried out using spring water, distilled water, Bolds Basal Medium (BBM), and three different dry weights of algal suspension in order to analyze the dissipation rate of the residual chlorine. The results showed that chlorine in distilled water and spring water rarely dissipated while chlorine concentration in algal suspension rapidly decreased by a maximum of 90% within the second hour. Second, acute chlorine toxicity tests were conducted in order to find the 24-hr LC50 of B. calyciflorus. The 24-hr LC50 of the test animal was 0.198 mg Cl/L. Third, chlorine toxicity tests were conducted in order to find the LC50 of Chlorella kessleri. The 24-hr LC50 of C. kessleri was 0.321 mg Cl/L. Based on these results, the test animal was more sensitive to chlorine than the test algae; therefore chlorine may be used to avoid algae pond crashes by B. calyciflorus. Fourth, C. kessleri and B. calyciflorus were combined into one test to determine how long it would take to observe an algal culture crash. The result demonstrated that the higher the population of predators in algal suspension, the faster it crashed. Finally, chlorine, C. kessleri, and B. calyciflorus were combined into one test to determine what chlorine concentration and dosing interval was needed to significantly reduce predation without significantly reducing algae growth. The results of the fifth experiment showed that the effective intermittent chlorine concentration was between 0.45 and 0.60 mg Cl/L, and a short interval of chlorine dosing was effective in inhibiting rotifers in algal suspension. Even though the rotifers in algal suspension were inhibited by 0.45 to 0.60 mg Cl/L, algae growth was greatly inhibited by chlorine. In this respect, future work is needed to reduce the effect on algae by chlorine or alternative chemicals.